RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3030
(116 letters)
>gnl|CDD|202474 pfam02932, Neur_chan_memb, Neurotransmitter-gated ion-channel
transmembrane region. This family includes the four
transmembrane helices that form the ion channel.
Length = 228
Score = 83.9 bits (208), Expect = 3e-21
Identities = 31/72 (43%), Positives = 45/72 (62%)
Query: 9 HASLADADNVIPRQLTPEILSAFEGVRFIAQHIKDADKDNEIVEDWKYVSMVLDRFFLCV 68
+ + P +L+PE+ A EGVRFIA+H++ D+ +E+ EDWKYV+MV+DR +
Sbjct: 156 LPGGSGSGLGSPFRLSPELKKALEGVRFIAEHLRSRDEFDEVKEDWKYVAMVIDRLSRWI 215
Query: 69 FTAACVLGTCGI 80
F A VLGT
Sbjct: 216 FPIAFVLGTLVY 227
>gnl|CDD|233155 TIGR00860, LIC, Cation transporter family protein. The
Ligand-gated Ion Channel (LIC) Family of
Neurotransmitter Receptors TC 1.A.9)Members of the LIC
family of ionotropic neurotransmitter receptors are
found only in vertebrate and invertebrate animals. They
exhibit receptor specificity for (1)acetylcholine, (2)
serotonin, (3) glycine, (4) glutamate and (5)
g-aminobutyric acid (GABA). All of these receptor
channels are probably hetero- orhomopentameric. The best
characterized are the nicotinic acetyl-choline receptors
which are pentameric channels of a2bgd subunit
composition. All subunits arehomologous. The three
dimensional structures of the protein complex in both
the open and closed configurations have been solved at
0.9 nm resolution.The channel protein complexes of the
LIC family preferentially transport cations or anions
depending on the channel (e.g., the acetylcholine
receptors are cationselective while glycine receptors
are anion selective) [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 459
Score = 34.3 bits (79), Expect = 0.007
Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 20 PRQLTPEILSAFEGVRFIAQHIKDADKDNEIVEDWKYVSMVLDRFFLCVFTAACVLGTCG 79
P + ++ E VR + D+ E+V DWK+ + V+D+ F A +L G
Sbjct: 396 PAEGDLDLAGILEEVRIA-HRFRKRDESEEVVRDWKFRAKVIDKLSRMAFPLAFLLFNIG 454
Query: 80 I 80
Sbjct: 455 Y 455
>gnl|CDD|187835 cd09704, Csx12, CRISPR/Cas system-associated protein Cas9. CRISPR
(Clustered Regularly Interspaced Short Palindromic
Repeats) and associated Cas proteins comprise a system
for heritable host defense by prokaryotic cells against
phage and other foreign DNA; Very large protein
containing McrA/HNH-nuclease related domain and a
RuvC-like nuclease domain; signature gene for type II.
Length = 804
Score = 28.8 bits (64), Expect = 0.59
Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 5/55 (9%)
Query: 16 DNVIP--RQLTPEILSAFEGVRFIAQHIKDADKDNEI---VEDWKYVSMVLDRFF 65
DN P RQ E+ FE +H KD + ++ D+K S +L R
Sbjct: 351 DNQYPNWRQYLQELKKLFETDLKDLKHSKDQPSNQQMASGQRDYKDDSRILQRIL 405
>gnl|CDD|233148 TIGR00844, c_cpa1, na(+)/h(+) antiporter. The Monovalent
Cation:Proton Antiporter-1 (CPA1) Family (TC 2.A.36) The
CPA1 family is a large family of proteins derived from
Gram-positive and Gram-negative bacteria, blue green
bacteria, yeast, plants and animals. Transporters from
eukaryotes have been functionally characterized, and all
of these catalyze Na+:H+ exchange. Their primary
physiological functions may be in (1) cytoplasmic pH
regulation, extruding the H+ generated during
metabolism, and (2) salt tolerance (in plants), due to
Na+ uptake into vacuoles. This model is specific for the
fungal members of this family [Transport and binding
proteins, Cations and iron carrying compounds].
Length = 810
Score = 27.6 bits (61), Expect = 1.7
Identities = 11/31 (35%), Positives = 19/31 (61%), Gaps = 2/31 (6%)
Query: 49 EIVEDWKYVSMVLDRFFLCVFTAACVLGTCG 79
EIV+DW V+++ + F + C++G CG
Sbjct: 198 EIVKDWICVTILWECIFGSIL--GCIIGYCG 226
>gnl|CDD|178346 PLN02745, PLN02745, Putative pectinesterase/pectinesterase
inhibitor.
