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= 048083
(692 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2O6S|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors B59
pdb|2O6S|B Chain B, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors B59
Length = 208
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 37/105 (35%), Positives = 53/105 (50%), Gaps = 5/105 (4%)
Query: 362 LVLLTVLDLEGVYKPKLSDHVIGKLLHLSYLGLRSTFIDSLPNSV-GNLRYLETLDVKHT 420
L LT L L G L + V KL L+YL L + + SLPN V L L+ L +
Sbjct: 51 LTSLTQLYLGGNKLQSLPNGVFNKLTSLTYLNLSTNQLQSLPNGVFDKLTQLKELALNTN 110
Query: 421 KLRYLPDSIW-KAKKLQ--HLYLNWIHSAISWLNFSSLNNLQTLW 462
+L+ LPD ++ K +L+ LY N + S + F L +LQ +W
Sbjct: 111 QLQSLPDGVFDKLTQLKDLRLYQNQLKSVPDGV-FDRLTSLQYIW 154
Score = 34.3 bits (77), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 366 TVLDLEGVYKPKLSDHVIGKLLHLSYLGLRSTFIDSLPNSVGN-LRYLETLDVKHTKLRY 424
T LDLE L + V +L L+ L L + SLPN V N L L L++ +L+
Sbjct: 31 TYLDLETNSLKSLPNGVFDELTSLTQLYLGGNKLQSLPNGVFNKLTSLTYLNLSTNQLQS 90
Query: 425 LPDSIW-KAKKLQHLYLN 441
LP+ ++ K +L+ L LN
Sbjct: 91 LPNGVFDKLTQLKELALN 108
>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 = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 38/105 (36%), Positives = 52/105 (49%), Gaps = 3/105 (2%)
Query: 360 RGLVLLTVLDLEGVYKPKLSDHVIGKLLHLSYLGLRSTFIDSLPNSV-GNLRYLETLDVK 418
RGL LT L+L+ LS V L L LGL + + SLP V +L L+ L +
Sbjct: 56 RGLTKLTWLNLDYNQLQTLSAGVFDDLTELGTLGLANNQLASLPLGVFDHLTQLDKLYLG 115
Query: 419 HTKLRYLPDSIW-KAKKLQHLYLNWIH-SAISWLNFSSLNNLQTL 461
+L+ LP ++ + KL+ L LN +I F L NLQTL
Sbjct: 116 GNQLKSLPSGVFDRLTKLKELRLNTNQLQSIPAGAFDKLTNLQTL 160
>pdb|3M18|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor
Vlra.R2.1 In Complex With Hen Egg Lysozyme
Length = 251
Score = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 38/105 (36%), Positives = 52/105 (49%), Gaps = 3/105 (2%)
Query: 360 RGLVLLTVLDLEGVYKPKLSDHVIGKLLHLSYLGLRSTFIDSLPNSV-GNLRYLETLDVK 418
RGL LT L+L+ LS V L L LGL + + SLP V +L L+ L +
Sbjct: 56 RGLTKLTWLNLDYNQLQTLSAGVFDDLTELGTLGLANNQLASLPLGVFDHLTQLDKLYLG 115
Query: 419 HTKLRYLPDSIW-KAKKLQHLYLNWIH-SAISWLNFSSLNNLQTL 461
+L+ LP ++ + KL+ L LN +I F L NLQTL
Sbjct: 116 GNQLKSLPSGVFDRLTKLKELRLNTNQLQSIPAGAFDKLTNLQTL 160
>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 = 38.9 bits (89), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 31/89 (34%), Positives = 47/89 (52%), Gaps = 5/89 (5%)
Query: 378 LSDHVIGKLLHLSYLGLRSTFIDSLPNSV-GNLRYLETLDVKHTKLRYLPDSIW-KAKKL 435
L D V KL +L+YL L + SLP V L L LD+ + +L+ LP+ ++ K +L
Sbjct: 124 LPDGVFDKLTNLTYLNLAHNQLQSLPKGVFDKLTNLTELDLSYNQLQSLPEGVFDKLTQL 183
Query: 436 Q--HLYLNWIHSAISWLNFSSLNNLQTLW 462
+ LY N + S + F L +LQ +W
Sbjct: 184 KDLRLYQNQLKSVPDGV-FDRLTSLQYIW 211
>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 = 36.6 bits (83), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 52/243 (21%), Positives = 103/243 (42%), Gaps = 21/243 (8%)
Query: 368 LDLEGVYKPKL----SDHVIGKLLHLSYLGLRSTFIDSLPNSVGNLRYLETLDVKHTKLR 423
LDL G+ PK S L+ Y+G + + +P ++ L L L + HT +
Sbjct: 55 LDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTNVS 114
