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= psy2501
(130 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 61.6 bits (148), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 33/57 (57%)
Query: 56 CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
C +C +PI G+V+ A+GK WH EHF+C C + +ER YCE Y+ LF
Sbjct: 8 CGACRRPIEGRVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLFG 64
>pdb|1X3H|A Chain A, Solution Structure Of The Lim Domain Of Human Leupaxin
Length = 80
Score = 59.7 bits (143), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 33/54 (61%)
Query: 56 CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHN 109
C C++P++ ++A+ WHPE F+C C T +FFE D RP+CE YH+
Sbjct: 18 CGGCNRPVLENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHH 71
Score = 26.2 bits (56), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 106 DYHNLFSPRCSYCNGPILD 124
D+ +FSP+C CN P+L+
Sbjct: 9 DFLAMFSPKCGGCNRPVLE 27
>pdb|2DAR|A Chain A, Solution Structure Of First Lim Domain Of Enigma-Like Pdz
And Lim Domains Protein
Length = 90
Score = 55.5 bits (132), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 30/57 (52%)
Query: 56 CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
C+ C++ I G + ALGK+WHPE F C HC + F E YCE Y F+
Sbjct: 28 CAHCNQVIRGPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFA 84
>pdb|2DJ7|A Chain A, Solution Structure Of 3rd Lim Domain Of Actin-Binding Lim
Protein 3
Length = 80
Score = 45.4 bits (106), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 56 CSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF 111
C+ C + I GQ + AL K WH F C C+ L T + +D PYCE DYH F
Sbjct: 18 CAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVIL-TGEYISKDGVPYCESDYHAQF 73
>pdb|1X64|A Chain A, Solution Structure Of The Lim Domain Of Alpha-Actinin-2
Associated Lim Protein
Length = 89
Score = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 25/49 (51%)
Query: 56 CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE 104
C C IVG V+ A K HPE F+C CN L + +F + YCE
Sbjct: 28 CDKCGSGIVGAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCE 76
>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 = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 30/57 (52%)
Query: 56 CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
C C KPI +T + WH E F+CT C ++L + F RD YC + +L++
Sbjct: 8 CVQCKKPITTGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYA 64
>pdb|2DLO|A Chain A, Solution Structure Of The Second Lim Domain Of Human
Thyroid Receptor-Interacting Protein 6
Length = 81
Score = 43.9 bits (102), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 39/66 (59%), Gaps = 3/66 (4%)
Query: 48 VTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNF-FERDSRPYCEPD 106
V T +K C++C +PI+ +++ A+GK +HP F C C++ L F + S+ +C D
Sbjct: 12 VATLEK--CATCSQPILDRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIED 69
Query: 107 YHNLFS 112
+H F+
Sbjct: 70 FHRKFA 75
>pdb|2D8X|A Chain A, Solution Structure Of The Second Lim Domain Of
Particularly Interesting New Cys-His Protein (Pinch)
Length = 70
Score = 43.9 bits (102), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 26/50 (52%)
Query: 56 CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEP 105
C C + I+G+VI A+ +WHPE F C C + L F + R C P
Sbjct: 8 CHQCGEFIIGRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRP 57
>pdb|2KBX|B Chain B, Solution Structure Of Ilk-Pinch Complex
Length = 70
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 13/78 (16%)
Query: 36 LDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFF 95
L S T E + G +K ++ + G+ +H + F+C C Q+ F+
Sbjct: 5 LASATCERCKGGFAPAEK-------------IVNSNGELYHEQCFVCAQCFQQFPEGLFY 51
Query: 96 ERDSRPYCEPDYHNLFSP 113
E + R YCE D+ LF+P
Sbjct: 52 EFEGRKYCEHDFQMLFAP 69
>pdb|1G47|A Chain A, 1st Lim Domain Of Pinch Protein
Length = 77
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 13/78 (16%)
Query: 36 LDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFF 95
L S T E + G +K ++ + G+ +H + F+C C Q+ F+
Sbjct: 9 LASATCERCKGGFAPAEK-------------IVNSNGELYHEQCFVCAQCFQQFPEGLFY 55
