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= 006658
(636 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 = 358 bits (918), Expect = 6e-99, Method: Compositional matrix adjust.
Identities = 196/440 (44%), Positives = 273/440 (62%), Gaps = 9/440 (2%)
Query: 4 ISTSAPTVLDVISTKELEKILVDEKLFASEEESLGRVEVLGRLDGIVKDWIKRVTMDKGI 63
IS +AP D + T++L + L +F EEE R+ +LG+L+ +VK+WI+ ++ K +
Sbjct: 26 ISLAAPKETDXLLTQKLVETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREISESKNL 85
Query: 64 SDEEQIQEANAKLFTFGSYRLGVAGPSTDIDALCVGPCYATRHDDFFGKLFRMLQETPLV 123
+ I+ K+FTFGSYRLGV DIDALCV P + R DFF + L+ V
Sbjct: 86 P-QSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDR-SDFFTSFYDKLKLQEEV 143
Query: 124 EDLTPVPDARVPVIKFKFNGVSVDLLYAQLQFSVIPEDLDSLQDSLLHNLDEQTVLSLNG 183
+DL V +A VPVIK F+G+ +D+L+A+L IPEDLD DSLL NLD + + SLNG
Sbjct: 144 KDLRAVEEAFVPVIKLXFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRXIRSLNG 203
Query: 184 CRVTDRILSLVPNIRNFRSTLRCLRFWAKRRGIYSNAMGFLGGINWALLVARVCQLYPNA 243
CRVTD IL LVPNI NFR TLR ++ WAKR IYSN +GFLGG++WA+LVAR CQLYPNA
Sbjct: 204 CRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNA 263
Query: 244 LPNVLVSRFFKIFAHWKWPNPVMLCPIQYQAMPHHVWDPRSNQRDRKHLMPIITPSYPCT 303
+ + LV +FF +F+ W+WPNPV+L + + VWDPR N DR HLMPIITP+YP
Sbjct: 264 IASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQ 323
Query: 304 NSSYNVSSTTLRIMQEEFQRAKELCEEIEAGKRTWITLFEPYHFFGSFKNYLQIHIAAKN 363
NS+YNVS +T +M EEF++ + +EI K W LFE +FF +K+Y+ + +A
Sbjct: 324 NSTYNVSVSTRMVMVEEFKQGLAITDEILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPT 383
Query: 364 AGDFRQWKGWVESRLRQLIHMIERDMGGVLQCRLYPGDF---SENSVKSSSQCHYFMGLG 420
+W G VES++R L+ +E++ L + P F EN K + + +GL
Sbjct: 384 EKQRLEWVGLVESKIRILVGSLEKNEFITL-AHVNPQSFPAPKENPDKEEFRTMWVIGLV 442
Query: 421 RKQGVSPQDGEKFDMRLTVE 440
K+ ++ E + LT +
Sbjct: 443 FKKT---ENSENLSVDLTYD 459
>pdb|1Q78|A Chain A, Crystal Structure Of Poly(A) Polymerase In Complex With
3'- Datp And Magnesium Chloride
Length = 514
Score = 357 bits (915), Expect = 1e-98, Method: Compositional matrix adjust.
