RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6286
(159 letters)
>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase,
tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A
{Saccharomyces cerevisiae}
Length = 1010
Score = 161 bits (407), Expect = 1e-46
Identities = 68/191 (35%), Positives = 108/191 (56%), Gaps = 41/191 (21%)
Query: 2 SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELS---------------------- 39
+++ +++L+ RKRVLRRLG+ T D+IE+KGRVACE+S
Sbjct: 812 AVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPE 871
Query: 40 -------------KSEETVILT------INDKLELARHIARISIESKLDLDEDSYVNQFK 80
+ +E L + E+A IA+I +SK+++ E YV F+
Sbjct: 872 QAAALLSCFAFQERCKEAPRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFR 931
Query: 81 PSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKF 140
LM+VV+ WC GA+F ++C +TD++EGS+IR +RLEE++++LV + IGN+ L+EK
Sbjct: 932 HELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKM 991
Query: 141 NEAIKTVKRDI 151
+K + RDI
Sbjct: 992 EAVLKLIHRDI 1002
>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix,
antiparallel-coiled-COI domain, ATP-binding, helicase,
hydrolase; 3.39A {Saccharomyces cerevisiae}
Length = 1108
Score = 160 bits (406), Expect = 1e-46
Identities = 68/192 (35%), Positives = 108/192 (56%), Gaps = 41/192 (21%)
Query: 1 MSLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELS--------------------- 39
+++ +++L+ RKRVLRRLG+ T D+IE+KGRVACE+S
Sbjct: 909 QAVIQLDDLRRRKRVLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKP 968
Query: 40 --------------KSEETVILT------INDKLELARHIARISIESKLDLDEDSYVNQF 79
+ +E L + E+A IA+I +SK+++ E YV F
Sbjct: 969 EQAAALLSCFAFQERCKEAPRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESF 1028
Query: 80 KPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEK 139
+ LM+VV+ WC GA+F ++C +TD++EGS+IR +RLEE++++LV + IGN+ L+EK
Sbjct: 1029 RHELMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEK 1088
Query: 140 FNEAIKTVKRDI 151
+K + RDI
Sbjct: 1089 MEAVLKLIHRDI 1100
>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation,
exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB:
4a4k_A
Length = 997
Score = 148 bits (374), Expect = 3e-42
Identities = 43/195 (22%), Positives = 88/195 (45%), Gaps = 45/195 (23%)
Query: 2 SLLHMEELKCRKRVLRRLGYATEADVIEMKGRVACELS---------------------- 39
+L + + + R VL+ + + + +KGRVACE++
Sbjct: 795 NLSLLPDYEKRLAVLKDTEFIDQNHNVLLKGRVACEINSGYELVLTELILDNFLGSFEPE 854
Query: 40 -------------KSEETVILTINDKL--------ELARHIARISIESKLDL--DEDSYV 76
K+ E + +L E+ + + + ++ L DE ++
Sbjct: 855 EIVALLSVFVYEGKTREEEPPIVTPRLAKGKQRIEEIYKKMLCVFNTHQIPLTQDEAEFL 914
Query: 77 NQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLL 136
++ + ++M+VV+ W G SF ++ ++ EG+++R + L+E+ R++ AS IGN+ L
Sbjct: 915 DRKRFAMMNVVYEWARGLSFKEIMEMSPEAEGTVVRVITWLDEICREVKTASIIIGNSTL 974
Query: 137 EEKFNEAIKTVKRDI 151
K + A + +KRDI
Sbjct: 975 HMKMSRAQELIKRDI 989
>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 = 38.3 bits (88), Expect = 5e-04
Identities = 19/113 (16%), Positives = 38/113 (33%), Gaps = 18/113 (15%)
Query: 55 LARHIARISIESKLDLDEDSYVN-QF-KPSLMDVVHAWCEGASFLKVCSITDIFEGSIIR 112
+ H+ I ++ L +++ +F + + AW S L ++ I
