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= 019740
(336 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 = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 29/114 (25%), Positives = 50/114 (43%), Gaps = 12/114 (10%)
Query: 1 MEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLI 60
++ WH C +C C + + D FS +G+ Y K + ++ KC CQ IP +
Sbjct: 25 LDRHWHSSCLKCADCQMQLADRCFSRAGS-VYCKEDFFKRFGTKCTACQQGIPPTQ---V 80
Query: 61 EYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSA 114
+A F +C + C C R ++ ++DGR +C E ++A
Sbjct: 81 VRKAQDFVYHLHCFA--------CIICNRQLATGDEFYLMEDGRLVCKEDYETA 126
>pdb|2CUP|A Chain A, Solution Structure Of The Skeletal Muscle Lim-Protein 1
Length = 101
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 16/45 (35%), Positives = 20/45 (44%)
Query: 4 FWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVC 48
FWH CFRC C P+ + F N+ C + PKC C
Sbjct: 28 FWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSPKCKGC 72
>pdb|2JTN|A Chain A, Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Complex
Length = 182
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/107 (25%), Positives = 47/107 (43%), Gaps = 12/107 (11%)
Query: 1 MEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLI 60
++ WH +C +C C++P+ + FS G Y K + ++ KC CQ IP +
Sbjct: 79 LDRHWHSKCLKCSDCHVPLAERCFS-RGESVYCKDDFFKRFGTKCAACQLGIPPTQ---V 134
Query: 61 EYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLC 107
RA F +C + C C+R ++ ++D R +C
Sbjct: 135 VRRAQDFVYHLHCFA--------CVVCKRQLATGDEFYLMEDSRLVC 173
>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 = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 27/107 (25%), Positives = 47/107 (43%), Gaps = 12/107 (11%)
Query: 1 MEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLI 60
++ WH +C +C C++P+ + FS G Y K + ++ KC CQ IP +
Sbjct: 25 LDRHWHSKCLKCSDCHVPLAERCFS-RGESVYCKDDFFKRFGTKCAACQLGIPPTQ---V 80
Query: 61 EYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLC 107
RA F +C + C C+R ++ ++D R +C
Sbjct: 81 VRRAQDFVYHLHCFA--------CVVCKRQLATGDEFYLMEDSRLVC 119
>pdb|2D8X|A Chain A, Solution Structure Of The Second Lim Domain Of
Particularly Interesting New Cys-His Protein (Pinch)
Length = 70
Score = 36.6 bits (83), Expect = 0.022, Method: Composition-based stats.
Identities = 14/40 (35%), Positives = 20/40 (50%)
Query: 1 MEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQ 40
M WHPECFRC C + D+ F + R + C+ +
Sbjct: 23 MNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNRE 62
>pdb|1X4K|A Chain A, Solution Structure Of Lim Domain In Lim-Protein 3
Length = 72
Score = 34.3 bits (77), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 19/37 (51%)
Query: 5 WHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQH 41
WH CF CH C PI F N+ + CY++QH
Sbjct: 29 WHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQH 65
>pdb|1X3H|A Chain A, Solution Structure Of The Lim Domain Of Human Leupaxin
Length = 80
Score = 33.5 bits (75), Expect = 0.18, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 18/42 (42%), Gaps = 3/42 (7%)
Query: 1 MEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHH 42
M+ WHPECF C C + F RP+ C HH
Sbjct: 33 MDTVWHPECFVCGDCFTSFSTGSFFELDGRPF---CELHYHH 71
>pdb|1CTL|A Chain A, Structure Of The Carboxy-Terminal Lim Domain From The
Cysteine Rich Protein Crp
Length = 85
Score = 33.1 bits (74), Expect = 0.23, Method: Composition-based stats.
Identities = 13/40 (32%), Positives = 16/40 (40%)
Query: 5 WHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPK 44
WH CFRC C + + Y K CY + PK
Sbjct: 31 WHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPK 70
>pdb|2CUQ|A Chain A, Solution Structure Of Second Lim Domain From Human
Skeletal Muscle Lim-Protein 2
Length = 80
Score = 32.7 bits (73), Expect = 0.29, Method: Composition-based stats.
