RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6621
(133 letters)
>4arc_A Leucine--tRNA ligase; ligase-RNA complex, nucleotide-binding,
protein biosynthesis I aminoacyl-tRNA synthetase,
ATP-binding; 2.00A {Escherichia coli} PDB: 4aq7_A
4ari_A* 4as1_A*
Length = 880
Score = 167 bits (426), Expect = 2e-49
Identities = 45/82 (54%), Positives = 56/82 (68%)
Query: 40 VFQPMGWDAFGLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKY 99
V QP+GWDAFGLPAE AA ++ P WT NIA MK+QL+ G ++W ELATC P+Y
Sbjct: 93 VLQPIGWDAFGLPAEGAAVKNNTAPAPWTYDNIAYMKNQLKMLGFGYDWSRELATCTPEY 152
Query: 100 YKWTQALFLDLYHAGLVYRKEV 121
Y+W Q F +LY GLVY+K
Sbjct: 153 YRWEQKFFTELYKKGLVYKKTS 174
>2v0c_A Aminoacyl-tRNA synthetase; ligase, nucleotide-binding, protein
biosynthesis; HET: LMS ANZ; 1.85A {Thermus thermophilus}
PDB: 1h3n_A* 1obc_A* 1obh_A* 2bte_A* 2byt_A 2v0g_A*
Length = 878
Score = 165 bits (420), Expect = 9e-49
Identities = 40/82 (48%), Positives = 56/82 (68%)
Query: 40 VFQPMGWDAFGLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGCKFNWESELATCDPKY 99
V PMGWDAFGLPAENAA + G+ P++WT NI K L+ G ++W+ E+ TC+P+Y
Sbjct: 73 VLHPMGWDAFGLPAENAALKFGVHPKDWTYANIRQAKESLRLMGILYDWDREVTTCEPEY 132
Query: 100 YKWTQALFLDLYHAGLVYRKEV 121
Y+W Q +FL ++ GL YR +
Sbjct: 133 YRWNQWIFLKMWEKGLAYRAKG 154
>1wkb_A Leucyl-tRNA synthetase; leucine, aminoacyl-tRNA, editing, amino
acid, aminoacylation, trnaLeu, structural genomics;
2.05A {Pyrococcus horikoshii}
Length = 810
Score = 101 bits (253), Expect = 3e-26
Identities = 20/114 (17%), Positives = 29/114 (25%), Gaps = 28/114 (24%)
Query: 39 RVFQPMGWDAFGLPAENAAHQ------------------------HGIDPREWTVGNIAT 74
V PM W G P A + DP +
Sbjct: 73 NVLFPMAWHITGSPIVGIAERIKNRDPKTIWIYRDVYKVPEEILWTFEDPINIVKYFMKA 132
Query: 75 MKSQLQGFGCKFNWESELATCD--PKYYKWTQALFLDLYHAGLVYRKE--VDYS 124
K G +W E T P + K+ + F L G + + V +
Sbjct: 133 AKETFIRAGFSVDWSREFYTTSLFPPFSKFIEWQFWKLKEKGYIVKGAHRVRWD 186
>1wz2_A Leucyl-tRNA synthetase; ligase, riken structural
genomics/proteomics initiativ structural genomics,
ligase-RNA complex; 3.21A {Pyrococcus horikoshii}
Length = 967
Score = 96.6 bits (240), Expect = 1e-24
Identities = 19/108 (17%), Positives = 27/108 (25%), Gaps = 26/108 (24%)
Query: 39 RVFQPMGWDAFGLPAENAAHQ------------------------HGIDPREWTVGNIAT 74
V PM W G P A + DP +
Sbjct: 73 NVLFPMAWHITGSPIVGIAERIKNRDPKTIWIYRDVYKVPEEILWTFEDPINIVKYFMKA 132
Query: 75 MKSQLQGFGCKFNWESELATCD--PKYYKWTQALFLDLYHAGLVYRKE 120
K G +W E T P + K+ + F L G + +
Sbjct: 133 AKETFIRAGFSVDWSREFYTTSLFPPFSKFIEWQFWKLKEKGYIVKGA 180
>1rqg_A Methionyl-tRNA synthetase; translation, dimerization, ligase; 2.90A
{Pyrococcus abyssi} SCOP: a.27.1.1 c.26.1.1 g.41.1.1
Length = 722
Score = 44.3 bits (105), Expect = 3e-06
Identities = 22/79 (27%), Positives = 29/79 (36%), Gaps = 4/79 (5%)
Query: 45 GWDAFGLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGCKF-NWESELATCDPKYYKWT 103
