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= 016325
(391 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 = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 47 AVAFLKEMRKRFRKQHDGIFVRFCQLLSDFTKSKIDRDSLGLEVKELFKGHDDLIHKYNV 106
A+++L +++ +F Q ++ F ++ +F ID + V +LFKGH DLI +N
Sbjct: 8 ALSYLDQVKLQFGSQPQ-VYNDFLDIMKEFKSQSIDTPGVISRVSQLFKGHPDLIMGFNT 66
Query: 107 FV 108
F+
Sbjct: 67 FL 68
>pdb|2CR7|A Chain A, Solution Structure Of The First Pah Domain Of The Mouse
Transcriptional Repressor Sin3b
Length = 80
Score = 32.7 bits (73), Expect = 0.34, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 47 AVAFLKEMRKRFRKQHDGIFVRFCQLLSDFTKSKIDRDSLGLEVKELFKGHDDLIHKYNV 106
A+ +L +++ RF + F +++ +F ID + V +LF H DLI +N
Sbjct: 13 ALTYLDQVKIRF-GSDPATYNGFLEIMKEFKSQSIDTPGVIRRVSQLFHEHPDLIVGFNA 71
Query: 107 FV 108
F+
Sbjct: 72 FL 73
>pdb|2CZY|A Chain A, Solution Structure Of The NrsfREST-Msin3b Pah1 Complex
Length = 77
Score = 32.7 bits (73), Expect = 0.34, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 47 AVAFLKEMRKRFRKQHDGIFVRFCQLLSDFTKSKIDRDSLGLEVKELFKGHDDLIHKYNV 106
A+ +L +++ RF + F +++ +F ID + V +LF H DLI +N
Sbjct: 7 ALTYLDQVKIRF-GSDPATYNGFLEIMKEFKSQSIDTPGVIRRVSQLFHEHPDLIVGFNA 65
Query: 107 FV 108
F+
Sbjct: 66 FL 67
>pdb|2F05|A Chain A, Solution Structure Of Free Pah2 Domain Of Msin3b
Length = 105
Score = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 38/72 (52%), Gaps = 11/72 (15%)
Query: 47 AVAFLKEMRKRFRKQHDGIFVRFCQLLSDFTKSKI---DRDSLGL-------EVKELFKG 96
A++++ +++ RF H I+ F ++L + K ++ R G+ EV LF+G
Sbjct: 10 AISYVNKIKTRFL-DHPEIYRSFLEILHTYQKEQLHTKGRPFRGMSEEEVFTEVANLFRG 68
Query: 97 HDDLIHKYNVFV 108
+DL+ ++ F+
Sbjct: 69 QEDLLSEFGQFL 80
>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 = 28.9 bits (63), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 38/72 (52%), Gaps = 11/72 (15%)
Query: 47 AVAFLKEMRKRFRKQHDGIFVRFCQLLSDFTKSKI---DRDSLGL-------EVKELFKG 96
A++++ +++ RF H I+ F ++L + K ++ R G+ EV LF+G
Sbjct: 10 AISYVNKIKTRFL-DHPEIYRSFLEILHTYQKEQLHTKGRPFRGMSEEEVFTEVANLFRG 68
Query: 97 HDDLIHKYNVFV 108
+DL+ ++ F+
Sbjct: 69 QEDLLSEFGQFL 80
>pdb|3N23|A Chain A, Crystal Structure Of The High Affinity Complex Between
Ouabain And The E2p Form Of The Sodium-Potassium Pump
pdb|3N23|C Chain C, Crystal Structure Of The High Affinity Complex Between
Ouabain And The E2p Form Of The Sodium-Potassium Pump
pdb|3N2F|A Chain A, Crystal Structure Of The Sodium-Potassium Pump
pdb|3N2F|C Chain C, Crystal Structure Of The Sodium-Potassium Pump
Length = 992
Score = 28.5 bits (62), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 9/56 (16%)
Query: 309 NLHKNPETALPVILKSLKQKVEELVERRSDCNKIWAHVCAKNHDKLQEMQRELKNS 364
++HKNP TA P L +K E +++R C+ I H K Q + ELK++
Sbjct: 460 SIHKNPNTAEPRHLLVMKGAPERILDR---CSSILI------HGKEQPLDEELKDA 506
>pdb|3B8E|A Chain A, Crystal Structure Of The Sodium-Potassium Pump
pdb|3B8E|C Chain C, Crystal Structure Of The Sodium-Potassium Pump
pdb|3KDP|A Chain A, Crystal Structure Of The Sodium-potassium Pump
pdb|3KDP|C Chain C, Crystal Structure Of The Sodium-potassium Pump
Length = 998
Score = 28.5 bits (62), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 9/56 (16%)
Query: 309 NLHKNPETALPVILKSLKQKVEELVERRSDCNKIWAHVCAKNHDKLQEMQRELKNS 364
++HKNP TA P L +K E +++R C+ I H K Q + ELK++
Sbjct: 466 SIHKNPNTAEPRHLLVMKGAPERILDR---CSSILI------HGKEQPLDEELKDA 512
>pdb|1MI1|A Chain A, Crystal Structure Of The Ph-Beach Domain Of Human
Neurobeachin
pdb|1MI1|B Chain B, Crystal Structure Of The Ph-Beach Domain Of Human
Neurobeachin
Length = 414
Score = 28.1 bits (61), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 22/95 (23%), Positives = 43/95 (45%), Gaps = 7/95 (7%)
Query: 175 DLSKCKQVSPSYWRLPEYYWMPLASNRSEIG---DQVLNDNLVCASTGTERSSFKQRRRT 231
D S K++ P ++ LPE + + SN +G D+V+ +++ + F + R
Sbjct: 278 DTSDVKELIPEFYYLPEXF---VNSNGYNLGVREDEVVVNDVDLPPWAKKPEDFVRINRX 334
Query: 232 KQEEVLFKCEDDRFELDLLLGWMHSAAENVEKLMI 266
E C+ ++ +DL+ G+ E V L +
Sbjct: 335 ALESEFVSCQLHQW-IDLIFGYKQRGPEAVRALNV 368
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
0.318 0.134 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,210,698
Number of Sequences: 62578
Number of extensions: 379842
Number of successful extensions: 1174
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1167
Number of HSP's gapped (non-prelim): 16
length of query: 391
length of database: 14,973,337
effective HSP length: 101
effective length of query: 290
effective length of database: 8,652,959
effective search space: 2509358110
effective search space used: 2509358110
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: 52 (24.6 bits)