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= 001686
(1029 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 = 407 bits (1046), Expect = e-113, Method: Compositional matrix adjust.
Identities = 192/338 (56%), Positives = 255/338 (75%), Gaps = 2/338 (0%)
Query: 676 SSLLDEFKTNKTRSFELSDIVDHVVEFSTDQYGSRFIQQKLEAATAEEKTRIFPEIIPHA 735
S LL++F+ N+ + +L D++ H+VEFS DQ+GSRFIQQKLE AT E+ +F EI+ A
Sbjct: 5 SRLLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAA 64
Query: 736 RTLMTDVFGNYVIQKFFEHGTESQRAQLASQLTGHVLRLSLQMYGCRVIQKALEVVHVDQ 795
LMTDVFGNYVIQKFFE G+ Q+ LA+++ GHVL L+LQMYGCRVIQKALE + DQ
Sbjct: 65 YQLMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQ 124
Query: 796 QTQMVAELDGSVMKCVHDQNGNHVIQKCIECIPQDRIQFIISSFYGQVVALSTHPYGCRV 855
Q++MV ELDG V+KCV DQNGNHV+QKCIEC+ +QFII +F GQV LSTHPYGCRV
Sbjct: 125 QSEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRV 184
Query: 856 IQRVLEHCDDANTQQIIMDEIMQHVCNLAQDQYGNYVIQHVLEHGKPHERTTVITQLAGQ 915
IQR+LEHC T I++E+ QH L QDQYGNYVIQHVLEHG+P +++ +++++ G+
Sbjct: 185 IQRILEHCTAEQTLP-ILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGK 243
Query: 916 IVRMSQQKFASNVVEKCLTFGSPEERQLLINEMLGSTD-ENEPLQAMMKDPFGNYVVQKV 974
++ +SQ KFASNVVEKC+T S ER LLI+E+ D + L MMKD + NYVVQK+
Sbjct: 244 VLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKM 303
Query: 975 LETCDDQSLELILSRIRVHLNVLKKYTYGKHIVSRIEK 1012
++ + ++I+ +IR H+ L+KYTYGKHI++++EK
Sbjct: 304 IDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKLEK 341
Score = 102 bits (253), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 70/253 (27%), Positives = 127/253 (50%), Gaps = 7/253 (2%)
Query: 767 LTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAELDGSVMKCVHDQNGNHVIQKCIEC 826
L GH++ S +G R IQ+ LE ++ + E+ + + + D GN+VIQK E
Sbjct: 24 LIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGNYVIQKFFEF 83
Query: 827 IPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEHCDDANTQQIIMDEIMQHVCNLAQD 886
D+ + + G V+ L+ YGCRVIQ+ LE ++ Q ++ E+ HV +D
Sbjct: 84 GSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESIS-SDQQSEMVKELDGHVLKCVKD 142
Query: 887 QYGNYVIQHVLEHGKPHERTTVITQLAGQIVRMSQQKFASNVVEKCLTFGSPEERQLLIN 946
Q GN+V+Q +E +P +I GQ+ +S + V+++ L + E+ ++
Sbjct: 143 QNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILE 202
Query: 947 EMLGSTDENEPLQAMMKDPFGNYVVQKVLETCDDQSLELILSRIRVHLNVLKKYTYGKHI 1006
E+ T++ +++D +GNYV+Q VLE + I+S IR + L ++ + ++
Sbjct: 203 ELHQHTEQ------LVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNV 256
Query: 1007 VSRIEKLIATGER 1019
V + + ER
Sbjct: 257 VEKCVTHASRAER 269
>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 = 402 bits (1032), Expect = e-112, Method: Compositional matrix adjust.
Identities = 192/340 (56%), Positives = 255/340 (75%), Gaps = 4/340 (1%)
Query: 676 SSLLDEFKTNKTRSFELSDIVDHVVEFSTDQYGSRFIQQKLEAATAEEKTRIFPEIIPHA 735
S LL++F+ N+ + +L D++ H+VEFS DQ+GSRFIQQKLE AT E+ +F EI+ A
Sbjct: 3 SRLLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAA 62
Query: 736 RTLMTDVFGNYVIQKFFEHGTESQRAQLASQLTGHVLRLSLQMYGCRVIQKALEVVHVDQ 795
LMTDVFGNYVIQKFFE G+ Q+ LA+++ GHVL L+LQMYGCRVIQKALE + DQ
Sbjct: 63 YQLMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQ 122
Query: 796 Q--TQMVAELDGSVMKCVHDQNGNHVIQKCIECIPQDRIQFIISSFYGQVVALSTHPYGC 853
Q ++MV ELDG V+KCV DQNGNHV+QKCIEC+ +QFII +F GQV LSTHPYGC
Sbjct: 123 QVISEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGC 182
Query: 854 RVIQRVLEHCDDANTQQIIMDEIMQHVCNLAQDQYGNYVIQHVLEHGKPHERTTVITQLA 913
RVIQR+LEHC T I++E+ QH L QDQYGNYVIQHVLEHG+P +++ +++++
Sbjct: 183 RVIQRILEHCTAEQTLP-ILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIR 241
Query: 914 GQIVRMSQQKFASNVVEKCLTFGSPEERQLLINEMLGSTD-ENEPLQAMMKDPFGNYVVQ 972
G+++ +SQ KFASNVVEKC+T S ER LLI+E+ D + L MMKD + NYVVQ
Sbjct: 242 GKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQ 301
Query: 973 KVLETCDDQSLELILSRIRVHLNVLKKYTYGKHIVSRIEK 1012
K+++ + ++I+ +IR H+ L+KYTYGKHI++++EK
Sbjct: 302 KMIDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKLEK 341
Score = 102 bits (254), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 72/256 (28%), Positives = 129/256 (50%), Gaps = 11/256 (4%)
Query: 767 LTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAELDGSVMKCVHDQNGNHVIQKCIEC 826
L GH++ S +G R IQ+ LE ++ + E+ + + + D GN+VIQK E
Sbjct: 22 LIGHIVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAAYQLMTDVFGNYVIQKFFEF 81
Query: 827 IPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEHCDDANTQQII---MDEIMQHVCNL 883
D+ + + G V+ L+ YGCRVIQ+ LE ++ QQ+I + E+ HV
Sbjct: 82 GSLDQKLALATRIRGHVLPLALQMYGCRVIQKALE--SISSDQQVISEMVKELDGHVLKC 139
Query: 884 AQDQYGNYVIQHVLEHGKPHERTTVITQLAGQIVRMSQQKFASNVVEKCLTFGSPEERQL 943
+DQ GN+V+Q +E +P +I GQ+ +S + V+++ L + E+
Sbjct: 140 VKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLP 199
Query: 944 LINEMLGSTDENEPLQAMMKDPFGNYVVQKVLETCDDQSLELILSRIRVHLNVLKKYTYG 1003
++ E+ T++ +++D +GNYV+Q VLE + I+S IR + L ++ +
Sbjct: 200 ILEELHQHTEQ------LVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFA 253
Query: 1004 KHIVSRIEKLIATGER 1019
++V + + ER
Sbjct: 254 SNVVEKCVTHASRAER 269
>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 (1011), Expect = e-109, Method: Compositional matrix adjust.
