RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3226
(111 letters)
>gnl|CDD|189714 pfam00778, DIX, DIX domain. The DIX domain is present in
Dishevelled and axin. This domain is involved in homo-
and hetero-oligomerisation. It is involved in the homo-
oligomerisation of mouse axin. The axin DIX domain also
interacts with the dishevelled DIX domain. The DIX
domain has also been called the DAX domain.
Length = 81
Score = 106 bits (266), Expect = 1e-31
Identities = 36/82 (43%), Positives = 52/82 (63%), Gaps = 3/82 (3%)
Query: 25 TTVVFTFCDEQYPYRTKIPSQS--VTLKQFKDYLPKKGNYRFFFKTECDDVDTKVIQEEI 82
T VV+ DE PYR KIP +TL FK L +KGNY++FFK D V++EE+
Sbjct: 1 TKVVYYLDDEPTPYRIKIPGPPGEITLGDFKAALTRKGNYKYFFKALDPDFG-CVVKEEV 59
Query: 83 VDDNEVLPLWEGKVMGQVKPLE 104
DD+ LPL+EGK++G ++ ++
Sbjct: 60 TDDSAKLPLFEGKIVGWLESVD 81
>gnl|CDD|197474 smart00021, DAX, Domain present in Dishevelled and axin. Domain of
unknown function.
Length = 83
Score = 67.1 bits (164), Expect = 4e-16
Identities = 32/78 (41%), Positives = 49/78 (62%), Gaps = 4/78 (5%)
Query: 25 TTVVFTFCDEQYPYRTKIPSQS--VTLKQFKDYLPKKGNYRFFFKTECDDVDTKVIQEEI 82
T V++ DE+ PY K+P + VTL FK+ L KK NY+++FK+ DD V++EEI
Sbjct: 4 TKVIYHLDDEETPYLVKVPVPAERVTLGDFKEVLTKK-NYKYYFKSMDDDFG-GVVKEEI 61
Query: 83 VDDNEVLPLWEGKVMGQV 100
DD+ LP + G+V+ +
Sbjct: 62 RDDSARLPCFNGRVVSWL 79
>gnl|CDD|227371 COG5038, COG5038, Ca2+-dependent lipid-binding protein, contains C2
domain [General function prediction only].
Length = 1227
Score = 32.0 bits (73), Expect = 0.044
Identities = 17/91 (18%), Positives = 27/91 (29%), Gaps = 6/91 (6%)
Query: 17 PEHQSGTFTTVVFTFCDEQYPYRT--KIPSQSVTLKQFKDYLPKKGNYRFFFKTECDDVD 74
+ + ++T E Y S L Q+ + + N T D
Sbjct: 594 LSSKKDNKSAELYTNAKEVYSTGKLKFTNHPSWNL-QYNVLVTDRKNSSIKVVTF-DVQS 651
Query: 75 TKVIQEEIVDDNEVLPLWEGKVMGQVKPLEN 105
KVI E +++ V PL N
Sbjct: 652 GKVIATEGSTLPDLID--RTLDTFLVFPLRN 680
>gnl|CDD|173127 PRK14664, PRK14664, tRNA-specific 2-thiouridylase MnmA;
Provisional.
Length = 362
Score = 27.6 bits (61), Expect = 1.5
Identities = 9/19 (47%), Positives = 15/19 (78%)
Query: 59 KGNYRFFFKTECDDVDTKV 77
KG+YR F + +C ++DT+V
Sbjct: 191 KGDYRDFLREQCPELDTEV 209
>gnl|CDD|233947 TIGR02600, Verru_Chthon_A, Verru_Chthon cassette protein A. In
Verrucomicrobium spinosum and Chthoniobacter flavus, a
four-gene operon that includes proteins with an
N-terminal signal sequence for cleavage and methylation
recurs many times. Each operon is likely to encode a
membrane complex, the function of which is unknown. This
model represents a long protein from this putative
membrame complex, with members averaging about 1300
amino acids. The N-terminal region includes an apparent
signal sequence. The function is unknown. Most cassettes
are adjacent to an unusually large protein with both an
outer membrane autotransporter region and PEP-CTERM
putative protein-sorting motif [Cell envelope, Surface
structures].
Length = 1265
Score = 27.1 bits (60), Expect = 2.1
Identities = 14/45 (31%), Positives = 20/45 (44%), Gaps = 3/45 (6%)
Query: 14 PRPPEHQSGTFTTVVFTFCDEQYPYRTKIPSQSVTLKQFKDYLPK 58
R P H + T + VFT D P T + + TL+ D P+
Sbjct: 274 QRFPGHPATTCLSAVFTPFDPLLPPST---ASAATLQNIYDLAPR 315
>gnl|CDD|235109 PRK03187, tgl, transglutaminase; Provisional.
Length = 272
Score = 26.5 bits (59), Expect = 2.8
Identities = 9/24 (37%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 19 HQSG-TFTTVVFTFCDEQYPYRTK 41
QSG F T + C+ +Y RT
Sbjct: 64 FQSGAQFATFRQSRCNPEYWKRTS 87
>gnl|CDD|216548 pfam01519, DUF16, Protein of unknown function DUF16. The function
of this protein is unknown. It appears to only occur in
Mycoplasma pneumoniae. The crystal structure revealed
that this domain is composed of two separated
homotrimeric coiled-coils.
