RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780949|ref|YP_003065362.1| tyrosyl-tRNA synthetase
[Candidatus Liberibacter asiaticus str. psy62]
(418 letters)
>gnl|CDD|30511 COG0162, TyrS, Tyrosyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 401
Score = 399 bits (1027), Expect = e-112
Identities = 182/410 (44%), Positives = 243/410 (59%), Gaps = 17/410 (4%)
Query: 5 KSDFLSILSERGFIHQISNPRELDILCSQGVVTAYIGYDLTASSLHAGHLTQLMLLFWLQ 64
L L +RG I QI++ EL L +G + YIG+D TA SLH GHL LM L Q
Sbjct: 2 MDVELLELIKRGLIEQITDEEELRKLLEEGPLRVYIGFDPTAPSLHLGHLVPLMKLRRFQ 61
Query: 65 KTGHKPISLMGGGTSIIGDPSFRDESRRMMRSQEIQENIEKIKGIFSSFIKYGTGKTDAL 124
GHKPI L+G T++IGDPS + E R+++ + + EN E IK F+ A
Sbjct: 62 DAGHKPIVLIGDATAMIGDPSGKSEERKLLTRETVLENAETIKKQLGKFLD-----NKAE 116
Query: 125 MLNNETWLCSIKYIDLLREIGSFFSVNRMLSFESVRSRLKREQSLSFLEFNYMILQAYDF 184
+NN WL + Y+D LR++G FSVNRML + V+ RL+REQ +SF EFNY +LQAYDF
Sbjct: 117 FVNNSDWLKKLNYLDFLRDVGKHFSVNRMLRRDDVKKRLEREQGISFTEFNYPLLQAYDF 176
Query: 185 VELAKNYDCRLQMGGSDQWGNIICGIDLGERLKTPKLFALTSPLLTTASGTKMGKTLSGA 244
V L K+ LQ+GGSDQWGNI+ G DL RL K+ LT+PLLT G KMGK+ GA
Sbjct: 177 VYLNKD----LQLGGSDQWGNILAGRDLIRRLGQKKVVGLTTPLLTGLDGKKMGKSEGGA 232
Query: 245 IWLNKEMTSPYNFWQYWRNIDDADVVSFAKRLTTLPMSEIDRMAK--LQGKEINEAKKII 302
+WL+ E TSPY+F+QYW NI+DADV F K LT L + EI+ + K L+G E EAKK++
Sbjct: 233 VWLDSEKTSPYDFYQYWMNIEDADVKRFLKLLTFLSLEEIEEIEKYVLKGPEPREAKKLL 292
Query: 303 ATEITTMVHGREEAEKAATAAMECFDMSIHSQHMPTISISKDEVSRGMGLLTLIVKAGFA 362
A E+T +VHG E AE A + F + ++P + + GL+ L+V AG A
Sbjct: 293 AKEVTKLVHGEEAAEAAEEEFEKLFSEGLPE-NLPPADLKQ---KLEDGLVDLLVDAGLA 348
Query: 363 TSTNEARRHLKSNAIKINNSIISNEKLQIKLQDFDSTGNIKLSFGKKNHI 412
S +EARR ++ +KIN + +E + D G + L GKK
Sbjct: 349 PSRSEARRLIQQGGVKINGEKVEDENYVL--SDLLDNGLLVLRRGKKKFA 396
>gnl|CDD|173902 cd00805, TyrRS_core, catalytic core domain of tyrosinyl-tRNA
synthetase. Tyrosinyl-tRNA synthetase (TyrRS) catalytic
core domain. TyrRS is a homodimer which attaches Tyr to
the appropriate tRNA. TyrRS is a class I tRNA
synthetases, so it aminoacylates the 2'-OH of the
nucleotide at the 3' end of the tRNA. The core domain is
based on the Rossman fold and is responsible for the
ATP-dependent formationof the enzyme bound
aminoacyl-adenylate. It contains the class I
characteristic HIGH and KMSKS motifs, which are involved
in ATP binding.
