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= 039899
(341 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3G06|A Chain A, The Salmonella Virulence Effector Ssph2 Functions As A
Novel E3 Ligase
Length = 622
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 28/65 (43%), Positives = 37/65 (56%), Gaps = 6/65 (9%)
Query: 35 LKELYLSKNRFFSLPASINLLSKLWIIELEECQRLQSLPQLPSNIEQVQV--NGCASLGT 92
L+EL +S N+ SLPA + L KLW +L SLP LPS ++++ V N ASL T
Sbjct: 143 LQELSVSDNQLASLPALPSELCKLWAYN----NQLTSLPMLPSGLQELSVSDNQLASLPT 198
Query: 93 LSHAL 97
L L
Sbjct: 199 LPSEL 203
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 41/80 (51%), Gaps = 11/80 (13%)
Query: 8 CSLTKLDISDCNLGE-GAIPSDIGNICSLKELYLSKNRFFSLPASINLLSKLWIIELEEC 66
L +L +SD L +PS+ L +L+ NR SLPA + L +L +
Sbjct: 181 SGLQELSVSDNQLASLPTLPSE------LYKLWAYNNRLTSLPALPSGLKELIV----SG 230
Query: 67 QRLQSLPQLPSNIEQVQVNG 86
RL SLP LPS ++++ V+G
Sbjct: 231 NRLTSLPVLPSELKELMVSG 250
Score = 32.3 bits (72), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 27/52 (51%), Gaps = 4/52 (7%)
Query: 33 CSLKELYLSKNRFFSLPASINLLSKLWIIELEECQRLQSLPQLPSNIEQVQV 84
LKEL +S NR SLP + L +L + RL SLP LPS + + V
Sbjct: 221 SGLKELIVSGNRLTSLPVLPSELKELMV----SGNRLTSLPMLPSGLLSLSV 268
Score = 31.6 bits (70), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 37/109 (33%), Positives = 50/109 (45%), Gaps = 23/109 (21%)
Query: 10 LTKLDISDCNLGE-GAIPSDI------GNICS--------LKELYLSKNRFFSLPASINL 54
+T L I D NL A+P ++ GN + L EL + N LPA +
Sbjct: 63 ITTLVIPDNNLTSLPALPPELRTLEVSGNQLTSLPVLPPGLLELSIFSNPLTHLPALPSG 122
Query: 55 LSKLWIIELEECQRLQSLPQLPSNIEQVQV--NGCASLGTLSHALKLCK 101
L KLWI +L SLP LP ++++ V N ASL L +LCK
Sbjct: 123 LCKLWIF----GNQLTSLPVLPPGLQELSVSDNQLASLPALPS--ELCK 165
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 32.3 bits (72), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 27/54 (50%)
Query: 21 GEGAIPSDIGNICSLKELYLSKNRFFSLPASINLLSKLWIIELEECQRLQSLPQ 74
G +P L+ L L++N +LPASI L++L + + C L LP+
Sbjct: 115 GLXELPDTXQQFAGLETLTLARNPLRALPASIASLNRLRELSIRACPELTELPE 168
Score = 31.6 bits (70), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 38/82 (46%), Gaps = 6/82 (7%)
Query: 2 PSLLGLCSLTKLDISDCNLGEGAIPSDIGNICSLKELYLSK-NRFFSLPASINLLSKLWI 60
P++ L L +LD+ C P G LK L L + +LP I+ L++L
Sbjct: 223 PAIHHLPKLEELDLRGCTALRN-YPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEK 281
Query: 61 IELEECQRLQSLP----QLPSN 78
++L C L LP QLP+N
Sbjct: 282 LDLRGCVNLSRLPSLIAQLPAN 303
>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 = 32.3 bits (72), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 29/43 (67%), Gaps = 2/43 (4%)
Query: 10 LTKLDISDCNLGEGAIPSDIGNICSLKELYLSKNRFFSLPASI 52
LT+L ++ +L E +P++I N+ +L+ L LS NR SLPA +
Sbjct: 249 LTRLYLNGNSLTE--LPAEIKNLSNLRVLDLSHNRLTSLPAEL 289
