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= 005802
(676 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1R86|A Chain A, Crystal Structure Of The Extracellular Xylanase From
Geobacillus Stearothermophilus T-6 (Xt6, Monoclinic
Form): The E159aE265A MUTANT AT 1.8A RESOLUTION
Length = 379
Score = 32.3 bits (72), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 33/58 (56%), Gaps = 2/58 (3%)
Query: 302 DVYCKCENMNYAESMLLLKGVRNSFSISSMIVGYSLQG--NMEEARRHFDSLTEKNVV 357
D Y K +++ + L + +N F+I + + Y LQ +++ +RHF+S+ +NV+
Sbjct: 4 DSYAKKPHISALNAPQLDQRYKNEFTIGAAVEPYQLQNEKDVQMLKRHFNSIVAENVM 61
>pdb|3MMD|A Chain A, Crystal Structure Of The W241a Mutant Of Xylanase From
Geobacillus Stearothermophilus T-6 (Xt6) Complexed With
Hydrolyzed Xylopentaose
Length = 379
Score = 32.3 bits (72), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 33/58 (56%), Gaps = 2/58 (3%)
Query: 302 DVYCKCENMNYAESMLLLKGVRNSFSISSMIVGYSLQG--NMEEARRHFDSLTEKNVV 357
D Y K +++ + L + +N F+I + + Y LQ +++ +RHF+S+ +NV+
Sbjct: 4 DSYAKKPHISALNAPQLDQRYKNEFTIGAAVEPYQLQNEKDVQMLKRHFNSIVAENVM 61
>pdb|1HIZ|A Chain A, Xylanase T6 (Xt6) From Bacillus Stearothermophilus
pdb|1R85|A Chain A, Crystal Structure Of The Extracellular Xylanase From
Geobacillus Stearothermophilus T-6 (Xt6): The Wt Enzyme
(Monoclinic Form) At 1.45a Resolution
pdb|1R87|A Chain A, Crystal Structure Of The Extracellular Xylanase From
Geobacillus Stearothermophilus T-6 (Xt6, Monoclinic
Form): The Complex Of The Wt Enzyme With Xylopentaose At
1.67a Resolution
Length = 379
Score = 32.3 bits (72), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 33/58 (56%), Gaps = 2/58 (3%)
Query: 302 DVYCKCENMNYAESMLLLKGVRNSFSISSMIVGYSLQG--NMEEARRHFDSLTEKNVV 357
D Y K +++ + L + +N F+I + + Y LQ +++ +RHF+S+ +NV+
Sbjct: 4 DSYAKKPHISALNAPQLDQRYKNEFTIGAAVEPYQLQNEKDVQMLKRHFNSIVAENVM 61
>pdb|3QK2|A Chain A, Structure-Based Analysis Of The Interaction Between The
Simian Virus 40 T-Antigen Origin Binding Domain And
Single-Stranded Dna
Length = 134
Score = 32.0 bits (71), Expect = 1.1, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 31/47 (65%), Gaps = 4/47 (8%)
Query: 459 VLYNVMIACYAHHGHEEKAILLFEEMLEKGIKPDAVTFVAILSAFRH 505
V N +AC+A + +EKA LL+++++EK +VTF++ +++ H
Sbjct: 22 VFSNRTLACFAIYTTKEKAALLYKKIMEKY----SVTFISRHNSYNH 64
>pdb|2NL8|A Chain A, The Origin Binding Domain Of The Sv40 Large T Antigen
Bound Non Specifically To A 17 Bp Palindrome Dna (Sites
1 And 3)
Length = 133
Score = 32.0 bits (71), Expect = 1.1, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 31/47 (65%), Gaps = 4/47 (8%)
