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= 047461
(312 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 = 55.1 bits (131), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 42/126 (33%), Positives = 59/126 (46%), Gaps = 22/126 (17%)
Query: 123 PTLMPRLNKLVTLNLRGSKSLKSLPSGIFNLEFLTKLDLSGCSKLKRLPEISSGNISWLF 182
P + L L +L +R S L +L I +L L +LDL GC+ L+ P I G
Sbjct: 199 PASIANLQNLKSLKIRNSP-LSALGPAIHHLPKLEELDLRGCTALRNYPPIFGGR----- 252
Query: 183 LRGIAIEELPSSIERLLRLGYLDLSDCKRLKSLPSSLYRLKSLGVLSLCGCSNLQRLPEC 242
+ ++RL+ L DC L +LP ++RL L L L GC NL RLP
Sbjct: 253 ----------APLKRLI------LKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSL 296
Query: 243 LGQLSS 248
+ QL +
Sbjct: 297 IAQLPA 302
Score = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 60/214 (28%), Positives = 83/214 (38%), Gaps = 41/214 (19%)
Query: 123 PTLMPRLNKLVTLNLRGSKSLKSLPSGIFNLEFLTKLDLSGCSKLKRLPEI-----SSG- 176
P + L TL L L++LP+ I +L L +L + C +L LPE +SG
Sbjct: 120 PDTXQQFAGLETLTL-ARNPLRALPASIASLNRLRELSIRACPELTELPEPLASTDASGE 178
Query: 177 -----NISWLFLRGIAIEELPSS-----------------------IERLLRLGYLDLSD 208
N+ L L I LP+S I L +L LDL
Sbjct: 179 HQGLVNLQSLRLEWTGIRSLPASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRG 238
Query: 209 CKRLKSLPSSLYRLKSLGVLSLCGCSNLQRLPECLGQLSSPITFNLAK-TNIERIPESII 267
C L++ P L L L CSNL LP + +L+ +L N+ R+P I
Sbjct: 239 CTALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSLIA 298
Query: 268 QLFVSGYLLLSYGIVEDTLRIQHTNHTPAVRWQE 301
QL + +L V L+ Q H P R E
Sbjct: 299 QLPANCIIL-----VPPHLQAQLDQHRPVARPAE 327
Score = 30.8 bits (68), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 27/94 (28%), Positives = 40/94 (42%), Gaps = 10/94 (10%)
Query: 185 GIAIEELPSSIERLLRLGYLDLSDCKRLKSLPSSLYRLKSLGVLSLCGCSNLQRLPECLG 244
+ ELP + ++ L L L+ L++LP+S+ L L LS+ C L LPE L
Sbjct: 113 AAGLXELPDTXQQFAGLETLTLARNP-LRALPASIASLNRLRELSIRACPELTELPEPLA 171
Query: 245 QLSSP---------ITFNLAKTNIERIPESIIQL 269
+ + L T I +P SI L
Sbjct: 172 STDASGEHQGLVNLQSLRLEWTGIRSLPASIANL 205
>pdb|3E6J|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor (Vlr)
Rbc36 In Complex With H-Trisaccharide
Length = 229
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 38/92 (41%), Positives = 51/92 (55%), Gaps = 7/92 (7%)
Query: 139 GSKSLKSLPSGIFN-LEFLTKLDLSGCSKLKRLPEISSG---NISWLFLRGIAIEELPSS 194
