RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy629
(166 letters)
>gnl|CDD|219464 pfam07555, NAGidase, beta-N-acetylglucosaminidase. This family has
previously been described as a hyaluronidase. However,
more recently it has been shown that this family has
beta-N-acetylglucosaminidase activity.
Length = 306
Score = 245 bits (627), Expect = 2e-82
Identities = 82/169 (48%), Positives = 106/169 (62%), Gaps = 10/169 (5%)
Query: 1 MDSYLYAPKDDYKHRAYWRDLYSVEEAEHLTGLISAAKEQGIDFYYALSPGLDITYSSGK 60
M++Y+YAPKDD HR+ WR+LY EE L L+ AA E +DF YA+SPGLDITYSS +
Sbjct: 29 MNTYIYAPKDDPYHRSKWRELYPEEELAKLKELVKAANENKVDFVYAISPGLDITYSSEE 88
Query: 61 EVATLKRKLEQVAQFGCRGFALLFDDIESEMSEADKEVFQSFAHAQVSVTNEVFEHLGQP 120
++ L K EQ+ G R FA+LFDDIE + ADK F SFA AQ + N+V + +P
Sbjct: 89 DLQALLAKFEQLYDLGVRSFAVLFDDIEYTLWNADKRRFGSFAEAQADLLNKVQKEFIKP 148
Query: 121 K-----FMLCPTQYCSTRAVPNVKNSEYLNTLGSKLAKEIDIMWTGPKV 164
K + CPT+Y + A P+ YL TLG L +IDIMWTG +V
Sbjct: 149 KGDVYPLIFCPTEYNGSWASPD-----YLQTLGETLDPDIDIMWTGDRV 192
>gnl|CDD|226230 COG3707, AmiR, Response regulator with putative antiterminator
output domain [Signal transduction mechanisms].
Length = 194
Score = 32.7 bits (75), Expect = 0.052
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 7/52 (13%)
Query: 27 AEHLTGLISAAKEQGIDFY-------YALSPGLDITYSSGKEVATLKRKLEQ 71
A LI AA E G+ Y L P LD+ S +E L+R+L +
Sbjct: 85 AYSDPALIEAAIEAGVMAYIVKPLDESRLLPILDVAVSRFEERRALRRELAK 136
>gnl|CDD|169386 PRK08334, PRK08334, translation initiation factor IF-2B subunit
beta; Validated.
Length = 356
Score = 31.1 bits (70), Expect = 0.22
Identities = 18/45 (40%), Positives = 27/45 (60%), Gaps = 4/45 (8%)
Query: 37 AKEQGIDFYYALSP--GLDITYSSGKEVATLKRKLEQVAQF-GCR 78
AKE GI F+ ++P +D++ SGKE+ +R E+V GCR
Sbjct: 268 AKEHGIPFF-TVAPLSTIDMSLKSGKEIPIEERSPEEVLTCGGCR 311
>gnl|CDD|178487 PLN02899, PLN02899, alpha-galactosidase.
Length = 633
Score = 30.1 bits (68), Expect = 0.55
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 3/53 (5%)
Query: 13 KHRAYWRDLYSVEEAEHLTGLISAAKEQGIDFYYALSPGLDITYSSGKEVATL 65
KH + D + +EE +++ ++ KE Y+LSPG T + KEV+ L
Sbjct: 213 KHDCVFGDDFDLEEITYVSEVL---KELDRPIVYSLSPGTSATPTMAKEVSGL 262
>gnl|CDD|240114 cd04801, CBS_pair_M50_like, This cd contains two tandem repeats
of the cystathionine beta-synthase (CBS pair) domains
in association with the metalloprotease peptidase M50.