Score = 31.6 bits (70), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 13 LDISDCNLGEGAIPSDIGNICSLKELYLSKNRFFSLPASINLLSKLWIIELEECQRLQSL 72
LD+S NL I ++I L LYL+ N LPA I LS L +++L RL SL
Sbjct: 229 LDLS--NLQIFNISANIFKYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSH-NRLTSL 285
Query: 73 P 73
P
Sbjct: 286 P 286
>pdb|3K8G|A Chain A, Structure Of Crystal Form I Of Tp0453
pdb|3K8G|B Chain B, Structure Of Crystal Form I Of Tp0453
pdb|3K8H|A Chain A, Structure Of Crystal Form I Of Tp0453
pdb|3K8H|B Chain B, Structure Of Crystal Form I Of Tp0453
pdb|3K8I|A Chain A, Structure Of Crystal Form Iv Of Tp0453
pdb|3K8J|A Chain A, Structure Of Crystal Form Iii Of Tp0453
Length = 262
Score = 31.6 bits (70), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 34/124 (27%), Positives = 52/124 (41%), Gaps = 8/124 (6%)
Query: 71 SLPQLPSNIEQVQVNGCASLGTLSHALKLCKSIDVEVSKPIPHLSIVVPGSEISKCFRYQ 130
S P +N+ + +G AS T H + +S +VS P PH S V+ GS SK R
Sbjct: 75 SYPYAFTNLIFSRSDGWASTKT-EHGITYYESEHTDVSIPAPHFSCVIFGS--SKRERMS 131
Query: 131 KEDSAMA-----VTMPLFLRENEVVGYAMCCVFNVRKGSCGIKRLRSFPTHQLSCHKNAS 185
K S + P F +E G + ++ G I +L +FP L
Sbjct: 132 KMLSRLVNPDRPQLPPRFEKECTSEGTSQTVALYIKNGGHFITKLLNFPQLNLPLGAMEL 191
Query: 186 YMSS 189
Y+++
Sbjct: 192 YLTA 195
>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 = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/42 (45%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 7 LCSLTKLDISDCNLGEGAIPSDIGNICSLKELYLSKNRFFSL 48
L +LT LD+S C L E P+ ++ SL+ L +S N FFSL
Sbjct: 469 LRNLTFLDLSQCQL-EQLSPTAFNSLSSLQVLNMSHNNFFSL 509
>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 = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/42 (45%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 7 LCSLTKLDISDCNLGEGAIPSDIGNICSLKELYLSKNRFFSL 48
L +LT LD+S C L E P+ ++ SL+ L +S N FFSL
Sbjct: 493 LRNLTFLDLSQCQL-EQLSPTAFNSLSSLQVLNMSHNNFFSL 533
>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 = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/42 (45%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 7 LCSLTKLDISDCNLGEGAIPSDIGNICSLKELYLSKNRFFSL 48
L +LT LD+S C L E P+ ++ SL+ L +S N FFSL
Sbjct: 174 LRNLTFLDLSQCQL-EQLSPTAFNSLSSLQVLNMSHNNFFSL 214
>pdb|1G9U|A Chain A, Crystal Structure Of Yopm-leucine Rich Effector Protein
From Yersinia Pestis
pdb|1JL5|A Chain A, Novel Molecular Architecture Of Yopm-A Leucine-Rich
Effector Protein From Yersinia Pestis
Length = 454
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 29/91 (31%), Positives = 45/91 (49%), Gaps = 19/91 (20%)
Query: 9 SLTKLDISD---CNLGE--------GAIPSDIGNIC----SLKELYLSKNRFFSLPASIN 53
SLT LD+S+ L E A ++I ++C SL+EL +S N+ LPA
Sbjct: 278 SLTFLDVSENIFSGLSELPPNLYYLNASSNEIRSLCDLPPSLEELNVSNNKLIELPALPP 337
Query: 54 LLSKLWIIELEECQRLQSLPQLPSNIEQVQV 84
L +L + L +P+LP N++Q+ V
Sbjct: 338 RLERL----IASFNHLAEVPELPQNLKQLHV 364