G D G P A + G PRE +K Q F + T P +YK +
Sbjct: 48 GTDEHGTPISFRALKEGRSPREIVDEFHEQIKITFQRAKISFDFFGR---TELPIHYKLS 104
Query: 104 QALFLDLYHAGLVYRKEVD 122
Q FL Y G + +K
Sbjct: 105 QEFFLKAYENGHLVKKVTK 123
>3h99_A Methionyl-tRNA synthetase; rossmann fold, aminoacyl-tRNA
synthetase, ATP-binding, ligas binding,
nucleotide-binding, protein biosynthesis; HET: CIT;
1.40A {Escherichia coli} PDB: 3h97_A* 3h9b_A* 1f4l_A
3h9c_A* 1pfv_A* 1pfu_A 1p7p_A* 1pfw_A* 1pfy_A* 1pg0_A*
1pg2_A* 1qqt_A 1mea_A 1med_A
Length = 560
Score = 43.0 bits (102), Expect = 8e-06
Identities = 16/77 (20%), Positives = 30/77 (38%), Gaps = 4/77 (5%)
Query: 47 DAFGLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGCKF-NWESELATCDPKYYKWTQA 105
DA G P A Q GI P + ++ GF + N+ S T + + ++
Sbjct: 65 DAHGTPIMLKAQQLGITPEQMIGEMSQEHQTDFAGFNISYDNYHS---THSEENRQLSEL 121
Query: 106 LFLDLYHAGLVYRKEVD 122
++ L G + + +
Sbjct: 122 IYSRLKENGFIKNRTIS 138
>3tun_A Methionyl-tRNA synthetase; aminoacyl-tRNA synthetase, AARS, metrs,
parasite, protein-IN complex, translation, nucleotide
binding; HET: C13; 2.55A {Trypanosoma brucei}
Length = 542
Score = 37.7 bits (87), Expect = 5e-04
Identities = 14/85 (16%), Positives = 26/85 (30%), Gaps = 10/85 (11%)
Query: 44 MGWDAF--------GLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGCKFNWESELATC 95
G F G AA Q + P ++T K + + + T
Sbjct: 45 KGERVFALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKXFEQMDYSID--YFIRTT 102
Query: 96 DPKYYKWTQALFLDLYHAGLVYRKE 120
+ ++ + L+ L G +Y
Sbjct: 103 NEQHKAVVKELWTKLEQKGDIYLGR 127
>1gax_A Valrs, valyl-tRNA synthetase; protein-RNA complex, rossmann fold,
coiled coil, riken structural genomics/proteomics
initiative, RSGI; HET: VAA; 2.90A {Thermus thermophilus}
SCOP: a.2.7.3 a.27.1.1 b.51.1.1 c.26.1.1 PDB: 1ivs_A*
1iyw_A
Length = 862
Score = 35.6 bits (83), Expect = 0.003
Identities = 22/85 (25%), Positives = 30/85 (35%), Gaps = 18/85 (21%)
Query: 66 EWTVGNIATMKSQLQGFGCKFNWESELATCDPKYYKWTQALFLDLYHAGLVYR------- 118
+W + T+ QL+ G +W E T D K + + F YH GL YR
Sbjct: 116 QWKEESGGTILKQLKRLGASADWSREAFTMDEKRSRAVRYAFSRYYHEGLAYRAPRLVNW 175
Query: 119 ----------KEVDYSQNLPTKFYH 133
EV+ P K Y
Sbjct: 176 CPRCETTLSDLEVETEPT-PGKLYT 199
>2d5b_A Methionyl-tRNA synthetase; rossmann fold, class 1A AARS, isomerase,
structural genomics, NPPSFA; 1.80A {Thermus
thermophilus} SCOP: a.27.1.1 c.26.1.1 PDB: 1woy_A 1a8h_A
2d54_A
Length = 500
Score = 33.0 bits (76), Expect = 0.021
Identities = 19/88 (21%), Positives = 29/88 (32%), Gaps = 16/88 (18%)
Query: 44 MGWDAF--------GLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGC---KFNWESEL 92
G+ F G AA G DP+ + K G F +
Sbjct: 39 DGYRTFFLTGTDEHGETVYRAAQAAGEDPKAFVDRVSGRFKRAWDLLGIAYDDF-----I 93
Query: 93 ATCDPKYYKWTQALFLDLYHAGLVYRKE 120
T + ++ K Q + +Y AG +Y E
Sbjct: 94 RTTEERHKKVVQLVLKKVYEAGDIYYGE 121
