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= 004281
(764 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4DZS|A Chain A, Crystal Structure Of Yeast Puf4p Rna Binding Domain In
Complex With Ho-4be Mutant Rna
pdb|4DZS|B Chain B, Crystal Structure Of Yeast Puf4p Rna Binding Domain In
Complex With Ho-4be Mutant Rna
Length = 357
Score = 217 bits (553), Expect = 2e-56, Method: Compositional matrix adjust.
Identities = 129/326 (39%), Positives = 196/326 (60%), Gaps = 21/326 (6%)
Query: 448 VEEVTGRIYLMAKDQHGCRFLQRKISEGTLEDIEKIFVEIIDHIVELMTDPFGNYLVQKL 507
+++ G I+ + KDQHGCRFLQ+++ + + IF E D+ VELMTD FGNYL+QKL
Sbjct: 30 LDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKL 89
Query: 508 LEVCNEDQRMQILQAITRKAGDLVRIS-----TRAVQKVIETLKSPEQFSLVVSSLKPGI 562
LE +QR+ +L I+ + V IS TRA+QK+IE +K+ E+ +VV SL+P
Sbjct: 90 LEEVTTEQRI-VLTKIS--SPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYT 146
Query: 563 VTLIKNMNGNHVAQRCLLYLLPEYSKFLFQATTNNCVELATDRHGCCVIQKCLTHSEGEQ 622
V L K++NGNHV Q+CL L PE +F+F A +++C+++AT RHGCCV+Q+CL H EQ
Sbjct: 147 VQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQ 206
Query: 623 RHRLVSKITSNALILSQDPFGNYVVQFVFELRLPWATMD----ILDQLEGNYGDLSMQKY 678
L K+ + L+ DPFGNYVVQ++ D I+ L+ +LS+ K+
Sbjct: 207 CDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKF 266
Query: 679 SSNVVEKCLKYGDDERRAHIIQELISNA---HLDQVMLDPYGNYVIQAAL---QQSKGGV 732
SNV+EK LK +I E+++N + ++ D YGNYV+Q AL + +
Sbjct: 267 GSNVIEKILKTAIVSEP--MILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQNDYL 324
Query: 733 HSALVDAIRP-HVPVLRTSPYGKKVL 757
+ L + + P V +R +P+GK+++
Sbjct: 325 YKRLSEIVAPLLVGPIRNTPHGKRII 350
>pdb|3BX2|A Chain A, Puf4 Rna Binding Domain Bound To Ho Endonuclease Rna 3'
Utr Recognition Sequence
pdb|3BX2|B Chain B, Puf4 Rna Binding Domain Bound To Ho Endonuclease Rna 3'
Utr Recognition Sequence
Length = 335
Score = 216 bits (549), Expect = 5e-56, Method: Compositional matrix adjust.
Identities = 129/326 (39%), Positives = 196/326 (60%), Gaps = 21/326 (6%)
Query: 448 VEEVTGRIYLMAKDQHGCRFLQRKISEGTLEDIEKIFVEIIDHIVELMTDPFGNYLVQKL 507
+++ G I+ + KDQHGCRFLQ+++ + + IF E D+ VELMTD FGNYL+QKL
Sbjct: 8 LDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKL 67
Query: 508 LEVCNEDQRMQILQAITRKAGDLVRIS-----TRAVQKVIETLKSPEQFSLVVSSLKPGI 562
LE +QR+ +L I+ + V IS TRA+QK+IE +K+ E+ +VV SL+P
Sbjct: 68 LEEVTTEQRI-VLTKIS--SPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYT 124
Query: 563 VTLIKNMNGNHVAQRCLLYLLPEYSKFLFQATTNNCVELATDRHGCCVIQKCLTHSEGEQ 622
V L K++NGNHV Q+CL L PE +F+F A +++C+++AT RHGCCV+Q+CL H EQ
Sbjct: 125 VQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQ 184
Query: 623 RHRLVSKITSNALILSQDPFGNYVVQFVFELRLPWATMD----ILDQLEGNYGDLSMQKY 678
L K+ + L+ DPFGNYVVQ++ D I+ L+ +LS+ K+
Sbjct: 185 CDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKF 244
Query: 679 SSNVVEKCLKYGDDERRAHIIQELISNA---HLDQVMLDPYGNYVIQAAL---QQSKGGV 732
SNV+EK LK +I E+++N + ++ D YGNYV+Q AL + +
Sbjct: 245 GSNVIEKILKTAIVSEP--MILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQNDYL 302
Query: 733 HSALVDAIRP-HVPVLRTSPYGKKVL 757
+ L + + P V +R +P+GK+++
Sbjct: 303 YKRLSEIVAPLLVGPIRNTPHGKRII 328
>pdb|3BWT|A Chain A, Crystal Structure Of The Rna Binding Domain Of Puf4 From
Saccharomyces Cerevisiae
Length = 333
Score = 215 bits (548), Expect = 7e-56, Method: Compositional matrix adjust.
Identities = 129/326 (39%), Positives = 196/326 (60%), Gaps = 21/326 (6%)
Query: 448 VEEVTGRIYLMAKDQHGCRFLQRKISEGTLEDIEKIFVEIIDHIVELMTDPFGNYLVQKL 507
+++ G I+ + KDQHGCRFLQ+++ + + IF E D+ VELMTD FGNYL+QKL
Sbjct: 8 LDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKL 67
Query: 508 LEVCNEDQRMQILQAITRKAGDLVRIS-----TRAVQKVIETLKSPEQFSLVVSSLKPGI 562
LE +QR+ +L I+ + V IS TRA+QK+IE +K+ E+ +VV SL+P
Sbjct: 68 LEEVTTEQRI-VLTKIS--SPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYT 124
Query: 563 VTLIKNMNGNHVAQRCLLYLLPEYSKFLFQATTNNCVELATDRHGCCVIQKCLTHSEGEQ 622
V L K++NGNHV Q+CL L PE +F+F A +++C+++AT RHGCCV+Q+CL H EQ
Sbjct: 125 VQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQ 184
Query: 623 RHRLVSKITSNALILSQDPFGNYVVQFVFELRLPWATMD----ILDQLEGNYGDLSMQKY 678
L K+ + L+ DPFGNYVVQ++ D I+ L+ +LS+ K+
Sbjct: 185 CDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKF 244
Query: 679 SSNVVEKCLKYGDDERRAHIIQELISNA---HLDQVMLDPYGNYVIQAAL---QQSKGGV 732
SNV+EK LK +I E+++N + ++ D YGNYV+Q AL + +
Sbjct: 245 GSNVIEKILKTAIVSEP--MILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQNDYL 302
Query: 733 HSALVDAIRP-HVPVLRTSPYGKKVL 757
+ L + + P V +R +P+GK+++
Sbjct: 303 YKRLSEIVAPLLVGPIRNTPHGKRII 328
>pdb|3BX3|A Chain A, Puf4 T650cC724R MUTANT BOUND TO COX17 RNA 3' UTR
Recognition Sequence
pdb|3BX3|B Chain B, Puf4 T650cC724R MUTANT BOUND TO COX17 RNA 3' UTR
Recognition Sequence
Length = 335
Score = 208 bits (530), Expect = 8e-54, Method: Compositional matrix adjust.
Identities = 127/326 (38%), Positives = 194/326 (59%), Gaps = 21/326 (6%)
Query: 448 VEEVTGRIYLMAKDQHGCRFLQRKISEGTLEDIEKIFVEIIDHIVELMTDPFGNYLVQKL 507
+++ G I+ + KDQHGCRFLQ+++ + + IF E D+ VELMTD FGNYL+QKL
Sbjct: 8 LDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKL 67
Query: 508 LEVCNEDQRMQILQAITRKAGDLVRIS-----TRAVQKVIETLKSPEQFSLVVSSLKPGI 562
LE +QR+ +L I+ + V IS RA+QK+IE +K+ E+ +VV SL+P
Sbjct: 68 LEEVTTEQRI-VLTKIS--SPHFVEISLNPHGCRALQKLIECIKTDEEAQIVVDSLRPYT 124
Query: 563 VTLIKNMNGNHVAQRCLLYLLPEYSKFLFQATTNNCVELATDRHGCCVIQKCLTHSEGEQ 622
V L K++NGNHV Q+CL L PE +F+F A +++C+++AT RHGC V+Q+CL H EQ
Sbjct: 125 VQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCRVLQRCLDHGTTEQ 184
Query: 623 RHRLVSKITSNALILSQDPFGNYVVQFVFELRLPWATMD----ILDQLEGNYGDLSMQKY 678
L K+ + L+ DPFGNYVVQ++ D I+ L+ +LS+ K+
Sbjct: 185 CDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKF 244
Query: 679 SSNVVEKCLKYGDDERRAHIIQELISNA---HLDQVMLDPYGNYVIQAAL---QQSKGGV 732
SNV+EK LK +I E+++N + ++ D YGNYV+Q AL + +
Sbjct: 245 GSNVIEKILKTAIVSEP--MILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQNDYL 302
Query: 733 HSALVDAIRP-HVPVLRTSPYGKKVL 757
+ L + + P V +R +P+GK+++
Sbjct: 303 YKRLSEIVAPLLVGPIRNTPHGKRII 328
>pdb|3Q0Q|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio2 In Complex With P38alpha Nrea
pdb|3Q0R|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio2 In Complex With P38alpha Nreb
pdb|3Q0S|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio2 In Complex With Erk2 Nre
Length = 351
Score = 186 bits (471), Expect = 6e-47, Method: Compositional matrix adjust.