Length = 269
Score = 300 bits (770), Expect = 6e-82
Identities = 115/276 (41%), Positives = 162/276 (58%), Gaps = 9/276 (3%)
Query: 36 VTAYIGYDLTASSLHAGHLTQLMLLFWLQKTGHKPISLMGGGTSIIGDPSFRDESRRMMR 95
+ YIG+D TA SLH GHL LM L Q+ GH+ I L+G T++IGDPS + E R+++
Sbjct: 1 LKVYIGFDPTAPSLHLGHLVPLMKLRDFQQAGHEVIVLIGDATAMIGDPSGKSEERKLLD 60
Query: 96 SQEIQENIEKIKGIFSSFIKYGTGKTDALMLNNETWLCSIKYIDLLREIGSFFSVNRMLS 155
+ I+EN + K + + + A +NN WL S+ +D LR +G F+VNRML
Sbjct: 61 LELIRENAKYYKKQLKAILDFI-PPEKAKFVNNSDWLLSLYTLDFLR-LGKHFTVNRMLR 118
Query: 156 FESVRSRLKREQSLSFLEFNYMILQAYDFVELAKNYDCRLQMGGSDQWGNIICGIDLGER 215
++V+ RL+ E+ +SF EF Y +LQAYDFV L LQ+GGSDQ GNI G DL +
Sbjct: 119 RDAVKVRLEEEEGISFSEFIYPLLQAYDFVYLDV----DLQLGGSDQRGNITLGRDLIRK 174
Query: 216 LKTPKLFALTSPLLTTASGTKMGKTLSGAIWLNKEMTSPYNFWQYWRNIDDADVVSFAKR 275
L K+ LT+PLLT G KM K+ AIW + + SPY+ +Q RN D DV+ F K
Sbjct: 175 LGYKKVVGLTTPLLTGLDGGKMSKSEGNAIW-DPVLDSPYDVYQKIRNAFDPDVLEFLKL 233
Query: 276 LTTLPMSEIDRMAKLQGKEI--NEAKKIIATEITTM 309
T L EI+ + + + +AKK +A E+T +
Sbjct: 234 FTFLDYEEIEELEEEHAEGPLPRDAKKALAEELTKL 269
>gnl|CDD|37834 KOG2623, KOG2623, KOG2623, Tyrosyl-tRNA synthetase [Translation,
ribosomal structure and biogenesis].
Length = 467
Score = 298 bits (764), Expect = 2e-81
Identities = 152/433 (35%), Positives = 233/433 (53%), Gaps = 26/433 (6%)
Query: 7 DFLSILSERGFIHQI---SNPRELDILCSQGV-VTAYIGYDLTASSLHAGHLTQLMLLFW 62
D+L+ L RG + + + L +G+ Y G+D TA SLH G+L LM+L
Sbjct: 31 DYLTELKARGLFQTSFPETLSKCSEDLNGRGLPQYVYCGFDPTAESLHVGNLLALMVLIH 90
Query: 63 LQKTGHKPISLMGGGTSIIGDPSFRDESRRMMRSQEIQENIEKI----KGIFSS---FIK 115
Q+ GH+PI+L+GG T+ +GDPS R R + + N I IF + + +
Sbjct: 91 FQRAGHRPIALIGGATASVGDPSGRKTERGQLAEDTREANSRSITQQLCKIFENHPEYYR 150
Query: 116 YGTGKTDALMLNNETWLCSIKYIDLLREIGSFFSVNRMLSFESVRSRLKREQSLSFLEFN 175
G+ + +++NN W IK +D L E+G F V ML+ +SV+SRL+ LSF EF
Sbjct: 151 DGSSQGKYIIVNNSDWYKDIKLLDFLAEVGRHFRVGSMLARDSVKSRLESPNGLSFTEFT 210
Query: 176 YMILQAYDFVELAKNYDCRLQMGGSDQWGNIICGIDLGERLKTPK--LFALTSPLLTTAS 233
Y +LQAYDF L +NY CR Q+GGSDQWGNI G DL ++ + +F LT PLLT+++
Sbjct: 211 YQLLQAYDFYHLYENYGCRFQLGGSDQWGNITAGTDLIRKIMPIQAFVFGLTFPLLTSST 270
Query: 234 GTKMGKTLSGAIWLNKEMTSPYNFWQYWRNIDDADVVSFAKRLTTLPMSEIDRMAKLQGK 293
G K+GK+ A+WL+ TSPY+ +Q++ ++ D DV F K T LP+ EI ++ + K
