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= 000557
(1423 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 = 87.4 bits (215), Expect = 5e-17, Method: Composition-based stats.
Identities = 41/71 (57%), Positives = 52/71 (73%)
Query: 74 QKLTTSDALTYLKEVKDMFQDQREKYDMFLEVMKDFKAQRTDTAGVIARVKDLFKGHNNL 133
Q+L DAL+YL +VK F Q + Y+ FL++MK+FK+Q DT GVI+RV LFKGH +L
Sbjct: 1 QRLKVEDALSYLDQVKLQFGSQPQVYNDFLDIMKEFKSQSIDTPGVISRVSQLFKGHPDL 60
Query: 134 IFGFNTFLPKG 144
I GFNTFLP G
Sbjct: 61 IMGFNTFLPPG 71
Score = 51.2 bits (121), Expect = 4e-06, Method: Composition-based stats.
Identities = 22/69 (31%), Positives = 43/69 (62%)
Query: 158 KTVEFEEAITFVNKIKKRFHNDEHVYKSFLEILNMYRKEHKDINEVYSEVASLFEDHADL 217
+ ++ E+A+++++++K +F + VY FL+I+ ++ + D V S V+ LF+ H DL
Sbjct: 1 QRLKVEDALSYLDQVKLQFGSQPQVYNDFLDIMKEFKSQSIDTPGVISRVSQLFKGHPDL 60
Query: 218 LEEFTRFLP 226
+ F FLP
Sbjct: 61 IMGFNTFLP 69
>pdb|2CZY|A Chain A, Solution Structure Of The NrsfREST-Msin3b Pah1 Complex
Length = 77
Score = 80.1 bits (196), Expect = 8e-15, Method: Composition-based stats.
Identities = 39/70 (55%), Positives = 46/70 (65%)
Query: 80 DALTYLKEVKDMFQDQREKYDMFLEVMKDFKAQRTDTAGVIARVKDLFKGHNNLIFGFNT 139
DALTYL +VK F Y+ FLE+MK+FK+Q DT GVI RV LF H +LI GFN
Sbjct: 6 DALTYLDQVKIRFGSDPATYNGFLEIMKEFKSQSIDTPGVIRRVSQLFHEHPDLIVGFNA 65
Query: 140 FLPKGYEITL 149
FLP GY I +
Sbjct: 66 FLPLGYRIDI 75
Score = 56.2 bits (134), Expect = 1e-07, Method: Composition-based stats.
Identities = 25/67 (37%), Positives = 40/67 (59%)
Query: 160 VEFEEAITFVNKIKKRFHNDEHVYKSFLEILNMYRKEHKDINEVYSEVASLFEDHADLLE 219
V E+A+T+++++K RF +D Y FLEI+ ++ + D V V+ LF +H DL+
Sbjct: 2 VHVEDALTYLDQVKIRFGSDPATYNGFLEIMKEFKSQSIDTPGVIRRVSQLFHEHPDLIV 61
Query: 220 EFTRFLP 226
F FLP
Sbjct: 62 GFNAFLP 68
>pdb|2CR7|A Chain A, Solution Structure Of The First Pah Domain Of The Mouse
Transcriptional Repressor Sin3b
Length = 80
Score = 76.6 bits (187), Expect = 8e-14, Method: Composition-based stats.
Identities = 38/72 (52%), Positives = 45/72 (62%)
Query: 73 SQKLTTSDALTYLKEVKDMFQDQREKYDMFLEVMKDFKAQRTDTAGVIARVKDLFKGHNN 132
S + DALTYL +VK F Y+ FLE+MK+FK+Q DT GVI RV LF H +
Sbjct: 5 SSGVHVEDALTYLDQVKIRFGSDPATYNGFLEIMKEFKSQSIDTPGVIRRVSQLFHEHPD 64
Query: 133 LIFGFNTFLPKG 144
LI GFN FLP G
Sbjct: 65 LIVGFNAFLPSG 76
Score = 55.8 bits (133), Expect = 1e-07, Method: Composition-based stats.
