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= 025027
(259 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3F67|A Chain A, Crystal Structure Of Putative Dienelactone Hydrolase From
Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578
Length = 241
Score = 34.7 bits (78), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 46/217 (21%), Positives = 86/217 (39%), Gaps = 31/217 (14%)
Query: 59 VLMISDIYGDEPPIYRSVADKVAGAGFLVVAPDFF--HGDAANPSNPKYDKDTWRKNHTT 116
V+++ +I+G I R + ++A G+L +AP+ + GD N +D T K +
Sbjct: 35 VIVVQEIFGVHEHI-RDLCRRLAQEGYLAIAPELYFRQGD----PNEYHDIPTLFKELVS 89
Query: 117 DKGYEDAKPVIXXXXXXX--------XXXXXXXXFCWGGKVA-VKLASNQDVQAAVLLHP 167
DA+ + FCWGG++ + A N ++AAV +
Sbjct: 90 K--VPDAQVLADLDHVASWAARHGGDAHRLLITGFCWGGRITWLYAAHNPQLKAAVAWYG 147
Query: 168 SNVTEDEIKAVKVPIAV----------LGAERDNGLPPAQMKRFDEILSAKPKFDHLVKT 217
V E + + K P+ + L +D +P ++ + L A +V
Sbjct: 148 KLVGEKSLNSPKHPVDIAVDLNAPVLGLYGAKDASIPQDTVETXRQALRAANATAEIV-V 206
Query: 218 YPGVCHGWTVRYFVNDTFAVNSAAEAHEDMINWFEKH 254
YP H + Y ++ SA + + + WF ++
Sbjct: 207 YPEADHAFNADY--RASYHEESAKDGWQRXLAWFAQY 241
>pdb|3K9C|A Chain A, Crystal Structure Of Laci Transcriptional Regulator From
Rhodococcus Species.
pdb|3K9C|B Chain B, Crystal Structure Of Laci Transcriptional Regulator From
Rhodococcus Species
Length = 289
Score = 30.8 bits (68), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 148 KVAVKLASNQDVQAAVLLHPSNVTEDEIKAVKVPIAVLGAERDNGLPPAQMKRFDEILSA 207
KVAV+ + +AA+LL + DE+ A+ + L R +GLP R D++
Sbjct: 56 KVAVQALXRERCEAAILL-GTRFDTDELGALADRVPALVVARASGLPGVGAVRGDDVAGI 114
Query: 208 KPKFDHLVK 216
DHL +
Sbjct: 115 TLAVDHLTE 123
>pdb|4EGB|A Chain A, 3.0 Angstrom Resolution Crystal Structure Of Dtdp-Glucose
4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str.
Ames In Complex With Nad
pdb|4EGB|B Chain B, 3.0 Angstrom Resolution Crystal Structure Of Dtdp-Glucose
4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str.
Ames In Complex With Nad
pdb|4EGB|C Chain C, 3.0 Angstrom Resolution Crystal Structure Of Dtdp-Glucose
4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str.
Ames In Complex With Nad
pdb|4EGB|D Chain D, 3.0 Angstrom Resolution Crystal Structure Of Dtdp-Glucose
4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str.
Ames In Complex With Nad
pdb|4EGB|E Chain E, 3.0 Angstrom Resolution Crystal Structure Of Dtdp-Glucose
4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str.
Ames In Complex With Nad
pdb|4EGB|F Chain F, 3.0 Angstrom Resolution Crystal Structure Of Dtdp-Glucose
4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str.
Ames In Complex With Nad
pdb|4EGB|G Chain G, 3.0 Angstrom Resolution Crystal Structure Of Dtdp-Glucose
4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str.
Ames In Complex With Nad
pdb|4EGB|H Chain H, 3.0 Angstrom Resolution Crystal Structure Of Dtdp-Glucose
4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str.
