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= psy8090
(242 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 35.4 bits (80), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 5/75 (6%)
Query: 79 FVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGD 138
F ++ C C D + ++ + A + WH CF C+ C + L +
Sbjct: 29 FAQKFGGAEKCSRCGDSVYAAEKVIGAGKP-----WHKNCFRCAKCGKSLESTTLTEKEG 83
Query: 139 KLYCGRHHAETLKPR 153
++YC +A+ P+
Sbjct: 84 EIYCKGCYAKNFGPK 98
>pdb|1CXX|A Chain A, Mutant R122a Of Quail Cysteine And Glycine-Rich Protein,
Nmr, Minimized Structure
Length = 113
Score = 35.0 bits (79), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 5/75 (6%)
Query: 79 FVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGD 138
F ++ C C D + ++ + A + WH CF C+ C + L +
Sbjct: 29 FAQKFGGAEKCSACGDSVYAAEKVIGAGKP-----WHKNCFRCAKCGKSLESTTLTEKEG 83
Query: 139 KLYCGRHHAETLKPR 153
++YC +A+ P+
Sbjct: 84 EIYCKGCYAKNFGPK 98
>pdb|1X63|A Chain A, Solution Structure Of The Second Lim Domain Of Skeletal
Muscle Lim Protein 1
Length = 82
Score = 34.7 bits (78), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 114 WHPGCFTCSVCNELLVDLIYFYRGDKLYC 142
WH CFTCS C +++ +F +G+ YC
Sbjct: 39 WHKDCFTCSNCKQVIGTGSFFPKGEDFYC 67
>pdb|2D8X|A Chain A, Solution Structure Of The Second Lim Domain Of
Particularly Interesting New Cys-His Protein (Pinch)
Length = 70
Score = 34.7 bits (78), Expect = 0.048, Method: Composition-based stats.
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 111 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 146
N+ WHP CF C +C E+L D+ + + C H
Sbjct: 24 NNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCH 59
>pdb|2CUP|A Chain A, Solution Structure Of The Skeletal Muscle Lim-Protein 1
Length = 101
Score = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 26/60 (43%)
Query: 114 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQDILYYLT 173
WH CF C+ C L + + + +K+ C + P+C C + Q++ Y T
Sbjct: 29 WHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSPKCKGCFKAIVAGDQNVEYKGT 88
>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 = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 6/64 (9%)
Query: 114 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE-----ECQTSSQDI 168
WH C C+ C L D F R +YC + +C+AC + + +QD
Sbjct: 29 WHSSCLKCADCQMQLADRC-FSRAGSVYCKEDFFKRFGTKCTACQQGIPPTQVVRKAQDF 87
Query: 169 LYYL 172
+Y+L
Sbjct: 88 VYHL 91
>pdb|2JTN|A Chain A, Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Complex
Length = 182
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 6/64 (9%)
Query: 114 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACD-----EECQTSSQDI 168
WH C CS C+ L + F RG+ +YC + +C+AC + +QD
Sbjct: 83 WHSKCLKCSDCHVPLAERC-FSRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVRRAQDF 141
Query: 169 LYYL 172
+Y+L
Sbjct: 142 VYHL 145
>pdb|2RGT|A Chain A, Crystal Structure Of Lhx3 Lim Domains 1 And 2 With The
Binding Domain Of Isl1
pdb|2RGT|B Chain B, Crystal Structure Of Lhx3 Lim Domains 1 And 2 With The
Binding Domain Of Isl1
Length = 169
Score = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 6/64 (9%)
Query: 114 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACD-----EECQTSSQDI 168
WH C CS C+ L + F RG+ +YC + +C+AC + +QD
Sbjct: 29 WHSKCLKCSDCHVPLAERC-FSRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVRRAQDF 87
Query: 169 LYYL 172
+Y+L
Sbjct: 88 VYHL 91
>pdb|3BBO|P Chain P, Homology Model For The Spinach Chloroplast 50s Subunit
Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome
Length = 205
Score = 30.4 bits (67), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 10/78 (12%)
Query: 22 KVPYVNSPGEQYR--IRQLLHQLPPHDNEVRYCHALSEDERKELRLF-------SAQRKR 72
KVP +N P +Q R +R L QL H ++ A + RK + S ++R
Sbjct: 95 KVPKLNRPPDQRRALLRGLTTQLLKH-GRIKTTKARARAVRKYVDKMITMAKDGSLHKRR 153
Query: 73 EALGRGFVKQLVAPMFCE 90
+ALG + KQ+V +F E
Sbjct: 154 QALGFIYEKQIVHALFAE 171
>pdb|1X64|A Chain A, Solution Structure Of The Lim Domain Of Alpha-Actinin-2
Associated Lim Protein
Length = 89
Score = 30.4 bits (67), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 115 HPGCFTCSVCNELLVDLIYFYRGDKLYCGRH-HAETLKP 152
HP CF C+ CN L YF+ +LYC H A T P
Sbjct: 48 HPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSGP 86