Identities = 196/440 (44%), Positives = 273/440 (62%), Gaps = 9/440 (2%)
Query: 4 ISTSAPTVLDVISTKELEKILVDEKLFASEEESLGRVEVLGRLDGIVKDWIKRVTMDKGI 63
IS +AP D + T++L + L +F EEE R+ +LG+L+ +VK+WI+ ++ K +
Sbjct: 26 ISLAAPKETDXLLTQKLVETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREISESKNL 85
Query: 64 SDEEQIQEANAKLFTFGSYRLGVAGPSTDIDALCVGPCYATRHDDFFGKLFRMLQETPLV 123
+ I+ K+FTFGSYRLGV DIDALCV P + R DFF + L+ V
Sbjct: 86 P-QSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDR-SDFFTSFYDKLKLQEEV 143
Query: 124 EDLTPVPDARVPVIKFKFNGVSVDLLYAQLQFSVIPEDLDSLQDSLLHNLDEQTVLSLNG 183
+DL V +A VPVIK F+G+ +D+L+A+L IPEDLD DSLL NLD + + SLNG
Sbjct: 144 KDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRXIRSLNG 203
Query: 184 CRVTDRILSLVPNIRNFRSTLRCLRFWAKRRGIYSNAMGFLGGINWALLVARVCQLYPNA 243
CRVTD IL LVPNI NFR TLR ++ WAKR IYSN +GFLGG++WA+LVAR CQLYPNA
Sbjct: 204 CRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNA 263
Query: 244 LPNVLVSRFFKIFAHWKWPNPVMLCPIQYQAMPHHVWDPRSNQRDRKHLMPIITPSYPCT 303
+ + LV +FF +F+ W+WPNPV+L + + VWDPR N DR HLMPIITP+YP
Sbjct: 264 IASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQ 323
Query: 304 NSSYNVSSTTLRIMQEEFQRAKELCEEIEAGKRTWITLFEPYHFFGSFKNYLQIHIAAKN 363
NS+YNVS +T +M EEF++ + +EI K W LFE +FF +K+Y+ + +A
Sbjct: 324 NSTYNVSVSTRMVMVEEFKQGLAITDEILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPT 383
Query: 364 AGDFRQWKGWVESRLRQLIHMIERDMGGVLQCRLYPGDF---SENSVKSSSQCHYFMGLG 420
+W G VES++R L+ +E++ L + P F EN K + + +GL
Sbjct: 384 EKQRLEWVGLVESKIRILVGSLEKNEFITL-AHVNPQSFPAPKENPDKEEFRTMWVIGLV 442
Query: 421 RKQGVSPQDGEKFDMRLTVE 440
K+ ++ E + LT +
Sbjct: 443 FKKT---ENSENLSVDLTYD 459
>pdb|1F5A|A Chain A, Crystal Structure Of Mammalian Poly(A) Polymerase
Length = 513
Score = 343 bits (880), Expect = 2e-94, Method: Compositional matrix adjust.
Identities = 194/440 (44%), Positives = 270/440 (61%), Gaps = 9/440 (2%)
Query: 4 ISTSAPTVLDVISTKELEKILVDEKLFASEEESLGRVEVLGRLDGIVKDWIKRVTMDKGI 63
IS +AP D + T++L + L +F EEE R+ +LG+L+ +VK+WI+ ++ K +
Sbjct: 26 ISLAAPKETDCLLTQKLVETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREISESKNL 85
Query: 64 SDEEQIQEANAKLFTFGSYRLGVAGPSTDIDALCVGPCYATRHDDFFGKLFRMLQETPLV 123
+ I+ K+FTFGSYRLGV DIDALCV P + R DFF + L+ V
Sbjct: 86 P-QSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDR-SDFFTSFYDKLKLQEEV 143
Query: 124 EDLTPVPDARVPVIKFKFNGVSVDLLYAQLQFSVIPEDLDSLQDSLLHNLDEQTVLSLNG 183
+DL V +A VPVIK F+G+ +D+L+A+L IPEDLD DSLL NLD + + SLNG
Sbjct: 144 KDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNG 203
Query: 184 CRVTDRILSLVPNIRNFRSTLRCLRFWAKRRGIYSNAMGFLGGINWALLVARVCQLYPNA 243
CRVTD IL LVPNI NFR TLR ++ WAKR IYSN +GFLGG++WA LVAR CQLYPNA
Sbjct: 204 CRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAXLVARTCQLYPNA 263
Query: 244 LPNVLVSRFFKIFAHWKWPNPVMLCPIQYQAMPHHVWDPRSNQRDRKHLMPIITPSYPCT 303
+ + LV +FF +F+ W+WPNPV+L + + VWDPR N DR HL PIITP+YP
Sbjct: 264 IASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLXPIITPAYPQQ 323
Query: 304 NSSYNVSSTTLRIMQEEFQRAKELCEEIEAGKRTWITLFEPYHFFGSFKNYLQIHIAAKN 363
NS+YNVS +T + EEF++ + +EI K W LFE +FF +K+Y+ + +A
Sbjct: 324 NSTYNVSVSTRXVXVEEFKQGLAITDEILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPT 383
Query: 364 AGDFRQWKGWVESRLRQLIHMIERDMGGVLQCRLYPGDF---SENSVKSSSQCHYFMGLG 420
+W G VES++R L+ +E++ L + P F EN K + + +GL
Sbjct: 384 EKQRLEWVGLVESKIRILVGSLEKNEFITL-AHVNPQSFPAPKENPDKEEFRTXWVIGLV 442
Query: 421 RKQGVSPQDGEKFDMRLTVE 440
K+ ++ E + LT +
Sbjct: 443 FKKT---ENSENLSVDLTYD 459
>pdb|2HHP|A Chain A, Structure Of Yeast Poly(A) Polymerase In A Closed
Conformation
Length = 530
Score = 320 bits (819), Expect = 2e-87, Method: Compositional matrix adjust.
