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= 028959
(201 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3O2Q|A Chain A, Crystal Structure Of The Human Symplekin-Ssu72-Ctd
Phosphopeptide Complex
pdb|3O2Q|D Chain D, Crystal Structure Of The Human Symplekin-Ssu72-Ctd
Phosphopeptide Complex
pdb|3O2S|A Chain A, Crystal Structure Of The Human Symplekin-Ssu72 Complex
pdb|4H3H|A Chain A, Crystal Structure Of A Ternary Complex Of Human Symplekin
Ntd, Human Ssu72 And A Rna Poymerase Ii Ctd Peptide
Phosphorylated At Ser-7
pdb|4H3H|D Chain D, Crystal Structure Of A Ternary Complex Of Human Symplekin
Ntd, Human Ssu72 And A Rna Poymerase Ii Ctd Peptide
Phosphorylated At Ser-7
pdb|4H3K|A Chain A, Crystal Structure Of A Ternary Complex Of Human Symplekin
Ntd, Human Ssu72 And A Rna Polymerase Ii Ctd Peptide
Phosphorylated At Ser-2, Ser-5 And Ser-7
pdb|4H3K|D Chain D, Crystal Structure Of A Ternary Complex Of Human Symplekin
Ntd, Human Ssu72 And A Rna Polymerase Ii Ctd Peptide
Phosphorylated At Ser-2, Ser-5 And Ser-7
Length = 351
Score = 40.0 bits (92), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 39/157 (24%), Positives = 72/157 (45%), Gaps = 5/157 (3%)
Query: 25 KLSSLKQVRGILSSADPSLAAELFPYLVELQSSPESLVRKSLIETIEDIGLKAMEHSSIL 84
K++ LKQV+ ++ + DP+L ++ Q+ VRK +I IE+ + +E L
Sbjct: 42 KITVLKQVQELIINKDPTLLDNFLDEIIAFQADKSIEVRKFVIGFIEEACKRDIELLLKL 101
Query: 85 MPVLLAFLRDGDSGVAGKSIVCGTNFFCRVLEEITMQFRWHGKVERWLEELWTWMVRFKD 144
+ L LRD + V K+I+ T + ++ +Q+ +V L+E MV
Sbjct: 102 IANLNMLLRDENVNVVKKAILTMTQLY-----KVALQWMVKSRVISELQEACWDMVSAMA 156
Query: 145 AVFAIALEPGLVGTKLLALKFLETHVLLFTSDSNDFE 181
+ L+ G + A+KF+E ++ + D E
Sbjct: 157 GDIILLLDSDNDGIRTHAIKFVEGLIVTLSPRMADSE 193
>pdb|3O2T|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human
Symplekin
Length = 386
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 39/157 (24%), Positives = 72/157 (45%), Gaps = 5/157 (3%)
Query: 25 KLSSLKQVRGILSSADPSLAAELFPYLVELQSSPESLVRKSLIETIEDIGLKAMEHSSIL 84
K++ LKQV+ ++ + DP+L ++ Q+ VRK +I IE+ + +E L
Sbjct: 42 KITVLKQVQELIINKDPTLLDNFLDEIIAFQADKSIEVRKFVIGFIEEACKRDIELLLKL 101
Query: 85 MPVLLAFLRDGDSGVAGKSIVCGTNFFCRVLEEITMQFRWHGKVERWLEELWTWMVRFKD 144
+ L LRD + V K+I+ T + ++ +Q+ +V L+E MV
Sbjct: 102 IANLNMLLRDENVNVVKKAILTMTQLY-----KVALQWMVKSRVISELQEACWDMVSAMA 156
Query: 145 AVFAIALEPGLVGTKLLALKFLETHVLLFTSDSNDFE 181
+ L+ G + A+KF+E ++ + D E
Sbjct: 157 GDIILLLDSDNDGIRTHAIKFVEGLIVTLSPRMADSE 193
>pdb|3ODR|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human
Symplekin
Length = 415
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 39/157 (24%), Positives = 72/157 (45%), Gaps = 5/157 (3%)
Query: 25 KLSSLKQVRGILSSADPSLAAELFPYLVELQSSPESLVRKSLIETIEDIGLKAMEHSSIL 84
K++ LKQV+ ++ + DP+L ++ Q+ VRK +I IE+ + +E L