>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 = 1.7, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 3/68 (4%)
Query: 9 SLTKLDISDCNLGE-GAIPSDI-GNICSLKELYLSKNRFFSLPASINLLSKLWIIELEEC 66
SLT+L + D + +PS + + LKEL++ N+ LP I L+ L + L++
Sbjct: 86 SLTQLTVLDLGTNQLTVLPSAVFDRLVHLKELFMCCNKLTELPRGIERLTHLTHLALDQN 145
Query: 67 QRLQSLPQ 74
Q L+S+P
Sbjct: 146 Q-LKSIPH 152
Score = 28.5 bits (62), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 31/55 (56%), Gaps = 5/55 (9%)
Query: 26 PSDIGNICSLKELYLSKNRFFSLPASI-NLLSKLWIIELEECQRLQSLPQLPSNI 79
P ++ +LKELYL N+ +LP + + L++L +++L Q L LPS +
Sbjct: 57 PGVFDSLINLKELYLGSNQLGALPVGVFDSLTQLTVLDLGTNQ----LTVLPSAV 107
>pdb|2BNH|A Chain A, Porcine Ribonuclease Inhibitor
pdb|1DFJ|I Chain I, Ribonuclease Inhibitor Complexed With Ribonuclease A
Length = 457
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 26/39 (66%), Gaps = 3/39 (7%)
Query: 8 CSLTKLDISDCNLGE---GAIPSDIGNICSLKELYLSKN 43
C + KL + +C+L E G +PS + ++ +L+EL+LS N
Sbjct: 81 CKIQKLSLQNCSLTEAGCGVLPSTLRSLPTLRELHLSDN 119
>pdb|2Z7X|A Chain A, Crystal Structure Of The Tlr1-Tlr2 Heterodimer Induced By
Binding Of A Tri-Acylated Lipopeptide
Length = 549
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 28/39 (71%), Gaps = 2/39 (5%)
Query: 35 LKELYLSKNRFFSLPASINLLSKLWIIELEECQRLQSLP 73
LKELY+S+N+ +LP + +LL L ++++ Q L+S+P
Sbjct: 453 LKELYISRNKLMTLPDA-SLLPMLLVLKISRNQ-LKSVP 489
Score = 28.1 bits (61), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 12/73 (16%)
Query: 23 GAIPSDIGNICSLKELYLSKNRFFSLPASINLLSKLWIIELEECQRLQSLPQLPSNIEQV 82
+IPS G ++K L LS NR + S +L+ C LQ+L + I +
Sbjct: 18 NSIPS--GLTEAVKSLDLSNNRITYISNS----------DLQRCVNLQALVLTSNGINTI 65
Query: 83 QVNGCASLGTLSH 95
+ + +SLG+L H
Sbjct: 66 EEDSFSSLGSLEH 78
>pdb|3S30|A Chain A, Crystal Structure Of A Hypothetical Glycoside Hydrolase
(Bvu_0247) From Bacteroides Vulgatus Atcc 8482 At 2.46 A
Resolution
pdb|3S30|B Chain B, Crystal Structure Of A Hypothetical Glycoside Hydrolase
(Bvu_0247) From Bacteroides Vulgatus Atcc 8482 At 2.46 A
Resolution
Length = 354
Score = 29.3 bits (64), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 35/89 (39%), Gaps = 16/89 (17%)
Query: 250 YRHE------VVKCDHATNRWTRSIIDYNLNGNLCTRFIDHLCELCQNQVKLNNVWYRLD 303
Y HE V+ H T+ WTR +D+N +H + Q KL N Y +
Sbjct: 271 YEHENXVAAAVITDTHETSEWTRFELDFNY---------EHYGKTIDPQ-KLANGGYNVS 320
Query: 304 DYLDENQVEDFYQTTNQWTWFIDRLSEFC 332
L ++ D +Q T ID L C
Sbjct: 321 IVLSASKDGDVFQGAPGSTLLIDDLELVC 349
>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 = 28.9 bits (63), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 19/43 (44%), Positives = 25/43 (58%), Gaps = 2/43 (4%)
Query: 32 ICSLKELYLSKNRFFSLPASI-NLLSKLWIIELEECQRLQSLP 73
+ SL +LYL N+ SLP + N L+ L + L Q LQSLP
Sbjct: 51 LTSLTQLYLGGNKLQSLPNGVFNKLTSLTYLNLSTNQ-LQSLP 92