Identities = 25/67 (37%), Positives = 40/67 (59%)
Query: 160 VEFEEAITFVNKIKKRFHNDEHVYKSFLEILNMYRKEHKDINEVYSEVASLFEDHADLLE 219
V E+A+T+++++K RF +D Y FLEI+ ++ + D V V+ LF +H DL+
Sbjct: 8 VHVEDALTYLDQVKIRFGSDPATYNGFLEIMKEFKSQSIDTPGVIRRVSQLFHEHPDLIV 67
Query: 220 EFTRFLP 226
F FLP
Sbjct: 68 GFNAFLP 74
>pdb|2L9S|B Chain B, Solution Structure Of Pf1 Sid1-Msin3a Pah2 Complex
Length = 94
Score = 75.9 bits (185), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 38/86 (44%), Positives = 53/86 (61%), Gaps = 13/86 (15%)
Query: 158 KTVEFEEAITFVNKIKKRFHNDEHVYKSFLEILNMYRKEHKDI-------------NEVY 204
+ VEF AI +VNKIK RF +YK+FLEIL+ Y+KE ++ EVY
Sbjct: 9 QPVEFNHAINYVNKIKNRFQGQPDIYKAFLEILHTYQKEQRNAKEAGGNYTPALTEQEVY 68
Query: 205 SEVASLFEDHADLLEEFTRFLPDTSA 230
++VA LF++ DLL EF +FLPD ++
Sbjct: 69 AQVARLFKNQEDLLSEFGQFLPDANS 94
Score = 40.4 bits (93), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 43/84 (51%), Gaps = 13/84 (15%)
Query: 72 TSQKLTTSDALTYLKEVKDMFQDQREKYDMFLEVMKDFKAQRTDT--AG----------- 118
+Q + + A+ Y+ ++K+ FQ Q + Y FLE++ ++ ++ + AG
Sbjct: 7 NNQPVEFNHAINYVNKIKNRFQGQPDIYKAFLEILHTYQKEQRNAKEAGGNYTPALTEQE 66
Query: 119 VIARVKDLFKGHNNLIFGFNTFLP 142
V A+V LFK +L+ F FLP
Sbjct: 67 VYAQVARLFKNQEDLLSEFGQFLP 90
>pdb|2F05|A Chain A, Solution Structure Of Free Pah2 Domain Of Msin3b
Length = 105
Score = 73.9 bits (180), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 42/102 (41%), Positives = 59/102 (57%), Gaps = 10/102 (9%)
Query: 159 TVEFEEAITFVNKIKKRFHNDEHVYKSFLEILNMYRKEHKDIN----------EVYSEVA 208
+VEF AI++VNKIK RF + +Y+SFLEIL+ Y+KE EV++EVA
Sbjct: 4 SVEFNNAISYVNKIKTRFLDHPEIYRSFLEILHTYQKEQLHTKGRPFRGMSEEEVFTEVA 63
Query: 209 SLFEDHADLLEEFTRFLPDTSATSLSHNIPFVRNSTQRGNER 250
+LF DLL EF +FLP+ + + N NS Q+ E+
Sbjct: 64 NLFRGQEDLLSEFGQFLPEAKRSLFTGNGSCEMNSGQKNEEK 105
Score = 43.9 bits (102), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 10/82 (12%)
Query: 73 SQKLTTSDALTYLKEVKDMFQDQREKYDMFLEVMKDFKAQRTDTAG----------VIAR 122
S + ++A++Y+ ++K F D E Y FLE++ ++ ++ T G V
Sbjct: 2 SDSVEFNNAISYVNKIKTRFLDHPEIYRSFLEILHTYQKEQLHTKGRPFRGMSEEEVFTE 61
Query: 123 VKDLFKGHNNLIFGFNTFLPKG 144
V +LF+G +L+ F FLP+
Sbjct: 62 VANLFRGQEDLLSEFGQFLPEA 83
>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 = 72.0 bits (175), Expect = 2e-12, Method: Composition-based stats.
Identities = 38/83 (45%), Positives = 51/83 (61%), Gaps = 13/83 (15%)
Query: 158 KTVEFEEAITFVNKIKKRFHNDEHVYKSFLEILNMYRKEHKDI-------------NEVY 204
+ VEF AI +VNKIK RF +YK+FLEIL+ Y+KE ++ EVY
Sbjct: 6 QPVEFNHAINYVNKIKNRFQGQPDIYKAFLEILHTYQKEQRNAKEAGGNYTPALTEQEVY 65
Query: 205 SEVASLFEDHADLLEEFTRFLPD 227
++VA LF++ DLL EF +FLPD
Sbjct: 66 AQVARLFKNQEDLLSEFGQFLPD 88
Score = 37.7 bits (86), Expect = 0.042, Method: Composition-based stats.
