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= 039176
(282 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2J8Q|A Chain A, Crystal Structure Of Human Cleavage And Polyadenylation
Specificity Factor 5 (Cpsf5) In Complex With A Sulphate
Ion.
pdb|2J8Q|B Chain B, Crystal Structure Of Human Cleavage And Polyadenylation
Specificity Factor 5 (Cpsf5) In Complex With A Sulphate
Ion
Length = 227
Score = 222 bits (566), Expect = 2e-58, Method: Compositional matrix adjust.
Identities = 105/171 (61%), Positives = 125/171 (73%), Gaps = 1/171 (0%)
Query: 50 VVNTYPLSSYTFGTKEPKMEKDTSVADRLARMKVNYMKEGMRTSVEAILLVQEHNHPHIL 109
+N YPL++YTFGTKEP EKD+SVA R RM+ + K GMR +VE +L+V EH PH+L
Sbjct: 36 TINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVL 95
Query: 110 LLQIGNTFCKLPGGRLKPGENEIEGLKRKLTSKLGANSPALVPDWQIGECVAIWWRPNFE 169
LLQ+G TF KLPGG L PGE+E+EGLKR +T LG ++ DW I +C+ WWRPNFE
Sbjct: 96 LLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQD-GVLQDWVIDDCIGNWWRPNFE 154
Query: 170 TIMYPYCPPHITKPKECKKLFLVHLSEREYFAVPKNLKLLAVPLFELYDNV 220
YPY P HITKPKE KKLFLV L E+ FAVPKN KL+A PLFELYDN
Sbjct: 155 PPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNA 205
>pdb|2CL3|A Chain A, Crystal Structure Of Human Cleavage And Polyadenylation
Specificity Factor 5 (Cpsf5)
pdb|3N9U|A Chain A, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|B Chain B, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 230
Score = 222 bits (565), Expect = 2e-58, Method: Compositional matrix adjust.
Identities = 105/171 (61%), Positives = 125/171 (73%), Gaps = 1/171 (0%)
Query: 50 VVNTYPLSSYTFGTKEPKMEKDTSVADRLARMKVNYMKEGMRTSVEAILLVQEHNHPHIL 109
+N YPL++YTFGTKEP EKD+SVA R RM+ + K GMR +VE +L+V EH PH+L
Sbjct: 39 TINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVL 98
Query: 110 LLQIGNTFCKLPGGRLKPGENEIEGLKRKLTSKLGANSPALVPDWQIGECVAIWWRPNFE 169
LLQ+G TF KLPGG L PGE+E+EGLKR +T LG ++ DW I +C+ WWRPNFE
Sbjct: 99 LLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQD-GVLQDWVIDDCIGNWWRPNFE 157
Query: 170 TIMYPYCPPHITKPKECKKLFLVHLSEREYFAVPKNLKLLAVPLFELYDNV 220
YPY P HITKPKE KKLFLV L E+ FAVPKN KL+A PLFELYDN
Sbjct: 158 PPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNA 208
>pdb|3BHO|A Chain A, Crystal Structure Of The 25kda Subunit Of Human Cleavage
Factor Im With Ap4a
Length = 208
Score = 221 bits (564), Expect = 2e-58, Method: Compositional matrix adjust.
Identities = 105/171 (61%), Positives = 125/171 (73%), Gaps = 1/171 (0%)
Query: 50 VVNTYPLSSYTFGTKEPKMEKDTSVADRLARMKVNYMKEGMRTSVEAILLVQEHNHPHIL 109
+N YPL++YTFGTKEP EKD+SVA R RM+ + K GMR +VE +L+V EH PH+L
Sbjct: 17 TINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVL 76
Query: 110 LLQIGNTFCKLPGGRLKPGENEIEGLKRKLTSKLGANSPALVPDWQIGECVAIWWRPNFE 169
LLQ+G TF KLPGG L PGE+E+EGLKR +T LG ++ DW I +C+ WWRPNFE
Sbjct: 77 LLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQD-GVLQDWVIDDCIGNWWRPNFE 135
Query: 170 TIMYPYCPPHITKPKECKKLFLVHLSEREYFAVPKNLKLLAVPLFELYDNV 220
YPY P HITKPKE KKLFLV L E+ FAVPKN KL+A PLFELYDN
Sbjct: 136 PPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNA 186
>pdb|3Q2S|A Chain A, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2S|B Chain B, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2T|A Chain A, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
pdb|3Q2T|B Chain B, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
Length = 207
Score = 221 bits (564), Expect = 3e-58, Method: Compositional matrix adjust.
