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= 040821
(220 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3PT9|A Chain A, Crystal Structure Of Mouse Dnmt1(731-1602) In The Free
State
pdb|4DA4|A Chain A, Structure Of Mouse Dnmt1 (731-1602) Bound To
Hemimethylated Cpg Dna
pdb|4DA4|B Chain B, Structure Of Mouse Dnmt1 (731-1602) Bound To
Hemimethylated Cpg Dna
Length = 873
Score = 33.5 bits (75), Expect = 0.10, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 63 KAAIDDEGLLTLTFEKLVPNHSETPSDLEKVSVQWKSKKGVFHFKAH-LPAGT 114
K +ID+E L ++P+ S P L +V+ W+ K G F AH AGT
Sbjct: 23 KVSIDEEMLEVGDCVSVIPDDSSKPLYLARVTALWEDKNGQMMFHAHWFCAGT 75
>pdb|3PT6|A Chain A, Crystal Structure Of Mouse Dnmt1(650-1602) In Complex With
Dna
pdb|3PT6|B Chain B, Crystal Structure Of Mouse Dnmt1(650-1602) In Complex With
Dna
Length = 954
Score = 33.5 bits (75), Expect = 0.10, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 63 KAAIDDEGLLTLTFEKLVPNHSETPSDLEKVSVQWKSKKGVFHFKAH-LPAGT 114
K +ID+E L ++P+ S P L +V+ W+ K G F AH AGT
Sbjct: 104 KVSIDEEMLEVGDCVSVIPDDSSKPLYLARVTALWEDKNGQMMFHAHWFCAGT 156
>pdb|3AV4|A Chain A, Crystal Structure Of Mouse Dna Methyltransferase 1
pdb|3AV5|A Chain A, Crystal Structure Of Mouse Dna Methyltransferase 1 With
Adohcy
pdb|3AV6|A Chain A, Crystal Structure Of Mouse Dna Methyltransferase 1 With
Adomet
Length = 1330
Score = 33.1 bits (74), Expect = 0.11, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 63 KAAIDDEGLLTLTFEKLVPNHSETPSDLEKVSVQWKSKKGVFHFKAH-LPAGT 114
K +ID+E L ++P+ S P L +V+ W+ K G F AH AGT
Sbjct: 462 KVSIDEEMLEVGDCVSVIPDDSSKPLYLARVTALWEDKNGQMMFHAHWFCAGT 514
>pdb|3L7Z|B Chain B, Crystal Structure Of The S. Solfataricus Archaeal Exosome
pdb|3L7Z|E Chain E, Crystal Structure Of The S. Solfataricus Archaeal Exosome
pdb|3L7Z|H Chain H, Crystal Structure Of The S. Solfataricus Archaeal Exosome
Length = 245
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 4/67 (5%)
Query: 112 AGTKMEDMMVGIEGRKSLMIGICDLSKTE----EGDTSTLMCVDGKNFRSFILPDGVNPN 167
AG M D++ G+ K+ + I DL++TE E D M F L + P+
Sbjct: 150 AGIPMRDLIAGVAVGKADGVIILDLNETEDMWGEADMPIAMMPSLNQVTLFQLNGSMTPD 209
Query: 168 GFKTAMD 174
F+ A D
Sbjct: 210 EFRQAFD 216
>pdb|2JE6|B Chain B, Structure Of A 9-Subunit Archaeal Exosome
pdb|2JEA|B Chain B, Structure Of A 9-Subunit Archaeal Exosome Bound To Rna
pdb|2JEB|B Chain B, Structure Of A 9-Subunit Archaeal Exosome Bound To Mn Ions
pdb|4BA1|B Chain B, Archaeal Exosome (rrp4-rrp41(d182a)-rrp42) Bound To
Inorganic Phosphate
pdb|4BA2|B Chain B, Archaeal Exosome (rrp4-rrp41(d182a)-rrp42) Bound To
Inorganic Phosphate
Length = 250
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 4/67 (5%)
Query: 112 AGTKMEDMMVGIEGRKSLMIGICDLSKTE----EGDTSTLMCVDGKNFRSFILPDGVNPN 167
AG M D++ G+ K+ + I DL++TE E D M F L + P+
Sbjct: 155 AGIPMRDLIAGVAVGKADGVIILDLNETEAMWGEADMPIAMMPSLNQVTLFQLNGSMTPD 214
Query: 168 GFKTAMD 174
F+ A D
Sbjct: 215 EFRQAFD 221
>pdb|2BR2|B Chain B, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|D Chain D, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|F Chain F, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|H Chain H, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|J Chain J, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|L Chain L, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|N Chain N, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|P Chain P, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|R Chain R, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|T Chain T, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|V Chain V, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|X Chain X, Rnase Ph Core Of The Archaeal Exosome
pdb|2C37|B Chain B, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|D Chain D, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|F Chain F, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|H Chain H, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|J Chain J, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|L Chain L, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|N Chain N, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|P Chain P, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|R Chain R, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|T Chain T, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|V Chain V, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|X Chain X, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C38|B Chain B, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|D Chain D, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|F Chain F, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|H Chain H, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|J Chain J, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|L