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= psy1332
(103 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2KDO|A Chain A, Structure Of The Human Shwachman-Bodian-Diamond Syndrome
Protein, Sbds
Length = 252
Score = 78.2 bits (191), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 45/100 (45%), Positives = 65/100 (65%), Gaps = 7/100 (7%)
Query: 6 QVIPTLKQCMSIERAQMRVR--VEVSAGXXXXXXXXXXXXXCATSVENEEWSGGGLLLIC 63
+VI LK+ M IERA MR+R + V+ G +E+E++ G L ++C
Sbjct: 158 EVIKQLKEKMKIERAHMRLRFILPVNEGKKLKEKLKPL----IKVIESEDY-GQQLEIVC 212
Query: 64 LIDPGKYREIDELVRTETRGQGTLELLNLKEVTEGEEVLE 103
LIDPG +REIDEL++ ET+G+G+LE+LNLK+V EG+E E
Sbjct: 213 LIDPGCFREIDELIKKETKGKGSLEVLNLKDVEEGDEKFE 252
>pdb|2L9N|A Chain A, Structure Of The Human Shwachman-Bodian-Diamond Syndrome
(Sbds) Protein
Length = 252
Score = 78.2 bits (191), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 45/100 (45%), Positives = 65/100 (65%), Gaps = 7/100 (7%)
Query: 6 QVIPTLKQCMSIERAQMRVR--VEVSAGXXXXXXXXXXXXXCATSVENEEWSGGGLLLIC 63
+VI LK+ M IERA MR+R + V+ G +E+E++ G L ++C
Sbjct: 158 EVIKQLKEKMKIERAHMRLRFILPVNEGKKLKEKLKPL----IKVIESEDY-GQQLEIVC 212
Query: 64 LIDPGKYREIDELVRTETRGQGTLELLNLKEVTEGEEVLE 103
LIDPG +REIDEL++ ET+G+G+LE+LNLK+V EG+E E
Sbjct: 213 LIDPGCFREIDELIKKETKGKGSLEVLNLKDVEEGDEKFE 252
>pdb|3TQC|A Chain A, Structure Of The Pantothenate Kinase (Coaa) From
Coxiella Burnetii
pdb|3TQC|B Chain B, Structure Of The Pantothenate Kinase (Coaa) From
Coxiella Burnetii
Length = 321
Score = 26.9 bits (58), Expect = 3.0, Method: Composition-based stats.
Identities = 14/33 (42%), Positives = 22/33 (66%), Gaps = 3/33 (9%)
Query: 68 GKYREIDELVRTET---RGQGTLELLNLKEVTE 97
G +R+ L TE+ + QG +E+++LKEVTE
Sbjct: 25 GNFRKDTPLTLTESDLDKLQGQIEIVSLKEVTE 57
>pdb|1PVO|A Chain A, X-Ray Crystal Structure Of Rho Transcription Termination
Factor In Complex With Ssrna Substrate And Anppnp
pdb|1PVO|B Chain B, X-Ray Crystal Structure Of Rho Transcription Termination
Factor In Complex With Ssrna Substrate And Anppnp
pdb|1PVO|C Chain C, X-Ray Crystal Structure Of Rho Transcription Termination
Factor In Complex With Ssrna Substrate And Anppnp
pdb|1PVO|D Chain D, X-Ray Crystal Structure Of Rho Transcription Termination
Factor In Complex With Ssrna Substrate And Anppnp
pdb|1PVO|E Chain E, X-Ray Crystal Structure Of Rho Transcription Termination
Factor In Complex With Ssrna Substrate And Anppnp
pdb|1PVO|F Chain F, X-Ray Crystal Structure Of Rho Transcription Termination
Factor In Complex With Ssrna Substrate And Anppnp
pdb|1XPR|A Chain A, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-formylbicyclomycin (fb)
pdb|1XPR|B Chain B, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-formylbicyclomycin (fb)
pdb|1XPR|C Chain C, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-formylbicyclomycin (fb)
pdb|1XPR|D Chain D, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-formylbicyclomycin (fb)
pdb|1XPR|E Chain E, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-formylbicyclomycin (fb)
pdb|1XPR|F Chain F, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-formylbicyclomycin (fb)
pdb|1XPU|A Chain A, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)
pdb|1XPU|B Chain B, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)
pdb|1XPU|C Chain C, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)