Query: 96 ERDSRPYCEPDYHNLFSP 113
E + R YCE D+ LF+P
Sbjct: 56 EFEGRKYCEHDFQMLFAP 73
>pdb|1V6G|A Chain A, Solution Structure Of The Lim Domain Of The Human Actin
Binding Lim Protein 2
Length = 81
Score = 42.7 bits (99), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 17/30 (56%), Positives = 24/30 (80%)
Query: 56 CSSCDKPIVGQVITALGKTWHPEHFICTHC 85
C SCD+ I G+V++ALGKT+HP+ F+C C
Sbjct: 18 CFSCDQFIEGEVVSALGKTYHPDCFVCAVC 47
>pdb|2CUQ|A Chain A, Solution Structure Of Second Lim Domain From Human
Skeletal Muscle Lim-Protein 2
Length = 80
Score = 42.4 bits (98), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 27/57 (47%)
Query: 56 CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
C+ C K + +T + WH E +CT C L + F RD PYC + LF+
Sbjct: 18 CARCSKTLTQGGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFA 74
>pdb|1IML|A Chain A, Cysteine Rich Intestinal Protein, Nmr, 48 Structures
Length = 76
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 2/61 (3%)
Query: 56 CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC-EPDYHNLFSP 113
C CDK + + +T+LGK WH C C + L + E + +PYC P Y +F P
Sbjct: 3 CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGP 62
Query: 114 R 114
+
Sbjct: 63 K 63
>pdb|1WYH|A Chain A, Solution Structure Of The Lim Domain From Human Skeletal
Muscle Lim-Protein 2
Length = 72
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 18/41 (43%), Positives = 24/41 (58%)
Query: 72 GKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
G+TWH F+C+ C Q LG+R+F YC P Y N F+
Sbjct: 26 GQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFA 66
>pdb|2JTN|A Chain A, Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Complex
Length = 182
Score = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 56 CSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 114
C+ CD+ I+ + ++ AL + WH + C+ C+ L R F R YC+ D+ F +
Sbjct: 63 CAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRFGTK 121
Query: 115 CSYCNGPI 122
C+ C I
Sbjct: 122 CAACQLGI 129
>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 = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 56 CSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 114
C+ CD+ I+ + ++ AL + WH + C+ C+ L R F R YC+ D+ F +
Sbjct: 9 CAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRFGTK 67
Query: 115 CSYCNGPI 122
C+ C I
Sbjct: 68 CAACQLGI 75
>pdb|1X4K|A Chain A, Solution Structure Of Lim Domain In Lim-Protein 3
Length = 72
Score = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 56 CSSCDKPIV--GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
C C K I+ + + G +WH FIC C Q +GT++F +D++ +C P Y
Sbjct: 8 CQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCY 61
>pdb|3F6Q|B Chain B, Crystal Structure Of Integrin-Linked Kinase Ankyrin Repeat
Domain In Complex With Pinch1 Lim1 Domain
Length = 72
Score = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 28/47 (59%)
Query: 66 QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
+++ + G+ +H + F+C C Q+ F+E + R YCE D+ LF+
Sbjct: 26 KIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFA 72
>pdb|2CUR|A Chain A, Solution Structure Of Skeletal Muscle Lim-Protein 1
Length = 69
Score = 40.0 bits (92), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 28/57 (49%)
Query: 56 CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
C C+K I IT + WH + F+C C+++L + F + + YC Y N S
Sbjct: 8 CVKCNKAITSGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVS 64
>pdb|1CTL|A Chain A, Structure Of The Carboxy-Terminal Lim Domain From The
Cysteine Rich Protein Crp
Length = 85
Score = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 56 CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 114
C C + + + + GK+WH F C C + L + ++D YC+ Y F P+
Sbjct: 11 CPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPK 70
>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 = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 2/68 (2%)
Query: 56 CSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 114
C+ C++ I+ + ++ L + WH C C +L R F R YC+ D+ F +
Sbjct: 9 CAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLADRCF-SRAGSVYCKEDFFKRFGTK 67
