RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy732
(119 letters)
>gnl|CDD|217283 pfam02913, FAD-oxidase_C, FAD linked oxidases, C-terminal domain.
This domain has a ferredoxin-like fold.
Length = 247
Score = 45.8 bits (109), Expect = 6e-07
Identities = 18/92 (19%), Positives = 43/92 (46%), Gaps = 5/92 (5%)
Query: 14 DHDAEKLNTFLQDGIENNIILDAVMCSEESKIQKIWPLRERIVE---SCLKDG-YIYNYD 69
+ E+L ++ +E D V+ +E++ +++W R+ + + G ++ D
Sbjct: 72 EVVEERLEAAVEAILEGAGAGDVVVAEDEAERERLWRARKYAMPLRDALGGAGPLVFTED 131
Query: 70 ISLSLKDFYSIIPIMKERLKDQPVVTVCGYGH 101
+S+ ++ +KE L +V +C +GH
Sbjct: 132 VSVPWSRLPDLVADIKELLAKYGLV-ICHFGH 162
>gnl|CDD|214416 MTH00066, ND5, NADH dehydrogenase subunit 5; Provisional.
Length = 598
Score = 30.3 bits (69), Expect = 0.18
Identities = 12/22 (54%), Positives = 16/22 (72%), Gaps = 3/22 (13%)
Query: 65 IYNYDISLSLK-DFYSII--PI 83
I+N++I+ S K D YSII PI
Sbjct: 69 IFNFNINSSFKFDQYSIIFLPI 90
>gnl|CDD|205122 pfam12875, DUF3826, Protein of unknown function (DUF3826). This is
a putative sugar-binding family.
Length = 187
Score = 29.8 bits (67), Expect = 0.24
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 51 LRERIVESCLKDGYIYNYDISLSLKDFYSIIPIMKERLKDQ 91
L E +E+ +KDG Y + ++ K + +IP + E K Q
Sbjct: 93 LTEEQIEA-VKDGMTYGV-LPVTYKAYQDMIPSLTEEEKAQ 131
>gnl|CDD|227468 COG5139, COG5139, Uncharacterized conserved protein [Function
unknown].
Length = 397
Score = 30.1 bits (67), Expect = 0.25
Identities = 23/72 (31%), Positives = 30/72 (41%), Gaps = 16/72 (22%)
Query: 22 TFLQDGIENNIILDAVMCSEESKIQKIWPLRERIVESCLKDGYIYNYDISLSLKDFYSII 81
LQD I +N ILD+V + W +E L D + N I SL D +
Sbjct: 199 KALQDTILDNNILDSV---------RGW------LEP-LPDKSLPNIKIQKSLLDVLKTL 242
Query: 82 PIMKERLKDQPV 93
PI E L + V
Sbjct: 243 PIHTEHLVESGV 254
>gnl|CDD|227376 COG5043, MRS6, Vacuolar protein sorting-associated protein
[Intracellular trafficking and secretion].
Length = 2552
Score = 29.5 bits (66), Expect = 0.40
Identities = 14/60 (23%), Positives = 22/60 (36%), Gaps = 12/60 (20%)
Query: 20 LNTFLQDGIENNIILDAVMCSEESKIQKIWPLRE-RIVESCLKDGYIYNYDISLSLKDFY 78
L + +GI+N + I LR R V DG + YD+ S ++
Sbjct: 2401 LTSNDSEGIKNTTTV--------LDYHDIPRLRLPRYVWD---DGCVAPYDLRESQGQYW 2449
>gnl|CDD|212512 cd09301, HDAC, Histone deacetylase (HDAC) classes I, II, IV and
related proteins. The HDAC/HDAC-like family includes
Zn-dependent histone deacetylase classes I, II and IV
(class III HDACs, also called sirtuins, are
NAD-dependent and structurally unrelated, and therefore
not part of this family). Histone deacetylases catalyze
hydrolysis of N(6)-acetyl-lysine residues in histone
amino termini to yield a deacetylated histone (EC
3.5.1.98), as opposed to the acetylation reaction by
some histone acetyltransferases (EC 2.3.1.48).
Deacetylases of this family are involved in signal
transduction through histone and other protein
modification, and can repress/activate transcription of
a number of different genes. They usually act via the
formation of large multiprotein complexes. They are
involved in various cellular processes, including cell
cycle regulation, DNA damage response, embryonic
development, cytokine signaling important for immune
response and post-translational control of the acetyl
coenzyme A synthetase. In mammals, they are known to be
involved in progression of different tumors. Specific
inhibitors of mammalian histone deacetylases are an
emerging class of promising novel anticancer drugs.