>4dlp_A Aminoacyl-tRNA synthetase, class I:aminoacyl-tRNA synthetase, class
IA:methionyl-tRNA...; structural genomics; 2.65A
{Brucella melitensis biovar abortus 230ORGANISM_TAXID}
Length = 536
Score = 32.2 bits (74), Expect = 0.033
Identities = 16/88 (18%), Positives = 35/88 (39%), Gaps = 16/88 (18%)
Query: 44 MGWDAF--------GLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGC---KFNWESEL 92
G D + G+ +A + GI PR+ N + + + + +
Sbjct: 61 NGMDVYFLTGTDEHGIKMLQSARKEGITPRDLADRNTSAFRRMAEVLNSSNDDY-----I 115
Query: 93 ATCDPKYYKWTQALFLDLYHAGLVYRKE 120
T + ++YK +QA++ + G +Y+
Sbjct: 116 RTSEERHYKASQAIWQAMVANGDIYKGG 143
>2csx_A Methionyl-tRNA synthetase; ligase, riken structural
genomics/proteomics initiative, RSGI, structural
genomics, ligase/RNA complex; 2.70A {Aquifex aeolicus}
PDB: 2ct8_A*
Length = 497
Score = 32.2 bits (74), Expect = 0.039
Identities = 23/88 (26%), Positives = 34/88 (38%), Gaps = 16/88 (18%)
Query: 44 MGWDAF--------GLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGC---KFNWESEL 92
+D F GL + A + GI P+E N K + KF +
Sbjct: 41 RDYDVFFLTGTDEHGLKIQKKAEELGISPKELVDRNAERFKKLWEFLKIEYTKF-----I 95
Query: 93 ATCDPKYYKWTQALFLDLYHAGLVYRKE 120
T DP + K+ Q +F + Y G +Y E
Sbjct: 96 RTTDPYHVKFVQKVFEECYKRGDIYLGE 123
>2x1l_A Methionyl-tRNA synthetase; nucleotide-binding, protein
biosynthesis, ligase, aminoacyl- synthetase; HET: ADN
CXS; 2.30A {Mycobacterium smegmatis} PDB: 2x1m_A*
Length = 524
Score = 32.2 bits (74), Expect = 0.040
Identities = 16/88 (18%), Positives = 30/88 (34%), Gaps = 16/88 (18%)
Query: 44 MGWDAF--------GLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGC---KFNWESEL 92
G+D G A + GI E N + + +F +
Sbjct: 48 DGYDVRYLTGTDVHGQKMAETAAKEGIPAAELARRNSDVFQRLQEKLNISFDRF-----I 102
Query: 93 ATCDPKYYKWTQALFLDLYHAGLVYRKE 120
T D +Y+ ++A++ + AG +Y
Sbjct: 103 RTSDADHYEASKAIWKRMADAGDIYLDA 130
>3kfl_A Methionyl-tRNA synthetase; parasite, aminoacyl-tRNA synthetase,
tRNA ligase metrs, methionine, translation, ATP-binding;
HET: ME8; 2.00A {Leishmania major}
Length = 564
Score = 30.7 bits (70), Expect = 0.10
Identities = 18/88 (20%), Positives = 31/88 (35%), Gaps = 16/88 (18%)
Query: 44 MGWDAF--------GLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGC---KFNWESEL 92
G + F G AA + G+ P ++T + K Q F +
Sbjct: 62 KGEEVFVMTGTDEHGQKVAEAAAKQGVSPMDFTTSVSSEFKQCFQEMNYDMNYF-----I 116
Query: 93 ATCDPKYYKWTQALFLDLYHAGLVYRKE 120
T +P + K Q ++ L G +Y +
Sbjct: 117 RTTNPTHEKLVQDIWKKLAAKGDIYLGK 144
>1ffy_A Isoleucyl-tRNA synthetase; protein-RNA complex, metal IONS, editing
tRNA synthetase, double-sieve, ligase/RNA, mupiroci;
HET: MRC; 2.20A {Staphylococcus aureus} SCOP: a.27.1.1
b.51.1.1 c.26.1.1 PDB: 1qu2_A* 1qu3_A*
Length = 917
Score = 30.6 bits (70), Expect = 0.13
Identities = 21/86 (24%), Positives = 36/86 (41%), Gaps = 12/86 (13%)
Query: 45 GWDAFGLPAENAAHQHGIDP------------REWTVGNIATMKSQLQGFGCKFNWESEL 92
