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= 044637
(370 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2FN9|A Chain A, Thermotoga Maritima Ribose Binding Protein Unliganded Form
pdb|2FN9|B Chain B, Thermotoga Maritima Ribose Binding Protein Unliganded Form
Length = 290
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 32/121 (26%), Positives = 55/121 (45%), Gaps = 13/121 (10%)
Query: 16 SLEFTSLALMAEKTIFVWNPGMEEESLSNVKRSKTDHLALIQCENFC-KKFKHLRVLNLG 74
S F ++ + A ++NP + S++NVKR+K + + FC + + R L +
Sbjct: 48 SAHFDAI-IAAGYDAIIFNPTDADGSIANVKRAKEAGIPV-----FCVDRGINARGLAVA 101
Query: 75 SAVLDQYPPG-LENFFYLKYLKLNIPSLKCLP--SLLCTLINLQTLEMPSSY---IDHSP 128
D Y G L +++K+LK P K +P LL L T + + + +D P
Sbjct: 102 QIYSDNYYGGVLAGEYFVKFLKEKYPDAKEIPYAELLGILSAQPTWDRSNGFHSVVDQYP 161
Query: 129 E 129
E
Sbjct: 162 E 162
>pdb|2FN8|A Chain A, Thermotoga Maritima Ribose Binding Protein Ribose Bound
Form
Length = 303
Score = 33.5 bits (75), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 32/121 (26%), Positives = 55/121 (45%), Gaps = 13/121 (10%)
Query: 16 SLEFTSLALMAEKTIFVWNPGMEEESLSNVKRSKTDHLALIQCENFC-KKFKHLRVLNLG 74
S F ++ + A ++NP + S++NVKR+K + + FC + + R L +
Sbjct: 48 SAHFDAI-IAAGYDAIIFNPTDADGSIANVKRAKEAGIPV-----FCVDRGINARGLAVA 101
Query: 75 SAVLDQYPPG-LENFFYLKYLKLNIPSLKCLP--SLLCTLINLQTLEMPSSY---IDHSP 128
D Y G L +++K+LK P K +P LL L T + + + +D P
Sbjct: 102 QIYSDNYYGGVLMGEYFVKFLKEKYPDAKEIPYAELLGILSAQPTWDRSNGFHSVVDQYP 161
Query: 129 E 129
E
Sbjct: 162 E 162
>pdb|1ZIW|A Chain A, Human Toll-Like Receptor 3 Extracellular Domain Structure
Length = 680
Score = 32.3 bits (72), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 2/66 (3%)
Query: 61 FCKKFKHLRVLNLGSAVLDQYPPGL-ENFFYLKYLKLNIPSLKCLP-SLLCTLINLQTLE 118
F K HL +LNL S D+ P + ++ F LK + L + +L LP S+ ++L++L
Sbjct: 531 FLKGLSHLHILNLESNGFDEIPVEVFKDLFELKIIDLGLNNLNTLPASVFNNQVSLKSLN 590
Query: 119 MPSSYI 124
+ + I
Sbjct: 591 LQKNLI 596
>pdb|3ULU|A Chain A, Structure Of Quaternary Complex Of Human Tlr3ecd With
Three Fabs (Form1)
pdb|3ULV|A Chain A, Structure Of Quaternary Complex Of Human Tlr3ecd With
Three Fabs (Form2)
Length = 694
Score = 32.3 bits (72), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 2/66 (3%)
Query: 61 FCKKFKHLRVLNLGSAVLDQYPPGL-ENFFYLKYLKLNIPSLKCLP-SLLCTLINLQTLE 118
F K HL +LNL S D+ P + ++ F LK + L + +L LP S+ ++L++L
Sbjct: 541 FLKGLSHLHILNLESNGFDEIPVEVFKDLFELKIIDLGLNNLNTLPASVFNNQVSLKSLN 600
Query: 119 MPSSYI 124
+ + I
Sbjct: 601 LQKNLI 606
>pdb|2A0Z|A Chain A, The Molecular Structure Of Toll-like Receptor 3 Ligand
Binding Domain
Length = 705
Score = 32.3 bits (72), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 2/66 (3%)
Query: 61 FCKKFKHLRVLNLGSAVLDQYPPGL-ENFFYLKYLKLNIPSLKCLP-SLLCTLINLQTLE 118