Identities = 160/383 (41%), Positives = 245/383 (63%), Gaps = 7/383 (1%)
Query: 5 STSAPTVLDVISTKELEKILVDEKLFASEEESLGRVEVLGRLDGIVKDWIKRVTMDKGIS 64
+T+A L+ +EL+K E F +E+E+ RV+VL L + + ++ V+ K +S
Sbjct: 18 ATAAENKLNDSLIQELKK----EGSFETEQETANRVQVLKILQELAQRFVYEVSKKKNMS 73
Query: 65 DEEQIQEANAKLFTFGSYRLGVAGPSTDIDALCVGPCYATRHDDFFGKLFRMLQETPLVE 124
D ++A K+FT+GSYRLGV GP +DID L V P + TR +DFF +L+E ++
Sbjct: 74 D-GMARDAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVTR-EDFFTVFDSLLRERKELD 131
Query: 125 DLTPVPDARVPVIKFKFNGVSVDLLYAQLQFSVIPEDLDSLQDSLLHNLDEQTVLSLNGC 184
++ PVPDA VP+IK KF+G+S+DL+ A+L +P L +LL NLDE+ + +LNG
Sbjct: 132 EIAPVPDAFVPIIKIKFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDEKDLRALNGT 191
Query: 185 RVTDRILSLVPNIRNFRSTLRCLRFWAKRRGIYSNAMGFLGGINWALLVARVCQLYPNAL 244
RVTD IL LVP FR LR ++ WA+RR +Y+N GF GG+ WA+LVAR+CQLYPNA
Sbjct: 192 RVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARICQLYPNAC 251
Query: 245 PNVLVSRFFKIFAHWKWPNPVMLCPIQYQAMPHHVWDPRSNQRDRKHLMPIITPSYPCTN 304
V+++RFF I + W WP PV+L PI+ + VW+P+ +DR H MP+ITP+YP
Sbjct: 252 SAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMC 311
Query: 305 SSYNVSSTTLRIMQEEFQRAKELCEEIEAGKRTWITLFEPYHFFGSFKNYLQIHIAAKNA 364
+++N++ +T +++ +EF R ++ +I + K++W LFE FF +K YL+I + +
Sbjct: 312 ATHNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLEITAYTRGS 371
Query: 365 GD-FRQWKGWVESRLRQLIHMIE 386
+ +W G VES++R L+ +E
Sbjct: 372 DEQHLKWSGLVESKVRLLVMKLE 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 = 319 bits (818), Expect = 2e-87, Method: Compositional matrix adjust.
