RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy938
(241 letters)
>gnl|CDD|235645 PRK05912, PRK05912, tyrosyl-tRNA synthetase; Validated.
Length = 408
Score = 146 bits (371), Expect = 1e-41
Identities = 69/197 (35%), Positives = 103/197 (52%), Gaps = 17/197 (8%)
Query: 8 GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
GLT P++ G+K GKS NA+WLD + +S +E+YQ + D++V+ LKL +F SL
Sbjct: 219 GLTMPLLTGLDGKKMGKSEGNAVWLDEEKTSPYEMYQKWMNISDADVWRYLKLLTFLSLE 278
Query: 68 AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
IE+ + + P R A+K LAE++T LVHGEE ++A+ A +AL+ G L
Sbjct: 279 EIEELEEELAEGPNPREAKKVLAEEITALVHGEEAAEAAEEAFEALFGS-----GELPD- 332
Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
VEL E G+ +L L + P EA I +GG +N +KV + V
Sbjct: 333 -------DLPEVEL--ELGIDLLALLVEAGLVPSKSEARRLIKQGGVKINGEKVSDENYV 383
Query: 188 LSPSAHILPNSLTLLRV 204
L +A T+L+
Sbjct: 384 L--TADDRFGKYTVLQR 398
>gnl|CDD|223240 COG0162, TyrS, Tyrosyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 401
Score = 126 bits (318), Expect = 3e-34
Identities = 71/197 (36%), Positives = 110/197 (55%), Gaps = 17/197 (8%)
Query: 8 GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
GLTTP++ G+K GKS A+WLDS+ +S ++ YQY + +D++V LKL +F SL
Sbjct: 211 GLTTPLLTGLDGKKMGKSEGGAVWLDSEKTSPYDFYQYWMNIEDADVKRFLKLLTFLSLE 270
Query: 68 AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
IE+ ++ PE R A+K LA+++T LVHGEE ++A+ + L+S+ L +L
Sbjct: 271 EIEEIEKYVLKGPEPREAKKLLAKEVTKLVHGEEAAEAAEEEFEKLFSEGLPE--NLPPA 328
Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
D + +V+LL ++ LA P EA I +GG +N +KV++ V
Sbjct: 329 DLKQKLE-DGLVDLL-------VDAGLA----PSRSEARRLIQQGGVKINGEKVEDENYV 376
Query: 188 LSPSAHILPNSLTLLRV 204
LS +L N L +LR
Sbjct: 377 LS---DLLDNGLLVLRR 390
>gnl|CDD|237360 PRK13354, PRK13354, tyrosyl-tRNA synthetase; Provisional.
Length = 410
Score = 125 bits (316), Expect = 7e-34
Identities = 63/187 (33%), Positives = 98/187 (52%), Gaps = 13/187 (6%)
Query: 8 GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
GLT P++E G K GKSA AIWLD + +S +E YQ+ + D +V LKLF+ S
Sbjct: 217 GLTMPLLEGADGTKMGKSAGGAIWLDPEKTSPYEFYQFWMNIDDRDVVKYLKLFTDLSPD 276
Query: 68 AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
I++ + Q E +P R A+K LAE++T VHGEE + A+ +AL+S D+ L +
Sbjct: 277 EIDELEAQLETEPNPRDAKKVLAEEITKFVHGEEAAEEAEKIFKALFSGDVKPLKDIPTF 336
Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
+ S +V+LL++ G+ P +EA I G +N +KV + +
Sbjct: 337 EVSA--ETKNLVDLLVDLGLE-----------PSKREARRLIQNGAIKINGEKVTDVDAI 383
Query: 188 LSPSAHI 194
++P
Sbjct: 384 INPEDAF 390
>gnl|CDD|232889 TIGR00234, tyrS, tyrosyl-tRNA synthetase. This tyrosyl-tRNA
synthetase model starts picking up tryptophanyl-tRNA
synthetases at scores of 0 and below. The proteins found
by this model have a deep split between two groups. One
group contains bacterial and organellar eukaryotic
examples. The other contains archaeal and cytosolic
eukaryotic examples [Protein synthesis, tRNA
aminoacylation].
