RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7344
(240 letters)
>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 = 73.3 bits (181), Expect = 8e-16
Identities = 23/55 (41%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 121 FCGNDSKNLTEAAKLAEP-HCDGIDINIGCPQMVAKRGHYGAYLQDDWPLLTNLV 174
G+D + L EAAK+ E DGID+N+GCP +G GA L D L+ +V
Sbjct: 61 LGGSDPETLAEAAKIVEELGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIV 115
Score = 57.1 bits (139), Expect = 6e-10
Identities = 16/40 (40%), Positives = 22/40 (55%)
Query: 67 FIAEPHCDGIDINIGCPQMVAKRGHYGAYLQDDWPLLTEL 106
+ E DGID+N+GCP +G GA L D L+ E+
Sbjct: 75 IVEELGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEI 114
Score = 56.7 bits (138), Expect = 8e-10
Identities = 17/38 (44%), Positives = 22/38 (57%)
Query: 12 EPHCDGIDINIGCPQMVAKRGHYGAYLQDDWPLLTELV 49
E DGID+N+GCP +G GA L D L+ E+V
Sbjct: 78 ELGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIV 115
Score = 50.6 bits (122), Expect = 1e-07
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 183 VIAEPHCDGNDINIGCPQMVAKRGHYGAYLQDDWPLLTEL 222
++ E DG D+N+GCP +G GA L D L+ E+
Sbjct: 75 IVEELGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEI 114
>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 = 61.6 bits (150), Expect = 3e-11
Identities = 24/59 (40%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 117 HSLMFCGNDSKNLTEAAKLAEPH-CDGIDINIGCPQMVAKRGHYGAYLQDDWPLLTNLV 174
++ G+D L EAAKL D IDIN+GCP RG GA L D L+ +V
Sbjct: 56 LAVQLGGSDPALLAEAAKLVADLGADIIDINMGCPAKKVTRGGAGAALLRDPDLVAQIV 114
Score = 41.9 bits (99), Expect = 1e-04
Identities = 16/35 (45%), Positives = 20/35 (57%)
Query: 15 CDGIDINIGCPQMVAKRGHYGAYLQDDWPLLTELV 49
D IDIN+GCP RG GA L D L+ ++V
Sbjct: 80 ADIIDINMGCPAKKVTRGGAGAALLRDPDLVAQIV 114
Score = 41.5 bits (98), Expect = 2e-04
Identities = 15/37 (40%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 68 IAEPH-CDGIDINIGCPQMVAKRGHYGAYLQDDWPLL 103
+ D IDIN+GCP RG GA L D L+
Sbjct: 74 LVADLGADIIDINMGCPAKKVTRGGAGAALLRDPDLV 110
Score = 36.5 bits (85), Expect = 0.007
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 184 IAEPH-CDGNDINIGCPQMVAKRGHYGAYLQDDWPLL 219
+ D DIN+GCP RG GA L D L+
Sbjct: 74 LVADLGADIIDINMGCPAKKVTRGGAGAALLRDPDLV 110
>gnl|CDD|223120 COG0042, COG0042, tRNA-dihydrouridine synthase [Translation,
ribosomal structure and biogenesis].
Length = 323
Score = 55.4 bits (134), Expect = 4e-09
Identities = 24/72 (33%), Positives = 33/72 (45%), Gaps = 1/72 (1%)
Query: 104 TELGFKTRSHMCGHSLMFCGNDSKNLTEAAKLAEPHC-DGIDINIGCPQMVAKRGHYGAY 162
L ++ G+D + L EAAK+AE D ID+N GCP +G GA
Sbjct: 56 FLLLLDELEEERPVAVQLGGSDPELLAEAAKIAEELGADIIDLNCGCPSPKVVKGGAGAA 115
Query: 163 LQDDWPLLTNLV 174
L + LL +V
Sbjct: 116 LLKNPELLAEIV 127
Score = 43.5 bits (103), Expect = 4e-05
Identities = 15/34 (44%), Positives = 19/34 (55%)
Query: 16 DGIDINIGCPQMVAKRGHYGAYLQDDWPLLTELV 49
D ID+N GCP +G GA L + LL E+V
Sbjct: 94 DIIDLNCGCPSPKVVKGGAGAALLKNPELLAEIV 127
Score = 41.5 bits (98), Expect = 2e-04
Identities = 14/33 (42%), Positives = 18/33 (54%)
Query: 74 DGIDINIGCPQMVAKRGHYGAYLQDDWPLLTEL 106
D ID+N GCP +G GA L + LL E+
Sbjct: 94 DIIDLNCGCPSPKVVKGGAGAALLKNPELLAEI 126
Score = 36.5 bits (85), Expect = 0.009
Identities = 13/33 (39%), Positives = 17/33 (51%)
Query: 190 DGNDINIGCPQMVAKRGHYGAYLQDDWPLLTEL 222
D D+N GCP +G GA L + LL E+
Sbjct: 94 DIIDLNCGCPSPKVVKGGAGAALLKNPELLAEI 126
>gnl|CDD|236991 PRK11815, PRK11815, tRNA-dihydrouridine synthase A; Provisional.
