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= 003515
(814 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 55.5 bits (132), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 69/293 (23%), Positives = 130/293 (44%), Gaps = 31/293 (10%)
Query: 180 KLELFKDGRQVIVVSAPGGYGKTTLVKKLCKDDQVL-GKFKDNIFFVTVSQTPN------ 232
KL K + + G GK+ L + +D +L G F + +V+V +
Sbjct: 139 KLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMK 198
Query: 233 VKGIVQKVYQHKGYAVPEFQTDEDAINDLERLLKPIRPEAILLVLDDVWSGSESLLQKFK 292
++ + ++ Q + ++ E+A + L L+ P + LL+LDDVW +L+ F
Sbjct: 199 LQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRS-LLILDDVWDSW--VLKAFD 255
Query: 293 FQLPYYKILVTSR--SVFPQ-FGSGYDL---KPLNDEAARTLFRYSANLQDGNSYIPDEN 346
Q +IL+T+R SV G Y + L E + N++ + +P++
Sbjct: 256 SQC---QILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKAD--LPEQ- 309
Query: 347 LVNKILRACKGCPLALTVVGGSLCGKHPAIWQKRVKEWTQDV------SVFHSNKEILSC 400
+ I++ CKG PL ++++G +L P W+ +K+ S + + +
Sbjct: 310 -AHSIIKECKGSPLVVSLIG-ALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEA 367
Query: 401 LERSLDALNNEVKECYMDLCSFPEDQRIPITALVDMW-MELYELVDELFAIAN 452
+ S++ L ++K+ Y DL +D ++P L +W ME E+ D L N
Sbjct: 368 MSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDMETEEVEDILQEFVN 420
>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 = 55.1 bits (131), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 69/293 (23%), Positives = 130/293 (44%), Gaps = 31/293 (10%)
Query: 180 KLELFKDGRQVIVVSAPGGYGKTTLVKKLCKDDQVL-GKFKDNIFFVTVSQTPN------ 232
KL K + + G GK+ L + +D +L G F + +V+V +
Sbjct: 145 KLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMK 204
Query: 233 VKGIVQKVYQHKGYAVPEFQTDEDAINDLERLLKPIRPEAILLVLDDVWSGSESLLQKFK 292
++ + ++ Q + ++ E+A + L L+ P + LL+LDDVW +L+ F
Sbjct: 205 LQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRS-LLILDDVWDSW--VLKAFD 261
Query: 293 FQLPYYKILVTSR--SVFPQ-FGSGYDL---KPLNDEAARTLFRYSANLQDGNSYIPDEN 346
Q +IL+T+R SV G Y + L E + N++ + +P++
Sbjct: 262 SQC---QILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKAD--LPEQ- 315
Query: 347 LVNKILRACKGCPLALTVVGGSLCGKHPAIWQKRVKEWTQDV------SVFHSNKEILSC 400
+ I++ CKG PL ++++G +L P W+ +K+ S + + +
Sbjct: 316 -AHSIIKECKGSPLVVSLIG-ALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEA 373
Query: 401 LERSLDALNNEVKECYMDLCSFPEDQRIPITALVDMW-MELYELVDELFAIAN 452
+ S++ L ++K+ Y DL +D ++P L +W ME E+ D L N
Sbjct: 374 MSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDMETEEVEDILQEFVN 426
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 61/231 (26%), Positives = 101/231 (43%), Gaps = 17/231 (7%)
Query: 549 EAPEVKVVVLNVRTKKYTLPKFLE---KMDKLKVMIVTNYGFFPAELSNI-QVFGALSNL 604
+A + V L +R+ LP+F + ++ L+ + G EL + Q F L L