Identities = 160/383 (41%), Positives = 245/383 (63%), Gaps = 7/383 (1%)
Query: 5 STSAPTVLDVISTKELEKILVDEKLFASEEESLGRVEVLGRLDGIVKDWIKRVTMDKGIS 64
+T+A L+ +EL+K E F +E+E+ RV+VL L + + ++ V+ K +S
Sbjct: 18 ATAAENKLNDSLIQELKK----EGSFETEQETANRVQVLKILQELAQRFVYEVSKKKNMS 73
Query: 65 DEEQIQEANAKLFTFGSYRLGVAGPSTDIDALCVGPCYATRHDDFFGKLFRMLQETPLVE 124
D ++A K+FT+GSYRLGV GP +DID L V P + TR +DFF +L+E ++
Sbjct: 74 D-GMARDAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVTR-EDFFTVFDSLLRERKELD 131
Query: 125 DLTPVPDARVPVIKFKFNGVSVDLLYAQLQFSVIPEDLDSLQDSLLHNLDEQTVLSLNGC 184
++ PVPDA VP+IK KF+G+S+DL+ A+L +P L +LL NLDE+ + +LNG
Sbjct: 132 EIAPVPDAFVPIIKIKFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDEKDLRALNGT 191
Query: 185 RVTDRILSLVPNIRNFRSTLRCLRFWAKRRGIYSNAMGFLGGINWALLVARVCQLYPNAL 244
RVTD IL LVP FR LR ++ WA+RR +Y+N GF GG+ WA+LVAR+CQLYPNA
Sbjct: 192 RVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARICQLYPNAC 251
Query: 245 PNVLVSRFFKIFAHWKWPNPVMLCPIQYQAMPHHVWDPRSNQRDRKHLMPIITPSYPCTN 304
V+++RFF I + W WP PV+L PI+ + VW+P+ +DR H MP+ITP+YP
Sbjct: 252 SAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMC 311
Query: 305 SSYNVSSTTLRIMQEEFQRAKELCEEIEAGKRTWITLFEPYHFFGSFKNYLQIHIAAKNA 364
+++N++ +T +++ +EF R ++ +I + K++W LFE FF +K YL+I + +
Sbjct: 312 ATHNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLEITAYTRGS 371
Query: 365 GD-FRQWKGWVESRLRQLIHMIE 386
+ +W G VES++R L+ +E
Sbjct: 372 DEQHLKWSGLVESKVRLLVMKLE 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 = 319 bits (818), Expect = 3e-87, Method: Compositional matrix adjust.
Identities = 160/383 (41%), Positives = 245/383 (63%), Gaps = 7/383 (1%)
Query: 5 STSAPTVLDVISTKELEKILVDEKLFASEEESLGRVEVLGRLDGIVKDWIKRVTMDKGIS 64
+T+A L+ +EL+K E F +E+E+ RV+VL L + + ++ V+ K +S
Sbjct: 18 ATAAENKLNDSLIQELKK----EGSFETEQETANRVQVLKILQELAQRFVYEVSKKKNMS 73
Query: 65 DEEQIQEANAKLFTFGSYRLGVAGPSTDIDALCVGPCYATRHDDFFGKLFRMLQETPLVE 124
D ++A K+FT+GSYRLGV GP +DID L V P + TR +DFF +L+E ++
Sbjct: 74 D-GMARDAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVTR-EDFFTVFDSLLRERKELD 131
Query: 125 DLTPVPDARVPVIKFKFNGVSVDLLYAQLQFSVIPEDLDSLQDSLLHNLDEQTVLSLNGC 184
++ PVPDA VP+IK KF+G+S+DL+ A+L +P L +LL NLDE+ + +LNG
Sbjct: 132 EIAPVPDAFVPIIKIKFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDEKDLRALNGT 191
Query: 185 RVTDRILSLVPNIRNFRSTLRCLRFWAKRRGIYSNAMGFLGGINWALLVARVCQLYPNAL 244
RVTD IL LVP FR LR ++ WA+RR +Y+N GF GG+ WA+LVAR+CQLYPNA
Sbjct: 192 RVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARICQLYPNAC 251
Query: 245 PNVLVSRFFKIFAHWKWPNPVMLCPIQYQAMPHHVWDPRSNQRDRKHLMPIITPSYPCTN 304
V+++RFF I + W WP PV+L PI+ + VW+P+ +DR H MP+ITP+YP
Sbjct: 252 SAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMC 311
Query: 305 SSYNVSSTTLRIMQEEFQRAKELCEEIEAGKRTWITLFEPYHFFGSFKNYLQIHIAAKNA 364
+++N++ +T +++ +EF R ++ +I + K++W LFE FF +K YL+I + +
Sbjct: 312 ATHNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLEITAYTRGS 371
Query: 365 GD-FRQWKGWVESRLRQLIHMIE 386
+ +W G VES++R L+ +E
Sbjct: 372 DEQHLKWSGLVESKVRLLVMKLE 394
>pdb|2Q66|A Chain A, Structure Of Yeast Poly(A) Polymerase With Atp And
Oligo(A)
Length = 525
Score = 316 bits (810), Expect = 2e-86, Method: Compositional matrix adjust.
