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= psy8111
(135 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2EHE|A Chain A, Solution Structure Of The First Lim Domain From Human Four
And A Half Lim Domains Protein 3
Length = 82
Score = 75.9 bits (185), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 31/70 (44%), Positives = 51/70 (72%)
Query: 55 KCYESVFANSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYC 114
CY++ FAN+C EC ++IG DS++L Y+D+H+HE CF C +C++SL D+ F + ++ C
Sbjct: 8 PCYDNTFANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLC 67
Query: 115 GNCYDAQFAS 124
+CY + F+S
Sbjct: 68 NDCYCSAFSS 77
>pdb|2CUP|A Chain A, Solution Structure Of The Skeletal Muscle Lim-Protein 1
Length = 101
Score = 64.7 bits (156), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 44/74 (59%)
Query: 62 ANSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQ 121
++ C EC K IG DSK++ YK++ WH+ CF C+KC L ++ F +K KI C C +
Sbjct: 5 SSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTRE 64
Query: 122 FASRCDGCSEIFKA 135
+ +C GC + A
Sbjct: 65 DSPKCKGCFKAIVA 78
Score = 39.3 bits (90), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 31/63 (49%)
Query: 30 FCCWQCDESLTGQRYVLRDDHPYCIKCYESVFANSCEECSKIIGIDSKDLSYKDKHWHEA 89
F C +C L + +V +D+ C KC + C+ C K I +++ YK WH+
Sbjct: 34 FRCAKCLHPLANETFVAKDNKILCNKCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKD 93
Query: 90 CFS 92
CFS
Sbjct: 94 CFS 96
>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 = 63.5 bits (153), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 30/90 (33%), Positives = 48/90 (53%), Gaps = 2/90 (2%)
Query: 28 QHFCCWQCDESLTGQRYVLRDDHPYCIKCYESVFANSCEECSKIIGIDSKDLSYKDKHWH 87
+HFCC+ CD L G+ YV+ +D P C CY A C+ C I + + ++Y + WH
Sbjct: 29 KHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAVVCQGCHNAIDPEVQRVTYNNFSWH 88
Query: 88 EA--CFSCSKCRQSLVDKQFGSKSEKIYCG 115
+ CF CS C + L+ ++F ++C
Sbjct: 89 ASTECFLCSCCSKCLIGQKFMPVEGMVFCS 118
Score = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 32/81 (39%), Gaps = 13/81 (16%)
Query: 49 DHPYCIKCYESVFANSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSK 108
+ P C C E +F+N + ++++WH F C C L + +
Sbjct: 2 EKPRCAGCDELIFSN-------------EYTQAENQNWHLKHFCCFDCDSILAGEIYVMV 48
Query: 109 SEKIYCGNCYDAQFASRCDGC 129
++K C CY A C GC
Sbjct: 49 NDKPVCKPCYVKNHAVVCQGC 69
>pdb|2CUQ|A Chain A, Solution Structure Of Second Lim Domain From Human
Skeletal Muscle Lim-Protein 2
Length = 80
Score = 58.9 bits (141), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 27/70 (38%), Positives = 38/70 (54%), Gaps = 2/70 (2%)
Query: 55 KCYESVFANSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYC 114
CYE+ FA C CSK + ++Y+D+ WH C C+ C+ L +QF S+ E YC
Sbjct: 8 PCYENKFAPRCARCSKTL--TQGGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYC 65
Query: 115 GNCYDAQFAS 124
C+ FAS
Sbjct: 66 VACFGELFAS 75
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 30 FCCWQCDESLTGQRYVLRDDHPYCIKCYESVFAN 63
C C L GQ++ RD+ PYC+ C+ +FA+
Sbjct: 42 LVCTGCQTPLAGQQFTSRDEDPYCVACFGELFAS 75
>pdb|1X4K|A Chain A, Solution Structure Of Lim Domain In Lim-Protein 3
Length = 72
Score = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 36/63 (57%)
Query: 62 ANSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQ 121
++ C+EC K I ++ + YK WHE CF C +C+Q + K F K + +C CY+ Q
Sbjct: 5 SSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQ 64
Query: 122 FAS 124
AS
Sbjct: 65 HAS 67
Score = 28.9 bits (63), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 12/43 (27%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 24 RGSGQH---FCCWQCDESLTGQRYVLRDDHPYCIKCYESVFAN 63
+GS H F C +C + + + ++ +D+ +C+ CYE A+
Sbjct: 25 KGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHAS 67
>pdb|1X63|A Chain A, Solution Structure Of The Second Lim Domain Of Skeletal
Muscle Lim Protein 1
Length = 82
Score = 52.8 bits (125), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 12/80 (15%)
Query: 45 VLRDDHPYCIKCYESVFANSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQ 104
R+D P C C++++ A +++ YK WH+ CF+CS C+Q +
