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= 000509
(1456 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2WJV|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJV|B Chain B, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJY|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2 Orthorhombic Form
Length = 800
Score = 93.2 bits (230), Expect = 9e-19, Method: Compositional matrix adjust.
Identities = 82/289 (28%), Positives = 131/289 (45%), Gaps = 41/289 (14%)
Query: 1027 RAFELLKSTADRANYLMTKQAKIVAMTCTHAALKRKDFLQLGFKYDNLLMEESAQILEIE 1086
+ + LK TA+R + A ++ TC A R +Q + ++L++ES Q E E
Sbjct: 479 KRYRALKRTAERE---LLMNADVICCTCVGAGDPRLAKMQ----FRSILIDESTQATEPE 531
Query: 1087 TFIPMLLNDRRM--------LPPVVKNMAFQKYSHMDQSLFTRFVRLGIPYIELNAQGRA 1138
+P++L +++ L PVV K + + QSLF R V LGI I L Q R
Sbjct: 532 CMVPVVLGAKQLILVGDHCQLGPVVMCKKAAK-AGLSQSLFERLVVLGIRPIRLQVQYRM 590
Query: 1139 RPSIAQLYNWRYRDLGDLPFLVDVPD---------------------YNGRGESAPSPWF 1177
P+++ + + + G L V D G+ E A S
Sbjct: 591 HPALSAFPSNIFYE-GSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTS 649
Query: 1178 YQNEGEAEYVVSVYIYMRLLGYPANKISILTTYNGQKLLIRDVINRQCVPYPFIGPPSKV 1237
Y N EA V + + G ++I I+T Y GQ+ + + + + ++
Sbjct: 650 YLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEI 709
Query: 1238 TTVDKFQGQQNDFILLSLVRT---RFVGHLRDVRRLVVAMSRARLGLYV 1283
+VD FQG++ DFI+LS VR + +G L D RRL VA++RAR G+ +
Sbjct: 710 ASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVII 758
Score = 41.6 bits (96), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 28/69 (40%), Positives = 40/69 (57%), Gaps = 11/69 (15%)
Query: 823 TQVGAIISGIQPGLTMVVGPPGTGKTDTAVQILNVLYH-----NCPSQRTLIITHSNQAL 877
+QV A+ + +Q L+++ GPPGTGKT T+ I +YH N P L+ SN A+
Sbjct: 360 SQVYAVKTVLQRPLSLIQGPPGTGKTVTSATI---VYHLARQGNGP---VLVCAPSNIAV 413
Query: 878 NDLFEKIMQ 886
+ L EKI Q
Sbjct: 414 DQLTEKIHQ 422
>pdb|2GJK|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|B Chain B, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK7|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
Length = 624
Score = 92.4 bits (228), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 84/289 (29%), Positives = 136/289 (47%), Gaps = 41/289 (14%)
Query: 1027 RAFELLKSTADRANYLMTKQAKIVAMTCTHAALKRKDFLQLGFKYDNLLMEESAQILEIE 1086
+ + LK TA+R + A ++ TC A R +Q + ++L++ES Q E E
Sbjct: 303 KRYRALKRTAERE---LLMNADVICCTCVGAGDPRLAKMQ----FRSILIDESTQATEPE 355
Query: 1087 TFIPMLLNDRRM--------LPPVVKNMAFQKYSHMDQSLFTRFVRLGIPYIELNAQGRA 1138
+P++L +++ L PVV K + + QSLF R V LGI I L Q R
Sbjct: 356 CMVPVVLGAKQLILVGDHCQLGPVVMCKKAAK-AGLSQSLFERLVVLGIRPIRLQVQYRM 414
Query: 1139 RPSIAQLYNWRYRDLGDLPFLVDVPDYNGRG--ESAPSP----WFYQNEGEAEYVVSVYI 1192
P+++ + + + G L V D +G P P +FY +G+ E S
Sbjct: 415 HPALSAFPSNIFYE-GSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTS 473
Query: 1193 YM-------------RLL--GYPANKISILTTYNGQKLLIRDVINRQCVPYPFIGPPSKV 1237
