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= psy12041
(153 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3VKG|A Chain A, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein Motor
Domain
pdb|3VKG|B Chain B, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein Motor
Domain
Length = 3245
Score = 70.1 bits (170), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 46/158 (29%), Positives = 80/158 (50%), Gaps = 26/158 (16%)
Query: 5 WNSEGLPPDELSIQNGILSTRGCHFPLCIDPQTQALKWIRNR-EDKNNLKVSYKLKLAES 63
W++ LP DEL I+N I+ R +PL IDP QA++++ N+ DK K S+ L S
Sbjct: 2162 WHANSLPSDELCIENAIMLKRFNRYPLVIDPSGQAMEFLMNQYADKKITKTSF---LDSS 2218
Query: 64 TAIDIDNLREGYRPVAKRGALLF---FVFSDISNVNPMYQYSLESYLE-------VPYGD 113
++++ AL F + D+ N++P+ L + + GD
Sbjct: 2219 FMKNLES------------ALRFGCPLLVQDVENIDPVLNPVLNKEIRKKGGRILIRLGD 2266
Query: 114 KEVDYDVNFRLYLTTKIPNPTFDPSLYTKATVINYSVT 151
++VD+ +F ++L T+ P F P L ++ T +N++VT
Sbjct: 2267 QDVDFSPSFMIFLFTRDPTAHFTPDLCSRVTFVNFTVT 2304
Score = 32.7 bits (73), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 50/95 (52%), Gaps = 8/95 (8%)
Query: 49 KNNLKVSYKLKLAESTAIDIDNLREGYRPVAKRGALLFFVFSDISNVNPMYQYSLESYLE 108
K +++ K++ E+ +I + Y P+A + ++F ++S + +YQ+SL ++L+
Sbjct: 2375 KETTEIALKVEETETVMQEISEVSALYNPMALSCSRVYFAMEELSQFH-LYQFSLRAFLD 2433
Query: 109 VPY-----GDKEVD-YDVNFRL-YLTTKIPNPTFD 136
+ Y VD D N RL YL+ I + TF+
Sbjct: 2434 IFYNLLNNNPNLVDKKDPNERLVYLSKDIFSMTFN 2468
>pdb|3VKH|A Chain A, X-Ray Structure Of A Functional Full-Length Dynein Motor
Domain
pdb|3VKH|B Chain B, X-Ray Structure Of A Functional Full-Length Dynein Motor
Domain
Length = 3367
Score = 70.1 bits (170), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 46/158 (29%), Positives = 80/158 (50%), Gaps = 26/158 (16%)
Query: 5 WNSEGLPPDELSIQNGILSTRGCHFPLCIDPQTQALKWIRNR-EDKNNLKVSYKLKLAES 63
W++ LP DEL I+N I+ R +PL IDP QA++++ N+ DK K S+ L S
Sbjct: 2284 WHANSLPSDELCIENAIMLKRFNRYPLVIDPSGQAMEFLMNQYADKKITKTSF---LDSS 2340
Query: 64 TAIDIDNLREGYRPVAKRGALLF---FVFSDISNVNPMYQYSLESYLE-------VPYGD 113
++++ AL F + D+ N++P+ L + + GD
Sbjct: 2341 FMKNLES------------ALRFGCPLLVQDVENIDPVLNPVLNKEIRKKGGRILIRLGD 2388
Query: 114 KEVDYDVNFRLYLTTKIPNPTFDPSLYTKATVINYSVT 151
++VD+ +F ++L T+ P F P L ++ T +N++VT
Sbjct: 2389 QDVDFSPSFMIFLFTRDPTAHFTPDLCSRVTFVNFTVT 2426
Score = 32.7 bits (73), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 50/95 (52%), Gaps = 8/95 (8%)
Query: 49 KNNLKVSYKLKLAESTAIDIDNLREGYRPVAKRGALLFFVFSDISNVNPMYQYSLESYLE 108
K +++ K++ E+ +I + Y P+A + ++F ++S + +YQ+SL ++L+
Sbjct: 2497 KETTEIALKVEETETVMQEISEVSALYNPMALSCSRVYFAMEELSQFH-LYQFSLRAFLD 2555
Query: 109 VPY-----GDKEVD-YDVNFRL-YLTTKIPNPTFD 136
+ Y VD D N RL YL+ I + TF+
Sbjct: 2556 IFYNLLNNNPNLVDKKDPNERLVYLSKDIFSMTFN 2590
>pdb|1ILG|A Chain A, Crystal Structure Of Apo Human Pregnane X Receptor Ligand
Binding Domain
pdb|1ILH|A Chain A, Crystal Structure Of Human Pregnane X Receptor Ligand
Binding Domain Bound To Sr12813
pdb|1M13|A Chain A, Crystal Structure Of The Human Pregane X Receptor Ligand
Binding Domain In Complex With Hyperforin, A Constituent
Of St. John's Wort
pdb|1NRL|A Chain A, Crystal Structure Of The Human Pxr-Lbd In Complex With An
Src-1 Coactivator Peptide And Sr12813
pdb|1NRL|B Chain B, Crystal Structure Of The Human Pxr-Lbd In Complex With An
Src-1 Coactivator Peptide And Sr12813
