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= 010849
(499 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 45.4 bits (106), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 37/130 (28%), Positives = 52/130 (40%), Gaps = 12/130 (9%)
Query: 138 CGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPK 197
C GCN I L + ++H +C +C C + + FS +G Y K F + K
Sbjct: 9 CAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLADRCFSRAGS-VYCKEDFFKRFGTK 67
Query: 198 CEVCHQYIPTNGAGLIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNTRYYSLEDGR 257
C C Q IP +K H H C C R + +Y +EDGR
Sbjct: 68 CTACQQGIPPTQV-----------VRKAQDFVYHLHCFACIICNRQLATGDEFYLMEDGR 116
Query: 258 SLCLECMESA 267
+C E E+A
Sbjct: 117 LVCKEDYETA 126
>pdb|2JTN|A Chain A, Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Complex
Length = 182
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 36/131 (27%), Positives = 52/131 (39%), Gaps = 12/131 (9%)
Query: 137 VCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELTHP 196
+C GC+ I L + ++H C +C C P+ E FS G+ Y K F +
Sbjct: 62 MCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFS-RGESVYCKDDFFKRFGT 120
Query: 197 KCEVCHQYIPTNGAGLIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNTRYYSLEDG 256
KC C IP + R F H H C C+R + +Y +ED
Sbjct: 121 KCAACQLGIPPTQ---VVRRAQDFVY--------HLHCFACVVCKRQLATGDEFYLMEDS 169
Query: 257 RSLCLECMESA 267
R +C E+A
Sbjct: 170 RLVCKADYETA 180
>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 = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 36/131 (27%), Positives = 52/131 (39%), Gaps = 12/131 (9%)
Query: 137 VCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELTHP 196
+C GC+ I L + ++H C +C C P+ E FS G+ Y K F +
Sbjct: 8 MCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFS-RGESVYCKDDFFKRFGT 66
Query: 197 KCEVCHQYIPTNGAGLIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNTRYYSLEDG 256
KC C IP + R F H H C C+R + +Y +ED
Sbjct: 67 KCAACQLGIPPTQ---VVRRAQDFVY--------HLHCFACVVCKRQLATGDEFYLMEDS 115
Query: 257 RSLCLECMESA 267
R +C E+A
Sbjct: 116 RLVCKADYETA 126
>pdb|1M3V|A Chain A, Flin4: Fusion Of The Lim Binding Domain Of Ldb1 And The N-
Terminal Lim Domain Of Lmo4
Length = 122
Score = 34.7 bits (78), Expect = 0.14, Method: Composition-based stats.
Identities = 14/35 (40%), Positives = 18/35 (51%)
Query: 134 SYKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSC 168
S+K C GC I L M +Y+H C +C SC
Sbjct: 4 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSC 38
>pdb|2CUP|A Chain A, Solution Structure Of The Skeletal Muscle Lim-Protein 1
Length = 101
Score = 34.3 bits (77), Expect = 0.18, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 1/60 (1%)
Query: 157 YFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPKCEVCHQYIPTNGAGLIEYR 216
++H CFRC C +P+ F C PKC+ C + I G +EY+
Sbjct: 28 FWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSPKCKGCFKAI-VAGDQNVEYK 86
>pdb|1B8T|A Chain A, Solution Structure Of The Chicken Crp1
Length = 192
Score = 34.3 bits (77), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 27/55 (49%)
Query: 136 KVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCF 190
K CG C + + + C G+ FH +CF C C + ++ G + Y KSC+
Sbjct: 8 KKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCY 62
Score = 29.3 bits (64), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 20/43 (46%)
Query: 155 GTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPK 197
G +H +CFRC CG + + + Y K C+ + PK
Sbjct: 135 GKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPK 177
>pdb|2DJ7|A Chain A, Solution Structure Of 3rd Lim Domain Of Actin-Binding Lim
Protein 3
Length = 80
Score = 34.3 bits (77), Expect = 0.18, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 138 CGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKS 188
C GC +I +G L + +H +CF+C++C +T S G PY +S
Sbjct: 18 CAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTGEYISKDGV-PYCES 67
>pdb|2L4Z|A Chain A, Nmr Structure Of Fusion Of Ctip (641-685) To Lmo4-Lim1
(18-82)
Length = 123
Score = 33.1 bits (74), Expect = 0.41, Method: Composition-based stats.
