RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15325
(102 letters)
>gnl|CDD|238105 cd00179, SynN, Syntaxin N-terminus domain; syntaxins are nervous
system-specific proteins implicated in the docking of
synaptic vesicles with the presynaptic plasma membrane;
they are a family of receptors for intracellular
transport vesicles; each target membrane may be
identified by a specific member of the syntaxin family;
syntaxins contain a moderately well conserved
amino-terminal domain, called Habc, whose structure is
an antiparallel three-helix bundle; a linker of about 30
amino acids connects this to the carboxy-terminal
region, designated H3 (t_SNARE), of the syntaxin
cytoplasmic domain; the highly conserved H3 region forms
a single, long alpha-helix when it is part of the core
SNARE complex and anchors the protein on the cytoplasmic
surface of cellular membranes; H3 is not included in
defining this domain.
Length = 151
Score = 68.5 bits (168), Expect = 4e-16
Identities = 29/48 (60%), Positives = 35/48 (72%)
Query: 7 EYNRTQTDYRERCKGRIQRQLEITGRTTTNEELEAMLDTGNPAVFTQG 54
E+N+ Q YRER K RIQRQLEITG T+EELE ML++GN +FT
Sbjct: 103 EFNKAQRKYRERYKERIQRQLEITGGEATDEELEDMLESGNSEIFTSQ 150
>gnl|CDD|227406 COG5074, COG5074, t-SNARE complex subunit, syntaxin [Intracellular
trafficking and secretion].
Length = 280
Score = 58.7 bits (142), Expect = 1e-11
Identities = 37/103 (35%), Positives = 56/103 (54%), Gaps = 9/103 (8%)
Query: 1 FLLYWREYNRTQTDYRERCKGRIQRQLEITGRTTTNEELEAML-DTGNPAVFTQ------ 53
FL ++Y ++YRE K + +RQ I T +E+EA + D VF+Q
Sbjct: 109 FLKLIQDYRIIDSNYREEEKEQARRQYIIAQPEATEDEVEAAINDVNGQQVFSQALLNAN 168
Query: 54 --GQAKQTLADIEARHADIIKLENSIRELHDMFMDMAMLVENQ 94
G+AK LA+++ARH +I K+E ++ EL +F DM LV Q
Sbjct: 169 RRGEAKTALAEVQARHQEIKKIEKTMAELTQLFNDMEELVIEQ 211
>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 = 39.5 bits (93), Expect = 1e-05
Identities = 16/41 (39%), Positives = 26/41 (63%)
Query: 57 KQTLADIEARHADIIKLENSIRELHDMFMDMAMLVENQDDR 97
+Q LA E R ++ +LE SI+EL +F+DM +E Q ++
Sbjct: 1 QQALAREEERDEELEQLEKSIQELKQIFLDMGTELEEQGEQ 41
>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 = 38.3 bits (90), Expect = 3e-05
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 66 RHADIIKLENSIRELHDMFMDMAMLVENQ 94
R + +LE+SI EL +F+DM VE Q
Sbjct: 1 RDEALEELESSIGELKQLFLDMGEEVEEQ 29
>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 = 35.5 bits (83), Expect = 3e-04
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 63 IEARHADIIKLENSIRELHDMFMDMAMLVENQDDR 97
+ R ++ +LE SI EL +F+D+ VE Q +
Sbjct: 1 EQERDEELEQLEASIGELKQIFLDLGTEVEEQGEL 35
>gnl|CDD|179571 PRK03369, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 488
Score = 31.3 bits (71), Expect = 0.056
Identities = 20/69 (28%), Positives = 30/69 (43%), Gaps = 3/69 (4%)
Query: 16 RERCKGRIQRQLEITG---RTTTNEELEAMLDTGNPAVFTQGQAKQTLADIEARHADIIK 72
C G +R L +TG +TTT L AML G + D+ A+++
Sbjct: 109 AAGCYGPPRRWLVVTGTNGKTTTTSMLHAMLIAAGRRSVLCGNIGSPVLDVLDEPAELLA 168
Query: 73 LENSIRELH 81
+E S +LH
Sbjct: 169 VELSSFQLH 177
>gnl|CDD|215215 PLN02384, PLN02384, ribose-5-phosphate isomerase.
