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= 001671
(1034 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 = 405 bits (1042), Expect = e-113, Method: Compositional matrix adjust.
Identities = 190/338 (56%), Positives = 260/338 (76%), Gaps = 2/338 (0%)
Query: 681 SSLLDEFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQA 740
S LL++F++N+ +L ++ GH+VEFS DQ+GSRFIQQKLE AT E+ +VF EI+ A
Sbjct: 5 SRLLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAA 64
Query: 741 LSLMTDVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQ 800
LMTDVFGNYVIQKFFE G+ Q LA ++ GHVL L+LQMYGCRVIQKA+E + DQ
Sbjct: 65 YQLMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQ 124
Query: 801 QTQMVKELDGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRV 860
Q++MVKELDGH+++CV+DQNGNHV+QKCIECV ++QFI+ F QV LSTHPYGCRV
Sbjct: 125 QSEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRV 184
Query: 861 IQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQ 920
IQR+LEHC E+T I ++E+ Q L QDQYGNYV+QHVLEHG+P ++S I+ ++ G+
Sbjct: 185 IQRILEHCTAEQTLPI-LEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGK 243
Query: 921 IVQMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSIE-ENEPLQVMMKDQFANYVVQKV 979
++ +SQ KFASNV+EKC++ + AER L++E+ + + L MMKDQ+ANYVVQK+
Sbjct: 244 VLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKM 303
Query: 980 LETCDDQQLELILNRIKVHLNALKKYTYGKHIVARVEK 1017
++ + Q ++I+++I+ H+ L+KYTYGKHI+A++EK
Sbjct: 304 IDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKLEK 341
Score = 94.7 bits (234), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 72/257 (28%), Positives = 124/257 (48%), Gaps = 7/257 (2%)
Query: 772 LTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKELDGHIMRCVRDQNGNHVIQKCIEC 831
L GH++ S +G R IQ+ +E ++ + E+ + + D GN+VIQK E
Sbjct: 24 LIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGNYVIQKFFEF 83
Query: 832 VPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQD 891
D + V+ L+ YGCRVIQ+ LE ++ QS M+ E+ V +D
Sbjct: 84 GSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQ-QSEMVKELDGHVLKCVKD 142
Query: 892 QYGNYVVQHVLEHGKPHERSAIIKKLTGQIVQMSQQKFASNVIEKCLSFGTPAERQALVN 951
Q GN+VVQ +E +P II GQ+ +S + VI++ L T + ++
Sbjct: 143 QNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILE 202
Query: 952 EMLGSIEENEPLQVMMKDQFANYVVQKVLETCDDQQLELILNRIKVHLNALKKYTYGKHI 1011
E+ E+ +++DQ+ NYV+Q VLE + I++ I+ + AL ++ + ++
Sbjct: 203 ELHQHTEQ------LVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNV 256
Query: 1012 VARVEKLVAAGERRISI 1028
V + + ER + I
Sbjct: 257 VEKCVTHASRAERALLI 273
>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 (1033), Expect = e-112, Method: Compositional matrix adjust.
Identities = 191/340 (56%), Positives = 260/340 (76%), Gaps = 4/340 (1%)
Query: 681 SSLLDEFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQA 740
S LL++F++N+ +L ++ GH+VEFS DQ+GSRFIQQKLE AT E+ MVF EI+ A
Sbjct: 3 SRLLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAA 62
Query: 741 LSLMTDVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQ 800
LMTDVFGNYVIQKFFE G+ Q LA ++ GHVL L+LQMYGCRVIQKA+E + DQ
Sbjct: 63 YQLMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQ 122
Query: 801 Q--TQMVKELDGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGC 858
Q ++MVKELDGH+++CV+DQNGNHV+QKCIECV ++QFI+ F QV LSTHPYGC
Sbjct: 123 QVISEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGC 182
Query: 859 RVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLT 918
RVIQR+LEHC E+T I ++E+ Q L QDQYGNYV+QHVLEHG+P ++S I+ ++
Sbjct: 183 RVIQRILEHCTAEQTLPI-LEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIR 241
Query: 919 GQIVQMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSIE-ENEPLQVMMKDQFANYVVQ 977
G+++ +SQ KFASNV+EKC++ + AER L++E+ + + L MMKDQ+ANYVVQ
Sbjct: 242 GKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQ 301
Query: 978 KVLETCDDQQLELILNRIKVHLNALKKYTYGKHIVARVEK 1017
K+++ + Q ++I+++I+ H+ L+KYTYGKHI+A++EK
Sbjct: 302 KMIDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKLEK 341
Score = 94.7 bits (234), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 72/258 (27%), Positives = 124/258 (48%), Gaps = 7/258 (2%)
Query: 772 LTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKELDGHIMRCVRDQNGNHVIQKCIEC 831
L GH++ S +G R IQ+ +E ++ + E+ + + D GN+VIQK E
Sbjct: 22 LIGHIVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAAYQLMTDVFGNYVIQKFFEF 81
Query: 832 VPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQRVLEHCH-DEKTQSIMMDEILQSVCMLAQ 890
D + V+ L+ YGCRVIQ+ LE D++ S M+ E+ V +
Sbjct: 82 GSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQVISEMVKELDGHVLKCVK 141
Query: 891 DQYGNYVVQHVLEHGKPHERSAIIKKLTGQIVQMSQQKFASNVIEKCLSFGTPAERQALV 950
DQ GN+VVQ +E +P II GQ+ +S + VI++ L T + ++
Sbjct: 142 DQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPIL 201
Query: 951 NEMLGSIEENEPLQVMMKDQFANYVVQKVLETCDDQQLELILNRIKVHLNALKKYTYGKH 1010
E+ E+ +++DQ+ NYV+Q VLE + I++ I+ + AL ++ + +
Sbjct: 202 EELHQHTEQ------LVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASN 255
Query: 1011 IVARVEKLVAAGERRISI 1028
+V + + ER + I
Sbjct: 256 VVEKCVTHASRAERALLI 273
Score = 59.3 bits (142), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 40/118 (33%), Positives = 64/118 (54%), Gaps = 8/118 (6%)
Query: 914 IKKLTGQIVQMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSIEENEPLQVMMKDQFAN 973
++ L G IV+ SQ + S I++ L TPAERQ + NE+L + + +M D F N
Sbjct: 19 LRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAAYQ------LMTDVFGN 72
Query: 974 YVVQKVLETCD-DQQLELILNRIKVHLNALKKYTYGKHIVARVEKLVAAGERRISIMT 1030
YV+QK E DQ+L L RI+ H+ L YG ++ + + +++ ++ IS M
Sbjct: 73 YVIQKFFEFGSLDQKLALA-TRIRGHVLPLALQMYGCRVIQKALESISSDQQVISEMV 129
>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 = 399 bits (1024), Expect = e-111, Method: Compositional matrix adjust.
