RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10664
(75 letters)
>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 = 111 bits (279), Expect = 6e-31
Identities = 39/74 (52%), Positives = 45/74 (60%)
Query: 1 MIDGVDSEAGAIVAGGRGYFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQ 60
+DG D E G + G RGYFL+ V L L+ Y LS KGY PL P M KEVM
Sbjct: 160 RLDGYDPERGVRIVGHRGYFLRNYGVFLNQALINYGLSFLSSKGYVPLQAPVMMNKEVMA 219
Query: 61 EVAQLAQFDEELYK 74
+ AQL+QFDEELYK
Sbjct: 220 KTAQLSQFDEELYK 233
>3vbb_A Seryl-tRNA synthetase, cytoplasmic; coiled-coil, ligase; 2.89A
{Homo sapiens}
Length = 522
Score = 110 bits (277), Expect = 1e-30
Identities = 51/75 (68%), Positives = 60/75 (80%)
Query: 1 MIDGVDSEAGAIVAGGRGYFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQ 60
M+DG + E GA+VAG RGYFLKG V L+ L+QYAL +GY P+YTPFFMRKEVMQ
Sbjct: 176 MVDGFEGEKGAVVAGSRGYFLKGVLVFLEQALIQYALRTLGSRGYIPIYTPFFMRKEVMQ 235
Query: 61 EVAQLAQFDEELYKM 75
EVAQL+QFDEELYK+
Sbjct: 236 EVAQLSQFDEELYKV 250
>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 = 103 bits (258), Expect = 5e-28
Identities = 40/75 (53%), Positives = 53/75 (70%), Gaps = 1/75 (1%)
Query: 1 MIDGVDSE-AGAIVAGGRGYFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVM 59
+ +D+ A +AGGR Y LKG V LQV LV Y+L +++GYTP Y PFF+ ++VM
Sbjct: 182 RLGMMDTSKAVTSMAGGRSYVLKGGLVQLQVALVSYSLDFLVKRGYTPFYPPFFLNRDVM 241
Query: 60 QEVAQLAQFDEELYK 74
EVAQL+QFDEELY+
Sbjct: 242 GEVAQLSQFDEELYQ 256
>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 = 81.9 bits (203), Expect = 2e-20
Identities = 25/73 (34%), Positives = 42/73 (57%)
Query: 3 DGVDSEAGAIVAGGRGYFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQEV 62
G D A V+G R Y+L V L + L+++AL + IEKG+TP+ P+ +R+ V +
Sbjct: 170 GGADFARAAKVSGSRFYYLLNEIVILDLALIRFALDRLIEKGFTPVIPPYMVRRFVEEGS 229
Query: 63 AQLAQFDEELYKM 75
F++ +YK+
Sbjct: 230 TSFEDFEDVIYKV 242
>1wle_A Seryl-tRNA synthetase; ligase; HET: SRP; 1.65A {Bos taurus}
Length = 501
Score = 71.5 bits (176), Expect = 1e-16
Identities = 21/72 (29%), Positives = 34/72 (47%)
Query: 3 DGVDSEAGAIVAGGRGYFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQEV 62
D + + + V+G R Y+L+G LQ GLV + L+K I +G+TP+ P +R V +
Sbjct: 196 DIIRQKRLSHVSGHRSYYLRGAGALLQHGLVNFTLNKLIHRGFTPMTVPDLLRGVVFEGC 255
Query: 63 AQLAQFDEELYK 74
Sbjct: 256 GMTPNAKPSQIY 267
>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 = 68.3 bits (168), Expect = 1e-15
Identities = 14/72 (19%), Positives = 34/72 (47%)
Query: 4 GVDSEAGAIVAGGRGYFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQEVA 63
G + V+G R Y LKG ++ L+++A+ +G+ P+ P + R++
