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= 010336
(513 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1YA9|A Chain A, Crystal Structure Of The 22kda N-Terminal Fragment Of
Mouse Apolipoprotein E
Length = 181
Score = 32.7 bits (73), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 47/83 (56%), Gaps = 3/83 (3%)
Query: 410 VDWLRNILNEISEAIEFSTQHQTIDAAKANCVNLLESTKKELESQMNELALKEKEVAGLK 469
+ W++ + +++ E ++ S Q + A + + +++ KKELE Q+ +A E+ A L
Sbjct: 28 LRWVQTLSDQVQEELQSSQVTQELTALMEDTMTEVKAYKKELEEQLGPVA--EETRARLG 85
Query: 470 ESVAKTKARL-SDLELESNRLEQ 491
+ V +ARL +D+E NRL Q
Sbjct: 86 KEVQAAQARLGADMEDLRNRLGQ 108
>pdb|2R9U|A Chain A, Crystal Structure Of Lamprey Variable Lymphocyte Receptor
2913 Ectodomain
pdb|2R9U|B Chain B, Crystal Structure Of Lamprey Variable Lymphocyte Receptor
2913 Ectodomain
pdb|2R9U|C Chain C, Crystal Structure Of Lamprey Variable Lymphocyte Receptor
2913 Ectodomain
pdb|2R9U|D Chain D, Crystal Structure Of Lamprey Variable Lymphocyte Receptor
2913 Ectodomain
Length = 174
Score = 32.7 bits (73), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 32/81 (39%), Gaps = 1/81 (1%)
Query: 434 DAAKANCVNL-LESTKKELESQMNELALKEKEVAGLKESVAKTKARLSDLELESNRLEQI 492
D NC N+ L S + + L L ++ L+ V L L SN+L I
Sbjct: 13 DQTLVNCQNIRLASVPAGIPTDKQRLWLNNNQITKLEPGVFDHLVNLQQLYFNSNKLTAI 72
Query: 493 IQATQSKVTKFSQKSLADEIL 513
K+T+ +Q L D L
Sbjct: 73 PTGVFDKLTQLTQLDLNDNHL 93
>pdb|2O6S|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors B59
pdb|2O6S|B Chain B, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors B59
Length = 208
Score = 31.2 bits (69), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 27/58 (46%)
Query: 453 SQMNELALKEKEVAGLKESVAKTKARLSDLELESNRLEQIIQATQSKVTKFSQKSLAD 510
+Q+ ELAL ++ L + V +L DL L N+L+ + ++T L D
Sbjct: 100 TQLKELALNTNQLQSLPDGVFDKLTQLKDLRLYQNQLKSVPDGVFDRLTSLQYIWLHD 157
>pdb|1LE2|A Chain A, Structural Basis For Altered Function In The Common
Mutants Of Human Apolipoprotein-E
Length = 144
Score = 30.0 bits (66), Expect = 3.1, Method: Composition-based stats.
Identities = 24/96 (25%), Positives = 48/96 (50%), Gaps = 3/96 (3%)
Query: 412 WLRNILNEISEAIEFSTQHQTIDAAKANCVNLLESTKKELESQMNELALKEKEVAGLKES 471
W++ + ++ E + S Q + A + L++ K ELE Q+ +A E+ A L +
Sbjct: 17 WVQTLSEQVQEELLSSQVTQELRALMDETMKELKAYKSELEEQLTPVA--EETRARLSKE 74
Query: 472 VAKTKARL-SDLELESNRLEQIIQATQSKVTKFSQK 506
+ +ARL +D+E RL Q Q+ + + +++
Sbjct: 75 LQAAQARLGADMEDVCGRLVQYRGEVQAMLGQSTEE 110
>pdb|1LE4|A Chain A, Structural Basis For Altered Function In The Common
Mutants Of Human Apolipoprotein-E
Length = 144
Score = 30.0 bits (66), Expect = 3.2, Method: Composition-based stats.