GWD GLP E A + G+D +E+ + I K + G + ++
Sbjct: 93 GWDTHGLPIEQALTKKGVDRKKMSTAEFREKCKEFALEQIELQKKDFRRLGVRGDFNDPY 152
Query: 93 ATCDPKYYKWTQALFLDLYHAGLVYR 118
T P+Y +F ++ GL+Y+
Sbjct: 153 ITLKPEYEAAQIRIFGEMADKGLIYK 178
>3a9s_A D-arabinose isomerase; rossmann fold, beta barrel, carbohydrate
metabolism, cytoplasm, fucose metabolism, manganese,
metal- binding; 1.60A {Geobacillus pallidus} PDB: 3a9r_A
3a9t_A*
Length = 595
Score = 30.2 bits (67), Expect = 0.17
Identities = 10/50 (20%), Positives = 17/50 (34%), Gaps = 6/50 (12%)
Query: 14 GVVVKTHSGAE----CRLAGINSIIKGP--VRVFQPMGWDAFGLPAENAA 57
+ H GA+ + I + ++F+P W FG A
Sbjct: 533 CSISYGHIGADLITLASILRIPVNMHNVPEEKIFRPDAWSMFGTKDLEGA 582
>1fui_A L-fucose isomerase; ketol isomerase, fucose metabolism, L-fucose to
L conversion; HET: FOC; 2.50A {Escherichia coli} SCOP:
b.43.2.1 c.85.1.1
Length = 591
Score = 28.6 bits (63), Expect = 0.65
Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 10/51 (19%)
Query: 14 GVVVKTHSGAECRLAGINSIIKGPV--------RVFQPMGWDAFGLPAENA 56
GV+ H GA+ + S+++ PV +V++P W A G+ E
Sbjct: 529 GVLTIGHVGAD--FITLASMLRIPVCMHNVEETKVYRPSAWAAHGMDIEGQ 577
>1ile_A Ilers, isoleucyl-tRNA synthetase; aminoacyl-tRNA synthetase, riken
structural genomics/proteom initiative, RSGI, structural
genomics; 2.50A {Thermus thermophilus} SCOP: a.27.1.1
b.51.1.1 c.26.1.1 PDB: 1jzq_A* 1jzs_A*
Length = 821
Score = 28.3 bits (64), Expect = 0.91
Identities = 23/100 (23%), Positives = 34/100 (34%), Gaps = 26/100 (26%)
Query: 39 RVFQPMGWDAFGLPAENAA------------HQHGIDP-----REWTVGNIATMKSQLQG 81
R GWD GLP E +GI+ RE ++ +
Sbjct: 80 RRA---GWDTHGLPVELEVEKKLGLKSKREIEAYGIERFNQACRESVFTYEKEWEAFTER 136
Query: 82 FGCKFNWESELATCDPKYYK---WTQALFLDLYHAGLVYR 118
+ E AT +P Y + W +L+ GL+YR
Sbjct: 137 IAYWVDLEDAYATLEPTYIESIWW---SLKNLFDRGLLYR 173
>4dd5_A Acetyl-COA acetyltransferase; structural genomics, center for
structural genomics of infec diseases, csgid, thiolase;
1.25A {Clostridium difficile}
Length = 396
Score = 26.6 bits (60), Expect = 2.7
Identities = 11/26 (42%), Positives = 12/26 (46%), Gaps = 6/26 (23%)
Query: 46 WDAF-----GLPAENAAHQHGIDPRE 66
D F G+ AEN A Q I RE
Sbjct: 154 SDIFNNYHMGITAENIAEQWNIT-RE 178
>4e1l_A Acetoacetyl-COA thiolase 2; 3-layer(ABA) sandwich, transferase;
2.00A {Clostridium difficile}
Length = 395
Score = 26.6 bits (60), Expect = 2.7
Identities = 10/26 (38%), Positives = 12/26 (46%), Gaps = 6/26 (23%)
Query: 46 WDAF-----GLPAENAAHQHGIDPRE 66
DAF G+ AEN A + RE
Sbjct: 152 IDAFNQYHMGITAENIATKFEFT-RE 176
>1zcc_A Glycerophosphodiester phosphodiesterase; NYSGXRC, agrobacterium
tumefaciens STR. C58, structural genomics; 2.50A
{Agrobacterium tumefaciens str} SCOP: c.1.18.3
Length = 248
Score = 26.5 bits (59), Expect = 3.1
Identities = 3/29 (10%), Positives = 12/29 (41%)
Query: 56 AAHQHGIDPREWTVGNIATMKSQLQGFGC 84
