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= psy6987
(204 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 = 58.5 bits (140), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 47/130 (36%), Positives = 71/130 (54%), Gaps = 19/130 (14%)
Query: 81 DFRELTISHYRTR------GPWIVKPVASSRGRGIYIVDTPDEVP--LEESV---VVAKY 129
D RE+ ++ Y R WI K A ++G GI I E+ ++E V+ KY
Sbjct: 126 DEREVFLAAYNRRREGREGNVWIAKSSAGAKGEGILISSEASELLDFIDEQGQVHVIQKY 185
Query: 130 IEKPLLVE-GH-KCDLRLYVVVTSYDPLI-IYMYEEGLVRFATVKYDSGRKHLWNPCMHL 186
+EKPLL+E GH K D+R +V+V D L IY+Y EG++R ++ Y+S + + HL
Sbjct: 186 LEKPLLLEPGHRKFDIRSWVLV---DHLYNIYLYREGVLRTSSEPYNSA--NFQDKTCHL 240
Query: 187 CNYSINKHHS 196
N+ I K +S
Sbjct: 241 TNHCIQKEYS 250
>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 = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 38/110 (34%), Positives = 59/110 (53%), Gaps = 15/110 (13%)
Query: 96 WIVKPVASSRGRGIYIVDTPDEVPLEESV-------VVAKYIEKPLLVE-GH-KCDLRLY 146
WI K + ++G GI I + D L + + V+ KY+E PLL+E GH K D+R +
Sbjct: 150 WIAKSSSGAKGEGILI--SSDATELLDFIDNQGQVHVIQKYLESPLLLEPGHRKFDIRSW 207
Query: 147 VVVTSYDPLIIYMYEEGLVRFATVKYDSGRKHLWNPCMHLCNYSINKHHS 196
V+V + IY+Y EG++R ++ Y + + HL N+ I K HS
Sbjct: 208 VLVD--NQYNIYLYREGVLRTSSEPYSD--TNFQDMTSHLTNHCIQKEHS 253
>pdb|1NKW|1 Chain 1, Crystal Structure Of The Large Ribosomal Subunit From
Deinococcus Radiodurans
pdb|1SM1|1 Chain 1, Complex Of The Large Ribosomal Subunit From Deinococcus
Radiodurans With Quinupristin And Dalfopristin
pdb|1YL3|6 Chain 6, Crystal Structure Of 70s Ribosome With Thrs Operator And
Trnas. Large Subunit. The Coordinates For The Small
Subunit Are In The Pdb Entry 1yl4.
pdb|2B66|6 Chain 6, 50s Ribosomal Subunit From A Crystal Structure Of Release
Factor Rf1, Trnas And Mrna Bound To The Ribosome. This
File Contains The 50s Subunit From A Crystal Structure
Of Release Factor Rf1, Trnas And Mrna Bound To The
Ribosome And Is Described In Remark 400
pdb|2B9N|6 Chain 6, 50s Ribosomal Subunit From A Crystal Structure Of Release
Factor Rf2, Trnas And Mrna Bound To The Ribosome. This
File Contains The 50s Subunit From A Crystal Structure
Of Release Factor Rf1, Trnas And Mrna Bound To The
Ribosome And Is Described In Remark 400.
