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= 040435
(1991 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3GKH|A Chain A, Npc1(ntd)
pdb|3GKI|A Chain A, Npc1(Ntd):cholesterol
pdb|3GKJ|A Chain A, Npc1d(ntd):25hydroxycholesterol
Length = 232
Score = 107 bits (267), Expect = 7e-23, Method: Compositional matrix adjust.
Identities = 73/223 (32%), Positives = 108/223 (48%), Gaps = 21/223 (9%)
Query: 1410 CAMYDICGERSDGKVLNCPY-GSPSVKPDELFSAKIESLCPSI---SGNVCCTETQFETL 1465
C Y CG K NC Y G P P + + ++ LCP ++CC Q +TL
Sbjct: 5 CVWYGECGIAYGDKRYNCEYSGPPKPLPKDGYDL-VQELCPGFFFGQVSLCCDVRQLQTL 63
Query: 1466 RAQVQQAIPFLVGCPACLRNFLNLFCELSCSPNQSQFINVTSVSEVNGNLT------VDG 1519
+ +Q + FL CP+C N LNLFCEL+CSP QSQF+ VT+ + +T V
Sbjct: 64 KDNLQLPLQFLSRCPSCFYNLLNLFCELTCSPRQSQFLQVTATEDYVDPVTNQTKTNVKE 123
Query: 1520 IDYYVTSTFGEELYNSCKDVKFGTMNTRAIDFI---GAGAKSFKEWFAFIGQKAPPGFPG 1576
+ YYV +F +YN+C+DV+ + N +A+ + A A W ++ K
Sbjct: 124 LQYYVGQSFANAMYNACRDVEAPSSNDKALGLLCGKDADACQATNWIEYMFNK---DNGQ 180
Query: 1577 SPYAINFKLSIPESSGLELMNVSTYSCGDT----SLGCSCGDC 1615
+P+ I S G+E MN +T C ++ + CSC DC
Sbjct: 181 APFTITPVFSDFPVHGMEPMNNATKGCDESVDEVTAPCSCQDC 223
>pdb|3QNT|A Chain A, Npc1l1 (Ntd) Structure
Length = 265
Score = 94.7 bits (234), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 73/235 (31%), Positives = 108/235 (45%), Gaps = 27/235 (11%)
Query: 1405 HSKEYCAMYDICGERSD--GKVL-----NCPYGSPSVKPDELFSAKIESLCPSI----SG 1453
H YCA YD CG+ + G ++ +C +P+ K ++ +CP + +
Sbjct: 9 HQPGYCAFYDECGKNPELSGSLMTLSNVSCLSNTPARKITGDHLILLQKICPRLYTGPNT 68
Query: 1454 NVCCTETQFETLRAQVQQAIPFLVGCPACLRNFLNLFCELSCSPNQSQFINVTSVSEVN- 1512
CC+ Q +L A + L CPAC NF+NL C +CSPNQS FINVT V+++
Sbjct: 69 QACCSAKQLVSLEASLSITKALLTRCPACSDNFVNLHCHNTCSPNQSLFINVTRVAQLGA 128
Query: 1513 GNL-TVDGIDYYVTSTFGEELYNSCKDVKFGTMNTRAIDFI----GAGAKSFKEWFAFIG 1567
G L V + + +F E+ Y+SC V+ T A+ + G+ + + W F G
Sbjct: 129 GQLPAVVAYEAFYQHSFAEQSYDSCSRVRVPAAATLAVGTMCGVYGSALCNAQRWLNFQG 188
Query: 1568 QKAPPGFPGSPYAINFKLSIPE---SSGLELMNVSTYSC----GDTSLGCSCGDC 1615
G +P I F L P SG++ +N C GD CSC DC
Sbjct: 189 DT---GNGLAPLDITFHLLEPGQAVGSGIQPLNEGVARCNESQGDDVATCSCQDC 240
>pdb|1G9R|A Chain A, Crystal Structure Of Galactosyltransferase Lgtc In Complex
With Mn And Udp-2f-Galactose
pdb|1GA8|A Chain A, Crystal Structure Of Galacosyltransferase Lgtc In Complex
With Donor And Acceptor Sugar Analogs
Length = 311
Score = 48.1 bits (113), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 45/190 (23%), Positives = 80/190 (42%), Gaps = 28/190 (14%)
Query: 475 NPKYLSMLNHLRFYLPEVYPKLEKILFLDDDIVVQKDLTPLWSVDL-HGMVNGAVETCKE 533
