BLASTP 2.2.1 [Apr-13-2001]
Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
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.
Query= gi|15644800|ref|NP_206970.1| peptide chain release
factor RF-2 (prfB) [Helicobacter pylori 26695]
(363 letters)
Database: /var/www/html/HP/blast_new/blast/db/pdbaa
13,198 sequences; 2,899,336 total letters
Searching...........................done
Score E
Sequences producing significant alignments: (bits) Value
pdb|1GQE|A Chain A, Polypeptide Chain Release Factor 2 (Rf2... 338 6e-94
pdb|1QBK|B Chain B, Structure Of The Karyopherin Beta2-Ran ... 29 0.96
pdb|1BSW|A Chain A, Acutolysin A From Snake Venom Of Agkist... 28 1.3
pdb|1BUD|A Chain A, Acutolysin A From Snake Venom Of Agkist... 28 1.3
pdb|1K83|H Chain H, Crystal Structure Of Yeast Rna Polymera... 28 1.6
pdb|1VOK|A Chain A, Arabidopsis Thaliana Tbp (Dimer) >gi|72... 28 2.1
pdb|1TGH|A Chain A, Human Tbp Complex With Tata Element Dna 27 2.8
pdb|1JFI|C Chain C, Crystal Structure Of The Nc2-Tbp-Dna Te... 27 2.8
pdb|1C9B|B Chain B, Crystal Structure Of A Human Tbp Core D... 27 2.8
pdb|1CDW|A Chain A, Human Tbp Core Domain Complexed With Dna 27 4.8
pdb|1FJD|A Chain A, Human Parvulin-Like Peptidyl Prolyl Cis... 27 4.8
pdb|1EQ3|A Chain A, Nmr Structure Of Human Parvulin Hpar14 26 6.2
>pdb|1GQE|A Chain A, Polypeptide Chain Release Factor 2 (Rf2) From Escherichia
Coli
Length = 365
Score = 338 bits (867), Expect = 6e-94
Identities = 173/354 (48%), Positives = 233/354 (64%), Gaps = 3/354 (0%)
Query: 10 LKSLQNKCDNIALIIKPEKIKQELERIEKEQEDPNFWQDVLKARDTNKEKVRLNRLLETY 69
++ L + D + + + K+ LE + E E P+ W + +A+ KE+ L +++T
Sbjct: 11 IQDLTERSDVLRGYLDYDAKKERLEEVNAELEQPDVWNEPERAQALGKERSSLEAVVDTL 70
Query: 70 QKTKNSLDESVELFELAQNDNDEVTLSLLYEEAPILENSVQKVEIEIMLSGENDASNAII 129
+ K L++ L ELA +DE T + E LE + ++E SGE D+++ +
Sbjct: 71 DQXKQGLEDVSGLLELAVEADDEETFNEAVAELDALEEKLAQLEFRRXFSGEYDSADCYL 130
Query: 130 TIQPGAGGTESQDWASILYRMYLRWAERRGFKSEILDYQDGEEAGIKGVAFIIKGENAYG 189
IQ G+GGTE+QDWAS L R YLRWAE RGFK+EI++ +GE AGIK V I G+ AYG
Sbjct: 131 DIQAGSGGTEAQDWASXLERXYLRWAESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYG 190
Query: 190 YLKNENGVHRLVRISPFDANAKRHTSFASVQISPELDDDIDIEIDEKDVRYDYYRSSGAG 249
+L+ E GVHRLVR SPFD+ +RHTSF+S + PE+DDDIDIEI+ D+R D YR+SGAG
Sbjct: 191 WLRTETGVHRLVRKSPFDSGGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRASGAG 250
Query: 250 GQHVNKTESAVRITHFPTGIVVQCQNDRSQHKNKASALKMLKSKLYELELEKQ--QSSAK 307
GQHVN+TESAVRITH PTGIV QCQNDRSQHKNK A K K+KLYE+E +K+ + A
Sbjct: 251 GQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAXKQXKAKLYEVEXQKKNAEKQAX 310
Query: 308 NEEKSEIGWGHQIRSYVLAPYQQVKDARSNTAYSNVEAILDGDIDAILEGVLIA 361
+ KS+IGWG QIRSYVL ++KD R+ N +A+LDG +D +E L A
Sbjct: 311 EDNKSDIGWGSQIRSYVLDD-SRIKDLRTGVETRNTQAVLDGSLDQFIEASLKA 363
>pdb|1QBK|B Chain B, Structure Of The Karyopherin Beta2-Ran Gppnhp Nuclear
Transport Complex
Length = 890