Identities = 106/322 (32%), Positives = 176/322 (54%), Gaps = 14/322 (4%)
Query: 448 VEEVTGRIYLMAKDQHGCRFLQRKISEGTLEDIEKIFVEIIDHIVELMTDPFGNYLVQKL 507
+ ++ G I ++DQHG RF+Q+K+ T + + +F EI+ +LMTD FGNY++QK
Sbjct: 19 LRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAAYQLMTDVFGNYVIQKF 78
Query: 508 LEVCNEDQRMQILQAITRKAGDLVRIS-----TRAVQKVIETLKSPEQ-FSLVVSSLKPG 561
E + DQ++ + TR G ++ ++ R +QK +E++ S +Q S +V L
Sbjct: 79 FEFGSLDQKLAL---ATRIRGHVLPLALQMYGCRVIQKALESISSDQQVISEMVKELDGH 135
Query: 562 IVTLIKNMNGNHVAQRCLLYLLPEYSKFLFQATTNNCVELATDRHGCCVIQKCLTHSEGE 621
++ +K+ NGNHV Q+C+ + P+ +F+ A L+T +GC VIQ+ L H E
Sbjct: 136 VLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAE 195
Query: 622 QRHRLVSKITSNALILSQDPFGNYVVQFVFELRLPWATMDILDQLEGNYGDLSMQKYSSN 681
Q ++ ++ + L QD +GNYV+Q V E P I+ ++ G LS K++SN
Sbjct: 196 QTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASN 255
Query: 682 VVEKCLKYGDDERRAHIIQELIS-----NAHLDQVMLDPYGNYVIQAALQQSKGGVHSAL 736
VVEKC+ + RA +I E+ ++ L +M D Y NYV+Q + ++ +
Sbjct: 256 VVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEPAQRKII 315
Query: 737 VDAIRPHVPVLRTSPYGKKVLS 758
+ IRPH+ LR YGK +L+
Sbjct: 316 MHKIRPHITTLRKYTYGKHILA 337
Score = 63.2 bits (152), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 61/256 (23%), Positives = 104/256 (40%), Gaps = 40/256 (15%)
Query: 540 KVIETLKSPEQFSLVVSSLKPGIVTLIKNMNGNHVAQRCLLYLLPEYSKFLFQATTNNCV 599
+++E ++ +L + L IV ++ +G+ Q+ L P + +F
Sbjct: 4 RLLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAAY 63
Query: 600 ELATDRHGCCVIQKCLTHSEGEQRHRLVSKITSNALILS--------------------- 638
+L TD G VIQK +Q+ L ++I + L L+
Sbjct: 64 QLMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQ 123
Query: 639 -----------------QDPFGNYVVQFVFELRLPWATMDILDQLEGNYGDLSMQKYSSN 681
+D GN+VVQ E P + I+D +G LS Y
Sbjct: 124 VISEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCR 183
Query: 682 VVEKCLKYGDDERRAHIIQELISNAHLDQVMLDPYGNYVIQAALQQSKGGVHSALVDAIR 741
V+++ L++ E+ I++EL + H +Q++ D YGNYVIQ L+ + S +V IR
Sbjct: 184 VIQRILEHCTAEQTLPILEEL--HQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIR 241
Query: 742 PHVPVLRTSPYGKKVL 757
V L + V+
Sbjct: 242 GKVLALSQHKFASNVV 257
Score = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 43/194 (22%), Positives = 83/194 (42%), Gaps = 47/194 (24%)
Query: 435 LKIIRPQPQKYNSVEEVTGRIYLMAKDQHGCRFLQRKISEGTLEDIEKIFVEIIDHIVEL 494
++ ++PQ ++ ++ G++++++ +GCR +QR + T E I E+ H +L
Sbjct: 153 IECVQPQSLQF-IIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQL 211
Query: 495 MTDPFGNYLVQKLLEVCNEDQRMQILQAITRKAGDL-------------VRISTRA---- 537
+ D +GNY++Q +LE + + +I+ I K L V ++RA
Sbjct: 212 VQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHASRAERAL 271
Query: 538 ----------------------------VQKVIETLKSPEQFSLVVSSLKPGIVTLIKNM 569
VQK+I+ + P Q +++ ++P I TL K
Sbjct: 272 LIDEVCCQNDGPHSALYTMMKDQYANYVVQKMID-MAEPAQRKIIMHKIRPHITTLRKYT 330
Query: 570 NGNHVAQRCLLYLL 583
G H+ + Y L
Sbjct: 331 YGKHILAKLEKYYL 344
>pdb|3GVO|A Chain A, Structure And Rna Binding Of The Mouse Pumilio-2 Puf
Domain
pdb|3GVT|A Chain A, Structure And Rna Binding Of The Mouse Pumilio-2 Puf
Domain
pdb|3GVT|B Chain B, Structure And Rna Binding Of The Mouse Pumilio-2 Puf
Domain
Length = 351
Score = 185 bits (470), Expect = 8e-47, Method: Compositional matrix adjust.
Identities = 106/321 (33%), Positives = 176/321 (54%), Gaps = 14/321 (4%)
Query: 448 VEEVTGRIYLMAKDQHGCRFLQRKISEGTLEDIEKIFVEIIDHIVELMTDPFGNYLVQKL 507
+ ++ G I ++DQHG RF+Q+K+ T + + +F EI+ +LMTD FGNY++QK
Sbjct: 21 LRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGNYVIQKF 80
Query: 508 LEVCNEDQRMQILQAITRKAGDLVRIS-----TRAVQKVIETLKSPEQFSLVVSSLKPGI 562
E + DQ++ + TR G ++ ++ R +QK +E++ S +Q S +V L +
Sbjct: 81 FEFGSLDQKLAL---ATRIRGHVLPLALQMYGCRVIQKALESISSDQQ-SEMVKELDGHV 136
Query: 563 VTLIKNMNGNHVAQRCLLYLLPEYSKFLFQATTNNCVELATDRHGCCVIQKCLTHSEGEQ 622
+ +K+ NGNHV Q+C+ + P+ +F+ A L+T +GC VIQ+ L H EQ
Sbjct: 137 LKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQ 196
Query: 623 RHRLVSKITSNALILSQDPFGNYVVQFVFELRLPWATMDILDQLEGNYGDLSMQKYSSNV 682
++ ++ + L QD +GNYV+Q V E P I+ ++ G LS K++SNV
Sbjct: 197 TLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNV 256
Query: 683 VEKCLKYGDDERRAHIIQELIS-----NAHLDQVMLDPYGNYVIQAALQQSKGGVHSALV 737
VEKC+ + RA +I E+ ++ L +M D Y NYV+Q + ++ ++
Sbjct: 257 VEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEPAQRKIIM 316
Query: 738 DAIRPHVPVLRTSPYGKKVLS 758
IRPH+ LR YGK +L+
Sbjct: 317 HKIRPHITTLRKYTYGKHILA 337
Score = 78.6 bits (192), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 60/259 (23%), Positives = 121/259 (46%), Gaps = 16/259 (6%)
Query: 443 QKYNSVEEVTGRIYLMAKDQHGCRFLQRKISEGTLEDIEKIFVEIIDHIVELMTDPFGNY 502
QK + G + +A +GCR +Q+ + + + ++ E+ H+++ + D GN+
Sbjct: 88 QKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQSEMVKELDGHVLKCVKDQNGNH 147
Query: 503 LVQKLLEVCNEDQRMQILQAITRKAGDLVRIST-----RAVQKVIETLKSPEQFSLVVSS 557
+VQK +E C + Q +Q + I G + +ST R +Q+++E + EQ ++
Sbjct: 148 VVQKCIE-CVQPQSLQFI--IDAFKGQVFVLSTHPYGCRVIQRILEHC-TAEQTLPILEE 203
Query: 558 LKPGIVTLIKNMNGNHVAQRCLLYLLPEYSKFLFQATTNNCVELATDRHGCCVIQKCLTH 617
L L+++ GN+V Q L + PE + + L+ + V++KC+TH
Sbjct: 204 LHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTH 263
Query: 618 SEGEQRHRLVSKIT-------SNALILSQDPFGNYVVQFVFELRLPWATMDILDQLEGNY 670
+ +R L+ ++ S + +D + NYVVQ + ++ P I+ ++ +
Sbjct: 264 ASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEPAQRKIIMHKIRPHI 323
Query: 671 GDLSMQKYSSNVVEKCLKY 689
L Y +++ K KY
Sbjct: 324 TTLRKYTYGKHILAKLEKY 342
Score = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 57/254 (22%), Positives = 104/254 (40%), Gaps = 38/254 (14%)
Query: 540 KVIETLKSPEQFSLVVSSLKPGIVTLIKNMNGNHVAQRCLLYLLPEYSKFLFQATTNNCV 599
+++E ++ +L + L IV ++ +G+ Q+ L P + +F
Sbjct: 6 RLLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAY 65
Query: 600 ELATDRHGCCVIQKCLTHSEGEQRHRLVSKITSNALILSQDPFGNYVVQFVFELRLPWAT 659
+L TD G VIQK +Q+ L ++I + L L+ +G V+Q E
Sbjct: 66 QLMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQ 125
Query: 660 MDILDQLEGNYGDLSMQKYSSNVVEKCLK-------------------------YG---- 690
+++ +L+G+ + ++VV+KC++ YG
Sbjct: 126 SEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVI 185
Query: 691 -------DDERRAHIIQELISNAHLDQVMLDPYGNYVIQAALQQSKGGVHSALVDAIRPH 743
E+ I++EL + H +Q++ D YGNYVIQ L+ + S +V IR
Sbjct: 186 QRILEHCTAEQTLPILEEL--HQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGK 243
Query: 744 VPVLRTSPYGKKVL 757
V L + V+
Sbjct: 244 VLALSQHKFASNVV 257
Score = 50.8 bits (120), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 43/194 (22%), Positives = 83/194 (42%), Gaps = 47/194 (24%)
Query: 435 LKIIRPQPQKYNSVEEVTGRIYLMAKDQHGCRFLQRKISEGTLEDIEKIFVEIIDHIVEL 494
++ ++PQ ++ ++ G++++++ +GCR +QR + T E I E+ H +L
Sbjct: 153 IECVQPQSLQF-IIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQL 211
Query: 495 MTDPFGNYLVQKLLEVCNEDQRMQILQAITRKAGDL-------------VRISTRA---- 537
+ D +GNY++Q +LE + + +I+ I K L V ++RA
Sbjct: 212 VQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHASRAERAL 271
Query: 538 ----------------------------VQKVIETLKSPEQFSLVVSSLKPGIVTLIKNM 569
VQK+I+ + P Q +++ ++P I TL K
Sbjct: 272 LIDEVCCQNDGPHSALYTMMKDQYANYVVQKMID-MAEPAQRKIIMHKIRPHITTLRKYT 330
Query: 570 NGNHVAQRCLLYLL 583
G H+ + Y L
Sbjct: 331 YGKHILAKLEKYYL 344
>pdb|1IB2|A Chain A, Crystal Structure Of A Pumilio-Homology Domain
pdb|1M8Z|A Chain A, Crystal Structure Of A Pumilio-Homology Domain
pdb|1M8W|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre1-19 Rna
pdb|1M8W|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre1-19 Rna
pdb|1M8X|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre1-14 Rna
pdb|1M8X|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre1-14 Rna
pdb|1M8Y|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre2-10 Rna
pdb|1M8Y|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Nre2-10 Rna
pdb|3Q0L|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With P38alpha Nrea
pdb|3Q0L|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With P38alpha Nrea
pdb|3Q0M|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With P38alpha Nreb
pdb|3Q0M|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With P38alpha Nreb
pdb|3Q0N|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Erk2 Nre
pdb|3Q0N|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Erk2 Nre
pdb|3Q0O|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Erk2 Nre
pdb|3Q0O|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Erk2 Nre
pdb|3Q0P|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Hunchback Nre
pdb|3Q0P|B Chain B, Crystal Structure Of The Pumilio-Homology Domain From
Human Pumilio1 In Complex With Hunchback Nre
Length = 349
Score = 180 bits (456), Expect = 3e-45, Method: Compositional matrix adjust.