Length = 96
Score = 25.9 bits (57), Expect = 2.9
Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 9/71 (12%)
Query: 36 YPYRTKIPSQSVTLKQFKDYLPKKGNYRFFFKTECDDVDTKVIQEEIVDDNEVLPLWEGK 95
+ + K + VT KQF ++ K N + K E Q E + +G+
Sbjct: 8 HMEKGKKKTGYVTHKQFDEF--KDANNQRLTKIE----TKLDAQGEQIRKLTQTVDKQGE 61
Query: 96 VMGQVKPLENE 106
Q+K L+ E
Sbjct: 62 ---QIKELQVE 69
>gnl|CDD|132335 TIGR03292, PhnH_redo, phosphonate C-P lyase system protein PhnH.
PhnH is a component of the C-P lyase system
(GenProp0232) for the catabolism of phosphonate
compounds. The specific function of this component is
unknown. This model is based on pfam05845.2, and has
been broadened to include sequences missed by that
model which are clearly true positive hits based on
genome context.
Length = 174
Score = 26.5 bits (59), Expect = 3.0
Identities = 11/33 (33%), Positives = 14/33 (42%)
Query: 1 MSNSCTLRSVTSTPRPPEHQSGTFTTVVFTFCD 33
MS T+R + S PP S V+ T D
Sbjct: 10 MSRPGTIRQLPSAASPPLPLSPATAAVLLTLLD 42
>gnl|CDD|188527 TIGR04012, poly_gGlu_PgsB, poly-gamma-glutamate synthase PgsB/CapB.
Of four genes commonly found to be involved in
biosynthesis and export of poly-gamma-glutamate,
pgsB(capB) and pgsC(capC) are found to be involved in
the synthesis per se. Members of this family are
designated PgsB, a nomeclature that covers both cases in
which the poly-gamma-glutamate is secreted and those in
which it is retained to form capsular material.PgsB has
been shown to have poly-gamma-glutamate activity by
itself but is bound tightly by PgsC (TIGR04011) [Cell
envelope, Other].
Length = 366
Score = 26.5 bits (59), Expect = 3.2
Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 10/53 (18%)
Query: 43 PSQSVTLKQFKDYLPKKG-------NYRFFFKTECDDVDTKVIQEEIVDDNEV 88
P+ + F +P G +Y FFK D +TK+I + D E+
Sbjct: 131 PTLDDVAEAFTATIPYNGDLFTAEDDYLDFFKEAAKDRNTKLI---VADAEEI 180
>gnl|CDD|173884 cd08519, PBP2_NikA_DppA_OppA_like_20, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 469
Score = 25.7 bits (57), Expect = 6.1
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 78 IQEEIVDDNEVLPLWEGK 95
IQ+ + +D +PLW+GK
Sbjct: 440 IQDILAEDVPYIPLWQGK 457
>gnl|CDD|226828 COG4393, COG4393, Predicted membrane protein [Function unknown].
Length = 405
Score = 25.5 bits (56), Expect = 6.2
Identities = 10/41 (24%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 21 SGTFTTVVFTFCDEQYPYRTKIPSQSVTLKQFKDYLPKKGN 61
S F +++ F + Y K+ S+ L + + P +GN
Sbjct: 251 SLAFFSILVVFSIQLY--WDKVASKPPALSEPQPVQPDEGN 289
>gnl|CDD|147348 pfam05124, S_layer_C, S-layer like family, C-terminal region.
Length = 223
Score = 25.4 bits (56), Expect = 7.5
Identities = 10/29 (34%), Positives = 13/29 (44%)
Query: 60 GNYRFFFKTECDDVDTKVIQEEIVDDNEV 88
GNY + DV T + EE + D E
Sbjct: 5 GNYGYADLVIYKDVKTLELGEEYIPDWEA 33
>gnl|CDD|200481 cd11343, AmyAc_Sucrose_phosphorylase-like, Alpha amylase catalytic
domain found in sucrose phosphorylase (also called
sucrose glucosyltransferase, disaccharide
glucosyltransferase, and sucrose-phosphate alpha-D
glucosyltransferase). Sucrose phosphorylase is a
bacterial enzyme that catalyzes the phosphorolysis of
sucrose to yield glucose-1-phosphate and fructose. These
enzymes do not have the conserved calcium ion present in
other alpha amylase family enzymes. The Alpha-amylase
family comprises the largest family of glycoside
hydrolases (GH), with the majority of enzymes acting on
starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 445
Score = 25.1 bits (56), Expect = 9.6
Identities = 9/37 (24%), Positives = 15/37 (40%), Gaps = 3/37 (8%)
Query: 42 IPSQSVTLKQFKDYLPKKGNYRFFFKTECDDVDTKVI 78
I SQS F+D+L + +F + D +
Sbjct: 89 ISSQS---PWFQDFLAGGDPSKDYFIEADPEEDLSKV 122
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 0.134 0.409
Gapped
Lambda K H
0.267 0.0680 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,508,241
Number of extensions: 449702
Number of successful extensions: 318
Number of sequences better than 10.0: 1
Number of HSP's gapped: 313
Number of HSP's successfully gapped: 17
Length of query: 111
Length of database: 10,937,602
Length adjustment: 75
Effective length of query: 36
Effective length of database: 7,611,052
Effective search space: 273997872
Effective search space used: 273997872
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 (24.3 bits)