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= 003398
(823 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 406 bits (1043), Expect = e-113, Method: Compositional matrix adjust.
Identities = 192/338 (56%), Positives = 255/338 (75%), Gaps = 2/338 (0%)
Query: 474 SSLLDEFKTNKTRSFELSDIVDHVVEFSTDQYGSRFIQQKLEAATAEEKTRIFPEIIPHA 533
S LL++F+ N+ + +L D++ H+VEFS DQ+GSRFIQQKLE AT E+ +F EI+ A
Sbjct: 5 SRLLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAA 64
Query: 534 RTLMTDVFGNYVIQKFFEHGTESQRAQLASQLTGHVLRLSLQMYGCRVIQKALEVVHVDQ 593
LMTDVFGNYVIQKFFE G+ Q+ LA+++ GHVL L+LQMYGCRVIQKALE + DQ
Sbjct: 65 YQLMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQ 124
Query: 594 QTQMVAELDGSVMKCVHDQNGNHVIQKCIECIPQDRIQFIISSFYGQVVALSTHPYGCRV 653
Q++MV ELDG V+KCV DQNGNHV+QKCIEC+ +QFII +F GQV LSTHPYGCRV
Sbjct: 125 QSEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRV 184
Query: 654 IQRVLEHCDDANTQQIIMDEIMQHVCNLAQDQYGNYVIQHVLEHGKPHERTTVITQLAGQ 713
IQR+LEHC T I++E+ QH L QDQYGNYVIQHVLEHG+P +++ +++++ G+
Sbjct: 185 IQRILEHCTAEQTLP-ILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGK 243
Query: 714 IVRMSQQKFASNVVEKCLTFGSPEERQLLINEMLGSTD-ENEPLQAMMKDPFGNYVVQKV 772
++ +SQ KFASNVVEKC+T S ER LLI+E+ D + L MMKD + NYVVQK+
Sbjct: 244 VLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKM 303
Query: 773 LETCDDQSLELILSRIRVHLNVLKKYTYGKHIVSRIEK 810
++ + ++I+ +IR H+ L+KYTYGKHI++++EK
Sbjct: 304 IDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKLEK 341
>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 = 401 bits (1031), Expect = e-112, Method: Compositional matrix adjust.
Identities = 192/340 (56%), Positives = 255/340 (75%), Gaps = 4/340 (1%)
Query: 474 SSLLDEFKTNKTRSFELSDIVDHVVEFSTDQYGSRFIQQKLEAATAEEKTRIFPEIIPHA 533
S LL++F+ N+ + +L D++ H+VEFS DQ+GSRFIQQKLE AT E+ +F EI+ A
Sbjct: 3 SRLLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAA 62
Query: 534 RTLMTDVFGNYVIQKFFEHGTESQRAQLASQLTGHVLRLSLQMYGCRVIQKALEVVHVDQ 593
LMTDVFGNYVIQKFFE G+ Q+ LA+++ GHVL L+LQMYGCRVIQKALE + DQ
Sbjct: 63 YQLMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQ 122
Query: 594 Q--TQMVAELDGSVMKCVHDQNGNHVIQKCIECIPQDRIQFIISSFYGQVVALSTHPYGC 651
Q ++MV ELDG V+KCV DQNGNHV+QKCIEC+ +QFII +F GQV LSTHPYGC
Sbjct: 123 QVISEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGC 182
Query: 652 RVIQRVLEHCDDANTQQIIMDEIMQHVCNLAQDQYGNYVIQHVLEHGKPHERTTVITQLA 711
RVIQR+LEHC T I++E+ QH L QDQYGNYVIQHVLEHG+P +++ +++++
Sbjct: 183 RVIQRILEHCTAEQTLP-ILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIR 241
Query: 712 GQIVRMSQQKFASNVVEKCLTFGSPEERQLLINEMLGSTD-ENEPLQAMMKDPFGNYVVQ 770
G+++ +SQ KFASNVVEKC+T S ER LLI+E+ D + L MMKD + NYVVQ
Sbjct: 242 GKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQ 301
Query: 771 KVLETCDDQSLELILSRIRVHLNVLKKYTYGKHIVSRIEK 810
K+++ + ++I+ +IR H+ L+KYTYGKHI++++EK
Sbjct: 302 KMIDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKLEK 341
>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 = 394 bits (1013), Expect = e-110, Method: Compositional matrix adjust.
Identities = 189/344 (54%), Positives = 250/344 (72%), Gaps = 2/344 (0%)
Query: 474 SSLLDEFKTNKTRSFELSDIVDHVVEFSTDQYGSRFIQQKLEAATAEEKTRIFPEIIPHA 533
S LL++F+ N+ + +L +I H++EFS DQ+GSRFIQ KLE AT E+ +F EI+ A
Sbjct: 3 SRLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAA 62
Query: 534 RTLMTDVFGNYVIQKFFEHGTESQRAQLASQLTGHVLRLSLQMYGCRVIQKALEVVHVDQ 593
LM DVFGNYVIQKFFE G+ Q+ LA ++ GHVL L+LQMYGCRVIQKALE + DQ
Sbjct: 63 YQLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQ 122
Query: 594 QTQMVAELDGSVMKCVHDQNGNHVIQKCIECIPQDRIQFIISSFYGQVVALSTHPYGCRV 653
Q +MV ELDG V+KCV DQNGNHV+QKCIEC+ +QFII +F GQV ALSTHPYGCRV
Sbjct: 123 QNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRV 182
Query: 654 IQRVLEHCDDANTQQIIMDEIMQHVCNLAQDQYGNYVIQHVLEHGKPHERTTVITQLAGQ 713
IQR+LEHC T I++E+ QH L QDQYGNYVIQHVLEHG+P +++ ++ ++ G
Sbjct: 183 IQRILEHCLPDQTLP-ILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGN 241
Query: 714 IVRMSQQKFASNVVEKCLTFGSPEERQLLINEMLGSTD-ENEPLQAMMKDPFGNYVVQKV 772
++ +SQ KFASNVVEKC+T S ER +LI+E+ D + L MMKD + NYVVQK+
Sbjct: 242 VLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKM 301
Query: 773 LETCDDQSLELILSRIRVHLNVLKKYTYGKHIVSRIEKLIATGG 816
++ + ++++ +IR H+ L+KYTYGKHI++++EK G
Sbjct: 302 IDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKLEKYYMKNG 345
Score = 55.1 bits (131), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 33/114 (28%), Positives = 57/114 (50%), Gaps = 6/114 (5%)
Query: 707 ITQLAGQIVRMSQQKFASNVVEKCLTFGSPEERQLLINEMLGSTDENEPLQAMMKDPFGN 766
+ ++AG I+ SQ + S ++ L +P ERQL+ NE+L + + +M D FGN
Sbjct: 19 LREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQ------LMVDVFGN 72
Query: 767 YVVQKVLETCDDQSLELILSRIRVHLNVLKKYTYGKHIVSRIEKLIATGGEGSL 820
YV+QK E + + RIR H+ L YG ++ + + I + + +
Sbjct: 73 YVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEM 126
>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 = 393 bits (1009), Expect = e-109, Method: Compositional matrix adjust.