Ames In Complex With Nad
Length = 346
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 13 NFASSKAQAPCYREPPPFCPTCGAGTVTELGGLKAYVTGPPHSKKAVLMISDIYG 67
NFA+ P PF T GTVT L +K Y PH K + ++YG
Sbjct: 104 NFAAESHVDRSIENPIPFYDTNVIGTVTLLELVKKY----PHIKLVQVSTDEVYG 154
>pdb|1ARO|P Chain P, T7 Rna Polymerase Complexed With T7 Lysozyme
Length = 883
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 4/55 (7%)
Query: 22 PCYREPPPFCPTCGAGTVTELGGLKAYVTGPPHSKKAVLMISDIYGDEPPIYRSV 76
PC P P+ G G G + HSKKA++ D+Y P +Y+++
Sbjct: 270 PCVVPPKPWTGITGGGYWA--NGRRPLALVRTHSKKALMRYEDVY--MPEVYKAI 320
>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 = 28.9 bits (63), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 4/55 (7%)
Query: 22 PCYREPPPFCPTCGAGTVTELGGLKAYVTGPPHSKKAVLMISDIYGDEPPIYRSV 76
PC P P+ G G G + HSKKA++ D+Y P +Y+++
Sbjct: 276 PCVVPPKPWTGITGGGYWA--NGRRPLALVRTHSKKALMRYEDVY--MPEVYKAI 326
>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 = 28.9 bits (63), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 4/55 (7%)
Query: 22 PCYREPPPFCPTCGAGTVTELGGLKAYVTGPPHSKKAVLMISDIYGDEPPIYRSV 76
PC P P+ G G G + HSKKA++ D+Y P +Y+++
Sbjct: 265 PCVVPPKPWTGITGGGYWA--NGRRPLALVRTHSKKALMRYEDVY--MPEVYKAI 315
>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 = 28.9 bits (63), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 4/55 (7%)
Query: 22 PCYREPPPFCPTCGAGTVTELGGLKAYVTGPPHSKKAVLMISDIYGDEPPIYRSV 76
PC P P+ G G G + HSKKA++ D+Y P +Y+++
Sbjct: 270 PCVVPPKPWTGITGGGYWA--NGRRPLALVRTHSKKALMRYEDVY--MPEVYKAI 320
>pdb|2OQ5|A Chain A, Crystal Structure Of Desc1, A New Member Of The Type Ii
Transmembrane Serine Proteinases Family
Length = 232
Score = 28.9 bits (63), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 36/89 (40%), Gaps = 2/89 (2%)
Query: 39 VTELGGLKAYVTGPPHSKKA-VLMISDIYGDEPPIYR-SVADKVAGAGFLVVAPDFFHGD 96
VT G LK H ++A V +I +EP Y ++ ++ AG L D GD
Sbjct: 122 VTGFGALKNDGYSQNHLRQAQVTLIDATTCNEPQAYNDAITPRMLCAGSLEGKTDACQGD 181
Query: 97 AANPSNPKYDKDTWRKNHTTDKGYEDAKP 125
+ P +D W G E AKP
Sbjct: 182 SGGPLVSSDARDIWYLAGIVSWGDECAKP 210
>pdb|4DTG|K Chain K, Hemostatic Effect Of A Monoclonal Antibody Mab 2021
Blocking The Interaction Between Fxa And Tfpi In A
Rabbit Hemophilia Model
Length = 66
Score = 28.5 bits (62), Expect = 3.5, Method: Composition-based stats.
Identities = 12/26 (46%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 208 KPKFDHLVKTYPGVCHGWTVRYFVND 233
KP F L + PG+C G+ RYF N+
Sbjct: 3 KPDFCFLEED-PGICRGYITRYFYNN 27
>pdb|1TFX|C Chain C, Complex Of The Second Kunitz Domain Of Tissue Factor
Pathway Inhibitor With Porcine Trypsin
pdb|1TFX|D Chain D, Complex Of The Second Kunitz Domain Of Tissue Factor
Pathway Inhibitor With Porcine Trypsin
Length = 58
Score = 28.5 bits (62), Expect = 3.5, Method: Composition-based stats.
