RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3902
(181 letters)
>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay,
zinc-finger, ATP-binding, metal-BIN UPF2, UPF1,
helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A
2iyk_A
Length = 800
Score = 120 bits (303), Expect = 3e-32
Identities = 38/119 (31%), Positives = 51/119 (42%), Gaps = 20/119 (16%)
Query: 62 PSGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELRI 121
F +IDE+ QATEPE +VP+ L + ++L GD QLGP V K + L
Sbjct: 512 AKMQFRSILIDESTQATEPECMVPVVLGAK---QLILVGDHCQLGPVVMCKKAAKAGLSQ 568
Query: 122 SLLERLTGRFLYSRDMSRFYATGGYDPRLVTRLVNNYRTMPEILKISSDLFYDASLVPH 180
SL ERL + RL YR P + S++FY+ SL
Sbjct: 569 SLFERLVVLGIR-----------------PIRLQVQYRMHPALSAFPSNIFYEGSLQNG 610
Score = 86.9 bits (215), Expect = 2e-20
Identities = 24/60 (40%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 2 PAGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELST 61
F +IDE+ QATEPE +VP+ L + ++L GD QLGP V K + LS
Sbjct: 512 AKMQFRSILIDESTQATEPECMVPVVLGAK---QLILVGDHCQLGPVVMCKKAAKAGLSQ 568
>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD,
hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A*
2gk7_A 2xzo_A* 2xzp_A
Length = 624
Score = 119 bits (299), Expect = 7e-32
Identities = 38/119 (31%), Positives = 51/119 (42%), Gaps = 20/119 (16%)
Query: 62 PSGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELRI 121
F +IDE+ QATEPE +VP+ L + ++L GD QLGP V K + L
Sbjct: 336 AKMQFRSILIDESTQATEPECMVPVVLGAK---QLILVGDHCQLGPVVMCKKAAKAGLSQ 392
Query: 122 SLLERLTGRFLYSRDMSRFYATGGYDPRLVTRLVNNYRTMPEILKISSDLFYDASLVPH 180
SL ERL + RL YR P + S++FY+ SL
Sbjct: 393 SLFERLVVLGIR-----------------PIRLQVQYRMHPALSAFPSNIFYEGSLQNG 434
Score = 85.6 bits (212), Expect = 4e-20
Identities = 24/60 (40%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 2 PAGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELST 61
F +IDE+ QATEPE +VP+ L + ++L GD QLGP V K + LS
Sbjct: 336 AKMQFRSILIDESTQATEPECMVPVVLGAK---QLILVGDHCQLGPVVMCKKAAKAGLSQ 392
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA
degradation, allosteric REGU; HET: ADP 1PE; 2.40A
{Saccharomyces cerevisiae}
Length = 802
Score = 118 bits (297), Expect = 2e-31
Identities = 36/119 (30%), Positives = 50/119 (42%), Gaps = 20/119 (16%)
Query: 62 PSGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELRI 121
F +IDE+ QA+EPE L+PI + V+L GD QLGP + + L+
Sbjct: 514 LDTKFRTVLIDESTQASEPECLIPIVKGAK---QVILVGDHQQLGPVILERKAADAGLKQ 570
Query: 122 SLLERLTGRFLYSRDMSRFYATGGYDPRLVTRLVNNYRTMPEILKISSDLFYDASLVPH 180
SL ERL RL YR P + + S++FY+ SL
Sbjct: 571 SLFERLISLGHV-----------------PIRLEVQYRMNPYLSEFPSNMFYEGSLQNG 612
Score = 84.6 bits (209), Expect = 9e-20
Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 2 PAGYFTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELST 61
F +IDE+ QA+EPE L+PI + V+L GD QLGP + + L
Sbjct: 514 LDTKFRTVLIDESTQASEPECLIPIVKGAK---QVILVGDHQQLGPVILERKAADAGLKQ 570
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 38.1 bits (88), Expect = 0.001
Identities = 30/147 (20%), Positives = 52/147 (35%), Gaps = 48/147 (32%)
Query: 11 IDEAGQATEPEVLVPISLLHRDNG--HVVLAGDPLQL-GPTVFSKLGQQLE-LSTPSGYF 66
+++ V ISL+ NG ++V++G P L G L L PSG
Sbjct: 353 VNKTNSHLPAGKQVEISLV---NGAKNLVVSGPPQSLYG------LNLTLRKAKAPSG-- 401
Query: 67 THCVIDEAGQATEP----------EVLVPIS-------------LLHRDNGHVVLAGDPL 103
+D Q+ P L P++ L+++D ++ +
Sbjct: 402 ----LD---QSRIPFSERKLKFSNRFL-PVASPFHSHLLVPASDLINKDLVKNNVSFNAK 453
Query: 104 QLGPTVFS-KLGQQL-ELRISLLERLT 128
+ V+ G L L S+ ER+
Sbjct: 454 DIQIPVYDTFDGSDLRVLSGSISERIV 480
>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase;
