Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
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.
Query= Dr_sW_027_J03
(745 letters)
Database: Non-redundant SwissProt sequences
184,735 sequences; 68,354,980 total letters
Score E
Sequences producing significant alignments: (bits) Value
sp|P21187|PABP_DROME Polyadenylate-binding protein (Poly(A)... 61 4e-09
sp|P20965|PABP1_XENLA Polyadenylate-binding protein 1 (Poly... 60 5e-09
sp|Q9EPH8|PABP1_RAT Polyadenylate-binding protein 1 (Poly(A... 55 2e-07
sp|P29341|PABP1_MOUSE Polyadenylate-binding protein 1 (Poly... 55 3e-07
sp|P11940|PABP1_HUMAN Polyadenylate-binding protein 1 (Poly... 54 3e-07
sp|Q13310|PABP4_HUMAN Polyadenylate-binding protein 4 (Poly... 52 2e-06
sp|O64380|PABP3_ARATH Polyadenylate-binding protein 3 (Poly... 52 2e-06
sp|Q9H361|PABP3_HUMAN Polyadenylate-binding protein 3 (Poly... 48 2e-05
sp|P42731|PABP2_ARATH Polyadenylate-binding protein 2 (Poly... 48 2e-05
sp|Q05196|PABP5_ARATH Polyadenylate-binding protein 5 (Poly... 39 0.011
>sp|P21187|PABP_DROME Polyadenylate-binding protein (Poly(A)-binding protein) (PABP)
Length = 634
Score = 60.8 bits (146), Expect = 4e-09
Identities = 69/244 (28%), Positives = 97/244 (39%), Gaps = 41/244 (16%)
Frame = +1
Query: 1 KPLYVALAQKKEDRVAHLRSQFQQ-----------RVHQPQPAVXXXXXXXXXXXXXXXX 147
KPLYVALAQ+KE+R AHL SQ+ + +++QP A
Sbjct: 355 KPLYVALAQRKEERKAHLASQYMRHMTGMRMQQLGQIYQPNAASGFFVPTLPSNQRFFGS 414
Query: 148 XXXARPGNILQSRW-PQNMPYIQPRNI---------------GMPANQNIMMAG----MP 267
+ N RW PQ P + + +P AG P
Sbjct: 415 QVATQMRNT--PRWVPQVRPPAAIQGVQAGAAAAGGFQGTAGAVPTQFRSAAAGARGAQP 472
Query: 268 QNQQRRNIIVDPIISQNRNARPITGNVQLNQPRPQYN--IVANGRQAGNMMYQY------ 423
Q Q +N AR ITG Q P Q +A G Q Y+Y
Sbjct: 473 QVQGTHAAAAAANNMRNTGARAITGQ-QTAAPNMQIPGAQIAGGAQQRTSNYKYTSNMRN 531
Query: 424 -PI-QDNQTMMNPDQMKMPDIESQIDLSTTSKIANADSMEAKQLLGEKIYPLVSKHAGDM 597
P+ Q +QT P Q++ + E I S +ANA E KQ+LGE++YP++ ++
Sbjct: 532 PPVPQLHQTQPIPQQLQGKNSEKLI----ASLLANAKPQEQKQILGERLYPMIEHMHANL 587
Query: 598 AGKL 609
AGK+
Sbjct: 588 AGKI 591
Score = 34.3 bits (77), Expect = 0.36
Identities = 14/21 (66%), Positives = 20/21 (95%)
Frame = +3
Query: 603 KITGMFLELDNAELLYMIENE 665
KITGM LE++N+ELL+MIE++
Sbjct: 590 KITGMLLEIENSELLHMIEDQ 610
>sp|P20965|PABP1_XENLA Polyadenylate-binding protein 1 (Poly(A)-binding protein 1) (PABP 1)
Length = 633
Score = 60.5 bits (145), Expect = 5e-09
Identities = 67/231 (29%), Positives = 90/231 (38%), Gaps = 28/231 (12%)
Frame = +1
Query: 1 KPLYVALAQKKEDRVAHLRSQFQQR---VHQPQPAVXXXXXXXXXXXXXXXXXXXAR--- 162
KPLYVALAQ+KE+R AHL +Q+ QR V P P + R