Sbjct: 144 GWWEPRISQVSGSRSYALKGDLALYELALLRFAMDFMARRGFLPMTLPSYAREKAFLGTG 203
Query: 64 QLAQFDEELYKM 75
+ ++++ +
Sbjct: 204 HFPAYRDQVWAI 215
>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 = 68.2 bits (167), Expect = 2e-15
Identities = 14/72 (19%), Positives = 34/72 (47%)
Query: 4 GVDSEAGAIVAGGRGYFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQEVA 63
G + V+G R Y LKG ++ L+++A+ +G+ P+ P + R++
Sbjct: 253 GWWEPRISQVSGSRSYALKGDLALYELALLRFAMDFMARRGFLPMTLPSYAREKAFLGTG 312
Query: 64 QLAQFDEELYKM 75
+ ++++ +
Sbjct: 313 HFPAYRDQVWAI 324
>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 = 56.4 bits (137), Expect = 2e-11
Identities = 21/73 (28%), Positives = 38/73 (52%)
Query: 3 DGVDSEAGAIVAGGRGYFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQEV 62
+D + GA ++G R + G L+ L+ + L +KGY + P ++ E++
Sbjct: 149 GILDFKRGAKLSGSRFTVIAGWGARLERALINFMLDLHTKKGYKEICPPHLVKPEILIGT 208
Query: 63 AQLAQFDEELYKM 75
QL +F+E+LYK
Sbjct: 209 GQLPKFEEDLYKC 221
>3mf2_A BLL0957 protein; aminoacyl-tRNA synthetase, seryl-tRNA synthetase,
zinc ION, amino acid:[carrier protein] ligase; HET: AMP;
2.15A {Bradyrhizobium japonicum} PDB: 3mey_A* 3mf1_A*
3pzc_A*
Length = 346
Score = 47.3 bits (112), Expect = 3e-08
Identities = 11/66 (16%), Positives = 21/66 (31%)
Query: 8 EAGAIVAGGRGYFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQEVAQLAQ 67
+ G G + + V + ++ E G L P M + +++ L
Sbjct: 45 DKLFHSMGSDGVYARTALYESIVERLAALITSHREAGTEALRFPPVMSRAQLEKSGYLKS 104
Query: 68 FDEELY 73
F L
Sbjct: 105 FPNLLG 110
>2cja_A Seryl-tRNA synthetase; ligase, zinc ION; HET: MSE ATP; 2.2A
{Methanosarcina barkeri} PDB: 2cim_A* 2cj9_A* 2cjb_A
Length = 522
Score = 45.9 bits (108), Expect = 1e-07
Identities = 12/74 (16%), Positives = 23/74 (31%), Gaps = 2/74 (2%)
Query: 2 IDGVDSEAGAIVAGGRG-YFLKGPAVCLQVGLVQYALSKWIEK-GYTPLYTPFFMRKEVM 59
+ E RG + + + + L + +E GY + P + EV
Sbjct: 206 TQAMMKEGWLKRGSSRGQWIHGPQSARIFRTFEKIVLEELLEPLGYREMIFPKLVTWEVW 265
Query: 60 QEVAQLAQFDEELY 73
+ E+Y
Sbjct: 266 MKSGHAKGVYPEIY 279
>2gov_A P22HBP, heme-binding protein 1; structural genomics, protein
structure initiative, PSI, center for eukaryotic
structural genomics, CESG; NMR {Mus musculus} SCOP:
d.60.1.4 PDB: 4a1m_A 2hva_A
Length = 195
Score = 26.0 bits (56), Expect = 1.0
Identities = 7/16 (43%), Positives = 8/16 (50%)
Query: 44 GYTPLYTPFFMRKEVM 59
GY P P+ R EV
Sbjct: 176 GYDPPMKPYGRRNEVW 191
>3nrb_A Formyltetrahydrofolate deformylase; N-terminal ACT domain,
structural genomics, joint center for structural
genomics, JCSG; HET: MSE FLC; 2.05A {Pseudomonas
putida}
Length = 287