Query: 424 -YLPDSIWKAKKLQHLYLNWIHSAISWLNFSSLNNLQTLWGLSMGDDSLFNQTFD----F 478
+PD + + K L + L++ ++A+S S+++L L G++ + + D F
Sbjct: 115 GAIPDFLSQIKTL--VTLDFSYNALSGTLPPSISSLPNLVGITFDGNRISGAIPDSYGSF 172
Query: 479 TKLASLRKLGVKCYSQRVIDSIAELVSRSTRLQSLKLVYAWRDDYSDIPFKAQANLQELY 538
+KL + + + ++ + A L L + L + + + F + N Q+++
Sbjct: 173 SKLFTSMTISRNRLTGKIPPTFANL-----NLAFVDLSRNMLEGDASVLFGSDKNTQKIH 227
Query: 539 LRGALRMFSAKTSSFPRNLKIVTLSMSRLYWDPMEALEKLCHLNILRI-----IGEAYEG 593
L F +NL + L +R+Y + L +L L+ L + GE +G
Sbjct: 228 LAKNSLAFDLGKVGLSKNLNGLDLRNNRIYGTLPQGLTQLKFLHSLNVSFNNLCGEIPQG 287
Query: 594 KKM 596
+
Sbjct: 288 GNL 290
>pdb|4FHO|A Chain A, Crystal Structure Of An Internalin C2 (Inlc2) From
Listeria Monocytogenes Str. 4b F2365 At 1.90 A
Resolution
pdb|4FHO|B Chain B, Crystal Structure Of An Internalin C2 (Inlc2) From
Listeria Monocytogenes Str. 4b F2365 At 1.90 A
Resolution
Length = 231
Score = 36.2 bits (82), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 41/136 (30%), Positives = 62/136 (45%), Gaps = 17/136 (12%)
Query: 405 SVGNLRYLETLDVKHTKLRYLPDSIWKAKKLQHLYLNWIHSAISWLNFSSLNNLQTLWGL 464
++ L+ ++TLD+ T++ + + LQ LYL+ N S L L L L
Sbjct: 108 AIAGLQSIKTLDLTSTQITDV-TPLAGLSNLQVLYLDLNQ----ITNISPLAGLTNLQYL 162
Query: 465 SMGDDSLFNQTFDFTKLASLRKLGVKCYSQRVIDSIAELVSRSTRLQSLKLVYAWRDDYS 524
S+G+ NQ D T LA+L KL I I+ L S L +L V+ + S
Sbjct: 163 SIGN----NQVNDLTPLANLSKLTTLRADDNKISDISPLAS----LPNLIEVHLKDNQIS 214
Query: 525 DI-PFKAQANLQELYL 539
D+ P ANL L++
Sbjct: 215 DVSPL---ANLSNLFI 227
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 1/74 (1%)
Query: 367 VLDLEGVYKPKLSDHVIGKLLHLSYLGLRSTFIDSLPNSVGNLRYLETLDVKHTKLRYLP 426
L+L V P+ D +L HL + + + + LP++ LETL + LR LP
Sbjct: 85 ALELRSVPLPQFPDQAF-RLSHLQHXTIDAAGLXELPDTXQQFAGLETLTLARNPLRALP 143
Query: 427 DSIWKAKKLQHLYL 440
SI +L+ L +
Sbjct: 144 ASIASLNRLRELSI 157
Score = 34.7 bits (78), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 44/157 (28%), Positives = 72/157 (45%), Gaps = 22/157 (14%)
Query: 360 RGLVLLTVLDLEGVYKPKLSDHVIGK---LLHLSYLGLRSTFIDSLPNSVGNLRYLETLD 416
R L + +L + +P S G+ L++L L L T I SLP S+ NL+ L++L
Sbjct: 153 RELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRLEWTGIRSLPASIANLQNLKSLK 212
Query: 417 VKHTKLRYLPDSIWKAKKLQHLYLNWIHSAISWLNFSSLNNLQTLWG-------LSMGDD 469
++++ L L +I KL+ L L ++L N ++G L + D
Sbjct: 213 IRNSPLSALGPAIHHLPKLEELDLR---------GCTALRNYPPIFGGRAPLKRLILKDC 263
Query: 470 S-LFNQTFDFTKLASLRKLGVK-CYS-QRVIDSIAEL 503
S L D +L L KL ++ C + R+ IA+L
Sbjct: 264 SNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSLIAQL 300
>pdb|3RFJ|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 279
Score = 35.0 bits (79), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 25/66 (37%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 378 LSDHVIGKLLHLSYLGLRSTFIDSLPNSV-GNLRYLETLDVKHTKLRYLPDSIW-KAKKL 435
L D V KL +L+YL L + SLP V L L LD+ + +L+ LP+ ++ K +L
Sbjct: 124 LPDGVFDKLTNLTYLYLYHNQLQSLPKGVFDKLTNLTRLDLDNNQLQSLPEGVFDKLTQL 183
Query: 436 QHLYLN 441
+ L LN
Sbjct: 184 KQLSLN 189
>pdb|2O6R|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors B61
Length = 177
