RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7749
(319 letters)
>3u5c_N S27A, YS15, 40S ribosomal protein S13; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_O 3o30_G 3o2z_G 3u5g_N 3iz6_O
3jyv_O* 1ysh_E 1s1h_O
Length = 151
Score = 252 bits (646), Expect = 2e-85
Identities = 111/150 (74%), Positives = 132/150 (88%)
Query: 169 MGRMHTPGKGISKSALPYRRSVPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGV 228
MGRMH+ GKGIS SA+PY R+ P W KL+SE V + I K ++KGLTPSQIGV+LRD+HGV
Sbjct: 1 MGRMHSAGKGISSSAIPYSRNAPAWFKLSSESVIEQIVKYARKGLTPSQIGVLLRDAHGV 60
Query: 229 AQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVES 288
Q R ++GNKI+RI+K+ GLAP +PEDLY LIKKAV++RKHLER+RKDKD+KFRLIL+ES
Sbjct: 61 TQARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKHLERNRKDKDAKFRLILIES 120
Query: 289 RIHRLARYYKTKAVLPPNWKYESATASALV 318
RIHRLARYY+T AVLPPNWKYESATASALV
Sbjct: 121 RIHRLARYYRTVAVLPPNWKYESATASALV 150
Score = 161 bits (409), Expect = 1e-49
Identities = 76/99 (76%), Positives = 91/99 (91%)
Query: 37 VILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDS 96
V+LRD+HGV Q R ++GNKI+RI+K+ GLAP +PEDLY LIKKAV++RKHLER+RKDKD+
Sbjct: 52 VLLRDAHGVTQARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKHLERNRKDKDA 111
Query: 97 KFRLILVESRIHRLARYYKTKAVLPPNWKYESATASAFI 135
KFRLIL+ESRIHRLARYY+T AVLPPNWKYESATASA +
Sbjct: 112 KFRLILIESRIHRLARYYRTVAVLPPNWKYESATASALV 150
>2xzm_O RPS13E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_O 1ysh_E 3jyv_O* 1s1h_O
Length = 153
Score = 249 bits (636), Expect = 6e-84
Identities = 105/152 (69%), Positives = 120/152 (78%), Gaps = 2/152 (1%)
Query: 169 MGRMHT--PGKGISKSALPYRRSVPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDSH 226
MGRM GKGIS SALP++R P WL +T V D KL+KKGLTPSQIGVILRD H
Sbjct: 1 MGRMQMKGKGKGISGSALPFKRRSPKWLHMTPSTVVDLSVKLAKKGLTPSQIGVILRDQH 60
Query: 227 GVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILV 286
G+ QVRF++G KILRI+K G AP LPEDLY LIKKA++IRKHLE++RKDKDSK+RLILV
Sbjct: 61 GIPQVRFLTGQKILRILKKNGCAPQLPEDLYFLIKKALSIRKHLEKNRKDKDSKYRLILV 120
Query: 287 ESRIHRLARYYKTKAVLPPNWKYESATASALV 318
ESRIHRL+RYYK LPP WKY + TASALV
Sbjct: 121 ESRIHRLSRYYKLNQKLPPKWKYNAQTASALV 152
Score = 163 bits (413), Expect = 3e-50
Identities = 71/99 (71%), Positives = 83/99 (83%)
Query: 37 VILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDS 96
VILRD HG+ QVRF++G KILRI+K G AP LPEDLY LIKKA++IRKHLE++RKDKDS
Sbjct: 54 VILRDQHGIPQVRFLTGQKILRILKKNGCAPQLPEDLYFLIKKALSIRKHLEKNRKDKDS 113
Query: 97 KFRLILVESRIHRLARYYKTKAVLPPNWKYESATASAFI 135
K+RLILVESRIHRL+RYYK LPP WKY + TASA +
Sbjct: 114 KYRLILVESRIHRLSRYYKLNQKLPPKWKYNAQTASALV 152
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 43.7 bits (102), Expect = 7e-05
Identities = 58/365 (15%), Positives = 103/365 (28%), Gaps = 117/365 (32%)
Query: 34 LFCVILRDSHGVAQVRFVSG------NKILRIMKAMGLAPNLPEDLYC-----LIKKAVA 82
LF +L + Q +FV ++ +K P++ +Y L
Sbjct: 67 LFWTLLSKQEEMVQ-KFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQV 125
Query: 83 IRKHLERSRKDKDSKFRLILVESR------IHRLARYYKTKAVLPPNWKYESATASAFIL 136
K+ SR K R L+E R I + KT +
Sbjct: 126 FAKY-NVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKT--WV---------ALDV--C 171
Query: 137 EGFRFRTRRGFRYKIDLVGLLDDNFYNKKSLKMGRMHTPGKGISKSALPYRRSVPNW--- 193