Sbjct: 77 DATQPGRVALELRS--VPLPQFPDQAFRLSHLQHXTIDAAGL--XELPDTXQQFAGLETL 132
Query: 605 KRIRLEHVSLPSLTTVRMKHLQNVSLVMCN-----VDQVVQNSTFHFSDAFPNLLEIDID 659
R +LP+ + + L+ +S+ C + + NL + ++
Sbjct: 133 TLARNPLRALPA-SIASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRLE 191
Query: 660 YCNDLIELPDGLCDIVSIKKLRITNCHKLSALPEGIGKLVNLQMLTLASCTDLSALPDTI 719
+ + LP + ++ ++K L+I N LSAL I L L+ L L CT L P
Sbjct: 192 WTG-IRSLPASIANLQNLKSLKIRNS-PLSALGPAIHHLPKLEELDLRGCTALRNYPPIF 249
Query: 720 GNLSNLNFLDISECLNIQELPERIGELCSLKTLCLKGC-SMFELPSSILNL 769
G + L L + +C N+ LP I L L+ L L+GC ++ LPS I L
Sbjct: 250 GGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSLIAQL 300
Score = 50.4 bits (119), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 41/122 (33%), Positives = 63/122 (51%), Gaps = 11/122 (9%)
Query: 664 LIELPDGLCDIVSIKKLRITNCHKLSALPEGIGKLVNLQMLTLASCTDLSALPDTIGNLS 723
L + PD + ++ I + L LP+ + L+ LTLA L ALP +I +L+
Sbjct: 93 LPQFPDQAFRLSHLQHXTI-DAAGLXELPDTXQQFAGLETLTLAR-NPLRALPASIASLN 150
Query: 724 NLNFLDISECLNIQELPERI------GE---LCSLKTLCLKGCSMFELPSSILNLENLEV 774
L L I C + ELPE + GE L +L++L L+ + LP+SI NL+NL+
Sbjct: 151 RLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRLEWTGIRSLPASIANLQNLKS 210
Query: 775 VK 776
+K
Sbjct: 211 LK 212
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 49.7 bits (117), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 75/324 (23%), Positives = 139/324 (42%), Gaps = 50/324 (15%)
Query: 191 IVVSAPGGYGKTTLVKKLCKDDQVL-GKFKDNIFFVTVSQTPN------VKGIVQKVYQH 243
+ + G GK+ L + +D +L G F + +V++ + ++ + ++ Q
Sbjct: 150 VTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQE 209
Query: 244 KGYAVPEFQTDEDAINDLERLLKPIRPEAILLVLDDVWSGSESLLQKFKFQLPYYKILVT 303
+ ++ E+A + L L+ P + LL+LDDVW +L+ F Q +IL+T
Sbjct: 210 ESFSQRLPLNIEEAKDRLRVLMLRKHPRS-LLILDDVWD--PWVLKAFDNQC---QILLT 263
Query: 304 SR--SVFPQFGSGYDLKP----LNDEAARTLFRYSANLQDGNSYIPDENLVNKILRACKG 357
+R SV + P L E + N++ + +P E + I++ CKG
Sbjct: 264 TRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKED--LPAE--AHSIIKECKG 319
Query: 358 CPLALTVVGGSLCGKHPAIWQ-----------KRVKEWTQDVSVFHSNKEILSCLERSLD 406
PL ++++G +L P W KR+++ S + + + + S++
Sbjct: 320 SPLVVSLIG-ALLRDFPNRWAYYLRQLQNKQFKRIRK-----SSSYDYEALDEAMSISVE 373
Query: 407 ALNNEVKECYMDLCSFPEDQRIPITALVDMWMELYELVDELFAIANLHELSNLNLANCVA 466
L ++K+ Y DL +D ++P L +W E V+++ L E N +L C
Sbjct: 374 MLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLETEEVEDI-----LQEFVNKSLLFCNR 428
Query: 467 TRKYASDDSCYNDHFVMQHDLLRE 490
K CY H +Q D L E
Sbjct: 429 NGK----SFCYYLH-DLQVDFLTE 447
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 74/324 (22%), Positives = 139/324 (42%), Gaps = 50/324 (15%)
Query: 191 IVVSAPGGYGKTTLVKKLCKDDQVL-GKFKDNIFFVTVSQTPN------VKGIVQKVYQH 243
