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= 013399
(444 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1Q79|A Chain A, Crystal Structure Of Mammalian Poly(A) Polymerase
Length = 514
Score = 238 bits (608), Expect = 4e-63, Method: Compositional matrix adjust.
Identities = 134/379 (35%), Positives = 212/379 (55%), Gaps = 9/379 (2%)
Query: 69 PLNPSVLDQMDEERSLSLVQLMTNEGLVPSTEEEDKRRNVIQKLKEIVLAWVKRVAWQRR 128
P++ + + D + LV+ + G+ EE +R ++ KL +V W++ ++ +
Sbjct: 25 PISLAAPKETDXLLTQKLVETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREISESKN 84
Query: 129 LPKEQIAETHATILTYGSYGLGVHGSESDIDALCLGPEFATMAEDFFVVLHNMLKSRPEV 188
LP+ I I T+GSY LGVH +DIDALC+ P + DFF ++ LK + EV
Sbjct: 85 LPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRS-DFFTSFYDKLKLQEEV 143
Query: 189 SEIHCVKDAKVPLMRFKFDGILIDLPYACLHVLSVPENVDVLNPFFLRDLDETSWKSLSG 248
++ V++A VP+++ FDGI ID+ +A L + ++PE++D+ + L++LD +SL+G
Sbjct: 144 KDLRAVEEAFVPVIKLXFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRXIRSLNG 203
Query: 249 VRANKCILQLVPDLEKFQPVLRCIKLWAKRRGVYGNLHGFLGGVHLAILVAHVCQNHPKG 308
R IL LVP+++ F+ LR IKLWAKR +Y N+ GFLGGV A+LVA CQ +P
Sbjct: 204 CRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNA 263
Query: 309 SLNTLVANFFKTYAYWPWPTPVMLQDPM-----LPAAG---YPSETRSLMPIRLPCSPHE 360
+TLV FF ++ W WP PV+L+ P LP PS+ LMPI P P +
Sbjct: 264 IASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQ 323
Query: 361 YCHSNITRSTFYKIRTEFLRGHNTTRDLMRPDFDWHFLFEPFPYSKKYARFVRVYLSASN 420
N++ ST + EF +G T +++ +W LFE + +KY ++ + SA
Sbjct: 324 NSTYNVSVSTRMVMVEEFKQGLAITDEILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPT 383
Query: 421 QDDLGDWVGWVKSRFRSLI 439
+ +WVG V+S+ R L+
Sbjct: 384 EKQRLEWVGLVESKIRILV 402
>pdb|1Q78|A Chain A, Crystal Structure Of Poly(A) Polymerase In Complex With
3'- Datp And Magnesium Chloride
Length = 514
Score = 237 bits (605), Expect = 9e-63, Method: Compositional matrix adjust.
Identities = 134/379 (35%), Positives = 212/379 (55%), Gaps = 9/379 (2%)
Query: 69 PLNPSVLDQMDEERSLSLVQLMTNEGLVPSTEEEDKRRNVIQKLKEIVLAWVKRVAWQRR 128
P++ + + D + LV+ + G+ EE +R ++ KL +V W++ ++ +
Sbjct: 25 PISLAAPKETDXLLTQKLVETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREISESKN 84
Query: 129 LPKEQIAETHATILTYGSYGLGVHGSESDIDALCLGPEFATMAEDFFVVLHNMLKSRPEV 188
LP+ I I T+GSY LGVH +DIDALC+ P + DFF ++ LK + EV
Sbjct: 85 LPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRS-DFFTSFYDKLKLQEEV 143
Query: 189 SEIHCVKDAKVPLMRFKFDGILIDLPYACLHVLSVPENVDVLNPFFLRDLDETSWKSLSG 248
++ V++A VP+++ FDGI ID+ +A L + ++PE++D+ + L++LD +SL+G
Sbjct: 144 KDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRXIRSLNG 203
Query: 249 VRANKCILQLVPDLEKFQPVLRCIKLWAKRRGVYGNLHGFLGGVHLAILVAHVCQNHPKG 308
R IL LVP+++ F+ LR IKLWAKR +Y N+ GFLGGV A+LVA CQ +P
Sbjct: 204 CRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNA 263
Query: 309 SLNTLVANFFKTYAYWPWPTPVMLQDPM-----LPAAG---YPSETRSLMPIRLPCSPHE 360
+TLV FF ++ W WP PV+L+ P LP PS+ LMPI P P +
Sbjct: 264 IASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQ 323
Query: 361 YCHSNITRSTFYKIRTEFLRGHNTTRDLMRPDFDWHFLFEPFPYSKKYARFVRVYLSASN 420
N++ ST + EF +G T +++ +W LFE + +KY ++ + SA
Sbjct: 324 NSTYNVSVSTRMVMVEEFKQGLAITDEILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPT 383
Query: 421 QDDLGDWVGWVKSRFRSLI 439
+ +WVG V+S+ R L+
Sbjct: 384 EKQRLEWVGLVESKIRILV 402
>pdb|1F5A|A Chain A, Crystal Structure Of Mammalian Poly(A) Polymerase
Length = 513
Score = 227 bits (579), Expect = 9e-60, Method: Compositional matrix adjust.
