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= 001681
(1031 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2RMR|A Chain A, Solution Structure Of Msin3a Pah1 Domain
pdb|2RMS|A Chain A, Solution Structure Of The Msin3a Pah1-Sap25 Sid Complex
Length = 71
Score = 92.4 bits (228), Expect = 1e-18, Method: Composition-based stats.
Identities = 43/71 (60%), Positives = 55/71 (77%)
Query: 41 QKLTTNDALAYLKAVKDIFQDKREKYDDFLEVMKDFKAQRIDTAGVIARVKELFKGHRDL 100
Q+L DAL+YL VK F + + Y+DFL++MK+FK+Q IDT GVI+RV +LFKGH DL
Sbjct: 1 QRLKVEDALSYLDQVKLQFGSQPQVYNDFLDIMKEFKSQSIDTPGVISRVSQLFKGHPDL 60
Query: 101 ILGFNTFLPKG 111
I+GFNTFLP G
Sbjct: 61 IMGFNTFLPPG 71
Score = 52.0 bits (123), Expect = 2e-06, Method: Composition-based stats.
Identities = 22/67 (32%), Positives = 40/67 (59%)
Query: 129 VEFEEAINFVNKIKTRFQGDDHVYKSFLDILNMYRKENKSITEVYQEVEALFQDHPDLLE 188
++ E+A+++++++K +F VY FLDI+ ++ ++ V V LF+ HPDL+
Sbjct: 3 LKVEDALSYLDQVKLQFGSQPQVYNDFLDIMKEFKSQSIDTPGVISRVSQLFKGHPDLIM 62
Query: 189 EFTHFLP 195
F FLP
Sbjct: 63 GFNTFLP 69
Score = 29.6 bits (65), Expect = 8.4, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 3/60 (5%)
Query: 353 LSFCEKVKDKLRDD---YQEFLRCLHLYTKEIITRSELQSLVGDLLGRYPDLMDGFNGFL 409
LS+ ++VK + Y +FL + + + I + S V L +PDL+ GFN FL
Sbjct: 9 LSYLDQVKLQFGSQPQVYNDFLDIMKEFKSQSIDTPGVISRVSQLFKGHPDLIMGFNTFL 68
>pdb|2CZY|A Chain A, Solution Structure Of The NrsfREST-Msin3b Pah1 Complex
Length = 77
Score = 84.7 bits (208), Expect = 2e-16, Method: Composition-based stats.
Identities = 41/71 (57%), Positives = 48/71 (67%)
Query: 47 DALAYLKAVKDIFQDKREKYDDFLEVMKDFKAQRIDTAGVIARVKELFKGHRDLILGFNT 106
DAL YL VK F Y+ FLE+MK+FK+Q IDT GVI RV +LF H DLI+GFN
Sbjct: 6 DALTYLDQVKIRFGSDPATYNGFLEIMKEFKSQSIDTPGVIRRVSQLFHEHPDLIVGFNA 65
Query: 107 FLPKGYEITLP 117
FLP GY I +P
Sbjct: 66 FLPLGYRIDIP 76
Score = 58.2 bits (139), Expect = 3e-08, Method: Composition-based stats.
