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= 045399
(802 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1HU3|A Chain A, Middle Domain Of Human Eif4gii
Length = 260
Score = 154 bits (390), Expect = 1e-37, Method: Compositional matrix adjust.
Identities = 104/266 (39%), Positives = 155/266 (58%), Gaps = 31/266 (11%)
Query: 220 ERVLKTVKGILNKLTPEKFDLLKGQLIDSGITSADILKEVISLIFDKAVLEPTFCPMYAQ 279
+ + + V+ ILNKLTP+ F+ L Q+ + + + LK VI L+F+KA+ EP+F YA
Sbjct: 9 QELFRKVRSILNKLTPQXFNQLXKQVSGLTVDTEERLKGVIDLVFEKAIDEPSFSVAYAN 68
Query: 280 LCSDL-NEKLPPFPSDEPGGKEITFKRVLLNICQEAFEG--AD-----KLREEVRQMTAP 331
C L K+P +D+PG + F+++LLN CQ+ FE AD K ++E+ +AP
Sbjct: 69 XCRCLVTLKVPX--ADKPGNT-VNFRKLLLNRCQKEFEKDKADDDVFEKKQKELEAASAP 125
Query: 332 -------DQESERRDKERLVKLRTLGNIRLIGELLKQKMVPEKIVHHIVQELL-GHDSST 383
D+ E +DK R R++GNI+ IGEL K K + E I H V +LL HD
Sbjct: 126 EERTRLHDELEEAKDKARR---RSIGNIKFIGELFKLKXLTEAIXHDCVVKLLKNHD--- 179
Query: 384 CPAEENVEAICQFVNTIGKQLD-EGPKSRRINDMYFSRLKELTTNPQLAPRLRFMVRDVL 442
EE++E +C+ + TIGK LD E K R D YF++ +++ + + R+RF ++DV+
Sbjct: 180 ---EESLECLCRLLTTIGKDLDFEKAKPR--XDQYFNQXEKIVKERKTSSRIRFXLQDVI 234
Query: 443 DLRANNWVPRREEVTAKTITEIHSEA 468
DLR NWV RR + KTI +IH EA
Sbjct: 235 DLRLCNWVSRRADQGPKTIEQIHKEA 260
>pdb|2VSO|E Chain E, Crystal Structure Of A Translation Initiation Complex
pdb|2VSO|F Chain F, Crystal Structure Of A Translation Initiation Complex
pdb|2VSX|E Chain E, Crystal Structure Of A Translation Initiation Complex
pdb|2VSX|F Chain F, Crystal Structure Of A Translation Initiation Complex
Length = 284
Score = 93.2 bits (230), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 75/257 (29%), Positives = 126/257 (49%), Gaps = 21/257 (8%)
Query: 213 RGNLSEKERVLKTVKGILNKLTPEKFDLLKGQL-----IDSGITSADILKEVISLIFDKA 267
+ L +K+ V + +K +LNKLT E FD + ++ I T+ + LK VI IF KA
Sbjct: 27 KTELLDKDEVERKMKSLLNKLTLEMFDAISSEILAIANISVWETNGETLKAVIEQIFLKA 86
Query: 268 VLEPTFCPMYAQLCSDLNEKLPPFPSDEPGGKEITFKRVLLNI---CQEAFE--GADKL- 321
EP + MYAQLC + ++L P +DE + K VL + C F+ DKL
Sbjct: 87 CDEPHWSSMYAQLCGKVVKELNPDITDETNEGKTGPKLVLHYLVARCHAEFDKGWTDKLP 146
Query: 322 REEVRQMTAPDQESERRDKERLVKLRTLGNIRLIGELLKQKMVPEKIVHHIVQELLGHDS 381
E P+ SE K R LG +R IG L + ++ K++ + L+ D
Sbjct: 147 TNEDGTPLEPEMMSEEYYAAASAKRRGLGLVRFIGFLYRLNLLTGKMMFECFRRLM-KDL 205
Query: 382 STCPAEENVEAICQFVNTIGKQLDEGP--------KSRRINDMYFSRLKELTTNPQLAPR 433
+ P+EE +E++ + +NT+G+Q + + ++ D F L + +++ R
Sbjct: 206 TDSPSEETLESVVELLNTVGEQFETDSFRTGQATLEGSQLLDSLFGILDNIIQTAKISSR 265
Query: 434 LRFMVRDVLDLRAN-NW 449
++F + D+ +LR + NW
Sbjct: 266 IKFKLIDIKELRHDKNW 282
>pdb|1UG3|A Chain A, C-Terminal Portion Of Human Eif4gi
pdb|1UG3|B Chain B, C-Terminal Portion Of Human Eif4gi
Length = 339
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 30/119 (25%), Positives = 60/119 (50%)
Query: 632 GKLNLDELCRKTISLLEEYFNIRVLEEALMCVEELKSPGYHPEVVKEAISLALEKNPPCV 691
L+ +EL +K+ +++EEY ++ ++EA+ CV+EL SP V+ + LE++
Sbjct: 3 AALSEEELEKKSKAIIEEYLHLNDMKEAVQCVQELASPSLLFIFVRHGVESTLERSAIAR 62
Query: 692 DPVTKLLEYLFTQKVITARDIGTGCLLFGALMDDVGIDLPRAPNNFGEIIGKLILAGGL 750
+ + +LL L ++ G L +D+ ID+P E++ ++ GG+
Sbjct: 63 EHMGQLLHQLLCAGHLSTAQYYQGLYEILELAEDMEIDIPHVWLYLAELVTPILQEGGV 121
>pdb|2HM8|A Chain A, Solution Structure Of The C-Terminal Ma-3 Domain Of Pdcd4
Length = 136
Score = 46.2 bits (108), Expect = 6e-05, Method: Composition-based stats.