Identities = 186/338 (55%), Positives = 258/338 (76%), Gaps = 2/338 (0%)
Query: 681 SSLLDEFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQA 740
S LL++F++N+ +L EIAGH++EFS DQ+GSRFIQ KLE AT E+ +VF EI+ A
Sbjct: 3 SRLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAA 62
Query: 741 LSLMTDVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQ 800
LM DVFGNYVIQKFFE G+ Q LA+++ GHVL+L+LQMYGCRVIQKA+E + DQ
Sbjct: 63 YQLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQ 122
Query: 801 QTQMVKELDGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRV 860
Q +MV+ELDGH+++CV+DQNGNHV+QKCIECV ++QFI+ F QV LSTHPYGCRV
Sbjct: 123 QNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRV 182
Query: 861 IQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQ 920
IQR+LEHC ++T I ++E+ Q L QDQYGNYV+QHVLEHG+P ++S I+ ++ G
Sbjct: 183 IQRILEHCLPDQTLPI-LEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGN 241
Query: 921 IVQMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSIE-ENEPLQVMMKDQFANYVVQKV 979
++ +SQ KFASNV+EKC++ + ER L++E+ + + L MMKDQ+ANYVVQK+
Sbjct: 242 VLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKM 301
Query: 980 LETCDDQQLELILNRIKVHLNALKKYTYGKHIVARVEK 1017
++ + Q ++++++I+ H+ L+KYTYGKHI+A++EK
Sbjct: 302 IDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKLEK 339
Score = 89.7 bits (221), Expect = 7e-18, Method: Compositional matrix adjust.
Identities = 72/265 (27%), Positives = 128/265 (48%), Gaps = 11/265 (4%)
Query: 764 QVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKELDGHIMRCVRDQNGNH 823
Q+RE+A GH++ S +G R IQ +E ++ + E+ + + D GN+
Sbjct: 18 QLREIA----GHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNY 73
Query: 824 VIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQ 883
VIQK E + + V++L+ YGCRVIQ+ LE ++ Q+ M+ E+
Sbjct: 74 VIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQ-QNEMVRELDG 132
Query: 884 SVCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQIVQMSQQKFASNVIEKCLSFGTP 943
V +DQ GN+VVQ +E +P II GQ+ +S + VI++ L P
Sbjct: 133 HVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLP 192
Query: 944 AERQALVNEMLGSIEENEPLQVMMKDQFANYVVQKVLETCDDQQLELILNRIKVHLNALK 1003
+ ++ E+ E+ +++DQ+ NYV+Q VLE + I+ I+ ++ L
Sbjct: 193 DQTLPILEELHQHTEQ------LVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLS 246
Query: 1004 KYTYGKHIVARVEKLVAAGERRISI 1028
++ + ++V + + ER + I
Sbjct: 247 QHKFASNVVEKCVTHASRTERAVLI 271
>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 = 398 bits (1023), Expect = e-111, Method: Compositional matrix adjust.
Identities = 186/338 (55%), Positives = 258/338 (76%), Gaps = 2/338 (0%)
Query: 681 SSLLDEFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQA 740
S LL++F++N+ +L EIAGH++EFS DQ+GSRFIQ KLE AT E+ +VF EI+ A
Sbjct: 3 SRLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAA 62
Query: 741 LSLMTDVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQ 800
LM DVFGNYVIQKFFE G+ Q LA+++ GHVL+L+LQMYGCRVIQKA+E + DQ
Sbjct: 63 YQLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQ 122
Query: 801 QTQMVKELDGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRV 860
Q +MV+ELDGH+++CV+DQNGNHV+QKCIECV ++QFI+ F QV LSTHPYGCRV
Sbjct: 123 QNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRV 182
Query: 861 IQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQ 920
IQR+LEHC ++T I ++E+ Q L QDQYGNYV+QHVLEHG+P ++S I+ ++ G
Sbjct: 183 IQRILEHCLPDQTLPI-LEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGN 241
Query: 921 IVQMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSIE-ENEPLQVMMKDQFANYVVQKV 979
++ +SQ KFASNV+EKC++ + ER L++E+ + + L MMKDQ+ANYVVQK+
Sbjct: 242 VLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKM 301
Query: 980 LETCDDQQLELILNRIKVHLNALKKYTYGKHIVARVEK 1017
++ + Q ++++++I+ H+ L+KYTYGKHI+A++EK
Sbjct: 302 IDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKLEK 339
Score = 89.0 bits (219), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 72/265 (27%), Positives = 128/265 (48%), Gaps = 11/265 (4%)
Query: 764 QVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKELDGHIMRCVRDQNGNH 823
Q+RE+A GH++ S +G R IQ +E ++ + E+ + + D GN+
Sbjct: 18 QLREIA----GHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNY 73
Query: 824 VIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQ 883
VIQK E + + V++L+ YGCRVIQ+ LE ++ Q+ M+ E+
Sbjct: 74 VIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQ-QNEMVRELDG 132
Query: 884 SVCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQIVQMSQQKFASNVIEKCLSFGTP 943
V +DQ GN+VVQ +E +P II GQ+ +S + VI++ L P
Sbjct: 133 HVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLP 192
Query: 944 AERQALVNEMLGSIEENEPLQVMMKDQFANYVVQKVLETCDDQQLELILNRIKVHLNALK 1003
+ ++ E+ E+ +++DQ+ NYV+Q VLE + I+ I+ ++ L
Sbjct: 193 DQTLPILEELHQHTEQ------LVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLS 246
Query: 1004 KYTYGKHIVARVEKLVAAGERRISI 1028
++ + ++V + + ER + I
Sbjct: 247 QHKFASNVVEKCVTHASRTERAVLI 271
>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 = 395 bits (1014), Expect = e-110, Method: Compositional matrix adjust.
