RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1486
(154 letters)
>gnl|CDD|217283 pfam02913, FAD-oxidase_C, FAD linked oxidases, C-terminal domain.
This domain has a ferredoxin-like fold.
Length = 247
Score = 49.3 bits (118), Expect = 1e-07
Identities = 30/149 (20%), Positives = 48/149 (32%), Gaps = 30/149 (20%)
Query: 1 RCQPSSIRLVDNVQLKAGQFFRPDPGYLELLTDGLKKLYVTKILGFRDDEMCAATVLFEG 60
P+++ L+D L T LG D A V FEG
Sbjct: 29 GIGPAALELMDKAALDLV--------------------LGTLGLGLPRDAPAALLVEFEG 68
Query: 61 DPEDVKNNEDKIYSIAKRYGGIPAG--------ESNGRRGYMLTYIIAYIRDFACDYYFI 112
+ E+V E ++ G AG R Y + +RD +
Sbjct: 69 NDEEV-VEERLEAAVEAILEGAGAGDVVVAEDEAERERLWRARKYAMP-LRDALGGAGPL 126
Query: 113 GDSFETSVPWDKTVLLCINVKKRLTRECT 141
+ + SVPW + L ++K+ L +
Sbjct: 127 VFTEDVSVPWSRLPDLVADIKELLAKYGL 155
>gnl|CDD|149059 pfam07785, DUF1623, Protein of unknown function (DUF1623). The
members of this family are all derived from relatively
short hypothetical proteins thought to be expressed by
various Nucleopolyhedroviruses.
Length = 90
Score = 28.9 bits (65), Expect = 0.44
Identities = 13/40 (32%), Positives = 19/40 (47%)
Query: 40 VTKILGFRDDEMCAATVLFEGDPEDVKNNEDKIYSIAKRY 79
+ F D + VL E + DV+ DKIY+I + Y
Sbjct: 50 IIDESQFDDFKRSDLEVLDEYELSDVELLLDKIYNIVEMY 89
>gnl|CDD|241412 cd13258, PH_PLEKHJ1, Pleckstrin homology domain containing, family
J member 1 Pleckstrin homology (PH) domain. PLEKHJ1
(also called GNRPX2/Guanine nucleotide-releasing protein
x ). It contains a single PH domain. Very little
information is known about PLEKHJ1. PLEKHJ1 has been
shown to interact with IKBKG (inhibitor of kappa light
polypeptide gene enhancer in B-cells, kinase gamma) and
KRT33B (keratin 33B). PH domains have diverse functions,
but in general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 144
Score = 28.6 bits (64), Expect = 0.83
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 99 IAYIRDFACDYYFIGDSFETSVPW 122
I++I + YYF S E V W
Sbjct: 86 ISFIDEPERKYYFECRSEEQCVEW 109
>gnl|CDD|218620 pfam05511, ATP-synt_F6, Mitochondrial ATP synthase coupling
factor 6. Coupling factor 6 (F6) is a component of
mitochondrial ATP synthase which is required for the
interactions of the catalytic and proton-translocating
segments.
Length = 99
Score = 27.8 bits (62), Expect = 0.97
Identities = 14/50 (28%), Positives = 28/50 (56%)
Query: 32 TDGLKKLYVTKILGFRDDEMCAATVLFEGDPEDVKNNEDKIYSIAKRYGG 81
D +++L+V KI ++ + L + PE K ++++ +AK+YGG
Sbjct: 34 LDPIQQLFVDKIREYKQKSKSSGGKLVDAGPEYEKELKEELEKLAKQYGG 83
>gnl|CDD|107332 cd06337, PBP1_ABC_ligand_binding_like_4, Type I periplasmic
ligand-binding domain of uncharacterized ABC (ATPase
Binding Cassette)-type active transport systems that are
predicted to be involved in transport of amino acids,
peptides, or inorganic ions. This subgroup includes the
type I periplasmic ligand-binding domain of
uncharacterized ABC (ATPase Binding Cassette)-type
active transport systems that are predicted to be
involved in transport of amino acids, peptides, or
inorganic ions. Members of this group are
sequence-similar to members of the family of ABC-type
hydrophobic amino acid transporters, such as
leucine-isoleucine-valine-binding protein (LIVBP);
however their ligand specificity has not been determined
experimentally.
Length = 357
Score = 28.9 bits (65), Expect = 1.0
Identities = 21/96 (21%), Positives = 35/96 (36%), Gaps = 15/96 (15%)
Query: 15 LKAGQFFRPDPGYLELLTDGLKKLYVTKILGFRDDEMCAATVLFEGDPEDVKN-----NE 69
L + DPG E TD + ++I F+ + + T P D +
Sbjct: 172 LADAGYKLVDPGRFEPGTDD----FSSQINAFKREGVDIVTGFA--IPPDFATFWRQAAQ 225
Query: 70 D----KIYSIAKRYGGIPAGESNGRRGYMLTYIIAY 101
KI +IAK E+ G RG ++ + +
Sbjct: 226 AGFKPKIVTIAKALLFPEDVEALGDRGDGMSTEVWW 261
>gnl|CDD|212071 cd11502, SLC6sbd_NTT5, Neurotransmitter transporter 5;
solute-binding domain. Human NTT5 is encoded by the
SLC6A16 gene. NTT5 is expressed in testis, pancreas, and
prostate; its expression is predominantly intracellular,
indicative of a vesicular location. Its substrates are
unknown. This subgroup belongs to the solute carrier 6
(SLC6) transporter family.