Length = 377
Score = 94.0 bits (234), Expect = 2e-22
Identities = 58/182 (31%), Positives = 87/182 (47%), Gaps = 17/182 (9%)
Query: 8 GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
GLT P++ GEK GKS A+ LD ++ YQ+ I T D +V +LKLF+F L
Sbjct: 208 GLTVPLLTPADGEKMGKSEGGAVSLDEGK---YDFYQFWINTPDEDVKKILKLFTFLGLE 264
Query: 68 AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
IE P R ++ LA+++T VHGEE +A+ ++AL+S L+
Sbjct: 265 EIEALV--ELKGPSPREVKENLAKEITKYVHGEEAALAAEEISEALFSGGLNPDE----L 318
Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
R + L +L LS FP EA I +GG Y+N +KV++ + +
Sbjct: 319 PIFRPEKFGGDITL-----ADLLVLSGL---FPSKSEARRDIKQGGVYINGEKVKDLEPI 370
Query: 188 LS 189
Sbjct: 371 RK 372
>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 = 91.1 bits (227), Expect = 4e-22
Identities = 37/89 (41%), Positives = 52/89 (58%), Gaps = 1/89 (1%)
Query: 8 GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
GLTTP++ G K KS NAIW D L S +++YQ + D +V + LKLF+F
Sbjct: 182 GLTTPLLTGLDGGKMSKSEGNAIW-DPVLDSPYDVYQKIRNAFDPDVLEFLKLFTFLDYE 240
Query: 68 AIEDFKRQNEHKPEERRAQKKLAEDLTLL 96
IE+ + ++ P R A+K LAE+LT L
Sbjct: 241 EIEELEEEHAEGPLPRDAKKALAEELTKL 269
>gnl|CDD|216003 pfam00579, tRNA-synt_1b, tRNA synthetases class I (W and Y).
Length = 291
Score = 76.2 bits (188), Expect = 2e-16
Identities = 41/110 (37%), Positives = 56/110 (50%), Gaps = 3/110 (2%)
Query: 8 GLTTPIIESESGE-KFGKSARN-AIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDS 65
GLT P++ G K KSA N AI+LD + S ++ Q D EV LKLF+ S
Sbjct: 183 GLTNPLLTGLDGGKKMSKSAGNSAIFLDDEKESVYKKIQKAYTDPDREVRKDLKLFTELS 242
Query: 66 LAAIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYS 115
IE + P +R A++ LA ++T LVHG + K+A A AL
Sbjct: 243 NEEIEILEAFLGKGP-KREAEELLAREVTGLVHGGDLKKAAAEAVNALLE 291
>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 = 72.7 bits (178), Expect = 3e-15
Identities = 37/87 (42%), Positives = 53/87 (60%)
Query: 8 GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
GLT P++ G KFGKS WLD++ +S +E YQ+ I DS+V ++LK F+F S
Sbjct: 185 GLTIPLVTKLDGPKFGKSESGPKWLDTEKTSPYEFYQFWINAVDSDVINILKYFTFLSKE 244
Query: 68 AIEDFKRQNEHKPEERRAQKKLAEDLT 94
IE +++ P R AQK LAE++T
Sbjct: 245 EIERLEQEQYEAPGYRVAQKTLAEEVT 271
>gnl|CDD|237029 PRK12268, PRK12268, methionyl-tRNA synthetase; Reviewed.
Length = 556
Score = 29.8 bits (68), Expect = 1.5
Identities = 18/69 (26%), Positives = 25/69 (36%), Gaps = 27/69 (39%)
Query: 18 SGEKFGKSARNAIWLDSKLSSSFELYQ------YLIR----TKDSEVYDLLKLFSFDSLA 67
G KF KS IW+D L E Y YL D++ F++
Sbjct: 331 EGGKFSKSRGWGIWVDDAL----ERYPPDYLRYYLAANAPENSDTD-------FTW---- 375
Query: 68 AIEDFKRQN 76
E+F R+
Sbjct: 376 --EEFVRRV 382
>gnl|CDD|234514 TIGR04231, seadorna_VP5, seadornavirus VP5 protein. This protein
family occurs in the seadornavirus virus group, with
designations VP5 in Banna virus, and VP6 in Kadipiro
virus and Liao ning virus. The function is unassigned.