Length = 333
Score = 40.1 bits (95), Expect = 5e-04
Identities = 20/42 (47%), Positives = 27/42 (64%), Gaps = 1/42 (2%)
Query: 123 GNDSKNLTEAAKLAEPH-CDGIDINIGCPQMVAKRGHYGAYL 163
G+D +L EAAKLAE D I++N+GCP + G +GA L
Sbjct: 73 GSDPADLAEAAKLAEDWGYDEINLNVGCPSDRVQNGRFGACL 114
Score = 27.4 bits (62), Expect = 6.7
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 16 DGIDINIGCPQMVAKRGHYGAYL 38
D I++N+GCP + G +GA L
Sbjct: 92 DEINLNVGCPSDRVQNGRFGACL 114
Score = 27.4 bits (62), Expect = 6.7
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 74 DGIDINIGCPQMVAKRGHYGAYL 96
D I++N+GCP + G +GA L
Sbjct: 92 DEINLNVGCPSDRVQNGRFGACL 114
>gnl|CDD|129825 TIGR00742, yjbN, tRNA dihydrouridine synthase A. This model
represents one branch of COG0042 (Predicted TIM-barrel
enzymes, possibly dehydrogenases, nifR3 family). It
represents a distinct subset by a set of shared unique
motifs, a conserved pattern of insertions/deletions
relative to other nifR3 homologs, and by subclustering
based on cross-genome bidirectional best hits. Members
are found in species as diverse as the proteobacteria, a
spirochete, a cyanobacterium, and Deinococcus
radiodurans. NifR3 itself, a protein of unknown function
associated with nitrogen regulation in Rhodobacter
capsulatus, is not a member of this branch. Members of
this family show a distant relationship to alpha/beta
(TIM) barrel enzymes such as dihydroorotate
dehydrogenase and glycolate oxidase [Protein synthesis,
tRNA and rRNA base modification].
Length = 318
Score = 36.0 bits (83), Expect = 0.012
Identities = 18/47 (38%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 118 SLMFCGNDSKNLTEAAKLAEPH-CDGIDINIGCPQMVAKRGHYGAYL 163
+L G+D +L + AK+AE D I++N+GCP + G++GA L
Sbjct: 58 ALQLGGSDPNDLAKCAKIAEKRGYDEINLNVGCPSDRVQNGNFGACL 104
>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 = 35.4 bits (82), Expect = 0.020
Identities = 21/50 (42%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 118 SLMFCGNDSKNLTEAAKLAEPH-CDGIDINIGCP-QMVAKRGHYGAYLQD 165
S+ G+D + EAAK+ E D IDIN+GCP + K+G A L+D
Sbjct: 66 SVQLFGSDPDTMAEAAKINEELGADIIDINMGCPVPKITKKGAGSALLRD 115
>gnl|CDD|239244 cd02940, DHPD_FMN, Dihydropyrimidine dehydrogenase (DHPD)
FMN-binding domain. DHPD catalyzes the first step in
pyrimidine degradation: the NADPH-dependent reduction of
uracil and thymine to the corresponding
5,6-dihydropyrimidines. DHPD contains two FAD, two FMN,
and eight [4Fe-4S] clusters, arranged in two electron
transfer chains that pass the dimer interface twice. Two
of the Fe-S clusters show a hitherto unobserved
coordination involving a glutamine residue.
