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= 029260
(196 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 148 bits (373), Expect = 2e-36, Method: Compositional matrix adjust.
Identities = 73/170 (42%), Positives = 106/170 (62%), Gaps = 1/170 (0%)
Query: 20 VVDIYPLSSYYFGSKEAIPFKDETLYNRVLRMKSNYDAHGLRTCVEAVLLVELFKHPHLL 79
+++YPL++Y FG+KE + KD ++ R RM+ +D G+R VE VL+V + PH+L
Sbjct: 39 TINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVL 98
Query: 80 LLQVRNSIFKLPGGRLRPGESDIYGLKRKLTRKLSLNXXXXXXXXXXXXCLGMWWKPDFE 139
LLQ+ + FKLPGG L PGE ++ GLKR +T L C+G WW+P+FE
Sbjct: 99 LLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILG-RQDGVLQDWVIDDCIGNWWRPNFE 157
Query: 140 TLLFPYFPPNVKRPKECTKLFLVKLPVSQKFFVPKNLKLLAVPLCQIHEN 189
+PY P ++ +PKE KLFLV+L F VPKN KL+A PL ++++N
Sbjct: 158 PPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDN 207
>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 = 148 bits (373), Expect = 2e-36, Method: Compositional matrix adjust.
Identities = 73/170 (42%), Positives = 106/170 (62%), Gaps = 1/170 (0%)
Query: 20 VVDIYPLSSYYFGSKEAIPFKDETLYNRVLRMKSNYDAHGLRTCVEAVLLVELFKHPHLL 79
+++YPL++Y FG+KE + KD ++ R RM+ +D G+R VE VL+V + PH+L
Sbjct: 36 TINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVL 95
Query: 80 LLQVRNSIFKLPGGRLRPGESDIYGLKRKLTRKLSLNXXXXXXXXXXXXCLGMWWKPDFE 139
LLQ+ + FKLPGG L PGE ++ GLKR +T L C+G WW+P+FE
Sbjct: 96 LLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILG-RQDGVLQDWVIDDCIGNWWRPNFE 154
Query: 140 TLLFPYFPPNVKRPKECTKLFLVKLPVSQKFFVPKNLKLLAVPLCQIHEN 189
+PY P ++ +PKE KLFLV+L F VPKN KL+A PL ++++N
Sbjct: 155 PPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDN 204
>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 = 147 bits (372), Expect = 3e-36, Method: Compositional matrix adjust.
Identities = 73/170 (42%), Positives = 106/170 (62%), Gaps = 1/170 (0%)
Query: 20 VVDIYPLSSYYFGSKEAIPFKDETLYNRVLRMKSNYDAHGLRTCVEAVLLVELFKHPHLL 79
+++YPL++Y FG+KE + KD ++ R RM+ +D G+R VE VL+V + PH+L
Sbjct: 36 TINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVL 95
Query: 80 LLQVRNSIFKLPGGRLRPGESDIYGLKRKLTRKLSLNXXXXXXXXXXXXCLGMWWKPDFE 139
LLQ+ + FKLPGG L PGE ++ GLKR +T L C+G WW+P+FE
Sbjct: 96 LLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILG-RQDGVLQDWVIDDCIGNWWRPNFE 154
Query: 140 TLLFPYFPPNVKRPKECTKLFLVKLPVSQKFFVPKNLKLLAVPLCQIHEN 189
+PY P ++ +PKE KLFLV+L F VPKN KL+A PL ++++N
Sbjct: 155 PPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDN 204
>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 = 147 bits (372), Expect = 3e-36, Method: Compositional matrix adjust.
Identities = 73/170 (42%), Positives = 106/170 (62%), Gaps = 1/170 (0%)
Query: 20 VVDIYPLSSYYFGSKEAIPFKDETLYNRVLRMKSNYDAHGLRTCVEAVLLVELFKHPHLL 79
+++YPL++Y FG+KE + KD ++ R RM+ +D G+R VE VL+V + PH+L
Sbjct: 16 TINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVL 75
Query: 80 LLQVRNSIFKLPGGRLRPGESDIYGLKRKLTRKLSLNXXXXXXXXXXXXCLGMWWKPDFE 139
LLQ+ + FKLPGG L PGE ++ GLKR +T L C+G WW+P+FE
Sbjct: 76 LLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILG-RQDGVLQDWVIDDCIGNWWRPNFE 134
Query: 140 TLLFPYFPPNVKRPKECTKLFLVKLPVSQKFFVPKNLKLLAVPLCQIHEN 189
+PY P ++ +PKE KLFLV+L F VPKN KL+A PL ++++N
Sbjct: 135 PPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDN 184
>pdb|3BHO|A Chain A, Crystal Structure Of The 25kda Subunit Of Human Cleavage
Factor Im With Ap4a
Length = 208
Score = 147 bits (372), Expect = 3e-36, Method: Compositional matrix adjust.
