RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8378
(230 letters)
>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 = 151 bits (384), Expect = 3e-42
Identities = 50/93 (53%), Positives = 62/93 (66%), Gaps = 14/93 (15%)
Query: 133 RYWGTPIPMVHCPSCGPVPVPYEALPITLPPSPPL---------PLASNAEWQHCSCPKC 183
RYWGTPIPMVHC +CG VPVP E LP+ LP + PL ++ E+ +CPKC
Sbjct: 428 RYWGTPIPMVHCEACGVVPVPEEELPVLLPDLKDVEDIRPKGKSPLEAHPEFYETTCPKC 487
Query: 184 GHGGARRETDTMDTFVDSAWYYVRYLGSGGDPN 216
G G A+R+TDTMDTF DS+WYY+RY DP+
Sbjct: 488 G-GPAKRDTDTMDTFFDSSWYYLRYT----DPH 515
>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 = 145 bits (367), Expect = 6e-40
Identities = 34/89 (38%), Positives = 44/89 (49%), Gaps = 12/89 (13%)
Query: 133 RYWGTPIPMVHCPSCGPVPVPYEALPITLP----PSPPL-PLASNAEWQHCSCPKCGHGG 187
RYWG PIPMV +P P + LP+ LP P+ ++ EW +
Sbjct: 446 RYWGAPIPMVTLEDGTVMPTPDDQLPVILPEDVVMDGITSPIKADPEWAKTTVNG---MP 502
Query: 188 ARRETDTMDTFVDSAWYYVRYLGSGGDPN 216
A RETDT DTF++S+WYY RY P
Sbjct: 503 ALRETDTFDTFMESSWYYARYT----CPQ 527
>1wkb_A Leucyl-tRNA synthetase; leucine, aminoacyl-tRNA, editing, amino
acid, aminoacylation, trnaLeu, structural genomics;
2.05A {Pyrococcus horikoshii}
Length = 810
Score = 41.1 bits (96), Expect = 2e-04
Identities = 9/83 (10%), Positives = 22/83 (26%), Gaps = 10/83 (12%)
Query: 131 KCRYWGTPIPM-----VHCPSCGPVPVPYEALPITLPPSPP----LPLASNAEWQHCSCP 181
+ GTP+P + S + + Y + + P E+
Sbjct: 510 RKIGLGTPLPWDPEWVIESLSDSTIYMAYYTISRHINKLRQEGKLDPEKLTPEFFDYIFL 569
Query: 182 KCGHGGARRETDTMDTFVDSAWY 204
+ + + T + +
Sbjct: 570 EEF-SEDKEKELEKKTGIPAEII 591
>1wz2_A Leucyl-tRNA synthetase; ligase, riken structural
genomics/proteomics initiativ structural genomics,
ligase-RNA complex; 3.21A {Pyrococcus horikoshii}
Length = 967
Score = 37.6 bits (87), Expect = 0.002
Identities = 13/104 (12%), Positives = 27/104 (25%), Gaps = 21/104 (20%)
Query: 131 KCRYWGTPIPMVHCPSC-----GPVPVPYEALPITLPPS----PPLPLASNAEWQHCSCP 181
+ GTP+P + + Y + + P E+
Sbjct: 510 RKIGLGTPLPWDPEWVIESLSDSTIYMAYYTISRHINKLRQEGKLDPEKLTPEFFDYIFL 569
Query: 182 KCGHGGARRETDTMDTFVDSA-----------WYYVRYLGSGGD 214
+ + + T + + WY + + SG D
Sbjct: 570 EEF-SEDKEKELEKKTGIPAEIIHEMKEEFEYWYPLDWRCSGKD 612
Score = 31.5 bits (71), Expect = 0.28
Identities = 11/99 (11%), Positives = 27/99 (27%), Gaps = 10/99 (10%)
Query: 133 RYWGTPIPMVHCPSCGPVPVPYEALPITLPPSPPLPLASNAEW-QHCSCPKCGHGGAR-- 189
+ I + E + LP + + +W +C + G
Sbjct: 461 IHDQWFIDYGNPEWKEKARKALERMK-ILPETRRAQFEAIIDWLDKKACARKIGLGTPLP 519
Query: 190 -RETDTMDTFVDS-----AWYYVRYLGSGGDPNVRLPDQ 222
+++ DS + R++ P++
Sbjct: 520 WDPEWVIESLSDSTIYMAYYTISRHINKLRQEGKLDPEK 558
>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 = 37.5 bits (88), Expect = 0.002