Score = 28.9 bits (63), Expect = 0.96
Identities = 13/56 (23%), Positives = 28/56 (49%)
Query: 197 VHRLVRISPFDANAKRHTSFASVQISPELDDDIDIEIDEKDVRYDYYRSSGAGGQH 252
V L ++ P N +++ + + ++++D I E+D+R ++RS QH
Sbjct: 294 VRHLPKLIPVLVNGXKYSDIDIILLKGDVEEDETIPDSEQDIRPRFHRSRTVAQQH 349
>pdb|1BSW|A Chain A, Acutolysin A From Snake Venom Of Agkistrodon Acutus At Ph
7.5
Length = 197
Score = 28.5 bits (62), Expect = 1.3
Identities = 29/121 (23%), Positives = 59/121 (47%), Gaps = 11/121 (9%)
Query: 89 DNDEVTLSLLYEEAPILENSVQKVEIEIMLSG-ENDASNAIITIQPGAGGTESQ--DWAS 145
D+D + + +YE + S ++I+I LSG E + +I ++ AG T +W +
Sbjct: 22 DSDSIK-AWVYEMINTITESYSYLKIDISLSGLEIWSGKDLIDVEASAGNTLKSFGEWRA 80
Query: 146 --ILYRMYLRWAERRGFKSEILDYQDGEEAGIKGVAFIIKGENAYGYLKNENGVHRLVRI 203
+++R+ + D+ DG G+ VA + + + G +++ + V+RLV I
Sbjct: 81 KDLIHRI----SHDNAQLLTATDF-DGATIGLAYVASMCNPKRSVGVIQDHSSVNRLVAI 135
Query: 204 S 204
+
Sbjct: 136 T 136
>pdb|1BUD|A Chain A, Acutolysin A From Snake Venom Of Agkistrodon Acutus At Ph
5.0
Length = 197
Score = 28.5 bits (62), Expect = 1.3
Identities = 29/121 (23%), Positives = 59/121 (47%), Gaps = 11/121 (9%)
Query: 89 DNDEVTLSLLYEEAPILENSVQKVEIEIMLSG-ENDASNAIITIQPGAGGTESQ--DWAS 145
D+D + + +YE + S ++I+I LSG E + +I ++ AG T +W +
Sbjct: 22 DSDSIK-AWVYEMINTITESYSYLKIDISLSGLEIWSGKDLIDVEASAGNTLKSFGEWRA 80
Query: 146 --ILYRMYLRWAERRGFKSEILDYQDGEEAGIKGVAFIIKGENAYGYLKNENGVHRLVRI 203
+++R+ + D+ DG G+ VA + + + G +++ + V+RLV I
Sbjct: 81 KDLIHRI----SHDNAQLLTATDF-DGATIGLAYVASMCNPKRSVGVIQDHSSVNRLVAI 135
Query: 204 S 204
+
Sbjct: 136 T 136
>pdb|1K83|H Chain H, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1I50|H Chain H, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I3Q|H Chain H, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I6H|H Chain H, Rna Polymerase Ii Elongation Complex
pdb|1A1D| Yeast Rna Polymerase Subunit Rpb8, Nmr, Minimized Average
Structure, Alpha Carbons Only
Length = 146
Score = 28.1 bits (61), Expect = 1.6
Identities = 18/53 (33%), Positives = 29/53 (53%), Gaps = 2/53 (3%)
Query: 61 RLNRLLETYQKTKNSLDESVELFELAQNDNDEVTL--SLLYEEAPILENSVQK 111
R+ T + K +LD +VELF +A D+ VT+ SL E+ P ++S +
Sbjct: 25 RIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASSLNLEDTPANDSSATR 77
>pdb|1VOK|A Chain A, Arabidopsis Thaliana Tbp (Dimer)
pdb|1QNE|B Chain B, Crystal Structure Of The Adenovirus Major Late Promoter
Tata Box Bound To Wild-Type Tbp (Arabidopsis Thaliana
Tbp Isoform 2).
pdb|1VOK|B Chain B, Arabidopsis Thaliana Tbp (Dimer)
pdb|1QN6|B Chain B, Crystal Structure Of The T(-26) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QNB|B Chain B, Crystal Structure Of The T(-25) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1VOL|B Chain B, Tfiib (Human Core Domain)TBP (A.THALIANA)TATA ELEMENT
Ternary Complex
pdb|1QNE|A Chain A, Crystal Structure Of The Adenovirus Major Late Promoter
Tata Box Bound To Wild-Type Tbp (Arabidopsis Thaliana
Tbp Isoform 2).
