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= 040718
(403 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3ZDK|A Chain A, Crystal Structure Of Human 5' Exonuclease Apollo
Length = 336
Score = 144 bits (364), Expect = 6e-35, Method: Compositional matrix adjust.
Identities = 110/350 (31%), Positives = 153/350 (43%), Gaps = 97/350 (27%)
Query: 6 ISVDRWT----EGSQVYFLTHLHSDHTQGLSSAWARGPLFCSRLTAKLFPLKFPGLDLSL 61
I+VD W+ ++++FL+H+HSDHT GLSS WAR PL+CS +TA L +
Sbjct: 12 IAVDFWSLRRAGTARLFFLSHMHSDHTVGLSSTWAR-PLYCSPITAHLLHRHL-QVSKQW 69
Query: 62 IRVLDIGXXXXXXXXXXXXGEKTFVEVIAIDANHCPGILGCSVMLLFRGDFGCLLYTGDF 121
I+ L++G G++T V +DANHCPG SVM LF G FG +LYTGDF
Sbjct: 70 IQALEVG--ESHVLPLDEIGQETMT-VTLLDANHCPG----SVMFLFEGYFGTILYTGDF 122
Query: 122 RWEASNERAEIGRNTLVKALKDDVVDILYLDNTYCNSSYAFPSREVAAQQI--------- 172
R+ S + TL K + LYLDNT CN + PSR+ AA QI
Sbjct: 123 RYTPSMLKEP--ALTLGKQ-----IHTLYLDNTNCNPALVLPSRQEAAHQIVQLIRKHPQ 175
Query: 173 -------------------------WVW--PERLQTMHLLGFHDIFTTKTSLTRVRAVPR 205
WV P RL+ + LLG D+FT + R+ AV
Sbjct: 176 HNIKIGLYSLGKESLLEQLALEFQTWVVLSPRRLELVQLLGLADVFTVEEKAGRIHAVDH 235
Query: 206 YSFSIDTLESLNTMHPTIGIMPSGLPWVVXXXXXXXXXXXXXXXXYQSKWRATGGTQTEK 265
+ N HPTI I+P+ + K
Sbjct: 236 MEICHSNMLRWNQTHPTIAILPT----------------------------------SRK 261
Query: 266 LKEALGSVDRFHKYIYSVPYSDHSCFTEIEEFLNLVQPSNIRGIVSSSSC 315
+ + H I+ +PYSDHS ++E+ F+ ++P + IVS C
Sbjct: 262 IHSS-------HPDIHVIPYSDHSSYSELRAFVAALKPCQVVPIVSRRPC 304
>pdb|4B87|A Chain A, Crystal Structure Of Human Dna Cross-Link Repair 1a
Length = 367
Score = 101 bits (251), Expect = 8e-22, Method: Compositional matrix adjust.
Identities = 88/316 (27%), Positives = 135/316 (42%), Gaps = 48/316 (15%)
Query: 13 EGSQVYFLTHLHSDHTQGLSSAWARGPLFCSRLTAKLFPLKFPGLDLSLIRVLDIGXXXX 72
EG YFLTH HSDH GLS + P++CS +T L K + I L +
Sbjct: 50 EGCTAYFLTHFHSDHYAGLSKHFTF-PVYCSEITGNLLKNKL-HVQEQYIHPLPLDTECI 107
Query: 73 XXXXXXXXGEKTFVEVIAIDANHCPGILGCSVMLLFRGDFG-CLLYTGDFRWEASNERAE 131
V+V+ +DANHCPG +VM+LF G +L+TGDFR + S ER+
Sbjct: 108 VNG----------VKVVLLDANHCPG----AVMILFYLPNGTVILHTGDFRADPSMERS- 152
Query: 132 IGRNTLVKALKDDVVDILYLDNTYCNSSYAFPSRE--------VAAQQIWVWPERL---- 179
L D V +LYLD TYC+ Y FPS++ A + + + P L
Sbjct: 153 --------LLADQKVHMLYLDTTYCSPEYTFPSQQEVIRFAINTAFEAVTLNPHALVVCG 204
Query: 180 -----QTMHLLGFHDIFTTKTSLTRVRAVPRYSFSIDTLESLNTMHPTIGIMPSGLPWVV 234
+ L D+ +K +++ + +I + SL T ++ LP +
Sbjct: 205 TYSIGKEKVFLAIADVLGSKVGMSQEKYKTLQCLNIPEINSLITTDMCSSLV-HLLPMMQ 263
Query: 235 XXXXXXXXXXXXXXXXYQS--KWRATGGTQTEKLKEALGSV--DRFHKYIYSVPYSDHSC 290
Y +R TG T + K + + + IY +PYS+HS
Sbjct: 264 INFKGLQSHLKKCGGKYNQILAFRPTGWTHSNKFTRIADVIPQTKGNISIYGIPYSEHSS 323
Query: 291 FTEIEEFLNLVQPSNI 306
+ E++ F+ ++P I
Sbjct: 324 YLEMKRFVQWLKPQKI 339
>pdb|3G1P|A Chain A, Crystals Structure Of Phnp From E.Coli K-12
pdb|3G1P|B Chain B, Crystals Structure Of Phnp From E.Coli K-12
pdb|3P2U|A Chain A, Crystal Structure Of Phnp In Complex With Orthovanadate
pdb|3P2U|B Chain B, Crystal Structure Of Phnp In Complex With Orthovanadate
Length = 258
Score = 34.3 bits (77), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 15/25 (60%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 8 VDRWTEGS-QVYFLTHLHSDHTQGL 31
DRW+ GS Q + LTH H DH QGL
Sbjct: 61 ADRWSPGSFQQFLLTHYHMDHVQGL 85
>pdb|1QI7|A Chain A, The Crystal Structure At 2.0 A Of Saporin So6, A Ribosome
Inactivating Protein From Saponaria Officinalis
Length = 253
Score = 29.6 bits (65), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 3/47 (6%)
Query: 134 RNTLVKALKDD---VVDILYLDNTYCNSSYAFPSREVAAQQIWVWPE 177
R T+ LK D VV L +DNT N +Y F S +A+ ++PE
Sbjct: 59 RGTVSLGLKRDNLYVVAYLAMDNTNVNRAYYFKSEITSAELTALFPE 105
>pdb|3J21|KK Chain k, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 339
Score = 28.5 bits (62), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 21/43 (48%)
Query: 293 EIEEFLNLVQPSNIRGIVSSSSCYVDPLYYFGRLCRANQPPLR 335
E+EE NL++ + +V SS PL RL R N LR
Sbjct: 11 EVEELANLIKSYPVVALVDVSSMPAYPLSQMRRLIRENNGLLR 53
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
0.322 0.136 0.420
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,495,233
Number of Sequences: 62578
Number of extensions: 391030
Number of successful extensions: 1008
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 996
Number of HSP's gapped (non-prelim): 9
length of query: 403
length of database: 14,973,337
effective HSP length: 101
effective length of query: 302
effective length of database: 8,652,959
effective search space: 2613193618
effective search space used: 2613193618
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: 53 (25.0 bits)