RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5542
(86 letters)
>gnl|CDD|238402 cd00779, ProRS_core_prok, Prolyl-tRNA synthetase (ProRS) class II
core catalytic domain. ProRS is a homodimer. It is
responsible for the attachment of proline to the 3' OH
group of ribose of the appropriate tRNA. This domain is
primarily responsible for ATP-dependent formation of the
enzyme bound aminoacyl-adenylate. Class II assignment is
based upon its structure and the presence of three
characteristic sequence motifs in the core domain. This
subfamily contains the core domain of ProRS from
prokaryotes and from the mitochondria of eukaryotes.
Length = 255
Score = 112 bits (282), Expect = 2e-32
Identities = 41/85 (48%), Positives = 54/85 (63%)
Query: 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
+VA+ S+K LPL LYQ +KFRDE+RP+FGLMR REFLMKD Y+F E + Y
Sbjct: 101 LVANEIKSYKQLPLNLYQIQTKFRDEIRPRFGLMRGREFLMKDAYSFDIDEESLEETYEK 160
Query: 61 VGKCYDDVFNTLGIKYRKVIVRHGA 85
+ + Y +F LG+ + KV GA
Sbjct: 161 MYQAYSRIFKRLGLPFVKVEADSGA 185
>gnl|CDD|236405 PRK09194, PRK09194, prolyl-tRNA synthetase; Provisional.
Length = 565
Score = 100 bits (252), Expect = 1e-26
Identities = 38/80 (47%), Positives = 55/80 (68%)
Query: 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
+V + S+K LPL LYQ +KFRDE+RP+FGLMR REF+MKD Y+F A E ++ Y+
Sbjct: 117 LVRNEIKSYKQLPLNLYQIQTKFRDEIRPRFGLMRGREFIMKDAYSFHADEESLDETYDA 176
Query: 61 VGKCYDDVFNTLGIKYRKVI 80
+ + Y +F+ LG+ +R V
Sbjct: 177 MYQAYSRIFDRLGLDFRAVE 196
>gnl|CDD|232962 TIGR00409, proS_fam_II, prolyl-tRNA synthetase, family II.
Prolyl-tRNA synthetase is a class II tRNA synthetase and
is recognized by pfam model tRNA-synt_2b, which
recognizes tRNA synthetases for Gly, His, Ser, and Pro.
The prolyl-tRNA synthetases are divided into two widely
divergent groups. This group includes enzymes from
Escherichia coli, Bacillus subtilis, Aquifex aeolicus,
the spirochete Treponema pallidum, Synechocystis
PCC6803, and one of the two prolyL-tRNA synthetases of
Saccharomyces cerevisiae. The other group includes the
Pro-specific domain of a human multifunctional tRNA
ligase and the prolyl-tRNA synthetases from the Archaea,
the Mycoplasmas, and the spirochete Borrelia burgdorferi
[Protein synthesis, tRNA aminoacylation].
Length = 568
Score = 99.1 bits (247), Expect = 4e-26
Identities = 38/86 (44%), Positives = 56/86 (65%)
Query: 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
+ + S+K LPL LYQ +KFRDE+RP+FGLMR REF+MKD Y+F + E + Y
Sbjct: 117 LARNEIKSYKQLPLNLYQIQTKFRDEIRPRFGLMRGREFIMKDAYSFHSDEESLDATYQK 176
Query: 61 VGKCYDDVFNTLGIKYRKVIVRHGAV 86
+ + Y ++F+ LG+ +R V GA+
Sbjct: 177 MYQAYSNIFSRLGLDFRPVQADSGAI 202
>gnl|CDD|223519 COG0442, ProS, Prolyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 500
Score = 97.7 bits (244), Expect = 1e-25
Identities = 39/80 (48%), Positives = 48/80 (60%)
Query: 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
M S+K LPL LYQ SKFRDE RP+FGL+R REFLMKD Y+F A E DA + Y
Sbjct: 117 MFRKWIRSYKDLPLKLYQIQSKFRDEKRPRFGLLRGREFLMKDAYSFHADEEDAEETYEK 176
Query: 61 VGKCYDDVFNTLGIKYRKVI 80
+ Y +F L + + V
Sbjct: 177 MLDAYSRIFLRLPLIFGPVP 196
>gnl|CDD|237059 PRK12325, PRK12325, prolyl-tRNA synthetase; Provisional.