Score = 25.6 bits (57), Expect = 1.3
Identities = 12/54 (22%), Positives = 20/54 (37%), Gaps = 11/54 (20%)
Query: 29 QVGLVQYALSKWI-EKG--------YTPLYTP-FFMRKEVMQEVAQLAQFDEEL 72
G+V +S ++ G + + FFMR V VA + F+
Sbjct: 17 APGIV-SEVSTFLFNNGANIVEAEQFNDEDSSKFFMRVSVEIPVAGVNDFNSAF 69
>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 = 24.6 bits (53), Expect = 3.6
Identities = 11/51 (21%), Positives = 21/51 (41%), Gaps = 7/51 (13%)
Query: 3 DGVDSEA---GAIVAGGRGYFLKGPAVCLQVGLVQ---YALSKWIEKGYTP 47
G++ + Y L P C +G++Q Y ++ + G+TP
Sbjct: 211 QGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKL-LGFTP 260
>4b0y_A Heme-binding protein 2; apoptosis; 3.50A {Homo sapiens}
Length = 227
Score = 24.5 bits (52), Expect = 3.7
Identities = 4/16 (25%), Positives = 4/16 (25%)
Query: 44 GYTPLYTPFFMRKEVM 59
GY EV
Sbjct: 200 GYNSPVKLLNRNNEVW 215
>1o97_D Electron transferring flavoprotein alpha-subunit; FAD binding; HET:
AMP FAD; 1.6A {Methylophilus methylotrophus} SCOP:
c.26.2.3 c.31.1.2 PDB: 1o95_D* 1o96_B* 1o94_D* 3clu_D*
3clt_D* 3clr_D* 3cls_D*
Length = 320
Score = 24.4 bits (54), Expect = 4.1
Identities = 5/17 (29%), Positives = 10/17 (58%), Gaps = 1/17 (5%)
Query: 3 DGVD-SEAGAIVAGGRG 18
+ +D + I++ GRG
Sbjct: 195 NDIDITTVDFIMSIGRG 211
>3r8j_A Heme-binding protein 2; HEBP family, SOUL protein, apoptosis; 1.60A
{Homo sapiens} PDB: 3r8k_A 2yc9_A 3r85_E
Length = 212
Score = 24.1 bits (51), Expect = 5.0
Identities = 4/16 (25%), Positives = 4/16 (25%)
Query: 44 GYTPLYTPFFMRKEVM 59
GY EV
Sbjct: 181 GYNSPVKLLNRNNEVW 196
>2fp4_A Succinyl-COA ligase [GDP-forming] alpha-chain, mitochondrial;
active site phosphohistidine residue; HET: NEP GTP;
2.08A {Sus scrofa} SCOP: c.2.1.8 c.23.4.1 PDB: 2fpg_A*
2fpi_A* 2fpp_A* 1euc_A* 1eud_A*
Length = 305
Score = 24.0 bits (53), Expect = 5.2
Identities = 8/10 (80%), Positives = 10/10 (100%)
Query: 9 AGAIVAGGRG 18
AGAI+AGG+G
Sbjct: 259 AGAIIAGGKG 268
>3fhr_A MAP kinase-activated protein kinase 3; kinase-inhibitor complex,
ATP-binding, cytoplasm, nucleotide-binding, nucleus,
phosphoprotein, polymorphism; HET: P4O; 1.90A {Homo
sapiens} PDB: 3fxw_A* 3r1n_A* 3she_A* 2oza_A 3fyk_X*
3fyj_X* 2p3g_X* 3ka0_A* 3fpm_A* 2pzy_A* 3a2c_A* 3kc3_A*
3gok_A* 2jbo_A* 2jbp_A* 3r2y_A* 3r30_A* 3r2b_A*
Length = 336
Score = 23.8 bits (52), Expect = 5.8
Identities = 8/27 (29%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 37 LSKWIEKG--YTPLYTPFFMRKEVMQE 61
+K + TP YTP+++ EV+
Sbjct: 177 FAKETTQNALQTPCYTPYYVAPEVLGP 203
>2yv1_A Succinyl-COA ligase [ADP-forming] subunit alpha; COA-binding
domain, structural genomics, NPPSFA; 1.70A
