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= 004993
(720 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 55.8 bits (133), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 44/124 (35%), Positives = 66/124 (53%), Gaps = 7/124 (5%)
Query: 368 LVNLKEIDLSYSRQLKKLP-DLSQARNLENLLLKACSSLVETHSSIQYLSKLVTLDMRLC 426
LVNL+ + L ++ ++ LP ++ +NL++L ++ S L +I +L KL LD+R C
Sbjct: 182 LVNLQSLRLEWT-GIRSLPASIANLQNLKSLKIRN-SPLSALGPAIHHLPKLEELDLRGC 239
Query: 427 KNLNRLPSSLCELISLQRLYLSGCSNLRRIPESIINLSKLELLHLKNCSKLLSLP----E 482
L P L+RL L CSNL +P I L++LE L L+ C L LP +
Sbjct: 240 TALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSLIAQ 299
Query: 483 LPCN 486
LP N
Sbjct: 300 LPAN 303
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 43/135 (31%), Positives = 65/135 (48%), Gaps = 13/135 (9%)
Query: 349 ISLQLRESKVEQLWDGVPNLVNLKEIDLSYSRQLKKLPDLSQA-RNLENLLLKACSSLVE 407
++L+LR + Q D L +L+ + + L +LPD Q LE L L A + L
Sbjct: 84 VALELRSVPLPQFPDQAFRLSHLQHXTIDAA-GLXELPDTXQQFAGLETLTL-ARNPLRA 141
Query: 408 THSSIQYLSKLVTLDMRLCKNLNRLPSSLCE---------LISLQRLYLSGCSNLRRIPE 458
+SI L++L L +R C L LP L L++LQ L L + +R +P
Sbjct: 142 LPASIASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRLE-WTGIRSLPA 200
Query: 459 SIINLSKLELLHLKN 473
SI NL L+ L ++N
Sbjct: 201 SIANLQNLKSLKIRN 215
>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 = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 50/194 (25%), Positives = 86/194 (44%), Gaps = 46/194 (23%)
Query: 265 EVLSKNLGTEAIEGILL--DMSKVNEIHLNSSTFKK------MPRLRFLKFHGENKFKIS 316
E + NL +++ + +++ +++I N+S K +P +R+L G IS
Sbjct: 20 ETIKANLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVRYLALGGNKLHDIS 79
Query: 317 HFEGEAFTELRYLYWDGYPSKSLPPVI--RLDTLISLQLRESKVEQLWDGV--------- 365
+ T L YL G +SLP + +L L L L E++++ L DGV
Sbjct: 80 ALK--ELTNLTYLILTGNQLQSLPNGVFDKLTNLKELVLVENQLQSLPDGVFDKLTNLTY 137
Query: 366 ----------------PNLVNLKEIDLSYSRQLKKLPD-----LSQARNL---ENLLLKA 401
L NL E+DLSY+ QL+ LP+ L+Q ++L +N L
Sbjct: 138 LNLAHNQLQSLPKGVFDKLTNLTELDLSYN-QLQSLPEGVFDKLTQLKDLRLYQNQLKSV 196
Query: 402 CSSLVETHSSIQYL 415
+ + +S+QY+
Sbjct: 197 PDGVFDRLTSLQYI 210
>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 = 33.1 bits (74), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 50/192 (26%), Positives = 79/192 (41%), Gaps = 31/192 (16%)
Query: 7 QELLSTLLNDDGNVKIIPNIGLNFESKR------LTRK--KVLIVFDDVTDRKQIEFLIG 58
Q L + L D+ + +P LN E + + RK + L++ DDV D
Sbjct: 206 QNLCTRLDQDESFSQRLP---LNIEEAKDRLRILMLRKHPRSLLILDDVWDS-------W 255
Query: 59 ELDSFASGSLIIITTRDKQVLINCWADKIYEVKE--LADADALKLFSRCAF--RQDHPVA 114
L +F S I++TTRDK V + K E L L++ S + D P
Sbjct: 256 VLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKADLP-- 313
Query: 115 CYMELTYKIIKYAQGVPLALKVLGLFLSARRKEEWESAITKLETVPHMEIQDVLKISYDG 174
E + IIK +G PL + ++G L WE + +L+ I+ Y+
Sbjct: 314 ---EQAHSIIKECKGSPLVVSLIGALLR-DFPNRWEYYLKQLQNKQFKRIRKSSSYDYEA 369