Sbjct: 71 KITVLKQVQELIINKDPTLLDNFLDEIIAFQADKSIEVRKFVIGFIEEACKRDIELLLKL 130
Query: 85 MPVLLAFLRDGDSGVAGKSIVCGTNFFCRVLEEITMQFRWHGKVERWLEELWTWMVRFKD 144
+ L LRD + V K+I+ T + ++ +Q+ +V L+E MV
Sbjct: 131 IANLNMLLRDENVNVVKKAILTMTQLY-----KVALQWMVKSRVISELQEACWDMVSAMA 185
Query: 145 AVFAIALEPGLVGTKLLALKFLETHVLLFTSDSNDFE 181
+ L+ G + A+KF+E ++ + D E
Sbjct: 186 GDIILLLDSDNDGIRTHAIKFVEGLIVTLSPRMADSE 222
>pdb|3ODS|A Chain A, Crystal Structure Of The K185a Mutant Of The N-Terminal
Domain Of Human Symplekin
Length = 415
Score = 36.2 bits (82), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 38/157 (24%), Positives = 71/157 (45%), Gaps = 5/157 (3%)
Query: 25 KLSSLKQVRGILSSADPSLAAELFPYLVELQSSPESLVRKSLIETIEDIGLKAMEHSSIL 84
K++ LKQV+ ++ + DP+L ++ Q+ VRK +I IE+ + +E L
Sbjct: 71 KITVLKQVQELIINKDPTLLDNFLDEIIAFQADKSIEVRKFVIGFIEEACKRDIELLLKL 130
Query: 85 MPVLLAFLRDGDSGVAGKSIVCGTNFFCRVLEEITMQFRWHGKVERWLEELWTWMVRFKD 144
+ L LRD + V K+I+ T + ++ +Q+ +V L+E MV
Sbjct: 131 IANLNMLLRDENVNVVKKAILTMTQLY-----KVALQWMVKSRVISELQEACWDMVSAMA 185
Query: 145 AVFAIALEPGLVGTKLLALKFLETHVLLFTSDSNDFE 181
+ L+ G + A+ F+E ++ + D E
Sbjct: 186 GDIILLLDSDNDGIRTHAIAFVEGLIVTLSPRMADSE 222
>pdb|3CTD|A Chain A, Crystal Structure Of A Putative Aaa Family Atpase From
Prochlorococcus Marinus Subsp. Pastoris
pdb|3CTD|B Chain B, Crystal Structure Of A Putative Aaa Family Atpase From
Prochlorococcus Marinus Subsp. Pastoris
Length = 213
Score = 30.4 bits (67), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 39/95 (41%), Gaps = 6/95 (6%)
Query: 3 AVSRD--QALSLLAAANNHGDLAVKLSSLKQVRGILSSADPSLAAELFPYLVELQSSPES 60
A++ D Q +++ N V + +K +RG +DP +VE P
Sbjct: 15 AIAEDSIQKKNIVYDKNGQNHFDVISAFIKSIRG----SDPDATLYWLANMVEAGEDPNF 70
Query: 61 LVRKSLIETIEDIGLKAMEHSSILMPVLLAFLRDG 95
+ R+ LI EDIGL ++ AF R G
Sbjct: 71 IFRRLLISACEDIGLADPNAIVVVQSCCDAFDRVG 105
>pdb|3MIP|A Chain A, I-Msoi Re-Designed For Altered Dna Cleavage Specificity
(-8gcg)
pdb|3MIP|B Chain B, I-Msoi Re-Designed For Altered Dna Cleavage Specificity
(-8gcg)
Length = 161
Score = 30.4 bits (67), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 48 FPYLVEL--QSSPESLVRKSLIETIEDIGLKAMEHSSILMPVLLAFLR 93
FPYL ++ Q ++RK + I D + H SI++P L+ +LR
Sbjct: 50 FPYLQDIYDQLGKRGILRKDRGDGIADYRIYGSTHLSIILPDLVPYLR 97
>pdb|3MIS|A Chain A, I-Msoi Re-Designed For Altered Dna Cleavage Specificity
(-8g)
pdb|3MIS|B Chain B, I-Msoi Re-Designed For Altered Dna Cleavage Specificity
(-8g)
Length = 161
Score = 28.9 bits (63), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 48 FPYLVEL--QSSPESLVRKSLIETIEDIGLKAMEHSSILMPVLLAFLR 93
FPYL ++ Q +RK + I D + H SI++P L+ +LR
Sbjct: 50 FPYLQDIYDQLGKRGNLRKDRGDGIADYTIYGSTHLSIILPDLVPYLR 97
>pdb|4B6J|A Chain A, Crystal Structure Of Phosphoserine Phosphatase From T.
Onnurineus
pdb|4B6J|B Chain B, Crystal Structure Of Phosphoserine Phosphatase From T.
