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= 005860
(673 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 = 34.7 bits (78), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 32/92 (34%), Positives = 47/92 (51%), Gaps = 4/92 (4%)
Query: 560 NSTNKILKGIEKLIHLRYLRLVGXXXXXXXXXXXXXXNLQVLEIEQCTSLKRLPLGI-GK 618
NS K ++GI+ L ++RYL L G NL L I L+ LP G+ K
Sbjct: 50 NSDIKSVQGIQYLPNVRYLAL-GGNKLHDISALKELTNLTYL-ILTGNQLQSLPNGVFDK 107
Query: 619 LVNLRHLTYDDSCLEFIPKGI-QRLTNLRTLS 649
L NL+ L ++ L+ +P G+ +LTNL L+
Sbjct: 108 LTNLKELVLVENQLQSLPDGVFDKLTNLTYLN 139
>pdb|3RFJ|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 279
Score = 34.3 bits (77), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 32/91 (35%), Positives = 46/91 (50%), Gaps = 4/91 (4%)
Query: 560 NSTNKILKGIEKLIHLRYLRLVGXXXXXXXXXXXXXXNLQVLEIEQCTSLKRLPLGI-GK 618
NS K ++GI+ L ++RYL L G NL L I L+ LP G+ K
Sbjct: 50 NSDIKSVQGIQYLPNVRYLAL-GGNKLHDISALKELTNLTYL-ILTGNQLQSLPNGVFDK 107
Query: 619 LVNLRHLTYDDSCLEFIPKGI-QRLTNLRTL 648
L NL+ L ++ L+ +P G+ +LTNL L
Sbjct: 108 LTNLKELVLVENQLQSLPDGVFDKLTNLTYL 138
>pdb|2Y3H|A Chain A, E63q Mutant Of Cupriavidus Metallidurans Ch34 Cnrxs
pdb|2Y3H|B Chain B, E63q Mutant Of Cupriavidus Metallidurans Ch34 Cnrxs
pdb|2Y3H|C Chain C, E63q Mutant Of Cupriavidus Metallidurans Ch34 Cnrxs
pdb|2Y3H|D Chain D, E63q Mutant Of Cupriavidus Metallidurans Ch34 Cnrxs
Length = 118
Score = 33.9 bits (76), Expect = 0.34, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 6/63 (9%)
Query: 115 GFSQTFQRRDIAVKIKAINGKLDDIAKQKDMYNFNVIRSTENSER----IQSTSLIDVSE 170
F+Q +RR+I +++A NGKL D + ++ V +T+ ER +Q +L+ V E
Sbjct: 35 AFAQ--RRREIETRLRAANGKLADAIAKNPAWSPEVEAATQEVERAAGDLQRATLVHVFE 92
Query: 171 IRG 173
+R
Sbjct: 93 MRA 95
>pdb|2Y39|A Chain A, Ni-Bound Form Of Cupriavidus Metallidurans Ch34 Cnrxs
pdb|2Y3B|A Chain A, Co-Bound Form Of Cupriavidus Metallidurans Ch34 Cnrxs
pdb|2Y3D|A Chain A, Zn-Bound Form Of Cupriavidus Metallidurans Ch34 Cnrxs
pdb|2Y3D|B Chain B, Zn-Bound Form Of Cupriavidus Metallidurans Ch34 Cnrxs
Length = 118
Score = 33.5 bits (75), Expect = 0.36, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 6/63 (9%)
Query: 115 GFSQTFQRRDIAVKIKAINGKLDDIAKQKDMYNFNVIRSTENSER----IQSTSLIDVSE 170
F+Q +RR+I +++A NGKL D + ++ V +T+ ER +Q +L+ V E
Sbjct: 35 AFAQ--RRREIETRLRAANGKLADAIAKNPAWSPEVEAATQEVERAAGDLQRATLVHVFE 92
Query: 171 IRG 173
+R
Sbjct: 93 MRA 95
>pdb|3E6J|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor (Vlr)
Rbc36 In Complex With H-Trisaccharide
Length = 229
Score = 33.1 bits (74), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 18/41 (43%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 606 CTSLKRLPLGIGKLVNLRHLTYDDSCLEFIPKG-IQRLTNL 645
C L LP GI +L +L HL D + L+ IP G RL++L
Sbjct: 121 CNKLTELPRGIERLTHLTHLALDQNQLKSIPHGAFDRLSSL 161