Identities = 12/35 (34%), Positives = 16/35 (45%)
Query: 5 WHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKE 39
WH EC C C P+ +F+ PY C+ E
Sbjct: 37 WHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGE 71
>pdb|1B8T|A Chain A, Solution Structure Of The Chicken Crp1
Length = 192
Score = 32.7 bits (73), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 16/40 (40%)
Query: 5 WHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPK 44
WH CFRC C + + Y K CY + PK
Sbjct: 138 WHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPK 177
>pdb|1CXX|A Chain A, Mutant R122a Of Quail Cysteine And Glycine-Rich Protein,
Nmr, Minimized Structure
Length = 113
Score = 32.0 bits (71), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 16/40 (40%)
Query: 5 WHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPK 44
WH CFRC C + + Y K CY + PK
Sbjct: 59 WHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAKNFGPK 98
>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 = 32.0 bits (71), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 16/40 (40%)
Query: 5 WHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPK 44
WH CFRC C + + Y K CY + PK
Sbjct: 59 WHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAKNFGPK 98
>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 = 31.2 bits (69), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 1 MEAFWHPECFRCHSCNLPITDVEFS 25
M+++WH C +C SC + D+ S
Sbjct: 24 MDSYWHSRCLKCSSCQAQLGDIGTS 48
>pdb|2L4Z|A Chain A, Nmr Structure Of Fusion Of Ctip (641-685) To Lmo4-Lim1
(18-82)
Length = 123
Score = 30.8 bits (68), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 1 MEAFWHPECFRCHSCNLPITDVEFS 25
M+++WH C +C SC + D+ S
Sbjct: 80 MDSYWHSRCLKCSSCQAQLGDIGTS 104
>pdb|1RUT|X Chain X, Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 Lid
Domain
Length = 188
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 1 MEAFWHPECFRCHSCNLPITDVEFS 25
M+++WH C +C SC + D+ S
Sbjct: 24 MDSYWHSRCLKCSSCQAQLGDIGTS 48
>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 = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 1 MEAFWHPECFRCHSCNLPITDVEFS 25
M+++WH C +C SC + D+ S
Sbjct: 22 MDSYWHSRCLKCSSCQAQLGDIGTS 46
>pdb|2CUR|A Chain A, Solution Structure Of Skeletal Muscle Lim-Protein 1
Length = 69
Score = 30.4 bits (67), Expect = 1.6, Method: Composition-based stats.
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 5 WHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYK 38
WH +CF C +C+ + F+ ++ Y CYK
Sbjct: 27 WHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYK 60
>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 = 3.8, Method: Composition-based stats.
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 5 WHPECFRCHSCNLPITD 21
+HPECF C SC + I D
Sbjct: 37 YHPECFACMSCKVIIED 53
>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 = 4.0, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 22/48 (45%)
Query: 5 WHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFI 52
WH + F C C+ + + M ++P K CY + H C C N I
Sbjct: 26 WHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAVVCQGCHNAI 73
>pdb|2DJ7|A Chain A, Solution Structure Of 3rd Lim Domain Of Actin-Binding
Lim Protein 3
Length = 80
Score = 28.9 bits (63), Expect = 4.8, Method: Composition-based stats.
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 5 WHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQ 40
WH CF+C +C++ +T S G PY + Y Q
Sbjct: 38 WHVSCFKCQTCSVILTGEYISKDG-VPYCESDYHAQ 72
>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 = 28.9 bits (63), Expect = 4.8, Method: Composition-based stats.