Identities = 188/338 (55%), Positives = 249/338 (73%), Gaps = 2/338 (0%)
Query: 676 SSLLDEFKTNKTRSFELSDIVDHVVEFSTDQYGSRFIQQKLEAATAEEKTRIFPEIIPHA 735
S LL++F+ N+ + +L +I H++EFS DQ+GSRFIQ KLE AT E+ +F EI+ A
Sbjct: 3 SRLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAA 62
Query: 736 RTLMTDVFGNYVIQKFFEHGTESQRAQLASQLTGHVLRLSLQMYGCRVIQKALEVVHVDQ 795
LM DVFGNYVIQKFFE G+ Q+ LA ++ GHVL L+LQMYGCRVIQKALE + DQ
Sbjct: 63 YQLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQ 122
Query: 796 QTQMVAELDGSVMKCVHDQNGNHVIQKCIECIPQDRIQFIISSFYGQVVALSTHPYGCRV 855
Q +MV ELDG V+KCV DQNGNHV+QKCIEC+ +QFII +F GQV ALSTHPYGCRV
Sbjct: 123 QNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRV 182
Query: 856 IQRVLEHCDDANTQQIIMDEIMQHVCNLAQDQYGNYVIQHVLEHGKPHERTTVITQLAGQ 915
IQR+LEHC T I++E+ QH L QDQYGNYVIQHVLEHG+P +++ ++ ++ G
Sbjct: 183 IQRILEHCLPDQTLP-ILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGN 241
Query: 916 IVRMSQQKFASNVVEKCLTFGSPEERQLLINEMLGSTD-ENEPLQAMMKDPFGNYVVQKV 974
++ +SQ KFASNVVEKC+T S ER +LI+E+ D + L MMKD + NYVVQK+
Sbjct: 242 VLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKM 301
Query: 975 LETCDDQSLELILSRIRVHLNVLKKYTYGKHIVSRIEK 1012
++ + ++++ +IR H+ L+KYTYGKHI++++EK
Sbjct: 302 IDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKLEK 339
Score = 99.4 bits (246), Expect = 9e-21, Method: Compositional matrix adjust.
Identities = 68/256 (26%), Positives = 130/256 (50%), Gaps = 7/256 (2%)
Query: 766 QLTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAELDGSVMKCVHDQNGNHVIQKCIE 825
++ GH++ S +G R IQ LE ++ + E+ + + + D GN+VIQK E
Sbjct: 21 EIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFE 80
Query: 826 CIPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEHCDDANTQQIIMDEIMQHVCNLAQ 885
++ + G V++L+ YGCRVIQ+ LE ++ Q ++ E+ HV +
Sbjct: 81 FGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIP-SDQQNEMVRELDGHVLKCVK 139
Query: 886 DQYGNYVIQHVLEHGKPHERTTVITQLAGQIVRMSQQKFASNVVEKCLTFGSPEERQLLI 945
DQ GN+V+Q +E +P +I GQ+ +S + V+++ L P++ ++
Sbjct: 140 DQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPIL 199
Query: 946 NEMLGSTDENEPLQAMMKDPFGNYVVQKVLETCDDQSLELILSRIRVHLNVLKKYTYGKH 1005
E+ T++ +++D +GNYV+Q VLE + I++ IR ++ VL ++ + +
Sbjct: 200 EELHQHTEQ------LVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASN 253
Query: 1006 IVSRIEKLIATGERRI 1021
+V + + ER +
Sbjct: 254 VVEKCVTHASRTERAV 269
>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 (1010), Expect = e-109, Method: Compositional matrix adjust.
Identities = 188/338 (55%), Positives = 249/338 (73%), Gaps = 2/338 (0%)
Query: 676 SSLLDEFKTNKTRSFELSDIVDHVVEFSTDQYGSRFIQQKLEAATAEEKTRIFPEIIPHA 735
S LL++F+ N+ + +L +I H++EFS DQ+GSRFIQ KLE AT E+ +F EI+ A
Sbjct: 3 SRLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAA 62
Query: 736 RTLMTDVFGNYVIQKFFEHGTESQRAQLASQLTGHVLRLSLQMYGCRVIQKALEVVHVDQ 795
LM DVFGNYVIQKFFE G+ Q+ LA ++ GHVL L+LQMYGCRVIQKALE + DQ
Sbjct: 63 YQLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQ 122
Query: 796 QTQMVAELDGSVMKCVHDQNGNHVIQKCIECIPQDRIQFIISSFYGQVVALSTHPYGCRV 855
Q +MV ELDG V+KCV DQNGNHV+QKCIEC+ +QFII +F GQV ALSTHPYGCRV
Sbjct: 123 QNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRV 182
Query: 856 IQRVLEHCDDANTQQIIMDEIMQHVCNLAQDQYGNYVIQHVLEHGKPHERTTVITQLAGQ 915
IQR+LEHC T I++E+ QH L QDQYGNYVIQHVLEHG+P +++ ++ ++ G
Sbjct: 183 IQRILEHCLPDQTLP-ILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGN 241
Query: 916 IVRMSQQKFASNVVEKCLTFGSPEERQLLINEMLGSTD-ENEPLQAMMKDPFGNYVVQKV 974
++ +SQ KFASNVVEKC+T S ER +LI+E+ D + L MMKD + NYVVQK+
Sbjct: 242 VLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKM 301
Query: 975 LETCDDQSLELILSRIRVHLNVLKKYTYGKHIVSRIEK 1012
++ + ++++ +IR H+ L+KYTYGKHI++++EK
Sbjct: 302 IDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKLEK 339
Score = 98.6 bits (244), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 68/256 (26%), Positives = 130/256 (50%), Gaps = 7/256 (2%)
Query: 766 QLTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAELDGSVMKCVHDQNGNHVIQKCIE 825
++ GH++ S +G R IQ LE ++ + E+ + + + D GN+VIQK E
Sbjct: 21 EIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFE 80
Query: 826 CIPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEHCDDANTQQIIMDEIMQHVCNLAQ 885
++ + G V++L+ YGCRVIQ+ LE ++ Q ++ E+ HV +
Sbjct: 81 FGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIP-SDQQNEMVRELDGHVLKCVK 139
Query: 886 DQYGNYVIQHVLEHGKPHERTTVITQLAGQIVRMSQQKFASNVVEKCLTFGSPEERQLLI 945
DQ GN+V+Q +E +P +I GQ+ +S + V+++ L P++ ++
Sbjct: 140 DQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPIL 199
Query: 946 NEMLGSTDENEPLQAMMKDPFGNYVVQKVLETCDDQSLELILSRIRVHLNVLKKYTYGKH 1005
E+ T++ +++D +GNYV+Q VLE + I++ IR ++ VL ++ + +
Sbjct: 200 EELHQHTEQ------LVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASN 253
Query: 1006 IVSRIEKLIATGERRI 1021
+V + + ER +
Sbjct: 254 VVEKCVTHASRTERAV 269
>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 = 390 bits (1001), Expect = e-108, Method: Compositional matrix adjust.