Identities = 31/108 (28%), Positives = 53/108 (49%), Gaps = 1/108 (0%)
Query: 627 PLRPAGKLNLDELCRKTISLLEEYFNIRVLEEALMCVEELKSPGYHPEVVKEAISLALEK 686
PL G+ ++ L ++ LL+EY + EA C++EL+ P +H E+V EAI + LE
Sbjct: 2 PLGSGGQQPVNHLVKEIDMLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIVMVLES 61
Query: 687 N-PPCVDPVTKLLEYLFTQKVITARDIGTGCLLFGALMDDVGIDLPRA 733
+ LL+ L+ IT + G + D+ +D+P +
Sbjct: 62 TGESAFKMILDLLKSLWKSSTITIDQMKRGYERIYNEIPDINLDVPHS 109
>pdb|3EIJ|A Chain A, Crystal Structure Of Pdcd4
pdb|3EIJ|B Chain B, Crystal Structure Of Pdcd4
Length = 321
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 31/119 (26%), Positives = 57/119 (47%), Gaps = 1/119 (0%)
Query: 631 AGKLNLDELCRKTISLLEEYFNIRVLEEALMCVEELKSPGYHPEVVKEAISLALEKN-PP 689
G+ +++ L ++ LL+EY + EA C++EL+ P +H E+V EAI + LE
Sbjct: 171 GGQQSVNHLVKEIDMLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIIMVLESTGES 230
Query: 690 CVDPVTKLLEYLFTQKVITARDIGTGCLLFGALMDDVGIDLPRAPNNFGEIIGKLILAG 748
+ LL+ L+ IT + G + D+ +D+P + + + + AG
Sbjct: 231 TFKMILDLLKSLWKSSTITVDQMKRGYERIYNEIPDINLDVPHSYSVLERFVEECFQAG 289
Score = 32.0 bits (71), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 40/153 (26%), Positives = 67/153 (43%), Gaps = 9/153 (5%)
Query: 642 KTIS-LLEEYFNIRVLEEALMCVEELKSPGYHPEVVKEAISLALEKNPPCVDPVTKLLEY 700
KT++ +++EYF E + +L V A+SLALE + +KLL
Sbjct: 18 KTLTPIIQEYFEHGDTNEVAEMLRDLNLGEMKSGVPVLAVSLALEGKASHREMTSKLLSD 77
Query: 701 LFTQKVITARDIGTGCLLFGALMDDV---GIDLPRAPNNFGEIIGKLILAGGLDFKVVQE 757
L V++ D+ F L+ D+ +D PRAP G+ I + + G+ +
Sbjct: 78 L-CGTVMSTTDVEKS---FDKLLKDLPELALDTPRAPQLVGQFIARAV-GDGILCNTYID 132
Query: 758 ILKKMEEEMYRKSVLDAALRIISCSPGQNILDS 790
K + + ++ LD A ++S S G DS
Sbjct: 133 SYKGTVDCVQARAALDKATVLLSMSKGGKRKDS 165
>pdb|2ION|A Chain A, Crystal Structure Of The C-terminal Ma3 Domain Of Pdcd4
(mouse); Form2
Length = 152
Score = 44.3 bits (103), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 31/118 (26%), Positives = 56/118 (47%), Gaps = 1/118 (0%)
Query: 632 GKLNLDELCRKTISLLEEYFNIRVLEEALMCVEELKSPGYHPEVVKEAISLALEKN-PPC 690
G+ ++ L ++ LL+EY + EA C++EL+ P +H E+V EAI + LE
Sbjct: 1 GQQPVNHLVKEIDMLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIVMVLESTGESA 60
Query: 691 VDPVTKLLEYLFTQKVITARDIGTGCLLFGALMDDVGIDLPRAPNNFGEIIGKLILAG 748
+ LL+ L+ IT + G + D+ +D+P + + + + AG
Sbjct: 61 FKMILDLLKSLWKSSTITIDQMKRGYERIYNEIPDINLDVPHSYSVLERFVEECFQAG 118
