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= psy10849
(267 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MMK|A Chain A, The Structural Basis For Partial Redundancy In A Class Of
Transcription Factors, The Lim-Homeodomain Proteins, In
Neural Cell Type Specification
pdb|3MMK|B Chain B, The Structural Basis For Partial Redundancy In A Class Of
Transcription Factors, The Lim-Homeodomain Proteins, In
Neural Cell Type Specification
Length = 169
Score = 63.2 bits (152), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 29/76 (38%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 3 SHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQ 62
S V C F+ +G KC C + P ++V +AQ VYHL CF C+IC + L G++
Sbjct: 49 SRAGSVYCKEDFFKRFGTKCTACQQGIPPTQVVRKAQDFVYHLHCFACIICNRQLATGDE 108
Query: 63 F-ILRSGQLFCRQDFE 77
F ++ G+L C++D+E
Sbjct: 109 FYLMEDGRLVCKEDYE 124
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 30/60 (50%), Gaps = 3/60 (5%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEM 80
+CA C +L + +++ +H C C C +Q ++ R+G ++C++DF K
Sbjct: 8 QCAGCNQHILD-KFILKVLDRHWHSSCLKCADC--QMQLADRCFSRAGSVYCKEDFFKRF 64
>pdb|2JTN|A Chain A, Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Complex
Length = 182
Score = 62.4 bits (150), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 3 SHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQ 62
S V C F+ +G KCA C + P ++V RAQ VYHL CF CV+C + L G++
Sbjct: 103 SRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDE 162
Query: 63 F-ILRSGQLFCRQDFE 77
F ++ +L C+ D+E
Sbjct: 163 FYLMEDSRLVCKADYE 178
>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 = 61.2 bits (147), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 3 SHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQ 62
S V C F+ +G KCA C + P ++V RAQ VYHL CF CV+C + L G++
Sbjct: 49 SRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDE 108
Query: 63 F-ILRSGQLFCRQDFE 77
F ++ +L C+ D+E
Sbjct: 109 FYLMEDSRLVCKADYE 124
>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 = 57.8 bits (138), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 41/77 (53%), Gaps = 2/77 (2%)
Query: 1 STSHNSHVSCHPRGFRLYG--VKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQ 58
S + + + C RL+G C+ CG + E+VMRAQ +VYHL CF C C L
Sbjct: 47 SYTKSGMILCRNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLV 106
Query: 59 KGEQFILRSGQLFCRQD 75
G++F +G LFC D
Sbjct: 107 PGDRFHYINGSLFCEHD 123
>pdb|1RUT|X Chain X, Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 Lid
Domain
Length = 188
Score = 57.8 bits (138), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 41/77 (53%), Gaps = 2/77 (2%)
Query: 1 STSHNSHVSCHPRGFRLYG--VKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQ 58
S + + + C RL+G C+ CG + E+VMRAQ +VYHL CF C C L
Sbjct: 49 SYTKSGMILCRNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLV 108
Query: 59 KGEQFILRSGQLFCRQD 75
G++F +G LFC D
Sbjct: 109 PGDRFHYINGSLFCEHD 125
>pdb|2LXD|A Chain A, Backbone 1h, 13c, And 15n Chemical Shift Assignments For
Lmo2(Lim2)- Ldb1(Lid)
Length = 125
Score = 53.9 bits (128), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 2/64 (3%)
Query: 15 FRLYGVK--CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFC 72
RL+G CA C R+ +EM MR + VYHL CF C C + G++++L + + C
Sbjct: 4 LRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFSVGDRYLLINSDIVC 63
Query: 73 RQDF 76
QD
Sbjct: 64 EQDI 67
>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 = 52.0 bits (123), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 2/64 (3%)
Query: 15 FRLYGVK--CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFC 72
RL+G CA C R+ +EM MR + VYHL CF C C + G++++L + + C
Sbjct: 2 LRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFSVGDRYLLINSDIVC 61
Query: 73 RQDF 76
QD
Sbjct: 62 EQDI 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 = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 36/69 (52%), Gaps = 2/69 (2%)