GS L +LP G+F+ L LT LDL G ++L LP ++ LF+ + ELP
Sbjct: 72 GSNQLGALPVGVFDSLTQLTVLDL-GTNQLTVLPSAVFDRLVHLKELFMCCNKLTELPRG 130
Query: 195 IERLLRLGYLDLSDCKRLKSLPSSLY-RLKSL 225
IERL L +L L D +LKS+P + RL SL
Sbjct: 131 IERLTHLTHLAL-DQNQLKSIPHGAFDRLSSL 161
>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 = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 41/153 (26%), Positives = 75/153 (49%), Gaps = 29/153 (18%)
Query: 123 PTLMPRLNKLVTLNLRGSKSLKSLPSGIFNLEFLTKLDLSGCSKLKRLPEISSGNISWLF 182
PT +P + L + SLKSLP+G+F+ E++S ++ L+
Sbjct: 23 PTGIPAQTTYLDLE---TNSLKSLPNGVFD-------------------ELTS--LTQLY 58
Query: 183 LRGIAIEELPSSI-ERLLRLGYLDLSDCKRLKSLPSSLY-RLKSLGVLSLCGCSNLQRLP 240
L G ++ LP+ + +L L YL+LS +L+SLP+ ++ +L L L+L + LQ LP
Sbjct: 59 LGGNKLQSLPNGVFNKLTSLTYLNLST-NQLQSLPNGVFDKLTQLKELAL-NTNQLQSLP 116
Query: 241 E-CLGQLSSPITFNLAKTNIERIPESIIQLFVS 272
+ +L+ L + ++ +P+ + S
Sbjct: 117 DGVFDKLTQLKDLRLYQNQLKSVPDGVFDRLTS 149
Score = 35.0 bits (79), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 45/137 (32%), Positives = 71/137 (51%), Gaps = 16/137 (11%)
Query: 117 IAKIPNPTLMPRLNKLVTLNLRGSKSLKSLPSGIFN-LEFLTKLDLSGCSKLKRLPEISS 175
+ +PN + L L L L G+K L+SLP+G+FN L LT L+LS ++L+ LP
Sbjct: 40 LKSLPN-GVFDELTSLTQLYLGGNK-LQSLPNGVFNKLTSLTYLNLS-TNQLQSLPNGVF 96
Query: 176 GNISW---LFLRGIAIEELPSSI-ERLLRLGYLDLSDCKRLKSLPSSLY-RLKSLGVLSL 230
++ L L ++ LP + ++L +L L L +LKS+P ++ RL SL + L
Sbjct: 97 DKLTQLKELALNTNQLQSLPDGVFDKLTQLKDLRLYQ-NQLKSVPDGVFDRLTSLQYIWL 155
Query: 231 ------CGCSNLQRLPE 241
C C ++ L E
Sbjct: 156 HDNPWDCTCPGIRYLSE 172
>pdb|2Z63|A Chain A, Crystal Structure Of The Tv8 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 570
Score = 33.1 bits (74), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 37/138 (26%), Positives = 56/138 (40%), Gaps = 15/138 (10%)
Query: 145 SLPSGIFNLEFLTKLDLSGCSKLKRLPEISSGNISWLFLRGIAIEELPSSIERLLRLGYL 204
++ S LE L LD S LK++ E S +L LR + ++ + R+ G
Sbjct: 387 TMSSNFLGLEQLEHLDFQH-SNLKQMSEFSV----FLSLRNLIYLDISHTHTRVAFNGIF 441
Query: 205 D-LSDCKRLKS---------LPSSLYRLKSLGVLSLCGCSNLQRLPECLGQLSSPITFNL 254
+ LS + LK LP L++L L L C Q P LSS N+
Sbjct: 442 NGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNM 501
Query: 255 AKTNIERIPESIIQLFVS 272
A ++ +P+ I S
Sbjct: 502 ASNQLKSVPDGIFDRLTS 519
>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 = 0.39, Method: Compositional matrix adjust.