Length = 439
Score = 91.5 bits (228), Expect = 2e-23
Identities = 36/68 (52%), Positives = 43/68 (63%)
Query: 8 SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDD 67
S+K LPL LY KFRDE+RP+FG+MR REFLMKD Y+F E A YN + Y
Sbjct: 124 SYKDLPLNLYHIQWKFRDEIRPRFGVMRGREFLMKDAYSFDLDEEGARHSYNRMFVAYLR 183
Query: 68 VFNTLGIK 75
F LG+K
Sbjct: 184 TFARLGLK 191
>gnl|CDD|216009 pfam00587, tRNA-synt_2b, tRNA synthetase class II core domain (G,
H, P, S and T). Other tRNA synthetase sub-families are
too dissimilar to be included. This domain is the core
catalytic domain of tRNA synthetases and includes
glycyl, histidyl, prolyl, seryl and threonyl tRNA
synthetases.
Length = 171
Score = 79.6 bits (197), Expect = 2e-20
Identities = 28/80 (35%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
+ + LS++ LPL LYQ FR E RP+ GL R REF D F E + +
Sbjct: 70 LFKNEILSYRELPLKLYQIGPCFRYEARPRRGLGRVREFTQVDAEIFGTPE-QSEEELEE 128
Query: 61 VGKCYDDVFNTLGIKYRKVI 80
+ K +++ LG+ YR V+
Sbjct: 129 LLKLAEEILQDLGLPYRVVL 148
>gnl|CDD|238395 cd00772, ProRS_core, Prolyl-tRNA synthetase (ProRS) class II core
catalytic domain. ProRS is a homodimer. It is
responsible for the attachment of proline to the 3' OH
group of ribose of the appropriate tRNA. This domain is
primarily responsible for ATP-dependent formation of the
enzyme bound aminoacyl-adenylate. Class II assignment is
based upon its structure and the presence of three
characteristic sequence motifs in the core domain.
Length = 264
Score = 60.1 bits (145), Expect = 2e-12
Identities = 30/86 (34%), Positives = 48/86 (55%), Gaps = 1/86 (1%)
Query: 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
+ A S K LP L Q +KFRDE+RP+FG +R+REF+MKD ++ A +A++ +
Sbjct: 107 IAAKFIKSWKDLPQHLNQIGNKFRDEIRPRFGFLRAREFIMKDGHSAHADAEEADEEFLN 166
Query: 61 VGKCYDDVFNTLG-IKYRKVIVRHGA 85
+ Y ++ L I + + GA
Sbjct: 167 MLSAYAEIARDLAAIDFIEGEADEGA 192
>gnl|CDD|238359 cd00670, Gly_His_Pro_Ser_Thr_tRS_core, Gly_His_Pro_Ser_Thr_tRNA
synthetase class II core domain. This domain is the core
catalytic domain of tRNA synthetases of the subgroup
containing glycyl, histidyl, prolyl, seryl and threonyl
tRNA synthetases. It is primarily responsible for
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. These enzymes belong to class II
aminoacyl-tRNA synthetases (aaRS) based upon their
structure and the presence of three characteristic
sequence motifs in the core domain. This domain is also
found at the C-terminus of eukaryotic GCN2 protein
kinase and at the N-terminus of the ATP
phosphoribosyltransferase accessory subunit, HisZ and
the accessory subunit of mitochondrial polymerase gamma
(Pol gamma b) . Most class II tRNA synthetases are
dimers, with this subgroup consisting of mostly
homodimers. These enzymes attach a specific amino acid
to the 3' OH group of ribose of the appropriate tRNA.
