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= psy4072
(191 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 98.6 bits (244), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 57/150 (38%), Positives = 74/150 (49%), Gaps = 32/150 (21%)
Query: 4 LSLCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDYVS 63
+ +C GC I D++IL+ A D WH+ CL+C++CH L E C
Sbjct: 6 IPMCAGCDQHILDRFILK-ALDRHWHSKCLKCSDCHVPLAERC----------------- 47
Query: 64 SEKNQFLDENCTCFVRDGKTYCKRDYVRLFGTKCEKCNLNFKREDFVMRAKNKIYHVQCF 123
F R YCK D+ + FGTKC C L V RA++ +YH+ CF
Sbjct: 48 -------------FSRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCF 94
Query: 124 CCVVCGKQLVPGDEFALREDG-LFCKDDHE 152
CVVC +QL GDEF L ED L CK D+E
Sbjct: 95 ACVVCKRQLATGDEFYLMEDSRLVCKADYE 124
>pdb|2JTN|A Chain A, Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Complex
Length = 182
Score = 98.2 bits (243), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 57/150 (38%), Positives = 74/150 (49%), Gaps = 32/150 (21%)
Query: 4 LSLCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDYVS 63
+ +C GC I D++IL+ A D WH+ CL+C++CH L E C
Sbjct: 60 IPMCAGCDQHILDRFILK-ALDRHWHSKCLKCSDCHVPLAERC----------------- 101
Query: 64 SEKNQFLDENCTCFVRDGKTYCKRDYVRLFGTKCEKCNLNFKREDFVMRAKNKIYHVQCF 123
F R YCK D+ + FGTKC C L V RA++ +YH+ CF
Sbjct: 102 -------------FSRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCF 148
Query: 124 CCVVCGKQLVPGDEFALREDG-LFCKDDHE 152
CVVC +QL GDEF L ED L CK D+E
Sbjct: 149 ACVVCKRQLATGDEFYLMEDSRLVCKADYE 178
>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 = 96.3 bits (238), Expect = 9e-21, Method: Compositional matrix adjust.
Identities = 54/152 (35%), Positives = 77/152 (50%), Gaps = 32/152 (21%)
Query: 2 RRLSLCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
+++ C GC I D++IL+V D WH++CL+CA+C L + CF R G
Sbjct: 4 QQIPQCAGCNQHILDKFILKVL-DRHWHSSCLKCADCQMQLADR--CFSRAGS------- 53
Query: 62 VSSEKNQFLDENCTCFVRDGKTYCKRDYVRLFGTKCEKCNLNFKREDFVMRAKNKIYHVQ 121
YCK D+ + FGTKC C V +A++ +YH+
Sbjct: 54 ---------------------VYCKEDFFKRFGTKCTACQQGIPPTQVVRKAQDFVYHLH 92
Query: 122 CFCCVVCGKQLVPGDEFALREDG-LFCKDDHE 152
CF C++C +QL GDEF L EDG L CK+D+E
Sbjct: 93 CFACIICNRQLATGDEFYLMEDGRLVCKEDYE 124
Score = 31.2 bits (69), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 1/67 (1%)
Query: 1 KRRLSLCVGCGGQIHDQYILRVAPDLEWHAACLRCAECH-QFLDENCTCFVRDGKTYCKR 59
KR + C C I ++R A D +H C C C+ Q + + DG+ CK
Sbjct: 62 KRFGTKCTACQQGIPPTQVVRKAQDFVYHLHCFACIICNRQLATGDEFYLMEDGRLVCKE 121
Query: 60 DYVSSEK 66
DY ++++
Sbjct: 122 DYETAKQ 128
>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 = 91.3 bits (225), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 48/146 (32%), Positives = 68/146 (46%), Gaps = 30/146 (20%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDYVSSEK 66
C GCGG+I D+++L A D WH+ CL+C+ C
Sbjct: 6 CAGCGGKIADRFLL-YAMDSYWHSRCLKCSSCQA-------------------------- 38
Query: 67 NQFLDENCTCFVRDGKTYCKRDYVRLFGTK--CEKCNLNFKREDFVMRAKNKIYHVQCFC 124
Q D + + + G C+ DY+RLFG C C + + VMRA+ +YH++CF
Sbjct: 39 -QLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFT 97
Query: 125 CVVCGKQLVPGDEFALREDGLFCKDD 150
C C +LVPGD F LFC+ D
Sbjct: 98 CSTCRNRLVPGDRFHYINGSLFCEHD 123
>pdb|1RUT|X Chain X, Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 Lid
Domain