++ + + F KI F+ L + ++P + + PNW
Sbjct: 172 LSYKVQCKMDF--KI---------FW----LNLKNCNSPETVLEMLQKLLYQIDPNWTSR 216
Query: 194 ------LKLTSEDVKDHIFKLSKKGLTP---------------------SQIGVILRDSH 226
+KL ++ + +L K +I + R
Sbjct: 217 SDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFK- 275
Query: 227 GVAQVRFVSGNKILRIM------------------KAMGLAPN-LPED-------LYCLI 260
V F+S I K + P LP + +I
Sbjct: 276 QVT--DFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSII 333
Query: 261 KKAVAIRKHLERS---RKDKDSKFRLILVESRIHRLA-----RYYKTKAVLPPNWKYESA 312
A +IR L + K I+ ES ++ L + + +V PP+ +
Sbjct: 334 --AESIRDGLATWDNWKHVNCDKLTTII-ESSLNVLEPAEYRKMFDRLSVFPPSAHIPTI 390
Query: 313 TASAL 317
S +
Sbjct: 391 LLSLI 395
Score = 42.5 bits (99), Expect = 1e-04
Identities = 54/325 (16%), Positives = 91/325 (28%), Gaps = 101/325 (31%)
Query: 8 QFNETTLGPNWFIKSGFYCN-LKTDIVL-----------F---CVIL---RDSHGVAQVR 49
+ + +KS Y N L +VL F C IL R V
Sbjct: 226 RIHSIQAELRRLLKSKPYENCL---LVLLNVQNAKAWNAFNLSCKILLTTRFK-QVT--D 279
Query: 50 FVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRL-ILVESRIH 108
F+S I P+++ L+ K + R + RL I+ ES
Sbjct: 280 FLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRD 339
Query: 109 RLAR--YYKTKAVLPPNWKYESATASAF-ILEGFRFRTRRGFRYKIDLVGLLDDNFYNKK 165
LA +K K + S+ +LE +R + L
Sbjct: 340 GLATWDNWKH----VNCDKLTTIIESSLNVLEPAEYRKM----FD-RLSVFPPS------ 384
Query: 166 SLKMGRMHTPGKGISKSALPYRRSVPNWLKLTSEDVKDHIFKLSKKGLTPSQIGVILRDS 225
H P +S + W + DV + KL K L + +
Sbjct: 385 ------AHIPTILLSL--I--------WFDVIKSDVMVVVNKLHKYSL-------VEKQP 421
Query: 226 HGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLIL 285
+ I +Y +K + L RS +
Sbjct: 422 K----------ESTISIP-----------SIYLELKVKLENEYALHRS-----------I 449
Query: 286 VESRIHRLARYYKTKAVLPPNW-KY 309
V+ + + + + ++PP +Y
Sbjct: 450 VDHY--NIPKTFDSDDLIPPYLDQY 472
Score = 28.3 bits (62), Expect = 4.7
Identities = 16/135 (11%), Positives = 38/135 (28%), Gaps = 25/135 (18%)
Query: 179 ISKSALPYRRSVPNWLK--LTSEDVKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFV-- 234
+ Y+ + + + + D KD + + K L+ +I I+ V+ +
Sbjct: 11 TGEHQYQYKDILSVFEDAFVDNFDCKD-VQDMPKSILSKEEIDHIIMSKDAVSGTLRLFW 69
Query: 235 ----SGNKILRIMKAMGLAPNLPEDLYCLIKKAVAIRKHLERSRKDKDSKFRLILVESRI 290
++++ L N Y + + + + +
Sbjct: 70 TLLSKQEEMVQKFVEEVLRIN-----YKFLMSPIKTE--------QRQPSMMTRMYIEQR 116
Query: 291 HRLARYYKTKAVLPP 305
RL Y V
Sbjct: 117 DRL---YNDNQVFAK 128
>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 = 39.3 bits (91), Expect = 0.002
Identities = 27/137 (19%), Positives = 45/137 (32%), Gaps = 30/137 (21%)
Query: 126 YESATASAFILE--GFRFRTRRGFRYKIDLVGLLDDNFYNKKSLKMGRMHTPG-KGISKS 182
Y+++ A+ + F+ GF +LD N +L + H G KG
Sbjct: 1636 YKTSKAAQDVWNRADNHFKDTYGFS-------ILDIVINNPVNLTI---HFGGEKG---- 1681
Query: 183 ALPYRRSVPNWLKLTSEDVKDHIFKLSK--KGLTPSQIGVILRDSHGV------AQVR-F 233
+R N+ + E + D K K K + R G+ Q
Sbjct: 1682 ----KRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALT 1737
Query: 234 VSGNKILRIMKAMGLAP 250
+ +K+ GL P
Sbjct: 1738 LMEKAAFEDLKSKGLIP 1754
Score = 38.9 bits (90), Expect = 0.002
Identities = 31/154 (20%), Positives = 59/154 (38%), Gaps = 47/154 (30%)
Query: 159 DNFYN--KKSLK----MG-RMH--TPGKGIS----KSALPYRRSVPNWL----KLTSEDV 201
++F+ +K++ +G R + P + + +L VP+ + LT E V
Sbjct: 290 ESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQV 349
