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= 009948
(522 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3CYM|A Chain A, Crystal Structure Of Protein Bad_0989 From Bifidobacterium
Adolescentis
Length = 440
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 39/68 (57%)
Query: 163 SLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222
LA + + L ++L+KE +DWS RPL + +NYAA+D LIE+ + ++ ++G
Sbjct: 134 GLAAVTEHFLGLTLAKEHSAADWSYRPLPRDWRNYAALDVELLIELETKMRAELKRQGKM 193
Query: 223 CSSISELD 230
+ E D
Sbjct: 194 EWAQEEFD 201
>pdb|2FBT|A Chain A, Wrn Exonuclease
pdb|2FBV|A Chain A, Wrn Exonuclease, Mn Complex
pdb|2FBX|A Chain A, Wrn Exonuclease, Mg Complex
pdb|2FBY|A Chain A, Wrn Exonuclease, Eu Complex
pdb|2FC0|A Chain A, Wrn Exonuclease, Mn Dgmp Complex
Length = 205
Score = 48.9 bits (115), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 53/193 (27%), Positives = 86/193 (44%), Gaps = 35/193 (18%)
Query: 25 LARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFXXXX 84
++ +LS +VG D EW P ++ +V+L+QL ES +
Sbjct: 38 ISMSLSDGDVVGFDMEWPPLY-NRGKLGKVALIQLCVS----------ESKCYLFHVSSM 86
Query: 85 XXXXXXXXWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSI 144
+ LK L + + K G + D L F DI +++ ++++T +
Sbjct: 87 SVFP-----QGLKMLLENKAVKKAGVGIEGDQWKLLRDF-----DI---KLKNFVELTDV 133
Query: 145 YNHLHHKQLGRKLP-KETKSLANICKELLDISL--SKELQCSDWSNRPLTEEQKNYAAID 201
N +KL ET SL ++ K LL L K ++CS+WS PLTE+QK YAA D
Sbjct: 134 AN--------KKLKCTETWSLNSLVKHLLGKQLLKDKSIRCSNWSKFPLTEDQKLYAATD 185
Query: 202 AHCLIEIFNIFQV 214
A+ I+ ++
Sbjct: 186 AYAGFIIYRNLEI 198
>pdb|2E6L|A Chain A, Structure Of Mouse Wrn Exonuclease Domain
pdb|2E6M|A Chain A, Structure Of Mouse Werner Exonuclease Domain
Length = 208
Score = 48.5 bits (114), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 58/204 (28%), Positives = 88/204 (43%), Gaps = 39/204 (19%)
Query: 13 LVTSTESPEFTHLAR----ALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFN 68
+V S E+ + + L+ LS +VG D EW P RV+++QL
Sbjct: 17 IVYSYEASDCSFLSEDISMRLSDGDVVGFDMEWPPIYKPGKR-SRVAVIQLCVS------ 69
Query: 69 PESDESNASVVFXXXXXXXXXXXXWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGC 128
ES + + LK L + I K G + D L F
Sbjct: 70 ----ESKCYLFHISSMSVFP-----QGLKMLLENKSIKKAGVGIEGDQWKLLRDF----- 115
Query: 129 DIGFDRVEPYLDITSIYNHLHHKQLGRKLP-KETKSLANICKELLDISL--SKELQCSDW 185
D+ ++E ++++T + N KL ET SL + K +L L K ++CS+W
Sbjct: 116 DV---KLESFVELTDVANE--------KLKCAETWSLNGLVKHVLGKQLLKDKSIRCSNW 164
Query: 186 SNRPLTEEQKNYAAIDAHCLIEIF 209
SN PLTE+QK YAA DA+ + I+
Sbjct: 165 SNFPLTEDQKLYAATDAYAGLIIY 188
>pdb|2HBJ|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain
pdb|2HBK|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain; Protein In Complex With Mn
pdb|2HBL|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain; Protein In Complex With Mn, Zn, And Amp
pdb|2HBM|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p,
Reveals An Interplay Between The Active Site And The
Hrdc Domain; Protein In Complex With Mn, Zn, And Ump
Length = 410
Score = 45.4 bits (106), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 35/135 (25%), Positives = 63/135 (46%), Gaps = 19/135 (14%)
