RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6240
(233 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 = 149 bits (378), Expect = 4e-42
Identities = 64/216 (29%), Positives = 97/216 (44%), Gaps = 29/216 (13%)
Query: 16 ENINIRGGT-QFHIDDDNVILPVDKTEFITQVLTSTGDKHVYKTQLNCTDKVVVEFSSPN 74
E + G QF + + I +LT + +L KV++EFSSPN
Sbjct: 101 EKVEANGPFIQFFFNPQFLA-----KLVIPDILT--RKEDYGSCKLVENKKVIIEFSSPN 153
Query: 75 IAKPFHVGHFRGTVLGNFVANLSNYFANNVVCLNYLGDWGTQFGLLQIGLKELNIKHTDL 134
IAKPFH GH R T++G F+ANL V+ +NYLGDWG QFGLL +G + + L
Sbjct: 154 IAKPFHAGHLRSTIIGGFLANLYEKLGWEVIRMNYLGDWGKQFGLLAVGFERYGNEEA-L 212
Query: 135 EQSPLDVLYKAYVKANELAKINPDVQEQAPLDVLYKAYVKANDLAKINPDVQEQASNIFQ 194
+ P+ L+ YV+ N+ + D +A F+
Sbjct: 213 VKDPIHHLFDVYVRINKDIEEEGDSIPL-------------------EQSTNGKAREYFK 253
Query: 195 QLECGKNTLHTKDWLDFQQVTLNELRGTYERLGIHF 230
++E G + K W F++ ++ + TY RL I +
Sbjct: 254 RMEDG-DEEALKIWKRFREFSIEKYIDTYARLNIKY 288
>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 = 131 bits (331), Expect = 2e-35
Identities = 40/196 (20%), Positives = 75/196 (38%), Gaps = 23/196 (11%)
Query: 37 VDKTEFITQVLTS--TGDKHVYKTQLNCTDKVVVEFSSPNIAKPFHVGHFRGTVLGNFVA 94
+D F ++ +++ KV+VE +S N KP H+GH R +LG+ +A
Sbjct: 90 IDYPHFARILINDILAKGDRFGSSEIGKGKKVIVEHTSVNPTKPLHMGHARNAILGDVMA 149
Query: 95 NLSNYFANNVVCLNYLGDWGTQFGLLQIGLKELNIKHTDLEQSPLDVLYKAYVKANELAK 154
+ + V NY+ D G QF + G L + + + K
Sbjct: 150 RILRFLGYEVEVQNYIDDLGIQFAQVYWGYLRLKEEFERIMNELRERGLK---------- 199
Query: 155 INPDVQEQAPLDVLYKAYVKANDLAKINPDVQEQASNIFQQLECGKNTLHTKDWLDFQQV 214
+ L YV+ N + NP+++ + +I ++LE G+ +
Sbjct: 200 ------DNPIDHALGLLYVEVNRRLEDNPELENEIRDIMKKLESGE-----LYGRKLAEE 248
Query: 215 TLNELRGTYERLGIHF 230
+ T +LG+ +
Sbjct: 249 VVRAQMVTTYKLGVKY 264
>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 = 127 bits (322), Expect = 3e-34
Identities = 43/221 (19%), Positives = 68/221 (30%), Gaps = 44/221 (19%)
Query: 13 DGSENINIRGG-TQFHIDDDNVILPVDKTEFITQVLTSTGDKHVYKTQLNCTDKVVVEFS 71
+ E GG F + E + + + V+VE +
Sbjct: 66 EFVEEAVPVGGYLNFRLRT----------EALLREALRPKAPFPRRPG-----VVLVEHT 110
Query: 72 SPNIAKPFHVGHFRGTVLGNFVANLSNYFANNVVCLNYLGDWGTQFGLLQIGLKELNIKH 131
S N K HVGH R LG+ +A + Y V+ LNY+ D G Q L+
Sbjct: 111 SVNPNKELHVGHLRNIALGDAIARILAYAGREVLVLNYIDDTGRQAAETLFALRHY--GL 168
Query: 132 TDLEQSPLDVLYKAYVKANELAKINPDVQEQAPLDVLYKAYVKANDLAKINPDVQEQASN 191
T + D +AYV+ + + +Q
Sbjct: 169 TWDGKEKYDHFAG-------------------------RAYVRLHQDPE-YERLQPAIEE 202