Identities = 24/68 (35%), Positives = 40/68 (58%)
Query: 128 PVEFEEAINFVNKIKTRFQGDDHVYKSFLDILNMYRKENKSITEVYQEVEALFQDHPDLL 187
PV E+A+ +++++K RF D Y FL+I+ ++ ++ V + V LF +HPDL+
Sbjct: 1 PVHVEDALTYLDQVKIRFGSDPATYNGFLEIMKEFKSQSIDTPGVIRRVSQLFHEHPDLI 60
Query: 188 EEFTHFLP 195
F FLP
Sbjct: 61 VGFNAFLP 68
Score = 30.8 bits (68), Expect = 3.8, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 353 LSFCEKVKDKLRDD---YQEFLRCLHLYTKEIITRSELQSLVGDLLGRYPDLMDGFNGFL 409
L++ ++VK + D Y FL + + + I + V L +PDL+ GFN FL
Sbjct: 8 LTYLDQVKIRFGSDPATYNGFLEIMKEFKSQSIDTPGVIRRVSQLFHEHPDLIVGFNAFL 67
>pdb|2CR7|A Chain A, Solution Structure Of The First Pah Domain Of The Mouse
Transcriptional Repressor Sin3b
Length = 80
Score = 80.1 bits (196), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 38/65 (58%), Positives = 44/65 (67%)
Query: 47 DALAYLKAVKDIFQDKREKYDDFLEVMKDFKAQRIDTAGVIARVKELFKGHRDLILGFNT 106
DAL YL VK F Y+ FLE+MK+FK+Q IDT GVI RV +LF H DLI+GFN
Sbjct: 12 DALTYLDQVKIRFGSDPATYNGFLEIMKEFKSQSIDTPGVIRRVSQLFHEHPDLIVGFNA 71
Query: 107 FLPKG 111
FLP G
Sbjct: 72 FLPSG 76
Score = 55.8 bits (133), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 43/74 (58%), Gaps = 2/74 (2%)
Query: 129 VEFEEAINFVNKIKTRFQGDDHVYKSFLDILNMYRKENKSITEVYQEVEALFQDHPDLLE 188
V E+A+ +++++K RF D Y FL+I+ ++ ++ V + V LF +HPDL+
Sbjct: 8 VHVEDALTYLDQVKIRFGSDPATYNGFLEIMKEFKSQSIDTPGVIRRVSQLFHEHPDLIV 67
Query: 189 EFTHFLPDSSGAAS 202
F FLP SG +S
Sbjct: 68 GFNAFLP--SGPSS 79
Score = 32.3 bits (72), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 3/66 (4%)
Query: 353 LSFCEKVKDKLRDD---YQEFLRCLHLYTKEIITRSELQSLVGDLLGRYPDLMDGFNGFL 409
L++ ++VK + D Y FL + + + I + V L +PDL+ GFN FL
Sbjct: 14 LTYLDQVKIRFGSDPATYNGFLEIMKEFKSQSIDTPGVIRRVSQLFHEHPDLIVGFNAFL 73
Query: 410 ARCEKS 415
S
Sbjct: 74 PSGPSS 79
>pdb|1G1E|B Chain B, Nmr Structure Of The Human Mad1 Transrepression Domain Sid
In Complex With Mammalian Sin3a Pah2 Domain
pdb|1S5Q|B Chain B, Solution Structure Of Mad1 Sid-Msin3a Pah2 Complex
pdb|1S5R|B Chain B, Solution Structure Of Hbp1 Sid-Msin3a Pah2 Complex
Length = 89
Score = 77.8 bits (190), Expect = 3e-14, Method: Composition-based stats.
Identities = 40/84 (47%), Positives = 53/84 (63%), Gaps = 13/84 (15%)
Query: 127 KPVEFEEAINFVNKIKTRFQGDDHVYKSFLDILNMYRKENKSI-------------TEVY 173
+PVEF AIN+VNKIK RFQG +YK+FL+IL+ Y+KE ++ EVY
Sbjct: 6 QPVEFNHAINYVNKIKNRFQGQPDIYKAFLEILHTYQKEQRNAKEAGGNYTPALTEQEVY 65
Query: 174 QEVEALFQDHPDLLEEFTHFLPDS 197
+V LF++ DLL EF FLPD+
Sbjct: 66 AQVARLFKNQEDLLSEFGQFLPDA 89
Score = 38.1 bits (87), Expect = 0.027, Method: Composition-based stats.
Identities = 26/82 (31%), Positives = 39/82 (47%), Gaps = 13/82 (15%)
Query: 41 QKLTTNDALAYLKAVKDIFQDKREKYDDFLEVMKDF-KAQR------------IDTAGVI 87
Q + N A+ Y+ +K+ FQ + + Y FLE++ + K QR + V
Sbjct: 6 QPVEFNHAINYVNKIKNRFQGQPDIYKAFLEILHTYQKEQRNAKEAGGNYTPALTEQEVY 65
Query: 88 ARVKELFKGHRDLILGFNTFLP 109
A+V LFK DL+ F FLP
Sbjct: 66 AQVARLFKNQEDLLSEFGQFLP 87
Score = 30.4 bits (67), Expect = 4.9, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 16/84 (19%)
Query: 342 KNAMKSMFSQELSFCEKVKDKLR---DDYQEFLRCLHLYTKE-------------IITRS 385
+N F+ +++ K+K++ + D Y+ FL LH Y KE +T
Sbjct: 3 QNNQPVEFNHAINYVNKIKNRFQGQPDIYKAFLEILHTYQKEQRNAKEAGGNYTPALTEQ 62
Query: 386 ELQSLVGDLLGRYPDLMDGFNGFL 409
E+ + V L DL+ F FL
Sbjct: 63 EVYAQVARLFKNQEDLLSEFGQFL 86
>pdb|2L9S|B Chain B, Solution Structure Of Pf1 Sid1-Msin3a Pah2 Complex
Length = 94
Score = 77.0 bits (188), Expect = 5e-14, Method: Composition-based stats.
