RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9896
(145 letters)
>gnl|CDD|239674 cd03703, aeIF5B_II, aeIF5B_II: This family represents the domain II
of archeal and eukaryotic aeIF5B. aeIF5B is a homologue
of prokaryotic Initiation Factor 2 (IF2). Disruption of
the eIF5B gene (FUN12) in yeast causes a severe
slow-growth phenotype, associated with a defect in
translation. eIF5B has a function analogous to
prokaryotic IF2 in mediating the joining of joining of
60S subunits. The eIF5B consists of three N-terminal
domains (I, II, II) connected by a long helix to domain
IV. Domain I is a G domain, domain II and IV are
beta-barrels and domain III has a novel alpha-beta-alpha
sandwich fold. The G domain and the beta-barrel domain
II display a similar structure and arrangement to the
homologous domains of EF1A, eEF1A and aeIF2gamma.
Length = 110
Score = 167 bits (426), Expect = 5e-55
Identities = 64/110 (58%), Positives = 82/110 (74%)
Query: 25 LQATVLEVKAIPGLGTTIDTILVNGTLYEGDTVVLAGTDGPIVTQIRSLLMPQPMQELRV 84
LQ TVLEVK GLGTTID IL +GTL EGDT+V+ G +GPIVT++R+LL PQP++ELRV
Sbjct: 1 LQGTVLEVKEEEGLGTTIDVILYDGTLREGDTIVVCGLNGPIVTKVRALLKPQPLKELRV 60
Query: 85 KNAYVEYKKIKGTQGVKIAAKDLEKTIAGLNLRVAKDQDEIDDLCDEVAR 134
K+ ++ K++K GVKI A DLEK IAG L V +DEI++L +EV
Sbjct: 61 KSRFIHVKEVKAAAGVKILAPDLEKAIAGSPLLVVGPEDEIEELKEEVME 110
>gnl|CDD|235195 PRK04004, PRK04004, translation initiation factor IF-2; Validated.
Length = 586
Score = 131 bits (332), Expect = 1e-36
Identities = 58/130 (44%), Positives = 88/130 (67%), Gaps = 4/130 (3%)
Query: 12 QTFLKKRLMFKNELQA--TVLEVKAIPGLGTTIDTILVNGTLYEGDTVVLAGTDGPIVTQ 69
Q +L++RL E TVLEVK GLGTTID IL +GTL +GDT+V+ G DGPIVT+
Sbjct: 218 QRYLEERLKIDVEGPGKGTVLEVKEERGLGTTIDVILYDGTLRKGDTIVVGGKDGPIVTK 277
Query: 70 IRSLLMPQPMQELR-VKNAYVEYKKIKGTQGVKIAAKDLEKTIAGLNLRVAKDQDEIDDL 128
+R+LL P+P+ E+R ++ + ++ GVKI+A DLE +AG LRV +D ++++++
Sbjct: 278 VRALLKPRPLDEMRDPEDKFKPVDEVVAAAGVKISAPDLEDALAGSPLRVVRD-EDVEEV 336
Query: 129 CDEVARELKS 138
+EV E++
Sbjct: 337 KEEVEEEIEE 346
>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 106 bits (267), Expect = 1e-27
Identities = 54/131 (41%), Positives = 85/131 (64%), Gaps = 3/131 (2%)
Query: 12 QTFLKKRLMFKNELQA--TVLEVKAIPGLGTTIDTILVNGTLYEGDTVVLAGTDGPIVTQ 69
Q +L++RL E A T+LEVK GLGTTID I+ +GTL GDT+V+ G D IVT+
Sbjct: 673 QKYLEERLKLNVEGYAKGTILEVKEEKGLGTTIDAIIYDGTLRRGDTIVVGGPDDVIVTK 732
Query: 70 IRSLLMPQPMQELRV-KNAYVEYKKIKGTQGVKIAAKDLEKTIAGLNLRVAKDQDEIDDL 128
+R+LL P+P+ E+R ++ + ++ GVKIAA LE+ +AG +R+ +++I+
Sbjct: 733 VRALLKPKPLDEIRDPRDKFDPVDEVTAAAGVKIAAPGLEEVLAGSPIRIVPTKEKIEKA 792
Query: 129 CDEVARELKSA 139
+EV +E++ A
Sbjct: 793 KEEVMKEVEEA 803
>gnl|CDD|129582 TIGR00491, aIF-2, translation initiation factor aIF-2/yIF-2. This
model describes archaeal and eukaryotic orthologs of
bacterial IF-2. Like IF-2, it helps convey the initiator
tRNA to the ribosome, although the initiator is
N-formyl-Met in bacteria and Met here. This protein is
not closely related to the subunits of eIF-2 of
eukaryotes, which is also involved in the initiation of
translation. The aIF-2 of Methanococcus jannaschii
contains a large intein interrupting a region of very
strongly conserved sequence very near the amino end; the
alignment generated by This model does not correctly
align the sequences from Methanococcus jannaschii and
Pyrococcus horikoshii in this region [Protein synthesis,
Translation factors].
