RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7111
(87 letters)
>gnl|CDD|203323 pfam05739, SNARE, SNARE domain. Most if not all vesicular
membrane fusion events in eukaryotic cells are believed
to be mediated by a conserved fusion machinery, the
SNARE [soluble N-ethylmaleimide-sensitive factor (NSF)
attachment protein (SNAP) receptors] machinery. The
SNARE domain is thought to act as a protein-protein
interaction module in the assembly of a SNARE protein
complex.
Length = 62
Score = 37.1 bits (87), Expect = 5e-05
Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 31 NEQLTSDLRNKIQALKSLTIDIGTEVKYQNEHLLRGMDDDFDRTGGFLNNSMAR 84
++ +L + I LK L +D+G EV+ Q E LL +DD+ D T + + R
Sbjct: 1 RDEALEELESSIGELKQLFLDMGEEVEEQGE-LLDRIDDNVDNTQSRVERANKR 53
>gnl|CDD|197699 smart00397, t_SNARE, Helical region found in SNAREs. All
alpha-helical motifs that form twisted and parallel
four-helix bundles in target soluble
N-ethylmaleimide-sensitive factor (NSF) attachment
protein (SNAP) receptor proteins. This motif found in
"Q-SNAREs".
Length = 66
Score = 33.7 bits (78), Expect = 0.001
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 25 DAIHQENEQLTSDLRNKIQALKSLTIDIGTEVKYQNEHLLRGMDDDFDRTGGFLNNSMAR 84
A +E ++ L IQ LK + +D+GTE++ Q E L ++D+ D L + R
Sbjct: 4 LAREEERDEELEQLEKSIQELKQIFLDMGTELEEQGE-QLDRIEDNVDDADVNLKKANKR 62
>gnl|CDD|238115 cd00193, t_SNARE, Soluble NSF (N-ethylmaleimide-sensitive fusion
protein)-Attachment protein (SNAP) REceptor domain;
these alpha-helical motifs form twisted and parallel
heterotetrameric helix bundles; the core complex
contains one helix from a protein that is anchored in
the vesicle membrane (synaptobrevin), one helix from a
protein of the target membrane (syntaxin), and two
helices from another protein anchored in the target
membrane (SNAP-25); their interaction forms a core
which is composed of a polar zero layer, a flanking
leucine-zipper layer acts as a water tight shield to
isolate ionic interactions in the zero layer from the
surrounding solvent.
Length = 60
Score = 33.6 bits (78), Expect = 0.001
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 28 HQENEQLTSDLRNKIQALKSLTIDIGTEVKYQNEHLLRGMDDDFDRTGGFLNNSMAR 84
QE ++ L I LK + +D+GTEV+ Q E L R ++D+ D + + R
Sbjct: 1 EQERDEELEQLEASIGELKQIFLDLGTEVEEQGELLDR-IEDNVDNADVNVKRANKR 56
>gnl|CDD|99746 cd06453, SufS_like, Cysteine desulfurase (SufS)-like. This family
belongs to the pyridoxal phosphate (PLP)-dependent
aspartate aminotransferase superfamily (fold I). The
major groups in this CD correspond to cysteine
desulfurase (SufS) and selenocysteine lyase. SufS
catalyzes the removal of elemental sulfur and selenium
atoms from L-cysteine, L-cystine, L-selenocysteine, and
L-selenocystine to produce L-alanine; and selenocysteine
lyase catalyzes the decomposition of L-selenocysteine.
