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_005_N12
(814 letters)
Database: Non-redundant SwissProt sequences
184,735 sequences; 68,354,980 total letters
Score E
Sequences producing significant alignments: (bits) Value
sp|Q5NVM8|RNPS1_PONPY RNA-binding protein with serine-rich ... 74 4e-13
sp|Q6AYK1|RNPS1_RAT RNA-binding protein with serine-rich do... 74 4e-13
sp|Q9W4D2|RNP4F_DROME RNA-binding protein 4F 40 0.010
sp|Q28165|PABP2_BOVIN Polyadenylate-binding protein 2 (Poly... 39 0.017
sp|Q8CCS6|PABP2_MOUSE Polyadenylate-binding protein 2 (Poly... 39 0.017
sp|Q86U42|PABP2_HUMAN Polyadenylate-binding protein 2 (Poly... 39 0.017
sp|O64380|PABP3_ARATH Polyadenylate-binding protein 3 (Poly... 39 0.022
sp|Q57014|RBPA_SYNY3 Putative RNA-binding protein rbpA 39 0.022
sp|O13620|MRD1_SCHPO Multiple RNA-binding domain-containing... 39 0.022
sp|P04147|PABP_YEAST Polyadenylate-binding protein, cytopla... 38 0.029
>sp|Q5NVM8|RNPS1_PONPY RNA-binding protein with serine-rich domain 1
sp|Q4R5N1|RNPS1_MACFA RNA-binding protein with serine-rich domain 1
sp|Q15287|RNPS1_HUMAN RNA-binding protein with serine-rich domain 1 (SR-related protein
LDC2)
Length = 305
Score = 74.3 bits (181), Expect = 4e-13
Identities = 27/62 (43%), Positives = 48/62 (77%)
Frame = +1
Query: 547 KIHITKLTRNITMAHLKEIFSTWGSVKHVEIPSDRFHPEFNRGFAYIEYDDPASAQQSIA 726
K+HI +LTRN+T H+ EIFST+G +K +++P +R HP ++G+AY+E+++P A++++
Sbjct: 162 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 221
Query: 727 EM 732
M
Sbjct: 222 HM 223
>sp|Q6AYK1|RNPS1_RAT RNA-binding protein with serine-rich domain 1
Length = 305
Score = 74.3 bits (181), Expect = 4e-13
Identities = 27/62 (43%), Positives = 48/62 (77%)
Frame = +1
Query: 547 KIHITKLTRNITMAHLKEIFSTWGSVKHVEIPSDRFHPEFNRGFAYIEYDDPASAQQSIA 726
K+HI +LTRN+T H+ EIFST+G +K +++P +R HP ++G+AY+E+++P A++++
Sbjct: 162 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 221
Query: 727 EM 732
M
Sbjct: 222 HM 223
>sp|Q9W4D2|RNP4F_DROME RNA-binding protein 4F
Length = 941
Score = 39.7 bits (91), Expect = 0.010
Identities = 20/61 (32%), Positives = 37/61 (60%)
Frame = +1
Query: 544 NKIHITKLTRNITMAHLKEIFSTWGSVKHVEIPSDRFHPEFNRGFAYIEYDDPASAQQSI 723
NKI + L + L E+FS +G++K V + + + +F +G AY+E++ P AQ+++
Sbjct: 724 NKIFVRNLHPACSKEELHELFSPFGTIKDVRL-VHKLNKQF-KGIAYVEFEKPGEAQRAV 781
Query: 724 A 726
A
Sbjct: 782 A 782
>sp|Q28165|PABP2_BOVIN Polyadenylate-binding protein 2 (Poly(A)-binding protein 2) (PolyA
binding protein II) (PABII) (Polyadenylate-binding
nuclear protein 1) (Nuclear poly(A)-binding protein 1)
Length = 306
Score = 38.9 bits (89), Expect = 0.017
Identities = 32/125 (25%), Positives = 57/125 (45%), Gaps = 3/125 (2%)
Frame = +1
Query: 361 QKPDVSTTKD-IKQIKEEKVKHEKLKPDHPKEADISVPXXXXXXXXXXXXXXXXXXXXXX 537
+ P++ K +++++EE K ++L+ + K+ ++S P
Sbjct: 115 EDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVIMSIEEKMEAD---- 170
Query: 538 XSNKIHITKLTRNITMAHLKEIFSTWGSVKHVEIPSDRF--HPEFNRGFAYIEYDDPASA 711
+ I++ + T L+ F GSV V I D+F HP +GFAYIE+ D S
Sbjct: 171 -ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHP---KGFAYIEFSDKESV 226
Query: 712 QQSIA 726
+ S+A
Sbjct: 227 RTSLA 231
>sp|Q8CCS6|PABP2_MOUSE Polyadenylate-binding protein 2 (Poly(A)-binding protein 2) (PolyA
binding protein II) (PABII) (Polyadenylate-binding
nuclear protein 1) (Nuclear poly(A)-binding protein 1)
Length = 302
Score = 38.9 bits (89), Expect = 0.017
Identities = 32/125 (25%), Positives = 57/125 (45%), Gaps = 3/125 (2%)
Frame = +1
Query: 361 QKPDVSTTKD-IKQIKEEKVKHEKLKPDHPKEADISVPXXXXXXXXXXXXXXXXXXXXXX 537
+ P++ K +++++EE K ++L+ + K+ ++S P