+ + G GK+ L + +D +L G F + +V++ + ++ + ++ Q
Sbjct: 157 VTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQE 216
Query: 244 KGYAVPEFQTDEDAINDLERLLKPIRPEAILLVLDDVWSGSESLLQKFKFQLPYYKILVT 303
+ ++ E+A + L L+ P + LL+LDDVW +L+ F Q +IL+T
Sbjct: 217 ESFSQRLPLNIEEAKDRLRVLMLRKHPRS-LLILDDVWD--PWVLKAFDNQC---QILLT 270
Query: 304 S--RSVFPQFGSGYDLKP----LNDEAARTLFRYSANLQDGNSYIPDENLVNKILRACKG 357
+ +SV + P L E + N++ + +P E + I++ CKG
Sbjct: 271 TSDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKED--LPAE--AHSIIKECKG 326
Query: 358 CPLALTVVGGSLCGKHPAIWQ-----------KRVKEWTQDVSVFHSNKEILSCLERSLD 406
PL ++++G +L P W KR+++ S + + + + S++
Sbjct: 327 SPLVVSLIG-ALLRDFPNRWAYYLRQLQNKQFKRIRK-----SSSYDYEALDEAMSISVE 380
Query: 407 ALNNEVKECYMDLCSFPEDQRIPITALVDMWMELYELVDELFAIANLHELSNLNLANCVA 466
L ++K+ Y DL +D ++P L +W E V+++ L E N +L C
Sbjct: 381 MLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLETEEVEDI-----LQEFVNKSLLFCNR 435
Query: 467 TRKYASDDSCYNDHFVMQHDLLRE 490
K CY H +Q D L E
Sbjct: 436 NGK----SFCYYLH-DLQVDFLTE 454
>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 = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 38/111 (34%), Positives = 61/111 (54%), Gaps = 7/111 (6%)
Query: 662 NDLIELPDGLCD-IVSIKKLRITNCHKLSALPEGI-GKLVNLQMLTLASCTDLSALPDTI 719
N L LP+G+ D + ++K+L + ++L +LP+G+ KL NL L LA L +LP +
Sbjct: 95 NQLQSLPNGVFDKLTNLKELVLVE-NQLQSLPDGVFDKLTNLTYLNLAH-NQLQSLPKGV 152
Query: 720 -GNLSNLNFLDISECLNIQELPERI-GELCSLKTLCLKGCSMFELPSSILN 768
L+NL LD+S +Q LPE + +L LK L L + +P + +
Sbjct: 153 FDKLTNLTELDLSYN-QLQSLPEGVFDKLTQLKDLRLYQNQLKSVPDGVFD 202
Score = 31.6 bits (70), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 33/112 (29%), Positives = 51/112 (45%), Gaps = 29/112 (25%)
Query: 597 VFGALSNLKRIRLEHVSLPSLTTVRMKHLQNVSLVMCNVDQVVQNSTFHFSDAFPNLLEI 656
VF L+NL + L H L SL F D NL E+
Sbjct: 128 VFDKLTNLTYLNLAHNQLQSLP----------------------KGVF---DKLTNLTEL 162
Query: 657 DIDYCNDLIELPDGLCD-IVSIKKLRITNCHKLSALPEGI-GKLVNLQMLTL 706
D+ Y N L LP+G+ D + +K LR+ ++L ++P+G+ +L +LQ + L
Sbjct: 163 DLSY-NQLQSLPEGVFDKLTQLKDLRLYQ-NQLKSVPDGVFDRLTSLQYIWL 212
>pdb|3RFJ|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 279
Score = 36.6 bits (83), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 36/111 (32%), Positives = 59/111 (53%), Gaps = 7/111 (6%)
Query: 662 NDLIELPDGLCD-IVSIKKLRITNCHKLSALPEGI-GKLVNLQMLTLASCTDLSALPDTI 719
N L LP+G+ D + ++K+L + ++L +LP+G+ KL NL L L L +LP +
Sbjct: 95 NQLQSLPNGVFDKLTNLKELVLVE-NQLQSLPDGVFDKLTNLTYLYLYH-NQLQSLPKGV 152
Query: 720 -GNLSNLNFLDISECLNIQELPERI-GELCSLKTLCLKGCSMFELPSSILN 768
L+NL LD+ +Q LPE + +L LK L L + +P + +
Sbjct: 153 FDKLTNLTRLDLDNN-QLQSLPEGVFDKLTQLKQLSLNDNQLKSVPDGVFD 202