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 135 YKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSC 168
+K C GC I L M +Y+H C +C SC
Sbjct: 61 WKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSC 94
>pdb|2O10|A Chain A, Solution Structure Of The N-Terminal Lim Domain Of MlpCRP3
Length = 60
Score = 32.7 bits (73), Expect = 0.48, Method: Composition-based stats.
Identities = 14/53 (26%), Positives = 22/53 (41%)
Query: 138 CGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCF 190
CG C + + + C G FH CF C +C + + + Y K C+
Sbjct: 4 CGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKVCY 56
>pdb|1J2O|A Chain A, Structure Of Flin2, A Complex Containing The N-Terminal
Lim Domain Of Lmo2 And Ldb1-Lid
Length = 114
Score = 32.0 bits (71), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 21/41 (51%)
Query: 134 SYKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITE 174
S CGGC +IG +L + Y+H +C C CG + E
Sbjct: 2 SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGE 42
>pdb|2CUQ|A Chain A, Solution Structure Of Second Lim Domain From Human
Skeletal Muscle Lim-Protein 2
Length = 80
Score = 31.6 bits (70), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 158 FHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKEL 193
+H C C C P+ +F+ +DPY +CF EL
Sbjct: 37 WHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGEL 72
>pdb|1X3H|A Chain A, Solution Structure Of The Lim Domain Of Human Leupaxin
Length = 80
Score = 31.6 bits (70), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 17/40 (42%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 138 CGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEF 177
CGGCN + NYL M T +HP CF C C + F
Sbjct: 18 CGGCNRPV-LENYLSAMDTVWHPECFVCGDCFTSFSTGSF 56
>pdb|2DFY|X Chain X, Crystal Structure Of A Cyclized Protein Fusion Of Lmo4 Lim
Domains 1 And 2 With The Lim Interacting Domain Of Ldb1
pdb|2DFY|C Chain C, Crystal Structure Of A Cyclized Protein Fusion Of Lmo4 Lim
Domains 1 And 2 With The Lim Interacting Domain Of Ldb1
Length = 195
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 32/84 (38%), Gaps = 14/84 (16%)
Query: 134 SYKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKS----C 189
S+K C GC I L M +Y+H C +C SC + + G Y KS C
Sbjct: 2 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSC-----QAQLGDIGTSSYTKSGMILC 56
Query: 190 FKEL-----THPKCEVCHQYIPTN 208
+ C C Q IP +
Sbjct: 57 RNDYIRLFGNSGACSACGQSIPAS 80
>pdb|2F37|A Chain A, Crystal Structure Of The Ankyrin Repeat Domain Of Human
Trpv2
pdb|2F37|B Chain B, Crystal Structure Of The Ankyrin Repeat Domain Of Human
Trpv2
Length = 251
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 37/85 (43%), Gaps = 10/85 (11%)
Query: 205 IPTNGAGLIEYRCHPFWAQKYCPSHEHDHTSRCCSCERLESWNTRYYSLEDGRSLCLECM 264
+P + AGL EY KY E+ S +C N L+DG + C+ +
Sbjct: 19 VPEDLAGLPEYLSK---TSKYLTDSEYTEGSTGKTCLXKAVLN-----LKDGVNACILPL 70
Query: 265 ESAIMDTGDCQPLYHA--IRDYYEG 287
D+G+ QPL +A DYY G
Sbjct: 71 LQIDRDSGNPQPLVNAQCTDDYYRG 95
>pdb|1RUT|X Chain X, Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 Lid
Domain
Length = 188
Score = 31.2 bits (69), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 32/84 (38%), Gaps = 14/84 (16%)
Query: 134 SYKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKS----C 189
S+K C GC I L M +Y+H C +C SC + + G Y KS C
Sbjct: 4 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSC-----QAQLGDIGTSSYTKSGMILC 58
Query: 190 FKEL-----THPKCEVCHQYIPTN 208
+ C C Q IP +
Sbjct: 59 RNDYIRLFGNSGACSACGQSIPAS 82
>pdb|2XJY|A Chain A, Crystal Structure Of The Lmo2:ldb1-Lid Complex, P21
Crystal Form
pdb|2XJZ|A Chain A, Crystal Structure Of The Lmo2:ldb1-Lid Complex, C2 Crystal
Form
