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= 041248
(813 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 37.0 bits (84), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 32/130 (24%), Positives = 61/130 (46%), Gaps = 23/130 (17%)
Query: 501 LVCSGAGVGAVPDVEGWENVRRLSLMQNQIEILSEVPTCPHLLTLFLDFNYKLEMITDGF 560
++ + + + +V ++ NVR L+L N++ +S + +L L L N +L+ + +G
Sbjct: 46 IIANNSDIKSVQGIQYLPNVRYLALGGNKLHDISALKELTNLTYLILTGN-QLQSLPNGV 104
Query: 561 FQCMPSLKVLKMS---------------------NCGHVKVLKLPFGM-SKLGSLQLLDI 598
F + +LK L + N H ++ LP G+ KL +L LD+
Sbjct: 105 FDKLTNLKELVLVENQLQSLPDGVFDKLTNLTYLNLAHNQLQSLPKGVFDKLTNLTELDL 164
Query: 599 SHAGIRELPE 608
S+ ++ LPE
Sbjct: 165 SYNQLQSLPE 174
>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 = 33.5 bits (75), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 38/158 (24%), Positives = 69/158 (43%), Gaps = 24/158 (15%)
Query: 249 EKALDIFRSL---REKRFVLLLDDIWERVDLTKMGIPLSGPKNTTSKVVFTTRFVDVCGS 305
E+A D R L + R +L+LDD+W+ L ++ +++ TTR V S
Sbjct: 221 EEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAF--------DSQCQILLTTRDKSVTDS 272
Query: 306 MEADKKFQV--ACLSEEDAWELFRKKVGEETLESDHDIVELAQTVAKECGGLPLALITIG 363
+ K + L +E E+ V + D+ E A ++ KEC G PL + IG
Sbjct: 273 VMGPKYVVPVESSLGKEKGLEILSLFVNMKKA----DLPEQAHSIIKECKGSPLVVSLIG 328
Query: 364 RAMA-FKKTAEEWIHAIE------VLRTSASEFAGLGE 394
+ F E ++ ++ + ++S+ ++ L E
Sbjct: 329 ALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDE 366
>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 = 32.7 bits (73), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 33/120 (27%), Positives = 53/120 (44%), Gaps = 17/120 (14%)
Query: 249 EKALDIFRSL---REKRFVLLLDDIWERVDLTKMGIPLSGPKNTTSKVVFTTRFVDVCGS 305
E+A D R L + R +L+LDD+W+ L ++ +++ TTR V S
Sbjct: 227 EEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAF--------DSQCQILLTTRDKSVTDS 278
Query: 306 MEADKKFQV--ACLSEEDAWELFRKKVGEETLESDHDIVELAQTVAKECGGLPLALITIG 363
+ K + L +E E+ V + D+ E A ++ KEC G PL + IG
Sbjct: 279 VMGPKYVVPVESSLGKEKGLEILSLFVNMKKA----DLPEQAHSIIKECKGSPLVVSLIG 334
>pdb|2Z7X|B Chain B, Crystal Structure Of The Tlr1-Tlr2 Heterodimer Induced By
Binding Of A Tri-Acylated Lipopeptide
Length = 520
Score = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 23/92 (25%), Positives = 50/92 (54%), Gaps = 5/92 (5%)
Query: 518 ENVRRLSLMQNQIEILSEVPTCPHLLTLFLDFNYKLEMITDGFFQCMPS-LKVLKMSNCG 576
+++++L + QN + + C +L L N ++TD F+C+P +KVL + +
Sbjct: 374 KSLQQLDISQNSVSYDEKKGDCSWTKSL-LSLNMSSNILTDTIFRCLPPRIKVLDLHSN- 431
Query: 577 HVKVLKLPFGMSKLGSLQLLDISHAGIRELPE 608
K+ +P + KL +LQ L+++ ++ +P+
Sbjct: 432 --KIKSIPKQVVKLEALQELNVASNQLKSVPD 461
>pdb|3HJ9|A Chain A, Crystal Structure Of A Putative Nitroreductase
(Reut_a1228) From Ralstonia Eutropha Jmp134 At 2.00 A
Resolution
pdb|3HJ9|B Chain B, Crystal Structure Of A Putative Nitroreductase
(Reut_a1228) From Ralstonia Eutropha Jmp134 At 2.00 A
Resolution
Length = 223
Score = 31.2 bits (69), Expect = 2.5, Method: Composition-based stats.
