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= psy16776
(214 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 = 310 bits (793), Expect = 5e-85, Method: Compositional matrix adjust.
Identities = 145/194 (74%), Positives = 169/194 (87%), Gaps = 4/194 (2%)
Query: 25 SKNLQYNRKKNLYPLSNYTFDIKDPLFEKDSSVPARFQRMRDEFEKIGMRRSVDGVLLVH 84
+K L R NLYPL+NYTF K+PL+EKDSSV ARFQRMR+EF+KIGMRR+V+GVL+VH
Sbjct: 28 TKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVH 87
Query: 85 EHGLPHVLMLQLGTTFFKLPGGELNQGEDEIEGLKRLLSDTLGRRDGVKQEWIVEDTIGN 144
EH LPHVL+LQLGTTFFKLPGGELN GEDE+EGLKRL+++ LGR+DGV Q+W+++D IGN
Sbjct: 88 EHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGN 147
Query: 145 WWRPNFEPPQYPYVPVHITSPKEHRRLFLVQLPER----VPKNYKLVAAPLVELYDNSQG 200
WWRPNFEPPQYPY+P HIT PKEH++LFLVQL E+ VPKNYKLVAAPL ELYDN+ G
Sbjct: 148 WWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPG 207
Query: 201 YGPIISSLPQALCR 214
YGPIISSLPQ L R
Sbjct: 208 YGPIISSLPQLLSR 221
>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 = 310 bits (793), Expect = 5e-85, Method: Compositional matrix adjust.
Identities = 145/194 (74%), Positives = 169/194 (87%), Gaps = 4/194 (2%)
Query: 25 SKNLQYNRKKNLYPLSNYTFDIKDPLFEKDSSVPARFQRMRDEFEKIGMRRSVDGVLLVH 84
+K L R NLYPL+NYTF K+PL+EKDSSV ARFQRMR+EF+KIGMRR+V+GVL+VH
Sbjct: 31 TKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVH 90
Query: 85 EHGLPHVLMLQLGTTFFKLPGGELNQGEDEIEGLKRLLSDTLGRRDGVKQEWIVEDTIGN 144
EH LPHVL+LQLGTTFFKLPGGELN GEDE+EGLKRL+++ LGR+DGV Q+W+++D IGN
Sbjct: 91 EHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGN 150
Query: 145 WWRPNFEPPQYPYVPVHITSPKEHRRLFLVQLPER----VPKNYKLVAAPLVELYDNSQG 200
WWRPNFEPPQYPY+P HIT PKEH++LFLVQL E+ VPKNYKLVAAPL ELYDN+ G
Sbjct: 151 WWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPG 210
Query: 201 YGPIISSLPQALCR 214
YGPIISSLPQ L R
Sbjct: 211 YGPIISSLPQLLSR 224
>pdb|3BHO|A Chain A, Crystal Structure Of The 25kda Subunit Of Human Cleavage
Factor Im With Ap4a
Length = 208
Score = 309 bits (791), Expect = 9e-85, Method: Compositional matrix adjust.
Identities = 145/194 (74%), Positives = 169/194 (87%), Gaps = 4/194 (2%)
Query: 25 SKNLQYNRKKNLYPLSNYTFDIKDPLFEKDSSVPARFQRMRDEFEKIGMRRSVDGVLLVH 84
+K L R NLYPL+NYTF K+PL+EKDSSV ARFQRMR+EF+KIGMRR+V+GVL+VH
Sbjct: 9 TKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVH 68
Query: 85 EHGLPHVLMLQLGTTFFKLPGGELNQGEDEIEGLKRLLSDTLGRRDGVKQEWIVEDTIGN 144
EH LPHVL+LQLGTTFFKLPGGELN GEDE+EGLKRL+++ LGR+DGV Q+W+++D IGN
Sbjct: 69 EHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGN 128
Query: 145 WWRPNFEPPQYPYVPVHITSPKEHRRLFLVQLPER----VPKNYKLVAAPLVELYDNSQG 200
WWRPNFEPPQYPY+P HIT PKEH++LFLVQL E+ VPKNYKLVAAPL ELYDN+ G
Sbjct: 129 WWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPG 188
Query: 201 YGPIISSLPQALCR 214
YGPIISSLPQ L R
Sbjct: 189 YGPIISSLPQLLSR 202
>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 = 308 bits (790), Expect = 1e-84, Method: Compositional matrix adjust.