Identities = 24/83 (28%), Positives = 43/83 (51%), Gaps = 13/83 (15%)
Query: 73 SQKLTTSDALTYLKEVKDMFQDQREKYDMFLEVMKDFKAQRTDT--AG-----------V 119
+Q + + A+ Y+ ++K+ FQ Q + Y FLE++ ++ ++ + AG V
Sbjct: 5 NQPVEFNHAINYVNKIKNRFQGQPDIYKAFLEILHTYQKEQRNAKEAGGNYTPALTEQEV 64
Query: 120 IARVKDLFKGHNNLIFGFNTFLP 142
A+V LFK +L+ F FLP
Sbjct: 65 YAQVARLFKNQEDLLSEFGQFLP 87
>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 = 68.6 bits (166), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 37/79 (46%), Positives = 50/79 (63%), Gaps = 10/79 (12%)
Query: 159 TVEFEEAITFVNKIKKRFHNDEHVYKSFLEILNMYRKEHKDIN----------EVYSEVA 208
+VEF AI++VNKIK RF + +Y+SFLEIL+ Y+KE EV++EVA
Sbjct: 4 SVEFNNAISYVNKIKTRFLDHPEIYRSFLEILHTYQKEQLHTKGRPFRGMSEEEVFTEVA 63
Query: 209 SLFEDHADLLEEFTRFLPD 227
+LF DLL EF +FLP+
Sbjct: 64 NLFRGQEDLLSEFGQFLPE 82
Score = 43.9 bits (102), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 10/82 (12%)
Query: 73 SQKLTTSDALTYLKEVKDMFQDQREKYDMFLEVMKDFKAQRTDTAG----------VIAR 122
S + ++A++Y+ ++K F D E Y FLE++ ++ ++ T G V
Sbjct: 2 SDSVEFNNAISYVNKIKTRFLDHPEIYRSFLEILHTYQKEQLHTKGRPFRGMSEEEVFTE 61
Query: 123 VKDLFKGHNNLIFGFNTFLPKG 144
V +LF+G +L+ F FLP+
Sbjct: 62 VANLFRGQEDLLSEFGQFLPEA 83
>pdb|2LD7|B Chain B, Solution Structure Of The Msin3a Pah3-Sap30 Sid Complex
Length = 75
Score = 45.8 bits (107), Expect = 2e-04, Method: Composition-based stats.
Identities = 23/58 (39%), Positives = 38/58 (65%), Gaps = 1/58 (1%)
Query: 371 IFCDKVKEKLCSDD-YQAFLKCLHIYSNGIIKRNDLQNLVTDLLGKYMDLMDEFNHFF 427
+F DKV++ L S + Y+ FL+CL I++ +I R +L LV+ LGK+ +L + F +F
Sbjct: 13 LFFDKVRKALRSAEAYENFLRCLVIFNQEVISRAELVQLVSPFLGKFPELFNWFKNFL 70
>pdb|3RCH|A Chain A, Crystal Structure Of Human Aromatic L-Amino Acid
Decarboxylase (Aadc) In The Open Conformation With Llp
And Plp Bound To Chain-A And Chain- B Respectively
Length = 480
Score = 33.9 bits (76), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 35/73 (47%), Gaps = 7/73 (9%)
Query: 535 GSEDYSFKHMRRNQYEESLFRCEDDRFE------LDMLLESVSSTAKRAEELLNSINENK 588
G + Y KH++ + ESL R +D RFE L ++ + + K E LL IN K
Sbjct: 373 GLQAYIRKHVQLSHEFESLVR-QDPRFEICVEVILGLVCFRLKGSNKVNEALLQRINSAK 431
Query: 589 ITLETPFHLKDHF 601
P HL+D F
Sbjct: 432 KIHLVPCHLRDKF 444
>pdb|3RBF|A Chain A, Crystal Structure Of Human Aromatic L-Amino Acid
Decarboxylase (Aadc) In The Apo Form
pdb|3RBF|B Chain B, Crystal Structure Of Human Aromatic L-Amino Acid
Decarboxylase (Aadc) In The Apo Form
pdb|3RBL|A Chain A, Crystal Structure Of Human Aromatic L-Amino Acid
Decarboxylase (Aadc) In The Apo Form
pdb|3RBL|B Chain B, Crystal Structure Of Human Aromatic L-Amino Acid
Decarboxylase (Aadc) In The Apo Form
pdb|3RCH|B Chain B, Crystal Structure Of Human Aromatic L-Amino Acid
Decarboxylase (Aadc) In The Open Conformation With Llp
And Plp Bound To Chain-A And Chain- B Respectively
Length = 480
Score = 33.9 bits (76), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 35/73 (47%), Gaps = 7/73 (9%)
Query: 535 GSEDYSFKHMRRNQYEESLFRCEDDRFE------LDMLLESVSSTAKRAEELLNSINENK 588
G + Y KH++ + ESL R +D RFE L ++ + + K E LL IN K
Sbjct: 373 GLQAYIRKHVQLSHEFESLVR-QDPRFEICVEVILGLVCFRLKGSNKVNEALLQRINSAK 431
Query: 589 ITLETPFHLKDHF 601
P HL+D F
Sbjct: 432 KIHLVPCHLRDKF 444
>pdb|2BV3|A Chain A, Crystal Structure Of A Mutant Elongation Factor G Trapped
