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= 004767
(732 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 = 422 bits (1084), Expect = e-118, Method: Compositional matrix adjust.
Identities = 223/478 (46%), Positives = 304/478 (63%), Gaps = 14/478 (2%)
Query: 10 GITEPISLAGPTDDDLMRTRKLEKYLRDVNLYESQEEAVSREEVLGRLDQIVKIWVKKIS 69
GIT PISLA P + D + T+KL + L+ ++E +EE R +LG+L+ +VK W+++IS
Sbjct: 21 GITSPISLAAPKETDXLLTQKLVETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREIS 80
Query: 70 RAKGLNDQLLQEANAKIFTFGSYRLGVHGPGADIDTLCVGPRHATREEDFFGELHQMLTE 129
+K L +++ KIFTFGSYRLGVH GADID LCV PRH R DFF + L
Sbjct: 81 ESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRS-DFFTSFYDKLKL 139
Query: 130 MPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTVR 189
EV +L V +A VPV+K F G+ ID+L+ARL+L IPEDLD+ DS+L+N D + +R
Sbjct: 140 QEEVKDLRAVEEAFVPVIKLXFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRXIR 199
Query: 190 SLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQL 249
SLNGCRVTD+IL LVP I NFR TLR ++ WAKR +YSN+ GFLGG++WA+LVAR CQL
Sbjct: 200 SLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQL 259
Query: 250 YPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPA 309
YPNA+ S LV +FF V+++W WPNPVLL EE +L L VWDPR NP D+YHLMPIITPA
Sbjct: 260 YPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPA 319
Query: 310 YPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKNYLRI 369
YP NS+YNVS ST +M++EF++G I + + ++A +W LFE FF+ YK+Y+ +
Sbjct: 320 YPQQNSTYNVSVSTRMVMVEEFKQGLAITDEILLSKA--EWSKLFEAPNFFQKYKHYIVL 377
Query: 370 DISAENADDLRNWKGWVESRLRQLTLKIERHTYNML-----QCHPHPGDFSDKSKPLYCS 424
SA W G VES++R L +E++ + L Q P P + DK +
Sbjct: 378 LASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKENPDKEE-FRTM 436
Query: 425 YFMGLQRKQGVPVGEGEQFDIRLTVKEFKQAVSMYTLR----KPGMQISVAHVTRRNL 478
+ +GL K+ E D+ ++ F V + + M+I+ HV R+ L
Sbjct: 437 WVIGLVFKK-TENSENLSVDLTYDIQSFTDTVYRQAINSKMFEVDMKIAAMHVKRKQL 493
>pdb|1Q78|A Chain A, Crystal Structure Of Poly(A) Polymerase In Complex With
3'- Datp And Magnesium Chloride
Length = 514
Score = 421 bits (1081), Expect = e-118, Method: Compositional matrix adjust.
Identities = 223/478 (46%), Positives = 304/478 (63%), Gaps = 14/478 (2%)
Query: 10 GITEPISLAGPTDDDLMRTRKLEKYLRDVNLYESQEEAVSREEVLGRLDQIVKIWVKKIS 69
GIT PISLA P + D + T+KL + L+ ++E +EE R +LG+L+ +VK W+++IS
Sbjct: 21 GITSPISLAAPKETDXLLTQKLVETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREIS 80
Query: 70 RAKGLNDQLLQEANAKIFTFGSYRLGVHGPGADIDTLCVGPRHATREEDFFGELHQMLTE 129
+K L +++ KIFTFGSYRLGVH GADID LCV PRH R DFF + L
Sbjct: 81 ESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRS-DFFTSFYDKLKL 139
Query: 130 MPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTVR 189
EV +L V +A VPV+K F G+ ID+L+ARL+L IPEDLD+ DS+L+N D + +R
Sbjct: 140 QEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRXIR 199
Query: 190 SLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQL 249
SLNGCRVTD+IL LVP I NFR TLR ++ WAKR +YSN+ GFLGG++WA+LVAR CQL
Sbjct: 200 SLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQL 259
Query: 250 YPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPA 309
YPNA+ S LV +FF V+++W WPNPVLL EE +L L VWDPR NP D+YHLMPIITPA
Sbjct: 260 YPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPA 319
Query: 310 YPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKNYLRI 369
YP NS+YNVS ST +M++EF++G I + + ++A +W LFE FF+ YK+Y+ +
Sbjct: 320 YPQQNSTYNVSVSTRMVMVEEFKQGLAITDEILLSKA--EWSKLFEAPNFFQKYKHYIVL 377
Query: 370 DISAENADDLRNWKGWVESRLRQLTLKIERHTYNML-----QCHPHPGDFSDKSKPLYCS 424
SA W G VES++R L +E++ + L Q P P + DK +
Sbjct: 378 LASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKENPDKEE-FRTM 436
Query: 425 YFMGLQRKQGVPVGEGEQFDIRLTVKEFKQAVSMYTLR----KPGMQISVAHVTRRNL 478
+ +GL K+ E D+ ++ F V + + M+I+ HV R+ L
Sbjct: 437 WVIGLVFKK-TENSENLSVDLTYDIQSFTDTVYRQAINSKMFEVDMKIAAMHVKRKQL 493
>pdb|1F5A|A Chain A, Crystal Structure Of Mammalian Poly(A) Polymerase
Length = 513
Score = 402 bits (1034), Expect = e-112, Method: Compositional matrix adjust.