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 = 114
Score = 27.2 bits (61), Expect = 2.2
Identities = 14/64 (21%), Positives = 21/64 (32%), Gaps = 7/64 (10%)
Query: 10 DDYKHRAYWRDLYSVEEAEHLTGLISAAKEQGIDFYYALSPGLDITYSSGKEVATLKRKL 69
+Y + R V+ G+IS A D + T + +V T KL
Sbjct: 17 REYVLGSNQRRFVVVDNEGRYVGIISLA-----DLRAIPTSQWAQT--TVIQVMTPAAKL 69
Query: 70 EQVA 73
V
Sbjct: 70 VTVL 73
>gnl|CDD|179366 PRK02102, PRK02102, ornithine carbamoyltransferase; Validated.
Length = 331
Score = 27.5 bits (62), Expect = 3.6
Identities = 11/32 (34%), Positives = 19/32 (59%), Gaps = 3/32 (9%)
Query: 84 FDDIESEMSEADKEVFQSFAHAQVSVTNEVFE 115
F D E+++ KE+ + + + VT+EVFE
Sbjct: 276 FHDTETKVG---KEIAEKYGLKGLEVTDEVFE 304
>gnl|CDD|218259 pfam04775, Bile_Hydr_Trans, Acyl-CoA thioester hydrolase/BAAT
N-terminal region. This family consists of the amino
termini of acyl-CoA thioester hydrolase and bile
acid-CoA:amino acid N-acetyltransferase (BAAT). This
region is not thought to contain the active site of
either enzyme. Thioesterase isoforms have been
identified in peroxisomes, cytoplasm and mitochondria,
where they are thought to have distinct functions in
lipid metabolism. For example, in peroxisomes, the
hydrolase acts on bile-CoA esters.
Length = 126
Score = 26.8 bits (60), Expect = 3.8
Identities = 5/28 (17%), Positives = 14/28 (50%)
Query: 86 DIESEMSEADKEVFQSFAHAQVSVTNEV 113
+ + +++ ++SFA + + EV
Sbjct: 19 TLRARLTDDKGVTWESFAVFRADASGEV 46
>gnl|CDD|213962 TIGR04349, rSAM_QueE_gams, putative 7-cyano-7-deazaguanosine
(preQ0) biosynthesis protein QueE, gammaproteobacterial
type. Members of this radical SAM domain protein
family appear to be a form of the queuosine
biosynthesis protein QueE. QueE is involved in making
preQ0 (7-cyano-7-deazaquanine), a precursor of both the
bacterial/eukaryotic modified tRNA base queuosine and
the archaeal modified base archaeosine. Members occur
in preQ0 operons species that lack members of related
protein family TIGR03365.
Length = 210
Score = 27.2 bits (61), Expect = 4.3
Identities = 12/27 (44%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 53 DITYS-SGKEVATLKRKLEQVAQFGCR 78
D Y+ SG E +L L QVA +G R
Sbjct: 37 DTAYAFSGGERMSLDDILAQVASYGAR 63
>gnl|CDD|163674 cd03174, DRE_TIM_metallolyase, DRE-TIM metallolyase superfamily.
The DRE-TIM metallolyase superfamily includes
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 265
Score = 26.6 bits (60), Expect = 5.8
Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 8/60 (13%)
Query: 25 EEAEHLTGLISAAKEQGIDFYYALSPGLDITYSSGKEV--ATLKRKLEQVAQFGCRGFAL 82
E+ E+ I AAKE G++ +L + G + + + + + G +L
Sbjct: 112 EDLENAEEAIEAAKEAGLEVEGSLE------DAFGCKTDPEYVLEVAKALEEAGADEISL 165
>gnl|CDD|235783 PRK06349, PRK06349, homoserine dehydrogenase; Provisional.
Length = 426
Score = 26.6 bits (60), Expect = 6.5
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 27 AEHLTGLISAAKEQGIDFYY 46
A H L +AA+E+G+D Y+
Sbjct: 109 AVHGAELFAAAEEKGVDLYF 128
>gnl|CDD|182361 PRK10294, PRK10294, 6-phosphofructokinase 2; Provisional.