>pdb|3EIQ|C Chain C, Crystal Structure Of Pdcd4-eif4a
Length = 358
Score = 44.3 bits (103), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 31/119 (26%), Positives = 56/119 (47%), Gaps = 1/119 (0%)
Query: 631 AGKLNLDELCRKTISLLEEYFNIRVLEEALMCVEELKSPGYHPEVVKEAISLALEKN-PP 689
G+ ++ L ++ LL+EY + EA C++EL+ P +H E+V EAI + LE
Sbjct: 208 GGQQPVNHLVKEIDMLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIVMVLESTGES 267
Query: 690 CVDPVTKLLEYLFTQKVITARDIGTGCLLFGALMDDVGIDLPRAPNNFGEIIGKLILAG 748
+ LL+ L+ IT + G + D+ +D+P + + + + AG
Sbjct: 268 AFKMILDLLKSLWKSSTITIDQMKRGYERIYNEIPDINLDVPHSYSVLERFVEECFQAG 326
Score = 32.3 bits (72), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 44/162 (27%), Positives = 71/162 (43%), Gaps = 10/162 (6%)
Query: 634 LNLDELC-RKTIS-LLEEYFNIRVLEEALMCVEELKSPGYHPEVVKEAISLALEKNPPCV 691
L LDE KT++ +++EYF E + +L V A+SLALE
Sbjct: 46 LPLDETAFEKTLTPIIQEYFEHGDTNEVAEMLRDLNLGEMKSGVPVLAVSLALEGKASHR 105
Query: 692 DPVTKLLEYLFTQKVITARDIGTGCLLFGALMDDV---GIDLPRAPNNFGEIIGKLILAG 748
+ +KLL L V++ D+ F L+ D+ +D PRAP G+ I + +
Sbjct: 106 EMTSKLLSDL-CGTVMSTNDVEKS---FDKLLKDLPELALDTPRAPQLVGQFIARAV-GD 160
Query: 749 GLDFKVVQEILKKMEEEMYRKSVLDAALRIISCSPGQNILDS 790
G+ + K + + ++ LD A ++S S G DS
Sbjct: 161 GILCNTYIDSYKGTVDCVQARAALDKATVLLSMSKGGKRKDS 202
>pdb|2ZU6|B Chain B, Crystal Structure Of The Eif4a-Pdcd4 Complex
pdb|2ZU6|E Chain E, Crystal Structure Of The Eif4a-Pdcd4 Complex
Length = 307
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 31/119 (26%), Positives = 55/119 (46%), Gaps = 1/119 (0%)
Query: 631 AGKLNLDELCRKTISLLEEYFNIRVLEEALMCVEELKSPGYHPEVVKEAISLALEKN-PP 689
G+ +++ L ++ LL+EY + EA C++EL+ P +H E+V EAI LE
Sbjct: 157 GGQQSVNHLVKEIDXLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIIXVLESTGES 216
Query: 690 CVDPVTKLLEYLFTQKVITARDIGTGCLLFGALMDDVGIDLPRAPNNFGEIIGKLILAG 748
+ LL+ L+ IT G + D+ +D+P + + + + AG
Sbjct: 217 TFKXILDLLKSLWKSSTITVDQXKRGYERIYNEIPDINLDVPHSYSVLERFVEECFQAG 275
Score = 30.8 bits (68), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 32/115 (27%), Positives = 51/115 (44%), Gaps = 8/115 (6%)
Query: 679 AISLALEKNPPCVDPVTKLLEYLFTQKVITARDIGTGCLLFGALMDDV---GIDLPRAPN 735
A+SLALE + +KLL L V + D+ F L+ D+ +D PRAP
Sbjct: 42 AVSLALEGKASHREXTSKLLSDL-CGTVXSTTDVEKS---FDKLLKDLPELALDTPRAPQ 97
Query: 736 NFGEIIGKLILAGGLDFKVVQEILKKMEEEMYRKSVLDAALRIISCSPGQNILDS 790
G+ I + + G+ + K + + ++ LD A ++S S G DS
