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= psy18158
(654 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 = 635 bits (1637), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 309/522 (59%), Positives = 382/522 (73%), Gaps = 28/522 (5%)
Query: 19 GKPQSQAPVT-YGMTTALNLSPPNQLDLQRTRELAECLKPYNVSETDEELSSRMEVLSKL 77
G Q+Q P YG+T+ ++L+ P + D T++L E LKP+ V E +EEL R+ +L KL
Sbjct: 9 GSQQTQPPQKHYGITSPISLAAPKETDXLLTQKLVETLKPFGVFEEEEELQRRILILGKL 68
Query: 78 NNLVKEWIKEVSIAKNIPPTVAEKVGGKIYTFGSYRLGVHHKGADIDALCVAPRHVDRAD 137
NNLVKEWI+E+S +KN+P +V E VGGKI+TFGSYRLGVH KGADIDALCVAPRHVDR+D
Sbjct: 69 NNLVKEWIREISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSD 128
Query: 138 YFSSFFEKLKTVDEVTDLRAVEEAFVPVIKMNFDGIEIDMLFARLALKEIPXXXXXXXXX 197
+F+SF++KLK +EV DLRAVEEAFVPVIK+ FDGIEID+LFARLAL+ IP
Sbjct: 129 FFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLXFDGIEIDILFARLALQTIPEDLDLRDDS 188
Query: 198 XXXXXXQKCVRSLNGCRVTDEILRLVPNIENFRLALRTIKLWAKKHGIYSNVLGYLGGVS 257
+ +RSLNGCRVTDEIL LVPNI+NFRL LR IKLWAK+H IYSN+LG+LGGVS
Sbjct: 189 LLKNLDIRXIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVS 248
Query: 258 WAMLVARICQLYPNAAASTLVCKFFLVFSQWKWPQPVLLKKPDNVNLGFPVWDPRVNVAD 317
WAMLVAR CQLYPNA ASTLV KFFLVFS+W+WP PVLLK+P+ NL PVWDPRVN +D
Sbjct: 249 WAMLVARTCQLYPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSD 308
Query: 318 RYHLMPIITPAYPQQNSTFNVSISTRTIMQEEFKQGKTISEDIYNGKTMWDKLFETPNFF 377
RYHLMPIITPAYPQQNST+NVS+STR +M EEFKQG I+++I K W KLFE PNFF
Sbjct: 309 RYHLMPIITPAYPQQNSTYNVSVSTRMVMVEEFKQGLAITDEILLSKAEWSKLFEAPNFF 368
Query: 378 TKYRHYLVLIASSVSAEDQLEWCGLIESKVRHLIGNLERNPHINLAHVNPECYTDTTGVI 437
KY+HY+VL+AS+ + + +LEW GL+ESK+R L+G+LE+N I LAHVNP+ +
Sbjct: 369 QKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFP------ 422
Query: 438 ANGSGSPEITAEGKEEGGENTSPPVSGVASMWFIGLDFI----AANVILNLTYDIQHFTN 493
+P +MW IGL F + N+ ++LTYDIQ FT+
Sbjct: 423 -----------------APKENPDKEEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTD 465
Query: 494 AVHWQATQSKMMKDGMKIEVRHVKKKQLSEYLPAHMLKKDKK 535
V+ QA SKM + MKI HVK+KQL + LP+H+L+K KK
Sbjct: 466 TVYRQAINSKMFEVDMKIAAMHVKRKQLHQLLPSHVLQKKKK 507
>pdb|1Q78|A Chain A, Crystal Structure Of Poly(A) Polymerase In Complex With