Length = 373
Score = 27.4 bits (62), Expect = 0.93
Identities = 8/59 (13%), Positives = 20/59 (33%), Gaps = 22/59 (37%)
Query: 14 YEPVPNQFDGG----------------------DAIHQENEQLTSDLRNKIQALKSLTI 50
Y +P++F+ G +AI +LT+ ++ + + +
Sbjct: 241 YADLPHKFEAGTPNIAGAIGLGAAIDYLEKIGMEAIAAHEHELTAYALERLSEIPGVRV 299
>gnl|CDD|241400 cd13246, PH_Scd1, Shape and Conjugation Deficiency 1 Pleckstrin
homology (PH) domain. Fission yeast Scd1 is an
exchange factor for Cdc42 and an effector of Ras1, the
homolog of the human H-Ras. Scd2/Bem1 mediates Cdc42
activation by binding to Scd1/Cdc24 and to Cdc42. Ras1
regulates Scd1/Cdc24/Ral1, which is a putative guanine
nucleotide exchange factor for Cdc42, a member of the
Rho family of Ras-like proteins. Cdc42 then activates
the Shk1/Orb2 protein kinase. Scd1 interacts with Klp5
and Klp6 kinesins to mediate cytokinesis. 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 = 148
Score = 26.5 bits (59), Expect = 1.3
Identities = 7/24 (29%), Positives = 15/24 (62%)
Query: 28 HQENEQLTSDLRNKIQALKSLTID 51
EN+Q+ DL+ +++ K ++D
Sbjct: 3 RAENQQVVDDLKARVEDWKGHSLD 26
>gnl|CDD|222701 pfam14349, SprA_N, Motility related/secretion protein. This domain
is found repeated three times in the N-terminal half of
the gliding motility-related SprA proteins. The role of
this domain in motility is uncertain. It is also found
in proteins required for secretion.
Length = 413
Score = 26.3 bits (58), Expect = 2.5
Identities = 12/54 (22%), Positives = 20/54 (37%), Gaps = 3/54 (5%)
Query: 8 QHAGNYYEPVPNQFDGGDAIHQENEQLTSDLRNKIQALKSLTIDIGTEVKYQNE 61
G EP N G + Q EQ L + L S + + ++ ++N
Sbjct: 187 LPPGVGREPGNNSLFGINTNLQFGEQ---SLTLVVSQLPSDSRAVSSKGGFKNT 237
>gnl|CDD|193523 cd05645, M20_peptidase_T, M20 Peptidase T specifically cleaves
tripeptides. Peptidase M20 family, Peptidase T (PepT;
tripeptide aminopeptidase; tripeptidase) subfamily and
similar proteins. PepT acts only on tripeptide
substrates, and is thus termed a tripeptidase. It
catalyzes the release of N-terminal amino acids with
hydrophobic side chains from tripeptides with high
specificity; dipeptides, tetrapeptides or tripeptides
with the N-terminus blocked are not cleaved.
Tripeptidases are known to function at the final stage
of proteolysis in lactococcal bacteria and release amino
acids from tripeptides produced during the digestion of
milk proteins such as casein.
Length = 398
Score = 26.0 bits (57), Expect = 3.2
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 16 PVPNQFDGGDAIHQENEQLTSDLRNK 41
P PN F GG+ H +NE +T + K
Sbjct: 362 PTPNLFTGGENYHTKNEFVTLEGMEK 387
>gnl|CDD|234846 PRK00844, glgC, glucose-1-phosphate adenylyltransferase;
Provisional.
Length = 407
Score = 25.2 bits (56), Expect = 4.9
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 8/28 (28%)
Query: 10 AGNYYEPVPNQ-------FDG-GDAIHQ 29
GNY PVP Q + G DAI+Q
Sbjct: 80 LGNYITPVPAQQRLGKRWYLGSADAIYQ 107
>gnl|CDD|206023 pfam13852, DUF4197, Protein of unknown function (DUF4197). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria. Proteins
in this family are typically between 228 and 249 amino
acids in length.
Length = 203
Score = 25.2 bits (56), Expect = 4.9
Identities = 9/39 (23%), Positives = 14/39 (35%), Gaps = 6/39 (15%)
Query: 49 TIDIGTEVKYQNEHLLRGMD---DDFDRTGGFLNNSMAR 84
+I +K E L G + + GFL N +
Sbjct: 7 DSEIAEGLK---EALSLGAERAVARLGKPDGFLGNPAVK 42
>gnl|CDD|239549 cd03466, Nitrogenase_NifN_2, Nitrogenase_nifN_2: A subgroup of
the NifN subunit of the NifEN complex: NifN forms an
alpha2beta2 tetramer with NifE. NifN and nifE are
structurally homologous to nitrogenase MoFe protein
beta and alpha subunits respectively. NifEN
participates in the synthesis of the iron-molybdenum
cofactor (FeMoco) of the MoFe protein. NifB-co (an
iron and sulfur containing precursor of the FeMoco)
from NifB is transferred to the NifEN complex where it
is further processed to FeMoco. The nifEN bound
precursor of FeMoco has been identified as a
molybdenum-free, iron- and sulfur- containing analog of
FeMoco. It has been suggested that this nifEN bound
precursor also acts as a cofactor precursor in
nitrogenase systems which require a cofactor other than
FeMoco: i.e. iron-vanadium cofactor (FeVco) or iron
only cofactor (FeFeco). This group also contains the
Clostidium fused NifN-NifB protein.
