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= psy15163
(176 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 62.0 bits (149), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 25/38 (65%), Positives = 31/38 (81%)
Query: 138 PRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKIIT 175
PRC CDELIF NEYT AEN+ +H+KHFCC++CD I+
Sbjct: 4 PRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILA 41
Score = 26.9 bits (58), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 99 WHP--QCFVCSTCDELLVDLMYFHYKGNVYC 127
WH +CF+CS C + L+ + +G V+C
Sbjct: 87 WHASTECFLCSCCSKCLIGQKFMPVEGMVFC 117
>pdb|1RUT|X Chain X, Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 Lid
Domain
Length = 188
Score = 43.1 bits (100), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 30/105 (28%), Positives = 45/105 (42%), Gaps = 9/105 (8%)
Query: 70 SGKTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHY--KGNVYC 127
S K C CG ++ L + WH +C CS+C L D+ Y G + C
Sbjct: 4 SWKRCAGCGGKIADRFLLYAMDSY-----WHSRCLKCSSCQAQLGDIGTSSYTKSGMILC 58
Query: 128 LRDYATML-DIPRCHACDELIFVNEYTL-AENKTFHVKHFCCYEC 170
DY + + C AC + I +E + A+ +H+K F C C
Sbjct: 59 RNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTC 103
Score = 40.0 bits (92), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
Query: 73 TCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHY-KGNVYCLRDY 131
C CGQ + + +L + + ++H +CF CSTC LV FHY G+++C D
Sbjct: 71 ACSACGQSIPASELVMRAQG----NVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDR 126
Query: 132 ATML 135
T L
Sbjct: 127 PTAL 130
>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 = 43.1 bits (100), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 30/105 (28%), Positives = 45/105 (42%), Gaps = 9/105 (8%)
Query: 70 SGKTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHY--KGNVYC 127
S K C CG ++ L + WH +C CS+C L D+ Y G + C
Sbjct: 2 SWKRCAGCGGKIADRFLLYAMDSY-----WHSRCLKCSSCQAQLGDIGTSSYTKSGMILC 56
Query: 128 LRDYATML-DIPRCHACDELIFVNEYTL-AENKTFHVKHFCCYEC 170
DY + + C AC + I +E + A+ +H+K F C C
Sbjct: 57 RNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTC 101
Score = 40.0 bits (92), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
Query: 73 TCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHY-KGNVYCLRDY 131
C CGQ + + +L + + ++H +CF CSTC LV FHY G+++C D
Sbjct: 69 ACSACGQSIPASELVMRAQG----NVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDR 124
Query: 132 ATML 135
T L
Sbjct: 125 PTAL 128
>pdb|3F6Q|B Chain B, Crystal Structure Of Integrin-Linked Kinase Ankyrin Repeat
Domain In Complex With Pinch1 Lim1 Domain
Length = 72
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 8/75 (10%)
Query: 63 NKLTQPRSGKTCKQCGQEVRSGDLAVYTEKL--GDQVLWHPQCFVCSTCDELLVDLMYFH 120
N Q + TC++C G A EK+ + L+H QCFVC+ C + + +++
Sbjct: 3 NLYFQGSASATCERC-----KGGFAP-AEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYE 56
Query: 121 YKGNVYCLRDYATML 135
++G YC D+ +
Sbjct: 57 FEGRKYCEHDFQMLF 71
>pdb|1X63|A Chain A, Solution Structure Of The Second Lim Domain Of Skeletal
Muscle Lim Protein 1
Length = 82
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 8/83 (9%)
Query: 53 GNGVTHGPCGNKLTQPRSGKTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDEL 112
G+ + G C + P+ CK C + + +GD V E G +WH CF CS C ++
Sbjct: 1 GSSGSSGKCTTREDSPK----CKGCFKAIVAGDQNV--EYKG--TVWHKDCFTCSNCKQV 52
Query: 113 LVDLMYFHYKGNVYCLRDYATML 135
+ +F + YC+ + T
Sbjct: 53 IGTGSFFPKGEDFYCVTCHETKF 75
>pdb|2KBX|B Chain B, Solution Structure Of Ilk-Pinch Complex
Length = 70
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 98 LWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIP 138
L+H QCFVC+ C + + +++ ++G YC D+ ML P
Sbjct: 30 LYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDF-QMLFAP 69
