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= 007979
(582 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 35.4 bits (80), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 35/85 (41%)
Query: 224 IPRNIEKLVHLRYLNLSSVTLIRKLPETLCELYNLEKLDISYCINLKALPQGIGKLINMK 283
IP I KL L YL ++ + +P+ L ++ L LD SY LP I L N+
Sbjct: 93 IPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKTLVTLDFSYNALSGTLPPSISSLPNLV 152
Query: 284 HLLNERTDSLGHMPAGIARLPSLRT 308
+ + G +P L T
Sbjct: 153 GITFDGNRISGAIPDSYGSFSKLFT 177
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 34.3 bits (77), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 42/145 (28%), Positives = 61/145 (42%), Gaps = 7/145 (4%)
Query: 414 PSWMMSLTNLRSLNLHLCENCEQLP-PLGKL-PSLEKLYISDMKSVKRVGNEILGIEXXX 471
P+ + SL LR L++ C +LP PL S E + +++S++ I +
Sbjct: 143 PASIASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRLEWTGIRSLPASI 202
Query: 472 XXXXXXXXVIIAFPKLQSL--FIEDLPELEEWDY-GIT--RTGHPFIDIMPRLSALAIAV 526
+ I L +L I LP+LEE D G T R P L L +
Sbjct: 203 ANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPPIFGGRAPLKRLILKD 262
Query: 527 CPKLKALPDHIHQTTTLKGLSIWGC 551
C L LP IH+ T L+ L + GC
Sbjct: 263 CSNLLTLPLDIHRLTQLEKLDLRGC 287
Score = 33.1 bits (74), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 31/113 (27%), Positives = 50/113 (44%), Gaps = 6/113 (5%)
Query: 193 KMLKELFGKLTSLRALDIGNWSATLCSSILDIPRNIEKLVHLRYLNLSSVTLIRKLPETL 252
+ L L +L++L I N S + + I L L L+L T +R P
Sbjct: 196 RSLPASIANLQNLKSLKIRN------SPLSALGPAIHHLPKLEELDLRGCTALRNYPPIF 249
Query: 253 CELYNLEKLDISYCINLKALPQGIGKLINMKHLLNERTDSLGHMPAGIARLPS 305
L++L + C NL LP I +L ++ L +L +P+ IA+LP+
Sbjct: 250 GGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSLIAQLPA 302
Score = 28.5 bits (62), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 37/149 (24%), Positives = 54/149 (36%), Gaps = 36/149 (24%)
Query: 193 KMLKELFGKLTSLRALDIGNWSATLCSSILDIPRNIEKL----VHLRYLNLSSVTL---- 244
+ L L LR L I C + ++P + H +NL S+ L
Sbjct: 140 RALPASIASLNRLRELSI-----RACPELTELPEPLASTDASGEHQGLVNLQSLRLEWTG 194
Query: 245 IRKLPETLCELYN-----------------------LEKLDISYCINLKALPQGIGKLIN 281
IR LP ++ L N LE+LD+ C L+ P G
Sbjct: 195 IRSLPASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPPIFGGRAP 254
Query: 282 MKHLLNERTDSLGHMPAGIARLPSLRTLD 310
+K L+ + +L +P I RL L LD
Sbjct: 255 LKRLILKDCSNLLTLPLDIHRLTQLEKLD 283
>pdb|3RG1|A Chain A, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|E Chain E, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|I Chain I, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|M Chain M, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|B Chain B, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|F Chain F, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|J Chain J, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|N Chain N, Crystal Structure Of The Rp105MD-1 Complex
Length = 612
Score = 33.5 bits (75), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 53/191 (27%), Positives = 89/191 (46%), Gaps = 46/191 (24%)
Query: 162 GASFPVSTCRIKRMRSLFISGNM--LDNSSLNGKMLKELFGKLTSLRALDIG--NWSATL 217
ASFP +R L+I GNM LD L + L+ KL +L+ LD+ + A+
Sbjct: 320 AASFP-------SLRDLYIKGNMRKLD---LGTRCLE----KLENLQKLDLSHSDIEASD 365