With A Gtp Analogue
Length = 691
Score = 31.2 bits (69), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 35/118 (29%), Positives = 51/118 (43%), Gaps = 13/118 (11%)
Query: 906 NSHGRTGSEMMSGYGAASLR-PCDAAKDDLKHEANVNPVPPSEVTQGCDLAKPTLLENGA 964
++H TGS ++SG G SL D K + K +ANV +V + KP +E
Sbjct: 441 STHPETGSTIISGMGELSLEIIVDRLKREFKVDANVG---KPQVAYRETITKPVDVEGKF 497
Query: 965 LRD-GAKGINYHEKSVGPTKIEKEEGELSPNGDFEEDNFGVYGDAAVKTLPKAKHGVE 1021
+R G +G H K K+E L FE N V G + +P + G+E
Sbjct: 498 IRQTGGRGQYGHVK----IKVEP----LPRGSGFEFVNAIVGGVIPKEYIPAVQKGIE 547
>pdb|3IYJ|F Chain F, Bovine Papillomavirus Type 1 Outer Capsid
pdb|3IYJ|A Chain A, Bovine Papillomavirus Type 1 Outer Capsid
pdb|3IYJ|B Chain B, Bovine Papillomavirus Type 1 Outer Capsid
pdb|3IYJ|C Chain C, Bovine Papillomavirus Type 1 Outer Capsid
pdb|3IYJ|D Chain D, Bovine Papillomavirus Type 1 Outer Capsid
pdb|3IYJ|E Chain E, Bovine Papillomavirus Type 1 Outer Capsid
Length = 495
Score = 31.2 bits (69), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 889 VGERVANSDASPAIGAENSHGRTGSEMMSGYGAASLRPCDAAKDDL 934
V +R+ N A P + +N H G M G+GAA+ + +A+K DL
Sbjct: 172 VTDRLENG-ACPPLELKNKHIEDGDMMEIGFGAANFKEINASKSDL 216
>pdb|3MKD|A Chain A, Crystal Structure Of Myosin-2 Dictyostelium Discoideum
Motor Domain S456y Mutant In Complex With
Adp-Orthovanadate
Length = 692
Score = 30.4 bits (67), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 4/79 (5%)
Query: 355 SYDDKDAL-KSIYNQGFIF-CDKVKEKLCSDDYQAFLKCLHIYSNGIIKRNDLQNLVTDL 412
S +DAL K++Y + F++ K+ LC + F+ L IY I K N + L +
Sbjct: 413 SSSSRDALVKALYGRLFLWLVKKINNVLCQERKAYFIGVLDIYGFEIFKVNSFEQLCINY 472
Query: 413 LGKYMDLMDEFNHFFERCE 431
+ L FNH + E
Sbjct: 473 TNE--KLQQFFNHHMFKLE 489
>pdb|1W9J|A Chain A, Myosin Ii Dictyostelium Discoideum Motor Domain S456y
Bound With Mgadp-Alf4
Length = 770
Score = 30.0 bits (66), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 4/79 (5%)
Query: 355 SYDDKDAL-KSIYNQGFIF-CDKVKEKLCSDDYQAFLKCLHIYSNGIIKRNDLQNLVTDL 412
S +DAL K++Y + F++ K+ LC + F+ L IY I K N + L +
Sbjct: 414 SSSSRDALVKALYGRLFLWLVKKINNVLCQERKAYFIGVLDIYGFEIFKVNSFEQLCINY 473
Query: 413 LGKYMDLMDEFNHFFERCE 431
+ L FNH + E
Sbjct: 474 TNE--KLQQFFNHHMFKLE 490
>pdb|1W9I|A Chain A, Myosin Ii Dictyostelium Discoideum Motor Domain S456y
Bound With Mgadp-Befx
Length = 770
Score = 30.0 bits (66), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 4/79 (5%)
Query: 355 SYDDKDAL-KSIYNQGFIF-CDKVKEKLCSDDYQAFLKCLHIYSNGIIKRNDLQNLVTDL 412
S +DAL K++Y + F++ K+ LC + F+ L IY I K N + L +
Sbjct: 414 SSSSRDALVKALYGRLFLWLVKKINNVLCQERKAYFIGVLDIYGFEIFKVNSFEQLCINY 473
Query: 413 LGKYMDLMDEFNHFFERCE 431
+ L FNH + E
Sbjct: 474 TNE--KLQQFFNHHMFKLE 490
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
0.316 0.132 0.380
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 39,247,666
Number of Sequences: 62578
Number of extensions: 1618651
Number of successful extensions: 4071
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 4043
Number of HSP's gapped (non-prelim): 36
length of query: 1423
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1312
effective length of database: 8,027,179
effective search space: 10531658848
effective search space used: 10531658848
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.9 bits)