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= psy4350
(107 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2JTN|A Chain A, Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Complex
Length = 182
Score = 69.7 bits (169), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 36/73 (49%), Positives = 45/73 (61%), Gaps = 4/73 (5%)
Query: 20 GGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFRY--SQ 77
GC Q I+DRF L A+DR WH CL+C+ CHVPL CFSR ++YCK DFF+ ++
Sbjct: 64 AGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAER--CFSRGESVYCKDDFFKRFGTK 121
Query: 78 ARYPDLPIPKTLV 90
L IP T V
Sbjct: 122 CAACQLGIPPTQV 134
>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 = 68.6 bits (166), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 36/73 (49%), Positives = 45/73 (61%), Gaps = 4/73 (5%)
Query: 20 GGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFRY--SQ 77
GC Q I+DRF L A+DR WH CL+C+ CHVPL CFSR ++YCK DFF+ ++
Sbjct: 10 AGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAER--CFSRGESVYCKDDFFKRFGTK 67
Query: 78 ARYPDLPIPKTLV 90
L IP T V
Sbjct: 68 CAACQLGIPPTQV 80
>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 = 64.3 bits (155), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 28/55 (50%), Positives = 37/55 (67%), Gaps = 2/55 (3%)
Query: 20 GGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
GC Q I+D+F L +DR WH CL+CA C + L CFSR G++YCK+DFF+
Sbjct: 10 AGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLADR--CFSRAGSVYCKEDFFK 62
>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 = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 21 GCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHS-ELSCFSRHGNIYCKQDFFR 74
GCG I DRF L A+D WH CL+C+ C L S +++ G I C+ D+ R
Sbjct: 10 GCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIR 64
>pdb|2L4Z|A Chain A, Nmr Structure Of Fusion Of Ctip (641-685) To Lmo4-Lim1
(18-82)
Length = 123
Score = 50.8 bits (120), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 21 GCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHS-ELSCFSRHGNIYCKQDFFR 74
GCG I DRF L A+D WH CL+C+ C L S +++ G I C+ D+ R
Sbjct: 66 GCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIR 120
>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 = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 21 GCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHS-ELSCFSRHGNIYCKQDFFR 74
GCG I DRF L A+D WH CL+C+ C L S +++ G I C+ D+ R
Sbjct: 8 GCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIR 62
>pdb|1RUT|X Chain X, Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 Lid
Domain
Length = 188
Score = 49.7 bits (117), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 21 GCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHS-ELSCFSRHGNIYCKQDFFR 74
GCG I DRF L A+D WH CL+C+ C L S +++ G I C+ D+ R
Sbjct: 10 GCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIR 64
>pdb|2DJ7|A Chain A, Solution Structure Of 3rd Lim Domain Of Actin-Binding
Lim Protein 3
Length = 80
Score = 42.4 bits (98), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 21 GCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
GC + I LLA+D+QWH+ C +C C V L E S+ G YC+ D+
Sbjct: 20 GCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTGEY--ISKDGVPYCESDY 69
>pdb|1J2O|A Chain A, Structure Of Flin2, A Complex Containing The N-Terminal
Lim Domain Of Lmo2 And Ldb1-Lid
Length = 114
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 20 GGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPL-HSELSCFSRHGNIYCKQDFFR 74
GGC Q I DR++L A+D+ WH CL C C L + + G C++D+ R
Sbjct: 7 GGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLR 62
>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 = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 20 GGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPL-HSELSCFSRHGNIYCKQDFFR 74
GGC Q I DR++L A+D+ WH CL C C L + + G C++D+ R
Sbjct: 6 GGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLR 61
>pdb|2DLO|A Chain A, Solution Structure Of The Second Lim Domain Of Human
Thyroid Receptor-Interacting Protein 6
Length = 81
Score = 37.0 bits (84), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 22 CGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
C QPI+DR L A+ + +H GC C CH L I+C +DF R
Sbjct: 21 CSQPILDRI-LRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHR 72
>pdb|1CTL|A Chain A, Structure Of The Carboxy-Terminal Lim Domain From The
Cysteine Rich Protein Crp
Length = 85
Score = 36.2 bits (82), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 22 CGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCK 69
CGQ + ++ + WH C +CA C L S + + G IYCK
Sbjct: 14 CGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLES-TTLADKDGEIYCK 60
>pdb|1B8T|A Chain A, Solution Structure Of The Chicken Crp1
Length = 192
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 22 CGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCK 69
CGQ + ++ + WH C +CA C L S + + G IYCK
Sbjct: 121 CGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLES-TTLADKDGEIYCK 167
>pdb|1CXX|A Chain A, Mutant R122a Of Quail Cysteine And Glycine-Rich Protein,
Nmr, Minimized Structure
Length = 113
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 22 CGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCK 69
CG + ++ + WH C +CA C L S + + G IYCK
Sbjct: 42 CGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLES-TTLTEKEGEIYCK 88
>pdb|1IBI|A Chain A, Quail Cysteine And Glycine-Rich Protein, Nmr, 15
Minimized Model Structures