Query: 10 CHPRGFRLYGVK--CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRS 67
C RL+G CA C R+ +EM MR + VYHL CF C C + G++++L +
Sbjct: 55 CRRDYLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLIN 114
Query: 68 GQLFCRQDF 76
+ C QD
Sbjct: 115 SDIVCEQDI 123
>pdb|1G47|A Chain A, 1st Lim Domain Of Pinch Protein
Length = 77
Score = 41.6 bits (96), Expect = 5e-04, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 17 LYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
L C RC P E ++ + +YH CFVC C Q +G F G+ +C DF
Sbjct: 9 LASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEG-LFYEFEGRKYCEHDF 67
Query: 77 E 77
+
Sbjct: 68 Q 68
>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 = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFE 77
C RC R P E ++ + +YH CFVC C +P +G F G+ +C DF+
Sbjct: 14 CQRCQARFSPAERIVNSNGELYHEHCFVCAQCFRPFPEG-LFYEFEGRKYCEHDFQ 68
>pdb|2KBX|B Chain B, Solution Structure Of Ilk-Pinch Complex
Length = 70
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 17 LYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
L C RC P E ++ + +YH CFVC C Q +G F G+ +C DF
Sbjct: 5 LASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEG-LFYEFEGRKYCEHDF 63
Query: 77 E 77
+
Sbjct: 64 Q 64
>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 = 0.001, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFE 77
C RC P E ++ + +YH CFVC C Q +G F G+ +C DF+
Sbjct: 14 CERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEG-LFYEFEGRKYCEHDFQ 68
>pdb|1V6G|A Chain A, Solution Structure Of The Lim Domain Of The Human Actin
Binding Lim Protein 2
Length = 81
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 16 RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQ 74
RLYG +C C D+ + E+V A YH CFVC +C P G++ + C++
Sbjct: 12 RLYGTRCFSC-DQFIEGEVV-SALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQK 68
>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 = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
KC+RCGD + E V+ A +H CF C C + L+ + G+++C+ + K
Sbjct: 38 KCSRCGDSVYAAEKVIGA-GKPWHKNCFRCAKCGKSLES-TTLTEKEGEIYCKGCYAK 93
>pdb|2DLO|A Chain A, Solution Structure Of The Second Lim Domain Of Human
Thyroid Receptor-Interacting Protein 6
Length = 81
Score = 37.4 bits (85), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEM 80
KCA C +L + ++RA YH CF CV+C + L + + Q+ C +DF ++
Sbjct: 17 KCATCSQPIL--DRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHRKF 74
>pdb|1X4K|A Chain A, Solution Structure Of Lim Domain In Lim-Protein 3
Length = 72
Score = 35.8 bits (81), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKE 79
C C ++P M + +H CF+C C QP+ + FI + Q FC +EK+
Sbjct: 8 CQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGT-KSFIPKDNQNFCVPCYEKQ 64
>pdb|1CXX|A Chain A, Mutant R122a Of Quail Cysteine And Glycine-Rich Protein,
Nmr, Minimized Structure
Length = 113
Score = 35.0 bits (79), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
KC+ CGD + E V+ A +H CF C C + L+ + G+++C+ + K
Sbjct: 38 KCSACGDSVYAAEKVIGA-GKPWHKNCFRCAKCGKSLES-TTLTEKEGEIYCKGCYAK 93
>pdb|2O13|A Chain A, Solution Structure Of The C-Terminal Lim Domain Of
MlpCRP3
Length = 58
Score = 33.9 bits (76), Expect = 0.090, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
KC RCG + E VM +H CF C IC + L+ + G+L+C+ + K
Sbjct: 1 KCPRCGKSVYAAEKVM-GGGKPWHKTCFRCAICGKSLES-TNVTDKDGELYCKVCYAK 56
>pdb|2D8Y|A Chain A, Solution Structure Of The Lim Domain Of Epithelial
Protein Lost In Neoplasm
Length = 91
Score = 32.0 bits (71), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 2/57 (3%)
Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
C C + P E ++ A V+H+ CF C C L G L G+++C+ F +
Sbjct: 18 CVECQKTVYPMERLL-ANQQVFHISCFRCSYCNNKLSLGTYASLH-GRIYCKPHFNQ 72
>pdb|3KHN|A Chain A, Crystal Structure Of Putative Motb Like Protein Dvu_2228
From Desulfovibrio Vulgaris.