>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 = 33.1 bits (74), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 53/200 (26%), Positives = 80/200 (40%), Gaps = 47/200 (23%)
Query: 204 GMGGIGKTTLAQFAYNDSDVFE--YFDKRMWVCV-----SDPFDELRIAKAIIEALEGFV 256
GM G GK+ LA A D + E + WV V S +L+ ++ E F
Sbjct: 154 GMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDESFS 213
Query: 257 PTVG-ELNSLLESIRASLVGK--KFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTT 313
+ + + +R ++ K + LLILDD+W + LK +IL+TT
Sbjct: 214 QRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDS---------WVLKAFDSQCQILLTT 264
Query: 314 RKETVA-RMMESIHVISIK---------------------ELSEQECW----CKGLPLAA 347
R ++V +M +V+ ++ +L EQ CKG PL
Sbjct: 265 RDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKADLPEQAHSIIKECKGSPLVV 324
Query: 348 KTIGSLLRFKRTREEWESIL 367
IG+LLR R WE L
Sbjct: 325 SLIGALLRDFPNR--WEYYL 342
>pdb|2Y3G|A Chain A, Se-Met Form Of Cupriavidus Metallidurans Ch34 Cnrxs
pdb|2Y3G|B Chain B, Se-Met Form Of Cupriavidus Metallidurans Ch34 Cnrxs
pdb|2Y3G|C Chain C, Se-Met Form Of Cupriavidus Metallidurans Ch34 Cnrxs
pdb|2Y3G|D Chain D, Se-Met Form Of Cupriavidus Metallidurans Ch34 Cnrxs
Length = 118
Score = 32.7 bits (73), Expect = 0.75, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 115 GFSQTFQRRDIAVKIKAINGKLDDIAKQKDMYNFNVIRSTENSER----IQSTSLIDVSE 170
F+Q +RR+I +++A NGKL D + ++ V +T+ ER +Q +L+ V E
Sbjct: 35 AFAQ--RRREIETRLRAANGKLADAIAKNPAWSPEVEAATQEVERAAGDLQRATLVHVFE 92
Query: 171 IRG 173
R
Sbjct: 93 XRA 95
>pdb|3EPV|A Chain A, X-Ray Structure Of The Metal-Sensor Cnrx In Both The Apo-
And Copper- Bound Forms
pdb|3EPV|B Chain B, X-Ray Structure Of The Metal-Sensor Cnrx In Both The Apo-
And Copper- Bound Forms
pdb|3EPV|C Chain C, X-Ray Structure Of The Metal-Sensor Cnrx In Both The Apo-
And Copper- Bound Forms
pdb|3EPV|D Chain D, X-Ray Structure Of The Metal-Sensor Cnrx In Both The Apo-
And Copper- Bound Forms
Length = 109
Score = 32.0 bits (71), Expect = 1.0, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 115 GFSQTFQRRDIAVKIKAINGKLDDIAKQKDMYNFNVIRSTENSER----IQSTSLIDVSE 170
F+Q +RR+I +++A NGKL D + ++ V +T+ ER +Q +L+ V E
Sbjct: 26 AFAQ--RRREIETRLRAANGKLADAIAKNPAWSPEVEAATQEVERAAGDLQRATLVHVFE 83
Query: 171 IRG 173
R
Sbjct: 84 XRA 86
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 50/188 (26%), Positives = 76/188 (40%), Gaps = 45/188 (23%)
Query: 204 GMGGIGKTTLAQFAYNDSDVFE--YFDKRMWVCV-----SDPFDELRIAKAIIEALEGFV 256
GM G GK+ LA A D + E + WV + S +L+ ++ E F
Sbjct: 154 GMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQEESFS 213
Query: 257 PTVG-ELNSLLESIRASLVGK--KFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTT 313
+ + + +R ++ K + LLILDD+ W+P + LK +IL+TT
Sbjct: 214 QRLPLNIEEAKDRLRVLMLRKHPRSLLILDDV-------WDP--WVLKAFDNQCQILLTT 264
Query: 314 RKETVA-RMMESIHVISI--------------------KELSEQECW-----CKGLPLAA 347
R ++V +M HV+ + KE E CKG PL
