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= psy5916
(190 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 57.0 bits (136), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 36/62 (58%), Positives = 42/62 (67%), Gaps = 6/62 (9%)
Query: 86 RLNINARERRRMHDLNDALDELRAVIPYAHSPSVRKLSKIATLLLAKNYILMQANALEEL 145
R+ NARER RMH LN ALD LR V+P +S + +KLSKI TL LAKNYI AL E+
Sbjct: 3 RMKANARERNRMHGLNAALDNLRKVVP-CYSKT-QKLSKIETLRLAKNYIW----ALSEI 56
Query: 146 RR 147
R
Sbjct: 57 LR 58
>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 = 31.6 bits (70), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 33/58 (56%), Gaps = 8/58 (13%)
Query: 63 PTHSGAMGSLQPLAKKNRQGKTVRLNINARERRRMHDLNDALDELRAVIPYAHSPSVR 120
PT S A + LAK+ RQ K N N ERRR ++ND + EL +IP ++ P +R
Sbjct: 13 PTESEA----RALAKE-RQKKD---NHNLIERRRRFNINDRIKELGTLIPKSNDPDMR 62
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 30.0 bits (66), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 27/43 (62%), Gaps = 1/43 (2%)
Query: 93 ERRRMHDLNDALDELRAVIPYAHSPSVRKLSKIATLLLAKNYI 135
E+RR +N +DEL +++P ++ S RKL K+ L +A ++
Sbjct: 21 EKRRRDKMNSFIDELASLVPTCNAMS-RKLDKLTVLRMAVQHM 62
>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 = 29.6 bits (65), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 27/43 (62%), Gaps = 1/43 (2%)
Query: 93 ERRRMHDLNDALDELRAVIPYAHSPSVRKLSKIATLLLAKNYI 135
E+RR +N +DEL +++P ++ S RKL K+ L +A ++
Sbjct: 17 EKRRRDKMNSFIDELASLVPTCNAMS-RKLDKLTVLRMAVQHM 58
>pdb|3L9F|A Chain A, The Crystal Structure Of Smu.1604c From Streptococcus
Mutans Ua159
pdb|3L9F|B Chain B, The Crystal Structure Of Smu.1604c From Streptococcus
Mutans Ua159
pdb|3L9F|C Chain C, The Crystal Structure Of Smu.1604c From Streptococcus
Mutans Ua159
pdb|3L9F|D Chain D, The Crystal Structure Of Smu.1604c From Streptococcus
Mutans Ua159
Length = 204
Score = 29.3 bits (64), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 35/65 (53%), Gaps = 4/65 (6%)
Query: 64 THSGAMGSLQPLAKKNRQGKTVRLNINARERRRMHDLNDAL-DELRAVIPYAHS---PSV 119
+H +M Q + + + QGK + L I +++ R +++ND L ++L + P++
Sbjct: 19 SHMASMTGGQQMGRGSMQGKDIILGILSKKERSGYEINDILQNQLSYFYDGTYGMIYPTL 78
Query: 120 RKLSK 124
RKL K
Sbjct: 79 RKLEK 83
>pdb|3N2T|A Chain A, Structure Of The Glycerol Dehydrogenase Akr11b4 From
Gluconobacter Oxydans
Length = 348
Score = 28.1 bits (61), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 6 GSYYSNETSQVPGRRTPLGNVGLGGF 31
GS+ +++T ++PG TPL V LG +
Sbjct: 14 GSHMASDTIRIPGIDTPLSRVALGTW 39
>pdb|2QL2|A Chain A, Crystal Structure Of The Basic-Helix-Loop-Helix Domains Of
The Heterodimer E47NEUROD1 BOUND TO DNA
pdb|2QL2|C Chain C, Crystal Structure Of The Basic-Helix-Loop-Helix Domains Of
The Heterodimer E47NEUROD1 BOUND TO DNA
Length = 60
Score = 26.9 bits (58), Expect = 7.8, Method: Composition-based stats.
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 86 RLNINARERRRMHDLNDALDEL 107
R+ NARER R+ D+N+A EL
Sbjct: 2 RMANNARERVRVRDINEAFREL 23
>pdb|3ADY|A Chain A, Crystal Structure Of Dotd From Legionella
Length = 148
Score = 26.6 bits (57), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 117 PSVRKLSKIATLLLAKNYILMQANALE--ELRRIITYIQAQGTMTMPPGFDLQA 168
P + S AT+ LA+ + + + LE ++ ++IT T+T+P ++LQA
Sbjct: 13 PPINNPSDDATIKLAEAAVSVSDSMLEMAKVEKVITPPSKDNTLTIPNAYNLQA 66
>pdb|2O8B|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T MISPAIR
pdb|2O8C|A Chain A, Human Mutsalpha (msh2/msh6) Bound To Adp And An
O6-methyl-guanine T Mispair
pdb|2O8D|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G DU MISPAIR
pdb|2O8F|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO DNA WITH A SINGLE BASE
T INSERT
pdb|3THW|A Chain A, Human Mutsbeta Complexed With An Idl Of 4 Bases (Loop4)
And Adp
pdb|3THX|A Chain A, Human Mutsbeta Complexed With An Idl Of 3 Bases (Loop3)
And Adp
pdb|3THY|A Chain A, Human Mutsbeta Complexed With An Idl Of 2 Bases (Loop2)
And Adp
pdb|3THZ|A Chain A, Human Mutsbeta Complexed With An Idl Of 6 Bases (Loop6)
And Adp
Length = 934
Score = 26.6 bits (57), Expect = 9.4, Method: Composition-based stats.
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 87 LNINARERRRMHDLNDALDELRAVIPYAH 115
+NI++ M LND L +L AV+ +AH
Sbjct: 582 VNISSGYVEPMQTLNDVLAQLDAVVSFAH 610
>pdb|2O8E|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO A G T MISPAIR, WITH
ADP BOUND TO Msh2 Only
Length = 934
Score = 26.6 bits (57), Expect = 9.5, Method: Composition-based stats.
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 87 LNINARERRRMHDLNDALDELRAVIPYAH 115
+NI++ M LND L +L AV+ +AH
Sbjct: 582 VNISSGYVEPMQTLNDVLAQLDAVVSFAH 610
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
0.317 0.133 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,417,002
Number of Sequences: 62578
Number of extensions: 143159
Number of successful extensions: 293
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 287
Number of HSP's gapped (non-prelim): 12
length of query: 190
length of database: 14,973,337
effective HSP length: 93
effective length of query: 97
effective length of database: 9,153,583
effective search space: 887897551
effective search space used: 887897551
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)