Y+ +LL G ++I I+T Y GQ+ + + + + ++
Sbjct: 474 YLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEI 533
Query: 1238 TTVDKFQGQQNDFILLSLVRT---RFVGHLRDVRRLVVAMSRARLGLYV 1283
+VD FQG++ DFI+LS VR + +G L D RRL VA++RAR G+ +
Sbjct: 534 ASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVII 582
Score = 41.6 bits (96), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 28/69 (40%), Positives = 40/69 (57%), Gaps = 11/69 (15%)
Query: 823 TQVGAIISGIQPGLTMVVGPPGTGKTDTAVQILNVLYH-----NCPSQRTLIITHSNQAL 877
+QV A+ + +Q L+++ GPPGTGKT T+ I +YH N P L+ SN A+
Sbjct: 184 SQVYAVKTVLQRPLSLIQGPPGTGKTVTSATI---VYHLARQGNGP---VLVCAPSNIAV 237
Query: 878 NDLFEKIMQ 886
+ L EKI Q
Sbjct: 238 DQLTEKIHQ 246
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 92.4 bits (228), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 82/289 (28%), Positives = 131/289 (45%), Gaps = 41/289 (14%)
Query: 1027 RAFELLKSTADRANYLMTKQAKIVAMTCTHAALKRKDFLQLGFKYDNLLMEESAQILEIE 1086
+ + LK TA+R + A ++ TC A R +Q + ++L++ES Q E E
Sbjct: 302 KRYRALKRTAERE---LLMNADVICCTCVGAGDPRLAKMQ----FRSILIDESTQATEPE 354
Query: 1087 TFIPMLLNDRRM--------LPPVVKNMAFQKYSHMDQSLFTRFVRLGIPYIELNAQGRA 1138
+P++L +++ L PVV K + + QSLF R V LGI I L Q R
Sbjct: 355 CMVPVVLGAKQLILVGDHCQLGPVVMCKKAAK-AGLSQSLFERLVVLGIRPIRLQVQYRM 413
Query: 1139 RPSIAQLYNWRYRDLGDLPFLVDVPD---------------------YNGRGESAPSPWF 1177
P+++ + + + G L V D G+ E A S
Sbjct: 414 HPALSAFPSNIFYE-GSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTS 472
Query: 1178 YQNEGEAEYVVSVYIYMRLLGYPANKISILTTYNGQKLLIRDVINRQCVPYPFIGPPSKV 1237
Y N EA V + + G ++I I+T Y GQ+ + + + + ++
Sbjct: 473 YLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEI 532
Query: 1238 TTVDKFQGQQNDFILLSLVRT---RFVGHLRDVRRLVVAMSRARLGLYV 1283
+VD FQG++ DFI+LS VR + +G L D RRL VA++RAR G+ +
Sbjct: 533 ASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVII 581
Score = 41.6 bits (96), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 28/69 (40%), Positives = 40/69 (57%), Gaps = 11/69 (15%)
Query: 823 TQVGAIISGIQPGLTMVVGPPGTGKTDTAVQILNVLYH-----NCPSQRTLIITHSNQAL 877
+QV A+ + +Q L+++ GPPGTGKT T+ I +YH N P L+ SN A+
Sbjct: 183 SQVYAVKTVLQRPLSLIQGPPGTGKTVTSATI---VYHLARQGNGP---VLVCAPSNIAV 236
Query: 878 NDLFEKIMQ 886
+ L EKI Q
Sbjct: 237 DQLTEKIHQ 245
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 87.4 bits (215), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 83/312 (26%), Positives = 133/312 (42%), Gaps = 41/312 (13%)
Query: 1007 RAAKGCFRHLQTLFQELEECRAFELLK--STADRANYLMTKQAKIVAMTCTHAALKRKDF 1064
R AKG ++L L E+ E A + + + + +A +V TC A KR D
Sbjct: 457 RGAKGELKNLLKLKDEVGELSASDTKRFVKLVRKTEAEILNKADVVCCTCVGAGDKRLDT 516
Query: 1065 LQLGFKYDNLLMEESAQILEIETFIPM--------LLNDRRMLPPVVKNMAFQKYSHMDQ 1116
K+ +L++ES Q E E IP+ L+ D + L PV+ + + Q
Sbjct: 517 -----KFRTVLIDESTQASEPECLIPIVKGAKQVILVGDHQQLGPVILERKAAD-AGLKQ 570
Query: 1117 SLFTRFVRLGIPYIELNAQGRARPSIAQLYNWRYRDLGDLPFLVDVPDYNGRGESAPSP- 1175