Sbjct: 361 KPLYVALAQRKEERQAHLTNQYMQRMASVRVPNPVINPYQPPPSSYFMAAIPPAQNRAAY 420
Query: 163 --PGNILQ----SRWP---------QNMPYIQPRNIGMPANQNIMMAGMPQNQQRRNIIV 297
PG I Q RW QNMP P + M Q V
Sbjct: 421 YPPGQIAQLRPSPRWTAQGARPHPFQNMPGAIRPTAPRPPTFSTMRPASNQ--------V 472
Query: 298 DPIISQNRNARPITGNVQLNQPRPQYNIVANG---RQAGNMMYQYPIQDNQTMMNPDQMK 468
++S R A T Q PRP A R Y +++ Q + Q+
Sbjct: 473 PRVMSAQRVANTST---QTMGPRPTTAAAAAASAVRAVPQYKYAAGVRNQQHLNTQPQVA 529
Query: 469 MPD----IESQIDLSTTSKIANADSMEAKQLLGEKIYPLVSKHAGDMAGKL 609
M ++ Q L T S +A A E KQ+LGE+++PL+ +AGK+
Sbjct: 530 MQQPAVHVQGQEPL-TASMLAAAPPQEQKQMLGERLFPLIQAMHPTLAGKI 579
Score = 34.3 bits (77), Expect = 0.36
Identities = 14/20 (70%), Positives = 19/20 (95%)
Frame = +3
Query: 603 KITGMFLELDNAELLYMIEN 662
KITGM LE+DN+ELL+M+E+
Sbjct: 578 KITGMLLEIDNSELLHMLES 597
>sp|Q9EPH8|PABP1_RAT Polyadenylate-binding protein 1 (Poly(A)-binding protein 1) (PABP 1)
Length = 636
Score = 55.5 bits (132), Expect = 2e-07
Identities = 62/229 (27%), Positives = 86/229 (37%), Gaps = 26/229 (11%)
Frame = +1
Query: 1 KPLYVALAQKKEDRVAHLRSQFQQRV-------------HQPQPAVXXXXXXXXXXXXXX 141
KPLYVALAQ+KE+R AHL +Q+ QR+ +QP P
Sbjct: 361 KPLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNRA 420
Query: 142 XXXXXARPGNILQS-RWP---------QNMPYIQPRNIGMPANQNIMMAGMPQNQQRRNI 291
++ + S RW QNMP P + A +
Sbjct: 421 AYYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPAAPRPPFSTMRPASSQVPRVMSTQ 480
Query: 292 IVDPIISQNRNARP---ITGNVQLNQPRPQYNIVANGRQAGNMMYQYPIQDNQTMMNPDQ 462
V +Q RP T + PQY A R N Q TM P
Sbjct: 481 RVANTSTQTMGPRPAAAATAATPAVRTVPQYKYAAGVR---NPQQHLNAQPQVTMQQP-- 535
Query: 463 MKMPDIESQIDLSTTSKIANADSMEAKQLLGEKIYPLVSKHAGDMAGKL 609
++ Q L T S +A+A E KQ+LGE+++PL+ +AGK+
Sbjct: 536 --AVHVQGQEPL-TASMLASAPPQEQKQMLGERLFPLIQAMHPSLAGKI 581
Score = 34.3 bits (77), Expect = 0.36
Identities = 14/20 (70%), Positives = 19/20 (95%)
Frame = +3
Query: 603 KITGMFLELDNAELLYMIEN 662
KITGM LE+DN+ELL+M+E+
Sbjct: 580 KITGMLLEIDNSELLHMLES 599
>sp|P29341|PABP1_MOUSE Polyadenylate-binding protein 1 (Poly(A)-binding protein 1) (PABP 1)
Length = 636
Score = 54.7 bits (130), Expect = 3e-07
Identities = 61/229 (26%), Positives = 85/229 (37%), Gaps = 26/229 (11%)
Frame = +1
Query: 1 KPLYVALAQKKEDRVAHLRSQFQQRV-------------HQPQPAVXXXXXXXXXXXXXX 141
KPLYVALAQ+KE+R AHL +Q+ QR+ +QP P
Sbjct: 361 KPLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNRA 420
Query: 142 XXXXXARPGNILQS-RWP---------QNMPYIQPRNIGMPANQNIMMAGMPQNQQRRNI 291
++ + S RW QNMP P + A +
Sbjct: 421 AYYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPAAPRPPFSTMRPASSQVPRVMSTQ 480