Length = 590
Score = 94.5 bits (235), Expect = 2e-23
Identities = 50/131 (38%), Positives = 86/131 (65%), Gaps = 4/131 (3%)
Query: 12 QTFLKKRLMFKNELQA--TVLEVKAIPGLGTTIDTILVNGTLYEGDTVVLAGTDGPIVTQ 69
Q +L+++L + E A T+LEVK GLG TID ++ +G L +GDT+ +AG+D IVT+
Sbjct: 216 QQYLEEQLKLEEEGPARGTILEVKEETGLGMTIDAVIYDGILRKGDTIAMAGSDDVIVTR 275
Query: 70 IRSLLMPQPMQELRV-KNAYVEYKKIKGTQGVKIAAKDLEKTIAGLNLRVAKDQDEIDDL 128
+R+LL P+P++E+R + + + ++ GVKIAA L+ +AG +RV D +EI+ +
Sbjct: 276 VRALLKPRPLEEMRESRKKFQKVDEVVAAAGVKIAAPGLDDVMAGSPIRVVTD-EEIEKV 334
Query: 129 CDEVARELKSA 139
+E+ +E++
Sbjct: 335 KEEILKEVEEI 345
>gnl|CDD|239672 cd03701, IF2_IF5B_II, IF2_IF5B_II: This family represents the
domain II of prokaryotic Initiation Factor 2 (IF2) and
its archeal and eukaryotic homologue aeIF5B. IF2, the
largest initiation factor is an essential GTP binding
protein. In E. coli three natural forms of IF2 exist in
the cell, IF2alpha, IF2beta1, and IF2beta2. Disruption
of the eIF5B gene (FUN12) in yeast causes a severe
slow-growth phenotype, associated with a defect in
translation. eIF5B has a function analogous to
prokaryotic IF2 in mediating the joining of the 60S
ribosomal subunit. The eIF5B consists of three
N-terminal domains (I, II, II) connected by a long
helix to domain IV. Domain I is a G domain, domain II
and IV are beta-barrels and domain III has a novel
alpha-beta-alpha sandwich fold. The G domain and the
beta-barrel domain II display a similar structure and
arrangement to the homologous domains in EF1A, eEF1A and
aeIF2gamma.
Length = 95
Score = 83.7 bits (208), Expect = 4e-22
Identities = 29/97 (29%), Positives = 40/97 (41%), Gaps = 7/97 (7%)
Query: 26 QATVLEVKAIPGLGTTIDTILVNGTLYEGDTVVLAGTDGPIVTQIR----SLLMPQPMQE 81
+ TV+E K G G I+ NGTL +GD +V GT G I T + +LL P
Sbjct: 2 EGTVIESKLDKGRGPVATVIVQNGTLKKGDVIVAGGTYGKIRTMVDENGKALLEAGPSTP 61
Query: 82 LRVKNAYVEYKKIKGTQGVKIAAKDLEKTIAGLNLRV 118
+ + K GV + A + E G V
Sbjct: 62 VEI---LGLKDVPKAGDGVLVVASEKEAKEIGSYRLV 95
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 89.1 bits (222), Expect = 1e-21
Identities = 34/123 (27%), Positives = 54/123 (43%), Gaps = 2/123 (1%)
Query: 22 KNELQATVLEVKAIPGLGTTIDTILVNGTLYEGDTVVLAGTDGPIVTQIRSLLMPQPMQE 81
+ + TV+EVK GLG I+ +GTL +GD +V G G + T + L P
Sbjct: 179 EGPARGTVIEVKLDKGLGPVATVIVQDGTLKKGDIIVAGGEYGRVRTMVDDLGKPIKEAG 238
Query: 82 LRVKNAYVEYKKIKGTQGVKIAAKDLEKTIAGLNLRVAKDQDEIDDLCDEVARELKSALS 141
+ ++ V I KD +K A LRV ++ +L + EL+ ++
Sbjct: 239 PSKPVEILGLSEVPAAGDVFIVVKDEKKARAIAELRVVLLREA--ELASKKKGELEELIA 296
Query: 142 TIK 144
IK
Sbjct: 297 EIK 299
>gnl|CDD|238652 cd01342, Translation_Factor_II_like, Translation_Factor_II_like:
Elongation factor Tu (EF-Tu) domain II-like proteins.