Identities = 188/338 (55%), Positives = 249/338 (73%), Gaps = 2/338 (0%)
Query: 474 SSLLDEFKTNKTRSFELSDIVDHVVEFSTDQYGSRFIQQKLEAATAEEKTRIFPEIIPHA 533
S LL++F+ N+ + +L +I H++EFS DQ+GSRFIQ KLE AT E+ +F EI+ A
Sbjct: 3 SRLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAA 62
Query: 534 RTLMTDVFGNYVIQKFFEHGTESQRAQLASQLTGHVLRLSLQMYGCRVIQKALEVVHVDQ 593
LM DVFGNYVIQKFFE G+ Q+ LA ++ GHVL L+LQMYGCRVIQKALE + DQ
Sbjct: 63 YQLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQ 122
Query: 594 QTQMVAELDGSVMKCVHDQNGNHVIQKCIECIPQDRIQFIISSFYGQVVALSTHPYGCRV 653
Q +MV ELDG V+KCV DQNGNHV+QKCIEC+ +QFII +F GQV ALSTHPYGCRV
Sbjct: 123 QNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRV 182
Query: 654 IQRVLEHCDDANTQQIIMDEIMQHVCNLAQDQYGNYVIQHVLEHGKPHERTTVITQLAGQ 713
IQR+LEHC T I++E+ QH L QDQYGNYVIQHVLEHG+P +++ ++ ++ G
Sbjct: 183 IQRILEHCLPDQTLP-ILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGN 241
Query: 714 IVRMSQQKFASNVVEKCLTFGSPEERQLLINEMLGSTD-ENEPLQAMMKDPFGNYVVQKV 772
++ +SQ KFASNVVEKC+T S ER +LI+E+ D + L MMKD + NYVVQK+
Sbjct: 242 VLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKM 301
Query: 773 LETCDDQSLELILSRIRVHLNVLKKYTYGKHIVSRIEK 810
++ + ++++ +IR H+ L+KYTYGKHI++++EK
Sbjct: 302 IDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKLEK 339
Score = 55.1 bits (131), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 33/114 (28%), Positives = 57/114 (50%), Gaps = 6/114 (5%)
Query: 707 ITQLAGQIVRMSQQKFASNVVEKCLTFGSPEERQLLINEMLGSTDENEPLQAMMKDPFGN 766
+ ++AG I+ SQ + S ++ L +P ERQL+ NE+L + + +M D FGN
Sbjct: 19 LREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQ------LMVDVFGN 72
Query: 767 YVVQKVLETCDDQSLELILSRIRVHLNVLKKYTYGKHIVSRIEKLIATGGEGSL 820
YV+QK E + + RIR H+ L YG ++ + + I + + +
Sbjct: 73 YVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEM 126
>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 = 391 bits (1004), Expect = e-108, Method: Compositional matrix adjust.
Identities = 187/344 (54%), Positives = 250/344 (72%), Gaps = 2/344 (0%)
Query: 474 SSLLDEFKTNKTRSFELSDIVDHVVEFSTDQYGSRFIQQKLEAATAEEKTRIFPEIIPHA 533
S LL++F+ N+ + +L +I H++EFS DQ+GSRFIQ KLE AT E+ +F EI+ A
Sbjct: 4 SRLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAA 63
Query: 534 RTLMTDVFGNYVIQKFFEHGTESQRAQLASQLTGHVLRLSLQMYGCRVIQKALEVVHVDQ 593
LM DVFGNYVIQKFFE G+ Q+ LA ++ GHVL L+LQMYGCRVIQKALE + DQ
Sbjct: 64 YQLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQ 123
Query: 594 QTQMVAELDGSVMKCVHDQNGNHVIQKCIECIPQDRIQFIISSFYGQVVALSTHPYGCRV 653
Q +MV ELDG V+KCV DQNGNHV+QKCIEC+ +QFII +F GQV ALSTHPYGCRV
Sbjct: 124 QNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRV 183
Query: 654 IQRVLEHCDDANTQQIIMDEIMQHVCNLAQDQYGNYVIQHVLEHGKPHERTTVITQLAGQ 713
IQR+LEHC T I++E+ QH L QDQYG+YVI+HVLEHG+P +++ ++ ++ G
Sbjct: 184 IQRILEHCLPDQTLP-ILEELHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGN 242
Query: 714 IVRMSQQKFASNVVEKCLTFGSPEERQLLINEMLGSTD-ENEPLQAMMKDPFGNYVVQKV 772
++ +SQ KFASNVVEKC+T S ER +LI+E+ D + L MMKD + NYVVQK+
Sbjct: 243 VLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKM 302
Query: 773 LETCDDQSLELILSRIRVHLNVLKKYTYGKHIVSRIEKLIATGG 816
++ + ++++ +IR H+ L+KYTYGKHI++++EK G
Sbjct: 303 IDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKLEKYYMKNG 346
Score = 55.1 bits (131), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 33/114 (28%), Positives = 57/114 (50%), Gaps = 6/114 (5%)
Query: 707 ITQLAGQIVRMSQQKFASNVVEKCLTFGSPEERQLLINEMLGSTDENEPLQAMMKDPFGN 766
+ ++AG I+ SQ + S ++ L +P ERQL+ NE+L + + +M D FGN
Sbjct: 20 LREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQ------LMVDVFGN 73
Query: 767 YVVQKVLETCDDQSLELILSRIRVHLNVLKKYTYGKHIVSRIEKLIATGGEGSL 820
YV+QK E + + RIR H+ L YG ++ + + I + + +
Sbjct: 74 YVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQNEM 127
>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 = 368 bits (945), Expect = e-102, Method: Compositional matrix adjust.