Identities = 133/379 (35%), Positives = 209/379 (55%), Gaps = 9/379 (2%)
Query: 69 PLNPSVLDQMDEERSLSLVQLMTNEGLVPSTEEEDKRRNVIQKLKEIVLAWVKRVAWQRR 128
P++ + + D + LV+ + G+ EE +R ++ KL +V W++ ++ +
Sbjct: 25 PISLAAPKETDCLLTQKLVETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREISESKN 84
Query: 129 LPKEQIAETHATILTYGSYGLGVHGSESDIDALCLGPEFATMAEDFFVVLHNMLKSRPEV 188
LP+ I I T+GSY LGVH +DIDALC+ P + DFF ++ LK + EV
Sbjct: 85 LPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRS-DFFTSFYDKLKLQEEV 143
Query: 189 SEIHCVKDAKVPLMRFKFDGILIDLPYACLHVLSVPENVDVLNPFFLRDLDETSWKSLSG 248
++ V++A VP+++ FDGI ID+ +A L + ++PE++D+ + L++LD +SL+G
Sbjct: 144 KDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNG 203
Query: 249 VRANKCILQLVPDLEKFQPVLRCIKLWAKRRGVYGNLHGFLGGVHLAILVAHVCQNHPKG 308
R IL LVP+++ F+ LR IKLWAKR +Y N+ GFLGGV A LVA CQ +P
Sbjct: 204 CRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAXLVARTCQLYPNA 263
Query: 309 SLNTLVANFFKTYAYWPWPTPVMLQDPM-----LPAAG---YPSETRSLMPIRLPCSPHE 360
+TLV FF ++ W WP PV+L+ P LP PS+ L PI P P +
Sbjct: 264 IASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLXPIITPAYPQQ 323
Query: 361 YCHSNITRSTFYKIRTEFLRGHNTTRDLMRPDFDWHFLFEPFPYSKKYARFVRVYLSASN 420
N++ ST EF +G T +++ +W LFE + +KY ++ + SA
Sbjct: 324 NSTYNVSVSTRXVXVEEFKQGLAITDEILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPT 383
Query: 421 QDDLGDWVGWVKSRFRSLI 439
+ +WVG V+S+ R L+
Sbjct: 384 EKQRLEWVGLVESKIRILV 402
>pdb|2O1P|A Chain A, Structure Of Yeast Poly(A) Polymerase In A Somewhat Closed
State
pdb|2O1P|B Chain B, Structure Of Yeast Poly(A) Polymerase In A Somewhat Closed
State
Length = 546
Score = 222 bits (566), Expect = 3e-58, Method: Compositional matrix adjust.
