RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10549
(103 letters)
>gnl|CDD|216175 pfam00888, Cullin, Cullin family.
Length = 603
Score = 60.7 bits (147), Expect = 3e-12
Identities = 22/53 (41%), Positives = 31/53 (58%)
Query: 42 WLLLKNAIQEIQKKNNSGLSFEELYRNAYTMVLHKHGERLYSGLKEVVTAHLE 94
W L +AI +I K+ S L + ELY Y V HK GE+LY+ LKE + ++
Sbjct: 1 WEKLLDAIDQILLKSFSSLDYMELYTAVYNYVPHKLGEKLYNRLKEYLEEYVA 53
>gnl|CDD|200526 cd11265, Sema_5C, The Sema domain, a protein interacting module,
of semaphorin 5C (sema5C). In Drosophila, Sema5C was
identified as an early development gene, which is
expressed in stage 2 embryos with a striped pattern
emerging at later stages. Sema5c may play a role in
odor-guided behavior and in tumorigenesis. Sema5C
belongs to class 5 semaphorin family of proteins, which
are transmembrane glycoproteins characterized by unique
thrombospondin specific repeats in the extracellular
region of the protein. Semaphorins are regulatory
molecules involved in the development of the nervous
system and in axonal guidance. They also play important
roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems
and cancer. The Sema domain is located at the
N-terminus and contains four disulfide bonds formed by
eight conserved cysteine residues. It serves as a
receptor-recognition and -binding module.
Length = 433
Score = 30.1 bits (68), Expect = 0.17
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 9/61 (14%)
Query: 27 RDHLMTMDEKYVQDI----WLLLKNAIQEIQKKNNSGLSFEELYRNAYTMVLHKHGERLY 82
RD+L + ++ + W ++ + Q K S EE N Y VL +G++L+
Sbjct: 26 RDNLYRLSLDGLELLERASWPAAESKVALCQNKGQS----EEDCHN-YVKVLLSYGKQLF 80
Query: 83 S 83
+
Sbjct: 81 A 81
>gnl|CDD|221176 pfam11707, Npa1, Ribosome 60S biogenesis N-terminal. Npa1p is
required for ribosome biogenesis and operates in the
same functional environment as Rsa3p and Dbp6p during
early maturation of 60S ribosomal subunits. The protein
partners of Npa1p include eight putative helicases as
well as the novel Npa2p factor. Npa1p can also
associate with a subset of H/ACA and C/D small
nucleolar RNPs (snoRNPs) involved in the chemical
modification of residues in the vicinity of the
peptidyl transferase centre. The protein has also been
referred to as Urb1, and this domain at the N-terminal
is one of several conserved regions along the length.
Length = 327
Score = 28.8 bits (65), Expect = 0.41
Identities = 13/53 (24%), Positives = 22/53 (41%)
Query: 34 DEKYVQDIWLLLKNAIQEIQKKNNSGLSFEELYRNAYTMVLHKHGERLYSGLK 86
+ + + L+ + +I K +S LSF +L H + LY GL
Sbjct: 14 AQVNNESLLSLITEVLAKILKTLSSDLSFRSYGLGLCKKILSNHLKLLYRGLN 66
>gnl|CDD|232953 TIGR00392, ileS, isoleucyl-tRNA synthetase. The isoleucyl tRNA
synthetase (IleS) is a class I amino acyl-tRNA ligase
and is particularly closely related to the valyl tRNA
synthetase. This model may recognize IleS from every
species, including eukaryotic cytosolic and
mitochondrial forms [Protein synthesis, tRNA
aminoacylation].
Length = 861
Score = 27.3 bits (61), Expect = 1.5
Identities = 8/19 (42%), Positives = 9/19 (47%)
Query: 31 MTMDEKYVQDIWLLLKNAI 49
TMD Y + W L K A
Sbjct: 146 KTMDPSYEESQWWLFKEAH 164
>gnl|CDD|225420 COG2865, COG2865, Predicted transcriptional regulator containing an
HTH domain and an uncharacterized domain shared with the
mammalian protein Schlafen [Transcription].