Query: 192 IFQQLECGKNTLHTKDWLDFQQVTLNELRGTYERLGIHFSV 232
+ LE G+ L Q T++ L Y+ L +
Sbjct: 203 VLHALERGELREEVNRILLAQMATMHALNARYDLLVWESDI 243
>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 = 47.7 bits (113), Expect = 1e-06
Identities = 36/190 (18%), Positives = 60/190 (31%), Gaps = 59/190 (31%)
Query: 71 SSPNIAKPFHV---GHFRGTVL-GNFVANL---SNYFANN-----VVCL--NYLG----- 111
S ++ V F + L F L + FA + L +LG
Sbjct: 12 SHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSL 71
Query: 112 ----DWGTQFGLLQIGLKELNIKHTDLEQSPLDVLYKAYVKANEL----AKINPDVQ-EQ 162
G +L + L E Y++ N++ AK+ +
Sbjct: 72 VEPSKVGQFDQVLNLCLTEFE---------------NCYLEGNDIHALAAKLLQENDTTL 116
Query: 163 APLDVLYKAYVKANDLAKINPDVQEQASNIFQQLECGKNTLH--------TKDWLDFQQV 214
L K Y+ A +AK P ++ S +F+ + G L T D+ +
Sbjct: 117 VKTKELIKNYITARIMAKR-PFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFE---- 171
Query: 215 TLNELRGTYE 224
ELR Y+
Sbjct: 172 ---ELRDLYQ 178
Score = 38.1 bits (88), Expect = 0.002
Identities = 47/268 (17%), Positives = 75/268 (27%), Gaps = 119/268 (44%)
Query: 12 IDGSENI-----NIRGGT----QFHIDDDNVILPVDKTEFITQVLTSTGDKHVYKTQLNC 62
++ +E + +I T Q +++ N LP K V + +N
Sbjct: 328 LENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLP--------------AGKQVEISLVNG 373
Query: 63 TDKVVVEFSSPNIAKPFHVGHFRGTVLGNFVANLSNYFANNVVCLNYLGDWGTQFGLLQ- 121
+VV S P P L L A + GL Q
Sbjct: 374 AKNLVV--SGP----P--------QSLYGLNLTLRKAKAPS--------------GLDQS 405
Query: 122 -IGLKE---------LNIK---HTDLEQSPLDVLYKAYVKANELAKINPDVQEQAPLDVL 168
I E L + H S L L A IN D+ + +V
Sbjct: 406 RIPFSERKLKFSNRFLPVASPFH-----SHL--LVPA------SDLINKDLVKN---NVS 449
Query: 169 YKAYVKANDLAKINP--------DVQEQASNIFQQLECGKNTLHTKDW-----------L 209
+ A D+ +I P D++ + +I +++ W L
Sbjct: 450 F----NAKDI-QI-PVYDTFDGSDLRVLSGSISERI-VDCIIRLPVKWETTTQFKATHIL 502
Query: 210 DF--------QQVTLNELRGTYERLGIH 229
DF +T GT G+
Sbjct: 503 DFGPGGASGLGVLTHRNKDGT----GVR 526
Score = 32.7 bits (74), Expect = 0.11
Identities = 24/122 (19%), Positives = 38/122 (31%), Gaps = 37/122 (30%)
Query: 122 IGLKELNIKHTDLEQSPLDVLYKAYVKANEL----AKINPDV-----QEQAPLDV--LYK 170
+ L + H LE L V ++ A++L KI P+ + P L
Sbjct: 4 YSTRPLTLSHGSLEHV-LLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVG 62
Query: 171 AYVKANDLAKINPDVQEQASNIFQQLECGKNTLHTKDWLDFQQVTLNELRGTYERLG--- 227
+ L ++ V+ F Q+ L + L E Y L
Sbjct: 63 KF-----LGYVSSLVEPSKVGQFDQV------L---------NLCLTEFENCY--LEGND 100
Query: 228 IH 229