Identities = 19/42 (45%), Positives = 27/42 (64%), Gaps = 1/42 (2%)
Query: 178 ISWLFLRGIAIEELPSSIERLLRLGYLDLSDCKRLKSLPSSL 219
++ L+L G ++ ELP+ I+ L L LDLS RL SLP+ L
Sbjct: 249 LTRLYLNGNSLTELPAEIKNLSNLRVLDLSH-NRLTSLPAEL 289
>pdb|3RDW|A Chain A, Putative Arsenate Reductase From Yersinia Pestis
pdb|3RDW|B Chain B, Putative Arsenate Reductase From Yersinia Pestis
Length = 121
Score = 31.6 bits (70), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 36/82 (43%), Gaps = 1/82 (1%)
Query: 190 ELPSSIERLLRL-GYLDLSDCKRLKSLPSSLYRLKSLGVLSLCGCSNLQRLPECLGQLSS 248
E P S+++L L L SD ++L LY+ +L L LQ + + +
Sbjct: 39 ETPPSVDKLKELLQQLGFSDARQLMRTKEDLYKTLNLDDRGLTQDQLLQAMADNPKLIER 98
Query: 249 PITFNLAKTNIERIPESIIQLF 270
PI K I R PE ++++
Sbjct: 99 PIVVTQGKARIGRPPEQVLEIL 120
>pdb|3G06|A Chain A, The Salmonella Virulence Effector Ssph2 Functions As A
Novel E3 Ligase
Length = 622
Score = 31.6 bits (70), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 47/133 (35%), Positives = 57/133 (42%), Gaps = 39/133 (29%)
Query: 123 PTLMPRLNKLVTLNLRGSKSLKSLPSGIFNLEFLTKLDLSGCSKLKRLPEISSGNISWLF 182
PTL L KL N R + SL +LPSG+ L I SGN
Sbjct: 197 PTLPSELYKLWAYNNRLT-SLPALPSGLKEL-------------------IVSGN----- 231
Query: 183 LRGIAIEELPSSIERLLRLGYLDLSDCKRLKSLPSSLYRLKSLGVLSLCGCSN-LQRLPE 241
R ++ LPS ++ L+ G RL SLP + G+LSL N L RLPE
Sbjct: 232 -RLTSLPVLPSELKELMVSG-------NRLTSLP-----MLPSGLLSLSVYRNQLTRLPE 278
Query: 242 CLGQLSSPITFNL 254
L LSS T NL
Sbjct: 279 SLIHLSSETTVNL 291
>pdb|3B2D|A Chain A, Crystal Structure Of Human Rp105MD-1 Complex
pdb|3B2D|B Chain B, Crystal Structure Of Human Rp105MD-1 Complex
Length = 603
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 8/74 (10%)
Query: 140 SKSLKSLPSGIFNLEFLTKLDLSGCSKLKRLPEISSGN---ISWLFLRGIAIEELP---S 193
+ LK LPSG+ L L KL LS + +L +IS+ N ++ L++RG +++L
Sbjct: 284 ATHLKGLPSGMKGLNLLKKLVLS-VNHFDQLCQISAANFPSLTHLYIRG-NVKKLHLGVG 341
Query: 194 SIERLLRLGYLDLS 207
+E+L L LDLS
Sbjct: 342 CLEKLGNLQTLDLS 355
>pdb|1IRX|A Chain A, Crystal Structure Of Class I Lysyl-Trna Synthetase
pdb|1IRX|B Chain B, Crystal Structure Of Class I Lysyl-Trna Synthetase
Length = 523
Score = 29.3 bits (64), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 3/55 (5%)
Query: 52 LQDPGFAEVKYLH-WHGYP-LKSLPSNLSAEKLMLLEVPDSDIKRLWDCVKHYSK 104
L+D G+ EV+++H W Y + +P N+ E L +P S++ W C + Y++
Sbjct: 52 LRDKGY-EVRHIHMWDDYDRFRKVPRNVPQEWKDYLGMPISEVPDPWGCHESYAE 105
>pdb|4AY9|X Chain X, Structure Of Follicle-Stimulating Hormone In Complex With
The Entire Ectodomain Of Its Receptor
pdb|4AY9|Y Chain Y, Structure Of Follicle-Stimulating Hormone In Complex With
The Entire Ectodomain Of Its Receptor
pdb|4AY9|Z Chain Z, Structure Of Follicle-Stimulating Hormone In Complex With
The Entire Ectodomain Of Its Receptor
Length = 350
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 41/83 (49%), Gaps = 6/83 (7%)
Query: 178 ISWLFLRGIAIEELPSSIERLLRLGYLDLSDCKRLKSLPSSLYRLKSLGVLSLCGCSNLQ 237
I WL GI +E+ +S +L L+LSD L+ LP+ ++ S V+ + +