Identities = 184/338 (54%), Positives = 258/338 (76%), Gaps = 2/338 (0%)
Query: 681 SSLLDEFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQA 740
S LL++F++N+ +L EIAGH++EFS DQ+GSRFIQ KLE AT E+ +VF EI+ A
Sbjct: 4 SRLLEDFRNNRYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAA 63
Query: 741 LSLMTDVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQ 800
LM DVFGNYVIQKFFE G+ Q LA+++ GHVL+L+LQMYGCRVIQKA+E + DQ
Sbjct: 64 YQLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQ 123
Query: 801 QTQMVKELDGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRV 860
Q +MV+ELDGH+++CV+DQNGNHV+QKCIECV ++QFI+ F QV LSTHPYGCRV
Sbjct: 124 QNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRV 183
Query: 861 IQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQ 920
IQR+LEHC ++T I ++E+ Q L QDQYG+YV++HVLEHG+P ++S I+ ++ G
Sbjct: 184 IQRILEHCLPDQTLPI-LEELHQHTEQLVQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGN 242
Query: 921 IVQMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSIE-ENEPLQVMMKDQFANYVVQKV 979
++ +SQ KFASNV+EKC++ + ER L++E+ + + L MMKDQ+ANYVVQK+
Sbjct: 243 VLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKM 302
Query: 980 LETCDDQQLELILNRIKVHLNALKKYTYGKHIVARVEK 1017
++ + Q ++++++I+ H+ L+KYTYGKHI+A++EK
Sbjct: 303 IDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILAKLEK 340
Score = 85.9 bits (211), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 70/265 (26%), Positives = 128/265 (48%), Gaps = 11/265 (4%)
Query: 764 QVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKELDGHIMRCVRDQNGNH 823
Q+RE+A GH++ S +G R IQ +E ++ + E+ + + D GN+
Sbjct: 19 QLREIA----GHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNY 74
Query: 824 VIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQ 883
VIQK E + + V++L+ YGCRVIQ+ LE ++ Q+ M+ E+
Sbjct: 75 VIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQ-QNEMVRELDG 133
Query: 884 SVCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQIVQMSQQKFASNVIEKCLSFGTP 943
V +DQ GN+VVQ +E +P II GQ+ +S + VI++ L P
Sbjct: 134 HVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLP 193
Query: 944 AERQALVNEMLGSIEENEPLQVMMKDQFANYVVQKVLETCDDQQLELILNRIKVHLNALK 1003
+ ++ E+ E+ +++DQ+ +YV++ VLE + I+ I+ ++ L
Sbjct: 194 DQTLPILEELHQHTEQ------LVQDQYGSYVIRHVLEHGRPEDKSKIVAEIRGNVLVLS 247
Query: 1004 KYTYGKHIVARVEKLVAAGERRISI 1028
++ + ++V + + ER + I
Sbjct: 248 QHKFASNVVEKCVTHASRTERAVLI 272
>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 = 375 bits (963), Expect = e-104, Method: Compositional matrix adjust.
Identities = 183/325 (56%), Positives = 243/325 (74%), Gaps = 3/325 (0%)
Query: 678 SFASSLLDEFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIM 737
S S LL++F++ + +L ++A H+VEFS DQ+GSRFIQQKLE AT EK MVF EI+
Sbjct: 2 SHMSRLLEDFRNQRYPNLQLRDLANHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEIL 61
Query: 738 PQALSLMTDVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVE 797
A SLMTDVFGNYVIQKFFE GT Q L Q+ GHVL L+LQMYGCRVIQKA+E +
Sbjct: 62 AAAYSLMTDVFGNYVIQKFFEFGTPEQKNTLGMQVKGHVLQLALQMYGCRVIQKALESIS 121
Query: 798 LDQQTQMVKELDGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYG 857
+QQ ++V ELDGH+++CV+DQNGNHV+QKCIECV A+QFI+ F QV +LSTHPYG
Sbjct: 122 PEQQQEIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYG 181
Query: 858 CRVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKL 917
CRVIQR+LEHC E+T I +DE+ + L QDQYGNYV+QHVLEHGK ++S +I +
Sbjct: 182 CRVIQRILEHCTAEQTTPI-LDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSV 240
Query: 918 TGQIVQMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSIEENEPLQVMMKDQFANYVVQ 977
G+++ +SQ KFASNV+EKC++ T ER L++E+ + +N L VMMKDQ+ANYVVQ
Sbjct: 241 RGKVLVLSQHKFASNVVEKCVTHATRGERTGLIDEVC-TFNDN-ALHVMMKDQYANYVVQ 298
Query: 978 KVLETCDDQQLELILNRIKVHLNAL 1002
K+++ + QL+ ++ +I+ ++ AL
Sbjct: 299 KMIDVSEPTQLKKLMTKIRKNMAAL 323
Score = 95.5 bits (236), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 71/261 (27%), Positives = 127/261 (48%), Gaps = 11/261 (4%)
Query: 764 QVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKELDGHIMRCVRDQNGNH 823
Q+R+LA+ H++ S +G R IQ+ +E ++ + E+ + D GN+
Sbjct: 20 QLRDLAN----HIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNY 75
Query: 824 VIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQ 883
VIQK E + + + V+ L+ YGCRVIQ+ LE E+ Q I+ E+
Sbjct: 76 VIQKFFEFGTPEQKNTLGMQVKGHVLQLALQMYGCRVIQKALESISPEQQQEIV-HELDG 134
Query: 884 SVCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQIVQMSQQKFASNVIEKCLSFGTP 943
V +DQ GN+VVQ +E P II GQ+ +S + VI++ L T
Sbjct: 135 HVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLSTHPYGCRVIQRILEHCTA 194
Query: 944 AERQALVNEMLGSIEENEPLQVMMKDQFANYVVQKVLETCDDQQLELILNRIKVHLNALK 1003
+ +++E+ +E + +++DQ+ NYV+Q VLE + +++N ++ + L
Sbjct: 195 EQTTPILDEL------HEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLS 248
Query: 1004 KYTYGKHIVARVEKLVAAGER 1024
++ + ++V + GER
Sbjct: 249 QHKFASNVVEKCVTHATRGER 269
>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 = 277 bits (708), Expect = 2e-74, Method: Compositional matrix adjust.