Length = 467
Score = 26.5 bits (59), Expect = 2.6
Identities = 7/27 (25%), Positives = 12/27 (44%)
Query: 41 IWLLLKNAIQEIQKKNNSGLSFEELYR 67
+ ++ AI I++ N E L R
Sbjct: 238 LPEQVERAISFIKRNLNVPYVVEGLRR 264
>gnl|CDD|241055 cd12611, RRM1_NGR1_NAM8_like, RNA recognition motif 1 in yeast
negative growth regulatory protein NGR1, yeast protein
NAM8 and similar proteins. This subgroup corresponds
to the RRM1 of NGR1 and NAM8. NGR1, also termed
RNA-binding protein RBP1, is a putative
glucose-repressible protein that binds both, RNA and
single-stranded DNA (ssDNA), in yeast. It may function
in regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two of which are followed by a glutamine-rich
stretch that may be involved in transcriptional
activity. In addition, NGR1 has an asparagine-rich
region near the carboxyl terminus which also harbors a
methionine-rich region. The subgroup also includes
NAM8, a putative RNA-binding protein that acts as a
suppressor of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. Like
NGR1, NAM8 contains two RRMs. .
Length = 81
Score = 25.5 bits (56), Expect = 2.6
Identities = 10/32 (31%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 32 TMDEKYVQDIW--LLLKNAIQEIQKKNNSGLS 61
MDE +++ +W L L+ ++ + NSGL+
Sbjct: 10 WMDENFIKQVWASLGLEPVNVKVIRSRNSGLN 41
>gnl|CDD|240407 PTZ00412, PTZ00412, leucyl aminopeptidase; Provisional.
Length = 569
Score = 26.1 bits (57), Expect = 4.6
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 38 VQDIWLLLKNAIQEIQKKNNSGLSFEELYRNAYTM 72
V+D L + A++E +K N S L L ++ ++M
Sbjct: 98 VRDYRLAVTAAVREAKKLNASALVLHSLPQDVFSM 132
>gnl|CDD|114111 pfam05369, MtmB, Monomethylamine methyltransferase MtmB.
Monomethylamine methyltransferase of the
archaebacterium Methanosarcina barkeri contains a novel
amino acid, pyrrolysine, encoded by the termination
codon UAG. The structure reveals a homohexamer
comprised of individual subunits with a TIM barrel
fold.
Length = 457
Score = 25.8 bits (56), Expect = 5.6
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 12/52 (23%)
Query: 35 EKYVQDIWLLLKNAIQEIQKKNNSGLSF------------EELYRNAYTMVL 74
EK QD W L+K ++ ++ K GL F E+L++ + M+L
Sbjct: 19 EKCTQDDWDLMKIPMKAMELKQKYGLDFKGEFVPTDKDMMEKLFQAGFEMLL 70
>gnl|CDD|227934 COG5647, COG5647, Cullin, a subunit of E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 773
Score = 25.5 bits (56), Expect = 5.6
Identities = 12/53 (22%), Positives = 24/53 (45%), Gaps = 9/53 (16%)
Query: 32 TMDEKYVQDIWLLLKNAIQEIQKKNNSGLSFEELYRNAYTMVLHKHGERLYSG 84
T+ E+ + W ++ AI +I FE LY + + L + ++Y+
Sbjct: 14 TLSEEDFESTWEFIERAIGQI---------FERLYDSMAILSLMEVYTKIYNY 57
>gnl|CDD|219814 pfam08385, DHC_N1, Dynein heavy chain, N-terminal region 1. Dynein
heavy chains interact with other heavy chains to form
dimers, and with intermediate chain-light chain
complexes to form a basal cargo binding unit. The region
featured in this family includes the sequences
implicated in mediating these interactions. It is
thought to be flexible and not to adopt a rigid
conformation.
Length = 577
Score = 25.7 bits (57), Expect = 6.1
Identities = 7/52 (13%), Positives = 18/52 (34%), Gaps = 6/52 (11%)
Query: 26 SRDHLMTMDEKYVQDIWLLLKNAIQEIQKKNNSGLSFEELYRNAYTMVLHKH 77
R + E+ + ++K I ++QK F++ + +
Sbjct: 342 KRPRIRGAIEEKQSRLLEMVKKEIDQLQKL------FKKQKQESEADNPPLL 387
>gnl|CDD|223080 COG0001, HemL, Glutamate-1-semialdehyde aminotransferase [Coenzyme
metabolism].
Length = 432
Score = 25.2 bits (56), Expect = 6.4
Identities = 11/34 (32%), Positives = 14/34 (41%), Gaps = 3/34 (8%)
Query: 61 SFEELYRNA--YTMVLHKHGERLYSGLKEVVTAH 92
+ EEL Y + GERL GL+ H
Sbjct: 314 TLEELMTEEGVYERLDAL-GERLAEGLRAAAERH 346
>gnl|CDD|223138 COG0060, IleS, Isoleucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 933
Score = 25.2 bits (56), Expect = 7.3
Identities = 6/20 (30%), Positives = 9/20 (45%)
Query: 31 MTMDEKYVQDIWLLLKNAIQ 50
TMD Y + +W K +
Sbjct: 158 KTMDPSYEESVWWAFKELYE 177
>gnl|CDD|236918 PRK11498, bcsA, cellulose synthase catalytic subunit; Provisional.