Sbjct: 98 LVGQFIARAV-GDGILCNTYIDSYKGTVDCVQARAALDKATVLLSXSKGGKRKDS 151
>pdb|3RK6|A Chain A, Crystal Structure Of The Middle Domain Of Human Paip1
pdb|3RK6|B Chain B, Crystal Structure Of The Middle Domain Of Human Paip1
Length = 234
Score = 43.5 bits (101), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 55/229 (24%), Positives = 103/229 (44%), Gaps = 26/229 (11%)
Query: 226 VKGILNKLT--PEKFDLLKGQL---IDSGITSADILKEVISLIFDKAVLEPTFCPMYAQL 280
V+ LN LT P F+ Q ++ +T+ D L+E++ LI+ +A P F M A+L
Sbjct: 23 VQDFLNHLTEQPGSFETEIEQFAETLNGCVTTDDALQELVELIYQQATSIPNFSYMGARL 82
Query: 281 CSDLNEKLPPFPSDEPGGKEITFKRVLLNICQEAFEGADKLREEVRQMTAPDQESERRDK 340
C+ L+ L P + G F+++LL C+ + EV+ A E R+
Sbjct: 83 CNYLSHHLTISP--QSG----NFRQLLLQRCRTEY--------EVKDQAAKGDEVTRKRF 128
Query: 341 ERLVKLRTLGNIRLIGEL--LKQKMVPEKIVHHIVQELLGHDSSTCPAEENVEAICQFVN 398
V LG + L E+ ++ I+ ++ELL S P ++N+ + +
Sbjct: 129 HAFVLF--LGELYLNLEIKGTNGQVTRADILQVGLRELLNALFSN-PMDDNLICAVKLLK 185
Query: 399 TIGKQLDEGPKSRRINDM--YFSRLKELTTNPQLAPRLRFMVRDVLDLR 445
G L++ K + DM R++ + + + ++ M+ +++LR
Sbjct: 186 LTGSVLEDAWKEKGKMDMEEIIQRIENVVLDANCSRDVKQMLLKLVELR 234
>pdb|2KZT|B Chain B, Structure Of The Tandem Ma-3 Region Of Pdcd4
Length = 131
Score = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 29/104 (27%), Positives = 51/104 (49%), Gaps = 1/104 (0%)
Query: 631 AGKLNLDELCRKTISLLEEYFNIRVLEEALMCVEELKSPGYHPEVVKEAISLALEKN-PP 689
G+ ++ L ++ LL+EY + EA C++EL+ P +H E+V EAI + LE
Sbjct: 1 GGQQPVNHLVKEIDMLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIVMVLESTGES 60
Query: 690 CVDPVTKLLEYLFTQKVITARDIGTGCLLFGALMDDVGIDLPRA 733
+ LL+ L+ IT + G + D+ +D+P +
Sbjct: 61 AFKMILDLLKSLWKSSTITIDQMKRGYERIYNEIPDINLDVPHS 104
>pdb|2NSZ|A Chain A, 1.15 Angstrom Crystal Structure Of The Ma3 Domain Of Pdcd4
Length = 129
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 28/99 (28%), Positives = 49/99 (49%), Gaps = 1/99 (1%)
Query: 636 LDELCRKTISLLEEYFNIRVLEEALMCVEELKSPGYHPEVVKEAISLALEKN-PPCVDPV 694
++ L ++ LL+EY + EA C++EL+ P +H E+V EAI + LE +
Sbjct: 3 VNHLVKEIDMLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIVMVLESTGESAFKMI 62
Query: 695 TKLLEYLFTQKVITARDIGTGCLLFGALMDDVGIDLPRA 733
LL+ L+ IT + G + D+ +D+P +
Sbjct: 63 LDLLKSLWKSSTITIDQMKRGYERIYNEIPDINLDVPHS 101
>pdb|2GGF|A Chain A, Solution Structure Of The Ma3 Domain Of Human Programmed
Cell Death 4
Length = 137
Score = 41.2 bits (95), Expect = 0.003, Method: Composition-based stats.
