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= 021860
(306 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3R2D|A Chain A, Crystal Structure Of Antitermination Factors Nusb And Nuse
In Complex With Dsrna
pdb|3R2D|B Chain B, Crystal Structure Of Antitermination Factors Nusb And Nuse
In Complex With Dsrna
Length = 149
Score = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 27/100 (27%), Positives = 48/100 (48%), Gaps = 8/100 (8%)
Query: 202 VVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVVGTRH-QIVINEA 260
+VD H+ ID ++ K W +D+ +E + L L ++E+ + ++ V +
Sbjct: 51 LVDTAVRHIEEIDSIIEKHLKGWSIDRLG--YVERNALRLGVAELIFLKSKEPGRVFIDI 108
Query: 261 VDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASK 300
VDL K++ D A + +NG L + A I +SK K
Sbjct: 109 VDLVKKYADEKAGKFVNGVLSAIYK-----AYITSSKEEK 143
>pdb|2JR0|A Chain A, Solution Structure Of Nusb From Aquifex Aeolicus
pdb|3R2C|A Chain A, Crystal Structure Of Antitermination Factors Nusb And Nuse
In Complex With Boxa Rna
pdb|3R2C|B Chain B, Crystal Structure Of Antitermination Factors Nusb And Nuse
In Complex With Boxa Rna
pdb|4EYA|A Chain A, Crystal Structure Of A Plectonemic Rna Supercoil
pdb|4EYA|B Chain B, Crystal Structure Of A Plectonemic Rna Supercoil
pdb|4EYA|C Chain C, Crystal Structure Of A Plectonemic Rna Supercoil
pdb|4EYA|D Chain D, Crystal Structure Of A Plectonemic Rna Supercoil
pdb|4EYA|E Chain E, Crystal Structure Of A Plectonemic Rna Supercoil
pdb|4EYA|F Chain F, Crystal Structure Of A Plectonemic Rna Supercoil
pdb|4EYA|G Chain G, Crystal Structure Of A Plectonemic Rna Supercoil
pdb|4EYA|H Chain H, Crystal Structure Of A Plectonemic Rna Supercoil
Length = 148
Score = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 27/100 (27%), Positives = 48/100 (48%), Gaps = 8/100 (8%)
Query: 202 VVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVVGTRH-QIVINEA 260
+VD H+ ID ++ K W +D+ +E + L L ++E+ + ++ V +
Sbjct: 50 LVDTAVRHIEEIDSIIEKHLKGWSIDRLG--YVERNALRLGVAELIFLKSKEPGRVFIDI 107
Query: 261 VDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASK 300
VDL K++ D A + +NG L + A I +SK K
Sbjct: 108 VDLVKKYADEKAGKFVNGVLSAIYK-----AYITSSKEEK 142
>pdb|1TZT|A Chain A, T. Maritima Nusb, P21
pdb|1TZT|B Chain B, T. Maritima Nusb, P21
pdb|1TZU|A Chain A, T. Maritima Nusb, P212121
pdb|1TZV|A Chain A, T. Maritima Nusb, P3121, Form 1
pdb|1TZW|A Chain A, T. Maritima Nusb, P3121, Form 2
pdb|1TZX|A Chain A, T. Maritima Nusb, P3221
pdb|1TZX|B Chain B, T. Maritima Nusb, P3221
Length = 142
Score = 30.8 bits (68), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 25/117 (21%), Positives = 57/117 (48%), Gaps = 11/117 (9%)
Query: 165 LRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVW 224
R DE+ I E+L Y K R+ + + + ++ +ID ++ + W
Sbjct: 21 FRRDEDLEQILEEILDE----TYDKKAKEDARRYIRGIKE----NLSMIDDLISRYLEKW 72
Query: 225 KMDQPAGRILELSILHLAMSEITV-VGTRHQIVINEAVDLAKRFCDGAAPRIINGCL 280
+++ + +++ ++L LA E+ ++ I+EA+++AKR+ + + +NG L
Sbjct: 73 SLNRLS--VVDRNVLRLATYELLFEKDIPIEVTIDEAIEIAKRYGTENSGKFVNGIL 127
>pdb|3IMQ|A Chain A, Crystal Structure Of The Nusb101-S10(Delta Loop) Complex
pdb|3IMQ|B Chain B, Crystal Structure Of The Nusb101-S10(Delta Loop) Complex
pdb|3IMQ|C Chain C, Crystal Structure Of The Nusb101-S10(Delta Loop) Complex
Length = 141
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 47/88 (53%), Gaps = 8/88 (9%)
Query: 194 FTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITV-VGTR 252
+ R+LL V + +D ++ P ++ + G++ E ++L +A+ E++
Sbjct: 49 YFRELLAGVA----TNTAYLDGLMKPYLS--RLLEELGQV-EKAVLRIALYELSKRSDVP 101
Query: 253 HQIVINEAVDLAKRFCDGAAPRIINGCL 280
+++ INEA++LAK F + + +NG L
Sbjct: 102 YKVAINEAIELAKSFGAENSHKFVNGVL 129
>pdb|1EY1|A Chain A, Solution Structure Of Escherichia Coli Nusb
Length = 139
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 234 LELSILHLAMSEITV-VGTRHQIVINEAVDLAKRFCDGAAPRIINGCL 280
+E ++L +A+ E++ +++ INEA++LAK F + + +NG L
Sbjct: 80 VEKAVLRIALYELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVL 127
>pdb|3D3B|A Chain A, Structural And Functional Analysis Of The E. Coli Nusb-s10
Transcription Antitermination Complex.