Score = 34.3 bits (77), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 34/101 (33%), Positives = 48/101 (47%), Gaps = 5/101 (4%)
Query: 366 TVLDLEGVYKPKLSDHVIGKLLHLSYLGLRSTFIDSLPNSV-GNLRYLETLDVKHTKLRY 424
T L+LE L V KL L+ L L I SLP+ V L L L + KL+
Sbjct: 31 TRLELESNKLQSLPHGVFDKLTQLTKLSLSQNQIQSLPDGVFDKLTKLTILYLHENKLQS 90
Query: 425 LPDSIW-KAKKLQHLYL--NWIHSAISWLNFSSLNNLQTLW 462
LP+ ++ K +L+ L L N + S + F L +LQ +W
Sbjct: 91 LPNGVFDKLTQLKELALDTNQLKSVPDGI-FDRLTSLQKIW 130
>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 = 34.3 bits (77), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 39/80 (48%), Gaps = 2/80 (2%)
Query: 383 IGKLLHLSYLGLRSTFIDSLPNSVGNLRYLETLDVKHTKLRYLPDSIWKAKKLQHLY-LN 441
I K L+ L L + LP + NL L LD+ H +L LP + +L++ Y +
Sbjct: 243 IFKYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFD 302
Query: 442 WIHSAISWLNFSSLNNLQTL 461
+ + + W F +L NLQ L
Sbjct: 303 NMVTTLPW-EFGNLCNLQFL 321
>pdb|4IFD|H Chain H, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 361
Score = 33.1 bits (74), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 9/53 (16%)
Query: 337 FDNRIYCSPAIEISTFLDKIISNRGLVLLTVLDLEGVYKPKLSDHVIGKLLHL 389
DN Y S A +S NR LL+V+ L+G Y P+ DHV+G++ +
Sbjct: 78 LDNMTYSSVAGTVSRV------NR---LLSVIPLKGRYAPETGDHVVGRIAEV 121
>pdb|3E6J|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor (Vlr)
Rbc36 In Complex With H-Trisaccharide
Length = 229
Score = 32.7 bits (73), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 36/80 (45%), Gaps = 1/80 (1%)
Query: 362 LVLLTVLDLEGVYKPKLSDHVIGKLLHLSYLGLRSTFIDSLPNSVGNLRYLETLDVKHTK 421
L LTVLDL L V +L+HL L + + LP + L +L L + +
Sbjct: 87 LTQLTVLDLGTNQLTVLPSAVFDRLVHLKELFMCCNKLTELPRGIERLTHLTHLALDQNQ 146
Query: 422 LRYLPDSIW-KAKKLQHLYL 440
L+ +P + + L H YL
Sbjct: 147 LKSIPHGAFDRLSSLTHAYL 166
>pdb|2O6Q|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors A29
Length = 270
Score = 32.3 bits (72), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 51/185 (27%), Positives = 79/185 (42%), Gaps = 27/185 (14%)
Query: 415 LDVKHTKLRYLPDSIW-KAKKLQHLYLN--WIHSAISWLNFSSLNNLQTLWGLSMGDDSL 471
LD++ KL LP + + KL+ LYLN + + + + F L NL+TLW +L
Sbjct: 42 LDLQSNKLSSLPSKAFHRLTKLRLLYLNDNKLQTLPAGI-FKELKNLETLWVTDNKLQAL 100
Query: 472 FNQTFD-FTKLASLR--KLGVKCYSQRVIDSIAELVSRSTRLQSLKLVYAWRDDYSDIPF 528
FD LA LR + +K RV DS+ T+L L L Y F
Sbjct: 101 PIGVFDQLVNLAELRLDRNQLKSLPPRVFDSL-------TKLTYLSLGYNELQSLPKGVF 153
Query: 529 KAQANLQELYLRGALRMFSAKTSSFPRN-------LKIVTLSMSRLYWDPMEALEKLCHL 581
+L+E LR+++ + P LK + L ++L P A + L L
Sbjct: 154 DKLTSLKE------LRLYNNQLKRVPEGAFDKLTELKTLKLDNNQLKRVPEGAFDSLEKL 207
Query: 582 NILRI 586
+L++
Sbjct: 208 KMLQL 212
>pdb|2Z7X|B Chain B, Crystal Structure Of The Tlr1-Tlr2 Heterodimer Induced By
Binding Of A Tri-Acylated Lipopeptide
Length = 520
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 392 LGLRSTFIDSLPNSVGNLRYLETLDVKHTKLRYLPDSIWKAKKLQHLYLNWIHS 445
L L S I S+P V L L+ L+V +L+ +PD I+ +L L W+H+
Sbjct: 426 LDLHSNKIKSIPKQVVKLEALQELNVASNQLKSVPDGIF--DRLTSLQKIWLHT 477
>pdb|3A79|B Chain B, Crystal Structure Of Tlr2-Tlr6-Pam2csk4 Complex
Length = 562