Score = 34.7 bits (78), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 31/100 (31%), Positives = 53/100 (53%), Gaps = 4/100 (4%)
Query: 597 VFGALSNLKRIRLEHVSLPSLTTVRMKHLQNVSLVMCNVDQVVQNSTFHFSDAFPNLLEI 656
VF L+NLK + L L SL L N++ + +Q+ Q+ D NL +
Sbjct: 104 VFDKLTNLKELVLVENQLQSLPDGVFDKLTNLTYLYLYHNQL-QSLPKGVFDKLTNLTRL 162
Query: 657 DIDYCNDLIELPDGLCD-IVSIKKLRITNCHKLSALPEGI 695
D+D N L LP+G+ D + +K+L + N ++L ++P+G+
Sbjct: 163 DLDN-NQLQSLPEGVFDKLTQLKQLSL-NDNQLKSVPDGV 200
>pdb|3M18|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor
Vlra.R2.1 In Complex With Hen Egg Lysozyme
Length = 251
Score = 35.8 bits (81), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 34/96 (35%), Positives = 51/96 (53%), Gaps = 14/96 (14%)
Query: 650 FPNLLEIDIDY--CNDLIELPDGLCD-IVSIKKLRITNCHKLSALPEG-IGKLVNLQMLT 705
F +L ++D Y N L LP G+ D + +K+LR+ N ++L ++P G KL NLQ L+
Sbjct: 103 FDHLTQLDKLYLGGNQLKSLPSGVFDRLTKLKELRL-NTNQLQSIPAGAFDKLTNLQTLS 161
Query: 706 LASCTDLSALP----DTIGNLSNL----NFLDISEC 733
L S L ++P D +G L + N D S C
Sbjct: 162 L-STNQLQSVPHGAFDRLGKLQTITLFGNQFDCSRC 196
>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 = 35.8 bits (81), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 40/84 (47%), Gaps = 1/84 (1%)
Query: 680 LRITNCHKLSALPEGIGKLVNLQMLTLASCT-DLSALPDTIGNLSNLNFLDISECLNIQE 738
L I++ H A L +L++L +A + + LPD L NL FLD+S+C Q
Sbjct: 450 LDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQL 509
Query: 739 LPERIGELCSLKTLCLKGCSMFEL 762
P L SL+ L + + F L
Sbjct: 510 SPTAFNSLSSLQVLNMSHNNFFSL 533
>pdb|2Z63|A Chain A, Crystal Structure Of The Tv8 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 570
Score = 35.8 bits (81), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 42/90 (46%), Gaps = 1/90 (1%)
Query: 680 LRITNCHKLSALPEGIGKLVNLQMLTLASCT-DLSALPDTIGNLSNLNFLDISECLNIQE 738
L I++ H A L +L++L +A + + LPD L NL FLD+S+C Q
Sbjct: 426 LDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQL 485
Query: 739 LPERIGELCSLKTLCLKGCSMFELPSSILN 768
P L SL+ L + + +P I +
Sbjct: 486 SPTAFNSLSSLQVLNMASNQLKSVPDGIFD 515
>pdb|3M19|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor
Vlra.R5.1
pdb|3M19|B Chain B, Crystal Structure Of Variable Lymphocyte Receptor
Vlra.R5.1
Length = 251
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 34/96 (35%), Positives = 51/96 (53%), Gaps = 14/96 (14%)
Query: 650 FPNLLEIDIDY--CNDLIELPDGLCD-IVSIKKLRITNCHKLSALPEG-IGKLVNLQMLT 705
F +L ++D Y N L LP G+ D + +K+LR+ N ++L ++P G KL NLQ L+
Sbjct: 103 FDHLTQLDKLYLGGNQLKSLPSGVFDRLTKLKELRL-NTNQLQSIPAGAFDKLTNLQTLS 161
Query: 706 LASCTDLSALP----DTIGNLSNL----NFLDISEC 733
L S L ++P D +G L + N D S C
Sbjct: 162 L-STNQLQSVPHGAFDRLGKLQTITLFGNQFDCSRC 196