>pdb|1G47|A Chain A, 1st Lim Domain Of Pinch Protein
Length = 77
Score = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 98 LWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIP 138
L+H QCFVC+ C + + +++ ++G YC D+ ML P
Sbjct: 34 LYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDF-QMLFAP 73
>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 = 0.017, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 82 RSGDLAVYTEK-LGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYA 132
R GD EK +G WH CF C+ C + L +G +YC YA
Sbjct: 41 RCGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYA 92
>pdb|1B8T|A Chain A, Solution Structure Of The Chicken Crp1
Length = 192
Score = 35.4 bits (80), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 6/74 (8%)
Query: 60 PCGNKLTQPRSGKT-CKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMY 118
P +++ Q G C +CGQ V + + + G WH CF C+ C + L
Sbjct: 103 PNASRMAQKVGGSDGCPRCGQAVYAAEKVI-----GAGKSWHKSCFRCAKCGKSLESTTL 157
Query: 119 FHYKGNVYCLRDYA 132
G +YC YA
Sbjct: 158 ADKDGEIYCKGCYA 171
>pdb|2D8X|A Chain A, Solution Structure Of The Second Lim Domain Of
Particularly Interesting New Cys-His Protein (Pinch)
Length = 70
Score = 35.0 bits (79), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 6/54 (11%)
Query: 74 CKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYC 127
C QCG+ + + + + + WHP+CF C C E+L D+ + G C
Sbjct: 8 CHQCGEFI----IGRVIKAMNNS--WHPECFRCDLCQEVLADIGFVKNAGRHLC 55
>pdb|3IXE|B Chain B, Structural Basis Of Competition Between Pinch1 And Pinch2
For Binding To The Ankyrin Repeat Domain Of
Integrin-Linked Kinase
Length = 72
Score = 35.0 bits (79), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 16/73 (21%), Positives = 32/73 (43%), Gaps = 4/73 (5%)
Query: 63 NKLTQPRSGKTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYK 122
N Q + C++C + V + + L+H CFVC+ C + +++ ++
Sbjct: 3 NLYFQGSANAVCQRCQARFSPAERIVNS----NGELYHEHCFVCAQCFRPFPEGLFYEFE 58
Query: 123 GNVYCLRDYATML 135
G YC D+ +
Sbjct: 59 GRKYCEHDFQMLF 71
>pdb|1CXX|A Chain A, Mutant R122a Of Quail Cysteine And Glycine-Rich Protein,
Nmr, Minimized Structure
Length = 113
Score = 34.7 bits (78), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 31/77 (40%), Gaps = 6/77 (7%)
Query: 57 THGPCGNKLTQPRSG-KTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVD 115
T P +K Q G + C CG V + + + G WH CF C+ C + L
Sbjct: 21 TTNPNTSKFAQKFGGAEKCSACGDSVYAAEKVI-----GAGKPWHKNCFRCAKCGKSLES 75
Query: 116 LMYFHYKGNVYCLRDYA 132
+G +YC YA
Sbjct: 76 TTLTEKEGEIYCKGCYA 92
Score = 27.7 bits (60), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 10/36 (27%), Positives = 18/36 (50%)
Query: 139 RCHACDELIFVNEYTLAENKTFHVKHFCCYECDKII 174
+C AC + ++ E + K +H F C +C K +
Sbjct: 38 KCSACGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSL 73
>pdb|1CTL|A Chain A, Structure Of The Carboxy-Terminal Lim Domain From The
Cysteine Rich Protein Crp
Length = 85
Score = 34.3 bits (77), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 25/59 (42%), Gaps = 5/59 (8%)
Query: 74 CKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYA 132
C +CGQ V + + + G WH CF C+ C + L G +YC YA
Sbjct: 11 CPRCGQAVYAAEKVI-----GAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYA 64
>pdb|1X64|A Chain A, Solution Structure Of The Lim Domain Of Alpha-Actinin-2
Associated Lim Protein
Length = 89
Score = 34.3 bits (77), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 10/70 (14%)
Query: 58 HGPCGNKLTQPRSGKTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLM 117
HG G+ P C +CG + G + +K HP+CFVC+ C+ L
Sbjct: 16 HGGAGSAQRMP----LCDKCGSGI-VGAVVKARDKY-----RHPECFVCADCNLNLKQKG 65
Query: 118 YFHYKGNVYC 127
YF +G +YC
Sbjct: 66 YFFVEGELYC 75
>pdb|2CUR|A Chain A, Solution Structure Of Skeletal Muscle Lim-Protein 1
Length = 69