Identities = 159/383 (41%), Positives = 244/383 (63%), Gaps = 7/383 (1%)
Query: 5 STSAPTVLDVISTKELEKILVDEKLFASEEESLGRVEVLGRLDGIVKDWIKRVTMDKGIS 64
+T+A L+ +EL+K E F +E+E+ RV+VL L + + ++ V+ K +S
Sbjct: 14 ATAAENKLNDSLIQELKK----EGSFETEQETANRVQVLKILQELAQRFVYEVSKKKNMS 69
Query: 65 DEEQIQEANAKLFTFGSYRLGVAGPSTDIDALCVGPCYATRHDDFFGKLFRMLQETPLVE 124
D ++A K+FT+GSYRLGV GP +DID L V P + TR +DFF +L+E ++
Sbjct: 70 D-GMARDAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVTR-EDFFTVFDSLLRERKELD 127
Query: 125 DLTPVPDARVPVIKFKFNGVSVDLLYAQLQFSVIPEDLDSLQDSLLHNLDEQTVLSLNGC 184
++ PVPDA VP+IK KF+G+S+ L+ A+L +P L +LL NLDE+ + +LNG
Sbjct: 128 EIAPVPDAFVPIIKIKFSGISIALICARLDQPQVPLSLTLSDKNLLRNLDEKDLRALNGT 187
Query: 185 RVTDRILSLVPNIRNFRSTLRCLRFWAKRRGIYSNAMGFLGGINWALLVARVCQLYPNAL 244
RVTD IL LVP FR LR ++ WA+RR +Y+N GF GG+ WA+LVAR+CQLYPNA
Sbjct: 188 RVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARICQLYPNAC 247
Query: 245 PNVLVSRFFKIFAHWKWPNPVMLCPIQYQAMPHHVWDPRSNQRDRKHLMPIITPSYPCTN 304
V+++RFF I + W WP PV+L PI+ + VW+P+ +DR H MP+ITP+YP
Sbjct: 248 SAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMC 307
Query: 305 SSYNVSSTTLRIMQEEFQRAKELCEEIEAGKRTWITLFEPYHFFGSFKNYLQIHIAAKNA 364
+++N++ +T +++ +EF R ++ +I + K++W LFE FF +K YL+I + +
Sbjct: 308 ATHNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLEITAYTRGS 367
Query: 365 GD-FRQWKGWVESRLRQLIHMIE 386
+ +W G VES++R L+ +E
Sbjct: 368 DEQHLKWSGLVESKVRLLVMKLE 390
>pdb|3NYB|A Chain A, Structure And Function Of The Polymerase Core Of Tramp, A
Rna Surveillance Complex
Length = 323
Score = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 41/196 (20%), Positives = 73/196 (37%), Gaps = 39/196 (19%)
Query: 73 NAKLFTFGSYRLGVAGPSTDIDALCVGPCYATRHDDFFGKLFRMLQETPLVEDLTPVPDA 132
+A L FGSY + P +DID + + L L++ L ++ V A
Sbjct: 59 DADLHVFGSYSTDLYLPGSDIDCVVTSELGGKESRNNLYSLASHLKKKNLATEVEVVAKA 118
Query: 133 RVPVIKF--KFNGVSVDLLYAQLQFSVIPEDLDSLQDSLLHNLDEQTVLSLNGCRVTDRI 190
RVP+IKF +G+ + + + E+T NG I
Sbjct: 119 RVPIIKFVEPHSGIHIAVSF------------------------ERT----NGIEAAKLI 150
Query: 191 LSLVPNIRNFRSTLRCLRFWAKRRGIYSNAMGFLGGINWALLVARVCQLYPNALPN---- 246
+ + R + ++ + R + + G LGG + LV ++P + N
Sbjct: 151 REWLDDTPGLRELVLIVKQFLHARRLNNVHTGGLGGFSIICLVFSFLHMHPRIITNEIDP 210
Query: 247 -----VLVSRFFKIFA 257
VL+ FF+++
Sbjct: 211 KDNLGVLLIEFFELYG 226
>pdb|2E73|A Chain A, Solution Structure Of The Phorbol EstersDIACYLGLYCEROL
Binding Domain Of Protein Kinase C Gamma
Length = 77
Score = 32.7 bits (73), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 6/77 (7%)
Query: 424 GVSPQDGEKFDMRLTVE-EFKSHVV-WMYSSWKQGMQIHVS----HLRCQDIPDFVFPGG 477