Identities = 181/326 (55%), Positives = 238/326 (73%), Gaps = 3/326 (0%)
Query: 470 GRLSSSLLDEFKTNKTRSFELSDIVDHVVEFSTDQYGSRFIQQKLEAATAEEKTRIFPEI 529
G S LL++F+ + + +L D+ +H+VEFS DQ+GSRFIQQKLE ATA EK +F EI
Sbjct: 1 GSHMSRLLEDFRNQRYPNLQLRDLANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEI 60
Query: 530 IPHARTLMTDVFGNYVIQKFFEHGTESQRAQLASQLTGHVLRLSLQMYGCRVIQKALEVV 589
+ A +LMTDVFGNYVIQKFFE GT Q+ L Q+ GHVL+L+LQMYGCRVIQKALE +
Sbjct: 61 LAAAYSLMTDVFGNYVIQKFFEFGTPEQKNTLGMQVKGHVLQLALQMYGCRVIQKALESI 120
Query: 590 HVDQQTQMVAELDGSVMKCVHDQNGNHVIQKCIECIPQDRIQFIISSFYGQVVALSTHPY 649
+QQ ++V ELDG V+KCV DQNGNHV+QKCIEC+ +QFII++F GQV +LSTHPY
Sbjct: 121 SPEQQQEIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPY 180
Query: 650 GCRVIQRVLEHCDDANTQQIIMDEIMQHVCNLAQDQYGNYVIQHVLEHGKPHERTTVITQ 709
GCRVIQR+LEHC T I+DE+ +H L QDQYGNYVIQHVLEHGK +++ +I
Sbjct: 181 GCRVIQRILEHCTAEQTTP-ILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINS 239
Query: 710 LAGQIVRMSQQKFASNVVEKCLTFGSPEERQLLINEMLGSTDENEPLQAMMKDPFGNYVV 769
+ G+++ +SQ KFASNVVEKC+T + ER LI+E+ D L MMKD + NYVV
Sbjct: 240 VRGKVLVLSQHKFASNVVEKCVTHATRGERTGLIDEVCTFND--NALHVMMKDQYANYVV 297
Query: 770 QKVLETCDDQSLELILSRIRVHLNVL 795
QK+++ + L+ ++++IR ++ L
Sbjct: 298 QKMIDVSEPTQLKKLMTKIRKNMAAL 323
Score = 102 bits (253), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 71/255 (27%), Positives = 129/255 (50%), Gaps = 12/255 (4%)
Query: 565 LTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAELDGSVMKCVHDQNGNHVIQKCIEC 624
L H++ S +G R IQ+ LE ++ + +E+ + + D GN+VIQK E
Sbjct: 24 LANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEF 83
Query: 625 IPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEHCDDANTQQIIMDEIMQHVCNLAQD 684
++ + G V+ L+ YGCRVIQ+ LE Q+I+ E+ HV +D
Sbjct: 84 GTPEQKNTLGMQVKGHVLQLALQMYGCRVIQKALESISPEQQQEIV-HELDGHVLKCVKD 142
Query: 685 QYGNYVIQHVLEHGKPHERTTVITQLAGQIVRMSQQKFASNVVEKCLTFGSPEERQLLIN 744
Q GN+V+Q +E P +I GQ+ +S + V+++ L + E+ +++
Sbjct: 143 QNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQTTPILD 202
Query: 745 EMLGSTDENEPLQAMMKDPFGNYVVQKVLETCDDQSLELILSRIRVHLNVLKKYTYGKHI 804
E+ +E + +++D +GNYV+Q VLE + ++++ +R + VL ++ + ++
Sbjct: 203 EL------HEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFASNV 256
Query: 805 VSRIEKLI--ATGGE 817
V EK + AT GE
Sbjct: 257 V---EKCVTHATRGE 268
>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 = 281 bits (719), Expect = 1e-75, Method: Compositional matrix adjust.
Identities = 153/338 (45%), Positives = 218/338 (64%), Gaps = 15/338 (4%)
Query: 490 LSDIVDHVVEFSTDQYGSRFIQQKLEAATAEEKTRIFPEIIPHARTLMTDVFGNYVIQKF 549
L DI H +EF DQ+GSRFIQ++L + A EK IF EI A L DVFGNYVIQKF
Sbjct: 26 LKDIFGHSLEFCKDQHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKF 85
Query: 550 FEHGTESQRAQLASQLTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAELDGSVMKCV 609
FE G++ Q+ L Q G++ +LSLQMY CRVIQKALE + +Q+ ++V EL SV++ +
Sbjct: 86 FEFGSKIQKNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLELSDSVLQMI 145
Query: 610 HDQNGNHVIQKCIECIPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEHCDDANTQQI 669
DQNGNHVIQK IE IP +++ FI+SS G + LSTH YGCRVIQR+LE + Q+
Sbjct: 146 KDQNGNHVIQKAIETIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEF-GSSEDQES 204
Query: 670 IMDEIMQHVCNLAQDQYGNYVIQHVLEHGKPHERTTV------ITQLAGQIVRMSQQKFA 723
I++E+ + L QDQYGNYVIQ+VL+ + + V I +A +V S+ KFA
Sbjct: 205 ILNELKDFIPYLIQDQYGNYVIQYVLQQDQFTNKEMVDIKQEIIETVANNVVEYSKHKFA 264
Query: 724 SNVVEKCLTFGSPEERQLLINEMLG-------STDENEPLQAMMKDPFGNYVVQKVLETC 776
SNVVEK + +GS ++ L+I+++L + +++ P+ M+KD F NYV+QK++
Sbjct: 265 SNVVEKSILYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFANYVIQKLVNVS 324
Query: 777 DDQSLELILSRIRVHLNVLKKY-TYGKHIVSRIEKLIA 813
+ + +LI+ IR +L+ L K + G ++ +EKL A
Sbjct: 325 EGEGKKLIVIAIRAYLDKLNKSNSLGNRHLASVEKLAA 362
>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 = 170 bits (430), Expect = 4e-42, Method: Compositional matrix adjust.