3'- Datp And Magnesium Chloride
Length = 514
Score = 634 bits (1634), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 309/522 (59%), Positives = 382/522 (73%), Gaps = 28/522 (5%)
Query: 19 GKPQSQAPVT-YGMTTALNLSPPNQLDLQRTRELAECLKPYNVSETDEELSSRMEVLSKL 77
G Q+Q P YG+T+ ++L+ P + D T++L E LKP+ V E +EEL R+ +L KL
Sbjct: 9 GSQQTQPPQKHYGITSPISLAAPKETDXLLTQKLVETLKPFGVFEEEEELQRRILILGKL 68
Query: 78 NNLVKEWIKEVSIAKNIPPTVAEKVGGKIYTFGSYRLGVHHKGADIDALCVAPRHVDRAD 137
NNLVKEWI+E+S +KN+P +V E VGGKI+TFGSYRLGVH KGADIDALCVAPRHVDR+D
Sbjct: 69 NNLVKEWIREISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSD 128
Query: 138 YFSSFFEKLKTVDEVTDLRAVEEAFVPVIKMNFDGIEIDMLFARLALKEIPXXXXXXXXX 197
+F+SF++KLK +EV DLRAVEEAFVPVIK+ FDGIEID+LFARLAL+ IP
Sbjct: 129 FFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDS 188
Query: 198 XXXXXXQKCVRSLNGCRVTDEILRLVPNIENFRLALRTIKLWAKKHGIYSNVLGYLGGVS 257
+ +RSLNGCRVTDEIL LVPNI+NFRL LR IKLWAK+H IYSN+LG+LGGVS
Sbjct: 189 LLKNLDIRXIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVS 248
Query: 258 WAMLVARICQLYPNAAASTLVCKFFLVFSQWKWPQPVLLKKPDNVNLGFPVWDPRVNVAD 317
WAMLVAR CQLYPNA ASTLV KFFLVFS+W+WP PVLLK+P+ NL PVWDPRVN +D
Sbjct: 249 WAMLVARTCQLYPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSD 308
Query: 318 RYHLMPIITPAYPQQNSTFNVSISTRTIMQEEFKQGKTISEDIYNGKTMWDKLFETPNFF 377
RYHLMPIITPAYPQQNST+NVS+STR +M EEFKQG I+++I K W KLFE PNFF
Sbjct: 309 RYHLMPIITPAYPQQNSTYNVSVSTRMVMVEEFKQGLAITDEILLSKAEWSKLFEAPNFF 368
Query: 378 TKYRHYLVLIASSVSAEDQLEWCGLIESKVRHLIGNLERNPHINLAHVNPECYTDTTGVI 437
KY+HY+VL+AS+ + + +LEW GL+ESK+R L+G+LE+N I LAHVNP+ +
Sbjct: 369 QKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFP------ 422
Query: 438 ANGSGSPEITAEGKEEGGENTSPPVSGVASMWFIGLDFI----AANVILNLTYDIQHFTN 493
+P +MW IGL F + N+ ++LTYDIQ FT+
Sbjct: 423 -----------------APKENPDKEEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTD 465
Query: 494 AVHWQATQSKMMKDGMKIEVRHVKKKQLSEYLPAHMLKKDKK 535
V+ QA SKM + MKI HVK+KQL + LP+H+L+K KK
Sbjct: 466 TVYRQAINSKMFEVDMKIAAMHVKRKQLHQLLPSHVLQKKKK 507
>pdb|1F5A|A Chain A, Crystal Structure Of Mammalian Poly(A) Polymerase
Length = 513
Score = 608 bits (1568), Expect = e-174, Method: Compositional matrix adjust.
