RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9518
(132 letters)
>gnl|CDD|223120 COG0042, COG0042, tRNA-dihydrouridine synthase [Translation,
ribosomal structure and biogenesis].
Length = 323
Score = 47.3 bits (113), Expect = 3e-07
Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 6/70 (8%)
Query: 1 MIGRGALIKPWIFQEIKE---KKLFDISSAERFDILKEYVNYGLEHWGSDTRGVETTRRF 57
MIGRGAL PW+F++I +L + AE DIL+E++ LE++G +G+ R+
Sbjct: 226 MIGRGALGNPWLFRQIDYLETGELLPPTLAEVLDILREHLELLLEYYG--KKGLRRLRKH 283
Query: 58 LLEWLSFLHR 67
L +
Sbjct: 284 LG-YYLKGLP 292
>gnl|CDD|239200 cd02801, DUS_like_FMN, Dihydrouridine synthase-like (DUS-like)
FMN-binding domain. Members of this family catalyze the
reduction of the 5,6-double bond of a uridine residue on
tRNA. Dihydrouridine modification of tRNA is widely
observed in prokaryotes and eukaryotes, and also in some
archaea. Most dihydrouridines are found in the D loop of
t-RNAs. The role of dihydrouridine in tRNA is currently
unknown, but may increase conformational flexibility of
the tRNA. It is likely that different family members
have different substrate specificities, which may
overlap. 1VHN, a putative flavin oxidoreductase, has
high sequence similarity to DUS. The enzymatic
mechanism of 1VHN is not known at the present.
Length = 231
Score = 44.0 bits (105), Expect = 4e-06
Identities = 14/18 (77%), Positives = 16/18 (88%)
Query: 1 MIGRGALIKPWIFQEIKE 18
MIGRGAL PW+F+EIKE
Sbjct: 211 MIGRGALGNPWLFREIKE 228
>gnl|CDD|129820 TIGR00737, nifR3_yhdG, putative TIM-barrel protein, nifR3 family.
This model represents one branch of COG0042 (Predicted
TIM-barrel enzymes, possibly dehydrogenases, nifR3
family). This branch includes NifR3 itself, from
Rhodobacter capsulatus. It excludes a broadly
distributed but more sparsely populated subfamily that
contains sll0926 from Synechocystis PCC6803, HI0634 from
Haemophilus influenzae, and BB0225 from Borrelia
burgdorferi. It also excludes a shorter and more distant
archaeal subfamily.The function of nifR3, a member of
this family, is unknown, but it is found in an operon
with nitrogen-sensing two component regulators in
Rhodobacter capsulatus.Members of this family show a
distant relationship to alpha/beta (TIM) barrel enzymes
such as dihydroorotate dehydrogenase and glycolate
oxidase [Unknown function, General].
Length = 319
Score = 40.4 bits (95), Expect = 7e-05
Identities = 18/61 (29%), Positives = 36/61 (59%), Gaps = 6/61 (9%)
Query: 1 MIGRGALIKPWIFQEIKE-----KKLFDISSAERFDILKEYVNYGLEHWGSDTRGVETTR 55
MIGRGAL PW+F++I++ K + AE+ D + ++ +++G +++G+ R
Sbjct: 220 MIGRGALGNPWLFRQIEQYLTTGKYKPPPTFAEKLDAILRHLQLLADYYG-ESKGLRIAR 278
Query: 56 R 56
+
Sbjct: 279 K 279
>gnl|CDD|216365 pfam01207, Dus, Dihydrouridine synthase (Dus). Members of this
family catalyze the reduction of the 5,6-double bond of
a uridine residue on tRNA. Dihydrouridine modification
of tRNA is widely observed in prokaryotes and
eukaryotes, and also in some archae. Most
dihydrouridines are found in the D loop of t-RNAs. The
role of dihydrouridine in tRNA is currently unknown, but
may increase conformational flexibility of the tRNA. It
is likely that different family members have different
substrate specificities, which may overlap. Dus 1 from
Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus
2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active
as a single subunit, requiring NADPH or NADH, and is
stimulated by the presence of FAD. Some family members
may be targeted to the mitochondria and even have a role
in mitochondria.
Length = 309
Score = 36.9 bits (86), Expect = 0.001
Identities = 21/54 (38%), Positives = 29/54 (53%), Gaps = 4/54 (7%)
Query: 1 MIGRGALIKPWIFQEIK--EKKLFDISS--AERFDILKEYVNYGLEHWGSDTRG 50
MIGRGAL PW+F E + FD AE +I+ E+++Y E +G D
Sbjct: 211 MIGRGALGNPWLFAEQHTVKTGEFDPRPPLAEEAEIVLEHLSYLEEFYGEDKGL 264
>gnl|CDD|182440 PRK10415, PRK10415, tRNA-dihydrouridine synthase B; Provisional.
Length = 321
Score = 31.1 bits (70), Expect = 0.12
Identities = 11/17 (64%), Positives = 14/17 (82%)
Query: 1 MIGRGALIKPWIFQEIK 17
MIGR A +PWIF+EI+
Sbjct: 222 MIGRAAQGRPWIFREIQ 238
>gnl|CDD|188029 TIGR00154, ispE, 4-diphosphocytidyl-2C-methyl-D-erythritol kinase.
Members of this family of GHMP kinases were previously
designated as conserved hypothetical protein YchB or as
isopentenyl monophosphate kinase. It is now known, in
tomato and E. coli, to encode
4-diphosphocytidyl-2C-methyl-D-erythritol kinase, an
enzyme of the deoxyxylulose phosphate pathway of
terpenoid biosynthesis [Biosynthesis of cofactors,
prosthetic groups, and carriers, Other].
