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= psy4164
(147 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1QGV|A Chain A, Human Spliceosomal Protein U5-15kd
pdb|1SYX|A Chain A, The Crystal Structure Of A Binary U5 Snrnp Complex
pdb|1SYX|C Chain C, The Crystal Structure Of A Binary U5 Snrnp Complex
pdb|1SYX|E Chain E, The Crystal Structure Of A Binary U5 Snrnp Complex
Length = 142
Score = 58.2 bits (139), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 25/27 (92%), Positives = 26/27 (96%)
Query: 1 MSYMLGHLHNGWQVDQAILSEEDRVVI 27
MSYML HLHNGWQVDQAILSEEDRVV+
Sbjct: 1 MSYMLPHLHNGWQVDQAILSEEDRVVV 27
>pdb|1PQN|A Chain A, Dominant Negative Human Hdim1 (Hdim1 1-128)
Length = 127
Score = 55.8 bits (133), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 24/26 (92%), Positives = 25/26 (96%)
Query: 2 SYMLGHLHNGWQVDQAILSEEDRVVI 27
SYML HLHNGWQVDQAILSEEDRVV+
Sbjct: 1 SYMLPHLHNGWQVDQAILSEEDRVVV 26
>pdb|2AV4|A Chain A, Crystal Structure Of Plasmodium Yoelii Thioredoxin-like
Protein 4a (dim1)
Length = 160
Score = 39.3 bits (90), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 15/26 (57%), Positives = 23/26 (88%)
Query: 2 SYMLGHLHNGWQVDQAILSEEDRVVI 27
S+ML HL++GW VDQAI++E++R+V
Sbjct: 20 SFMLQHLNSGWAVDQAIVNEDERLVC 45
>pdb|2OM5|A Chain A, N-Terminal Fragment Of Human Tax1
Length = 381
Score = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 58 YRAVVSTMIPQLVTLDSVLYGNPIEKIREYRAVVSTMIPQLVTLDSVFILPS 109
+ A ++ Q VTL+ +GNP+ +I+ +R V ++ PQ T + +PS
Sbjct: 212 FPAETYALVGQQVTLECFAFGNPVPRIK-WRKVDGSLSPQWTTAEPTLQIPS 262
>pdb|2JE0|A Chain A, Crystal Structure Of Pp32
pdb|2JE0|B Chain B, Crystal Structure Of Pp32
pdb|2JE0|C Chain C, Crystal Structure Of Pp32
pdb|2JE0|D Chain D, Crystal Structure Of Pp32
pdb|2JE0|E Chain E, Crystal Structure Of Pp32
pdb|2JE0|F Chain F, Crystal Structure Of Pp32
pdb|2JE1|A Chain A, The Crystal Structure Of The Tumor Supressor Protein Pp32
( Anp32a):structural Insights Into The Anp32 Family Of
Proteins
pdb|2JE1|B Chain B, The Crystal Structure Of The Tumor Supressor Protein Pp32
( Anp32a):structural Insights Into The Anp32 Family Of
Proteins
pdb|2JE1|C Chain C, The Crystal Structure Of The Tumor Supressor Protein Pp32
( Anp32a):structural Insights Into The Anp32 Family Of
Proteins
pdb|2JE1|D Chain D, The Crystal Structure Of The Tumor Supressor Protein Pp32
( Anp32a):structural Insights Into The Anp32 Family Of
Proteins
Length = 149
Score = 31.2 bits (69), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 29/48 (60%)
Query: 27 IEEYLSVFVLRRVNSLRTLSLYGNPIEKIREYRAVVSTMIPQLVTLDS 74
I++ ++ L+++ +L++L L+ + + +YR V ++PQL LD
Sbjct: 100 IKDLSTIEPLKKLENLKSLDLFNCEVTNLNDYRENVFKLLPQLTYLDG 147
Score = 26.9 bits (58), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 10/66 (15%)
Query: 41 SLRTLSLYGNPIEKIREYRAVVSTMIP--QLVTLDSV-LYGNPIEKIREYRAVVSTMIPQ 97
+L L+L GN I+ + ST+ P +L L S+ L+ + + +YR V ++PQ