pdb|1XPU|D Chain D, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)
pdb|1XPU|E Chain E, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)
pdb|1XPU|F Chain F, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
5a-(3-Formylphenylsulfanyl)- Dihydrobicyclomycin (Fpdb)
pdb|1XPO|A Chain A, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
Bicyclomycin
pdb|1XPO|B Chain B, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
Bicyclomycin
pdb|1XPO|C Chain C, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
Bicyclomycin
pdb|1XPO|D Chain D, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
Bicyclomycin
pdb|1XPO|E Chain E, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
Bicyclomycin
pdb|1XPO|F Chain F, Structural Mechanism Of Inhibition Of The Rho
Transcription Termination Factor By The Antibiotic
Bicyclomycin
Length = 419
Score = 25.8 bits (55), Expect = 5.7, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 4/44 (9%)
Query: 56 GGGLLLIC--LIDPGKYREIDELVRTETRGQGTLELLNLKEVTE 97
GG L +I LID G ++DE++ E +G G +EL +++ E
Sbjct: 310 GGSLTIIATALIDTGS--KMDEVIYEEFKGTGNMELHLSRKIAE 351
>pdb|2HT1|A Chain A, The Closed Ring Structure Of The Rho Transcription
Termination Factor In Complex With Nucleic Acid In The
Motor Domains
pdb|2HT1|B Chain B, The Closed Ring Structure Of The Rho Transcription
Termination Factor In Complex With Nucleic Acid In The
Motor Domains
Length = 433
Score = 25.8 bits (55), Expect = 5.8, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 4/44 (9%)
Query: 56 GGGLLLIC--LIDPGKYREIDELVRTETRGQGTLELLNLKEVTE 97
GG L +I LID G ++DE++ E +G G +EL +++ E
Sbjct: 332 GGSLTIIATALIDTGS--KMDEVIYEEFKGTGNMELHLSRKIAE 373
>pdb|4GWP|E Chain E, Structure Of The Mediator Head Module From S. Cerevisiae
pdb|4GWQ|E Chain E, Structure Of The Mediator Head Module From S. Cerevisiae
In Complex With The Carboxy-Terminal Domain (Ctd) Of Rna
Polymerase Ii Rpb1 Subunit
Length = 307
Score = 25.8 bits (55), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 6/48 (12%)
Query: 51 NEEWSGGGLLLICLIDPGKYREIDELVRTETRGQGTLELLNLKEVTEG 98
N + + GG LL I+ + +ID + TET L+NLK+ +G
Sbjct: 243 NSQITSGGFLLKAYINVSRGTDIDRINYTET------ALMNLKKELQG 284
>pdb|2HZM|B Chain B, Structure Of The Mediator Head Subcomplex Med18/20
pdb|2HZM|D Chain D, Structure Of The Mediator Head Subcomplex Med18/20
pdb|2HZM|F Chain F, Structure Of The Mediator Head Subcomplex Med18/20
pdb|2HZM|H Chain H, Structure Of The Mediator Head Subcomplex Med18/20
Length = 317
Score = 25.8 bits (55), Expect = 7.1, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 6/48 (12%)
Query: 51 NEEWSGGGLLLICLIDPGKYREIDELVRTETRGQGTLELLNLKEVTEG 98
N + + GG LL I+ + +ID + TET L+NLK+ +G
Sbjct: 242 NSQITSGGFLLKAYINVSRGTDIDRINYTET------VLMNLKKELQG 283
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
0.315 0.135 0.383
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,509,583
Number of Sequences: 62578
Number of extensions: 72057
Number of successful extensions: 179
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 174
Number of HSP's gapped (non-prelim): 9
length of query: 103
length of database: 14,973,337
effective HSP length: 68
effective length of query: 35
effective length of database: 10,718,033
effective search space: 375131155
effective search space used: 375131155
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)