Identities = 104/318 (32%), Positives = 171/318 (53%), Gaps = 8/318 (2%)
Query: 448 VEEVTGRIYLMAKDQHGCRFLQRKISEGTLEDIEKIFVEIIDHIVELMTDPFGNYLVQKL 507
+ E+ G I ++DQHG RF+Q K+ T + + +F EI+ +LM D FGNY++QK
Sbjct: 19 LREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKF 78
Query: 508 LEVCNEDQRMQILQAITRKAGDLV--RISTRAVQKVIETLKSPEQFSLVVSSLKPGIVTL 565
E + +Q++ + + I L R +QK +E + S +Q +V L ++
Sbjct: 79 FEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMV-RELDGHVLKC 137
Query: 566 IKNMNGNHVAQRCLLYLLPEYSKFLFQATTNNCVELATDRHGCCVIQKCLTHSEGEQRHR 625
+K+ NGNHV Q+C+ + P+ +F+ A L+T +GC VIQ+ L H +Q
Sbjct: 138 VKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLP 197
Query: 626 LVSKITSNALILSQDPFGNYVVQFVFELRLPWATMDILDQLEGNYGDLSMQKYSSNVVEK 685
++ ++ + L QD +GNYV+Q V E P I+ ++ GN LS K++SNVVEK
Sbjct: 198 ILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEK 257
Query: 686 CLKYGDDERRAHIIQELIS-----NAHLDQVMLDPYGNYVIQAALQQSKGGVHSALVDAI 740
C+ + RA +I E+ + ++ L +M D Y NYV+Q + ++ G ++ I
Sbjct: 258 CVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKI 317
Query: 741 RPHVPVLRTSPYGKKVLS 758
RPH+ LR YGK +L+
Sbjct: 318 RPHIATLRKYTYGKHILA 335
Score = 80.1 bits (196), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 61/259 (23%), Positives = 122/259 (47%), Gaps = 16/259 (6%)
Query: 443 QKYNSVEEVTGRIYLMAKDQHGCRFLQRKISEGTLEDIEKIFVEIIDHIVELMTDPFGNY 502
QK E + G + +A +GCR +Q+ + + ++ E+ H+++ + D GN+
Sbjct: 86 QKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVKDQNGNH 145
Query: 503 LVQKLLEVCNEDQRMQILQAITRKAGDLVRIST-----RAVQKVIETLKSPEQFSLVVSS 557
+VQK +E C + Q +Q + I G + +ST R +Q+++E P+Q ++
Sbjct: 146 VVQKCIE-CVQPQSLQFI--IDAFKGQVFALSTHPYGCRVIQRILEHC-LPDQTLPILEE 201
Query: 558 LKPGIVTLIKNMNGNHVAQRCLLYLLPEYSKFLFQATTNNCVELATDRHGCCVIQKCLTH 617
L L+++ GN+V Q L + PE + N + L+ + V++KC+TH
Sbjct: 202 LHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTH 261
Query: 618 SEGEQRHRLVSKIT-------SNALILSQDPFGNYVVQFVFELRLPWATMDILDQLEGNY 670
+ +R L+ ++ S + +D + NYVVQ + ++ P ++ ++ +
Sbjct: 262 ASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHI 321
Query: 671 GDLSMQKYSSNVVEKCLKY 689
L Y +++ K KY
Sbjct: 322 ATLRKYTYGKHILAKLEKY 340
Score = 74.3 bits (181), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 45/172 (26%), Positives = 88/172 (51%), Gaps = 2/172 (1%)
Query: 586 YSKFLFQATTNNCVELATDRHGCCVIQKCLTHSEGEQRHRLVSKITSNALILSQDPFGNY 645
Y + + +E + D+HG IQ L + +R + ++I A L D FGNY
Sbjct: 14 YPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNY 73
Query: 646 VVQFVFELRLPWATMDILDQLEGNYGDLSMQKYSSNVVEKCLKYGDDERRAHIIQELISN 705
V+Q FE + + +++ G+ L++Q Y V++K L++ +++ +++EL +
Sbjct: 74 VIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVREL--D 131
Query: 706 AHLDQVMLDPYGNYVIQAALQQSKGGVHSALVDAIRPHVPVLRTSPYGKKVL 757
H+ + + D GN+V+Q ++ + ++DA + V L T PYG +V+
Sbjct: 132 GHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVI 183
Score = 50.8 bits (120), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 54/252 (21%), Positives = 102/252 (40%), Gaps = 34/252 (13%)
Query: 540 KVIETLKSPEQFSLVVSSLKPGIVTLIKNMNGNHVAQRCLLYLLPEYSKFLFQATTNNCV 599
+++E ++ +L + + I+ ++ +G+ Q L P + +F
Sbjct: 4 RLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAY 63
Query: 600 ELATDRHGCCVIQKCLTHSEGEQRHRLVSKITSNALILSQDPFGNYVVQFVFELRLPWAT 659
+L D G VIQK EQ+ L +I + L L+ +G V+Q E
Sbjct: 64 QLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQ 123
Query: 660 MDILDQLEGNYGDLSMQKYSSNVVEKC--------LKYGDDERRAH------------II 699
+++ +L+G+ + ++VV+KC L++ D + +I
Sbjct: 124 NEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVI 183
Query: 700 QELISNA--------------HLDQVMLDPYGNYVIQAALQQSKGGVHSALVDAIRPHVP 745
Q ++ + H +Q++ D YGNYVIQ L+ + S +V IR +V
Sbjct: 184 QRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVL 243
Query: 746 VLRTSPYGKKVL 757
VL + V+
Sbjct: 244 VLSQHKFASNVV 255
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 45/194 (23%), Positives = 82/194 (42%), Gaps = 18/194 (9%)
Query: 407 CLSLSTPNAGCFQIDGLNS--WPLSSDSMDLKIIRP------QPQKYNSVEEVTGRIYLM 458
C+ P + F ID + LS+ ++I+ Q +EE+ +
Sbjct: 150 CIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQL 209
Query: 459 AKDQHGCRFLQRKISEGTLEDIEKIFVEIIDHIVELMTDPFGNYLVQKLLEVCNEDQRMQ 518
+DQ+G +Q + G ED KI EI +++ L F + +V+K + + +R
Sbjct: 210 VQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAV 269
Query: 519 ILQAI-TRKAGDLVRISTR--------AVQKVIETLKSPEQFSLVVSSLKPGIVTLIKNM 569
++ + T G + T VQK+I+ + P Q +V+ ++P I TL K
Sbjct: 270 LIDEVCTMNDGPHSALYTMMKDQYANYVVQKMID-VAEPGQRKIVMHKIRPHIATLRKYT 328
Query: 570 NGNHVAQRCLLYLL 583
G H+ + Y +
Sbjct: 329 YGKHILAKLEKYYM 342
>pdb|3BSB|A Chain A, Crystal Structure Of Human Pumilio1 In Complex With
Cyclinb Reverse Rna
pdb|3BSB|B Chain B, Crystal Structure Of Human Pumilio1 In Complex With
Cyclinb Reverse Rna
pdb|3BSX|A Chain A, Crystal Structure Of Human Pumilio 1 In Complex With Puf5
Rna
pdb|3BSX|B Chain B, Crystal Structure Of Human Pumilio 1 In Complex With Puf5
Rna
Length = 343
Score = 179 bits (455), Expect = 4e-45, Method: Compositional matrix adjust.