Query: 459 VLYNVMIACYAHHGHEEKAILLFEEMLEKGIKPDAVTFVAILSAFRH 505
V N +AC+A + +EKA LL+++++EK +VTF++ +++ H
Sbjct: 24 VFSNRTLACFAIYTTKEKAALLYKKIMEKY----SVTFISRHNSYNH 66
>pdb|1Z1D|B Chain B, Structural Model For The Interaction Between Rpa32 C-
Terminal Domain And Sv40 T Antigen Origin Binding Domain
Length = 131
Score = 32.0 bits (71), Expect = 1.1, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 31/47 (65%), Gaps = 4/47 (8%)
Query: 459 VLYNVMIACYAHHGHEEKAILLFEEMLEKGIKPDAVTFVAILSAFRH 505
V N +AC+A + +EKA LL+++++EK +VTF++ +++ H
Sbjct: 22 VFSNRTLACFAIYTTKEKAALLYKKIMEKY----SVTFISRHNSYNH 64
>pdb|1GJI|A Chain A, Crystal Structure Of C-Rel Bound To Dna
pdb|1GJI|B Chain B, Crystal Structure Of C-Rel Bound To Dna
Length = 275
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 3/69 (4%)
Query: 52 PERNVFSWNTIISACIKSHDLKQARSLFDSSPHKDLVTYNSMLCGYINAEGYEADALKLF 111
PER V S+ + C+K DLK++ SL S K + +N N + Y+ + ++L
Sbjct: 88 PERRVLSFQNLGIQCVKKKDLKESISLRIS---KKINPFNVPEEQLHNIDEYDLNVVRLC 144
Query: 112 IEMQSADEH 120
+ DEH
Sbjct: 145 FQAFLPDEH 153
>pdb|2IF9|A Chain A, Crystal Structure Of Sv40 T-Antigen Origin Binding Domain
Disulfide-Linked Dimer
pdb|2IF9|B Chain B, Crystal Structure Of Sv40 T-Antigen Origin Binding Domain
Disulfide-Linked Dimer
pdb|2NTC|A Chain A, Crystal Structure Of Sv40 Large T Antigen Origin Binding
Domain With Dna
pdb|2NTC|B Chain B, Crystal Structure Of Sv40 Large T Antigen Origin Binding
Domain With Dna
pdb|1TBD|A Chain A, Solution Structure Of The Origin Dna Binding Domain Of
Sv40 T-Antigen, Nmr, Minimized Average Structure
pdb|2TBD|A Chain A, Sv40 T Antigen Dna-Binding Domain, Nmr, 30 Structures
Length = 134
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 31/47 (65%), Gaps = 4/47 (8%)
Query: 459 VLYNVMIACYAHHGHEEKAILLFEEMLEKGIKPDAVTFVAILSAFRH 505
V N +AC+A + +EKA LL+++++EK +VTF++ +++ H
Sbjct: 22 VFSNRTLACFAIYTTKEKAALLYKKIMEKY----SVTFISRHNSYNH 64
>pdb|4FGN|A Chain A, Crystal Structure Of The Sv40 Large T-antigen Origin
Bining Domain Bound To Site I Dna
pdb|4FGN|B Chain B, Crystal Structure Of The Sv40 Large T-antigen Origin
Bining Domain Bound To Site I Dna
Length = 132
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 31/47 (65%), Gaps = 4/47 (8%)
Query: 459 VLYNVMIACYAHHGHEEKAILLFEEMLEKGIKPDAVTFVAILSAFRH 505
V N +AC+A + +EKA LL+++++EK +VTF++ +++ H
Sbjct: 22 VFSNRTLACFAIYTTKEKAALLYKKIMEKY----SVTFISRHNSYNH 64
>pdb|2ENK|A Chain A, Solution Structure Of A Putativ Dna-Binding Domain Of The
Humansolute Carrier Family 30 (Zinc Transporter) Protein
Length = 101
Score = 31.2 bits (69), Expect = 1.9, Method: Composition-based stats.