Elongation factor Tu consists of three structural
domains, this family represents the second domain.
Domain II adopts a beta barrel structure and is
involved in binding to charged tRNA. Domain II is found
in other proteins such as elongation factor G and
translation initiation factor IF-2. This group also
includes the C2 subdomain of domain IV of IF-2 that has
the same fold as domain II of (EF-Tu). Like IF-2 from
certain prokaryotes such as Thermus thermophilus,
mitochondrial IF-2 lacks domain II, which is thought
to be involved in binding of E.coli IF-2 to 30S
subunits.
Length = 83
Score = 45.8 bits (109), Expect = 2e-07
Identities = 16/53 (30%), Positives = 27/53 (50%)
Query: 25 LQATVLEVKAIPGLGTTIDTILVNGTLYEGDTVVLAGTDGPIVTQIRSLLMPQ 77
L+A V +V G GT + +GTL +GD V + G + +++SL +
Sbjct: 1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGGGVKGKVKSLKRFK 53
>gnl|CDD|217388 pfam03144, GTP_EFTU_D2, Elongation factor Tu domain 2. Elongation
factor Tu consists of three structural domains, this is
the second domain. This domain adopts a beta barrel
structure. This the second domain is involved in binding
to charged tRNA. This domain is also found in other
proteins such as elongation factor G and translation
initiation factor IF-2. This domain is structurally
related to pfam03143, and in fact has weak sequence
matches to this domain.
Length = 70
Score = 36.1 bits (84), Expect = 6e-04
Identities = 18/75 (24%), Positives = 27/75 (36%), Gaps = 9/75 (12%)
Query: 39 GTTIDTILVNGTLYEGDTVVLAGTDGPIVTQIRSLLMPQPMQELRVKNAYVEYKKIKGTQ 98
GT + +GTL +GD VV+ ++ SL M V A
Sbjct: 1 GTVATGRVESGTLKKGDKVVIGPNGTGKKGRVTSLEMFHGDLREAVAGANA--------- 51
Query: 99 GVKIAAKDLEKTIAG 113
G+ +A L+ G
Sbjct: 52 GIILAGIGLKDIKRG 66
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 35.6 bits (83), Expect = 0.005
Identities = 26/53 (49%), Positives = 29/53 (54%), Gaps = 16/53 (30%)
Query: 25 LQATVLEVKAIP---GLGTTID-----------TILV-NGTLYEGDTVVLAGT 62
LQA VLE+KA P GT I+ T+LV NGTL GD VV AGT
Sbjct: 408 LQAEVLELKANPDRPARGTVIEAKLDKGRGPVATVLVQNGTLKVGDIVV-AGT 459
>gnl|CDD|239673 cd03702, IF2_mtIF2_II, This family represents the domain II of
bacterial Initiation Factor 2 (IF2) and its eukaryotic
mitochondrial homologue mtIF2. IF2, the largest
initiation factor is an essential GTP binding protein.
In E. coli three natural forms of IF2 exist in the
cell, IF2alpha, IF2beta1, and IF2beta2. Bacterial IF-2
is structurally and functionally related to eukaryotic
mitochondrial mtIF-2.
Length = 95
Score = 32.1 bits (74), Expect = 0.024
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 26 QATVLEVKAIPGLGTTIDTILVNGTLYEGDTVVLAGTDGPIVTQIRSLL 74
+ V+E K G G ++ NGTL GD +V T G ++R++
Sbjct: 2 EGVVIESKLDKGRGPVATVLVQNGTLKVGDVLVAGTTYG----KVRAMF 46
>gnl|CDD|239665 cd03694, GTPBP_II, Domain II of the GP-1 family of GTPase. This
group includes proteins similar to GTPBP1 and GTPBP2.