Length = 235
Score = 54.7 bits (132), Expect = 1e-10
Identities = 25/76 (32%), Positives = 37/76 (48%), Gaps = 1/76 (1%)
Query: 6 KLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCY 65
LS++ALPL L Q FR E + GLMR REF + F E +A + +
Sbjct: 81 ILSYRALPLRLDQIGPCFRHEPSGRRGLMRVREFRQVEYVVFGEPE-EAEEERREWLELA 139
Query: 66 DDVFNTLGIKYRKVIV 81
+++ LG+ R V+
Sbjct: 140 EEIARELGLPVRVVVA 155
>gnl|CDD|238391 cd00768, class_II_aaRS-like_core, Class II tRNA amino-acyl
synthetase-like catalytic core domain. Class II amino
acyl-tRNA synthetases (aaRS) share a common fold and
generally attach an amino acid to the 3' OH of ribose of
the appropriate tRNA. PheRS is an exception in that it
attaches the amino acid at the 2'-OH group, like class I
aaRSs. These enzymes are usually homodimers. This domain
is primarily responsible for ATP-dependent formation of
the enzyme bound aminoacyl-adenylate. The substrate
specificity of this reaction is further determined by
additional domains. Intererestingly, this domain is also
found is asparagine synthase A (AsnA), in the accessory
subunit of mitochondrial polymerase gamma and in the
bacterial ATP phosphoribosyltransferase regulatory
subunit HisZ.
Length = 211
Score = 45.2 bits (107), Expect = 3e-07
Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 2/72 (2%)
Query: 10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVF 69
+ LPL L + FR+E GL R REF + F +A++ L+ +++
Sbjct: 72 RKLPLRLAEIGPAFRNEGGR-RGLRRVREFTQLEGEVFGEDGEEASEFEELIEL-TEELL 129
Query: 70 NTLGIKYRKVIV 81
LGIK V V
Sbjct: 130 RALGIKLDIVFV 141
>gnl|CDD|238401 cd00778, ProRS_core_arch_euk, Prolyl-tRNA synthetase (ProRS) class
II core catalytic domain. ProRS is a homodimer. It is
responsible for the attachment of proline to the 3' OH
group of ribose of the appropriate tRNA. This domain is
primarily responsible for ATP-dependent formation of the
enzyme bound aminoacyl-adenylate. Class II assignment is
based upon its structure and the presence of three
characteristic sequence motifs in the core domain. This
subfamily contains the core domain of ProRS from
archaea, the cytoplasm of eukaryotes and some bacteria.
Length = 261
Score = 44.5 bits (106), Expect = 7e-07
Identities = 19/70 (27%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 8 SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDD 67
S++ LPL + Q+ + FR E + +R+REFL ++ + A+E +A + + Y +
Sbjct: 114 SYRDLPLKINQWVNVFRWETKTTRPFLRTREFLWQEGHTAHATEEEAEEEVLQILDLYKE 173
Query: 68 VFNT-LGIKY 76
+ L I
Sbjct: 174 FYEDLLAIPV 183
>gnl|CDD|232961 TIGR00408, proS_fam_I, prolyl-tRNA synthetase, family I.
Prolyl-tRNA synthetase is a class II tRNA synthetase and
is recognized by pfam model tRNA-synt_2b, which
recognizes tRNA synthetases for Gly, His, Ser, and Pro.
The prolyl-tRNA synthetases are divided into two widely
divergent families. This family includes the archaeal
enzyme, the Pro-specific domain of a human
multifunctional tRNA ligase, and the enzyme from the
spirochete Borrelia burgdorferi. The other family
includes enzymes from Escherichia coli, Bacillus
subtilis, Synechocystis PCC6803, and one of the two
prolyL-tRNA synthetases of Saccharomyces cerevisiae
[Protein synthesis, tRNA aminoacylation].
Length = 472
Score = 43.6 bits (103), Expect = 2e-06
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 1/77 (1%)
Query: 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60
M S+ LPL + Q+ + FR E + +R+REF ++ + A+ +A +
Sbjct: 113 MFKKWVKSYTDLPLKINQWVNVFRYETKHTRPFLRTREFTWQEAHTAHATAEEAEEQVLR 172
Query: 61 VGKCYDDVF-NTLGIKY 76
Y + N+L I Y
Sbjct: 173 ALDIYKEFIENSLAIPY 189
>gnl|CDD|232967 TIGR00418, thrS, threonyl-tRNA synthetase. This model represents
the threonyl-tRNA synthetase found in most organisms.