Identities = 22/81 (27%), Positives = 28/81 (34%), Gaps = 21/81 (25%)
Query: 133 RYWGTPIPMVHCPSCGPVPVP-----YEALPITLPPSPPLPLASNAEWQHCS-------C 180
RYWGTP+P+ C +CG +A P P H
Sbjct: 450 RYWGTPLPIWVCQACGKEEAIGSFQELKARATKPLPEPF--------DPHRPYVDQVELA 501
Query: 181 PKCGHGGARRETDTMDTFVDS 201
CG G RR +D + DS
Sbjct: 502 CACG-GTMRRVPYVIDVWYDS 521
>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 = 36.0 bits (84), Expect = 0.007
Identities = 21/70 (30%), Positives = 26/70 (37%), Gaps = 16/70 (22%)
Query: 135 WGTPIPMVHCPSCGPVPVPYEALPITLPPSPPLPLASNAEWQHCSCPKCGHGGARRETDT 194
WG IP +C C V VP + P SC CG +R+ D
Sbjct: 408 WGHQIPAWYCEDCQAVNVPRPERYLEDP---------------TSCEACGSPRLKRDEDV 452
Query: 195 MDTFVDSA-W 203
DT+ SA W
Sbjct: 453 FDTWFSSALW 462
>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 = 34.4 bits (80), Expect = 0.028
Identities = 17/89 (19%), Positives = 28/89 (31%), Gaps = 22/89 (24%)
Query: 133 RYWGTPIPMVHCPSCGPVPVP---------YEALPI----TLPPSPPLPLASNAEWQHCS 179
R WG P+P+ + + + + LP + +
Sbjct: 457 RVWGVPLPVFYAENGEIIMTKETVNHVADLFAEHGSNIWFEREAKDLLP-------EGFT 509
Query: 180 CPKCGHGGARRETDTMDTFVDSA--WYYV 206
P +G +ETD MD + DS V
Sbjct: 510 HPGSPNGTFTKETDIMDVWFDSGSSHRGV 538
>3a43_A HYPD, hydrogenase nickel incorporation protein HYPA; [NIFE]
hydrogenase maturation, zinc-finger, nickel binding,
metal-binding; HET: FME; 2.30A {Pyrococcus
kodakaraensis} PDB: 3a44_A*
Length = 139
Score = 29.6 bits (66), Expect = 0.46
Identities = 7/51 (13%), Positives = 12/51 (23%), Gaps = 1/51 (1%)
Query: 140 PMVHCPSCG-PVPVPYEALPITLPPSPPLPLASNAEWQHCSCPKCGHGGAR 189
+ C +C + + +CPKCG
Sbjct: 69 AVFKCRNCNYEWKLKEVKDKFDERIKEDIHFIPEVVHAFLACPKCGSHDFE 119
>4acr_A Glypican-1; proteoglycan, glycosaminoglycans, heparan sulfate,
helical B glycoprotein, membrane protein; HET: NAG;
2.55A {Homo sapiens} PDB: 4ad7_A*
Length = 478
Score = 30.1 bits (67), Expect = 0.65
Identities = 15/61 (24%), Positives = 19/61 (31%), Gaps = 1/61 (1%)
Query: 120 LAHHVIAVWFLKCRYWGTPIPMVHCPSCGPVPVPYEALPITLPPSPPLPLASNAEWQHCS 179
L HH + + G P SCG V Y A +L P S + C
Sbjct: 4 LHHHHHHDLYENLYFQGKLDPASKSRSCGEVRQIYGAKGFSLSDVPQAE-ISGEHLRICP 62
Query: 180 C 180
Sbjct: 63 Q 63
>1ob8_A Holliday-junction resolvase; hydrolase, enzyme, homologous
recombination, holliday junction resolving enzyme,
nuclease, archaea; 1.8A {Sulfolobus solfataricus} SCOP:
c.52.1.18 PDB: 1ob9_A
Length = 135
Score = 28.6 bits (63), Expect = 0.89
Identities = 10/35 (28%), Positives = 13/35 (37%), Gaps = 1/35 (2%)
Query: 187 GARRETDTMDTFVDSAWYYVRYLGSGGDPNVRLPD 221
G E + + + VR S PN LPD
Sbjct: 6 GKNAERELVSILRGEGFNAVRIPTSNSSPN-PLPD 39
>1hh1_A Holliday junction resolving enzyme HJC; holliday junction
resolvase, homologous recombination, nuclease domain,