Query: 218 CSSILDIPRNIEKLVHLRYLNLSSVTLIRKLPETLCELYNLEKLDISYC-INLKALPQG- 275
C ++ ++ L HL+YLNLS + + E LE LD+++ +++KA P
Sbjct: 366 CCNL-----QLKNLRHLQYLNLSYNEPLGLEDQAFKECPQLELLDVAFTHLHVKA-PHSP 419
Query: 276 -----IGKLINMKHLLNERTDSLGHMPAGIARLPSLRTLDEFHVSGGEGVDGRKGCRLES 330
+ +++N+ H L + ++ H+ AG L+ L ++ G DG S
Sbjct: 420 FQNLHLLRVLNLSHCLLDTSNQ--HLLAG------LQDLRHLNLQGNSFQDG-------S 464
Query: 331 LKNMELLQVCG 341
+ LLQ+ G
Sbjct: 465 ISKTNLLQMVG 475
>pdb|3E6J|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor (Vlr)
Rbc36 In Complex With H-Trisaccharide
Length = 229
Score = 32.3 bits (72), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 36/83 (43%), Gaps = 24/83 (28%)
Query: 175 MRSLFISGNMLDNSSLNGKMLKELFGKLTSLRALDIGNWSATL----------------- 217
++ L++ N L G + +F LT L LD+G T+
Sbjct: 66 LKELYLGSNQL------GALPVGVFDSLTQLTVLDLGTNQLTVLPSAVFDRLVHLKELFM 119
Query: 218 -CSSILDIPRNIEKLVHLRYLNL 239
C+ + ++PR IE+L HL +L L
Sbjct: 120 CCNKLTELPRGIERLTHLTHLAL 142
>pdb|2Z63|A Chain A, Crystal Structure Of The Tv8 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 570
Score = 31.2 bits (69), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 248 LPETLCELYNLEKLDISYCINLKALPQGIGKLINMKHLLNERTDSLGHMPAGIA-RLPSL 306
LP+ EL NL LD+S C + P L +++ +LN ++ L +P GI RL SL
Sbjct: 462 LPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQ-VLNMASNQLKSVPDGIFDRLTSL 520
Query: 307 RTL 309
+ +
Sbjct: 521 QKI 523
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 35/112 (31%), Positives = 55/112 (49%), Gaps = 21/112 (18%)
Query: 172 IKRMRSLFISGNMLDNSSLNGKMLKELFGKLTSLRALDIGNWSATLCSSILDIPRNIEKL 231
+ + +L ++GN + + +L F L+SL+ L T +S+ + P I L
Sbjct: 75 LSHLSTLILTGNPIQSLALGA------FSGLSSLQKLVA---VETNLASLENFP--IGHL 123
Query: 232 VHLRYLNLSSVTLIR--KLPETLCELYNLEKLDIS-------YCINLKALPQ 274
L+ LN++ LI+ KLPE L NLE LD+S YC +L+ L Q
Sbjct: 124 KTLKELNVAH-NLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQ 174
>pdb|3ULA|A Chain A, Crystal Structure Of The Tv3 Mutant F63w-Md-2-Eritoran
Complex
pdb|3ULA|C Chain C, Crystal Structure Of The Tv3 Mutant F63w-Md-2-Eritoran
Complex
Length = 279
Score = 31.2 bits (69), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 35/112 (31%), Positives = 55/112 (49%), Gaps = 21/112 (18%)
Query: 172 IKRMRSLFISGNMLDNSSLNGKMLKELFGKLTSLRALDIGNWSATLCSSILDIPRNIEKL 231
+ + +L ++GN + + +L F L+SL+ L T +S+ + P I L
Sbjct: 77 LSHLSTLILTGNPIQSLALGA------FSGLSSLQKLVA---VETNLASLENFP--IGHL 125
Query: 232 VHLRYLNLSSVTLIR--KLPETLCELYNLEKLDIS-------YCINLKALPQ 274
L+ LN++ LI+ KLPE L NLE LD+S YC +L+ L Q
Sbjct: 126 KTLKELNVAH-NLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQ 176
>pdb|3UL9|A Chain A, Structure Of The Tv3 Mutant M41e
Length = 278
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 35/112 (31%), Positives = 55/112 (49%), Gaps = 21/112 (18%)
Query: 172 IKRMRSLFISGNMLDNSSLNGKMLKELFGKLTSLRALDIGNWSATLCSSILDIPRNIEKL 231
+ + +L ++GN + + +L F L+SL+ L T +S+ + P I L
Sbjct: 76 LSHLSTLILTGNPIQSLALGA------FSGLSSLQKLVA---VETNLASLENFP--IGHL 124
Query: 232 VHLRYLNLSSVTLIR--KLPETLCELYNLEKLDIS-------YCINLKALPQ 274
L+ LN++ LI+ KLPE L NLE LD+S YC +L+ L Q
Sbjct: 125 KTLKELNVAH-NLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQ 175
>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 = 2.1, Method: Compositional matrix adjust.