Sbjct: 271 GAKLGKSAGNAVWLDPSKTSPYHLYQFFASLPDDDVEKFLKLFTFLPLEEIKQILEEHRK 330
Query: 294 EI--NEAKKIIATEITTMVHGRE---EAEKAATA-------AMECFDMSIHSQHMPTISI 341
E A+K++A E+T MVHG+E AE+ A + +S Q +
Sbjct: 331 EPSQRIAQKLLAAEVTRMVHGKEGLEVAERCTKALFGAKKAGLSGLSLSEILQLFKDATF 390
Query: 342 SKDEVSRGMGLLTLIVKAGFATSTNEARRHLKSNAIKINNSIISNEKLQIKLQDFDSTGN 401
+ G+ +L L+ KA S EARR ++ + +N+ + +E + I +
Sbjct: 391 IDLKDEPGVSILDLLRKASRFPSGKEARRMIQQGGVSLNHEKVRDESVSIAGPFILNNRG 450
Query: 402 IK-LSFGKKNHII 413
+ L GK+N +I
Sbjct: 451 LSLLRAGKRNFVI 463
>gnl|CDD|173893 cd00395, Tyr_Trp_RS_core, catalytic core domain of tyrosinyl-tRNA
and tryptophanyl-tRNA synthetase. Tyrosinyl-tRNA
synthetase (TyrRS)/Tryptophanyl-tRNA synthetase (TrpRS)
catalytic core domain. These enzymes attach Tyr or Trp,
respectively, to the appropriate tRNA. These class I
enzymes are homodimers, which aminoacylate the 2'-OH of
the nucleotide at the 3' of the appropriate tRNA. The
core domain is based on the Rossman fold and is
responsible for the ATP-dependent formation of the
enzyme bound aminoacyl-adenylate. It contains the class
I characteristic HIGH and KMSKS motifs, which are
involved in ATP binding.
Length = 273
Score = 230 bits (588), Expect = 4e-61
Identities = 110/274 (40%), Positives = 148/274 (54%), Gaps = 6/274 (2%)
Query: 37 TAYIGYDLTASSLHAGHLTQLMLLFWLQKTGHKPISLMGGGTSIIGDPSFRDESRRMMRS 96
T Y G D TA SLH GHL L+ Q GH+PI L+GG T IIGDPS + R +
Sbjct: 1 TLYCGIDPTADSLHIGHLIGLLTFRRFQHAGHRPIFLIGGQTGIIGDPSGKKSERTLNDP 60
Query: 97 QEIQENIEKIKGIFSSFIKYGTGKTDALMLNNETWLCSIKYIDLLREIGSFFSVNRMLSF 156
+E+++NI +I + + + T A + NN W + +I LR++G VN M
Sbjct: 61 EEVRQNIRRIAAQYLAVGIFEDP-TQATLFNNSDWPGPLAHIQFLRDLGKHVYVNYMERK 119
Query: 157 ESVRSRLKREQSLSFLEFNYMILQAYDFVELAKNYDCRLQMGGSDQWGNIICGIDLGERL 216
S +SR E+ +S EF Y LQA DF+ L C +Q GGSDQWGNI G +L R
Sbjct: 120 TSFQSRS--EEGISATEFTYPPLQAADFLLLNTTEGCDIQPGGSDQWGNITLGRELARRF 177
Query: 217 K-TPKLFALTSPLLTTASGTKMGKTLSGAIWLNKEMTSPYNFWQYWRNIDDADVVSFAKR 275
LT PL+T G K GK+ SG WL+ E TSPY F+Q+W N D+DV++ K
Sbjct: 178 NGFTIAEGLTIPLVTKLDGPKFGKSESGPKWLDTEKTSPYEFYQFWINAVDSDVINILKY 237
Query: 276 LTTLPMSEIDRMAKLQ--GKEINEAKKIIATEIT 307
T L EI+R+ + Q A+K +A E+T
Sbjct: 238 FTFLSKEEIERLEQEQYEAPGYRVAQKTLAEEVT 271
>gnl|CDD|144245 pfam00579, tRNA-synt_1b, tRNA synthetases class I (W and Y).