Length = 309
Score = 26.7 bits (59), Expect = 7.2
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 11/58 (18%)
Query: 28 EHLTGLISAAKEQGID---------FYYALSPG-LDITYSSGKEVATL-KRKLEQVAQ 74
E LT LISAA++QGI AL+ G +++ + KE++ L R L Q
Sbjct: 147 EKLTQLISAAQKQGIRCIIDSSGDALSAALAIGNIELVKPNQKELSALVNRDLTQPDD 204
>gnl|CDD|187751 cd09270, RNase_H2-B, Ribonuclease H2-B is a subunit of the
eukaryotic RNase H complex which cleaves RNA-DNA
hybrids. Ribonuclease H2B is one of the three proteins
of eukaryotic RNase H2 complex that is required for
nucleic acid binding and hydrolysis. RNase H is
classified into two families, type I (prokaryotic RNase
HI, eukaryotic RNase H1 and viral RNase H) and type II
(prokaryotic RNase HII and HIII, and eukaryotic RNase
H2/HII). RNase H endonucleolytically hydrolyzes an RNA
strand when it is annealed to a complementary DNA strand
in the presence of divalent cations, in DNA replication
and repair. The enzyme can be found in bacteria,
archaea, and eukaryotes. Most prokaryotic and eukaryotic
genomes contain multiple RNase H genes. Despite a lack
of evidence for homology from sequence comparisons, type
I and type II RNase H share a common fold and similar
steric configurations of the four acidic active-site
residues, suggesting identical or very similar catalytic
mechanisms. Eukaryotic RNase HII is active during
replication and is believed to play a role in removal of
Okazaki fragment primers and single ribonucleotides in
DNA-DNA duplexes. Eukaryotic RNase HII is functional
when it forms a complex with RNase H2B and RNase H2C
proteins. It is speculated that the two accessory
subunits are required for correct folding of the
catalytic subunit of RNase HII. Mutations in the three
subunits of human RNase HII cause neurological disorder.
Length = 211
Score = 26.1 bits (58), Expect = 9.1
Identities = 21/92 (22%), Positives = 32/92 (34%), Gaps = 18/92 (19%)
Query: 2 DSYLYAPKDDYKHRAYWRDLYSVEEAEHLTGLISAAKEQGIDFYYALSPGLDITYSSGKE 61
D L DL + E I KE+G D +Y YS K
Sbjct: 97 DDILDD--LSSPSSHLLEDL-PLPILESSLAKICDVKEEGDDKFY--------KYSDEKL 145
Query: 62 VATLKRKLEQVAQFGCRGFALLFDDIESEMSE 93
+A L +K+E++ + D E+E +
Sbjct: 146 LAWLLKKVERLKK-------KELDIKEAEAAR 170
>gnl|CDD|217006 pfam02382, RTX, RTX N-terminal domain. The RTX family of
bacterial toxins are a group of cytolysins and
cytotoxins. This Pfam family represents the N-terminal
domain which is found in association with a
glycine-rich repeat domain and hemolysinCabind
pfam00353.
Length = 653
Score = 26.3 bits (58), Expect = 10.0
Identities = 15/54 (27%), Positives = 20/54 (37%), Gaps = 11/54 (20%)
Query: 5 LYAPKDDYKHRAYWRDLYSVEEAEHLTGLISAAKEQGIDFYYALSPGLDITYSS 58
LY PK+ Y + L L+ AA+E GI+ G I S
Sbjct: 47 LYIPKN-----------YDASQGNGLNDLVKAAEELGIEVQREERNGTAIAKQS 89
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 0.133 0.393
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,299,648
Number of extensions: 726520
Number of successful extensions: 749
Number of sequences better than 10.0: 1
Number of HSP's gapped: 746
Number of HSP's successfully gapped: 22
Length of query: 166
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 76
Effective length of database: 6,945,742
Effective search space: 527876392
Effective search space used: 527876392
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: 55 (24.9 bits)