Query: 115 CSYCNGPI 122
C+ C I
Sbjct: 68 CTACQQGI 75
Score = 26.9 bits (58), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 56 CSSCDKPI--VGQVITALGKTWHPEHFICTHCNQELGTRN--FFERDSRPYCEPDY 107
C++C + I V A +H F C CN++L T + + D R C+ DY
Sbjct: 68 CTACQQGIPPTQVVRKAQDFVYHLHCFACIICNRQLATGDEFYLMEDGRLVCKEDY 123
>pdb|1X63|A Chain A, Solution Structure Of The Second Lim Domain Of Skeletal
Muscle Lim Protein 1
Length = 82
Score = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 56 CSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
C C K IV Q + G WH + F C++C Q +GT +FF + YC + F+
Sbjct: 18 CKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFA 76
>pdb|1B8T|A Chain A, Solution Structure Of The Chicken Crp1
Length = 192
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 56 CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 114
C C + + + + GK+WH F C C + L + ++D YC+ Y F P+
Sbjct: 118 CPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPK 177
>pdb|1CXX|A Chain A, Mutant R122a Of Quail Cysteine And Glycine-Rich Protein,
Nmr, Minimized Structure
Length = 113
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 56 CSSC-DKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 114
CS+C D + + GK WH F C C + L + E++ YC+ Y F P+
Sbjct: 39 CSACGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAKNFGPK 98
>pdb|2CU8|A Chain A, Solution Structure Of The Lim Domain Of Human
Cysteine-Rich Protein 2
Length = 76
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 56 CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYC-EPDYHNLF 111
C CDK + + +++LGK WH C C++ L E D +P+C +P Y LF
Sbjct: 12 CPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLF 69
>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 = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 1/60 (1%)
Query: 56 CSSC-DKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 114
CS C D + + GK WH F C C + L + E++ YC+ Y F P+
Sbjct: 39 CSRCGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAKNFGPK 98
>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 = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 1/68 (1%)
Query: 56 CSSCDKPIVGQVIT-ALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 114
C+ CD+ I T A + WH +HF C C+ L + + +P C+P Y +
Sbjct: 6 CAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAVV 65
Query: 115 CSYCNGPI 122
C C+ I
Sbjct: 66 CQGCHNAI 73
>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 = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 26/47 (55%)
Query: 66 QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFS 112
+++ + G+ +H F+C C + F+E + R YCE D+ LF+
Sbjct: 26 RIVNSNGELYHEHCFVCAQCFRPFPEGLFYEFEGRKYCEHDFQMLFA 72
>pdb|1X61|A Chain A, Solution Structure Of The First Lim Domain Of Thyroid
Receptor Interacting Protein 6 (Trip6)
Length = 72
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 24/43 (55%)
Query: 65 GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
G + AL + +H F+C+ C +L ++F+ + R YCE Y
Sbjct: 19 GAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCY 61
>pdb|1X62|A Chain A, Solution Structure Of The Lim Domain Of Carboxyl Terminal
Lim Domain Protein 1
Length = 79
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 23/49 (46%)
Query: 56 CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE 104
C C IVG + + HPE ++CT C L + F + + YCE
Sbjct: 18 CDKCGTGIVGVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCE 66
>pdb|2D8Y|A Chain A, Solution Structure Of The Lim Domain Of Epithelial Protein
Lost In Neoplasm
Length = 91
Score = 34.7 bits (78), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 56 CSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 114
C C K + + + A + +H F C++CN +L + R YC+P ++ LF +
Sbjct: 18 CVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSK 77
Query: 115 CSYCNG 120
+Y G
Sbjct: 78 GNYDEG 83
>pdb|2O13|A Chain A, Solution Structure Of The C-Terminal Lim Domain Of MlpCRP3
Length = 58
Score = 34.3 bits (77), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 1/57 (1%)