Length = 299
Score = 34.6 bits (80), Expect = 0.036
Identities = 15/41 (36%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 118 SLMFCGNDSKNLTEAAKLAEPH-CDGIDINIGCPQMVAKRG 157
S+M C + ++ TE AKL E D +++N CP + +RG
Sbjct: 105 SIM-CEYNKEDWTELAKLVEEAGADALELNFSCPHGMPERG 144
Score = 28.4 bits (64), Expect = 2.9
Identities = 13/56 (23%), Positives = 21/56 (37%), Gaps = 19/56 (33%)
Query: 35 GAYLQDDWPLLTELVVHFSWVSKNGPLFMGPLFIAEPHCDGIDINIGCPQMVAKRG 90
Y ++DW L +LV E D +++N CP + +RG
Sbjct: 108 CEYNKEDWTELAKLV-------------------EEAGADALELNFSCPHGMPERG 144
Score = 28.0 bits (63), Expect = 4.7
Identities = 6/17 (35%), Positives = 11/17 (64%)
Query: 16 DGIDINIGCPQMVAKRG 32
D +++N CP + +RG
Sbjct: 128 DALELNFSCPHGMPERG 144
Score = 27.2 bits (61), Expect = 7.1
Identities = 13/47 (27%), Positives = 19/47 (40%), Gaps = 10/47 (21%)
Query: 160 GAYLQDDWPLLTNLVYSPNMVHFVIAEPHCDGNDINIGCPQMVAKRG 206
Y ++DW L LV E D ++N CP + +RG
Sbjct: 108 CEYNKEDWTELAKLV----------EEAGADALELNFSCPHGMPERG 144
>gnl|CDD|236048 PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated.
Length = 859
Score = 34.0 bits (79), Expect = 0.071
Identities = 21/94 (22%), Positives = 35/94 (37%), Gaps = 37/94 (39%)
Query: 85 MVAKRGHYGAYLQDDWPLLTELGFKTRSHMCGHSLMFCGNDSKNLTEAAKLAEPHCDGID 144
MV + G +G Y+Q+ E R + GN+ P C G++
Sbjct: 655 MVLRSGRFGPYVQEG-----EGDKPRRLSLPK------GNN------------PECVGLE 691
Query: 145 INIG----------CP----QMVAKRGHYGAYLQ 164
I +G P ++ AK G +G Y++
Sbjct: 692 IALGLLSLPRPVGEHPECGSEIQAKIGRFGPYVK 725
Score = 33.6 bits (78), Expect = 0.089
Identities = 35/165 (21%), Positives = 53/165 (32%), Gaps = 40/165 (24%)
Query: 74 DGIDIN------IGCP----QMVAKRGHYGAYLQDDWPLLTELGFKTRSHMCGHSLMFCG 123
G+ N CP M + G G +L L E R C +
Sbjct: 576 GGMRPNQMVITDRDCPTCGRGMGIRTGKTGVFLGCSGYALKE-----R---CKTTRNLTP 627
Query: 124 NDSKNLTEAAKLAEPHCDGIDINIGCPQMVAKRGHYGAYLQDDWPLLTNLVYSPNMVH-F 182
+ + AE G D G MV + G +G Y+Q+ P +
Sbjct: 628 EEETLNVLEGEDAETRALGADPECGTA-MVLRSGRFGPYVQEGEGD------KPRRLSLP 680
Query: 183 VIAEPHCDGNDINIG----------CP----QMVAKRGHYGAYLQ 213
P C G +I +G P ++ AK G +G Y++
Sbjct: 681 KGNNPECVGLEIALGLLSLPRPVGEHPECGSEIQAKIGRFGPYVK 725
>gnl|CDD|236237 PRK08318, PRK08318, dihydropyrimidine dehydrogenase subunit B;
Validated.