Score = 34.3 bits (77), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 27/65 (41%), Gaps = 6/65 (9%)
Query: 74 CKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYAT 133
C +C + + SG + + WH CFVC TC + L + + YC+ Y
Sbjct: 8 CVKCNKAITSGGITYQDQP------WHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKN 61
Query: 134 MLDIP 138
+ P
Sbjct: 62 FVSGP 66
>pdb|2DJ7|A Chain A, Solution Structure Of 3rd Lim Domain Of Actin-Binding Lim
Protein 3
Length = 80
Score = 34.3 bits (77), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 28/69 (40%), Gaps = 6/69 (8%)
Query: 63 NKLTQPRSGKTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYK 122
K + R C C +E++ G + +K WH CF C TC +L Y
Sbjct: 7 GKPIKIRGPSHCAGCKEEIKHGQSLLALDKQ-----WHVSCFKCQTCSVILTG-EYISKD 60
Query: 123 GNVYCLRDY 131
G YC DY
Sbjct: 61 GVPYCESDY 69
Score = 27.3 bits (59), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 18/36 (50%)
Query: 140 CHACDELIFVNEYTLAENKTFHVKHFCCYECDKIIT 175
C C E I + LA +K +HV F C C I+T
Sbjct: 18 CAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILT 53
>pdb|1X3H|A Chain A, Solution Structure Of The Lim Domain Of Human Leupaxin
Length = 80
Score = 32.3 bits (72), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 16/35 (45%)
Query: 97 VLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 131
+WHP+CFVC C +F G +C Y
Sbjct: 35 TVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHY 69
>pdb|2DAR|A Chain A, Solution Structure Of First Lim Domain Of Enigma-Like Pdz
And Lim Domains Protein
Length = 90
Score = 31.6 bits (70), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 6/54 (11%)
Query: 74 CKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYC 127
C C Q +R L LG WHP+ F C+ C + + + KG +YC
Sbjct: 28 CAHCNQVIRGPFLVA----LGKS--WHPEEFNCAHCKNTMAYIGFVEEKGALYC 75
>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 = 0.25, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 6/80 (7%)
Query: 57 THGPCGNKLTQPRSGKTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDL 116
+ G G K P + +TC +C + V + L +Q ++H CF CS C+ L
Sbjct: 2 SSGSSGMKFQAP-ARETCVECQKTVYPME-----RLLANQQVFHISCFRCSYCNNKLSLG 55
Query: 117 MYFHYKGNVYCLRDYATMLD 136
Y G +YC + +
Sbjct: 56 TYASLHGRIYCKPHFNQLFK 75
>pdb|1WYH|A Chain A, Solution Structure Of The Lim Domain From Human Skeletal
Muscle Lim-Protein 2
Length = 72
Score = 31.2 bits (69), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 18/33 (54%)
Query: 99 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 131
WH CF+CS C++ L + KG YC+ Y
Sbjct: 29 WHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCY 61
>pdb|2CUQ|A Chain A, Solution Structure Of Second Lim Domain From Human
Skeletal Muscle Lim-Protein 2
Length = 80
Score = 30.8 bits (68), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 18/83 (21%), Positives = 32/83 (38%), Gaps = 10/83 (12%)
Query: 53 GNGVTHGPCGNKLTQPRSGKTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDEL 112
G+ + GPC PR C +C + + G + + WH +C VC+ C
Sbjct: 1 GSSGSSGPCYENKFAPR----CARCSKTLTQGGVTYRDQP------WHRECLVCTGCQTP 50
Query: 113 LVDLMYFHYKGNVYCLRDYATML 135
L + + YC+ + +
Sbjct: 51 LAGQQFTSRDEDPYCVACFGELF 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 = 30.8 bits (68), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 6/55 (10%)
Query: 74 CKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCL 128
C QC + + +G + Y E+ WH +CFVC+ C + L + YCL
Sbjct: 8 CVQCKKPITTGGV-TYREQP-----WHKECFVCTACRKQLSGQRFTARDDFAYCL 56
>pdb|2CUP|A Chain A, Solution Structure Of The Skeletal Muscle Lim-Protein 1
Length = 101
Score = 30.4 bits (67), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 23/57 (40%), Gaps = 1/57 (1%)
Query: 98 LWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIFVNEYTL 154
WH CF C+ C L + + + C + T D P+C C + I + +