Identities = 186/338 (55%), Positives = 249/338 (73%), Gaps = 2/338 (0%)
Query: 676 SSLLDEFKTNKTRSFELSDIVDHVVEFSTDQYGSRFIQQKLEAATAEEKTRIFPEIIPHA 735
S LL++F+ N+ + +L +I H++EFS DQ+GSRFIQ KLE AT E+ +F EI+ A
Sbjct: 4 SRLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAA 63
Query: 736 RTLMTDVFGNYVIQKFFEHGTESQRAQLASQLTGHVLRLSLQMYGCRVIQKALEVVHVDQ 795
LM DVFGNYVIQKFFE G+ Q+ LA ++ GHVL L+LQMYGCRVIQKALE + DQ
Sbjct: 64 YQLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQ 123
Query: 796 QTQMVAELDGSVMKCVHDQNGNHVIQKCIECIPQDRIQFIISSFYGQVVALSTHPYGCRV 855
Q +MV ELDG V+KCV DQNGNHV+QKCIEC+ +QFII +F GQV ALSTHPYGCRV
Sbjct: 124 QNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRV 183
Query: 856 IQRVLEHCDDANTQQIIMDEIMQHVCNLAQDQYGNYVIQHVLEHGKPHERTTVITQLAGQ 915
IQR+LEHC T I++E+ QH L QDQYG+YVI+HVLEHG+P +++ ++ ++ G
Sbjct: 184 IQRILEHCLPDQTLP-ILEELHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGN 242
Query: 916 IVRMSQQKFASNVVEKCLTFGSPEERQLLINEMLGSTD-ENEPLQAMMKDPFGNYVVQKV 974
++ +SQ KFASNVVEKC+T S ER +LI+E+ D + L MMKD + NYVVQK+
Sbjct: 243 VLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKM 302
Query: 975 LETCDDQSLELILSRIRVHLNVLKKYTYGKHIVSRIEK 1012
++ + ++++ +IR H+ L+KYTYGKHI++++EK
Sbjct: 303 IDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKLEK 340
Score = 95.5 bits (236), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 66/256 (25%), Positives = 130/256 (50%), Gaps = 7/256 (2%)
Query: 766 QLTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAELDGSVMKCVHDQNGNHVIQKCIE 825
++ GH++ S +G R IQ LE ++ + E+ + + + D GN+VIQK E
Sbjct: 22 EIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFE 81
Query: 826 CIPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEHCDDANTQQIIMDEIMQHVCNLAQ 885
++ + G V++L+ YGCRVIQ+ LE ++ Q ++ E+ HV +
Sbjct: 82 FGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIP-SDQQNEMVRELDGHVLKCVK 140
Query: 886 DQYGNYVIQHVLEHGKPHERTTVITQLAGQIVRMSQQKFASNVVEKCLTFGSPEERQLLI 945
DQ GN+V+Q +E +P +I GQ+ +S + V+++ L P++ ++
Sbjct: 141 DQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPIL 200
Query: 946 NEMLGSTDENEPLQAMMKDPFGNYVVQKVLETCDDQSLELILSRIRVHLNVLKKYTYGKH 1005
E+ T++ +++D +G+YV++ VLE + I++ IR ++ VL ++ + +
Sbjct: 201 EELHQHTEQ------LVQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASN 254
Query: 1006 IVSRIEKLIATGERRI 1021
+V + + ER +
Sbjct: 255 VVEKCVTHASRTERAV 270
Score = 54.7 bits (130), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 33/111 (29%), Positives = 57/111 (51%), Gaps = 6/111 (5%)
Query: 909 ITQLAGQIVRMSQQKFASNVVEKCLTFGSPEERQLLINEMLGSTDENEPLQAMMKDPFGN 968
+ ++AG I+ SQ + S ++ L +P ERQL+ NE+L + + +M D FGN
Sbjct: 20 LREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQ------LMVDVFGN 73
Query: 969 YVVQKVLETCDDQSLELILSRIRVHLNVLKKYTYGKHIVSRIEKLIATGER 1019
YV+QK E + + RIR H+ L YG ++ + + I + ++
Sbjct: 74 YVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQ 124
>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 = 369 bits (947), Expect = e-102, Method: Compositional matrix adjust.
Identities = 181/326 (55%), Positives = 238/326 (73%), Gaps = 3/326 (0%)
Query: 672 GRLSSSLLDEFKTNKTRSFELSDIVDHVVEFSTDQYGSRFIQQKLEAATAEEKTRIFPEI 731
G S LL++F+ + + +L D+ +H+VEFS DQ+GSRFIQQKLE ATA EK +F EI
Sbjct: 1 GSHMSRLLEDFRNQRYPNLQLRDLANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEI 60
Query: 732 IPHARTLMTDVFGNYVIQKFFEHGTESQRAQLASQLTGHVLRLSLQMYGCRVIQKALEVV 791
+ A +LMTDVFGNYVIQKFFE GT Q+ L Q+ GHVL+L+LQMYGCRVIQKALE +
Sbjct: 61 LAAAYSLMTDVFGNYVIQKFFEFGTPEQKNTLGMQVKGHVLQLALQMYGCRVIQKALESI 120
Query: 792 HVDQQTQMVAELDGSVMKCVHDQNGNHVIQKCIECIPQDRIQFIISSFYGQVVALSTHPY 851
+QQ ++V ELDG V+KCV DQNGNHV+QKCIEC+ +QFII++F GQV +LSTHPY
Sbjct: 121 SPEQQQEIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPY 180
Query: 852 GCRVIQRVLEHCDDANTQQIIMDEIMQHVCNLAQDQYGNYVIQHVLEHGKPHERTTVITQ 911
GCRVIQR+LEHC T I+DE+ +H L QDQYGNYVIQHVLEHGK +++ +I
Sbjct: 181 GCRVIQRILEHCTAEQTTP-ILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINS 239
Query: 912 LAGQIVRMSQQKFASNVVEKCLTFGSPEERQLLINEMLGSTDENEPLQAMMKDPFGNYVV 971
+ G+++ +SQ KFASNVVEKC+T + ER LI+E+ D L MMKD + NYVV
Sbjct: 240 VRGKVLVLSQHKFASNVVEKCVTHATRGERTGLIDEVCTFND--NALHVMMKDQYANYVV 297
Query: 972 QKVLETCDDQSLELILSRIRVHLNVL 997
QK+++ + L+ ++++IR ++ L
Sbjct: 298 QKMIDVSEPTQLKKLMTKIRKNMAAL 323
Score = 103 bits (258), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 71/263 (26%), Positives = 130/263 (49%), Gaps = 8/263 (3%)
Query: 767 LTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAELDGSVMKCVHDQNGNHVIQKCIEC 826
L H++ S +G R IQ+ LE ++ + +E+ + + D GN+VIQK E
Sbjct: 24 LANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEF 83
Query: 827 IPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEHCDDANTQQIIMDEIMQHVCNLAQD 886
++ + G V+ L+ YGCRVIQ+ LE Q+I+ E+ HV +D
Sbjct: 84 GTPEQKNTLGMQVKGHVLQLALQMYGCRVIQKALESISPEQQQEIV-HELDGHVLKCVKD 142
Query: 887 QYGNYVIQHVLEHGKPHERTTVITQLAGQIVRMSQQKFASNVVEKCLTFGSPEERQLLIN 946
Q GN+V+Q +E P +I GQ+ +S + V+++ L + E+ +++
Sbjct: 143 QNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTAEQTTPILD 202
Query: 947 EMLGSTDENEPLQAMMKDPFGNYVVQKVLETCDDQSLELILSRIRVHLNVLKKYTYGKHI 1006
E+ +E + +++D +GNYV+Q VLE + ++++ +R + VL ++ + ++
Sbjct: 203 EL------HEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFASNV 256
Query: 1007 VSRIEKLIATGERRIGLSSSVSS 1029
V + GE R GL V +
Sbjct: 257 VEKCVTHATRGE-RTGLIDEVCT 278
>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 (720), Expect = 9e-76, Method: Compositional matrix adjust.
