RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6239
(151 letters)
>1f7u_A Arginyl-tRNA synthetase; RNA-protein complex, aminoacylation; HET:
PSU 1MG 2MG H2U M2G 5MC 5MU 1MA ARG; 2.20A
{Saccharomyces cerevisiae} SCOP: a.27.1.1 c.26.1.1
d.67.2.1 PDB: 1bs2_A* 1f7v_A*
Length = 607
Score = 143 bits (364), Expect = 3e-41
Identities = 53/153 (34%), Positives = 88/153 (57%), Gaps = 2/153 (1%)
Query: 1 MSALIVYNLKIRRLKSYNFNWDECLHMSGDGGVKLQYSHCRLVSLAQECNAIQPPD--HC 58
+SA+++ +++ +R+ +Y F W+ L GD G LQY+H RL S+ + + I +
Sbjct: 455 ISAVMIQDMQGKRINNYEFKWERMLSFEGDTGPYLQYAHSRLRSVERNASGITQEKWINA 514
Query: 59 DPKLLAEPVALQLILDIARFDEVLYQAHESYDSSIVVRYLFNLTNSINKALKQLQVKGTE 118
D LL EP A LI + ++ +VL A ++++ + VV YLF LT+ ++ L V G
Sbjct: 515 DFSLLKEPAAKLLIRLLGQYPDVLRNAIKTHEPTTVVTYLFKLTHQVSSCYDVLWVAGQT 574
Query: 119 YHVSQHRLLLFNKARLVLNQGMCVLGLKPLDKM 151
++ RL L+ AR VL GM +LGL P+++M
Sbjct: 575 EELATARLALYGAARQVLYNGMRLLGLTPVERM 607
>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 = 104 bits (261), Expect = 4e-27
Identities = 33/157 (21%), Positives = 66/157 (42%), Gaps = 6/157 (3%)
Query: 1 MSALIVYNLKIRRLKSYNFNWDECLHMSGDGGVKLQYSHCRLVSL---AQECNAIQPPDH 57
+ A+ +K K F W++ L+ G+ +QY+H R S+ A+E P+
Sbjct: 473 IGAIRYNLIKYSPDKKIIFRWEDVLNFEGESAPYIQYAHARCSSILRKAEEEGIKVDPET 532
Query: 58 CDPK---LLAEPVALQLILDIARFDEVLYQAHESYDSSIVVRYLFNLTNSINKALKQLQV 114
+L++ +++F ++ QA + ++ + L + NK V
Sbjct: 533 LFKNADFTKLSERERELVIMLSKFPRIVEQAGKDVKPHLIAWFANELASLFNKFYMDHPV 592
Query: 115 KGTEYHVSQHRLLLFNKARLVLNQGMCVLGLKPLDKM 151
E V + RLLL VL + ++G++ ++M
Sbjct: 593 LKAEEGVREARLLLVMAVEQVLKNALYLMGIEAPERM 629
>1iq0_A Arginyl-tRNA synthetase; riken structural genomics/proteomics
initiative, RSGI, structural genomics, ligase; 2.30A
{Thermus thermophilus} SCOP: a.27.1.1 c.26.1.1 d.67.2.1
Length = 592
Score = 103 bits (258), Expect = 1e-26
Identities = 39/158 (24%), Positives = 64/158 (40%), Gaps = 11/158 (6%)
Query: 1 MSALIVYNLKIRRLKSYNFNWDECLHMSGDGGVKLQYSHCRLVSLAQECNAIQPPDHCDP 60