Sbjct: 28 FWHDTCFRCAKCLHPLANETFVAKDNKILCNK-CTTREDSPKCKGCFKAIVAGDQNV 83
>pdb|2O13|A Chain A, Solution Structure Of The C-Terminal Lim Domain Of MlpCRP3
Length = 58
Score = 30.4 bits (67), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 25/59 (42%), Gaps = 5/59 (8%)
Query: 74 CKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYA 132
C +CG+ V + + +G WH CF C+ C + L G +YC YA
Sbjct: 2 CPRCGKSVYAAEKV-----MGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYA 55
>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 = 30.0 bits (66), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 93 LGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATML 135
+G Q WH + FVC+ C++ + ++ KG YC Y +
Sbjct: 23 MGKQ--WHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLF 63
Score = 28.1 bits (61), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 135 LDIPRCHACDELIFVNEYTLAENKTFHVKHFCCYECDK 172
+ +P C AC I A K +HV+HF C +C+K
Sbjct: 3 MGVPICGACRRPI-EGRVVNAMGKQWHVEHFVCAKCEK 39
>pdb|1X62|A Chain A, Solution Structure Of The Lim Domain Of Carboxyl Terminal
Lim Domain Protein 1
Length = 79
Score = 30.0 bits (66), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 6/65 (9%)
Query: 74 CKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYAT 133
C +CG +G + V+ KL D+ HP+C+VC+ C L +F + +YC +
Sbjct: 18 CDKCG----TGIVGVFV-KLRDR-HRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARE 71
Query: 134 MLDIP 138
+ P
Sbjct: 72 RVSGP 76
>pdb|3TSQ|A Chain A, Crystal Structure Of E. Coli Hypf With Atp And Carbamoyl
Phosphate
pdb|3TTD|A Chain A, Crystal Structure Of E. Coli Hypf With Amp-Cpp And
Carbamoyl Phosphate
Length = 658
Score = 29.6 bits (65), Expect = 0.83, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 5/42 (11%)
Query: 129 RDYATMLDIPRCHACDELIFVNEYTLAENKTFHVKHFCCYEC 170
R + M P C ACD+ EY ++ FH + C EC
Sbjct: 59 RPFTVMAAFPLCPACDK-----EYRDPLDRRFHAQPVACPEC 95
>pdb|3TSP|A Chain A, Crystal Structure Of E. Coli Hypf
pdb|3TSU|A Chain A, Crystal Structure Of E. Coli Hypf With Amp-Pnp And
Carbamoyl Phosphate
pdb|3TTC|A Chain A, Crystal Structure Of E. Coli Hypf With Adp And Carbamoyl
Phosphate
pdb|3TTF|A Chain A, Crystal Structure Of E. Coli Hypf With Amp And Carbamoyl
Phosphate
Length = 657
Score = 29.6 bits (65), Expect = 0.83, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 5/42 (11%)
Query: 129 RDYATMLDIPRCHACDELIFVNEYTLAENKTFHVKHFCCYEC 170
R + M P C ACD+ EY ++ FH + C EC
Sbjct: 59 RPFTVMAAFPLCPACDK-----EYRDPLDRRFHAQPVACPEC 95
>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp
Length = 386
Score = 29.6 bits (65), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 17/27 (62%), Gaps = 3/27 (11%)
Query: 153 TLAENKTF---HVKHFCCYECDKIITQ 176
LA NK+ H+KHF ECDK++ Q
Sbjct: 141 ALARNKSLNLKHIKHFILDECDKMLEQ 167
>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 = 29.6 bits (65), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 27/68 (39%), Gaps = 7/68 (10%)
Query: 70 SGKTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHY--KGNVYC 127
S K C CG ++ L + WH +C CS+C L D+ Y G + C
Sbjct: 4 SWKRCAGCGGKIADRFLLYAMDSY-----WHSRCLKCSSCQAQLGDIGTSSYTKSGMILC 58
Query: 128 LRDYATML 135
DY +
Sbjct: 59 RNDYIRLF 66
>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56
Length = 391
Score = 29.6 bits (65), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 17/27 (62%), Gaps = 3/27 (11%)
Query: 153 TLAENKTF---HVKHFCCYECDKIITQ 176
LA NK+ H+KHF ECDK++ Q
Sbjct: 141 ALARNKSLNLKHIKHFILDECDKMLEQ 167
>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56
pdb|1T6N|B Chain B, Crystal Structure Of The N-Terminal Domain Of Human Uap56
Length = 220
Score = 29.3 bits (64), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 17/27 (62%), Gaps = 3/27 (11%)