Identities = 40/85 (47%), Positives = 54/85 (63%), Gaps = 13/85 (15%)
Query: 127 KPVEFEEAINFVNKIKTRFQGDDHVYKSFLDILNMYRKENKSI-------------TEVY 173
+PVEF AIN+VNKIK RFQG +YK+FL+IL+ Y+KE ++ EVY
Sbjct: 9 QPVEFNHAINYVNKIKNRFQGQPDIYKAFLEILHTYQKEQRNAKEAGGNYTPALTEQEVY 68
Query: 174 QEVEALFQDHPDLLEEFTHFLPDSS 198
+V LF++ DLL EF FLPD++
Sbjct: 69 AQVARLFKNQEDLLSEFGQFLPDAN 93
Score = 37.4 bits (85), Expect = 0.038, Method: Composition-based stats.
Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 13/82 (15%)
Query: 41 QKLTTNDALAYLKAVKDIFQDKREKYDDFLEVMKDFKAQRIDT--AG-----------VI 87
Q + N A+ Y+ +K+ FQ + + Y FLE++ ++ ++ + AG V
Sbjct: 9 QPVEFNHAINYVNKIKNRFQGQPDIYKAFLEILHTYQKEQRNAKEAGGNYTPALTEQEVY 68
Query: 88 ARVKELFKGHRDLILGFNTFLP 109
A+V LFK DL+ F FLP
Sbjct: 69 AQVARLFKNQEDLLSEFGQFLP 90
Score = 30.0 bits (66), Expect = 6.8, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 16/84 (19%)
Query: 342 KNAMKSMFSQELSFCEKVKDKLR---DDYQEFLRCLHLYTKE-------------IITRS 385
+N F+ +++ K+K++ + D Y+ FL LH Y KE +T
Sbjct: 6 QNNQPVEFNHAINYVNKIKNRFQGQPDIYKAFLEILHTYQKEQRNAKEAGGNYTPALTEQ 65
Query: 386 ELQSLVGDLLGRYPDLMDGFNGFL 409
E+ + V L DL+ F FL
Sbjct: 66 EVYAQVARLFKNQEDLLSEFGQFL 89
>pdb|2F05|A Chain A, Solution Structure Of Free Pah2 Domain Of Msin3b
Length = 105
Score = 67.0 bits (162), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 37/79 (46%), Positives = 48/79 (60%), Gaps = 10/79 (12%)
Query: 129 VEFEEAINFVNKIKTRFQGDDHVYKSFLDILNMYRKE----------NKSITEVYQEVEA 178
VEF AI++VNKIKTRF +Y+SFL+IL+ Y+KE S EV+ EV
Sbjct: 5 VEFNNAISYVNKIKTRFLDHPEIYRSFLEILHTYQKEQLHTKGRPFRGMSEEEVFTEVAN 64
Query: 179 LFQDHPDLLEEFTHFLPDS 197
LF+ DLL EF FLP++
Sbjct: 65 LFRGQEDLLSEFGQFLPEA 83
Score = 48.5 bits (114), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 10/76 (13%)
Query: 46 NDALAYLKAVKDIFQDKREKYDDFLEVMKDFKAQRIDTAG----------VIARVKELFK 95
N+A++Y+ +K F D E Y FLE++ ++ +++ T G V V LF+
Sbjct: 8 NNAISYVNKIKTRFLDHPEIYRSFLEILHTYQKEQLHTKGRPFRGMSEEEVFTEVANLFR 67
Query: 96 GHRDLILGFNTFLPKG 111
G DL+ F FLP+
Sbjct: 68 GQEDLLSEFGQFLPEA 83
Score = 31.6 bits (70), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 36/80 (45%), Gaps = 13/80 (16%)
Query: 349 FSQELSFCEKVKDKLRDD---YQEFLRCLHLYTKEII----------TRSELQSLVGDLL 395
F+ +S+ K+K + D Y+ FL LH Y KE + + E+ + V +L
Sbjct: 7 FNNAISYVNKIKTRFLDHPEIYRSFLEILHTYQKEQLHTKGRPFRGMSEEEVFTEVANLF 66
Query: 396 GRYPDLMDGFNGFLARCEKS 415
DL+ F FL ++S
Sbjct: 67 RGQEDLLSEFGQFLPEAKRS 86