Query: 56 CSSCDKPI-VGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLF 111
C C K + + + GK WH F C C + L + N ++D YC+ Y F
Sbjct: 2 CPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNF 58
>pdb|2EGQ|A Chain A, Solution Structure Of The Fourth Lim Domain From Human
Four And A Half Lim Domains 1
Length = 77
Score = 33.9 bits (76), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 6/56 (10%)
Query: 56 CSSCDKPIVG-----QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPD 106
C+ C PI G V+ G++WH F C C+ L + F + YC PD
Sbjct: 18 CAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYC-PD 72
>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 = 32.3 bits (72), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 19/32 (59%)
Query: 56 CSSCDKPIVGQVITALGKTWHPEHFICTHCNQ 87
C SC+K I G+V+ A K +HP +C C Q
Sbjct: 8 CDSCEKYITGRVLEAGEKHYHPSCALCVRCGQ 39
>pdb|1X68|A Chain A, Solution Structures Of The C-Terminal Lim Domain Of Human
Fhl5 Protein
Length = 76
Score = 32.0 bits (71), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 4/53 (7%)
Query: 56 CSSCDKPIVG----QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCE 104
C +C KPI G + I WH E F C C+ L + F ++ +C+
Sbjct: 8 CVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQ 60
>pdb|3H4N|A Chain A, Ppcd, A Cytochrome C7 From Geobacter Sulfurreducens
pdb|3H4N|B Chain B, Ppcd, A Cytochrome C7 From Geobacter Sulfurreducens
Length = 72
Score = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 53 KGCCSSCDKPIVGQVITALGKTWHPEHFICTHCNQELG 90
KG C +C + G I +GK W H CT C++E+G
Sbjct: 25 KGECKACHETEAGGKIAGMGKDW--AHKTCTGCHKEMG 60
>pdb|1RUT|X Chain X, Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 Lid
Domain
Length = 188
Score = 30.8 bits (68), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 30/72 (41%), Gaps = 5/72 (6%)
Query: 56 CSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELG--TRNFFERDSRPYCEPDYHNLF- 111
C+ C I + ++ A+ WH C+ C +LG + + + C DY LF
Sbjct: 8 CAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG 67
Query: 112 -SPRCSYCNGPI 122
S CS C I
Sbjct: 68 NSGACSACGQSI 79
>pdb|2COR|A Chain A, Solution Structure Of The Third Lim Domain Of Particularly
Interesting New Cys-His Protein
Length = 79
Score = 30.8 bits (68), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 56 CSSCDKPIVGQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEP 105
C C I Q + +HP+HF C +C +EL T + E YC P
Sbjct: 18 CQKCHAIIDEQPLIFKNDPYHPDHFNCANCGKEL-TADARELKGELYCLP 66
>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 = 30.8 bits (68), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 30/72 (41%), Gaps = 5/72 (6%)
Query: 56 CSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELG--TRNFFERDSRPYCEPDYHNLF- 111
C+ C I + ++ A+ WH C+ C +LG + + + C DY LF
Sbjct: 6 CAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG 65
Query: 112 -SPRCSYCNGPI 122
S CS C I
Sbjct: 66 NSGACSACGQSI 77
>pdb|2CUP|A Chain A, Solution Structure Of The Skeletal Muscle Lim-Protein 1
Length = 101
Score = 30.4 bits (67), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 27/70 (38%), Gaps = 2/70 (2%)
Query: 56 CSSCDKPIVG--QVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSP 113
C C KPI + + + WH F C C L F +D++ C SP
Sbjct: 8 CVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSP 67
Query: 114 RCSYCNGPIL 123
+C C I+
Sbjct: 68 KCKGCFKAIV 77
>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 = 30.0 bits (66), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 52 QKGCCSSCDKPIVGQVIT--ALGKTWHPEHFICTHCNQELGTRN-FFERDSRPYCEPDYH 108
Q G C+SCDK I +T K +H E F C C + + + +S CE D +
Sbjct: 7 QDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFSVGDRYLLINSDIVCEQDIY 66
>pdb|2LXD|A Chain A, Backbone 1h, 13c, And 15n Chemical Shift Assignments For
Lmo2(Lim2)- Ldb1(Lid)
Length = 125
Score = 29.6 bits (65), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 52 QKGCCSSCDKPIVGQVIT--ALGKTWHPEHFICTHCNQELGTRN-FFERDSRPYCEPDYH 108
Q G C+SCDK I +T K +H E F C C + + + +S CE D +
Sbjct: 9 QDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFSVGDRYLLINSDIVCEQDIY 68
>pdb|2L4Z|A Chain A, Nmr Structure Of Fusion Of Ctip (641-685) To Lmo4-Lim1