>pdb|1B8T|A Chain A, Solution Structure Of The Chicken Crp1
Length = 192
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/65 (21%), Positives = 28/65 (43%), Gaps = 5/65 (7%)
Query: 89 CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAE 148
C C + ++ + A ++ WH CF C+ C + L + ++YC +A+
Sbjct: 118 CPRCGQAVYAAEKVIGAGKS-----WHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAK 172
Query: 149 TLKPR 153
P+
Sbjct: 173 NFGPK 177
Score = 27.3 bits (59), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 16/32 (50%)
Query: 111 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYC 142
S +H CF C VC + L GD++YC
Sbjct: 27 GSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYC 58
>pdb|1CTL|A Chain A, Structure Of The Carboxy-Terminal Lim Domain From The
Cysteine Rich Protein Crp
Length = 85
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/65 (21%), Positives = 28/65 (43%), Gaps = 5/65 (7%)
Query: 89 CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAE 148
C C + ++ + A ++ WH CF C+ C + L + ++YC +A+
Sbjct: 11 CPRCGQAVYAAEKVIGAGKS-----WHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAK 65
Query: 149 TLKPR 153
P+
Sbjct: 66 NFGPK 70
>pdb|1X62|A Chain A, Solution Structure Of The Lim Domain Of Carboxyl Terminal
Lim Domain Protein 1
Length = 79
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 115 HPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETL 150
HP C+ C+ C L +F+ D++YC +H E +
Sbjct: 38 HPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERV 73
>pdb|1X68|A Chain A, Solution Structures Of The C-Terminal Lim Domain Of Human
Fhl5 Protein
Length = 76
Score = 28.1 bits (61), Expect = 4.3, Method: Composition-based stats.
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 111 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGR 144
+S WH CF C C+ LV + + +++C +
Sbjct: 28 DSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQK 61
>pdb|2DLO|A Chain A, Solution Structure Of The Second Lim Domain Of Human
Thyroid Receptor-Interacting Protein 6
Length = 81
Score = 28.1 bits (61), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 114 WHPGCFTCSVCNELL 128
+HPGCFTC VC+ L
Sbjct: 37 YHPGCFTCVVCHRGL 51
>pdb|2CUR|A Chain A, Solution Structure Of Skeletal Muscle Lim-Protein 1
Length = 69
Score = 27.3 bits (59), Expect = 7.0, Method: Composition-based stats.
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 114 WHPGCFTCSVCNELLVDLIYFYRGDKLYC 142
WH CF C C++ L + D+ YC
Sbjct: 27 WHADCFVCVTCSKKLAGQRFTAVEDQYYC 55
>pdb|2O13|A Chain A, Solution Structure Of The C-Terminal Lim Domain Of MlpCRP3
Length = 58
Score = 27.3 bits (59), Expect = 7.4, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 2/43 (4%)
Query: 102 SVFASRA--GPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYC 142
SV+A+ G WH CF C++C + L + +LYC
Sbjct: 8 SVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYC 50
>pdb|2D8Y|A Chain A, Solution Structure Of The Lim Domain Of Epithelial Protein
Lost In Neoplasm
Length = 91
Score = 27.3 bits (59), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 18/40 (45%)
Query: 114 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPR 153
+H CF CS CN L Y ++YC H + K +
Sbjct: 38 FHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSK 77
>pdb|2DJ7|A Chain A, Solution Structure Of 3rd Lim Domain Of Actin-Binding Lim
Protein 3
Length = 80
Score = 27.3 bits (59), Expect = 7.5, Method: Composition-based stats.
Identities = 12/47 (25%), Positives = 21/47 (44%), Gaps = 5/47 (10%)
Query: 82 QLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELL 128
++ P C C++E++ S + WH CF C C+ +L
Sbjct: 11 KIRGPSHCAGCKEEIKHGQ-----SLLALDKQWHVSCFKCQTCSVIL 52
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
0.320 0.135 0.425
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,847,079
Number of Sequences: 62578
Number of extensions: 268661
Number of successful extensions: 619
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 593
Number of HSP's gapped (non-prelim): 36
length of query: 242
length of database: 14,973,337
effective HSP length: 96
effective length of query: 146
effective length of database: 8,965,849
effective search space: 1309013954
effective search space used: 1309013954
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)