RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5646
(106 letters)
>gnl|CDD|238403 cd00780, NTF2, Nuclear transport factor 2 (NTF2) domain plays an
important role in the trafficking of macromolecules,
ions and small molecules between the cytoplasm and
nucleus. This bi-directional transport of macromolecules
across the nuclear envelope requires many soluble
factors that includes GDP-binding protein Ran (RanGDP).
RanGDP is required for both import and export of
proteins and poly(A) RNA. RanGDP also has been
implicated in cell cycle control, specifically in
mitotic spindle assembly. In interphase cells, RanGDP is
predominately nuclear and thought to be GTP bound, but
it is also present in the cytoplasm, probably in the
GDP-bound state. NTF2 mediates the nuclear import of
RanGDP. NTF2 binds to both RanGDP and FxFG
repeat-containing nucleoporins.
Length = 119
Score = 63.5 bits (155), Expect = 2e-14
Identities = 23/102 (22%), Positives = 48/102 (47%), Gaps = 10/102 (9%)
Query: 1 MGKLYKDEDAVLSWNG-HGTKGSQAIVKYISELPP--CDHELKSMDIHRLPEEAAQNQIA 57
+ +LY D ++LS G G AIV+ +S LP H++ ++D P
Sbjct: 24 LHRLYGDT-SMLSREGMKQVTGRDAIVEKLSSLPFQKTKHKITTVDSQPTPSGG------ 76
Query: 58 YLISTSGTVVYKNMKKTGFNQNFIISAEGARWKIISDVFRLQ 99
++ +G++ F+Q F+++ + + +++D+FR
Sbjct: 77 VIVMVTGSLKLDEQPPRKFSQTFVLAPQNGGYFVLNDIFRFV 118
>gnl|CDD|216894 pfam02136, NTF2, Nuclear transport factor 2 (NTF2) domain. This
family includes the NTF2-like Delta-5-3-ketosteroid
isomerase proteins.
Length = 116
Score = 52.4 bits (126), Expect = 4e-10
Identities = 22/100 (22%), Positives = 45/100 (45%), Gaps = 8/100 (8%)
Query: 2 GKLYKDEDAVLSWNGHGT-KGSQAIVKYISELPP--CDHELKSMDIHRLPEEAAQNQIAY 58
LY D+ +V G G +AI ++ LP H + S+D A +
Sbjct: 22 AALYYDDASVEDPPGQSPVTGREAINEFFDSLPFTRIQHLITSVDAQP-----ASHSDGV 76
Query: 59 LISTSGTVVYKNMKKTGFNQNFIISAEGARWKIISDVFRL 98
L+ +G + + + F+Q F+++ + + +++D+FR
Sbjct: 77 LVMVTGELTVDDFPRRRFSQTFLLTPQRGGYFVLNDIFRY 116
>gnl|CDD|238296 cd00531, NTF2_like, Nuclear transport factor 2 (NTF2-like)
superfamily. This family includes members of the NTF2
family, Delta-5-3-ketosteroid isomerases, Scytalone
Dehydratases, and the beta subunit of Ring hydroxylating
dioxygenases. This family is a classic example of
divergent evolution wherein the proteins have many
common structural details but diverge greatly in their
function. For example, nuclear transport factor 2
(NTF2) mediates the nuclear import of RanGDP and binds
to both RanGDP and FxFG repeat-containing nucleoporins
while Ketosteroid isomerases catalyze the isomerization
of delta-5-3-ketosteroid to delta-4-3-ketosteroid, by
intramolecular transfer of the C4-beta proton to the
C6-beta position. While the function of the beta
sub-unit of the Ring hydroxylating dioxygenases is not
known, Scytalone Dehydratases catalyzes two reactions in
the biosynthetic pathway that produces fungal melanin.
Members of the NTF2-like superfamily are widely
distributed among bacteria, archaea and eukaryotes.