Identities = 28/96 (29%), Positives = 47/96 (48%), Gaps = 1/96 (1%)
Query: 639 LCRKTISLLEEYFNIRVLEEALMCVEELKSPGYHPEVVKEAISLALEKN-PPCVDPVTKL 697
L ++ LL+EY + EA C++EL+ P +H E+V EAI + LE + L
Sbjct: 8 LVKEIDMLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIIMVLESTGESTFKMILDL 67
Query: 698 LEYLFTQKVITARDIGTGCLLFGALMDDVGIDLPRA 733
L+ L+ IT + G + D+ +D+P +
Sbjct: 68 LKSLWKSSTITVDQMKRGYERIYNEIPDINLDVPHS 103
>pdb|2IOL|A Chain A, Crystal Structure Of The C-Terminal Ma3 Domain Of Pdcd4
(Mouse); Form 1
pdb|2IOL|B Chain B, Crystal Structure Of The C-Terminal Ma3 Domain Of Pdcd4
(Mouse); Form 1
Length = 150
Score = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 29/103 (28%), Positives = 49/103 (47%), Gaps = 1/103 (0%)
Query: 632 GKLNLDELCRKTISLLEEYFNIRVLEEALMCVEELKSPGYHPEVVKEAISLALEKN-PPC 690
G+ ++ L ++ LL+EY + EA C++EL+ P +H E+V EAI LE
Sbjct: 1 GQQPVNHLVKEIDXLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIVXVLESTGESA 60
Query: 691 VDPVTKLLEYLFTQKVITARDIGTGCLLFGALMDDVGIDLPRA 733
+ LL+ L+ IT G + D+ +D+P +
Sbjct: 61 FKXILDLLKSLWKSSTITIDQXKRGYERIYNEIPDINLDVPHS 103
>pdb|2IOS|A Chain A, Crystal Structure Of The C-Terminal Ma3 Domain Of Pdcd4
(Mouse); Form 3
Length = 150
Score = 38.1 bits (87), Expect = 0.022, Method: Composition-based stats.
Identities = 35/155 (22%), Positives = 66/155 (42%), Gaps = 23/155 (14%)
Query: 632 GKLNLDELCRKTISLLEEYFNIRVLEEALMCVEELKSPGYHPEVVKEAISLALEKN-PPC 690
G+ ++ L ++ LL+EY + EA ++EL+ P +H E+V EAI + LE
Sbjct: 1 GQQPVNHLVKEIDMLLKEYLLSGDISEAEHXLKELEVPHFHHELVYEAIVMVLESTGESA 60
Query: 691 VDPVTKLLEYLFTQKVITARDIGTGCLLFGALMDDVGIDLPRAPNNFGEIIGKLILAGGL 750
+ LL+ L+ IT + G + D+ +D+P +
Sbjct: 61 FKMILDLLKSLWKSSTITIDQMKRGYERIYNEIPDINLDVPHS----------------- 103
Query: 751 DFKVVQEILKKMEEEMYRKSVLDAALRIISCSPGQ 785
+L++ EE ++ ++ LR + S G+
Sbjct: 104 -----YSVLERFVEECFQAGIISKQLRDLXPSRGR 133
>pdb|2I2O|A Chain A, Crystal Structure Of An Eif4g-Like Protein From Danio
Rerio
pdb|2I2O|B Chain B, Crystal Structure Of An Eif4g-Like Protein From Danio
Rerio
Length = 224
Score = 34.7 bits (78), Expect = 0.24, Method: Composition-based stats.
Identities = 56/217 (25%), Positives = 97/217 (44%), Gaps = 30/217 (13%)
Query: 236 EKFDLLKGQLIDSGITSADILKEVISLIFDKAVLEPTFCPMYAQLCSDLNEKLPPFPSDE 295
E LLK L D G S D L++V S+I D+++ + F ++C + + + +
Sbjct: 19 ETQKLLKTALKDPG--SVD-LEKVSSVIVDQSLKDQVFSREAGRICYTIVQA----EAKQ 71
Query: 296 PGGKEITFKRVLLNICQEAFEGADKLREEVRQMTAPDQESERRDKERLVKLRTLGNIRLI 355
G F+R LLN Q+ F K REE R+ R +E + + + NI
Sbjct: 72 TNGS--VFRRNLLNRLQQEF----KAREETRK---------RSTQEWVCLVSFICNIF-- 114
Query: 356 GELLKQKMVPEKIVHHIVQELLGH--DSSTCPAEENVEAICQFVNTIGKQLDEGPKSRRI 413
+ LK P + H V + L S EE V+ + ++ IG QL++ + ++
Sbjct: 115 -DYLKVNNXPXVALVHPVYDCLFRLAQSDALKNEEEVDCLVLQLHRIGDQLEK--XNVQL 171
Query: 414 NDMYFSRLKE-LTTNPQLAPRLRFMVRDVLDLRANNW 449
D F+ L++ L+ R ++ ++L+ RA W
Sbjct: 172 XDELFNLLRDGFLLQEDLSSXGRLLLLEILEFRAGGW 208
>pdb|1UW4|B Chain B, The Structural Basis Of The Interaction Between Nonsense
Mediated Decay Factors Upf2 And Upf3
pdb|1UW4|D Chain D, The Structural Basis Of The Interaction Between Nonsense
Mediated Decay Factors Upf2 And Upf3
Length = 248
Score = 34.7 bits (78), Expect = 0.24, Method: Composition-based stats.