pdb|2XJZ|B Chain B, Crystal Structure Of The Lmo2:ldb1-Lid Complex, C2 Crystal
Form
pdb|2XJZ|C Chain C, Crystal Structure Of The Lmo2:ldb1-Lid Complex, C2 Crystal
Form
pdb|2XJZ|D Chain D, Crystal Structure Of The Lmo2:ldb1-Lid Complex, C2 Crystal
Form
pdb|2XJZ|E Chain E, Crystal Structure Of The Lmo2:ldb1-Lid Complex, C2 Crystal
Form
Length = 131
Score = 30.4 bits (67), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 5/54 (9%)
Query: 134 SYKVCGGCNCDIGYGNYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHK 187
S CGGC +IG +L + Y+H +C C CG + E G+ Y+K
Sbjct: 1 SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGE-----VGRRLYYK 49
>pdb|1CTL|A Chain A, Structure Of The Carboxy-Terminal Lim Domain From The
Cysteine Rich Protein Crp
Length = 85
Score = 30.4 bits (67), Expect = 2.6, Method: Composition-based stats.
Identities = 13/43 (30%), Positives = 20/43 (46%)
Query: 155 GTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPK 197
G +H +CFRC CG + + + Y K C+ + PK
Sbjct: 28 GKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPK 70
>pdb|2EGQ|A Chain A, Solution Structure Of The Fourth Lim Domain From Human
Four And A Half Lim Domains 1
Length = 77
Score = 30.0 bits (66), Expect = 3.1, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 4/62 (6%)
Query: 136 KVCGGCNCDI-GYG---NYLGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFK 191
K C GC I G+G + + G +H CF C+ C + F + Y C K
Sbjct: 16 KKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAK 75
Query: 192 EL 193
+L
Sbjct: 76 KL 77
>pdb|1X63|A Chain A, Solution Structure Of The Second Lim Domain Of Skeletal
Muscle Lim Protein 1
Length = 82
Score = 30.0 bits (66), Expect = 3.3, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 138 CGGCNCDIGYGNY-LGCMGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSC 189
C GC I G+ + GT +H +CF C +C I F G+D Y +C
Sbjct: 18 CKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTC 70
>pdb|2O13|A Chain A, Solution Structure Of The C-Terminal Lim Domain Of MlpCRP3
Length = 58
Score = 29.6 bits (65), Expect = 4.6, Method: Composition-based stats.
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 6/38 (15%)
Query: 164 RCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPKCEVC 201
+C CG + E + G P+HK+CF +C +C
Sbjct: 1 KCPRCGKSVYAAEKVMGGGKPWHKTCF------RCAIC 32
>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 = 29.3 bits (64), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 20/44 (45%)
Query: 154 MGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPK 197
G +H NCFRC CG + + + Y K C+ + PK
Sbjct: 55 AGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAKNFGPK 98
>pdb|1CXX|A Chain A, Mutant R122a Of Quail Cysteine And Glycine-Rich Protein,
Nmr, Minimized Structure
Length = 113
Score = 29.3 bits (64), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 20/44 (45%)
Query: 154 MGTYFHPNCFRCRSCGYPITEHEFSLSGKDPYHKSCFKELTHPK 197
G +H NCFRC CG + + + Y K C+ + PK
Sbjct: 55 AGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAKNFGPK 98
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 0.138 0.456
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,152,699
Number of Sequences: 62578
Number of extensions: 635533
Number of successful extensions: 1335
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 24
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1298
Number of HSP's gapped (non-prelim): 40
length of query: 499
length of database: 14,973,337
effective HSP length: 103
effective length of query: 396
effective length of database: 8,527,803
effective search space: 3377009988
effective search space used: 3377009988
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)