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 66 CIKSHDLKQARSLFDSSPHKDLVTYNSMLCGYINAEGYE 104
C+KS DL+Q R + SPH+D ++ L + A+ E
Sbjct: 25 CLKSSDLEQLRKIRRRSPHEDTESFTVYLRSDVEAKSLE 63
>pdb|2FUF|A Chain A, Crystal Structure Of The Sv40 Large T Antigen
Origin-Binding Domain
Length = 134
Score = 30.8 bits (68), Expect = 2.7, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 30/47 (63%), Gaps = 4/47 (8%)
Query: 459 VLYNVMIACYAHHGHEEKAILLFEEMLEKGIKPDAVTFVAILSAFRH 505
V N +AC+A + +EKA LL++++ EK +VTF++ +++ H
Sbjct: 22 VFSNRTLACFAIYTTKEKAALLYKKIXEKY----SVTFISRHNSYNH 64
>pdb|2IPR|A Chain A, Origin Binding Domain Of The Sv40 Large T Antigen
(Residues 131-259). P21 Crystal Form
pdb|2IPR|B Chain B, Origin Binding Domain Of The Sv40 Large T Antigen
(Residues 131-259). P21 Crystal Form
pdb|2ITJ|A Chain A, Origin Binding Domain Of The Sv40 Large T Antigen
(Residues 131-259). P212121 Crystal Form
pdb|2ITJ|B Chain B, Origin Binding Domain Of The Sv40 Large T Antigen
(Residues 131-259). P212121 Crystal Form
pdb|2ITL|A Chain A, The Origin Binding Domain Of The Sv40 Large T Antigen
Bound To The Functional Pen Palindrome Dna (23 Bp)
pdb|2ITL|B Chain B, The Origin Binding Domain Of The Sv40 Large T Antigen
Bound To The Functional Pen Palindrome Dna (23 Bp)
Length = 133
Score = 30.8 bits (68), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 31/47 (65%), Gaps = 4/47 (8%)
Query: 459 VLYNVMIACYAHHGHEEKAILLFEEMLEKGIKPDAVTFVAILSAFRH 505
V N +AC+A + +EKA LL+++++EK +VTF++ +++ H
Sbjct: 24 VFSNRTLACFAIYTTKEKAALLYKKIMEKY----SVTFISRHNSYNH 66
>pdb|1P9R|A Chain A, Crystal Structure Of Vibrio Cholerae Putative Ntpase Epse
pdb|1P9W|A Chain A, Crystal Structure Of Vibrio Cholerae Putative Ntpase Epse
Length = 418
Score = 30.0 bits (66), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 15/65 (23%)
Query: 73 KQARSLFDSSPHKDLVTYNSMLCGYINAEGYEA-----------DALKLFIEM----QSA 117
K+ R LFDS + L+ Y + C N +GY DAL+ I Q+
Sbjct: 318 KEQRKLFDSKKKEPLILYRATGCPKCNHKGYRGRTGIHELLLVDDALQELIHSEAGEQAX 377
Query: 118 DEHIR 122
++HIR
Sbjct: 378 EKHIR 382
>pdb|1IRU|D Chain D, Crystal Structure Of The Mammalian 20s Proteasome At 2.75
A Resolution
pdb|1IRU|R Chain R, Crystal Structure Of The Mammalian 20s Proteasome At 2.75
A Resolution
Length = 248
Score = 30.0 bits (66), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 36/80 (45%), Gaps = 6/80 (7%)
Query: 63 ISACIKSHDLKQARSLFDSSPHKDLVTYNSMLCGYINAEGYEADALKLFIEMQSADEHIR 122
ISA I D L+ + P TY++ NA G A +++ F+E DE I
Sbjct: 129 ISALIVGFDFDGTPRLYQTDPSG---TYHAWKA---NAIGRGAKSVREFLEKNYTDEAIE 182
Query: 123 MDEFTVTSTLNLCVKLLNVG 142
D+ T+ + ++++ G
Sbjct: 183 TDDLTIKLVIKALLEVVQSG 202
>pdb|2PMD|A Chain A, The Structures Of Aif2gamma Subunit From The Archaeon
Sulfolobus Solfataricus In The Gdp-Bound Form.
pdb|2PMD|B Chain B, The Structures Of Aif2gamma Subunit From The Archaeon
Sulfolobus Solfataricus In The Gdp-Bound Form.
pdb|3CW2|A Chain A, Crystal Structure Of The Intact Archaeal Translation
Initiation Factor 2 From Sulfolobus Solfataricus .
pdb|3CW2|B Chain B, Crystal Structure Of The Intact Archaeal Translation
Initiation Factor 2 From Sulfolobus Solfataricus .
pdb|3CW2|E Chain E, Crystal Structure Of The Intact Archaeal Translation
Initiation Factor 2 From Sulfolobus Solfataricus .
pdb|3CW2|F Chain F, Crystal Structure Of The Intact Archaeal Translation
Initiation Factor 2 From Sulfolobus Solfataricus .
