RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7609
(226 letters)
>gnl|CDD|222307 pfam13671, AAA_33, AAA domain. This family of domains contain only
a P-loop motif, that is characteristic of the AAA
superfamily. Many of the proteins in this family are
just short fragments so there is no Walker B motif.
Length = 143
Score = 58.9 bits (143), Expect = 3e-11
Identities = 21/92 (22%), Positives = 35/92 (38%), Gaps = 4/92 (4%)
Query: 28 DKTTKCLNRLLELGFSRRRNYILDQTNVYVSAQKR--KMRSYFGFQRKAIVVVPTNEDYL 85
+ + L L R I+D TN+ + R + +G + + + E
Sbjct: 53 GRVYQRLLELAREALRAGRPVIVDATNLSREERARLIDLARRYGAPVRIVYLEAPEEVLR 112
Query: 86 ARLEMHREKEGKDDVP-PDNVILEMKANFKLP 116
R RE+ G D P+ V+ M A F+ P
Sbjct: 113 ERNA-QRERSGGDPSDVPEAVLDRMLARFEPP 143
>gnl|CDD|185752 cd08961, GH64-TLP-SF, glycoside hydrolase family 64
(beta-1,3-glucanases which produce specific
pentasaccharide oligomers) and thaumatin-like proteins.
This superfamily includes glycoside hydrolases of family
64 (GH64), these are mostly bacterial
beta-1,3-glucanases which cleave long-chain
polysaccharide beta-1,3-glucans, into specific
pentasaccharide oligomers and are implicated in fungal
cell wall degradation. Also included in this superfamily
are thaumatin, the sweet-tasting protein from the
African berry Thaumatococcus daniellii, and
thaumatin-like proteins (TLPs) which are involved in
host defense and a wide range of developmental processes
in fungi, plants, and animals. Like GH64s, some TLPs
also hydrolyze the beta-1,3-glucans of the type commonly
found in fungal walls. Plant TLPs are classified as
pathogenesis-related (PR) protein family 5 (PR5), their
expression is induced by environmental stresses such as
pathogen/pest attack, drought and cold. Several members
of the plant TLP family have been reported as food
allergens from fruits, and pollen allergens from
conifers. Streptomyces matensis
laminaripentaose-producing, beta-1,3-glucanase
(GH64-LPHase), and TLPs have in common, a core
N-terminal barrel domain (domain I) composed of 10
beta-strands, two coming from the C-terminal region of
the protein. In TLPs, this core domain is flanked by two
shorter domains (domains II and III). Small TLPs, such
as Triticum aestivum thaumatin-like xylanase inhibitor,
have a deletion in the third domain (domain II).
GH64-LPHase has a second C-terminal domain which
corresponds positional to, but is much larger than,
domain III of TLP. GH64-LPHase and TLPs are described as
crescent-fold structures. Critical functional residues,
common to GH64-LPHase and TLPs are a Glu and an Asp
residue. LPHase has an electronegative,
substrate-binding cleft and the afore mentioned
conserved Glu and Asp residues are the catalytic
residues essential for beta-1,3-glucan cleavage. In
TLPs, these residues are two of the four conserved
residues which contribute to the strong electronegative
character of the cleft which is associated with the
antifungal activity of TLPs.
Length = 153
Score = 29.5 bits (66), Expect = 0.81
Identities = 15/96 (15%), Positives = 23/96 (23%), Gaps = 18/96 (18%)
Query: 131 QHPEAEKIIDEYNKNADGTYNYPQNWNAQNWQGYGYSTTGQTGTTGQTGQSTQ----GAS 186
+ T P+ ++ + W G S T T +
Sbjct: 20 LSSAPDASGPGLAPGRSTTIQIPKGFSGRIWFRTGCSMDFSGTTGCLTQDPGVVNPTDPN 79
Query: 187 KMISAA-------DFESGGWWFESKSRYKISLVQLF 215
+ DF SG + SLV F
Sbjct: 80 RDPPFTLAEFTLNDFNSGDF-------IDSSLVDGF 108
>gnl|CDD|225761 COG3220, COG3220, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 282
Score = 30.0 bits (68), Expect = 0.99
Identities = 34/122 (27%), Positives = 43/122 (35%), Gaps = 51/122 (41%)
Query: 50 LDQTNVYVSAQKRKMRSYFGFQRKAIVVVPTNEDYLARLEMHR-----------EKEG-- 96
LD N+YV+A GF E+YLA L + R E+EG
Sbjct: 171 LDVNNIYVNAV------NHGF---------DPEEYLAALPVERVGEIHLAGHDEEEEGEL 215
Query: 97 ---------KDDV-----------PPDNVILEMKANFKLPEVGELFEEVTYI-ELQHPEA 135
KD+V P +LE +F +P EL EV I ELQ A
Sbjct: 216 LIDTHGAPVKDEVWDLLEAAYARLGPRPTLLER--DFNIPPFAELLAEVEAIAELQDRIA 273
Query: 136 EK 137
Sbjct: 274 AL 275
>gnl|CDD|184287 PRK13735, PRK13735, conjugal transfer mating pair stabilization
protein TraG; Provisional.
