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= psy12053
(167 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XRP|I Chain I, Human Doublecortin N-Dc Repeat (1mjd) And Mammalian
Tubulin (1jff And 3hke) Docked Into The 8-Angstrom
Cryo-Em Map Of Doublecortin-Stabilised Microtubules
Length = 95
Score = 63.5 bits (153), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 37/85 (43%), Positives = 53/85 (62%), Gaps = 6/85 (7%)
Query: 73 RARKVTFFKNGDPYFPGVEYRFKPGRDIPSLEA----LQDKLSVRMDLPRGARYVFSMDG 128
+A+KV F++NGD YF G+ Y R S +A L LS ++LP+G RY++++DG
Sbjct: 6 KAKKVRFYRNGDRYFKGIVYAVSSDR-FRSFDALLADLTRSLSDNINLPQGVRYIYTIDG 64
Query: 129 VR-ILTLDELEDNASYVVSSYKTFK 152
R I ++DELE+ SYV SS FK
Sbjct: 65 SRKIGSMDELEEGESYVCSSDNFFK 89
>pdb|1MJD|A Chain A, Structure Of N-Terminal Domain Of Human Doublecortin
Length = 113
Score = 63.5 bits (153), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 37/85 (43%), Positives = 53/85 (62%), Gaps = 6/85 (7%)
Query: 73 RARKVTFFKNGDPYFPGVEYRFKPGRDIPSLEA----LQDKLSVRMDLPRGARYVFSMDG 128
+A+KV F++NGD YF G+ Y R S +A L LS ++LP+G RY++++DG
Sbjct: 14 KAKKVRFYRNGDRYFKGIVYAVSSDR-FRSFDALLADLTRSLSDNINLPQGVRYIYTIDG 72
Query: 129 VR-ILTLDELEDNASYVVSSYKTFK 152
R I ++DELE+ SYV SS FK
Sbjct: 73 SRKIGSMDELEEGESYVCSSDNFFK 97
>pdb|4ATU|I Chain I, Human Doublecortin N-Dc Repeat Plus Linker, And Tubulin
(2xrp) Docked Into An 8a Cryo-Em Map Of
Doublecortin-Stabilised Microtubules Reconstructed In
Absence Of Kinesin
Length = 373
Score = 63.2 bits (152), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 37/85 (43%), Positives = 53/85 (62%), Gaps = 6/85 (7%)
Query: 73 RARKVTFFKNGDPYFPGVEYRFKPGRDIPSLEA----LQDKLSVRMDLPRGARYVFSMDG 128
+A+KV F++NGD YF G+ Y R S +A L LS ++LP+G RY++++DG
Sbjct: 64 KAKKVRFYRNGDRYFKGIVYAVSSDR-FRSFDALLADLTRSLSDNINLPQGVRYIYTIDG 122
Query: 129 VR-ILTLDELEDNASYVVSSYKTFK 152
R I ++DELE+ SYV SS FK
Sbjct: 123 SRKIGSMDELEEGESYVCSSDNFFK 147
>pdb|1UF0|A Chain A, Solution Structure Of The N-Terminal Dcx Domain Of Human
Doublecortin-Like Kinase
Length = 116
Score = 62.0 bits (149), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 35/85 (41%), Positives = 53/85 (62%), Gaps = 6/85 (7%)
Query: 73 RARKVTFFKNGDPYFPGVEYRFKPGRDIPSLEA----LQDKLSVRMDLPRGARYVFSMDG 128
+A+KV F++NGD YF G+ Y P R S EA L LS ++LP+G R ++++DG
Sbjct: 9 KAKKVRFYRNGDRYFKGIVYAISPDR-FRSFEALLADLTRTLSDNVNLPQGVRTIYTIDG 67
Query: 129 V-RILTLDELEDNASYVVSSYKTFK 152
+ +I +LD+L + SYV S + FK
Sbjct: 68 LKKISSLDQLVEGESYVCGSIEPFK 92