Length = 279
Score = 28.9 bits (65), Expect = 0.59
Identities = 25/95 (26%), Positives = 42/95 (44%), Gaps = 5/95 (5%)
Query: 16 DAEKLNTFLQDGIENNIILDAVMCSEESKIQKIWPLRERIVESCLKDGYIYNY--DISLS 73
K+N L+DG+ + LDAV +++ P E +V D + + +LS
Sbjct: 178 KGYKINVPLEDGLGDEEYLDAVERVISKVLEEFEP--EVVVLQFGHDTHEGDRLGGFNLS 235
Query: 74 LKDFYSIIPIMKERLKDQPVVTVCGYGH-LERLKD 107
K F + I+KE + P++ V G G+ E
Sbjct: 236 EKGFVKLAEIVKEFARGGPILMVLGGGYNPEAAAR 270
>gnl|CDD|132431 TIGR03390, ascorbOXfungal, L-ascorbate oxidase, fungal type. This
model describes a family of fungal ascorbate oxidases,
within a larger family of multicopper oxidases that also
includes plant ascorbate oxidases (TIGR03388), plant
laccases and laccase-like proteins (TIGR03389), and
related proteins. The member from Acremonium sp. HI-25
is characterized.
Length = 538
Score = 27.9 bits (62), Expect = 1.3
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 55 IVESCLKDGYIYNYDISLSLKDFYS 79
IVE C Y Y+ + L + DF+S
Sbjct: 126 IVEDCEPPPYKYDDERILLVSDFFS 150
>gnl|CDD|184403 PRK13929, PRK13929, rod-share determining protein MreBH;
Provisional.
Length = 335
Score = 27.9 bits (62), Expect = 1.3
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 14/69 (20%)
Query: 60 LKDGYIYNYDISLSLKDFYSIIPIMKERLKD------QPVVTVC---GYGHLERLKDQPV 110
+KDG I +YD++ L + IMK+ K+ +P V VC G +ER
Sbjct: 66 MKDGVIADYDMTTDL-----LKQIMKKAGKNIGMTFRKPNVVVCTPSGSTAVERRAISDA 120
Query: 111 VTVCGYGHL 119
V CG ++
Sbjct: 121 VKNCGAKNV 129
>gnl|CDD|130300 TIGR01233, lacG, 6-phospho-beta-galactosidase. This enzyme is part
of the tagatose-6-phosphate pathway of
galactose-6-phosphate degradation [Energy metabolism,
Biosynthesis and degradation of polysaccharides].
Length = 467
Score = 27.0 bits (59), Expect = 3.1
Identities = 10/31 (32%), Positives = 13/31 (41%), Gaps = 4/31 (12%)
Query: 11 SCVDHDAEKLNTFLQDGIENNIILDAVMCSE 41
+ D A +L +D I N ILDA
Sbjct: 227 NPADVRAAEL----EDIIHNKFILDATYLGH 253
>gnl|CDD|118672 pfam10144, SMP_2, Bacterial virulence factor haemolysin. Members
of this family of bacterial proteins are membrane
proteins that effect the expression of haemolysin under
anaerobic conditions.
Length = 210
Score = 25.9 bits (57), Expect = 4.7
Identities = 15/62 (24%), Positives = 29/62 (46%), Gaps = 4/62 (6%)
Query: 13 VDHDAEKLNTFLQDGIENNIILDAVMCSEE----SKIQKIWPLRERIVESCLKDGYIYNY 68
+ + E+L LQ ++ ILDA + SE+ + + +R+R+ + G +N
Sbjct: 67 QNENGERLQAILQQLTLDSRILDASVYSEDGVLLAHSGESVNVRDRLALDGKEAGSYFNQ 126
Query: 69 DI 70
I
Sbjct: 127 QI 128
>gnl|CDD|234836 PRK00782, PRK00782, hypothetical protein; Provisional.
Length = 267
Score = 26.1 bits (58), Expect = 5.5
Identities = 12/40 (30%), Positives = 16/40 (40%), Gaps = 8/40 (20%)
Query: 61 KDGYIYNYDISLSLKDFYSIIPIMKERLKDQPVVTVCGYG 100
KD + + L + FY I R+ T CGYG
Sbjct: 191 KDMILIEAILDLDVDGFYDEI----YRMN----ATACGYG 222
>gnl|CDD|215922 pfam00443, UCH, Ubiquitin carboxyl-terminal hydrolase.