pdb|3KHN|B Chain B, Crystal Structure Of Putative Motb Like Protein Dvu_2228
From Desulfovibrio Vulgaris
Length = 174
Score = 30.8 bits (68), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 24/108 (22%), Positives = 50/108 (46%), Gaps = 18/108 (16%)
Query: 124 SSFEVSPKPCRKVSTMNS----KRAKNI--------LTPNQRRQFKSSFEISSMPCRKVG 171
+ E++P R ++T+ +R +NI + P+ +FK ++E+S++ R V
Sbjct: 58 GAVELAPGADRVLATLKDLFIRRREQNINIKGFTDDVQPSANARFKDNWEVSAL--RSVN 115
Query: 172 VHGHYLSLGMSLQDSSDSIFASSTKPLNPNHPYSPDDSYAMHSNDSFC 219
V ++L G+ + A+ L+P P + D++ A + F
Sbjct: 116 VLRYFLGAGI----EPARLTATGLGELDPLFPNTSDENRARNRRVEFV 159
>pdb|1X64|A Chain A, Solution Structure Of The Lim Domain Of Alpha-Actinin-2
Associated Lim Protein
Length = 89
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 5/52 (9%)
Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPL-QKGEQFILRSGQLFC 72
C +CG ++ V++A+ H CFVC C L QKG F+ G+L+C
Sbjct: 28 CDKCGSGIV--GAVVKARDKYRHPECFVCADCNLNLKQKGYFFV--EGELYC 75
>pdb|1A7I|A Chain A, Amino-Terminal Lim Domain From Quail Cysteine And
Glycine- Rich Protein, Nmr, Minimized Average Structure
Length = 81
Score = 30.4 bits (67), Expect = 1.1, Method: Composition-based stats.
Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 19 GVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
G KC CG R + H ++ +H CF+C++C + L + +++C+ + K
Sbjct: 7 GNKCGACG-RTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDS-TTVAIHDAEVYCKSCYGK 64
Query: 79 E 79
+
Sbjct: 65 K 65
>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 = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 35 VMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLF---CRQDFEKE 79
V+ A YH C +CV C Q +GE+ L+ ++ CRQ E
Sbjct: 19 VLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAARTE 66
>pdb|1X3H|A Chain A, Solution Structure Of The Lim Domain Of Human Leupaxin
Length = 80
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 25/57 (43%), Gaps = 3/57 (5%)
Query: 17 LYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCR 73
++ KC C +L E + A V+H CFVC C G F L G+ FC
Sbjct: 13 MFSPKCGGCNRPVL--ENYLSAMDTVWHPECFVCGDCFTSFSTGSFFEL-DGRPFCE 66
>pdb|2HNY|B Chain B, Crystal Structure Of E138k Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
pdb|2HNZ|B Chain B, Crystal Structure Of E138k Mutant Hiv-1 Reverse
Transcriptase In Complex With Pett-2
Length = 422
Score = 29.3 bits (64), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 2/71 (2%)
Query: 158 SSFEISSMPCRKVGVHGHYLSLGMSLQDSSDSIFASS-TKPLNPNHPYSPDDSYAMHSND 216
++F I S+ + G+ Y L + S +IF SS TK L P +PD + +D
Sbjct: 122 TAFTIPSINNKTPGIRYQYNVLPQGWK-GSPAIFQSSMTKILEPFRKQNPDIVIYQYMDD 180
Query: 217 SFCSSDISLDE 227
+ SD+ + +
Sbjct: 181 LYVGSDLEIGQ 191
>pdb|2HNY|A Chain A, Crystal Structure Of E138k Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
pdb|2HNZ|A Chain A, Crystal Structure Of E138k Mutant Hiv-1 Reverse
Transcriptase In Complex With Pett-2
Length = 534
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 2/71 (2%)
Query: 158 SSFEISSMPCRKVGVHGHYLSLGMSLQDSSDSIFASS-TKPLNPNHPYSPDDSYAMHSND 216