Length = 124
Score = 30.9 bits (70), Expect = 0.047
Identities = 23/108 (21%), Positives = 38/108 (35%), Gaps = 18/108 (16%)
Query: 4 LYKDEDAVLSWNGHGT-----KGSQAIVKYISEL---PPCDHELKSM-DIHRLPEEAAQN 54
LY +DA G G +AI + L P L S D+ + +
Sbjct: 23 LY-ADDAYFEPPGGDGLIYPDDGREAIEDRVRRLPFGPSRTRHLVSNVDV-----QPGDD 76
Query: 55 QIAYLISTSGTVVYKNMKKTG---FNQNFIISAEGARWKIISDVFRLQ 99
++S G + + + Q F++ +G KI + FRL
Sbjct: 77 GEGVVVSVFGVLRTRGDGEQDVFAGGQTFVLRPQGGGGKIANRRFRLD 124
>gnl|CDD|176913 cd08904, START_STARD6-like, Lipid-binding START domain of
mammalian STARD6 and related proteins. This subgroup
includes the steroidogenic acute regulatory protein
(StAR)-related lipid transfer (START) domains of
mammalian STARD6 and related domains. It belongs to the
START domain family, and in turn to the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. STARD6 is expressed in male germ cells of
normal rats, and in the steroidogenic Leydig cells of
perinatal hypothyroid testes. It may play a pivotal
role in the steroidogenesis as well as in the
spermatogenesis of normal rats. STARD6 has also been
detected in the rat nervous system, and may participate
in neurosteroid synthesis.
Length = 204
Score = 26.8 bits (59), Expect = 1.8
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 42 MDIHRLPEEAAQNQIAYLISTSGTVVYKNMKK 73
MD ++ +E +Q + Y TSG V K KK
Sbjct: 1 MDFKKIAQETSQEVLGYSRDTSGWKVVKTSKK 32
>gnl|CDD|239276 cd02978, KaiB_like, KaiB-like family; composed of the circadian
clock proteins, KaiB and the N-terminal KaiB-like
sensory domain of SasA. KaiB is an essential protein in
maintaining circadian rhythm. It was originally
discovered from the cyanobacterium Synechococcus as
part of the circadian clock gene cluster, kaiABC. KaiB
attenuates KaiA-enhanced KaiC autokinase activity by
interacting with KaiA-KaiC complexes in a circadian
fashion. KaiB is membrane-associated as well as
cytosolic. The amount of membrane-associated protein
peaks in the evening (at circadian time (CT) 12-16)
while the cytosolic form peaks later (at CT 20). The
rhythmic localization of KaiB may function in
regulating the formation of Kai complexes. SasA is a
sensory histidine kinase which associates with KaiC.
Although it is not an essential oscillator component,
it is important in enhancing kaiABC expression and is
important in metabolic growth control under day/night
cycle conditions. SasA contains an N-terminal sensory
domain with a TRX fold which is involved in the
SasA-KaiC interaction. This domain shows high sequence
similarity with KaiB. However, the KaiB structure does
not show a classical TRX fold. The N-terminal half of
KaiB shares the same beta-alpha-beta topology as TRX,
but the topology of its C-terminal half diverges.
Length = 72
Score = 25.6 bits (57), Expect = 2.6
Identities = 9/34 (26%), Positives = 21/34 (61%)
Query: 23 QAIVKYISELPPCDHELKSMDIHRLPEEAAQNQI 56
Q + + + EL +EL+ +D+ + P+ A +++I
Sbjct: 20 QNLKRILEELLGGPYELEVIDVLKQPQLAEEDKI 53
>gnl|CDD|213322 cd12114, A_NRPS_TlmIV_like, The adenylation domain of nonribosomal
peptide synthetases (NRPS), including Streptoalloteichus
tallysomycin biosynthesis genes. The adenylation (A)
domain of NRPS recognizes a specific amino acid or
hydroxy acid and activates it as an (amino) acyl
adenylate by hydrolysis of ATP. The activated acyl
moiety then forms a thioester to the enzyme-bound
cofactor phosphopantetheine of a peptidyl carrier
protein domain. NRPSs are large multifunctional enzymes
which synthesize many therapeutically useful peptides in
bacteria and fungi via a template-directed, nucleic acid
independent nonribosomal mechanism. These natural
products include antibiotics, immunosuppressants, plant
and animal toxins, and enzyme inhibitors. NRPS has a
distinct modular structure in which each module is
responsible for the recognition, activation, and in some
cases, modification of a single amino acid residue of
the final peptide product. The modules can be subdivided
into domains that catalyze specific biochemical
reactions. This family includes the TLM biosynthetic
gene cluster from Streptoalloteichus that consists of
nine NRPS genes; the N-terminal module of TlmVI (NRPS-5)
and the starter module of BlmVI (NRPS-5) are comprised
of the acyl CoA ligase (AL) and acyl carrier protein
(ACP)-like domains, which are thought to be involved in
the biosynthesis of the beta-aminoalaninamide moiety.