Query: 95 LLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLH-HKQL 153
+L E+F +P I+K+ D+I+L D+G L + +++ H K +
Sbjct: 150 ILNEVFTNPSIVKVFHGAFMDIIWLQR-------DLG-------LYVVGLFDTYHASKAI 195
Query: 154 GRKLPKETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213
G LP+ SLA + + + SK+ Q +DW RPL++ A D H L+ I++ +
Sbjct: 196 G--LPRH--SLAYLLENFANFKTSKKYQLADWRIRPLSKPMTAAARADTHFLLNIYDQLR 251
Query: 214 VKVAQKGNSCSSISE 228
K+ + + E
Sbjct: 252 NKLIESNKLAGVLYE 266
>pdb|3SAF|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
pdb|3SAF|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
pdb|3SAG|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
pdb|3SAG|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
D313n Mutation In The Active Site
Length = 428
Score = 45.4 bits (106), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 42/79 (53%)
Query: 144 IYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAH 203
+ N Q R L SL ++ K ++ +K+ Q +DW RPL EE +YA D H
Sbjct: 205 VVNMFDTHQAARLLNLGRHSLDHLLKLYCNVDSNKQYQLADWRIRPLPEEMLSYARDDTH 264
Query: 204 CLIEIFNIFQVKVAQKGNS 222
L+ I++ ++++ ++GN
Sbjct: 265 YLLYIYDKMRLEMWERGNG 283
>pdb|3SAH|A Chain A, Crystal Structure Of The Human Rrp6 Catalytic Domain With
Y436a Mutation In The Catalytic Site
pdb|3SAH|B Chain B, Crystal Structure Of The Human Rrp6 Catalytic Domain With
Y436a Mutation In The Catalytic Site
Length = 428
Score = 42.0 bits (97), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 41/79 (51%)
Query: 144 IYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAH 203
+ N Q R L SL ++ K ++ +K+ Q +DW RPL EE + A D H
Sbjct: 205 VVNMFDTHQAARLLNLGRHSLDHLLKLYCNVDSNKQYQLADWRIRPLPEEMLSAARDDTH 264
Query: 204 CLIEIFNIFQVKVAQKGNS 222
L+ I++ ++++ ++GN
Sbjct: 265 YLLYIYDKMRLEMWERGNG 283
>pdb|1YT3|A Chain A, Crystal Structure Of Escherichia Coli Rnase D, An
Exoribonuclease Involved In Structured Rna Processing
Length = 375
Score = 38.1 bits (87), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 32/66 (48%)
Query: 163 SLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222
A++ +E ++L K +DW RPLTE Q YAA D L+ I V+ G
Sbjct: 117 GFASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVWYLLPITAKLMVETEASGWL 176
Query: 223 CSSISE 228
+++ E
Sbjct: 177 PAALDE 182
>pdb|1E6I|A Chain A, Bromodomain From Gcn5 Complexed With Acetylated H4 Peptide
Length = 121
Score = 28.9 bits (63), Expect = 7.6, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 460 FIQKP--LSTEEAVEAAKGFQRIPDCLFDKNLQFWQCMDCNQLYWEGTQYHNAVQKFID 516
FI++P LST E + +Q++ D ++D L F C N +Y N ++KF +
Sbjct: 49 FIKEPMDLSTMEIKLESNKYQKMEDFIYDARLVFNNCRMYNGENTSYYKYANRLEKFFN 107
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
0.320 0.136 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,713,661
Number of Sequences: 62578
Number of extensions: 579293
Number of successful extensions: 1408
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1396
Number of HSP's gapped (non-prelim): 13
length of query: 522
length of database: 14,973,337
effective HSP length: 103
effective length of query: 419
effective length of database: 8,527,803
effective search space: 3573149457
effective search space used: 3573149457
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)