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= 003265
(835 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3RFJ|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 279
Score = 31.6 bits (70), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 35/69 (50%)
Query: 427 LVCAGAGLKEAPDVKRWENVRRLSLMQNQIETLSEVPKCPHLLTLFLDFNQELKIADGFF 486
++ + +K ++ NVR L+L N++ +S + + +L L L NQ + +G F
Sbjct: 46 IIANNSDIKSVQGIQYLPNVRYLALGGNKLHDISALKELTNLTYLILTGNQLQSLPNGVF 105
Query: 487 QFMPSLKVL 495
+ +LK L
Sbjct: 106 DKLTNLKEL 114
>pdb|3RFS|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
pdb|3RFS|B Chain B, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 272
Score = 31.2 bits (69), Expect = 2.7, Method: Composition-based stats.
Identities = 30/99 (30%), Positives = 49/99 (49%), Gaps = 8/99 (8%)
Query: 427 LVCAGAGLKEAPD--VKRWENVRRLSLMQNQIETLSE--VPKCPHLLTLFLDFNQELKIA 482
LV L+ PD + N+ L+L NQ+++L + K +L L L +NQ +
Sbjct: 114 LVLVENQLQSLPDGVFDKLTNLTYLNLAHNQLQSLPKGVFDKLTNLTELDLSYNQLQSLP 173
Query: 483 DGFFQFMPSLKVLKMSYCGQSWSSFQLPVGMSELGSSLQ 521
+G F + LK L++ Y Q S +P G+ + +SLQ
Sbjct: 174 EGVFDKLTQLKDLRL-YQNQLKS---VPDGVFDRLTSLQ 208
Score = 30.8 bits (68), Expect = 2.9, Method: Composition-based stats.
Identities = 18/69 (26%), Positives = 35/69 (50%)
Query: 427 LVCAGAGLKEAPDVKRWENVRRLSLMQNQIETLSEVPKCPHLLTLFLDFNQELKIADGFF 486
++ + +K ++ NVR L+L N++ +S + + +L L L NQ + +G F
Sbjct: 46 IIANNSDIKSVQGIQYLPNVRYLALGGNKLHDISALKELTNLTYLILTGNQLQSLPNGVF 105
Query: 487 QFMPSLKVL 495
+ +LK L
Sbjct: 106 DKLTNLKEL 114
>pdb|3T6Q|A Chain A, Crystal Structure Of Mouse Rp105MD-1 Complex
pdb|3T6Q|B Chain B, Crystal Structure Of Mouse Rp105MD-1 Complex
Length = 606
Score = 30.8 bits (68), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 45/95 (47%), Gaps = 8/95 (8%)
Query: 440 VKRWENVRRLSLMQNQIETLS----EVPKCPHLLTLFLDFNQELKIADGFFQFMPSLKVL 495
++ EN+R L L + IET ++ HL +L L +N+ L + F+ P L++L
Sbjct: 346 LENLENLRELDLSHDDIETSDCCNLQLRNLSHLQSLNLSYNEPLSLKTEAFKECPQLELL 405
Query: 496 KMSYC----GQSWSSFQLPVGMSELGSSLQLFDIS 526
+++ + S FQ + L S L DIS
Sbjct: 406 DLAFTRLKVKDAQSPFQNLHLLKVLNLSHSLLDIS 440
>pdb|1Z6T|A Chain A, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|B Chain B, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|C Chain C, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|D Chain D, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
Length = 591
Score = 30.8 bits (68), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 43/150 (28%), Positives = 64/150 (42%), Gaps = 30/150 (20%)
Query: 186 EKALDIFRSL---RGKRIVLLLDDIWERVDLTKVGVPLPGPQNTTSKVVFTTRFIDVCGS 242
E+A D R L + R +L+LDD+W+ L ++ +++ TTR V S
Sbjct: 221 EEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAF--------DSQCQILLTTRDKSVTDS 272
Query: 243 MEADRKFLVACLSEKDAWELFREKVGEETLK-----SDHDIAELAQIVAKECVGLPLALI 297
+ K++V S L +EK G E L D+ E A + KEC G PL +
Sbjct: 273 VMGP-KYVVPVESS-----LGKEK-GLEILSLFVNMKKADLPEQAHSIIKECKGSPLVVS 325
Query: 298 TIGRAM-------AYRKKAEQWRQFAGLGK 320
IG + Y K Q +QF + K
Sbjct: 326 LIGALLRDFPNRWEYYLKQLQNKQFKRIRK 355
