RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4709
(86 letters)
>gnl|CDD|221996 pfam13232, Complex1_LYR_1, Complex1_LYR-like. This is a family
of proteins carrying the LYR motif of family
Complex1_LYR, pfam05347, likely to be involved in Fe-S
cluster biogenesis in mitochondria.
Length = 61
Score = 63.0 bits (154), Expect = 3e-15
Identities = 22/61 (36%), Positives = 39/61 (63%)
Query: 19 AEVLGLYKTFLRTAKEIPDESSRKEMIDWIRSEFKHNKHLSDETSIKMMIQYGQRSLKEV 78
EVL LY+ LR A++ PD + R+ + IR EF+ NK L+D I+ +++ G++ L+ +
Sbjct: 1 KEVLSLYRQLLRAARKFPDYNFREYIRRRIRDEFRKNKDLTDPEKIEKLLKEGKKQLELL 60
Query: 79 E 79
+
Sbjct: 61 K 61
>gnl|CDD|203236 pfam05347, Complex1_LYR, Complex 1 protein (LYR family).
Proteins in this family have been identified as a
component of the higher eukaryotic NADH complex. In
Saccharomyces cerevisiae, the Isd11 protein has been
shown to play a role in Fe/S cluster biogenesis in
mitochondria. We have named this family LYR after a
highly conserved tripeptide motif close to the
N-terminus of these proteins.
Length = 59
Score = 62.2 bits (152), Expect = 6e-15
Identities = 22/59 (37%), Positives = 38/59 (64%)
Query: 19 AEVLGLYKTFLRTAKEIPDESSRKEMIDWIRSEFKHNKHLSDETSIKMMIQYGQRSLKE 77
EVL LY+ LR A++ PD ++R+ IR EF+ NK+L+D I+ +++ G++ L+
Sbjct: 1 KEVLSLYRQLLREARKFPDYNAREYFRRRIRDEFRKNKNLTDPEKIEALLKEGKKQLEV 59
>gnl|CDD|237678 PRK14335, PRK14335, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 455
Score = 27.6 bits (61), Expect = 0.70
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 27 TFLRTAKEIPDESSRKEMIDWIRSEFKHNKHLSDE 61
TF + + I + + I WIR H K LSD+
Sbjct: 222 TFPQLLRHIVRRAEVTDQIRWIRFMSSHPKDLSDD 256
>gnl|CDD|221997 pfam13233, Complex1_LYR_2, Complex1_LYR-like. This is a family
of proteins carrying the LYR motif of family
Complex1_LYR, pfam05347, likely to be involved in Fe-S
cluster biogenesis in mitochondria.
Length = 97
Score = 27.0 bits (60), Expect = 0.77
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 4/53 (7%)
Query: 21 VLGLYKTFLRTAKEIPDE----SSRKEMIDWIRSEFKHNKHLSDETSIKMMIQ 69
VL LY+ LR + P SS ++R EF+ + +D+ K +Q
Sbjct: 1 VLRLYRELLRELPKYPLRYNLLSSLSLGRRYVRKEFRRHAGATDDELAKEFLQ 53
>gnl|CDD|219423 pfam07477, Glyco_hydro_67C, Glycosyl hydrolase family 67
C-terminus. Alpha-glucuronidases, components of an
ensemble of enzymes central to the recycling of
photosynthetic biomass, remove the alpha-1,2 linked
4-O-methyl glucuronic acid from xylans. This family
represents the C terminal region of alpha-glucuronidase
which is mainly alpha-helical. It wraps around the
catalytic domain (pfam07488), making additional
interactions both with the N-terminal domain
(pfam03648) of its parent monomer and also forming the
majority of the dimer-surface with the equivalent
C-terminal domain of the other monomer of the dimer.
Length = 225
Score = 27.2 bits (61), Expect = 0.97
Identities = 11/34 (32%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 36 PDESSRKEMIDWIRSEFKHNKHLSDETSIKMMIQ 69
PD SS + +WIR F ++ + D S +M+++
Sbjct: 20 PDLSSEEIADEWIRLTFGNDPKVVDTIS-EMLME 52
>gnl|CDD|234375 TIGR03860, FMN_nitrolo, FMN-dependent oxidoreductase,
nitrilotriacetate monooxygenase family. This model
represents a distinctive clade, in which all
characterized members are FMN-binding, within the larger
family of luciferase-like monooxygenases (LLM), among
which there are both FMN- and F420-binding enzymes. A
well-characterized member is nitrilotriacetate
monooxygenase from Aminobacter aminovorans
(Chelatobacter heintzii), where nitrilotriacetate is a
chelating agent used in detergents [Unknown function,
Enzymes of unknown specificity].
Length = 422
Score = 27.1 bits (61), Expect = 1.1
Identities = 7/38 (18%), Positives = 15/38 (39%), Gaps = 5/38 (13%)
Query: 13 RQFLLRAEVLGLYKTFLRTAKEIPDESSRKEMIDWIRS 50
RQ R + F+ T +++ D ++ +W
Sbjct: 344 RQLAERLAGGRGHPVFVGTPEQVAD-----QLEEWFEE 376
>gnl|CDD|181619 PRK09039, PRK09039, hypothetical protein; Validated.
Length = 343
Score = 26.5 bits (59), Expect = 1.7
Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 6/31 (19%)
Query: 18 RAEVLGLYKTFLRTAKEIPDESSRKEMIDWI 48
+AE+ L + AKEIP E I+W+
Sbjct: 240 QAEIAKLAAALIELAKEIPPE------INWV 264
>gnl|CDD|233476 TIGR01574, miaB-methiolase, tRNA-N(6)-(isopentenyl)adenosine-37
thiotransferase enzyme MiaB. This model represents
homologs of the MiaB enzyme responsible for the
modification of the isopentenylated adenine-37 base of
most bacterial and eukaryotic tRNAs that read codons
beginning with uracil (all except tRNA(I,V) Ser).