GTPB1 is structurally, related to elongation factor 1
alpha, a key component of protein biosynthesis
machinery. Immunohistochemical analyses on mouse
tissues revealed that GTPBP1 is expressed in some
neurons and smooth muscle cells of various organs as
well as macrophages. Immunofluorescence analyses
revealed that GTPBP1 is localized exclusively in
cytoplasm and shows a diffuse granular network forming
a gradient from the nucleus to the periphery of the
cells in smooth muscle cell lines and macrophages. No
significant difference was observed in the immune
response to protein antigen between mutant mice and
wild-type mice, suggesting normal function of
antigen-presenting cells of the mutant mice. The
absence of an eminent phenotype in GTPBP1-deficient
mice may be due to functional compensation by GTPBP2,
which is similar to GTPBP1 in structure and tissue
distribution.
Length = 87
Score = 28.3 bits (64), Expect = 0.50
Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 10/49 (20%)
Query: 31 EVKAIPGLGTTIDTILVNGTLYEGDTVVLAGTDGP------IVTQIRSL 73
E+ ++PG+GT + + G + GDT++L GP ++S+
Sbjct: 7 EIYSVPGVGTVVGGTVSKGVIRLGDTLLL----GPDQDGSFRPVTVKSI 51
>gnl|CDD|235774 PRK06292, PRK06292, dihydrolipoamide dehydrogenase; Validated.
Length = 460
Score = 29.0 bits (66), Expect = 0.89
Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 31 EVKAIPGLGTTID--TILVNGTLYEGDTVVLA-GTDGPIV 67
++ I G +D T+ VNG E +V+A G+ P +
Sbjct: 106 KIDKIKGTARFVDPNTVEVNGERIEAKNIVIATGSRVPPI 145
>gnl|CDD|232995 TIGR00487, IF-2, translation initiation factor IF-2. This model
discriminates eubacterial (and mitochondrial)
translation initiation factor 2 (IF-2), encoded by the
infB gene in bacteria, from similar proteins in the
Archaea and Eukaryotes. In the bacteria and in
organelles, the initiator tRNA is charged with
N-formyl-Met instead of Met. This translation factor
acts in delivering the initator tRNA to the ribosome. It
is one of a number of GTP-binding translation factors
recognized by the pfam model GTP_EFTU [Protein
synthesis, Translation factors].
Length = 587
Score = 28.6 bits (64), Expect = 1.2
Identities = 18/61 (29%), Positives = 25/61 (40%), Gaps = 15/61 (24%)
Query: 25 LQATVLEVKAIP---------------GLGTTIDTILVNGTLYEGDTVVLAGTDGPIVTQ 69
LQ+ V E+KA P G G ++ +GTL GD VV+ G +
Sbjct: 247 LQSEVEELKANPNGQASGVVIEAQLDKGRGPVATVLVQSGTLRVGDIVVVGAAYGRVRAM 306
Query: 70 I 70
I
Sbjct: 307 I 307
>gnl|CDD|225035 COG2124, CypX, Cytochrome P450 [Secondary metabolites biosynthesis,
transport, and catabolism].
Length = 411
Score = 27.8 bits (62), Expect = 2.3
Identities = 16/68 (23%), Positives = 22/68 (32%), Gaps = 16/68 (23%)
Query: 9 QYCQTFLKKRLMFKNELQATVLEVKAIPGLGTTIDTILVNGTLYEGDTVVLAGTDGPIVT 68
+ L+ F + L A + P LG L DGP T
Sbjct: 57 ADVREVLRDPRFFSSALGAGLRPRLLRPVLGDG----------------SLLTLDGPEHT 100
Query: 69 QIRSLLMP 76
++R LL P
Sbjct: 101 RLRKLLAP 108
>gnl|CDD|222883 PHA02572, nrdA, ribonucleoside-diphosphate reductase subunit alpha;
Provisional.
Length = 753
Score = 27.8 bits (62), Expect = 2.7
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 110 TIAGLNLRVAKDQDEIDDLCDEVARELKSAL 140
T++ + L +DQDEI++L + R L + L
Sbjct: 458 TLSAIVLGNFEDQDEIEELAEVAVRALDNLL 488
>gnl|CDD|221952 pfam13166, AAA_13, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. This family includes the
PrrC protein that is thought to be the active component
of the anticodon nuclease.