Onnurineus
pdb|4B6J|C Chain C, Crystal Structure Of Phosphoserine Phosphatase From T.
Onnurineus
pdb|4B6J|D Chain D, Crystal Structure Of Phosphoserine Phosphatase From T.
Onnurineus
Length = 201
Score = 28.5 bits (62), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 28/105 (26%), Positives = 47/105 (44%), Gaps = 19/105 (18%)
Query: 57 SPESLVRKSLIETIEDIGLKAMEHSSILMPVLLAFLRDGDSGVAGKSIVCGTNFFCRVLE 116
SPE+ + L+ET+ + G K + S VL F GD +A ++I F +
Sbjct: 81 SPEA---RELVETLREKGFKVVLISGSFEEVLEPFKELGDEFMANRAIFEDGKF-----Q 132
Query: 117 EITMQFRWHGKVERWLEELWTWMVRFKDAVFAIALEPGLVGTKLL 161
I ++FR G+ ++ RF+D F +A+ G K+
Sbjct: 133 GIRLRFRDKGE----------FLKRFRDG-FILAMGDGYADAKMF 166
>pdb|3FD2|A Chain A, Crystal Structure Of MmsoiDNA COMPLEX WITH CALCIUM
Length = 373
Score = 28.1 bits (61), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 48 FPYLVEL--QSSPESLVRKSLIETIEDIGLKAMEHSSILMPVLLAFLR 93
FPYL ++ Q +RK + I D + H SI++P L+ +LR
Sbjct: 55 FPYLQDIYDQLGKRGNLRKDRGDGIADYTIIGSTHLSIILPDLVPYLR 102
Score = 28.1 bits (61), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 48 FPYLVEL--QSSPESLVRKSLIETIEDIGLKAMEHSSILMPVLLAFLR 93
FPYL ++ Q +RK + I D + H SI++P L+ +LR
Sbjct: 258 FPYLQDIYDQLGKRGNLRKDRGDGIADYTIIGSTHLSIILPDLVPYLR 305
>pdb|3KO2|A Chain A, I-Msoi Re-Designed For Altered Dna Cleavage Specificity
(-7c)
pdb|3KO2|B Chain B, I-Msoi Re-Designed For Altered Dna Cleavage Specificity
(-7c)
pdb|3KO2|F Chain F, I-Msoi Re-Designed For Altered Dna Cleavage Specificity
(-7c)
pdb|3KO2|G Chain G, I-Msoi Re-Designed For Altered Dna Cleavage Specificity
(-7c)
Length = 170
Score = 28.1 bits (61), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 48 FPYLVEL--QSSPESLVRKSLIETIEDIGLKAMEHSSILMPVLLAFLR 93
FPYL ++ Q +RK + I D + H SI++P L+ +LR
Sbjct: 55 FPYLQDIYDQLGKRGTLRKDRGDGIADYTIWGSTHLSIILPDLVPYLR 102
>pdb|1M5X|A Chain A, Crystal Structure Of The Homing Endonuclease I-Msoi Bound
To Its Dna Substrate
pdb|1M5X|B Chain B, Crystal Structure Of The Homing Endonuclease I-Msoi Bound
To Its Dna Substrate
Length = 170
Score = 27.7 bits (60), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 48 FPYLVEL--QSSPESLVRKSLIETIEDIGLKAMEHSSILMPVLLAFLR 93
FPYL ++ Q +RK + I D + H SI++P L+ +LR
Sbjct: 55 FPYLQDIYDQLGKRGNLRKDRGDGIADYTIIGSTHLSIILPDLVPYLR 102
>pdb|2FLD|A Chain A, I-Msoi Re-Designed For Altered Dna Cleavage Specificity
pdb|2FLD|B Chain B, I-Msoi Re-Designed For Altered Dna Cleavage Specificity
Length = 165
Score = 27.7 bits (60), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 48 FPYLVEL--QSSPESLVRKSLIETIEDIGLKAMEHSSILMPVLLAFLR 93
FPYL ++ Q +RK + I D + H SI++P L+ +LR
Sbjct: 50 FPYLQDIYDQLGKRGNLRKDRGDGIADYRIIGSTHLSIILPDLVPYLR 97
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
0.324 0.137 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,361,494
Number of Sequences: 62578
Number of extensions: 198726
Number of successful extensions: 630
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 623
Number of HSP's gapped (non-prelim): 20
length of query: 201
length of database: 14,973,337
effective HSP length: 94
effective length of query: 107
effective length of database: 9,091,005
effective search space: 972737535
effective search space used: 972737535
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 49 (23.5 bits)