Identities = 108/317 (34%), Positives = 172/317 (54%), Gaps = 17/317 (5%)
Query: 500 FSTDQYGSRFIQQKLEAATAEEKTRIFPEIIPHARTLMTDVFGNYVIQKFFEHGTESQRA 559
DQ+G RF+Q++L+ ++ IF E + LMTD FGNY+IQK E T QR
Sbjct: 18 LCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQRI 77
Query: 560 QLASQLTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAE-LDGSVMKCVHDQNGNHVI 618
L + H + +SL +GCR +QK +E + D++ Q+V + L ++ D NGNHVI
Sbjct: 78 VLTKISSPHFVEISLNPHGCRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVI 137
Query: 619 QKCIECIPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEHCDDANTQQI--IMDEIMQ 676
QKC++ + + QFI + + ++TH +GCRV+QR L+H T+Q + D+++
Sbjct: 138 QKCLQRLKPENFQFIFDAISDSCIDIATHRHGCRVLQRCLDH---GTTEQCDNLCDKLLA 194
Query: 677 HVCNLAQDQYGNYVIQHVL----EHGKPHERTTVITQLAGQIVRMSQQKFASNVVEKCLT 732
V L D +GNYV+Q+++ E K ++ L + + +S KF SNV+EK L
Sbjct: 195 LVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILK 254
Query: 733 FGSPEERQLLINEMLGSTDENEPLQAMMKDPFGNYVVQKVLETCDDQSLELI--LSRIRV 790
E +L E+L + E +Q+++ D +GNYV+Q L+ Q+ L LS I
Sbjct: 255 TAIVSEPMIL--EILNNGGET-GIQSLLNDSYGNYVLQTALDISHKQNDYLYKRLSEIVA 311
Query: 791 HLNV--LKKYTYGKHIV 805
L V ++ +GK I+
Sbjct: 312 PLLVGPIRNTPHGKRII 328
Score = 97.1 bits (240), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 55/210 (26%), Positives = 106/210 (50%), Gaps = 6/210 (2%)
Query: 564 QLTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAELDGSVMKCVHDQNGNHVIQKCIE 623
Q G + L +GCR +QK L+++ + E ++ + D GN++IQK +E
Sbjct: 10 QYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLE 69
Query: 624 CIPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEHCDDANTQQIIMDEIMQHVCNLAQ 683
+ ++ + V +S +P+GCR +Q+++E QI++D + + L++
Sbjct: 70 EVTTEQRIVLTKISSPHFVEISLNPHGCRALQKLIECIKTDEEAQIVVDSLRPYTVQLSK 129
Query: 684 DQYGNYVIQHVLEHGKPHERTTVITQLAGQIVRMSQQKFASNVVEKCLTFGSPEERQLLI 743
D GN+VIQ L+ KP + ++ + ++ + V+++CL G+ E+ L
Sbjct: 130 DLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCRVLQRCLDHGTTEQCDNLC 189
Query: 744 NEMLGSTDENEPLQAMMKDPFGNYVVQKVL 773
+++L D+ + DPFGNYVVQ ++
Sbjct: 190 DKLLALVDK------LTLDPFGNYVVQYII 213
Score = 54.3 bits (129), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 55/231 (23%), Positives = 94/231 (40%), Gaps = 40/231 (17%)
Query: 471 RLSSSLLDEFKTNKTRSFELSDIVDHVVEFSTDQYGSRFIQQKLEAATAEEKTRIFPEII 530
R L++ KT++ + + + V+ S D G+ IQ+ L+ E IF I
Sbjct: 98 RALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAIS 157
Query: 531 PHARTLMTDVFGNYVIQKFFEHGTESQRAQLASQLTGHVLRLSLQMYGCRVIQKALEVVH 590
+ T G V+Q+ +HGT Q L +L V +L+L +G V+Q
Sbjct: 158 DSCIDIATHRHGCRVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQ------- 210
Query: 591 VDQQTQMVAELDGSVMKCVHDQNGNHVIQKCIECIPQDRIQFIISSFYGQVVALSTHPYG 650
++I K E D I+ + + LS H +G
Sbjct: 211 -------------------------YIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFG 245
Query: 651 CRVIQRVLEHCDDANTQQIIMDEIMQH-----VCNLAQDQYGNYVIQHVLE 696
VI+++L+ A + ++ EI+ + + +L D YGNYV+Q L+
Sbjct: 246 SNVIEKILK---TAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALD 293
Score = 29.3 bits (64), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 27/140 (19%), Positives = 63/140 (45%), Gaps = 9/140 (6%)
Query: 670 IMDEIMQHVCNLAQDQYGNYVIQHVLEHGKPHERTTVITQLAGQIVRMSQQKFASNVVEK 729
++D+ + + +L +DQ+G +Q L+ + + V + F + +++K
Sbjct: 7 VLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQK 66
Query: 730 CLTFGSPEERQLLINEMLGSTDENEP-LQAMMKDPFGNYVVQKVLETCD-DQSLELILSR 787
L + E+R +L T + P + +P G +QK++E D+ ++++
Sbjct: 67 LLEEVTTEQRIVL-------TKISSPHFVEISLNPHGCRALQKLIECIKTDEEAQIVVDS 119
Query: 788 IRVHLNVLKKYTYGKHIVSR 807
+R + L K G H++ +
Sbjct: 120 LRPYTVQLSKDLNGNHVIQK 139
>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 = 163 bits (413), Expect = 3e-40, Method: Compositional matrix adjust.
Identities = 106/320 (33%), Positives = 170/320 (53%), Gaps = 23/320 (7%)
Query: 500 FSTDQYGSRFIQQKLEAATAEEKTRIFPEIIPHARTLMTDVFGNYVIQKFFEHGTESQRA 559
DQ+G RF+Q++L+ ++ IF E + LMTD FGNY+IQK E T QR
Sbjct: 40 LCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQRI 99
Query: 560 QLASQLTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAE-LDGSVMKCVHDQNGNHVI 618
L + H + +SL +G R +QK +E + D++ Q+V + L ++ D NGNHVI
Sbjct: 100 VLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVI 159
Query: 619 QKCIECIPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEH-----CDDANTQQIIMDE 673
QKC++ + + QFI + + ++TH +GC V+QR L+H CD+ + D+
Sbjct: 160 QKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDN------LCDK 213
Query: 674 IMQHVCNLAQDQYGNYVIQHVL----EHGKPHERTTVITQLAGQIVRMSQQKFASNVVEK 729
++ V L D +GNYV+Q+++ E K ++ L + + +S KF SNV+EK
Sbjct: 214 LLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEK 273
Query: 730 CLTFGSPEERQLLINEMLGSTDENEPLQAMMKDPFGNYVVQKVLETCDDQSLELI--LSR 787
L E +L E+L + E +Q+++ D +GNYV+Q L+ Q+ L LS
Sbjct: 274 ILKTAIVSEPMIL--EILNNGGET-GIQSLLNDSYGNYVLQTALDISHKQNDYLYKRLSE 330
Query: 788 IRVHLNV--LKKYTYGKHIV 805
I L V ++ +GK I+
Sbjct: 331 IVAPLLVGPIRNTPHGKRII 350
Score = 93.6 bits (231), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 54/210 (25%), Positives = 105/210 (50%), Gaps = 6/210 (2%)
Query: 564 QLTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAELDGSVMKCVHDQNGNHVIQKCIE 623
Q G + L +GCR +QK L+++ + E ++ + D GN++IQK +E
Sbjct: 32 QYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLE 91
Query: 624 CIPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEHCDDANTQQIIMDEIMQHVCNLAQ 683
+ ++ + V +S +P+G R +Q+++E QI++D + + L++
Sbjct: 92 EVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSK 151
Query: 684 DQYGNYVIQHVLEHGKPHERTTVITQLAGQIVRMSQQKFASNVVEKCLTFGSPEERQLLI 743
D GN+VIQ L+ KP + ++ + ++ + V+++CL G+ E+ L
Sbjct: 152 DLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLC 211
Query: 744 NEMLGSTDENEPLQAMMKDPFGNYVVQKVL 773
+++L D+ + DPFGNYVVQ ++
Sbjct: 212 DKLLALVDK------LTLDPFGNYVVQYII 235
Score = 29.3 bits (64), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 7/83 (8%)
Query: 706 VITQLAGQIVRMSQQKFASNVVEKCLTFGSPEERQLLINEMLGSTDENEPLQAMMKDPFG 765
V+ Q G I + + + ++K L + + E T E +M D FG
Sbjct: 29 VLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVE------LMTDSFG 82
Query: 766 NYVVQKVLETCDDQSLELILSRI 788
NY++QK+LE + ++L++I
Sbjct: 83 NYLIQKLLEEVTTEQ-RIVLTKI 104
>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 = 162 bits (410), Expect = 7e-40, Method: Compositional matrix adjust.