Identities = 145/194 (74%), Positives = 169/194 (87%), Gaps = 4/194 (2%)
Query: 25 SKNLQYNRKKNLYPLSNYTFDIKDPLFEKDSSVPARFQRMRDEFEKIGMRRSVDGVLLVH 84
+K L R NLYPL+NYTF K+PL+EKDSSV ARFQRMR+EF+KIGMRR+V+GVL+VH
Sbjct: 8 TKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVH 67
Query: 85 EHGLPHVLMLQLGTTFFKLPGGELNQGEDEIEGLKRLLSDTLGRRDGVKQEWIVEDTIGN 144
EH LPHVL+LQLGTTFFKLPGGELN GEDE+EGLKRL+++ LGR+DGV Q+W+++D IGN
Sbjct: 68 EHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGN 127
Query: 145 WWRPNFEPPQYPYVPVHITSPKEHRRLFLVQLPER----VPKNYKLVAAPLVELYDNSQG 200
WWRPNFEPPQYPY+P HIT PKEH++LFLVQL E+ VPKNYKLVAAPL ELYDN+ G
Sbjct: 128 WWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPG 187
Query: 201 YGPIISSLPQALCR 214
YGPIISSLPQ L R
Sbjct: 188 YGPIISSLPQLLSR 201
>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 = 308 bits (789), Expect = 1e-84, Method: Compositional matrix adjust.
Identities = 145/194 (74%), Positives = 169/194 (87%), Gaps = 4/194 (2%)
Query: 25 SKNLQYNRKKNLYPLSNYTFDIKDPLFEKDSSVPARFQRMRDEFEKIGMRRSVDGVLLVH 84
+K L R NLYPL+NYTF K+PL+EKDSSV ARFQRMR+EF+KIGMRR+V+GVL+VH
Sbjct: 28 TKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVH 87
Query: 85 EHGLPHVLMLQLGTTFFKLPGGELNQGEDEIEGLKRLLSDTLGRRDGVKQEWIVEDTIGN 144
EH LPHVL+LQLGTTFFKLPGGELN GEDE+EGLKRL+++ LGR+DGV Q+W+++D IGN
Sbjct: 88 EHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGN 147
Query: 145 WWRPNFEPPQYPYVPVHITSPKEHRRLFLVQLPER----VPKNYKLVAAPLVELYDNSQG 200
WWRPNFEPPQYPY+P HIT PKEH++LFLVQL E+ VPKNYKLVAAPL ELYDN+ G
Sbjct: 148 WWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPG 207
Query: 201 YGPIISSLPQALCR 214
YGPIISSLPQ L R
Sbjct: 208 YGPIISSLPQLLSR 221
>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 = 306 bits (783), Expect = 6e-84, Method: Compositional matrix adjust.
Identities = 143/187 (76%), Positives = 166/187 (88%), Gaps = 4/187 (2%)
Query: 32 RKKNLYPLSNYTFDIKDPLFEKDSSVPARFQRMRDEFEKIGMRRSVDGVLLVHEHGLPHV 91
R NLYPL+NYTF K+PL+EKDSSV ARFQRMR+EF+KIGMRR+V+GVL+VHEH LPHV
Sbjct: 2 RTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHV 61
Query: 92 LMLQLGTTFFKLPGGELNQGEDEIEGLKRLLSDTLGRRDGVKQEWIVEDTIGNWWRPNFE 151
L+LQLGTTFFKLPGGELN GEDE+EGLKRL+++ LGR+DGV Q+W+++D IGNWWRPNFE
Sbjct: 62 LLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGNWWRPNFE 121
Query: 152 PPQYPYVPVHITSPKEHRRLFLVQLPER----VPKNYKLVAAPLVELYDNSQGYGPIISS 207
PPQYPY+P HIT PKEH++LFLVQL E+ VPKNYKLVAAPL ELYDN+ GYGPIISS
Sbjct: 122 PPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISS 181
Query: 208 LPQALCR 214
LPQ L R
Sbjct: 182 LPQLLSR 188
>pdb|3BAP|A Chain A, Crystal Structure Of The 25 Kda Subunit Of Human Cleavage
Factor Im
Length = 227
Score = 301 bits (771), Expect = 2e-82, Method: Compositional matrix adjust.