Identities = 104/318 (32%), Positives = 171/318 (53%), Gaps = 8/318 (2%)
Query: 448 VEEVTGRIYLMAKDQHGCRFLQRKISEGTLEDIEKIFVEIIDHIVELMTDPFGNYLVQKL 507
+ E+ G I ++DQHG RF+Q K+ T + + +F EI+ +LM D FGNY++QK
Sbjct: 19 LREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKF 78
Query: 508 LEVCNEDQRMQILQAITRKAGDLV--RISTRAVQKVIETLKSPEQFSLVVSSLKPGIVTL 565
E + +Q++ + + I L R +QK +E + S +Q +V L ++
Sbjct: 79 FEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMV-RELDGHVLKC 137
Query: 566 IKNMNGNHVAQRCLLYLLPEYSKFLFQATTNNCVELATDRHGCCVIQKCLTHSEGEQRHR 625
+K+ NGNHV Q+C+ + P+ +F+ A L+T +GC VIQ+ L H +Q
Sbjct: 138 VKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLP 197
Query: 626 LVSKITSNALILSQDPFGNYVVQFVFELRLPWATMDILDQLEGNYGDLSMQKYSSNVVEK 685
++ ++ + L QD +GNYV+Q V E P I+ ++ GN LS K++SNVVEK
Sbjct: 198 ILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEK 257
Query: 686 CLKYGDDERRAHIIQELIS-----NAHLDQVMLDPYGNYVIQAALQQSKGGVHSALVDAI 740
C+ + RA +I E+ + ++ L +M D Y NYV+Q + ++ G ++ I
Sbjct: 258 CVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKI 317
Query: 741 RPHVPVLRTSPYGKKVLS 758
RPH+ LR YGK +L+
Sbjct: 318 RPHIATLRKYTYGKHILA 335
Score = 79.7 bits (195), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 61/259 (23%), Positives = 122/259 (47%), Gaps = 16/259 (6%)
Query: 443 QKYNSVEEVTGRIYLMAKDQHGCRFLQRKISEGTLEDIEKIFVEIIDHIVELMTDPFGNY 502
QK E + G + +A +GCR +Q+ + + ++ E+ H+++ + D GN+
Sbjct: 86 QKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVKDQNGNH 145
Query: 503 LVQKLLEVCNEDQRMQILQAITRKAGDLVRIST-----RAVQKVIETLKSPEQFSLVVSS 557
+VQK +E C + Q +Q + I G + +ST R +Q+++E P+Q ++
Sbjct: 146 VVQKCIE-CVQPQSLQFI--IDAFKGQVFALSTHPYGCRVIQRILEHC-LPDQTLPILEE 201
Query: 558 LKPGIVTLIKNMNGNHVAQRCLLYLLPEYSKFLFQATTNNCVELATDRHGCCVIQKCLTH 617
L L+++ GN+V Q L + PE + N + L+ + V++KC+TH
Sbjct: 202 LHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTH 261
Query: 618 SEGEQRHRLVSKIT-------SNALILSQDPFGNYVVQFVFELRLPWATMDILDQLEGNY 670
+ +R L+ ++ S + +D + NYVVQ + ++ P ++ ++ +
Sbjct: 262 ASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHI 321
Query: 671 GDLSMQKYSSNVVEKCLKY 689
L Y +++ K KY
Sbjct: 322 ATLRKYTYGKHILAKLEKY 340
Score = 73.9 bits (180), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 45/172 (26%), Positives = 88/172 (51%), Gaps = 2/172 (1%)
Query: 586 YSKFLFQATTNNCVELATDRHGCCVIQKCLTHSEGEQRHRLVSKITSNALILSQDPFGNY 645
Y + + +E + D+HG IQ L + +R + ++I A L D FGNY
Sbjct: 14 YPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNY 73
Query: 646 VVQFVFELRLPWATMDILDQLEGNYGDLSMQKYSSNVVEKCLKYGDDERRAHIIQELISN 705
V+Q FE + + +++ G+ L++Q Y V++K L++ +++ +++EL +
Sbjct: 74 VIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVREL--D 131
Query: 706 AHLDQVMLDPYGNYVIQAALQQSKGGVHSALVDAIRPHVPVLRTSPYGKKVL 757
H+ + + D GN+V+Q ++ + ++DA + V L T PYG +V+
Sbjct: 132 GHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVI 183
Score = 50.4 bits (119), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 54/252 (21%), Positives = 102/252 (40%), Gaps = 34/252 (13%)
Query: 540 KVIETLKSPEQFSLVVSSLKPGIVTLIKNMNGNHVAQRCLLYLLPEYSKFLFQATTNNCV 599
+++E ++ +L + + I+ ++ +G+ Q L P + +F
Sbjct: 4 RLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAY 63
Query: 600 ELATDRHGCCVIQKCLTHSEGEQRHRLVSKITSNALILSQDPFGNYVVQFVFELRLPWAT 659
+L D G VIQK EQ+ L +I + L L+ +G V+Q E
Sbjct: 64 QLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQ 123
Query: 660 MDILDQLEGNYGDLSMQKYSSNVVEKC--------LKYGDDERRAH------------II 699
+++ +L+G+ + ++VV+KC L++ D + +I
Sbjct: 124 NEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVI 183
Query: 700 QELISNA--------------HLDQVMLDPYGNYVIQAALQQSKGGVHSALVDAIRPHVP 745
Q ++ + H +Q++ D YGNYVIQ L+ + S +V IR +V
Sbjct: 184 QRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVL 243
Query: 746 VLRTSPYGKKVL 757
VL + V+
Sbjct: 244 VLSQHKFASNVV 255
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 45/194 (23%), Positives = 82/194 (42%), Gaps = 18/194 (9%)
Query: 407 CLSLSTPNAGCFQIDGLNS--WPLSSDSMDLKIIRP------QPQKYNSVEEVTGRIYLM 458
C+ P + F ID + LS+ ++I+ Q +EE+ +
Sbjct: 150 CIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQL 209
Query: 459 AKDQHGCRFLQRKISEGTLEDIEKIFVEIIDHIVELMTDPFGNYLVQKLLEVCNEDQRMQ 518
+DQ+G +Q + G ED KI EI +++ L F + +V+K + + +R
Sbjct: 210 VQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAV 269
Query: 519 ILQAI-TRKAGDLVRISTR--------AVQKVIETLKSPEQFSLVVSSLKPGIVTLIKNM 569
++ + T G + T VQK+I+ + P Q +V+ ++P I TL K
Sbjct: 270 LIDEVCTMNDGPHSALYTMMKDQYANYVVQKMID-VAEPGQRKIVMHKIRPHIATLRKYT 328
Query: 570 NGNHVAQRCLLYLL 583
G H+ + Y +
Sbjct: 329 YGKHILAKLEKYYM 342
>pdb|2YJY|A Chain A, A Specific And Modular Binding Code For Cytosine
Recognition In Puf Domains
pdb|2YJY|B Chain B, A Specific And Modular Binding Code For Cytosine
Recognition In Puf Domains
Length = 350
Score = 176 bits (445), Expect = 5e-44, Method: Compositional matrix adjust.
Identities = 102/318 (32%), Positives = 171/318 (53%), Gaps = 8/318 (2%)
Query: 448 VEEVTGRIYLMAKDQHGCRFLQRKISEGTLEDIEKIFVEIIDHIVELMTDPFGNYLVQKL 507
+ E+ G I ++DQHG RF+Q K+ T + + +F EI+ +LM D FGNY++QK
Sbjct: 20 LREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKF 79
Query: 508 LEVCNEDQRMQILQAITRKAGDLV--RISTRAVQKVIETLKSPEQFSLVVSSLKPGIVTL 565
E + +Q++ + + I L R +QK +E + S +Q +V L ++
Sbjct: 80 FEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMV-RELDGHVLKC 138
Query: 566 IKNMNGNHVAQRCLLYLLPEYSKFLFQATTNNCVELATDRHGCCVIQKCLTHSEGEQRHR 625
+K+ NGNHV Q+C+ + P+ +F+ A L+T +GC VIQ+ L H +Q
Sbjct: 139 VKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLP 198
Query: 626 LVSKITSNALILSQDPFGNYVVQFVFELRLPWATMDILDQLEGNYGDLSMQKYSSNVVEK 685
++ ++ + L QD +G+YV++ V E P I+ ++ GN LS K++SNVVEK
Sbjct: 199 ILEELHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEK 258
Query: 686 CLKYGDDERRAHIIQELIS-----NAHLDQVMLDPYGNYVIQAALQQSKGGVHSALVDAI 740
C+ + RA +I E+ + ++ L +M D Y NYV+Q + ++ G ++ I
Sbjct: 259 CVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKI 318
Query: 741 RPHVPVLRTSPYGKKVLS 758
RPH+ LR YGK +L+
Sbjct: 319 RPHIATLRKYTYGKHILA 336
Score = 76.3 bits (186), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 59/259 (22%), Positives = 122/259 (47%), Gaps = 16/259 (6%)
Query: 443 QKYNSVEEVTGRIYLMAKDQHGCRFLQRKISEGTLEDIEKIFVEIIDHIVELMTDPFGNY 502
QK E + G + +A +GCR +Q+ + + ++ E+ H+++ + D GN+
Sbjct: 87 QKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVRELDGHVLKCVKDQNGNH 146
Query: 503 LVQKLLEVCNEDQRMQILQAITRKAGDLVRIST-----RAVQKVIETLKSPEQFSLVVSS 557
+VQK +E C + Q +Q + I G + +ST R +Q+++E P+Q ++
Sbjct: 147 VVQKCIE-CVQPQSLQFI--IDAFKGQVFALSTHPYGCRVIQRILEHC-LPDQTLPILEE 202
Query: 558 LKPGIVTLIKNMNGNHVAQRCLLYLLPEYSKFLFQATTNNCVELATDRHGCCVIQKCLTH 617