Identities = 12/26 (46%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 208 KPKFDHLVKTYPGVCHGWTVRYFVND 233
KP F L + PG+C G+ RYF N+
Sbjct: 1 KPDFCFLEED-PGICRGYITRYFYNN 25
>pdb|2ISI|A Chain A, Crystal Structure Of Ape1 From Homo Sapiens In A New
Crystal Form Complexed With A Ligand
pdb|2ISI|B Chain B, Crystal Structure Of Ape1 From Homo Sapiens In A New
Crystal Form Complexed With A Ligand
pdb|2ISI|C Chain C, Crystal Structure Of Ape1 From Homo Sapiens In A New
Crystal Form Complexed With A Ligand
pdb|4IEM|A Chain A, Human Apurinic/apyrimidinic Endonuclease (ape1) With
Product Dna And Mg2+
pdb|4IEM|B Chain B, Human Apurinic/apyrimidinic Endonuclease (ape1) With
Product Dna And Mg2+
pdb|4IEM|C Chain C, Human Apurinic/apyrimidinic Endonuclease (ape1) With
Product Dna And Mg2+
pdb|4IEM|D Chain D, Human Apurinic/apyrimidinic Endonuclease (ape1) With
Product Dna And Mg2+
Length = 317
Score = 28.5 bits (62), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 4/76 (5%)
Query: 163 VLLHPSNVTEDEIKAVKVPIAVLGAERDNGLPPAQMKRFDEILSAKPKFDHLVKTYPGVC 222
VL NV +EI ++ P G +++ G P + + F E+L A P D YP
Sbjct: 205 VLCGDLNVAHEEID-LRNPK---GNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTP 260
Query: 223 HGWTVRYFVNDTFAVN 238
+ +T ++ + + N
Sbjct: 261 YAYTFWTYMMNARSKN 276
>pdb|1BIX|A Chain A, The Crystal Structure Of The Human Dna Repair Endonuclease
Hap1 Suggests The Recognition Of Extra-Helical
Deoxyribose At Dna Abasic Sites
Length = 287
Score = 28.5 bits (62), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 4/76 (5%)
Query: 163 VLLHPSNVTEDEIKAVKVPIAVLGAERDNGLPPAQMKRFDEILSAKPKFDHLVKTYPGVC 222
VL NV +EI ++ P G +++ G P + + F E+L A P D YP
Sbjct: 175 VLCGDLNVAHEEID-LRNPK---GNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTP 230
Query: 223 HGWTVRYFVNDTFAVN 238
+ +T ++ + + N
Sbjct: 231 YAYTFWTYMMNARSKN 246
>pdb|2O3H|A Chain A, Crystal Structure Of The Human C65a Ape
Length = 285
Score = 28.1 bits (61), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 4/76 (5%)
Query: 163 VLLHPSNVTEDEIKAVKVPIAVLGAERDNGLPPAQMKRFDEILSAKPKFDHLVKTYPGVC 222
VL NV +EI ++ P G +++ G P + + F E+L A P D YP
Sbjct: 173 VLCGDLNVAHEEID-LRNPK---GNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTP 228
Query: 223 HGWTVRYFVNDTFAVN 238
+ +T ++ + + N
Sbjct: 229 YAYTFWTYMMNARSKN 244
>pdb|1E9N|A Chain A, A Second Divalent Metal Ion In The Active Site Of A New
Crystal Form Of Human ApurinicAPYRIMIDINIC ENDONUCLEASE,
Ape1, And Its Implications For The Catalytic Mechanism
pdb|1E9N|B Chain B, A Second Divalent Metal Ion In The Active Site Of A New
Crystal Form Of Human ApurinicAPYRIMIDINIC ENDONUCLEASE,
Ape1, And Its Implications For The Catalytic Mechanism
pdb|1HD7|A Chain A, A Second Divalent Metal Ion In The Active Site Of A New
Crystal Form Of Human ApurinicAPYRIDINIMIC ENDONUCLEASE,
Ape1, And Its Implications For The Catalytic Mechanism
pdb|3U8U|A Chain A, Crystal Structure Of Human ApurinicAPYRIDINIMIC
ENDONUCLEASE, APE1 IN A New Crystal Form
pdb|3U8U|B Chain B, Crystal Structure Of Human ApurinicAPYRIDINIMIC
ENDONUCLEASE, APE1 IN A New Crystal Form