Query: 175 LDYVEQAMFLDI 186
LD +AM + +
Sbjct: 370 LD---EAMSISV 378
>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 = 32.7 bits (73), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 46/178 (25%), Positives = 72/178 (40%), Gaps = 20/178 (11%)
Query: 7 QELLSTLLNDDGNVKIIPNIGLNFESKR------LTRK--KVLIVFDDVTDRKQIEFLIG 58
Q L + L D+ + +P LN E + + RK + L++ DDV D
Sbjct: 200 QNLCTRLDQDESFSQRLP---LNIEEAKDRLRILMLRKHPRSLLILDDVWDS-------W 249
Query: 59 ELDSFASGSLIIITTRDKQVLINCWADKIYEVKELADADALKLFSRCAFRQDHPVACYME 118
L +F S I++TTRDK V + K Y V + K + + A E
Sbjct: 250 VLKAFDSQCQILLTTRDKSVTDSVMGPK-YVVPVESSLGKEKGLEILSLFVNMKKADLPE 308
Query: 119 LTYKIIKYAQGVPLALKVLGLFLSARRKEEWESAITKLETVPHMEIQDVLKISYDGLD 176
+ IIK +G PL + ++G L WE + +L+ I+ Y+ LD
Sbjct: 309 QAHSIIKECKGSPLVVSLIGALLRD-FPNRWEYYLKQLQNKQFKRIRKSSSYDYEALD 365
>pdb|3RMW|A Chain A, Crystal Structure Of Human Glycogenin-1 (Gyg1) T83m Mutant
Complexed With Manganese And Udp-Glucose
pdb|3RMV|A Chain A, Crystal Structure Of Human Glycogenin-1 (Gyg1) T83m Mutant
Complexed With Manganese And Udp
Length = 263
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 29/108 (26%), Positives = 48/108 (44%), Gaps = 11/108 (10%)
Query: 5 LRQELLSTLLNDDGNVKIIPNIGLNFESKRLTRKKVLIVFDDVTD--RKQIEFLIGE--- 59
+ + TL +D K +G + + R TR+ V++ V+D RK +E + E
Sbjct: 2 MTDQAFVTLTTNDAYAKGALVLGSSLKQHRTTRRLVVLATPQVSDSMRKVLETVFDEVIM 61
Query: 60 ---LDSFASGSLIIITTRDKQVL---INCWADKIYEVKELADADALKL 101
LDS S L ++ + V+ ++CW+ Y DAD L L
Sbjct: 62 VDVLDSGDSAHLTLMKRPELGVMLTKLHCWSLTQYSKCVFMDADTLVL 109
>pdb|3RP9|A Chain A, Crystal Structure Of The Apo Mapk From Toxoplasma Gondii,
25.M01780 Or Tgme49_007820
Length = 458
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 9/77 (11%)
Query: 30 FESKRLTRKKVLIVFDDVTDRKQIEFLIGELDSFASGSLI----IITTRDKQVLINCWAD 85
E + + KK+L VF+D+ D K+I I L+ ++ I+ +D + D
Sbjct: 76 LEKRVVAIKKILRVFEDLIDCKRILREIAILNRLNHDHVVKVLDIVIPKDVEKF-----D 130
Query: 86 KIYEVKELADADALKLF 102
++Y V E+AD+D KLF
Sbjct: 131 ELYVVLEIADSDFKKLF 147
>pdb|3U2T|A Chain A, Crystal Structure Of Human Glycogenin-1 (Gyg1) Complexed
With Manganese
Length = 284
Score = 30.8 bits (68), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 29/108 (26%), Positives = 47/108 (43%), Gaps = 11/108 (10%)
Query: 5 LRQELLSTLLNDDGNVKIIPNIGLNFESKRLTRKKVLIVFDDVTD--RKQIEFLIGE--- 59
+ + TL +D K +G + + R TR+ V++ V+D RK +E + E
Sbjct: 23 MTDQAFVTLTTNDAYAKGALVLGSSLKQHRTTRRLVVLATPQVSDSMRKVLETVFDEVIM 82
Query: 60 ---LDSFASGSLIIITTRDKQVL---INCWADKIYEVKELADADALKL 101
LDS S L ++ + V ++CW+ Y DAD L L
Sbjct: 83 VDVLDSGDSAHLTLMKRPELGVTLTKLHCWSLTQYSKCVFMDADTLVL 130
>pdb|3Q4S|A Chain A, Crystal Structure Of Human Glycogenin-1 (Gyg1), Apo Form
pdb|3QVB|A Chain A, Crystal Structure Of Human Glycogenin-1 (Gyg1) Complexed
With Manganese And Udp
pdb|3U2W|A Chain A, Crystal Structure Of Human Glycogenin-1 (Gyg1) Complexed