Identities = 146/341 (42%), Positives = 222/341 (65%), Gaps = 15/341 (4%)
Query: 697 LSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQALSLMTDVFGNYVIQKF 756
L +I GH +EF DQ+GSRFIQ++L T+ EK ++F EI A+ L DVFGNYVIQKF
Sbjct: 26 LKDIFGHSLEFCKDQHGSRFIQRELATSPASEKEVIFNEIRDDAIELSNDVFGNYVIQKF 85
Query: 757 FEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKELDGHIMRCV 816
FE G+ Q L DQ G++ LSLQMY CRVIQKA+E ++ +Q+ ++V EL +++ +
Sbjct: 86 FEFGSKIQKNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQRIELVLELSDSVLQMI 145
Query: 817 RDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQRVLEHCHDEKTQSI 876
+DQNGNHVIQK IE +P + + FI+ + + LSTH YGCRVIQR+LE E +SI
Sbjct: 146 KDQNGNHVIQKAIETIPIEKLPFILSSLTGHIYHLSTHSYGCRVIQRLLEFGSSEDQESI 205
Query: 877 MMDEILQSVCMLAQDQYGNYVVQHVLEHGKPHERS------AIIKKLTGQIVQMSQQKFA 930
++E+ + L QDQYGNYV+Q+VL+ + + II+ + +V+ S+ KFA
Sbjct: 206 -LNELKDFIPYLIQDQYGNYVIQYVLQQDQFTNKEMVDIKQEIIETVANNVVEYSKHKFA 264
Query: 931 SNVIEKCLSFGTPAERQALVNEMLG-------SIEENEPLQVMMKDQFANYVVQKVLETC 983
SNV+EK + +G+ ++ +++++L ++E++ P+ +M+KDQFANYV+QK++
Sbjct: 265 SNVVEKSILYGSKNQKDLIISKILPRDKNHALNLEDDSPMILMIKDQFANYVIQKLVNVS 324
Query: 984 DDQQLELILNRIKVHLNALKKY-TYGKHIVARVEKLVAAGE 1023
+ + +LI+ I+ +L+ L K + G +A VEKL A E
Sbjct: 325 EGEGKKLIVIAIRAYLDKLNKSNSLGNRHLASVEKLAALVE 365
Score = 32.7 bits (73), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/111 (19%), Positives = 51/111 (45%), Gaps = 6/111 (5%)
Query: 914 IKKLTGQIVQMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSIEENEPLQVMMKDQFAN 973
+K + G ++ + + S I++ L+ +E++ + NE+ E + D F N
Sbjct: 26 LKDIFGHSLEFCKDQHGSRFIQRELATSPASEKEVIFNEIRDDAIE------LSNDVFGN 79
Query: 974 YVVQKVLETCDDQQLELILNRIKVHLNALKKYTYGKHIVARVEKLVAAGER 1024
YV+QK E Q ++++ K ++ L Y ++ + + + + +R
Sbjct: 80 YVIQKFFEFGSKIQKNTLVDQFKGNMKQLSLQMYACRVIQKALEYIDSNQR 130
>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 = 178 bits (452), Expect = 1e-44, Method: Composition-based stats.
Identities = 102/295 (34%), Positives = 166/295 (56%), Gaps = 9/295 (3%)
Query: 697 LSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQALSLMTDVFGNYVIQKF 756
L + G + DQ+G RF+Q++L+ ++ + +F+E + LMTD FGNY+IQK
Sbjct: 8 LDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKL 67
Query: 757 FEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKE-LDGHIMRC 815
E T Q L + H + +SL +GCR +QK IE ++ D++ Q+V + L + ++
Sbjct: 68 LEEVTTEQRIVLTKISSPHFVEISLNPHGCRALQKLIECIKTDEEAQIVVDSLRPYTVQL 127
Query: 816 VRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQRVLEHCHDEKTQS 875
+D NGNHVIQKC++ + + QFI D + ++TH +GCRV+QR L+H E+ +
Sbjct: 128 SKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCRVLQRCLDHGTTEQCDN 187
Query: 876 IMMDEILQSVCMLAQDQYGNYVVQHVL----EHGKPHERSAIIKKLTGQIVQMSQQKFAS 931
+ D++L V L D +GNYVVQ+++ E K I+ L + +++S KF S
Sbjct: 188 -LCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGS 246
Query: 932 NVIEKCLSFGTPAERQALVNEMLGSIEENEPLQVMMKDQFANYVVQKVLETCDDQ 986
NVIEK L T + ++ E+L + E +Q ++ D + NYV+Q L+ Q
Sbjct: 247 NVIEKILK--TAIVSEPMILEILNNGGET-GIQSLLNDSYGNYVLQTALDISHKQ 298
Score = 100 bits (249), Expect = 4e-21, Method: Composition-based stats.
Identities = 65/263 (24%), Positives = 128/263 (48%), Gaps = 14/263 (5%)
Query: 770 DQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKELDGHIMRCVRDQNGNHVIQKCI 829
DQ G + +L +GCR +QK ++++ + +E + + + D GN++IQK +
Sbjct: 9 DQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLL 68
Query: 830 ECVPEDAIQFIVLTFYD--QVVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQSVCM 887
E V + Q IVLT V +S +P+GCR +Q+++E ++ I++D +
Sbjct: 69 EEVTTE--QRIVLTKISSPHFVEISLNPHGCRALQKLIECIKTDEEAQIVVDSLRPYTVQ 126
Query: 888 LAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQIVQMSQQKFASNVIEKCLSFGTPAERQ 947
L++D GN+V+Q L+ KP I ++ + ++ + V+++CL GT +
Sbjct: 127 LSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCRVLQRCLDHGTTEQCD 186
Query: 948 ALVNEMLGSIEENEPLQVMMKDQFANYVVQKVL----ETCDDQQLELILNRIKVHLNALK 1003
L +++L +++ + D F NYVVQ ++ E I++ +K L
Sbjct: 187 NLCDKLLALVDK------LTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELS 240
Query: 1004 KYTYGKHIVARVEKLVAAGERRI 1026
+ +G +++ ++ K E I
Sbjct: 241 IHKFGSNVIEKILKTAIVSEPMI 263
Score = 61.6 bits (148), Expect = 2e-09, Method: Composition-based stats.
Identities = 59/245 (24%), Positives = 100/245 (40%), Gaps = 42/245 (17%)
Query: 683 LLDEFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQALS 742
L++ K+++ + + + V+ S D G+ IQ+ L+ E +F I +
Sbjct: 103 LIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCID 162
Query: 743 LMTDVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQT 802
+ T G V+Q+ +HGT Q L D+L V L+L +G V+Q
Sbjct: 163 IATHRHGCRVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQ------------ 210
Query: 803 QMVKELDGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQ 862
++I K E D IV + + LS H +G VI+
Sbjct: 211 --------------------YIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIE 250
Query: 863 RVLEHCHDEKTQSIMMDEILQS-----VCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKL 917
++L+ M+ EIL + + L D YGNYV+Q L+ H+++ + K
Sbjct: 251 KILK---TAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALD--ISHKQNDYLYKR 305
Query: 918 TGQIV 922
+IV
Sbjct: 306 LSEIV 310
>pdb|3BWT|A Chain A, Crystal Structure Of The Rna Binding Domain Of Puf4 From
Saccharomyces Cerevisiae
Length = 333
Score = 171 bits (433), Expect = 2e-42, Method: Composition-based stats.