Length = 713
Score = 27.3 bits (61), Expect = 3.7
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 10/60 (16%)
Query: 85 KNAYVEYKKIKGTQGVKIAAKDLEKTIAGLNLRVAKDQDEIDDLCDEVARELKSALSTIK 144
K Y+K K K LEK I L + + + EI L E+ +EL+ L+ I+
Sbjct: 407 KEDIDAYQKEK---------KGLEKAINSLEKEIKQLEAEIKALEKEI-KELEKQLTNIE 456
>gnl|CDD|206777 cd11372, RNase_PH_RRP46, RRP46 subunit of eukaryotic exosome. The
RRP46 subunit of eukaryotic exosome is a member of the
RNase_PH family, named after the bacterial Ribonuclease
PH, a 3'-5' exoribonuclease. Structurally all members of
this family form hexameric rings (trimers of
Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The
eukaryotic exosome core is composed of six individually
encoded RNase PH-like subunits and three additional
proteins (Rrp4, Csl4 and Rrp40) that form a stable cap
and contain RNA-binding domains. The RNase PH-like
subunits are no longer phosphorolytic enzymes, the
exosome directly associates with Rrp44 and Rrp6,
hydrolytic exoribonucleases related to bacterial RNase
II/R and RNase D. The exosome plays an important role in
RNA turnover. It plays a crucial role in the maturation
of stable RNA species such as rRNA, snRNA and snoRNA,
quality control of mRNA, and the degradation of RNA
processing by-products and non-coding transcripts.
Length = 199
Score = 26.8 bits (60), Expect = 4.1
Identities = 20/62 (32%), Positives = 25/62 (40%), Gaps = 13/62 (20%)
Query: 54 GDTVVLAGTDGPIVTQIRSLLMPQPMQELRVKNAYVE--YKKIKGTQGVKIAAKDLEKTI 111
GDT VLA GPI ++R L A +E + G GVK K LE +
Sbjct: 23 GDTSVLAAVYGPIEVKLRKEL---------PDRATLEVIVRPKSGLPGVK--EKLLELLL 71
Query: 112 AG 113
Sbjct: 72 RS 73
>gnl|CDD|223651 COG0578, GlpA, Glycerol-3-phosphate dehydrogenase [Energy
production and conversion].
Length = 532
Score = 26.9 bits (60), Expect = 4.3
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 117 RVAKDQDEIDDLCDEVARELKSALS 141
++EID L D V R L L+
Sbjct: 297 DPRITEEEIDYLLDAVNRYLAPPLT 321
>gnl|CDD|219050 pfam06478, Corona_RPol_N, Coronavirus RPol N-terminus. This family
covers the N-terminal region of the coronavirus
RNA-directed RNA Polymerase.
Length = 356
Score = 26.6 bits (59), Expect = 5.8
Identities = 13/38 (34%), Positives = 17/38 (44%), Gaps = 2/38 (5%)
Query: 41 TIDTILVNGTLYE-GD-TVVLAGTDGPIVTQIRSLLMP 76
T+D +NG Y+ GD G PI S +MP
Sbjct: 195 TLDNQDLNGNFYDFGDFVQTAPGAGVPICDSYYSYMMP 232
>gnl|CDD|221948 pfam13161, DUF3996, Protein of unknown function (DUF3996). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 172 and 203 amino
acids in length.
Length = 153
Score = 26.1 bits (58), Expect = 5.9
Identities = 12/22 (54%), Positives = 14/22 (63%), Gaps = 3/22 (13%)
Query: 33 KAIPGLGTTIDTILVNGTLYEG 54
K PG+G TI +NG LYEG
Sbjct: 122 KIAPGIGI---TIWLNGPLYEG 140
>gnl|CDD|233903 TIGR02512, FeFe_hydrog_A, [FeFe] hydrogenase, group A. This model
describes iron-only hydrogenases of anaerobic and
microaerophilic bacteria and protozoa. This model is
narrower, and covers a longer stretch of sequence, than
pfam02906. This family represents a division among
families that belong to pfam02906, which also includes
proteins such as nuclear prelamin A recognition factor
in animals. Note that this family shows some
heterogeneity in terms of periplasmic, cytosolic, or
hydrogenosome location, NAD or NADP dependence, and
overal protein protein length.
Length = 374
Score = 26.5 bits (59), Expect = 6.1
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 4/35 (11%)
Query: 85 KNAYVEYKKIKGTQGVKIAAKDLEKTIAGLNLRVA 119
+ +E+K ++G GVK A D I G ++VA
Sbjct: 301 ELELIEFKAVRGLDGVKEATVD----IGGTKVKVA 331
>gnl|CDD|217894 pfam04102, SlyX, SlyX. The SlyX protein has no known function. It
is short less than 80 amino acids and is found close to
the slyD gene. The SlyX protein has a conserved PPH(Y/W)
motif at its C-terminus. The protein may be a
coiled-coil structure.