pdb|1QLI|A Chain A, Quail Cysteine And Glycine-Rich Protein, Nmr, Minimized
Average Structure
Length = 113
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 22 CGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCK 69
CG + ++ + WH C +CA C L S + + G IYCK
Sbjct: 42 CGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLES-TTLTEKEGEIYCK 88
>pdb|1X3H|A Chain A, Solution Structure Of The Lim Domain Of Human Leupaxin
Length = 80
Score = 33.9 bits (76), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 20 GGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCK 69
GGC +P+++ YL A+D WH C C C S S F G +C+
Sbjct: 19 GGCNRPVLEN-YLSAMDTVWHPECFVCGDCFTSF-STGSFFELDGRPFCE 66
>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 = 0.11, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 22 CGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
C + + LLA + +H+ C +C++C+ L S + S HG IYCK F
Sbjct: 21 CQKTVYPMERLLANQQVFHISCFRCSYCNNKL-SLGTYASLHGRIYCKPHF 70
>pdb|2O13|A Chain A, Solution Structure Of The C-Terminal Lim Domain Of
MlpCRP3
Length = 58
Score = 30.0 bits (66), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 22 CGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCK 69
CG+ + ++ + WH C +CA C L S + + G +YCK
Sbjct: 5 CGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLES-TNVTDKDGELYCK 51
>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 = 29.3 bits (64), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 2/53 (3%)
Query: 20 GGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
G C +PI R + A+ +QWH+ CA C P + R G YC+ +
Sbjct: 9 GACRRPIEGRV-VNAMGKQWHVEHFVCAKCEKPFLGHRH-YERKGLAYCETHY 59
>pdb|2LXD|A Chain A, Backbone 1h, 13c, And 15n Chemical Shift Assignments For
Lmo2(Lim2)- Ldb1(Lid)
Length = 125
Score = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 11/42 (26%), Positives = 21/42 (50%)
Query: 36 DRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFRYSQ 77
D+ +HL C +CA C + +I C+QD + +++
Sbjct: 31 DKVYHLECFKCAACQKHFSVGDRYLLINSDIVCEQDIYEWTK 72
>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 = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 11/42 (26%), Positives = 21/42 (50%)
Query: 36 DRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFRYSQ 77
D+ +HL C +CA C + +I C+QD + +++
Sbjct: 29 DKVYHLECFKCAACQKHFSVGDRYLLINSDIVCEQDIYEWTK 70
>pdb|1X61|A Chain A, Solution Structure Of The First Lim Domain Of Thyroid
Receptor Interacting Protein 6 (Trip6)
Length = 72
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 26 IIDRFYLLAVDRQWHLGCLQCAHCHVPLHSE 56
+ D ++A+DR +H+GC C+ C L +
Sbjct: 16 VGDGAGVVALDRVFHVGCFVCSTCRAQLRGQ 46
>pdb|1X68|A Chain A, Solution Structures Of The C-Terminal Lim Domain Of
Human Fhl5 Protein
Length = 76
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 15/35 (42%), Gaps = 3/35 (8%)
Query: 22 CGQPI---IDRFYLLAVDRQWHLGCLQCAHCHVPL 53
C +PI ++ D QWH C C C V L
Sbjct: 11 CSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSL 45
>pdb|2DAR|A Chain A, Solution Structure Of First Lim Domain Of Enigma-Like
Pdz And Lim Domains Protein
Length = 90
Score = 26.9 bits (58), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 26 IIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCK---QDFF 73
+I +L+A+ + WH CAHC + + + G +YC+ + FF
Sbjct: 34 VIRGPFLVALGKSWHPEEFNCAHCKNTM-AYIGFVEEKGALYCELCYEKFF 83
>pdb|2OLM|A Chain A, Arfgap Domain Of Hiv-1 Rev Binding Protein
Length = 140
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 3/46 (6%)
Query: 54 HSELSCFSRHGNIYCKQ---DFFRYSQARYPDLPIPKTLVSFLYDK 96
E+ +HGN CKQ F + PD P+ + FL +K
Sbjct: 74 QQEIEFLQKHGNEVCKQIWLGLFDDRSSAIPDFRDPQKVKEFLQEK 119
>pdb|2D9L|A Chain A, Solution Structure Of The Arfgap Domain Of Human Rip
Length = 134
Score = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 3/46 (6%)
Query: 54 HSELSCFSRHGNIYCKQ---DFFRYSQARYPDLPIPKTLVSFLYDK 96
E+ +HGN CKQ F + PD P+ + FL +K
Sbjct: 69 QQEIEFLQKHGNEVCKQIWLGLFDDRSSAIPDFRDPQKVKEFLQEK 114
>pdb|1X4L|A Chain A, Solution Structure Of Lim Domain In Four And A Half Lim
Domains Protein 2
Length = 72
Score = 26.2 bits (56), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 31 YLLAVDRQWHLGCLQCAHCHVPL 53
Y+ +RQWH C C C + L
Sbjct: 23 YISFEERQWHNDCFNCKKCSLSL 45
>pdb|2CUQ|A Chain A, Solution Structure Of Second Lim Domain From Human
Skeletal Muscle Lim-Protein 2
Length = 80
Score = 26.2 bits (56), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 36 DRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYC 68
D+ WH CL C C PL + SR + YC
Sbjct: 34 DQPWHRECLVCTGCQTPLAGQQF-TSRDEDPYC 65
>pdb|2CUP|A Chain A, Solution Structure Of The Skeletal Muscle Lim-Protein 1
Length = 101
Score = 25.8 bits (55), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 22 CGQPI-IDRFYLLAVDRQWHLGCLQCAHCHVPLHSEL 57
C +PI D + +R WH C +CA C PL +E
Sbjct: 11 CRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANET 47
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
0.328 0.144 0.492
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,054,575
Number of Sequences: 62578
Number of extensions: 108120
Number of successful extensions: 344
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 24
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 315
Number of HSP's gapped (non-prelim): 33
length of query: 107
length of database: 14,973,337
effective HSP length: 72
effective length of query: 35
effective length of database: 10,467,721
effective search space: 366370235
effective search space used: 366370235
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)