Length = 188
Score = 91.3 bits (225), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 48/146 (32%), Positives = 68/146 (46%), Gaps = 30/146 (20%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDYVSSEK 66
C GCGG+I D+++L A D WH+ CL+C+ C
Sbjct: 8 CAGCGGKIADRFLL-YAMDSYWHSRCLKCSSCQA-------------------------- 40
Query: 67 NQFLDENCTCFVRDGKTYCKRDYVRLFGTK--CEKCNLNFKREDFVMRAKNKIYHVQCFC 124
Q D + + + G C+ DY+RLFG C C + + VMRA+ +YH++CF
Sbjct: 41 -QLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFT 99
Query: 125 CVVCGKQLVPGDEFALREDGLFCKDD 150
C C +LVPGD F LFC+ D
Sbjct: 100 CSTCRNRLVPGDRFHYINGSLFCEHD 125
>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 = 64.3 bits (155), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 46/149 (30%), Positives = 64/149 (42%), Gaps = 30/149 (20%)
Query: 4 LSLCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDYVS 63
L C GC I D+Y L+ A D WH CL C C L E G+
Sbjct: 2 LLTCGGCQQNIGDRYFLK-AIDQYWHEDCLSCDLCGCRLGEV-------GRRL------- 46
Query: 64 SEKNQFLDENCTCFVRDGKTYCKRDYVRLFGTK--CEKCNLNFKREDFVMRAKNKIYHVQ 121
+ + G+ C+RDY+RLFG C C+ + + MR K+K+YH++
Sbjct: 47 -------------YYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLE 93
Query: 122 CFCCVVCGKQLVPGDEFALREDGLFCKDD 150
CF C C K GD + L + C+ D
Sbjct: 94 CFKCAACQKHFCVGDRYLLINSDIVCEQD 122
>pdb|2L6Y|B Chain B, Haddock Model Of Gata1nf:lmo2lim2-Ldb1lid
pdb|2L6Z|C Chain C, Haddock Model Of Gata1nf:lmo2lim2-Ldb1lid With Fog
Length = 96
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 89 YVRLFGTK--CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLF 146
Y+RLFG C C+ + + MR K+K+YH++CF C C K GD + L +
Sbjct: 1 YLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFSVGDRYLLINSDIV 60
Query: 147 CKDD 150
C+ D
Sbjct: 61 CEQD 64
>pdb|2LXD|A Chain A, Backbone 1h, 13c, And 15n Chemical Shift Assignments For
Lmo2(Lim2)- Ldb1(Lid)
Length = 125
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 89 YVRLFGTK--CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLF 146
Y+RLFG C C+ + + MR K+K+YH++CF C C K GD + L +
Sbjct: 3 YLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFSVGDRYLLINSDIV 62
Query: 147 CKDD 150
C+ D
Sbjct: 63 CEQD 66
>pdb|2L4Z|A Chain A, Nmr Structure Of Fusion Of Ctip (641-685) To Lmo4-Lim1
(18-82)
Length = 123
Score = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 38/88 (43%), Gaps = 28/88 (31%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDYVSSEK 66
C GCGG+I D+++L A D WH+ CL+C+ C
Sbjct: 64 CAGCGGKIADRFLL-YAMDSYWHSRCLKCSSCQA-------------------------- 96
Query: 67 NQFLDENCTCFVRDGKTYCKRDYVRLFG 94
Q D + + + G C+ DY+RLFG
Sbjct: 97 -QLGDIGTSSYTKSGMILCRNDYIRLFG 123
>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 = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 37/87 (42%), Gaps = 28/87 (32%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDYVSSEK 66
C GCGG+I D+++L A D WH+ CL+C+ C
Sbjct: 8 CAGCGGKIADRFLL-YAMDSYWHSRCLKCSSCQA-------------------------- 40
Query: 67 NQFLDENCTCFVRDGKTYCKRDYVRLF 93
Q D + + + G C+ DY+RLF
Sbjct: 41 -QLGDIGTSSYTKSGMILCRNDYIRLF 66
>pdb|1V6G|A Chain A, Solution Structure Of The Lim Domain Of The Human Actin
Binding Lim Protein 2
Length = 81
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 88 DYVRLFGTKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFAL 140