Identities = 26/116 (22%), Positives = 49/116 (42%), Gaps = 18/116 (15%)
Query: 347 RTLGNIRLIGELLKQKMVPEKIVHHIVQELL-------GHDSSTCPAEE--NVEAICQFV 397
R + + + +GEL +MV ++ + G SS P E + +C +
Sbjct: 100 RRISSAKFLGELYNYRMVESAVIFRTLYSFTSFGVNPDGSPSSLDPPEHLFRIRLVCTIL 159
Query: 398 NTIGKQLDEGPKSRRIND--MYFSR-------LKELTTNPQLAPRLRFMVRDVLDL 444
+T G+ D G R+++ +YF R L+ T + + +M+ D L+L
Sbjct: 160 DTCGQYFDRGSSKRKLDCFLVYFQRYVWWKKSLEVWTKDHPFPIDIDYMISDTLEL 215
>pdb|2KZT|A Chain A, Structure Of The Tandem Ma-3 Region Of Pdcd4
Length = 163
Score = 32.3 bits (72), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 40/153 (26%), Positives = 67/153 (43%), Gaps = 9/153 (5%)
Query: 642 KTIS-LLEEYFNIRVLEEALMCVEELKSPGYHPEVVKEAISLALEKNPPCVDPVTKLLEY 700
KT++ +++EYF E + +L V A+SLALE + +KLL
Sbjct: 11 KTLTPIIQEYFEHGDTNEVAEMLRDLNLGEMKSGVPVLAVSLALEGKASHREMTSKLLSD 70
Query: 701 LFTQKVITARDIGTGCLLFGALMDDV---GIDLPRAPNNFGEIIGKLILAGGLDFKVVQE 757
L V++ D+ F L+ D+ +D PRAP G+ I + + G+ +
Sbjct: 71 L-CGTVMSTTDVEKS---FDKLLKDLPELALDTPRAPQLVGQFIARAV-GDGILCNTYID 125
Query: 758 ILKKMEEEMYRKSVLDAALRIISCSPGQNILDS 790
K + + ++ LD A ++S S G DS
Sbjct: 126 SYKGTVDCVQARAALDKATVLLSMSKGGKRKDS 158
>pdb|3OD1|A Chain A, The Crystal Structure Of An Atp Phosphoribosyltransferase
Regulatory SubunitHISTIDYL-Trna Synthetase From Bacillus
Halodurans C
pdb|3OD1|B Chain B, The Crystal Structure Of An Atp Phosphoribosyltransferase
Regulatory SubunitHISTIDYL-Trna Synthetase From Bacillus
Halodurans C
Length = 400
Score = 32.3 bits (72), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 33/76 (43%), Gaps = 6/76 (7%)
Query: 421 LKELTTNPQLAPRLRFMVRDVLDLRANNWVPRREEVTAKTITEIHSEAEKNLGLRPGATA 480
L ++ N Q A RLR L N+V RE V + ++ I NL G A
Sbjct: 175 LXDVVGNEQRADRLRRF------LYEKNYVGYREHVKSLNLSTIDKSRLXNLLSLRGGRA 228
Query: 481 SIRNSRGMISGAPGVT 496
+I +RG+I G T
Sbjct: 229 AIEEARGLIQTEKGKT 244
>pdb|2RG8|A Chain A, Crystal Structure Of Programmed For Cell Death 4 Middle
Ma3 Domain
pdb|2RG8|B Chain B, Crystal Structure Of Programmed For Cell Death 4 Middle
Ma3 Domain
Length = 165
Score = 31.2 bits (69), Expect = 2.4, Method: Composition-based stats.
