RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6240
(233 letters)
>gnl|CDD|223097 COG0018, ArgS, Arginyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 577
Score = 123 bits (310), Expect = 2e-32
Identities = 46/168 (27%), Positives = 76/168 (45%), Gaps = 27/168 (16%)
Query: 65 KVVVEFSSPNIAKPFHVGHFRGTVLGNFVANLSNYFANNVVCLNYLGDWGTQFGLLQIGL 124
KVV+E+SS N P H+GH R ++G+ +A + + +V NY+ DWGTQ G+L +
Sbjct: 118 KVVIEYSSANPTGPLHIGHLRNAIIGDSLARILEFLGYDVTRENYVNDWGTQIGMLALSY 177
Query: 125 KELNIKHTDLEQSPLDVLYKAYVKANELAKINPDVQEQAPLDVLYKAYVKANDLAKINPD 184
++ + L P L + YVK + + +P E
Sbjct: 178 EKRGREALGLTPEPDGYLGEYYVKIAKDLEEDPGNDE----------------------- 214
Query: 185 VQEQASNIFQQLECGKNTLHTKDWLDFQQVTLNELRGTYERLGIHFSV 232
E+A ++LE G + W F ++L ++ T +RLG+ F V
Sbjct: 215 --EEAREEVEKLESGD--EEAELWRKFVDLSLEGIKETLDRLGVKFDV 258
>gnl|CDD|232981 TIGR00456, argS, arginyl-tRNA synthetase. This model recognizes
arginyl-tRNA synthetase in every completed genome to
date. An interesting feature of the alignment of all
arginyl-tRNA synthetases is a fairly deep split between
two families. One family includes archaeal, eukaryotic
and organellar, spirochete, E. coli, and Synechocystis
sp. The second, sharing a deletion of about 25 residues
in the central region relative to the first, includes
Bacillus subtilis, Aquifex aeolicus, the Mycoplasmas and
Mycobacteria, and the Gram-negative bacterium
Helicobacter pylori [Protein synthesis, tRNA
aminoacylation].
Length = 566
Score = 114 bits (287), Expect = 2e-29
Identities = 48/195 (24%), Positives = 87/195 (44%), Gaps = 27/195 (13%)
Query: 37 VDKTEFITQVLTS-TGDKHVYKTQLNCTDKVVVEFSSPNIAKPFHVGHFRGTVLGNFVAN 95
+ + + +++ K Y ++ K+++EFSS N A P H+GH R ++G+ +A
Sbjct: 84 LSPQKLLERLIQKILTQKEDYGSKKLKNKKIIIEFSSANPAGPLHIGHLRNAIIGDSLAR 143
Query: 96 LSNYFANNVVCLNYLGDWGTQFGLLQIGLKELNIKHTDLEQSPLDVLYKAYVKANELAKI 155
+ + +V+ Y+ DWG QFGLL +G+++ + +
Sbjct: 144 ILEFLGYDVIREYYVNDWGRQFGLLALGVEKFGNEKLNEAVKK----------------- 186
Query: 156 NPDVQEQAPLDVLYKAYVKANDLAKINPDVQEQASNIFQQLECGKNTLHTKDWLDFQQVT 215
P L YV+ N + N +++E+A +F +LE G K W + +
Sbjct: 187 --------PDHGLEGFYVEINKRLEENEELEEEARELFVKLESGDE-EAIKLWKRLVEYS 237
Query: 216 LNELRGTYERLGIHF 230
L ++ T RL IHF
Sbjct: 238 LEGIKETLARLNIHF 252
>gnl|CDD|183534 PRK12451, PRK12451, arginyl-tRNA synthetase; Reviewed.