Query: 292 IVDPIISQNRNARPITGNVQLN---QPRPQYNIVANGRQAGNMMYQYPIQDNQTMMNPDQ 462
V +Q RP + PQY A R N Q TM P
Sbjct: 481 RVANTSTQTMGPRPAAAAAAATPAVRTVPQYKYAAGVR---NPQQHLNAQPQVTMQQP-- 535
Query: 463 MKMPDIESQIDLSTTSKIANADSMEAKQLLGEKIYPLVSKHAGDMAGKL 609
++ Q L T S +A+A E KQ+LGE+++PL+ +AGK+
Sbjct: 536 --AVHVQGQEPL-TASMLASAPPQEQKQMLGERLFPLIQAMHPSLAGKI 581
Score = 34.3 bits (77), Expect = 0.36
Identities = 14/20 (70%), Positives = 19/20 (95%)
Frame = +3
Query: 603 KITGMFLELDNAELLYMIEN 662
KITGM LE+DN+ELL+M+E+
Sbjct: 580 KITGMLLEIDNSELLHMLES 599
>sp|P11940|PABP1_HUMAN Polyadenylate-binding protein 1 (Poly(A)-binding protein 1) (PABP 1)
sp|P61286|PABP1_BOVIN Polyadenylate-binding protein 1 (Poly(A)-binding protein 1) (PABP 1)
Length = 636
Score = 54.3 bits (129), Expect = 3e-07
Identities = 61/229 (26%), Positives = 85/229 (37%), Gaps = 26/229 (11%)
Frame = +1
Query: 1 KPLYVALAQKKEDRVAHLRSQFQQRV-------------HQPQPAVXXXXXXXXXXXXXX 141
KPLYVALAQ+KE+R AHL +Q+ QR+ +QP P
Sbjct: 361 KPLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNRA 420
Query: 142 XXXXXARPGNILQS-RWP---------QNMPYIQPRNIGMPANQNIMMAGMPQNQQRRNI 291
++ + S RW QNMP P + A +
Sbjct: 421 AYYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPAAPRPPFSTMRPASSQVPRVMSTQ 480
Query: 292 IVDPIISQNRNARPITGNVQLN---QPRPQYNIVANGRQAGNMMYQYPIQDNQTMMNPDQ 462
V +Q RP + PQY A R N Q TM P
Sbjct: 481 RVANTSTQTMGPRPAAAAAAATPAVRTVPQYKYAAGVR---NPQQHLNAQPQVTMQQP-- 535
Query: 463 MKMPDIESQIDLSTTSKIANADSMEAKQLLGEKIYPLVSKHAGDMAGKL 609
++ Q L T S +A+A E KQ+LGE+++PL+ +AGK+
Sbjct: 536 --AVHVQGQEPL-TASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKI 581
Score = 34.3 bits (77), Expect = 0.36
Identities = 14/20 (70%), Positives = 19/20 (95%)
Frame = +3
Query: 603 KITGMFLELDNAELLYMIEN 662
KITGM LE+DN+ELL+M+E+
Sbjct: 580 KITGMLLEIDNSELLHMLES 599
>sp|Q13310|PABP4_HUMAN Polyadenylate-binding protein 4 (Poly(A)-binding protein 4) (PABP 4)
(Inducible poly(A)-binding protein) (iPABP)
(Activated-platelet protein 1) (APP-1)
Length = 644
Score = 52.0 bits (123), Expect = 2e-06
Identities = 61/237 (25%), Positives = 91/237 (38%), Gaps = 34/237 (14%)
Frame = +1
Query: 1 KPLYVALAQKKEDRVAHLRSQFQQRV------------HQPQPAVXXXXXXXXXXXXXXX 144
KPLYVALAQ+KE+R AHL +Q+ QRV +Q QPA
Sbjct: 361 KPLYVALAQRKEERKAHLTNQYMQRVAGMRALPANAILNQFQPAA-------GGYFVPAV 413
Query: 145 XXXXARPGNILQSRWPQNMPYIQPRNIGMPANQNIMMAGMPQNQQR---RNIIVDPIISQ 315
RP ++ Q P + + G P M + + Q+ R R++
Sbjct: 414 PQAQGRPPYYTPNQLAQMRPNPRWQQGGRPQGFQGMPSAIRQSGPRPTLRHLAPTGSECP 473
Query: 316 NRNARPITGNVQLNQ-----------PRPQYNI-------VANGRQAGNMMYQYPIQDNQ 441