Identities = 44/162 (27%), Positives = 70/162 (43%), Gaps = 10/162 (6%)
Query: 634 LNLDELC-RKTIS-LLEEYFNIRVLEEALMCVEELKSPGYHPEVVKEAISLALEKNPPCV 691
L LDE KT++ +++EYF E + +L V A+SLALE
Sbjct: 2 LPLDERAFEKTLTPIIQEYFEHGDTNEVAEXLRDLNLGEXKSGVPVLAVSLALEGKASHR 61
Query: 692 DPVTKLLEYLFTQKVITARDIGTGCLLFGALMDDV---GIDLPRAPNNFGEIIGKLILAG 748
+ +KLL L V + D+ F L+ D+ +D PRAP G+ I + +
Sbjct: 62 EXTSKLLSDL-CGTVXSTTDVEKS---FDKLLKDLPELALDTPRAPQLVGQFIARAV-GD 116
Query: 749 GLDFKVVQEILKKMEEEMYRKSVLDAALRIISCSPGQNILDS 790
G+ + K + + ++ LD A ++S S G DS
Sbjct: 117 GILCNTYIDSYKGTVDCVQARAALDKATVLLSXSKGGKRKDS 158
>pdb|3L6A|A Chain A, Crystal Structure Of The C-Terminal Region Of Human P97
Length = 364
Score = 30.8 bits (68), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 23/112 (20%), Positives = 55/112 (49%), Gaps = 1/112 (0%)
Query: 637 DELCRKTISLLEEYFNIRVLEEALMCVEELKSPGYH-PEVVKEAISLALEKNPPCVDPVT 695
+EL + T +++ EY N EA+ V E+++P + PE++ + I L+L+++ + +
Sbjct: 9 EELLKLTETVVTEYLNSGNANEAVNGVREMRAPKHFLPEMLSKVIILSLDRSDEDKEKAS 68
Query: 696 KLLEYLFTQKVITARDIGTGCLLFGALMDDVGIDLPRAPNNFGEIIGKLILA 747
L+ L + + T+ + L + +D+P + + + I++
Sbjct: 69 SLISLLKQEGIATSDNFMQAFLNVLDQCPKLEVDIPLVKSYLAQFAARAIIS 120
>pdb|1RY2|A Chain A, Crystal Structure Of Yeast Acetyl-Coenzyme A Synthetase In
Complex With Amp
Length = 663
Score = 30.0 bits (66), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 285 NEKLPPFPSDEPG-GKEITFKRVLLNICQEA 314
N+K F DEPG G IT+K +L +CQ A
Sbjct: 97 NKKAIIFEGDEPGQGYSITYKELLEEVCQVA 127
>pdb|3VJ6|A Chain A, Structure Of The Mhc Class Ib Molecule Qa-1b
Length = 277
Score = 29.6 bits (65), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 305 RVLLNICQEAFEGAD--KLREEVRQMTAPDQESE 336
R+L CQEA++G D L E++R TA D S+
Sbjct: 108 RLLRGYCQEAYDGQDYISLNEDLRSWTANDIASQ 141
>pdb|1F5S|A Chain A, Crystal Structure Of Phosphoserine Phosphatase From
Methanococcus Jannaschii
pdb|1F5S|B Chain B, Crystal Structure Of Phosphoserine Phosphatase From
Methanococcus Jannaschii
Length = 211
Score = 29.3 bits (64), Expect = 8.8, Method: Composition-based stats.
Identities = 35/132 (26%), Positives = 60/132 (45%), Gaps = 26/132 (19%)
Query: 632 GKLNLDELCRKTISLLEEYFNIRVLEEALM----------CVEELKSPGYHPEVVKEAIS 681
GKLN ++ RK +SLL++ I +E+A+ ++ELK+ GY VV
Sbjct: 45 GKLNFEQSLRKRVSLLKD-LPIEKVEKAIKRITPTEGAEETIKELKNRGYVVAVVSGGFD 103
Query: 682 LALEKNPPCVDPVTKLLEYLFTQKVITARDIGTGCLLFGALMDDVGIDLPRAPNNFGEII 741
+A+ K + L+Y F ++I G L DV ++ + N GEI+
Sbjct: 104 IAVNKIKEKLG-----LDYAFANRLIVKD---------GKLTGDVEGEVLKE-NAKGEIL 148
Query: 742 GKLILAGGLDFK 753
K+ G++ +
Sbjct: 149 EKIAKIEGINLE 160
>pdb|1J97|A Chain A, Phospho-Aspartyl Intermediate Analogue Of Phosphoserine
Phosphatase
pdb|1J97|B Chain B, Phospho-Aspartyl Intermediate Analogue Of Phosphoserine
Phosphatase
Length = 211
Score = 29.3 bits (64), Expect = 8.9, Method: Composition-based stats.