F K HL +LNL S D+ P + ++ F LK + L + +L LP S+ ++L++L
Sbjct: 536 FLKGLSHLHILNLESNGFDEIPVEVFKDLFELKIIDLGLNNLNTLPASVFNNQVSLKSLN 595
Query: 119 MPSSYI 124
+ + I
Sbjct: 596 LQKNLI 601
>pdb|3CIG|A Chain A, Crystal Structure Of Mouse Tlr3 Ectodomain
pdb|3CIY|A Chain A, Mouse Toll-Like Receptor 3 Ectodomain Complexed With
Double-Stranded Rna
pdb|3CIY|B Chain B, Mouse Toll-Like Receptor 3 Ectodomain Complexed With
Double-Stranded Rna
Length = 697
Score = 31.2 bits (69), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 17/34 (50%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 60 NFCKKFKHLRVLNLGSAVLDQYPPGL-ENFFYLK 92
NF K HL +LNL S LD+ P G+ +N F LK
Sbjct: 530 NFLKGLSHLHILNLESNGLDEIPVGVFKNLFELK 563
>pdb|2RFK|A Chain A, Substrate Rna Positioning In The Archaeal HACA
Ribonucleoprotein Complex
Length = 334
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 22/49 (44%), Gaps = 5/49 (10%)
Query: 138 MHLNFGSITLPAPPKNNSSTL-----KNLIFISALHPGSCTPDILGRLP 181
MH+ FG I L PP S + K L A H G+ P + G LP
Sbjct: 38 MHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLAPKVSGVLP 86
>pdb|3ZYN|A Chain A, Crystal Structure Of The N-Terminal Leucine Rich Repeats
Of Netrin-G Ligand-3
pdb|3ZYN|B Chain B, Crystal Structure Of The N-Terminal Leucine Rich Repeats
Of Netrin-G Ligand-3
Length = 321
Score = 28.5 bits (62), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 68 LRVLNLGSAVLDQY--PPGLENFFYLKYLKLNIPSLKCLPSLLCTLINLQTLEMPSSYID 125
LR L+LG +Y E L+YL L + +LK +P+ L L+ L+ LE+ + +D
Sbjct: 133 LRRLDLGELKRLEYISEAAFEGLVNLRYLNLGMCNLKDIPN-LTALVRLEELELSGNRLD 191
>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 = 28.5 bits (62), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 31/125 (24%), Positives = 60/125 (48%), Gaps = 12/125 (9%)
Query: 191 DLSYYHSGVSKSLCQLHKLECLKLVNEGNMRQLSRMILSEYKFPPSLTQLSLSNTELMED 250
D Y S + LC + +E + L + S + S ++ + +L L+ L +
Sbjct: 238 DDQYLTSATFEGLCDM-SVESINL----QKHRFSDLSSSTFRCFTRVQELDLTAAHL--N 290
Query: 251 PMPT-LEELPHLEVLKLKQNSYLERKLVCVGCSSFPQLKILHLKSMLWLEEWTMGAGAMP 309
+P+ +E + L+ L L NS+ +L + +SFP L+ L++K + + +G +
Sbjct: 291 GLPSGIEGMNSLKKLVLNANSF--DQLCQINAASFPSLRDLYIKGN--MRKLDLGTRCLE 346
Query: 310 KLESL 314
KLE+L
Sbjct: 347 KLENL 351
>pdb|3ZYI|A Chain A, Netring2 In Complex With Ngl2
Length = 452
Score = 28.5 bits (62), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 4/46 (8%)
Query: 84 GLENFFYLKYLKLNIPSLKCLPSLLCTLINLQTLEMPSSYIDHSPE 129
E F LKYL L + ++K +P+ L L+ L+ LEM +H PE
Sbjct: 191 AFEGLFNLKYLNLGMCNIKDMPN-LTPLVGLEELEMSG---NHFPE 232
>pdb|3ZYO|A Chain A, Crystal Structure Of The N-Terminal Leucine Rich Repeats
And Immunoglobulin Domain Of Netrin-G Ligand-3
Length = 411