pdb|2QNV|A Chain A, Crystal Structure Of The Pregnane X Receptor Bound To
Colupulone
pdb|3R8D|A Chain A, Activation Of The Human Nuclear Xenobiotic Receptor Pxr By
The Reverse Transcriptase-Targeted Anti-Hiv Drug
Pnu-142721
Length = 316
Score = 29.6 bits (65), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 42/84 (50%), Gaps = 12/84 (14%)
Query: 20 GILSTRGCHFPLCIDP--QTQALKWIRNREDKNNLKVSYKLKLAESTAIDIDNLREGYRP 77
G+LS+ GC P + + +A KW + R+D +LKVS +L+ + + + Y+P
Sbjct: 58 GVLSS-GCELPESLQAPSREEAAKWSQVRKDLCSLKVSLQLRGEDGSVWN-------YKP 109
Query: 78 VAKRGALLFFVFSDISNVNPMYQY 101
A G +FS + ++ M Y
Sbjct: 110 PADSGGKE--IFSLLPHMADMSTY 131
>pdb|2O9I|A Chain A, Crystal Structure Of The Human Pregnane X Receptor Lbd
In Complex With An Src-1 Coactivator Peptide And
T0901317
pdb|2O9I|B Chain B, Crystal Structure Of The Human Pregnane X Receptor Lbd
In Complex With An Src-1 Coactivator Peptide And
T0901317
Length = 293
Score = 29.6 bits (65), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 10/66 (15%)
Query: 20 GILSTRGCHFPLCIDP--QTQALKWIRNREDKNNLKVSYKLKLAESTAIDIDNLREGYRP 77
G+LS+ GC P + + +A KW + R+D +LKVS +L+ + + + Y+P
Sbjct: 35 GVLSS-GCELPESLQAPSREEAAKWSQVRKDLCSLKVSLQLRGEDGSVWN-------YKP 86
Query: 78 VAKRGA 83
A G
Sbjct: 87 PADSGG 92
>pdb|1SKX|A Chain A, Structural Disorder In The Complex Of Human Pxr And The
Macrolide Antibiotic Rifampicin
Length = 313
Score = 29.6 bits (65), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 42/84 (50%), Gaps = 12/84 (14%)
Query: 20 GILSTRGCHFPLCIDP--QTQALKWIRNREDKNNLKVSYKLKLAESTAIDIDNLREGYRP 77
G+LS+ GC P + + +A KW + R+D +LKVS +L+ + + + Y+P
Sbjct: 58 GVLSS-GCELPESLQAPSREEAAKWSQVRKDLCSLKVSLQLRGEDGSVWN-------YKP 109
Query: 78 VAKRGALLFFVFSDISNVNPMYQY 101
A G +FS + ++ M Y
Sbjct: 110 PADSGGKE--IFSLLPHMADMSTY 131
>pdb|3CTB|A Chain A, Tethered Pxr-LbdSRC-1p Apoprotein
pdb|3CTB|B Chain B, Tethered Pxr-LbdSRC-1p Apoprotein
pdb|3HVL|A Chain A, Tethered Pxr-LbdSRC-1p Complexed With Sr-12813
pdb|3HVL|B Chain B, Tethered Pxr-LbdSRC-1p Complexed With Sr-12813
Length = 344
Score = 29.6 bits (65), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 42/84 (50%), Gaps = 12/84 (14%)
Query: 20 GILSTRGCHFPLCIDP--QTQALKWIRNREDKNNLKVSYKLKLAESTAIDIDNLREGYRP 77
G+LS+ GC P + + +A KW + R+D +LKVS +L+ + + + Y+P
Sbjct: 58 GVLSS-GCELPESLQAPSREEAAKWSQVRKDLCSLKVSLQLRGEDGSVWN-------YKP 109
Query: 78 VAKRGALLFFVFSDISNVNPMYQY 101
A G +FS + ++ M Y
Sbjct: 110 PADSGGKE--IFSLLPHMADMSTY 131
>pdb|4F5X|W Chain W, Location Of The Dsrna-dependent Polymerase, Vp1, In
Rotavirus Particles
Length = 1089
Score = 27.7 bits (60), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 29/59 (49%), Gaps = 12/59 (20%)
Query: 103 LESY----LEVPYGDKEVDYDVN-------FRLYLTTKIPNPTFDPSLYTKATVINYSV 150
LESY L + YG ++ +D N R+ KIP TF LY K VINY++
Sbjct: 989 LESYVYNLLSINYGCYQL-FDFNSPDLEKLIRIPFKGKIPAVTFILHLYAKLEVINYAI 1046
>pdb|2R7Q|A Chain A, Crystal Structure Of Vp1 Apoenzyme Of Rotavirus Sa11 (C-
Terminal Hexahistidine-Tagged)
pdb|2R7R|A Chain A, Crystal Structure Of Rotavirus Sa11 Vp1RNA (UGUGACC) Complex
pdb|2R7S|A Chain A, Crystal Structure Of Rotavirus Sa11 Vp1 RNA (UGUGCC)
Complex
pdb|2R7T|A Chain A, Crystal Structure Of Rotavirus Sa11 Vp1RNA (UGUGAACC)
Complex
pdb|2R7U|A Chain A, Crystal Structure Of Rotavirus Sa11 Vp1RNA (AAAAGCC) Complex
pdb|2R7V|A Chain A, Crystal Structure Of Rotavirus Sa11 Vp1RNA (GGCUUU) COMPLEX