Sbjct: 89 NLTHLNLSGNKIKDL-------STIEPLKKLENLKSLDLFNCEVTNLNDYRENVFKLLPQ 141
Query: 98 LVTLDS 103
L LD
Sbjct: 142 LTYLDG 147
>pdb|2ELL|A Chain A, Solution Structure Of The Leucine Rich Repeat Of Human
Acidic Leucine- Rich Nuclear Phosphoprotein 32 Family
Member B
pdb|2RR6|A Chain A, Solution Structure Of The Leucine Rich Repeat Of Human
Acidic Leucine- Rich Nuclear Phosphoprotein 32 Family
Member B
Length = 168
Score = 31.2 bits (69), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 23/39 (58%)
Query: 36 LRRVNSLRTLSLYGNPIEKIREYRAVVSTMIPQLVTLDS 74
L+++ L++L L+ + + +YR V ++PQL LD
Sbjct: 116 LKKLECLKSLDLFNCEVTNLNDYRESVFKLLPQLTYLDG 154
Score = 27.7 bits (60), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 10/66 (15%)
Query: 41 SLRTLSLYGNPIEKIREYRAVVSTMIP--QLVTLDSV-LYGNPIEKIREYRAVVSTMIPQ 97
+L L+L GN ++ I ST+ P +L L S+ L+ + + +YR V ++PQ
Sbjct: 96 NLTHLNLSGNKLKDI-------STLEPLKKLECLKSLDLFNCEVTNLNDYRESVFKLLPQ 148
Query: 98 LVTLDS 103
L LD
Sbjct: 149 LTYLDG 154
>pdb|3BJC|A Chain A, Crystal Structure Of The Pde5a Catalytic Domain In Complex
With A Novel Inhibitor
Length = 878
Score = 29.3 bits (64), Expect = 0.77, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 12/76 (15%)
Query: 28 EEYLSVFVLRRVNSLRTLSLYGNPIEKIREYRAVVSTMIPQLVTLDSVLYGNPI--EKIR 85
E++L FV+ G I+ + Y AV M Q+VTL+ + Y E+ R
Sbjct: 492 EQFLEAFVI----------FCGLGIQNTQMYEAVERAMAKQMVTLEVLSYHASAAEEETR 541
Query: 86 EYRAVVSTMIPQLVTL 101
E +++ + ++P TL
Sbjct: 542 ELQSLAAAVVPSAQTL 557
>pdb|2JQD|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of Lanp
Length = 169
Score = 29.3 bits (64), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 12/48 (25%), Positives = 29/48 (60%)
Query: 27 IEEYLSVFVLRRVNSLRTLSLYGNPIEKIREYRAVVSTMIPQLVTLDS 74
I++ ++ L+++ +L++L L+ + + YR V ++PQ++ LD
Sbjct: 105 IKDLSTIEPLKKLENLKSLDLFNCEVTNLNAYRENVFKLLPQVMYLDG 152
>pdb|2A91|A Chain A, Crystal Structure Of Erbb2 Domains 1-3
Length = 517
Score = 26.9 bits (58), Expect = 4.4, Method: Composition-based stats.
Identities = 22/67 (32%), Positives = 29/67 (43%), Gaps = 5/67 (7%)
Query: 75 VLYGNPIEKIREYRAVVSTMIPQLVTLDSVF----ILPSEKQETNALN-AEIRSYLLPKY 129
V YG +E +RE RAV S I + +F LP A N A ++ L +
Sbjct: 320 VCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVF 379
Query: 130 EKLEAAT 136
E LE T
Sbjct: 380 ETLEEIT 386
>pdb|1S78|A Chain A, Insights Into Erbb Signaling From The Structure Of The
Erbb2- Pertuzumab Complex
pdb|1S78|B Chain B, Insights Into Erbb Signaling From The Structure Of The
Erbb2- Pertuzumab Complex
pdb|3BE1|A Chain A, Dual Specific Bh1 Fab In Complex With The Extracellular
Domain Of Her2ERBB-2
pdb|3MZW|A Chain A, Her2 Extracelluar Region With Affinity Matured 3-Helix
Affibody Zher2:342
pdb|3N85|A Chain A, Crystallographic Trimer Of Her2 Extracellular Regions In
Complex With Tryptophan-Rich Antibody Fragment
Length = 624
Score = 26.9 bits (58), Expect = 4.4, Method: Composition-based stats.