Identities = 100/295 (33%), Positives = 164/295 (55%), Gaps = 9/295 (3%)
Query: 697 LSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQALSLMTDVFGNYVIQKF 756
L + G + DQ+G RF+Q++L+ ++ + +F+E + LMTD FGNY+IQK
Sbjct: 8 LDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKL 67
Query: 757 FEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKE-LDGHIMRC 815
E T Q L + H + +SL +G R +QK IE ++ D++ Q+V + L + ++
Sbjct: 68 LEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQL 127
Query: 816 VRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQRVLEHCHDEKTQS 875
+D NGNHVIQKC++ + + QFI D + ++TH +GC V+QR L+H E+ +
Sbjct: 128 SKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDN 187
Query: 876 IMMDEILQSVCMLAQDQYGNYVVQHVL----EHGKPHERSAIIKKLTGQIVQMSQQKFAS 931
+ D++L V L D +GNYVVQ+++ E K I+ L + +++S KF S
Sbjct: 188 -LCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGS 246
Query: 932 NVIEKCLSFGTPAERQALVNEMLGSIEENEPLQVMMKDQFANYVVQKVLETCDDQ 986
NVIEK L T + ++ E+L + E +Q ++ D + NYV+Q L+ Q
Sbjct: 247 NVIEKILK--TAIVSEPMILEILNNGGET-GIQSLLNDSYGNYVLQTALDISHKQ 298
Score = 95.9 bits (237), Expect = 1e-19, Method: Composition-based stats.
Identities = 64/263 (24%), Positives = 127/263 (48%), Gaps = 14/263 (5%)
Query: 770 DQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKELDGHIMRCVRDQNGNHVIQKCI 829
DQ G + +L +GCR +QK ++++ + +E + + + D GN++IQK +
Sbjct: 9 DQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLL 68
Query: 830 ECVPEDAIQFIVLTFYD--QVVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQSVCM 887
E V + Q IVLT V +S +P+G R +Q+++E ++ I++D +
Sbjct: 69 EEVTTE--QRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQ 126
Query: 888 LAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQIVQMSQQKFASNVIEKCLSFGTPAERQ 947
L++D GN+V+Q L+ KP I ++ + ++ + V+++CL GT +
Sbjct: 127 LSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCD 186
Query: 948 ALVNEMLGSIEENEPLQVMMKDQFANYVVQKVL----ETCDDQQLELILNRIKVHLNALK 1003
L +++L +++ + D F NYVVQ ++ E I++ +K L
Sbjct: 187 NLCDKLLALVDK------LTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELS 240
Query: 1004 KYTYGKHIVARVEKLVAAGERRI 1026
+ +G +++ ++ K E I
Sbjct: 241 IHKFGSNVIEKILKTAIVSEPMI 263
Score = 61.6 bits (148), Expect = 2e-09, Method: Composition-based stats.
Identities = 59/245 (24%), Positives = 100/245 (40%), Gaps = 42/245 (17%)
Query: 683 LLDEFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQALS 742
L++ K+++ + + + V+ S D G+ IQ+ L+ E +F I +
Sbjct: 103 LIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCID 162
Query: 743 LMTDVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQT 802
+ T G V+Q+ +HGT Q L D+L V L+L +G V+Q
Sbjct: 163 IATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQ------------ 210
Query: 803 QMVKELDGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQ 862
++I K E D IV + + LS H +G VI+
Sbjct: 211 --------------------YIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIE 250
Query: 863 RVLEHCHDEKTQSIMMDEILQS-----VCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKL 917
++L+ M+ EIL + + L D YGNYV+Q L+ H+++ + K
Sbjct: 251 KILK---TAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALD--ISHKQNDYLYKR 305
Query: 918 TGQIV 922
+IV
Sbjct: 306 LSEIV 310
>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 = 171 bits (432), Expect = 2e-42, Method: Composition-based stats.
Identities = 100/295 (33%), Positives = 164/295 (55%), Gaps = 9/295 (3%)
Query: 697 LSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQALSLMTDVFGNYVIQKF 756
L + G + DQ+G RF+Q++L+ ++ + +F+E + LMTD FGNY+IQK
Sbjct: 8 LDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKL 67
Query: 757 FEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKE-LDGHIMRC 815
E T Q L + H + +SL +G R +QK IE ++ D++ Q+V + L + ++
Sbjct: 68 LEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQL 127
Query: 816 VRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQRVLEHCHDEKTQS 875
+D NGNHVIQKC++ + + QFI D + ++TH +GC V+QR L+H E+ +
Sbjct: 128 SKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDN 187
Query: 876 IMMDEILQSVCMLAQDQYGNYVVQHVL----EHGKPHERSAIIKKLTGQIVQMSQQKFAS 931
+ D++L V L D +GNYVVQ+++ E K I+ L + +++S KF S
Sbjct: 188 -LCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGS 246
Query: 932 NVIEKCLSFGTPAERQALVNEMLGSIEENEPLQVMMKDQFANYVVQKVLETCDDQ 986
NVIEK L T + ++ E+L + E +Q ++ D + NYV+Q L+ Q
Sbjct: 247 NVIEKILK--TAIVSEPMILEILNNGGET-GIQSLLNDSYGNYVLQTALDISHKQ 298
Score = 95.5 bits (236), Expect = 1e-19, Method: Composition-based stats.
Identities = 64/263 (24%), Positives = 127/263 (48%), Gaps = 14/263 (5%)
Query: 770 DQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKELDGHIMRCVRDQNGNHVIQKCI 829
DQ G + +L +GCR +QK ++++ + +E + + + D GN++IQK +
Sbjct: 9 DQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLL 68
Query: 830 ECVPEDAIQFIVLTFYD--QVVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQSVCM 887
E V + Q IVLT V +S +P+G R +Q+++E ++ I++D +
Sbjct: 69 EEVTTE--QRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQ 126
Query: 888 LAQDQYGNYVVQHVLEHGKPHERSAIIKKLTGQIVQMSQQKFASNVIEKCLSFGTPAERQ 947
L++D GN+V+Q L+ KP I ++ + ++ + V+++CL GT +
Sbjct: 127 LSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCD 186
Query: 948 ALVNEMLGSIEENEPLQVMMKDQFANYVVQKVL----ETCDDQQLELILNRIKVHLNALK 1003
L +++L +++ + D F NYVVQ ++ E I++ +K L
Sbjct: 187 NLCDKLLALVDK------LTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELS 240
Query: 1004 KYTYGKHIVARVEKLVAAGERRI 1026
+ +G +++ ++ K E I
Sbjct: 241 IHKFGSNVIEKILKTAIVSEPMI 263
Score = 61.2 bits (147), Expect = 3e-09, Method: Composition-based stats.