A+ + G++ + G+ + ++
Sbjct: 189 ASRKAGLEIMVYYGGDDMAVHREIATSDV 217
>2ib8_A Acetyl-COA acetyltransferase; thiolase fold, potassium ION,
chloride, beta-alpha-beta-ALPH alpha-beta-BETA topology;
HET: MES; 1.85A {Homo sapiens} PDB: 2ib7_A* 2ib9_A*
2ibu_A* 2ibw_A* 2iby_A* 2f2s_A*
Length = 395
Score = 26.3 bits (59), Expect = 3.2
Identities = 8/26 (30%), Positives = 10/26 (38%), Gaps = 6/26 (23%)
Query: 46 WDAF-----GLPAENAAHQHGIDPRE 66
D + G AEN A + I R
Sbjct: 153 TDVYNKIHMGSCAENTAKKLNIA-RN 177
>3ss6_A Acetyl-COA acetyltransferase; structural genomics, csgid, center
for structural genomics O infectious diseases, alpha
beta; HET: CSO; 1.70A {Bacillus anthracis}
Length = 394
Score = 26.3 bits (59), Expect = 3.2
Identities = 9/26 (34%), Positives = 10/26 (38%), Gaps = 6/26 (23%)
Query: 46 WDAF-----GLPAENAAHQHGIDPRE 66
D G AEN Q+ I RE
Sbjct: 151 EDPIHHIMMGETAENLVEQYEIT-RE 175
>2vu1_A Acetyl-COA acetyltransferase; acyltransferase, PHB biosynthesis,
thiolase FOL; HET: CSO OPI; 1.51A {Zoogloea ramigera}
PDB: 1nl7_A* 1ou6_A* 2vu0_A* 1m4s_A* 2vu2_A* 2wkv_A*
2wku_A* 1m1t_A 1m3k_A 1m1o_A 1m3z_A* 2vtz_A* 2wl5_A*
2wkt_A* 2wl4_A* 1m4t_A* 2wl6_A 1qfl_A* 1dlv_A* 1dlu_A*
...
Length = 392
Score = 26.3 bits (59), Expect = 3.3
Identities = 10/26 (38%), Positives = 12/26 (46%), Gaps = 6/26 (23%)
Query: 46 WDAF-----GLPAENAAHQHGIDPRE 66
DAF G AEN A Q + R+
Sbjct: 149 TDAFYGYHMGTTAENVAKQWQLS-RD 173
>3bbo_6 Ribosomal protein L36; large ribosomal subunit, spinach
chloroplast ribosome, ribonucleoprotein particle,
macromolecular complex; 9.40A {Spinacea oleracea} SCOP:
i.1.1.1
Length = 104
Score = 25.1 bits (54), Expect = 4.7
Identities = 8/45 (17%), Positives = 16/45 (35%)
Query: 50 GLPAENAAHQHGIDPREWTVGNIATMKSQLQGFGCKFNWESELAT 94
A+ + P + +A++ + F W S LA+
Sbjct: 53 LFAEPIASQELVRLPGQGVSAGLASLLHKRPMPTAYFGWRSGLAS 97
>1ulq_A Putative acetyl-COA acetyltransferase; structural genomics, riken
structural genomics/proteomics initiative, RSGI; 3.00A
{Thermus thermophilus} SCOP: c.95.1.1 c.95.1.1
Length = 401
Score = 25.1 bits (56), Expect = 8.1
Identities = 11/33 (33%), Positives = 13/33 (39%), Gaps = 6/33 (18%)
Query: 39 RVFQPMGWDAF-----GLPAENAAHQHGIDPRE 66
R P + G AEN A +GI RE
Sbjct: 148 RFVNPKMQALYGTESMGETAENLAEMYGIR-RE 179
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
0.321 0.137 0.456
Gapped
Lambda K H
0.267 0.0864 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,198,613
Number of extensions: 119995
Number of successful extensions: 239
Number of sequences better than 10.0: 1
Number of HSP's gapped: 234
Number of HSP's successfully gapped: 28
Length of query: 133
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 50
Effective length of database: 4,384,350
Effective search space: 219217500
Effective search space used: 219217500
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: 52 (23.6 bits)