Length = 543
Score = 28.1 bits (63), Expect = 1.9
Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 4/31 (12%)
Query: 110 YFIGDSFETSVPWDKTVLLCINVKKRLTREC 140
+++G SF+ +PW++ C VK EC
Sbjct: 107 FYLGHSFQFPLPWEQ----CPLVKNSSDPEC 133
>gnl|CDD|204905 pfam12399, BCA_ABC_TP_C, Branched-chain amino acid ATP-binding
cassette transporter. This domain family is found in
bacteria, archaea and eukaryotes, and is approximately
30 amino acids in length. The family is found in
association with pfam00005. There is a conserved AYLG
sequence motif. This family is the C terminal of an ATP
dependent branched-chain amino acid transporter.
Length = 23
Score = 24.5 bits (55), Expect = 4.2
Identities = 5/16 (31%), Positives = 9/16 (56%)
Query: 55 TVLFEGDPEDVKNNED 70
V+ EG P +V+ +
Sbjct: 1 RVIAEGTPAEVRADPA 16
>gnl|CDD|213186 cd03219, ABC_Mj1267_LivG_branched, ATP-binding cassette component
of branched chain amino acids transport system. The
Mj1267/LivG ABC transporter subfamily is involved in the
transport of the hydrophobic amino acids leucine,
isoleucine and valine. MJ1267 is a branched-chain amino
acid transporter with 29% similarity to both the LivF
and LivG components of the E. coli branched-chain amino
acid transporter. MJ1267 contains an insertion from
residues 114 to 123 characteristic of LivG
(Leucine-Isoleucine-Valine) homologs. The branched-chain
amino acid transporter from E. coli comprises a
heterodimer of ABCs (LivF and LivG), a heterodimer of
six-helix TM domains (LivM and LivH), and one of two
alternative soluble periplasmic substrate binding
proteins (LivK or LivJ).
Length = 236
Score = 27.0 bits (61), Expect = 4.4
Identities = 7/15 (46%), Positives = 11/15 (73%)
Query: 56 VLFEGDPEDVKNNED 70
V+ EG P++V+NN
Sbjct: 221 VIAEGTPDEVRNNPR 235
>gnl|CDD|233571 TIGR01778, TonB-copper, TonB-dependent copper receptor. This model
represents a family of proteobacterial TonB-dependent
outer membrane receptor/transporters which bind and
translocate copper ions. Two characterized members of
this family exist, outer membrane protein C (OprC) from
Pseudomonas aeruginosa and NosA from Pseudomonas
stutzeri which is responsible for providing copper for
the copper-containing N2O reducatse [Transport and
binding proteins, Cations and iron carrying compounds,
Transport and binding proteins, Porins].
Length = 636
Score = 27.1 bits (60), Expect = 4.6
Identities = 16/43 (37%), Positives = 20/43 (46%), Gaps = 7/43 (16%)
Query: 53 AATVLFEGDPEDVKNNEDKIYSIAKRYGGIPAGESNGRRGYML 95
A TVLFE PE + + ++Y A G SNGR L
Sbjct: 98 AGTVLFERQPE--RFDALELYGGASGLRG-----SNGRFDAYL 133
>gnl|CDD|163616 cd00840, MPP_Mre11_N, Mre11 nuclease, N-terminal metallophosphatase
domain. Mre11 (also known as SbcD in Escherichia coli)
is a subunit of the MRX protein complex. This complex
includes: Mre11, Rad50, and Xrs2/Nbs1, and plays a vital
role in several nuclear processes including DNA
double-strand break repair, telomere length maintenance,
cell cycle checkpoint control, and meiotic
recombination, in eukaryotes. During double-strand
break repair, the MRX complex is required to hold the
two ends of a broken chromosome together. In vitro
studies show that Mre11 has 3'-5' exonuclease activity
on dsDNA templates and endonuclease activity on dsDNA
and ssDNA templates. In addition to the N-terminal
phosphatase domain, the eukaryotic MRE11 members of this
family have a C-terminal DNA binding domain (not
included in this alignment model). MRE11-like proteins
are found in prokaryotes and archaea was well as in
eukaryotes. Mre11 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 = 223
Score = 26.6 bits (59), Expect = 5.2
Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 5/56 (8%)
Query: 95 LTYIIAYIRDFACDYYFI-GDSFETSVPWDKTVLLCINVKKRLTRECTGRWLPVLV 149
I+ + D+ I GD F+++ P + + L I +RL +PV +
Sbjct: 30 FEEIVELAIEEKVDFVLIAGDLFDSNNPSPEALELLIEALRRLKEAG----IPVFI 81
>gnl|CDD|176073 cd08691, C2_NEDL1-like, C2 domain present in NEDL1 (NEDD4-like
ubiquitin protein ligase-1). NEDL1 (AKA HECW1(HECT,
C2 and WW domain containing E3 ubiquitin protein ligase
1)) is a newly identified HECT-type E3 ubiquitin
protein ligase highly expressed in favorable
neuroblastomas. In vertebrates it is found primarily in
neuronal tissues, including the spinal cord. NEDL1 is
thought to normally function in the quality control of
cellular proteins by eliminating misfolded proteins.