Length = 562
Score = 110 bits (277), Expect = 6e-28
Identities = 56/174 (32%), Positives = 88/174 (50%), Gaps = 28/174 (16%)
Query: 57 KTQLNCTDKVVVEFSSPNIAKPFHVGHFRGTVLGNFVANLSNYFANNVVCLNYLGDWGTQ 116
+ C VV+++SSPNIAKPF +GH R T++GN + +++ VV +NY+GDWGTQ
Sbjct: 106 QNHFGCEKTVVIDYSSPNIAKPFSMGHLRSTMIGNALKHIAEKCGYEVVGINYIGDWGTQ 165
Query: 117 FGLLQIGLKELNIKHTDLEQSPLDVLYKAYVKANELAKINPDVQEQAPLDVLYKAYVKAN 176
FG L AY K N V ++ P+ L+K YV+ +
Sbjct: 166 FGKLIT----------------------AYKKWG-----NEAVVKEDPIRELFKLYVQFH 198
Query: 177 DLAKINPDVQEQASNIFQQLECGKNTLHTKDWLDFQQVTLNELRGTYERLGIHF 230
+ K + +++E+ F++LE G + + W F+ +L E YE LG+ F
Sbjct: 199 EEVKDDEELEEEGRAWFKKLEEG-DEEAVELWNWFRHESLKEFSRIYELLGVEF 251
>gnl|CDD|234964 PRK01611, argS, arginyl-tRNA synthetase; Reviewed.
Length = 507
Score = 93.3 bits (233), Expect = 5e-22
Identities = 26/63 (41%), Positives = 36/63 (57%)
Query: 65 KVVVEFSSPNIAKPFHVGHFRGTVLGNFVANLSNYFANNVVCLNYLGDWGTQFGLLQIGL 124
KVVVE+ S N P HVGH R V+G+ +A + + +V Y+ D GTQ G+L L
Sbjct: 112 KVVVEYVSANPTGPLHVGHLRSAVIGDALARILEFAGYDVTREYYVNDAGTQIGMLIASL 171
Query: 125 KEL 127
+ L
Sbjct: 172 ELL 174
>gnl|CDD|185675 cd00671, ArgRS_core, catalytic core domain of arginyl-tRNA
synthetases. Arginyl tRNA synthetase (ArgRS) catalytic
core domain. This class I enzyme is a monomer which
aminoacylates 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. There
are at least three subgroups of ArgRS. One type contains
both characteristic class I HIGH and KMSKS motifs, which
are involved in ATP binding. The second subtype lacks
the KMSKS motif; however, it has a lysine N-terminal to
the HIGH motif, which serves as the functional
counterpart to the second lysine of the KMSKS motif. A
third group, which is found primarily in archaea and a
few bacteria, lacks both the KMSKS motif and the HIGH
loop lysine.
Length = 212
Score = 88.0 bits (219), Expect = 2e-21
Identities = 24/62 (38%), Positives = 37/62 (59%)
Query: 65 KVVVEFSSPNIAKPFHVGHFRGTVLGNFVANLSNYFANNVVCLNYLGDWGTQFGLLQIGL 124
K++VEF S N P HVGH R ++G+ +A + + +V Y+ DWG Q GLL + L
Sbjct: 1 KILVEFVSANPTGPLHVGHLRNAIIGDSLARILEFLGYDVTREYYINDWGRQIGLLILSL 60
Query: 125 KE 126
++
Sbjct: 61 EK 62
>gnl|CDD|216097 pfam00750, tRNA-synt_1d, tRNA synthetases class I (R). Other tRNA
synthetase sub-families are too dissimilar to be
included. This family includes only arginyl tRNA
synthetase.
Length = 345
Score = 87.5 bits (217), Expect = 2e-20
Identities = 38/86 (44%), Positives = 50/86 (58%), Gaps = 1/86 (1%)
Query: 65 KVVVEFSSPNIAKPFHVGHFRGTVLGNFVANLSNYFANNVVCLNYLGDWGTQFGLLQIGL 124
KVVVEFSSPN AKP HVGH R T++G+ ++ L + +VV NY+GDWGTQFG+L L
Sbjct: 20 KVVVEFSSPNPAKPIHVGHLRSTIIGDALSRLLEFLGYDVVRENYVGDWGTQFGMLIASL 79
Query: 125 KELNIKHTDLEQSPLDVLYKAYVKAN 150
+ + P+ L Y
Sbjct: 80 EAAAKEEL-TVPMPIQDLEDGYRGIK 104
>gnl|CDD|215160 PLN02286, PLN02286, arginine-tRNA ligase.