Query: 153 TLAENKTF---HVKHFCCYECDKIITQ 176
LA NK+ H+KHF ECDK++ Q
Sbjct: 147 ALARNKSLNLKHIKHFILDECDKMLEQ 173
>pdb|1X6A|A Chain A, Solution Structures Of The Second Lim Domain Of Human Lim-
Kinase 2 (limk2)
Length = 81
Score = 28.9 bits (63), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 8/49 (16%)
Query: 93 LGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCH 141
+ + +HP+CF C +C ++ D G+ Y L +AT L +CH
Sbjct: 31 VAGEFKYHPECFACMSCKVIIED-------GDAYALVQHAT-LYCGKCH 71
>pdb|1AXE|A Chain A, Crystal Structure Of The Active-Site Mutant Phe93->trp Of
Horse Liver Alcohol Dehydrogenase In Complex With Nad
And Inhibitor Trifluoroethanol
pdb|1AXE|B Chain B, Crystal Structure Of The Active-Site Mutant Phe93->trp Of
Horse Liver Alcohol Dehydrogenase In Complex With Nad
And Inhibitor Trifluoroethanol
Length = 374
Score = 28.9 bits (63), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 27/56 (48%), Gaps = 12/56 (21%)
Query: 81 VRSGDLAVYTEKLGDQV--LWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATM 134
V S V T + GD+V LW PQC C C H +GN +CL++ +M
Sbjct: 73 VESIGEGVTTVRPGDKVIPLWTPQCGKCRVCK---------HPEGN-FCLKNDLSM 118
>pdb|1A71|A Chain A, Ternary Complex Of An Active Site Double Mutant Of Horse
Liver Alcohol Dehydrogenase, Phe93>trp, Val203>ala With
Nad And Trifluoroethanol
pdb|1A71|B Chain B, Ternary Complex Of An Active Site Double Mutant Of Horse
Liver Alcohol Dehydrogenase, Phe93>trp, Val203>ala With
Nad And Trifluoroethanol
pdb|1A72|A Chain A, An Active-Site Double Mutant (Phe93->trp, Val203->ala) Of
Horse Liver Alcohol Dehydrogenase In Complex With The
Isosteric Nad Analog Cpad
Length = 374
Score = 28.9 bits (63), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 27/56 (48%), Gaps = 12/56 (21%)
Query: 81 VRSGDLAVYTEKLGDQV--LWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATM 134
V S V T + GD+V LW PQC C C H +GN +CL++ +M
Sbjct: 73 VESIGEGVTTVRPGDKVIPLWTPQCGKCRVCK---------HPEGN-FCLKNDLSM 118
>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 = 28.9 bits (63), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 25/67 (37%), Gaps = 6/67 (8%)
Query: 69 RSGKTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLV--DLMYFHYKGNVY 126
R G C C Q + + + ++H CF C C+ L D Y G +
Sbjct: 63 RFGTKCTACQQGIPPTQVV----RKAQDFVYHLHCFACIICNRQLATGDEFYLMEDGRLV 118
Query: 127 CLRDYAT 133
C DY T
Sbjct: 119 CKEDYET 125
>pdb|1X61|A Chain A, Solution Structure Of The First Lim Domain Of Thyroid
Receptor Interacting Protein 6 (Trip6)
Length = 72
Score = 28.9 bits (63), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 19/39 (48%)
Query: 98 LWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLD 136
++H CFVCSTC L ++ + YC Y L+
Sbjct: 28 VFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATLE 66
>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 = 2.2, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 26/66 (39%), Gaps = 7/66 (10%)
Query: 72 KTCKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHY--KGNVYCLR 129
K C CG ++ L + WH +C CS+C L D+ Y G + C
Sbjct: 62 KRCAGCGGKIADRFLLYAMDSY-----WHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRN 116
Query: 130 DYATML 135
DY +
Sbjct: 117 DYIRLF 122
>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 = 28.5 bits (62), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 33/78 (42%), Gaps = 3/78 (3%)
Query: 99 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIFVNEYT-LAEN 157
WH +C CS C L + F +VYC D+ +C AC I + A++
Sbjct: 29 WHSKCLKCSDCHVPLAERC-FSRGESVYCKDDFFKRFGT-KCAACQLGIPPTQVVRRAQD 86
Query: 158 KTFHVKHFCCYECDKIIT 175
+H+ F C C + +
Sbjct: 87 FVYHLHCFACVVCKRQLA 104
>pdb|1RQG|A Chain A, Methionyl-Trna Synthetase From Pyrococcus Abyssi
Length = 722
Score = 28.1 bits (61), Expect = 2.4, Method: Composition-based stats.