Length = 596
Score = 26.7 bits (59), Expect = 2.8
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 80 IIFQAPSLYDNTAPIDIQMTRITQYGISSPPTV 112
+I+ +YD T +D +M +T YG S T+
Sbjct: 316 VIYVKQGIYDETVTVDKKMVNVTMYGDGSQKTI 348
>gnl|CDD|215893 pfam00389, 2-Hacid_dh, D-isomer specific 2-hydroxyacid
dehydrogenase, catalytic domain. This family
represents the largest portion of the catalytic domain
of 2-hydroxyacid dehydrogenases as the NAD binding
domain is inserted within the structural domain.
Length = 312
Score = 26.5 bits (59), Expect = 3.5
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 12 LADADNVIPRQ---LTPEILSAFEGVRFIAQH 40
DAD +I R +T E+L A G++ IA+
Sbjct: 36 AKDADALIVRSTTPVTAEVLEAAPGLKVIARR 67
>gnl|CDD|133056 cd06434, GT2_HAS, Hyaluronan synthases catalyze polymerization of
hyaluronan. Hyaluronan synthases (HASs) are
bi-functional glycosyltransferases that catalyze
polymerization of hyaluronan. HASs transfer both GlcUA
and GlcNAc in beta-(1,3) and beta-(1,4) linkages,
respectively to the hyaluronan chain using UDP-GlcNAc
and UDP-GlcUA as substrates. HA is made as a free
glycan, not attached to a protein or lipid. HASs do not
need a primer for HA synthesis; they initiate HA
biosynthesis de novo with only UDP-GlcNAc, UDP-GlcUA,
and Mg2+. Hyaluronan (HA) is a linear
heteropolysaccharide composed of (1-3)-linked
beta-D-GlcUA-beta-D-GlcNAc disaccharide repeats. It can
be found in vertebrates and a few microbes and is
typically on the cell surface or in the extracellular
space, but is also found inside mammalian cells.
Hyaluronan has several physiochemical and biological
functions such as space filling, lubrication, and
providing a hydrated matrix through which cells can
migrate.
Length = 235
Score = 26.1 bits (58), Expect = 4.7
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 12 LADADNVIPRQLTPEILSAFE 32
L D+D V P PE+L FE
Sbjct: 83 LLDSDTVWPPNALPEMLKPFE 103
>gnl|CDD|240622 cd05198, formate_dh_like, Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxy acid
dehydrogenase family. Formate dehydrogenase,
D-specific 2-hydroxy acid dehydrogenase,
Phosphoglycerate Dehydrogenase, Lactate dehydrogenase,
Thermostable Phosphite Dehydrogenase, and
Hydroxy(phenyl)pyruvate reductase, among others, share
a characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form.
2-hydroxyacid dehydrogenases are enzymes that catalyze
the conversion of a wide variety of D-2-hydroxy acids
to their corresponding keto acids. The general
mechanism is (R)-lactate + acceptor to pyruvate +
reduced acceptor. The NAD+ binding domain is inserted
within the linear sequence of the mostly N-terminal
catalytic domain, which has a similar domain structure
to the internal NAD binding domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD is bound, primarily to the
C-terminal portion of the 2nd (internal) domain. Some
related proteins have similar structural subdomain but
with a tandem arrangement of the catalytic and
NAD-binding subdomains in the linear sequence. Formate
dehydrogenase (FDH) catalyzes the NAD+-dependent
oxidation of formate ion to carbon dioxide with the
concomitant reduction of NAD+ to NADH. FDHs of this
family contain no metal ions or prosthetic groups.
Catalysis occurs though direct transfer of hydride ion
to NAD+ without the stages of acid-base catalysis
typically found in related dehydrogenases. FDHs are
found in all methylotrophic microorganisms in energy
production and in the stress responses of plants.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-Adenosylhomocysteine Hydrolase, among others. While
many members of this family are dimeric, alanine DH is
hexameric and phosphoglycerate DH is tetrameric.
Length = 302
Score = 26.1 bits (58), Expect = 5.2
Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 10/52 (19%)
Query: 10 ASLADADNVIPRQ---LTPEILSAFEGVRFIAQ------HI-KDADKDNEIV 51
A LADAD +I +T E+L+ ++FI +I DA K I
Sbjct: 37 ALLADADALIVSSTTPVTAEVLAKAPKLKFIQVAGAGVDNIDLDAAKKRGIT 88
>gnl|CDD|173241 PRK14780, PRK14780, lipoprotein signal peptidase; Provisional.
Length = 263
Score = 25.7 bits (56), Expect = 6.3
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 45 DKDNEIVEDWKYVSMVLDRFFLCVFTAACVLGTCGII 81
D N +V+ WK+V+ +++ F + + CVL II
Sbjct: 184 DVINGVVDYWKFVNSIINLFDVYIVVGVCVLVVILII 220
>gnl|CDD|226121 COG3593, COG3593, Predicted ATP-dependent endonuclease of the OLD
family [DNA replication, recombination, and repair].
