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= psy8727
(300 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3HY5|A Chain A, Crystal Structure Of Cralbp
Length = 316
Score = 66.2 bits (160), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 59/222 (26%), Positives = 97/222 (43%), Gaps = 18/222 (8%)
Query: 2 TKDRKPEELSVETSVSKQGLQIAKAELREDESTREDALIQLRQWITKNS----------- 50
TKD P + + + LQ AK EL E E TRE+A+ +L++ + +
Sbjct: 26 TKDHGPV-FGPCSQLPRHTLQKAKDELNEREETREEAVRELQEMVQAQAASGEELAVAVA 84
Query: 51 -RIQTCXXXXXXXXXXXXSKKFSVPMAEEALERYILLRNTYGDLAFSKLDPKNPTMQELL 109
R+Q ++KF+V A E L Y+ R Y +L F L P+ ++ +
Sbjct: 85 ERVQ--EKDSGFFLRFIRARKFNVGRAYELLRGYVNFRLQYPEL-FDSLSPE--AVRCTI 139
Query: 110 KLGYLFATPKRDKLGRRVIIARPGVFNPHKYTNSHMLQIHGMTYETLMEDEENQVRGFVH 169
+ GY RDK GR V++ + + T +LQ + E L+E+EE Q+ GF
Sbjct: 140 EAGYPGVLSSRDKYGRVVMLFNIENWQSQEITFDEILQAYCFILEKLLENEETQINGFCI 199
Query: 170 FNDGAGVSFPHLTLFTPKEAVRIVKNGERTLPMRHKEIHIIN 211
+ G + + ++V + + P R K IH I+
Sbjct: 200 IENFKGFTMQQAASLRTSDLRKMVDMLQDSFPARFKAIHFIH 241
Score = 34.7 bits (78), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 35/59 (59%), Gaps = 8/59 (13%)
Query: 227 VSEKIRKRIKVSVIVNARFLLRFLRSKKFSVPMAEEALERYILLRNTYGDLAFSKLDPK 285
V+E+++++ ++ F LRF+R++KF+V A E L Y+ R Y +L F L P+
Sbjct: 83 VAERVQEK-------DSGFFLRFIRARKFNVGRAYELLRGYVNFRLQYPEL-FDSLSPE 133
>pdb|3HX3|A Chain A, Crystal Structure Of Cralbp Mutant R234w
Length = 316
Score = 61.2 bits (147), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 58/222 (26%), Positives = 94/222 (42%), Gaps = 18/222 (8%)
Query: 2 TKDRKPEELSVETSVSKQGLQIAKAELREDESTREDALIQLRQWITKNS----------- 50
TKD P + + + LQ AK EL E E TRE+A+ +L++ + +
Sbjct: 26 TKDHGPV-FGPCSQLPRHTLQKAKDELNEREETREEAVRELQEXVQAQAASGEELAVAVA 84
Query: 51 -RIQTCXXXXXXXXXXXXSKKFSVPMAEEALERYILLRNTYGDLAFSKLDPKNPTMQELL 109
R+Q ++KF+V A E L Y+ R Y +L F L P+ ++ +
Sbjct: 85 ERVQ--EKDSGFFLRFIRARKFNVGRAYELLRGYVNFRLQYPEL-FDSLSPE--AVRCTI 139
Query: 110 KLGYLFATPKRDKLGRRVIIARPGVFNPHKYTNSHMLQIHGMTYETLMEDEENQVRGFVH 169
+ GY RDK GR V + + + T +LQ + E L+E+EE Q+ GF
Sbjct: 140 EAGYPGVLSSRDKYGRVVXLFNIENWQSQEITFDEILQAYCFILEKLLENEETQINGFCI 199
Query: 170 FNDGAGVSFPHLTLFTPKEAVRIVKNGERTLPMRHKEIHIIN 211
+ G + + + V + + P K IH I+
Sbjct: 200 IENFKGFTXQQAASLRTSDLRKXVDXLQDSFPAWFKAIHFIH 241
Score = 34.7 bits (78), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 35/59 (59%), Gaps = 8/59 (13%)
Query: 227 VSEKIRKRIKVSVIVNARFLLRFLRSKKFSVPMAEEALERYILLRNTYGDLAFSKLDPK 285
V+E+++++ ++ F LRF+R++KF+V A E L Y+ R Y +L F L P+
Sbjct: 83 VAERVQEK-------DSGFFLRFIRARKFNVGRAYELLRGYVNFRLQYPEL-FDSLSPE 133
>pdb|1R5L|A Chain A, Crystal Structure Of Human Alpha-tocopherol Transfer
Protein Bound To Its Ligand
Length = 262
Score = 58.5 bits (140), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 45/169 (26%), Positives = 84/169 (49%), Gaps = 5/169 (2%)
Query: 68 SKKFSVPMAEEALERYILLRNTYGDLAFSKLDPKNPTMQELLKLGYLFATPKRDKLGRRV 127
++ F + +A L+ Y R +++ + L P+ ++ LLK GY RD G +V
Sbjct: 42 ARDFDLDLAWRLLKNYYKWRAECPEIS-ADLHPR--SIIGLLKAGYHGVLRSRDPTGSKV 98
Query: 128 IIARPGVFNPHKYTNSHMLQIHGMTYETLMEDEENQVRGFVHFNDGAGVSFPHLTLFTPK 187
+I R ++P +T + ++ +T E ++++ E Q G D G F H TP