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 73 TCKQCGQEVRSGD-LAVYTEKLGDQVLWHPQCFVC 106
TC CG E + GD V L ++L +P+C +C
Sbjct: 142 TCPYCGAEDQKGDQCEVCGRPLTPEILINPRCAIC 176
>pdb|2JTN|A Chain A, Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Complex
Length = 182
Score = 28.1 bits (61), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 33/78 (42%), Gaps = 3/78 (3%)
Query: 99 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIPRCHACDELIFVNEYT-LAEN 157
WH +C CS C L + F +VYC D+ +C AC I + A++
Sbjct: 83 WHSKCLKCSDCHVPLAERC-FSRGESVYCKDDFFKRFGT-KCAACQLGIPPTQVVRRAQD 140
Query: 158 KTFHVKHFCCYECDKIIT 175
+H+ F C C + +
Sbjct: 141 FVYHLHCFACVVCKRQLA 158
>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 = 27.3 bits (59), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 99 WHP--QCFVCSTCDELLVDLMYFHYKGNVYC 127
WH +CF+CS C + L+ + +G V+C
Sbjct: 26 WHASTECFLCSCCSKCLIGQKFMPVEGMVFC 56
>pdb|1X68|A Chain A, Solution Structures Of The C-Terminal Lim Domain Of Human
Fhl5 Protein
Length = 76
Score = 27.3 bits (59), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 10/36 (27%), Positives = 16/36 (44%)
Query: 99 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATM 134
WH +CF C C LV + ++C + + M
Sbjct: 31 WHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGM 66
>pdb|1UB2|A Chain A, Crystal Structure Of Catalase-Peroxidase From
Synechococcus Pcc 7942
Length = 720
Score = 27.3 bits (59), Expect = 4.3, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 5/55 (9%)
Query: 6 GHPNGAPTSATVRVTNLDDLVDDLSRASVNGGRQNINGSVNGLTHGSGNGVTHGP 60
G+P+ T+ VRVT ++D ++ G G G HG+GN GP
Sbjct: 229 GNPDPLKTAHDVRVTFARMAMNDEETVALTAG-----GHTVGKCHGNGNAALLGP 278
>pdb|1IML|A Chain A, Cysteine Rich Intestinal Protein, Nmr, 48 Structures
Length = 76
Score = 27.3 bits (59), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 25/63 (39%), Gaps = 6/63 (9%)
Query: 74 CKQCGQEVRSGDLAVYTEKLGDQVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRD-YA 132
C +C +EV A LG WH C C C + L + ++G YC Y+
Sbjct: 3 CPKCDKEVY---FAERVTSLGKD--WHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYS 57
Query: 133 TML 135
M
Sbjct: 58 AMF 60
Score = 26.6 bits (57), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 11/39 (28%), Positives = 19/39 (48%)
Query: 138 PRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKIITQ 176
P+C CD+ ++ E + K +H C +C K +T
Sbjct: 1 PKCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTS 39
>pdb|2HAI|A Chain A, Crystal Structure Of Hcv Ns5b Rna Polymerase In Complex
With Novel Class Of Dihydropyrone-Containing Inhibitor
Length = 576
Score = 26.6 bits (57), Expect = 8.0, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 26/72 (36%), Gaps = 6/72 (8%)
Query: 31 RASVNGGRQNINGSVNGLTHGSGNGVTHGPCGNKLT-QPRSGKTCK-----QCGQEVRSG 84
R + G N G G +GV CGN LT ++ C+ C V
Sbjct: 259 RLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKASAACRAAKLQDCTMLVNGD 318
Query: 85 DLAVYTEKLGDQ 96
DL V E G Q
Sbjct: 319 DLVVICESAGTQ 330
>pdb|1NHU|A Chain A, Hepatitis C Virus Rna Polymerase In Complex With Non-
