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= psy2231
(201 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1IML|A Chain A, Cysteine Rich Intestinal Protein, Nmr, 48 Structures
Length = 76
Score = 88.6 bits (218), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 36/57 (63%), Positives = 43/57 (75%)
Query: 49 NSMYLAERKTSLGKDWHGSCLRCENCNKTLVPGSHSEHDGKPYCNYPCYSALFSERS 105
+Y AER TSLGKDWH CL+CE C KTL G H+EH+GKPYCN+PCYSA+F +
Sbjct: 8 KEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKG 64
>pdb|2CU8|A Chain A, Solution Structure Of The Lim Domain Of Human
Cysteine-Rich Protein 2
Length = 76
Score = 84.7 bits (208), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 34/62 (54%), Positives = 44/62 (70%)
Query: 41 TSNAINLPNSMYLAERKTSLGKDWHGSCLRCENCNKTLVPGSHSEHDGKPYCNYPCYSAL 100
S ++Y AE+ +SLGKDWH CL+CE C+KTL PG H+EHDGKP+C+ PCY+ L
Sbjct: 9 ASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATL 68
Query: 101 FS 102
F
Sbjct: 69 FG 70
>pdb|1CTL|A Chain A, Structure Of The Carboxy-Terminal Lim Domain From The
Cysteine Rich Protein Crp
Length = 85
Score = 47.0 bits (110), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 49 NSMYLAERKTSLGKDWHGSCLRCENCNKTLVPGSHSEHDGKPYCNYPCYSALFSER 104
++Y AE+ GK WH SC RC C K+L + ++ DG+ YC CY+ F +
Sbjct: 16 QAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCK-GCYAKNFGPK 70
>pdb|1B8T|A Chain A, Solution Structure Of The Chicken Crp1
Length = 192
Score = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 49 NSMYLAERKTSLGKDWHGSCLRCENCNKTLVPGSHSEHDGKPYCNYPCYSALFSER 104
++Y AE+ GK WH SC RC C K+L + ++ DG+ YC CY+ F +
Sbjct: 123 QAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCK-GCYAKNFGPK 177
>pdb|1CXX|A Chain A, Mutant R122a Of Quail Cysteine And Glycine-Rich Protein,
Nmr, Minimized Structure
Length = 113
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 49 NSMYLAERKTSLGKDWHGSCLRCENCNKTLVPGSHSEHDGKPYCNYPCYSALFSERS 105
+S+Y AE+ GK WH +C RC C K+L + +E +G+ YC CY+ F +
Sbjct: 44 DSVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKG-CYAKNFGPKG 99
>pdb|1IBI|A Chain A, Quail Cysteine And Glycine-Rich Protein, Nmr, 15 Minimized
Model Structures
pdb|1QLI|A Chain A, Quail Cysteine And Glycine-Rich Protein, Nmr, Minimized
Average Structure
Length = 113
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 49 NSMYLAERKTSLGKDWHGSCLRCENCNKTLVPGSHSEHDGKPYCNYPCYSALFSERS 105
+S+Y AE+ GK WH +C RC C K+L + +E +G+ YC CY+ F +
Sbjct: 44 DSVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKG-CYAKNFGPKG 99
>pdb|2O13|A Chain A, Solution Structure Of The C-Terminal Lim Domain Of MlpCRP3
Length = 58
Score = 43.9 bits (102), Expect = 6e-05, Method: Composition-based stats.
Identities = 21/52 (40%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 50 SMYLAERKTSLGKDWHGSCLRCENCNKTLVPGSHSEHDGKPYCNYPCYSALF 101
S+Y AE+ GK WH +C RC C K+L + ++ DG+ YC CY+ F
Sbjct: 8 SVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKV-CYAKNF 58
>pdb|2CO8|A Chain A, Solution Structures Of The Lim Domain Of Human Nedd9
Interacting Protein With Calponin Homology And Lim
Domains
Length = 82
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 30/61 (49%), Gaps = 6/61 (9%)
Query: 38 QHHTSNAINL----PNSMYLAERKTSLGKDWHGSCLRCENCNKTLVPGSHSEH--DGKPY 91
QH + A +L +Y+ ER G +H SC RC C TL PG + +H DG Y
Sbjct: 8 QHQEAGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFY 67
Query: 92 C 92
C
Sbjct: 68 C 68
>pdb|2DJ7|A Chain A, Solution Structure Of 3rd Lim Domain Of Actin-Binding
Lim Protein 3
Length = 80
Score = 33.5 bits (75), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 59 SLGKDWHGSCLRCENCNKTLVPGSHSEHDGKPYCN 93
+L K WH SC +C+ C+ ++ G + DG PYC
Sbjct: 33 ALDKQWHVSCFKCQTCS-VILTGEYISKDGVPYCE 66
>pdb|2D8Y|A Chain A, Solution Structure Of The Lim Domain Of Epithelial Protein
Lost In Neoplasm
Length = 91
Score = 33.1 bits (74), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 45 INLPNSMYLAERKTSLGKDWHGSCLRCENCNKTLVPGSHSEHDGKPYCNYPCYSALFSER 104
+ ++Y ER + + +H SC RC CN L G+++ G+ YC P ++ LF +
Sbjct: 19 VECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCK-PHFNQLFKSK 77
Query: 105 SKF 107
+
Sbjct: 78 GNY 80
>pdb|1X3H|A Chain A, Solution Structure Of The Lim Domain Of Human Leupaxin
Length = 80
Score = 32.3 bits (72), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 64 WHGSCLRCENCNKTLVPGSHSEHDGKPYCN 93
WH C C +C + GS E DG+P+C
Sbjct: 37 WHPECFVCGDCFTSFSTGSFFELDGRPFCE 66
>pdb|2DAR|A Chain A, Solution Structure Of First Lim Domain Of Enigma-Like Pdz
And Lim Domains Protein
Length = 90
Score = 32.3 bits (72), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 36/92 (39%), Gaps = 8/92 (8%)
Query: 11 NSRGAGLQQYAMILDLLLSSSGRRYVLQHHTSNAINLPNSMYLAERKTSLGKDWHGSCLR 70
S G+ Q ++ +G+R + H + I P +L +LGK WH
Sbjct: 1 GSSGSSGDQDTLVQRAEHIPAGKRTPMCAHCNQVIRGP---FL----VALGKSWHPEEFN 53
Query: 71 CENCNKTLVPGSHSEHDGKPYCNYPCYSALFS 102
C +C T+ E G YC CY F+
Sbjct: 54 CAHCKNTMAYIGFVEEKGALYCEL-CYEKFFA 84
>pdb|1NYP|A Chain A, 4th Lim Domain Of Pinch Protein
pdb|1U5S|B Chain B, Nmr Structure Of The Complex Between Nck-2 Sh3 Domain And
Pinch-1 Lim4 Domain
Length = 66
Score = 31.6 bits (70), Expect = 0.30, Method: Composition-based stats.
Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 1/45 (2%)
Query: 59 SLGKDWHGSCLRCENCNKTLVPGSHSEHDGKPYCNYPCYSALFSE 103
++GK WH C C K + H E G YC Y+ LF +
Sbjct: 22 AMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETH-YNQLFGD 65
>pdb|2CUQ|A Chain A, Solution Structure Of Second Lim Domain From Human
Skeletal Muscle Lim-Protein 2
Length = 80
Score = 30.0 bits (66), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 18/41 (43%), Gaps = 1/41 (2%)
Query: 62 KDWHGSCLRCENCNKTLVPGSHSEHDGKPYCNYPCYSALFS 102
+ WH CL C C L + D PYC C+ LF+
Sbjct: 35 QPWHRECLVCTGCQTPLAGQQFTSRDEDPYC-VACFGELFA 74
>pdb|2O10|A Chain A, Solution Structure Of The N-Terminal Lim Domain Of
MlpCRP3
Length = 60
Score = 30.0 bits (66), Expect = 0.84, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 50 SMYLAERKTSLGKDWHGSCLRCENCNKTLVPGSHSEHDGKPYCNYPCY 97
++Y AE G+ +H +C C C K L + + H+ + YC CY
Sbjct: 10 TVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKV-CY 56
>pdb|1WYH|A Chain A, Solution Structure Of The Lim Domain From Human Skeletal
Muscle Lim-Protein 2
Length = 72
Score = 28.1 bits (61), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 18/42 (42%), Gaps = 1/42 (2%)
Query: 61 GKDWHGSCLRCENCNKTLVPGSHSEHDGKPYCNYPCYSALFS 102
G+ WH C C C + L S G YC PCY F+
Sbjct: 26 GQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYC-VPCYENKFA 66
>pdb|1V6G|A Chain A, Solution Structure Of The Lim Domain Of The Human Actin
Binding Lim Protein 2
Length = 81
Score = 27.3 bits (59), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 16/36 (44%)
Query: 54 AERKTSLGKDWHGSCLRCENCNKTLVPGSHSEHDGK 89
E ++LGK +H C C C PG +GK
Sbjct: 27 GEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGK 62
>pdb|3MMK|A Chain A, The Structural Basis For Partial Redundancy In A Class
Of Transcription Factors, The Lim-Homeodomain Proteins,
In Neural Cell Type Specification
pdb|3MMK|B Chain B, The Structural Basis For Partial Redundancy In A Class
Of Transcription Factors, The Lim-Homeodomain Proteins,
In Neural Cell Type Specification
Length = 169
Score = 26.9 bits (58), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 60 LGKDWHGSCLRCENCNKTLVPGSHSEHDGKPYCN 93
L + WH SCL+C +C L S G YC
Sbjct: 25 LDRHWHSSCLKCADCQMQLADRCFSRA-GSVYCK 57
>pdb|1A7I|A Chain A, Amino-Terminal Lim Domain From Quail Cysteine And Glycine-
Rich Protein, Nmr, Minimized Average Structure
Length = 81
Score = 26.9 bits (58), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 1/56 (1%)
Query: 50 SMYLAERKTSLGKDWHGSCLRCENCNKTLVPGSHSEHDGKPYCNYPCYSALFSERS 105
++Y AE G+ +H C C C K L + + HD + YC CY + +
Sbjct: 16 TVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCK-SCYGKKYGPKG 70
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
0.322 0.133 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,761,597
Number of Sequences: 62578
Number of extensions: 214071
Number of successful extensions: 380
Number of sequences better than 100.0: 36
Number of HSP's better than 100.0 without gapping: 25
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 352
Number of HSP's gapped (non-prelim): 39
length of query: 201
length of database: 14,973,337
effective HSP length: 94
effective length of query: 107
effective length of database: 9,091,005
effective search space: 972737535
effective search space used: 972737535
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)