Length = 313
Score = 25.8 bits (57), Expect = 6.2
Identities = 18/98 (18%), Positives = 36/98 (36%), Gaps = 10/98 (10%)
Query: 15 HDAEKLNTFLQDGIENNIILDAVMCS----EESKIQKIWPLRERIVESCLKDGYIYNYDI 70
DA + FL D + ++ S ES I K++ + CLK +
Sbjct: 92 QDAHEFLLFLLDQLHEDLNSLKKRKSHAAENESLITKLFQGQLESRLKCLKCKKESSTP- 150
Query: 71 SLSLKDFYSIIPIMKERLKDQPVVTVCGYGHLERLKDQ 108
+ F + +++ ++T + LE L+ +
Sbjct: 151 ----EPFSDLSLPIEDSSSVLKLLTGN-FLKLEELEKE 183
>gnl|CDD|215513 PLN02951, PLN02951, Molybderin biosynthesis protein CNX2.
Length = 373
Score = 25.9 bits (57), Expect = 6.7
Identities = 19/96 (19%), Positives = 40/96 (41%), Gaps = 20/96 (20%)
Query: 14 DHDAEKLNTFLQDGIENNIILDAVMCSEESKIQKIWPLRERIVESCLKDGYIYNYDISLS 73
++ K+N + G ++ I D V + + P+ R +E DG ++N +
Sbjct: 198 GYNPVKVNCVVMRGFNDDEICDFVELTRDK------PINVRFIEFMPFDGNVWNVKKLVP 251
Query: 74 LKDFYSIIPIMKERLKDQPVVTVCGYGHLERLKDQP 109
+ M +R++ + + L+RL+D P
Sbjct: 252 YAE-------MMDRIEQR-------FPSLKRLQDHP 273
>gnl|CDD|238134 cd00217, INT_Flp, Flp recombinase, C-terminal catalytic domain.
Yeast Flp-like recombinases mediate the amplification of
the 2 micron circular plasmid copy number by catalyzing
the intra-molecular recombination between two inverted
repeats during replication. They belong to the DNA
breaking-rejoining enzyme superfamily, which also
includes prokaryotic tyrosine recombinases and type IB
topoisomerases. These enzymes share the same fold in
their catalytic domain containing six conserved active
site residues and the overall reaction mechanism.
Flp-like recombinases are almost exclusively found in
yeast and are highly diverged in sequence from the
prokaryotic tyrosine recombinases. They cleave their
target DNA in trans with a composite active site in
which the catalytic tyrosine is provided by a promoter
bound to a site other than the one being cleaved. Thus
each active site within Flp complexes is assembled by
domain swapping and contains catalytic residues from two
different monomers. Two DNA segments are synapsed by the
tetrameric enzyme, carrying the nucleophilic tyrosine in
each active site with only two of the four monomers
active at a given time. The catalytic domain is linked
through a flexible loop to the N-terminal domain, which
is largely responsible for non-specific DNA binding and
isomerization. Its overall fold is similar to the SAM
domain fold also found in the N-terminal domains of
lambda integrase and XerD recombinase.
Length = 339
Score = 25.5 bits (56), Expect = 8.2
Identities = 6/27 (22%), Positives = 10/27 (37%), Gaps = 1/27 (3%)
Query: 67 NYDISLSLKDFYSII-PIMKERLKDQP 92
D ++L D P K R ++
Sbjct: 227 RCDPLVALHDLLRHTTPTKKSRTSNRN 253
>gnl|CDD|187861 cd09730, Cas8a1_I-A, CRISPR/Cas system-associated protein Cas8a1.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Large proteins, some contain Zn-finger domain; signature
gene for I-A subtype; also known as TM1802 family.
Length = 579
Score = 25.4 bits (56), Expect = 9.0
Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 43 SKIQKIWPLRERIVESCLKDGYIYNYDISLSLKDFYSIIPIMKERLKD 90
S+ +KI+ ++ V S +K+ NY + L+L Y ++P K K+
Sbjct: 340 SRFKKIFEALKK-VNSIVKEDNGMNYLLKLTLNQIYYLLPGNKSGSKN 386
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
0.325 0.144 0.460
Gapped
Lambda K H
0.267 0.0706 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,188,599
Number of extensions: 540232
Number of successful extensions: 664
Number of sequences better than 10.0: 1
Number of HSP's gapped: 663
Number of HSP's successfully gapped: 24
Length of query: 119
Length of database: 10,937,602
Length adjustment: 82
Effective length of query: 37
Effective length of database: 7,300,574
Effective search space: 270121238
Effective search space used: 270121238
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.2 bits)