Identities = 105/171 (61%), Positives = 125/171 (73%), Gaps = 1/171 (0%)
Query: 50 VVNTYPLSSYTFGTKEPKMEKDTSVADRLARMKVNYMKEGMRTSVEAILLVQEHNHPHIL 109
+N YPL++YTFGTKEP EKD+SVA R RM+ + K GMR +VE +L+V EH PH+L
Sbjct: 16 TINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVL 75
Query: 110 LLQIGNTFCKLPGGRLKPGENEIEGLKRKLTSKLGANSPALVPDWQIGECVAIWWRPNFE 169
LLQ+G TF KLPGG L PGE+E+EGLKR +T LG ++ DW I +C+ WWRPNFE
Sbjct: 76 LLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQD-GVLQDWVIDDCIGNWWRPNFE 134
Query: 170 TIMYPYCPPHITKPKECKKLFLVHLSEREYFAVPKNLKLLAVPLFELYDNV 220
YPY P HITKPKE KKLFLV L E+ FAVPKN KL+A PLFELYDN
Sbjct: 135 PPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNA 185
>pdb|3MDG|A Chain A, Crystal Structure Of The 25kda Subunit Of Human Cleavage
Factor Im In Complex With Rna Uuguau
pdb|3MDG|B Chain B, Crystal Structure Of The 25kda Subunit Of Human Cleavage
Factor Im In Complex With Rna Uuguau
pdb|3MDI|A Chain A, Crystal Structure Of The 25kda Subunit Of Human Cleavage
Factor Im In Complex With Rna Uguaaa
pdb|3MDI|B Chain B, Crystal Structure Of The 25kda Subunit Of Human Cleavage
Factor Im In Complex With Rna Uguaaa
Length = 227
Score = 221 bits (564), Expect = 3e-58, Method: Compositional matrix adjust.
Identities = 105/171 (61%), Positives = 125/171 (73%), Gaps = 1/171 (0%)
Query: 50 VVNTYPLSSYTFGTKEPKMEKDTSVADRLARMKVNYMKEGMRTSVEAILLVQEHNHPHIL 109
+N YPL++YTFGTKEP EKD+SVA R RM+ + K GMR +VE +L+V EH PH+L
Sbjct: 36 TINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVL 95
Query: 110 LLQIGNTFCKLPGGRLKPGENEIEGLKRKLTSKLGANSPALVPDWQIGECVAIWWRPNFE 169
LLQ+G TF KLPGG L PGE+E+EGLKR +T LG ++ DW I +C+ WWRPNFE
Sbjct: 96 LLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQD-GVLQDWVIDDCIGNWWRPNFE 154
Query: 170 TIMYPYCPPHITKPKECKKLFLVHLSEREYFAVPKNLKLLAVPLFELYDNV 220
YPY P HITKPKE KKLFLV L E+ FAVPKN KL+A PLFELYDN
Sbjct: 155 PPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNA 205
>pdb|3P5T|A Chain A, Cfim25-Cfim68 Complex
pdb|3P5T|B Chain B, Cfim25-Cfim68 Complex
pdb|3P5T|C Chain C, Cfim25-Cfim68 Complex
pdb|3P5T|D Chain D, Cfim25-Cfim68 Complex
pdb|3P5T|E Chain E, Cfim25-Cfim68 Complex
pdb|3P5T|F Chain F, Cfim25-Cfim68 Complex
pdb|3P6Y|A Chain A, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|B Chain B, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|E Chain E, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|F Chain F, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|I Chain I, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|J Chain J, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|M Chain M, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|N Chain N, Cf Im25-Cf Im68-Uguaa Complex
Length = 202
Score = 221 bits (563), Expect = 3e-58, Method: Compositional matrix adjust.