Length = 291
Score = 229 bits (586), Expect = 1e-60
Identities = 109/302 (36%), Positives = 156/302 (51%), Gaps = 19/302 (6%)
Query: 32 SQGVVTAYIGYDLTASSLHAGHLTQLMLLFWLQKTGHKPISLMGGGTSIIGDPSFRDESR 91
+ + Y G+D T LH G+L LM L Q+ GH+ L+G T+IIGDPS + E R
Sbjct: 2 KERPLRVYTGFDPTGP-LHLGYLVPLMKLVQFQQAGHEVFFLIGDLTAIIGDPS-KSEER 59
Query: 92 RMMRSQEIQENIEKIKGIFSSFIKYGTGKTDALMLNNETWLCSIKYIDLLREIGSFFSVN 151
+++ +E+ EN + K + ++NN WL ++ LLR++G+ FS+N
Sbjct: 60 KLLSREEVLENAKAQLACGLDPEK-------SEIVNNSDWLEHLELAWLLRDLGNHFSLN 112
Query: 152 RMLSFESVRSRLKREQSLSFLEFNYMILQAYDFVELAKNYDCRLQMGGSDQWGNIICGID 211
RML F+ V+ RLK+ +S EF Y +LQA D + L + LQ GGSDQWG+I G D
Sbjct: 113 RMLQFKDVKKRLKQNPGISLGEFTYPLLQAADILLLKAD----LQPGGSDQWGHIELGRD 168
Query: 212 LGERLKT---PKLFALTSPLLTTASGT-KMGKTLSG-AIWLNKEMTSPYNFWQYWRNIDD 266
L R K LT+PLLT G KM K+ AI+L+ E S Y Q D
Sbjct: 169 LARRFNKKVFKKPVGLTNPLLTGLDGGKKMSKSAGNSAIFLDDEKESVYKKIQKAYTDPD 228
Query: 267 ADVVSFAKRLTTLPMSEIDRMAKLQGK-EINEAKKIIATEITTMVHGREEAEKAATAAME 325
+V K T L EI+ + GK EA++++A E+T +VHG + + AA A
Sbjct: 229 REVRKDLKLFTELSNEEIEILEAFLGKGPKREAEELLAREVTGLVHGGDLKKAAAEAVNA 288
Query: 326 CF 327
Sbjct: 289 LL 290
>gnl|CDD|173901 cd00802, class_I_aaRS_core, catalytic core domain of class I amino
acyl-tRNA synthetase. Class I amino acyl-tRNA
synthetase (aaRS) catalytic core domain. These enzymes
are mostly monomers which aminoacylate the 2'-OH of the
nucleotide at the 3' of the appropriate tRNA. The core
domain is based on the Rossman fold and is responsible
for the ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in ATP
binding.
Length = 143
Score = 52.5 bits (126), Expect = 2e-07
Identities = 28/70 (40%), Positives = 40/70 (57%), Gaps = 2/70 (2%)
Query: 173 EFNYMILQAYDFVELAKNYDCRLQMGGSDQWGNIICGIDLGERLKTPK-LFALTSPLLTT 231
+ YM LQA DF+ L + C + +GGSDQ G+I G++L ++ P F LT +
Sbjct: 75 DVEYMFLQAADFLLLYETE-CDIHLGGSDQLGHIELGLELLKKAGGPARPFGLTFGRVMG 133
Query: 232 ASGTKMGKTL 241
A GTKM K+
Sbjct: 134 ADGTKMSKSK 143
>gnl|CDD|29105 cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding domain; The domain
surface is populated by conserved, charged residues that
define a likely RNA-binding site; Found in stress
proteins, ribosomal proteins and tRNA synthetases; This
may imply a hitherto unrecognized functional similarity
between these three protein classes..