Identities = 154/341 (45%), Positives = 219/341 (64%), Gaps = 15/341 (4%)
Query: 692 LSDIVDHVVEFSTDQYGSRFIQQKLEAATAEEKTRIFPEIIPHARTLMTDVFGNYVIQKF 751
L DI H +EF DQ+GSRFIQ++L + A EK IF EI A L DVFGNYVIQKF
Sbjct: 26 LKDIFGHSLEFCKDQHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKF 85
Query: 752 FEHGTESQRAQLASQLTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAELDGSVMKCV 811
FE G++ Q+ L Q G++ +LSLQMY CRVIQKALE + +Q+ ++V EL SV++ +
Sbjct: 86 FEFGSKIQKNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLELSDSVLQMI 145
Query: 812 HDQNGNHVIQKCIECIPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEHCDDANTQQI 871
DQNGNHVIQK IE IP +++ FI+SS G + LSTH YGCRVIQR+LE + Q+
Sbjct: 146 KDQNGNHVIQKAIETIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEF-GSSEDQES 204
Query: 872 IMDEIMQHVCNLAQDQYGNYVIQHVLEHGKPHERTTV------ITQLAGQIVRMSQQKFA 925
I++E+ + L QDQYGNYVIQ+VL+ + + V I +A +V S+ KFA
Sbjct: 205 ILNELKDFIPYLIQDQYGNYVIQYVLQQDQFTNKEMVDIKQEIIETVANNVVEYSKHKFA 264
Query: 926 SNVVEKCLTFGSPEERQLLINEMLG-------STDENEPLQAMMKDPFGNYVVQKVLETC 978
SNVVEK + +GS ++ L+I+++L + +++ P+ M+KD F NYV+QK++
Sbjct: 265 SNVVEKSILYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFANYVIQKLVNVS 324
Query: 979 DDQSLELILSRIRVHLNVLKKY-TYGKHIVSRIEKLIATGE 1018
+ + +LI+ IR +L+ L K + G ++ +EKL A E
Sbjct: 325 EGEGKKLIVIAIRAYLDKLNKSNSLGNRHLASVEKLAALVE 365
>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 (431), Expect = 4e-42, Method: Compositional matrix adjust.
Identities = 99/288 (34%), Positives = 159/288 (55%), Gaps = 13/288 (4%)
Query: 702 FSTDQYGSRFIQQKLEAATAEEKTRIFPEIIPHARTLMTDVFGNYVIQKFFEHGTESQRA 761
DQ+G RF+Q++L+ ++ IF E + LMTD FGNY+IQK E T QR
Sbjct: 18 LCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQRI 77
Query: 762 QLASQLTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAE-LDGSVMKCVHDQNGNHVI 820
L + H + +SL +GCR +QK +E + D++ Q+V + L ++ D NGNHVI
Sbjct: 78 VLTKISSPHFVEISLNPHGCRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVI 137
Query: 821 QKCIECIPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEHCDDANTQQI--IMDEIMQ 878
QKC++ + + QFI + + ++TH +GCRV+QR L+H T+Q + D+++
Sbjct: 138 QKCLQRLKPENFQFIFDAISDSCIDIATHRHGCRVLQRCLDH---GTTEQCDNLCDKLLA 194
Query: 879 HVCNLAQDQYGNYVIQHVL----EHGKPHERTTVITQLAGQIVRMSQQKFASNVVEKCLT 934
V L D +GNYV+Q+++ E K ++ L + + +S KF SNV+EK L
Sbjct: 195 LVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILK 254
Query: 935 FGSPEERQLLINEMLGSTDENEPLQAMMKDPFGNYVVQKVLETCDDQS 982
E +L E+L + E +Q+++ D +GNYV+Q L+ Q+
Sbjct: 255 TAIVSEPMIL--EILNNGGET-GIQSLLNDSYGNYVLQTALDISHKQN 299
Score = 97.4 bits (241), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 55/210 (26%), Positives = 106/210 (50%), Gaps = 6/210 (2%)
Query: 766 QLTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAELDGSVMKCVHDQNGNHVIQKCIE 825
Q G + L +GCR +QK L+++ + E ++ + D GN++IQK +E
Sbjct: 10 QYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLE 69
Query: 826 CIPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEHCDDANTQQIIMDEIMQHVCNLAQ 885
+ ++ + V +S +P+GCR +Q+++E QI++D + + L++
Sbjct: 70 EVTTEQRIVLTKISSPHFVEISLNPHGCRALQKLIECIKTDEEAQIVVDSLRPYTVQLSK 129
Query: 886 DQYGNYVIQHVLEHGKPHERTTVITQLAGQIVRMSQQKFASNVVEKCLTFGSPEERQLLI 945
D GN+VIQ L+ KP + ++ + ++ + V+++CL G+ E+ L
Sbjct: 130 DLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCRVLQRCLDHGTTEQCDNLC 189
Query: 946 NEMLGSTDENEPLQAMMKDPFGNYVVQKVL 975
+++L D+ + DPFGNYVVQ ++
Sbjct: 190 DKLLALVDK------LTLDPFGNYVVQYII 213
Score = 53.9 bits (128), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 55/231 (23%), Positives = 94/231 (40%), Gaps = 40/231 (17%)
Query: 673 RLSSSLLDEFKTNKTRSFELSDIVDHVVEFSTDQYGSRFIQQKLEAATAEEKTRIFPEII 732
R L++ KT++ + + + V+ S D G+ IQ+ L+ E IF I
Sbjct: 98 RALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAIS 157
Query: 733 PHARTLMTDVFGNYVIQKFFEHGTESQRAQLASQLTGHVLRLSLQMYGCRVIQKALEVVH 792
+ T G V+Q+ +HGT Q L +L V +L+L +G V+Q
Sbjct: 158 DSCIDIATHRHGCRVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQ------- 210
Query: 793 VDQQTQMVAELDGSVMKCVHDQNGNHVIQKCIECIPQDRIQFIISSFYGQVVALSTHPYG 852
++I K E D I+ + + LS H +G
Sbjct: 211 -------------------------YIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFG 245
Query: 853 CRVIQRVLEHCDDANTQQIIMDEIMQH-----VCNLAQDQYGNYVIQHVLE 898
VI+++L+ A + ++ EI+ + + +L D YGNYV+Q L+
Sbjct: 246 SNVIEKILK---TAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALD 293
>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 = 164 bits (414), Expect = 3e-40, Method: Compositional matrix adjust.