Length = 476
Score = 25.6 bits (57), Expect = 5.6
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 46 RLPEEAAQNQIAYLISTSGT 65
P + +AY+I TSG+
Sbjct: 118 PPPPRVDPDDLAYVIFTSGS 137
>gnl|CDD|238679 cd01383, MYSc_type_VIII, Myosin motor domain, plant-specific type
VIII myosins, a subgroup which has been associated with
endocytosis, cytokinesis, cell-to-cell coupling and
gating at plasmodesmata. This catalytic (head) domain
has ATPase activity and belongs to the larger group of
P-loop NTPases. Myosins are actin-dependent molecular
motors that play important roles in muscle contraction,
cell motility, and organelle transport. The head domain
is a molecular motor, which utilizes ATP hydrolysis to
generate directed movement toward the plus end along
actin filaments. A cyclical interaction between myosin
and actin provides the driving force. Rates of ATP
hydrolysis and consequently the speed of movement along
actin filaments vary widely, from about 0.04 micrometer
per second for myosin I to 4.5 micrometer per second for
myosin II in skeletal muscle. Myosin II moves in
discrete steps about 5-10 nm long and generates 1-5
piconewtons of force. Upon ATP binding, the myosin head
dissociates from an actin filament. ATP hydrolysis
causes the head to pivot and associate with a new actin
subunit. The release of Pi causes the head to pivot and
move the filament (power stroke). Release of ADP
completes the cycle.
Length = 677
Score = 25.9 bits (57), Expect = 5.6
Identities = 10/32 (31%), Positives = 14/32 (43%)
Query: 68 YKNMKKTGFNQNFIISAEGARWKIISDVFRLQ 99
Y M + NQ+ IIS E K + +Q
Sbjct: 83 YNEMMRDEVNQSIIISGESGAGKTETAKIAMQ 114
>gnl|CDD|131084 TIGR02029, AcsF, magnesium-protoporphyrin IX monomethyl ester
aerobic oxidative cyclase. This model respresents the
oxidative cyclase responsible for forming the
distinctive E-ring of the chlorin ring system under
aerobic conditions. This enzyme is believed to utilize a
binuclear iron center and molecular oxygen. There are
two isoforms of this enzyme in some plants and
cyanobacterai which are differentially regulated based
on the levels of copper and oxygen. This step is
essential in the biosynthesis of both
bacteriochlorophyll and chlorophyll under aerobic
conditions (a separate enzyme, BchE, acts under
anaerobic conditions). This enzyme is found in plants,
cyanobacteria and other photosynthetic bacteria
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Chlorophyll and bacteriochlorphyll].
Length = 337
Score = 25.5 bits (56), Expect = 6.0
Identities = 9/39 (23%), Positives = 20/39 (51%), Gaps = 5/39 (12%)
Query: 50 EAAQNQIAYLIST-----SGTVVYKNMKKTGFNQNFIIS 83
E Q I +L + SG ++YK + + N++ +++
Sbjct: 69 ELRQAFIEFLERSCTSEFSGFLLYKELSRRLKNRDPVVA 107
>gnl|CDD|215954 pfam00501, AMP-binding, AMP-binding enzyme.