DY RL+GT+C C+ + E V+ A K YH CF C VC PGD
Sbjct: 9 DYQRLYGTRCFSCDQFIEGE--VVSALGKTYHPDCFVCAVCRLPFPPGDRVTF 59
>pdb|2DJ7|A Chain A, Solution Structure Of 3rd Lim Domain Of Actin-Binding
Lim Protein 3
Length = 80
Score = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 30/61 (49%), Gaps = 5/61 (8%)
Query: 2 RRLSLCVGCGGQI-HDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRD 60
R S C GC +I H Q +L + D +WH +C +C C L +DG YC+ D
Sbjct: 13 RGPSHCAGCKEEIKHGQSLLAL--DKQWHVSCFKCQTCSVILTGE--YISKDGVPYCESD 68
Query: 61 Y 61
Y
Sbjct: 69 Y 69
>pdb|1CTL|A Chain A, Structure Of The Carboxy-Terminal Lim Domain From The
Cysteine Rich Protein Crp
Length = 85
Score = 33.9 bits (76), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 22 VAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDYV 62
+ WH +C RCA+C + L E+ T +DG+ YCK Y
Sbjct: 25 IGAGKSWHKSCFRCAKCGKSL-ESTTLADKDGEIYCKGCYA 64
>pdb|1B8T|A Chain A, Solution Structure Of The Chicken Crp1
Length = 192
Score = 33.5 bits (75), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 22 VAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDYV 62
+ WH +C RCA+C + L E+ T +DG+ YCK Y
Sbjct: 132 IGAGKSWHKSCFRCAKCGKSL-ESTTLADKDGEIYCKGCYA 171
>pdb|2KBX|B Chain B, Solution Structure Of Ilk-Pinch Complex
Length = 70
Score = 33.5 bits (75), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 22/44 (50%)
Query: 92 LFGTKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPG 135
L CE+C F + ++ + ++YH QCF C C +Q G
Sbjct: 5 LASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEG 48
>pdb|1G47|A Chain A, 1st Lim Domain Of Pinch Protein
Length = 77
Score = 33.5 bits (75), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 22/44 (50%)
Query: 92 LFGTKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPG 135
L CE+C F + ++ + ++YH QCF C C +Q G
Sbjct: 9 LASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEG 52
>pdb|3F6Q|B Chain B, Crystal Structure Of Integrin-Linked Kinase Ankyrin Repeat
Domain In Complex With Pinch1 Lim1 Domain
Length = 72
Score = 33.5 bits (75), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 21/41 (51%)
Query: 95 TKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPG 135
CE+C F + ++ + ++YH QCF C C +Q G
Sbjct: 12 ATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEG 52
>pdb|1X6A|A Chain A, Solution Structures Of The Second Lim Domain Of Human Lim-
Kinase 2 (limk2)
Length = 81
Score = 33.1 bits (74), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 3/66 (4%)
Query: 87 RDYVRLFGTKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDG-L 145
+DY FG C C+L F++ + K YH +CF C+ C + GD +AL + L
Sbjct: 8 KDYWGKFGEFCHGCSL-LMTGPFMVAGEFK-YHPECFACMSCKVIIEDGDAYALVQHATL 65
Query: 146 FCKDDH 151
+C H
Sbjct: 66 YCGKCH 71
>pdb|1CXX|A Chain A, Mutant R122a Of Quail Cysteine And Glycine-Rich Protein,
Nmr, Minimized Structure
Length = 113
Score = 32.7 bits (73), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDYV 62
C CG ++ + + WH C RCA+C + L E+ T ++G+ YCK Y
Sbjct: 39 CSACGDSVYAAEKV-IGAGKPWHKNCFRCAKCGKSL-ESTTLTEKEGEIYCKGCYA 92
Score = 26.6 bits (57), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 28/62 (45%), Gaps = 4/62 (6%)
Query: 89 YVRLFGT--KCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLF 146
+ + FG KC C + + V+ A K +H CF C CGK L +E ++