Identities = 106/317 (33%), Positives = 170/317 (53%), Gaps = 17/317 (5%)
Query: 702 FSTDQYGSRFIQQKLEAATAEEKTRIFPEIIPHARTLMTDVFGNYVIQKFFEHGTESQRA 761
DQ+G RF+Q++L+ ++ IF E + LMTD FGNY+IQK E T QR
Sbjct: 40 LCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQRI 99
Query: 762 QLASQLTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAE-LDGSVMKCVHDQNGNHVI 820
L + H + +SL +G R +QK +E + D++ Q+V + L ++ D NGNHVI
Sbjct: 100 VLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVI 159
Query: 821 QKCIECIPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEHCDDANTQQI--IMDEIMQ 878
QKC++ + + QFI + + ++TH +GC V+QR L+H T+Q + D+++
Sbjct: 160 QKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDH---GTTEQCDNLCDKLLA 216
Query: 879 HVCNLAQDQYGNYVIQHVL----EHGKPHERTTVITQLAGQIVRMSQQKFASNVVEKCLT 934
V L D +GNYV+Q+++ E K ++ L + + +S KF SNV+EK L
Sbjct: 217 LVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILK 276
Query: 935 FGSPEERQLLINEMLGSTDENEPLQAMMKDPFGNYVVQKVLETCDDQSLELI--LSRIRV 992
E +L E+L + E +Q+++ D +GNYV+Q L+ Q+ L LS I
Sbjct: 277 TAIVSEPMIL--EILNNGGET-GIQSLLNDSYGNYVLQTALDISHKQNDYLYKRLSEIVA 333
Query: 993 HLNV--LKKYTYGKHIV 1007
L V ++ +GK I+
Sbjct: 334 PLLVGPIRNTPHGKRII 350
Score = 93.6 bits (231), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 54/210 (25%), Positives = 105/210 (50%), Gaps = 6/210 (2%)
Query: 766 QLTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAELDGSVMKCVHDQNGNHVIQKCIE 825
Q G + L +GCR +QK L+++ + E ++ + D GN++IQK +E
Sbjct: 32 QYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLE 91
Query: 826 CIPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEHCDDANTQQIIMDEIMQHVCNLAQ 885
+ ++ + V +S +P+G R +Q+++E QI++D + + L++
Sbjct: 92 EVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSK 151
Query: 886 DQYGNYVIQHVLEHGKPHERTTVITQLAGQIVRMSQQKFASNVVEKCLTFGSPEERQLLI 945
D GN+VIQ L+ KP + ++ + ++ + V+++CL G+ E+ L
Sbjct: 152 DLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLC 211
Query: 946 NEMLGSTDENEPLQAMMKDPFGNYVVQKVL 975
+++L D+ + DPFGNYVVQ ++
Sbjct: 212 DKLLALVDK------LTLDPFGNYVVQYII 235
>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 = 8e-40, Method: Compositional matrix adjust.
Identities = 96/282 (34%), Positives = 155/282 (54%), Gaps = 13/282 (4%)
Query: 702 FSTDQYGSRFIQQKLEAATAEEKTRIFPEIIPHARTLMTDVFGNYVIQKFFEHGTESQRA 761
DQ+G RF+Q++L+ ++ IF E + LMTD FGNY+IQK E T QR
Sbjct: 18 LCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQRI 77
Query: 762 QLASQLTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAE-LDGSVMKCVHDQNGNHVI 820
L + H + +SL +G R +QK +E + D++ Q+V + L ++ D NGNHVI
Sbjct: 78 VLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVI 137
Query: 821 QKCIECIPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEHCDDANTQQI--IMDEIMQ 878
QKC++ + + QFI + + ++TH +GC V+QR L+H T+Q + D+++
Sbjct: 138 QKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDH---GTTEQCDNLCDKLLA 194
Query: 879 HVCNLAQDQYGNYVIQHVL----EHGKPHERTTVITQLAGQIVRMSQQKFASNVVEKCLT 934
V L D +GNYV+Q+++ E K ++ L + + +S KF SNV+EK L
Sbjct: 195 LVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILK 254
Query: 935 FGSPEERQLLINEMLGSTDENEPLQAMMKDPFGNYVVQKVLE 976
E +L E+L + E +Q+++ D +GNYV+Q L+
Sbjct: 255 TAIVSEPMIL--EILNNGGET-GIQSLLNDSYGNYVLQTALD 293
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: 766 QLTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAELDGSVMKCVHDQNGNHVIQKCIE 825
Q G + L +GCR +QK L+++ + E ++ + D GN++IQK +E
Sbjct: 10 QYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLE 69
Query: 826 CIPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEHCDDANTQQIIMDEIMQHVCNLAQ 885
+ ++ + V +S +P+G R +Q+++E QI++D + + L++
Sbjct: 70 EVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSK 129
Query: 886 DQYGNYVIQHVLEHGKPHERTTVITQLAGQIVRMSQQKFASNVVEKCLTFGSPEERQLLI 945
D GN+VIQ L+ KP + ++ + ++ + V+++CL G+ E+ L
Sbjct: 130 DLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLC 189
Query: 946 NEMLGSTDENEPLQAMMKDPFGNYVVQKVL 975
+++L D+ + DPFGNYVVQ ++
Sbjct: 190 DKLLALVDK------LTLDPFGNYVVQYII 213
Score = 53.9 bits (128), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 55/231 (23%), Positives = 94/231 (40%), Gaps = 40/231 (17%)
Query: 673 RLSSSLLDEFKTNKTRSFELSDIVDHVVEFSTDQYGSRFIQQKLEAATAEEKTRIFPEII 732
R L++ KT++ + + + V+ S D G+ IQ+ L+ E IF I
Sbjct: 98 RALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAIS 157
Query: 733 PHARTLMTDVFGNYVIQKFFEHGTESQRAQLASQLTGHVLRLSLQMYGCRVIQKALEVVH 792
+ T G V+Q+ +HGT Q L +L V +L+L +G V+Q
Sbjct: 158 DSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQ------- 210
Query: 793 VDQQTQMVAELDGSVMKCVHDQNGNHVIQKCIECIPQDRIQFIISSFYGQVVALSTHPYG 852
++I K E D I+ + + LS H +G
Sbjct: 211 -------------------------YIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFG 245
Query: 853 CRVIQRVLEHCDDANTQQIIMDEIMQH-----VCNLAQDQYGNYVIQHVLE 898
VI+++L+ A + ++ EI+ + + +L D YGNYV+Q L+
Sbjct: 246 SNVIEKILK---TAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALD 293
Score = 29.6 bits (65), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 27/140 (19%), Positives = 63/140 (45%), Gaps = 9/140 (6%)
Query: 872 IMDEIMQHVCNLAQDQYGNYVIQHVLEHGKPHERTTVITQLAGQIVRMSQQKFASNVVEK 931
++D+ + + +L +DQ+G +Q L+ + + V + F + +++K
Sbjct: 7 VLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQK 66
Query: 932 CLTFGSPEERQLLINEMLGSTDENEP-LQAMMKDPFGNYVVQKVLETCD-DQSLELILSR 989
L + E+R +L T + P + +P G +QK++E D+ ++++
Sbjct: 67 LLEEVTTEQRIVL-------TKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDS 119
Query: 990 IRVHLNVLKKYTYGKHIVSR 1009
+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 (409), Expect = 1e-39, Method: Compositional matrix adjust.
