RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1520
(107 letters)
>gnl|CDD|234743 PRK00390, leuS, leucyl-tRNA synthetase; Validated.
Length = 805
Score = 101 bits (255), Expect = 1e-26
Identities = 35/62 (56%), Positives = 40/62 (64%)
Query: 20 NAEVSFNTDKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQG 79
N E F+ + A WLPVD YIGG EHAVLHL YARF L G + EPFK+LL QG
Sbjct: 508 NDEAPFDKEAANYWLPVDQYIGGIEHAVLHLLYARFFTKVLRDLGLVSSDEPFKKLLTQG 567
Query: 80 MI 81
M+
Sbjct: 568 MV 569
>gnl|CDD|232956 TIGR00396, leuS_bact, leucyl-tRNA synthetase, eubacterial and
mitochondrial family. The leucyl-tRNA synthetases
belong to two families so broadly different that they
are represented by separate models. This model includes
both eubacterial and mitochondrial leucyl-tRNA
synthetases. It generates higher scores for some
valyl-tRNA synthetases than for any archaeal or
eukaryotic cytosolic leucyl-tRNA synthetase. Note that
the enzyme from Aquifex aeolicus is split into alpha and
beta chains; neither chain is long enough to score above
the trusted cutoff, but the alpha chain scores well
above the noise cutoff. The beta chain must be found by
a model and search designed for partial length matches
[Protein synthesis, tRNA aminoacylation].
Length = 842
Score = 97.5 bits (243), Expect = 4e-25
Identities = 38/86 (44%), Positives = 50/86 (58%), Gaps = 2/86 (2%)
Query: 19 INAEVSFNTDKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQ 78
N + F+ +KA+ WLPVD+YIGG EHA+LHL YARF FL G +EPFK+L+ Q
Sbjct: 505 KNTDGPFDKEKAEYWLPVDLYIGGIEHAILHLLYARFFHKFLRDIGYVNTKEPFKKLINQ 564
Query: 79 GMIMGQTYREKTSGKYLKPDEVFTKG 104
GM++G Y +GK
Sbjct: 565 GMVLGFYYPP--NGKVPADVLTERDE 588
>gnl|CDD|173906 cd00812, LeuRS_core, catalytic core domain of leucyl-tRNA
synthetases. Leucyl tRNA synthetase (LeuRS) 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. It
contains the characteristic class I HIGH and KMSKS
motifs, which are involved in ATP binding. In Aquifex
aeolicus, the gene encoding LeuRS is split in two, just
before the KMSKS motif. Consequently, LeuRS is a
heterodimer, which likely superimposes with the LeuRS
monomer found in most other organisms. LeuRS has an
insertion in the core domain, which is subject to both
deletions and rearrangements and thus differs between
prokaryotic LeuRS and archaeal/eukaryotic LeuRS. This
editing region hydrolyzes mischarged cognate tRNAs and
thus prevents the incorporation of chemically similar
amino acids.
Length = 314
Score = 87.3 bits (217), Expect = 5e-22
Identities = 37/90 (41%), Positives = 51/90 (56%), Gaps = 6/90 (6%)
Query: 17 RDINAEVSFNTDKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLL 76
+ ++ F+ ++ + W PVDIYIGGKEHA HL Y+RF L +G EP K L+
Sbjct: 206 QPYEGDLEFDREEFEYWYPVDIYIGGKEHAPNHLLYSRFNHKALFDEG-LVTDEPPKGLI 264
Query: 77 VQGMIMGQTYREKTS---GKYLKPDEVFTK 103
VQGM++ + EK S G + PDE K
Sbjct: 265 VQGMVLLEG--EKMSKSKGNVVTPDEAIKK 292
>gnl|CDD|223569 COG0495, LeuS, Leucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 814
Score = 88.5 bits (220), Expect = 6e-22
Identities = 39/85 (45%), Positives = 52/85 (61%), Gaps = 4/85 (4%)
Query: 22 EVSFNTDKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMI 81
E+ F+ ++ W PVD+YIGG EHAVLHL Y RF L +G P EPFK+L+ QGM+
Sbjct: 513 ELPFDREEFNYWYPVDLYIGGIEHAVLHLLYFRFFHKALFDEGLVPKDEPFKKLITQGMV 572
Query: 82 MGQTYREKTS---GKYLKPDEVFTK 103
+G+ EK S G + P+E K
Sbjct: 573 LGEE-GEKMSKSKGNVVDPEEAVEK 596
>gnl|CDD|178177 PLN02563, PLN02563, aminoacyl-tRNA ligase.
Length = 963
Score = 84.9 bits (210), Expect = 1e-20
Identities = 35/82 (42%), Positives = 52/82 (63%), Gaps = 3/82 (3%)
Query: 20 NAEVSFNTDKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQG 79
N+ + +K + W+PVD+Y+GG EHAVLHL YARF L+ G +EPF+ L+ QG
Sbjct: 601 NSNALVDKEKEKYWMPVDLYVGGAEHAVLHLLYARFWHKVLYDIGVVSTKEPFQCLVNQG 660
Query: 80 MIMGQ---TYREKTSGKYLKPD 98
MI+G+ T + + G+Y+ D
Sbjct: 661 MILGEVEYTAFKDSDGEYVSAD 682
>gnl|CDD|185674 cd00668, Ile_Leu_Val_MetRS_core, catalytic core domain of
isoleucyl, leucyl, valyl and methioninyl tRNA
synthetases. Catalytic core domain of isoleucyl,
leucyl, valyl and methioninyl tRNA synthetases. These
class I enzymes are all monomers. However, in some
species, MetRS functions as a homodimer, as a result of
an additional C-terminal domain. These enzymes
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. Enzymes in
this subfamily share an insertion in the core domain,
which is subject to both deletions and rearrangements.