Identities = 106/317 (33%), Positives = 170/317 (53%), Gaps = 17/317 (5%)
Query: 500 FSTDQYGSRFIQQKLEAATAEEKTRIFPEIIPHARTLMTDVFGNYVIQKFFEHGTESQRA 559
DQ+G RF+Q++L+ ++ IF E + LMTD FGNY+IQK E T QR
Sbjct: 18 LCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQRI 77
Query: 560 QLASQLTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAE-LDGSVMKCVHDQNGNHVI 618
L + H + +SL +G R +QK +E + D++ Q+V + L ++ D NGNHVI
Sbjct: 78 VLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVI 137
Query: 619 QKCIECIPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEHCDDANTQQI--IMDEIMQ 676
QKC++ + + QFI + + ++TH +GC V+QR L+H T+Q + D+++
Sbjct: 138 QKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDH---GTTEQCDNLCDKLLA 194
Query: 677 HVCNLAQDQYGNYVIQHVL----EHGKPHERTTVITQLAGQIVRMSQQKFASNVVEKCLT 732
V L D +GNYV+Q+++ E K ++ L + + +S KF SNV+EK L
Sbjct: 195 LVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILK 254
Query: 733 FGSPEERQLLINEMLGSTDENEPLQAMMKDPFGNYVVQKVLETCDDQSLELI--LSRIRV 790
E +L E+L + E +Q+++ D +GNYV+Q L+ Q+ L LS I
Sbjct: 255 TAIVSEPMIL--EILNNGGET-GIQSLLNDSYGNYVLQTALDISHKQNDYLYKRLSEIVA 311
Query: 791 HLNV--LKKYTYGKHIV 805
L V ++ +GK I+
Sbjct: 312 PLLVGPIRNTPHGKRII 328
Score = 92.4 bits (228), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 54/210 (25%), Positives = 105/210 (50%), Gaps = 6/210 (2%)
Query: 564 QLTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAELDGSVMKCVHDQNGNHVIQKCIE 623
Q G + L +GCR +QK L+++ + E ++ + D GN++IQK +E
Sbjct: 10 QYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLE 69
Query: 624 CIPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEHCDDANTQQIIMDEIMQHVCNLAQ 683
+ ++ + V +S +P+G R +Q+++E QI++D + + L++
Sbjct: 70 EVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSK 129
Query: 684 DQYGNYVIQHVLEHGKPHERTTVITQLAGQIVRMSQQKFASNVVEKCLTFGSPEERQLLI 743
D GN+VIQ L+ KP + ++ + ++ + V+++CL G+ E+ L
Sbjct: 130 DLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLC 189
Query: 744 NEMLGSTDENEPLQAMMKDPFGNYVVQKVL 773
+++L D+ + DPFGNYVVQ ++
Sbjct: 190 DKLLALVDK------LTLDPFGNYVVQYII 213
Score = 54.3 bits (129), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 55/231 (23%), Positives = 94/231 (40%), Gaps = 40/231 (17%)
Query: 471 RLSSSLLDEFKTNKTRSFELSDIVDHVVEFSTDQYGSRFIQQKLEAATAEEKTRIFPEII 530
R L++ KT++ + + + V+ S D G+ IQ+ L+ E IF I
Sbjct: 98 RALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAIS 157
Query: 531 PHARTLMTDVFGNYVIQKFFEHGTESQRAQLASQLTGHVLRLSLQMYGCRVIQKALEVVH 590
+ T G V+Q+ +HGT Q L +L V +L+L +G V+Q
Sbjct: 158 DSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQ------- 210
Query: 591 VDQQTQMVAELDGSVMKCVHDQNGNHVIQKCIECIPQDRIQFIISSFYGQVVALSTHPYG 650
++I K E D I+ + + LS H +G
Sbjct: 211 -------------------------YIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFG 245
Query: 651 CRVIQRVLEHCDDANTQQIIMDEIMQH-----VCNLAQDQYGNYVIQHVLE 696
VI+++L+ A + ++ EI+ + + +L D YGNYV+Q L+
Sbjct: 246 SNVIEKILK---TAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALD 293
Score = 30.0 bits (66), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 27/140 (19%), Positives = 63/140 (45%), Gaps = 9/140 (6%)
Query: 670 IMDEIMQHVCNLAQDQYGNYVIQHVLEHGKPHERTTVITQLAGQIVRMSQQKFASNVVEK 729
++D+ + + +L +DQ+G +Q L+ + + V + F + +++K
Sbjct: 7 VLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQK 66
Query: 730 CLTFGSPEERQLLINEMLGSTDENEP-LQAMMKDPFGNYVVQKVLETCD-DQSLELILSR 787
L + E+R +L T + P + +P G +QK++E D+ ++++
Sbjct: 67 LLEEVTTEQRIVL-------TKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDS 119
Query: 788 IRVHLNVLKKYTYGKHIVSR 807
+R + L K G H++ +
Sbjct: 120 LRPYTVQLSKDLNGNHVIQK 139
>pdb|3BWT|A Chain A, Crystal Structure Of The Rna Binding Domain Of Puf4 From
Saccharomyces Cerevisiae
Length = 333
Score = 162 bits (410), Expect = 8e-40, Method: Compositional matrix adjust.