Identities = 105/171 (61%), Positives = 125/171 (73%), Gaps = 1/171 (0%)
Query: 50 VVNTYPLSSYTFGTKEPKMEKDTSVADRLARMKVNYMKEGMRTSVEAILLVQEHNHPHIL 109
+N YPL++YTFGTKEP EKD+SVA R RM+ + K GMR +VE +L+V EH PH+L
Sbjct: 3 TINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVL 62
Query: 110 LLQIGNTFCKLPGGRLKPGENEIEGLKRKLTSKLGANSPALVPDWQIGECVAIWWRPNFE 169
LLQ+G TF KLPGG L PGE+E+EGLKR +T LG ++ DW I +C+ WWRPNFE
Sbjct: 63 LLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQD-GVLQDWVIDDCIGNWWRPNFE 121
Query: 170 TIMYPYCPPHITKPKECKKLFLVHLSEREYFAVPKNLKLLAVPLFELYDNV 220
YPY P HITKPKE KKLFLV L E+ FAVPKN KL+A PLFELYDN
Sbjct: 122 PPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNA 172
>pdb|3BAP|A Chain A, Crystal Structure Of The 25 Kda Subunit Of Human Cleavage
Factor Im
Length = 227
Score = 215 bits (548), Expect = 2e-56, Method: Compositional matrix adjust.
Identities = 103/171 (60%), Positives = 122/171 (71%), Gaps = 1/171 (0%)
Query: 50 VVNTYPLSSYTFGTKEPKMEKDTSVADRLARMKVNYMKEGMRTSVEAILLVQEHNHPHIL 109
+N YPL++YTFGTKEP EKD+SVA R R + + K G R +VE +L+V EH PH+L
Sbjct: 36 TINLYPLTNYTFGTKEPLYEKDSSVAARFQRXREEFDKIGXRRTVEGVLIVHEHRLPHVL 95
Query: 110 LLQIGNTFCKLPGGRLKPGENEIEGLKRKLTSKLGANSPALVPDWQIGECVAIWWRPNFE 169
LLQ+G TF KLPGG L PGE+E+EGLKR T LG ++ DW I +C+ WWRPNFE
Sbjct: 96 LLQLGTTFFKLPGGELNPGEDEVEGLKRLXTEILGRQD-GVLQDWVIDDCIGNWWRPNFE 154
Query: 170 TIMYPYCPPHITKPKECKKLFLVHLSEREYFAVPKNLKLLAVPLFELYDNV 220
YPY P HITKPKE KKLFLV L E+ FAVPKN KL+A PLFELYDN
Sbjct: 155 PPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNA 205
>pdb|3GG6|A Chain A, Crystal Structure Of The Nudix Domain Of Human Nudt18
Length = 156
Score = 34.3 bits (77), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 4/52 (7%)
Query: 97 ILLVQEHNHPHILLLQIGNTFCK----LPGGRLKPGENEIEGLKRKLTSKLG 144
+L V +LL+Q C+ LP GR++PGE +E L+R++ + G
Sbjct: 23 VLAVFLSEQDEVLLIQEAKRECRGSWYLPAGRMEPGETIVEALQREVKEEAG 74
>pdb|2YVM|A Chain A, Crystal Structure Of Ndx2 In Complex With Mg2+ From
Thermus Thermophilus Hb8
pdb|2YVN|A Chain A, Crystal Structure Of Ndx2 From Thermus Thermophilus Hb8
pdb|2YVO|A Chain A, Crystal Structure Of Ndx2 In Complex With Mg2+ And Amp
From Thermus Thermophilus Hb8
pdb|2YVP|A Chain A, Crystal Structure Of Ndx2 In Complex With Mg2+ And Ampcpr
From Thermus Thermophilus Hb8
Length = 182
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 6/55 (10%)
Query: 98 LLVQEHNHPHILLLQIGNTFCKLPGGRLKPGENEIEGLKRKLTSKLGANSPALVP 152
LLV+++ HP G ++P G++ GE +R+L ++GA + L+P
Sbjct: 56 LLVRQYRHP------TGKFLLEVPAGKVDEGETPEAAARRELREEVGAEAETLIP 104
>pdb|3R03|A Chain A, The Crystal Structure Of Nudix Hydrolase From
Rhodospirillum Rubrum
pdb|3R03|B Chain B, The Crystal Structure Of Nudix Hydrolase From
Rhodospirillum Rubrum
Length = 144
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 119 KLPGGRLKPGENEIEGLKRKLTSKLGANS 147
+ PGG+L+PGE L R+L +LG ++
Sbjct: 38 EFPGGKLEPGETPEAALVRELAEELGVDT 66
>pdb|2AZW|A Chain A, Crystal Structure Of The Mutt/nudix Family Protein From