Identities = 304/522 (58%), Positives = 377/522 (72%), Gaps = 28/522 (5%)
Query: 19 GKPQSQAPVT-YGMTTALNLSPPNQLDLQRTRELAECLKPYNVSETDEELSSRMEVLSKL 77
G Q+Q P YG+T+ ++L+ P + D T++L E LKP+ V E +EEL R+ +L KL
Sbjct: 9 GSQQTQPPQKHYGITSPISLAAPKETDCLLTQKLVETLKPFGVFEEEEELQRRILILGKL 68
Query: 78 NNLVKEWIKEVSIAKNIPPTVAEKVGGKIYTFGSYRLGVHHKGADIDALCVAPRHVDRAD 137
NNLVKEWI+E+S +KN+P +V E VGGKI+TFGSYRLGVH KGADIDALCVAPRHVDR+D
Sbjct: 69 NNLVKEWIREISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSD 128
Query: 138 YFSSFFEKLKTVDEVTDLRAVEEAFVPVIKMNFDGIEIDMLFARLALKEIPXXXXXXXXX 197
+F+SF++KLK +EV DLRAVEEAFVPVIK+ FDGIEID+LFARLAL+ IP
Sbjct: 129 FFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDS 188
Query: 198 XXXXXXQKCVRSLNGCRVTDEILRLVPNIENFRLALRTIKLWAKKHGIYSNVLGYLGGVS 257
+C+RSLNGCRVTDEIL LVPNI+NFRL LR IKLWAK+H IYSN+LG+LGGVS
Sbjct: 189 LLKNLDIRCIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVS 248
Query: 258 WAMLVARICQLYPNAAASTLVCKFFLVFSQWKWPQPVLLKKPDNVNLGFPVWDPRVNVAD 317
WA LVAR CQLYPNA ASTLV KFFLVFS+W+WP PVLLK+P+ NL PVWDPRVN +D
Sbjct: 249 WAXLVARTCQLYPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSD 308
Query: 318 RYHLMPIITPAYPQQNSTFNVSISTRTIMQEEFKQGKTISEDIYNGKTMWDKLFETPNFF 377
RYHL PIITPAYPQQNST+NVS+STR + EEFKQG I+++I K W KLFE PNFF
Sbjct: 309 RYHLXPIITPAYPQQNSTYNVSVSTRXVXVEEFKQGLAITDEILLSKAEWSKLFEAPNFF 368
Query: 378 TKYRHYLVLIASSVSAEDQLEWCGLIESKVRHLIGNLERNPHINLAHVNPECYTDTTGVI 437
KY+HY+VL+AS+ + + +LEW GL+ESK+R L+G+LE+N I LAHVNP+ +
Sbjct: 369 QKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFP------ 422
Query: 438 ANGSGSPEITAEGKEEGGENTSPPVSGVASMWFIGLDFI----AANVILNLTYDIQHFTN 493
+P + W IGL F + N+ ++LTYDIQ FT+
Sbjct: 423 -----------------APKENPDKEEFRTXWVIGLVFKKTENSENLSVDLTYDIQSFTD 465
Query: 494 AVHWQATQSKMMKDGMKIEVRHVKKKQLSEYLPAHMLKKDKK 535
V+ QA SK + KI HVK+KQL + LP+H+L+K KK
Sbjct: 466 TVYRQAINSKXFEVDXKIAAXHVKRKQLHQLLPSHVLQKKKK 507
>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 = 360 bits (925), Expect = 1e-99, Method: Compositional matrix adjust.
Identities = 190/467 (40%), Positives = 281/467 (60%), Gaps = 21/467 (4%)
Query: 28 TYGMTTALNLSPPNQLDLQRTRELAECLKPYNVSETDEELSSRMEVLSKLNNLVKEWIKE 87
+G+T ++ + + L + LK ET++E ++R++VL L L + ++ E
Sbjct: 6 VFGITGPVSTVGATAAENKLNDSLIQELKKEGSFETEQETANRVQVLKILQELAQRFVYE 65
Query: 88 VSIAKNIPPTVAEKVGGKIYTFGSYRLGVHHKGADIDALCVAPRHVDRADYFSSFFEKLK 147
VS KN+ +A GGKI+T+GSYRLGVH G+DID L V P+HV R D+F+ F L+
Sbjct: 66 VSKKKNMSDGMARDAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVTREDFFTVFDSLLR 125
Query: 148 TVDEVTDLRAVEEAFVPVIKMNFDGIEIDMLFARLALKEIPXXXXXXXXXXXXXXXQKCV 207
E+ ++ V +AFVP+IK+ F GI ID++ ARL ++P +K +
Sbjct: 126 ERKELDEIAPVPDAFVPIIKIKFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDEKDL 185
Query: 208 RSLNGCRVTDEILRLVPNIENFRLALRTIKLWAKKHGIYSNVLGYLGGVSWAMLVARICQ 267
R+LNG RVTDEIL LVP FR+ALR IKLWA++ +Y+N+ G+ GGV+WAMLVARICQ