Identities = 35/112 (31%), Positives = 55/112 (49%), Gaps = 21/112 (18%)
Query: 172 IKRMRSLFISGNMLDNSSLNGKMLKELFGKLTSLRALDIGNWSATLCSSILDIPRNIEKL 231
+ + +L ++GN + + +L F L+SL+ L T +S+ + P I L
Sbjct: 99 LSHLSTLILTGNPIQSLALGA------FSGLSSLQKLVA---VETNLASLENFP--IGHL 147
Query: 232 VHLRYLNLSSVTLIR--KLPETLCELYNLEKLDIS-------YCINLKALPQ 274
L+ LN++ LI+ KLPE L NLE LD+S YC +L+ L Q
Sbjct: 148 KTLKELNVAH-NLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQ 198
>pdb|3UL7|A Chain A, Crystal Structure Of The Tv3 Mutant F63w
Length = 278
Score = 30.8 bits (68), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 35/112 (31%), Positives = 55/112 (49%), Gaps = 21/112 (18%)
Query: 172 IKRMRSLFISGNMLDNSSLNGKMLKELFGKLTSLRALDIGNWSATLCSSILDIPRNIEKL 231
+ + +L ++GN + + +L F L+SL+ L T +S+ + P I L
Sbjct: 76 LSHLSTLILTGNPIQSLALGA------FSGLSSLQKLVA---VETNLASLENFP--IGHL 124
Query: 232 VHLRYLNLSSVTLIR--KLPETLCELYNLEKLDIS-------YCINLKALPQ 274
L+ LN++ LI+ KLPE L NLE LD+S YC +L+ L Q
Sbjct: 125 KTLKELNVAH-NLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQ 175
>pdb|2Z62|A Chain A, Crystal Structure Of The Tv3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
pdb|2Z65|A Chain A, Crystal Structure Of The Human Tlr4 Tv3
Hybrid-Md-2-Eritoran Complex
pdb|2Z65|B Chain B, Crystal Structure Of The Human Tlr4 Tv3
Hybrid-Md-2-Eritoran Complex
Length = 276
Score = 30.8 bits (68), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 35/112 (31%), Positives = 55/112 (49%), Gaps = 21/112 (18%)
Query: 172 IKRMRSLFISGNMLDNSSLNGKMLKELFGKLTSLRALDIGNWSATLCSSILDIPRNIEKL 231
+ + +L ++GN + + +L F L+SL+ L T +S+ + P I L
Sbjct: 75 LSHLSTLILTGNPIQSLALGA------FSGLSSLQKLVA---VETNLASLENFP--IGHL 123
Query: 232 VHLRYLNLSSVTLIR--KLPETLCELYNLEKLDIS-------YCINLKALPQ 274
L+ LN++ LI+ KLPE L NLE LD+S YC +L+ L Q
Sbjct: 124 KTLKELNVAH-NLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQ 174
>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 = 2.3, Method: Compositional matrix adjust.