Sbjct: 477 IGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICD 536
Query: 113 CMRRLEEVLRQLVQASRNIGNTLLEEK----------------FNEAIKTVKR 149
+ E ++ ++ I L+ K F EA K V+R
Sbjct: 537 NDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQVQR 589
>1muk_A Minor core protein lambda 3; single subunit polymerase fold, fingers,
PALM, thumb, right hand configuration, viral protein;
2.50A {Reovirus SP} SCOP: e.8.1.4 PDB: 1mwh_A* 1n1h_A*
1n35_A* 1n38_A* 1uon_A* 2cse_1
Length = 1267
Score = 31.2 bits (70), Expect = 0.12
Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 2/49 (4%)
Query: 81 PSLMDVVHAWCEGASFLKVCSITDIFE--GSIIRCMRRLEEVLRQLVQA 127
PSL DV H W +GA + + ++ E +++R R +L++A
Sbjct: 1007 PSLFDVPHKWYQGAQEAAIATREELAEMDETLMRARRHSYSSFSKLLEA 1055
>3tql_A Arginine-binding protein; transport and binding proteins, transport
protein; HET: MSE ARG; 1.59A {Coxiella burnetii}
Length = 227
Score = 29.5 bits (67), Expect = 0.37
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 132 GNTLLEEKFNEAIKTVKRD 150
GN L K N+A+ +K +
Sbjct: 198 GNQALLLKLNKALAAIKAN 216
>2y7i_A STM4351; arginine-binding protein; HET: ARG; 1.90A {Salmonella
enterica subsp}
Length = 229
Score = 28.7 bits (65), Expect = 0.59
Identities = 6/19 (31%), Positives = 9/19 (47%)
Query: 132 GNTLLEEKFNEAIKTVKRD 150
N L ++ N A+ VK
Sbjct: 198 DNDALLQEINAALDKVKAS 216
>1lst_A Lysine, arginine, ornithine-binding protein; amino-acid binding
protein; HET: LYS; 1.80A {Salmonella typhimurium} SCOP:
c.94.1.1 PDB: 2lao_A 1lag_E* 1lah_E 1laf_E 1hsl_A*
1hpb_P*
Length = 239
Score = 28.8 bits (65), Expect = 0.65
Identities = 5/19 (26%), Positives = 13/19 (68%)
Query: 132 GNTLLEEKFNEAIKTVKRD 150
+T L+ F++A+ +++D
Sbjct: 202 DDTELKAAFDKALTELRQD 220
>3kzg_A Arginine 3RD transport system periplasmic binding protein; arginine
transport system, protein structure initiative II(PSI
II); 2.06A {Legionella pneumophila subsp}
Length = 237
Score = 28.8 bits (65), Expect = 0.74
Identities = 4/19 (21%), Positives = 10/19 (52%)
Query: 132 GNTLLEEKFNEAIKTVKRD 150
+L +K N+ + ++ D
Sbjct: 200 DQFVLIKKINKILLEMEAD 218
>2nyy_A Botulinum neurotoxin type A; neurotoxin, FAB, protein antibody
complex, toxin- system complex; 2.61A {Clostridium
botulinum} PDB: 2nz9_A 3bta_A 3v0a_A* 3v0b_A 3v0c_A
3zus_A 3zur_A
Length = 1295
Score = 29.1 bits (64), Expect = 0.79
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 130 NIGNTLLEEKFNEAIKTVKRDIFLEILENL 159
NIGN L ++ F A+ I LE + +
Sbjct: 641 NIGNMLYKDDFVGALIFSGAVILLEFIPEI 670
>1wdn_A GLNBP, glutamine binding protein; closed form, complex, peptide,
complex (binding protein/peptide); 1.94A {Escherichia
coli} SCOP: c.94.1.1 PDB: 1ggg_A
Length = 226
Score = 28.3 bits (64), Expect = 0.85
Identities = 7/19 (36%), Positives = 13/19 (68%)
Query: 132 GNTLLEEKFNEAIKTVKRD 150
G+ L +K N A+KT++ +
Sbjct: 192 GSDELRDKVNGALKTLREN 210
>1epw_A Bontoxilysin B, botulinum neurotoxin type B; zinc, metalloprotease,
transmembrane, hydrolase; 1.90A {Clostridium botulinum}
SCOP: b.29.1.6 b.42.4.2 d.92.1.7 h.4.2.1 PDB: 1f31_A*
1g9a_A* 1g9b_A* 1g9c_A* 1g9d_A* 1i1e_A* 1s0b_A 1s0c_A
1s0d_A 1s0e_A 1s0f_A 1s0g_A 2np0_A 3zuq_A 2etf_A 2xhl_A
1z0h_A 2nm1_A 3g94_A 1f82_A ...