G S G KF R + F SH +++ KQG+Q V H RC + F PG
Sbjct: 1 GSSGSSGHKFTARFFKQPTFCSHCTDFIWGIGKQGLQCQVCSFVVHRRCHEFVTFECPGA 60
Query: 478 VRPPKSLNEKKRKRIEV 494
+ P++ + + + + +
Sbjct: 61 GKGPQTDDPRNKHKFRL 77
>pdb|1BHT|A Chain A, Nk1 Fragment Of Human Hepatocyte Growth Factor
pdb|1BHT|B Chain B, Nk1 Fragment Of Human Hepatocyte Growth Factor
Length = 176
Score = 30.4 bits (67), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 6/88 (6%)
Query: 380 QLIHMIERDMGGVLQCRLYPGDFSENSVKSSSQCHYFMGLGRKQGVSPQDGEKFDMRLTV 439
Q + R+ G C+ + D K+ QC +F GV + G +FD+
Sbjct: 35 QCANRCTRNKGLPFTCKAFVFD------KARKQCLWFPFNSMSSGVKKEFGHEFDLYENK 88
Query: 440 EEFKSHVVWMYSSWKQGMQIHVSHLRCQ 467
+ ++ ++ S+K + I S ++CQ
Sbjct: 89 DYIRNCIIGKGRSYKGTVSITKSGIKCQ 116
>pdb|1GP9|A Chain A, A New Crystal Form Of The Nk1 Splice Variant Of HgfSF
Demonstrates Extensive Hinge Movement And Suggests That
The Nk1 Dimer Originates By Domain Swapping
pdb|1GP9|B Chain B, A New Crystal Form Of The Nk1 Splice Variant Of HgfSF
Demonstrates Extensive Hinge Movement And Suggests That
The Nk1 Dimer Originates By Domain Swapping
pdb|1GP9|C Chain C, A New Crystal Form Of The Nk1 Splice Variant Of HgfSF
Demonstrates Extensive Hinge Movement And Suggests That
The Nk1 Dimer Originates By Domain Swapping
pdb|1GP9|D Chain D, A New Crystal Form Of The Nk1 Splice Variant Of HgfSF
Demonstrates Extensive Hinge Movement And Suggests That
The Nk1 Dimer Originates By Domain Swapping
Length = 177
Score = 30.0 bits (66), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 6/88 (6%)
Query: 380 QLIHMIERDMGGVLQCRLYPGDFSENSVKSSSQCHYFMGLGRKQGVSPQDGEKFDMRLTV 439
Q + R+ G C+ + D K+ QC +F GV + G +FD+
Sbjct: 36 QCANRCTRNKGLPFTCKAFVFD------KARKQCLWFPFNSMSSGVKKEFGHEFDLYENK 89
Query: 440 EEFKSHVVWMYSSWKQGMQIHVSHLRCQ 467
+ ++ ++ S+K + I S ++CQ
Sbjct: 90 DYIRNCIIGKGRSYKGTVSITKSGIKCQ 117
>pdb|1NK1|A Chain A, Nk1 Fragment Of Human Hepatocyte Growth FactorSCATTER
Factor (HgfSF) AT 2.5 ANGSTROM RESOLUTION
pdb|1NK1|B Chain B, Nk1 Fragment Of Human Hepatocyte Growth FactorSCATTER
Factor (HgfSF) AT 2.5 ANGSTROM RESOLUTION
Length = 183
Score = 30.0 bits (66), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 6/88 (6%)
Query: 380 QLIHMIERDMGGVLQCRLYPGDFSENSVKSSSQCHYFMGLGRKQGVSPQDGEKFDMRLTV 439
Q + R+ G C+ + D K+ QC +F GV + G +FD+
Sbjct: 42 QCANRCTRNKGLPFTCKAFVFD------KARKQCLWFPFNSMSSGVKKEFGHEFDLYENK 95
Query: 440 EEFKSHVVWMYSSWKQGMQIHVSHLRCQ 467
+ ++ ++ S+K + I S ++CQ
Sbjct: 96 DYIRNCIIGKGRSYKGTVSITKSGIKCQ 123
>pdb|3MKP|A Chain A, Crystal Structure Of 1k1 Mutant Of Hepatocyte Growth
FactorSCATTER Factor Fragment Nk1 In Complex With
Heparin
