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= 006388
(647 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1W3B|A Chain A, The Superhelical Tpr Domain Of O-Linked Glcnac Transferase
Reveals Structural Similarities To Importin Alpha.
pdb|1W3B|B Chain B, The Superhelical Tpr Domain Of O-Linked Glcnac Transferase
Reveals Structural Similarities To Importin Alpha
Length = 388
Score = 33.1 bits (74), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 39/151 (25%), Positives = 67/151 (44%), Gaps = 13/151 (8%)
Query: 343 SWTALVSGYAKFGKANETIDLFEKMLSHGLKPDEVT-LIGVLSACSRAGLVEKGRHYFEI 401
+++ L + Y + G+ E I+ + L LKPD + I + +A AG +E +
Sbjct: 69 AYSNLGNVYKERGQLQEAIEHYRHALR--LKPDFIDGYINLAAALVAAGDMEGA---VQA 123
Query: 402 MVKEYGIRPIHDHYTCMIDI---LSRAGRLEEAKS-FINKMPFPPD-AIGWATLLSSCRI 456
V P D Y D+ L GRLEEAK+ ++ + P+ A+ W+ L
Sbjct: 124 YVSALQYNP--DLYCVRSDLGNLLKALGRLEEAKACYLKAIETQPNFAVAWSNLGCVFNA 181
Query: 457 HGNVEIGKWAAESLLELDPYNPASYVLLSSI 487
G + + E + LDP +Y+ L ++
Sbjct: 182 QGEIWLAIHHFEKAVTLDPNFLDAYINLGNV 212
>pdb|2WAQ|B Chain B, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|B Chain B, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|R Chain R, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|B Chain B, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|R Chain R, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|B Chain B, Rnap At 3.2ang
pdb|4B1O|B Chain B, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|R Chain R, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 1131
Score = 30.4 bits (67), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 21/31 (67%)
Query: 544 LEKLNRKMIKEGYVPDMSSVLHDVELSEKIK 574
+E+L +++K GY+PD + V +D +KIK
Sbjct: 953 IEQLQNEILKYGYLPDATEVTYDGRTGQKIK 983
>pdb|2PMZ|B Chain B, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|R Chain R, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|B Chain B, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|J Chain J, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 1124
Score = 30.4 bits (67), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 22/31 (70%)
Query: 544 LEKLNRKMIKEGYVPDMSSVLHDVELSEKIK 574
+E+L ++++ GY+PD + V++D +KIK
Sbjct: 950 IEQLQNEILRYGYLPDATEVVYDGRTGQKIK 980
>pdb|2K9N|A Chain A, Solution Nmr Structure Of The R2r3 Dna Binding Domain Of
Myb1 Protein From Protozoan Parasite Trichomonas
Vaginalis
pdb|2KDZ|A Chain A, Structure Of The R2r3 Dna Binding Domain Of Myb1 Protein
From Protozoan Parasite Trichomonas Vaginalis In Complex
With Mre-1MRE-2r Dna
Length = 107
Score = 29.6 bits (65), Expect = 5.0, Method: Composition-based stats.
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 471 LELDPYNPASYVLLSSIYASKG-KWDHVSQLRRTMREKGVR 510
L DP++P +LL YA G KW+ +S+ + + +R
Sbjct: 51 LRTDPWSPEEDMLLDQKYAEYGPKWNKISKFLKNRSDNNIR 91
>pdb|1ELW|A Chain A, Crystal Structure Of The Tpr1 Domain Of Hop In Complex
With A Hsc70 Peptide
pdb|1ELW|B Chain B, Crystal Structure Of The Tpr1 Domain Of Hop In Complex
With A Hsc70 Peptide
Length = 118
Score = 29.6 bits (65), Expect = 5.0, Method: Composition-based stats.
Identities = 25/92 (27%), Positives = 35/92 (38%), Gaps = 22/92 (23%)
Query: 458 GNVEIGKWAAESLLELDPYNPASYVLLSSIYASKGKWDHVSQLRRTMREKGVRKDPGCSW 517
GN++ ++LDP+N Y S+ YA KG + + GC
Sbjct: 18 GNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYE-------------DGCKT 64
Query: 518 IKYKSRVHIFSADDWSSPYSDQIYAELEKLNR 549
+ K DW YS + A LE LNR
Sbjct: 65 VDLKP--------DWGKGYSRKA-AALEFLNR 87
>pdb|2UY1|A Chain A, Crystal Structure Of Cstf-77
Length = 493
Score = 29.6 bits (65), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 39/151 (25%), Positives = 68/151 (45%), Gaps = 17/151 (11%)
Query: 18 SHGSVNDAVKVYNLMLKDGLGNLSRITFSTMLIMSSSRRCVDLGRQIHGHILKFGFGSYV 77
S G A KV++ L +L RI ++ +R ++L R++ + G G +V
Sbjct: 270 SMGEAESAEKVFSKEL-----DLLRINHLNYVL---KKRGLELFRKLFIELGNEGVGPHV 321
Query: 78 FVGSPLVDMYA--KLGLIYDA-KRGFDELPEKNIVMYNTMITGLLRRGLVEESRRLFRGM 134
F+ ++ YA Y+ G + P+ ++ LLR G E +R LF+ +
Sbjct: 322 FIYCAFIEYYATGSRATPYNIFSSGLLKHPDSTLLK-EEFFLFLLRIGDEENARALFKRL 380
Query: 135 KDKDSISWTTMITGLMQNGLEREAIDLFREM 165
+K S W +MI G +++LFRE+
Sbjct: 381 -EKTSRMWDSMIEYEFMVG----SMELFREL 406
>pdb|2UY1|B Chain B, Crystal Structure Of Cstf-77
Length = 493
Score = 29.6 bits (65), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 39/151 (25%), Positives = 68/151 (45%), Gaps = 17/151 (11%)
Query: 18 SHGSVNDAVKVYNLMLKDGLGNLSRITFSTMLIMSSSRRCVDLGRQIHGHILKFGFGSYV 77
S G A KV++ L +L RI ++ +R ++L R++ + G G +V
Sbjct: 270 SMGEAESAEKVFSKEL-----DLLRINHLNYVL---KKRGLELFRKLFIELGNEGVGPHV 321
Query: 78 FVGSPLVDMYA--KLGLIYDA-KRGFDELPEKNIVMYNTMITGLLRRGLVEESRRLFRGM 134
F+ ++ YA Y+ G + P+ ++ LLR G E +R LF+ +
Sbjct: 322 FIYCAFIEYYATGSRATPYNIFSSGLLKHPDSTLLK-EEFFLFLLRIGDEENARALFKRL 380
Query: 135 KDKDSISWTTMITGLMQNGLEREAIDLFREM 165
+K S W +MI G +++LFRE+
Sbjct: 381 -EKTSRMWDSMIEYEFMVG----SMELFREL 406
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
0.322 0.138 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,603,285
Number of Sequences: 62578
Number of extensions: 805555
Number of successful extensions: 1852
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1850
Number of HSP's gapped (non-prelim): 9
length of query: 647
length of database: 14,973,337
effective HSP length: 105
effective length of query: 542
effective length of database: 8,402,647
effective search space: 4554234674
effective search space used: 4554234674
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)