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= psy2507
(111 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4I4T|F Chain F, Crystal Structure Of Tubulin-rb3-ttl-zampanolide Complex
pdb|4I50|F Chain F, Crystal Structure Of Tubulin-stathmin-ttl-epothilone A
Complex
pdb|4I55|F Chain F, Crystal Structure Of Tubulin-stathmin-ttl Complex
pdb|4IIJ|F Chain F, Crystal Structure Of Tubulin-stathmin-ttl-apo Complex
pdb|4IHJ|F Chain F, Crystal Structure Of Tubulin-stathmin-ttl-adp Complex
Length = 384
Score = 41.2 bits (95), Expect = 2e-04, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 8/55 (14%)
Query: 4 EKYELYGFDILIDSDLKPWLLEVNLSPSLG-------CDTPLDTRLKSAM-LADT 50
+ ++L+GFD ++D +LK WL+EVN +P+ C +D + S LADT
Sbjct: 310 QSFQLFGFDFMVDEELKVWLIEVNGAPACAQKLYAELCQGIVDVAISSVFPLADT 364
>pdb|3TIG|A Chain A, Tubulin Tyrosine Ligase
pdb|3TII|A Chain A, Tubulin Tyrosine Ligase
pdb|3TII|B Chain B, Tubulin Tyrosine Ligase
pdb|3TIN|A Chain A, Tubulin Tyrosine Ligase
Length = 380
Score = 38.5 bits (88), Expect = 9e-04, Method: Composition-based stats.
Identities = 13/26 (50%), Positives = 22/26 (84%)
Query: 6 YELYGFDILIDSDLKPWLLEVNLSPS 31
++L+GFD ++D +LK WL+EVN +P+
Sbjct: 315 FQLFGFDFMVDKNLKVWLIEVNGAPA 340
>pdb|2B1W|A Chain A, Solution Structure Of The Nod1 Caspase Activating And
Recruitment Domain
Length = 127
Score = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 15/30 (50%), Positives = 20/30 (66%), Gaps = 2/30 (6%)
Query: 5 KYELYGFDILIDS--DLKPWLLEVNLSPSL 32
++ LY L D+ DL+PWLLE+ SPSL
Sbjct: 73 EFFLYLLQQLADAYVDLRPWLLEIGFSPSL 102
>pdb|4E9M|A Chain A, Nod1 Card Domain With Three Disulfide-clinched,
Domain-swapped Dimers In The Asymmetric Unit
pdb|4E9M|B Chain B, Nod1 Card Domain With Three Disulfide-clinched,
Domain-swapped Dimers In The Asymmetric Unit
pdb|4E9M|C Chain C, Nod1 Card Domain With Three Disulfide-clinched,
Domain-swapped Dimers In The Asymmetric Unit
pdb|4E9M|D Chain D, Nod1 Card Domain With Three Disulfide-clinched,
Domain-swapped Dimers In The Asymmetric Unit
pdb|4E9M|E Chain E, Nod1 Card Domain With Three Disulfide-clinched,
Domain-swapped Dimers In The Asymmetric Unit
pdb|4E9M|F Chain F, Nod1 Card Domain With Three Disulfide-clinched,
Domain-swapped Dimers In The Asymmetric Unit
Length = 144
Score = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 15/30 (50%), Positives = 20/30 (66%), Gaps = 2/30 (6%)
Query: 5 KYELYGFDILIDS--DLKPWLLEVNLSPSL 32
++ LY L D+ DL+PWLLE+ SPSL
Sbjct: 90 EFFLYLLQQLADAYVDLRPWLLEIGFSPSL 119
>pdb|4E2C|A Chain A, Crystal Structure Of The Periplasmic Domain Of The
Chimeric Lps O- Antigen Chain Length Regulator Protein
pdb|4E2C|B Chain B, Crystal Structure Of The Periplasmic Domain Of The
Chimeric Lps O- Antigen Chain Length Regulator Protein
Length = 245
Score = 30.4 bits (67), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 27/41 (65%), Gaps = 2/41 (4%)
Query: 49 DTLTLVGIPALDPMLRHNSTKRSPFLSSSHTLRTKCSLGDM 89
DTL L+G AL+ M++H +T+ P + S + +TK +L D+
Sbjct: 180 DTLFLLGSEALESMIKHEATR--PLVFSPNYYQTKQTLLDI 218
>pdb|4E2H|A Chain A, Crystal Structure Of The Periplasmic Domain Of Shigella
Flexneri Wzzb
pdb|4E2H|C Chain C, Crystal Structure Of The Periplasmic Domain Of Shigella
Flexneri Wzzb
pdb|4E2H|B Chain B, Crystal Structure Of The Periplasmic Domain Of Shigella
Flexneri Wzzb
Length = 240
Score = 29.3 bits (64), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 30/46 (65%), Gaps = 3/46 (6%)
Query: 49 DTLTLVGIPALDPMLRHNSTKRSPFLSSSHTLRTKCSLGDMD-LKF 93
DTL L+G AL+ ++H +T+ P + S + +T+ +L D++ LKF
Sbjct: 181 DTLFLLGSEALESXIKHEATR--PLVFSPNYYQTRQNLLDIEKLKF 224
>pdb|4EGJ|A Chain A, Crystal Structure Of D-Alanine-D-Alanine Ligase From
Burkholderia Xenovorans
pdb|4EGJ|B Chain B, Crystal Structure Of D-Alanine-D-Alanine Ligase From
Burkholderia Xenovorans
pdb|4EGJ|C Chain C, Crystal Structure Of D-Alanine-D-Alanine Ligase From
Burkholderia Xenovorans
pdb|4EGJ|D Chain D, Crystal Structure Of D-Alanine-D-Alanine Ligase From
Burkholderia Xenovorans
Length = 334
Score = 27.7 bits (60), Expect = 1.6, Method: Composition-based stats.