Sbjct: 158 ILWLNKNGI--QEIHNSAFNGTQLDELNLSDNNNLEELPNDVFHGASGPVILDISRTRIH 215
Query: 238 RLP----ECLGQLSSPITFNLAK 256
LP E L +L + T+NL K
Sbjct: 216 SLPSYGLENLKKLRARSTYNLKK 238
>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 = 29.3 bits (64), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 78/311 (25%), Positives = 130/311 (41%), Gaps = 59/311 (18%)
Query: 23 NTFTKMPKL-RFLKFYSSLFNGENKCKMSYLQDPGFAEVKYLHWHGYPLKSLPSNLSAEK 81
N+ T++P+L + LK S L + N +S L P E YL L+ LP ++
Sbjct: 101 NSLTELPELPQSLK--SLLVDNNNLKALSDL--PPLLE--YLGVSNNQLEKLPELQNSSF 154
Query: 82 LMLLEVPDSDIKRLWDCVKHYSKLNQIIHAACHKLIAKIPNPTLMPRLNKLVTLNLRGSK 141
L +++V ++ +K+L D + AA + + ++P +P L + N
Sbjct: 155 LKIIDVDNNSLKKLPDLPPSLEFI-----AAGNNQLEELPELQNLPFLTAIYADN----N 205
Query: 142 SLKSLPSGIFNLEFLTKLDLSGCSKLKRLPEISSGNISWLFLRGI--------AIEELPS 193
SLK LP +LE + ++G + L+ LPE+ + FL I + +LP
Sbjct: 206 SLKKLPDLPLSLESI----VAGNNILEELPELQ----NLPFLTTIYADNNLLKTLPDLPP 257
Query: 194 SIERL-LRLGYL-DLSDCKR--------------LKSLPSSLYRLK--SLGVLSLCGCSN 235
S+E L +R YL DL + + L LP +LY L S + SLC
Sbjct: 258 SLEALNVRDNYLTDLPELPQSLTFLDVSENIFSGLSELPPNLYYLNASSNEIRSLCD--- 314
Query: 236 LQRLPECLGQLSSPITFNLAKTNIERIPESIIQLFVSGYLLLSYGIVEDTLRIQHTNHTP 295
LP L +L+ N + +P + +L S L + L+ H + P
Sbjct: 315 ---LPPSLEELN---VSNNKLIELPALPPRLERLIASFNHLAEVPELPQNLKQLHVEYNP 368
Query: 296 AVRWQEIWQEV 306
+ +I + V
Sbjct: 369 LREFPDIPESV 379
>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 = 28.1 bits (61), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 183 LRGIAIEE--LPSSIERLLRLGYLDLSDCKRLKSLPSSLYRLKSLGVLSL 230
+ G + +E LP L L +LDLS C+ + P++ L SL VL++
Sbjct: 452 MAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNM 501
>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 = 28.1 bits (61), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 183 LRGIAIEE--LPSSIERLLRLGYLDLSDCKRLKSLPSSLYRLKSLGVLSL 230
+ G + +E LP L L +LDLS C+ + P++ L SL VL++
Sbjct: 476 MAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNM 525
>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 = 28.1 bits (61), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 183 LRGIAIEE--LPSSIERLLRLGYLDLSDCKRLKSLPSSLYRLKSLGVLSL 230
+ G + +E LP L L +LDLS C+ + P++ L SL VL++
Sbjct: 157 MAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNM 206
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 0.138 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,386,768
Number of Sequences: 62578
Number of extensions: 369735
Number of successful extensions: 987
Number of sequences better than 100.0: 33
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 27
Number of HSP's that attempted gapping in prelim test: 934
Number of HSP's gapped (non-prelim): 67
length of query: 312
length of database: 14,973,337
effective HSP length: 99
effective length of query: 213
effective length of database: 8,778,115
effective search space: 1869738495
effective search space used: 1869738495
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)