Length = 942
Score = 28.9 bits (65), Expect = 2.2
Identities = 14/60 (23%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 134 EAEKIIDEYNKNADGTYNYPQNWNAQNWQGYGYSTTGQTGTTGQTGQSTQGASKMISAAD 193
+AE + ++ + +N + + G S TG +T + Q + AS+M SA +
Sbjct: 539 QAESALHGFSSSIASAWNQLSQFGSNR--GSSDSVTGGADST-MSAQDSMMASRMRSAVE 595
>gnl|CDD|171679 PRK12717, flgL, flagellar hook-associated protein FlgL;
Provisional.
Length = 523
Score = 28.9 bits (65), Expect = 2.4
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 6/56 (10%)
Query: 142 YNKNADGTYNYPQNWNAQNWQGYGYSTTGQTGTTG-----QTGQSTQGASKMISAA 192
Y +NADGTY+Y + + Q G + TG Q +++ + + S A
Sbjct: 146 YVRNADGTYSYQGDQTQLSLQ-VGDTLNLAANDTGYSAFEQAVNTSRTQTTLTSPA 200
>gnl|CDD|218160 pfam04587, ADP_PFK_GK, ADP-specific Phosphofructokinase/Glucokinase
conserved region. In archaea a novel type of glycolytic
pathway exists that is deviant from the classical
Embden-Meyerhof pathway. This pathway utilises two novel
proteins: an ADP-dependent Glucokinase and an
ADP-dependent Phosphofructokinase. This conserved region
is present at the C-terminal of both these proteins.
Interestingly this family contains sequences from higher
eukaryotes..
Length = 444
Score = 28.2 bits (63), Expect = 3.4
Identities = 18/64 (28%), Positives = 26/64 (40%), Gaps = 4/64 (6%)
Query: 55 VYVSAQKRKMRSYFGFQRKAIVVVPTNEDYLARLEMHREKEGKDDVPPDNVILEMKANFK 114
Y +K+ F ++VPT E+ L+ RE D + I E KA FK
Sbjct: 115 AYTPFLSKKLAELF----LDNILVPTVENGELVLKHPREAYRDGDPDKIHRIFEFKAGFK 170
Query: 115 LPEV 118
E+
Sbjct: 171 WGEI 174
>gnl|CDD|222334 pfam13710, ACT_5, ACT domain. ACT domains bind to amino acids and
regulate associated enzyme domains. These ACT domains
are found at the C-terminus of the RelA protein.
Length = 63
Score = 26.0 bits (58), Expect = 3.8
Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 6/50 (12%)
Query: 69 GFQRKAIVVVPTNEDYLARLEMHREKEGKDDVPPDNVILEMKANFKLPEV 118
GF ++ + T +D +ARL + EG + P D ++ +++ KL +V
Sbjct: 17 GFNIASLNMSTTEDDGVARLTL--TVEGHER-PVDLLVNQLE---KLIDV 60
>gnl|CDD|173713 cd05624, STKc_MRCK_beta, Catalytic domain of the Protein
Serine/Threonine Kinase, DMPK-related cell division
control protein 42 binding kinase beta.
Serine/Threonine Kinases (STKs), DMPK-like subfamily,
DMPK-related cell division control protein 42 (Cdc42)
binding kinase (MRCK) beta isoform, catalytic (c)
domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The DMPK-like subfamily
is part of a larger superfamily that includes the
catalytic domains of other protein STKs, protein
tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. MRCK is activated via interaction with the
small GTPase Cdc42. MRCK/Cdc42 signaling mediates
myosin-dependent cell motility. MRCKbeta is expressed
ubiquitously in many tissues.
Length = 331
Score = 27.7 bits (61), Expect = 5.1
Identities = 13/38 (34%), Positives = 21/38 (55%)
Query: 82 EDYLARLEMHREKEGKDDVPPDNVILEMKANFKLPEVG 119
E LA +H+ D+ PDNV+L+M + +L + G
Sbjct: 110 EMVLAIHSIHQLHYVHRDIKPDNVLLDMNGHIRLADFG 147
>gnl|CDD|99979 cd03807, GT1_WbnK_like, This family is most closely related to the
GT1 family of glycosyltransferases. WbnK in Shigella
dysenteriae has been shown to be involved in the type 7
O-antigen biosynthesis.