pdb|2R7W|A Chain A, Crystal Structure Of Rotavirus Sa11 Vp1RNA (UGUGACC)MRNA
5'-Cap (M7gpppg) Complex
pdb|2R7X|A Chain A, Crystal Structure Of Rotavirus Sa11 Vp1RNA (UGUGACC)GTP
Complex
pdb|2R7X|B Chain B, Crystal Structure Of Rotavirus Sa11 Vp1RNA (UGUGACC)GTP
Complex
Length = 1095
Score = 27.7 bits (60), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 29/59 (49%), Gaps = 12/59 (20%)
Query: 103 LESY----LEVPYGDKEVDYDVN-------FRLYLTTKIPNPTFDPSLYTKATVINYSV 150
LESY L + YG ++ +D N R+ KIP TF LY K VINY++
Sbjct: 989 LESYVYNLLSINYGCYQL-FDFNSPDLEKLIRIPFKGKIPAVTFILHLYAKLEVINYAI 1046
>pdb|2R7O|A Chain A, Crystal Structure Of Vp1 Apoenzyme Of Rotavirus Sa11 (N-
Terminal Hexahistidine-Tagged)
pdb|4AU6|A Chain A, Location Of The Dsrna-dependent Polymerase, Vp1, In
Rotavirus Particles
pdb|4AU6|B Chain B, Location Of The Dsrna-dependent Polymerase, Vp1, In
Rotavirus Particles
pdb|4AU6|C Chain C, Location Of The Dsrna-dependent Polymerase, Vp1, In
Rotavirus Particles
pdb|4AU6|D Chain D, Location Of The Dsrna-dependent Polymerase, Vp1, In
Rotavirus Particles
pdb|4AU6|E Chain E, Location Of The Dsrna-dependent Polymerase, Vp1, In
Rotavirus Particles
Length = 1095
Score = 27.7 bits (60), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 29/59 (49%), Gaps = 12/59 (20%)
Query: 103 LESY----LEVPYGDKEVDYDVN-------FRLYLTTKIPNPTFDPSLYTKATVINYSV 150
LESY L + YG ++ +D N R+ KIP TF LY K VINY++
Sbjct: 995 LESYVYNLLSINYGCYQL-FDFNSPDLEKLIRIPFKGKIPAVTFILHLYAKLEVINYAI 1052
>pdb|2ODH|A Chain A, Restriction Endonuclease Bcni In The Absence Of Dna
pdb|2Q10|A Chain A, Restriction Endonuclease Bcni (Wild Type)-Cognate Dna
Substrate Complex
pdb|2Q10|B Chain B, Restriction Endonuclease Bcni (Wild Type)-Cognate Dna
Substrate Complex
pdb|3IMB|A Chain A, Alternative Binding Mode Of Restriction Endonuclease
Bcni To Cognate Dna
pdb|3IMB|B Chain B, Alternative Binding Mode Of Restriction Endonuclease
Bcni To Cognate Dna
pdb|3IMB|C Chain C, Alternative Binding Mode Of Restriction Endonuclease
Bcni To Cognate Dna
pdb|3IMB|D Chain D, Alternative Binding Mode Of Restriction Endonuclease
Bcni To Cognate Dna
Length = 238
Score = 27.7 bits (60), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 40 LKWIRNREDKNNLKVSYKLKLAESTAIDIDNLREGY 75
LK +RNR+ K+NL + +K +A T I I N R GY
Sbjct: 61 LKGMRNRKAKSNLTLFHKKPVAGQTVIQIFN-RFGY 95
>pdb|2ODI|A Chain A, Restriction Endonuclease Bcni-Cognate Dna Substrate
Complex
pdb|2ODI|B Chain B, Restriction Endonuclease Bcni-Cognate Dna Substrate
Complex
Length = 238
Score = 26.2 bits (56), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 40 LKWIRNREDKNNLKVSYKLKLAESTAIDIDNLREGY 75
LK RNR+ K+NL + +K +A T I I N R GY
Sbjct: 61 LKGXRNRKAKSNLTLFHKKPVAGQTVIQIFN-RFGY 95
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
0.318 0.136 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,774,508
Number of Sequences: 62578
Number of extensions: 182949
Number of successful extensions: 344
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 332
Number of HSP's gapped (non-prelim): 19
length of query: 153
length of database: 14,973,337
effective HSP length: 90
effective length of query: 63
effective length of database: 9,341,317
effective search space: 588502971
effective search space used: 588502971
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)