Length = 264
Score = 30.2 bits (68), Expect = 0.13
Identities = 22/77 (28%), Positives = 33/77 (42%), Gaps = 9/77 (11%)
Query: 20 KGRIQRQLEITG-----RTTTNEELEAMLDTGNPAVFTQGQAKQTLADIEARHADIIKLE 74
++Q E G RT N E + D GN V K+ + D++ I++L
Sbjct: 179 AEKLQSLFEYAGCVAKLRTKNNGEEPFVTDNGNYIV--DLYFKRDIGDLKVASDAILRLA 236
Query: 75 NSIRELHDMFMDMAMLV 91
+ H MF+DMA V
Sbjct: 237 GVVE--HGMFLDMATTV 251
>gnl|CDD|162358 TIGR01437, selA_rel, uncharacterized pyridoxal phosphate-dependent
enzyme. This model describes a protein related to a
number of pyridoxal phosphate-dependent enzymes, and in
particular to selenocysteine synthase (SelA), which
converts Ser to selenocysteine on its tRNA. While
resembling SelA, this protein is found only in species
that have a better candidate SelA or else lack the other
genes (selB, selC, and selD) required for selenocysteine
incorporation [Unknown function, Enzymes of unknown
specificity].
Length = 363
Score = 29.7 bits (67), Expect = 0.18
Identities = 16/69 (23%), Positives = 32/69 (46%), Gaps = 6/69 (8%)
Query: 16 RERCKGRIQRQLEITGRTTTNEELEAMLDTGNPAVFTQG-QAKQTLADIEAR---HADII 71
R+ + I+ G T ++ L G PA++T+G +A + + +I+ R +
Sbjct: 296 RDIARAEIRFDESELGMTA--ADVVQALRQGEPAIYTRGYKANEGIIEIDPRSVTGGQLD 353
Query: 72 KLENSIREL 80
+ IRE+
Sbjct: 354 IIVERIREI 362
>gnl|CDD|223841 COG0770, MurF, UDP-N-acetylmuramyl pentapeptide synthase [Cell
envelope biogenesis, outer membrane].
Length = 451
Score = 27.7 bits (62), Expect = 0.93
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 6/43 (13%)
Query: 15 YRERCKGRIQRQLEITG---RTTTNEELEAMLDTGNPAVFTQG 54
YR++ ++ + ITG +TTT E L A+L T T G
Sbjct: 97 YRQKFNAKV---IAITGSNGKTTTKEMLAAILSTKGKVHATPG 136
>gnl|CDD|237621 PRK14139, PRK14139, heat shock protein GrpE; Provisional.
Length = 185
Score = 26.5 bits (59), Expect = 2.0
Identities = 16/69 (23%), Positives = 23/69 (33%), Gaps = 8/69 (11%)
Query: 33 TTTNEELEAMLDTGNPAVFTQGQAKQTLADIEARHADIIKLENSIRELHDMFMDMAMLVE 92
+ +E E A A+ +EA A+ E EL D F+ E
Sbjct: 7 NPSEQEAEEAGAAAQAAAAAAAAAEDAAPALEAELAE---AEAKAAELQDSFLRAKAETE 63
Query: 93 N-----QDD 96
N Q+D
Sbjct: 64 NVRRRAQED 72
>gnl|CDD|227635 COG5325, COG5325, t-SNARE complex subunit, syntaxin [Intracellular
trafficking and secretion].
Length = 283
Score = 26.7 bits (59), Expect = 2.1
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 53 QGQAKQTLAD----IEARHADIIKLENSIRELHDMFMDMAMLVENQ 94
QG + + L I R +I L I EL+++F D+ LV Q
Sbjct: 176 QGLSNEELEYQQILITERDEEIKNLARGIYELNEIFRDLGSLVGEQ 221
>gnl|CDD|181238 PRK08124, PRK08124, flagellar motor protein MotA; Validated.
Length = 263
Score = 26.5 bits (59), Expect = 2.4
Identities = 9/34 (26%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 64 EARHADIIKLENSIRELHDMFMD--MAMLVENQD 95
E+R ++ LE + E+ D F+ + M+++ Q
Sbjct: 88 ESRREGLLALEAQLDEIDDPFLKRGLKMVIDGQS 121
>gnl|CDD|239982 cd04609, CBS_pair_PALP_assoc2, This cd contains two tandem
repeats of the cystathionine beta-synthase (CBS pair)
domains associated with the pyridoxal-phosphate (PALP)
dependent enzyme domain upstream. The vitamin B6
complex comprises pyridoxine, pyridoxal, and
pyridoxamine, as well as the 5'-phosphate esters of
pyridoxal (PALP) and pyridoxamine, the last two being
the biologically active coenzyme derivatives. The
members of the PALP family are principally involved in
the biosynthesis of amino acids and amino acid-derived
metabolites, but they are also found in the
biosynthetic pathways of amino sugars and other
amine-containing compounds. CBS is a small domain
originally identified in cystathionine beta-synthase
and subsequently found in a wide range of different
proteins. CBS domains usually come in tandem repeats,
which associate to form a so-called Bateman domain or a
CBS pair which is reflected in this model. The
interface between the two CBS domains forms a cleft
that is a potential ligand binding site. The CBS pair
coexists with a variety of other functional domains.