>pdb|2BQQ|A Chain A, X-Ray Strucure Of The N-Terminal Domain Of Human
Doublecortin
Length = 113
Score = 61.6 bits (148), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 36/84 (42%), Positives = 52/84 (61%), Gaps = 6/84 (7%)
Query: 73 RARKVTFFKNGDPYFPGVEYRFKPGRDIPSLEA----LQDKLSVRMDLPRGARYVFSMDG 128
+A+KV F++NGD YF G+ Y R S +A L LS ++LP+G RY++++DG
Sbjct: 14 KAKKVRFYRNGDRYFKGIVYAVSSDR-FRSFDALLADLTRSLSDNINLPQGVRYIYTIDG 72
Query: 129 VR-ILTLDELEDNASYVVSSYKTF 151
R I ++DELE+ SYV SS F
Sbjct: 73 SRKIGSMDELEEGESYVCSSDNFF 96
>pdb|1MG4|A Chain A, Structure Of N-Terminal Doublecortin Domain From Dclk:
Wild Type Protein
Length = 113
Score = 60.8 bits (146), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 35/85 (41%), Positives = 53/85 (62%), Gaps = 6/85 (7%)
Query: 73 RARKVTFFKNGDPYFPGVEYRFKPGRDIPSLEA----LQDKLSVRMDLPRGARYVFSMDG 128
+A+KV F++NGD YF G+ Y P R S EA L LS ++LP+G R ++++DG
Sbjct: 14 KAKKVRFYRNGDRYFKGIVYAISPDR-FRSFEALLADLTRTLSDNVNLPQGVRTIYTIDG 72
Query: 129 V-RILTLDELEDNASYVVSSYKTFK 152
+ +I +LD+L + SYV S + FK
Sbjct: 73 LKKISSLDQLVEGESYVCGSIEPFK 97
>pdb|1MFW|A Chain A, Structure Of N-Terminal Doublecortin Domain From Dclk:
Selenomethionine Labeled Protein
Length = 107
Score = 58.9 bits (141), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 34/85 (40%), Positives = 52/85 (61%), Gaps = 6/85 (7%)
Query: 73 RARKVTFFKNGDPYFPGVEYRFKPGRDIPSLEA----LQDKLSVRMDLPRGARYVFSMDG 128
+A+KV F++NGD YF G+ Y P R S EA L LS ++LP+G R ++++DG
Sbjct: 8 KAKKVRFYRNGDRYFKGIVYAISPDR-FRSFEALLADLTRTLSDNVNLPQGVRTIYTIDG 66
Query: 129 V-RILTLDELEDNASYVVSSYKTFK 152
+ +I + D+L + SYV S + FK
Sbjct: 67 LKKISSXDQLVEGESYVCGSIEPFK 91
>pdb|3QF4|A Chain A, Crystal Structure Of A Heterodimeric Abc Transporter In
Its Inward- Facing Conformation
Length = 587
Score = 29.6 bits (65), Expect = 0.78, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 8/73 (10%)
Query: 79 FFKNGDPYFPGVEYRFKPGRDIPSL-------EALQDKLSVRMDLPRGARYVFSMDGVRI 131
+F+N DP GV + KPG + L L + + +D RG V +D VR
Sbjct: 351 YFENTDPVLSGVNFSVKPGSLVAVLGETGSGKSTLMNLIPRLIDPERGRVEVDELD-VRT 409
Query: 132 LTLDELEDNASYV 144
+ L +L + S V
Sbjct: 410 VKLKDLRGHISAV 422
>pdb|3E2E|A Chain A, Crystal Structure Of An Intermediate Complex Of T7 Rnap
And 7nt Of Rna
pdb|3E3J|C Chain C, Crystal Structure Of An Intermediate Complex Of T7 Rnap
And 8nt Of Rna
pdb|3E3J|B Chain B, Crystal Structure Of An Intermediate Complex Of T7 Rnap
And 8nt Of Rna
Length = 889
Score = 29.6 bits (65), Expect = 0.88, Method: Composition-based stats.