Sbjct: 186 RALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARICQ 245
Query: 268 LYPNAAASTLVCKFFLVFSQWKWPQPVLLKKPDNVNLGFPVWDPRVNVADRYHLMPIITP 327
LYPNA ++ ++ +FF++ S+W WPQPV+LK ++ L VW+P++ DR H MP+ITP
Sbjct: 246 LYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITP 305
Query: 328 AYPQQNSTFNVSISTRTIMQEEFKQGKTISEDIYNGKTMWDKLFETPNFFTKYRHYLVLI 387
AYP +T N++ ST+ ++ +EF +G I+ DI++ K W LFE +FF +Y+ YL +
Sbjct: 306 AYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLEIT 365
Query: 388 ASSVSAEDQ-LEWCGLIESKVRHLIGNLERNPHINLAHVNPE-------CYT-DTTGVIA 438
A + +++Q L+W GL+ESKVR L+ LE I +AH + C T D +I
Sbjct: 366 AYTRGSDEQHLKWSGLVESKVRLLVMKLEVLAGIKIAHPFTKPFESSYCCPTEDDYEMIQ 425
Query: 439 NGSGSPE----------ITAEGKEEGGENTSPPVSGVASMWFIGLDF 475
+ GS + +T E KEE +P S +IGLDF
Sbjct: 426 DKYGSHKTETALNALKLVTDENKEEESIKDAP--KAYLSTMYIGLDF 470
>pdb|2HHP|A Chain A, Structure Of Yeast Poly(A) Polymerase In A Closed
Conformation
Length = 530
Score = 360 bits (924), Expect = 1e-99, Method: Compositional matrix adjust.
Identities = 190/467 (40%), Positives = 281/467 (60%), Gaps = 21/467 (4%)
Query: 28 TYGMTTALNLSPPNQLDLQRTRELAECLKPYNVSETDEELSSRMEVLSKLNNLVKEWIKE 87
+G+T ++ + + L + LK ET++E ++R++VL L L + ++ E
Sbjct: 6 VFGITGPVSTVGATAAENKLNDSLIQELKKEGSFETEQETANRVQVLKILQELAQRFVYE 65
Query: 88 VSIAKNIPPTVAEKVGGKIYTFGSYRLGVHHKGADIDALCVAPRHVDRADYFSSFFEKLK 147
VS KN+ +A GGKI+T+GSYRLGVH G+DID L V P+HV R D+F+ F L+
Sbjct: 66 VSKKKNMSDGMARDAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVTREDFFTVFDSLLR 125
Query: 148 TVDEVTDLRAVEEAFVPVIKMNFDGIEIDMLFARLALKEIPXXXXXXXXXXXXXXXQKCV 207
E+ ++ V +AFVP+IK+ F GI ID++ ARL ++P +K +
Sbjct: 126 ERKELDEIAPVPDAFVPIIKIKFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDEKDL 185
Query: 208 RSLNGCRVTDEILRLVPNIENFRLALRTIKLWAKKHGIYSNVLGYLGGVSWAMLVARICQ 267
R+LNG RVTDEIL LVP FR+ALR IKLWA++ +Y+N+ G+ GGV+WAMLVARICQ
Sbjct: 186 RALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARICQ 245
Query: 268 LYPNAAASTLVCKFFLVFSQWKWPQPVLLKKPDNVNLGFPVWDPRVNVADRYHLMPIITP 327
LYPNA ++ ++ +FF++ S+W WPQPV+LK ++ L VW+P++ DR H MP+ITP
Sbjct: 246 LYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITP 305
Query: 328 AYPQQNSTFNVSISTRTIMQEEFKQGKTISEDIYNGKTMWDKLFETPNFFTKYRHYLVLI 387
AYP +T N++ ST+ ++ +EF +G I+ DI++ K W LFE +FF +Y+ YL +
Sbjct: 306 AYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLEIT 365
Query: 388 ASSVSAEDQ-LEWCGLIESKVRHLIGNLERNPHINLAHVNPE-------CYT-DTTGVIA 438
A + +++Q L+W GL+ESKVR L+ LE I +AH + C T D +I
Sbjct: 366 AYTRGSDEQHLKWSGLVESKVRLLVMKLEVLAGIKIAHPFTKPFESSYCCPTEDDYEMIQ 425
Query: 439 NGSGSPE----------ITAEGKEEGGENTSPPVSGVASMWFIGLDF 475
+ GS + +T E KEE +P S +IGLDF
Sbjct: 426 DKYGSHKTETALNALKLVTDENKEEESIKDAP--KAYLSTMYIGLDF 470
>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 = 360 bits (923), Expect = 2e-99, Method: Compositional matrix adjust.