IH
Sbjct: 101 IH 102
Score = 26.6 bits (58), Expect = 9.3
Identities = 12/78 (15%), Positives = 22/78 (28%), Gaps = 38/78 (48%)
Query: 61 NCTDKVVVEFSSPNIAKPFHVGHFRGTVLGNFVANLSNYFANNVVCLNYLGDWGTQFGLL 120
N ++ V A G R + ++N LN++
Sbjct: 1847 NVENQQYV------AA-----GDLRA------LDTVTN-------VLNFI---------- 1872
Query: 121 QIGLKELNIKHTDLEQSP 138
K I +L++S
Sbjct: 1873 ----KLQKIDIIELQKSL 1886
>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 = 43.7 bits (102), Expect = 3e-05
Identities = 37/229 (16%), Positives = 63/229 (27%), Gaps = 76/229 (33%)
Query: 3 KTFTIHYHIIDGSENINIRGGTQFH---IDDDNVILPVDKTEFITQVLTSTGDKHVYKTQ 59
K TI I + + H +D N+ D + I L D++ Y
Sbjct: 422 KESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYL----DQYFY--- 474
Query: 60 LNCTDKVVVEFSSPNIAKPFHVG-HFRGTVLGNFVANLSNYFANNVVCLNYLGDWGTQFG 118
H+G H + + F L++ +
Sbjct: 475 -------------------SHIGHHLKNIEHPERMTLFRMVF------LDF--RF----- 502
Query: 119 LLQIGLKELNIKHTDLEQSPLDVLYKAYVKANELAKINPDVQEQAPLDV-LYKAYVKAND 177
+ K I+H N I +Q + YK Y+ ND
Sbjct: 503 ---LEQK---IRHDSTAW-------------NASGSILNTLQ-----QLKFYKPYICDND 538
Query: 178 LAKINPDVQEQASNIFQQLE-CGKNTLHTKDWLDFQQVTL-NELRGTYE 224
P + + I L +N + +K D ++ L E +E
Sbjct: 539 -----PKYERLVNAILDFLPKIEENLICSKY-TDLLRIALMAEDEAIFE 581
Score = 37.9 bits (87), Expect = 0.002
Identities = 29/228 (12%), Positives = 66/228 (28%), Gaps = 46/228 (20%)
Query: 11 IIDGSENINIRGGTQFHIDDDNVILPVDKTEFITQVLTSTGDKHVYKTQLNCTDKVVVEF 70
+++ + + + + D+ + I L Y+ L V
Sbjct: 198 VLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNV---- 253
Query: 71 SSPNIAKPFHVG-----HFRGTVLGNFVANLSNYFANNVVCLNYLGDWGTQFGLLQIGLK 125
+ F++ R + +F++ + + L++ T + + LK
Sbjct: 254 QNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTT----HISLDHHSMTLTPDEVKSLLLK 309
Query: 126 ELNIKHTDLEQSPLDVLYKAYVKANELAKINPDVQEQAPLDVLYKAYVKANDLAKINPDV 185
L+ + DL P E+ NP + + +
Sbjct: 310 YLDCRPQDL---P-----------REVLTTNP----------RRLSIIAE--SIRDGLAT 343
Query: 186 QEQASNIFQQLECGKNTLHTKDWLDFQQVTLNELRGTYERLGIHFSVD 233
+ ++ + C K L T + E R ++RL + F
Sbjct: 344 WDN----WKHVNCDK--LTTIIESSLNVLEPAEYRKMFDRLSV-FPPS 384
Score = 35.6 bits (81), Expect = 0.014
Identities = 36/218 (16%), Positives = 65/218 (29%), Gaps = 76/218 (34%)
Query: 8 HYHIIDGSENINIRGGTQFHIDDDNVILPV------------DKTEFITQVLTSTGDKHV 55
H+H +D E G Q+ D IL V D + +L+ H+
Sbjct: 3 HHHHMD-FET----GEHQYQYKD---ILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHI 54