This is thought to be accomplished via a mechanism
analogous to that of ER-associated degradation by
forming tight complexes and aggregating misfolded
proteins that have escaped ubiquitin-mediated
degradation. NEDL1, is composed of a C2 domain, two WW
domains, and a ubiquitin ligase Hect domain. 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 = 137
Score = 26.2 bits (58), Expect = 5.4
Identities = 9/16 (56%), Positives = 12/16 (75%), Gaps = 1/16 (6%)
Query: 15 LKAGQFFRPDPGYLEL 30
LK G FF PDP Y+++
Sbjct: 13 LKKGMFFNPDP-YVKI 27
>gnl|CDD|223488 COG0411, LivG, ABC-type branched-chain amino acid transport
systems, ATPase component [Amino acid transport and
metabolism].
Length = 250
Score = 26.4 bits (59), Expect = 5.8
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 55 TVLFEGDPEDVKNNEDKI 72
V+ EG PE+V+NN I
Sbjct: 227 EVIAEGTPEEVRNNPRVI 244
>gnl|CDD|224060 COG1137, YhbG, ABC-type (unclassified) transport system, ATPase
component [General function prediction only].
Length = 243
Score = 26.4 bits (59), Expect = 6.7
Identities = 11/25 (44%), Positives = 16/25 (64%), Gaps = 2/25 (8%)
Query: 51 MCAATVLFEGDPEDVKNNED--KIY 73
+ VL EG PE++ NNED ++Y
Sbjct: 212 ISDGKVLAEGSPEEIVNNEDVRRVY 236
>gnl|CDD|213185 cd03218, ABC_YhbG, ATP-binding cassette component of YhbG transport
system. The ABC transporters belonging to the YhbG
family are similar to members of the Mj1267_LivG family,
which is involved in the transport of branched-chain
amino acids. The genes yhbG and yhbN are located in a
single operon and may function together in cell envelope
during biogenesis. YhbG is the putative ATP-binding
cassette component and YhbN is the putative
periplasmic-binding protein. Depletion of each gene
product leads to growth arrest, irreversible cell damage
and loss of viability in E. coli. The YhbG homolog
(NtrA) is essential in Rhizobium meliloti, a symbiotic
nitrogen-fixing bacterium.
Length = 232
Score = 26.0 bits (58), Expect = 7.7
Identities = 10/20 (50%), Positives = 13/20 (65%), Gaps = 2/20 (10%)
Query: 56 VLFEGDPEDVKNNED--KIY 73
VL EG PE++ NE K+Y
Sbjct: 211 VLAEGTPEEIAANELVRKVY 230
>gnl|CDD|176990 CHL00049, ndhB, NADH dehydrogenase subunit 2.
Length = 494
Score = 26.5 bits (59), Expect = 7.8
Identities = 15/33 (45%), Positives = 19/33 (57%), Gaps = 8/33 (24%)
Query: 81 GIPAGESNGRRGY--MLTYIIAYI----RDFAC 107
GI G+SN GY M+TY++ YI FAC
Sbjct: 322 GIIVGDSND--GYASMITYMLFYIFMNLGTFAC 352
>gnl|CDD|225566 COG3022, COG3022, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 253
Score = 26.1 bits (58), Expect = 8.7
Identities = 14/38 (36%), Positives = 18/38 (47%), Gaps = 12/38 (31%)
Query: 63 EDVKNNEDKIYS-IAKRYGGIPAGESNGRRGYMLTYII 99
+D KN + K+ S AK+ RG ML YII
Sbjct: 190 KDEKNGKYKVISFYAKKA-----------RGLMLRYII 216
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
0.324 0.144 0.448
Gapped
Lambda K H
0.267 0.103 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,131,503
Number of extensions: 754377
Number of successful extensions: 606
Number of sequences better than 10.0: 1
Number of HSP's gapped: 604
Number of HSP's successfully gapped: 21
Length of query: 154
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 65
Effective length of database: 6,990,096
Effective search space: 454356240
Effective search space used: 454356240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (24.5 bits)