This protein is a class II tRNA synthetase, and is
recognized by the pfam model tRNA-synt_2b. Note that B.
subtilis has closely related isozymes thrS and thrZ. The
N-terminal regions are quite dissimilar between archaeal
and eubacterial forms, while some eukaryotic forms are
missing sequence there altogether. [Protein synthesis,
tRNA aminoacylation].
Length = 563
Score = 41.5 bits (98), Expect = 9e-06
Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 2/80 (2%)
Query: 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKF-GLMRSREFLMKDLYAFTASEVDANDVYN 59
+ S++ LPL + + R E + GLMR R F D + F + + N
Sbjct: 270 IFKSSLRSYRDLPLRIAELGYSHRYEQSGELHGLMRVRGFTQDDAHIFCTEDQIKEEFKN 329
Query: 60 LVGKCYDDVFNTLGIKYRKV 79
V++ G + K
Sbjct: 330 QFRLIQ-KVYSDFGFSFDKY 348
>gnl|CDD|236327 PRK08661, PRK08661, prolyl-tRNA synthetase; Provisional.
Length = 477
Score = 40.5 bits (96), Expect = 2e-05
Identities = 13/33 (39%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 8 SHKALPLLLYQFTSKFRDELRPKFGLMRSREFL 40
S++ LPLL Q+ + R E + + +R+REFL
Sbjct: 126 SYRDLPLLYNQWVNVVRWETKTRP-FLRTREFL 157
>gnl|CDD|223518 COG0441, ThrS, Threonyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 589
Score = 40.7 bits (96), Expect = 2e-05
Identities = 19/83 (22%), Positives = 34/83 (40%), Gaps = 2/83 (2%)
Query: 1 MVADMKLSHKALPLLLYQFTSKFRDELR-PKFGLMRSREFLMKDLYAFTASEVDANDVYN 59
+ S++ LPL L +F +R E GLMR R F D + F + ++
Sbjct: 289 IFKSGLRSYRELPLRLAEFGYVYRYEKSGALHGLMRVRGFTQDDAHIFCTPDQIKDEFKG 348
Query: 60 LVGKCYDDVFNTLGIKYRKVIVR 82
++ +V+ G +V +
Sbjct: 349 ILELIL-EVYKDFGFTDYEVKLS 370
>gnl|CDD|235190 PRK03991, PRK03991, threonyl-tRNA synthetase; Validated.
Length = 613
Score = 37.9 bits (89), Expect = 2e-04
Identities = 26/85 (30%), Positives = 40/85 (47%), Gaps = 5/85 (5%)
Query: 1 MVADMKLSHKALPLLLYQFTSK-FRDELRPKF-GLMRSREFLMKDLYAFTASEVDANDV- 57
M+ DM +S+K LPL +Y+ ++ FR E R + GL R R F M D++ A +
Sbjct: 296 MLKDMTISYKNLPLKMYELSTYSFRLEQRGELVGLKRLRAFTMPDMHTLCKDMEQAMEEF 355
Query: 58 YNLVGKCYDDVFNTLGIKYRKVIVR 82
+ LG Y +V +R
Sbjct: 356 EKQYEMIL-ETGEDLGRDY-EVAIR 378
>gnl|CDD|232951 TIGR00389, glyS_dimeric, glycyl-tRNA synthetase, dimeric type.
This model describes a glycyl-tRNA synthetase distinct
from the two alpha and two beta chains of the tetrameric
E. coli glycyl-tRNA synthetase. This enzyme is a
homodimeric class II tRNA synthetase and is recognized
by pfam model tRNA-synt_2b, which recognizes His, Ser,
Pro, and this set of glycyl-tRNA synthetases [Protein
synthesis, tRNA aminoacylation].
