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= psy6495
(235 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1W66|A Chain A, Structure Of A Lipoate-protein Ligase B From Mycobacterium
Tuberculosis
Length = 232
Score = 138 bits (348), Expect = 2e-33, Method: Compositional matrix adjust.
Identities = 81/201 (40%), Positives = 112/201 (55%), Gaps = 17/201 (8%)
Query: 5 VQLVRLGVVSYSNGIKIQEHYVNKLKTLISKPSNHSGTLLLLEHKPVYTIGIRSLKEYDE 64
+ + +LG V Y ++Q + ++ + + TLLLLEH VYT G R+ E
Sbjct: 14 IDVRQLGTVDYRTAWQLQRELAD------ARVAGGADTLLLLEHPAVYTAGRRT-----E 62
Query: 65 NLELKLNKLGADFYKTNRGGLITFHGPGQLVAYPIINLKHFTPSIKWFVQSIEQTVIQLC 124
E ++ G T+RGG IT+HGPGQLV YPII L + +V+ +E+++IQ+C
Sbjct: 63 THERPID--GTPVVDTDRGGKITWHGPGQLVGYPIIGLAEPLDVVN-YVRRLEESLIQVC 119
Query: 125 KQEFSLNAGLIPKYTGVFLDDE--YKVCAIGVHSSLYITHHGLAINCDTDLTWFNHITPC 182
+ L+AG + +GV+L KV AIGV S T HG A+NCD DL F I PC
Sbjct: 120 A-DLGLHAGRVDGRSGVWLPGRPARKVAAIGVRVSRATTLHGFALNCDCDLAAFTAIVPC 178
Query: 183 GIKDKQVTSLSKHLSKDITVD 203
GI D VTSLS L + +TVD
Sbjct: 179 GISDAAVTSLSAELGRTVTVD 199
>pdb|2QHT|A Chain A, Structural Basis Of Octanoic Acid Recognition By
Lipoate-Protein Ligase B
pdb|2QHU|A Chain A, Structural Basis Of Octanoic Acid Recognition By
Lipoate-Protein Ligase B
pdb|2QHV|A Chain A, Structural Basis Of Octanoic Acid Recognition By
Lipoate-protein Ligase B
Length = 210
Score = 116 bits (291), Expect = 8e-27, Method: Compositional matrix adjust.
Identities = 68/194 (35%), Positives = 106/194 (54%), Gaps = 10/194 (5%)
Query: 10 LGVVSYSNGIKIQEHYVNKLKTLISKPSNHSGTLLLLEHKPVYTIGIRSLKEYDENLELK 69
LG+V Y Q+ ++ N TLLLLEH V T+G ++ E E
Sbjct: 8 LGLVPYGEAWAYQKRVHREVVA-----GNRPPTLLLLEHPRVITLGRKATGENLLFPESW 62
Query: 70 LNKLGADFYKTNRGGLITFHGPGQLVAYPIINLKHFTPSIKWFVQSIEQTVIQLCKQEFS 129
+ G + Y RGG +T+HGPGQLV YPI + ++ F++ IE+ ++++ +
Sbjct: 63 YRENGFELYWVERGGDVTYHGPGQLVGYPIFPVGR---EVRRFLRQIEEAIVRVAAG-YG 118
Query: 130 LNAGLIPKYTGVFLDDEYKVCAIGVHSSLYITHHGLAINCDTDLTWFNHITPCGIKDKQV 189
++A P Y GV++ ++ K+CAIGV ++ HG A+N +TDL F I PCG+K K V
Sbjct: 119 ISAYPTPGYAGVWVGED-KLCAIGVAVKEGVSFHGFALNVNTDLNDFTVIVPCGLKGKGV 177
Query: 190 TSLSKHLSKDITVD 203
TSL K L + + ++
Sbjct: 178 TSLEKLLGRKVPME 191
>pdb|2QHS|A Chain A, Structural Basis Of Octanoic Acid Recognition By
Lipoate-protein Ligase B
Length = 237
Score = 116 bits (291), Expect = 8e-27, Method: Compositional matrix adjust.