Identities = 190/467 (40%), Positives = 281/467 (60%), Gaps = 21/467 (4%)
Query: 28 TYGMTTALNLSPPNQLDLQRTRELAECLKPYNVSETDEELSSRMEVLSKLNNLVKEWIKE 87
+G+T ++ + + L + LK ET++E ++R++VL L L + ++ E
Sbjct: 6 VFGITGPVSTVGATAAENKLNDSLIQELKKEGSFETEQETANRVQVLKILQELAQRFVYE 65
Query: 88 VSIAKNIPPTVAEKVGGKIYTFGSYRLGVHHKGADIDALCVAPRHVDRADYFSSFFEKLK 147
VS KN+ +A GGKI+T+GSYRLGVH G+DID L V P+HV R D+F+ F L+
Sbjct: 66 VSKKKNMSDGMARDAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVTREDFFTVFDSLLR 125
Query: 148 TVDEVTDLRAVEEAFVPVIKMNFDGIEIDMLFARLALKEIPXXXXXXXXXXXXXXXQKCV 207
E+ ++ V +AFVP+IK+ F GI ID++ ARL ++P +K +
Sbjct: 126 ERKELDEIAPVPDAFVPIIKIKFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDEKDL 185
Query: 208 RSLNGCRVTDEILRLVPNIENFRLALRTIKLWAKKHGIYSNVLGYLGGVSWAMLVARICQ 267
R+LNG RVTDEIL LVP FR+ALR IKLWA++ +Y+N+ G+ GGV+WAMLVARICQ
Sbjct: 186 RALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARICQ 245
Query: 268 LYPNAAASTLVCKFFLVFSQWKWPQPVLLKKPDNVNLGFPVWDPRVNVADRYHLMPIITP 327
LYPNA ++ ++ +FF++ S+W WPQPV+LK ++ L VW+P++ DR H MP+ITP
Sbjct: 246 LYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITP 305
Query: 328 AYPQQNSTFNVSISTRTIMQEEFKQGKTISEDIYNGKTMWDKLFETPNFFTKYRHYLVLI 387
AYP +T N++ ST+ ++ +EF +G I+ DI++ K W LFE +FF +Y+ YL +
Sbjct: 306 AYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLEIT 365
Query: 388 ASSVSAEDQ-LEWCGLIESKVRHLIGNLERNPHINLAHVNPE-------CYT-DTTGVIA 438
A + +++Q L+W GL+ESKVR L+ LE I +AH + C T D +I
Sbjct: 366 AYTRGSDEQHLKWSGLVESKVRLLVMKLEVLAGIKIAHPFTKPFESSYCCPTEDDYEMIQ 425
Query: 439 NGSGSPE----------ITAEGKEEGGENTSPPVSGVASMWFIGLDF 475
+ GS + +T E KEE +P S +IGLDF
Sbjct: 426 DKYGSHKTETALNALKLVTDENKEEESIKDAP--KAYLSTMYIGLDF 470
>pdb|2Q66|A Chain A, Structure Of Yeast Poly(A) Polymerase With Atp And
Oligo(A)
Length = 525
Score = 357 bits (916), Expect = 1e-98, Method: Compositional matrix adjust.