Length = 1290
Score = 28.6 bits (63), Expect = 0.92
Identities = 9/30 (30%), Positives = 13/30 (43%)
Query: 130 NIGNTLLEEKFNEAIKTVKRDIFLEILENL 159
N+GN + F A + I LE + L
Sbjct: 628 NVGNETAKGNFENAFEIAGASILLEFIPEL 657
>2zue_A Arginyl-tRNA synthetase; aminoacyl-tRNA synthetase, ATP-binding,
cytoplasm, ligase, nucleotide-binding, protein
biosynthesis, ligase/RNA complex; HET: ANP; 2.00A
{Pyrococcus horikoshii} PDB: 2zuf_A
Length = 629
Score = 28.5 bits (64), Expect = 0.92
Identities = 16/84 (19%), Positives = 27/84 (32%), Gaps = 24/84 (28%)
Query: 4 LHMEELKCRKRVLRRLGYATEADVIE-------------MKGRVACELSKSEETVILTIN 50
+K L+ LG+ A + GR V T++
Sbjct: 389 HPQLAIK---YALQLLGFEDAAANLYHLAYEHVERPEGKFSGR-------KGTWVGFTVD 438
Query: 51 DKLELARHIARISIESKL-DLDED 73
+ ++ A AR IE K L ++
Sbjct: 439 EVIQEAVKRARELIEEKNPALSDE 462
>3ffz_A Botulinum neurotoxin type E; botulinum neurotoxin serotype E,
botulism, domain organization, endopeptidase,
translocation, hydrolase; 2.65A {Clostridium botulinum}
Length = 1252
Score = 28.6 bits (63), Expect = 1.0
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 130 NIGNTLLEEKFNEAIKTVKRDIFLEILENL 159
NIGN + F +A++ + I LE L
Sbjct: 611 NIGNEAQKGNFKDALELLGAGILLEFEPEL 640
>3i6v_A Periplasmic His/Glu/Gln/Arg/opine family-binding; structural
genomics, transporter, PSI-2, protein structure
initiative; HET: LYS; 2.00A {Silicibacter pomeroyi}
Length = 232
Score = 28.3 bits (64), Expect = 1.0
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 132 GNTLLEEKFNEAIKTVKRD 150
+ L KF+ AI ++K D
Sbjct: 187 SDGELRGKFDAAITSMKED 205
>3del_B Arginine binding protein; alpha and beta protein (A/B), periplasmic
protein, arginine protein binding, transport protein;
1.92A {Chlamydia trachomatis}
Length = 242
Score = 28.0 bits (63), Expect = 1.3
Identities = 3/19 (15%), Positives = 9/19 (47%)
Query: 132 GNTLLEEKFNEAIKTVKRD 150
L K A++ ++++
Sbjct: 202 DRPALALKIEAAVQEIRKE 220
>2yln_A Putative ABC transporter, periplasmic binding Pro amino acid;
transport protein, solute-BIND protein; HET: CYS GOL;
1.12A {Neisseria gonorrhoeae} PDB: 3zsf_A
Length = 283
Score = 27.7 bits (62), Expect = 1.5
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 132 GNTLLEEKFNEAIKTVKRD 150
GN KF+ AI +K D
Sbjct: 247 GNDEAVAKFSTAINELKAD 265
>3h7m_A Sensor protein; histidine kinase sensor domain, kinase,
phosphoprotein, transferase; 2.40A {Geobacter
sulfurreducens}
Length = 234
Score = 27.6 bits (62), Expect = 1.5
Identities = 4/19 (21%), Positives = 11/19 (57%)
Query: 132 GNTLLEEKFNEAIKTVKRD 150
G+ L +F+E + +++
Sbjct: 200 GDAELLARFSEGLAILRKT 218
>3qax_A Probable ABC transporter arginine-binding protein; periplasmic,
transport PR; HET: ARG; 2.00A {Chlamydophila pneumoniae}
PDB: 3g41_A* 3n26_A*
Length = 268
Score = 27.7 bits (62), Expect = 1.8
Identities = 3/19 (15%), Positives = 7/19 (36%)
Query: 132 GNTLLEEKFNEAIKTVKRD 150
+ +AI +K +
Sbjct: 223 DRPEEIQTIQQAITDLKSE 241
>3hv1_A Polar amino acid ABC uptake transporter substrate binding protein;
protein structure initiative II(PSI II), nysgxrc; 1.90A
{Streptococcus thermophilus lmg 18311}
Length = 268
Score = 27.3 bits (61), Expect = 2.0
Identities = 4/19 (21%), Positives = 11/19 (57%)
Query: 132 GNTLLEEKFNEAIKTVKRD 150
+ L +K N+ +T+ ++
Sbjct: 218 VDKTLIKKINQGFETLYKN 236
>2iee_A ORF2, probable ABC transporter extracellular-binding protein YCKB;
SR574, NESG, X-RAY, structural genomics, PSI-2; 2.20A
{Bacillus subtilis}
Length = 271
Score = 26.9 bits (60), Expect = 2.6
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 132 GNTLLEEKFNEAIKTVKRD 150
N L++K NEA+K + +D