Identities = 137/369 (37%), Positives = 194/369 (52%), Gaps = 12/369 (3%)
Query: 85 SLVQLMTNEGLVPSTEEEDKRRNVIQKLKEIVLAWVKRVAWQRRLPKEQIAETHATILTY 144
SL+Q + EG + +E R V++ L+E+ +V V+ ++ + + I TY
Sbjct: 28 SLIQELKKEGSFETEQETANRVQVLKILQELAQRFVYEVSKKKNMSDGMARDAGGKIFTY 87
Query: 145 GSYGLGVHGSESDIDALCLGPEFATMAEDFFVVLHNMLKSRPEVSEIHCVKDAKVPLMRF 204
GSY LGVHG SDID L + P+ T EDFF V ++L+ R E+ EI V DA VP+++
Sbjct: 88 GSYRLGVHGPGSDIDTLVVVPKHVTR-EDFFTVFDSLLRERKELDEIAPVPDAFVPIIKI 146
Query: 205 KFDGILIDLPYACLHVLSVPENVDVLNPFFLRDLDETSWKSLSGVRANKCILQLVPDLEK 264
KF GI IDL A L VP ++ + + LR+LDE ++L+G R IL+LVP
Sbjct: 147 KFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDEKDLRALNGTRVTDEILELVPKPNV 206
Query: 265 FQPVLRCIKLWAKRRGVYGNLHGFLGGVHLAILVAHVCQNHPKGSLNTLVANFFKTYAYW 324
F+ LR IKLWA+RR VY N+ GF GGV A+LVA +CQ +P ++ FF + W
Sbjct: 207 FRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARICQLYPNACSAVILNRFFIILSEW 266
Query: 325 PWPTPVML---QDPMLPA-----AGYPSETRSLMPIRLPCSPHEYCHSNITRSTFYKIRT 376
WP PV+L +D L Y + MP+ P P NIT ST I
Sbjct: 267 NWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMCATHNITESTKKVILQ 326
Query: 377 EFLRGHNTTRDLMRPDFDWHFLFEP--FPYSKKYARFVRVYLSASNQDDLGDWVGWVKSR 434
EF+RG T D+ W LFE F + K+ + Y S++ L W G V+S+
Sbjct: 327 EFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLEITAYTRGSDEQHL-KWSGLVESK 385
Query: 435 FRSLILKVS 443
R L++K+
Sbjct: 386 VRLLVMKLE 394
>pdb|1FA0|A Chain A, Structure Of Yeast Poly(A) Polymerase Bound To Manganate
And 3'-Datp
pdb|1FA0|B Chain B, Structure Of Yeast Poly(A) Polymerase Bound To Manganate
And 3'-Datp
pdb|3C66|A Chain A, Yeast Poly(A) Polymerase In Complex With Fip1 Residues
80-105
pdb|3C66|B Chain B, Yeast Poly(A) Polymerase In Complex With Fip1 Residues
80-105
Length = 537
Score = 222 bits (566), Expect = 3e-58, Method: Compositional matrix adjust.
Identities = 137/369 (37%), Positives = 194/369 (52%), Gaps = 12/369 (3%)
Query: 85 SLVQLMTNEGLVPSTEEEDKRRNVIQKLKEIVLAWVKRVAWQRRLPKEQIAETHATILTY 144
SL+Q + EG + +E R V++ L+E+ +V V+ ++ + + I TY
Sbjct: 28 SLIQELKKEGSFETEQETANRVQVLKILQELAQRFVYEVSKKKNMSDGMARDAGGKIFTY 87
Query: 145 GSYGLGVHGSESDIDALCLGPEFATMAEDFFVVLHNMLKSRPEVSEIHCVKDAKVPLMRF 204
GSY LGVHG SDID L + P+ T EDFF V ++L+ R E+ EI V DA VP+++
Sbjct: 88 GSYRLGVHGPGSDIDTLVVVPKHVTR-EDFFTVFDSLLRERKELDEIAPVPDAFVPIIKI 146
Query: 205 KFDGILIDLPYACLHVLSVPENVDVLNPFFLRDLDETSWKSLSGVRANKCILQLVPDLEK 264
KF GI IDL A L VP ++ + + LR+LDE ++L+G R IL+LVP
Sbjct: 147 KFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDEKDLRALNGTRVTDEILELVPKPNV 206
Query: 265 FQPVLRCIKLWAKRRGVYGNLHGFLGGVHLAILVAHVCQNHPKGSLNTLVANFFKTYAYW 324
F+ LR IKLWA+RR VY N+ GF GGV A+LVA +CQ +P ++ FF + W
Sbjct: 207 FRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARICQLYPNACSAVILNRFFIILSEW 266
Query: 325 PWPTPVML---QDPMLPA-----AGYPSETRSLMPIRLPCSPHEYCHSNITRSTFYKIRT 376
WP PV+L +D L Y + MP+ P P NIT ST I
Sbjct: 267 NWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMCATHNITESTKKVILQ 326
Query: 377 EFLRGHNTTRDLMRPDFDWHFLFEP--FPYSKKYARFVRVYLSASNQDDLGDWVGWVKSR 434
EF+RG T D+ W LFE F + K+ + Y S++ L W G V+S+
Sbjct: 327 EFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLEITAYTRGSDEQHL-KWSGLVESK 385
Query: 435 FRSLILKVS 443
R L++K+
Sbjct: 386 VRLLVMKLE 394
>pdb|2HHP|A Chain A, Structure Of Yeast Poly(A) Polymerase In A Closed
Conformation
Length = 530
Score = 222 bits (566), Expect = 3e-58, Method: Compositional matrix adjust.