Identities = 189/467 (40%), Positives = 280/467 (59%), Gaps = 21/467 (4%)
Query: 28 TYGMTTALNLSPPNQLDLQRTRELAECLKPYNVSETDEELSSRMEVLSKLNNLVKEWIKE 87
+G+T ++ + + L + LK ET++E ++R++VL L L + ++ E
Sbjct: 2 VFGITGPVSTVGATAAENKLNDSLIQELKKEGSFETEQETANRVQVLKILQELAQRFVYE 61
Query: 88 VSIAKNIPPTVAEKVGGKIYTFGSYRLGVHHKGADIDALCVAPRHVDRADYFSSFFEKLK 147
VS KN+ +A GGKI+T+GSYRLGVH G+DID L V P+HV R D+F+ F L+
Sbjct: 62 VSKKKNMSDGMARDAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVTREDFFTVFDSLLR 121
Query: 148 TVDEVTDLRAVEEAFVPVIKMNFDGIEIDMLFARLALKEIPXXXXXXXXXXXXXXXQKCV 207
E+ ++ V +AFVP+IK+ F GI I ++ ARL ++P +K +
Sbjct: 122 ERKELDEIAPVPDAFVPIIKIKFSGISIALICARLDQPQVPLSLTLSDKNLLRNLDEKDL 181
Query: 208 RSLNGCRVTDEILRLVPNIENFRLALRTIKLWAKKHGIYSNVLGYLGGVSWAMLVARICQ 267
R+LNG RVTDEIL LVP FR+ALR IKLWA++ +Y+N+ G+ GGV+WAMLVARICQ
Sbjct: 182 RALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARICQ 241
Query: 268 LYPNAAASTLVCKFFLVFSQWKWPQPVLLKKPDNVNLGFPVWDPRVNVADRYHLMPIITP 327
LYPNA ++ ++ +FF++ S+W WPQPV+LK ++ L VW+P++ DR H MP+ITP
Sbjct: 242 LYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITP 301
Query: 328 AYPQQNSTFNVSISTRTIMQEEFKQGKTISEDIYNGKTMWDKLFETPNFFTKYRHYLVLI 387
AYP +T N++ ST+ ++ +EF +G I+ DI++ K W LFE +FF +Y+ YL +
Sbjct: 302 AYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLEIT 361
Query: 388 ASSVSAEDQ-LEWCGLIESKVRHLIGNLERNPHINLAHVNPE-------CYT-DTTGVIA 438
A + +++Q L+W GL+ESKVR L+ LE I +AH + C T D +I
Sbjct: 362 AYTRGSDEQHLKWSGLVESKVRLLVMKLEVLAGIKIAHPFTKPFESSYCCPTEDDYEMIQ 421
Query: 439 NGSGSPE----------ITAEGKEEGGENTSPPVSGVASMWFIGLDF 475
+ GS + +T E KEE +P S +IGLDF
Sbjct: 422 DKYGSHKTETALNALKLVTDENKEEESIKDAP--KAYLSTMYIGLDF 466
>pdb|3NYB|A Chain A, Structure And Function Of The Polymerase Core Of Tramp, A
Rna Surveillance Complex
Length = 323
Score = 36.2 bits (82), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 52/246 (21%), Positives = 91/246 (36%), Gaps = 53/246 (21%)
Query: 86 KEVSIAKNIPPTVAEKV-----GGKIYTFGSYRLGVHHKGADIDALCVAPRHV---DRAD 137
+E+ I T+ E V ++ FGSY ++ G+DID CV + + +
Sbjct: 37 EEIEIRNQTISTIREAVKQLWPDADLHVFGSYSTDLYLPGSDID--CVVTSELGGKESRN 94
Query: 138 YFSSFFEKLKTVDEVTDLRAVEEAFVPVIKM--NFDGIEIDMLFARLALKEIPXXXXXXX 195
S LK + T++ V +A VP+IK GI I + F R
Sbjct: 95 NLYSLASHLKKKNLATEVEVVAKARVPIIKFVEPHSGIHIAVSFER-------------- 140
Query: 196 XXXXXXXXQKCVRSLNGCRVTDEILRLVPNIENFRLALRTIKLWAKKHGIYSNVLGYLGG 255
+ ++ E L P + L ++ + + +++ G LGG
Sbjct: 141 -----------TNGIEAAKLIREWLDDTPGLRELVLIVKQFLHARRLNNVHT---GGLGG 186
Query: 256 VSWAMLVARICQLYPNAAAS---------TLVCKFFLVFSQWKWPQPVLLKKPDNVNLGF 306
S LV ++P + L+ +FF ++ + V L D G+