Sbjct: 29 FAQKFGGAEKCSACGDSVYAAEKVIGA-GKPWHKNCFRCAKCGKSLE-STTLTEKEGEIY 86
Query: 147 CK 148
CK
Sbjct: 87 CK 88
>pdb|2CUR|A Chain A, Solution Structure Of Skeletal Muscle Lim-Protein 1
Length = 69
Score = 32.7 bits (73), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 95 TKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKD 149
+ C KCN + ++ +H CF CV C K+L G F ED +C D
Sbjct: 6 SGCVKCNKAITSGGITYQ--DQPWHADCFVCVTCSKKLA-GQRFTAVEDQYYCVD 57
>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 = 31.6 bits (70), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 22 VAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDYV 62
+ WH C RCA+C + L E+ T ++G+ YCK Y
Sbjct: 53 IGAGKPWHKNCFRCAKCGKSL-ESTTLTEKEGEIYCKGCYA 92
Score = 27.3 bits (59), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 4/62 (6%)
Query: 89 YVRLFGT--KCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLF 146
+ + FG KC +C + + V+ A K +H CF C CGK L +E ++
Sbjct: 29 FAQKFGGAEKCSRCGDSVYAAEKVIGA-GKPWHKNCFRCAKCGKSLE-STTLTEKEGEIY 86
Query: 147 CK 148
CK
Sbjct: 87 CK 88
>pdb|2DLO|A Chain A, Solution Structure Of The Second Lim Domain Of Human
Thyroid Receptor-Interacting Protein 6
Length = 81
Score = 31.2 bits (69), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 96 KCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQL 132
KC C+ D ++RA K YH CF CVVC + L
Sbjct: 17 KCATCSQPIL--DRILRAMGKAYHPGCFTCVVCHRGL 51
>pdb|1X3H|A Chain A, Solution Structure Of The Lim Domain Of Human Leupaxin
Length = 80
Score = 31.2 bits (69), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 2/54 (3%)
Query: 87 RDYVRLFGTKCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFAL 140
+D++ +F KC CN + A + ++H +CF C C G F L
Sbjct: 8 KDFLAMFSPKCGGCNRPVLEN--YLSAMDTVWHPECFVCGDCFTSFSTGSFFEL 59
Score = 29.3 bits (64), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 3/55 (5%)
Query: 7 CVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDY 61
C GC + + Y+ A D WH C C +C + F DG+ +C+ Y
Sbjct: 18 CGGCNRPVLENYL--SAMDTVWHPECFVCGDCFTSFSTG-SFFELDGRPFCELHY 69
>pdb|1WIG|A Chain A, Solution Structure Of Rsgi Ruh-019, A Lim Domain Of Actin
Binding Lim Protein 2 (kiaa1808 Protein) From Human Cdna
Length = 73
Score = 31.2 bits (69), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 110 VMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLF 146
V+ A K YH C CV CG+ G+E L+ ++
Sbjct: 19 VLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIW 55
>pdb|3IXE|B Chain B, Structural Basis Of Competition Between Pinch1 And Pinch2
For Binding To The Ankyrin Repeat Domain Of
Integrin-Linked Kinase
Length = 72
Score = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 10/39 (25%), Positives = 19/39 (48%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPG 135
C++C F + ++ + ++YH CF C C + G
Sbjct: 14 CQRCQARFSPAERIVNSNGELYHEHCFVCAQCFRPFPEG 52
>pdb|2O13|A Chain A, Solution Structure Of The C-Terminal Lim Domain Of
MlpCRP3
Length = 58
Score = 28.5 bits (62), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 27 EWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDYV 62
WH C RCA C + L E+ +DG+ YCK Y
Sbjct: 21 PWHKTCFRCAICGKSL-ESTNVTDKDGELYCKVCYA 55
Score = 27.7 bits (60), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 2/53 (3%)