Length = 551
Score = 37.5 bits (87), Expect = 2e-04
Identities = 15/50 (30%), Positives = 24/50 (48%)
Query: 12 LPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLV 61
LP + Q FR+E+ P+ GL R REF ++ F ++ + V
Sbjct: 182 LPFGVAQIGKSFRNEISPRNGLFRVREFEQAEIEFFVHPLDKSHPKFEEV 231
>gnl|CDD|238394 cd00771, ThrRS_core, Threonyl-tRNA synthetase (ThrRS) class II core
catalytic domain. ThrRS is a homodimer. It is
responsible for the attachment of threonine to the 3' OH
group of ribose of the appropriate tRNA. This domain is
primarily responsible for ATP-dependent formation of the
enzyme bound aminoacyl-adenylate. Class II assignment is
based upon its structure and the presence of three
characteristic sequence motifs in the core domain.
Length = 298
Score = 34.4 bits (80), Expect = 0.003
Identities = 22/83 (26%), Positives = 32/83 (38%), Gaps = 9/83 (10%)
Query: 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKF-GLMRSREFLMKDLYAFTA-----SEVDA 54
+ S++ LPL L +F + R E GL R R F D + F E+
Sbjct: 99 IFKSKPRSYRDLPLRLAEFGTVHRYEQSGALHGLTRVRGFTQDDAHIFCTPDQIKEEI-- 156
Query: 55 NDVYNLVGKCYDDVFNTLGIKYR 77
V +L+ + Y D F K
Sbjct: 157 KGVLDLIKEVYSD-FGFFDYKVE 178
>gnl|CDD|178335 PLN02734, PLN02734, glycyl-tRNA synthetase.
Length = 684
Score = 33.6 bits (77), Expect = 0.006
Identities = 14/36 (38%), Positives = 21/36 (58%)
Query: 12 LPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAF 47
LP Q FR+E+ P+ GL+R REF + ++ F
Sbjct: 274 LPFAAAQIGQAFRNEISPRQGLLRVREFTLAEIEHF 309
>gnl|CDD|223500 COG0423, GRS1, Glycyl-tRNA synthetase (class II) [Translation,
ribosomal structure and biogenesis].
Length = 558
Score = 30.4 bits (69), Expect = 0.065
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 12 LPLLLYQFTSKFRDELRPKFGLMRSREFLM 41
LP + Q FR+E+ P+ GL R+REF
Sbjct: 186 LPFGIAQIGKSFRNEISPRNGLFRTREFEQ 215
>gnl|CDD|184826 PRK14799, thrS, threonyl-tRNA synthetase; Provisional.
Length = 545
Score = 30.6 bits (69), Expect = 0.071
Identities = 17/69 (24%), Positives = 36/69 (52%), Gaps = 2/69 (2%)
Query: 8 SHKALPLLLYQFTSKFRDELRPK-FGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYD 66
+++ LP+ +F +R E + + +GL+R R F+ D + F + ++ L+ K
Sbjct: 244 TYRDLPIRFSEFGHVYRWEKKGELYGLLRVRGFVQDDGHIFLREDQLREEIKMLISKTV- 302
Query: 67 DVFNTLGIK 75
+V++ G K
Sbjct: 303 EVWHKFGFK 311
>gnl|CDD|223250 COG0172, SerS, Seryl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 29.5 bits (67), Expect = 0.13
Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 5/85 (5%)
Query: 1 MVADMKLSHKALPLLLYQFTSKFRDEL--RPKF--GLMRSREFLMKDLYAFTASEVDAND 56
+ D L + LP+ ++ FR E K GL+R +F +L T E ++ +
Sbjct: 241 LHRDEILDEEDLPIKYTAYSPCFRSEAGSAGKDTRGLIRVHQFDKVELVVITKPE-ESEE 299
Query: 57 VYNLVGKCYDDVFNTLGIKYRKVIV 81
+ ++V L + YR V +
Sbjct: 300 ELEEMLGNAEEVLQELELPYRVVNL 324
>gnl|CDD|237851 PRK14894, PRK14894, glycyl-tRNA synthetase; Provisional.
