RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4403
(101 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 = 37.5 bits (88), Expect = 3e-04
Identities = 11/41 (26%), Positives = 16/41 (39%)
Query: 9 EIVDYGGILKFKADTNASSVMIARAAQDNCSIFSPTKGIQD 49
+I L+ T VMI R A N +F K + +
Sbjct: 191 DIFSLEDALRCLEQTGVDGVMIGRGALGNPWLFREIKELLE 231
>gnl|CDD|223120 COG0042, COG0042, tRNA-dihydrouridine synthase [Translation,
ribosomal structure and biogenesis].
Length = 323
Score = 31.1 bits (71), Expect = 0.056
Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 13/71 (18%)
Query: 5 GGSKEIVDYGGILKFKADTNASSVMIARAAQDNCSIFSPTKGIQD----------IHQMI 54
G K + D +L++ T A VMI R A N +F ++ + ++
Sbjct: 205 GDIKSLEDAKEMLEY---TGADGVMIGRGALGNPWLFRQIDYLETGELLPPTLAEVLDIL 261
Query: 55 KEYLRYCVDYD 65
+E+L ++Y
Sbjct: 262 REHLELLLEYY 272
>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 = 29.0 bits (65), Expect = 0.29
Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 8/73 (10%)
Query: 27 SVMIARAAQDNCS--------IFSPTKGIQDIHQMIKEYLRYCVDYDNSAPNSKYCVQSM 78
VM+ R A +N IF+ T I +++++ L Y +Y + + + + +
Sbjct: 219 GVMVGREAYENPYLLANVDREIFNETDEILTRKEIVEQMLPYIEEYLSQGLSLNHITRHL 278
Query: 79 LGSQQESPLGKKF 91
LG Q P K++
Sbjct: 279 LGLFQGKPGAKQW 291
>gnl|CDD|181635 PRK09065, PRK09065, glutamine amidotransferase; Provisional.
Length = 237
Score = 28.4 bits (64), Expect = 0.51
Identities = 20/74 (27%), Positives = 32/74 (43%), Gaps = 12/74 (16%)
Query: 27 SVMIARAAQDNCSIF--SP-TKGIQ-----DIHQMIKEYLRYCVDYDNSAPNSKYCVQSM 78
+V++AR+AQD F P G+Q H M + YLR + +++
Sbjct: 159 AVVLARSAQDPHQAFRYGPHAWGVQFHPEFTAHIM-RAYLRA---RADCLRREGLDARTL 214
Query: 79 LGSQQESPLGKKFL 92
L E+P +K L
Sbjct: 215 LREVSEAPWARKLL 228
>gnl|CDD|219256 pfam06991, Prp19_bind, Splicing factor, Prp19-binding domain. This
family represents the C-terminus (approximately 300
residues) of proteins that are involved as binding
partners for Prp19 as part of the nuclear pore complex.
The family in Drosophila is necessary for pre-mRNA
splicing, and the human protein has been found in
purifications of the spliceosome. In the past this
family was thought, erroneously, to be associated with
microfibrillin.
Length = 277
Score = 28.0 bits (62), Expect = 0.86
Identities = 10/29 (34%), Positives = 14/29 (48%), Gaps = 2/29 (6%)
Query: 64 YDNSAPNSKYCVQSMLGSQQ--ESPLGKK 90
Y S N K+ + G + + PLGKK
Sbjct: 248 YSESNLNLKFSNKRAGGMRSVFDKPLGKK 276
>gnl|CDD|177113 MTH00038, COX2, cytochrome c oxidase subunit II; Provisional.
Length = 229
Score = 27.4 bits (61), Expect = 1.1
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 85 SPLGKKFLESQTLEQIW 101
SP + FLE Q LE IW
Sbjct: 49 SPTNRFFLEGQELETIW 65
>gnl|CDD|233881 TIGR02470, sucr_synth, sucrose synthase. This model represents
sucrose synthase, an enzyme that, despite its name,
generally uses rather produces sucrose. Sucrose plus
UDP (or ADP) becomes D-fructose plus UDP-glucose (or
ADP-glucose), which is then available for cell wall (or
starch) biosynthesis. The enzyme is homologous to
sucrose phosphate synthase, which catalyzes the
penultimate step in sucrose synthesis. Sucrose synthase
is found, so far, exclusively in plants and
cyanobacteria [Energy metabolism, Biosynthesis and
degradation of polysaccharides].