Sbjct: 187 FSIICLVFSFLHMHPRIITNEIDPKDNLGVLLIEFFELYGKNFGYDDVALGSSD----GY 242
Query: 307 PVWDPR 312
PV+ P+
Sbjct: 243 PVYFPK 248
>pdb|3K7X|A Chain A, Crystal Structure Of The Lin0763 Protein From Listeria
Innocua. Northeast Structural Genomics Consortium Target
Lkr23
Length = 349
Score = 30.0 bits (66), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 28/120 (23%), Positives = 49/120 (40%), Gaps = 17/120 (14%)
Query: 320 HLMPIITPAYPQQNSTFNVSISTRTIMQEEFKQGKTISEDIYNGKTMWDKLFETPNFFTK 379
HL+ + AY + ++ ++ +T + + + G T+ D Y+ +W+ L
Sbjct: 50 HLVEVRLDAYLRTKKQADLEVAEKTYLHNKNRNGGTLIHDFYD-DXLWNAL-------AA 101
Query: 380 YRHYLVLIASSVSAED-QLEWCGLIESKVRHLIGNLERNPHINLAHVNPECYTDTTGVIA 438
YR Y S+ ED QL W L+++ + G A P+ Y T V A
Sbjct: 102 YRLYKA-TGKSIYLEDAQLVWQDLVDTGWNDIXGG-------GFAWRRPQXYYKNTPVNA 153
>pdb|1B3Q|A Chain A, Crystal Structure Of Chea-289, A Signal Transducing
Histidine Kinase
pdb|1B3Q|B Chain B, Crystal Structure Of Chea-289, A Signal Transducing
Histidine Kinase
Length = 379
Score = 29.3 bits (64), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 17/40 (42%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 42 QLDLQRTRELAECLKPYNVSETDEELSSRMEVLSKLNNLV 81
+L + R+R L E LK YN+ E DE LS + L N+V
Sbjct: 20 ELVIARSRIL-ETLKKYNIKELDESLSHLSRITLDLQNVV 58
>pdb|2YIB|A Chain A, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus
pdb|2YIB|B Chain B, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus
pdb|2YIB|C Chain C, Structure Of The Rna Polymerase Vp1 From Infectious
Pancreatic Necrosis Virus
pdb|3ZED|A Chain A, X-ray Structure Of The Birnavirus Vp1-vp3 Complex
pdb|3ZED|B Chain B, X-ray Structure Of The Birnavirus Vp1-vp3 Complex
pdb|3ZED|C Chain C, X-ray Structure Of The Birnavirus Vp1-vp3 Complex
Length = 853
Score = 28.9 bits (63), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 5/55 (9%)
Query: 42 QLDLQRTRELAECLKPY-----NVSETDEELSSRMEVLSKLNNLVKEWIKEVSIA 91
+L + R+ A LKP N +E EEL+ + ++L K NNL+K + E A
Sbjct: 734 KLRVSTLRDQALALKPASSSVDNWAEATEELAQQQQLLMKANNLLKSSLTETREA 788
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
0.316 0.132 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,603,458
Number of Sequences: 62578
Number of extensions: 764743
Number of successful extensions: 1606
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1583
Number of HSP's gapped (non-prelim): 21
length of query: 654
length of database: 14,973,337
effective HSP length: 105
effective length of query: 549
effective length of database: 8,402,647
effective search space: 4613053203
effective search space used: 4613053203
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)