(18-82)
Length = 123
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 3/59 (5%)
Query: 56 CSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGT--RNFFERDSRPYCEPDYHNLF 111
C+ C I + ++ A+ WH C+ C +LG + + + C DY LF
Sbjct: 64 CAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLF 122
>pdb|1A7I|A Chain A, Amino-Terminal Lim Domain From Quail Cysteine And Glycine-
Rich Protein, Nmr, Minimized Average Structure
Length = 81
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/60 (21%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 56 CSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDYHNLFSPR 114
C +C + + + + G+++H F+C C + L + D+ YC+ Y + P+
Sbjct: 10 CGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKYGPK 69
>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 = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 3/59 (5%)
Query: 56 CSSCDKPIVGQ-VITALGKTWHPEHFICTHCNQELGT--RNFFERDSRPYCEPDYHNLF 111
C+ C I + ++ A+ WH C+ C +LG + + + C DY LF
Sbjct: 8 CAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLF 66
>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 = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 29/61 (47%), Gaps = 5/61 (8%)
Query: 52 QKGCCSSCDKPIVGQVIT--ALGKTWHPEHFICTHCNQE--LGTRNFFERDSRPYCEPDY 107
Q G C+SCDK I +T K +H E F C C + +G R + +S CE D
Sbjct: 65 QDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDR-YLLINSDIVCEQDI 123
Query: 108 H 108
+
Sbjct: 124 Y 124
>pdb|2HVR|A Chain A, Structure Of T4 Rna Ligase 2 With Nicked 5'-Adenylated
Nucleic Acid Duplex Containing A 3'-Deoxyribonucleotide
At The Nick
pdb|2HVR|B Chain B, Structure Of T4 Rna Ligase 2 With Nicked 5'-Adenylated
Nucleic Acid Duplex Containing A 3'-Deoxyribonucleotide
At The Nick
pdb|2HVS|A Chain A, Structure Of T4 Rna Ligase 2 With Nicked 5'-Adenylated
Nucleic Acid Duplex Containing A 2'-Deoxyribonucleotide
At The Nick
pdb|2HVS|B Chain B, Structure Of T4 Rna Ligase 2 With Nicked 5'-Adenylated
Nucleic Acid Duplex Containing A 2'-Deoxyribonucleotide
At The Nick
Length = 335
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 21/47 (44%)
Query: 29 GKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTW 75
GK + + + E SR+G+T TQ S K +V V L W
Sbjct: 284 GKVMGLTVQDILEETSREGITLTQADNPSLIKKELVKMVQDVLRPAW 330
>pdb|2HVQ|A Chain A, Structure Of Adenylated Full-length T4 Rna Ligase 2
Length = 335
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 21/47 (44%)
Query: 29 GKQLDCMLDSLTAEMSRQGVTTTQKGCCSSCDKPIVGQVITALGKTW 75
GK + + + E SR+G+T TQ S K +V V L W
Sbjct: 284 GKVMGLTVQDILEETSREGITLTQADNPSLIKKELVKMVQDVLRPAW 330
>pdb|2O10|A Chain A, Solution Structure Of The N-Terminal Lim Domain Of MlpCRP3
Length = 60
Score = 27.3 bits (59), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 56 CSSCDKPIV-GQVITALGKTWHPEHFICTHCNQELGTRNFFERDSRPYCEPDY 107
C +C+K + + I G+++H F C C + L + +S YC+ Y
Sbjct: 4 CGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKVCY 56
>pdb|1X6H|A Chain A, Solution Structures Of The C2h2 Type Zinc Finger Domain Of
Human Transcriptional Repressor Ctcf
Length = 86
Score = 25.8 bits (55), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 6/57 (10%)
Query: 56 CSSCDKPIV-GQVITALGKTWH-----PEHFICTHCNQELGTRNFFERDSRPYCEPD 106
CS CDK Q++ K +H P F+C+ C + RN R + PD
Sbjct: 18 CSHCDKTFRQKQLLDMHFKRYHDPNFVPAAFVCSKCGKTFTRRNTMARHADNCAGPD 74
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
0.321 0.135 0.449
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,772,896
Number of Sequences: 62578
Number of extensions: 135437
Number of successful extensions: 234
Number of sequences better than 100.0: 51
Number of HSP's better than 100.0 without gapping: 37
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 187
Number of HSP's gapped (non-prelim): 58
length of query: 130
length of database: 14,973,337
effective HSP length: 88
effective length of query: 42
effective length of database: 9,466,473
effective search space: 397591866
effective search space used: 397591866
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: 45 (21.9 bits)