Query: 96 KCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCK 148
KC +C + + VM K +H CF C +CGK L ++ L+CK
Sbjct: 1 KCPRCGKSVYAAEKVM-GGGKPWHKTCFRCAICGKSL-ESTNVTDKDGELYCK 51
>pdb|2D8Z|A Chain A, Solution Structure Of The Third Lim Domain Of Four And A
Half Lim Domains Protein 2 (Fhl-2)
Length = 70
Score = 28.5 bits (62), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 114 KNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFC 147
+ + +H +CF C C KQL G F R+D +C
Sbjct: 23 REQPWHKECFVCTACRKQLS-GQRFTARDDFAYC 55
>pdb|2XQN|T Chain T, Complex Of The 2nd And 3rd Lim Domains Of Tes With The
Evh1 Domain Of Mena And The N-Terminal Domain Of
Actin-Like Protein Arp7a
Length = 126
Score = 28.5 bits (62), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 3/71 (4%)
Query: 80 DGKTYCKRDYVRLFGTKCEKCNLNFKREDFVMRAKNKIYH--VQCFCCVVCGKQLVPGDE 137
+ K CK YV+ C+ C+ E + N +H +CF C C K L+ G +
Sbjct: 49 NDKPVCKPCYVKNHAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLI-GQK 107
Query: 138 FALREDGLFCK 148
F E +FC
Sbjct: 108 FMPVEGMVFCS 118
>pdb|1EJI|A Chain A, Recombinant Serine Hydroxymethyltransferase (Mouse)
pdb|1EJI|B Chain B, Recombinant Serine Hydroxymethyltransferase (Mouse)
pdb|1EJI|C Chain C, Recombinant Serine Hydroxymethyltransferase (Mouse)
pdb|1EJI|D Chain D, Recombinant Serine Hydroxymethyltransferase (Mouse)
Length = 478
Score = 27.3 bits (59), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 124 CCVVCGKQLVPGDEFALREDGL 145
C + C K PGD+ ALR GL
Sbjct: 374 CSIACNKNTCPGDKSALRPSGL 395
>pdb|2COR|A Chain A, Solution Structure Of The Third Lim Domain Of Particularly
Interesting New Cys-His Protein
Length = 79
Score = 27.3 bits (59), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 97 CEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLV 133
C+KC+ + + KN YH F C CGK+L
Sbjct: 18 CQKCHAIIDEQPLIF--KNDPYHPDHFNCANCGKELT 52
>pdb|3P2O|A Chain A, Crystal Structure Of Fold Bifunctional Protein From
Campylobacter Jejuni
pdb|3P2O|B Chain B, Crystal Structure Of Fold Bifunctional Protein From
Campylobacter Jejuni
Length = 285
Score = 27.3 bits (59), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 4/42 (9%)
Query: 65 EKNQFLD----ENCTCFVRDGKTYCKRDYVRLFGTKCEKCNL 102
EKNQFL E+C + G + YV+ CE+C +
Sbjct: 22 EKNQFLKSKGIESCLAVILVGDNPASQTYVKSKAKACEECGI 63
>pdb|1J2O|A Chain A, Structure Of Flin2, A Complex Containing The N-Terminal
Lim Domain Of Lmo2 And Ldb1-Lid
Length = 114
Score = 27.3 bits (59), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 33/89 (37%), Gaps = 28/89 (31%)
Query: 4 LSLCVGCGGQIHDQYILRVAPDLEWHAACLRCAECHQFLDENCTCFVRDGKTYCKRDYVS 63
L C GC I D+Y L+ A D WH CL C C C+ V
Sbjct: 3 LLTCGGCQQNIGDRYFLK-AIDQYWHEDCLSCDLCG-----------------CRLGEVG 44
Query: 64 SEKNQFLDENCTCFVRDGKTYCKRDYVRL 92
+ + G+ C+RDY+RL
Sbjct: 45 RR----------LYYKLGRKLCRRDYLRL 63
>pdb|1RVU|A Chain A, E75q Mutant Of Rabbit Cytosolic Serine
Hydroxymethyltransferase
pdb|1RVU|B Chain B, E75q Mutant Of Rabbit Cytosolic Serine
Hydroxymethyltransferase
pdb|1RVY|A Chain A, E75q Mutant Of Rabbit Cytosolic Serine
Hydroxymethyltransferase, Complex With Glycine
pdb|1RVY|B Chain B, E75q Mutant Of Rabbit Cytosolic Serine
Hydroxymethyltransferase, Complex With Glycine
Length = 483
Score = 27.3 bits (59), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 124 CCVVCGKQLVPGDEFALREDGL 145