Identities = 11/36 (30%), Positives = 18/36 (50%)
Query: 2 EAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCY 37
E WH ECF C +C ++ F+ + Y +C+
Sbjct: 24 EQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCF 59
>pdb|2HHJ|A Chain A, Human Bisphosphoglycerate Mutase Complexed With 2,3-
Bisphosphoglycerate (15 Days)
pdb|2HHJ|B Chain B, Human Bisphosphoglycerate Mutase Complexed With 2,3-
Bisphosphoglycerate (15 Days)
Length = 267
Score = 28.5 bits (62), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 30/124 (24%), Positives = 50/124 (40%), Gaps = 15/124 (12%)
Query: 31 PYHKHCYKEQHHPKCDVCQNFIP-TNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCS--- 86
PY++ Y ++ + CDV + +P + S + R P+W ++ P R T +
Sbjct: 131 PYYQEIYNDRRYKVCDVPLDQLPRSESLKDVLERLLPYWNERIAPEVLRGKTILISAHGN 190
Query: 87 --------CERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMK 138
E + D ++L G + LE LD + Q +L QE + K
Sbjct: 191 SSRALLKHLEGISDEDIINITLPTGVPILLE-LDENLRAVGPHQ--FLGDQEAIQAAIKK 247
Query: 139 VEQQ 142
VE Q
Sbjct: 248 VEDQ 251
>pdb|1T8P|A Chain A, Crystal Structure Of Human Erythrocyte 2,3-
Bisphosphoglycerate Mutase
pdb|1T8P|B Chain B, Crystal Structure Of Human Erythrocyte 2,3-
Bisphosphoglycerate Mutase
pdb|2A9J|A Chain A, Human Bisphosphoglycerate Mutase Complexed With 3-
Phosphoglycerate (17 Days)
pdb|2A9J|B Chain B, Human Bisphosphoglycerate Mutase Complexed With 3-
Phosphoglycerate (17 Days)
pdb|2F90|A Chain A, Crystal Structure Of Bisphosphoglycerate Mutase In Complex
With 3-Phosphoglycerate And Alf4-
pdb|2F90|B Chain B, Crystal Structure Of Bisphosphoglycerate Mutase In Complex
With 3-Phosphoglycerate And Alf4-
pdb|2H4X|A Chain A, Human Bisphosphoglycerate Mutase Complex With 3-
Phosphoglycerate With Crystal Growth 90 Days
pdb|2H4X|B Chain B, Human Bisphosphoglycerate Mutase Complex With 3-
Phosphoglycerate With Crystal Growth 90 Days
pdb|2H4Z|A Chain A, Human Bisphosphoglycerate Mutase Complexed With 2,3-
Bisphosphoglycerate
pdb|2H4Z|B Chain B, Human Bisphosphoglycerate Mutase Complexed With 2,3-
Bisphosphoglycerate
pdb|2H52|A Chain A, Crystal Structure Of Human Bisphosphoglycerate Mutase
Complex With 3-Phosphoglycerate (18 Days)
pdb|2H52|B Chain B, Crystal Structure Of Human Bisphosphoglycerate Mutase
Complex With 3-Phosphoglycerate (18 Days)
pdb|3NFY|A Chain A, The Structure Of Human Bisphosphoglycerate Mutase To 1.94a
pdb|3NFY|B Chain B, The Structure Of Human Bisphosphoglycerate Mutase To 1.94a
Length = 267
Score = 28.5 bits (62), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 30/124 (24%), Positives = 50/124 (40%), Gaps = 15/124 (12%)
Query: 31 PYHKHCYKEQHHPKCDVCQNFIP-TNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCS--- 86
PY++ Y ++ + CDV + +P + S + R P+W ++ P R T +
Sbjct: 131 PYYQEIYNDRRYKVCDVPLDQLPRSESLKDVLERLLPYWNERIAPEVLRGKTILISAHGN 190
Query: 87 --------CERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMK 138
E + D ++L G + LE LD + Q +L QE + K
Sbjct: 191 SSRALLKHLEGISDEDIINITLPTGVPILLE-LDENLRAVGPHQ--FLGDQEAIQAAIKK 247
Query: 139 VEQQ 142
VE Q
Sbjct: 248 VEDQ 251
>pdb|2EGQ|A Chain A, Solution Structure Of The Fourth Lim Domain From Human
Four And A Half Lim Domains 1
Length = 77
Score = 27.7 bits (60), Expect = 8.7, Method: Composition-based stats.
Identities = 10/35 (28%), Positives = 16/35 (45%)
Query: 5 WHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKE 39
WH CF C C++ + + F + Y C K+
Sbjct: 42 WHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKK 76
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 0.450
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,082,370
Number of Sequences: 62578
Number of extensions: 391150
Number of successful extensions: 944
Number of sequences better than 100.0: 39
Number of HSP's better than 100.0 without gapping: 28
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 906
Number of HSP's gapped (non-prelim): 49
length of query: 336
length of database: 14,973,337
effective HSP length: 99
effective length of query: 237
effective length of database: 8,778,115
effective search space: 2080413255
effective search space used: 2080413255
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: 52 (24.6 bits)