Length = 539
Score = 29.2 bits (65), Expect = 0.22
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 8 SHKALPLLLYQFTSKFRDELRPKFGLMRSREF 39
S + LP + Q FR+E+ P+ L R REF
Sbjct: 160 SARKLPFGIAQVGKAFRNEINPRNFLFRVREF 191
>gnl|CDD|237050 PRK12305, thrS, threonyl-tRNA synthetase; Reviewed.
Length = 575
Score = 28.6 bits (65), Expect = 0.27
Identities = 21/77 (27%), Positives = 31/77 (40%), Gaps = 18/77 (23%)
Query: 8 SHKALPLLLYQFTSKFRDELRPK----FGLMRSREFLMKDLYAFT-----ASEVDANDVY 58
S++ LPL L +F + +R E K GL R R F D + F E+ V
Sbjct: 283 SYRDLPLRLAEFGTVYRYE---KSGVLHGLTRVRGFTQDDAHIFCTPDQIEDEI--LKVL 337
Query: 59 NLVGKCYDDVFNTLGIK 75
+ V ++ G K
Sbjct: 338 DFV----LELLKDFGFK 350
>gnl|CDD|238397 cd00774, GlyRS-like_core, Glycyl-tRNA synthetase (GlyRS)-like class
II core catalytic domain. GlyRS functions as a homodimer
in eukaryotes, archaea and some bacteria and as a
heterotetramer in the remainder of prokaryotes. It is
responsible for the attachment of glycine to the 3' OH
group of ribose of the appropriate tRNA. This domain is
primarily responsible for ATP binding and hydrolysis.
This alignment contains only sequences from the GlyRS
form which homodimerizes. The heterotetramer glyQ is in
a different family of class II aaRS. Class II assignment
is based upon its structure and the presence of three
characteristic sequence motifs. This domain is also
found at the N-terminus of the accessory subunit of
mitochondrial polymerase gamma (Pol gamma b). Pol gamma
b stimulates processive DNA synthesis and is functional
as a homodimer, which can associate with the catalytic
subunit Pol gamma alpha to form a heterotrimer. Despite
significant both structural and sequence similarity with
GlyRS, Pol gamma b lacks conservation of several class
II functional residues.
Length = 254
Score = 28.3 bits (64), Expect = 0.33
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 5 MKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLM 41
++ + + LP + Q FR+E+ P+ GL R REF
Sbjct: 99 LEFNRRKLPFGVAQIGKSFRNEISPRNGLFRVREFTQ 135
>gnl|CDD|178496 PLN02908, PLN02908, threonyl-tRNA synthetase.
Length = 686
Score = 27.8 bits (62), Expect = 0.62
Identities = 23/77 (29%), Positives = 33/77 (42%), Gaps = 2/77 (2%)
Query: 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKF-GLMRSREFLMKDLYAFTASEVDANDVYN 59
M A S++ LPL L F R+EL GL R R F D + F + ++V
Sbjct: 390 MFAHRVRSYRELPLRLADFGVLHRNELSGALTGLTRVRRFQQDDAHIFCREDQIKDEVKG 449
Query: 60 LVGKCYDDVFNTLGIKY 76
++ D V+ G Y
Sbjct: 450 VL-DFLDYVYEVFGFTY 465
>gnl|CDD|219094 pfam06583, Neogenin_C, Neogenin C-terminus. This family represents
the C-terminus of eukaryotic neogenin precursor
proteins, which contains several potential
phosphorylation sites. Neogenin is a member of the N-CAM
family of cell adhesion molecules (and therefore
contains multiple copies of pfam00047 and pfam00041) and
is closely related to the DCC tumour suppressor gene
product - these proteins may play an integral role in
regulating differentiation programmes and/or cell
migration events within many adult and embryonic
tissues.
Length = 295
Score = 27.6 bits (61), Expect = 0.67
Identities = 14/26 (53%), Positives = 16/26 (61%), Gaps = 3/26 (11%)
Query: 25 DELRPKFGLMRSREFLMKDLYAFTAS 50
DEL + M S E LMKDL A TA+
Sbjct: 273 DELSEE---MASLEGLMKDLNAITAA 295
>gnl|CDD|213530 TIGR00442, hisS, histidyl-tRNA synthetase. This model finds a
histidyl-tRNA synthetase in every completed genome.
