RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5866
(98 letters)
>gnl|CDD|219745 pfam08205, C2-set_2, CD80-like C2-set immunoglobulin domain.
These domains belong to the immunoglobulin superfamily.
Length = 89
Score = 30.1 bits (68), Expect = 0.059
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 61 PKISPGANPVATEGRAIELVCSTSGGSPDPQIS 93
P I P + + E + CS++GG P P+I+
Sbjct: 1 PTIEPPVSLLEGENLEVVATCSSAGGKPAPRIT 33
>gnl|CDD|218123 pfam04516, CP2, CP2 transcription factor. This family represents
a conserved region in the CP2 transcription factor
family.
Length = 237
Score = 28.4 bits (64), Expect = 0.45
Identities = 12/76 (15%), Positives = 25/76 (32%), Gaps = 10/76 (13%)
Query: 1 MDKVEIIDYRPDSGRYDLIISNASFERDNGKFECRLKAAGS-GQDLH---------SQVY 50
+ K +P+S +N +F+ L+A + + Q Y
Sbjct: 12 ILKQPPQSVQPESSSMSEDYVFIPPPSENFRFQYTLEAPTAMAKKSDEIPLTYLNKGQAY 71
Query: 51 TVTVLTPPQPPKISPG 66
++++L P K
Sbjct: 72 SISLLDTAPPLKGLQP 87
>gnl|CDD|188823 cd09439, LIM_Mical, The LIM domain of Mical (molecule interacting
with CasL). The LIM domain of Mical (molecule
interacting with CasL): MICAL is a large, multidomain,
cytosolic protein with a single LIM domain, a calponin
homology (CH) domain and a flavoprotein monooxygenase
domain. In Drosophila, MICAL is expressed in axons,
interacts with the neuronal A (PlexA) receptor and is
required for Semapho-rin 1a (Sema-1a)-PlexA-mediated
repulsive axon guidance. The LIM domain and calporin
homology domain are known for interactions with the
cytoskeleton, cytoskeletal adaptor proteins, and other
signaling proteins. The flavoprotein monooxygenase (MO)
is required for semaphorin-plexin repulsive axon
guidance during axonal pathfinding in the Drosophila
neuromuscular system. In addition, MICAL was
characterized to interact with Rab13 and Rab8 to
coordinate the assembly of tight junctions and adherens
junctions in epithelial cells. Thus, MICAL was also
named junctional Rab13-binding protein (JRAB). As in
other LIM domains, this domain family is 50-60 amino
acids in size and shares two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 55
Score = 26.5 bits (59), Expect = 0.73
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 18 LIISNASFERDNGKFECRL 36
L + +F+RD+GKF C+
Sbjct: 35 LRLGAYAFDRDDGKFYCKP 53
>gnl|CDD|222457 pfam13927, Ig_3, Immunoglobulin domain. This family contains
immunoglobulin-like domains.
Length = 74
Score = 27.0 bits (59), Expect = 0.75
Identities = 14/34 (41%), Positives = 17/34 (50%)
Query: 60 PPKISPGANPVATEGRAIELVCSTSGGSPDPQIS 93
P I+ +P T G + L CS GG P P IS
Sbjct: 1 KPVITVSPSPSVTSGGGVTLTCSAEGGPPPPTIS 34
>gnl|CDD|176228 cd08267, MDR1, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 319
Score = 28.0 bits (63), Expect = 0.81
Identities = 9/47 (19%), Positives = 15/47 (31%), Gaps = 9/47 (19%)
Query: 5 EIIDYR--------PDSGRYDLIISNASFERDNGKFECRLKAAGSGQ 43
E+IDY +YD+I + + L G+
Sbjct: 190 EVIDYTTEDFVALTAGGEKYDVIFDAVGNSPFS-LYRASLALKPGGR 235
>gnl|CDD|183282 PRK11705, PRK11705, cyclopropane fatty acyl phospholipid synthase;
Provisional.
Length = 383
Score = 27.5 bits (62), Expect = 1.0
Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 2/25 (8%)
Query: 4 VEII--DYRPDSGRYDLIISNASFE 26
VEI DYR +G++D I+S FE
Sbjct: 215 VEIRLQDYRDLNGQFDRIVSVGMFE 239
>gnl|CDD|143168 cd04967, Ig1_Contactin, First Ig domain of contactin.
Ig1_Contactin: First Ig domain of contactins.
Contactins are neural cell adhesion molecules and are
comprised of six Ig domains followed by four
fibronectin type III(FnIII) domains anchored to the
membrane by glycosylphosphatidylinositol. The first
four Ig domains form the intermolecular binding
fragment, which arranges as a compact U-shaped module
via contacts between Ig domains 1 and 4, and between Ig
domains 2 and 3. Contactin-2 (TAG-1, axonin-1) may play
a part in the neuronal processes of neurite outgrowth,
axon guidance and fasciculation, and neuronal
migration. This group also includes contactin-1 and
contactin-5. The different contactins show different
expression patterns in the central nervous system.