pdb|1QN8|B Chain B, Crystal Structure Of The T(-28) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QNC|B Chain B, Crystal Structure Of The A(-31) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QNA|B Chain B, Crystal Structure Of The T(-30) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN5|B Chain B, Crystal Structure Of The G(-26) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN4|B Chain B, Crystal Structure Of The T(-24) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN9|B Chain B, Crystal Structure Of The C(-29) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN3|B Chain B, Crystal Structure Of The C(-25) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN7|A Chain A, Crystal Structure Of The T(-27) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN7|B Chain B, Crystal Structure Of The T(-27) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN6|A Chain A, Crystal Structure Of The T(-26) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN5|A Chain A, Crystal Structure Of The G(-26) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QNB|A Chain A, Crystal Structure Of The T(-25) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QNC|A Chain A, Crystal Structure Of The A(-31) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN4|A Chain A, Crystal Structure Of The T(-24) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN9|A Chain A, Crystal Structure Of The C(-29) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN3|A Chain A, Crystal Structure Of The C(-25) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN8|A Chain A, Crystal Structure Of The T(-28) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QNA|A Chain A, Crystal Structure Of The T(-30) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution
Length = 200
Score = 27.7 bits (60), Expect = 2.1
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 137 GTESQDWASILYRMYLRWAERRGFKSEILDYQDGEEAGIKGVAFIIKGEN-AYGY 190
G +S+D++ + R Y R ++ GF ++ D++ G V F I+ E AY +
Sbjct: 83 GAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSH 137
>pdb|1TGH|A Chain A, Human Tbp Complex With Tata Element Dna
Length = 185
Score = 27.3 bits (59), Expect = 2.8
Identities = 14/49 (28%), Positives = 26/49 (52%)
Query: 137 GTESQDWASILYRMYLRWAERRGFKSEILDYQDGEEAGIKGVAFIIKGE 185
G +S++ + + R Y R ++ GF ++ LD++ G V F I+ E
Sbjct: 69 GAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLE 117
>pdb|1JFI|C Chain C, Crystal Structure Of The Nc2-Tbp-Dna Ternary Complex
Length = 185
Score = 27.3 bits (59), Expect = 2.8
Identities = 14/49 (28%), Positives = 26/49 (52%)
Query: 137 GTESQDWASILYRMYLRWAERRGFKSEILDYQDGEEAGIKGVAFIIKGE 185
G +S++ + + R Y R ++ GF ++ LD++ G V F I+ E
Sbjct: 69 GAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLE 117
>pdb|1C9B|B Chain B, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
Core Domain Complex Bound To An Extended, Modified
Adenoviral Major Late Promoter (Admlp)
pdb|1C9B|F Chain F, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
Core Domain Complex Bound To An Extended, Modified
Adenoviral Major Late Promoter (Admlp)
pdb|1C9B|J Chain J, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
Core Domain Complex Bound To An Extended, Modified
Adenoviral Major Late Promoter (Admlp)
pdb|1C9B|N Chain N, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
Core Domain Complex Bound To An Extended, Modified
Adenoviral Major Late Promoter (Admlp)
pdb|1C9B|R Chain R, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
Core Domain Complex Bound To An Extended, Modified
Adenoviral Major Late Promoter (Admlp)
Length = 180
Score = 27.3 bits (59), Expect = 2.8
Identities = 14/49 (28%), Positives = 26/49 (52%)
Query: 137 GTESQDWASILYRMYLRWAERRGFKSEILDYQDGEEAGIKGVAFIIKGE 185
G +S++ + + R Y R ++ GF ++ LD++ G V F I+ E
Sbjct: 66 GAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLE 114
>pdb|1CDW|A Chain A, Human Tbp Core Domain Complexed With Dna
Length = 179
Score = 26.6 bits (57), Expect = 4.8
Identities = 14/49 (28%), Positives = 26/49 (52%)
Query: 137 GTESQDWASILYRMYLRWAERRGFKSEILDYQDGEEAGIKGVAFIIKGE 185
G +S++ + + R Y R ++ GF ++ LD++ G V F I+ E
Sbjct: 65 GAKSEENSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLE 113
>pdb|1FJD|A Chain A, Human Parvulin-Like Peptidyl Prolyl CisTRANS ISOMERASE,
Hpar14
Length = 104
Score = 26.6 bits (57), Expect = 4.8
Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 12/73 (16%)
Query: 258 SAVRITHFPTGIVVQCQNDRSQHKNKASALKMLKSKLYELELEKQQSSAKNEEKSEIGWG 317
+AV++ H + C+ +H A++ LKS + E+ Q S K + ++GW
Sbjct: 9 NAVKVRH------ILCE----KHGKIMEAMEKLKSGMRFNEVAAQYSEDKARQGGDLGW- 57
Query: 318 HQIRSYVLAPYQQ 330
R ++ P+Q+
Sbjct: 58 -MTRGSMVGPFQE 69
>pdb|1EQ3|A Chain A, Nmr Structure Of Human Parvulin Hpar14
Length = 96
Score = 26.2 bits (56), Expect = 6.2
Identities = 14/52 (26%), Positives = 26/52 (49%), Gaps = 2/52 (3%)
Query: 279 QHKNKASALKMLKSKLYELELEKQQSSAKNEEKSEIGWGHQIRSYVLAPYQQ 330
+H A++ LKS + E+ Q S K + ++GW R ++ P+Q+
Sbjct: 12 KHGKIMEAMEKLKSGMRFNEVAAQYSEDKARQGGDLGW--MTRGSMVGPFQE 61
Database: /var/www/html/HP/blast_new/blast/db/pdbaa
Posted date: Dec 20, 2002 11:08 AM
Number of letters in database: 2,899,336
Number of sequences in database: 13,198
Lambda K H
0.312 0.131 0.360
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,107,059
Number of Sequences: 13198
Number of extensions: 91240
Number of successful extensions: 196
Number of sequences better than 10.0: 12
Number of HSP's better than 10.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 187
Number of HSP's gapped (non-prelim): 12
length of query: 363
length of database: 2,899,336
effective HSP length: 89
effective length of query: 274
effective length of database: 1,724,714
effective search space: 472571636
effective search space used: 472571636
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 55 (25.8 bits)