archaea; 2.15A {Sulfolobus solfataricus} SCOP: c.52.1.18
Length = 143
Score = 28.2 bits (62), Expect = 1.6
Identities = 9/35 (25%), Positives = 14/35 (40%)
Query: 187 GARRETDTMDTFVDSAWYYVRYLGSGGDPNVRLPD 221
G+ E + + D + VR SG +PD
Sbjct: 8 GSAVERNIVSRLRDKGFAVVRAPASGSKRKDPIPD 42
>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 = 28.5 bits (63), Expect = 2.2
Identities = 24/140 (17%), Positives = 36/140 (25%), Gaps = 50/140 (35%)
Query: 60 LNLSKISITTSIAIP--------IL--EFVSML-------------TRLPKLFSNFVGDQ 96
L LS S+ + +P L +F +L T +L F+G
Sbjct: 9 LTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLG-- 66
Query: 97 YMSVFAICMPCTNPFKYNHYTVSLAHHVIAVWFLKCRY-WGTPIPMVHCPSCGPVPVPYE 155
+ P K + L + + + Y G I H
Sbjct: 67 ----Y--VSSLVEPSKVGQFDQVLN---LCLTEFENCYLEGNDI---H------------ 102
Query: 156 ALPITLPPSPPLPLASNAEW 175
AL L L E
Sbjct: 103 ALAAKLLQENDTTLVKTKEL 122
>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 = 28.7 bits (63), Expect = 2.2
Identities = 11/57 (19%), Positives = 22/57 (38%), Gaps = 6/57 (10%)
Query: 44 TLEMEREMVKLLPEVLLNLS----KISITTSIAIPILEFVSMLTRLPKLFSNFVGDQ 96
+E E + L V L+ KI ++ ++ L +L K + ++ D
Sbjct: 483 NIEHP-ERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQL-KFYKPYICDN 537
>2vq8_A RNAse ZF-1A; evolution, zebrafish, polymorphism, ribonucleases,
hydrolase; 1.35A {Danio rerio} PDB: 3ljd_A 3ln8_A
Length = 139
Score = 26.8 bits (59), Expect = 3.3
Identities = 12/81 (14%), Positives = 20/81 (24%), Gaps = 6/81 (7%)
Query: 87 KLFSNFVGDQYMSVFAICMPCTNPFKYNHYTVSLAH-----HVIAVWFLKCRYWGTPIPM 141
K + F+ + +C +P + C Y GT
Sbjct: 58 KPVNTFILANKRLIKTVCGRAGSPQGNMVRSNQPFPVVKCVLNNGERHPYCEYRGTRSTR 117
Query: 142 VHCPSC-GPVPVPYEALPITL 161
C PV Y + +
Sbjct: 118 YIVLKCEEGWPVHYHEDEVNV 138
>3riy_A NAD-dependent deacetylase sirtuin-5; desuccinylase, demalonylase,
posttranslational modification, binding domain, rossmann
fold domain; HET: SLL NAD; 1.55A {Homo sapiens} PDB:
3rig_A* 2b4y_A* 2nyr_A*
Length = 273
Score = 27.6 bits (62), Expect = 3.5
Identities = 15/50 (30%), Positives = 17/50 (34%), Gaps = 7/50 (14%)
Query: 142 VHCPSCGPVPVPYE-----ALPITLPPSPPLPLASNAEWQ--HCSCPKCG 184
C SCG V Y+ AL P P AS + C CG
Sbjct: 135 TRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCG 184
>3bbn_F Ribosomal protein S6; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 168
Score = 26.4 bits (58), Expect = 5.6
Identities = 10/56 (17%), Positives = 16/56 (28%)
Query: 131 KCRYWGTPIPMVHCPSCGPVPVPYEALPITLPPSPPLPLASNAEWQHCSCPKCGHG 186
+ Y P V + +E L PP + + P+C G
Sbjct: 6 RHHYLSNYGPYVKAIALDFSGSFFEGGFGGLDEDPPSTPPAGLAVEEKPEPQCPPG 61
>1h7b_A Anaerobic ribonucleotide-triphosphate reductase large chain;
oxidoreductase, allosteric regulation, substrate