>pdb|3RIZ|A Chain A, Crystal Structure Of The Plant Steroid Receptor Bri1
Ectodomain
pdb|3RJ0|A Chain A, Plant Steroid Receptor Bri1 Ectodomain In Complex With
Brassinolide
Length = 772
Score = 35.4 bits (80), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 46/83 (55%), Gaps = 1/83 (1%)
Query: 662 NDLI-ELPDGLCDIVSIKKLRITNCHKLSALPEGIGKLVNLQMLTLASCTDLSALPDTIG 720
NDL E+P GL + ++ + ++N +P+ IG+L NL +L L++ + +P +G
Sbjct: 473 NDLTGEIPSGLSNCTNLNWISLSNNRLTGEIPKWIGRLENLAILKLSNNSFSGNIPAELG 532
Query: 721 NLSNLNFLDISECLNIQELPERI 743
+ +L +LD++ L +P +
Sbjct: 533 DCRSLIWLDLNTNLFNGTIPAAM 555
Score = 32.0 bits (71), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 34/132 (25%), Positives = 57/132 (43%), Gaps = 21/132 (15%)
Query: 691 LPEGIGKLVNLQMLTLASCTDLSALPDTIGNLSNLNFLDISECLNIQELPERIGELCSLK 750
+P+ IG + L +L L ++PD +G+L LN LD+S +P+ + L L
Sbjct: 645 IPKEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLSSNKLDGRIPQAMSALTMLT 704
Query: 751 TLCLKGCSM---------FEL--PSSILNLENL---EVVKCDEETAYQWEYFQLGQAKFR 796
+ L ++ FE P+ LN L + +CD A + + Q + R
Sbjct: 705 EIDLSNNNLSGPIPEMGQFETFPPAKFLNNPGLCGYPLPRCDPSNADGYAHHQRSHGR-R 763
Query: 797 IEVIQEDINLYW 808
+E NLY+
Sbjct: 764 LE------NLYF 769
>pdb|3FXI|A Chain A, Crystal Structure Of The Human Tlr4-Human Md-2-E.Coli Lps
Ra Complex
pdb|3FXI|B Chain B, Crystal Structure Of The Human Tlr4-Human Md-2-E.Coli Lps
Ra Complex
Length = 605
Score = 35.0 bits (79), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 40/84 (47%), Gaps = 1/84 (1%)
Query: 680 LRITNCHKLSALPEGIGKLVNLQMLTLASCT-DLSALPDTIGNLSNLNFLDISECLNIQE 738
L I++ H A L +L++L +A + + LPD L NL FLD+S+C Q
Sbjct: 426 LDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQL 485
Query: 739 LPERIGELCSLKTLCLKGCSMFEL 762
P L SL+ L + + F L
Sbjct: 486 SPTAFNSLSSLQVLNMSHNNFFSL 509
>pdb|3RGX|A Chain A, Structural Insight Into Brassinosteroid Perception By Bri1
pdb|3RGZ|A Chain A, Structural Insight Into Brassinosteroid Perception By Bri1
Length = 768
Score = 35.0 bits (79), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 46/83 (55%), Gaps = 1/83 (1%)
Query: 662 NDLI-ELPDGLCDIVSIKKLRITNCHKLSALPEGIGKLVNLQMLTLASCTDLSALPDTIG 720
NDL E+P GL + ++ + ++N +P+ IG+L NL +L L++ + +P +G
Sbjct: 476 NDLTGEIPSGLSNCTNLNWISLSNNRLTGEIPKWIGRLENLAILKLSNNSFSGNIPAELG 535
Query: 721 NLSNLNFLDISECLNIQELPERI 743
+ +L +LD++ L +P +
Sbjct: 536 DCRSLIWLDLNTNLFNGTIPAAM 558
>pdb|2G7R|A Chain A, X-Ray Structure Of The Death Domain Of The Human Mucosa
Associated Lymphoid Tissue Lymphoma Translocation
Protein 1
pdb|2G7R|B Chain B, X-Ray Structure Of The Death Domain Of The Human Mucosa
Associated Lymphoid Tissue Lymphoma Translocation
Protein 1
Length = 117
Score = 33.5 bits (75), Expect = 0.50, Method: Composition-based stats.