Identities = 106/317 (33%), Positives = 170/317 (53%), Gaps = 17/317 (5%)
Query: 500 FSTDQYGSRFIQQKLEAATAEEKTRIFPEIIPHARTLMTDVFGNYVIQKFFEHGTESQRA 559
DQ+G RF+Q++L+ ++ IF E + LMTD FGNY+IQK E T QR
Sbjct: 18 LCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQRI 77
Query: 560 QLASQLTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAE-LDGSVMKCVHDQNGNHVI 618
L + H + +SL +G R +QK +E + D++ Q+V + L ++ D NGNHVI
Sbjct: 78 VLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVI 137
Query: 619 QKCIECIPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEHCDDANTQQI--IMDEIMQ 676
QKC++ + + QFI + + ++TH +GC V+QR L+H T+Q + D+++
Sbjct: 138 QKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDH---GTTEQCDNLCDKLLA 194
Query: 677 HVCNLAQDQYGNYVIQHVL----EHGKPHERTTVITQLAGQIVRMSQQKFASNVVEKCLT 732
V L D +GNYV+Q+++ E K ++ L + + +S KF SNV+EK L
Sbjct: 195 LVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILK 254
Query: 733 FGSPEERQLLINEMLGSTDENEPLQAMMKDPFGNYVVQKVLETCDDQSLELI--LSRIRV 790
E +L E+L + E +Q+++ D +GNYV+Q L+ Q+ L LS I
Sbjct: 255 TAIVSEPMIL--EILNNGGET-GIQSLLNDSYGNYVLQTALDISHKQNDYLYKRLSEIVA 311
Query: 791 HLNV--LKKYTYGKHIV 805
L V ++ +GK I+
Sbjct: 312 PLLVGPIRNTPHGKRII 328
Score = 92.0 bits (227), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 54/210 (25%), Positives = 105/210 (50%), Gaps = 6/210 (2%)
Query: 564 QLTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAELDGSVMKCVHDQNGNHVIQKCIE 623
Q G + L +GCR +QK L+++ + E ++ + D GN++IQK +E
Sbjct: 10 QYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLE 69
Query: 624 CIPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEHCDDANTQQIIMDEIMQHVCNLAQ 683
+ ++ + V +S +P+G R +Q+++E QI++D + + L++
Sbjct: 70 EVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSK 129
Query: 684 DQYGNYVIQHVLEHGKPHERTTVITQLAGQIVRMSQQKFASNVVEKCLTFGSPEERQLLI 743
D GN+VIQ L+ KP + ++ + ++ + V+++CL G+ E+ L
Sbjct: 130 DLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLC 189
Query: 744 NEMLGSTDENEPLQAMMKDPFGNYVVQKVL 773
+++L D+ + DPFGNYVVQ ++
Sbjct: 190 DKLLALVDK------LTLDPFGNYVVQYII 213
Score = 54.3 bits (129), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 55/231 (23%), Positives = 94/231 (40%), Gaps = 40/231 (17%)
Query: 471 RLSSSLLDEFKTNKTRSFELSDIVDHVVEFSTDQYGSRFIQQKLEAATAEEKTRIFPEII 530
R L++ KT++ + + + V+ S D G+ IQ+ L+ E IF I
Sbjct: 98 RALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAIS 157
Query: 531 PHARTLMTDVFGNYVIQKFFEHGTESQRAQLASQLTGHVLRLSLQMYGCRVIQKALEVVH 590
+ T G V+Q+ +HGT Q L +L V +L+L +G V+Q
Sbjct: 158 DSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQ------- 210
Query: 591 VDQQTQMVAELDGSVMKCVHDQNGNHVIQKCIECIPQDRIQFIISSFYGQVVALSTHPYG 650
++I K E D I+ + + LS H +G
Sbjct: 211 -------------------------YIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFG 245
Query: 651 CRVIQRVLEHCDDANTQQIIMDEIMQH-----VCNLAQDQYGNYVIQHVLE 696
VI+++L+ A + ++ EI+ + + +L D YGNYV+Q L+
Sbjct: 246 SNVIEKILK---TAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALD 293
Score = 30.0 bits (66), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 27/140 (19%), Positives = 63/140 (45%), Gaps = 9/140 (6%)
Query: 670 IMDEIMQHVCNLAQDQYGNYVIQHVLEHGKPHERTTVITQLAGQIVRMSQQKFASNVVEK 729
++D+ + + +L +DQ+G +Q L+ + + V + F + +++K
Sbjct: 7 VLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQK 66
Query: 730 CLTFGSPEERQLLINEMLGSTDENEP-LQAMMKDPFGNYVVQKVLETCD-DQSLELILSR 787
L + E+R +L T + P + +P G +QK++E D+ ++++
Sbjct: 67 LLEEVTTEQRIVL-------TKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDS 119
Query: 788 IRVHLNVLKKYTYGKHIVSR 807
+R + L K G H++ +
Sbjct: 120 LRPYTVQLSKDLNGNHVIQK 139
>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 = 128 bits (321), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 98/362 (27%), Positives = 172/362 (47%), Gaps = 63/362 (17%)
Query: 460 WHLDAGINMEGRLSSSLLDEFKTNKTRSFELSDIVD--HVVEFSTDQYGSRFIQQKLEAA 517
W LD+ M RLS LS+++D +++F+ D+ G +F+++ ++ +
Sbjct: 8 WSLDSNGEMRSRLS----------------LSEVLDSGDLMKFAVDKTGCQFLEKAVKGS 51