Identities = 35/112 (31%), Positives = 55/112 (49%), Gaps = 21/112 (18%)
Query: 172 IKRMRSLFISGNMLDNSSLNGKMLKELFGKLTSLRALDIGNWSATLCSSILDIPRNIEKL 231
+ + +L ++GN + + +L F L+SL+ L T +S+ + P I L
Sbjct: 75 LSHLSTLILTGNPIQSLALGA------FSGLSSLQKLVA---VETNLASLENFP--IGHL 123
Query: 232 VHLRYLNLSSVTLIR--KLPETLCELYNLEKLDIS-------YCINLKALPQ 274
L+ LN++ LI+ KLPE L NLE LD+S YC +L+ L Q
Sbjct: 124 KTLKELNVAH-NLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQ 174
>pdb|3UL8|A Chain A, Crystal Structure Of The Tv3 Mutant V134l
Length = 279
Score = 30.4 bits (67), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 35/112 (31%), Positives = 55/112 (49%), Gaps = 21/112 (18%)
Query: 172 IKRMRSLFISGNMLDNSSLNGKMLKELFGKLTSLRALDIGNWSATLCSSILDIPRNIEKL 231
+ + +L ++GN + + +L F L+SL+ L T +S+ + P I L
Sbjct: 77 LSHLSTLILTGNPIQSLALGA------FSGLSSLQKLVA---LETNLASLENFP--IGHL 125
Query: 232 VHLRYLNLSSVTLIR--KLPETLCELYNLEKLDIS-------YCINLKALPQ 274
L+ LN++ LI+ KLPE L NLE LD+S YC +L+ L Q
Sbjct: 126 KTLKELNVAH-NLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQ 176
>pdb|3LPX|A Chain A, Crystal Structure Of Gyra
pdb|3LPX|B Chain B, Crystal Structure Of Gyra
Length = 500
Score = 30.4 bits (67), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 22/36 (61%)
Query: 251 TLCELYNLEKLDISYCINLKALPQGIGKLINMKHLL 286
L LY L ++ +S+ +N+ AL G K+ N+K +L
Sbjct: 286 VLNNLYKLTQMQVSFGLNMVALTNGQPKIFNIKEML 321
>pdb|1AB4|A Chain A, 59kda Fragment Of Gyrase A From E. Coli
Length = 493
Score = 29.6 bits (65), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 23/36 (63%)
Query: 251 TLCELYNLEKLDISYCINLKALPQGIGKLINMKHLL 286
L LY+ +L +S+ IN+ AL G K++N+K ++
Sbjct: 287 VLNNLYSQTQLQVSFGINMVALHHGQPKIMNLKDII 322
>pdb|2Y3P|A Chain A, Crystal Structure Of N-Terminal Domain Of Gyra With The
Antibiotic Simocyclinone D8
pdb|2Y3P|B Chain B, Crystal Structure Of N-Terminal Domain Of Gyra With The
Antibiotic Simocyclinone D8
Length = 522
Score = 29.6 bits (65), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 23/36 (63%)
Query: 251 TLCELYNLEKLDISYCINLKALPQGIGKLINMKHLL 286
L LY+ +L +S+ IN+ AL G K++N+K ++
Sbjct: 315 VLNNLYSQTQLQVSFGINMVALHHGQPKIMNLKDII 350
>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 = 29.3 bits (64), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 61/226 (26%), Positives = 98/226 (43%), Gaps = 43/226 (19%)
Query: 167 VSTCRIKRMRSLFISGNMLDNSSLNGKMLKELFG---KLTSLRALDIG--NWSATLCSSI 221
+S + L+I GN+ K L G KL +L+ LD+ + A+ C S+
Sbjct: 316 ISAANFPSLTHLYIRGNV--------KKLHLGVGCLEKLGNLQTLDLSHNDIEASDCCSL 367
Query: 222 LDIPRNIEKLVHLRYLNLSSVTLIRKLPETLCELYNLEKLDISYC-INLKALPQGIGKLI 280
++ L HL+ LNLS + + E LE LD+++ +++ A PQ + +
Sbjct: 368 -----QLKNLSHLQTLNLSHNEPLGLQSQAFKECPQLELLDLAFTRLHINA-PQSPFQNL 421
Query: 281 NMKHLLNER----TDSLGHMPAGIARLPSLRTLDEFHVSGGEGVDG--RKGCRLESLKNM 334
+ +LN S H+ AG LP LR L+ + G DG K L+++ ++
Sbjct: 422 HFLQVLNLTYCFLDTSNQHLLAG---LPVLRHLN---LKGNHFQDGTITKTNLLQTVGSL 475
Query: 335 E--LLQVCGI--------RRLGNVSDVD-EAKRLKLDKKKYLSCLR 369
E +L CG+ LG +S VD L D LS L+
Sbjct: 476 EVLILSSCGLLSIDQQAFHSLGKMSHVDLSHNSLTCDSIDSLSHLK 521
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 0.139 0.420
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,042,263
Number of Sequences: 62578
Number of extensions: 680850
Number of successful extensions: 1399
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 1360
Number of HSP's gapped (non-prelim): 61
length of query: 582
length of database: 14,973,337
effective HSP length: 104
effective length of query: 478
effective length of database: 8,465,225
effective search space: 4046377550
effective search space used: 4046377550
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: 54 (25.4 bits)