1.90A {Tomato mosaic virus}
Length = 446
Score = 31.7 bits (71), Expect = 0.12
Identities = 10/59 (16%), Positives = 14/59 (23%), Gaps = 2/59 (3%)
Query: 66 FTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLGPTVFSKLGQQLELRISLL 124
F IDE V + + D + GD Q+ L
Sbjct: 235 FKRLFIDEGLMLHTGCVNFLVEMSLCD--IAYVYGDTQQIPYINRVTGFPYPAHFAKLE 291
Score = 30.9 bits (69), Expect = 0.20
Identities = 9/41 (21%), Positives = 13/41 (31%), Gaps = 2/41 (4%)
Query: 6 FTHCVIDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQLG 46
F IDE V + + D + GD Q+
Sbjct: 235 FKRLFIDEGLMLHTGCVNFLVEMSLCD--IAYVYGDTQQIP 273
>2vr5_A Glycogen operon protein GLGX; hydrolase, glycosidase, glycosyl
hydrolase, glycogen debraching; HET: GLC A16; 2.8A
{Sulfolobus solfataricus} PDB: 2vnc_A* 2vuy_A
Length = 718
Score = 31.1 bits (71), Expect = 0.17
Identities = 17/87 (19%), Positives = 30/87 (34%), Gaps = 25/87 (28%)
Query: 27 SLLHRDNGHVVLAGDPLQLGPT-----------VFSKLGQQLELSTPSGYFTHCVIDEAG 75
+L R + GDP LG +FS+ +++EL +
Sbjct: 2 ALFFRTRDRPLRPGDPYPLGSNWIEDDDGVNFSLFSENAEKVEL---------LLYSLTN 52
Query: 76 QATEPEVLVPISLLHRDNG--HVVLAG 100
Q E+ I + ++ HV + G
Sbjct: 53 QKYPKEI---IEVKNKTGDIWHVFVPG 76
>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase,
hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli}
SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*
Length = 608
Score = 29.3 bits (66), Expect = 0.64
Identities = 21/124 (16%), Positives = 34/124 (27%), Gaps = 28/124 (22%)
Query: 57 LELSTPSGYFTHC----------VIDEAGQATEPEVLVPISLLHR------DNGHVVLAG 100
L S H V+DEA ++ + ++ R D+ V+ G
Sbjct: 244 LGAQPGSQRLRHHAGNPLHLDVLVVDEAS-------MIDLPMMSRLIDALPDHARVIFLG 296
Query: 101 DPLQL---GP-TVFSKLGQQLELRISLLERLTGRFLYSRDMSRFYATGGYDPRL-VTRLV 155
D QL V + + L + T R + L
Sbjct: 297 DRDQLASVEAGAVLGDICAYANAGFTAERARQLSRLTGTHVPAGTGTEAASLRDSLCLLQ 356
Query: 156 NNYR 159
+YR
Sbjct: 357 KSYR 360
>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein,
ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus
radiodurans} PDB: 3gp8_A 3gpl_A*
Length = 574
Score = 27.0 bits (60), Expect = 4.4
Identities = 10/44 (22%), Positives = 16/44 (36%), Gaps = 13/44 (29%)
Query: 10 VIDEAGQATEPEVLVPISLLHR------DNGHVVLAGDPLQLGP 47
++DE + +L+ V+L GD QL P
Sbjct: 284 IVDEVSM-------MGDALMLSLLAAVPPGARVLLVGDTDQLPP 320
Score = 27.0 bits (60), Expect = 4.4
Identities = 10/44 (22%), Positives = 16/44 (36%), Gaps = 13/44 (29%)
Query: 70 VIDEAGQATEPEVLVPISLLHR------DNGHVVLAGDPLQLGP 107
++DE + +L+ V+L GD QL P
Sbjct: 284 IVDEVSM-------MGDALMLSLLAAVPPGARVLLVGDTDQLPP 320
>3v2a_R Vascular endothelial growth factor receptor 2; IG-homology
domain, vegfr-2, growth factor receptor, VEGF LI
hormone-signaling protein complex, angiogenesis; 3.20A
{Homo sapiens} PDB: 3v6b_R
Length = 772
Score = 26.6 bits (58), Expect = 6.3
Identities = 8/44 (18%), Positives = 13/44 (29%), Gaps = 2/44 (4%)
Query: 3 AGYFTHCV-IDEAGQATEPEVLVPISLLHRDNGHVVLAGDPLQL 45
+ CV A L L + + + A LQ+
Sbjct: 9 VALWL-CVETRAASVGLPSVSLDLPRLSIQKDILTIKANTTLQI 51
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.320 0.140 0.415
Gapped
Lambda K H
0.267 0.0491 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,815,384
Number of extensions: 165146
Number of successful extensions: 443
Number of sequences better than 10.0: 1
Number of HSP's gapped: 433
Number of HSP's successfully gapped: 20
Length of query: 181
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 93
Effective length of database: 4,244,745
Effective search space: 394761285
Effective search space used: 394761285
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.1 bits)