RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16988
(103 letters)
>gnl|CDD|225030 COG2119, COG2119, Predicted membrane protein [Function unknown].
Length = 190
Score = 53.5 bits (129), Expect = 4e-10
Identities = 18/43 (41%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 38 VVIQAFTLTFLAEWGDRSQLTTIILAARE-DVYGVTLGGVLGH 79
V + F FLAE GD++Q+ TI LAA + V G LG
Sbjct: 101 VFVTTFITFFLAELGDKTQIATIALAADYHSPWAVFAGTTLGM 143
Score = 29.6 bits (67), Expect = 0.17
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 44 TLTFLAEWGDRSQLTTIILAAR 65
+ LAE GD++QL ++LA R
Sbjct: 9 LMVALAEIGDKTQLIAMLLAMR 30
>gnl|CDD|216341 pfam01169, UPF0016, Uncharacterized protein family UPF0016. This
family contains integral membrane proteins of unknown
function. Most members of the family contain two copies
of a region that contains an EXGD motif. Each of these
regions contains three predicted transmembrane regions.
Length = 78
Score = 50.9 bits (123), Expect = 5e-10
Identities = 20/42 (47%), Positives = 25/42 (59%), Gaps = 2/42 (4%)
Query: 40 IQAFTLTFLAEWGDRSQLTTIILAARE--DVYGVTLGGVLGH 79
+ +F L FLAE GD++QL TI LAAR + V LG L
Sbjct: 2 LTSFLLIFLAELGDKTQLATIALAARYSRSPWAVFLGATLAL 43
>gnl|CDD|182492 PRK10483, PRK10483, tryptophan permease; Provisional.
Length = 414
Score = 29.0 bits (65), Expect = 0.41
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 4/45 (8%)
Query: 42 AFTLTFLAEWGDR--SQLTTIILAAREDVYGVTLGGVLGH--PAV 82
A + F+ + S++T I+L A+ + +T G +LGH PA
Sbjct: 135 ALLVAFVVWLSTKAVSRMTAIVLGAKVITFFLTFGSLLGHVQPAT 179
>gnl|CDD|197295 cd09199, PLDc_pPLDalpha_2, Catalytic domain, repeat 2, of plant
alpha-type phospholipase D. Catalytic domain, repeat 2,
of plant alpha-type phospholipase D (PLDalpha, EC
3.1.4.4). Plant PLDalpha is a phosphatidylinositol
4,5-bisphosphate (PIP2)-independent PLD that possesses a
regulatory calcium-dependent phospholipid-binding C2
domain in the N-terminus and require millimolar calcium
for optimal activity. The C2 domain is unique to plant
PLDs and is not present in animal or fungal PLDs. Like
other PLD enzymes, the monomer of plant PLDalpha
consists of two catalytic domains, each of which
contains one copy of the conserved HKD motif
(H-x-K-x(4)-D, where x represents any amino acid
residue). Two HKD motifs from two domains form a single
active site. Plant PLDalpha may utilize a common
two-step ping-pong catalytic mechanism involving an
enzyme-substrate intermediate to cleave phosphodiester
bonds. The two histidine residues from the two HKD
motifs play key roles in the catalysis. Upon substrate
binding, a histidine residue from one HKD motif could
function as the nucleophile, attacking the
phosphodiester bond to create a covalent
phosphohistidine intermediate, while the other histidine
residue from the second HKD motif could serve as a
general acid, stabilizing the leaving group.
Length = 211
Score = 28.0 bits (62), Expect = 0.63
Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 4/64 (6%)
Query: 3 VVREWPTAVFEKEALTGDVESGKSYQAQTISLLSRVVIQAFTLTFLAEWGDRSQLTTIIL 62
VV WP + E +G V++ +Q +T+ ++ + QA + + R LT L
Sbjct: 77 VVPMWPEGIPE----SGSVQAILDWQKRTMEMMYTDIAQALRAQGIDDEDPRDYLTFFCL 132
Query: 63 AARE 66
A RE
Sbjct: 133 ANRE 136
>gnl|CDD|200458 cd11319, AmyAc_euk_AmyA, Alpha amylase catalytic domain found in
eukaryotic 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 eukaryotic alpha-amylases including proteins
from fungi, sponges, and protozoans. 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 = 375
Score = 27.5 bits (62), Expect = 1.0
Identities = 14/61 (22%), Positives = 20/61 (32%)
Query: 15 EALTGDVESGKSYQAQTISLLSRVVIQAFTLTFLAEWGDRSQLTTIILAAREDVYGVTLG 74
E GD YQ +L+ + F + G S L I + + TL
Sbjct: 230 EVFDGDPNYVCPYQNYLDGVLNYPLYYPLVDAFQSTKGSMSALVDTINSVQSSCKDPTLL 289
Query: 75 G 75
G
Sbjct: 290 G 290
>gnl|CDD|221536 pfam12335, SBF2, Myotubularin protein. This domain family is found
in eukaryotes, and is approximately 220 amino acids in
length. The family is found in association with
pfam02141, pfam03456, pfam03455. This family is the
middle region of SBF2, a member of the myotubularin
family. Myotubularin-related proteins have been
suggested to work in phosphoinositide-mediated
signalling events that may also convey control of
myelination. Mutations of SBF2 are implicated in
Charcot-Marie-Tooth disease.
Length = 224
Score = 26.2 bits (58), Expect = 2.9
Identities = 12/37 (32%), Positives = 17/37 (45%), Gaps = 3/37 (8%)
Query: 2 DVVREWPTAVFEKE-ALTGDVESGKSYQAQTISLLSR 37
+ +R WPT EK+ L ES +Q I +R
Sbjct: 189 EQLRLWPTLSKEKQQELVQSEESTV--FSQAIHFANR 223
>gnl|CDD|221410 pfam12077, DUF3556, Transmembrane protein of unknown function
(DUF3556). This family of transmembrane proteins is
functionally uncharacterized. This protein is found in
bacteria. Proteins in this family are typically between
576 to 592 amino acids in length.
Length = 574
Score = 26.2 bits (58), Expect = 3.7
Identities = 17/43 (39%), Positives = 20/43 (46%), Gaps = 3/43 (6%)
Query: 31 TISLLSRVVIQAFTLTFLAEWGDRSQLTTIILAAREDVYGVTL 73
I LL + A L LA G R + I LAAR +VY L
Sbjct: 176 EIGLLPPWQLVAI-LALLAVLGLRDK--VIFLAARGEVYAPML 215
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 0.394
Gapped
Lambda K H
0.267 0.0681 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,378,887
Number of extensions: 457227
Number of successful extensions: 326
Number of sequences better than 10.0: 1
Number of HSP's gapped: 326
Number of HSP's successfully gapped: 15
Length of query: 103
Length of database: 10,937,602
Length adjustment: 69
Effective length of query: 34
Effective length of database: 7,877,176
Effective search space: 267823984
Effective search space used: 267823984
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 (24.3 bits)