pdb|3U8U|C Chain C, Crystal Structure Of Human ApurinicAPYRIDINIMIC
ENDONUCLEASE, APE1 IN A New Crystal Form
pdb|3U8U|D Chain D, Crystal Structure Of Human ApurinicAPYRIDINIMIC
ENDONUCLEASE, APE1 IN A New Crystal Form
pdb|3U8U|E Chain E, Crystal Structure Of Human ApurinicAPYRIDINIMIC
ENDONUCLEASE, APE1 IN A New Crystal Form
pdb|3U8U|F Chain F, Crystal Structure Of Human ApurinicAPYRIDINIMIC
ENDONUCLEASE, APE1 IN A New Crystal Form
Length = 318
Score = 28.1 bits (61), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 4/76 (5%)
Query: 163 VLLHPSNVTEDEIKAVKVPIAVLGAERDNGLPPAQMKRFDEILSAKPKFDHLVKTYPGVC 222
VL NV +EI ++ P G +++ G P + + F E+L A P D YP
Sbjct: 206 VLCGDLNVAHEEID-LRNPK---GNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTP 261
Query: 223 HGWTVRYFVNDTFAVN 238
+ +T ++ + + N
Sbjct: 262 YAYTFWTYMMNARSKN 277
>pdb|1DE8|B Chain B, Human ApurinicAPYRIMIDINIC ENDONUCLEASE-1 (Ape1) Bound To
Abasic Dna
pdb|1DE8|A Chain A, Human ApurinicAPYRIMIDINIC ENDONUCLEASE-1 (Ape1) Bound To
Abasic Dna
pdb|1DE9|A Chain A, Human Ape1 Endonuclease With Bound Abasic Dna And Mn2+ Ion
pdb|1DE9|B Chain B, Human Ape1 Endonuclease With Bound Abasic Dna And Mn2+ Ion
Length = 276
Score = 28.1 bits (61), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 4/76 (5%)
Query: 163 VLLHPSNVTEDEIKAVKVPIAVLGAERDNGLPPAQMKRFDEILSAKPKFDHLVKTYPGVC 222
VL NV +EI ++ P G +++ G P + + F E+L A P D YP
Sbjct: 164 VLCGDLNVAHEEID-LRNPK---GNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTP 219
Query: 223 HGWTVRYFVNDTFAVN 238
+ +T ++ + + N
Sbjct: 220 YAYTFWTYMMNARSKN 235
>pdb|1DEW|A Chain A, Crystal Structure Of Human Ape1 Bound To Abasic Dna
pdb|1DEW|B Chain B, Crystal Structure Of Human Ape1 Bound To Abasic Dna
Length = 279
Score = 28.1 bits (61), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 4/76 (5%)
Query: 163 VLLHPSNVTEDEIKAVKVPIAVLGAERDNGLPPAQMKRFDEILSAKPKFDHLVKTYPGVC 222
VL NV +EI ++ P G +++ G P + + F E+L A P D YP
Sbjct: 167 VLCGDLNVAHEEID-LRNPK---GNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTP 222
Query: 223 HGWTVRYFVNDTFAVN 238
+ +T ++ + + N
Sbjct: 223 YAYTFWTYMMNARSKN 238
>pdb|1ADZ|A Chain A, The Solution Structure Of The Second Kunitz Domain Of
Tissue Factor Pathway Inhibitor, Nmr, 30 Structures
Length = 71
Score = 27.7 bits (60), Expect = 7.5, Method: Composition-based stats.
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 219 PGVCHGWTVRYFVND 233
PG+C G+ RYF N+
Sbjct: 20 PGICRGYITRYFYNN 34
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
0.318 0.135 0.427
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,661,451
Number of Sequences: 62578
Number of extensions: 299681
Number of successful extensions: 718
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 716
Number of HSP's gapped (non-prelim): 20
length of query: 259
length of database: 14,973,337
effective HSP length: 97
effective length of query: 162
effective length of database: 8,903,271
effective search space: 1442329902
effective search space used: 1442329902
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)