Sbjct: 10 TTREDSPKCKGCFKAIVAGD------------QNVEYKGTVWHKDCFTCSNCKQVIGTGS 57
Query: 105 FGSKSEKIYCGNCYDAQFAS 124
F K E YC C++ +FAS
Sbjct: 58 FFPKGEDFYCVTCHETKFAS 77
>pdb|2EGQ|A Chain A, Solution Structure Of The Fourth Lim Domain From Human
Four And A Half Lim Domains 1
Length = 77
Score = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 3/65 (4%)
Query: 56 CYESVFANSCEECSKII---GIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKI 112
CY++ A C C I G S ++Y+ + WH+ CF C KC +L +K+F E++
Sbjct: 9 CYKNFVAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQV 68
Query: 113 YCGNC 117
YC +C
Sbjct: 69 YCPDC 73
>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 = 45.8 bits (107), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 39/63 (61%), Gaps = 2/63 (3%)
Query: 62 ANSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQ 121
++ C +C K I + ++Y+++ WH+ CF C+ CR+ L ++F ++ + YC NC+
Sbjct: 5 SSGCVQCKKPI--TTGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDL 62
Query: 122 FAS 124
+AS
Sbjct: 63 YAS 65
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 22/34 (64%)
Query: 30 FCCWQCDESLTGQRYVLRDDHPYCIKCYESVFAN 63
F C C + L+GQR+ RDD YC+ C+ ++A+
Sbjct: 32 FVCTACRKQLSGQRFTARDDFAYCLNCFCDLYAS 65
>pdb|1WYH|A Chain A, Solution Structure Of The Lim Domain From Human Skeletal
Muscle Lim-Protein 2
Length = 72
Score = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 28/55 (50%)
Query: 70 KIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFAS 124
+ + S+ L Y + WHE CF CS C Q L + F YC CY+ +FAS
Sbjct: 13 ETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFAS 67
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 30 FCCWQCDESLTGQRYVLRDDHPYCIKCYESVFAN 63
F C C++ L + +V YC+ CYE+ FA+
Sbjct: 34 FLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFAS 67
>pdb|1X68|A Chain A, Solution Structures Of The C-Terminal Lim Domain Of Human
Fhl5 Protein
Length = 76
Score = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 35/58 (60%), Gaps = 2/58 (3%)
Query: 62 ANSCEECSKIIG--IDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNC 117
++ C CSK I +K + ++D WH CF+C KC SLV K F +++++I+C C
Sbjct: 5 SSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKC 62
>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 = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 34/73 (46%), Gaps = 13/73 (17%)
Query: 53 CIKCYESVFANSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKI 112
C +C +SV+A K+IG K WH+ CF C+KC +SL K +I
Sbjct: 39 CSRCGDSVYA-----AEKVIGAG--------KPWHKNCFRCAKCGKSLESTTLTEKEGEI 85
Query: 113 YCGNCYDAQFASR 125
YC CY F +
Sbjct: 86 YCKGCYAKNFGPK 98
>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 = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 37/67 (55%), Gaps = 2/67 (2%)
Query: 65 CEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFAS 124
C C++ I +D L D+HWH +C C+ C+ L D+ F S++ +YC + +F +
Sbjct: 9 CAGCNQHI-LDKFILKVLDRHWHSSCLKCADCQMQLADRCF-SRAGSVYCKEDFFKRFGT 66
Query: 125 RCDGCSE 131
+C C +
Sbjct: 67 KCTACQQ 73
>pdb|1B8T|A Chain A, Solution Structure Of The Chicken Crp1
Length = 192
Score = 43.5 bits (101), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 13/73 (17%)
Query: 53 CIKCYESVFANSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKI 112
C +C ++V+A K+IG K WH++CF C+KC +SL K +I
Sbjct: 118 CPRCGQAVYAAE-----KVIGAG--------KSWHKSCFRCAKCGKSLESTTLADKDGEI 164
Query: 113 YCGNCYDAQFASR 125
YC CY F +
Sbjct: 165 YCKGCYAKNFGPK 177
Score = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 86 WHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCY 118
+H++CF C C+++L ++IYC +CY
Sbjct: 30 FHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCY 62
>pdb|1CTL|A Chain A, Structure Of The Carboxy-Terminal Lim Domain From The
Cysteine Rich Protein Crp
Length = 85
Score = 43.5 bits (101), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 13/73 (17%)
Query: 53 CIKCYESVFANSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKI 112
C +C ++V+A K+IG K WH++CF C+KC +SL K +I
Sbjct: 11 CPRCGQAVYAAE-----KVIGAG--------KSWHKSCFRCAKCGKSLESTTLADKDGEI 57
Query: 113 YCGNCYDAQFASR 125
YC CY F +