Length = 576
Score = 87.8 bits (218), Expect = 5e-20
Identities = 41/104 (39%), Positives = 55/104 (52%), Gaps = 16/104 (15%)
Query: 65 KVVVEFSSPNIAKPFHVGHFRGTVLGNFVANLSNYFANNVVCLNYLGDWGTQFGLLQIGL 124
+ VV+FSSPNIAK HVGH R T++G+ +A + + V+ N++GDWGTQFG+L L
Sbjct: 118 RAVVDFSSPNIAKEMHVGHLRSTIIGDTLARMLEFSGVEVLRRNHVGDWGTQFGMLIEHL 177
Query: 125 KELNIKHTDLEQSP------LDVLYKAYVKANELAKINPDVQEQ 162
E K + E L YKA AK D E+
Sbjct: 178 FE---KFPNWESVSDQAIGDLQEFYKA-------AKKRFDEDEE 211
>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 = 54.8 bits (132), Expect = 1e-09
Identities = 17/66 (25%), Positives = 22/66 (33%), Gaps = 1/66 (1%)
Query: 68 VEFSSPNIAKPFHVGHFRGTVLGNFVANLSNYFANNVVCLNYLGDWGTQFGLLQIGLKEL 127
FS H+GH R V +F+A V C+ + D G G K
Sbjct: 1 TTFSGITPNGYLHIGHLRTIVTFDFLAQAYRKLGYKVRCIALIDDAGGLIGDPANK-KGE 59
Query: 128 NIKHTD 133
N K
Sbjct: 60 NAKAFV 65
>gnl|CDD|232985 TIGR00463, gltX_arch, glutamyl-tRNA synthetase, archaeal and
eukaryotic family. The glutamyl-tRNA synthetases of the
eukaryotic cytosol and of the Archaea are more similar
to glutaminyl-tRNA synthetases than to bacterial
glutamyl-tRNA synthetases. This model models just the
eukaryotic cytosolic and archaeal forms of the enzyme.
In some eukaryotes, the glutamyl-tRNA synthetase is part
of a longer, multifunctional aminoacyl-tRNA ligase. In
many species, the charging of tRNA(gln) proceeds first
through misacylation with Glu and then transamidation.
For this reason, glutamyl-tRNA synthetases, including
all known archaeal enzymes (as of 2010) may act on both
tRNA(gln) and tRNA(glu) [Protein synthesis, tRNA
aminoacylation].
Length = 556
Score = 30.6 bits (69), Expect = 0.80
Identities = 12/31 (38%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 64 DKVVVEFSSPNIAKPFHVGHFRGTVLGNFVA 94
+VV+ F+ PN + P H+GH R +L + A
Sbjct: 92 GEVVMRFA-PNPSGPLHIGHARAAILNHEYA 121
>gnl|CDD|185768 cd09245, BRO1_UmRIM23-like, Protein-interacting, Bro1-like domain
of Ustilago maydis Rim23 (PalC), and related domains.
This family contains the Bro1-like domain of Ustilago
maydis Rim23 (also known as PalC), and related proteins.
It belongs to the BRO1_Alix_like superfamily which
includes the Bro1-like domains of mammalian Alix
(apoptosis-linked gene-2 interacting protein X),
His-Domain type N23 protein tyrosine phosphatase
(HD-PTP, also known as PTPN23), RhoA-binding proteins
Rhophilin-1 and -2, Brox, Bro1 and Rim20 (also known as
PalA) from Saccharomyces cerevisiae, and related
domains. Alix, HD-PTP, Brox, Bro1, Rim20, and Rim23
interact with the ESCRT (Endosomal Sorting Complexes
Required for Transport) system. Rim20 and Rim23
participate in the response to the external pH via the
Rim101 pathway. Through its Bro1-like domain, Rim23
allows the interaction between the endosomal and plasma
membrane complexes. Bro1-like domains are
boomerang-shape, and part of the domain is a
tetratricopeptide repeat (TPR)-like structure.
Intermediates in the Rim101 pathway may play roles in
the pathogenesis of fungal corneal infection during
Candida albicans keratitis. This family lacks the
V-shaped (V) domain found in many members of the
BRO1_Alix_like superfamily.