It has been proposed that the CBS domain may play a
regulatory role, although its exact function is
unknown.
Length = 110
Score = 25.6 bits (57), Expect = 3.1
Identities = 10/24 (41%), Positives = 11/24 (45%)
Query: 27 LEITGRTTTNEELEAMLDTGNPAV 50
L EEL +LD GN AV
Sbjct: 67 LPTVDPDAPIEELSELLDRGNVAV 90
>gnl|CDD|236475 PRK09352, PRK09352, 3-oxoacyl-(acyl carrier protein) synthase
III; Reviewed.
Length = 319
Score = 26.2 bits (59), Expect = 3.3
Identities = 7/11 (63%), Positives = 10/11 (90%)
Query: 35 TNEELEAMLDT 45
TN++LE M+DT
Sbjct: 19 TNDDLEKMVDT 29
>gnl|CDD|237681 PRK14342, PRK14342, lipoate-protein ligase B; Provisional.
Length = 213
Score = 25.6 bits (57), Expect = 4.2
Identities = 8/9 (88%), Positives = 8/9 (88%)
Query: 48 PAVFTQGQA 56
P VFTQGQA
Sbjct: 44 PPVFTQGQA 52
>gnl|CDD|234344 TIGR03754, conj_TOL_TraD, conjugative coupling factor TraD, TOL
family. Members of this protein are assigned by
homology to the TraD family of conjugative coupling
factor. This particular clade serves as a marker for an
extended gene region that occurs occasionally on
plasmids, including the toluene catabolism TOL plasmid.
More commonly, the gene region is chromosomal, flanked
by various markers of conjugative transfer and
insertion.
Length = 643
Score = 25.8 bits (57), Expect = 4.5
Identities = 11/28 (39%), Positives = 14/28 (50%)
Query: 58 QTLADIEARHADIIKLENSIRELHDMFM 85
QTL+DIEAR K I + + M
Sbjct: 528 QTLSDIEARIGSKAKAGQVIGNFNTLIM 555
>gnl|CDD|205692 pfam13514, AAA_27, AAA domain. This domain is found in a number of
double-strand DNA break proteins. This domain contains a
P-loop motif.
Length = 1118
Score = 25.9 bits (57), Expect = 4.9
Identities = 16/98 (16%), Positives = 32/98 (32%), Gaps = 15/98 (15%)
Query: 14 DYRERCKGRIQRQLEITGRTTTNEELEAMLDTGNPAV--------------FTQGQAKQT 59
D R R + ++ L+ EEL +L+ + A++
Sbjct: 636 DRRARLRAALRAALKAVAIVLPGEELAELLELARQLLEEAEKQAARKASLDERLRDAERA 695
Query: 60 LADIEARHADIIK-LENSIRELHDMFMDMAMLVENQDD 96
L + E RH + LE + +D ++ +
Sbjct: 696 LEEAEERHDEAQSALEAWQEQWYDALLEAGLGGRASPA 733
>gnl|CDD|179297 PRK01438, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 480
Score = 25.8 bits (57), Expect = 5.0
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 15 YRERCKGRIQRQLEITG---RTTTNEELEAML 43
+R R R L +TG +TTT + L +ML
Sbjct: 113 WRLRDPDRPAPWLAVTGTNGKTTTVQMLASML 144
>gnl|CDD|181156 PRK07878, PRK07878, molybdopterin biosynthesis-like protein MoeZ;
Validated.
Length = 392
Score = 25.4 bits (56), Expect = 6.5
Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 3/37 (8%)
Query: 14 DYRERCKGRI--QRQLEITGRTTTNEELEAMLDTGNP 48
DY C G + + Q G T T EL+ LD+G
Sbjct: 268 DYEAFC-GVVSDEAQQAAAGSTITPRELKEWLDSGKK 303
>gnl|CDD|237245 PRK12879, PRK12879, 3-oxoacyl-(acyl carrier protein) synthase
III; Reviewed.
Length = 325
Score = 25.2 bits (56), Expect = 6.8
Identities = 10/25 (40%), Positives = 13/25 (52%), Gaps = 7/25 (28%)
Query: 28 EITG-------RTTTNEELEAMLDT 45
ITG R TN++LE +DT
Sbjct: 6 RITGIGTYVPPRVLTNDDLETFIDT 30
>gnl|CDD|106978 PHA00670, PHA00670, hypothetical protein.