Adenine-37 is next to the anticodon on the 3' side in
these tRNA's, and lack of modification at this site
leads to an increased spontaneous mutation frequency.
Isopentenylated A-37 is modified by methylthiolation at
position 2, either by MiaB alone or in concert with a
separate methylase yet to be discovered (MiaC?). MiaB
contains a 4Fe-4S cluster which is labile under
oxidizing conditions. Additionally, the sequence is
homologous (via PSI-BLAST searches) to the biotin
synthetase, BioB, which utilizes both an iron-sulfur
cluster and S-adenosym methionine (SAM) to generate a
radical which is responsible for initiating the
insertion of sulfur into the substrate. It is reasonable
to surmise that the methyl group of SAM becomes the
methyl group of the product, but this has not been
shown, and the possibility of a separate methylase
exists. This equivalog is a member of a subfamily
(TIGR00089) which contains several other hypothetical
equivalogs which are all probably enzymes with similar
function acting on different substrates. These enzymes
contain a TRAM domain (pfam01938) which is believed to
be responsible for binding to tRNAs. Hits to this model
span all major groups of bacteria and eukaryotes, but
not archaea, which are known to lack this particular
tRNA modification. The enzyme from Thermotoga maritima
has been cloned, expressed, spectroscopically
characterized and shown to complement the E. coli MiaB
enzyme [Protein synthesis, tRNA and rRNA base
modification].
Length = 438
Score = 26.3 bits (58), Expect = 1.9
Identities = 7/25 (28%), Positives = 10/25 (40%)
Query: 37 DESSRKEMIDWIRSEFKHNKHLSDE 61
E S + I+ IR H D+
Sbjct: 221 RELSTIDGIERIRFTSSHPLDFDDD 245
>gnl|CDD|222692 pfam14338, Mrr_N, Mrr N-terminal domain. This domain is found at
the N-terminus of the Mrr restriction endonuclease
catalytic domain, pfam04471. Fold recognition analysis
predicts that it is a diverged member of the winged
helix variant of helix turn helix proteins. It may play
a role in DNA sequence recognition.
Length = 92
Score = 25.3 bits (56), Expect = 3.0
Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 4/38 (10%)
Query: 24 LYKTFLRTAKEIPDESSRKEMIDWIRSEFKHNKHLSDE 61
L L+ K++ E+ KE+I+ + F LS+E
Sbjct: 5 LMLPLLKALKDLGGEARIKEIIERVAERFN----LSEE 38
>gnl|CDD|240573 cd12953, MMP_TTHA0227, Minimal MMP-like domain found in Thermus
thermophilus hypothetical protein TTHA0227 and similar
proteins. The subfamily includes an uncharacterized
protein from Thermus thermophilus (TTHA0227) and its
homologs from bacteria. Although its biological role
remains unclear, TTHA0227 contains a minimal
metalloprotease (MMP)-like domain consisting of
3-stranded mixed 2-beta sheets and a HExxH (x could be
any amino acid) motif. It may belong to a superfamily
of bacterial zinc metallo-peptidases, which is
characterized by a conserved HExxHxxGxxD motif.
Length = 112
Score = 25.3 bits (56), Expect = 3.8
Identities = 8/34 (23%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 25 YKTFLRTAKEIPDESSRKEMIDWIRSEFKHNKHL 58
Y +F + E ++E+ + + E +H HL
Sbjct: 64 YGSFAAVYGDESREDWKEELRETLLHELRH--HL 95
>gnl|CDD|219155 pfam06741, LsmAD, LsmAD domain. This domain is found associated
with Lsm domain.
Length = 72
Score = 24.2 bits (53), Expect = 5.1
Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 9/59 (15%)
Query: 4 KLPKSTLNFRQFLLRAEVLGLYKTFLRTAKEIPDESSRKEMIDWIRSEFKHNKHLSDET 62
+L KS +++ RAE R A+EI ++ I R + + + +E
Sbjct: 15 RLDKSNPIYKEREARAE---------RIAREIEGSATGNIHIAEERGDLVDDSGVDEED 64
>gnl|CDD|223676 COG0603, COG0603, Predicted PP-loop superfamily ATPase [General
function prediction only].
Length = 222
Score = 24.9 bits (55), Expect = 5.5
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 68 IQYGQRSLKEVESSVSLIK 86
YGQR KE+E++ L K
Sbjct: 34 FDYGQRHRKELEAAKELAK 52
>gnl|CDD|237539 PRK13878, PRK13878, conjugal transfer relaxase TraI; Provisional.
Length = 746
Score = 25.1 bits (55), Expect = 5.8
Identities = 7/35 (20%), Positives = 20/35 (57%)
Query: 17 LRAEVLGLYKTFLRTAKEIPDESSRKEMIDWIRSE 51
L++E+ + K + + + + ++ R+ DW++ E
Sbjct: 347 LKSEIQAINKQYQQERQALYEKHRRRTWADWLKKE 381
>gnl|CDD|234925 PRK01233, glyS, glycyl-tRNA synthetase subunit beta; Validated.
Length = 682
Score = 24.7 bits (55), Expect = 8.0
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 25 YKTFLRTAKEIPDESSRKEMI 45
Y+ LR AK I D RK +I
Sbjct: 203 YEEKLREAKVIADPEERKAII 223
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
0.316 0.129 0.349
Gapped
Lambda K H
0.267 0.0776 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,056,483
Number of extensions: 313082
Number of successful extensions: 401
Number of sequences better than 10.0: 1
Number of HSP's gapped: 401
Number of HSP's successfully gapped: 21
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: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.1 bits)