Identities = 68/194 (35%), Positives = 106/194 (54%), Gaps = 10/194 (5%)
Query: 10 LGVVSYSNGIKIQEHYVNKLKTLISKPSNHSGTLLLLEHKPVYTIGIRSLKEYDENLELK 69
LG+V Y Q+ ++ N TLLLLEH V T+G ++ E E
Sbjct: 28 LGLVPYGEAWAYQKRVHREVVA-----GNRPPTLLLLEHPRVITLGRKATGENLLFPESW 82
Query: 70 LNKLGADFYKTNRGGLITFHGPGQLVAYPIINLKHFTPSIKWFVQSIEQTVIQLCKQEFS 129
+ G + Y RGG +T+HGPGQLV YPI + ++ F++ IE+ ++++ +
Sbjct: 83 YRENGFELYWVERGGDVTYHGPGQLVGYPIFPVGR---EVRRFLRQIEEAIVRVAAG-YG 138
Query: 130 LNAGLIPKYTGVFLDDEYKVCAIGVHSSLYITHHGLAINCDTDLTWFNHITPCGIKDKQV 189
++A P Y GV++ ++ K+CAIGV ++ HG A+N +TDL F I PCG+K K V
Sbjct: 139 ISAYPTPGYAGVWVGED-KLCAIGVAVKEGVSFHGFALNVNTDLNDFTVIVPCGLKGKGV 197
Query: 190 TSLSKHLSKDITVD 203
TSL K L + + ++
Sbjct: 198 TSLEKLLGRKVPME 211
>pdb|3ISP|A Chain A, Crystal Structure Of Argp From Mycobacterium Tuberculosis
pdb|3ISP|B Chain B, Crystal Structure Of Argp From Mycobacterium Tuberculosis
Length = 303
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 7/83 (8%)
Query: 104 HFTPS-IKWFVQSIEQTVIQLC----KQEFSLNAG--LIPKYTGVFLDDEYKVCAIGVHS 156
H TPS + ++S+EQ V Q+ K + AG L+ L + + +G ++
Sbjct: 31 HVTPSAVSQRIKSLEQQVGQVLVVREKPCRATTAGIPLLRLAAQTALLESEALAEMGGNA 90
Query: 157 SLYITHHGLAINCDTDLTWFNHI 179
SL T +A+N D+ TWF+ +
Sbjct: 91 SLKRTRITIAVNADSMATWFSAV 113
>pdb|2J6J|A Chain A, Prefusion Form Of The Vesicular Stomatitis Virus
Glycoprotein G Ectodomain
Length = 422
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 9/53 (16%)
Query: 88 FHGPGQLVAYPIINLKHFTPSIKWFVQSIEQTVIQLCKQEFSLNAGLIPKYTG 140
++GP Y +++ FTPS++ +SIEQT KQ LN G P+ G
Sbjct: 72 WYGP----KYITQSIRSFTPSVEQCKESIEQT-----KQGTWLNPGFPPQSCG 115
>pdb|2CMZ|A Chain A, Crystal Structure Of Vsv-Indiana (Mudd-Summers Strain)
Glycoprotein Under Its Acidic Conformation
pdb|2CMZ|B Chain B, Crystal Structure Of Vsv-Indiana (Mudd-Summers Strain)
Glycoprotein Under Its Acidic Conformation
pdb|2CMZ|C Chain C, Crystal Structure Of Vsv-Indiana (Mudd-Summers Strain)
Glycoprotein Under Its Acidic Conformation
Length = 423
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 9/53 (16%)
Query: 88 FHGPGQLVAYPIINLKHFTPSIKWFVQSIEQTVIQLCKQEFSLNAGLIPKYTG 140
++GP Y +++ FTPS++ +SIEQT KQ LN G P+ G
Sbjct: 72 WYGP----KYITQSIRSFTPSVEQCKESIEQT-----KQGTWLNPGFPPQSCG 115
>pdb|2VV4|B Chain B, Hppargamma Ligand Binding Domain In Complex With 6-Oxoote
Length = 276
Score = 27.3 bits (59), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 19/87 (21%), Positives = 38/87 (43%), Gaps = 8/87 (9%)
Query: 80 TNRGGLITFHGPGQLVAYPIINLKHFTPSIKWFVQSIEQTVIQLCK-------QEFSLNA 132
T++ + + ++ I KH TP ++ + + + Q C+ QE + A
Sbjct: 41 TDKSPFVIYDMQSLMMGEDKIKFKHITP-LQEQSKEVAIRIFQGCQFRSVEAVQEITEYA 99
Query: 133 GLIPKYTGVFLDDEYKVCAIGVHSSLY 159
IP + + L+D+ + GVH +Y
Sbjct: 100 KSIPGFVNLDLNDQVTLLKYGVHEIIY 126