SLF R + LG I L Q R P +++ + + + G L V + P P
Sbjct: 571 SLFERLISLGHVPIRLEVQYRMNPYLSEFPSNMFYE-GSLQNGVTIEQRTVPNSKFPWPI 629
Query: 1176 -----WFYQNEGEAEYVVSVYIYMRLL---------------GYPANKISILTTYNGQKL 1215
F+ N G E + ++ + G +I ++T Y GQ+
Sbjct: 630 RGIPMMFWANYGREEISANGTSFLNRIEAMNCERIITKLFRDGVKPEQIGVITPYEGQRA 689
Query: 1216 LIRDVINRQCVPYPFIGPPSKVTTVDKFQGQQNDFILLSLVRT---RFVGHLRDVRRLVV 1272
I + + +V +VD FQG++ D+I+LS VR + +G LRD RRL V
Sbjct: 690 YILQYMQMNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVRANEQQAIGFLRDPRRLNV 749
Query: 1273 AMSRARLGLYVF 1284
++RA+ GL +
Sbjct: 750 GLTRAKYGLVIL 761
Score = 38.9 bits (89), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 5/71 (7%)
Query: 816 NSVRFTPTQVGAIISGIQPGLTMVVGPPGTGKTDTAVQILNVLYH--NCPSQRTLIITHS 873
N + +Q A+ +Q L+++ GPPGTGKT T+ I +YH R L+ S
Sbjct: 357 NFAQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATI---VYHLSKIHKDRILVCAPS 413
Query: 874 NQALNDLFEKI 884
N A++ L K+
Sbjct: 414 NVAVDHLAAKL 424
>pdb|4B3G|A Chain A, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
pdb|4B3G|B Chain B, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
Length = 646
Score = 58.9 bits (141), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 84/333 (25%), Positives = 140/333 (42%), Gaps = 66/333 (19%)
Query: 996 IFTGDSFEKDMRAAKGCFRHLQTLFQELEECRAFELLKSTADRANYLMTKQAKIVAMTCT 1055
+F + +D R ++ L +EL+E +L+S A +V T T
Sbjct: 301 VFVKNKKTQDKREKSNFRNEIKLLRKELKEREEAAMLESLTS---------ANVVLATNT 351
Query: 1056 HAALKRKDFLQLGFKYDNLLMEESAQILEIETFIPML-------LNDRRMLPP------- 1101
A+ L +D ++++E AQ LE +IP+L D + LPP
Sbjct: 352 GASADGPLKLLPESYFDVVVIDECAQALEASCWIPLLKARKCILAGDHKQLPPTTVSHKA 411
Query: 1102 VVKNMAFQKYSHMDQSLFTRFVR-LGIPYIELNA------------QGRARPSIAQLYNW 1148
+ ++ + + R VR L + Y A Q A S+A+
Sbjct: 412 ALAGLSLSLMERLAEEYGARVVRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHL-- 469
Query: 1149 RYRDLGDLPFLV-----DVP----DYNGRGESAPSPWFYQNEGEAEYVVSVYIYMRLL-- 1197
L DLP + VP D G G Q++G V V ++++ L
Sbjct: 470 ----LRDLPGVAATEETGVPLLLVDTAGCGLFELEEEDEQSKGNPGEVRLVSLHIQALVD 525
Query: 1198 -GYPANKISILTTYNGQKLLIR-DVINRQCVPYPFIGPPSKVTTVDKFQGQQNDFILLSL 1255
G PA I++++ YN Q L+R +++R P ++ +VD FQG++ + ++LS
Sbjct: 526 AGVPARDIAVVSPYNLQVDLLRQSLVHRH--------PELEIKSVDGFQGREKEAVILSF 577
Query: 1256 VRTRF---VGHLRDVRRLVVAMSRARLGLYVFC 1285
VR+ VG L + RR+ VA++RAR + V C
Sbjct: 578 VRSNRKGEVGFLAEDRRINVAVTRARRHVAVIC 610
Score = 38.5 bits (88), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 37/67 (55%), Gaps = 5/67 (7%)
Query: 833 QPGLTMVVGPPGTGKTDTAVQILNVLYHNCPSQRTLIITHSNQALNDLFEKIMQRDVPAR 892
Q L ++ GPPGTGKT T V+I +L + L SN A+++L E++ + +
Sbjct: 204 QKELAIIHGPPGTGKTTTVVEI--ILQAVKQGLKVLCCAPSNIAVDNLVERLA---LCKQ 258
Query: 893 YLLRLGQ 899
+LRLG
Sbjct: 259 RILRLGH 265
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 58.5 bits (140), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 84/333 (25%), Positives = 140/333 (42%), Gaps = 66/333 (19%)