pdb|3I1F|A Chain A, Gamma-Subunit Of The Translation Initiation Factor 2 From
S. Solfataricus In Complex With Gpp(Ch2)p
pdb|3I1F|B Chain B, Gamma-Subunit Of The Translation Initiation Factor 2 From
S. Solfataricus In Complex With Gpp(Ch2)p
pdb|3P3M|A Chain A, Gamma-Subunit Of The Translation Initiation Factor 2 From
S. Solfataricus Complexed With Gtp
pdb|3P3M|B Chain B, Gamma-Subunit Of The Translation Initiation Factor 2 From
S. Solfataricus Complexed With Gtp
pdb|3P3M|C Chain C, Gamma-Subunit Of The Translation Initiation Factor 2 From
S. Solfataricus Complexed With Gtp
pdb|3P3M|D Chain D, Gamma-Subunit Of The Translation Initiation Factor 2 From
S. Solfataricus Complexed With Gtp
pdb|3P3M|E Chain E, Gamma-Subunit Of The Translation Initiation Factor 2 From
S. Solfataricus Complexed With Gtp
pdb|3P3M|F Chain F, Gamma-Subunit Of The Translation Initiation Factor 2 From
S. Solfataricus Complexed With Gtp
pdb|3QSY|A Chain A, Recognition Of The Methionylated Initiator Trna By The
Translation Initiation Factor 2 In Archaea
Length = 415
Score = 30.0 bits (66), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 633 SWVYVEHEIHIFTVGDVSHPKTNAIYSVLAIFT 665
+W V+ E++I VG V H KT + ++ I+T
Sbjct: 2 AWPKVQPEVNIGVVGHVDHGKTTLVQAITGIWT 34
>pdb|3QN2|A Chain A, Structure-Based Design Of A Disulfide-Linked Oligomeric
Form Of The Simian Virus 40 (Sv40) Large T Antigen Dna
Binding Domain
Length = 134
Score = 30.0 bits (66), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 30/44 (68%), Gaps = 4/44 (9%)
Query: 462 NVMIACYAHHGHEEKAILLFEEMLEKGIKPDAVTFVAILSAFRH 505
N +AC+A + +EKA LL+++++EK +VTF++ +++ H
Sbjct: 25 NRTLACFAIYTTKEKAALLYKKIMEKY----SVTFISRHNSYNH 64
>pdb|1E9Z|B Chain B, Crystal Structure Of Helicobacter Pylori Urease
Length = 569
Score = 29.6 bits (65), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 4/67 (5%)
Query: 468 YAHHG---HEEKAILLFEEMLEKGIKPDAVTFVAILSAFRHCGSVEMGEKYFNSMTADYK 524
+AHHG ++ + + +KGIK + +L ++C +V + FN+ TA +
Sbjct: 479 FAHHGKAKYDANITFVSQAAYDKGIKEELGLERQVLP-VKNCRNVTKKDMQFNNTTAHIE 537
Query: 525 ISPETDH 531
++PET H
Sbjct: 538 VNPETYH 544
>pdb|1E9Y|B Chain B, Crystal Structure Of Helicobacter Pylori Urease In Complex
With Acetohydroxamic Acid
Length = 569
Score = 29.6 bits (65), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 4/67 (5%)
Query: 468 YAHHG---HEEKAILLFEEMLEKGIKPDAVTFVAILSAFRHCGSVEMGEKYFNSMTADYK 524
+AHHG ++ + + +KGIK + +L ++C +V + FN+ TA +
Sbjct: 479 FAHHGKAKYDANITFVSQAAYDKGIKEELGLERQVLP-VKNCRNVTKKDMQFNNTTAHIE 537
Query: 525 ISPETDH 531
++PET H
Sbjct: 538 VNPETYH 544
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 0.135 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,404,483
Number of Sequences: 62578
Number of extensions: 713893
Number of successful extensions: 1424
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 1422
Number of HSP's gapped (non-prelim): 24
length of query: 676
length of database: 14,973,337
effective HSP length: 105
effective length of query: 571
effective length of database: 8,402,647
effective search space: 4797911437
effective search space used: 4797911437
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (25.8 bits)