Sbjct: 58 YCKGCYAKNFGPK 70
>pdb|2CUR|A Chain A, Solution Structure Of Skeletal Muscle Lim-Protein 1
Length = 69
Score = 43.1 bits (100), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 62 ANSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCY 118
++ C +C+K I S ++Y+D+ WH CF C C + L ++F + ++ YC +CY
Sbjct: 5 SSGCVKCNK--AITSGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCY 59
Score = 32.0 bits (71), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 30 FCCWQCDESLTGQRYVLRDDHPYCIKCYESVFAN 63
F C C + L GQR+ +D YC+ CY++ +
Sbjct: 32 FVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVSG 65
>pdb|1CXX|A Chain A, Mutant R122a Of Quail Cysteine And Glycine-Rich Protein,
Nmr, Minimized Structure
Length = 113
Score = 43.1 bits (100), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 33/73 (45%), Gaps = 13/73 (17%)
Query: 53 CIKCYESVFANSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKI 112
C C +SV+A K+IG K WH+ CF C+KC +SL K +I
Sbjct: 39 CSACGDSVYA-----AEKVIGAG--------KPWHKNCFRCAKCGKSLESTTLTEKEGEI 85
Query: 113 YCGNCYDAQFASR 125
YC CY F +
Sbjct: 86 YCKGCYAKNFGPK 98
>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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 34/65 (52%), Gaps = 2/65 (3%)
Query: 65 CEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFAS 124
C C + I +D L D+HWH C CS C L ++ F S+ E +YC + + +F +
Sbjct: 9 CAGCDQHI-LDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRFGT 66
Query: 125 RCDGC 129
+C C
Sbjct: 67 KCAAC 71
>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 = 19/56 (33%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 74 IDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFASRCDGC 129
+D L D+HWH C CS C L ++ F S+ E +YC + + +F ++C C
Sbjct: 71 LDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRFGTKCAAC 125
>pdb|1X4L|A Chain A, Solution Structure Of Lim Domain In Four And A Half Lim
Domains Protein 2
Length = 72
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 28/42 (66%)
Query: 76 SKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNC 117
+K +S++++ WH CF+C KC SLV + F ++ + I C +C
Sbjct: 21 TKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDC 62
>pdb|1X61|A Chain A, Solution Structure Of The First Lim Domain Of Thyroid
Receptor Interacting Protein 6 (Trip6)
Length = 72
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 71 IIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFAS 124
++G D + D+ +H CF CS CR L + F + + YC CY A S
Sbjct: 15 VVG-DGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATLES 67
>pdb|2O13|A Chain A, Solution Structure Of The C-Terminal Lim Domain Of MlpCRP3
Length = 58
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 26/58 (44%), Gaps = 1/58 (1%)
Query: 65 CEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQF 122
C C K + K + K WH+ CF C+ C +SL K ++YC CY F
Sbjct: 2 CPRCGKSVYAAEKVMG-GGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNF 58
>pdb|2DAR|A Chain A, Solution Structure Of First Lim Domain Of Enigma-Like Pdz
And Lim Domains Protein
Length = 90
Score = 34.3 bits (77), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 2/60 (3%)
Query: 65 CEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFAS 124
C C+++I L K WH F+C+ C+ ++ F + +YC CY+ FAS
Sbjct: 28 CAHCNQVI--RGPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFAS 85
>pdb|1IML|A Chain A, Cysteine Rich Intestinal Protein, Nmr, 48 Structures
Length = 76
Score = 33.9 bits (76), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 26/62 (41%), Gaps = 2/62 (3%)
Query: 65 CEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGN-CYDAQFA 123
C +C K + + S K WH C C KC ++L K YC + CY A F
Sbjct: 3 CPKCDKEVYFAERVTSL-GKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFG 61
Query: 124 SR 125
+
Sbjct: 62 PK 63
>pdb|2DJ7|A Chain A, Solution Structure Of 3rd Lim Domain Of Actin-Binding Lim
Protein 3
Length = 80
Score = 33.1 bits (74), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 77 KDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFAS 124
+ L DK WH +CF C C ++ ++ SK YC + Y AQF S