+ A+ +K K +F + E L GD G +QY+H R S+ ++ PD
Sbjct: 439 LGAIRFSMVKTEPKKQIDFRYQEALSFEGDTGPYVQYAHARAHSILRKAGEWGAPD---- 494
Query: 61 KLLAEPVALQLILDIARFDEVLYQAHESYDSSIVVRYLFNLTNSINK-------ALKQLQ 113
A P L LD+ F+E + +A E ++ +YL +L S N
Sbjct: 495 LSQATPYERALALDLLDFEEAVLEAAEERTPHVLAQYLLDLAASWNAYYNARENGQPATP 554
Query: 114 VKGTEYHVSQHRLLLFNKARLVLNQGMCVLGLKPLDKM 151
V + + RL L + L G+ +LG+ + M
Sbjct: 555 VLTAPEGLRELRLSLVQSLQRTLATGLDLLGIPAPEVM 592
>3fnr_A Arginyl-tRNA synthetase; transferase, PSI-2, NYSGXRC, struc
genomics, protein structure initiative; 2.20A
{Campylobacter jejuni}
Length = 464
Score = 56.5 bits (137), Expect = 2e-10
Identities = 25/117 (21%), Positives = 48/117 (41%), Gaps = 4/117 (3%)
Query: 36 QYSHCRLVSLAQECN-AIQPPDHCDPKLLAEPVALQLILDIARFDEVLYQAHESYDSSIV 94
Y+H R+ + + I D + L + + L+ + VL A E+ +
Sbjct: 341 NYAHARIHQVFAKAGKKIDDVMKADLQSLNQD-GVNLLFEALNLKAVLNDAFEARALQKI 399
Query: 95 VRYLFNLTNSINKALKQLQVKGTEYHVSQHRLLLFNKARLVLNQGMCVLGLKPLDKM 151
YL NL + +K + +V G+ L LF+ L + ++G++ +KM
Sbjct: 400 PDYLKNLAANFHKFYNENKVVGSA--NENDLLKLFSLVALSIKTAFSLMGIEAKNKM 454
>1air_A Pectate lyase C, PELC; pectate cleavage, pectinolyitc activity,
trans-elimination; 2.20A {Erwinia chrysanthemi} SCOP:
b.80.1.1 PDB: 1o88_A 1o8d_A 1o8e_A 1o8f_A 1o8g_A 1o8h_A
1o8i_A 1o8j_A 1o8k_A 1o8l_A 1o8m_A 1plu_A 2pec_A 2ewe_A*
Length = 353
Score = 28.6 bits (63), Expect = 0.87
Identities = 10/48 (20%), Positives = 18/48 (37%), Gaps = 3/48 (6%)
Query: 5 IVYNLKIRRLKSYNFNWDECLHMSGDGGVKLQYSHCRLVSLAQECNAI 52
+V N++I L + D + D + H L + EC+
Sbjct: 114 VVQNMRIGYLPGGAKDGD---MIRVDDSPNVWVDHNELFAANHECDGT 158
>1mqi_A Glutamate receptor 2; GLUR2, ligand binding core, S1S2, partial
agonist, WILLARDIINES, fluoro-WILLARDIINE, membrane
protein; HET: FWD; 1.35A {Rattus norvegicus} SCOP:
c.94.1.1 PDB: 1ftj_A* 1ftl_A* 1fto_A 1fw0_A* 1m5b_A*
1ftm_A* 1m5c_A* 1mm6_A* 1mm7_A* 1mqg_A* 1m5e_A* 1mqj_A*
1ms7_A* 1mxu_A* 1mxv_A 1mxw_A 1mxx_A 1mxy_A 1mxz_A
1my0_A ...