Identities = 97/288 (33%), Positives = 157/288 (54%), Gaps = 13/288 (4%)
Query: 702 FSTDQYGSRFIQQKLEAATAEEKTRIFPEIIPHARTLMTDVFGNYVIQKFFEHGTESQRA 761
DQ+G RF+Q++L+ ++ IF E + LMTD FGNY+IQK E T QR
Sbjct: 18 LCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQRI 77
Query: 762 QLASQLTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAE-LDGSVMKCVHDQNGNHVI 820
L + H + +SL +G R +QK +E + D++ Q+V + L ++ D NGNHVI
Sbjct: 78 VLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVI 137
Query: 821 QKCIECIPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEHCDDANTQQI--IMDEIMQ 878
QKC++ + + QFI + + ++TH +GC V+QR L+H T+Q + D+++
Sbjct: 138 QKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDH---GTTEQCDNLCDKLLA 194
Query: 879 HVCNLAQDQYGNYVIQHVL----EHGKPHERTTVITQLAGQIVRMSQQKFASNVVEKCLT 934
V L D +GNYV+Q+++ E K ++ L + + +S KF SNV+EK L
Sbjct: 195 LVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILK 254
Query: 935 FGSPEERQLLINEMLGSTDENEPLQAMMKDPFGNYVVQKVLETCDDQS 982
E +L E+L + E +Q+++ D +GNYV+Q L+ Q+
Sbjct: 255 TAIVSEPMIL--EILNNGGET-GIQSLLNDSYGNYVLQTALDISHKQN 299
Score = 91.7 bits (226), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 54/210 (25%), Positives = 105/210 (50%), Gaps = 6/210 (2%)
Query: 766 QLTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAELDGSVMKCVHDQNGNHVIQKCIE 825
Q G + L +GCR +QK L+++ + E ++ + D GN++IQK +E
Sbjct: 10 QYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLE 69
Query: 826 CIPQDRIQFIISSFYGQVVALSTHPYGCRVIQRVLEHCDDANTQQIIMDEIMQHVCNLAQ 885
+ ++ + V +S +P+G R +Q+++E QI++D + + L++
Sbjct: 70 EVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSK 129
Query: 886 DQYGNYVIQHVLEHGKPHERTTVITQLAGQIVRMSQQKFASNVVEKCLTFGSPEERQLLI 945
D GN+VIQ L+ KP + ++ + ++ + V+++CL G+ E+ L
Sbjct: 130 DLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLC 189
Query: 946 NEMLGSTDENEPLQAMMKDPFGNYVVQKVL 975
+++L D+ + DPFGNYVVQ ++
Sbjct: 190 DKLLALVDK------LTLDPFGNYVVQYII 213
Score = 53.5 bits (127), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 55/231 (23%), Positives = 94/231 (40%), Gaps = 40/231 (17%)
Query: 673 RLSSSLLDEFKTNKTRSFELSDIVDHVVEFSTDQYGSRFIQQKLEAATAEEKTRIFPEII 732
R L++ KT++ + + + V+ S D G+ IQ+ L+ E IF I
Sbjct: 98 RALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAIS 157
Query: 733 PHARTLMTDVFGNYVIQKFFEHGTESQRAQLASQLTGHVLRLSLQMYGCRVIQKALEVVH 792
+ T G V+Q+ +HGT Q L +L V +L+L +G V+Q
Sbjct: 158 DSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQ------- 210
Query: 793 VDQQTQMVAELDGSVMKCVHDQNGNHVIQKCIECIPQDRIQFIISSFYGQVVALSTHPYG 852
++I K E D I+ + + LS H +G
Sbjct: 211 -------------------------YIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFG 245
Query: 853 CRVIQRVLEHCDDANTQQIIMDEIMQH-----VCNLAQDQYGNYVIQHVLE 898
VI+++L+ A + ++ EI+ + + +L D YGNYV+Q L+
Sbjct: 246 SNVIEKILK---TAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALD 293
>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 = 129 bits (324), Expect = 9e-30, Method: Compositional matrix adjust.
Identities = 99/362 (27%), Positives = 174/362 (48%), Gaps = 63/362 (17%)
Query: 662 WHLDAGINMEGRLSSSLLDEFKTNKTRSFELSDIVD--HVVEFSTDQYGSRFIQQKLEAA 719
W LD+ M RLS LS+++D +++F+ D+ G +F+++ ++ +
Sbjct: 8 WSLDSNGEMRSRLS----------------LSEVLDSGDLMKFAVDKTGCQFLEKAVKGS 51
Query: 720 -TAEEKTRIFPEIIPHARTLM---TDVFGNYVIQKFF-------EHGTESQRAQLASQLT 768
T+ +K ++F ++I + T++FGNY++Q + G ++ +L + ++
Sbjct: 52 LTSYQKFQLFEQVIGRKDDFLKLSTNIFGNYLVQSVIGISLATNDDGYTKRQEKLKNFIS 111
Query: 769 GHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAEL--DGSVMKCVHDQNGNHVIQKCIEC 826
+ + L + CRVIQ +L+ + + ++V L D ++ DQN NHVIQK +
Sbjct: 112 SQMTDMCLDKFACRVIQSSLQNMDLSLACKLVQALPRDARLIAICVDQNANHVIQKVVAV 171
Query: 827 IPQDRIQFIISSFYG--QVVALSTHPYGCRVIQRVLEH--CDDANTQ------------- 869
IP +FI+ + + + YGCRV+Q ++E D N
Sbjct: 172 IPLKNWEFIVDFVATPEHLRQICSDKYGCRVVQTIIEKLTADSMNVDLTSAAQNLRERAL 231
Query: 870 QIIMDEIMQHVCNLAQDQYGNYVIQHVLEHGK-PHERTTVITQ-LAGQIVRMSQQKFASN 927
Q +M + LA ++Y NY+IQH++ + R +I + L ++ +SQ+KFAS+
Sbjct: 232 QRLMTSVTNRCQELATNEYANYIIQHIVSNDDLAVYRECIIEKCLMRNLLSLSQEKFASH 291
Query: 928 VVEKCLTFGSPEERQLLINEMLGSTDE---------NEPLQAMMKDPFGNYVVQKVLETC 978
VVEK +P E L+ EM+ + + L MM FGNYVVQ +L C
Sbjct: 292 VVEKAF-LHAPLE---LLAEMMDEIFDGYIPHPDTGKDALDIMMFHQFGNYVVQCMLTIC 347
Query: 979 DD 980
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 = 129 bits (323), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 99/362 (27%), Positives = 174/362 (48%), Gaps = 63/362 (17%)