Length = 294
Score = 28.2 bits (63), Expect = 1.1
Identities = 14/45 (31%), Positives = 20/45 (44%), Gaps = 10/45 (22%)
Query: 73 LLESTQKMN-------QRPPMYHGRNELETLMTSSNCSDWIKISE 110
+ + K+N +RP YH EL+ LM + D I IS
Sbjct: 4 VFPAPAKINLFLYILGKRPDGYH---ELQMLMQFIDLGDKIIISV 45
>gnl|CDD|225599 COG3057, SeqA, Negative regulator of replication initiationR [DNA
replication, recombination, and repair].
Length = 181
Score = 27.1 bits (60), Expect = 2.6
Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 56 RFLLEWLSFLHRYIPVGLLESTQKMNQRPPMYHGRNELETLMTSSN 101
RF+L LS L+R E+T+ ++ R +Y +E +TL+ + N
Sbjct: 90 RFML-ILSTLYRLDAQAFAEATESLHGRTRVYFAADE-QTLLKNGN 133
>gnl|CDD|236991 PRK11815, PRK11815, tRNA-dihydrouridine synthase A; Provisional.
Length = 333
Score = 27.0 bits (61), Expect = 3.4
Identities = 12/41 (29%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 1 MIGRGALIKPWIFQEIKEKKLFDISSAE--RFDILKEYVNY 39
MIGR A P++ E+ +++LF + R ++L+ + Y
Sbjct: 231 MIGRAAYHNPYLLAEV-DRELFGEPAPPLSRSEVLEAMLPY 270
>gnl|CDD|224858 COG1947, IspE, 4-diphosphocytidyl-2C-methyl-D-erythritol
2-phosphate synthase [Lipid metabolism].
Length = 289
Score = 26.8 bits (60), Expect = 3.6
Identities = 10/29 (34%), Positives = 13/29 (44%), Gaps = 3/29 (10%)
Query: 82 QRPPMYHGRNELETLMTSSNCSDWIKISE 110
+R YH ELETL + D + I
Sbjct: 21 KRADGYH---ELETLFQFIDLGDELTIRP 46
>gnl|CDD|180937 PRK07337, PRK07337, aminotransferase; Validated.
Length = 388
Score = 26.6 bits (59), Expect = 4.3
Identities = 11/27 (40%), Positives = 12/27 (44%), Gaps = 3/27 (11%)
Query: 25 SSAERFDILKEYVNYGLEHWGSDTRGV 51
AERF + V WG TRGV
Sbjct: 144 GPAERFQLTAADVE---AAWGERTRGV 167
>gnl|CDD|110179 pfam01157, Ribosomal_L21e, Ribosomal protein L21e.
Length = 99
Score = 25.5 bits (56), Expect = 5.9
Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 2/48 (4%)
Query: 72 GLLESTQKMNQRPPMYHGRNELETLMTSSNCSDWIKISEMLLGKIPAG 119
G T+ M +RP HG + L T + D++ I G + G
Sbjct: 5 GPRRGTRYMFKRPFRKHGLSPLSTYLREYKVGDYVDIKIN--GSVQKG 50
>gnl|CDD|226375 COG3857, AddB, ATP-dependent nuclease, subunit B [DNA replication,
recombination, and repair].
Length = 1108
Score = 26.2 bits (58), Expect = 6.1
Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 4/37 (10%)
Query: 12 IFQEIKEKKLFDISSAERFDILKEYVNY----GLEHW 44
+ +K LFD + +E D+L+ YV G + W
Sbjct: 388 VLNLLKTDVLFDSNESEDIDLLENYVLAAGIKGKKKW 424
>gnl|CDD|223093 COG0014, ProA, Gamma-glutamyl phosphate reductase [Amino acid
transport and metabolism].
Length = 417
Score = 26.0 bits (58), Expect = 7.0
Identities = 11/24 (45%), Positives = 14/24 (58%), Gaps = 5/24 (20%)
Query: 76 STQKMNQRPPMYHGRNELETLMTS 99
STQK++ R PM G LE L +
Sbjct: 387 STQKLHARGPM--G---LEALTSY 405
>gnl|CDD|221753 pfam12753, Nro1, Nuclear pore complex subunit Nro1. In fission
yeast, this protein is a positive regulator of the
stability of Sre1N, the sterol regulatory
element-binding protein which is an ER membrane-bound
transcription factor that controls adaptation to low
oxygen-growth. In addition, the fission yeast Nro1 is a
direct inhibitor of a protein that inhibits SreN1
degradation, Ofd1 (an oxoglutamate deoxygenase). The
outcome of this reactivity is that Ofd1 acts as an
oxygen sensor that regulates the binding of Nro1 to Ofd1
to control the stability of Sre1N. Solution of the
structure of Nro1 reveals it to be made up of a number
of TPR coils.
Length = 401
Score = 26.0 bits (57), Expect = 8.4
Identities = 16/55 (29%), Positives = 26/55 (47%)
Query: 6 ALIKPWIFQEIKEKKLFDISSAERFDILKEYVNYGLEHWGSDTRGVETTRRFLLE 60
AL + IF+ +E++L D S E FD E + GL R + + +L+
Sbjct: 105 ALSELAIFKAEEEERLKDESVEEFFDAALERADLGLAPGPDSVRLLLAKAKIILQ 159
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
0.321 0.137 0.434
Gapped
Lambda K H
0.267 0.0708 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,882,968
Number of extensions: 587170
Number of successful extensions: 465
Number of sequences better than 10.0: 1
Number of HSP's gapped: 464
Number of HSP's successfully gapped: 21
Length of query: 132
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 46
Effective length of database: 7,123,158
Effective search space: 327665268
Effective search space used: 327665268
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 (21.9 bits)
S2: 53 (24.2 bits)