Identities = 59/245 (24%), Positives = 100/245 (40%), Gaps = 42/245 (17%)
Query: 683 LLDEFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQALS 742
L++ K+++ + + + V+ S D G+ IQ+ L+ E +F I +
Sbjct: 103 LIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCID 162
Query: 743 LMTDVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQT 802
+ T G V+Q+ +HGT Q L D+L V L+L +G V+Q
Sbjct: 163 IATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQ------------ 210
Query: 803 QMVKELDGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQ 862
++I K E D IV + + LS H +G VI+
Sbjct: 211 --------------------YIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIE 250
Query: 863 RVLEHCHDEKTQSIMMDEILQS-----VCMLAQDQYGNYVVQHVLEHGKPHERSAIIKKL 917
++L+ M+ EIL + + L D YGNYV+Q L+ H+++ + K
Sbjct: 251 KILK---TAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALD--ISHKQNDYLYKR 305
Query: 918 TGQIV 922
+IV
Sbjct: 306 LSEIV 310
>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 = 167 bits (423), Expect = 3e-41, Method: Compositional matrix adjust.
Identities = 105/320 (32%), Positives = 175/320 (54%), Gaps = 24/320 (7%)
Query: 669 SEAGGSLDES--FASSLLDEFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATT 726
+E ++ES FA ++LD++ G + DQ+G RF+Q++L+ +
Sbjct: 13 AEKQRKIEESSRFADAVLDQY-------------IGSIHSLCKDQHGCRFLQKQLDILGS 59
Query: 727 EEKNMVFQEIMPQALSLMTDVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGC 786
+ + +F+E + LMTD FGNY+IQK E T Q L + H + +SL +G
Sbjct: 60 KAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGT 119
Query: 787 RVIQKAIEVVELDQQTQMVKE-LDGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFY 845
R +QK IE ++ D++ Q+V + L + ++ +D NGNHVIQKC++ + + QFI
Sbjct: 120 RALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAIS 179
Query: 846 DQVVTLSTHPYGCRVIQRVLEHCHDEKTQSIMMDEILQSVCMLAQDQYGNYVVQHVL--- 902
D + ++TH +GC V+QR L+H E+ + + D++L V L D +GNYVVQ+++
Sbjct: 180 DSCIDIATHRHGCCVLQRCLDHGTTEQCDN-LCDKLLALVDKLTLDPFGNYVVQYIITKE 238
Query: 903 -EHGKPHERSAIIKKLTGQIVQMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSIEENE 961
E K I+ L + +++S KF SNVIEK L +E ++ E+L + E
Sbjct: 239 AEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILKTAIVSE--PMILEILNNGGET- 295
Query: 962 PLQVMMKDQFANYVVQKVLE 981
+Q ++ D + NYV+Q L+
Sbjct: 296 GIQSLLNDSYGNYVLQTALD 315
Score = 59.3 bits (142), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 61/248 (24%), Positives = 102/248 (41%), Gaps = 48/248 (19%)
Query: 683 LLDEFKSNKTKCFELSEIAGHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQALS 742
L++ K+++ + + + V+ S D G+ IQ+ L+ E +F I +
Sbjct: 125 LIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCID 184
Query: 743 LMTDVFGNYVIQKFFEHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQT 802
+ T G V+Q+ +HGT Q L D+L V L+L +G V+Q
Sbjct: 185 IATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQ------------ 232
Query: 803 QMVKELDGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVTLSTHPYGCRVIQ 862
++I K E D IV + + LS H +G VI+
Sbjct: 233 --------------------YIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIE 272
Query: 863 RVLEHCHDEKTQSI---MMDEILQS-----VCMLAQDQYGNYVVQHVLEHGKPHERSAII 914
++L KT + M+ EIL + + L D YGNYV+Q L+ H+++ +
Sbjct: 273 KIL------KTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALD--ISHKQNDYL 324
Query: 915 KKLTGQIV 922
K +IV
Sbjct: 325 YKRLSEIV 332
>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 = 133 bits (334), Expect = 6e-31, Method: Compositional matrix adjust.
Identities = 96/336 (28%), Positives = 172/336 (51%), Gaps = 55/336 (16%)
Query: 697 LSEI--AGHVVEFSADQYGSRFIQQKLE-TATTEEKNMVFQEIMPQA---LSLMTDVFGN 750
LSE+ +G +++F+ D+ G +F+++ ++ + T+ +K +F++++ + L L T++FGN
Sbjct: 22 LSEVLDSGDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNIFGN 81
Query: 751 YVIQKFF-------EHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQ 803
Y++Q + G + +L + ++ + + L + CRVIQ +++ ++L +
Sbjct: 82 YLVQSVIGISLATNDDGYTKRQEKLKNFISSQMTDMCLDKFACRVIQSSLQNMDLSLACK 141
Query: 804 MVKEL--DGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVT------LSTHP 855
+V+ L D ++ DQN NHVIQK + +P +FIV D V T + +
Sbjct: 142 LVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIV----DFVATPEHLRQICSDK 197
Query: 856 YGCRVIQRVLEHCH---------------DEKTQSIMMDEILQSVCMLAQDQYGNYVVQH 900
YGCRV+Q ++E E+ +M + LA ++Y NY++QH
Sbjct: 198 YGCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQH 257
Query: 901 VLEHGK-PHERSAIIKK-LTGQIVQMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSIE 958
++ + R II+K L ++ +SQ+KFAS+V+EK P E L+ EM+ I
Sbjct: 258 IVSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAF-LHAPLE---LLAEMMDEIF 313
Query: 959 E---------NEPLQVMMKDQFANYVVQKVLETCDD 985
+ + L +MM QF NYVVQ +L C D
Sbjct: 314 DGYIPHPDTGKDALDIMMFHQFGNYVVQCMLTICCD 349
Score = 43.1 bits (100), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 37/143 (25%), Positives = 67/143 (46%), Gaps = 14/143 (9%)
Query: 888 LAQDQYGNYVVQHVL-------EHGKPHERSAIIKKLTGQIVQMSQQKFASNVIEKCLSF 940
L+ + +GNY+VQ V+ + G + + ++ Q+ M KFA VI+ L
Sbjct: 74 LSTNIFGNYLVQSVIGISLATNDDGYTKRQEKLKNFISSQMTDMCLDKFACRVIQSSLQ- 132
Query: 941 GTPAERQALVNEMLGSIEENEPLQVMMKDQFANYVVQKVLETCDDQQLELILNRIKV--H 998
+L +++ ++ + L + DQ AN+V+QKV+ + E I++ + H
Sbjct: 133 ---NMDLSLACKLVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEH 189
Query: 999 LNALKKYTYGKHIVAR-VEKLVA 1020
L + YG +V +EKL A
Sbjct: 190 LRQICSDKYGCRVVQTIIEKLTA 212
>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 = 133 bits (334), Expect = 6e-31, Method: Compositional matrix adjust.
