RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10035
(102 letters)
>3vbb_A Seryl-tRNA synthetase, cytoplasmic; coiled-coil, ligase; 2.89A
{Homo sapiens}
Length = 522
Score = 100 bits (250), Expect = 2e-26
Identities = 51/86 (59%), Positives = 66/86 (76%)
Query: 1 MVLDLDLFRTEKGGDPEKVRKNQKDRFKNVELVDKVIENDLKWRQFRHKADNFNKFKNLC 60
MVLDLDLFR +KGGDP +R+ Q+ RFK+ LVD++++ D +WR+ R +ADN NK KNLC
Sbjct: 1 MVLDLDLFRVDKGGDPALIRETQEKRFKDPGLVDQLVKADSEWRRCRFRADNLNKLKNLC 60
Query: 61 SKVIGEKMKAKEPVGDSSTLPGETLN 86
SK IGEKMK KEPVGD ++P L+
Sbjct: 61 SKTIGEKMKKKEPVGDDESVPENVLS 86
>3lss_A Seryl-tRNA synthetase; aminoacyl-tRNA synthetase, tRNA ligase,
AARS, serrs, translation, ATP-binding,
nucleotide-binding, structural genomics; HET: ATP;
1.95A {Trypanosoma brucei} PDB: 3lsq_A*
Length = 484
Score = 92.8 bits (231), Expect = 8e-24
Identities = 36/88 (40%), Positives = 53/88 (60%), Gaps = 2/88 (2%)
Query: 1 MVLDLDLFRTEKGGDPEKVRKNQKDRFKNVELVDKVIENDLKWRQFRHKADNFNKFKNLC 60
MVLD+ LFR E G +R++Q+ RF + ++VD +IE D KWR+ + + K N+C
Sbjct: 6 MVLDIQLFRDETG--ANIIRESQRRRFADPDIVDAIIEADKKWRRTQFLTEASKKLINIC 63
Query: 61 SKVIGEKMKAKEPVGDSSTLPGETLNVC 88
SK +G K KAKE GD+S +P +
Sbjct: 64 SKAVGAKKKAKEADGDTSEIPPQVKEAY 91
>3qne_A Seryl-tRNA synthetase, cytoplasmic; amino acid biosynthesis,
CTG-clade, codon ambiguity, pathoge II aminoacyl-tRNA
synthetase family; 2.00A {Candida albicans} PDB:
3qo7_A* 3qo8_A* 3qo5_A
Length = 485
Score = 90.8 bits (226), Expect = 4e-23
Identities = 33/75 (44%), Positives = 46/75 (61%)
Query: 2 VLDLDLFRTEKGGDPEKVRKNQKDRFKNVELVDKVIENDLKWRQFRHKADNFNKFKNLCS 61
+LD++ F EKGGDPE ++ +QK R +VELVD++I +W + R D NK N
Sbjct: 1 MLDINAFLVEKGGDPEIIKASQKKRGDSVELVDEIIAEYKEWVKLRFDLDEHNKKLNSVQ 60
Query: 62 KVIGEKMKAKEPVGD 76
K IG++ KAKE D
Sbjct: 61 KEIGKRFKAKEDAKD 75
>2dq0_A Seryl-tRNA synthetase; coiled-coil, homodimer, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; HET: SSA; 2.60A
{Pyrococcus horikoshii} PDB: 2dq1_A* 2dq2_A 2zr2_A*
2zr3_A
Length = 455
Score = 52.2 bits (126), Expect = 1e-09
Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 6/72 (8%)
Query: 3 LDLDLFRTEKGGDPEKVRKNQKDRFK--NVELVDKVIENDLKWRQFRHKADNFNKFKNLC 60
LD+ L R +PE V+ + R + V+ VD++++ D +WR + + +N
Sbjct: 2 LDIKLIRE----NPELVKNDLIKRGELEKVKWVDEILKLDTEWRTKLKEINRLRHERNKI 57
Query: 61 SKVIGEKMKAKE 72
+ IG++ K E
Sbjct: 58 AVEIGKRRKKGE 69
>1wle_A Seryl-tRNA synthetase; ligase; HET: SRP; 1.65A {Bos taurus}
Length = 501
Score = 46.9 bits (112), Expect = 1e-07
Identities = 11/85 (12%), Positives = 30/85 (35%), Gaps = 6/85 (7%)
Query: 3 LDLDLFRTEKGGDPEKVRKNQKDRFKNV--ELVDKVIENDLKWRQFRHKADNFNKFKNLC 60
LD++ PE + R + + + +I + RQ R + + + K
Sbjct: 41 LDMESLCA----YPEDAARALDLRKGELRSKDLPGIISTWQELRQLREQIRSLEEEKEAV 96
Query: 61 SKVIGEKMKAKEPVGDSSTLPGETL 85
++ + + ++ ++L
Sbjct: 97 TEAVRALVVNQDNSQVQQDPQYQSL 121
>2dq3_A Seryl-tRNA synthetase; coiled-coil, homodimer, structural
genomics, NPPSFA, nationa on protein structural and
functional analyses; HET: SSA; 3.00A {Aquifex aeolicus}
Length = 425
Score = 43.3 bits (103), Expect = 2e-06
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 3 LDLDLFRTEKGGDPEKVRKNQKDR-FKNVELVDKVIENDLKWRQFRHKADNFNKFKNLCS 61
+D++L R P+ V++ R + V LVDKV+E D + R+ + + +N S
Sbjct: 2 IDINLIRE----KPDYVKERLATRDKELVSLVDKVLELDKRRREIIKRLEALRSERNKLS 57
Query: 62 KVIGEKMKAKE 72
K IG+ + +
Sbjct: 58 KEIGKLKREGK 68
>1ses_A Seryl-tRNA synthetase; ligase; HET: AHX AMP; 2.50A {Thermus
thermophilus} SCOP: a.2.7.1 d.104.1.1 PDB: 1ser_A*