Length = 420
Score = 31.8 bits (73), Expect = 0.25
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 118 SLMFCGNDSKNLTEAAKLAEPH-CDGIDINIGCPQMVAKRG 157
S+M + + E A L E DGI++N GCP +++RG
Sbjct: 105 SIMV-ECNEEEWKEIAPLVEETGADGIELNFGCPHGMSERG 144
Score = 29.1 bits (66), Expect = 2.4
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 15 CDGIDINIGCPQMVAKRG 32
DGI++N GCP +++RG
Sbjct: 127 ADGIELNFGCPHGMSERG 144
Score = 29.1 bits (66), Expect = 2.4
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 73 CDGIDINIGCPQMVAKRG 90
DGI++N GCP +++RG
Sbjct: 127 ADGIELNFGCPHGMSERG 144
>gnl|CDD|213244 cd03277, ABC_SMC5_euk, ATP-binding cassette domain of eukaryotic
SMC5 proteins. The structural maintenance of
chromosomes (SMC) proteins are large (approximately 110
to 170 kDa), and each is arranged into five recognizable
domains. Amino-acid sequence homology of SMC proteins
between species is largely confined to the amino- and
carboxy-terminal globular domains. The amino-terminal
domain contains a 'Walker A' nucleotide-binding domain
(GxxGxGKS/T, in the single-letter amino-acid code),
which by mutational studies has been shown to be
essential in several proteins. The carboxy-terminal
domain contains a sequence (the DA-box) that resembles a
'Walker B' motif, and a motif with homology to the
signature sequence of the ATP-binding cassette (ABC)
family of ATPases. The sequence homology within the
carboxy-terminal domain is relatively high within the
SMC1-SMC4 group, whereas SMC5 and SMC6 show some
divergence in both of these sequences. In eukaryotic
cells, the proteins are found as heterodimers of SMC1
paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6
(formerly known as Rad18).
Length = 213
Score = 29.5 bits (67), Expect = 1.2
Identities = 9/22 (40%), Positives = 9/22 (40%), Gaps = 1/22 (4%)
Query: 169 LLTNLVYSPNM-VHFVIAEPHC 189
LL L Y M V V PH
Sbjct: 192 LLPGLNYHEKMTVLCVYNGPHI 213
>gnl|CDD|182440 PRK10415, PRK10415, tRNA-dihydrouridine synthase B; Provisional.
Length = 321
Score = 28.8 bits (64), Expect = 2.4
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 118 SLMFCGNDSKNLTEAAKL-AEPHCDGIDINIGCPQMVAKRGHYGAYL 163
++ G+D K + +AA++ E IDIN+GCP R G+ L
Sbjct: 68 TVQIAGSDPKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSAL 114
>gnl|CDD|240091 cd04740, DHOD_1B_like, Dihydroorotate dehydrogenase (DHOD) class 1B
FMN-binding domain. DHOD catalyzes the oxidation of
(S)-dihydroorotate to orotate. This is the fourth step
and the only redox reaction in the de novo biosynthesis
of UMP, the precursor of all pyrimidine nucleotides.
DHOD requires FMN as co-factor. DHOD divides into class
1 and class 2 based on their amino acid sequences and
cellular location. Members of class 1 are cytosolic
enzymes and multimers while class 2 enzymes are membrane
associated and monomeric. The class 1 enzymes can be
further divided into subtypes 1A and 1B which are
homodimers and heterotetrameric proteins, respectively.
Length = 296
Score = 28.3 bits (64), Expect = 3.6
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 132 AAKLAEPHCDGIDINIGCP 150
A KLA+ D I++NI CP
Sbjct: 108 AEKLADAGADAIELNISCP 126
>gnl|CDD|223245 COG0167, PyrD, Dihydroorotate dehydrogenase [Nucleotide transport
and metabolism].
Length = 310
Score = 27.6 bits (62), Expect = 5.7
Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 5/41 (12%)
Query: 9 IETEPHCDGIDINIGCPQMVAKRGHYGAYLQDDWPLLTELV 49
+E D I++NI CP R L D LL +L+
Sbjct: 118 LEEAGDADAIELNISCPNTPGGRA-----LGQDPELLEKLL 153
>gnl|CDD|182308 PRK10209, PRK10209, acid-resistance membrane protein; Provisional.
Length = 190
Score = 26.9 bits (60), Expect = 8.6
Identities = 10/45 (22%), Positives = 20/45 (44%), Gaps = 12/45 (26%)
Query: 27 MVAKRGHYGAYLQDDWPLLTELVVHFSWVSKNGPLFMGPLFIAEP 71
+ A R + WP+L+ +++ ++ L +G FI P
Sbjct: 68 LFANR------SHNFWPMLSGILLGVAY------LVLGYFFIRNP 100
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
0.322 0.142 0.480
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,150,396
Number of extensions: 1107034
Number of successful extensions: 720
Number of sequences better than 10.0: 1
Number of HSP's gapped: 713
Number of HSP's successfully gapped: 40
Length of query: 240
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 146
Effective length of database: 6,768,326
Effective search space: 988175596
Effective search space used: 988175596
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: 57 (25.7 bits)