Sbjct: 111 EDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVIMSLEEKMEAD---- 166
Query: 538 XSNKIHITKLTRNITMAHLKEIFSTWGSVKHVEIPSDRF--HPEFNRGFAYIEYDDPASA 711
+ I++ + T L+ F GSV V I D+F HP +GFAYIE+ D S
Sbjct: 167 -ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHP---KGFAYIEFSDKESV 222
Query: 712 QQSIA 726
+ S+A
Sbjct: 223 RTSLA 227
>sp|Q86U42|PABP2_HUMAN Polyadenylate-binding protein 2 (Poly(A)-binding protein 2) (PolyA
binding protein II) (PABII) (Polyadenylate-binding
nuclear protein 1) (Nuclear poly(A)-binding protein 1)
Length = 306
Score = 38.9 bits (89), Expect = 0.017
Identities = 32/125 (25%), Positives = 57/125 (45%), Gaps = 3/125 (2%)
Frame = +1
Query: 361 QKPDVSTTKD-IKQIKEEKVKHEKLKPDHPKEADISVPXXXXXXXXXXXXXXXXXXXXXX 537
+ P++ K +++++EE K ++L+ + K+ ++S P
Sbjct: 115 EDPELEAIKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVIMSIEEKMEAD---- 170
Query: 538 XSNKIHITKLTRNITMAHLKEIFSTWGSVKHVEIPSDRF--HPEFNRGFAYIEYDDPASA 711
+ I++ + T L+ F GSV V I D+F HP +GFAYIE+ D S
Sbjct: 171 -ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHP---KGFAYIEFSDKESV 226
Query: 712 QQSIA 726
+ S+A
Sbjct: 227 RTSLA 231
>sp|O64380|PABP3_ARATH Polyadenylate-binding protein 3 (Poly(A)-binding protein 3) (PABP
3)
Length = 660
Score = 38.5 bits (88), Expect = 0.022
Identities = 19/69 (27%), Positives = 41/69 (59%), Gaps = 1/69 (1%)
Frame = +1
Query: 550 IHITKLTRNITMAHLKEIFSTWGSVKHVEIPSDRFHPE-FNRGFAYIEYDDPASAQQSIA 726
+++ L ++ LKE+FS +G+V ++ +P+ +RGF ++ Y +P A ++++
Sbjct: 334 LYLKNLDDSVDDEKLKEMFSEYGNVTSSKV---MLNPQGMSRGFGFVAYSNPEEALRALS 390
Query: 727 EMK*RPVGR 753
EM + +GR
Sbjct: 391 EMNGKMIGR 399
>sp|Q57014|RBPA_SYNY3 Putative RNA-binding protein rbpA
Length = 101
Score = 38.5 bits (88), Expect = 0.022
Identities = 19/58 (32%), Positives = 35/58 (60%)
Frame = +1
Query: 550 IHITKLTRNITMAHLKEIFSTWGSVKHVEIPSDRFHPEFNRGFAYIEYDDPASAQQSI 723
I++ L+ +++ A L +F+ +GSVK V++P+DR RGF ++E + A +I
Sbjct: 3 IYVGNLSYDVSEADLTAVFAEYGSVKRVQLPTDRETGRM-RGFGFVELEADAEETAAI 59
>sp|O13620|MRD1_SCHPO Multiple RNA-binding domain-containing protein 1
Length = 833
Score = 38.5 bits (88), Expect = 0.022
Identities = 23/87 (26%), Positives = 45/87 (51%), Gaps = 1/87 (1%)
Frame = +1
Query: 541 SNKIHITKLTRNITMAHLKEIFSTWGSVKHVEIPSDRFHPEFNRGFAYIEYDDPASAQQS 720
+ ++ + LT + LK +F +G ++ V +P D+ +GFAYI++ D A ++
Sbjct: 322 TKRLFLRNLTYSCAEDDLKSLFGPFGQLEQVHMPIDK-KTNNPKGFAYIDFHDADDAVRA 380
Query: 721 IAEMK*RPV-GRPRNISCGKCRFPVLI 798
E+ +P GR ++ K R +L+
Sbjct: 381 YLELDAKPFQGRLLHVLPAKARSSILL 407
>sp|P04147|PABP_YEAST Polyadenylate-binding protein, cytoplasmic and nuclear
(Poly(A)-binding protein) (PABP) (ARS consensus binding
protein ACBP-67) (Polyadenylate tail-binding protein)
Length = 577
Score = 38.1 bits (87), Expect = 0.029
Identities = 18/69 (26%), Positives = 40/69 (57%)
Frame = +1
Query: 541 SNKIHITKLTRNITMAHLKEIFSTWGSVKHVEIPSDRFHPEFNRGFAYIEYDDPASAQQS 720
S +++ L +++ AHL +IFS GSV + + D + + G+AY+ ++D + +++
Sbjct: 37 SASLYVGDLEPSVSEAHLYDIFSPIGSVSSIRVCRDAI-TKTSLGYAYVNFNDHEAGRKA 95
Query: 721 IAEMK*RPV 747
I ++ P+
Sbjct: 96 IEQLNYTPI 104
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: 56,134,253
Number of Sequences: 369166
Number of extensions: 894014
Number of successful extensions: 3645
Number of sequences better than 10.0: 10
Number of HSP's better than 10.0 without gapping: 3444
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): 3614
length of database: 68,354,980
effective HSP length: 109
effective length of database: 48,218,865
effective search space used: 7763237265
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)