Identities = 35/132 (26%), Positives = 60/132 (45%), Gaps = 26/132 (19%)
Query: 632 GKLNLDELCRKTISLLEEYFNIRVLEEALM----------CVEELKSPGYHPEVVKEAIS 681
GKLN ++ RK +SLL++ I +E+A+ ++ELK+ GY VV
Sbjct: 45 GKLNFEQSLRKRVSLLKD-LPIEKVEKAIKRITPTEGAEETIKELKNRGYVVAVVSGGFD 103
Query: 682 LALEKNPPCVDPVTKLLEYLFTQKVITARDIGTGCLLFGALMDDVGIDLPRAPNNFGEII 741
+A+ K + L+Y F ++I G L DV ++ + N GEI+
Sbjct: 104 IAVNKIKEKLG-----LDYAFANRLIVKD---------GKLTGDVEGEVLKE-NAKGEIL 148
Query: 742 GKLILAGGLDFK 753
K+ G++ +
Sbjct: 149 EKIAKIEGINLE 160
>pdb|1L7M|A Chain A, High Resolution Liganded Structure Of Phosphoserine
Phosphatase (Pi Complex)
pdb|1L7M|B Chain B, High Resolution Liganded Structure Of Phosphoserine
Phosphatase (Pi Complex)
pdb|1L7N|A Chain A, Transition State Analogue Of Phosphoserine Phosphatase
(Aluminum Fluoride Complex)
pdb|1L7N|B Chain B, Transition State Analogue Of Phosphoserine Phosphatase
(Aluminum Fluoride Complex)
Length = 211
Score = 29.3 bits (64), Expect = 9.5, Method: Composition-based stats.
Identities = 35/132 (26%), Positives = 60/132 (45%), Gaps = 26/132 (19%)
Query: 632 GKLNLDELCRKTISLLEEYFNIRVLEEALM----------CVEELKSPGYHPEVVKEAIS 681
GKLN ++ RK +SLL++ I +E+A+ ++ELK+ GY VV
Sbjct: 45 GKLNFEQSLRKRVSLLKD-LPIEKVEKAIKRITPTEGAEETIKELKNRGYVVAVVSGGFD 103
Query: 682 LALEKNPPCVDPVTKLLEYLFTQKVITARDIGTGCLLFGALMDDVGIDLPRAPNNFGEII 741
+A+ K + L+Y F ++I G L DV ++ + N GEI+
Sbjct: 104 IAVNKIKEKLG-----LDYAFANRLIVKD---------GKLTGDVEGEVLKE-NAKGEIL 148
Query: 742 GKLILAGGLDFK 753
K+ G++ +
Sbjct: 149 EKIAKIEGINLE 160
>pdb|1L7O|A Chain A, Crystal Structure Of Phosphoserine Phosphatase In Apo Form
pdb|1L7O|B Chain B, Crystal Structure Of Phosphoserine Phosphatase In Apo Form
pdb|1L7P|A Chain A, Substrate Bound Phosphoserine Phosphatase Complex
Structure
pdb|1L7P|B Chain B, Substrate Bound Phosphoserine Phosphatase Complex
Structure
Length = 211
Score = 29.3 bits (64), Expect = 9.6, Method: Composition-based stats.
Identities = 35/132 (26%), Positives = 60/132 (45%), Gaps = 26/132 (19%)
Query: 632 GKLNLDELCRKTISLLEEYFNIRVLEEALM----------CVEELKSPGYHPEVVKEAIS 681
GKLN ++ RK +SLL++ I +E+A+ ++ELK+ GY VV
Sbjct: 45 GKLNFEQSLRKRVSLLKD-LPIEKVEKAIKRITPTEGAEETIKELKNRGYVVAVVSGGFD 103
Query: 682 LALEKNPPCVDPVTKLLEYLFTQKVITARDIGTGCLLFGALMDDVGIDLPRAPNNFGEII 741
+A+ K + L+Y F ++I G L DV ++ + N GEI+
Sbjct: 104 IAVNKIKEKLG-----LDYAFANRLIVKD---------GKLTGDVEGEVLKE-NAKGEIL 148
Query: 742 GKLILAGGLDFK 753
K+ G++ +
Sbjct: 149 EKIAKIEGINLE 160
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 0.136 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,145,962
Number of Sequences: 62578
Number of extensions: 1065726
Number of successful extensions: 2586
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 29
Number of HSP's that attempted gapping in prelim test: 2544
Number of HSP's gapped (non-prelim): 54
length of query: 802
length of database: 14,973,337
effective HSP length: 107
effective length of query: 695
effective length of database: 8,277,491
effective search space: 5752856245
effective search space used: 5752856245
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)