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= 039126
(295 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 = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 40/122 (32%), Positives = 61/122 (50%), Gaps = 6/122 (4%)
Query: 36 QRLVNLKSINLNHSEHLTEIPSLSLATNLESLNFQRYTSLLETHSSIRHLNKFVARNLKH 95
Q LVNL+S+ L + + S++ NL+SL R + L +I HL K +L+
Sbjct: 180 QGLVNLQSLRLEWTGIRSLPASIANLQNLKSLKI-RNSPLSALGPAIHHLPKLEELDLRG 238
Query: 96 CRSLTNLSTSIHLES-LKKLILSGCSNLMSFP---ELFYNIKELSLDGTA-INELPSSIE 150
C +L N + LK+LIL CSNL++ P +++L L G ++ LPS I
Sbjct: 239 CTALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSLIA 298
Query: 151 YL 152
L
Sbjct: 299 QL 300
>pdb|1CB8|A Chain A, Chondroitinase Ac Lyase From Flavobacterium Heparinum
Length = 678
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 26/99 (26%), Positives = 46/99 (46%), Gaps = 3/99 (3%)
Query: 36 QRLVNLKSINLNHSEHLTEIPSLSLATNLESLNFQRYTSLLETHSSIRHLNKFVARNLKH 95
+RL+ K I+L H+E + + + +T + Y ++HL + N++
Sbjct: 281 KRLLVAKMIDLKHTEEWADAIARTDSTVAAGYKIEPYHHQFWNGDYVQHLRPAYSFNVRM 340
Query: 96 CRSLTNLSTSIHLESLKKLILS-GCSNL-MSFPELFYNI 132
T S S + E+L LS G +N+ + PE +YNI
Sbjct: 341 VSKRTRRSESGNKENLLGRYLSDGATNIQLRGPE-YYNI 378
>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 = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 42/74 (56%), Gaps = 4/74 (5%)
Query: 132 IKELSLDGTAINELPSSIEYLSKLVILNLGNSSRLEGLPSKICKLKSLQHLNLSCCSNLE 191
+ L L+G ++ ELP+ I+ LS L +L+L + +RL LP+++ L++ + +
Sbjct: 249 LTRLYLNGNSLTELPAEIKNLSNLRVLDLSH-NRLTSLPAELGSCFQLKYFYF-FDNMVT 306
Query: 192 SFPNELRNLFPCDL 205
+ P E NL C+L
Sbjct: 307 TLPWEFGNL--CNL 318
>pdb|1HM2|A Chain A, Active Site Of Chondroitinase Ac Lyase Revealed By The
Structure Of Enzyme-Oligosaccharide Complexes And
Mutagenesis
pdb|1HM3|A Chain A, Active Site Of Chondroitinase Ac Lyase Revealed By The
Structure Of Enzyme-Oligosaccharide Complexes And
Mutagenesis
pdb|1HMU|A Chain A, Active Site Of Chondroitinase Ac Lyase Revealed By The
Structure Of Enzyme-oligosaccharide Complexes And
Mutagenesis
pdb|1HMW|A Chain A, Active Site Of Chondroitinase Ac Lyase Revealed By The
Structure Of Enzyme-oligosaccharide Complexes And
Mutagenesis
Length = 700
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 26/99 (26%), Positives = 46/99 (46%), Gaps = 3/99 (3%)
Query: 36 QRLVNLKSINLNHSEHLTEIPSLSLATNLESLNFQRYTSLLETHSSIRHLNKFVARNLKH 95
+RL+ K I+L H+E + + + +T + Y ++HL + N++
Sbjct: 303 KRLLVAKMIDLKHTEEWADAIARTDSTVAAGYKIEPYHHQFWNGDYVQHLRPAYSFNVRM 362
Query: 96 CRSLTNLSTSIHLESLKKLILS-GCSNL-MSFPELFYNI 132
T S S + E+L LS G +N+ + PE +YNI
Sbjct: 363 VSKRTRRSESGNKENLLGRYLSDGATNIQLRGPE-YYNI 400
>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 = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 30/50 (60%), Gaps = 7/50 (14%)
Query: 107 HLESLKKLILSGCSNLMSFPELFYNIKELSLDGT---AINELPSSIEYLS 153
HLESL ++ C++L PEL ++K L +D A+++LP +EYL
Sbjct: 92 HLESL----VASCNSLTELPELPQSLKSLLVDNNNLKALSDLPPLLEYLG 137
>pdb|4FMZ|A Chain A, Crystal Structure Of An Internalin (Inlf) From Listeria
Monocytogenes Str. 4b F2365 At 1.91 A Resolution
pdb|4FMZ|B Chain B, Crystal Structure Of An Internalin (Inlf) From Listeria
Monocytogenes Str. 4b F2365 At 1.91 A Resolution
Length = 347
Score = 28.9 bits (63), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 27/94 (28%), Positives = 50/94 (53%), Gaps = 12/94 (12%)
Query: 91 RNLKHCRSLTNLSTSIHLESLKKLILSG--CSNLMSFPELFYNIKELSLDGTAINELPSS 148
R + S+T++ T LES+ KL+++G +++ E N++ L+L+G I ++ S
Sbjct: 26 RAVLQKASVTDVVTQEELESITKLVVAGEKVASIQGI-EYLTNLEYLNLNGNQITDI-SP 83
Query: 149 IEYLSKLVILNLGNSSRLEGLPSKICKLKSLQHL 182
+ L KL L +G +KI + +LQ+L
Sbjct: 84 LSNLVKLTNLYIG--------TNKITDISALQNL 109