+R A G Q P N+ A R Y ++
Sbjct: 474 DRLAMDFGGAGAAQQGLTDSCQSGGVPTAVQNLAPRAAVAAAAPRAVAPYKYASSVRSPH 533
Query: 442 TMMNPDQMKMPDIESQ-IDLSTTSKIANADSMEAKQLLGEKIYPLVSKHAGDMAGKL 609
+ P Q P + Q + T S +A A E KQ+LGE+++PL+ ++AGK+
Sbjct: 534 PAIQPLQAPQPAVHVQGQEPLTASMLAAAPPQEQKQMLGERLFPLIQTMHSNLAGKI 590
Score = 34.3 bits (77), Expect = 0.36
Identities = 14/20 (70%), Positives = 19/20 (95%)
Frame = +3
Query: 603 KITGMFLELDNAELLYMIEN 662
KITGM LE+DN+ELL+M+E+
Sbjct: 589 KITGMLLEIDNSELLHMLES 608
>sp|O64380|PABP3_ARATH Polyadenylate-binding protein 3 (Poly(A)-binding protein 3) (PABP 3)
Length = 660
Score = 52.0 bits (123), Expect = 2e-06
Identities = 61/225 (27%), Positives = 90/225 (40%), Gaps = 30/225 (13%)
Frame = +1
Query: 1 KPLYVALAQKKEDRVAHLRSQFQQRVHQPQPAVXXXXXXXXXXXXXXXXXXXARPGNILQ 180
KPLY+ALAQ+KEDR AHL++ F Q + P P PG +
Sbjct: 400 KPLYIALAQRKEDRRAHLQALFSQ-IRAPGPMSGFHHP----------------PGGPMP 442
Query: 181 SRWPQNMPYIQPRNIGMPANQNI-------MMAGMPQNQQRRNIIVDPIISQNRNARPIT 339
PQ+M Y+ M +Q I M GM N IV + + P
Sbjct: 443 GP-PQHM-YVGQNGASMVPSQPIGYGFQPQFMPGMRPGSGPGNFIVPYPLQRQPQTGPRM 500
Query: 340 G------NVQLNQPRPQYNIVANGRQAGNMMYQYPIQDNQTMMN---PDQMKMPDIESQI 492
G NVQ + + Q + + + M Y + + M+ P + P I I
Sbjct: 501 GFRRGATNVQQHIQQQQ---LMHRNPSPGMRYMNGASNGRNGMDSSVPQGILPPIIPLPI 557
Query: 493 DLST--------------TSKIANADSMEAKQLLGEKIYPLVSKH 585
D S+ TS +A+A + ++LGE++YPLV +H
Sbjct: 558 DASSISHQKAPLLPISKLTSSLASASPADRTRMLGEQLYPLVERH 602
Score = 30.4 bits (67), Expect = 5.2
Identities = 11/20 (55%), Positives = 18/20 (90%)
Frame = +3
Query: 603 KITGMFLELDNAELLYMIEN 662
K+TGM LE+D AE+L+++E+
Sbjct: 609 KVTGMLLEMDQAEILHLMES 628
>sp|Q9H361|PABP3_HUMAN Polyadenylate-binding protein 3 (Poly(A)-binding protein 3) (PABP 3)
(Testis-specific poly(A)-binding protein)
Length = 631
Score = 48.1 bits (113), Expect = 2e-05
Identities = 57/226 (25%), Positives = 90/226 (39%), Gaps = 23/226 (10%)
Frame = +1
Query: 1 KPLYVALAQKKEDRVAHLRSQFQQRVHQ----PQPAVXXXXXXXXXXXXXXXXXXXARPG 168
KPLYVALAQ+KE+R A+L +++ QR+ P P
Sbjct: 361 KPLYVALAQRKEERQAYLTNEYMQRMASVRAVPNQRAPPSGYFMTAVPQTQNHAAYYPPS 420
Query: 169 NILQ----SRW----PQNMPYIQPRNIGMPANQNIMMAGM-PQNQQRRNIIVDPIISQNR 321
I + RW + P+ + P + + M P + Q V ++S R
Sbjct: 421 QIARLRPSPRWTAQGARPHPFQNKPSAIRPGAPRVPFSTMRPASSQ-----VPRVMSTQR 475
Query: 322 NARPITGNVQLNQPRPQYNIVANGRQAGNMMYQYPIQDNQTMMNPDQMK--MPDIESQ-- 489
A T V PRP A A + +Y + NP Q + P + Q
Sbjct: 476 VANTSTQTV---GPRPAAAAAAAATPAVRTVPRYKYAAG--VRNPQQHRNAQPQVTMQQL 530
Query: 490 ------IDLSTTSKIANADSMEAKQLLGEKIYPLVSKHAGDMAGKL 609