Length = 365
Score = 27.6 bits (62), Expect = 6.1
Identities = 21/99 (21%), Positives = 38/99 (38%), Gaps = 11/99 (11%)
Query: 19 IKGSWVQVVDKTTKCLNRLLELGFSRRRNYILDQTNVYVSAQKRKMRSYFGFQRKAIVVV 78
I+ S + + K+T+ L R + + V SA + G+ K IVV+
Sbjct: 111 IRHSDLDLGKKSTR-----LVARLRRLLSSFIPLI-VANSAAAAEYHQAIGYPPKKIVVI 164
Query: 79 PTN----EDYLARLEMHREKEGKDDVPPDNVILEMKANF 113
P N E + L+ + +P D ++ + A
Sbjct: 165 P-NGVDTERFSPDLDARARLREELGLPEDTFLIGIVARL 202
>gnl|CDD|226277 COG3754, RgpF, Lipopolysaccharide biosynthesis protein [Cell
envelope biogenesis, outer membrane].
Length = 595
Score = 27.4 bits (61), Expect = 7.4
Identities = 10/35 (28%), Positives = 13/35 (37%), Gaps = 5/35 (14%)
Query: 56 YVSAQKRKMRSYFGFQRKAIVVV--PTNEDYLARL 88
YV +R K +VV +E L RL
Sbjct: 19 YVIYLLESLRPLVE---KIVVVSNGEVSELALGRL 50
>gnl|CDD|212504 cd11645, Precorrin_2_C20_MT, Precorrin-2 C20-methyltransferase,
also named CobI or CbiL. Precorrin-2
C20-methyltransferase participates in the pathway toward
the biosynthesis of cobalamin (vitamin B12). There are
two distinct cobalamin biosynthetic pathways in
bacteria. The aerobic pathway requires oxygen, and
cobalt is inserted late in the pathway; the anaerobic
pathway does not require oxygen, and cobalt insertion is
the first committed step towards cobalamin synthesis.
Precorrin-2 C20-methyltransferase catalyzes methylation
at the C-20 position of a cyclic tetrapyrrole ring of
precorrin-2 using S-adenosylmethionine as a methyl group
source to produce precorrin-3A. In the anaerobic
pathway, cobalt is inserted into precorrin-2 by CbiK to
generate cobalt-precorrin-2, which is the substrate for
CbiL, a C20 methyltransferase. In Clostridium difficile,
CbiK and CbiL are fused into a bifunctional enzyme. In
the aerobic pathway, the precorrin-2
C20-methyltransferase is named CobI. This family
includes CbiL and CobI precorrin-2
C20-methyltransferases, both as stand-alone enzymes and
when CbiL forms part of a bifunctional enzyme.
Length = 226
Score = 27.1 bits (61), Expect = 7.9
Identities = 12/23 (52%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 102 PDNVILEMKANFKLPEVGELFEE 124
D V+L MK L EV EL EE
Sbjct: 165 FDTVVL-MKVGRNLDEVRELLEE 186
>gnl|CDD|218808 pfam05913, DUF871, Bacterial protein of unknown function (DUF871).
This family consists of several conserved hypothetical
proteins from bacteria and archaea. The function of this
family is unknown.
Length = 357
Score = 27.1 bits (61), Expect = 8.4
Identities = 9/28 (32%), Positives = 12/28 (42%)
Query: 83 DYLARLEMHREKEGKDDVPPDNVILEMK 110
Y+ R R K +D+PP N K
Sbjct: 271 RYVIRSTESRVKYKDEDIPPHNTSDPRK 298
>gnl|CDD|236275 PRK08486, PRK08486, single-stranded DNA-binding protein;
Provisional.
Length = 182
Score = 26.7 bits (59), Expect = 8.8
Identities = 8/49 (16%), Positives = 14/49 (28%), Gaps = 1/49 (2%)
Query: 140 DEYNKNADGTYNYPQNWNAQNWQGYGYSTTGQTGTTGQ-TGQSTQGASK 187
+ + + + NYP N+N + Y Q Q
Sbjct: 118 QDNSFHENFNNNYPGNYNNPSQDPYMNQAQSYNQNAYAKENQQAQPPKY 166
>gnl|CDD|235090 PRK02951, PRK02951, DNA replication terminus site-binding protein;
Provisional.
Length = 309
Score = 26.8 bits (60), Expect = 9.0
Identities = 17/59 (28%), Positives = 25/59 (42%), Gaps = 13/59 (22%)
Query: 68 FGFQRKAIVVVPTNEDYLARLEMHREKEGKD--DVPPDN-------VILEMKANFKLPE 117
FG+ K I+ T ++ LA+L EK K V P + E++ LPE
Sbjct: 170 FGWANKHIIKNLTRDELLAQL----EKSLKSGRAVAPWTREQWQEKLEQEIQDIASLPE 224
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
0.316 0.133 0.395
Gapped
Lambda K H
0.267 0.0807 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,596,322
Number of extensions: 1078423
Number of successful extensions: 1031
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1029
Number of HSP's successfully gapped: 22
Length of query: 226
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 133
Effective length of database: 6,812,680
Effective search space: 906086440
Effective search space used: 906086440
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: 57 (25.6 bits)