Query: 56 YK--TQLNCTDKVVVEFSSPNIAKPFHVGHFRGTVLGNFVANLSNYFANNVVCLNYLGDW 113
++ T ++ L + + F V+ +NY +
Sbjct: 55 IMSKDAVSGTLRLF-------------------WTLLSKQEEMVQKFVEEVLRINY--KF 93
Query: 114 GTQFGLLQIGLKELNIKHTDLEQSPLDVLYKAYVKANELAKINPDVQEQAPLDV----LY 169
L IK + S + +Y ++ D Q A +V Y
Sbjct: 94 ----------LMS-PIKTEQRQPSMMTRMYIEQRD-----RLYNDNQVFAKYNVSRLQPY 137
Query: 170 KAYVKANDLAKINPDVQEQASNIFQQLE----CGKNTL 203
+A L ++ P A N+ ++ GK +
Sbjct: 138 LKLRQA--LLELRP-----AKNVL--IDGVLGSGKTWV 166
Score = 31.7 bits (71), Expect = 0.19
Identities = 18/114 (15%), Positives = 35/114 (30%), Gaps = 22/114 (19%)
Query: 131 HTDLEQSPLDVLYKAYVKANELA-KINPDVQ--EQAPLDVLYKAYVKANDLAKINPDVQE 187
H D E YK + E A N D + + P +L K + + + D
Sbjct: 6 HMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEID--HIIM-SKDAVS 62
Query: 188 QASNIFQQLEC-GKNT-------LHTKD--WL------DFQQVTLNELRGTYER 225
+F L + + + +L + +Q ++ +R
Sbjct: 63 GTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQR 116
>3fnr_A Arginyl-tRNA synthetase; transferase, PSI-2, NYSGXRC, struc
genomics, protein structure initiative; 2.20A
{Campylobacter jejuni}
Length = 464
Score = 39.5 bits (93), Expect = 5e-04
Identities = 18/56 (32%), Positives = 27/56 (48%)
Query: 65 KVVVEFSSPNIAKPFHVGHFRGTVLGNFVANLSNYFANNVVCLNYLGDWGTQFGLL 120
++E+ S N P H+GH RG V G+ + L+ + Y+ D G Q LL
Sbjct: 31 SFLLEYVSANPTGPLHIGHARGAVFGDTLTRLARHLGYKFNTEYYVNDAGNQIYLL 86
>2ks0_A Uncharacterized protein; YABP family, structural genomi 2, protein
structure initiative, northeast structural genom
consortium; NMR {Desulfitobacterium hafniense} PDB:
2kyi_A 3ipf_A
Length = 71
Score = 25.0 bits (55), Expect = 7.0
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 115 TQFGLLQIGLKELNIKHTDLEQSPLDV 141
T G+L I ++L IKH DL+ ++V
Sbjct: 27 TIQGVLSIKGEKLGIKHLDLKAGQVEV 53
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
0.319 0.137 0.408
Gapped
Lambda K H
0.267 0.0596 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,545,314
Number of extensions: 200519
Number of successful extensions: 352
Number of sequences better than 10.0: 1
Number of HSP's gapped: 343
Number of HSP's successfully gapped: 16
Length of query: 233
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 143
Effective length of database: 4,188,903
Effective search space: 599013129
Effective search space used: 599013129
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 (21.7 bits)
S2: 56 (25.6 bits)