L L+++ G++V + L + PE + N + L+ + V++KC+TH
Sbjct: 203 LHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTH 262
Query: 618 SEGEQRHRLVSKIT-------SNALILSQDPFGNYVVQFVFELRLPWATMDILDQLEGNY 670
+ +R L+ ++ S + +D + NYVVQ + ++ P ++ ++ +
Sbjct: 263 ASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHI 322
Query: 671 GDLSMQKYSSNVVEKCLKY 689
L Y +++ K KY
Sbjct: 323 ATLRKYTYGKHILAKLEKY 341
Score = 74.3 bits (181), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 45/172 (26%), Positives = 88/172 (51%), Gaps = 2/172 (1%)
Query: 586 YSKFLFQATTNNCVELATDRHGCCVIQKCLTHSEGEQRHRLVSKITSNALILSQDPFGNY 645
Y + + +E + D+HG IQ L + +R + ++I A L D FGNY
Sbjct: 15 YPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNY 74
Query: 646 VVQFVFELRLPWATMDILDQLEGNYGDLSMQKYSSNVVEKCLKYGDDERRAHIIQELISN 705
V+Q FE + + +++ G+ L++Q Y V++K L++ +++ +++EL +
Sbjct: 75 VIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEMVREL--D 132
Query: 706 AHLDQVMLDPYGNYVIQAALQQSKGGVHSALVDAIRPHVPVLRTSPYGKKVL 757
H+ + + D GN+V+Q ++ + ++DA + V L T PYG +V+
Sbjct: 133 GHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVI 184
Score = 47.0 bits (110), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 52/252 (20%), Positives = 102/252 (40%), Gaps = 34/252 (13%)
Query: 540 KVIETLKSPEQFSLVVSSLKPGIVTLIKNMNGNHVAQRCLLYLLPEYSKFLFQATTNNCV 599
+++E ++ +L + + I+ ++ +G+ Q L P + +F
Sbjct: 5 RLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAY 64
Query: 600 ELATDRHGCCVIQKCLTHSEGEQRHRLVSKITSNALILSQDPFGNYVVQFVFELRLPWAT 659
+L D G VIQK EQ+ L +I + L L+ +G V+Q E
Sbjct: 65 QLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQ 124
Query: 660 MDILDQLEGNYGDLSMQKYSSNVVEKC--------LKYGDDERRAH------------II 699
+++ +L+G+ + ++VV+KC L++ D + +I
Sbjct: 125 NEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVI 184
Query: 700 QELISNA--------------HLDQVMLDPYGNYVIQAALQQSKGGVHSALVDAIRPHVP 745
Q ++ + H +Q++ D YG+YVI+ L+ + S +V IR +V
Sbjct: 185 QRILEHCLPDQTLPILEELHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGNVL 244
Query: 746 VLRTSPYGKKVL 757
VL + V+
Sbjct: 245 VLSQHKFASNVV 256
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 44/194 (22%), Positives = 82/194 (42%), Gaps = 18/194 (9%)
Query: 407 CLSLSTPNAGCFQIDGLNS--WPLSSDSMDLKIIRP------QPQKYNSVEEVTGRIYLM 458
C+ P + F ID + LS+ ++I+ Q +EE+ +
Sbjct: 151 CIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQL 210
Query: 459 AKDQHGCRFLQRKISEGTLEDIEKIFVEIIDHIVELMTDPFGNYLVQKLLEVCNEDQRMQ 518
+DQ+G ++ + G ED KI EI +++ L F + +V+K + + +R
Sbjct: 211 VQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAV 270
Query: 519 ILQAI-TRKAGDLVRISTR--------AVQKVIETLKSPEQFSLVVSSLKPGIVTLIKNM 569
++ + T G + T VQK+I+ + P Q +V+ ++P I TL K
Sbjct: 271 LIDEVCTMNDGPHSALYTMMKDQYANYVVQKMID-VAEPGQRKIVMHKIRPHIATLRKYT 329
Query: 570 NGNHVAQRCLLYLL 583
G H+ + Y +
Sbjct: 330 YGKHILAKLEKYYM 343
>pdb|3H3D|X Chain X, Drosophila Pumilio Rna Binding Domain (Puf Domain)
pdb|3H3D|Y Chain Y, Drosophila Pumilio Rna Binding Domain (Puf Domain)
Length = 323
Score = 155 bits (392), Expect = 7e-38, Method: Compositional matrix adjust.
Identities = 100/307 (32%), Positives = 161/307 (52%), Gaps = 11/307 (3%)
Query: 448 VEEVTGRIYLMAKDQHGCRFLQRKISEGTLEDIEKIFVEIIDHIVELMTDPFGNYLVQKL 507
+ ++ I ++DQHG RF+Q+K+ T + + +F EI+ LMTD FGNY++QK
Sbjct: 21 LRDLANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKF 80
Query: 508 LEVCNEDQR----MQILQAITRKAGDLVRISTRAVQKVIETLKSPEQFSLVVSSLKPGIV 563
E +Q+ MQ+ + + A L R +QK +E++ SPEQ +V L ++
Sbjct: 81 FEFGTPEQKNTLGMQVKGHVLQLA--LQMYGCRVIQKALESI-SPEQQQEIVHELDGHVL 137
Query: 564 TLIKNMNGNHVAQRCLLYLLPEYSKFLFQATTNNCVELATDRHGCCVIQKCLTHSEGEQR 623
+K+ NGNHV Q+C+ + P +F+ A L+T +GC VIQ+ L H EQ
Sbjct: 138 KCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQT 197
Query: 624 HRLVSKITSNALILSQDPFGNYVVQFVFELRLPWATMDILDQLEGNYGDLSMQKYSSNVV 683
++ ++ + L QD +GNYV+Q V E +++ + G LS K++SNVV
Sbjct: 198 TPILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFASNVV 257
Query: 684 EKCLKYGDDERRAHIIQELIS---NAHLDQVMLDPYGNYVIQAALQQSKGGVHSALVDAI 740
EKC+ + R +I E+ + NA L +M D Y NYV+Q + S+ L+ I
Sbjct: 258 EKCVTHATRGERTGLIDEVCTFNDNA-LHVMMKDQYANYVVQKMIDVSEPTQLKKLMTKI 316
Query: 741 RPHVPVL 747
R ++ L
Sbjct: 317 RKNMAAL 323
Score = 99.0 bits (245), Expect = 9e-21, Method: Compositional matrix adjust.
Identities = 66/223 (29%), Positives = 113/223 (50%), Gaps = 3/223 (1%)
Query: 535 TRAVQKVIETLKSPEQFSLVVSSLKPGIVTLIKNMNGNHVAQRCLLYLLPEYSKFLFQAT 594
+R +Q+ +E + E+ +V S + +L+ ++ GN+V Q+ + PE L
Sbjct: 38 SRFIQQKLERATAAEK-QMVFSEILAAAYSLMTDVFGNYVIQKFFEFGTPEQKNTLGMQV 96
Query: 595 TNNCVELATDRHGCCVIQKCLTHSEGEQRHRLVSKITSNALILSQDPFGNYVVQFVFELR 654
+ ++LA +GC VIQK L EQ+ +V ++ + L +D GN+VVQ E
Sbjct: 97 KGHVLQLALQMYGCRVIQKALESISPEQQQEIVHELDGHVLKCVKDQNGNHVVQKCIECV 156
Query: 655 LPWATMDILDQLEGNYGDLSMQKYSSNVVEKCLKYGDDERRAHIIQELISNAHLDQVMLD 714
P A I++ +G LS Y V+++ L++ E+ I+ EL + H +Q++ D
Sbjct: 157 DPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQTTPILDEL--HEHTEQLIQD 214
Query: 715 PYGNYVIQAALQQSKGGVHSALVDAIRPHVPVLRTSPYGKKVL 757
YGNYVIQ L+ K S L++++R V VL + V+
Sbjct: 215 QYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFASNVV 257
Score = 81.6 bits (200), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 52/187 (27%), Positives = 95/187 (50%), Gaps = 2/187 (1%)
Query: 571 GNHVAQRCLLYLLPEYSKFLFQATTNNCVELATDRHGCCVIQKCLTHSEGEQRHRLVSKI 630
G+H+++ + Y + N+ VE + D+HG IQ+ L + ++ + S+I
Sbjct: 1 GSHMSRLLEDFRNQRYPNLQLRDLANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEI 60
Query: 631 TSNALILSQDPFGNYVVQFVFELRLPWATMDILDQLEGNYGDLSMQKYSSNVVEKCLKYG 690
+ A L D FGNYV+Q FE P + Q++G+ L++Q Y V++K L+
Sbjct: 61 LAAAYSLMTDVFGNYVIQKFFEFGTPEQKNTLGMQVKGHVLQLALQMYGCRVIQKALESI 120
Query: 691 DDERRAHIIQELISNAHLDQVMLDPYGNYVIQAALQQSKGGVHSALVDAIRPHVPVLRTS 750
E++ I+ EL + H+ + + D GN+V+Q ++ +++A + V L T
Sbjct: 121 SPEQQQEIVHEL--DGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTH 178
Query: 751 PYGKKVL 757
PYG +V+
Sbjct: 179 PYGCRVI 185
>pdb|3K49|A Chain A, Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr
Recognition Sequence Site B
pdb|3K49|C Chain C, Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr
Recognition Sequence Site B
pdb|3K49|E Chain E, Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr
Recognition Sequence Site B
pdb|3K4E|A Chain A, Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr
Recognition Sequence Site A
pdb|3K4E|C Chain C, Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr
Recognition Sequence Site A
pdb|3K4E|E Chain E, Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr
Recognition Sequence Site A
Length = 369
Score = 145 bits (367), Expect = 7e-35, Method: Compositional matrix adjust.
