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= 006806
(630 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1W4S|A Chain A, Crystal Structure Of The Proximal Bah Domain Of Polybromo
Length = 174
Score = 57.8 bits (138), Expect = 2e-08, Method: Composition-based stats.
Identities = 35/137 (25%), Positives = 65/137 (47%), Gaps = 10/137 (7%)
Query: 118 RSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWFYRPEEA 177
R++ + F + Y + D V + P + N +P++ I+ + + G + G WFYRP E
Sbjct: 14 RTYSQDCSFKNSMYHVGDYVYVEPAEANLQPHIVCIERLWEDSAGEKWLYGCWFYRPNET 73
Query: 178 DRKGGGNWLSRDTRELFYSFHRDEVPAESVMHKCVVHFVPIHKQL--PNRKQHPGFIVQK 235
+L +E+F S + ++VP ++ KCVV FV + +L N + ++ +
Sbjct: 74 FHLATRKFLE---KEVFKSDYYNKVPVSKILGKCVVMFVKEYFKLCPENFRDEDVYVCES 130
Query: 236 VYDTVER-----KLWKL 247
Y + KLW +
Sbjct: 131 RYSAKTKSFKKIKLWTM 147
>pdb|2DME|A Chain A, Solution Structure Of The Tfiis Domain Ii Of Human Phd
Finger Protein 3
Length = 120
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/43 (44%), Positives = 27/43 (62%), Gaps = 2/43 (4%)
Query: 439 KYNQKLRQLLFNLK--STALLARRLLNGELEPSKILNMSPNEL 479
KY K R L+FNLK +L +++L GE+ P ++ MSP EL
Sbjct: 61 KYKNKYRSLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEEL 103
>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 = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 30/54 (55%)
Query: 118 RSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWF 171
R++Y+ D E+ D V + P+D+++ Y+A + + + K+G MM WF
Sbjct: 99 RTYYQKVSIDEEMLEVGDCVSVIPDDSSKPLYLARVTALWEDKNGQMMFHAHWF 152
>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 = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 30/54 (55%)
Query: 118 RSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWF 171
R++Y+ D E+ D V + P+D+++ Y+A + + + K+G MM WF
Sbjct: 457 RTYYQKVSIDEEMLEVGDCVSVIPDDSSKPLYLARVTALWEDKNGQMMFHAHWF 510
>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 = 39.3 bits (90), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 30/54 (55%)
Query: 118 RSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGSMMVTGQWF 171
R++Y+ D E+ D V + P+D+++ Y+A + + + K+G MM WF
Sbjct: 18 RTYYQKVSIDEEMLEVGDCVSVIPDDSSKPLYLARVTALWEDKNGQMMFHAHWF 71
>pdb|3SWR|A Chain A, Structure Of Human Dnmt1 (601-1600) In Complex With
Sinefungin
Length = 1002
Score = 36.2 bits (82), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 4/68 (5%)
Query: 104 VGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGS 163
VGE V+ GK +S+Y+ D E+ D V + P+D+++ Y+A + + +
Sbjct: 136 VGEAVKTDGK----KSYYKKVCIDAETLEVGDCVSVIPDDSSKPLYLARVTALWEDSSNG 191
Query: 164 MMVTGQWF 171
M WF
Sbjct: 192 QMFHAHWF 199
>pdb|3PTA|A Chain A, Crystal Structure Of Human Dnmt1(646-1600) In Complex With
Dna
Length = 956
Score = 36.2 bits (82), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 4/68 (5%)
Query: 104 VGELVRFSGKGRGRRSHYEAFEFDGNKYELEDPVLLTPEDTNQKPYVAIIKEITQSKDGS 163
VGE V+ GK +S+Y+ D E+ D V + P+D+++ Y+A + + +
Sbjct: 90 VGEAVKTDGK----KSYYKKVCIDAETLEVGDCVSVIPDDSSKPLYLARVTALWEDSSNG 145
Query: 164 MMVTGQWF 171
M WF
Sbjct: 146 QMFHAHWF 153