Sbjct: 29 QSLLALDKQWHVSCFKCQTC-SVILTGEYISKDGVPYCESDYHAQFGS 75
>pdb|1A7I|A Chain A, Amino-Terminal Lim Domain From Quail Cysteine And Glycine-
Rich Protein, Nmr, Minimized Average Structure
Length = 81
Score = 33.1 bits (74), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 14/64 (21%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 62 ANSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQ 121
N C C + + ++++ + +H CF C CR++L ++YC +CY +
Sbjct: 7 GNKCGACGRTV-YHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKK 65
Query: 122 FASR 125
+ +
Sbjct: 66 YGPK 69
>pdb|2D8X|A Chain A, Solution Structure Of The Second Lim Domain Of
Particularly Interesting New Cys-His Protein (Pinch)
Length = 70
Score = 32.7 bits (73), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 2/63 (3%)
Query: 62 ANSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQ 121
++ C +C + I + + + WH CF C C++ L D F + + C C++ +
Sbjct: 5 SSGCHQCGEFI--IGRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNRE 62
Query: 122 FAS 124
AS
Sbjct: 63 KAS 65
>pdb|2O10|A Chain A, Solution Structure Of The N-Terminal Lim Domain Of MlpCRP3
Length = 60
Score = 32.3 bits (72), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 65 CEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCY 118
C C K + ++++ + +H+ CF C CR++L + +IYC CY
Sbjct: 4 CGACEKTV-YHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKVCY 56
>pdb|2CU8|A Chain A, Solution Structure Of The Lim Domain Of Human
Cysteine-Rich Protein 2
Length = 76
Score = 32.0 bits (71), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 2/65 (3%)
Query: 61 FANSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYC-GNCYD 119
A+ C +C K + K +S K WH+ C C +C ++L K +C CY
Sbjct: 8 MASKCPKCDKTVYFAEK-VSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYA 66
Query: 120 AQFAS 124
F S
Sbjct: 67 TLFGS 71
>pdb|2IYB|E Chain E, Structure Of Complex Between The 3rd Lim Domain Of Tes And
The Evh1 Domain Of Mena
pdb|2IYB|F Chain F, Structure Of Complex Between The 3rd Lim Domain Of Tes And
The Evh1 Domain Of Mena
pdb|2IYB|G Chain G, Structure Of Complex Between The 3rd Lim Domain Of Tes And
The Evh1 Domain Of Mena
pdb|2IYB|H Chain H, Structure Of Complex Between The 3rd Lim Domain Of Tes And
The Evh1 Domain Of Mena
Length = 65
Score = 32.0 bits (71), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 62 ANSCEECSKIIGIDSKDLSYKDKHWHEA--CFSCSKCRQSLVDKQFGSKSEKIYC 114
A C+ C I + + ++Y + WH + CF CS C + L+ ++F ++C
Sbjct: 2 AVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFC 56
>pdb|2D8Y|A Chain A, Solution Structure Of The Lim Domain Of Epithelial Protein
Lost In Neoplasm
Length = 91
Score = 31.6 bits (70), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 64 SCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFA 123
+C EC K + + L + +H +CF CS C L + S +IYC ++ F
Sbjct: 17 TCVECQKTV-YPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFK 75
Query: 124 SR 125
S+
Sbjct: 76 SK 77
>pdb|2KBX|B Chain B, Solution Structure Of Ilk-Pinch Complex
Length = 70
Score = 30.8 bits (68), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 27/61 (44%)
Query: 64 SCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFA 123
+CE C K ++ + +HE CF C++C Q + F + YC + + FA
Sbjct: 9 TCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFA 68
Query: 124 S 124
Sbjct: 69 P 69
>pdb|3F6Q|B Chain B, Crystal Structure Of Integrin-Linked Kinase Ankyrin Repeat
Domain In Complex With Pinch1 Lim1 Domain
Length = 72
Score = 30.8 bits (68), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 27/60 (45%)
Query: 64 SCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFA 123
+CE C K ++ + +HE CF C++C Q + F + YC + + FA
Sbjct: 13 TCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFA 72
>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 = 0.25, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 57 YESVFANS--CEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLV 101
Y +F NS C C + I + + +H CF+CS CR LV
Sbjct: 62 YIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLV 108
Score = 30.4 bits (67), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 25/61 (40%), Gaps = 4/61 (6%)