{Methanocaldococcus jannaschii}
Length = 294
Score = 24.0 bits (53), Expect = 6.0
Identities = 7/10 (70%), Positives = 8/10 (80%)
Query: 9 AGAIVAGGRG 18
AGAIV G+G
Sbjct: 252 AGAIVEKGKG 261
>2nu8_A Succinyl-COA ligase [ADP-forming] subunit alpha; citric acid cycle,
heterotetramer, ligase, ATP-grAsp fold, R fold; HET:
COA; 2.15A {Escherichia coli} SCOP: c.2.1.8 c.23.4.1
PDB: 2nu9_A* 2nu7_A* 2nua_A* 2nu6_A* 2scu_A* 1jll_A*
1scu_A* 1jkj_A* 1cqj_A* 1cqi_A*
Length = 288
Score = 24.0 bits (53), Expect = 6.0
Identities = 8/10 (80%), Positives = 10/10 (100%)
Query: 9 AGAIVAGGRG 18
AGAI+AGG+G
Sbjct: 247 AGAIIAGGKG 256
>2yv2_A Succinyl-COA synthetase alpha chain; COA-binding domain, ligase,
structural genomics, NPPSFA; 2.20A {Aeropyrum pernix}
Length = 297
Score = 24.0 bits (53), Expect = 6.2
Identities = 6/10 (60%), Positives = 7/10 (70%)
Query: 9 AGAIVAGGRG 18
AGAI+ G G
Sbjct: 255 AGAIIMMGTG 264
>1oi7_A Succinyl-COA synthetase alpha chain; SCS, ligase, riken structural
genomics/proteomics initiative, RSGI, structural
genomics; 1.23A {Thermus thermophilus} SCOP: c.2.1.8
c.23.4.1
Length = 288
Score = 23.6 bits (52), Expect = 7.2
Identities = 6/10 (60%), Positives = 7/10 (70%)
Query: 9 AGAIVAGGRG 18
AGAI+ G G
Sbjct: 247 AGAIIMGNVG 256
>1efp_A ETF, protein (electron transfer flavoprotein); electron transport,
glutaric acidemia type II; HET: FAD AMP; 2.60A
{Paracoccus denitrificans} SCOP: c.26.2.3 c.31.1.2
Length = 307
Score = 23.6 bits (52), Expect = 7.3
Identities = 6/12 (50%), Positives = 9/12 (75%)
Query: 7 SEAGAIVAGGRG 18
+ A +V+GGRG
Sbjct: 190 TSARRVVSGGRG 201
>1efv_A Electron transfer flavoprotein; electron transport, glutaric
acidemia type II; HET: FAD AMP; 2.10A {Homo sapiens}
SCOP: c.26.2.3 c.31.1.2 PDB: 2a1u_A* 1t9g_R* 2a1t_R*
Length = 315
Score = 23.6 bits (52), Expect = 7.5
Identities = 6/12 (50%), Positives = 9/12 (75%)
Query: 7 SEAGAIVAGGRG 18
+ A +V+GGRG
Sbjct: 195 TGAKVVVSGGRG 206
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
0.323 0.140 0.420
Gapped
Lambda K H
0.267 0.0452 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,223,573
Number of extensions: 59432
Number of successful extensions: 171
Number of sequences better than 10.0: 1
Number of HSP's gapped: 171
Number of HSP's successfully gapped: 26
Length of query: 75
Length of database: 6,701,793
Length adjustment: 44
Effective length of query: 31
Effective length of database: 5,473,269
Effective search space: 169671339
Effective search space used: 169671339
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: 51 (24.1 bits)