Nucleoside Analogue Inhibitor
pdb|1NHU|B Chain B, Hepatitis C Virus Rna Polymerase In Complex With Non-
Nucleoside Analogue Inhibitor
pdb|1NHV|A Chain A, Hepatitis C Virus Rna Polymerase In Complex With Non-
Nucleoside Analogue Inhibitor
pdb|1NHV|B Chain B, Hepatitis C Virus Rna Polymerase In Complex With Non-
Nucleoside Analogue Inhibitor
Length = 578
Score = 26.6 bits (57), Expect = 8.8, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 26/72 (36%), Gaps = 6/72 (8%)
Query: 31 RASVNGGRQNINGSVNGLTHGSGNGVTHGPCGNKLT-QPRSGKTCK-----QCGQEVRSG 84
R + G N G G +GV CGN LT ++ C+ C V
Sbjct: 267 RLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKASAACRAAKLQDCTMLVNGD 326
Query: 85 DLAVYTEKLGDQ 96
DL V E G Q
Sbjct: 327 DLVVICESAGTQ 338
>pdb|1OS5|A Chain A, Crystal Structure Of Hcv Ns5b Rna Polymerase Complexed
With A Novel Non-Competitive Inhibitor
Length = 576
Score = 26.6 bits (57), Expect = 8.9, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 26/72 (36%), Gaps = 6/72 (8%)
Query: 31 RASVNGGRQNINGSVNGLTHGSGNGVTHGPCGNKLT-QPRSGKTCK-----QCGQEVRSG 84
R + G N G G +GV CGN LT ++ C+ C V
Sbjct: 259 RLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKASAACRAAKLQDCTMLVNGD 318
Query: 85 DLAVYTEKLGDQ 96
DL V E G Q
Sbjct: 319 DLVVICESAGTQ 330
>pdb|2E8Y|A Chain A, Crystal Structure Of Pullulanase Type I From Bacillus
Subtilis Str. 168
pdb|2E8Y|B Chain B, Crystal Structure Of Pullulanase Type I From Bacillus
Subtilis Str. 168
pdb|2E8Z|A Chain A, Crystal Structure Of Pullulanase Type I From Bacillus
Subtilis Str. 168 Complexed With Alpha-Cyclodextrin
pdb|2E8Z|B Chain B, Crystal Structure Of Pullulanase Type I From Bacillus
Subtilis Str. 168 Complexed With Alpha-Cyclodextrin
pdb|2E9B|A Chain A, Crystal Structure Of Pullulanase Type I From Bacillus
Subtilis Str. 168 Complexed With Maltose
pdb|2E9B|B Chain B, Crystal Structure Of Pullulanase Type I From Bacillus
Subtilis Str. 168 Complexed With Maltose
Length = 718
Score = 26.2 bits (56), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 25/60 (41%), Gaps = 9/60 (15%)
Query: 8 PNGAPTSATVRVTNLDDLVDDLSRASVNGGR---------QNINGSVNGLTHGSGNGVTH 58
P P A + T+L D + +N G+ Q NGS +GL + GVTH
Sbjct: 208 PFSHPVDAVIYETHLRDFSIHENSGMINKGKYLALTETDTQTANGSSSGLAYVKELGVTH 267
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
0.323 0.139 0.455
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,702,054
Number of Sequences: 62578
Number of extensions: 233906
Number of successful extensions: 660
Number of sequences better than 100.0: 75
Number of HSP's better than 100.0 without gapping: 35
Number of HSP's successfully gapped in prelim test: 40
Number of HSP's that attempted gapping in prelim test: 608
Number of HSP's gapped (non-prelim): 97
length of query: 176
length of database: 14,973,337
effective HSP length: 92
effective length of query: 84
effective length of database: 9,216,161
effective search space: 774157524
effective search space used: 774157524
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)