Identities = 18/40 (45%), Positives = 26/40 (65%), Gaps = 6/40 (15%)
Query: 500 FLVCSGAGVGAVPDVEGWENVRRL----SLMQNQIEILSE 535
+L C+ AG+GAV V GW N R+L SL +++ ILS+
Sbjct: 172 YLYCASAGLGAV--VRGWLNRRQLAEHXSLNEDEEPILSQ 209
>pdb|4AY9|X Chain X, Structure Of Follicle-Stimulating Hormone In Complex With
The Entire Ectodomain Of Its Receptor
pdb|4AY9|Y Chain Y, Structure Of Follicle-Stimulating Hormone In Complex With
The Entire Ectodomain Of Its Receptor
pdb|4AY9|Z Chain Z, Structure Of Follicle-Stimulating Hormone In Complex With
The Entire Ectodomain Of Its Receptor
Length = 350
Score = 31.2 bits (69), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 550 NYKLEMITDGFFQCMPSLKVLKMSNCGHVKVLKLPFGMSKLGSLQLLDISHAGIRELPE 608
N LE+I F +P L +++ ++ + P L +LQ L IS+ GI+ LP+
Sbjct: 64 NDVLEVIEADVFSNLPKLHEIRIEKANNLLYIN-PEAFQNLPNLQYLLISNTGIKHLPD 121
>pdb|1XWD|C Chain C, Crystal Structure Of Human Follicle Stimulating Hormone
Complexed With Its Receptor
pdb|1XWD|F Chain F, Crystal Structure Of Human Follicle Stimulating Hormone
Complexed With Its Receptor
Length = 252
Score = 30.0 bits (66), Expect = 5.5, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 550 NYKLEMITDGFFQCMPSLKVLKMSNCGHVKVLKLPFGMSKLGSLQLLDISHAGIRELPE 608
N LE+I F +P L +++ ++ + P L +LQ L IS+ GI+ LP+
Sbjct: 64 NDVLEVIEADVFSNLPKLHEIRIEKANNLLYIN-PEAFQNLPNLQYLLISNTGIKHLPD 121
>pdb|4AW4|A Chain A, Engineered Variant Of Listeria Monocytogenes Inlb
Internalin Domain With An Additional Leucine Rich Repeat
Inserted
pdb|4AW4|B Chain B, Engineered Variant Of Listeria Monocytogenes Inlb
Internalin Domain With An Additional Leucine Rich Repeat
Inserted
pdb|4AW4|C Chain C, Engineered Variant Of Listeria Monocytogenes Inlb
Internalin Domain With An Additional Leucine Rich Repeat
Inserted
Length = 311
Score = 29.6 bits (65), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 28/50 (56%)
Query: 501 LVCSGAGVGAVPDVEGWENVRRLSLMQNQIEILSEVPTCPHLLTLFLDFN 550
++ + + + +V ++ N+ L+L NQI +S + P++ LFL+ N
Sbjct: 49 IIANNSDIKSVQGIQYLPNLTSLNLSNNQITDISPIQYLPNVTKLFLNGN 98
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 29.3 bits (64), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 32/120 (26%), Positives = 50/120 (41%), Gaps = 17/120 (14%)
Query: 249 EKALDIFRSL---REKRFVLLLDDIWERVDLTKMGIPLSGPKNTTSKVVFTTRFVDVCGS 305
E+A D R L + R +L+LDD+W+ L + +++ TTR V S
Sbjct: 221 EEAKDRLRVLMLRKHPRSLLILDDVWDPWVLKAF--------DNQCQILLTTRDKSVTDS 272
Query: 306 MEADKKFQV--ACLSEEDAWELFRKKVGEETLESDHDIVELAQTVAKECGGLPLALITIG 363
+ K + L E E+ V + D+ A ++ KEC G PL + IG
Sbjct: 273 VMGPKHVVPVESGLGREKGLEILSLFVNMKK----EDLPAEAHSIIKECKGSPLVVSLIG 328
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
0.321 0.136 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,594,590
Number of Sequences: 62578
Number of extensions: 822894
Number of successful extensions: 2008
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 1998
Number of HSP's gapped (non-prelim): 23
length of query: 813
length of database: 14,973,337
effective HSP length: 107
effective length of query: 706
effective length of database: 8,277,491
effective search space: 5843908646
effective search space used: 5843908646
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)