Length = 852
Score = 25.4 bits (56), Expect = 7.6
Identities = 16/59 (27%), Positives = 25/59 (42%), Gaps = 5/59 (8%)
Query: 38 VQDIWLLLKNAIQEIQKKNNSGLSFEELYRNAYTMVLHKHGERLYSGLKEVVTAHLETK 96
+Q +WLL+ + +E K S + R Y L + ER+ T HL+ K
Sbjct: 71 IQTLWLLIGRSRKETPKPRRRAFSGLQNIRGRYHQWLEELPERV-----SHKTQHLDEK 124
>gnl|CDD|223491 COG0414, PanC, Panthothenate synthetase [Coenzyme metabolism].
Length = 285
Score = 24.9 bits (55), Expect = 8.8
Identities = 7/26 (26%), Positives = 10/26 (38%)
Query: 76 KHGERLYSGLKEVVTAHLETKVGVEP 101
GER + + E LE V+
Sbjct: 216 AGGERDPAKIIEAARQVLEEAGFVKV 241
>gnl|CDD|176713 cd09011, Glo_EDI_BRP_like_23, This conserved domain belongs to a
superfamily including the bleomycin resistance protein,
glyoxalase I, and type I ring-cleaving dioxygenases.
This protein family belongs to a conserved domain
superfamily that is found in a variety of structurally
related metalloproteins, including the bleomycin
resistance protein, glyoxalase I, and type I
ring-cleaving dioxygenases. A bound metal ion is
required for protein activities for the members of this
superfamily. A variety of metal ions have been found in
the catalytic centers of these proteins including
Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein
superfamily contains members with or without domain
swapping.
Length = 120
Score = 24.6 bits (54), Expect = 9.2
Identities = 10/24 (41%), Positives = 12/24 (50%)
Query: 41 IWLLLKNAIQEIQKKNNSGLSFEE 64
WL + I+K NN L FEE
Sbjct: 49 SWLEGISKADIIEKSNNFELYFEE 72
>gnl|CDD|191604 pfam06760, DUF1221, Protein of unknown function (DUF1221). This is
a family of plant proteins, most of which are
hypothetical and of unknown function. All members
contain the pfam00069 domain, suggesting that they may
possess kinase activity.
Length = 217
Score = 24.8 bits (54), Expect = 9.3
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 26 SRDHLMTMDEKYVQDIWLLLKNAIQEIQKKNNSGLSFEE 64
+RD MD + +D W+L +QE + +S LS E
Sbjct: 150 TRDLCARMDMAWKEDRWILS-QELQEKKGSGSSKLSKHE 187
>gnl|CDD|99934 cd05502, Bromo_tif1_like, Bromodomain; tif1_like subfamily. Tif1
(transcription intermediary factor 1) is a member of
the tripartite motif (TRIM) protein family, which is
characterized by a particular domain architecture. It
functions by recruiting coactivators and/or
corepressors to modulate transcription. Vertebrate
Tif1-gamma, also labeled E3 ubiquitin-protein ligase
TRIM33, plays a role in the control of hematopoiesis.
Its homologue in Xenopus laevis, Ectodermin, has been
shown to function in germ-layer specification and
control of cell growth during embryogenesis.
Bromodomains are 110 amino acid long domains, that are
found in many chromatin associated proteins.
Bromodomains can interact specifically with acetylated
lysine.
Length = 109
Score = 24.6 bits (54), Expect = 9.3
Identities = 10/33 (30%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 16 SLVKSNGHRTSRDHLMTMDEKYVQDIWLLLKNA 48
SL++ S H + E++V D+ L+ KN
Sbjct: 47 SLIRKKLQPKSPQHYSSP-EEFVADVRLMFKNC 78
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
0.312 0.126 0.343
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,851,587
Number of extensions: 394929
Number of successful extensions: 296
Number of sequences better than 10.0: 1
Number of HSP's gapped: 296
Number of HSP's successfully gapped: 34
Length of query: 103
Length of database: 10,937,602
Length adjustment: 69
Effective length of query: 34
Effective length of database: 7,877,176
Effective search space: 267823984
Effective search space used: 267823984
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.1 bits)