Identities = 137/369 (37%), Positives = 194/369 (52%), Gaps = 12/369 (3%)
Query: 85 SLVQLMTNEGLVPSTEEEDKRRNVIQKLKEIVLAWVKRVAWQRRLPKEQIAETHATILTY 144
SL+Q + EG + +E R V++ L+E+ +V V+ ++ + + I TY
Sbjct: 28 SLIQELKKEGSFETEQETANRVQVLKILQELAQRFVYEVSKKKNMSDGMARDAGGKIFTY 87
Query: 145 GSYGLGVHGSESDIDALCLGPEFATMAEDFFVVLHNMLKSRPEVSEIHCVKDAKVPLMRF 204
GSY LGVHG SDID L + P+ T EDFF V ++L+ R E+ EI V DA VP+++
Sbjct: 88 GSYRLGVHGPGSDIDTLVVVPKHVTR-EDFFTVFDSLLRERKELDEIAPVPDAFVPIIKI 146
Query: 205 KFDGILIDLPYACLHVLSVPENVDVLNPFFLRDLDETSWKSLSGVRANKCILQLVPDLEK 264
KF GI IDL A L VP ++ + + LR+LDE ++L+G R IL+LVP
Sbjct: 147 KFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDEKDLRALNGTRVTDEILELVPKPNV 206
Query: 265 FQPVLRCIKLWAKRRGVYGNLHGFLGGVHLAILVAHVCQNHPKGSLNTLVANFFKTYAYW 324
F+ LR IKLWA+RR VY N+ GF GGV A+LVA +CQ +P ++ FF + W
Sbjct: 207 FRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARICQLYPNACSAVILNRFFIILSEW 266
Query: 325 PWPTPVML---QDPMLPA-----AGYPSETRSLMPIRLPCSPHEYCHSNITRSTFYKIRT 376
WP PV+L +D L Y + MP+ P P NIT ST I
Sbjct: 267 NWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMCATHNITESTKKVILQ 326
Query: 377 EFLRGHNTTRDLMRPDFDWHFLFEP--FPYSKKYARFVRVYLSASNQDDLGDWVGWVKSR 434
EF+RG T D+ W LFE F + K+ + Y S++ L W G V+S+
Sbjct: 327 EFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLEITAYTRGSDEQHL-KWSGLVESK 385
Query: 435 FRSLILKVS 443
R L++K+
Sbjct: 386 VRLLVMKLE 394
>pdb|2Q66|A Chain A, Structure Of Yeast Poly(A) Polymerase With Atp And
Oligo(A)
Length = 525
Score = 219 bits (557), Expect = 3e-57, Method: Compositional matrix adjust.