++F I S+ + G+ Y L + S +IF SS TK L P +PD + +D
Sbjct: 125 TAFTIPSINNKTPGIRYQYNVLPQGWK-GSPAIFQSSMTKILEPFRKQNPDIVIYQYMDD 183
Query: 217 SFCSSDISLDE 227
+ SD+ + +
Sbjct: 184 LYVGSDLEIGQ 194
>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 = 28.9 bits (63), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 3/73 (4%)
Query: 10 CHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHL--PCFVCVICCQPLQKGEQFILRS 67
C P + + V C C + + P + + +H CF+C CC G++F+
Sbjct: 54 CKPCYVKNHAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCS-CCSKCLIGQKFMPVE 112
Query: 68 GQLFCRQDFEKEM 80
G +FC + +K M
Sbjct: 113 GMVFCSVECKKRM 125
>pdb|3OEO|A Chain A, The Crystal Structure E. Coli Spy
pdb|3OEO|B Chain B, The Crystal Structure E. Coli Spy
pdb|3OEO|C Chain C, The Crystal Structure E. Coli Spy
pdb|3OEO|D Chain D, The Crystal Structure E. Coli Spy
Length = 138
Score = 28.9 bits (63), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 18/26 (69%), Gaps = 2/26 (7%)
Query: 146 NILTPNQRRQFKSSFE--ISSMPCRK 169
NILTP Q++QF ++FE ++ P K
Sbjct: 105 NILTPEQKKQFNANFEKRLTERPAAK 130
>pdb|2CUR|A Chain A, Solution Structure Of Skeletal Muscle Lim-Protein 1
Length = 69
Score = 28.5 bits (62), Expect = 4.5, Method: Composition-based stats.
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 39 QSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFC 72
Q +H CFVCV C + L G++F Q +C
Sbjct: 23 QDQPWHADCFVCVTCSKKL-AGQRFTAVEDQYYC 55
>pdb|2DJ7|A Chain A, Solution Structure Of 3rd Lim Domain Of Actin-Binding
Lim Protein 3
Length = 80
Score = 28.1 bits (61), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 3/59 (5%)
Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEM 80
CA C + + H + A +H+ CF C C L ++I + G +C D+ +
Sbjct: 18 CAGCKEEI-KHGQSLLALDKQWHVSCFKCQTCSVILTG--EYISKDGVPYCESDYHAQF 73
>pdb|3O39|A Chain A, Crystal Structure Of Spy
pdb|3O39|B Chain B, Crystal Structure Of Spy
Length = 108
Score = 28.1 bits (61), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 10/16 (62%), Positives = 14/16 (87%)
Query: 146 NILTPNQRRQFKSSFE 161
NILTP Q++QF ++FE
Sbjct: 89 NILTPEQKKQFNANFE 104
>pdb|1JKH|B Chain B, Crystal Structure Of Y181c Mutant Hiv-1 Reverse
Transcriptase In Complex With Dmp-266(Efavirenz)
pdb|1JLA|B Chain B, Crystal Structure Of Y181c Mutant Hiv-1 Reverse
Transcriptase In Complex With Tnk-651
pdb|1JLB|B Chain B, Crystal Structure Of Y181c Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
pdb|1JLC|B Chain B, Crystal Structure Of Y181c Mutant Hiv-1 Reverse
Transcriptase In Complex With Pett-2
Length = 440
Score = 27.7 bits (60), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 158 SSFEISSMPCRKVGVHGHYLSLGMSLQDSSDSIFASS-TKPLNPNHPYSPDDSYAMHSND 216
++F I S+ G+ Y L + S +IF SS TK L P +PD + +D
Sbjct: 128 TAFTIPSINNETPGIRYQYNVLPQGWK-GSPAIFQSSMTKILEPFRKQNPDIVICQYMDD 186
Query: 217 SFCSSDISLDE 227
+ SD+ + +
Sbjct: 187 LYVGSDLEIGQ 197
>pdb|3DMJ|B Chain B, Crystal Structure Of Hiv-1 V106a And Y181c Mutant Reverse
Transcriptase In Complex With Gw564511
Length = 440
Score = 27.7 bits (60), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 158 SSFEISSMPCRKVGVHGHYLSLGMSLQDSSDSIFASS-TKPLNPNHPYSPDDSYAMHSND 216