Identities = 24/96 (25%), Positives = 48/96 (50%), Gaps = 3/96 (3%)
Query: 412 WLRNILNEISEAIEFSTQHQTIDAAKANCVNLLESTKKELESQMNELALKEKEVAGLKES 471
W++ + ++ E + S Q + A + L++ K ELE Q+ +A E+ A L +
Sbjct: 17 WVQTLSEQVQEELLSSQVTQELRALMDETMKELKAYKSELEEQLTPVA--EETRARLSKE 74
Query: 472 VAKTKARL-SDLELESNRLEQIIQATQSKVTKFSQK 506
+ +ARL +D+E RL Q Q+ + + +++
Sbjct: 75 LQAAQARLGADMEDVRGRLVQYRGEVQAMLGQSTEE 110
>pdb|1LPE|A Chain A, Three-Dimensional Structure Of The Ldl Receptor-Binding
Domain Of Human Apolipoprotein E
Length = 144
Score = 30.0 bits (66), Expect = 3.3, Method: Composition-based stats.
Identities = 24/96 (25%), Positives = 48/96 (50%), Gaps = 3/96 (3%)
Query: 412 WLRNILNEISEAIEFSTQHQTIDAAKANCVNLLESTKKELESQMNELALKEKEVAGLKES 471
W++ + ++ E + S Q + A + L++ K ELE Q+ +A E+ A L +
Sbjct: 17 WVQTLSEQVQEELLSSQVTQELRALMDETMKELKAYKSELEEQLTPVA--EETRARLSKE 74
Query: 472 VAKTKARL-SDLELESNRLEQIIQATQSKVTKFSQK 506
+ +ARL +D+E RL Q Q+ + + +++
Sbjct: 75 LQAAQARLGADMEDVCGRLVQYRGEVQAMLGQSTEE 110
>pdb|1BZ4|A Chain A, Apolipoprotein E3 (Apo-E3), Truncation Mutant 165
Length = 144
Score = 30.0 bits (66), Expect = 3.5, Method: Composition-based stats.
Identities = 24/96 (25%), Positives = 48/96 (50%), Gaps = 3/96 (3%)
Query: 412 WLRNILNEISEAIEFSTQHQTIDAAKANCVNLLESTKKELESQMNELALKEKEVAGLKES 471
W++ + ++ E + S Q + A + L++ K ELE Q+ +A E+ A L +
Sbjct: 18 WVQTLSEQVQEELLSSQVTQELRALMDETMKELKAYKSELEEQLTPVA--EETRARLSKE 75
Query: 472 VAKTKARL-SDLELESNRLEQIIQATQSKVTKFSQK 506
+ +ARL +D+E RL Q Q+ + + +++
Sbjct: 76 LQAAQARLGADMEDVCGRLVQYRGEVQAMLGQSTEE 111
>pdb|4H5F|A Chain A, Crystal Structure Of An Amino Acid Abc Transporter
Substrate-Binding Protein From Streptococcus Pneumoniae
Canada Mdr_19a Bound To L- Arginine, Form 1
pdb|4H5F|B Chain B, Crystal Structure Of An Amino Acid Abc Transporter
Substrate-Binding Protein From Streptococcus Pneumoniae
Canada Mdr_19a Bound To L- Arginine, Form 1
pdb|4H5F|C Chain C, Crystal Structure Of An Amino Acid Abc Transporter
Substrate-Binding Protein From Streptococcus Pneumoniae
Canada Mdr_19a Bound To L- Arginine, Form 1
pdb|4H5F|D Chain D, Crystal Structure Of An Amino Acid Abc Transporter
Substrate-Binding Protein From Streptococcus Pneumoniae
Canada Mdr_19a Bound To L- Arginine, Form 1
pdb|4H5G|A Chain A, Crystal Structure Of An Amino Acid Abc Transporter
Substrate-Binding Protein From Streptococcus Pneumoniae
Canada Mdr_19a Bound To L- Arginine, Form 2
pdb|4H5G|B Chain B, Crystal Structure Of An Amino Acid Abc Transporter
Substrate-Binding Protein From Streptococcus Pneumoniae
Canada Mdr_19a Bound To L- Arginine, Form 2
Length = 243
Score = 29.3 bits (64), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 86 RNGEANALGFKKQSDNHNGVTEGVISVKKNEG 117
++G+ANA+ +K SD+ V + VI K+EG
Sbjct: 195 KDGDANAVALRKNSDDLKEVVDKVIQKLKDEG 226
>pdb|3RFJ|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 279
Score = 29.3 bits (64), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 30/58 (51%)
Query: 453 SQMNELALKEKEVAGLKESVAKTKARLSDLELESNRLEQIIQATQSKVTKFSQKSLAD 510
+ + L L ++ L + V L+ L+L++N+L+ + + K+T+ Q SL D
Sbjct: 133 TNLTYLYLYHNQLQSLPKGVFDKLTNLTRLDLDNNQLQSLPEGVFDKLTQLKQLSLND 190
>pdb|1OR3|A Chain A, Apolipoprotein E3 (Apoe3), Trigonal Truncation Mutant 165
Length = 165
Score = 28.9 bits (63), Expect = 6.3, Method: Composition-based stats.