Length = 505
Score = 29.5 bits (66), Expect = 1.6
Identities = 14/70 (20%), Positives = 22/70 (31%), Gaps = 7/70 (10%)
Query: 162 DKEANLTISEGGFYVNYKKVQNPQE-------VLSPSAHILPNSLTLLRVEVSANIIAKS 214
DK NL + Y+ + S+ +L N T ++ A S
Sbjct: 429 DKRHNLESAVVDDVQKYRLEEVKTGNSASGLLKAKESSGVLINDNTTFKINSDVVFDASS 488
Query: 215 ANIIAKSANI 224
+ I S I
Sbjct: 489 SVIADTSKGI 498
>gnl|CDD|214638 smart00363, S4, S4 RNA-binding domain.
Length = 60
Score = 26.4 bits (59), Expect = 2.5
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 164 EANLTISEGGFYVNYKKVQNPQEVLSPSAHI 194
+A I +G VN KKV P ++ P I
Sbjct: 18 QARRLIEQGRVKVNGKKVTKPSYIVKPGDVI 48
>gnl|CDD|201819 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 = 25.9 bits (58), Expect = 3.3
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 169 ISEGGFYVNYKKVQNPQEVLSPSAHI 194
I G VN K V++P + P I
Sbjct: 23 IRHGHVRVNGKVVKDPSYRVKPGDVI 48
>gnl|CDD|219978 pfam08701, GN3L_Grn1, GNL3L/Grn1 putative GTPase. Grn1 (yeast)
and GNL3L (human) are putative GTPases which are
required for growth and play a role in processing of
nucleolar pre-rRNA. This family contains a potential
nuclear localisation signal.
Length = 80
Score = 26.1 bits (58), Expect = 5.7
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 66 LAAIEDFKRQNEHKPEERRAQKKLAEDLTL 95
L IE+ KR+ E + E R+ +K
Sbjct: 48 LEEIEEKKRKQEEEKERRKEARKAERAEAR 77
>gnl|CDD|182465 PRK10443, rihA, ribonucleoside hydrolase 1; Provisional.
Length = 311
Score = 27.3 bits (61), Expect = 7.8
Identities = 12/34 (35%), Positives = 14/34 (41%), Gaps = 2/34 (5%)
Query: 85 AQKKLAEDLTLL--VHGEEGLKSAKLATQALYSQ 116
A K L +L + VHGE GL L Q
Sbjct: 67 AVKPLMRELIIADNVHGESGLDGPALPEPTFAPQ 100
>gnl|CDD|220916 pfam10962, DUF2764, Protein of unknown function (DUF2764). This
bacterial family of proteins has no known function.
Length = 271
Score = 26.9 bits (60), Expect = 9.2
Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 6/74 (8%)
Query: 33 DSKLSSSFELYQYLIR----TKDSEVYDLLKLFSFDSLAAIEDFKRQNEHK-PEERRAQK 87
DSKLS +F ++ + KD ++ DLL L FD+ + P R Q
Sbjct: 18 DSKLSYTFADFKDELYLNLSEKDKKLIDLLYLK-FDNENLLAFLWDGEPLPDPRGRITQD 76
Query: 88 KLAEDLTLLVHGEE 101
+L E ++ ++
Sbjct: 77 ELEELISAQRESDK 90
>gnl|CDD|226408 COG3892, COG3892, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 310
Score = 27.0 bits (60), Expect = 9.9
Identities = 14/68 (20%), Positives = 24/68 (35%), Gaps = 6/68 (8%)
Query: 54 VYDLLKLFSFDSLAAIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSA------K 107
+ L + +FD + +ED + K+LA V G GL+ +
Sbjct: 25 DWPELCVLAFDHRSQLEDIAAEAGADESRIPTFKQLALRAARKVAGGRGLQGYGMLIDGR 84
Query: 108 LATQALYS 115
AL +
Sbjct: 85 FGRDALAA 92
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.314 0.131 0.356
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,727,502
Number of extensions: 1080653
Number of successful extensions: 708
Number of sequences better than 10.0: 1
Number of HSP's gapped: 700
Number of HSP's successfully gapped: 23
Length of query: 241
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 147
Effective length of database: 6,768,326
Effective search space: 994943922
Effective search space used: 994943922
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: 42 (22.0 bits)
S2: 58 (26.0 bits)