Length = 263
Score = 27.3 bits (60), Expect = 2.1
Identities = 6/17 (35%), Positives = 11/17 (64%)
Query: 101 LTNSINKALKQLQVKGT 117
L N++N A+ +L +G
Sbjct: 230 LGNAVNLAVLKLNEQGL 246
>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 = 27.5 bits (60), Expect = 2.3
Identities = 21/139 (15%), Positives = 44/139 (31%), Gaps = 30/139 (21%)
Query: 6 VYNLKIRRLKSYNFNWDECLHMSGDGGVK------LQYSHCRLVS-LAQECNAIQPPDHC 58
+ K + W L + V+ L+ ++ L+S + E
Sbjct: 54 IIMSKDAVSGTLRLFW--TLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQR-------- 103
Query: 59 DPKLLAEPVALQLILDIARFDEVLYQAHESYDSSIVVRYLFNLTNSINKALKQLQVKGTE 118
P ++ Q + LY ++ + V R + +AL +L+
Sbjct: 104 QPSMMTRMYIEQR--------DRLYNDNQVFAKYNVSR--LQPYLKLRQALLELRP---A 150
Query: 119 YHVSQHRLLLFNKARLVLN 137
+V +L K + L+
Sbjct: 151 KNVLIDGVLGSGKTWVALD 169
>3g3k_A Glutamate receptor, ionotropic kainate 2; membrane protein, cell
junction, cell membrane, glycoprotein, ION transport,
ionic channel, membrane; HET: GLU IPA; 1.24A {Rattus
norvegicus} PDB: 3g3j_A* 3g3i_A* 2i0b_A* 3g3h_A* 3g3g_A*
3g3f_A* 1s7y_A* 1s9t_A* 1sd3_A* 1tt1_A* 1s50_A* 2xxr_A*
2xxt_A* 2xxx_A* 2xxw_A* 2xxy_A* 2xxu_A* 2xxv_A* 3qxm_A*
2i0c_A* ...
Length = 259
Score = 26.1 bits (57), Expect = 4.6
Identities = 5/17 (29%), Positives = 9/17 (52%)
Query: 101 LTNSINKALKQLQVKGT 117
+ I A+ +LQ +G
Sbjct: 227 YRDKITLAILKLQEQGK 243
>2v3u_A Glutamate receptor delta-2 subunit; postsynaptic membrane,
ionotropic glutamate receptors, transmembrane, membrane
protein; 1.74A {Rattus norvegicus} PDB: 2v3t_A
Length = 265
Score = 26.2 bits (57), Expect = 5.5
Identities = 3/17 (17%), Positives = 8/17 (47%)
Query: 101 LTNSINKALKQLQVKGT 117
+ ++ + +LQ G
Sbjct: 232 YRDVFSQRILELQQSGD 248
>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 = 25.8 bits (57), Expect = 6.1
Identities = 6/17 (35%), Positives = 11/17 (64%)
Query: 101 LTNSINKALKQLQVKGT 117
L +N+ALK++ G+
Sbjct: 220 LQKKMNEALKEMSKDGS 236
>3bv4_A Fructose-bisphosphate aldolase A; lyase, acetylation, glycolysis,
phosphoprotein, schiff base; HET: 13P; 1.70A
{Oryctolagus cuniculus} PDB: 1ado_A* 1ewd_A 1zai_A*
1zah_A* 1zaj_A* 1zal_A 2ot0_A 2ot1_A* 2qut_A 2quv_A
3lge_A 3tu9_A* 3b8d_A 6ald_A* 1ex5_A 1ewe_A 2quu_A
3dfn_A 3dfo_A 3dfp_A ...
Length = 341
Score = 25.8 bits (57), Expect = 7.6
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 102 TNSINKALKQLQVKGTEYHVSQHRLLLF 129
T SI K L+ + + TE + +R LL
Sbjct: 33 TGSIAKRLQSIGTENTEENRRFYRQLLL 60
>3bbn_C Ribosomal protein S3; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 218
Score = 25.6 bits (57), Expect = 7.7
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 59 DPKLLAEPVALQL 71
DP +LAE +A QL
Sbjct: 123 DPNILAEFIAGQL 135
>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 = 25.4 bits (56), Expect = 8.3
Identities = 4/17 (23%), Positives = 9/17 (52%)
Query: 101 LTNSINKALKQLQVKGT 117
+I +A+ L+ +G
Sbjct: 227 EIQTIQQAITDLKSEGV 243
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 0.414
Gapped
Lambda K H
0.267 0.0721 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,280,173
Number of extensions: 123653
Number of successful extensions: 269
Number of sequences better than 10.0: 1
Number of HSP's gapped: 264
Number of HSP's successfully gapped: 15
Length of query: 151
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 66
Effective length of database: 4,328,508
Effective search space: 285681528
Effective search space used: 285681528
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: 53 (24.2 bits)