Length = 413
Score = 30.1 bits (68), Expect = 1.1
Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 3/67 (4%)
Query: 114 GTQFGLLQIGLKELNIKHTDLEQSPLDVLYKAYVKANELAKINPD---VQEQAPLDVLYK 170
G G L+ KEL + + L K++ + E K+ +E L++L K
Sbjct: 313 GEAIGWLRAAKKELEDLKSPSGVASKAKLKKSWKEKREDRKVEKGAGVEEELRTLEMLLK 372
Query: 171 AYVKAND 177
Y K ND
Sbjct: 373 KYKKMND 379
>gnl|CDD|185682 cd09287, GluRS_non_core, catalytic core domain of
non-discriminating glutamyl-tRNA synthetase.
Non-discriminating Glutamyl-tRNA synthetase (GluRS)
cataytic core domain. These enzymes attach Glu to the
appropriate tRNA. Like other class I tRNA synthetases,
they aminoacylate 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
formation of the enzyme bound aminoacyl-adenylate. It
contains the characteristic class I HIGH and KMSKS
motifs, which are involved in ATP binding. These
enzymes function as monomers. Archaea and most bacteria
lack GlnRS. In these organisms, the
"non-discriminating" form of GluRS aminoacylates both
tRNA(Glu) and tRNA(Gln) with Glu, which is converted to
Gln when appropriate by a transamidation enzyme.
Length = 240
Score = 29.6 bits (67), Expect = 1.3
Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 65 KVVVEFSSPNIAKPFHVGHFRGTVL 89
KVV+ F+ PN P H+GH R +L
Sbjct: 1 KVVMRFA-PNPNGPLHLGHARAAIL 24
>gnl|CDD|235229 PRK04156, gltX, glutamyl-tRNA synthetase; Provisional.
Length = 567
Score = 28.7 bits (65), Expect = 3.0
Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 64 DKVVVEFSSPNIAKPFHVGHFRGTVL 89
KVV+ F+ PN + P H+GH R +L
Sbjct: 100 GKVVMRFA-PNPSGPLHLGHARAAIL 124
>gnl|CDD|227434 COG5103, CDC39, Cell division control protein, negative regulator
of transcription [Cell division and chromosome
partitioning / Transcription].
Length = 2005
Score = 28.0 bits (62), Expect = 5.8
Identities = 7/26 (26%), Positives = 12/26 (46%)
Query: 171 AYVKANDLAKINPDVQEQASNIFQQL 196
N D++E+AS+ QQ+
Sbjct: 587 IVAATNTTRSKEIDIEEEASSYIQQI 612
>gnl|CDD|177351 PHA02117, PHA02117, glutathionylspermidine synthase
domain-containing protein.
Length = 397
Score = 27.5 bits (61), Expect = 6.4
Identities = 14/65 (21%), Positives = 28/65 (43%), Gaps = 7/65 (10%)
Query: 89 LGNFVANLSNYFANNVVCLNYLGDWGTQFGLL-------QIGLKELNIKHTDLEQSPLDV 141
L + ++ + V + YL + T+ G + +I L + D E +P+D+
Sbjct: 175 LNGCLNIVATGQVEDFVTIAYLAETATEAGAVVKFFDIQEIQLSDRGPFFVDGEDAPIDM 234
Query: 142 LYKAY 146
+K Y
Sbjct: 235 CFKLY 239
>gnl|CDD|173158 PRK14695, PRK14695, serine/threonine transporter SstT; Provisional.
Length = 319
Score = 26.9 bits (59), Expect = 10.0
Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 9/82 (10%)
Query: 65 KVVVEFSSPNIAKPFHVGHFRGTVLGNFVANLSNYFANNVVCLNYLG--DWGTQFGLLQI 122
++ + ++ IA P +G VL N + L + N ++ NY+G W FG I
Sbjct: 21 EITLNSANTEIAPPDGIGQ----VLSNLLLKLVDSPVNALLTANYIGILSWAVIFG---I 73
Query: 123 GLKELNIKHTDLEQSPLDVLYK 144
++E + +L ++ DV K
Sbjct: 74 AMREASKNSKELLKTIADVTSK 95
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
0.319 0.137 0.408
Gapped
Lambda K H
0.267 0.0752 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,657,183
Number of extensions: 1069891
Number of successful extensions: 885
Number of sequences better than 10.0: 1
Number of HSP's gapped: 879
Number of HSP's successfully gapped: 27
Length of query: 233
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 139
Effective length of database: 6,768,326
Effective search space: 940797314
Effective search space used: 940797314
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: 57 (25.7 bits)