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= 027312
(225 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2C35|A Chain A, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
pdb|2C35|C Chain C, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
pdb|2C35|E Chain E, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
pdb|2C35|G Chain G, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
Length = 152
Score = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 29/97 (29%), Positives = 52/97 (53%), Gaps = 2/97 (2%)
Query: 108 KNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLF 167
+ A+ L++ E +LE ++Q SA+ ++ F K L Y S F N + + +
Sbjct: 37 ETAETLLNSEVHMLLEHRKQQNE--SAEDEQELSEVFMKTLNYTARFSRFKNRETIASVR 94
Query: 168 QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAK 204
L + + E+ +AN+CPET EE+ A++PSL+ +
Sbjct: 95 SLLLQKKLHKFELACLANLCPETAEESKALIPSLEGR 131
>pdb|1WCM|D Chain D, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
Length = 177
Score = 34.3 bits (77), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 150 YAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLN 209
Y S F + + V + Q L G+ E+ + ++ +T +EA ++PSL K S +
Sbjct: 103 YLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKIS--D 160
Query: 210 DLLKEVLIQLAKFKS 224
D L+ +L +L+ ++
Sbjct: 161 DELERILKELSNLET 175
>pdb|1Y14|A Chain A, Crystal Structure Of Yeast Subcomplex Of Rpb4 And Rpb7
pdb|1Y14|C Chain C, Crystal Structure Of Yeast Subcomplex Of Rpb4 And Rpb7
Length = 187
Score = 34.3 bits (77), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 150 YAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLN 209
Y S F + + V + Q L G+ E+ + ++ +T +EA ++PSL K S +
Sbjct: 113 YLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKIS--D 170
Query: 210 DLLKEVLIQLAKFKS 224
D L+ +L +L+ ++
Sbjct: 171 DELERILKELSNLET 185
>pdb|1PQV|D Chain D, Rna Polymerase Ii-Tfiis Complex
Length = 221
Score = 34.3 bits (77), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 150 YAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLN 209
Y S F + + V + Q L G+ E+ + ++ +T +EA ++PSL K S +
Sbjct: 147 YLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKIS--D 204
Query: 210 DLLKEVLIQLAKFKS 224
D L+ +L +L+ ++
Sbjct: 205 DELERILKELSNLET 219
>pdb|3QT1|D Chain D, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
Length = 219
Score = 34.3 bits (77), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 150 YAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLN 209
Y S F + + V + Q L G+ E+ + ++ +T +EA ++PSL K S +
Sbjct: 145 YLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKIS--D 202
Query: 210 DLLKEVLIQLAKFKS 224
D L+ +L +L+ ++
Sbjct: 203 DELERILKELSNLET 217
>pdb|1NT9|D Chain D, Complete 12-Subunit Rna Polymerase Ii
pdb|1Y1W|D Chain D, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|D Chain D, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|D Chain D, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|D Chain D, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|D Chain D, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|D Chain D, 12-Subunit Rna Polymerase Ii
pdb|2JA5|D Chain D, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|D Chain D, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|D Chain D, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|P Chain P, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|D Chain D, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2R7Z|D Chain D, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|D Chain D, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|D Chain D, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|D Chain D, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3FKI|D Chain D, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3H3V|E Chain E, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|D Chain D, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|P Chain P, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|D Chain D, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|D Chain D, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|D Chain D, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|D Chain D, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|D Chain D, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|D Chain D, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|D Chain D, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|D Chain D, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3PO2|D Chain D, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|D Chain D, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3J0K|D Chain D, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
pdb|4A3C|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|D Chain D, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|D Chain D, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
pdb|4BBR|D Chain D, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|D Chain D, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 221
Score = 34.3 bits (77), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 150 YAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKAKRSRLN 209
Y S F + + V + Q L G+ E+ + ++ +T +EA ++PSL K S +
Sbjct: 147 YLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKIS--D 204
Query: 210 DLLKEVLIQLAKFKS 224
D L+ +L +L+ ++
Sbjct: 205 DELERILKELSNLET 219
>pdb|2BE7|D Chain D, Crystal Structure Of The Unliganded (T-State) Aspartate
Transcarbamoylase Of The Psychrophilic Bacterium
Moritella Profunda
pdb|2BE7|E Chain E, Crystal Structure Of The Unliganded (T-State) Aspartate
Transcarbamoylase Of The Psychrophilic Bacterium
Moritella Profunda
pdb|2BE7|F Chain F, Crystal Structure Of The Unliganded (T-State) Aspartate
Transcarbamoylase Of The Psychrophilic Bacterium
Moritella Profunda
Length = 153
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 109 NAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ 168
NAK L+ E I + Q+ALL+ + TI I +F HS T P V+ +F
Sbjct: 53 NAKDLIKVENTEITKSQANQLALLAPNATINIIENFK----VTDKHS-LTLPNEVENVFP 107
Query: 169 SLSEHGVTDGE 179
+ + +T GE
Sbjct: 108 CPNSNCITHGE 118
>pdb|2HP3|A Chain A, Crystal Structure Of Iminodisuccinate Epimerase
pdb|2HP3|B Chain B, Crystal Structure Of Iminodisuccinate Epimerase
Length = 446
Score = 28.1 bits (61), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 1/67 (1%)
Query: 115 DCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTH-SHFTNPQAVKGLFQSLSEH 173
D E + G Q L +A P + LY K+ S + N + + GLF + EH
Sbjct: 229 DAEGILAMYGAQPGPELFNAMQKFGTPWAIIAPGLYKKSWPSCYANHKPLAGLFAIMKEH 288
Query: 174 GVTDGEI 180
G+T +I
Sbjct: 289 GLTGQDI 295
>pdb|1XR6|A Chain A, Crystal Structure Of Rna-Dependent Rna Polymerase 3d From
Human Rhinovirus Serotype 1b
Length = 460
Score = 26.9 bits (58), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 40/86 (46%), Gaps = 6/86 (6%)
Query: 139 KIPVSFDKGLLYAKTHSHF---TNP---QAVKGLFQSLSEHGVTDGEICVIANICPETVE 192
KIPV D + A ++++ +P QA+K + ++LS +C ++ T
Sbjct: 220 KIPVMLDGDCIMAFDYTNYDGSIHPVWFQALKKVLENLSFQSNLIDRLCYSKHLFKSTYY 279
Query: 193 EAYAIVPSLKAKRSRLNDLLKEVLIQ 218
E VPS + S N ++ ++I+
Sbjct: 280 EVAGGVPSGCSGTSIFNTMINNIIIR 305
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
0.313 0.130 0.356
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,366,920
Number of Sequences: 62578
Number of extensions: 189779
Number of successful extensions: 257
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 251
Number of HSP's gapped (non-prelim): 11
length of query: 225
length of database: 14,973,337
effective HSP length: 95
effective length of query: 130
effective length of database: 9,028,427
effective search space: 1173695510
effective search space used: 1173695510
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)