Sbjct: 99 LIYRIAHWDPKVFTAYDVFRVSLITSELIVQEVETQRNGIKAIFDLEGWQFSHAFQITPS 158
Query: 188 EAVRIVKNGERTLPMRHKEIHIINCHPSVKYALDFGLN-LVSEKIRKRI 235
A +I + P++ + IH+IN P + +A+ + ++EKI++RI
Sbjct: 159 VAKKIAAVLTDSFPLKVRGIHLIN-EPVIFHAVFSXIKPFLTEKIKERI 206
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 31/53 (58%), Gaps = 3/53 (5%)
Query: 245 FLLRFLRSKKFSVPMAEEALERYILLRNTYGDLAFSKLDPKNPTMQELLKLGY 297
FLLRFLR++ F + +A L+ Y R +++ + L P+ ++ LLK GY
Sbjct: 35 FLLRFLRARDFDLDLAWRLLKNYYKWRAECPEIS-ADLHPR--SIIGLLKAGY 84
>pdb|1OIP|A Chain A, The Molecular Basis Of Vitamin E Retention: Structure Of
Human Alpha-tocopherol Transfer Protein
pdb|1OIZ|A Chain A, The Molecular Basis Of Vitamin E Retention: Structure Of
Human Alpha-Tocopherol Transfer Protein
pdb|1OIZ|B Chain B, The Molecular Basis Of Vitamin E Retention: Structure Of
Human Alpha-Tocopherol Transfer Protein
Length = 278
Score = 58.5 bits (140), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 46/172 (26%), Positives = 86/172 (50%), Gaps = 7/172 (4%)
Query: 68 SKKFSVPMAEEALERYILLRNTYGDLAFSKLDPKNPTMQELLKLGYLFATPKRDKLGRRV 127
++ F + +A L+ Y R +++ + L P+ ++ LLK GY RD G +V
Sbjct: 58 ARDFDLDLAWRLLKNYYKWRAECPEIS-ADLHPR--SIIGLLKAGYHGVLRSRDPTGSKV 114
Query: 128 IIARPGVFNPHKYTNSHMLQIHGMTYETLMEDEENQVRGFVHFNDGAGVSFPHLTLFTPK 187
+I R ++P +T + ++ +T E ++++ E Q G D G F H TP
Sbjct: 115 LIYRIAHWDPKVFTAYDVFRVSLITSELIVQEVETQRNGIKAIFDLEGWQFSHAFQITPS 174
Query: 188 EAVRIVKNGERTLPMRHKEIHIINCHPSVKYALDFGL--NLVSEKIRKRIKV 237
A +I + P++ + IH+IN P + +A+ F + ++EKI++RI +
Sbjct: 175 VAKKIAAVLTDSFPLKVRGIHLIN-EPVIFHAV-FSMIKPFLTEKIKERIHM 224
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 31/53 (58%), Gaps = 3/53 (5%)
Query: 245 FLLRFLRSKKFSVPMAEEALERYILLRNTYGDLAFSKLDPKNPTMQELLKLGY 297
FLLRFLR++ F + +A L+ Y R +++ + L P+ ++ LLK GY
Sbjct: 51 FLLRFLRARDFDLDLAWRLLKNYYKWRAECPEIS-ADLHPR--SIIGLLKAGY 100
>pdb|3BF5|A Chain A, Crystal Structure Of Putative Ribokinase (10640157) From
Thermoplasma Acidophilum At 1.91 A Resolution
pdb|3BF5|B Chain B, Crystal Structure Of Putative Ribokinase (10640157) From
Thermoplasma Acidophilum At 1.91 A Resolution
Length = 306
Score = 32.7 bits (73), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 17/69 (24%)
Query: 134 VFNP----HKYTNSHMLQIHGMTYETLMEDEENQVRGFVHFNDGAGVSFPHLTLFTPKEA 189
+F+P HKY+ + + H ++Y ++ D E +V F + G+S P +T
Sbjct: 164 IFDPSQEIHKYSKDELKKFHEISYXSIFNDHEYRV-----FREXTGLSSPKVTT------ 212
Query: 190 VRIVKNGER 198
IV NGER
Sbjct: 213 --IVTNGER 219
>pdb|1AUA|A Chain A, Phosphatidylinositol Transfer Protein Sec14p From
Saccharomyces Cerevisiae
Length = 296
Score = 32.7 bits (73), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 34/72 (47%), Gaps = 7/72 (9%)
Query: 211 NCHPSVKYALDFGLNLVSEK----IRKRIKVSVIV---NARFLLRFLRSKKFSVPMAEEA 263
NC P L+ EK +RK ++ + + + LLRFLR++KF V +A+E
Sbjct: 13 NCPPDALPGTPGNLDSAQEKALAELRKLLEDAGFIERLDDSTLLRFLRARKFDVQLAKEM 72
Query: 264 LERYILLRNTYG 275
E R YG
Sbjct: 73 FENCEKWRKDYG 84
>pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|Q Chain Q, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|A Chain A, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|I Chain I, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 880