This editing region hydrolyzes mischarged cognate tRNAs
and thus prevents the incorporation of chemically
similar amino acids. MetRS has a significantly shorter
insertion, which lacks the editing function.
Length = 312
Score = 31.6 bits (72), Expect = 0.041
Identities = 18/75 (24%), Positives = 33/75 (44%), Gaps = 8/75 (10%)
Query: 31 QDWLPVDIYIGGKEHAVLHLYYARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTYRE-- 88
+D P D ++ GK+ + +I + G P K LLV G ++ + ++
Sbjct: 222 KDSYPADWHLIGKDILRGWANF--WITMLVALFG----EIPPKNLLVHGFVLDEGGQKMS 275
Query: 89 KTSGKYLKPDEVFTK 103
K+ G + P +V K
Sbjct: 276 KSKGNVIDPSDVVEK 290
>gnl|CDD|217156 pfam02634, FdhD-NarQ, FdhD/NarQ family. A pan-bacterial lineage
of proteins. Nitrate assimilation protein, NarQ, and
FdhD are required for formate dehydrogenase activity.
Structurally, they possess a deaminase fold with a
characteristic binding pocket, suggesting that they
might bind a nucleotide or related molecule
allosterically to regulate the formate dehydrogenase
catalytic subunit.
Length = 235
Score = 27.1 bits (61), Expect = 1.6
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 7/35 (20%)
Query: 35 PVDIYIGGKEHAVL-----HLYYARFIAHFLHAQG 64
P+ IY+ G+E A L L FL ++G
Sbjct: 5 PLAIYLNGRELATLMATPADLED--LALGFLLSEG 37
>gnl|CDD|220146 pfam09228, Prok-TraM, Prokaryotic Transcriptional repressor TraM.
Members of this family of transcriptional repressors
adopt a T-shaped structure, with a core composed of two
antiparallel alpha-helices. These proteins can be
divided into two parts, a 'globular head' and an
'elongated tail', and they negatively regulate
conjugation and the expression of tra genes by
antagonising traR/AAI-dependent activation.
Length = 99
Score = 26.6 bits (59), Expect = 1.7
Identities = 11/34 (32%), Positives = 12/34 (35%), Gaps = 3/34 (8%)
Query: 31 QDWLPVDIYIGGKEHAVLHL-YYARFIAHFLHAQ 63
Q+W D I L L Y I HAQ
Sbjct: 51 QEWASADPKISPAVLGTLQLEYIEAQIES--HAQ 82
>gnl|CDD|234823 PRK00724, PRK00724, formate dehydrogenase accessory protein;
Reviewed.
Length = 263
Score = 26.7 bits (60), Expect = 2.0
Identities = 8/22 (36%), Positives = 11/22 (50%), Gaps = 4/22 (18%)
Query: 31 QDWL----PVDIYIGGKEHAVL 48
+D + PV I G HAV+
Sbjct: 23 EDTVAEEVPVAIVYNGISHAVM 44
>gnl|CDD|65145 pfam01324, Diphtheria_R, Diphtheria toxin, R domain. C-terminal
receptor binding (R) domain - binds to cell surface
receptor, permitting the toxin to enter the cell by
receptor mediated endocytosis.
Length = 154
Score = 26.2 bits (57), Expect = 3.5
Identities = 14/52 (26%), Positives = 27/52 (51%), Gaps = 6/52 (11%)
Query: 11 KTKTKSRDINAEVSFNTDKAQDWLPVDIYIGGKEHAVLHLYYARFIAHFLHA 62
K + + R I+ +V+F K+ +Y+G HA LH+ + R + +H+
Sbjct: 76 KIRMRCRAIDGDVTFCRPKSP------VYVGNGVHANLHVAFHRSSSEKIHS 121
>gnl|CDD|237770 PRK14618, PRK14618, NAD(P)H-dependent glycerol-3-phosphate
dehydrogenase; Provisional.
Length = 328
Score = 25.2 bits (55), Expect = 8.0
Identities = 14/40 (35%), Positives = 18/40 (45%)
Query: 52 YARFIAHFLHAQGKTPAREPFKRLLVQGMIMGQTYREKTS 91
+A IA FL A + EP VQ G ++R TS
Sbjct: 137 HAEEIARFLPAATVVASPEPGLARRVQAAFSGPSFRVYTS 176
>gnl|CDD|215739 pfam00133, tRNA-synt_1, tRNA synthetases class I (I, L, M and V).
Other tRNA synthetase sub-families are too dissimilar to
be included.
Length = 606
Score = 25.0 bits (55), Expect = 9.2
Identities = 11/36 (30%), Positives = 20/36 (55%), Gaps = 2/36 (5%)
Query: 70 EPFKRLLVQGMIMGQTYRE--KTSGKYLKPDEVFTK 103
P+K +LV G++ + R+ K+ G + P +V K
Sbjct: 549 APYKNVLVHGLVRDEQGRKMSKSLGNVIDPLDVIDK 584
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
0.320 0.134 0.398
Gapped
Lambda K H
0.267 0.0702 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,354,256
Number of extensions: 450557
Number of successful extensions: 325
Number of sequences better than 10.0: 1
Number of HSP's gapped: 324
Number of HSP's successfully gapped: 19
Length of query: 107
Length of database: 10,937,602
Length adjustment: 72
Effective length of query: 35
Effective length of database: 7,744,114
Effective search space: 271043990
Effective search space used: 271043990
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: 53 (24.2 bits)