Identities = 73/170 (42%), Positives = 106/170 (62%), Gaps = 1/170 (0%)
Query: 20 VVDIYPLSSYYFGSKEAIPFKDETLYNRVLRMKSNYDAHGLRTCVEAVLLVELFKHPHLL 79
+++YPL++Y FG+KE + KD ++ R RM+ +D G+R VE VL+V + PH+L
Sbjct: 17 TINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVL 76
Query: 80 LLQVRNSIFKLPGGRLRPGESDIYGLKRKLTRKLSLNXXXXXXXXXXXXCLGMWWKPDFE 139
LLQ+ + FKLPGG L PGE ++ GLKR +T L C+G WW+P+FE
Sbjct: 77 LLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILG-RQDGVLQDWVIDDCIGNWWRPNFE 135
Query: 140 TLLFPYFPPNVKRPKECTKLFLVKLPVSQKFFVPKNLKLLAVPLCQIHEN 189
+PY P ++ +PKE KLFLV+L F VPKN KL+A PL ++++N
Sbjct: 136 PPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDN 185
>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 = 147 bits (372), Expect = 3e-36, Method: Compositional matrix adjust.
Identities = 73/170 (42%), Positives = 106/170 (62%), Gaps = 1/170 (0%)
Query: 20 VVDIYPLSSYYFGSKEAIPFKDETLYNRVLRMKSNYDAHGLRTCVEAVLLVELFKHPHLL 79
+++YPL++Y FG+KE + KD ++ R RM+ +D G+R VE VL+V + PH+L
Sbjct: 3 TINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVL 62
Query: 80 LLQVRNSIFKLPGGRLRPGESDIYGLKRKLTRKLSLNXXXXXXXXXXXXCLGMWWKPDFE 139
LLQ+ + FKLPGG L PGE ++ GLKR +T L C+G WW+P+FE
Sbjct: 63 LLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILG-RQDGVLQDWVIDDCIGNWWRPNFE 121
Query: 140 TLLFPYFPPNVKRPKECTKLFLVKLPVSQKFFVPKNLKLLAVPLCQIHEN 189
+PY P ++ +PKE KLFLV+L F VPKN KL+A PL ++++N
Sbjct: 122 PPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDN 171
>pdb|3BAP|A Chain A, Crystal Structure Of The 25 Kda Subunit Of Human Cleavage
Factor Im
Length = 227
Score = 143 bits (360), Expect = 7e-35, Method: Compositional matrix adjust.