During development and in adulthood, contactin-2 is
transiently expressed in subsets of central and
peripheral neurons. Contactin-5 is expressed
specifically in the rat postnatal nervous system,
peaking at about 3 weeks postnatal, and a lack of
contactin-5 (NB-2) results in an impairment of neuronal
activity in the rat auditory system. Contactin-5 is
highly expressed in the adult human brain in the
occipital lobe and in the amygdala. Contactin-1 is
differentially expressed in tumor tissues and may,
through a RhoA mechanism, facilitate invasion and
metastasis of human lung adenocarcinoma.
Length = 91
Score = 26.6 bits (59), Expect = 1.3
Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 6/34 (17%)
Query: 7 IDYRPDSGRY-----DLIISNASFERDNGKFECR 35
ID PDS RY +L+ISN S +D G+++C
Sbjct: 45 IDDEPDS-RYSLVGGNLVISNPSKAKDAGRYQCL 77
>gnl|CDD|181902 PRK09489, rsmC, 16S ribosomal RNA m2G1207 methyltransferase;
Provisional.
Length = 342
Score = 27.2 bits (61), Expect = 1.4
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 13 SGRYDLIISNASF 25
GR+D+IISN F
Sbjct: 259 KGRFDMIISNPPF 271
>gnl|CDD|143209 cd05732, Ig5_NCAM-1_like, Fifth immunoglobulin (Ig)-like domain
of Neural Cell Adhesion Molecule NCAM-1 (NCAM) and
similar proteins. Ig5_NCAM-1 like: domain similar to
the fifth immunoglobulin (Ig)-like domain of Neural
Cell Adhesion Molecule NCAM-1 (NCAM). NCAM plays
important roles in the development and regeneration of
the central nervous system, in synaptogenesis and
neural migration. NCAM mediates cell-cell and
cell-substratum recognition and adhesion via homophilic
(NCAM-NCAM), and heterophilic (NCAM-non-NCAM),
interactions. NCAM is expressed as three major isoforms
having different intracellular extensions. The
extracellular portion of NCAM has five N-terminal
Ig-like domains and two fibronectin type III domains.
The double zipper adhesion complex model for NCAM
homophilic binding involves Ig1, Ig2, and Ig3. By this
model, Ig1 and Ig2 mediate dimerization of NCAM
molecules situated on the same cell surface (cis
interactions), and Ig3 domains mediate interactions
between NCAM molecules expressed on the surface of
opposing cells (trans interactions), through binding to
the Ig1 and Ig2 domains. The adhesive ability of NCAM
is modulated by the addition of polysialic acid chains
to the fifth Ig-like domain. Also included in this
group is NCAM-2 (also known as OCAM/mamFas II and
RNCAM) NCAM-2 is differentially expressed in the
developing and mature olfactory epithelium (OE).
Length = 96
Score = 26.3 bits (58), Expect = 1.5
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 61 PKISPGANPVATEGRAIELVCSTSGGSPDPQIS 93
PKI+ N A E I L C G P P+I+
Sbjct: 3 PKITYLENQTAVELEQITLTCEAE-GDPIPEIT 34
>gnl|CDD|143256 cd05848, Ig1_Contactin-5, First Ig domain of contactin-5.
Ig1_Contactin-5: First Ig domain of the neural cell
adhesion molecule contactin-5. Contactins are comprised
of six Ig domains followed by four fibronectin type III
(FnIII) domains, anchored to the membrane by
glycosylphosphatidylinositol. The different contactins
show different expression patterns in the central
nervous system. In rats, a lack of contactin-5 (NB-2)
results in an impairment of the neuronal activity in
the auditory system. Contactin-5 is expressed
specifically in the postnatal nervous system, peaking
at about 3 weeks postnatal. Contactin-5 is highly
expressed in the adult human brain in the occipital
lobe and in the amygdala; lower levels of expression
have been detected in the corpus callosum, caudate
nucleus, and spinal cord.
Length = 94
Score = 26.4 bits (58), Expect = 1.5
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 8 DYRPDSGRYDLIISNASFERDNGKFECR 35
DYR +LIISN S +D+G+++C
Sbjct: 50 DYRYSLIDGNLIISNPSEVKDSGRYQCL 77
>gnl|CDD|163512 TIGR03800, PLP_synth_Pdx2, pyridoxal 5'-phosphate synthase,
glutaminase subunit Pdx2. Pyridoxal 5'-phosphate (PLP)
is synthesized by the PdxA/PdxJ pathway in some species
(mostly within the gamma subdivision of the
proteobacteria) and by the Pdx1/Pdx2 pathway in most
other organisms. This family describes Pdx2, the
glutaminase subunit of the PLP synthase [Biosynthesis of
cofactors, prosthetic groups, and carriers, Pyridoxine].