pdb|2B9P|6 Chain 6, 50s Ribosomal Subunit From A Crystal Structure Of The
Ribosome In Complex With Trnas And Mrna With A Stop
Codon In The A-Site. This File Contains The 50s Subunit
From A Crystal Structure Of The Ribosome In Complex With
Trnas And Mrna With A Stop Codon In The A-Site And Is
Described In Remark 400
Length = 82
Score = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 28/60 (46%), Gaps = 2/60 (3%)
Query: 72 IPSTFVMPGDFRELTI--SHYRTRGPWIVKPVASSRGRGIYIVDTPDEVPLEESVVVAKY 129
+ +TF +PGD RE S GP I+ + SS G G Y T + + + + KY
Sbjct: 8 LGATFPVPGDQREGCAKESIMAKDGPRIIVKMESSAGTGFYYTTTKNRRNTQAKLELKKY 67
>pdb|2QUF|A Chain A, Crystal Structure Of Transcription Factor Axxa-pf0095 From
Pyrococcus Furiosus
pdb|2QUF|B Chain B, Crystal Structure Of Transcription Factor Axxa-pf0095 From
Pyrococcus Furiosus
Length = 232
Score = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 10/88 (11%)
Query: 4 LNLGVTSDVADFNLLWSGLHPKPQTLRSLAPHQRVNHFPRSYELTRKDRLYKNIEKMQHS 63
L+LG +++ DF + SGL +P TL+ + + + EL + +K IE + S
Sbjct: 94 LDLG-DAELRDFEISLSGLDTEPSTLKEMI----TDFIKANKELEKVLEAFKTIESYRSS 148
Query: 64 KGFKHFDFIPSTFVMP-GDFRELTISHY 90
K I ++ GD +L I HY
Sbjct: 149 LMRK----IKEAYLKEIGDMTQLAILHY 172
>pdb|2CZG|A Chain A, Crystal Structure Of Probable Phosphoribosylglycinamide
Formyl Transferase (Ph0318) From Pyrococcus Horikoshii
Ot3
pdb|2CZG|B Chain B, Crystal Structure Of Probable Phosphoribosylglycinamide
Formyl Transferase (Ph0318) From Pyrococcus Horikoshii
Ot3
pdb|2DWC|A Chain A, Crystal Structure Of Probable Phosphoribosylglycinamide
Formyl Transferase From Pyrococcus Horikoshii Ot3
Complexed With Adp
pdb|2DWC|B Chain B, Crystal Structure Of Probable Phosphoribosylglycinamide
Formyl Transferase From Pyrococcus Horikoshii Ot3
Complexed With Adp
Length = 433
Score = 28.9 bits (63), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 2/47 (4%)
Query: 95 PWIVKPVASSRGRGIYIVDTPDEVP--LEESVVVAKYIEKPLLVEGH 139
P K + SS G+G Y V P+++P EE+ A+ + ++VE H
Sbjct: 158 PCHTKAIMSSSGKGSYFVKGPEDIPKAWEEAKTKARGSAEKIIVEEH 204
>pdb|2QLZ|A Chain A, Crystal Structure Of Transcription Factor Pf0095 From
Pyrococcus Furiosus
pdb|2QLZ|B Chain B, Crystal Structure Of Transcription Factor Pf0095 From
Pyrococcus Furiosus
pdb|2QLZ|C Chain C, Crystal Structure Of Transcription Factor Pf0095 From
Pyrococcus Furiosus
pdb|2QLZ|D Chain D, Crystal Structure Of Transcription Factor Pf0095 From
Pyrococcus Furiosus
Length = 232
Score = 28.1 bits (61), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 43/89 (48%), Gaps = 12/89 (13%)
Query: 4 LNLGVTSDVADFNLLWSGLHPKPQTLRSLAPHQRVNHFPRS-YELTRKDRLYKNIEKMQH 62
L+LG +++ DF + SGL +P TL+ + + F ++ EL + +K IE +
Sbjct: 94 LDLG-DAELRDFEISLSGLDTEPSTLK-----EXITDFIKANKELEKVLEAFKTIESYRS 147
Query: 63 SKGFKHFDFIPSTFVMP-GDFRELTISHY 90
S K I ++ GD +L I HY
Sbjct: 148 SLXRK----IKEAYLKEIGDXTQLAILHY 172
>pdb|3RRM|C Chain C, S. Cerevisiae Dbp5 L327v Bound To Nup159, Gle1 H337r, Ip6
And Adp
Length = 388
Score = 26.6 bits (57), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 27/115 (23%), Positives = 50/115 (43%), Gaps = 11/115 (9%)
Query: 20 SGLHPKPQTLRSLAPHQRVNHFP---RSYELTRKDRLYKNIEKMQHSKGFKHFDFIPSTF 76
S L + ++ + LA Q V F + KDR +++ ++ + K F+F
Sbjct: 149 SALDLRTKSTKQLA--QNVTSFDVTNSQLAVLLKDRSFQSF-AWRNGEMEKQFEF----- 200
Query: 77 VMPGDFRELTISHYRTRGPWIVKPVASSRGRGIYIVDTPDEVPLEESVVVAKYIE 131
+P + EL + Y I+ P G I +T DEV ++ + + K+I+
Sbjct: 201 SLPSELEELPVEEYSPLSVTILSPQDFLAVFGNVISETDDEVSYDQKMYIIKHID 255
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
0.324 0.140 0.444
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,688,738
Number of Sequences: 62578
Number of extensions: 276189
Number of successful extensions: 581
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 577
Number of HSP's gapped (non-prelim): 8
length of query: 204
length of database: 14,973,337
effective HSP length: 94
effective length of query: 110
effective length of database: 9,091,005
effective search space: 1000010550
effective search space used: 1000010550
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)