Length = 68
Score = 24.8 bits (55), Expect = 6.7
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 108 EKTIAGLNLRVAKDQDEIDDLCDEVAR 134
E TI LN VA+ Q +ID L ++
Sbjct: 17 EDTIEELNQVVAEQQRQIDRLQRQLRL 43
>gnl|CDD|163687 cd08056, MPN_PRP8, Mpr1p, Pad1p N-terminal (MPN) domains without
isopeptidase activity found in splicing factor Prp8.
Members of this family are found in pre-mRNA-processing
factor 8 (Prp8) which is a critical splicing factor,
interacting with several other spliceosomal proteins,
snRNAs, and the pre-mRNA, thus organizing and
stabilizing the spliceosome catalytic core. Prp8 is one
of the largest and most highly conserved of nuclear
proteins, occupying a central position in the catalytic
core of the spliceosome. Its C-terminal domain exhibits
a JAB1/MPN-like core similar to deubiquitinating
enzymes, but does not show catalytic isopeptidase
activity, possibly because the putative isopeptidase
center is covered by insertions and terminal appendices
that are grafted onto this core, thus impairing the
metal binding site. It is proposed that this domain is a
protein interaction domain instead of a Zn(2+)-dependent
metalloenzyme as proposed for some MPN proteins. The
DEAD-box protein Brr2 and the GTPase Snu114 bind to the
Prp8 C-terminus, a region where mutations in human Prp8
(hPrp8) cause a severe form of the genetic disorder
retinitis pigmentosa, RP13, which leads to progressive
photoreceptor degeneration in the retina and eventual
blindness. At the N-terminus of Prp8, there are several
domains, including a highly variable nuclear
localization signal (NLS) motif rich in prolines, a
conserved RNA recognition motif (RRM), and U5 and U6
snRNA binding sites.
Length = 252
Score = 26.1 bits (58), Expect = 6.8
Identities = 17/52 (32%), Positives = 20/52 (38%), Gaps = 11/52 (21%)
Query: 82 LRVKNAYVEYKKIKGTQGVKIAAKDLEKTIAGLNLRVAKDQDEIDDLCDEVA 133
LR KN YV IK T I K+L K I DL ++A
Sbjct: 19 LRTKNIYVSSDDIKETGYTYILPKNLLKKFI-----------SISDLRTQIA 59
>gnl|CDD|187574 cd05264, UDP_G4E_5_SDR_e, UDP-glucose 4-epimerase (G4E), subgroup
5, extended (e) SDRs. This subgroup partially conserves
the characteristic active site tetrad and NAD-binding
motif of the extended SDRs, and has been identified as
possible UDP-glucose 4-epimerase (aka UDP-galactose
4-epimerase), a homodimeric member of the extended SDR
family. UDP-glucose 4-epimerase catalyzes the
NAD-dependent conversion of UDP-galactose to
UDP-glucose, the final step in Leloir galactose
synthesis. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 300
Score = 26.1 bits (58), Expect = 7.0
Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 6/54 (11%)
Query: 82 LRVKNAYVEYKKIKGTQGV-----KIAAKDLEKTIAGLNLRVAKDQDEIDDLCD 130
LR+ N Y ++ G QGV + I G + +D IDDL +
Sbjct: 163 LRISNPYGPGQRPDGKQGVIPIALNKILRGEPIEIWG-DGESIRDYIYIDDLVE 215
>gnl|CDD|236892 PRK11281, PRK11281, hypothetical protein; Provisional.
Length = 1113
Score = 26.0 bits (58), Expect = 9.8
Identities = 12/52 (23%), Positives = 25/52 (48%)
Query: 94 IKGTQGVKIAAKDLEKTIAGLNLRVAKDQDEIDDLCDEVARELKSALSTIKL 145
+ K + L++ +A ++ + Q E++ L D+ E + LST+ L
Sbjct: 72 LDKIDRQKEETEQLKQQLAQAPAKLRQAQAELEALKDDNDEETRETLSTLSL 123
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
0.317 0.134 0.362
Gapped
Lambda K H
0.267 0.0833 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,178,180
Number of extensions: 654264
Number of successful extensions: 916
Number of sequences better than 10.0: 1
Number of HSP's gapped: 910
Number of HSP's successfully gapped: 60
Length of query: 145
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 57
Effective length of database: 7,034,450
Effective search space: 400963650
Effective search space used: 400963650
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 (21.6 bits)
S2: 54 (24.4 bits)