Score = 28.5 bits (62), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 68 LRVLNLGSAVLDQY--PPGLENFFYLKYLKLNIPSLKCLPSLLCTLINLQTLEMPSSYID 125
LR L+LG +Y E L+YL L + +LK +P+ L L+ L+ LE+ + +D
Sbjct: 133 LRRLDLGELKRLEYISEAAFEGLVNLRYLNLGMCNLKDIPN-LTALVRLEELELSGNRLD 191
>pdb|1SQ0|B Chain B, Crystal Structure Of The Complex Of The Wild-Type Von
Willebrand Factor A1 Domain And Glycoprotein Ib Alpha At
2.6 Angstrom Resolution
Length = 288
Score = 28.5 bits (62), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 23/36 (63%)
Query: 235 PSLTQLSLSNTELMEDPMPTLEELPHLEVLKLKQNS 270
P L +LSL+N +L E P L L +L+ L L++NS
Sbjct: 148 PKLEKLSLANNDLTELPAGLLNGLENLDTLLLQENS 183
>pdb|1U0N|D Chain D, The Ternary Von Willebrand Factor A1-Glycoprotein Ibalpha-
Botrocetin Complex
Length = 265
Score = 28.5 bits (62), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 23/36 (63%)
Query: 235 PSLTQLSLSNTELMEDPMPTLEELPHLEVLKLKQNS 270
P L +LSL+N +L E P L L +L+ L L++NS
Sbjct: 148 PKLEKLSLANNQLTELPAGLLNGLENLDTLLLQENS 183
>pdb|3P72|A Chain A, Structure Of Platelet Glycoprotein 1b Alpha With A Bound
Peptide Inhibitor
Length = 269
Score = 28.1 bits (61), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 23/36 (63%)
Query: 235 PSLTQLSLSNTELMEDPMPTLEELPHLEVLKLKQNS 270
P L +LSL+N +L E P L L +L+ L L++NS
Sbjct: 148 PKLEKLSLANNQLTELPAGLLNGLENLDTLLLQENS 183
>pdb|1M10|B Chain B, Crystal Structure Of The Complex Of Glycoprotein Ib Alpha
And The Von Willebrand Factor A1 Domain
Length = 290
Score = 28.1 bits (61), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 23/36 (63%)
Query: 235 PSLTQLSLSNTELMEDPMPTLEELPHLEVLKLKQNS 270
P L +LSL+N +L E P L L +L+ L L++NS
Sbjct: 148 PKLEKLSLANNQLTELPAGLLNGLENLDTLLLQENS 183
>pdb|1M0Z|A Chain A, Crystal Structure Of The Von Willebrand Factor Binding
Domain Of Glycoprotein Ib Alpha
pdb|1M0Z|B Chain B, Crystal Structure Of The Von Willebrand Factor Binding
Domain Of Glycoprotein Ib Alpha
Length = 290
Score = 28.1 bits (61), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 23/36 (63%)
Query: 235 PSLTQLSLSNTELMEDPMPTLEELPHLEVLKLKQNS 270
P L +LSL+N +L E P L L +L+ L L++NS
Sbjct: 148 PKLEKLSLANNQLTELPAGLLNGLENLDTLLLQENS 183
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 0.137 0.424
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,369,833
Number of Sequences: 62578
Number of extensions: 459971
Number of successful extensions: 834
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 807
Number of HSP's gapped (non-prelim): 47
length of query: 370
length of database: 14,973,337
effective HSP length: 100
effective length of query: 270
effective length of database: 8,715,537
effective search space: 2353194990
effective search space used: 2353194990
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)