specificity; 2.45A {Bacteriophage T4} SCOP: c.7.1.3 PDB:
1h79_A* 1h7a_A* 1h78_A 1hk8_A*
Length = 605
Score = 26.9 bits (59), Expect = 6.1
Identities = 9/55 (16%), Positives = 13/55 (23%), Gaps = 18/55 (32%)
Query: 131 KCRYWGTPIPMVHCPSCGPVPVPYEALPITLPPSPPLPLASNAEWQHCSCPKCGH 185
Y+G +P+ C +CG C CG
Sbjct: 530 HLDYFGVNMPVDKCFTCGSTHE------------------MTPTENGFVCSICGE 566
>1l5a_A Amide synthase, VIBH; nonribosomal peptide synthetase, NRPS
condensation domain, vibriobactin, biosynthetic protein;
2.55A {Vibrio cholerae} SCOP: c.43.1.2 c.43.1.2
Length = 436
Score = 26.8 bits (60), Expect = 6.1
Identities = 4/16 (25%), Positives = 6/16 (37%)
Query: 162 PPSPPLPLASNAEWQH 177
P + P S E +
Sbjct: 154 PTAAFKPYQSYLEEEA 169
>2gek_A Phosphatidylinositol mannosyltransferase (PIMA); GT4
glycosyltransferase, rossmann fold, complex; HET: GDP;
2.40A {Mycobacterium smegmatis} PDB: 2gej_A*
Length = 406
Score = 26.9 bits (60), Expect = 6.6
Identities = 11/61 (18%), Positives = 16/61 (26%), Gaps = 4/61 (6%)
Query: 114 NHYTVSLAHHVIA----VWFLKCRYWGTPIPMVHCPSCGPVPVPYEALPITLPPSPPLPL 169
+ + LA + V L +P VP+PY L P
Sbjct: 38 QSHVLQLAEVLRDAGHEVSVLAPASPHVKLPDYVVSGGKAVPIPYNGSVARLRFGPATHR 97
Query: 170 A 170
Sbjct: 98 K 98
>1k19_A Chemosensory protein CSP2; pheromone, lipid transport; NMR
{Mamestra brassicae} SCOP: a.118.21.1 PDB: 1kx8_A
1kx9_A 1n8u_A* 1n8v_A* 2jnt_A
Length = 112
Score = 25.2 bits (55), Expect = 9.6
Identities = 7/37 (18%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 25 ESERGYSRQEKCITALTTCTLEMEREMVKLLPEVLLN 61
++R C+ C+ E +E+ + L + + N
Sbjct: 18 ANKRLLVAYVNCVMERGKCSPEG-KELKEHLQDAIEN 53
>2ph1_A Nucleotide-binding protein; alpha-beta protein, structural
genomics, PSI-2, protein STRU initiative; 2.70A
{Archaeoglobus fulgidus dsm 4304} PDB: 3kb1_A*
Length = 262
Score = 26.0 bits (58), Expect = 9.8
Identities = 9/68 (13%), Positives = 15/68 (22%), Gaps = 28/68 (41%)
Query: 180 CPKCGH-------GGARRETDTMDTFVDSAWYYVRYLGS------------GGDPNVRLP 220
CP CGH G + + + S G
Sbjct: 196 CPNCGHKSYIFGEGKGESLAKKYN---------IGFFTSIPIEEELIKLADSGRIEEYEK 246
Query: 221 DQPDGSRY 228
D + + +
Sbjct: 247 DWFESAPF 254
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 0.139 0.465
Gapped
Lambda K H
0.267 0.0540 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,711,047
Number of extensions: 212056
Number of successful extensions: 663
Number of sequences better than 10.0: 1
Number of HSP's gapped: 657
Number of HSP's successfully gapped: 34
Length of query: 230
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 140
Effective length of database: 4,188,903
Effective search space: 586446420
Effective search space used: 586446420
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 56 (25.8 bits)