Query: 79 LSYKDKHWHEACFSCSKCRQSLVDKQFGS--KSEKIYCGNCYDAQFASR--CDGCSEIFK 134
L D +WH C CS C+ L D S KS I C N Y F + C C +
Sbjct: 21 LYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIP 80
Query: 135 A 135
A
Sbjct: 81 A 81
>pdb|1G47|A Chain A, 1st Lim Domain Of Pinch Protein
Length = 77
Score = 30.8 bits (68), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 27/61 (44%)
Query: 64 SCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFA 123
+CE C K ++ + +HE CF C++C Q + F + YC + + FA
Sbjct: 13 TCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFA 72
Query: 124 S 124
Sbjct: 73 P 73
>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 = 0.26, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 57 YESVFANS--CEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLV 101
Y +F NS C C + I + + +H CF+CS CR LV
Sbjct: 60 YIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLV 106
Score = 30.8 bits (68), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 25/61 (40%), Gaps = 4/61 (6%)
Query: 79 LSYKDKHWHEACFSCSKCRQSLVDKQFGS--KSEKIYCGNCYDAQFASR--CDGCSEIFK 134
L D +WH C CS C+ L D S KS I C N Y F + C C +
Sbjct: 19 LYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIP 78
Query: 135 A 135
A
Sbjct: 79 A 79
>pdb|1X3H|A Chain A, Solution Structure Of The Lim Domain Of Human Leupaxin
Length = 80
Score = 29.3 bits (64), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 24/58 (41%), Gaps = 2/58 (3%)
Query: 57 YESVFANSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYC 114
+ ++F+ C C++ + LS D WH CF C C S F + +C
Sbjct: 10 FLAMFSPKCGGCNRPV--LENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFC 65
>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 = 29.3 bits (64), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 20/46 (43%), Gaps = 2/46 (4%)
Query: 79 LSYKDKHWHEACFSCSKCRQSLVDKQFGS--KSEKIYCGNCYDAQF 122
L D +WH C CS C+ L D S KS I C N Y F
Sbjct: 21 LYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLF 66
>pdb|1X62|A Chain A, Solution Structure Of The Lim Domain Of Carboxyl Terminal
Lim Domain Protein 1
Length = 79
Score = 29.3 bits (64), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 65 CEEC-SKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYC 114
C++C + I+G+ K +D+H H C+ C+ C +L K ++IYC
Sbjct: 18 CDKCGTGIVGVFVK---LRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYC 65
>pdb|2L4Z|A Chain A, Nmr Structure Of Fusion Of Ctip (641-685) To Lmo4-Lim1
(18-82)
Length = 123
Score = 28.9 bits (63), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 20/47 (42%), Gaps = 2/47 (4%)
Query: 79 LSYKDKHWHEACFSCSKCRQSLVDKQFGS--KSEKIYCGNCYDAQFA 123
L D +WH C CS C+ L D S KS I C N Y F
Sbjct: 77 LYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG 123
>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 = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 12/50 (24%), Positives = 22/50 (44%)
Query: 74 IDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFA 123
I+ + ++ K WH F C+KC + + + + YC Y+ F
Sbjct: 15 IEGRVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLFG 64
Score = 27.3 bits (59), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 18/36 (50%)
Query: 28 QHFCCWQCDESLTGQRYVLRDDHPYCIKCYESVFAN 63
+HF C +C++ G R+ R YC Y +F +
Sbjct: 30 EHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLFGD 65
>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 = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 2/61 (3%)
Query: 40 TGQRYVLRDDHPYCIKCYESVFANS--CEECSKIIGIDSKDLSYKDKHWHEACFSCSKCR 97
G+R + C + Y +F C C K I + KDK +H CF C+ C+
Sbjct: 42 VGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQ 101
Query: 98 Q 98
+
Sbjct: 102 K 102
Score = 26.9 bits (58), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 64 SCEECSKIIGIDSKDLSYKDKHWHEACFSCSKC 96
+C C + IG D L D++WHE C SC C
Sbjct: 4 TCGGCQQNIG-DRYFLKAIDQYWHEDCLSCDLC 35
>pdb|1X64|A Chain A, Solution Structure Of The Lim Domain Of Alpha-Actinin-2
Associated Lim Protein
Length = 89
Score = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 65 CEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYC 114