pdb|3MKP|B Chain B, Crystal Structure Of 1k1 Mutant Of Hepatocyte Growth
FactorSCATTER Factor Fragment Nk1 In Complex With
Heparin
pdb|3MKP|C Chain C, Crystal Structure Of 1k1 Mutant Of Hepatocyte Growth
FactorSCATTER Factor Fragment Nk1 In Complex With
Heparin
pdb|3MKP|D Chain D, Crystal Structure Of 1k1 Mutant Of Hepatocyte Growth
FactorSCATTER Factor Fragment Nk1 In Complex With
Heparin
Length = 183
Score = 29.6 bits (65), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 6/88 (6%)
Query: 380 QLIHMIERDMGGVLQCRLYPGDFSENSVKSSSQCHYFMGLGRKQGVSPQDGEKFDMRLTV 439
Q + R+ G C+ + D K+ QC +F GV + G +FD+
Sbjct: 42 QCANRCTRNKGLPFTCKAFVFD------KARKQCLWFPFNSMSSGVKKEFGHEFDLYENK 95
Query: 440 EEFKSHVVWMYSSWKQGMQIHVSHLRCQ 467
+ ++ ++ S+K + I S ++CQ
Sbjct: 96 DYIRNCIIGEGESYKGTVSITKSGIKCQ 123
>pdb|2QJ2|A Chain A, A Mechanistic Basis For Converting A Receptor Tyrosine
Kinase Agonist To An Antagonist
pdb|2QJ2|B Chain B, A Mechanistic Basis For Converting A Receptor Tyrosine
Kinase Agonist To An Antagonist
Length = 184
Score = 29.6 bits (65), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 6/88 (6%)
Query: 380 QLIHMIERDMGGVLQCRLYPGDFSENSVKSSSQCHYFMGLGRKQGVSPQDGEKFDMRLTV 439
Q + R+ G C+ + D K+ QC +F GV + G +FD+
Sbjct: 44 QCANRCTRNKGLPFTCKAFVFD------KARKQCLWFPFNSMSSGVKKEFGHEFDLYENK 97
Query: 440 EEFKSHVVWMYSSWKQGMQIHVSHLRCQ 467
+ ++ ++ S+K + I S ++CQ
Sbjct: 98 DYIRNCIIGKGRSYKGTVSITKSGIKCQ 125
>pdb|3PFQ|A Chain A, Crystal Structure And Allosteric Activation Of Protein
Kinase C Beta Ii
Length = 674
Score = 29.3 bits (64), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 25/102 (24%), Positives = 45/102 (44%), Gaps = 11/102 (10%)
Query: 399 PGDFSENSVKSSSQCHYFMGLGRKQGVSPQDGEKFDMRLTVE-EFKSHVV-WMYSSWKQG 456
P + E++V+ + + G R++ V KF R + F SH +++ KQG
Sbjct: 11 PSEGEESTVRFARK-----GALRQKNVHEVKNHKFTARFFKQPTFCSHCTDFIWGFGKQG 65
Query: 457 MQIHVS----HLRCQDIPDFVFPGGVRPPKSLNEKKRKRIEV 494
Q V H RC + F PG + P S + + + + ++
Sbjct: 66 FQCQVCSFVVHKRCHEFVTFSCPGADKGPASDDPRSKHKFKI 107
>pdb|1GMN|A Chain A, Crystal Structures Of Nk1-Heparin Complexes Reveal The
Basis For Nk1 Activity And Enable Engineering Of Potent
Agonists Of The Met Receptor
pdb|1GMN|B Chain B, Crystal Structures Of Nk1-Heparin Complexes Reveal The
Basis For Nk1 Activity And Enable Engineering Of Potent
Agonists Of The Met Receptor
pdb|1GMO|A Chain A, Crystal Structures Of Nk1-Heparin Complexes Reveal The
Basis For Nk1 Activity And Enable Engineering Of Potent
Agonists Of The Met Receptor
pdb|1GMO|B Chain B, Crystal Structures Of Nk1-Heparin Complexes Reveal The
Basis For Nk1 Activity And Enable Engineering Of Potent
