RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15162
(70 letters)
>gnl|CDD|223555 COG0479, FrdB, Succinate dehydrogenase/fumarate reductase, Fe-S
protein subunit [Energy production and conversion].
Length = 234
Score = 27.3 bits (61), Expect = 0.49
Identities = 9/20 (45%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 49 DLGEPFGVYHCVTC-ECVQV 67
L +P GV+ C TC C +V
Sbjct: 190 ILEDPDGVWRCTTCGNCTEV 209
>gnl|CDD|172778 PRK14290, PRK14290, chaperone protein DnaJ; Provisional.
Length = 365
Score = 27.2 bits (60), Expect = 0.53
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 37 KEFYEIGAKWHPDL 50
K F E+ KWHPDL
Sbjct: 22 KAFRELAKKWHPDL 35
>gnl|CDD|215712 pfam00093, VWC, von Willebrand factor type C domain. The high
cutoff was used to prevent overlap with pfam00094.
Length = 57
Score = 25.5 bits (56), Expect = 1.1
Identities = 11/33 (33%), Positives = 11/33 (33%), Gaps = 8/33 (24%)
Query: 33 CVFGKEFYEIGAKWHPDLGEPFGVYHCVTCECV 65
CV YE G W PD C C C
Sbjct: 1 CVQNGVVYENGETWKPD--------LCTICTCD 25
>gnl|CDD|225918 COG3383, COG3383, Uncharacterized anaerobic dehydrogenase [General
function prediction only].
Length = 978
Score = 25.5 bits (56), Expect = 2.5
Identities = 8/21 (38%), Positives = 9/21 (42%), Gaps = 1/21 (4%)
Query: 48 PDLGEPFGVYHCVTC-ECVQV 67
D P CV+C CV V
Sbjct: 183 WDNDVPINESSCVSCGACVTV 203
>gnl|CDD|235652 PRK05950, sdhB, succinate dehydrogenase iron-sulfur subunit;
Reviewed.
Length = 232
Score = 24.8 bits (55), Expect = 4.2
Identities = 10/20 (50%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 49 DLGEPFGVYHCVTC-ECVQV 67
L +PFGV+ C T CV+V
Sbjct: 190 ILDDPFGVFRCHTIMNCVEV 209
>gnl|CDD|200457 cd11318, AmyAc_bac_fung_AmyA, Alpha amylase catalytic domain found
in bacterial and fungal Alpha amylases (also called
1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC
3.2.1.1) catalyzes the hydrolysis of alpha-(1,4)
glycosidic linkages of glycogen, starch, related
polysaccharides, and some oligosaccharides. This group
includes bacterial and fungal proteins. 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 = 391
Score = 24.4 bits (54), Expect = 5.5
Identities = 15/61 (24%), Positives = 19/61 (31%), Gaps = 13/61 (21%)
Query: 1 MTWYIWYI--------RLQ-STHIDFIHMTLLCTALDHCSKCVFGKEFYEIGAKWHPDLG 51
W WYI RL HI + L GK+ + +G W DL
Sbjct: 213 KRWGKWYINTTGLDGFRLDAVKHISASFIKDWIDHLRR----ETGKDLFAVGEYWSGDLE 268
Query: 52 E 52
Sbjct: 269 A 269
>gnl|CDD|188837 cd09453, LIM1_ENH, The first LIM domain of the Enigma Homolog
(ENH) family. The first LIM domain of the Enigma
Homolog (ENH) family: ENH was initially identified in
rat brain. Same as enigma, it contains three LIM
domains at the C-terminus and a PDZ domain at
N-terminus. ENH is implicated in signal transduction
processes involving protein kinases. It has also been
shown that ENH interacts with protein kinase D1 (PKD1)
via its LIM domains and forms a complex with PKD1 and
the alpha1C subunit of cardiac L-type voltage-gated
calcium channel in rat neonatal cardiomyocytes. The
N-terminal PDZ domain interacts with alpha-actinin at
the Z-line. ENH is expressed in multiple tissues, such
as skeletal muscle, heart, bone, and brain. LIM domains
are 50-60 amino acids in size and share 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 complexes.
Length = 52
Score = 23.4 bits (50), Expect = 6.4
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 3/33 (9%)
Query: 29 HCSKCVFGKEFYEIGAKWHPDLGEPFGVYHCVT 61
C++ + G +G WHP E F HC +
Sbjct: 3 TCNQVIRGPFLVALGKSWHP---EEFNCAHCKS 32
>gnl|CDD|188722 cd09336, LIM1_Paxillin_like, The first LIM domain of the paxillin
like protein family. The first LIM domain of the
paxillin like protein family: This family consists of
paxillin, leupaxin, Hic-5 (ARA55), and other related
proteins. There are four LIM domains in the C-terminal
of the proteins and leucine-rich LD-motifs in the
N-terminal region. Members of this family are adaptor
proteins to recruit key components of
signal-transduction machinery to specific sub-cellular
locations. Paxillin is found at the interface between
the plasma membrane and the actin cytoskeleton.
Paxillin serves as a platform for the recruitment of
numerous regulatory and structural proteins that
together control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression that
are necessary for cell migration and survival. Leupaxin
is a cytoskeleton adaptor protein, which is
preferentially expressed in hematopoietic cells. It
associates with focal adhesion kinases PYK2 and
pp125FAK and identified to be a component of the
osteoclast pososomal signaling complex. Hic-5 controls
cell proliferation, migration and senescence by
functioning as coactivator for steroid receptors such
as androgen receptor, glucocorticoid receptor and
progesterone receptor. LIM domains are 50-60 amino
acids in size and share 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 complexes.
Length = 53
Score = 23.1 bits (50), Expect = 7.1
Identities = 10/30 (33%), Positives = 13/30 (43%), Gaps = 3/30 (10%)
Query: 30 CSKCVFGKEFYEIGAKWHPDLGEPFGVYHC 59
C K + G+ +G WHP E F C
Sbjct: 4 CKKPIVGQVVTALGKTWHP---EHFVCAEC 30
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
0.332 0.144 0.540
Gapped
Lambda K H
0.267 0.0632 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,398,703
Number of extensions: 230886
Number of successful extensions: 269
Number of sequences better than 10.0: 1
Number of HSP's gapped: 268
Number of HSP's successfully gapped: 14
Length of query: 70
Length of database: 10,937,602
Length adjustment: 40
Effective length of query: 30
Effective length of database: 9,163,442
Effective search space: 274903260
Effective search space used: 274903260
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)
S2: 53 (24.4 bits)