With Manganese And Glucose Or A Glucal Species
pdb|3U2W|B Chain B, Crystal Structure Of Human Glycogenin-1 (Gyg1) Complexed
With Manganese And Glucose Or A Glucal Species
Length = 263
Score = 30.8 bits (68), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 29/108 (26%), Positives = 47/108 (43%), Gaps = 11/108 (10%)
Query: 5 LRQELLSTLLNDDGNVKIIPNIGLNFESKRLTRKKVLIVFDDVTD--RKQIEFLIGE--- 59
+ + TL +D K +G + + R TR+ V++ V+D RK +E + E
Sbjct: 2 MTDQAFVTLTTNDAYAKGALVLGSSLKQHRTTRRLVVLATPQVSDSMRKVLETVFDEVIM 61
Query: 60 ---LDSFASGSLIIITTRDKQVL---INCWADKIYEVKELADADALKL 101
LDS S L ++ + V ++CW+ Y DAD L L
Sbjct: 62 VDVLDSGDSAHLTLMKRPELGVTLTKLHCWSLTQYSKCVFMDADTLVL 109
>pdb|3T7M|A Chain A, Crystal Structure Of Human Glycogenin-1 (Gyg1) Complexed
With Manganese And Udp, In A Triclinic Closed Form
pdb|3T7M|B Chain B, Crystal Structure Of Human Glycogenin-1 (Gyg1) Complexed
With Manganese And Udp, In A Triclinic Closed Form
pdb|3T7N|A Chain A, Crystal Structure Of Human Glycogenin-1 (Gyg1) Complexed
With Manganese And Udp, In A Monoclinic Closed Form
pdb|3T7N|B Chain B, Crystal Structure Of Human Glycogenin-1 (Gyg1) Complexed
With Manganese And Udp, In A Monoclinic Closed Form
pdb|3T7O|A Chain A, Crystal Structure Of Human Glycogenin-1 (Gyg1) Complexed
With Manganese, Udp-Glucose And Glucose
pdb|3T7O|B Chain B, Crystal Structure Of Human Glycogenin-1 (Gyg1) Complexed
With Manganese, Udp-Glucose And Glucose
pdb|3U2U|A Chain A, Crystal Structure Of Human Glycogenin-1 (Gyg1) Complexed
With Manganese, Udp And Maltotetraose
pdb|3U2U|B Chain B, Crystal Structure Of Human Glycogenin-1 (Gyg1) Complexed
With Manganese, Udp And Maltotetraose
pdb|3U2X|A Chain A, Crystal Structure Of Human Glycogenin-1 (Gyg1) Complexed
With Manganese, Udp And 1'-Deoxyglucose
pdb|3U2X|B Chain B, Crystal Structure Of Human Glycogenin-1 (Gyg1) Complexed
With Manganese, Udp And 1'-Deoxyglucose
pdb|3U2V|A Chain A, Crystal Structure Of Human Glycogenin-1 (Gyg1) Complexed
With Manganese, Udp And Maltohexaose
pdb|3U2V|B Chain B, Crystal Structure Of Human Glycogenin-1 (Gyg1) Complexed
With Manganese, Udp And Maltohexaose
Length = 263
Score = 30.8 bits (68), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 29/108 (26%), Positives = 47/108 (43%), Gaps = 11/108 (10%)
Query: 5 LRQELLSTLLNDDGNVKIIPNIGLNFESKRLTRKKVLIVFDDVTD--RKQIEFLIGE--- 59
+ + TL +D K +G + + R TR+ V++ V+D RK +E + E
Sbjct: 2 MTDQAFVTLTTNDAYAKGALVLGSSLKQHRTTRRLVVLATPQVSDSMRKVLETVFDEVIM 61
Query: 60 ---LDSFASGSLIIITTRDKQVL---INCWADKIYEVKELADADALKL 101
LDS S L ++ + V ++CW+ Y DAD L L
Sbjct: 62 VDVLDSGDSAHLTLMKRPELGVTLTKLHCWSLTQYSKCVFMDADTLVL 109
>pdb|1OGQ|A Chain A, The Crystal Structure Of Pgip (Polygalacturonase
Inhibiting Protein), A Leucine Rich Repeat Protein
Involved In Plant Defense
Length = 313