Identities = 143/194 (73%), Positives = 166/194 (85%), Gaps = 4/194 (2%)
Query: 25 SKNLQYNRKKNLYPLSNYTFDIKDPLFEKDSSVPARFQRMRDEFEKIGMRRSVDGVLLVH 84
+K L R NLYPL+NYTF K+PL+EKDSSV ARFQR R+EF+KIG RR+V+GVL+VH
Sbjct: 28 TKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRXREEFDKIGXRRTVEGVLIVH 87
Query: 85 EHGLPHVLMLQLGTTFFKLPGGELNQGEDEIEGLKRLLSDTLGRRDGVKQEWIVEDTIGN 144
EH LPHVL+LQLGTTFFKLPGGELN GEDE+EGLKRL ++ LGR+DGV Q+W+++D IGN
Sbjct: 88 EHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLXTEILGRQDGVLQDWVIDDCIGN 147
Query: 145 WWRPNFEPPQYPYVPVHITSPKEHRRLFLVQLPER----VPKNYKLVAAPLVELYDNSQG 200
WWRPNFEPPQYPY+P HIT PKEH++LFLVQL E+ VPKNYKLVAAPL ELYDN+ G
Sbjct: 148 WWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPG 207
Query: 201 YGPIISSLPQALCR 214
YGPIISSLPQ L R
Sbjct: 208 YGPIISSLPQLLSR 221
>pdb|1I5P|A Chain A, Insecticidal Crystal Protein Cry2aa
Length = 633
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 34/98 (34%), Positives = 47/98 (47%), Gaps = 12/98 (12%)
Query: 103 LPGGELNQGED---EIEGL--KRLLSDTLGRRDGVKQEWI-VEDTIG--NWWRPNFEPPQ 154
P G N +D E E +RL +DTL R V E I ++ I N NF P
Sbjct: 82 FPSGSTNLMQDILRETEQFLNQRLNTDTLAR---VNAELIGLQANIREFNQQVDNFLNPT 138
Query: 155 YPYVPVHITSP-KEHRRLFLVQLPERVPKNYKLVAAPL 191
VP+ ITS ++LFL +LP+ + Y+L+ PL
Sbjct: 139 QNPVPLSITSSVNTMQQLFLNRLPQFQIQGYQLLLLPL 176
>pdb|3I6V|A Chain A, Crystal Structure Of A Periplasmic HisGLUGLNARGOPINE
FAMILY- Binding Protein From Silicibacter Pomeroyi In
Complex With Lysine
Length = 232
Score = 28.9 bits (63), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 26/62 (41%), Gaps = 8/62 (12%)
Query: 114 EIEGLKRLLSDTLGRRDGVKQEWIVEDTIGNWWR---PNFEPPQYPYVPVHITSPKEHRR 170
E++G +R L D L +R G+ EW+ D W PN Y + ++ E
Sbjct: 26 EVDGFERELGDELCKRAGLTCEWVKND-----WDSIIPNLVSGNYDTIIAGMSITDERDE 80
Query: 171 LF 172
+
Sbjct: 81 VI 82
>pdb|4F6C|A Chain A, Crystal Structure Of Aureusimine Biosynthetic Cluster
Reductase Domain
pdb|4F6C|B Chain B, Crystal Structure Of Aureusimine Biosynthetic Cluster
Reductase Domain
Length = 427
Score = 28.5 bits (62), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 23/37 (62%), Gaps = 2/37 (5%)
Query: 66 DEFEKIGMRRSVDGVLLVHEHG--LPHVLMLQLGTTF 100
DEFEK+ ++ +VD + L +H L +V + +GT F
Sbjct: 168 DEFEKVNVQGTVDVIRLAQQHHARLIYVSTISVGTYF 204
>pdb|4F6L|B Chain B, Crystal Structure Of Aureusimine Biosynthetic Cluster
Reductase Domain
pdb|4F6L|A Chain A, Crystal Structure Of Aureusimine Biosynthetic Cluster
Reductase Domain
Length = 508
Score = 27.7 bits (60), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 23/37 (62%), Gaps = 2/37 (5%)
Query: 66 DEFEKIGMRRSVDGVLLVHEHG--LPHVLMLQLGTTF 100
DEFEK+ ++ +VD + L +H L +V + +GT F
Sbjct: 249 DEFEKVNVQGTVDVIRLAQQHHARLIYVSTISVGTYF 285
>pdb|2QJO|A Chain A, Crystal Structure Of A Bifunctional Nmn
AdenylyltransferaseADP RIBOSE Pyrophosphatase (Nadm)
Complexed With Adprp And Nad From Synechocystis Sp.
pdb|2QJO|B Chain B, Crystal Structure Of A Bifunctional Nmn
AdenylyltransferaseADP RIBOSE Pyrophosphatase (Nadm)
Complexed With Adprp And Nad From Synechocystis Sp.
pdb|2QJO|C Chain C, Crystal Structure Of A Bifunctional Nmn
AdenylyltransferaseADP RIBOSE Pyrophosphatase (Nadm)
Complexed With Adprp And Nad From Synechocystis Sp
Length = 341
Score = 26.9 bits (58), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 4/39 (10%)
Query: 90 HVLMLQL----GTTFFKLPGGELNQGEDEIEGLKRLLSD 124
HVLM++ G LPGG + Q E +EG+ R L +
Sbjct: 215 HVLMVRRQAKPGLGLIALPGGFIKQNETLVEGMLRELKE 253
>pdb|2FGN|A Chain A, Structural Studies Examining The Substrate Specificity
Profiles Of Pc-Plcbc Protein Variants
Length = 245
Score = 26.9 bits (58), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 12/48 (25%), Positives = 28/48 (58%)
Query: 11 NSTLVTVNRTINLISKNLQYNRKKNLYPLSNYTFDIKDPLFEKDSSVP 58
NS L VNR I+++S+N ++ + L+ + ++++ ++ D+ P
Sbjct: 12 NSHLWIVNRAIDIMSRNTTLVKQDRVAQLNEWRTELENGIYAADTENP 59
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
0.319 0.139 0.423
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,895,683
Number of Sequences: 62578
Number of extensions: 292991
Number of successful extensions: 621
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 599
Number of HSP's gapped (non-prelim): 21
length of query: 214
length of database: 14,973,337
effective HSP length: 95
effective length of query: 119
effective length of database: 9,028,427
effective search space: 1074382813
effective search space used: 1074382813
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)