>pdb|2Z80|A Chain A, Crystal Structure Of The Tlr1-Tlr2 Heterodimer Induced By
Binding Of A Tri-Acylated Lipopeptide
pdb|2Z80|B Chain B, Crystal Structure Of The Tlr1-Tlr2 Heterodimer Induced By
Binding Of A Tri-Acylated Lipopeptide
Length = 353
Score = 28.1 bits (61), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 12/72 (16%)
Query: 24 AIPSDIGNICSLKELYLSKNRFFSLPASINLLSKLWIIELEECQRLQSLPQLPSNIEQVQ 83
+IPS G ++K L LS NR + S +L+ C LQ+L + I ++
Sbjct: 45 SIPS--GLTEAVKSLDLSNNRITYISNS----------DLQRCVNLQALVLTSNGINTIE 92
Query: 84 VNGCASLGTLSH 95
+ +SLG+L H
Sbjct: 93 EDSFSSLGSLEH 104
>pdb|2P1M|B Chain B, Tir1-ask1 Complex Structure
pdb|2P1N|B Chain B, Mechanism Of Auxin Perception By The Tir1 Ubiqutin Ligase
pdb|2P1N|E Chain E, Mechanism Of Auxin Perception By The Tir1 Ubiqutin Ligase
pdb|2P1O|B Chain B, Mechanism Of Auxin Perception By The Tir1 Ubiquitin Ligase
pdb|2P1P|B Chain B, Mechanism Of Auxin Perception By The Tir1 Ubiquitin Ligase
pdb|2P1Q|B Chain B, Mechanism Of Auxin Perception By The Tir1 Ubiquitin Ligase
pdb|3C6N|B Chain B, Small Molecule Agonists And Antagonists Of F-Box Protein-
Substrate Interactions In Auxin Perception And Signaling
pdb|3C6O|B Chain B, Small Molecule Agonists And Antagonists Of F-Box
Protein-Substrate Interactions In Auxin Perception And
Signaling
pdb|3C6P|B Chain B, Small Molecule Agonists And Antagonists Of F-Box Protein-
Substrate Interactions In Auxin Perception And Signaling
Length = 594
Score = 28.1 bits (61), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 24/38 (63%)
Query: 4 LLGLCSLTKLDISDCNLGEGAIPSDIGNICSLKELYLS 41
L G SL KL+I DC G+ A+ ++ + +++ L++S
Sbjct: 477 LSGCDSLRKLEIRDCPFGDKALLANASKLETMRSLWMS 514
>pdb|2BMB|A Chain A, X-Ray Structure Of The Bifunctional 6-Hydroxymethyl-7,8-
Dihydroxypterin Pyrophosphokinase Dihydropteroate
Synthase From Saccharomyces Cerevisiae
Length = 545
Score = 27.7 bits (60), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 3/75 (4%)
Query: 43 NRFFSLPASINLLSKLWIIELEECQRLQSLPQLPSNIEQVQVNGCASLGTL---SHALKL 99
+RF + ++ LLS+ ++L + + + +NGC + TL S LKL
Sbjct: 31 DRFKHIQMALQLLSREKTVKLRNISSIFESEPMYFKDQTPFMNGCVEVETLLTPSELLKL 90
Query: 100 CKSIDVEVSKPIPHL 114
CK I+ E + + H
Sbjct: 91 CKKIEYEELQRVKHF 105
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
0.322 0.137 0.439
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,515,435
Number of Sequences: 62578
Number of extensions: 434068
Number of successful extensions: 898
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 872
Number of HSP's gapped (non-prelim): 44
length of query: 341
length of database: 14,973,337
effective HSP length: 100
effective length of query: 241
effective length of database: 8,715,537
effective search space: 2100444417
effective search space used: 2100444417
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: 52 (24.6 bits)