>pdb|1J2W|A Chain A, Tetrameric Structure Of Aldolase From Thermus Thermophilus
Hb8
pdb|1J2W|B Chain B, Tetrameric Structure Of Aldolase From Thermus Thermophilus
Hb8
pdb|1J2W|C Chain C, Tetrameric Structure Of Aldolase From Thermus Thermophilus
Hb8
pdb|1J2W|D Chain D, Tetrameric Structure Of Aldolase From Thermus Thermophilus
Hb8
pdb|1UB3|A Chain A, Crystal Structure Of Tetrameric Structure Of Aldolase From
Thermus Thermophilus Hb8
pdb|1UB3|B Chain B, Crystal Structure Of Tetrameric Structure Of Aldolase From
Thermus Thermophilus Hb8
pdb|1UB3|C Chain C, Crystal Structure Of Tetrameric Structure Of Aldolase From
Thermus Thermophilus Hb8
pdb|1UB3|D Chain D, Crystal Structure Of Tetrameric Structure Of Aldolase From
Thermus Thermophilus Hb8
Length = 220
Score = 33.9 bits (76), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 259 EIDLLVQKTQARLGDLPDIEPEETAAREQEDQLKAKRSLRKKNISPLDVSREEDSTTRSD 318
E+D+++ +A+ GDL +E E A RE Q K L SP +++R ++ R
Sbjct: 87 EVDMVLHLGRAKAGDLDYLEAEVRAVREAVPQAVLKVILETGYFSPEEIARLAEAAIRGG 146
Query: 319 Q-YVKAET 325
++K T
Sbjct: 147 ADFLKTST 154
>pdb|3B5X|A Chain A, Crystal Structure Of Msba From Vibrio Cholerae
pdb|3B5X|B Chain B, Crystal Structure Of Msba From Vibrio Cholerae
Length = 582
Score = 29.6 bits (65), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 30/121 (24%), Positives = 50/121 (41%), Gaps = 4/121 (3%)
Query: 321 VKAE-TPGSCTSNASEYYNILSKFKALTGETHRDKWLERLLQGLQYICNSADSIHADQNG 379
++AE TPG+ T S + ++ KALT T +R + Q + D NG
Sbjct: 275 IRAELTPGTFTVVFSAMFGLMRPLKALTSVTSE---FQRGMAACQTLFGLMDLETERDNG 331
Query: 380 KGGCKGVDHESEDKSVGTENGSREKGQKNGKSFIWPDTAIAAVTALEKASHDTLSLDFQK 439
K + V+ E + K V +EK + SF P A+ + T++ F +
Sbjct: 332 KYEAERVNGEVDVKDVTFTYQGKEKPALSHVSFSIPQGKTVALVGRSGSGKSTIANLFTR 391
Query: 440 Y 440
+
Sbjct: 392 F 392
>pdb|1KSF|X Chain X, Crystal Structure Of Clpa, An Hsp100 Chaperone And
Regulator Of Clpap Protease: Structural Basis Of
Differences In Function Of The Two Aaa+ Atpase Domains
pdb|1R6B|X Chain X, High Resolution Crystal Structure Of Clpa
Length = 758
Score = 29.3 bits (64), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 39/90 (43%), Gaps = 14/90 (15%)
Query: 286 EQEDQLKAKRSLRKKNISPLDVSREEDSTTRSDQYVKAETPGSCTS------------NA 333
EQE Q A LRK +S LDV TR D+ ++ PGS + N
Sbjct: 115 EQESQ--AAYLLRKHEVSRLDVVNFISHGTRKDEPTQSSDPGSQPNSEEQAGGEERLENF 172
Query: 334 SEYYNILSKFKALTGETHRDKWLERLLQGL 363
+ N L++ + R+K LER +Q L
Sbjct: 173 TTNLNQLARVGGIDPLIGREKELERAIQVL 202
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
0.311 0.128 0.365
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,834,874
Number of Sequences: 62578
Number of extensions: 746695
Number of successful extensions: 1223
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1214
Number of HSP's gapped (non-prelim): 14
length of query: 630
length of database: 14,973,337
effective HSP length: 105
effective length of query: 525
effective length of database: 8,402,647
effective search space: 4411389675
effective search space used: 4411389675
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 54 (25.4 bits)