Enterococcus Faecalis
Length = 148
Score = 28.9 bits (63), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 30/54 (55%)
Query: 91 RTSVEAILLVQEHNHPHILLLQIGNTFCKLPGGRLKPGENEIEGLKRKLTSKLG 144
+T A ++V + + ++L+Q N LPGG ++ E + E + R++ +LG
Sbjct: 16 QTRYAAYIIVSKPENNTMVLVQAPNGAYFLPGGEIEGTETKEEAIHREVLEELG 69
>pdb|1V8V|A Chain A, Crystal Structure Analysis Of The Adp-Ribose
Pyrophosphatase Of E86q Mutant, Complexed With
Adp-Ribose And Mg
pdb|1V8Y|A Chain A, Crystal Structure Analysis Of The Adp-Ribose
Pyrophosphatase Of E86q Mutant, Complexed With
Adp-Ribose And Zn
Length = 170
Score = 27.3 bits (59), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 10/35 (28%), Positives = 21/35 (60%)
Query: 113 IGNTFCKLPGGRLKPGENEIEGLKRKLTSKLGANS 147
+G ++P G ++PGE+ +E +R+L + G +
Sbjct: 57 VGLAPLEIPAGLIEPGEDPLEAARRELAEQTGLSG 91
>pdb|1V8U|A Chain A, Crystal Structure Analysis Of The Adp-Ribose
Pyrophosphatase Of E82q Mutant With So4 And Mg
pdb|1V8W|A Chain A, Crystal Structure Analysis Of The Adp-Ribose
Pyrophosphatase Of E82q Mutant, Complexed With So4 And
Zn
Length = 170
Score = 27.3 bits (59), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 10/35 (28%), Positives = 21/35 (60%)
Query: 113 IGNTFCKLPGGRLKPGENEIEGLKRKLTSKLGANS 147
+G ++P G ++PGE+ +E +R+L + G +
Sbjct: 57 VGLAPLEIPAGLIEPGEDPLEAARRQLAEETGLSG 91
>pdb|1OIR|A Chain A, Imidazopyridines: A Potent And Selective Class Of
Cyclin-Dependent Kinase Inhibitors Identified Through
Structure-Based Hybridisation
Length = 299
Score = 27.3 bits (59), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 60 TFGTKEPKMEKDTSVADRLARMKVNYMKEGM-RTSVEAILLVQEHNHPHIL-LLQIGNTF 117
T+G K T L +++++ EG+ T++ I L++E NHP+I+ LL + +T
Sbjct: 15 TYGVVYKARNKLTGEVVALXKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTE 74
Query: 118 CKL 120
KL
Sbjct: 75 NKL 77
>pdb|1H01|A Chain A, Cdk2 In Complex With A Disubstituted 2, 4-Bis Anilino
Pyrimidine Cdk4 Inhibitor
Length = 298
Score = 27.3 bits (59), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 60 TFGTKEPKMEKDTSVADRLARMKVNYMKEGM-RTSVEAILLVQEHNHPHIL-LLQIGNTF 117
T+G K T L +++++ EG+ T++ I L++E NHP+I+ LL + +T
Sbjct: 14 TYGVVYKARNKLTGEVVALXKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTE 73
Query: 118 CKL 120
KL
Sbjct: 74 NKL 76
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 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,485,236
Number of Sequences: 62578
Number of extensions: 331986
Number of successful extensions: 656
Number of sequences better than 100.0: 53
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 38
Number of HSP's that attempted gapping in prelim test: 634
Number of HSP's gapped (non-prelim): 53
length of query: 282
length of database: 14,973,337
effective HSP length: 98
effective length of query: 184
effective length of database: 8,840,693
effective search space: 1626687512
effective search space used: 1626687512
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: 51 (24.3 bits)