Identities = 96/336 (28%), Positives = 172/336 (51%), Gaps = 55/336 (16%)
Query: 697 LSEI--AGHVVEFSADQYGSRFIQQKLE-TATTEEKNMVFQEIMPQA---LSLMTDVFGN 750
LSE+ +G +++F+ D+ G +F+++ ++ + T+ +K +F++++ + L L T++FGN
Sbjct: 23 LSEVLDSGDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNIFGN 82
Query: 751 YVIQKFF-------EHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQ 803
Y++Q + G + +L + ++ + + L + CRVIQ +++ ++L +
Sbjct: 83 YLVQSVIGISLATNDDGYTKRQEKLKNFISSQMTDMCLDKFACRVIQSSLQNMDLSLACK 142
Query: 804 MVKEL--DGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVT------LSTHP 855
+V+ L D ++ DQN NHVIQK + +P +FIV D V T + +
Sbjct: 143 LVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIV----DFVATPEHLRQICSDK 198
Query: 856 YGCRVIQRVLEHCH---------------DEKTQSIMMDEILQSVCMLAQDQYGNYVVQH 900
YGCRV+Q ++E E+ +M + LA ++Y NY++QH
Sbjct: 199 YGCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQH 258
Query: 901 VLEHGK-PHERSAIIKK-LTGQIVQMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSIE 958
++ + R II+K L ++ +SQ+KFAS+V+EK P E L+ EM+ I
Sbjct: 259 IVSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAF-LHAPLE---LLAEMMDEIF 314
Query: 959 E---------NEPLQVMMKDQFANYVVQKVLETCDD 985
+ + L +MM QF NYVVQ +L C D
Sbjct: 315 DGYIPHPDTGKDALDIMMFHQFGNYVVQCMLTICCD 350
Score = 43.1 bits (100), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 37/143 (25%), Positives = 67/143 (46%), Gaps = 14/143 (9%)
Query: 888 LAQDQYGNYVVQHVL-------EHGKPHERSAIIKKLTGQIVQMSQQKFASNVIEKCLSF 940
L+ + +GNY+VQ V+ + G + + ++ Q+ M KFA VI+ L
Sbjct: 75 LSTNIFGNYLVQSVIGISLATNDDGYTKRQEKLKNFISSQMTDMCLDKFACRVIQSSLQ- 133
Query: 941 GTPAERQALVNEMLGSIEENEPLQVMMKDQFANYVVQKVLETCDDQQLELILNRIKV--H 998
+L +++ ++ + L + DQ AN+V+QKV+ + E I++ + H
Sbjct: 134 ---NMDLSLACKLVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEH 190
Query: 999 LNALKKYTYGKHIVAR-VEKLVA 1020
L + YG +V +EKL A
Sbjct: 191 LRQICSDKYGCRVVQTIIEKLTA 213
>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 = 130 bits (326), Expect = 4e-30, Method: Compositional matrix adjust.
Identities = 95/336 (28%), Positives = 171/336 (50%), Gaps = 55/336 (16%)
Query: 697 LSEI--AGHVVEFSADQYGSRFIQQKLE-TATTEEKNMVFQEIMPQA---LSLMTDVFGN 750
LSE+ +G +++F+ D+ G +F+++ ++ + T+ +K +F++++ + L L T++FGN
Sbjct: 23 LSEVLDSGDLMKFAVDKTGCQFLEKAVKGSLTSYQKFQLFEQVIGRKDDFLKLSTNIFGN 82
Query: 751 YVIQKFF-------EHGTASQVRELADQLTGHVLTLSLQMYGCRVIQKAIEVVELDQQTQ 803
Y++Q + G + +L + ++ + + L + C VIQ +++ ++L +
Sbjct: 83 YLVQSVIGISLATNDDGYTKRQEKLKNFISSQMTDMCLDKFACYVIQSSLQNMDLSLACK 142
Query: 804 MVKEL--DGHIMRCVRDQNGNHVIQKCIECVPEDAIQFIVLTFYDQVVT------LSTHP 855
+V+ L D ++ DQN NHVIQK + +P +FIV D V T + +
Sbjct: 143 LVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIV----DFVATPEHLRQICSDK 198
Query: 856 YGCRVIQRVLEHCH---------------DEKTQSIMMDEILQSVCMLAQDQYGNYVVQH 900
YGCRV+Q ++E E+ +M + LA ++Y NY++QH
Sbjct: 199 YGCRVVQTIIEKLTADSMNVDLTSAAQNLRERALQRLMTSVTNRCQELATNEYANYIIQH 258
Query: 901 VLEHGK-PHERSAIIKK-LTGQIVQMSQQKFASNVIEKCLSFGTPAERQALVNEMLGSIE 958
++ + R II+K L ++ +SQ+KFAS+V+EK P E L+ EM+ I
Sbjct: 259 IVSNDDLAVYRECIIEKCLMRNLLSLSQEKFASHVVEKAF-LHAPLE---LLAEMMDEIF 314
Query: 959 E---------NEPLQVMMKDQFANYVVQKVLETCDD 985
+ + L +MM QF NYVVQ +L C D
Sbjct: 315 DGYIPHPDTGKDALDIMMFHQFGNYVVQCMLTICCD 350
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 37/143 (25%), Positives = 67/143 (46%), Gaps = 14/143 (9%)
Query: 888 LAQDQYGNYVVQHVL-------EHGKPHERSAIIKKLTGQIVQMSQQKFASNVIEKCLSF 940
L+ + +GNY+VQ V+ + G + + ++ Q+ M KFA VI+ L
Sbjct: 75 LSTNIFGNYLVQSVIGISLATNDDGYTKRQEKLKNFISSQMTDMCLDKFACYVIQSSLQ- 133
Query: 941 GTPAERQALVNEMLGSIEENEPLQVMMKDQFANYVVQKVLETCDDQQLELILNRIKV--H 998
+L +++ ++ + L + DQ AN+V+QKV+ + E I++ + H
Sbjct: 134 ---NMDLSLACKLVQALPRDARLIAICVDQNANHVIQKVVAVIPLKNWEFIVDFVATPEH 190
Query: 999 LNALKKYTYGKHIVAR-VEKLVA 1020
L + YG +V +EKL A
Sbjct: 191 LRQICSDKYGCRVVQTIIEKLTA 213
>pdb|3V71|A Chain A, Crystal Structure Of Puf-6 In Complex With 5be13 Rna
Length = 382
Score = 120 bits (302), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 93/361 (25%), Positives = 180/361 (49%), Gaps = 45/361 (12%)
Query: 702 GHVVEFSADQYGSRFIQQKLETATTEEKNMVFQEIMPQALSLMTDVF----GNYVIQKFF 757
G +++F+ D G +F++ + ++ E ++ +L + GN+++QK
Sbjct: 20 GQLIDFAIDPSGVKFLEANYPLDSEDQIRKAVFEKFTESTTLFVGLCHSRNGNFIVQKLV 79