Length = 429
Score = 25.0 bits (55), Expect = 5.0
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 3/53 (5%)
Query: 5 MRRQHAGNYYEPV---PNQFDGGDAIHQENEQLTSDLRNKIQALKSLTIDIGT 54
+RR A +Y EPV + + ++ + L L+N I+ I I T
Sbjct: 40 IRRHMARHYNEPVDIASSSLNEETTVYGGEKNLKKGLKNVIEQYNPEVIGIAT 92
>gnl|CDD|222604 pfam14222, MOR2-PAG1_N, Cell morphogenesis N-terminal. This family
is the conserved N-terminal region of proteins that are
involved in cell morphogenesis.
Length = 538
Score = 25.3 bits (56), Expect = 5.5
Identities = 13/54 (24%), Positives = 26/54 (48%), Gaps = 10/54 (18%)
Query: 42 IQALKSLTIDIGTEVKYQNEHLLRGM---------DDDFDRTGGFLNNSMARSF 86
I L+ L + + + + E L+RGM ++ F+ + F+ S+A+ F
Sbjct: 85 IAELEKLRKEDSPDAESKIELLIRGMRYLRLKTYPEEAFEESADFM-QSLAKLF 137
>gnl|CDD|236152 PRK08115, PRK08115, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 858
Score = 25.2 bits (55), Expect = 5.9
Identities = 11/43 (25%), Positives = 19/43 (44%), Gaps = 5/43 (11%)
Query: 19 NQFDGGD-----AIHQENEQLTSDLRNKIQALKSLTIDIGTEV 56
N D + +E + L + IQ ++S + IG+EV
Sbjct: 784 NDLDEQLLLLPEELEEEETKKPVVLVDTIQDVRSTDVTIGSEV 826
>gnl|CDD|227285 COG4949, COG4949, Uncharacterized membrane-anchored protein
conserved in bacteria [Function unknown].
Length = 424
Score = 24.9 bits (54), Expect = 6.4
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 29 QENEQLTSDLRNKI-QALKSLTIDIGTEVKYQNEHLLRGMD 68
Q E+ ++L K+ +A L I E++ QN+ LL MD
Sbjct: 308 QSVEERQANLSRKLARATALLRTWIDVELERQNQELLNSMD 348
>gnl|CDD|192445 pfam10018, Med4, Vitamin-D-receptor interacting Mediator subunit
4. Members of this family function as part of the
Mediator (Med) complex, which links DNA-bound
transcriptional regulators and the general
transcription machinery, particularly the RNA
polymerase II enzyme. They play a role in basal
transcription by mediating activation or repression
according to the specific complement of transcriptional
regulators bound to the promoter.
Length = 176
Score = 24.7 bits (54), Expect = 8.0
Identities = 13/36 (36%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 28 HQENEQLTSDLRNKIQALKSLTIDIGTEVK-YQNEH 62
HQEN+Q +LR ++++L DI E+K + E
Sbjct: 24 HQENQQRILELRAEVESLDEKIKDILKELKEAEKEL 59
>gnl|CDD|235316 PRK04863, mukB, cell division protein MukB; Provisional.
Length = 1486
Score = 24.5 bits (54), Expect = 9.0
Identities = 8/31 (25%), Positives = 15/31 (48%)
Query: 18 PNQFDGGDAIHQENEQLTSDLRNKIQALKSL 48
P QF+ +Q+ +Q D + + AL +
Sbjct: 934 PEQFEQLKQDYQQAQQTQRDAKQQAFALTEV 964
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
0.317 0.135 0.393
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: 4,458,620
Number of extensions: 349300
Number of successful extensions: 370
Number of sequences better than 10.0: 1
Number of HSP's gapped: 369
Number of HSP's successfully gapped: 24
Length of query: 87
Length of database: 10,937,602
Length adjustment: 55
Effective length of query: 32
Effective length of database: 8,498,132
Effective search space: 271940224
Effective search space used: 271940224
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 (24.1 bits)