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/31 (54%), Positives = 20/31 (64%), Gaps = 5/31 (16%)
Query: 77 EEALERYIL-----LRNTYGDLAFSKLDPKN 102
EE+LE YIL LR+T GD+A LDP N
Sbjct: 693 EESLENYILDTLDKLRSTAGDIASKYLDPFN 723
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/31 (54%), Positives = 20/31 (64%), Gaps = 5/31 (16%)
Query: 261 EEALERYIL-----LRNTYGDLAFSKLDPKN 286
EE+LE YIL LR+T GD+A LDP N
Sbjct: 693 EESLENYILDTLDKLRSTAGDIASKYLDPFN 723
>pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|W Chain W, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|A Chain A, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|W Chain W, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|A Chain A, Rnap At 3.2ang
pdb|4B1O|A Chain A, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|W Chain W, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 880
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/31 (54%), Positives = 20/31 (64%), Gaps = 5/31 (16%)
Query: 77 EEALERYIL-----LRNTYGDLAFSKLDPKN 102
EE+LE YIL LR+T GD+A LDP N
Sbjct: 693 EESLENYILDTLDKLRSTAGDIASKYLDPFN 723
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/31 (54%), Positives = 20/31 (64%), Gaps = 5/31 (16%)
Query: 261 EEALERYIL-----LRNTYGDLAFSKLDPKN 286
EE+LE YIL LR+T GD+A LDP N
Sbjct: 693 EESLENYILDTLDKLRSTAGDIASKYLDPFN 723
>pdb|3DQZ|A Chain A, Structure Of The Hydroxynitrile Lyase From Arabidopsis
Thaliana
pdb|3DQZ|B Chain B, Structure Of The Hydroxynitrile Lyase From Arabidopsis
Thaliana
pdb|3DQZ|C Chain C, Structure Of The Hydroxynitrile Lyase From Arabidopsis
Thaliana
pdb|3DQZ|D Chain D, Structure Of The Hydroxynitrile Lyase From Arabidopsis
Thaliana
Length = 258
Score = 28.9 bits (63), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 38/76 (50%), Gaps = 11/76 (14%)
Query: 223 GLN--LVSEKIRKRIKVSVIVNARFLLRFLRSKKFSVPMAEEALERYILLRNTYGDLAFS 280
G+N L ++ +IKV V +NA FL VP L++Y+ + GD FS
Sbjct: 84 GINIALAADIFPAKIKVLVFLNA-----FLPDTT-HVP--SHVLDKYMEMPGGLGDCEFS 135
Query: 281 KLDPKNPTMQELLKLG 296
+ +N TM LLK+G
Sbjct: 136 SHETRNGTMS-LLKMG 150
>pdb|1D2E|A Chain A, Crystal Structure Of Mitochondrial Ef-Tu In Complex With
Gdp
pdb|1D2E|B Chain B, Crystal Structure Of Mitochondrial Ef-Tu In Complex With
Gdp
pdb|1D2E|C Chain C, Crystal Structure Of Mitochondrial Ef-Tu In Complex With
Gdp
pdb|1D2E|D Chain D, Crystal Structure Of Mitochondrial Ef-Tu In Complex With
Gdp
Length = 397
Score = 28.1 bits (61), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 111 LGYLFATPKRDKLGRRVIIARPGVFNPHKYTNSHM 145
LG L KR+ L R +++A+PG PH+ + +
Sbjct: 268 LGALVRGLKREDLRRGLVMAKPGSIQPHQKVEAQV 302
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 0.136 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,079,804
Number of Sequences: 62578
Number of extensions: 308073
Number of successful extensions: 693
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 681
Number of HSP's gapped (non-prelim): 21
length of query: 300
length of database: 14,973,337
effective HSP length: 98
effective length of query: 202
effective length of database: 8,840,693
effective search space: 1785819986
effective search space used: 1785819986
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)