Identities = 97/322 (30%), Positives = 165/322 (51%), Gaps = 20/322 (6%)
Query: 448 VEEVTGRIYLMAKDQHGCRFLQRKISEGTLEDIEKIFVEIIDHIVELMTDPFGNYLVQKL 507
++++ G KDQHG RF+QR+++ + E IF EI D +EL D FGNY++QK
Sbjct: 26 LKDIFGHSLEFCKDQHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKF 85
Query: 508 LEVCNEDQRMQILQAI--TRKAGDLVRISTRAVQKVIETLKSPEQFSLVVSSLKPGIVTL 565
E ++ Q+ ++ K L + R +QK +E + S ++ LV+ L ++ +
Sbjct: 86 FEFGSKIQKNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLE-LSDSVLQM 144
Query: 566 IKNMNGNHVAQRCLLYLLPEYSKFLFQATTNNCVELATDRHGCCVIQKCLTHSEGEQRHR 625
IK+ NGNHV Q+ + + E F+ + T + L+T +GC VIQ+ L E +
Sbjct: 145 IKDQNGNHVIQKAIETIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQES 204
Query: 626 LVSKITSNALILSQDPFGNYVVQFVFE------LRLPWATMDILDQLEGNYGDLSMQKYS 679
+++++ L QD +GNYV+Q+V + + +I++ + N + S K++
Sbjct: 205 ILNELKDFIPYLIQDQYGNYVIQYVLQQDQFTNKEMVDIKQEIIETVANNVVEYSKHKFA 264
Query: 680 SNVVEKCLKYGDDERRAHIIQELI-------SNAHLDQVML----DPYGNYVIQAALQQS 728
SNVVEK + YG ++ II +++ N D M+ D + NYVIQ + S
Sbjct: 265 SNVVEKSILYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFANYVIQKLVNVS 324
Query: 729 KGGVHSALVDAIRPHVPVLRTS 750
+G +V AIR ++ L S
Sbjct: 325 EGEGKKLIVIAIRAYLDKLNKS 346
Score = 87.8 bits (216), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 53/161 (32%), Positives = 90/161 (55%), Gaps = 2/161 (1%)
Query: 597 NCVELATDRHGCCVIQKCLTHSEGEQRHRLVSKITSNALILSQDPFGNYVVQFVFELRLP 656
+ +E D+HG IQ+ L S ++ + ++I +A+ LS D FGNYV+Q FE
Sbjct: 32 HSLEFCKDQHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKFFEFGSK 91
Query: 657 WATMDILDQLEGNYGDLSMQKYSSNVVEKCLKYGDDERRAHIIQELISNAHLDQVMLDPY 716
++DQ +GN LS+Q Y+ V++K L+Y D +R ++ EL S++ L Q++ D
Sbjct: 92 IQKNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLEL-SDSVL-QMIKDQN 149
Query: 717 GNYVIQAALQQSKGGVHSALVDAIRPHVPVLRTSPYGKKVL 757
GN+VIQ A++ ++ ++ H+ L T YG +V+
Sbjct: 150 GNHVIQKAIETIPIEKLPFILSSLTGHIYHLSTHSYGCRVI 190
Score = 65.5 bits (158), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 54/230 (23%), Positives = 112/230 (48%), Gaps = 28/230 (12%)
Query: 443 QKYNSVEEVTGRIYLMAKDQHGCRFLQRKISEGTLEDIEKIFVEIIDHIVELMTDPFGNY 502
QK V++ G + ++ + CR +Q+ + ++ +E+ D +++++ D GN+
Sbjct: 93 QKNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLELSDSVLQMIKDQNGNH 152
Query: 503 LVQKLLEVCNEDQRMQILQAITRKAGDLVRIST-----RAVQKVIETLKSPEQFSLVVSS 557
++QK +E ++ IL ++T G + +ST R +Q+++E S +Q S +++
Sbjct: 153 VIQKAIETIPIEKLPFILSSLT---GHIYHLSTHSYGCRVIQRLLEFGSSEDQES-ILNE 208
Query: 558 LKPGIVTLIKNMNGNHVAQRCLLY------LLPEYSKFLFQATTNNCVELATDRHGCCVI 611
LK I LI++ GN+V Q L + + + + + NN VE + + V+
Sbjct: 209 LKDFIPYLIQDQYGNYVIQYVLQQDQFTNKEMVDIKQEIIETVANNVVEYSKHKFASNVV 268
Query: 612 QKCLTHSEGEQRHRLVSKIT-------------SNALILSQDPFGNYVVQ 648
+K + + Q+ ++SKI S +++ +D F NYV+Q
Sbjct: 269 EKSILYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFANYVIQ 318
>pdb|3QG9|A Chain A, Crystal Structure Of Fbf-2GLD-1 Fbea A7u Mutant Complex
pdb|3V6Y|A Chain A, Crystal Structure Of Fbf-2 In Complex With A Mutant Gld-1
Fbea13 Rna
pdb|3V74|A Chain A, Crystal Structure Of Fbf-2 In Complex With Gld-1 Fbea13
Rna
Length = 413
Score = 80.1 bits (196), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 82/325 (25%), Positives = 158/325 (48%), Gaps = 47/325 (14%)
Query: 447 SVEEV--TGRIYLMAKDQHGCRFLQRKISEGTLEDIEK--IFVEII---DHIVELMTDPF 499
S+ EV +G + A D+ GC+FL++ + +G+L +K +F ++I D ++L T+ F
Sbjct: 22 SLSEVLDSGDLMKFAVDKTGCQFLEKAV-KGSLTSYQKFQLFEQVIGRKDDFLKLSTNIF 80
Query: 500 GNYLVQKLLEV---CNED---QRMQILQ-AITRKAGDLV--RISTRAVQKVIETLKSPEQ 550
GNYLVQ ++ + N+D +R + L+ I+ + D+ + + R +Q ++ +
Sbjct: 81 GNYLVQSVIGISLATNDDGYTKRQEKLKNFISSQMTDMCLDKFACRVIQSSLQNMDLSLA 140
Query: 551 FSLVVSSLKPG-IVTLIKNMNGNHVAQRCLLYLLPEYSKFL--FQATTNNCVELATDRHG 607
LV + + ++ + + N NHV Q+ + + + +F+ F AT + ++ +D++G
Sbjct: 141 CKLVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEHLRQICSDKYG 200
Query: 608 CCVIQKC------------LTHSEGEQR----HRLVSKITSNALILSQDPFGNYVVQFVF 651
C V+Q LT + R RL++ +T+ L+ + + NY++Q +
Sbjct: 201 CRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQHIV 260
Query: 652 --ELRLPWATMDILDQLEGNYGDLSMQKYSSNVVEKCLKYGDDERRAHIIQELISNA--- 706
+ + I L N LS +K++S+VVEK + E A ++ E+
Sbjct: 261 SNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIPH 320
Query: 707 ------HLDQVMLDPYGNYVIQAAL 725
LD +M +GNYV+Q L
Sbjct: 321 PDTGKDALDIMMFHQFGNYVVQCML 345
Score = 35.4 bits (80), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 39/184 (21%), Positives = 76/184 (41%), Gaps = 53/184 (28%)
Query: 595 TNNCVELATDRHGCCVIQKCLTHS-EGEQRHRLVSKIT---SNALILSQDPFGNYVVQFV 650
+ + ++ A D+ GC ++K + S Q+ +L ++ + L LS + FGNY+VQ V
Sbjct: 29 SGDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNIFGNYLVQSV 88
Query: 651 FELRLPWATMD---------ILDQLEGNYGDLSMQKYSSNVVEKCLKYGD---------- 691
+ L AT D + + + D+ + K++ V++ L+ D
Sbjct: 89 IGISL--ATNDDGYTKRQEKLKNFISSQMTDMCLDKFACRVIQSSLQNMDLSLACKLVQA 146
Query: 692 ------------DERRAHIIQELISNA----------------HLDQVMLDPYGNYVIQA 723
D+ H+IQ++++ HL Q+ D YG V+Q
Sbjct: 147 LPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEHLRQICSDKYGCRVVQT 206
Query: 724 ALQQ 727
+++
Sbjct: 207 IIEK 210
>pdb|3K5Q|A Chain A, Crystal Structure Of Fbf-2FBE COMPLEX
pdb|3K5Y|A Chain A, Crystal Structure Of Fbf-2GLD-1 Fbea Complex
pdb|3K5Z|A Chain A, Crystal Structure Of Fbf-2GLD-1 Fbea G4a Mutant Complex
pdb|3K61|A Chain A, Crystal Structure Of Fbf-2FOG-1 Fbea Complex
pdb|3K62|A Chain A, Crystal Structure Of Fbf-2GLD-1 Fbeb Complex
pdb|3K64|A Chain A, Crystal Structure Of Fbf-2FEM-3 Pme Complex
Length = 412
Score = 80.1 bits (196), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 82/325 (25%), Positives = 158/325 (48%), Gaps = 47/325 (14%)
Query: 447 SVEEV--TGRIYLMAKDQHGCRFLQRKISEGTLEDIEK--IFVEII---DHIVELMTDPF 499
S+ EV +G + A D+ GC+FL++ + +G+L +K +F ++I D ++L T+ F
Sbjct: 21 SLSEVLDSGDLMKFAVDKTGCQFLEKAV-KGSLTSYQKFQLFEQVIGRKDDFLKLSTNIF 79
Query: 500 GNYLVQKLLEV---CNED---QRMQILQ-AITRKAGDLV--RISTRAVQKVIETLKSPEQ 550
GNYLVQ ++ + N+D +R + L+ I+ + D+ + + R +Q ++ +
Sbjct: 80 GNYLVQSVIGISLATNDDGYTKRQEKLKNFISSQMTDMCLDKFACRVIQSSLQNMDLSLA 139
Query: 551 FSLVVSSLKPG-IVTLIKNMNGNHVAQRCLLYLLPEYSKFL--FQATTNNCVELATDRHG 607
LV + + ++ + + N NHV Q+ + + + +F+ F AT + ++ +D++G
Sbjct: 140 CKLVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEHLRQICSDKYG 199
Query: 608 CCVIQKC------------LTHSEGEQR----HRLVSKITSNALILSQDPFGNYVVQFVF 651