>pdb|3RJ1|A Chain A, Architecture Of The Mediator Head Module
pdb|3RJ1|H Chain H, Architecture Of The Mediator Head Module
pdb|3RJ1|O Chain O, Architecture Of The Mediator Head Module
Length = 131
Score = 28.5 bits (62), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 205 LYDIEAHWCSSLETLSGLSIIFTKISRNTQS 235
L DIE CS L+ S ++ IF ++ R +S
Sbjct: 29 LNDIETQLCSXLQEASQVTFIFGELKRGNES 59
>pdb|3R84|A Chain A, Structure Of The Mediator Head Subcomplex Med1122
pdb|3R84|C Chain C, Structure Of The Mediator Head Subcomplex Med1122
pdb|3R84|E Chain E, Structure Of The Mediator Head Subcomplex Med1122
pdb|3R84|G Chain G, Structure Of The Mediator Head Subcomplex Med1122
pdb|3R84|I Chain I, Structure Of The Mediator Head Subcomplex Med1122
pdb|3R84|K Chain K, Structure Of The Mediator Head Subcomplex Med1122
pdb|3R84|M Chain M, Structure Of The Mediator Head Subcomplex Med1122
pdb|3R84|O Chain O, Structure Of The Mediator Head Subcomplex Med1122
pdb|3R84|Q Chain Q, Structure Of The Mediator Head Subcomplex Med1122
pdb|3R84|S Chain S, Structure Of The Mediator Head Subcomplex Med1122
pdb|3R84|U Chain U, Structure Of The Mediator Head Subcomplex Med1122
pdb|3R84|W Chain W, Structure Of The Mediator Head Subcomplex Med1122
Length = 86
Score = 28.5 bits (62), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 205 LYDIEAHWCSSLETLSGLSIIFTKISRNTQS 235
L DIE CS L+ S ++ IF ++ R +S
Sbjct: 10 LNDIETQLCSXLQEASQVTFIFGELKRGNES 40
>pdb|4GWP|A Chain A, Structure Of The Mediator Head Module From S. Cerevisiae
pdb|4GWQ|A Chain A, Structure Of The Mediator Head Module From S. Cerevisiae
In Complex With The Carboxy-Terminal Domain (Ctd) Of Rna
Polymerase Ii Rpb1 Subunit
Length = 115
Score = 28.1 bits (61), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 205 LYDIEAHWCSSLETLSGLSIIFTKISRNTQS 235
L DIE CS L+ S ++ IF ++ R +S
Sbjct: 13 LNDIETQLCSMLQEASQVTFIFGELKRGNES 43
>pdb|3V47|A Chain A, Crystal Structure Of The N-Tetminal Fragment Of Zebrafish
Tlr5 In Complex With Salmonella Flagellin
pdb|3V47|B Chain B, Crystal Structure Of The N-Tetminal Fragment Of Zebrafish
Tlr5 In Complex With Salmonella Flagellin
Length = 455
Score = 28.1 bits (61), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 28/104 (26%), Positives = 46/104 (44%), Gaps = 15/104 (14%)
Query: 51 HLTEIPSLSLATN----LESLNFQRYTSLLETHSSIRHLNKFVARNLKHCRSLTNLSTSI 106
H T++ L+LA N ++ F T LL+ + S L +R ++ L L S
Sbjct: 297 HFTDLEQLTLAQNEINKIDDNAFWGLTHLLKLNLSQNFLGSIDSRMFENLDKLEVLDLSY 356
Query: 107 -HLESLKKLILSGCSNLMSFPELFYNIKELSLDGTAINELPSSI 149
H+ +L G + + P N+KEL+LD + +P I
Sbjct: 357 NHIRAL------GDQSFLGLP----NLKELALDTNQLKSVPDGI 390
>pdb|3CVR|A Chain A, Crystal Structure Of The Full Length Ipah3
Length = 571
Score = 27.3 bits (59), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 4/41 (9%)
Query: 116 LSGCSNLMS-FPELFYNIKELSLDG---TAINELPSSIEYL 152
L C N +S PEL ++K L +D T + ELP+ +EY+
Sbjct: 105 LDACDNRLSTLPELPASLKHLDVDNNQLTXLPELPALLEYI 145
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
0.319 0.133 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,469,635
Number of Sequences: 62578
Number of extensions: 264487
Number of successful extensions: 837
Number of sequences better than 100.0: 36
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 32
Number of HSP's that attempted gapping in prelim test: 803
Number of HSP's gapped (non-prelim): 52
length of query: 295
length of database: 14,973,337
effective HSP length: 98
effective length of query: 197
effective length of database: 8,840,693
effective search space: 1741616521
effective search space used: 1741616521
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: 51 (24.3 bits)