>pdb|1E91|A Chain A, Structure Of The Complex Of The Mad1-Sin3b Interaction
Domains
pdb|1PD7|A Chain A, Extended Sid Of Mad1 Bound To The Pah2 Domain Of Msin3b
Length = 85
Score = 65.9 bits (159), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 37/79 (46%), Positives = 48/79 (60%), Gaps = 10/79 (12%)
Query: 129 VEFEEAINFVNKIKTRFQGDDHVYKSFLDILNMYRKEN----------KSITEVYQEVEA 178
VEF AI++VNKIKTRF +Y+SFL+IL+ Y+KE S EV+ EV
Sbjct: 5 VEFNNAISYVNKIKTRFLDHPEIYRSFLEILHTYQKEQLHTKGRPFRGMSEEEVFTEVAN 64
Query: 179 LFQDHPDLLEEFTHFLPDS 197
LF+ DLL EF FLP++
Sbjct: 65 LFRGQEDLLSEFGQFLPEA 83
Score = 47.4 bits (111), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 10/76 (13%)
Query: 46 NDALAYLKAVKDIFQDKREKYDDFLEVMKDFKAQRIDTAG----------VIARVKELFK 95
N+A++Y+ +K F D E Y FLE++ ++ +++ T G V V LF+
Sbjct: 8 NNAISYVNKIKTRFLDHPEIYRSFLEILHTYQKEQLHTKGRPFRGMSEEEVFTEVANLFR 67
Query: 96 GHRDLILGFNTFLPKG 111
G DL+ F FLP+
Sbjct: 68 GQEDLLSEFGQFLPEA 83
Score = 30.4 bits (67), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 13/79 (16%)
Query: 349 FSQELSFCEKVKDKLRDD---YQEFLRCLHLYTKEII----------TRSELQSLVGDLL 395
F+ +S+ K+K + D Y+ FL LH Y KE + + E+ + V +L
Sbjct: 7 FNNAISYVNKIKTRFLDHPEIYRSFLEILHTYQKEQLHTKGRPFRGMSEEEVFTEVANLF 66
Query: 396 GRYPDLMDGFNGFLARCEK 414
DL+ F FL ++
Sbjct: 67 RGQEDLLSEFGQFLPEAKR 85
>pdb|2LD7|B Chain B, Solution Structure Of The Msin3a Pah3-Sap30 Sid Complex
Length = 75
Score = 58.5 bits (140), Expect = 2e-08, Method: Composition-based stats.
Identities = 30/73 (41%), Positives = 44/73 (60%), Gaps = 2/73 (2%)
Query: 343 NAMKSMFSQELSFCEKVKDKLR--DDYQEFLRCLHLYTKEIITRSELQSLVGDLLGRYPD 400
NA K E F +KV+ LR + Y+ FLRCL ++ +E+I+R+EL LV LG++P+
Sbjct: 2 NASKHGVGTESLFFDKVRKALRSAEAYENFLRCLVIFNQEVISRAELVQLVSPFLGKFPE 61
Query: 401 LMDGFNGFLARCE 413
L + F FL E
Sbjct: 62 LFNWFKNFLGYKE 74
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
0.314 0.131 0.377
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 27,728,317
Number of Sequences: 62578
Number of extensions: 1087780
Number of successful extensions: 2089
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 2058
Number of HSP's gapped (non-prelim): 25
length of query: 1031
length of database: 14,973,337
effective HSP length: 109
effective length of query: 922
effective length of database: 8,152,335
effective search space: 7516452870
effective search space used: 7516452870
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 56 (26.2 bits)