Apparent second copies from Bacillus subtilis,
Synechocystis sp., and Aquifex aeolicus are slightly
shorter, more closely related to each other than to
other hisS proteins, and actually serve as regulatory
subunits for an enzyme of histidine biosynthesis. They
were excluded from the seed alignment and score much
lower than do single copy histidyl-tRNA synthetases of
other genomes not included in the seed alignment. These
putative second copies of HisS score below the trusted
cutoff. The regulatory protein kinase GCN2 of
Saccharomyces cerevisiae (YDR283c), and related proteins
from other species designated eIF-2 alpha kinase, have a
domain closely related to histidyl-tRNA synthetase that
may serve to detect and respond to uncharged tRNA(his),
an indicator of amino acid starvation; these regulatory
proteins are not orthologous and so score below the
noise cutoff [Protein synthesis, tRNA aminoacylation].
Length = 397
Score = 27.4 bits (62), Expect = 0.84
Identities = 15/39 (38%), Positives = 18/39 (46%), Gaps = 4/39 (10%)
Query: 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREF 39
V + KL P LY FR E RP+ G R R+F
Sbjct: 86 AVIENKL-LLPKPFKLYYIGPMFRYE-RPQKG--RYRQF 120
>gnl|CDD|223845 COG0774, LpxC, UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell
envelope biogenesis, outer membrane].
Length = 300
Score = 26.1 bits (58), Expect = 2.1
Identities = 20/68 (29%), Positives = 26/68 (38%), Gaps = 18/68 (26%)
Query: 23 FRDELRP--KFGLMRSREFLMKDLYAFTAS-----EVDANDVYNLVGKCYDDVFNTLGIK 75
FR E+ FG MR E+L A S +D + V N G ++D F
Sbjct: 182 FRKEIARARTFGFMRDVEYLRSKGLALGGSLENAIVIDDDRVLNPEGLRFEDEF------ 235
Query: 76 YRKVIVRH 83
VRH
Sbjct: 236 -----VRH 238
>gnl|CDD|200397 TIGR04146, GGGPS_Afulg, phosphoglycerol geranylgeranyltransferase.
This enzyme, known also as GGGP synthase and GGGPS,
catalyzes the stereospecific first step in the
biosynthesis of the characteristic membrane diether
lipids of archaea. Interestingly, the closest homologs
outside this family are not the functionally equivalent
enzymes of other archaea, but rather functionally
distinct bacterial enzymes.
Length = 221
Score = 25.8 bits (57), Expect = 2.9
Identities = 14/36 (38%), Positives = 18/36 (50%)
Query: 45 YAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVI 80
Y F S ++ D +VGK D V N I + KVI
Sbjct: 76 YLFVPSVLNTKDPEWIVGKHKDWVRNYDNIVWDKVI 111
>gnl|CDD|234586 PRK00037, hisS, histidyl-tRNA synthetase; Reviewed.
Length = 412
Score = 25.9 bits (58), Expect = 2.9
Identities = 14/33 (42%), Positives = 17/33 (51%), Gaps = 3/33 (9%)
Query: 7 LSHKALPLLLYQFTSKFRDELRPKFGLMRSREF 39
+ HK P LY FR E RP+ G R R+F
Sbjct: 92 IEHKLQPFKLYYIGPMFRYE-RPQKG--RYRQF 121
>gnl|CDD|238393 cd00770, SerRS_core, Seryl-tRNA synthetase (SerRS) class II core
catalytic domain. SerRS is responsible for the
attachment of serine to the 3' OH group of ribose of the
appropriate tRNA. This domain It is primarily
responsible for ATP-dependent formation of the enzyme
bound aminoacyl-adenylate. Class II assignment is based
upon its structure and the presence of three
characteristic sequence motifs in the core domain. SerRS
synthetase is a homodimer.