Identities = 12/19 (63%), Positives = 14/19 (73%), Gaps = 2/19 (10%)
Query: 15 PRPNTVLTGGGYW--GSRP 31
P+P T +TGGGYW G RP
Sbjct: 281 PKPWTGITGGGYWANGRRP 299
>pdb|4RNP|A Chain A, Bacteriophage T7 Rna Polymerase, High Salt Crystal Form,
Low Temperature Data, Alpha-Carbons Only
pdb|4RNP|B Chain B, Bacteriophage T7 Rna Polymerase, High Salt Crystal Form,
Low Temperature Data, Alpha-Carbons Only
pdb|4RNP|C Chain C, Bacteriophage T7 Rna Polymerase, High Salt Crystal Form,
Low Temperature Data, Alpha-Carbons Only
pdb|1CEZ|A Chain A, Crystal Structure Of A T7 Rna Polymerase-T7 Promoter
Complex
pdb|1QLN|A Chain A, Structure Of A Transcribing T7 Rna Polymerase Initiation
Complex
pdb|1H38|A Chain A, Structure Of A T7 Rna Polymerase Elongation Complex At
2.9a Resolution
pdb|1H38|B Chain B, Structure Of A T7 Rna Polymerase Elongation Complex At
2.9a Resolution
pdb|1H38|C Chain C, Structure Of A T7 Rna Polymerase Elongation Complex At
2.9a Resolution
pdb|1H38|D Chain D, Structure Of A T7 Rna Polymerase Elongation Complex At
2.9a Resolution
pdb|1MSW|D Chain D, Structural Basis For The Transition From Initiation To
Elongation Transcription In T7 Rna Polymerase
pdb|1S0V|A Chain A, Structural Basis For Substrate Selection By T7 Rna
Polymerase
pdb|1S0V|B Chain B, Structural Basis For Substrate Selection By T7 Rna
Polymerase
pdb|1S0V|C Chain C, Structural Basis For Substrate Selection By T7 Rna
Polymerase
pdb|1S0V|D Chain D, Structural Basis For Substrate Selection By T7 Rna
Polymerase
pdb|1S76|D Chain D, T7 Rna Polymerase Alpha Beta Methylene Atp Elongation
Complex
pdb|1S77|D Chain D, T7 Rnap Product Pyrophosphate Elongation Complex
Length = 883
Score = 29.6 bits (65), Expect = 0.89, Method: Composition-based stats.
Identities = 12/19 (63%), Positives = 14/19 (73%), Gaps = 2/19 (10%)
Query: 15 PRPNTVLTGGGYW--GSRP 31
P+P T +TGGGYW G RP
Sbjct: 275 PKPWTGITGGGYWANGRRP 293
>pdb|2PI4|A Chain A, T7rnap Complexed With A Phi10 Protein And Initiating Gtps.
pdb|2PI5|A Chain A, T7 Rna Polymerase Complexed With A Phi10 Promoter
Length = 878
Score = 29.6 bits (65), Expect = 0.89, Method: Composition-based stats.
Identities = 12/19 (63%), Positives = 14/19 (73%), Gaps = 2/19 (10%)
Query: 15 PRPNTVLTGGGYW--GSRP 31
P+P T +TGGGYW G RP
Sbjct: 270 PKPWTGITGGGYWANGRRP 288
>pdb|1ARO|P Chain P, T7 Rna Polymerase Complexed With T7 Lysozyme
Length = 883
Score = 29.3 bits (64), Expect = 1.00, Method: Composition-based stats.
Identities = 12/19 (63%), Positives = 14/19 (73%), Gaps = 2/19 (10%)
Query: 15 PRPNTVLTGGGYW--GSRP 31
P+P T +TGGGYW G RP
Sbjct: 275 PKPWTGITGGGYWANGRRP 293
>pdb|1SI8|A Chain A, Crystal Structure Of E. Faecalis Catalase
pdb|1SI8|B Chain B, Crystal Structure Of E. Faecalis Catalase
pdb|1SI8|C Chain C, Crystal Structure Of E. Faecalis Catalase
pdb|1SI8|D Chain D, Crystal Structure Of E. Faecalis Catalase
Length = 484
Score = 26.9 bits (58), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 77 VTFFKNGDPYFPGVEY-RFKPGRDIPSLEALQDKL 110
+T +N + YF VE F PG +P +EA DKL
Sbjct: 295 MTLNRNPENYFAEVEQVTFSPGNFVPGIEASPDKL 329
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
0.317 0.135 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,008,583
Number of Sequences: 62578
Number of extensions: 183644
Number of successful extensions: 381
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 356
Number of HSP's gapped (non-prelim): 13
length of query: 167
length of database: 14,973,337
effective HSP length: 92
effective length of query: 75
effective length of database: 9,216,161
effective search space: 691212075
effective search space used: 691212075
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: 48 (23.1 bits)