1set_A* 1sry_A
Length = 421
Score = 39.4 bits (93), Expect = 5e-05
Identities = 9/69 (13%), Positives = 30/69 (43%), Gaps = 5/69 (7%)
Query: 3 LDLDLFRTEKGGDPEKVRKNQKDRFKNVELVDKVIENDLKWRQFRHKADNFNKFKNLCSK 62
+DL R +PE + +++ ++L + ++ D + ++ + + +N +K
Sbjct: 2 VDLKRLRQ----EPEVFHRAIREKGVALDL-EALLALDREVQELKKRLQEVQTERNQVAK 56
Query: 63 VIGEKMKAK 71
+ + +
Sbjct: 57 RVPKAPPEE 65
>3err_A Fusion protein of microtubule binding domain from mouse cytoplasmic
dynein and seryl-tRNA...; coiled coil, ligase; HET: AMP;
2.27A {Mus musculus}
Length = 536
Score = 30.8 bits (70), Expect = 0.048
Identities = 14/87 (16%), Positives = 27/87 (31%), Gaps = 12/87 (13%)
Query: 1 MVLDLDLFRTEKGGDPEKVRKNQKDR-FKNV------ELVDKVIENDLKWRQFRHKADNF 53
+ L L T D +++R F E + I +K + + N+
Sbjct: 97 IALLLGESTT----DWKQIRSIIMRENFIPTIVNFSAEEISDAIREKMKKNYMSNPSYNY 152
Query: 54 NKFKNLCSKVIGEKMKAKEPVGDSSTL 80
N S G +K + + +
Sbjct: 153 EI-VNRASLAAGPMVKWAIAQLNYADM 178
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 28.2 bits (62), Expect = 0.40
Identities = 12/61 (19%), Positives = 32/61 (52%), Gaps = 10/61 (16%)
Query: 15 DPEKVRKNQKDRFKNVELVDKVIENDL-KWR-QFRHKADNFNKFKNLCSKVIGEKM-KAK 71
+PE +RK ++++ K ++ +D + +WR + + + +N+ ++ E++ K K
Sbjct: 83 EPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQS-------EQVEKNK 135
Query: 72 E 72
Sbjct: 136 I 136
>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 = 0.89
Identities = 21/99 (21%), Positives = 35/99 (35%), Gaps = 32/99 (32%)
Query: 6 DLFRTEKGGDP-------EKVR--KNQKDRFKNVEL--VDKVIE---NDLKWRQFRHKAD 51
DL R +P E +R D +K+V + +IE N L+ ++R D
Sbjct: 317 DLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFD 376
Query: 52 NFNKFKNLCSKVIGEKMKAKEPVGDSSTLPGETLNVCWS 90
+ F P S+ +P L++ W
Sbjct: 377 RLSVF----------------P--PSAHIPTILLSLIWF 397
>3seb_A SEB, staphylococcal enterotoxin B; superantigen; 1.48A
{Staphylococcus aureus} SCOP: b.40.2.2 d.15.6.1 PDB:
1se4_A* 1d5x_C* 1d5z_C* 1d6e_C* 1sbb_B 1se3_A* 1d5m_C*
2seb_D* 3r8b_A 1goz_A 3gp7_A 1seb_D
Length = 238
Score = 25.9 bits (56), Expect = 2.8
Identities = 11/47 (23%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 27 FKNVELVDKVIENDLKWRQFRHKADNFNKFK-NLCSKVIGEKMKAKE 72
NV+ +D+ + DL + K N++ + +K + +K K K
Sbjct: 35 AINVKSIDQFLYFDLIYSIKDTKLGNYDNVRVEFKNKDLADKYKDKY 81
>2cxi_A Phenylalanyl-tRNA synthetase beta chain; aminoacyl-tRNA synthetase,
ligase, structural genomics; HET: MSE; 1.94A {Pyrococcus
horikoshii}
Length = 348
Score = 25.3 bits (55), Expect = 5.2
Identities = 13/78 (16%), Positives = 24/78 (30%), Gaps = 8/78 (10%)
Query: 4 DLDLFRTEKGGDPEKVRK-------NQKDRFKNVELVDKVIENDLKWRQFRHKADNFNKF 56
++F G EKV +R + V +V+ D + F
Sbjct: 228 TKNVFIDVTGWKLEKVMLALNVMVTALAERGGKIRSV-RVVYKDFEIETPDLTPKEFEVE 286
Query: 57 KNLCSKVIGEKMKAKEPV 74
+ K+ G ++ E
Sbjct: 287 LDYIRKLSGLELNDGEIK 304
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
0.317 0.135 0.405
Gapped
Lambda K H
0.267 0.0600 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,503,829
Number of extensions: 74092
Number of successful extensions: 164
Number of sequences better than 10.0: 1
Number of HSP's gapped: 162
Number of HSP's successfully gapped: 25
Length of query: 102
Length of database: 6,701,793
Length adjustment: 67
Effective length of query: 35
Effective length of database: 4,831,086
Effective search space: 169088010
Effective search space used: 169088010
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (23.7 bits)