Query: 996 IFTGDSFEKDMRAAKGCFRHLQTLFQELEECRAFELLKSTADRANYLMTKQAKIVAMTCT 1055
+F + +D R ++ L +EL+E +L+S A +V T T
Sbjct: 301 VFVKNKKTQDKREKSNFRNEIKLLRKELKEREEAAMLESLTS---------ANVVLATNT 351
Query: 1056 HAALKRKDFLQLGFKYDNLLMEESAQILEIETFIPML-------LNDRRMLPP------- 1101
A+ L +D ++++E AQ LE +IP+L D + LPP
Sbjct: 352 GASADGPLKLLPESYFDVVVIDECAQALEASCWIPLLKARKCILAGDHKQLPPTTVSHKA 411
Query: 1102 VVKNMAFQKYSHMDQSLFTRFVR-LGIPYIELNA------------QGRARPSIAQLYNW 1148
+ ++ + + R VR L + Y A Q A S+A+
Sbjct: 412 ALAGLSLSLMERLAEEYGARVVRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHL-- 469
Query: 1149 RYRDLGDLPFLV-----DVP----DYNGRGESAPSPWFYQNEGEAEYVVSVYIYMRLL-- 1197
L DLP + VP D G G Q++G V V ++++ L
Sbjct: 470 ----LRDLPGVAATEETGVPLLLVDTAGCGLFELEEEDEQSKGNPGEVRLVSLHIQALVD 525
Query: 1198 -GYPANKISILTTYNGQKLLIR-DVINRQCVPYPFIGPPSKVTTVDKFQGQQNDFILLSL 1255
G PA I++++ YN Q L+R +++R P ++ +VD FQG++ + ++LS
Sbjct: 526 AGVPARDIAVVSPYNLQVDLLRQSLVHRH--------PELEIKSVDGFQGREKEAVILSF 577
Query: 1256 VRTRF---VGHLRDVRRLVVAMSRARLGLYVFC 1285
VR+ VG L + RR+ VA++RAR + V C
Sbjct: 578 VRSNRKGEVGFLAEDRRINVAVTRARRHVAVIC 610
Score = 38.1 bits (87), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 37/67 (55%), Gaps = 5/67 (7%)
Query: 833 QPGLTMVVGPPGTGKTDTAVQILNVLYHNCPSQRTLIITHSNQALNDLFEKIMQRDVPAR 892
Q L ++ GPPGTGKT T V+I +L + L SN A+++L E++ + +
Sbjct: 204 QKELAIIHGPPGTGKTTTVVEI--ILQAVKQGLKVLCCAPSNIAVDNLVERLA---LCKQ 258
Query: 893 YLLRLGQ 899
+LRLG
Sbjct: 259 RILRLGH 265
>pdb|1ODF|A Chain A, Structure Of Ygr205w Protein
Length = 290
Score = 31.6 bits (70), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 12/78 (15%)
Query: 834 PGLTMVVGPPGTGKTDTAVQILNVLYHNCPSQRTL--------IITHSNQ-ALNDLFE-- 882
P GP G+GK+ T++QI N L ++++ +TH +Q LN+ F+
Sbjct: 31 PLFIFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFYLTHEDQLKLNEQFKNN 90
Query: 883 KIMQ-RDVPARYLLRLGQ 899
K++Q R +P + ++L Q
Sbjct: 91 KLLQGRGLPGTHDMKLLQ 108
>pdb|3RB8|A Chain A, Structure Of The Phage Tubulin Phuz(semet)-gdp
Length = 315
Score = 30.0 bits (66), Expect = 9.2, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 26/48 (54%)
Query: 454 LQFLTLHDYLLRNFNLFRLESTYEIREDIQEAVPHLLAYINNEGEAAF 501
++F H+YL+ +E+T + E++ EA+ L Y++ E AF
Sbjct: 195 VRFTDKHNYLIPQVCELHIETTRKDAENVPEAISQLSLYLDPSKEVAF 242
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
0.320 0.136 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 41,964,954
Number of Sequences: 62578
Number of extensions: 1748341
Number of successful extensions: 3740
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 3702
Number of HSP's gapped (non-prelim): 27
length of query: 1456
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1345
effective length of database: 8,027,179
effective search space: 10796555755
effective search space used: 10796555755
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.9 bits)