Identities = 72/170 (42%), Positives = 103/170 (60%), Gaps = 1/170 (0%)
Query: 20 VVDIYPLSSYYFGSKEAIPFKDETLYNRVLRMKSNYDAHGLRTCVEAVLLVELFKHPHLL 79
+++YPL++Y FG+KE + KD ++ R R + +D G R VE VL+V + PH+L
Sbjct: 36 TINLYPLTNYTFGTKEPLYEKDSSVAARFQRXREEFDKIGXRRTVEGVLIVHEHRLPHVL 95
Query: 80 LLQVRNSIFKLPGGRLRPGESDIYGLKRKLTRKLSLNXXXXXXXXXXXXCLGMWWKPDFE 139
LLQ+ + FKLPGG L PGE ++ GLKR T L C+G WW+P+FE
Sbjct: 96 LLQLGTTFFKLPGGELNPGEDEVEGLKRLXTEILG-RQDGVLQDWVIDDCIGNWWRPNFE 154
Query: 140 TLLFPYFPPNVKRPKECTKLFLVKLPVSQKFFVPKNLKLLAVPLCQIHEN 189
+PY P ++ +PKE KLFLV+L F VPKN KL+A PL ++++N
Sbjct: 155 PPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDN 204
>pdb|3GG6|A Chain A, Crystal Structure Of The Nudix Domain Of Human Nudt18
Length = 156
Score = 30.8 bits (68), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 6/55 (10%)
Query: 67 VLLVELFKHPHLLLLQ-----VRNSIFKLPGGRLRPGESDIYGLKRKLTRKLSLN 116
VL V L + +LL+Q R S + LP GR+ PGE+ + L+R++ + L+
Sbjct: 23 VLAVFLSEQDEVLLIQEAKRECRGSWY-LPAGRMEPGETIVEALQREVKEEAGLH 76
>pdb|2EQI|A Chain A, Solution Structure Of The Sh3 Domain From Phospholipase C,
Gamma 2
Length = 69
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 131 GMWWKPDFETLLFPYFPPN 149
G WWK D+ T + YFP N
Sbjct: 40 GGWWKGDYGTRIQQYFPSN 58
>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 = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 20/31 (64%)
Query: 86 SIFKLPGGRLRPGESDIYGLKRKLTRKLSLN 116
+++ PGG+L PGE+ L R+L +L ++
Sbjct: 35 GLWEFPGGKLEPGETPEAALVRELAEELGVD 65
>pdb|3I7U|A Chain A, Crystal Structure Of Ap4a Hydrolase (Aq_158) From Aquifex
Aeolicus Vf5
pdb|3I7U|B Chain B, Crystal Structure Of Ap4a Hydrolase (Aq_158) From Aquifex
Aeolicus Vf5
pdb|3I7U|C Chain C, Crystal Structure Of Ap4a Hydrolase (Aq_158) From Aquifex
Aeolicus Vf5
pdb|3I7U|D Chain D, Crystal Structure Of Ap4a Hydrolase (Aq_158) From Aquifex
Aeolicus Vf5
pdb|3I7V|A Chain A, Crystal Structure Of Ap4a Hydrolase Complexed With Ap4a
(atp) (aq_158) From Aquifex Aeolicus Vf5
pdb|3I7V|B Chain B, Crystal Structure Of Ap4a Hydrolase Complexed With Ap4a
(atp) (aq_158) From Aquifex Aeolicus Vf5
Length = 134
Score = 28.1 bits (61), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 11/50 (22%)
Query: 51 MKSNYDAHGLRTCVEAVLLVELFKHPHLLLLQVRNSIFKLPGGRLRPGES 100
MK + A G+ LFK +LL++ ++++ P G + PGE
Sbjct: 1 MKKEFSAGGV-----------LFKDGEVLLIKTPSNVWSFPKGNIEPGEK 39
>pdb|3P8T|A Chain A, Crystal Structure Of The Archaeal Asparagine Synthetase A
pdb|3P8T|B Chain B, Crystal Structure Of The Archaeal Asparagine Synthetase A
pdb|3P8V|A Chain A, Crystal Structure Of The Archaeal Asparagine Synthetase A
Complexed With L-Aspartic Acid
pdb|3P8V|B Chain B, Crystal Structure Of The Archaeal Asparagine Synthetase A
Complexed With L-Aspartic Acid
pdb|3P8Y|A Chain A, Crystal Structure Of The Archaeal Asparagine Synthetase A
Complexed With L-Asparagine
pdb|3P8Y|B Chain B, Crystal Structure Of The Archaeal Asparagine Synthetase A
Complexed With L-Asparagine
pdb|3REU|A Chain A, Crystal Structure Of The Archaeal Asparagine Synthetase A
Complexed With L-Aspartic Acid And Adenosine
Triphosphate
pdb|3REU|B Chain B, Crystal Structure Of The Archaeal Asparagine Synthetase A
Complexed With L-Aspartic Acid And Adenosine
Triphosphate
pdb|3REX|A Chain A, Crystal Structure Of The Archaeal Asparagine Synthetase A
Complexed With Adenosine Monophosphate
pdb|3REX|B Chain B, Crystal Structure Of The Archaeal Asparagine Synthetase A