Sbjct: 216 SNAALQKKMNEALKEMSKD 234
>3k4u_A Binding component of ABC transporter; structural genomics, protein
structure INI NEW YORK structural genomix research
consortium, nysgxrc; HET: LYS; 2.62A {Wolinella
succinogenes}
Length = 245
Score = 26.9 bits (60), Expect = 2.7
Identities = 4/19 (21%), Positives = 7/19 (36%)
Query: 132 GNTLLEEKFNEAIKTVKRD 150
G+ N + +K D
Sbjct: 198 GDPDFLNWLNHFLAQIKHD 216
>4eq9_A ABC transporter substrate-binding protein-amino A transport;
structural genomics, niaid; HET: GSH; 1.40A
{Streptococcus pneumoniae}
Length = 246
Score = 26.9 bits (60), Expect = 2.9
Identities = 5/19 (26%), Positives = 10/19 (52%)
Query: 132 GNTLLEEKFNEAIKTVKRD 150
G L+ ++ IK + +D
Sbjct: 205 GQDELKSFVDKRIKELYKD 223
>2o1m_A Probable amino-acid ABC transporter extracellular-binding protein
YTMK; NESG X-RAY O34852 YTMK_bacsu, structural genomics,
PSI-2; 2.00A {Bacillus subtilis}
Length = 258
Score = 26.5 bits (59), Expect = 3.5
Identities = 3/19 (15%), Positives = 9/19 (47%)
Query: 132 GNTLLEEKFNEAIKTVKRD 150
L + ++A++ + D
Sbjct: 212 NEQTLSDDIDKALQEIIDD 230
>1h2v_C 80 kDa nuclear CAP binding protein; CAP-binding-complex, RNP
domain, MIF4G domain, RNA maturation, RNA export,
nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP:
a.118.1.14 a.118.1.14 a.118.1.14 PDB: 1n52_A* 1n54_A
3fex_A 3fey_A 1h6k_A 1h2t_C* 1h2u_A*
Length = 771
Score = 26.7 bits (58), Expect = 3.8
Identities = 18/119 (15%), Positives = 39/119 (32%), Gaps = 4/119 (3%)
Query: 37 ELSKSEETVILTINDKLELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGAS- 95
+L++ + + + + IE + E + Q K + + + +
Sbjct: 646 KLARQHKRRSDDDDRSSDRKDGVLEEQIERLQEKVESAQSEQ-KNLFLVIFQRFIMILTE 704
Query: 96 FLKVCS--ITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDIF 152
L C T + C+ RL+++ Q Q + TL F + +F
Sbjct: 705 HLVRCETDGTSVLTPWYKNCIERLQQIFLQHHQIIQQYMVTLENLLFTAELDPHILAVF 763
>2q88_A EHUB, putative ABC transporter amino acid-binding prote;
substrate-binding protein, compatible solues,
ABC-transporte osmoprotection; HET: 4CS; 1.90A
{Sinorhizobium meliloti} PDB: 2q89_A*
Length = 257
Score = 26.5 bits (59), Expect = 4.5
Identities = 4/19 (21%), Positives = 9/19 (47%)
Query: 132 GNTLLEEKFNEAIKTVKRD 150
G+ L + F+ + +K
Sbjct: 210 GDEALRDAFDVELAKLKES 228
>2pvu_A ARTJ; basic amino acid binding protein, ABC transport system, THER
bacterium, transport protein; HET: LYS; 1.79A
{Geobacillus stearothermophilus} PDB: 2q2a_A* 2q2c_A*
Length = 272
Score = 26.1 bits (58), Expect = 5.2
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 133 NTLLEEKFNEAIKTVKRD 150
N+ L+ K +EA+K V
Sbjct: 233 NSELKAKVDEALKNVINS 250
>2pyy_A Ionotropic glutamate receptor bacterial homologue; GLUR0 ligand
binding domain, transport protein; HET: GLU; 2.10A
{Nostoc punctiforme}
Length = 228
Score = 25.7 bits (57), Expect = 7.7
Identities = 4/19 (21%), Positives = 10/19 (52%)
Query: 132 GNTLLEEKFNEAIKTVKRD 150
N+ + N+A+ +K +
Sbjct: 192 NNSPYRKPINQALLNLKEN 210
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
0.322 0.136 0.379
Gapped
Lambda K H
0.267 0.0839 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,430,101
Number of extensions: 138762
Number of successful extensions: 415
Number of sequences better than 10.0: 1
Number of HSP's gapped: 415
Number of HSP's successfully gapped: 49
Length of query: 159
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 73
Effective length of database: 4,300,587
Effective search space: 313942851
Effective search space used: 313942851
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 (21.9 bits)
S2: 53 (24.0 bits)