C + C K PGD+ ALR GL
Sbjct: 379 CSIACNKNTCPGDKSALRPSGL 400
>pdb|1RV3|A Chain A, E75l Mutant Of Rabbit Cytosolic Serine
Hydroxymethyltransferase, Complex With Glycine
pdb|1RV4|A Chain A, E75l Mutant Of Rabbit Cytosolic Serine
Hydroxymethyltransferase
pdb|1RV4|B Chain B, E75l Mutant Of Rabbit Cytosolic Serine
Hydroxymethyltransferase
pdb|1RV3|B Chain B, E75l Mutant Of Rabbit Cytosolic Serine
Hydroxymethyltransferase, Complex With Glycine
Length = 483
Score = 27.3 bits (59), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 124 CCVVCGKQLVPGDEFALREDGL 145
C + C K PGD+ ALR GL
Sbjct: 379 CSIACNKNTCPGDKSALRPSGL 400
>pdb|1CJ0|A Chain A, Crystal Structure Of Rabbit Cytosolic Serine
Hydroxymethyltransferase At 2.8 Angstrom Resolution
pdb|1CJ0|B Chain B, Crystal Structure Of Rabbit Cytosolic Serine
Hydroxymethyltransferase At 2.8 Angstrom Resolution
Length = 470
Score = 27.3 bits (59), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 124 CCVVCGKQLVPGDEFALREDGL 145
C + C K PGD+ ALR GL
Sbjct: 366 CSIACNKNTCPGDKSALRPSGL 387
>pdb|1LS3|B Chain B, Crystal Structure Of The Complex Between Rabbit Cytosolic
Serine Hydroxymethyltransferase And
Triglu-5-Formyl-Tetrahydrofolate
pdb|1LS3|D Chain D, Crystal Structure Of The Complex Between Rabbit Cytosolic
Serine Hydroxymethyltransferase And
Triglu-5-Formyl-Tetrahydrofolate
pdb|1LS3|A Chain A, Crystal Structure Of The Complex Between Rabbit Cytosolic
Serine Hydroxymethyltransferase And
Triglu-5-Formyl-Tetrahydrofolate
pdb|1LS3|C Chain C, Crystal Structure Of The Complex Between Rabbit Cytosolic
Serine Hydroxymethyltransferase And
Triglu-5-Formyl-Tetrahydrofolate
Length = 483
Score = 27.3 bits (59), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 124 CCVVCGKQLVPGDEFALREDGL 145
C + C K PGD+ ALR GL
Sbjct: 379 CSIACNKNTCPGDKSALRPSGL 400
>pdb|1BJ4|A Chain A, Recombinant Serine Hydroxymethyltransferase (human)
Length = 470
Score = 26.9 bits (58), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 12/22 (54%)
Query: 124 CCVVCGKQLVPGDEFALREDGL 145
C + C K PGD ALR GL
Sbjct: 370 CSIACNKNTCPGDRSALRPSGL 391
>pdb|1X63|A Chain A, Solution Structure Of The Second Lim Domain Of Skeletal
Muscle Lim Protein 1
Length = 82
Score = 26.6 bits (57), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 1/57 (1%)
Query: 96 KCEKCNLNFKREDFVMRAKNKIYHVQCFCCVVCGKQLVPGDEFALREDGLFCKDDHE 152
KC+ C D + K ++H CF C C KQ++ F + + +C HE
Sbjct: 17 KCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNC-KQVIGTGSFFPKGEDFYCVTCHE 72
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
0.329 0.144 0.495
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,297,600
Number of Sequences: 62578
Number of extensions: 205531
Number of successful extensions: 543
Number of sequences better than 100.0: 56
Number of HSP's better than 100.0 without gapping: 30
Number of HSP's successfully gapped in prelim test: 26
Number of HSP's that attempted gapping in prelim test: 452
Number of HSP's gapped (non-prelim): 90
length of query: 191
length of database: 14,973,337
effective HSP length: 93
effective length of query: 98
effective length of database: 9,153,583
effective search space: 897051134
effective search space used: 897051134
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 bits)