Identities = 136/369 (36%), Positives = 193/369 (52%), Gaps = 12/369 (3%)
Query: 85 SLVQLMTNEGLVPSTEEEDKRRNVIQKLKEIVLAWVKRVAWQRRLPKEQIAETHATILTY 144
SL+Q + EG + +E R V++ L+E+ +V V+ ++ + + I TY
Sbjct: 24 SLIQELKKEGSFETEQETANRVQVLKILQELAQRFVYEVSKKKNMSDGMARDAGGKIFTY 83
Query: 145 GSYGLGVHGSESDIDALCLGPEFATMAEDFFVVLHNMLKSRPEVSEIHCVKDAKVPLMRF 204
GSY LGVHG SDID L + P+ T EDFF V ++L+ R E+ EI V DA VP+++
Sbjct: 84 GSYRLGVHGPGSDIDTLVVVPKHVTR-EDFFTVFDSLLRERKELDEIAPVPDAFVPIIKI 142
Query: 205 KFDGILIDLPYACLHVLSVPENVDVLNPFFLRDLDETSWKSLSGVRANKCILQLVPDLEK 264
KF GI I L A L VP ++ + + LR+LDE ++L+G R IL+LVP
Sbjct: 143 KFSGISIALICARLDQPQVPLSLTLSDKNLLRNLDEKDLRALNGTRVTDEILELVPKPNV 202
Query: 265 FQPVLRCIKLWAKRRGVYGNLHGFLGGVHLAILVAHVCQNHPKGSLNTLVANFFKTYAYW 324
F+ LR IKLWA+RR VY N+ GF GGV A+LVA +CQ +P ++ FF + W
Sbjct: 203 FRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARICQLYPNACSAVILNRFFIILSEW 262
Query: 325 PWPTPVML---QDPMLPA-----AGYPSETRSLMPIRLPCSPHEYCHSNITRSTFYKIRT 376
WP PV+L +D L Y + MP+ P P NIT ST I
Sbjct: 263 NWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMCATHNITESTKKVILQ 322
Query: 377 EFLRGHNTTRDLMRPDFDWHFLFEP--FPYSKKYARFVRVYLSASNQDDLGDWVGWVKSR 434
EF+RG T D+ W LFE F + K+ + Y S++ L W G V+S+
Sbjct: 323 EFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLEITAYTRGSDEQHL-KWSGLVESK 381
Query: 435 FRSLILKVS 443
R L++K+
Sbjct: 382 VRLLVMKLE 390
>pdb|3NYB|A Chain A, Structure And Function Of The Polymerase Core Of Tramp, A
Rna Surveillance Complex
Length = 323
Score = 48.5 bits (114), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 67/297 (22%), Positives = 116/297 (39%), Gaps = 68/297 (22%)
Query: 95 LVPSTEEEDKRRNVIQKLKEIVLAWVKRVAWQRRLPKEQIAETHATILTYGSYGLGVHGS 154
+ PS EE + R I ++E V + W A + +GSY ++
Sbjct: 32 ISPSREEIEIRNQTISTIREAV-----KQLW-----------PDADLHVFGSYSTDLYLP 75
Query: 155 ESDIDALCLGPEFATMAEDFFVVLHNMLKSRPEVSEIHCVKDAKVPLMRFKFDGILIDLP 214
SDID + + + L + LK + +E+ V A+VP+++F P
Sbjct: 76 GSDIDCVVTSELGGKESRNNLYSLASHLKKKNLATEVEVVAKARVPIIKFV-------EP 128
Query: 215 YACLHVLSVPENVDVLNPFFLRDLDETSWKSLSGVRANKCILQLVPDLEKFQPVLRCIKL 274
++ +H+ S++ +G+ A K I + + D + ++ +K
Sbjct: 129 HSGIHI-------------------AVSFERTNGIEAAKLIREWLDDTPGLRELVLIVKQ 169
Query: 275 WAKRRGVYGNLH-GFLGGVHLAILVAHVCQNH---------PKGSLNTLVANFFKTYAYW 324
+ R + N+H G LGG + LV H PK +L L+ FF+ Y
Sbjct: 170 FLHARRL-NNVHTGGLGGFSIICLVFSFLHMHPRIITNEIDPKDNLGVLLIEFFELYGKN 228
Query: 325 PWPTPVMLQDPMLPAAGYP-----SETRSLMPIRLPCS-----PHEYCHSNITRSTF 371
V L + GYP S ++ PI+ P S P + +NI+R +F
Sbjct: 229 FGYDDVALG----SSDGYPVYFPKSTWSAIQPIKNPFSLAIQDPGDES-NNISRGSF 280
>pdb|2XNT|A Chain A, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNT|B Chain B, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNT|C Chain C, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNT|D Chain D, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNT|E Chain E, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNT|F Chain F, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNT|G Chain G, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNT|H Chain H, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNT|I Chain I, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNT|J Chain J, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNU|A Chain A, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNU|B