>pdb|3IZA|A Chain A, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|B Chain B, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|C Chain C, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|D Chain D, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|E Chain E, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|F Chain F, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|G Chain G, Structure Of An Apoptosome-Procaspase-9 Card Complex
Length = 1263
Score = 30.0 bits (66), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 43/150 (28%), Positives = 64/150 (42%), Gaps = 30/150 (20%)
Query: 186 EKALDIFRSL---RGKRIVLLLDDIWERVDLTKVGVPLPGPQNTTSKVVFTTRFIDVCGS 242
E+A D R L + R +L+LDD+W+ L ++ +++ TTR V S
Sbjct: 227 EEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAF--------DSQCQILLTTRDKSVTDS 278
Query: 243 MEADRKFLVACLSEKDAWELFREKVGEETLK-----SDHDIAELAQIVAKECVGLPLALI 297
+ K++V S L +EK G E L D+ E A + KEC G PL +
Sbjct: 279 VMGP-KYVVPVESS-----LGKEK-GLEILSLFVNMKKADLPEQAHSIIKECKGSPLVVS 331
Query: 298 TIGRAM-------AYRKKAEQWRQFAGLGK 320
IG + Y K Q +QF + K
Sbjct: 332 LIGALLRDFPNRWEYYLKQLQNKQFKRIRK 361
>pdb|2O8E|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO A G T MISPAIR, WITH
ADP BOUND TO Msh2 Only
Length = 934
Score = 30.0 bits (66), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 25/44 (56%)
Query: 359 LIDCWIGEGFLGESDRFGAENQGYDILDTLVRACLLEEVEDDKV 402
+I+C + E ++ E+QGYDI++ + C LE + +K+
Sbjct: 840 VIECAKQKALELEEFQYIGESQGYDIMEPAAKKCYLEREQGEKI 883
>pdb|2O8B|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T MISPAIR
pdb|2O8C|A Chain A, Human Mutsalpha (msh2/msh6) Bound To Adp And An
O6-methyl-guanine T Mispair
pdb|2O8D|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G DU MISPAIR
pdb|2O8F|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO DNA WITH A SINGLE BASE
T INSERT
pdb|3THW|A Chain A, Human Mutsbeta Complexed With An Idl Of 4 Bases (Loop4)
And Adp
pdb|3THX|A Chain A, Human Mutsbeta Complexed With An Idl Of 3 Bases (Loop3)
And Adp
pdb|3THY|A Chain A, Human Mutsbeta Complexed With An Idl Of 2 Bases (Loop2)
And Adp
pdb|3THZ|A Chain A, Human Mutsbeta Complexed With An Idl Of 6 Bases (Loop6)
And Adp
Length = 934
Score = 30.0 bits (66), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 25/44 (56%)
Query: 359 LIDCWIGEGFLGESDRFGAENQGYDILDTLVRACLLEEVEDDKV 402
+I+C + E ++ E+QGYDI++ + C LE + +K+
Sbjct: 840 VIECAKQKALELEEFQYIGESQGYDIMEPAAKKCYLEREQGEKI 883
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
0.322 0.137 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,105,741
Number of Sequences: 62578
Number of extensions: 907318
Number of successful extensions: 1845
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1833
Number of HSP's gapped (non-prelim): 15
length of query: 835
length of database: 14,973,337
effective HSP length: 107
effective length of query: 728
effective length of database: 8,277,491
effective search space: 6026013448
effective search space used: 6026013448
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: 56 (26.2 bits)