+ T S++A+A + KQ+LGE+++PL+ +AGK+
Sbjct: 531 AVHVQGQETLTASRLASAPPQKQKQMLGERLFPLIQAMHPTLAGKI 576
Score = 36.2 bits (82), Expect = 0.095
Identities = 15/20 (75%), Positives = 19/20 (95%)
Frame = +3
Query: 603 KITGMFLELDNAELLYMIEN 662
KITGM LE+DN+ELLYM+E+
Sbjct: 575 KITGMLLEIDNSELLYMLES 594
>sp|P42731|PABP2_ARATH Polyadenylate-binding protein 2 (Poly(A)-binding protein 2) (PABP
2)
Length = 629
Score = 48.1 bits (113), Expect = 2e-05
Identities = 57/214 (26%), Positives = 89/214 (41%), Gaps = 11/214 (5%)
Frame = +1
Query: 1 KPLYVALAQKKEDRVAHLRSQFQQ-RVHQPQPAVXXXXXXXXXXXXXXXXXXXARPGNIL 177
KPLYVA+AQ+KEDR L++QF Q R QP+V PG
Sbjct: 386 KPLYVAIAQRKEDRRVRLQAQFSQVRPVAMQPSV----------GPRMPVYPPGGPGIGQ 435
Query: 178 QSRWPQNMPYIQPRNIGMPANQNIMMAGMPQNQQRRNIIVDPIISQNR----NARPITGN 345
Q + Q P + P G Q ++ P + + + Q + RP G
Sbjct: 436 QMFYGQAPPAMIPPQPGYGYQQQLVPGMRPGGGPVPSFFMPMVQPQQQRPGGGRRP--GG 493
Query: 346 VQLNQ---PRPQYNIVANGRQAGNMMYQYPIQDNQTMMNPDQMKMPDIESQIDL---STT 507
+Q +Q P Q + GR M++YP Q + D+ + + L +
Sbjct: 494 IQHSQQQNPMMQQQMHPRGR-----MFRYP----QGRGGSGDVPPYDMGNNMPLTIGALA 544
Query: 508 SKIANADSMEAKQLLGEKIYPLVSKHAGDMAGKL 609
S ++NA + + +LGE +YPLV + + A K+
Sbjct: 545 SNLSNATPEQQRTMLGEVLYPLVEQVEAESAAKV 578
>sp|Q05196|PABP5_ARATH Polyadenylate-binding protein 5 (Poly(A)-binding protein 5) (PABP
5)
Length = 668
Score = 39.3 bits (90), Expect = 0.011
Identities = 18/24 (75%), Positives = 21/24 (87%)
Frame = +1
Query: 1 KPLYVALAQKKEDRVAHLRSQFQQ 72
KPLYVALAQ+KE+R AHL+S F Q
Sbjct: 396 KPLYVALAQRKEERQAHLQSLFTQ 419
Score = 30.8 bits (68), Expect = 4.0
Identities = 11/20 (55%), Positives = 18/20 (90%)
Frame = +3
Query: 603 KITGMFLELDNAELLYMIEN 662
K+TGM LE+D AE+L+++E+
Sbjct: 612 KVTGMLLEMDQAEILHLLES 631
Database: Non-redundant SwissProt sequences
Posted date: Dec 6, 2005 7:40 AM
Number of letters in database: 68,354,980
Number of sequences in database: 184,735
Database: swissprot.01
Posted date: Dec 6, 2005 8:18 AM
Number of letters in database: 66,202,850
Number of sequences in database: 184,431
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 87,802,296
Number of Sequences: 369166
Number of extensions: 1802920
Number of successful extensions: 4813
Number of sequences better than 10.0: 10
Number of HSP's better than 10.0 without gapping: 4614
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 4809
length of database: 68,354,980
effective HSP length: 108
effective length of database: 48,403,600
effective search space used: 6728100400
frameshift window, decay const: 40, 0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)