N +++S+ + R L E +K+L+LD D++V+ LTPLW DL + +++ E
Sbjct: 75 NIRHISITTYARLKLGEYIADCDKVLYLDIDVLVRDSLTPLWDTDLGDNWLGASIDLFVE 134
Query: 534 SFHRFDKYLNFSNPLISENFSPNACGWAFGMNMFDLKEWRKRNITGIYHYWQDANEDRTL 593
+ + + ++ + NA G+ + +LK+WR+ +I W + +D
Sbjct: 135 RQEGYKQKIGXADG----EYYFNA-----GVLLINLKKWRRHDIFKXSSEWVEQYKDVXQ 185
Query: 594 WKLGTLPPGL-----------ITFYNLTYPLDRSW----HVLGLGYDPALNLTQIDNGAV 638
++ + GL F Y +W H L D + + AV
Sbjct: 186 YQDQDILNGLFKGGVCYANSRFNFXPTNYAFXANWFASRHTDPLYRDRTNTVXPV---AV 242
Query: 639 VHYNGNNKPW 648
HY G KPW
Sbjct: 243 SHYCGPAKPW 252
>pdb|1SS9|A Chain A, Crystal Structural Analysis Of Active Site Mutant Q189e Of
Lgtc
Length = 311
Score = 47.4 bits (111), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 48/189 (25%), Positives = 82/189 (43%), Gaps = 26/189 (13%)
Query: 475 NPKYLSMLNHLRFYLPEVYPKLEKILFLDDDIVVQKDLTPLWSVDLHGMVNGAVETCKES 534
N +++S+ + R L E +K+L+LD D++V+ LTPLW DL GA C +
Sbjct: 75 NIRHISITTYARLKLGEYIADCDKVLYLDIDVLVRDSLTPLWDTDLGDNWLGA---CIDL 131
Query: 535 FHRFDKYLNFSNPLISENFSPNACGWAFGMNMFDLKEWRKRNITGIYHYWQDANEDRTLW 594
F + + + NA G+ + +LK+WR+ +I + W + +D +
Sbjct: 132 FVERQEGYKQKIGMADGEYYFNA-----GVLLINLKKWRRHDIFKMSCEWVEQYKDVMQY 186
Query: 595 K----LGTLPPGLITFYNLTY---PLDRSW--------HVLGLGYDPALNLTQIDNGAVV 639
+ L L G + + N + P + ++ H L D + + AV
Sbjct: 187 QDEDILNGLFKGGVCYANSRFNFMPTNYAFMANRFASRHTDPLYRDRTNTVMPV---AVS 243
Query: 640 HYNGNNKPW 648
HY G KPW
Sbjct: 244 HYCGPAKPW 252
>pdb|2Z23|A Chain A, Crystal Structure Of Y.Pestis Oligo Peptide Binding Protein
Oppa With Tri-Lysine Ligand
Length = 517
Score = 33.1 bits (74), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 1540 KFGTMNTRAIDFIGAGAKSFKEWFA---FIGQKAPPGFPGSPYAINFKLSIPESSGLELM 1596
KFG T+ +F+G GA K+W + +++P + + IN +P SS E+
Sbjct: 174 KFGEKWTQPQNFVGNGAYKLKDWIVNERIVLERSPTYWDNAKTVINQVTYLPISS--EVT 231
Query: 1597 NVSTYSCGDTSL 1608
+V+ Y G+ +
Sbjct: 232 DVNRYRSGEIDM 243
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
0.320 0.134 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 57,717,597
Number of Sequences: 62578
Number of extensions: 2395774
Number of successful extensions: 4998
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 4985
Number of HSP's gapped (non-prelim): 6
length of query: 1991
length of database: 14,973,337
effective HSP length: 113
effective length of query: 1878
effective length of database: 7,902,023
effective search space: 14839999194
effective search space used: 14839999194
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: 59 (27.3 bits)