Identities = 220/478 (46%), Positives = 299/478 (62%), Gaps = 14/478 (2%)
Query: 10 GITEPISLAGPTDDDLMRTRKLEKYLRDVNLYESQEEAVSREEVLGRLDQIVKIWVKKIS 69
GIT PISLA P + D + T+KL + L+ ++E +EE R +LG+L+ +VK W+++IS
Sbjct: 21 GITSPISLAAPKETDCLLTQKLVETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREIS 80
Query: 70 RAKGLNDQLLQEANAKIFTFGSYRLGVHGPGADIDTLCVGPRHATREEDFFGELHQMLTE 129
+K L +++ KIFTFGSYRLGVH GADID LCV PRH R DFF + L
Sbjct: 81 ESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRS-DFFTSFYDKLKL 139
Query: 130 MPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTVR 189
EV +L V +A VPV+K F G+ ID+L+ARL+L IPEDLD+ DS+L+N D + +R
Sbjct: 140 QEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIR 199
Query: 190 SLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQL 249
SLNGCRVTD+IL LVP I NFR TLR ++ WAKR +YSN+ GFLGG++WA LVAR CQL
Sbjct: 200 SLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAXLVARTCQL 259
Query: 250 YPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITPA 309
YPNA+ S LV +FF V+++W WPNPVLL EE +L L VWDPR NP D+YHL PIITPA
Sbjct: 260 YPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLXPIITPA 319
Query: 310 YPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKNYLRI 369
YP NS+YNVS ST + ++EF++G I + + ++A +W LFE FF+ YK+Y+ +
Sbjct: 320 YPQQNSTYNVSVSTRXVXVEEFKQGLAITDEILLSKA--EWSKLFEAPNFFQKYKHYIVL 377
Query: 370 DISAENADDLRNWKGWVESRLRQLTLKIERHTYNML-----QCHPHPGDFSDKSKPLYCS 424
SA W G VES++R L +E++ + L Q P P + DK +
Sbjct: 378 LASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKENPDKEE-FRTX 436
Query: 425 YFMGLQRKQGVPVGEGEQFDIRLTVKEFKQAVSMYTLRKPGMQ----ISVAHVTRRNL 478
+ +GL K+ E D+ ++ F V + + I+ HV R+ L
Sbjct: 437 WVIGLVFKK-TENSENLSVDLTYDIQSFTDTVYRQAINSKXFEVDXKIAAXHVKRKQL 493
>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 = 371 bits (952), Expect = e-103, Method: Compositional matrix adjust.
Identities = 180/396 (45%), Positives = 265/396 (66%), Gaps = 4/396 (1%)
Query: 4 SNGQRLGITEPISLAGPTDDDLMRTRKLEKYLRDVNLYESQEEAVSREEVLGRLDQIVKI 63
S+ + GIT P+S G T + L + L+ +E+++E +R +VL L ++ +
Sbjct: 2 SSQKVFGITGPVSTVGATAAENKLNDSLIQELKKEGSFETEQETANRVQVLKILQELAQR 61
Query: 64 WVKKISRAKGLNDQLLQEANAKIFTFGSYRLGVHGPGADIDTLCVGPRHATREEDFFGEL 123
+V ++S+ K ++D + ++A KIFT+GSYRLGVHGPG+DIDTL V P+H TRE DFF
Sbjct: 62 FVYEVSKKKNMSDGMARDAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVTRE-DFFTVF 120
Query: 124 HQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLWVIPEDLDISQDSILQNA 183
+L E E+ E+ PVPDA VP++K KFSG+SIDL+ ARL +P L +S ++L+N
Sbjct: 121 DSLLRERKELDEIAPVPDAFVPIIKIKFSGISIDLICARLDQPQVPLSLTLSDKNLLRNL 180
Query: 184 DEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLV 243
DE+ +R+LNG RVTD+IL LVPK FR LR ++ WA+RR VY+N+ GF GG+ WA+LV
Sbjct: 181 DEKDLRALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLV 240
Query: 244 ARICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLM 303
ARICQLYPNA +++++RFF + ++W WP PV+L IE+G L ++VW+P+ +D+ H M
Sbjct: 241 ARICQLYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRM 300
Query: 304 PIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAY 363
P+ITPAYP M +++N++ ST ++++ EF RG +I + N+ W LFE FF Y
Sbjct: 301 PVITPAYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKK--SWANLFEKNDFFFRY 358
Query: 364 KNYLRIDISAENADDLR-NWKGWVESRLRQLTLKIE 398
K YL I +D+ W G VES++R L +K+E
Sbjct: 359 KFYLEITAYTRGSDEQHLKWSGLVESKVRLLVMKLE 394
>pdb|2HHP|A Chain A, Structure Of Yeast Poly(A) Polymerase In A Closed
Conformation
Length = 530
Score = 370 bits (951), Expect = e-102, Method: Compositional matrix adjust.
