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= 009783
(526 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 = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 36/58 (62%)
Query: 163 SLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKG 220
LA + + L ++L+KE +DWS RPL + +NYAA+D LIE+ + ++ ++G
Sbjct: 134 GLAAVTEHFLGLTLAKEHSAADWSYRPLPRDWRNYAALDVELLIELETKMRAELKRQG 191
>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 = 7e-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 = 54/188 (28%), Positives = 81/188 (43%), Gaps = 35/188 (18%)
Query: 25 LARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFXXXX 84
++ LS +VG D EW P RV+++QL ES +
Sbjct: 33 ISMRLSDGDVVGFDMEWPPIYKPGKR-SRVAVIQLCVS----------ESKCYLFHISSM 81
Query: 85 XXXXXXXXWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSI 144
+ LK L + I K G + D L F D+ ++E ++++T +
Sbjct: 82 SVFP-----QGLKMLLENKSIKKAGVGIEGDQWKLLRDF-----DV---KLESFVELTDV 128
Query: 145 YNHLHHKQLGRKLP-KETKSLANICKELLDISL--SKELQCSDWSNRPLTEEQKNYAAID 201
N KL ET SL + K +L L K ++CS+WSN PLTE+QK YAA D
Sbjct: 129 ANE--------KLKCAETWSLNGLVKHVLGKQLLKDKSIRCSNWSNFPLTEDQKLYAATD 180
Query: 202 AHCLIEIF 209
A+ + I+
Sbjct: 181 AYAGLIIY 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 = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 36/131 (27%), Positives = 63/131 (48%), Gaps = 19/131 (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 VKVAQKGFAAG 224
K+ + AG
Sbjct: 252 NKLIESNKLAG 262
>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 = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 41/77 (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 CLIEIFNIFQVKVAQKG 220
L+ I++ ++++ ++G
Sbjct: 265 YLLYIYDKMRLEMWERG 281
>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 = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 40/77 (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 CLIEIFNIFQVKVAQKG 220
L+ I++ ++++ ++G
Sbjct: 265 YLLYIYDKMRLEMWERG 281
>pdb|1YT3|A Chain A, Crystal Structure Of Escherichia Coli Rnase D, An
Exoribonuclease Involved In Structured Rna Processing
Length = 375
Score = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 2/67 (2%)
Query: 163 SLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGF- 221
A++ +E ++L K +DW RPLTE Q YAA D L+ I V+ G+
Sbjct: 117 GFASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVWYLLPITAKLMVETEASGWL 176
Query: 222 -AAGNSC 227
AA + C
Sbjct: 177 PAALDEC 183
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
0.321 0.137 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,740,748
Number of Sequences: 62578
Number of extensions: 579743
Number of successful extensions: 1181
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1169
Number of HSP's gapped (non-prelim): 12
length of query: 526
length of database: 14,973,337
effective HSP length: 103
effective length of query: 423
effective length of database: 8,527,803
effective search space: 3607260669
effective search space used: 3607260669
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)