C++C GI + +DK+ H CF C+ C +L K + ++YC
Sbjct: 28 CDKCGS--GIVGAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYC 75
>pdb|1J2O|A Chain A, Structure Of Flin2, A Complex Containing The N-Terminal
Lim Domain Of Lmo2 And Ldb1-Lid
Length = 114
Score = 28.1 bits (61), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 64 SCEECSKIIGIDSKDLSYKDKHWHEACFSCSKC 96
+C C + IG D L D++WHE C SC C
Sbjct: 5 TCGGCQQNIG-DRYFLKAIDQYWHEDCLSCDLC 36
>pdb|3CKL|A Chain A, Crystal Structure Of Human Cytosolic Sulfotransferase
Sult1b1 In Complex With Pap And Resveratrol
pdb|3CKL|B Chain B, Crystal Structure Of Human Cytosolic Sulfotransferase
Sult1b1 In Complex With Pap And Resveratrol
Length = 298
Score = 28.1 bits (61), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 2/51 (3%)
Query: 47 RDDHPYCIKCYESVFANSCEECSKIIGIDSKDLS--YKDKHWHEACFSCSK 95
+++HP YE + N EE KII K+L+ D+ H F K
Sbjct: 186 KEEHPILFLYYEDMKENPKEEIKKIIRFLEKNLNDEILDRIIHHTSFEVMK 236
>pdb|2Z5F|A Chain A, Human Sulfotransferase Sult1b1 In Complex With Pap
pdb|2Z5F|B Chain B, Human Sulfotransferase Sult1b1 In Complex With Pap
Length = 298
Score = 28.1 bits (61), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 2/51 (3%)
Query: 47 RDDHPYCIKCYESVFANSCEECSKIIGIDSKDLS--YKDKHWHEACFSCSK 95
+++HP YE + N EE KII K+L+ D+ H F K
Sbjct: 186 KEEHPILFLYYEDMKENPKEEIKKIIRFLEKNLNDEILDRIIHHTSFEVMK 236
>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 = 27.3 bits (59), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 13/59 (22%), Positives = 26/59 (44%)
Query: 65 CEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFA 123
C+ C + ++ + +HE CF C++C + + F + YC + + FA
Sbjct: 14 CQRCQARFSPAERIVNSNGELYHEHCFVCAQCFRPFPEGLFYEFEGRKYCEHDFQMLFA 72
>pdb|1V6G|A Chain A, Solution Structure Of The Lim Domain Of The Human Actin
Binding Lim Protein 2
Length = 81
Score = 26.9 bits (58), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 57 YESVFANSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCR 97
Y+ ++ C C + I + + +S K +H CF C+ CR
Sbjct: 10 YQRLYGTRCFSCDQFI--EGEVVSALGKTYHPDCFVCAVCR 48
>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 = 26.2 bits (56), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 65 CEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQ 98
C C K I + KDK +H CF C+ C++
Sbjct: 11 CASCDKRIRAYEMTMRVKDKVYHLECFKCAACQK 44
>pdb|2LXD|A Chain A, Backbone 1h, 13c, And 15n Chemical Shift Assignments For
Lmo2(Lim2)- Ldb1(Lid)
Length = 125
Score = 25.8 bits (55), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 65 CEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQ 98
C C K I + KDK +H CF C+ C++
Sbjct: 13 CASCDKRIRAYEMTMRVKDKVYHLECFKCAACQK 46
>pdb|3EB0|A Chain A, Crystal Structure Of Cgd4_240 From Cryptosporidium
Parvum In Complex With Indirubin E804
pdb|3EB0|C Chain C, Crystal Structure Of Cgd4_240 From Cryptosporidium
Parvum In Complex With Indirubin E804
Length = 383
Score = 25.8 bits (55), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 14 EDYNKLGGKDRGSGQH 29
+D+NKLGGK+ G H
Sbjct: 84 DDHNKLGGKNNGVNNH 99
>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 = 25.4 bits (54), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 65 CEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQ 104
C+ C K I + L +KH+H +C C +C Q + +
Sbjct: 8 CDSCEKYI--TGRVLEAGEKHYHPSCALCVRCGQMFAEGE 45
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 0.135 0.455
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,299,118
Number of Sequences: 62578
Number of extensions: 172398
Number of successful extensions: 465
Number of sequences better than 100.0: 67
Number of HSP's better than 100.0 without gapping: 53
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 364
Number of HSP's gapped (non-prelim): 108
length of query: 135
length of database: 14,973,337
effective HSP length: 88
effective length of query: 47
effective length of database: 9,466,473
effective search space: 444924231
effective search space used: 444924231
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: 46 (22.3 bits)