Length = 70
Score = 40.6 bits (95), Expect = 9e-04
Identities = 13/67 (19%), Positives = 30/67 (44%), Gaps = 3/67 (4%)
Query: 350 MGLLTLIVKAGFATSTNEARRHLKSNAIKINNSIISNEKLQIKLQD---FDSTGNIKLSF 406
M L ++ + G A S +EAR+ +K + +N +++ ++K D D +
Sbjct: 1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIV 60
Query: 407 GKKNHII 413
+ ++
Sbjct: 61 YEDKKLL 67
>gnl|CDD|144902 pfam01479, S4, S4 domain. The S4 domain is a small domain
consisting of 60-65 amino acid residues that was
detected in the bacterial ribosomal protein S4,
eukaryotic ribosomal S9, two families of pseudouridine
synthases, a novel family of predicted RNA methylases, a
yeast protein containing a pseudouridine synthetase and
a deaminase domain, bacterial tyrosyl-tRNA synthetases,
and a number of uncharacterized, small proteins that may
be involved in translation regulation. The S4 domain
probably mediates binding to RNA.
Length = 48
Score = 39.0 bits (92), Expect = 0.002
Identities = 11/46 (23%), Positives = 27/46 (58%)
Query: 350 MGLLTLIVKAGFATSTNEARRHLKSNAIKINNSIISNEKLQIKLQD 395
M L ++ + G A+S +EAR+ ++ +++N ++ + ++K D
Sbjct: 1 MRLDKVLARLGLASSRSEARQLIRHGHVRVNGKVVKDPSYRVKPGD 46
>gnl|CDD|35956 KOG0737, KOG0737, KOG0737, AAA+-type ATPase [Posttranslational
modification, protein turnover, chaperones].
Length = 386
Score = 29.5 bits (66), Expect = 2.0
Identities = 28/114 (24%), Positives = 48/114 (42%), Gaps = 19/114 (16%)
Query: 216 LKTPKLFA---LTSP----LLTTASGTKMGKTL--------SGAIWLNKEMTSPYNFWQY 260
L+ P+LFA L P LL GT GKT+ +GA ++N +++ + W
Sbjct: 112 LRRPELFAKGKLLRPPKGILLYGPPGT--GKTMLAKAIAKEAGANFINVSVSNLTSKWFG 169
Query: 261 WRNIDDADVVSFAKRL--TTLPMSEIDRMAKLQGKEINEAKKIIATEITTMVHG 312
V S A +L + + + E+D + +EA ++ E + G
Sbjct: 170 EAQKLVKAVFSLASKLQPSIIFIDEVDSFLGQRRSTDHEATAMMKNEFMALWDG 223
>gnl|CDD|37356 KOG2145, KOG2145, KOG2145, Cytoplasmic tryptophanyl-tRNA synthetase
[Translation, ribosomal structure and biogenesis].
Length = 397
Score = 28.0 bits (62), Expect = 5.1
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 39 YIGYDLTASSLHAGHLTQLMLLFWLQKTGHKPI 71
Y G ++ S+H GHL + WLQ P+
Sbjct: 89 YTGRGPSSESMHLGHLIPFIFTKWLQDVFDVPL 121
>gnl|CDD|36810 KOG1597, KOG1597, KOG1597, Transcription initiation factor TFIIB
[Transcription].
Length = 308
Score = 27.6 bits (61), Expect = 7.6
Identities = 10/30 (33%), Positives = 14/30 (46%)
Query: 281 MSEIDRMAKLQGKEINEAKKIIATEITTMV 310
EI +A + KEI K+I + T V
Sbjct: 167 FKEISAVANVSKKEIGRCVKLIGEALETSV 196
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.320 0.134 0.392
Gapped
Lambda K H
0.267 0.0690 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,879,614
Number of extensions: 252052
Number of successful extensions: 683
Number of sequences better than 10.0: 1
Number of HSP's gapped: 660
Number of HSP's successfully gapped: 15
Length of query: 418
Length of database: 6,263,737
Length adjustment: 96
Effective length of query: 322
Effective length of database: 4,189,273
Effective search space: 1348945906
Effective search space used: 1348945906
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 (21.8 bits)
S2: 59 (26.6 bits)