Identities = 24/66 (36%), Positives = 38/66 (57%), Gaps = 3/66 (4%)
Query: 712 LSALPDTIGNLSNLNFLDISEC-LNIQELPERIGELCSLKTLCLKGCSMFELPSSILNLE 770
L+ L + G L L+ LD+ +C L + E PE LC LK + KGC++ EL + +E
Sbjct: 48 LAELAGSRGRL-RLSCLDLEQCSLKVLE-PEGSPSLCLLKLMGEKGCTVTELSDFLQAME 105
Query: 771 NLEVVK 776
+ EV++
Sbjct: 106 HTEVLQ 111
>pdb|2Z66|A Chain A, Crystal Structure Of The Vt3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
pdb|2Z66|B Chain B, Crystal Structure Of The Vt3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
pdb|2Z66|C Chain C, Crystal Structure Of The Vt3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
pdb|2Z66|D Chain D, Crystal Structure Of The Vt3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 306
Score = 33.1 bits (74), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 40/84 (47%), Gaps = 1/84 (1%)
Query: 680 LRITNCHKLSALPEGIGKLVNLQMLTLASCT-DLSALPDTIGNLSNLNFLDISECLNIQE 738
L I++ H A L +L++L +A + + LPD L NL FLD+S+C Q
Sbjct: 131 LDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQL 190
Query: 739 LPERIGELCSLKTLCLKGCSMFEL 762
P L SL+ L + + F L
Sbjct: 191 SPTAFNSLSSLQVLNMSHNNFFSL 214
>pdb|2O6Q|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors A29
Length = 270
Score = 33.1 bits (74), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 34/114 (29%), Positives = 56/114 (49%), Gaps = 5/114 (4%)
Query: 595 IQVFGALSNLKRIRLEHVSLPSLTTVRMKHLQNVSLVMCNVDQVVQNSTFHFSDAFPNLL 654
I VF L NL +RL+ L SL L ++ + +++ Q+ D +L
Sbjct: 102 IGVFDQLVNLAELRLDRNQLKSLPPRVFDSLTKLTYLSLGYNEL-QSLPKGVFDKLTSLK 160
Query: 655 EIDIDYCNDLIELPDGLCD-IVSIKKLRITNCHKLSALPEG-IGKLVNLQMLTL 706
E+ + Y N L +P+G D + +K L++ N ++L +PEG L L+ML L
Sbjct: 161 ELRL-YNNQLKRVPEGAFDKLTELKTLKLDN-NQLKRVPEGAFDSLEKLKMLQL 212
>pdb|4B8C|D Chain D, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|J Chain J, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|K Chain K, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|L Chain L, Nuclease Module Of The Yeast Ccr4-Not Complex
Length = 727
Score = 32.7 bits (73), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 31/67 (46%), Gaps = 1/67 (1%)
Query: 712 LSALPDTIGNLSNLNFLDISECLNIQELPERIGELCSLKTLCLKGCSMFELPSSILNLEN 771
L+ LP I NLSNL LD+S + LP +G LK + LP NL N
Sbjct: 259 LTELPAEIKNLSNLRVLDLSHN-RLTSLPAELGSCFQLKYFYFFDNMVTTLPWEFGNLCN 317
Query: 772 LEVVKCD 778
L+ + +
Sbjct: 318 LQFLGVE 324
Score = 32.3 bits (72), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 662 NDLIELPDGLCDIVSIKKLRITNCHKLSALPEGIGKLVNLQMLTLASCTDLSALPDTIGN 721
N L ELP + ++ +++ L +++ ++L++LP +G L+ ++ LP GN
Sbjct: 257 NSLTELPAEIKNLSNLRVLDLSH-NRLTSLPAELGSCFQLKYFYFFDNM-VTTLPWEFGN 314
Query: 722 LSNLNFLDI 730
L NL FL +
Sbjct: 315 LCNLQFLGV 323
>pdb|1LVG|A Chain A, Crystal Structure Of Mouse Guanylate Kinase In Complex
With Gmp And Adp
Length = 198
Score = 31.2 bits (69), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 26/44 (59%), Gaps = 7/44 (15%)
Query: 187 GRQVIVVSAPGGYGKTTLVKKLCKDDQVLGKFKDNIFFVTVSQT 230
G + +V+S P G GK+TL+KKL ++ +IF +VS T
Sbjct: 3 GPRPVVLSGPSGAGKSTLLKKLFQE-------HSSIFGFSVSHT 39
>pdb|3QQ6|A Chain A, The N-Terminal Dna Binding Domain Of Sinr From Bacillus
Subtilis
pdb|3QQ6|B Chain B, The N-Terminal Dna Binding Domain Of Sinr From Bacillus
Subtilis
Length = 78
Score = 30.8 bits (68), Expect = 2.9, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 8/55 (14%)
Query: 21 AVSEAKDKAVMFKDLLEQLESTLQNSTPMIKEIEKLNQVLDLP-------KHETD 68
++SE +KA + K L +E LQ + P I+ +EK++ VLD+ KHET+
Sbjct: 25 SLSELAEKAGVAKSYLSSIERNLQ-TNPSIQFLEKVSAVLDVSVHTLLDEKHETE 78
>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 = 3.2, Method: Compositional matrix adjust.