Chain L, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|N Chain N, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|P Chain P, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|R Chain R, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|T Chain T, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|V Chain V, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|X Chain X, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C39|B Chain B, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|D Chain D, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|F Chain F, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|H Chain H, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|J Chain J, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|L Chain L, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|N Chain N, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|P Chain P, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|R Chain R, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|T Chain T, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|V Chain V, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|X Chain X, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
Length = 248
Score = 28.9 bits (63), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 4/67 (5%)
Query: 112 AGTKMEDMMVGIEGRKSLMIGICDLSKTE----EGDTSTLMCVDGKNFRSFILPDGVNPN 167
AG M D++ G+ K+ + I DL++TE E D M F L + P+
Sbjct: 153 AGIPMRDLIAGVAVGKADGVIILDLNETEDMWGEADMPIAMMPSLNQVTLFQLNGSMTPD 212
Query: 168 GFKTAMD 174
F+ A D
Sbjct: 213 EFRQAFD 219
>pdb|1DD9|A Chain A, Structure Of The Dnag Catalytic Core
pdb|1DDE|A Chain A, Structure Of The Dnag Catalytic Core
Length = 338
Score = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 30/73 (41%), Gaps = 10/73 (13%)
Query: 143 DTSTLMCVDGKNFRSFILPDGVNPN---------GFKTAMDDAGVLTV-TFTKLKPEKKK 192
+T+ DG+ R LPDG +P+ F+ M+ A L+ F L P+
Sbjct: 228 ETALPYMTDGRQLRFMFLPDGEDPDTLVRKEGKEAFEARMEQAMPLSAFLFNSLMPQVDL 287
Query: 193 LRPIAKKSLGCLA 205
P + L LA
Sbjct: 288 STPDGRARLSTLA 300
>pdb|3B39|A Chain A, Structure Of The Dnag Primase Catalytic Domain Bound To
Ssdna
pdb|3B39|B Chain B, Structure Of The Dnag Primase Catalytic Domain Bound To
Ssdna
Length = 322
Score = 28.5 bits (62), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 30/73 (41%), Gaps = 10/73 (13%)
Query: 143 DTSTLMCVDGKNFRSFILPDGVNPN---------GFKTAMDDAGVLTV-TFTKLKPEKKK 192
+T+ DG+ R LPDG +P+ F+ M+ A L+ F L P+
Sbjct: 216 ETALPYMTDGRQLRFMFLPDGEDPDTLVRKEGKEAFEARMEQAMPLSAFLFNSLMPQVDL 275
Query: 193 LRPIAKKSLGCLA 205
P + L LA
Sbjct: 276 STPDGRARLSTLA 288
>pdb|1GME|A Chain A, Crystal Structure And Assembly Of An Eukaryotic Small Heat
Shock Protein
pdb|1GME|B Chain B, Crystal Structure And Assembly Of An Eukaryotic Small Heat
Shock Protein
pdb|1GME|C Chain C, Crystal Structure And Assembly Of An Eukaryotic Small Heat
Shock Protein
pdb|1GME|D Chain D, Crystal Structure And Assembly Of An Eukaryotic Small Heat
Shock Protein
Length = 151
Score = 27.7 bits (60), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 35/129 (27%), Positives = 57/129 (44%), Gaps = 11/129 (8%)
Query: 75 TFEKLVP----NHSETPSDLEKVSVQWKSKKGVFHFKAHLPAGTKMEDMMVGIEGRKSLM 130
TF +VP SET + + WK FKA LP K E + +G +++
Sbjct: 23 TFRSIVPAISGGGSETAA-FANARMDWKETPEAHVFKADLPGVKKEEVKVEVEDG--NVL 79
Query: 131 IGICDLSKTEEGDTSTLMCVD---GKNFRSFILPDGVNPNGFKTAMDDAGVLTVTFTKLK 187
+ + +K +E V+ GK R F L + K +++ GVLTVT K +
Sbjct: 80 VVSGERTKEKEDKNDKWHRVERSSGKFVRRFRLLEDAKVEEVKAGLEN-GVLTVTVPKAE 138
Query: 188 PEKKKLRPI 196
+K +++ I
Sbjct: 139 VKKPEVKAI 147
>pdb|2XNC|A Chain A, Crystal Structure Of An Engineered Ferredoxin Nadp
Reductase (Fnr) From Pisum Sativum
pdb|2XNC|B Chain B, Crystal Structure Of An Engineered Ferredoxin Nadp
Reductase (Fnr) From Pisum Sativum
Length = 315
Score = 26.9 bits (58), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 29/63 (46%), Gaps = 19/63 (30%)
Query: 159 ILPDGVNPNGFKTAMDDAGVLTVTFTKLKPEKKKLRPIAKKSLGCLAHAACLLIC-EKIS 217
I+PDG++ NG KP K +L IA ++G + + +C +++
Sbjct: 87 IVPDGIDKNG------------------KPHKLRLYSIASSAIGDFGDSKTVSLCVKRVP 128
Query: 218 DGI 220
DG+
Sbjct: 129 DGV 131
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 0.135 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,727,188
Number of Sequences: 62578
Number of extensions: 282522
Number of successful extensions: 631
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 627
Number of HSP's gapped (non-prelim): 12
length of query: 220
length of database: 14,973,337
effective HSP length: 95
effective length of query: 125
effective length of database: 9,028,427
effective search space: 1128553375
effective search space used: 1128553375
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)