Query: 518 -TAEEKTRIFPEIIPHARTLM---TDVFGNYVIQKFF-------EHGTESQRAQLASQLT 566
T+ +K ++F ++I + T++FGNY++Q + G ++ +L + ++
Sbjct: 52 LTSYQKFQLFEQVIGRKDDFLKLSTNIFGNYLVQSVIGISLATNDDGYTKRQEKLKNFIS 111
Query: 567 GHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAEL--DGSVMKCVHDQNGNHVIQKCIEC 624
+ + L + CRVIQ +L+ + + ++V L D ++ DQN NHVIQK +
Sbjct: 112 SQMTDMCLDKFACRVIQSSLQNMDLSLACKLVQALPRDARLIAICVDQNANHVIQKVVAV 171
Query: 625 IPQDRIQFIISSFYG--QVVALSTHPYGCRVIQRVLEH--CDDANTQ------------- 667
IP +FI+ + + + YGCRV+Q ++E D N
Sbjct: 172 IPLKNWEFIVDFVATPEHLRQICSDKYGCRVVQTIIEKLTADSMNVDLTSAAQNLRERAL 231
Query: 668 QIIMDEIMQHVCNLAQDQYGNYVIQHVLEHGK-PHERTTVITQ-LAGQIVRMSQQKFASN 725
Q +M + LA ++Y NY+IQH++ + R +I + L ++ +SQ+KFAS+
Sbjct: 232 QRLMTSVTNRCQELATNEYANYIIQHIVSNDDLAVYRECIIEKCLMRNLLSLSQEKFASH 291
Query: 726 VVEKCLTFGSPEERQLLINEMLGSTDE---------NEPLQAMMKDPFGNYVVQKVLETC 776
VVEK E L+ EM+ + + L MM FGNYVVQ +L C
Sbjct: 292 VVEKAFLHAPLE----LLAEMMDEIFDGYIPHPDTGKDALDIMMFHQFGNYVVQCMLTIC 347
Query: 777 DD 778
D
Sbjct: 348 CD 349
>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 = 128 bits (321), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 98/362 (27%), Positives = 172/362 (47%), Gaps = 63/362 (17%)
Query: 460 WHLDAGINMEGRLSSSLLDEFKTNKTRSFELSDIVD--HVVEFSTDQYGSRFIQQKLEAA 517
W LD+ M RLS LS+++D +++F+ D+ G +F+++ ++ +
Sbjct: 9 WSLDSNGEMRSRLS----------------LSEVLDSGDLMKFAVDKTGCQFLEKAVKGS 52
Query: 518 -TAEEKTRIFPEIIPHARTLM---TDVFGNYVIQKFF-------EHGTESQRAQLASQLT 566
T+ +K ++F ++I + T++FGNY++Q + G ++ +L + ++
Sbjct: 53 LTSYQKFQLFEQVIGRKDDFLKLSTNIFGNYLVQSVIGISLATNDDGYTKRQEKLKNFIS 112
Query: 567 GHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAEL--DGSVMKCVHDQNGNHVIQKCIEC 624
+ + L + CRVIQ +L+ + + ++V L D ++ DQN NHVIQK +
Sbjct: 113 SQMTDMCLDKFACRVIQSSLQNMDLSLACKLVQALPRDARLIAICVDQNANHVIQKVVAV 172
Query: 625 IPQDRIQFIISSFYG--QVVALSTHPYGCRVIQRVLEH--CDDANTQ------------- 667
IP +FI+ + + + YGCRV+Q ++E D N
Sbjct: 173 IPLKNWEFIVDFVATPEHLRQICSDKYGCRVVQTIIEKLTADSMNVDLTSAAQNLRERAL 232
Query: 668 QIIMDEIMQHVCNLAQDQYGNYVIQHVLEHGK-PHERTTVITQ-LAGQIVRMSQQKFASN 725
Q +M + LA ++Y NY+IQH++ + R +I + L ++ +SQ+KFAS+
Sbjct: 233 QRLMTSVTNRCQELATNEYANYIIQHIVSNDDLAVYRECIIEKCLMRNLLSLSQEKFASH 292
Query: 726 VVEKCLTFGSPEERQLLINEMLGSTDE---------NEPLQAMMKDPFGNYVVQKVLETC 776
VVEK E L+ EM+ + + L MM FGNYVVQ +L C
Sbjct: 293 VVEKAFLHAPLE----LLAEMMDEIFDGYIPHPDTGKDALDIMMFHQFGNYVVQCMLTIC 348
Query: 777 DD 778
D
Sbjct: 349 CD 350
>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 = 125 bits (313), Expect = 1e-28, Method: Compositional matrix adjust.
Identities = 97/362 (26%), Positives = 171/362 (47%), Gaps = 63/362 (17%)
Query: 460 WHLDAGINMEGRLSSSLLDEFKTNKTRSFELSDIVD--HVVEFSTDQYGSRFIQQKLEAA 517
W LD+ M RLS LS+++D +++F+ D+ G +F+++ ++ +
Sbjct: 9 WSLDSNGEMRSRLS----------------LSEVLDSGDLMKFAVDKTGCQFLEKAVKGS 52
Query: 518 -TAEEKTRIFPEIIPHARTLM---TDVFGNYVIQKFF-------EHGTESQRAQLASQLT 566
T+ +K ++F ++I + T++FGNY++Q + G ++ +L + ++
Sbjct: 53 LTSYQKFQLFEQVIGRKDDFLKLSTNIFGNYLVQSVIGISLATNDDGYTKRQEKLKNFIS 112
Query: 567 GHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAEL--DGSVMKCVHDQNGNHVIQKCIEC 624
+ + L + C VIQ +L+ + + ++V L D ++ DQN NHVIQK +
Sbjct: 113 SQMTDMCLDKFACYVIQSSLQNMDLSLACKLVQALPRDARLIAICVDQNANHVIQKVVAV 172
Query: 625 IPQDRIQFIISSFYG--QVVALSTHPYGCRVIQRVLEH--CDDANTQ------------- 667
IP +FI+ + + + YGCRV+Q ++E D N
Sbjct: 173 IPLKNWEFIVDFVATPEHLRQICSDKYGCRVVQTIIEKLTADSMNVDLTSAAQNLRERAL 232
Query: 668 QIIMDEIMQHVCNLAQDQYGNYVIQHVLEHGK-PHERTTVITQ-LAGQIVRMSQQKFASN 725
Q +M + LA ++Y NY+IQH++ + R +I + L ++ +SQ+KFAS+
Sbjct: 233 QRLMTSVTNRCQELATNEYANYIIQHIVSNDDLAVYRECIIEKCLMRNLLSLSQEKFASH 292
Query: 726 VVEKCLTFGSPEERQLLINEMLGSTDE---------NEPLQAMMKDPFGNYVVQKVLETC 776
VVEK E L+ EM+ + + L MM FGNYVVQ +L C
Sbjct: 293 VVEKAFLHAPLE----LLAEMMDEIFDGYIPHPDTGKDALDIMMFHQFGNYVVQCMLTIC 348
Query: 777 DD 778
D
Sbjct: 349 CD 350
>pdb|3V71|A Chain A, Crystal Structure Of Puf-6 In Complex With 5be13 Rna
Length = 382
Score = 105 bits (263), Expect = 7e-23, Method: Compositional matrix adjust.