>pdb|2Y1I|A Chain A, Crystal Structure Of A S-Diastereomer Analogue Of The
Spore Photoproduct In Complex With Fragment Dna
Polymerase I From Bacillus Stearothermophilus
pdb|2Y1J|A Chain A, Crystal Structure Of A R-Diastereomer Analogue Of The
Spore Photoproduct In Complex With Fragment Dna
Polymerase I From Bacillus Stearothermophilus
Length = 580
Score = 27.3 bits (59), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 21/31 (67%), Gaps = 3/31 (9%)
Query: 113 VQSIEQTVIQLCKQEFSLNAGLIPKYTGVFL 143
++++EQ + +L QEF++N+ PK GV L
Sbjct: 215 LRTVEQRIYELAGQEFNINS---PKQLGVIL 242
>pdb|2XY5|A Chain A, Crystal Structure Of An Artificial Salen-Copper Basepair
In Complex With Fragment Dna Polymerase I From Bacillus
Stearothermophilus
Length = 581
Score = 27.3 bits (59), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 21/31 (67%), Gaps = 3/31 (9%)
Query: 113 VQSIEQTVIQLCKQEFSLNAGLIPKYTGVFL 143
++++EQ + +L QEF++N+ PK GV L
Sbjct: 216 LRTVEQRIYELAGQEFNINS---PKQLGVIL 243
>pdb|2XY6|A Chain A, Crystal Structure Of A Salicylic Aldehyde Basepair In
Complex With Fragment Dna Polymerase I From Bacillus
Stearothermophilus
Length = 581
Score = 27.3 bits (59), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 21/31 (67%), Gaps = 3/31 (9%)
Query: 113 VQSIEQTVIQLCKQEFSLNAGLIPKYTGVFL 143
++++EQ + +L QEF++N+ PK GV L
Sbjct: 216 LRTVEQRIYELAGQEFNINS---PKQLGVIL 243
>pdb|2XO7|A Chain A, Crystal Structure Of A Da:o-Allylhydroxylamine-Dc Basepair
In Complex With Fragment Dna Polymerase I From Bacillus
Stearothermophilus
Length = 580
Score = 27.3 bits (59), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 21/31 (67%), Gaps = 3/31 (9%)
Query: 113 VQSIEQTVIQLCKQEFSLNAGLIPKYTGVFL 143
++++EQ + +L QEF++N+ PK GV L
Sbjct: 215 LRTVEQRIYELAGQEFNINS---PKQLGVIL 242
>pdb|2XY7|A Chain A, Crystal Structure Of A Salicylic Aldehyde Base In The
Pre-Insertion Site Of Fragment Dna Polymerase I From
Bacillus Stearothermophilus
Length = 580
Score = 27.3 bits (59), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 21/31 (67%), Gaps = 3/31 (9%)
Query: 113 VQSIEQTVIQLCKQEFSLNAGLIPKYTGVFL 143
++++EQ + +L QEF++N+ PK GV L
Sbjct: 215 LRTVEQRIYELAGQEFNINS---PKQLGVIL 242
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 0.138 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,710,212
Number of Sequences: 62578
Number of extensions: 272503
Number of successful extensions: 1084
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1073
Number of HSP's gapped (non-prelim): 14
length of query: 235
length of database: 14,973,337
effective HSP length: 96
effective length of query: 139
effective length of database: 8,965,849
effective search space: 1246253011
effective search space used: 1246253011
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: 50 (23.9 bits)