Length = 184
Score = 26.2 bits (58), Expect = 2.3
Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 5/77 (6%)
Query: 5 EIIDYRPDS-GRYDLIISNASFERDNGKFECRLKAAGSGQDLHSQVYTVTVLTPPQPPKI 63
EII + G D+ + ++ R FE + G G D + V+ + P+ +
Sbjct: 86 EIIGQKEGYLGLLDMTVERNAYGRQVDSFEAEVDIKGVGDDPITGVF----IRAPKIVSV 141
Query: 64 SPGANPVATEGRAIELV 80
G +A G I V
Sbjct: 142 GNGVEILAKVGNRIVAV 158
>gnl|CDD|236577 PRK09581, pleD, response regulator PleD; Reviewed.
Length = 457
Score = 25.6 bits (57), Expect = 4.3
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 13 SGRYDLIISNASFERDNG 30
YDL+I +A+FE +
Sbjct: 196 ETNYDLVIVSANFENYDP 213
>gnl|CDD|238401 cd00778, ProRS_core_arch_euk, Prolyl-tRNA synthetase (ProRS)
class II core catalytic domain. ProRS is a homodimer.
It is responsible for the attachment of proline to the
3' OH group of ribose of the appropriate tRNA. This
domain is primarily responsible for ATP-dependent
formation of the enzyme bound aminoacyl-adenylate.
Class II assignment is based upon its structure and the
presence of three characteristic sequence motifs in the
core domain. This subfamily contains the core domain of
ProRS from archaea, the cytoplasm of eukaryotes and
some bacteria.
Length = 261
Score = 25.6 bits (57), Expect = 4.3
Identities = 13/53 (24%), Positives = 19/53 (35%), Gaps = 10/53 (18%)
Query: 1 MDKVEIIDYRPDSGRYDLIISNASF---ERDNGKFECRLKAAGSGQDLHSQVY 50
+ K E+IDY P G + + E + +K G H VY
Sbjct: 10 ITKAELIDYGPVKGCM--VFRPYGYAIWENIQKILDKEIKETG-----HENVY 55
>gnl|CDD|225969 COG3435, COG3435, Gentisate 1,2-dioxygenase [Secondary metabolites
biosynthesis, transport, and catabolism].
Length = 351
Score = 25.5 bits (56), Expect = 5.0
Identities = 7/25 (28%), Positives = 11/25 (44%)
Query: 73 EGRAIELVCSTSGGSPDPQISVTLQ 97
+G + V +GG P I +Q
Sbjct: 242 DGYKMRYVNPVTGGYAMPTIGAFMQ 266
>gnl|CDD|197509 smart00086, PAC, Motif C-terminal to PAS motifs (likely to
contribute to PAS structural domain). PAC motif occurs
C-terminal to a subset of all known PAS motifs. It is
proposed to contribute to the PAS domain fold.
Length = 43
Score = 24.1 bits (53), Expect = 5.0
Identities = 7/32 (21%), Positives = 14/32 (43%)
Query: 3 KVEIIDYRPDSGRYDLIISNASFERDNGKFEC 34
VE R D +++S + ++G+ E
Sbjct: 1 TVEYRLRRKDGSYIWVLVSASPIRDEDGEVEG 32
>gnl|CDD|225443 COG2890, HemK, Methylase of polypeptide chain release factors
[Translation, ribosomal structure and biogenesis].
Length = 280
Score = 25.4 bits (56), Expect = 6.2
Identities = 8/25 (32%), Positives = 16/25 (64%), Gaps = 3/25 (12%)
Query: 1 MDKVEIID---YRPDSGRYDLIISN 22
+ +V ++ + P G++DLI+SN
Sbjct: 159 LVRVLVVQSDLFEPLRGKFDLIVSN 183
>gnl|CDD|214653 smart00410, IG_like, Immunoglobulin like. IG domains that cannot
be classified into one of IGv1, IGc1, IGc2, IG.
Length = 85
Score = 24.4 bits (53), Expect = 6.2
Identities = 9/24 (37%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 70 VATEGRAIELVCSTSGGSPDPQIS 93
EG ++ L C S GSP P+++
Sbjct: 5 TVKEGESVTLSCEAS-GSPPPEVT 27
>gnl|CDD|214652 smart00409, IG, Immunoglobulin.