Identities = 24/96 (25%), Positives = 48/96 (50%), Gaps = 3/96 (3%)
Query: 412 WLRNILNEISEAIEFSTQHQTIDAAKANCVNLLESTKKELESQMNELALKEKEVAGLKES 471
W++ + ++ E + S Q + A + L++ K ELE Q+ +A E+ A L +
Sbjct: 39 WVQTLSEQVQEELLSSQVTQELRALMDETMKELKAYKSELEEQLTPVA--EETRARLSKE 96
Query: 472 VAKTKARL-SDLELESNRLEQIIQATQSKVTKFSQK 506
+ +ARL +D+E RL Q Q+ + + +++
Sbjct: 97 LQAAQARLGADMEDVCGRLVQYRGEVQAMLGQSTEE 132
>pdb|2O6R|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors B61
Length = 177
Score = 28.9 bits (63), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 13/56 (23%), Positives = 30/56 (53%)
Query: 453 SQMNELALKEKEVAGLKESVAKTKARLSDLELESNRLEQIIQATQSKVTKFSQKSL 508
+Q+ +L+L + ++ L + V +L+ L L N+L+ + K+T+ + +L
Sbjct: 52 TQLTKLSLSQNQIQSLPDGVFDKLTKLTILYLHENKLQSLPNGVFDKLTQLKELAL 107
>pdb|1GS9|A Chain A, Apolipoprotein E4, 22k Domain
Length = 165
Score = 28.9 bits (63), Expect = 6.4, Method: Composition-based stats.
Identities = 24/96 (25%), Positives = 48/96 (50%), Gaps = 3/96 (3%)
Query: 412 WLRNILNEISEAIEFSTQHQTIDAAKANCVNLLESTKKELESQMNELALKEKEVAGLKES 471
W++ + ++ E + S Q + A + L++ K ELE Q+ +A E+ A L +
Sbjct: 39 WVQTLSEQVQEELLSSQVTQELRALMDETMKELKAYKSELEEQLTPVA--EETRARLSKE 96
Query: 472 VAKTKARL-SDLELESNRLEQIIQATQSKVTKFSQK 506
+ +ARL +D+E RL Q Q+ + + +++
Sbjct: 97 LQAAQARLGADMEDVRGRLVQYRGEVQAMLGQSTEE 132
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
0.308 0.125 0.353
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,984,547
Number of Sequences: 62578
Number of extensions: 616252
Number of successful extensions: 1269
Number of sequences better than 100.0: 58
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 40
Number of HSP's that attempted gapping in prelim test: 1242
Number of HSP's gapped (non-prelim): 72
length of query: 513
length of database: 14,973,337
effective HSP length: 103
effective length of query: 410
effective length of database: 8,527,803
effective search space: 3496399230
effective search space used: 3496399230
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 54 (25.4 bits)