C V+Q LT + R RL++ +T+ L+ + + NY++Q +
Sbjct: 200 CRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQHIV 259
Query: 652 --ELRLPWATMDILDQLEGNYGDLSMQKYSSNVVEKCLKYGDDERRAHIIQELISNA--- 706
+ + I L N LS +K++S+VVEK + E A ++ E+
Sbjct: 260 SNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIPH 319
Query: 707 ------HLDQVMLDPYGNYVIQAAL 725
LD +M +GNYV+Q L
Sbjct: 320 PDTGKDALDIMMFHQFGNYVVQCML 344
Score = 35.0 bits (79), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 39/184 (21%), Positives = 76/184 (41%), Gaps = 53/184 (28%)
Query: 595 TNNCVELATDRHGCCVIQKCLTHS-EGEQRHRLVSKIT---SNALILSQDPFGNYVVQFV 650
+ + ++ A D+ GC ++K + S Q+ +L ++ + L LS + FGNY+VQ V
Sbjct: 28 SGDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNIFGNYLVQSV 87
Query: 651 FELRLPWATMD---------ILDQLEGNYGDLSMQKYSSNVVEKCLKYGD---------- 691
+ L AT D + + + D+ + K++ V++ L+ D
Sbjct: 88 IGISL--ATNDDGYTKRQEKLKNFISSQMTDMCLDKFACRVIQSSLQNMDLSLACKLVQA 145
Query: 692 ------------DERRAHIIQELISNA----------------HLDQVMLDPYGNYVIQA 723
D+ H+IQ++++ HL Q+ D YG V+Q
Sbjct: 146 LPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEHLRQICSDKYGCRVVQT 205
Query: 724 ALQQ 727
+++
Sbjct: 206 IIEK 209
>pdb|3QGB|A Chain A, Crystal Structure Of Fbf-2 R288y Mutant In Complex With
Gld-1 Fbea
pdb|3QGC|A Chain A, Crystal Structure Of Fbf-2 R288y Mutant In Complex With
Gld-1 Fbea A7u Mutant
Length = 413
Score = 77.4 bits (189), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 81/325 (24%), Positives = 157/325 (48%), Gaps = 47/325 (14%)
Query: 447 SVEEV--TGRIYLMAKDQHGCRFLQRKISEGTLEDIEK--IFVEII---DHIVELMTDPF 499
S+ EV +G + A D+ GC+FL++ + +G+L +K +F ++I D ++L T+ F
Sbjct: 22 SLSEVLDSGDLMKFAVDKTGCQFLEKAV-KGSLTSYQKFQLFEQVIGRKDDFLKLSTNIF 80
Query: 500 GNYLVQKLLEV---CNED---QRMQILQ-AITRKAGDLV--RISTRAVQKVIETLKSPEQ 550
GNYLVQ ++ + N+D +R + L+ I+ + D+ + + +Q ++ +
Sbjct: 81 GNYLVQSVIGISLATNDDGYTKRQEKLKNFISSQMTDMCLDKFACYVIQSSLQNMDLSLA 140
Query: 551 FSLVVSSLKPG-IVTLIKNMNGNHVAQRCLLYLLPEYSKFL--FQATTNNCVELATDRHG 607
LV + + ++ + + N NHV Q+ + + + +F+ F AT + ++ +D++G
Sbjct: 141 CKLVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEHLRQICSDKYG 200
Query: 608 CCVIQKC------------LTHSEGEQR----HRLVSKITSNALILSQDPFGNYVVQFVF 651
C V+Q LT + R RL++ +T+ L+ + + NY++Q +
Sbjct: 201 CRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQHIV 260
Query: 652 --ELRLPWATMDILDQLEGNYGDLSMQKYSSNVVEKCLKYGDDERRAHIIQELISNA--- 706
+ + I L N LS +K++S+VVEK + E A ++ E+
Sbjct: 261 SNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAFLHAPLELLAEMMDEIFDGYIPH 320
Query: 707 ------HLDQVMLDPYGNYVIQAAL 725
LD +M +GNYV+Q L
Sbjct: 321 PDTGKDALDIMMFHQFGNYVVQCML 345
Score = 34.7 bits (78), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 39/184 (21%), Positives = 76/184 (41%), Gaps = 53/184 (28%)
Query: 595 TNNCVELATDRHGCCVIQKCLTHS-EGEQRHRLVSKIT---SNALILSQDPFGNYVVQFV 650
+ + ++ A D+ GC ++K + S Q+ +L ++ + L LS + FGNY+VQ V
Sbjct: 29 SGDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNIFGNYLVQSV 88
Query: 651 FELRLPWATMD---------ILDQLEGNYGDLSMQKYSSNVVEKCLKYGD---------- 691
+ L AT D + + + D+ + K++ V++ L+ D
Sbjct: 89 IGISL--ATNDDGYTKRQEKLKNFISSQMTDMCLDKFACYVIQSSLQNMDLSLACKLVQA 146
Query: 692 ------------DERRAHIIQELISNA----------------HLDQVMLDPYGNYVIQA 723
D+ H+IQ++++ HL Q+ D YG V+Q
Sbjct: 147 LPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEHLRQICSDKYGCRVVQT 206
Query: 724 ALQQ 727
+++
Sbjct: 207 IIEK 210
>pdb|3V71|A Chain A, Crystal Structure Of Puf-6 In Complex With 5be13 Rna
Length = 382
Score = 67.8 bits (164), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 78/351 (22%), Positives = 148/351 (42%), Gaps = 38/351 (10%)
Query: 440 PQPQKYNSVEEV--TGRIYLMAKDQHGCRFLQRKISEGTLEDIEKI----FVEIIDHIVE 493
P + S+E+V G++ A D G +FL+ + + I K F E V
Sbjct: 5 PVAPIFISLEDVLLNGQLIDFAIDPSGVKFLEANYPLDSEDQIRKAVFEKFTESTTLFVG 64
Query: 494 LMTDPFGNYLVQKLLEVCNEDQRMQILQAITRKAGDLV-----RISTRAVQKVIETLKSP 548
L GN++VQKL+E+ ++ ++L+ + G L+ + + R VQ ++
Sbjct: 65 LCHSRNGNFIVQKLVELATPAEQRELLRQMID--GGLLAMCKDKFACRVVQLALQKFDHS 122
Query: 549 EQFSLVVSSLKPGIVTLIKNMNGNHVAQRCLLYLLPEYSKFL--FQATTNNCVELATDRH 606
F L+ + + + HV QR + L + F F ++ ++ + + D++
Sbjct: 123 NVFQLIQELSTFDLAAMCTDQISIHVIQRVVKQLPVDMWTFFVHFLSSGDSLMAVCQDKY 182
Query: 607 GCCVIQKCLTHSEGEQR-----------HRLVSKITSNALILSQDPFGNYVVQFVFELR- 654
GC ++Q+ + + H L++ I N LS + F NYV+Q+V +
Sbjct: 183 GCRLVQQVIDRLAENPKLPCFKFRIQLLHSLMTCIVRNCYRLSSNEFANYVIQYVIKSSG 242
Query: 655 -LPWATMDILDQ-LEGNYGDLSMQKYSSNVVEKCLKYGDDERRAHIIQELISNA------ 706
+ I+D+ L N +S KY+S+V+E + +++E+ S
Sbjct: 243 IMEMYRDTIIDKCLLRNLLSMSQDKYASHVIEGAFLFAPPALLHEMMEEIFSGYVKDVES 302
Query: 707 ---HLDQVMLDPYGNYVIQAALQQSKGGVHSALVDAIRPHVPVLRTSPYGK 754
LD ++ YGNYV+Q + + + P + +L + Y K
Sbjct: 303 NRDALDILLFHQYGNYVVQQMISICTAALIGKEERELPPAILLLYSGWYEK 353
>pdb|3ICJ|A Chain A, Crystal Structure Of An Uncharacterized Metal-Dependent
Hydrolase From Pyrococcus Furiosus
Length = 534
Score = 32.3 bits (72), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 25/50 (50%)
Query: 81 IKRIPQEEANLPDDQSLTSAFAELRFNGGIPIEPVSPWANCNSSPNYAVL 130
+ R+ +E A S+ +L F+ PIEP PW + +++ N V+
Sbjct: 406 VNRVGEERAKWAYRLKTLSSITKLGFSTDSPIEPADPWVSIDAAVNRYVV 455
>pdb|3PND|A Chain A, Fad Binding By Apbe Protein From Salmonella Enterica: A
New Class Of Fad Binding Proteins
pdb|3PND|B Chain B, Fad Binding By Apbe Protein From Salmonella Enterica: A
New Class Of Fad Binding Proteins
pdb|3PND|C Chain C, Fad Binding By Apbe Protein From Salmonella Enterica: A
New Class Of Fad Binding Proteins
pdb|3PND|D Chain D, Fad Binding By Apbe Protein From Salmonella Enterica: A
New Class Of Fad Binding Proteins
Length = 337
Score = 30.4 bits (67), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 40/91 (43%), Gaps = 19/91 (20%)
Query: 423 LNSWPLSSDSMDLKIIRPQPQKYNSVEEVTGRIYLMAKDQHGCRFLQRKISEGTLEDIEK 482
+N W D L I P P + ++ + TG +L D+ G +FLQ+ D+
Sbjct: 109 VNLWGFGPDRQPLHI--PTPAQIDAAKAKTGLQHLQVIDRAGHQFLQK--------DLPD 158
Query: 483 IFVEI--------IDHIVELMT-DPFGNYLV 504
++V++ DH+ LM + YLV
Sbjct: 159 LYVDLSTVGEGYAADHLARLMEQEGIARYLV 189
>pdb|3MOI|A Chain A, The Crystal Structure Of The Putative Dehydrogenase From
Bordetella Bronchiseptica Rb50
Length = 387
Score = 30.4 bits (67), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 30/109 (27%), Positives = 46/109 (42%), Gaps = 14/109 (12%)
Query: 662 ILDQLEGNYGDLSMQKYS-SNVVEKCLKYGD-DERRAHIIQELISNAHLDQVMLDPYGNY 719