Chain B, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNU|C Chain C, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNU|D Chain D, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNU|E Chain E, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNV|A Chain A, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNV|B Chain B, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNV|C Chain C, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNV|D Chain D, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNV|E Chain E, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNV|F Chain F, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNV|G Chain G, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNV|H Chain H, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNV|I Chain I, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNV|J Chain J, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
Length = 236
Score = 32.3 bits (72), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 288 FLGGVHLAILVAHVCQNHPKGSLNTLVANFFKTYAYWPWPTPVMLQDPMLPAAGY 342
L V+LA+LVA V Q H + +L L ++ F +P PT DP+ G+
Sbjct: 1 MLVSVYLALLVACVGQAHSQANLMRLKSDLFNRSPMYPGPTK---DDPLTVTLGF 52
>pdb|3G40|A Chain A, Crystal Structure Of The Cytoplasmic Domain Of A
Prokaryotic Cation Chloride Cotransporter
Length = 294
Score = 32.0 bits (71), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 10/63 (15%)
Query: 271 CIKLWAKRRGVYGNLHGFLGGVHLAILVAHVCQNHPKGSLNTLVANFFKTYAYWPWPTPV 330
I LW + RG+ ++ LG + LA+L+A+ +++ K SL+ F T+A PT +
Sbjct: 157 LINLWIENRGLDWDISMELGNMDLALLIAYKLKSNWKASLS------FMTFA----PTAI 206
Query: 331 MLQ 333
Q
Sbjct: 207 QAQ 209
>pdb|2YLX|A Chain A, Snapshots Of Enzymatic Baeyer-Villiger Catalysis: Oxygen
Activation And Intermediate Stabilization: Asp66ala
Mutant In Complex With Nadp And Mes
Length = 542
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 7/77 (9%)
Query: 4 YACNNNQSNNLVVYPYNFVDFYPQNANFGVVTPQSLGV-INPNLI-SPSQVLVPCNSPVF 61
+A N + N +P+ VDF Q GV+ S G+ ++P + +++ V +P F
Sbjct: 167 FAGNLYHTGN---WPHEPVDFSGQRV--GVIGTGSSGIQVSPQIAKQAAELFVFQRTPHF 221
Query: 62 LVPSFNFPLNPSVLDQM 78
VP+ N PL+P L +
Sbjct: 222 AVPARNAPLDPEFLADL 238
>pdb|2YLZ|A Chain A, Snapshots Of Enzymatic Baeyer-Villiger Catalysis: Oxygen
Activation And Intermediate Stabilization: Met446gly
Mutant
Length = 542
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 7/77 (9%)
Query: 4 YACNNNQSNNLVVYPYNFVDFYPQNANFGVVTPQSLGV-INPNLI-SPSQVLVPCNSPVF 61
+A N + N +P+ VDF Q GV+ S G+ ++P + +++ V +P F
Sbjct: 167 FAGNLYHTGN---WPHEPVDFSGQRV--GVIGTGSSGIQVSPQIAKQAAELFVFQRTPHF 221
Query: 62 LVPSFNFPLNPSVLDQM 78
VP+ N PL+P L +
Sbjct: 222 AVPARNAPLDPEFLADL 238
>pdb|1W4X|A Chain A, Phenylacetone Monooxygenase, A Baeyer-villiger
Monooxygenase
pdb|2YLR|A Chain A, Snapshots Of Enzymatic Baeyer-Villiger Catalysis: Oxygen
Activation And Intermediate Stabilization: Complex With
Nadp
pdb|2YLS|A Chain A, Snapshots Of Enzymatic Baeyer-Villiger Catalysis: Oxygen
Activation And Intermediate Stabilization: Reduced
Enzyme Bound To Nadp
pdb|2YLT|A Chain A, Snapshots Of Enzymatic Baeyer-Villiger Catalysis: Oxygen
Activation And Intermediate Stabilization: Complex With
Nadp And Mes
Length = 542
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 7/77 (9%)