Query: 662 WHLDAGINMEGRLSSSLLDEFKTNKTRSFELSDIVD--HVVEFSTDQYGSRFIQQKLEAA 719
W LD+ M RLS LS+++D +++F+ D+ G +F+++ ++ +
Sbjct: 9 WSLDSNGEMRSRLS----------------LSEVLDSGDLMKFAVDKTGCQFLEKAVKGS 52
Query: 720 -TAEEKTRIFPEIIPHARTLM---TDVFGNYVIQKFF-------EHGTESQRAQLASQLT 768
T+ +K ++F ++I + T++FGNY++Q + G ++ +L + ++
Sbjct: 53 LTSYQKFQLFEQVIGRKDDFLKLSTNIFGNYLVQSVIGISLATNDDGYTKRQEKLKNFIS 112
Query: 769 GHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAEL--DGSVMKCVHDQNGNHVIQKCIEC 826
+ + L + CRVIQ +L+ + + ++V L D ++ DQN NHVIQK +
Sbjct: 113 SQMTDMCLDKFACRVIQSSLQNMDLSLACKLVQALPRDARLIAICVDQNANHVIQKVVAV 172
Query: 827 IPQDRIQFIISSFYG--QVVALSTHPYGCRVIQRVLEH--CDDANTQ------------- 869
IP +FI+ + + + YGCRV+Q ++E D N
Sbjct: 173 IPLKNWEFIVDFVATPEHLRQICSDKYGCRVVQTIIEKLTADSMNVDLTSAAQNLRERAL 232
Query: 870 QIIMDEIMQHVCNLAQDQYGNYVIQHVLEHGK-PHERTTVITQ-LAGQIVRMSQQKFASN 927
Q +M + LA ++Y NY+IQH++ + R +I + L ++ +SQ+KFAS+
Sbjct: 233 QRLMTSVTNRCQELATNEYANYIIQHIVSNDDLAVYRECIIEKCLMRNLLSLSQEKFASH 292
Query: 928 VVEKCLTFGSPEERQLLINEMLGSTDE---------NEPLQAMMKDPFGNYVVQKVLETC 978
VVEK +P E L+ EM+ + + L MM FGNYVVQ +L C
Sbjct: 293 VVEKAF-LHAPLE---LLAEMMDEIFDGYIPHPDTGKDALDIMMFHQFGNYVVQCMLTIC 348
Query: 979 DD 980
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 = 126 bits (316), Expect = 7e-29, Method: Compositional matrix adjust.
Identities = 98/362 (27%), Positives = 173/362 (47%), Gaps = 63/362 (17%)
Query: 662 WHLDAGINMEGRLSSSLLDEFKTNKTRSFELSDIVD--HVVEFSTDQYGSRFIQQKLEAA 719
W LD+ M RLS LS+++D +++F+ D+ G +F+++ ++ +
Sbjct: 9 WSLDSNGEMRSRLS----------------LSEVLDSGDLMKFAVDKTGCQFLEKAVKGS 52
Query: 720 -TAEEKTRIFPEIIPHARTLM---TDVFGNYVIQKFF-------EHGTESQRAQLASQLT 768
T+ +K ++F ++I + T++FGNY++Q + G ++ +L + ++
Sbjct: 53 LTSYQKFQLFEQVIGRKDDFLKLSTNIFGNYLVQSVIGISLATNDDGYTKRQEKLKNFIS 112
Query: 769 GHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAEL--DGSVMKCVHDQNGNHVIQKCIEC 826
+ + L + C VIQ +L+ + + ++V L D ++ DQN NHVIQK +
Sbjct: 113 SQMTDMCLDKFACYVIQSSLQNMDLSLACKLVQALPRDARLIAICVDQNANHVIQKVVAV 172
Query: 827 IPQDRIQFIISSFYG--QVVALSTHPYGCRVIQRVLEH--CDDANTQ------------- 869
IP +FI+ + + + YGCRV+Q ++E D N
Sbjct: 173 IPLKNWEFIVDFVATPEHLRQICSDKYGCRVVQTIIEKLTADSMNVDLTSAAQNLRERAL 232
Query: 870 QIIMDEIMQHVCNLAQDQYGNYVIQHVLEHGK-PHERTTVITQ-LAGQIVRMSQQKFASN 927
Q +M + LA ++Y NY+IQH++ + R +I + L ++ +SQ+KFAS+
Sbjct: 233 QRLMTSVTNRCQELATNEYANYIIQHIVSNDDLAVYRECIIEKCLMRNLLSLSQEKFASH 292
Query: 928 VVEKCLTFGSPEERQLLINEMLGSTDE---------NEPLQAMMKDPFGNYVVQKVLETC 978
VVEK +P E L+ EM+ + + L MM FGNYVVQ +L C
Sbjct: 293 VVEKAF-LHAPLE---LLAEMMDEIFDGYIPHPDTGKDALDIMMFHQFGNYVVQCMLTIC 348
Query: 979 DD 980
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 = 9e-23, Method: Compositional matrix adjust.
Identities = 80/309 (25%), Positives = 154/309 (49%), Gaps = 30/309 (9%)
Query: 698 HVVEFSTDQYGSRFIQQKLEAATAEEKTRIFPEIIPHARTLMTDVF----GNYVIQKFFE 753
+++F+ D G +F++ + ++ + E + TL + GN+++QK E
Sbjct: 21 QLIDFAIDPSGVKFLEANYPLDSEDQIRKAVFEKFTESTTLFVGLCHSRNGNFIVQKLVE 80
Query: 754 HGTESQRAQLASQLT-GHVLRLSLQMYGCRVIQKALEVV---HVDQQTQMVAELDGSVMK 809
T +++ +L Q+ G +L + + CRV+Q AL+ +V Q Q ++ D + M
Sbjct: 81 LATPAEQRELLRQMIDGGLLAMCKDKFACRVVQLALQKFDHSNVFQLIQELSTFDLAAM- 139
Query: 810 CVHDQNGNHVIQKCIECIPQDRIQFIISSFYG--QVVALSTHPYGCRVIQRVLEH----- 862
C DQ HVIQ+ ++ +P D F + ++A+ YGCR++Q+V++
Sbjct: 140 CT-DQISIHVIQRVVKQLPVDMWTFFVHFLSSGDSLMAVCQDKYGCRLVQQVIDRLAENP 198
Query: 863 ---CDDANTQQI--IMDEIMQHVCNLAQDQYGNYVIQHVLEHGKPHE--RTTVITQ-LAG 914
C Q + +M I+++ L+ +++ NYVIQ+V++ E R T+I + L
Sbjct: 199 KLPCFKFRIQLLHSLMTCIVRNCYRLSSNEFANYVIQYVIKSSGIMEMYRDTIIDKCLLR 258
Query: 915 QIVRMSQQKFASNVVEKCLTFGSPEERQLLINEMLGSTDEN-----EPLQAMMKDPFGNY 969
++ MSQ K+AS+V+E F P ++ E+ ++ + L ++ +GNY
Sbjct: 259 NLLSMSQDKYASHVIEGAFLFAPPALLHEMMEEIFSGYVKDVESNRDALDILLFHQYGNY 318
Query: 970 VVQKVLETC 978
VVQ+++ C
Sbjct: 319 VVQQMISIC 327
Score = 33.9 bits (76), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 50/211 (23%), Positives = 85/211 (40%), Gaps = 29/211 (13%)
Query: 697 DHVVEFSTDQYGSRFIQQKLEAATAEEKTRIFPEIIPHARTLMTDV-----------FGN 745
D ++ D+YG R +QQ ++ K F I +LMT + F N
Sbjct: 172 DSLMAVCQDKYGCRLVQQVIDRLAENPKLPCFKFRIQLLHSLMTCIVRNCYRLSSNEFAN 231
Query: 746 YVIQKFFEHG--TESQRAQLASQ-LTGHVLRLSLQMYGCRVIQKALEVVHVDQQTQMVAE 802
YVIQ + E R + + L ++L +S Y VI+ A +M+ E
Sbjct: 232 YVIQYVIKSSGIMEMYRDTIIDKCLLRNLLSMSQDKYASHVIEGAFLFAPPALLHEMMEE 291