+L QLEG+ +L +Y + K ++ G+ D ++ H L++ H D + P G
Sbjct: 262 VLRQLEGDEAELRRSRYGFGGPISKSMESGNTDRKQPHFGVMLVTCEHAD-LRASPEGVL 320
Query: 720 V-----------IQAALQQSKGGVHSALVDAIRPHVPVLRTSPYGKKVL 757
V I S+G L DAI P LR + +GK L
Sbjct: 321 VYGDEGVREVPAITGRGPFSQGDTIDELRDAIAGVAPALRDARWGKDTL 369
>pdb|2A6Z|A Chain A, Crystal Structure Of Emp47p Carbohydrate Recognition
Domain (Crd), Monoclinic Crystal Form 1
pdb|2A70|A Chain A, Crystal Structure Of Emp47p Carbohydrate Recognition
Domain (Crd), Monoclinic Crystal Form 2
pdb|2A70|B Chain B, Crystal Structure Of Emp47p Carbohydrate Recognition
Domain (Crd), Monoclinic Crystal Form 2
pdb|2A71|A Chain A, Crystal Structure Of Emp47p Carbohydrate Recognition
Domain (Crd), Orthorhombic Crystal Form
pdb|2A71|B Chain B, Crystal Structure Of Emp47p Carbohydrate Recognition
Domain (Crd), Orthorhombic Crystal Form
pdb|2A71|C Chain C, Crystal Structure Of Emp47p Carbohydrate Recognition
Domain (Crd), Orthorhombic Crystal Form
pdb|2A71|D Chain D, Crystal Structure Of Emp47p Carbohydrate Recognition
Domain (Crd), Orthorhombic Crystal Form
Length = 222
Score = 30.0 bits (66), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 37 RVSSNYILPPITVNSSKGPLAEKLKNNGNLDEGKILVNKSQQSPIKRIPQEEANLPDDQS 96
++SS+Y LP + +N+ K P + +L+EG+I++ +Q S ++ +L D +
Sbjct: 6 KLSSDYSLPDL-INTRKVPNNWQTGEQASLEEGRIVLTSNQNSKGSLWLKQGFDLKDSFT 64
Query: 97 LTSAFAELRFNG 108
+ F + ++G
Sbjct: 65 MEWTFRSVGYSG 76
>pdb|2O8B|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T MISPAIR
pdb|2O8C|A Chain A, Human Mutsalpha (msh2/msh6) Bound To Adp And An
O6-methyl-guanine T Mispair
pdb|2O8D|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G DU MISPAIR
pdb|2O8F|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO DNA WITH A SINGLE BASE
T INSERT
pdb|3THW|A Chain A, Human Mutsbeta Complexed With An Idl Of 4 Bases (Loop4)
And Adp
pdb|3THX|A Chain A, Human Mutsbeta Complexed With An Idl Of 3 Bases (Loop3)
And Adp
pdb|3THY|A Chain A, Human Mutsbeta Complexed With An Idl Of 2 Bases (Loop2)
And Adp
pdb|3THZ|A Chain A, Human Mutsbeta Complexed With An Idl Of 6 Bases (Loop6)
And Adp
Length = 934
Score = 29.6 bits (65), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 34/144 (23%), Positives = 64/144 (44%), Gaps = 12/144 (8%)
Query: 96 SLTSAFAELRFNGGIPIEPVSPWANCNSSPNYAVLLDCQHPNGLK--EPVSNVDSQLMVA 153
+L SA +L + G I+ + ++ Y + C+ L+ + S VD Q
Sbjct: 495 TLISAARDLGLDPGKQIK-----LDSSAQFGYYFRVTCKEEKVLRNNKNFSTVDIQ---K 546
Query: 154 SSFQSTNSVPSGFDEFDLTKVRQESSNMVNLDVQELKKLQVGYRQPVENFSGALPNAHSL 213
+ + TNS + +E + TK + E + V+E+ + GY +P++ + L ++
Sbjct: 547 NGVKFTNSKLTSLNE-EYTKNKTEYEEAQDAIVKEIVNISSGYVEPMQTLNDVLAQLDAV 605
Query: 214 QGFRFLSN-VPVPGVEFPVMSDPQ 236
F +SN PVP V ++ Q
Sbjct: 606 VSFAHVSNGAPVPYVRPAILEKGQ 629
>pdb|2A6Y|A Chain A, Crystal Structure Of Emp47p Carbohydrate Recognition
Domain (Crd), Tetragonal Crystal Form
Length = 256
Score = 29.6 bits (65), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 37 RVSSNYILPPITVNSSKGPLAEKLKNNGNLDEGKILVNKSQQSPIKRIPQEEANLPDDQS 96
++SS+Y LP + +N+ K P + +L+EG+I++ +Q S ++ +L D +
Sbjct: 13 KLSSDYSLPDL-INTRKVPNNWQTGEQASLEEGRIVLTSNQNSKGSLWLKQGFDLKDSFT 71
Query: 97 LTSAFAELRFNG 108
+ F + ++G
Sbjct: 72 MEWTFRSVGYSG 83
>pdb|2O8E|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO A G T MISPAIR, WITH
ADP BOUND TO Msh2 Only
Length = 934
Score = 29.6 bits (65), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 34/144 (23%), Positives = 64/144 (44%), Gaps = 12/144 (8%)
Query: 96 SLTSAFAELRFNGGIPIEPVSPWANCNSSPNYAVLLDCQHPNGLK--EPVSNVDSQLMVA 153
+L SA +L + G I+ + ++ Y + C+ L+ + S VD Q
Sbjct: 495 TLISAARDLGLDPGKQIK-----LDSSAQFGYYFRVTCKEEKVLRNNKNFSTVDIQ---K 546
Query: 154 SSFQSTNSVPSGFDEFDLTKVRQESSNMVNLDVQELKKLQVGYRQPVENFSGALPNAHSL 213
+ + TNS + +E + TK + E + V+E+ + GY +P++ + L ++
Sbjct: 547 NGVKFTNSKLTSLNE-EYTKNKTEYEEAQDAIVKEIVNISSGYVEPMQTLNDVLAQLDAV 605
Query: 214 QGFRFLSN-VPVPGVEFPVMSDPQ 236
F +SN PVP V ++ Q
Sbjct: 606 VSFAHVSNGAPVPYVRPAILEKGQ 629
>pdb|3N7Z|A Chain A, Crystal Structure Of Acetyltransferase From Bacillus
Anthrac
pdb|3N7Z|B Chain B, Crystal Structure Of Acetyltransferase From Bacillus
Anthrac
pdb|3N7Z|C Chain C, Crystal Structure Of Acetyltransferase From Bacillus
Anthrac
pdb|3N7Z|D Chain D, Crystal Structure Of Acetyltransferase From Bacillus
Anthrac
pdb|3N7Z|E Chain E, Crystal Structure Of Acetyltransferase From Bacillus
Anthrac
pdb|3N7Z|F Chain F, Crystal Structure Of Acetyltransferase From Bacillus
Anthrac
Length = 388
Score = 29.6 bits (65), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 13/52 (25%), Positives = 25/52 (48%)
Query: 150 LMVASSFQSTNSVPSGFDEFDLTKVRQESSNMVNLDVQELKKLQVGYRQPVE 201
L + SF N++ ++T + + + LD+ L + GYR+P+E
Sbjct: 305 LHITDSFAQWNNITVRIANHEITIIEEPIDKGIKLDINALSTILFGYRRPLE 356
>pdb|2ZR5|A Chain A, Crystal Structure Of A Mutant Pin1 Peptidyl-Prolyl
Cis-Trans Isomerase
Length = 163
Score = 29.3 bits (64), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 34/68 (50%), Gaps = 3/68 (4%)
Query: 137 NGLKEPVSNVDSQLMVASSFQSTNSVPSGFDEFDLTKVRQESSNMVNLDVQELKKLQVGY 196
NG EP S L+VA S + PS + + +T+ ++E+ ++N +Q++K + +
Sbjct: 47 NGQGEPARVRCSHLLVA---HSQSRRPSSWRQEKITRTKEEALELINGYIQKIKSGEEDF 103
Query: 197 RQPVENFS 204
FS
Sbjct: 104 ESLASQFS 111
>pdb|2WNK|A Chain A, Structure Of Sporosag From Toxoplasma Gondii
pdb|2X28|A Chain A, Cadmium Bound Structure Of Sporosag
Length = 238
Score = 29.3 bits (64), Expect = 9.7, Method: Composition-based stats.
Identities = 20/69 (28%), Positives = 30/69 (43%), Gaps = 7/69 (10%)
Query: 104 LRFNGGIPIEPVSPWANCNSSPNYAVLLDCQHPNGLKEPVSNVDSQLMVASSFQSTNSVP 163
+RFN +E + P S DC + LK+ + + AS Q+ S P
Sbjct: 24 VRFNCPSTLEEIKPAYEAGDSTKVCTTADCSNEAALKDVLKS-------ASLAQAEGSGP 76
Query: 164 SGFDEFDLT 172
SG ++F LT
Sbjct: 77 SGGNDFTLT 85
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 0.133 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,099,000
Number of Sequences: 62578
Number of extensions: 910549
Number of successful extensions: 2331
Number of sequences better than 100.0: 33
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 2058
Number of HSP's gapped (non-prelim): 78
length of query: 764
length of database: 14,973,337
effective HSP length: 106
effective length of query: 658
effective length of database: 8,340,069
effective search space: 5487765402
effective search space used: 5487765402
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)