Query: 4 YACNNNQSNNLVVYPYNFVDFYPQNANFGVVTPQSLGV-INPNLI-SPSQVLVPCNSPVF 61
+A N + N +P+ VDF Q GV+ S G+ ++P + +++ V +P F
Sbjct: 167 FAGNLYHTGN---WPHEPVDFSGQRV--GVIGTGSSGIQVSPQIAKQAAELFVFQRTPHF 221
Query: 62 LVPSFNFPLNPSVLDQM 78
VP+ N PL+P L +
Sbjct: 222 AVPARNAPLDPEFLADL 238
>pdb|2YLW|A Chain A, Snapshots Of Enzymatic Baeyer-Villiger Catalysis: Oxygen
Activation And Intermediate Stabilization: Arg337lys
Mutant In Complex With Mes
pdb|2YM1|A Chain A, Snapshots Of Enzymatic Baeyer-Villiger Catalysis: Oxygen
Activation And Intermediate Stabilization: Arg337lys
Mutant In Complex With Nadp
pdb|2YM2|A Chain A, Snapshots Of Enzymatic Baeyer-Villiger Catalysis: Oxygen
Activation And Intermediate Stabilization: Arg337lys
Mutant Reduced State With Nadp
Length = 542
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 7/77 (9%)
Query: 4 YACNNNQSNNLVVYPYNFVDFYPQNANFGVVTPQSLGV-INPNLI-SPSQVLVPCNSPVF 61
+A N + N +P+ VDF Q GV+ S G+ ++P + +++ V +P F
Sbjct: 167 FAGNLYHTGN---WPHEPVDFSGQRV--GVIGTGSSGIQVSPQIAKQAAELFVFQRTPHF 221
Query: 62 LVPSFNFPLNPSVLDQM 78
VP+ N PL+P L +
Sbjct: 222 AVPARNAPLDPEFLADL 238
>pdb|1JLN|A Chain A, Crystal Structure Of The Catalytic Domain Of Protein
Tyrosine Phosphatase Ptp-SlBR7
Length = 297
Score = 29.6 bits (65), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 30/112 (26%), Positives = 44/112 (39%), Gaps = 22/112 (19%)
Query: 270 RCIKLWAKRRGVYGNLHGFLGGVHLAILVAHVCQNHPKGSLNTLV------ANFFKTYAY 323
+C+ W ++RG+YG + + GV C N+ ++ LV K Y Y
Sbjct: 141 KCVLYWPEKRGIYGKVEVLVTGV-------TECDNY---TIRNLVLKQGSHTQHVKHYWY 190
Query: 324 WPWP---TPVMLQDPMLPAAGYPSETRSLMPIRLPCSPHEYCHSNITRSTFY 372
WP TP Q P+L E R R P H C + I R+ +
Sbjct: 191 TSWPDHKTPDSAQ-PLLQLMLDVEEDRLASEGRGPVVVH--CSAGIGRTGCF 239
>pdb|2A8B|A Chain A, Crystal Structure Of The Catalytic Domain Of Human
Tyrosine Phosphatase Receptor, Type R
Length = 283
Score = 29.6 bits (65), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 29/112 (25%), Positives = 45/112 (40%), Gaps = 22/112 (19%)
Query: 270 RCIKLWAKRRGVYGNLHGFLGGVHLAILVAHVCQNHPKGSLNTLV------ANFFKTYAY 323
+C+ W ++RG+YG V + ++ + C N+ ++ LV K Y Y
Sbjct: 128 KCVLYWPEKRGIYGK-------VEVLVISVNECDNY---TIRNLVLKQGSHTQHVKHYWY 177
Query: 324 WPWP---TPVMLQDPMLPAAGYPSETRSLMPIRLPCSPHEYCHSNITRSTFY 372
WP TP Q P+L E R R P H C + I R+ +
Sbjct: 178 TSWPDHKTPDSAQ-PLLQLMLDVEEDRLASQGRGPVVVH--CSAGIGRTGCF 226
>pdb|3IYG|Q Chain Q, Ca Model Of Bovine TricCCT DERIVED FROM A 4.0 ANGSTROM
Cryo-Em Map
Length = 512
Score = 29.3 bits (64), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 22/42 (52%)
Query: 177 VLHNMLKSRPEVSEIHCVKDAKVPLMRFKFDGILIDLPYACL 218
VLH M+ + ++ VKDAK+ + FDG++ + L
Sbjct: 201 VLHGMVFKKETEGDVTSVKDAKIAVYSCPFDGMITETKGTVL 242
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
0.323 0.139 0.440
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,836,703
Number of Sequences: 62578
Number of extensions: 589150
Number of successful extensions: 1273
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1247
Number of HSP's gapped (non-prelim): 19
length of query: 444
length of database: 14,973,337
effective HSP length: 102
effective length of query: 342
effective length of database: 8,590,381
effective search space: 2937910302
effective search space used: 2937910302
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 bits)