Complexed With Adenosine Monophosphate
pdb|3RL6|A Chain A, Crystal Structure Of The Archaeal Asparagine Synthetase A
Complexed With L-Asparagine And Adenosine Monophosphate
pdb|3RL6|B Chain B, Crystal Structure Of The Archaeal Asparagine Synthetase A
Complexed With L-Asparagine And Adenosine Monophosphate
Length = 294
Score = 28.1 bits (61), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 25/40 (62%), Gaps = 1/40 (2%)
Query: 78 LLLLQVRNSIFKLPGGR-LRPGESDIYGLKRKLTRKLSLN 116
++L + + ++ P G +RP E D+YG++ +LT + L+
Sbjct: 40 IMLSPITDPLWPDPAGEGIRPAEVDVYGVRMRLTHSMILH 79
>pdb|2RQA|A Chain A, Solution Structure Of Lgp2 Ctd
Length = 137
Score = 27.7 bits (60), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 5/76 (6%)
Query: 21 VDIYPLSSYYFGSKEAIPFKDETLYNRVLRMKSNYDAHGLRTCVEAVLLVELFKHPHLLL 80
V++ P S Y+ +D + N+V + R C E L ++K L +
Sbjct: 37 VNVNPNFSNYYNVS-----RDPVVINKVFKDWKPGGVISCRNCGEVWGLQMIYKSVKLPV 91
Query: 81 LQVRNSIFKLPGGRLR 96
L+VR+ + + P GR++
Sbjct: 92 LKVRSMLLETPQGRIQ 107
>pdb|2W4R|A Chain A, Crystal Structure Of The Regulatory Domain Of Human Lgp2
pdb|2W4R|B Chain B, Crystal Structure Of The Regulatory Domain Of Human Lgp2
pdb|2W4R|C Chain C, Crystal Structure Of The Regulatory Domain Of Human Lgp2
pdb|2W4R|D Chain D, Crystal Structure Of The Regulatory Domain Of Human Lgp2
Length = 142
Score = 27.3 bits (59), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 5/76 (6%)
Query: 21 VDIYPLSSYYFGSKEAIPFKDETLYNRVLRMKSNYDAHGLRTCVEAVLLVELFKHPHLLL 80
V++ P S Y+ +D + N+V + R C E L ++K L +
Sbjct: 42 VNVNPNFSNYYNVS-----RDPVVINKVFKDWKPGGVISCRNCGEVWGLQMIYKSVKLPV 96
Query: 81 LQVRNSIFKLPGGRLR 96
L+VR+ + + P GR++
Sbjct: 97 LKVRSMLLETPQGRIQ 112
>pdb|1W36|B Chain B, Recbcd:dna Complex
pdb|1W36|E Chain E, Recbcd:dna Complex
pdb|3K70|B Chain B, Crystal Structure Of The Complete Initiation Complex Of
Recbcd
pdb|3K70|E Chain E, Crystal Structure Of The Complete Initiation Complex Of
Recbcd
Length = 1180
Score = 26.9 bits (58), Expect = 7.2, Method: Composition-based stats.
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 42 ETLYNRVLRMKSNYDAHGLRTCVEAV 67
++ R+L+ DA GLRTC+EA+
Sbjct: 835 QSALGRLLQKGEPQDAAGLRTCIEAL 860
>pdb|3EQT|A Chain A, Crystal Structure Of Human Lgp2 C-Terminal Domain In
Complex With Dsrna
pdb|3EQT|B Chain B, Crystal Structure Of Human Lgp2 C-Terminal Domain In
Complex With Dsrna
Length = 145
Score = 26.6 bits (57), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 40/89 (44%), Gaps = 9/89 (10%)
Query: 12 NGSD----RNGYVVDIYPLSSYYFGSKEAIPFKDETLYNRVLRMKSNYDAHGLRTCVEAV 67
+GSD + V++ P S Y+ +D + N+V + R C E
Sbjct: 25 HGSDLRKVEGTHHVNVNPNFSNYYNVS-----RDPVVINKVFKDWKPGGVISCRNCGEVW 79
Query: 68 LLVELFKHPHLLLLQVRNSIFKLPGGRLR 96
L ++K L +L+VR+ + + P GR++
Sbjct: 80 GLQMIYKSVKLPVLKVRSMLLETPQGRIQ 108
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 0.142 0.441
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,695,456
Number of Sequences: 62578
Number of extensions: 204931
Number of successful extensions: 312
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 292
Number of HSP's gapped (non-prelim): 16
length of query: 196
length of database: 14,973,337
effective HSP length: 94
effective length of query: 102
effective length of database: 9,091,005
effective search space: 927282510
effective search space used: 927282510
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)