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 12 DILIDSDLKPWLLEVNLSPSL 32
D ++D+D P+ LEVN +P +
Sbjct: 283 DFMLDADGNPYFLEVNTAPGM 303
>pdb|3ULY|B Chain B, Crystal Structure Of Brox Bro1 Domain In Complex With
The C-Terminal Tails Of Chmp5
pdb|3UM1|B Chain B, Crystal Structure Of The Brox Bro1 Domain In Complex
With The C- Terminal Tail Of Chmp5
pdb|3UM1|E Chain E, Crystal Structure Of The Brox Bro1 Domain In Complex
With The C- Terminal Tail Of Chmp5
Length = 69
Score = 27.3 bits (59), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 10 GFDILIDSDLKPWLLEVNLSPSLGCDTPLDTRLKSAMLADTLTLVGIPA 58
G ++L D D +L E +P++ P DT+ K +L D L IPA
Sbjct: 21 GDELLADEDSS-YLDEAASAPAIPEGVPTDTKNKDGVLVDEFGLPQIPA 68
>pdb|3VAR|A Chain A, Crystal Structure Of Dnpep, Znzn Form
pdb|3VAT|A Chain A, Crystal Structure Of Dnpep, Znmg Form
Length = 496
Score = 26.9 bits (58), Expect = 3.1, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 4/59 (6%)
Query: 42 LKSAMLADTLTLVGIPALDPMLRHNS---TKRSPFLSSSHTLRTKCSLGDMDLKFHQNR 97
+ A++ + + VG+P D M+R++S T P L+S LR LG L H R
Sbjct: 407 VSEALIREVASSVGVPLQDLMVRNDSPCGTTIGPILASRLGLRV-LDLGSPQLAMHSIR 464
>pdb|1IOV|A Chain A, Complex Of D-Ala:d-Ala Ligase With Adp And A Phosphoryl
Phosphonate
pdb|2DLN|A Chain A, Vancomycin Resistance: Structure Of D-Alanine:d-Alanine
Ligase At 2.3 Angstroms Resolution
Length = 306
Score = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 11 FDILIDSDLKPWLLEVNLSPSL 32
D+++DSD + +LLE N SP +
Sbjct: 256 IDVMLDSDGQFYLLEANTSPGM 277
>pdb|1IOW|A Chain A, Complex Of Y216f D-Ala:d-Ala Ligase With Adp And A
Phosphoryl Phosphinate
Length = 306
Score = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 11 FDILIDSDLKPWLLEVNLSPSL 32
D+++DSD + +LLE N SP +
Sbjct: 256 IDVMLDSDGQFYLLEANTSPGM 277
>pdb|2DBD|A Chain A, Solution Structure Of The Card Domain In Human Caspase
Recruitment Domain Protein 4 (Nod1 Protein)
Length = 107
Score = 25.8 bits (55), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 20/33 (60%), Gaps = 4/33 (12%)
Query: 5 KYELYGFDILIDS--DLKPWLLEVNLS--PSLG 33
++ LY L D+ DL+PWLLE+ S PS G
Sbjct: 75 EFFLYLLQQLADAYVDLRPWLLEIGFSSGPSSG 107
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
0.319 0.134 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,085,140
Number of Sequences: 62578
Number of extensions: 102606
Number of successful extensions: 191
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 180
Number of HSP's gapped (non-prelim): 14
length of query: 111
length of database: 14,973,337
effective HSP length: 75
effective length of query: 36
effective length of database: 10,279,987
effective search space: 370079532
effective search space used: 370079532
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)