pdb|3D3C|A Chain A, Structural And Functional Analysis Of The E. Coli Nusb-S10
Transcription Antitermination Complex.
pdb|3D3C|B Chain B, Structural And Functional Analysis Of The E. Coli Nusb-S10
Transcription Antitermination Complex.
pdb|3D3C|C Chain C, Structural And Functional Analysis Of The E. Coli Nusb-S10
Transcription Antitermination Complex
Length = 141
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 47/88 (53%), Gaps = 8/88 (9%)
Query: 194 FTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITV-VGTR 252
+ R+LL V + +D ++ P ++ + G++ E ++L +A+ E++
Sbjct: 49 YFRELLAGVA----TNTAYLDGLMKPYLS--RLLEELGQV-EKAVLRIALYELSKRSDVP 101
Query: 253 HQIVINEAVDLAKRFCDGAAPRIINGCL 280
+++ INEA++LAK F + + +NG L
Sbjct: 102 YKVAINEAIELAKSFGAEDSHKFVNGVL 129
>pdb|1EYV|A Chain A, The Crystal Structure Of Nusb From Mycobacterium
Tuberculosis
pdb|1EYV|B Chain B, The Crystal Structure Of Nusb From Mycobacterium
Tuberculosis
Length = 156
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 5/74 (6%)
Query: 209 HVHIIDKVVPPIWKVWKMDQ-PAGRILELSILHLAMSEIT-VVGTRHQIVINEAVDLAKR 266
H ID ++ + W +D+ PA ++ +IL +++ E+ +V++EAV LAK
Sbjct: 65 HAAHIDDLITAHLRGWTLDRLPA---VDRAILRVSVWELLHAADVPEPVVVDEAVQLAKE 121
Query: 267 FCDGAAPRIINGCL 280
+P +NG L
Sbjct: 122 LSTDDSPGFVNGVL 135
>pdb|3AAD|A Chain A, Structure Of The Histone Chaperone Cia/asf1-double
Bromodomain Complex Linking Histone Modifications And
Site-specific Histone Eviction
Length = 292
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 31/112 (27%), Positives = 51/112 (45%), Gaps = 15/112 (13%)
Query: 123 KRLNSRREPGYEF-DKSSLLEYNHMSFGGPP-----VTTETVEEADELLRSDEE-----E 171
KRL RE EF + L+ N ++ GP ++ ++ DE L+ E+ E
Sbjct: 99 KRLYPSRE---EFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARLE 155
Query: 172 SAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKV 223
AI +L ++ +S +L + ++AV D W H + K VP +KV
Sbjct: 156 KAINP-LLDDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKV 206
>pdb|3UV5|A Chain A, Crystal Structure Of The Tandem Bromodomains Of Human
Transcription Initiation Factor Tfiid Subunit 1 (Taf1)
Length = 265
Score = 29.3 bits (64), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 31/112 (27%), Positives = 51/112 (45%), Gaps = 15/112 (13%)
Query: 123 KRLNSRREPGYEF-DKSSLLEYNHMSFGGP-----PVTTETVEEADELLRSDEE-----E 171
KRL RE EF + L+ N ++ GP ++ ++ DE L+ E+ E
Sbjct: 66 KRLYPSRE---EFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARLE 122
Query: 172 SAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKV 223
AI +L ++ +S +L + ++AV D W H + K VP +KV
Sbjct: 123 KAINP-LLDDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKV 173
>pdb|1EQF|A Chain A, Crystal Structure Of The Double Bromodomain Module From
Human Tafii250
Length = 280
Score = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 31/112 (27%), Positives = 51/112 (45%), Gaps = 15/112 (13%)
Query: 123 KRLNSRREPGYEF-DKSSLLEYNHMSFGGPP-----VTTETVEEADELLRSDEE-----E 171
KRL RE EF + L+ N ++ GP ++ ++ DE L+ E+ E
Sbjct: 78 KRLYPSRE---EFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARLE 134
Query: 172 SAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKV 223
AI +L ++ +S +L + ++AV D W H + K VP +KV
Sbjct: 135 KAINP-LLDDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKV 185
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
0.317 0.130 0.374
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,171,789
Number of Sequences: 62578
Number of extensions: 293996
Number of successful extensions: 642
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 640
Number of HSP's gapped (non-prelim): 12
length of query: 306
length of database: 14,973,337
effective HSP length: 98
effective length of query: 208
effective length of database: 8,840,693
effective search space: 1838864144
effective search space used: 1838864144
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: 51 (24.3 bits)