Score = 30.4 bits (67), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 432 LPSSLCELISLQRLYLSGCSNL-RRIPESIINLSKLELLHLKNCSKLLSLPE 482
+PSSL L L LY+ G +NL IP +I L++L L++ + + ++P+
Sbjct: 68 IPSSLANLPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTNVSGAIPD 119
>pdb|4G8A|A Chain A, Crystal Structure Of Human Tlr4 Polymorphic Variant D299g
And T399i In Complex With Md-2 And Lps
pdb|4G8A|B Chain B, Crystal Structure Of Human Tlr4 Polymorphic Variant D299g
And T399i In Complex With Md-2 And Lps
Length = 635
Score = 29.6 bits (65), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 54/197 (27%), Positives = 81/197 (41%), Gaps = 17/197 (8%)
Query: 297 KKMPRLRFLKFHGENKFKISHFEGEAFTELRY--LYWDGYPSKSLPPVIRLDTLISLQLR 354
K + RL F G N F F +L L + G S+S I L L L
Sbjct: 349 KSLKRLTFTSNKGGNAFSEVDLPSLEFLDLSRNGLSFKGCCSQSDFGTISLKYL---DLS 405
Query: 355 ESKVEQLWDGVPNLVNLKEIDLSYSRQLKKLPDLSQARNLENLLLKACSSLVETHSSIQY 414
+ V + L L+ +D +S LK++ + S +L NL+ S TH+ + +
Sbjct: 406 FNGVITMSSNFLGLEQLEHLDFQHSN-LKQMSEFSVFLSLRNLIYLDIS---HTHTRVAF 461
Query: 415 ------LSKLVTLDMRLCK-NLNRLPSSLCELISLQRLYLSGCSNLRRIPESIINLSKLE 467
LS L L M N LP EL +L L LS C + P + +LS L+
Sbjct: 462 NGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQ 521
Query: 468 LLHLKNCSKLLSLPELP 484
+L++ + + SL P
Sbjct: 522 VLNMSH-NNFFSLDTFP 537
>pdb|2Z63|A Chain A, Crystal Structure Of The Tv8 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 570
Score = 29.3 bits (64), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 53/195 (27%), Positives = 84/195 (43%), Gaps = 17/195 (8%)
Query: 297 KKMPRLRFLKFHGENKFKISHFEGEAFTELRY--LYWDGYPSKSLPPVIRLDTLISLQLR 354
K + RL F G N F F +L L + G S+S +L L L
Sbjct: 325 KSLKRLTFTSNKGGNAFSEVDLPSLEFLDLSRNGLSFKGCCSQS---DFGTTSLKYLDLS 381
Query: 355 ESKVEQLWDGVPNLVNLKEIDLSYSRQLKKLPDLSQARNLENLLLKACSSLVETHSSIQY 414
+ V + L L+ +D +S LK++ + S +L NL+ S TH+ + +
Sbjct: 382 FNGVITMSSNFLGLEQLEHLDFQHSN-LKQMSEFSVFLSLRNLIYLDIS---HTHTRVAF 437
Query: 415 ------LSKLVTLDMRLCK-NLNRLPSSLCELISLQRLYLSGCSNLRRIPESIINLSKLE 467
LS L L M N LP EL +L L LS C + P + +LS L+
Sbjct: 438 NGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQ 497
Query: 468 LLHLKNCSKLLSLPE 482
+L++ + ++L S+P+
Sbjct: 498 VLNMAS-NQLKSVPD 511
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 0.423
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,808,710
Number of Sequences: 62578
Number of extensions: 856304
Number of successful extensions: 1988
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 31
Number of HSP's that attempted gapping in prelim test: 1970
Number of HSP's gapped (non-prelim): 42
length of query: 720
length of database: 14,973,337
effective HSP length: 106
effective length of query: 614
effective length of database: 8,340,069
effective search space: 5120802366
effective search space used: 5120802366
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)