Identities = 22/67 (32%), Positives = 29/67 (43%), Gaps = 5/67 (7%)
Query: 75 VLYGNPIEKIREYRAVVSTMIPQLVTLDSVF----ILPSEKQETNALN-AEIRSYLLPKY 129
V YG +E +RE RAV S I + +F LP A N A ++ L +
Sbjct: 319 VCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVF 378
Query: 130 EKLEAAT 136
E LE T
Sbjct: 379 ETLEEIT 385
>pdb|1N8Z|C Chain C, Crystal Structure Of Extracellular Domain Of Human Her2
Complexed With Herceptin Fab
Length = 607
Score = 26.9 bits (58), Expect = 4.4, Method: Composition-based stats.
Identities = 22/67 (32%), Positives = 29/67 (43%), Gaps = 5/67 (7%)
Query: 75 VLYGNPIEKIREYRAVVSTMIPQLVTLDSVF----ILPSEKQETNALN-AEIRSYLLPKY 129
V YG +E +RE RAV S I + +F LP A N A ++ L +
Sbjct: 319 VCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVF 378
Query: 130 EKLEAAT 136
E LE T
Sbjct: 379 ETLEEIT 385
>pdb|3LGD|A Chain A, Crystal Structure Of Human Adenosine Deaminase Growth
Factor, Adenosine Deaminase Type 2 (Ada2)
pdb|3LGD|B Chain B, Crystal Structure Of Human Adenosine Deaminase Growth
Factor, Adenosine Deaminase Type 2 (Ada2)
pdb|3LGG|A Chain A, Crystal Structure Of Human Adenosine Deaminase Growth
Factor Adenosine Deaminase Type 2 (Ada2) Complexed With
Transition Analogue, Coformycin
pdb|3LGG|B Chain B, Crystal Structure Of Human Adenosine Deaminase Growth
Factor Adenosine Deaminase Type 2 (Ada2) Complexed With
Transition Analogue, Coformycin
Length = 508
Score = 26.9 bits (58), Expect = 4.5, Method: Composition-based stats.
Identities = 15/29 (51%), Positives = 16/29 (55%)
Query: 102 DSVFILPSEKQETNALNAEIRSYLLPKYE 130
D VF E E N L EIR+ LLP YE
Sbjct: 200 DYVFRSMQEFYEDNVLYMEIRARLLPVYE 228
>pdb|1M9L|A Chain A, Relaxation-Based Refined Structure Of Chlamydomonas Outer
Arm Dynein Light Chain 1
Length = 199
Score = 25.8 bits (55), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 40/95 (42%), Gaps = 19/95 (20%)
Query: 32 SVFVLRRVNSLRTLSLYGNPIEKIREYRAVVSTMIPQLVTLDSV----LYGNPI------ 81
S+ + ++ +LR L + N I E I +L LD + L GNP+
Sbjct: 108 SLSGIEKLVNLRVLYMSNNKITNWGE--------IDKLAALDKLEDLLLAGNPLYNDYKE 159
Query: 82 -EKIREYRAVVSTMIPQLVTLDSVFILPSEKQETN 115
EYR V +P L LD + + E+++ N
Sbjct: 160 NNATSEYRIEVVKRLPNLKKLDGMPVDVDEREQAN 194
>pdb|1DS9|A Chain A, Solution Structure Of Chlamydomonas Outer Arm Dynein Light
Chain 1
Length = 198
Score = 25.8 bits (55), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 40/95 (42%), Gaps = 19/95 (20%)
Query: 32 SVFVLRRVNSLRTLSLYGNPIEKIREYRAVVSTMIPQLVTLDSV----LYGNPI------ 81
S+ + ++ +LR L + N I E I +L LD + L GNP+
Sbjct: 107 SLSGIEKLVNLRVLYMSNNKITNWGE--------IDKLAALDKLEDLLLAGNPLYNDYKE 158
Query: 82 -EKIREYRAVVSTMIPQLVTLDSVFILPSEKQETN 115
EYR V +P L LD + + E+++ N
Sbjct: 159 NNATSEYRIEVVKRLPNLKKLDGMPVDVDEREQAN 193
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
0.318 0.133 0.361
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,746,671
Number of Sequences: 62578
Number of extensions: 125790
Number of successful extensions: 350
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 329
Number of HSP's gapped (non-prelim): 29
length of query: 147
length of database: 14,973,337
effective HSP length: 90
effective length of query: 57
effective length of database: 9,341,317
effective search space: 532455069
effective search space used: 532455069
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)