Score = 31.2 bits (69), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 30/53 (56%), Gaps = 2/53 (3%)
Query: 392 LGLRSTFIDSLPNSVGNLRYLETLDVKHTKLRYLPDSIWKAKKLQHLYLNWIH 444
L L + I S+P V +L+ L+ L+V +L+ +PD ++ +L L W+H
Sbjct: 455 LDLHNNRIMSIPKDVTHLQALQELNVASNQLKSVPDGVF--DRLTSLQYIWLH 505
>pdb|4ES1|A Chain A, Double-Stranded Endonuclease Activity In B. Halodurans
Clustered Regularly Interspaced Short Palindromic
Repeats (Crispr)-Associated Cas2 Protein
pdb|4ES2|A Chain A, Double-Stranded Endonuclease Activity In B. Halodurans
Clustered Regularly Interspaced Short Palindromic
Repeats (Crispr)-Associated Cas2 Protein
pdb|4ES3|A Chain A, Double-Stranded Endonuclease Activity In B. Halodurans
Clustered Regularly Interspaced Short Palindromic
Repeats (Crispr)-Associated Cas2 Protein
Length = 100
Score = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 474 QTFDFTKLASLRKLGVKC--YSQRVIDSIAELVSRSTRLQSLKL 515
QT LRK+ C Y QRV +S+ E + ST+L SLKL
Sbjct: 14 QTSSMGGTKRLRKVAKACQNYGQRVQNSVFECIVDSTQLTSLKL 57
>pdb|1PUJ|A Chain A, Structure Of B. Subtilis Ylqf Gtpase
Length = 282
Score = 30.0 bits (66), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 34/66 (51%), Gaps = 3/66 (4%)
Query: 365 LTVLDLEGVYKPKLSDHVIGKLLHLSYLG-LRSTFIDSLPNSVGNLRYLETLDVKHTKLR 423
L +LD G+ PK D ++G L L+ G ++ + I+ +V LR+LE + K R
Sbjct: 167 LELLDTPGILWPKFEDELVG--LRLAVTGAIKDSIINLQDVAVFGLRFLEEHYPERLKER 224
Query: 424 YLPDSI 429
Y D I
Sbjct: 225 YGLDEI 230
>pdb|3G3B|A Chain A, Structure Of A Lamprey Variable Lymphocyte Receptor Mutant
In Complex With A Protein Antigen
pdb|3G3B|C Chain C, Structure Of A Lamprey Variable Lymphocyte Receptor Mutant
In Complex With A Protein Antigen
pdb|3G3B|E Chain E, Structure Of A Lamprey Variable Lymphocyte Receptor Mutant
In Complex With A Protein Antigen
pdb|3G3B|G Chain G, Structure Of A Lamprey Variable Lymphocyte Receptor Mutant
In Complex With A Protein Antigen
Length = 170
Score = 29.6 bits (65), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 39/122 (31%), Positives = 53/122 (43%), Gaps = 21/122 (17%)
Query: 337 FDNRIYCSPAIEISTFLDKIISNRGLVLLTVLDLEGVYKPKLSDHVIGKLLHLSYLGLRS 396
+DNRI T L+ + +R L LT LDL+ L V KL L+ L L
Sbjct: 38 YDNRI---------TKLEPGVFDR-LTQLTRLDLDNNQLTVLPAGVFDKLTQLTQLSLND 87
Query: 397 TFIDSLP-NSVGNLRYLETLDVKHTKLRYLPDSIWKAKKLQHLYLN-WIHSAISWLNFSS 454
+ S+P + NLR L + +L ++ W LYL+ WI S WL F
Sbjct: 88 NQLKSIPRGAFDNLRSLTHI--------WLLNNPWDCACSDILYLSRWI-SQHPWLVFGY 138
Query: 455 LN 456
LN
Sbjct: 139 LN 140
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
0.320 0.135 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,672,534
Number of Sequences: 62578
Number of extensions: 788909
Number of successful extensions: 1837
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 22
Number of HSP's that attempted gapping in prelim test: 1814
Number of HSP's gapped (non-prelim): 43
length of query: 692
length of database: 14,973,337
effective HSP length: 106
effective length of query: 586
effective length of database: 8,340,069
effective search space: 4887280434
effective search space used: 4887280434
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: 55 (25.8 bits)