Length = 540
Score = 25.2 bits (55), Expect = 6.8
Identities = 13/62 (20%), Positives = 26/62 (41%), Gaps = 6/62 (9%)
Query: 43 LDTGNPAVFTQGQAKQTLADIEARHADIIKLENSIRELHDMFMDM------AMLVENQDD 96
L T +P + + K L ++ + N EL++ ++ + AM+VE +D
Sbjct: 83 LATRDPELNEDAEVKAWLENVTRDMYSAFQKSNFYLELNETYISLGGFGTAAMVVEEDED 142
Query: 97 RG 98
Sbjct: 143 EV 144
>gnl|CDD|143333 cd05118, STKc_CMGC, Catalytic domain of CMGC family
Serine/Threonine Kinases. Serine/Threonine Kinases
(STKs), CMGC family, catalytic (c) domain. STKs
catalyze the transfer of the gamma-phosphoryl group
from ATP to serine/threonine residues on protein
substrates. The CMGC family is part of a larger
superfamily that includes the catalytic domains of
other protein STKs, protein tyrosine kinases, RIO
kinases, aminoglycoside phosphotransferase, choline
kinase, and phosphoinositide 3-kinase. The CMGC family
consists of Cyclin-Dependent protein Kinases (CDKs),
Mitogen-activated protein kinases (MAPKs) such as
Extracellular signal-regulated kinase (ERKs), c-Jun
N-terminal kinases (JNKs), and p38, and similar
proteins. CDKs belong to a large subfamily of STKs that
are regulated by their cognate cyclins. Together, they
are involved in the control of cell-cycle progression,
transcription, and neuronal function. MAPKs serve as
important mediators of cellular responses to
extracellular signals. They control critical cellular
functions including differentiation, proliferation,
migration, and apoptosis. They are also implicated in
the pathogenesis of many diseases including multiple
types of cancer, stroke, diabetes, and chronic
inflammation.
Length = 283
Score = 25.4 bits (56), Expect = 7.0
Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 9/55 (16%)
Query: 52 TQGQAKQTLADIEA----RHADIIKLENSIRELHDM-----FMDMAMLVENQDDR 97
++G K L +I+ H +IIKL + R D+ FMD + +D +
Sbjct: 38 SEGIPKTALREIKLLKELNHPNIIKLLDVFRHKGDLYLVFEFMDTDLYKLIKDRQ 92
>gnl|CDD|237445 PRK13609, PRK13609, diacylglycerol glucosyltransferase;
Provisional.
Length = 380
Score = 25.1 bits (55), Expect = 7.8
Identities = 7/28 (25%), Positives = 17/28 (60%)
Query: 57 KQTLADIEARHADIIKLENSIRELHDMF 84
KQ+L D++ + D +K+ + + ++F
Sbjct: 244 KQSLEDLQETNPDALKVFGYVENIDELF 271
>gnl|CDD|206160 pfam13990, YjcZ, YjcZ-like protein. This family of proteins is
functionally uncharacterized. The family includes the
YjcZ protein from E. coli. This family of proteins is
found in enteric bacteria. Proteins in this family are
approximately 300 amino acids in length. There are two
conserved sequence motifs: FGD and MPR.
Length = 270
Score = 25.1 bits (55), Expect = 8.7
Identities = 12/49 (24%), Positives = 19/49 (38%), Gaps = 1/49 (2%)
Query: 37 EELEAMLDTGNPAVFTQGQAKQTLADIEARHADII-KLENSIRELHDMF 84
E+L + LD G+ A+ Q L + A A + L + F
Sbjct: 58 EKLTSSLDPGHLALTLVNQRLTRLQNDVADLAHFSPGTRQQLLALTEQF 106
>gnl|CDD|224327 COG1409, Icc, Predicted phosphohydrolases [General function
prediction only].
Length = 301
Score = 24.9 bits (54), Expect = 8.7
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 43 LDTGNPAVFTQGQAKQTLADIEARHADII 71
L G V ++ + LA IE D++
Sbjct: 9 LHLGALGVDSEELLEALLAAIEQLKPDLL 37
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
0.318 0.132 0.382
Gapped
Lambda K H
0.267 0.0712 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,174,392
Number of extensions: 430613
Number of successful extensions: 572
Number of sequences better than 10.0: 1
Number of HSP's gapped: 571
Number of HSP's successfully gapped: 59
Length of query: 102
Length of database: 10,937,602
Length adjustment: 68
Effective length of query: 34
Effective length of database: 7,921,530
Effective search space: 269332020
Effective search space used: 269332020
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 (21.7 bits)
S2: 53 (24.2 bits)