Identities = 88/362 (24%), Positives = 175/362 (48%), Gaps = 49/362 (13%)
Query: 496 HVVEFSTDQYGSRFIQQKLEAATAEEKTRIFPEIIPHARTLMTDVF----GNYVIQKFFE 551
+++F+ D G +F++ + ++ + E + TL + GN+++QK E
Sbjct: 21 QLIDFAIDPSGVKFLEANYPLDSEDQIRKAVFEKFTESTTLFVGLCHSRNGNFIVQKLVE 80
Query: 552 HGTESQRAQLASQLT-GHVLRLSLQMYGCRVIQKALEVV---HVDQQTQMVAELDGSVMK 607
T +++ +L Q+ G +L + + CRV+Q AL+ +V Q Q ++ D + M
Sbjct: 81 LATPAEQRELLRQMIDGGLLAMCKDKFACRVVQLALQKFDHSNVFQLIQELSTFDLAAM- 139
Query: 608 CVHDQNGNHVIQKCIECIPQDRIQFIISSFYG--QVVALSTHPYGCRVIQRVLEH----- 660
C DQ HVIQ+ ++ +P D F + ++A+ YGCR++Q+V++
Sbjct: 140 CT-DQISIHVIQRVVKQLPVDMWTFFVHFLSSGDSLMAVCQDKYGCRLVQQVIDRLAENP 198
Query: 661 ---CDDANTQQI--IMDEIMQHVCNLAQDQYGNYVIQHVLEHGKPHE--RTTVITQ-LAG 712
C Q + +M I+++ L+ +++ NYVIQ+V++ E R T+I + L
Sbjct: 199 KLPCFKFRIQLLHSLMTCIVRNCYRLSSNEFANYVIQYVIKSSGIMEMYRDTIIDKCLLR 258
Query: 713 QIVRMSQQKFASNVVEKCLTFGSPEERQLLINEMLGSTDEN-----EPLQAMMKDPFGNY 767
++ MSQ K+AS+V+E F P ++ E+ ++ + L ++ +GNY
Sbjct: 259 NLLSMSQDKYASHVIEGAFLFAPPALLHEMMEEIFSGYVKDVESNRDALDILLFHQYGNY 318
Query: 768 VVQKVLETC-------DDQSL------------ELILSRIRVHLNVLKKYTYGKHIVSRI 808
VVQ+++ C +++ L E + R+ H + L++++ GK I+ +
Sbjct: 319 VVQQMISICTAALIGKEERELPPAILLLYSGWYEKMKQRVLQHASRLERFSSGKKIIDSV 378
Query: 809 EK 810
+
Sbjct: 379 MR 380
Score = 35.0 bits (79), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 50/211 (23%), Positives = 85/211 (40%), Gaps = 29/211 (13%)
Query: 495 DHVVEFSTDQYGSRFIQQKLEAATAEEKTRIFPEIIPHARTLMTDV-----------FGN 543
D ++ D+YG R +QQ ++ K F I +LMT + F N
Sbjct: 172 DSLMAVCQDKYGCRLVQQVIDRLAENPKLPCFKFRIQLLHSLMTCIVRNCYRLSSNEFAN 231
Query: 544 YVIQKFFEHG--TESQRAQLASQ-LTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAE 600
YVIQ + E R + + L ++L +S Y VI+ A +M+ E
Sbjct: 232 YVIQYVIKSSGIMEMYRDTIIDKCLLRNLLSMSQDKYASHVIEGAFLFAPPALLHEMMEE 291
Query: 601 LDGSVMKCVHD-----------QNGNHVIQKCIECIPQDRIQFIISSFYGQVVALSTHPY 649
+ +K V Q GN+V+Q+ I I ++ L + Y
Sbjct: 292 IFSGYVKDVESNRDALDILLFHQYGNYVVQQMISICTAALIGKEERELPPAILLLYSGWY 351
Query: 650 GCRVIQRVLEHC---DDANTQQIIMDEIMQH 677
++ QRVL+H + ++ + I+D +M+H
Sbjct: 352 E-KMKQRVLQHASRLERFSSGKKIIDSVMRH 381
>pdb|1JW1|A Chain A, Crystallization And Structure Determination Of Goat
Lactoferrin At 4.0 Resolution: A New Form Of Packing In
Lactoferrins With A High Solvent Content In Crystals
Length = 689
Score = 30.0 bits (66), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 22/34 (64%)
Query: 710 LAGQIVRMSQQKFASNVVEKCLTFGSPEERQLLI 743
L +++R +Q+KF N ++ FGSPE R+ L+
Sbjct: 266 LIWELLRKAQEKFGKNKSQRFQLFGSPEGRRDLL 299
>pdb|2VG9|A Chain A, Crystal Structure Of Loop Swap Mutant Of Necallimastix
Patriciarum Xyn11a
Length = 217
Score = 29.6 bits (65), Expect = 7.8, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 189 QSDFLYDTSNGHNQSMKQQF---MDKSTADNLAFSTHYIDFTRKNGIVPNLNASAINSNG 245
Q D T NG +++ KQ F K T+ ++ S H+ ++ ++ + NL A+N+ G
Sbjct: 141 QMDHTGPTINGGSETFKQYFSVRQQKRTSGHITVSDHFKEWAKQGWGIGNLYEVALNAEG 200
>pdb|2C1F|A Chain A, The Structure Of The Family 11 Xylanase From
Neocallimastix Patriciarum
Length = 234
Score = 29.3 bits (64), Expect = 8.3, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 189 QSDFLYDTSNGHNQSMKQQF---MDKSTADNLAFSTHYIDFTRKNGIVPNLNASAINSNG 245
Q D T NG +++ KQ F K T+ ++ S H+ ++ ++ + NL A+N+ G
Sbjct: 143 QMDHTGPTINGGSETFKQYFSVRQQKRTSGHITVSDHFKEWAKQGWGIGNLYEVALNAEG 202
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 0.131 0.377
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,321,596
Number of Sequences: 62578
Number of extensions: 932865
Number of successful extensions: 2588
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 2252
Number of HSP's gapped (non-prelim): 53
length of query: 823
length of database: 14,973,337
effective HSP length: 107
effective length of query: 716
effective length of database: 8,277,491
effective search space: 5926683556
effective search space used: 5926683556
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: 56 (26.2 bits)