Identities = 180/396 (45%), Positives = 265/396 (66%), Gaps = 4/396 (1%)
Query: 4 SNGQRLGITEPISLAGPTDDDLMRTRKLEKYLRDVNLYESQEEAVSREEVLGRLDQIVKI 63
S+ + GIT P+S G T + L + L+ +E+++E +R +VL L ++ +
Sbjct: 2 SSQKVFGITGPVSTVGATAAENKLNDSLIQELKKEGSFETEQETANRVQVLKILQELAQR 61
Query: 64 WVKKISRAKGLNDQLLQEANAKIFTFGSYRLGVHGPGADIDTLCVGPRHATREEDFFGEL 123
+V ++S+ K ++D + ++A KIFT+GSYRLGVHGPG+DIDTL V P+H TRE DFF
Sbjct: 62 FVYEVSKKKNMSDGMARDAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVTRE-DFFTVF 120
Query: 124 HQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLWVIPEDLDISQDSILQNA 183
+L E E+ E+ PVPDA VP++K KFSG+SIDL+ ARL +P L +S ++L+N
Sbjct: 121 DSLLRERKELDEIAPVPDAFVPIIKIKFSGISIDLICARLDQPQVPLSLTLSDKNLLRNL 180
Query: 184 DEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLV 243
DE+ +R+LNG RVTD+IL LVPK FR LR ++ WA+RR VY+N+ GF GG+ WA+LV
Sbjct: 181 DEKDLRALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLV 240
Query: 244 ARICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLM 303
ARICQLYPNA +++++RFF + ++W WP PV+L IE+G L ++VW+P+ +D+ H M
Sbjct: 241 ARICQLYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRM 300
Query: 304 PIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAY 363
P+ITPAYP M +++N++ ST ++++ EF RG +I + N+ W LFE FF Y
Sbjct: 301 PVITPAYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKK--SWANLFEKNDFFFRY 358
Query: 364 KNYLRIDISAENADDLR-NWKGWVESRLRQLTLKIE 398
K YL I +D+ W G VES++R L +K+E
Sbjct: 359 KFYLEITAYTRGSDEQHLKWSGLVESKVRLLVMKLE 394
>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 = 370 bits (951), Expect = e-102, Method: Compositional matrix adjust.
Identities = 180/396 (45%), Positives = 265/396 (66%), Gaps = 4/396 (1%)
Query: 4 SNGQRLGITEPISLAGPTDDDLMRTRKLEKYLRDVNLYESQEEAVSREEVLGRLDQIVKI 63
S+ + GIT P+S G T + L + L+ +E+++E +R +VL L ++ +
Sbjct: 2 SSQKVFGITGPVSTVGATAAENKLNDSLIQELKKEGSFETEQETANRVQVLKILQELAQR 61
Query: 64 WVKKISRAKGLNDQLLQEANAKIFTFGSYRLGVHGPGADIDTLCVGPRHATREEDFFGEL 123
+V ++S+ K ++D + ++A KIFT+GSYRLGVHGPG+DIDTL V P+H TRE DFF
Sbjct: 62 FVYEVSKKKNMSDGMARDAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVTRE-DFFTVF 120
Query: 124 HQMLTEMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLWVIPEDLDISQDSILQNA 183
+L E E+ E+ PVPDA VP++K KFSG+SIDL+ ARL +P L +S ++L+N
Sbjct: 121 DSLLRERKELDEIAPVPDAFVPIIKIKFSGISIDLICARLDQPQVPLSLTLSDKNLLRNL 180
Query: 184 DEQTVRSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLV 243
DE+ +R+LNG RVTD+IL LVPK FR LR ++ WA+RR VY+N+ GF GG+ WA+LV
Sbjct: 181 DEKDLRALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLV 240
Query: 244 ARICQLYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLM 303
ARICQLYPNA +++++RFF + ++W WP PV+L IE+G L ++VW+P+ +D+ H M
Sbjct: 241 ARICQLYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRM 300
Query: 304 PIITPAYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAY 363
P+ITPAYP M +++N++ ST ++++ EF RG +I + N+ W LFE FF Y
Sbjct: 301 PVITPAYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKK--SWANLFEKNDFFFRY 358
Query: 364 KNYLRIDISAENADDLR-NWKGWVESRLRQLTLKIE 398
K YL I +D+ W G VES++R L +K+E
Sbjct: 359 KFYLEITAYTRGSDEQHLKWSGLVESKVRLLVMKLE 394
>pdb|2Q66|A Chain A, Structure Of Yeast Poly(A) Polymerase With Atp And
Oligo(A)
Length = 525
Score = 366 bits (940), Expect = e-101, Method: Compositional matrix adjust.