Query: 202 KDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFV-SGNKILRIMKAMGLAPNLPEDLYCLI 260
+D++ K + Q+ + L + V SG P+ LY L
Sbjct: 350 QDYVNKTNSHLPAGKQVEISLVNGA----KNLVVSGP---------------PQSLYGL- 389
Query: 261 KKAVAIRK-----HLERSRKDKDSKFRLILVESR 289
+ +RK L++SR S+ R + +R
Sbjct: 390 --NLTLRKAKAPSGLDQSRI-PFSE-RKLKFSNR 419
Score = 38.9 bits (90), Expect = 0.002
Identities = 47/284 (16%), Positives = 92/284 (32%), Gaps = 81/284 (28%)
Query: 19 FIKSGFYCNL--KTDIVLFCVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPED---- 72
F+ G+ +L + + F +L + ++ GN I LA L ++
Sbjct: 64 FL--GYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDI------HALAAKLLQENDTT 115
Query: 73 ---LYCLIKKAVAIRKHLERS----------RKDKDSKFRLILV-------ESRIHRLAR 112
LIK + R +R R + +L+ + + L
Sbjct: 116 LVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRD 175
Query: 113 YYKTKAVLPPNWKYESA-----TASAFILEGF---RFRTRRGFRYKIDLVGLLDDNFYNK 164
Y+T Y SA L + F ++++ L++
Sbjct: 176 LYQT---------YHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLEN----- 221
Query: 165 KSLKMGRMHTPGKGISKSALPYRRSVPNWLKLTSEDVKDHIFKLSKK-GLTPSQIGVILR 223
+TP K S P S P + + H +K G TP ++ L+
Sbjct: 222 ------PSNTPDKDYLLSI-PI--SCP-LIGVIQ---LAHYVVTAKLLGFTPGELRSYLK 268
Query: 224 DSHGVAQVRFVSGNKILRIMKAMGLAP-NLPEDLYCLIKKAVAI 266
+ G +Q ++ A+ +A + E + ++KA+ +
Sbjct: 269 GATGHSQ----------GLVTAVAIAETDSWESFFVSVRKAITV 302
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA
degradation, allosteric REGU; HET: ADP 1PE; 2.40A
{Saccharomyces cerevisiae}
Length = 802
Score = 31.1 bits (70), Expect = 0.63
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 11/61 (18%)
Query: 201 VKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLI 260
+ I KL + G+ P QIGVI + Q I++ M + +L +DLY +
Sbjct: 661 CERIITKLFRDGVKPEQIGVI---TPYEGQRA--------YILQYMQMNGSLDKDLYIKV 709
Query: 261 K 261
+
Sbjct: 710 E 710
>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 = 30.3 bits (68), Expect = 0.86
Identities = 15/61 (24%), Positives = 25/61 (40%), Gaps = 11/61 (18%)
Query: 201 VKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLI 260
V+ KL K G P QIG+I + Q +++ M + +L LY +
Sbjct: 659 VEKITTKLLKAGAKPDQIGII---TPYEGQRS--------YLVQYMQFSGSLHTKLYQEV 707
Query: 261 K 261
+
Sbjct: 708 E 708
>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 = 30.2 bits (68), Expect = 1.1
Identities = 15/61 (24%), Positives = 25/61 (40%), Gaps = 11/61 (18%)
Query: 201 VKDHIFKLSKKGLTPSQIGVILRDSHGVAQVRFVSGNKILRIMKAMGLAPNLPEDLYCLI 260
V+ KL K G P QIG+I + Q +++ M + +L LY +
Sbjct: 483 VEKITTKLLKAGAKPDQIGII---TPYEGQRS--------YLVQYMQFSGSLHTKLYQEV 531
Query: 261 K 261
+
Sbjct: 532 E 532
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
0.324 0.138 0.413
Gapped
Lambda K H
0.267 0.0612 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,920,702
Number of extensions: 293069
Number of successful extensions: 744
Number of sequences better than 10.0: 1
Number of HSP's gapped: 738
Number of HSP's successfully gapped: 15
Length of query: 319
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 225
Effective length of database: 4,077,219
Effective search space: 917374275
Effective search space used: 917374275
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 57 (26.0 bits)