++F I S+ G+ Y L + S +IF SS TK L P +PD + +D
Sbjct: 128 TAFTIPSINNETPGIRYQYNVLPQGWK-GSPAIFQSSMTKILEPFRKQNPDIVICQYMDD 186
Query: 217 SFCSSDISLDE 227
+ SD+ + +
Sbjct: 187 LYVGSDLEIGQ 197
>pdb|3DRR|A Chain A, Hiv Reverse Transcriptase Y181c Mutant In Complex With
Inhibitor R8e
Length = 563
Score = 27.3 bits (59), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 158 SSFEISSMPCRKVGVHGHYLSLGMSLQDSSDSIFASS-TKPLNPNHPYSPDDSYAMHSND 216
++F I S+ G+ Y L + S +IF SS TK L P +PD + +D
Sbjct: 131 TAFTIPSINNETPGIRYQYNVLPQGWK-GSPAIFQSSMTKILEPFRKQNPDIVICQYMDD 189
Query: 217 SFCSSDISLDE 227
+ SD+ + +
Sbjct: 190 LYVGSDLEIGQ 200
>pdb|3DRR|B Chain B, Hiv Reverse Transcriptase Y181c Mutant In Complex With
Inhibitor R8e
Length = 443
Score = 27.3 bits (59), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 158 SSFEISSMPCRKVGVHGHYLSLGMSLQDSSDSIFASS-TKPLNPNHPYSPDDSYAMHSND 216
++F I S+ G+ Y L + S +IF SS TK L P +PD + +D
Sbjct: 131 TAFTIPSINNETPGIRYQYNVLPQGWK-GSPAIFQSSMTKILEPFRKQNPDIVICQYMDD 189
Query: 217 SFCSSDISLDE 227
+ SD+ + +
Sbjct: 190 LYVGSDLEIGQ 200
>pdb|3DMJ|A Chain A, Crystal Structure Of Hiv-1 V106a And Y181c Mutant Reverse
Transcriptase In Complex With Gw564511
Length = 560
Score = 27.3 bits (59), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 158 SSFEISSMPCRKVGVHGHYLSLGMSLQDSSDSIFASS-TKPLNPNHPYSPDDSYAMHSND 216
++F I S+ G+ Y L + S +IF SS TK L P +PD + +D
Sbjct: 128 TAFTIPSINNETPGIRYQYNVLPQGWK-GSPAIFQSSMTKILEPFRKQNPDIVICQYMDD 186
Query: 217 SFCSSDISLDE 227
+ SD+ + +
Sbjct: 187 LYVGSDLEIGQ 197
>pdb|1JKH|A Chain A, Crystal Structure Of Y181c Mutant Hiv-1 Reverse
Transcriptase In Complex With Dmp-266(Efavirenz)
pdb|1JLA|A Chain A, Crystal Structure Of Y181c Mutant Hiv-1 Reverse
Transcriptase In Complex With Tnk-651
pdb|1JLB|A Chain A, Crystal Structure Of Y181c Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
pdb|1JLC|A Chain A, Crystal Structure Of Y181c Mutant Hiv-1 Reverse
Transcriptase In Complex With Pett-2
Length = 560
Score = 27.3 bits (59), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 158 SSFEISSMPCRKVGVHGHYLSLGMSLQDSSDSIFASS-TKPLNPNHPYSPDDSYAMHSND 216
++F I S+ G+ Y L + S +IF SS TK L P +PD + +D
Sbjct: 128 TAFTIPSINNETPGIRYQYNVLPQGWK-GSPAIFQSSMTKILEPFRKQNPDIVICQYMDD 186
Query: 217 SFCSSDISLDE 227
+ SD+ + +
Sbjct: 187 LYVGSDLEIGQ 197
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
0.320 0.131 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,624,496
Number of Sequences: 62578
Number of extensions: 219136
Number of successful extensions: 886
Number of sequences better than 100.0: 45
Number of HSP's better than 100.0 without gapping: 29
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 851
Number of HSP's gapped (non-prelim): 49
length of query: 267
length of database: 14,973,337
effective HSP length: 97
effective length of query: 170
effective length of database: 8,903,271
effective search space: 1513556070
effective search space used: 1513556070
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: 50 (23.9 bits)