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= psy5800
(152 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2VSZ|A Chain A, Crystal Structure Of The Elmo1 Ph Domain
pdb|2VSZ|B Chain B, Crystal Structure Of The Elmo1 Ph Domain
Length = 149
Score = 117 bits (294), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 61/101 (60%), Positives = 74/101 (73%), Gaps = 5/101 (4%)
Query: 53 AKPIVELKELITPEIVDLIQQQRLGYLVEGTRFTKYSSRGQVIILDKFWYVRLSPNHKVF 112
PI+ELKE I PEI++LI+QQRL LVEGT F K ++R + DKFWY RLSPNHKV
Sbjct: 4 GSPILELKEKIQPEILELIKQQRLNRLVEGTCFRKLNARRRQ---DKFWYCRLSPNHKVL 60
Query: 113 QYGDCDEKSIPQLDH--LPNKLPVADIKALLVGKDCPHMKE 151
YGD +E ++ H L +KLPVADIKA++ GKDCPHMKE
Sbjct: 61 HYGDLEESPQGEVPHDSLQDKLPVADIKAVVTGKDCPHMKE 101
>pdb|3A98|B Chain B, Crystal Structure Of The Complex Of The Interacting
Regions Of Dock2 And Elmo1
pdb|3A98|D Chain D, Crystal Structure Of The Complex Of The Interacting
Regions Of Dock2 And Elmo1
Length = 203
Score = 115 bits (287), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 60/101 (59%), Positives = 74/101 (73%), Gaps = 5/101 (4%)
Query: 53 AKPIVELKELITPEIVDLIQQQRLGYLVEGTRFTKYSSRGQVIILDKFWYVRLSPNHKVF 112
+ PI+ELKE I PEI++LI+QQRL LVEGT F K ++R + DKFWY RLSPNHKV
Sbjct: 6 SGPILELKEKIQPEILELIKQQRLNRLVEGTCFRKLNARRRQ---DKFWYCRLSPNHKVL 62
Query: 113 QYGDCDEKSIPQLDH--LPNKLPVADIKALLVGKDCPHMKE 151
YGD +E ++ H L +KLPVADIKA++ GKDCPH KE
Sbjct: 63 HYGDLEESPQGEVPHDSLQDKLPVADIKAVVTGKDCPHXKE 103
>pdb|2AIZ|P Chain P, Solution Structure Of Peptidoglycan Associated Lipoprotein
From Haemophilus Influenza Bound To
Udp-N-Acetylmuramoyl-L-
Alanyl-D-Glutamyl-Meso-2,6-Diaminopimeloyl-D-Alanyl-D-
Alanine
Length = 134
Score = 31.2 bits (69), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 38/86 (44%), Gaps = 6/86 (6%)
Query: 67 IVDLIQQQRLGYLVEGTRFTKYSSRGQVI-ILDKFW-YVRLSPNHKVFQYGDCDEKSIPQ 124
+ DL QQR + G F KY G+ + ILD Y+ +P KV G+ DE+ P+
Sbjct: 22 VADL--QQRYNTVYFG--FDKYDITGEYVQILDAHAAYLNATPAAKVLVEGNTDERGTPE 77
Query: 125 LDHLPNKLPVADIKALLVGKDCPHMK 150
+ + +K L GK K
Sbjct: 78 YNIALGQRRADAVKGYLAGKGVDAGK 103
>pdb|3H11|A Chain A, Zymogen Caspase-8:c-Flipl Protease Domain Complex
pdb|3H13|A Chain A, C-Flipl Protease-Like Domain
Length = 272
Score = 29.6 bits (65), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 11/80 (13%)
Query: 76 LGYLVEGTRFTKYSSRGQVIILDKFWYVRLSPNHKVFQYGDC------DEKSIPQLDHLP 129
LGY V+ +F S G IL +F + P H+ + C +S+ +D
Sbjct: 66 LGYEVQ--KFLHLSMHGISQILGQFACM---PEHRDYDSFVCVLVSRGGSQSVYGVDQTH 120
Query: 130 NKLPVADIKALLVGKDCPHM 149
+ LP+ I+ + +G CP++
Sbjct: 121 SGLPLHHIRRMFMGDSCPYL 140
>pdb|4DJ2|A Chain A, Unwinding The Differences Of The Mammalian Period Clock
Proteins From Crystal Structure To Cellular Function
pdb|4DJ2|B Chain B, Unwinding The Differences Of The Mammalian Period Clock
Proteins From Crystal Structure To Cellular Function
pdb|4DJ2|C Chain C, Unwinding The Differences Of The Mammalian Period Clock
Proteins From Crystal Structure To Cellular Function
pdb|4DJ2|D Chain D, Unwinding The Differences Of The Mammalian Period Clock
Proteins From Crystal Structure To Cellular Function
Length = 320
Score = 26.6 bits (57), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 8/54 (14%)
Query: 104 RLSPNHKVFQ--------YGDCDEKSIPQLDHLPNKLPVADIKALLVGKDCPHM 149
R+ P+ ++F + D DE++ P L +LP L A + L +D P M
Sbjct: 170 RIPPDKRIFTTRHTPSCLFQDVDERAAPLLGYLPQDLLGAPVLLFLHPEDRPLM 223
>pdb|1Q5D|A Chain A, Epothilone B-Bound Cytochrome P450epok
pdb|1Q5E|A Chain A, Substrate-Free Cytochrome P450epok
Length = 419
Score = 25.8 bits (55), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 21/33 (63%), Gaps = 2/33 (6%)
Query: 32 YSEITNLWQQER--TSREEWESHAKPIVELKEL 62
Y +++ +++ ER SREEWES A+ + EL
Sbjct: 55 YHDVSAVFRDERFAVSREEWESSAEYSSAIPEL 87
>pdb|1PKF|A Chain A, Crystal Structure Of Epothilone D-Bound Cytochrome
P450epok
Length = 419
Score = 25.8 bits (55), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 21/33 (63%), Gaps = 2/33 (6%)
Query: 32 YSEITNLWQQER--TSREEWESHAKPIVELKEL 62
Y +++ +++ ER SREEWES A+ + EL
Sbjct: 55 YHDVSAVFRDERFAVSREEWESSAEYSSAIPEL 87
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 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,507,056
Number of Sequences: 62578
Number of extensions: 173534
Number of successful extensions: 478
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 471
Number of HSP's gapped (non-prelim): 8
length of query: 152
length of database: 14,973,337
effective HSP length: 90
effective length of query: 62
effective length of database: 9,341,317
effective search space: 579161654
effective search space used: 579161654
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: 47 (22.7 bits)