Length = 581
Score = 25.8 bits (57), Expect = 7.1
Identities = 11/33 (33%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 16 DNVIPRQLTPEILSAFEGVRFIAQHIKDADKDN 48
V QL P S E R I +H+ DA + +
Sbjct: 361 SRVAAFQLGPNNFSKEEDKRRIKRHL-DATRSS 392
>gnl|CDD|221649 pfam12580, TPPII, Tripeptidyl peptidase II. This domain family
is found in bacteria and eukaryotes, and is
approximately 190 amino acids in length. The family is
found in association with pfam00082. Tripeptidyl
peptidase II (TPPII) is a crucial component of the
proteolytic cascade acting downstream of the 26S
proteasome in the ubiquitin-proteasome pathway. It is
an amino peptidase belonging to the subtilase family
removing tripeptides from the free N terminus of
oligopeptides.
Length = 188
Score = 25.3 bits (56), Expect = 7.3
Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 6/43 (13%)
Query: 7 TYHASLADADNVIPR-QLTPEIL--SAFEGVRFIAQHIKDADK 46
TY+ +LA A V PR L ++L S FE + I DA+K
Sbjct: 49 TYNFNLAKAAEVTPRLPLLSDLLYESEFESQLW---MIFDANK 88
>gnl|CDD|216296 pfam01094, ANF_receptor, Receptor family ligand binding region.
This family includes extracellular ligand binding
domains of a wide range of receptors. This family also
includes the bacterial amino acid binding proteins of
known structure.
Length = 343
Score = 25.5 bits (56), Expect = 7.7
Identities = 14/77 (18%), Positives = 23/77 (29%), Gaps = 8/77 (10%)
Query: 8 YHASLADADNVIPRQLTPEILSAFEGVRFIAQHIKDADKDNEIVEDWK--------YVSM 59
Y L D + + A +GV D+ E VE K +
Sbjct: 207 YVWILTDLWSDSLDIDNDKAREAAKGVLGFTLKPPDSPGFQEFVERLKKLANRCTPALDT 266
Query: 60 VLDRFFLCVFTAACVLG 76
+ + L + A +L
Sbjct: 267 EPNGYALLAYDAVYLLA 283
>gnl|CDD|146969 pfam04584, Pox_A28, Poxvirus A28 family. Family of conserved
Poxvirus A28 family proteins. Conserved region spans
entire protein in the majority of family members.
Length = 140
Score = 25.0 bits (55), Expect = 8.1
Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 4/27 (14%)
Query: 64 FFLCVFTAACVLGTCGIIFQAPSLYDN 90
FF+ + TAA C I+FQ +Y+N
Sbjct: 7 FFIILATAA----VCFILFQLYYIYEN 29
>gnl|CDD|240650 cd12173, PGDH_4, Phosphoglycerate dehydrogenases, NAD-binding and
catalytic domains. Phosphoglycerate dehydrogenases
(PGDHs) catalyze the initial step in the biosynthesis
of L-serine from D-3-phosphoglycerate. PGDHs come in 3
distinct structural forms, with this first group being
related to 2-hydroxy acid dehydrogenases, sharing
structural similarity to formate and glycerate
dehydrogenases. PGDH in E. coli and Mycobacterium
tuberculosis form tetramers, with subunits containing a
Rossmann-fold NAD binding domain. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as
formate dehydrogenase, glycerate dehydrogenase,
L-alanine dehydrogenase, and S-adenosylhomocysteine
hydrolase. Despite often low sequence identity, these
proteins typically have a characteristic arrangement of
2 similar subdomains of the alpha/beta Rossmann fold
NAD+ binding form. The NAD+ binding domain is inserted
within the linear sequence of the mostly N-terminal
catalytic domain, which has a similar domain structure
to the internal NAD binding domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD is bound, primarily to the
C-terminal portion of the 2nd (internal) domain. Some
related proteins have similar structural subdomain but
with a tandem arrangement of the catalytic and
NAD-binding subdomains in the linear sequence.
Length = 304
Score = 25.1 bits (56), Expect = 9.1
Identities = 11/39 (28%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 5 PNTYHASLADADNVIPR---QLTPEILSAFEGVRFIAQH 40
A +ADAD +I R ++T E++ A ++ I +
Sbjct: 31 EEELLAIIADADALIVRSATKVTAEVIEAAPRLKVIGRA 69
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 0.138 0.423
Gapped
Lambda K H
0.267 0.0803 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,986,270
Number of extensions: 509277
Number of successful extensions: 557
Number of sequences better than 10.0: 1
Number of HSP's gapped: 557
Number of HSP's successfully gapped: 21
Length of query: 116
Length of database: 10,937,602
Length adjustment: 79
Effective length of query: 37
Effective length of database: 7,433,636
Effective search space: 275044532
Effective search space used: 275044532
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: 40 (21.6 bits)
S2: 53 (24.1 bits)