Length = 297
Score = 25.6 bits (57), Expect = 3.2
Identities = 22/83 (26%), Positives = 36/83 (43%), Gaps = 5/83 (6%)
Query: 1 MVADMKLSHKALPLLLYQFTSKFRDE----LRPKFGLMRSREFLMKDLYAFTASEVDAND 56
+ D L + LPL ++ FR E R GL R +F + + FT E +
Sbjct: 119 LHRDEILEEEELPLKYAGYSPCFRKEAGSAGRDTRGLFRVHQFEKVEQFVFTKPEESWEE 178
Query: 57 VYNLVGKCYDDVFNTLGIKYRKV 79
+ L+ +++ LG+ YR V
Sbjct: 179 LEELISNA-EEILQELGLPYRVV 200
>gnl|CDD|238396 cd00773, HisRS-like_core, Class II Histidinyl-tRNA synthetase
(HisRS)-like catalytic core domain. HisRS is a
homodimer. It is responsible for the attachment of
histidine to the 3' OH group of ribose of the
appropriate tRNA. This domain is primarily responsible
for ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. Class II assignment is based upon
its structure and the presence of three characteristic
sequence motifs. This domain is also found at the
C-terminus of eukaryotic GCN2 protein kinase and at the
N-terminus of the ATP phosphoribosyltransferase
accessory subunit, HisZ. HisZ along with HisG catalyze
the first reaction in histidine biosynthesis. HisZ is
found only in a subset of bacteria and differs from
HisRS in lacking a C-terminal anti-codon binding domain.
Length = 261
Score = 25.3 bits (56), Expect = 4.8
Identities = 16/35 (45%), Positives = 17/35 (48%), Gaps = 3/35 (8%)
Query: 5 MKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREF 39
L LPL LY FR E RP+ G R REF
Sbjct: 74 ENLLSLPLPLKLYYIGPVFRYE-RPQKG--RYREF 105
>gnl|CDD|214580 smart00242, MYSc, Myosin. Large ATPases. ATPase; molecular motor.
Muscle contraction consists of a cyclical interaction
between myosin and actin. The core of the myosin
structure is similar in fold to that of kinesin.
Length = 677
Score = 24.8 bits (55), Expect = 6.9
Identities = 6/23 (26%), Positives = 12/23 (52%)
Query: 17 YQFTSKFRDELRPKFGLMRSREF 39
YQ + +EL+ + GL ++
Sbjct: 200 YQLLAGASEELKKELGLKSPEDY 222
>gnl|CDD|215307 PLN02567, PLN02567, alpha,alpha-trehalase.
Length = 554
Score = 24.6 bits (54), Expect = 7.9
Identities = 8/18 (44%), Positives = 12/18 (66%), Gaps = 2/18 (11%)
Query: 4 DMKLSHKALPLLL--YQF 19
D++L +ALP LL + F
Sbjct: 221 DVELVRRALPALLKEHAF 238
>gnl|CDD|235240 PRK04173, PRK04173, glycyl-tRNA synthetase; Provisional.
Length = 456
Score = 24.3 bits (54), Expect = 8.6
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 23 FRDELRPKFGLMRSREF 39
FR+E+ P+ + R+REF
Sbjct: 196 FRNEITPRNFIFRTREF 212
>gnl|CDD|225309 COG2511, GatE, Archaeal Glu-tRNAGln amidotransferase subunit E
(contains GAD domain) [Translation, ribosomal structure
and biogenesis].
Length = 631
Score = 24.6 bits (54), Expect = 9.4
Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 22 KFRDELRPKFGLMRSREFL-MKDLYAFTASEV 52
K RDEL+ + G S E + DL+A T S++
Sbjct: 265 KIRDELKERGGADVSEEVFDVTDLFANTKSKI 296
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
0.327 0.142 0.413
Gapped
Lambda K H
0.267 0.0809 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,394,442
Number of extensions: 353697
Number of successful extensions: 386
Number of sequences better than 10.0: 1
Number of HSP's gapped: 380
Number of HSP's successfully gapped: 41
Length of query: 86
Length of database: 10,937,602
Length adjustment: 54
Effective length of query: 32
Effective length of database: 8,542,486
Effective search space: 273359552
Effective search space used: 273359552
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.0 bits)