Sbjct: 265 RDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKEDLPAEAHSIIKECKGSPLVV 324
Query: 348 KTIGSLLR 355
IG+LLR
Sbjct: 325 SLIGALLR 332
>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 = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 51/196 (26%), Positives = 79/196 (40%), Gaps = 45/196 (22%)
Query: 204 GMGGIGKTTLAQFAYNDSDVFE--YFDKRMWVCV-----SDPFDELRIAKAIIEALEGFV 256
GM G GK+ LA A D + E + WV V S +L+ ++ E F
Sbjct: 160 GMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDESFS 219
Query: 257 PTVG-ELNSLLESIRASLVGK--KFLLILDDMWTDDYSKWEPFHYCLKNGVRGSKILVTT 313
+ + + +R ++ K + LLILDD+W + LK +IL+TT
Sbjct: 220 QRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDS---------WVLKAFDSQCQILLTT 270
Query: 314 RKETVA-RMMESIHVISIK---------------------ELSEQECW----CKGLPLAA 347
R ++V +M +V+ ++ +L EQ CKG PL
Sbjct: 271 RDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKADLPEQAHSIIKECKGSPLVV 330
Query: 348 KTIGSLLRFKRTREEW 363
IG+LLR R E+
Sbjct: 331 SLIGALLRDFPNRWEY 346
>pdb|2IDY|A Chain A, Nmr Structure Of The Sars-Cov Non-Structural Protein Nsp3a
pdb|2GRI|A Chain A, Nmr Structure Of The Sars-Cov Non-Structural Protein Nsp3a
Length = 112
Score = 29.6 bits (65), Expect = 6.0, Method: Composition-based stats.
Identities = 23/90 (25%), Positives = 38/90 (42%), Gaps = 3/90 (3%)
Query: 23 EQMKLVVGIDNEVAKLKHNFLAIQAVLVDAEQRQFK---EETVRLWLDQLKDVSYYMGDV 79
+ +++ +D V K+ + ++ V E +F E V L + D+ MG
Sbjct: 20 KNVRITFELDERVDKVLNEKCSVYTVESGTEVTEFACVVAEAVVKTLQPVSDLLTNMGID 79
Query: 80 LDEWNTARLKLRIEGVDALVPQRKVCSFLP 109
LDEW+ A L + + R CSF P
Sbjct: 80 LDEWSVATFYLFDDAGEENFSSRMYCSFYP 109
>pdb|2J9R|A Chain A, Thymidine Kinase From B. Anthracis In Complex With Dt
Length = 214
Score = 29.3 bits (64), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 31/54 (57%), Gaps = 3/54 (5%)
Query: 31 IDNEVAK---LKHNFLAIQAVLVDAEQRQFKEETVRLWLDQLKDVSYYMGDVLD 81
IDN ++ + HN L ++AV V A + FK T + + + +V ++ GD+++
Sbjct: 66 IDNRYSEEDVVSHNGLKVKAVPVSASKDIFKHITEEMDVIAIDEVQFFDGDIVE 119
>pdb|2YF0|A Chain A, Human Myotubularin Related Protein 6 (Mtmr6)
Length = 512
Score = 29.3 bits (64), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 22/36 (61%)
Query: 135 KLDDIAKQKDMYNFNVIRSTENSERIQSTSLIDVSE 170
+L AK +D+Y F+ +SER+Q LID++E
Sbjct: 97 QLSKQAKYEDLYAFSYNPKQNDSERLQGWQLIDLAE 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
0.323 0.139 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,510,100
Number of Sequences: 62578
Number of extensions: 678528
Number of successful extensions: 1507
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 1499
Number of HSP's gapped (non-prelim): 27
length of query: 673
length of database: 14,973,337
effective HSP length: 105
effective length of query: 568
effective length of database: 8,402,647
effective search space: 4772703496
effective search space used: 4772703496
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: 55 (25.8 bits)