Agonists Of The Met Receptor
pdb|1GMO|C Chain C, Crystal Structures Of Nk1-Heparin Complexes Reveal The
Basis For Nk1 Activity And Enable Engineering Of Potent
Agonists Of The Met Receptor
pdb|1GMO|D Chain D, Crystal Structures Of Nk1-Heparin Complexes Reveal The
Basis For Nk1 Activity And Enable Engineering Of Potent
Agonists Of The Met Receptor
pdb|1GMO|E Chain E, Crystal Structures Of Nk1-Heparin Complexes Reveal The
Basis For Nk1 Activity And Enable Engineering Of Potent
Agonists Of The Met Receptor
pdb|1GMO|F Chain F, Crystal Structures Of Nk1-Heparin Complexes Reveal The
Basis For Nk1 Activity And Enable Engineering Of Potent
Agonists Of The Met Receptor
pdb|1GMO|G Chain G, Crystal Structures Of Nk1-Heparin Complexes Reveal The
Basis For Nk1 Activity And Enable Engineering Of Potent
Agonists Of The Met Receptor
pdb|1GMO|H Chain H, Crystal Structures Of Nk1-Heparin Complexes Reveal The
Basis For Nk1 Activity And Enable Engineering Of Potent
Agonists Of The Met Receptor
Length = 183
Score = 28.9 bits (63), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 20/88 (22%), Positives = 37/88 (42%), Gaps = 6/88 (6%)
Query: 380 QLIHMIERDMGGVLQCRLYPGDFSENSVKSSSQCHYFMGLGRKQGVSPQDGEKFDMRLTV 439
Q R+ G C+ + D K+ QC +F GV + G +FD+
Sbjct: 42 QCADRCTRNKGLPFTCKAFVFD------KARKQCLWFPFNSMSSGVKKEFGHEFDLYENK 95
Query: 440 EEFKSHVVWMYSSWKQGMQIHVSHLRCQ 467
+ ++ ++ S+K + I S ++CQ
Sbjct: 96 DYIRNCIIGKGRSYKGTVSITKSGIKCQ 123
>pdb|3SP8|A Chain A, Crystal Structure Of Nk2 In Complex With Fractionated
Heparin Dp10
pdb|3SP8|B Chain B, Crystal Structure Of Nk2 In Complex With Fractionated
Heparin Dp10
Length = 264
Score = 28.9 bits (63), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 6/88 (6%)
Query: 380 QLIHMIERDMGGVLQCRLYPGDFSENSVKSSSQCHYFMGLGRKQGVSPQDGEKFDMRLTV 439
Q + R+ G C+ + D K+ QC +F GV + G +FD+
Sbjct: 44 QCANRCTRNKGLPFTCKAFVFD------KARKQCLWFPFNSMSSGVKKEFGHEFDLYENK 97
Query: 440 EEFKSHVVWMYSSWKQGMQIHVSHLRCQ 467
+ ++ ++ S+K + I S ++CQ
Sbjct: 98 DYIRNCIIGKGRSYKGTVSITKSDIKCQ 125
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
0.321 0.136 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,264,266
Number of Sequences: 62578
Number of extensions: 692704
Number of successful extensions: 1263
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: 1226
Number of HSP's gapped (non-prelim): 25
length of query: 636
length of database: 14,973,337
effective HSP length: 105
effective length of query: 531
effective length of database: 8,402,647
effective search space: 4461805557
effective search space used: 4461805557
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)