Identities = 42/141 (29%), Positives = 61/141 (43%), Gaps = 22/141 (15%)
Query: 639 VQNSTFHFSDAFPNLLEIDIDYCNDLIELPDGLCDIVSIKKLRITNCHKLSALPE-GIGK 697
+ ++TFH F L E+D+ L ELP GL + ++KKL + + +K L +
Sbjct: 269 ISSNTFH---CFSGLQELDLT-ATHLSELPSGLVGLSTLKKL-VLSANKFENLCQISASN 323
Query: 698 LVNLQMLTLASCTD-LSALPDTIGNLSNLNFLDI-------SECLN--------IQELPE 741
+L L++ T L + NL NL LD+ S+C N +Q L
Sbjct: 324 FPSLTHLSIKGNTKRLELGTGCLENLENLRELDLSHDDIETSDCCNLQLRNLSHLQSLNL 383
Query: 742 RIGELCSLKTLCLKGCSMFEL 762
E SLKT K C EL
Sbjct: 384 SYNEPLSLKTEAFKECPQLEL 404
>pdb|3E6J|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor (Vlr)
Rbc36 In Complex With H-Trisaccharide
Length = 229
Score = 30.0 bits (66), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 34/60 (56%), Gaps = 3/60 (5%)
Query: 648 DAFPNLLEIDIDYCNDLIELPDGLCD-IVSIKKLRITNCHKLSALPEGIGKLVNLQMLTL 706
D+ L +D+ N L LP + D +V +K+L + C+KL+ LP GI +L +L L L
Sbjct: 85 DSLTQLTVLDLGT-NQLTVLPSAVFDRLVHLKELFMC-CNKLTELPRGIERLTHLTHLAL 142
>pdb|3J16|B Chain B, Models Of Ribosome-Bound Dom34p And Rli1p And Their
Ribosomal Binding Partners
Length = 608
Score = 29.6 bits (65), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 44/92 (47%), Gaps = 15/92 (16%)
Query: 189 QVIVVSAPGGYGKTTLVKKLC---KDDQVLGKFKDNIFFVTVSQTPNVKGIVQKVYQHK- 244
+++V+ G GKTTL+K L K D+ K N+ P G V++++ K
Sbjct: 379 EILVMMGENGTGKTTLIKLLAGALKPDEGQDIPKLNVSMKPQKIAPKFPGTVRQLFFKKI 438
Query: 245 --GYAVPEFQTDEDAINDLERLLKPIRPEAIL 274
+ P+FQTD ++KP+R + I+
Sbjct: 439 RGQFLNPQFQTD---------VVKPLRIDDII 461
>pdb|1B0N|A Chain A, Sinr ProteinSINI PROTEIN COMPLEX
Length = 111
Score = 29.6 bits (65), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 29/89 (32%), Positives = 45/89 (50%), Gaps = 11/89 (12%)
Query: 21 AVSEAKDKAVMFKDLLEQLESTLQNSTPMIKEIEKLNQVLDLP-------KHETDTLIEM 73
++SE +KA + K L +E LQ + P I+ +EK++ VLD+ KHET+ ++
Sbjct: 16 SLSELAEKAGVAKSYLSSIERNLQ-TNPSIQFLEKVSAVLDVSVHTLLDEKHETEYDGQL 74
Query: 74 MRRGEHLVHKC--SRVKWNCFKRY-DYAK 99
E LV S V F+ + DY K
Sbjct: 75 DSEWEKLVRDAMTSGVSKKQFREFLDYQK 103
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 0.137 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,655,317
Number of Sequences: 62578
Number of extensions: 999736
Number of successful extensions: 2720
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 24
Number of HSP's that attempted gapping in prelim test: 2669
Number of HSP's gapped (non-prelim): 54
length of query: 814
length of database: 14,973,337
effective HSP length: 107
effective length of query: 707
effective length of database: 8,277,491
effective search space: 5852186137
effective search space used: 5852186137
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)