Length = 85
Score = 24.4 bits (53), Expect = 6.2
Identities = 9/24 (37%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 70 VATEGRAIELVCSTSGGSPDPQIS 93
EG ++ L C S GSP P+++
Sbjct: 5 TVKEGESVTLSCEAS-GSPPPEVT 27
>gnl|CDD|236988 PRK11805, PRK11805, N5-glutamine S-adenosyl-L-methionine-dependent
methyltransferase; Provisional.
Length = 307
Score = 25.1 bits (56), Expect = 7.4
Identities = 7/8 (87%), Positives = 8/8 (100%)
Query: 15 RYDLIISN 22
RYDLI+SN
Sbjct: 201 RYDLIVSN 208
>gnl|CDD|184130 PRK13545, tagH, teichoic acids export protein ATP-binding
subunit; Provisional.
Length = 549
Score = 25.2 bits (55), Expect = 7.6
Identities = 13/43 (30%), Positives = 22/43 (51%)
Query: 1 MDKVEIIDYRPDSGRYDLIISNASFERDNGKFECRLKAAGSGQ 43
DK++ + +R G Y ++N SFE G+ + GSG+
Sbjct: 21 FDKLKDLFFRSKDGEYHYALNNISFEVPEGEIVGIIGLNGSGK 63
>gnl|CDD|234248 TIGR03534, RF_mod_PrmC, protein-(glutamine-N5) methyltransferase,
release factor-specific. Members of this protein family
are HemK (PrmC), a protein once thought to be involved
in heme biosynthesis but now recognized to be a
protein-glutamine methyltransferase that modifies the
peptide chain release factors. All members of the seed
alignment are encoded next to the release factor 1 gene
(prfA) and confirmed by phylogenetic analysis. SIMBAL
analysis (manuscript in prep.) shows the motif
[LIV]PRx[DE]TE (in Escherichia coli, IPRPDTE) confers
specificity for the release factors rather than for
ribosomal protein L3 [Protein fate, Protein modification
and repair].
Length = 251
Score = 24.7 bits (55), Expect = 8.8
Identities = 6/10 (60%), Positives = 9/10 (90%)
Query: 13 SGRYDLIISN 22
G++DLI+SN
Sbjct: 152 GGKFDLIVSN 161
>gnl|CDD|143225 cd05748, Ig_Titin_like, Immunoglobulin (Ig)-like domain of titin
and similar proteins. Ig_Titin_like: immunoglobulin
(Ig)-like domain found in titin-like proteins. Titin
(also called connectin) is a fibrous sarcomeric protein
specifically found in vertebrate striated muscle. Titin
is gigantic, depending on isoform composition it ranges
from 2970 to 3700 kDa, and is of a length that spans
half a sarcomere. Titin largely consists of multiple
repeats of Ig-like and fibronectin type 3 (FN-III)-like
domains. Titin connects the ends of myosin thick
filaments to Z disks and extends along the thick
filament to the H zone. It appears to function
similarly to an elastic band, keeping the myosin
filaments centered in the sarcomere during muscle
contraction or stretching. Within the sarcomere, titin
is also attached to or is associated with myosin
binding protein C (MyBP-C). MyBP-C appears to
contribute to the generation of passive tension by
titin, and similar to titin has repeated Ig-like and
FN-III domains. Also included in this group are worm
twitchin and insect projectin, thick filament proteins
of invertebrate muscle, which also have repeated
Ig-like and FN-III domains.
Length = 74
Score = 24.1 bits (53), Expect = 9.1
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 10 RPDSGRYDLIISNASFE 26
R DSG+Y L + N + E
Sbjct: 49 RSDSGKYTLTLKNPAGE 65
>gnl|CDD|234247 TIGR03533, L3_gln_methyl, protein-(glutamine-N5) methyltransferase,
ribosomal protein L3-specific. Members of this protein
family methylate ribosomal protein L3 on a glutamine
side chain. This family is related to HemK, a
protein-glutamine methyltranferase for peptide chain
release factors [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 284
Score = 24.8 bits (55), Expect = 9.7
Identities = 6/8 (75%), Positives = 8/8 (100%)
Query: 15 RYDLIISN 22
+YDLI+SN
Sbjct: 189 KYDLIVSN 196
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
0.313 0.133 0.387
Gapped
Lambda K H
0.267 0.0637 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,991,993
Number of extensions: 403561
Number of successful extensions: 310
Number of sequences better than 10.0: 1
Number of HSP's gapped: 310
Number of HSP's successfully gapped: 36
Length of query: 98
Length of database: 10,937,602
Length adjustment: 64
Effective length of query: 34
Effective length of database: 8,098,946
Effective search space: 275364164
Effective search space used: 275364164
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 (24.4 bits)