Query: 758 EHGTASQVRELADQLT-GHVLTLSLQMYGCRVIQKAIEVVELDQQTQMVKELDGH-IMRC 815
E T ++ REL Q+ G +L + + CRV+Q A++ + Q+++EL +
Sbjct: 80 ELATPAEQRELLRQMIDGGLLAMCKDKFACRVVQLALQKFDHSNVFQLIQELSTFDLAAM 139
Query: 816 VRDQNGNHVIQKCIECVPEDAIQFIV--LTFYDQVVTLSTHPYGCRVIQRVLEH------ 867
DQ HVIQ+ ++ +P D F V L+ D ++ + YGCR++Q+V++
Sbjct: 140 CTDQISIHVIQRVVKQLPVDMWTFFVHFLSSGDSLMAVCQDKYGCRLVQQVIDRLAENPK 199
Query: 868 --CHDEKTQSI--MMDEILQSVCMLAQDQYGNYVVQHVLEHGKPHE--RSAIIKK-LTGQ 920
C + Q + +M I+++ L+ +++ NYV+Q+V++ E R II K L
Sbjct: 200 LPCFKFRIQLLHSLMTCIVRNCYRLSSNEFANYVIQYVIKSSGIMEMYRDTIIDKCLLRN 259
Query: 921 IVQMSQQKFASNVIEKCLSFGTPAERQALVNEMLG----SIEEN-EPLQVMMKDQFANYV 975
++ MSQ K+AS+VIE F PA ++ E+ +E N + L +++ Q+ NYV
Sbjct: 260 LLSMSQDKYASHVIEGAFLFAPPALLHEMMEEIFSGYVKDVESNRDALDILLFHQYGNYV 319
Query: 976 VQKVLETC-------DDQQL------------ELILNRIKVHLNALKKYTYGKHIVARVE 1016
VQ+++ C ++++L E + R+ H + L++++ GK I+ V
Sbjct: 320 VQQMISICTAALIGKEERELPPAILLLYSGWYEKMKQRVLQHASRLERFSSGKKIIDSVM 379
Query: 1017 K 1017
+
Sbjct: 380 R 380
>pdb|2IHM|A Chain A, Polymerase Mu In Ternary Complex With Gapped 11mer Dna
Duplex And Bound Incoming Nucleotide
pdb|2IHM|B Chain B, Polymerase Mu In Ternary Complex With Gapped 11mer Dna
Duplex And Bound Incoming Nucleotide
Length = 360
Score = 30.8 bits (68), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 4/67 (5%)
Query: 711 QYGSRFIQQKLETATTEEKNMVFQEIMPQALSLMTDVFGNYV--IQKFFEHG--TASQVR 766
++ +R IQ+ LE T EE V Q + L T VFG V ++++ G T ++R
Sbjct: 71 EHSTRVIQELLEHGTCEEVKQVRCSERYQTMKLFTQVFGVGVKTANRWYQEGLRTLDELR 130
Query: 767 ELADQLT 773
E +LT
Sbjct: 131 EQPQRLT 137
>pdb|2CUN|A Chain A, Crystal Structure Of Phosphoglycerate Kinase From
Pyrococcus Horikoshii Ot3
pdb|2CUN|B Chain B, Crystal Structure Of Phosphoglycerate Kinase From
Pyrococcus Horikoshii Ot3
Length = 410
Score = 30.4 bits (67), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 44/95 (46%), Gaps = 16/95 (16%)
Query: 725 TTEEKNMVFQEIMPQALSLMTDVFGNYVIQKFFEHGTASQVRELADQLTGHVLTL-SLQM 783
TTEE V E++ Q + + D+FG Y +K ++EL +G V L +L+
Sbjct: 68 TTEEHARVLSELLDQHVEYIEDIFGRYAREK---------IKELK---SGEVAILENLRF 115
Query: 784 YGCRVIQKAIEVVELDQQTQMVKELDGHIMRCVRD 818
V K IE E +T +VK+L I V D
Sbjct: 116 SAEEVKNKPIEECE---KTFLVKKLSKVIDYVVND 147
>pdb|2RGH|A Chain A, Structure Of Alpha-Glycerophosphate Oxidase From
Streptococcus Sp.: A Template For The Mitochondrial
Alpha- Glycerophosphate Dehydrogenase
Length = 571
Score = 30.0 bits (66), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 50/177 (28%), Positives = 70/177 (39%), Gaps = 21/177 (11%)
Query: 587 YLGALLSPQKSQYGVPYLNKSGSLNNNLYGNPAFGLG---MSYPG-GPLLPNSPVGSGSP 642
Y G P+ +Q V YL + N+ Y L S+ G PLL + GS S
Sbjct: 317 YQGDFTDPKVTQEDVDYLL---DVINHRYPEANITLADIEASWAGLRPLLIGNS-GSPST 372
Query: 643 VRHGDRNMRFPSGMRNLSGGVMGPWHSEAGGSLDESFASSLLDEFKSNKTKCFELSEIAG 702
+ G R P G+ LSGG + + A G+L LL E +TK EI
Sbjct: 373 ISRGSSLEREPDGLLTLSGGKITDYRKXAEGAL--RLIRQLLKEEYGIETK-----EIDS 425
Query: 703 HVVEFSADQYGSRFIQQKLETATTE-EKNMVFQEIMPQALSLMTDVFGNYVIQKFFE 758
+ S G F KLE TE K V + + + + D +G ++ FE
Sbjct: 426 KKYQIS----GGNFDPTKLEETVTELAKEGVAAGLEEEDATYIADFYGTNA-RRIFE 477
>pdb|3C38|A Chain A, Crystal Structure Of The Periplasmic Domain Of Vibrio
Cholerae Luxq
Length = 270
Score = 30.0 bits (66), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 3/78 (3%)
Query: 370 HMKQHPFLGRSESGHLLMHSASHSTKGSYPNMGKSGVGIDMNNASLMADGHKSALSSSNS 429
H+ Q P G+S H+LM +S G+ +G VGI +N+ + + +S +S N
Sbjct: 123 HLVQTPSEGKSV--HILMRRSSLIEAGTGQVVGYLYVGIVLNDNFALLENIRSGSNSENL 180
Query: 430 YLKGPCTPTLNG-GGNSP 446
L TP ++ GN P
Sbjct: 181 VLAVDTTPLVSTLKGNEP 198
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
0.314 0.130 0.370
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 26,486,428
Number of Sequences: 62578
Number of extensions: 1026225
Number of successful extensions: 2202
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1874
Number of HSP's gapped (non-prelim): 49
length of query: 1034
length of database: 14,973,337
effective HSP length: 109
effective length of query: 925
effective length of database: 8,152,335
effective search space: 7540909875
effective search space used: 7540909875
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 56 (26.2 bits)