Length = 784
Score = 27.4 bits (61), Expect = 1.5
Identities = 13/45 (28%), Positives = 21/45 (46%)
Query: 40 IFSPTKGIQDIHQMIKEYLRYCVDYDNSAPNSKYCVQSMLGSQQE 84
S K HQ++ E+ +YC D D S+ + ++ S QE
Sbjct: 11 YVSQGKRYLLRHQLLDEFEQYCSDADKEKKLSESPLGKLIFSTQE 55
>gnl|CDD|225414 COG2859, COG2859, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 237
Score = 27.1 bits (60), Expect = 1.5
Identities = 10/45 (22%), Positives = 15/45 (33%)
Query: 17 LKFKADTNASSVMIARAAQDNCSIFSPTKGIQDIHQMIKEYLRYC 61
L+F + + I A+Q IFS + D K
Sbjct: 185 LEFAKHSGSKLGKIKDASQGVFQIFSNDSDLDDPTAYPKNIRVVV 229
>gnl|CDD|163637 cd07394, MPP_Vps29, Homo sapiens Vps29 and related proteins,
metallophosphatase domain. Vps29 (vacuolar sorting
protein 29), also known as vacuolar membrane protein
Pep11, is a subunit of the retromer complex which is
responsible for the retrieval of mannose-6-phosphate
receptors (MPRs) from the endosomes for retrograde
transport back to the Golgi. Vps29 has a
phosphoesterase fold that acts as a protein interaction
scaffold for retromer complex assembly as well as a
phosphatase with specificity for the cytoplasmic tail
of the MPR. The retromer includes the following 5
subunits: Vps35, Vps26, Vps29, and a dimer of the
sorting nexins Vps5 (Snx1), and Vps17 (Snx2). Vps29
belongs to the metallophosphatase (MPP) superfamily.
MPPs are functionally diverse, but all share a
conserved domain with an active site consisting of two
metal ions (usually manganese, iron, or zinc)
coordinated with octahedral geometry by a cage of
histidine, aspartate, and asparagine residues. The MPP
superfamily includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and
acid sphingomyelinases (ASMases). The conserved domain
is a double beta-sheet sandwich with a di-metal active
site made up of residues located at the C-terminal side
of the sheets. This domain is thought to allow for
productive metal coordination.
Length = 178
Score = 25.6 bits (57), Expect = 4.4
Identities = 16/43 (37%), Positives = 17/43 (39%), Gaps = 7/43 (16%)
Query: 6 GSKEIVDYGGILKFKADTNASSVMIARAAQDNCSIFSPTKGIQ 48
SKE DY LK T A V I R D + TK I
Sbjct: 40 CSKETYDY---LK----TIAPDVHIVRGDFDENLNYPETKVIT 75
>gnl|CDD|233505 TIGR01646, vgr_GE, Rhs element Vgr protein. This model represents
the Vgr family of proteins, associated with some classes
of Rhs elements. This model does not include a large
octapeptide repeat region, VGXXXXXX, found in the Vgr of
Rhs classes G and E.
Length = 483
Score = 25.1 bits (55), Expect = 7.9
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 2/42 (4%)
Query: 37 NCSIFSPTKGIQDIHQMIKEY--LRYCVDYDNSAPNSKYCVQ 76
N IF T I ++++EY + D P +YCVQ
Sbjct: 90 NNRIFQDTSVPDIIEEILREYGFADFRFDVAREYPQREYCVQ 131
>gnl|CDD|239458 cd03342, TCP1_zeta, TCP-1 (CTT or eukaryotic type II) chaperonin
family, zeta subunit. Chaperonins are involved in
productive folding of proteins. They share a common
general morphology, a double toroid of 2 stacked rings.
In contrast to bacterial group I chaperonins (GroEL),
each ring of the eukaryotic cytosolic chaperonin (CTT)
consists of eight different, but homologous subunits.
Their common function is to sequester nonnative
proteins inside their central cavity and promote
folding by using energy derived from ATP hydrolysis.
The best studied in vivo substrates of CTT are actin
and tubulin.
Length = 484
Score = 24.9 bits (55), Expect = 8.3
Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 12/49 (24%)
Query: 1 MDPSGGSKEIVDYGGILKFKAD----------TNASSVMIARAA--QDN 37
+ P G K +V G +K D + ++ MIARAA QD+
Sbjct: 32 LGPKGTLKMLVSGAGDIKLTKDGNVLLSEMQIQHPTASMIARAATAQDD 80
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
0.315 0.131 0.382
Gapped
Lambda K H
0.267 0.0592 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,813,314
Number of extensions: 368016
Number of successful extensions: 269
Number of sequences better than 10.0: 1
Number of HSP's gapped: 267
Number of HSP's successfully gapped: 14
Length of query: 101
Length of database: 10,937,602
Length adjustment: 67
Effective length of query: 34
Effective length of database: 7,965,884
Effective search space: 270840056
Effective search space used: 270840056
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: 53 (24.5 bits)