Query: 803 LDGSVMKCVHD-----------QNGNHVIQKCIECIPQDRIQFIISSFYGQVVALSTHPY 851
+ +K V Q GN+V+Q+ I I ++ L + Y
Sbjct: 292 IFSGYVKDVESNRDALDILLFHQYGNYVVQQMISICTAALIGKEERELPPAILLLYSGWY 351
Query: 852 GCRVIQRVLEHC---DDANTQQIIMDEIMQH 879
++ QRVL+H + ++ + I+D +M+H
Sbjct: 352 E-KMKQRVLQHASRLERFSSGKKIIDSVMRH 381
>pdb|1PYS|B Chain B, Phenylalanyl-Trna Synthetase From Thermus Thermophilus
pdb|1B7Y|B Chain B, Phenylalanyl Trna Synthetase Complexed With
Phenylalaninyl-Adenylate
pdb|1EIY|B Chain B, The Crystal Structure Of Phenylalanyl-Trna Synthetase From
Thermus Thermophilus Complexed With Cognate Trnaphe
pdb|1B70|B Chain B, Phenylalanyl Trna Synthetase Complexed With Phenylalanine
pdb|1JJC|B Chain B, Crystal Structure At 2.6a Resolution Of Phenylalanyl-trna
Synthetase Complexed With Phenylalanyl-adenylate In The
Presence Of Manganese
pdb|2AKW|B Chain B, Crystal Structure Of T.thermophilus Phenylalanyl-trna
Synthetase Complexed With P-cl-phenylalanine
pdb|2ALY|B Chain B, Crystal Structure Of T.Thermophilus Phenylalanyl-Trna
Synthetase Complexed With
5'-O-[n-(L-Tyrosyl)sulphamoyl]adenosine
pdb|2AMC|B Chain B, Crystal Structure Of Phenylalanyl-Trna Synthetase
Complexed With L- Tyrosine
pdb|3HFZ|B Chain B, Crystal Structure Of Thermus Thermophilus
Phenylalanyl-Trna Synthetase Comlexed With M-Tyrosine
pdb|3TEH|B Chain B, Crystal Structure Of Thermus Thermophilus
Phenylalanyl-Trna Synthetase Comlexed With L-Dopa
Length = 785
Score = 31.6 bits (70), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 34/73 (46%), Gaps = 8/73 (10%)
Query: 153 IADWRKK--------GVNGGDRSSLFSMQPGISVLQAENDLMELRNAARRNLSRDASAEW 204
IA WR + GV GG S + I++ A D + +R ARR+ R ++
Sbjct: 300 IAGWRGEESFPLGLAGVMGGAESEVREDTEAIALEVACFDPVSIRKTARRHGLRTEASHR 359
Query: 205 LERGSDRLIGVPA 217
ERG D L VPA
Sbjct: 360 FERGVDPLGQVPA 372
>pdb|2IY5|B Chain B, Phenylalanyl-Trna Synthetase From Thermus Thermophilus
Complexed With Trna And A Phenylalanyl-Adenylate Analog
Length = 785
Score = 31.6 bits (70), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 34/73 (46%), Gaps = 8/73 (10%)
Query: 153 IADWRKK--------GVNGGDRSSLFSMQPGISVLQAENDLMELRNAARRNLSRDASAEW 204
IA WR + GV GG S + I++ A D + +R ARR+ R ++
Sbjct: 300 IAGWRGEESFPLGLAGVMGGAESEVREDTEAIALEVACFDPVSIRKTARRHGLRTEASHR 359
Query: 205 LERGSDRLIGVPA 217
ERG D L VPA
Sbjct: 360 FERGVDPLGQVPA 372
>pdb|2R8R|A Chain A, Crystal Structure Of The N-Terminal Region (19..243) Of
Sensor Protein Kdpd From Pseudomonas Syringae Pv. Tomato
Str. Dc3000
pdb|2R8R|B Chain B, Crystal Structure Of The N-Terminal Region (19..243) Of
Sensor Protein Kdpd From Pseudomonas Syringae Pv. Tomato
Str. Dc3000
Length = 228
Score = 30.0 bits (66), Expect = 6.5, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 4/78 (5%)
Query: 6 NIEMLPNLEDGLRGQNG---NLSLED-SLQTELELILQRQPDRQIVNRERDVNIYRSGSA 61
N++ L +L D +RG G +L D LQ +L+L P R+++ R RD +Y A
Sbjct: 125 NVQHLESLNDQVRGITGVQVRETLPDWVLQEAFDLVLIDLPPRELLERLRDGKVYVPEQA 184
Query: 62 PPTVEGSLNAVGSLFLRD 79
++ LR+
Sbjct: 185 RAAIDAFFTQTNLTALRE 202
>pdb|3U46|L Chain L, Ch04hCH02L P212121
pdb|3U46|B Chain B, Ch04hCH02L P212121
pdb|3U4B|L Chain L, Ch04hCH02L FAB P4
Length = 215
Score = 29.6 bits (65), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 20/41 (48%)
Query: 110 HPAYLSYYYSHENINPRLPPPLVSKEDWRVAQRFQGGGSSL 150
HP Y ++Y +PRL S +A RF GGGS +
Sbjct: 30 HPRYFAWYQQKRGQSPRLLIHSGSTRAAGIADRFSGGGSGM 70
>pdb|2VG9|A Chain A, Crystal Structure Of Loop Swap Mutant Of Necallimastix
Patriciarum Xyn11a
Length = 217
Score = 29.6 bits (65), Expect = 9.8, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 391 QSDFLYDTSNGHNQSMKQQF---MDKSTADNLAFSTHYIDFTRKNGIVPNLNASAINSNG 447
Q D T NG +++ KQ F K T+ ++ S H+ ++ ++ + NL A+N+ G
Sbjct: 141 QMDHTGPTINGGSETFKQYFSVRQQKRTSGHITVSDHFKEWAKQGWGIGNLYEVALNAEG 200
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
0.315 0.131 0.374
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 29,001,022
Number of Sequences: 62578
Number of extensions: 1167058
Number of successful extensions: 3426
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 3091
Number of HSP's gapped (non-prelim): 49
length of query: 1029
length of database: 14,973,337
effective HSP length: 109
effective length of query: 920
effective length of database: 8,152,335
effective search space: 7500148200
effective search space used: 7500148200
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)