Identities = 178/391 (45%), Positives = 261/391 (66%), Gaps = 4/391 (1%)
Query: 9 LGITEPISLAGPTDDDLMRTRKLEKYLRDVNLYESQEEAVSREEVLGRLDQIVKIWVKKI 68
GIT P+S G T + L + L+ +E+++E +R +VL L ++ + +V ++
Sbjct: 3 FGITGPVSTVGATAAENKLNDSLIQELKKEGSFETEQETANRVQVLKILQELAQRFVYEV 62
Query: 69 SRAKGLNDQLLQEANAKIFTFGSYRLGVHGPGADIDTLCVGPRHATREEDFFGELHQMLT 128
S+ K ++D + ++A KIFT+GSYRLGVHGPG+DIDTL V P+H TRE DFF +L
Sbjct: 63 SKKKNMSDGMARDAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVTRE-DFFTVFDSLLR 121
Query: 129 EMPEVTELHPVPDAHVPVMKFKFSGVSIDLLYARLSLWVIPEDLDISQDSILQNADEQTV 188
E E+ E+ PVPDA VP++K KFSG+SI L+ ARL +P L +S ++L+N DE+ +
Sbjct: 122 ERKELDEIAPVPDAFVPIIKIKFSGISIALICARLDQPQVPLSLTLSDKNLLRNLDEKDL 181
Query: 189 RSLNGCRVTDQILRLVPKIQNFRTTLRCMRFWAKRRGVYSNVAGFLGGINWALLVARICQ 248
R+LNG RVTD+IL LVPK FR LR ++ WA+RR VY+N+ GF GG+ WA+LVARICQ
Sbjct: 182 RALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARICQ 241
Query: 249 LYPNAVPSMLVSRFFRVYTQWRWPNPVLLCAIEEGSLGLQVWDPRRNPKDKYHLMPIITP 308
LYPNA +++++RFF + ++W WP PV+L IE+G L ++VW+P+ +D+ H MP+ITP
Sbjct: 242 LYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITP 301
Query: 309 AYPCMNSSYNVSTSTLRIMMDEFQRGHEICEAMEKNEADVDWDTLFEPFTFFEAYKNYLR 368
AYP M +++N++ ST ++++ EF RG +I + N+ W LFE FF YK YL
Sbjct: 302 AYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKK--SWANLFEKNDFFFRYKFYLE 359
Query: 369 IDISAENADDLR-NWKGWVESRLRQLTLKIE 398
I +D+ W G VES++R L +K+E
Sbjct: 360 ITAYTRGSDEQHLKWSGLVESKVRLLVMKLE 390
>pdb|3NYB|A Chain A, Structure And Function Of The Polymerase Core Of Tramp, A
Rna Surveillance Complex
Length = 323
Score = 38.9 bits (89), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 2/82 (2%)
Query: 83 NAKIFTFGSYRLGVHGPGADIDTLCVGPRHATREEDFFGELHQMLTEMPEVTELHPVPDA 142
+A + FGSY ++ PG+DID + + L L + TE+ V A
Sbjct: 59 DADLHVFGSYSTDLYLPGSDIDCVVTSELGGKESRNNLYSLASHLKKKNLATEVEVVAKA 118
Query: 143 HVPVMKF--KFSGVSIDLLYAR 162
VP++KF SG+ I + + R
Sbjct: 119 RVPIIKFVEPHSGIHIAVSFER 140
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
0.318 0.134 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,994,427
Number of Sequences: 62578
Number of extensions: 864898
Number of successful extensions: 1703
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1677
Number of HSP's gapped (non-prelim): 11
length of query: 732
length of database: 14,973,337
effective HSP length: 106
effective length of query: 626
effective length of database: 8,340,069
effective search space: 5220883194
effective search space used: 5220883194
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)