Length = 412
Score = 25.4 bits (56), Expect = 6.4
Identities = 9/30 (30%), Positives = 12/30 (40%)
Query: 36 DHELKSMDIHRLPEEAAQNQIAYLISTSGT 65
D L + +AY+I TSGT
Sbjct: 113 DELLAGASAEPPAPPVDPDDLAYIIYTSGT 142
>gnl|CDD|176068 cd08686, C2_ABR, C2 domain in the Active BCR (Breakpoint cluster
region) Related protein. The ABR protein is similar to
the breakpoint cluster region protein. It has homology
to guanine nucleotide exchange proteins and
GTPase-activating proteins (GAPs). ABR is expressed
primarily in the brain, but also includes non-neuronal
tissues such as the heart. It has been associated with
human diseases such as Miller-Dieker syndrome in which
mental retardation and malformations of the heart are
present. ABR contains a RhoGEF domain and a PH-like
domain upstream of its C2 domain and a RhoGAP domain
downstream of this domain. A few members also contain
a Bcr-Abl oncoprotein oligomerization domain at the
very N-terminal end. Splice variants of ABR have been
identified. ABR is found in a wide variety of organisms
including chimpanzee, dog, mouse, rat, fruit fly, and
mosquito. The C2 domain was first identified in PKC. C2
domains fold into an 8-standed beta-sandwich that can
adopt 2 structural arrangements: Type I and Type II,
distinguished by a circular permutation involving their
N- and C-terminal beta strands. Many C2 domains are
Ca2+-dependent membrane-targeting modules that bind a
wide variety of substances including bind
phospholipids, inositol polyphosphates, and
intracellular proteins. Most C2 domain proteins are
either signal transduction enzymes that contain a
single C2 domain, such as protein kinase C, or membrane
trafficking proteins which contain at least two C2
domains, such as synaptotagmin 1. However, there are a
few exceptions to this including RIM isoforms and some
splice variants of piccolo/aczonin and intersectin
which only have a single C2 domain. C2 domains with a
calcium binding region have negatively charged
residues, primarily aspartates, that serve as ligands
for calcium ions.
Length = 118
Score = 24.8 bits (54), Expect = 7.1
Identities = 8/31 (25%), Positives = 17/31 (54%)
Query: 58 YLISTSGTVVYKNMKKTGFNQNFIISAEGAR 88
Y + + T V ++ + +N+ F I EG++
Sbjct: 28 YFVKKAKTRVCRDTTEPNWNEEFEIELEGSQ 58
>gnl|CDD|188569 TIGR04054, rSAM_NirJ1, putative heme d1 biosynthesis radical SAM
protein NirJ1. Members of this radical SAM protein
subfamily, designated NirJ1, occur in genomic contexts
with a paralog NirJ2 and with other nitrite reductase
operon genes associated with heme d1 biosynthesis, as
in Heliobacillus mobilis and Heliophilum fasciatum.
NirJ1 is presumed by bioinformatics analysis (Xiong, et
al.) to be a heme d1 biosynthesis protein by context,
perhaps involved in conversions of acetate groups to
methyl groups in conversion from uroporphyrinogen III.
Length = 351
Score = 25.4 bits (56), Expect = 7.4
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 4/37 (10%)
Query: 43 DIHRLPEEAAQNQIAYLISTSGTV----VYKNMKKTG 75
D+ L A + I IST+GT+ K +KK G
Sbjct: 62 DLFELAAYATKRGIRPTISTNGTLITKETAKELKKIG 98
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
0.316 0.131 0.387
Gapped
Lambda K H
0.267 0.0809 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,315,168
Number of extensions: 429318
Number of successful extensions: 348
Number of sequences better than 10.0: 1
Number of HSP's gapped: 346
Number of HSP's successfully gapped: 19
Length of query: 106
Length of database: 10,937,602
Length adjustment: 71
Effective length of query: 35
Effective length of database: 7,788,468
Effective search space: 272596380
Effective search space used: 272596380
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 (24.0 bits)