RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3115
(226 letters)
>gnl|CDD|143500 cd06827, PLPDE_III_AR_proteobact, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes, Proteobacterial Alanine
Racemases. This subfamily is composed mainly of
proteobacterial alanine racemases (EC 5.1.1.1), fold
type III PLP-dependent enzymes that catalyze the
interconversion between L- and D-alanine, which is an
essential component of the peptidoglycan layer of
bacterial cell walls. hese proteins are similar to other
bacterial ARs and are fold type III PLP-dependent
enzymes containing contains an N-terminal PLP-binding
TIM-barrel domain and a C-terminal beta-sandwich domain.
They exist as homodimers with active sites that lie at
the interface between the TIM barrel domain of one
subunit and the beta-sandwich domain of the other
subunit. Homodimer formation and the presence of the PLP
cofactor are required for catalytic activity.
Length = 354
Score = 33.6 bits (78), Expect = 0.055
Identities = 16/62 (25%), Positives = 25/62 (40%), Gaps = 16/62 (25%)
Query: 114 IYLK---------FTPNEI---YKALQANNKVPFIA----FQDASDENSKYTLELLECFN 157
++LK F+P E Y+ L+A+ V I F A + +S T + L F
Sbjct: 117 VWLKLDSGMHRLGFSPEEYAAAYQRLKASPNVASIVLMTHFACADEPDSPGTAKQLAIFE 176
Query: 158 AV 159
Sbjct: 177 QA 178
>gnl|CDD|139376 PRK13150, PRK13150, cytochrome c-type biogenesis protein CcmE;
Reviewed.
Length = 159
Score = 28.4 bits (63), Expect = 1.9
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 118 FTPNEIYKALQANNKVPFIAFQDAS 142
+TP E+ KA+Q N++ P A +D S
Sbjct: 134 YTPPEVEKAMQENHRRPQRADKDTS 158
>gnl|CDD|232960 TIGR00406, prmA, ribosomal protein L11 methyltransferase.
Ribosomal protein L11 methyltransferase is an
S-adenosyl-L-methionine-dependent methyltransferase
required for the modification of ribosomal protein L11.
This protein is found in bacteria and (with a probable
transit peptide) in Arabidopsis [Protein synthesis,
Ribosomal proteins: synthesis and modification].
Length = 288
Score = 27.9 bits (62), Expect = 4.1
Identities = 23/77 (29%), Positives = 30/77 (38%), Gaps = 6/77 (7%)
Query: 120 PNEIYKALQANNKVPFIAFQDASDENSKYTLELLECFNAVFKARQHNLFDFDDFDVDE-- 177
P E K L N V IA DA + + + LLE F FD D +
Sbjct: 44 PGE--KRLWGNLDV--IALFDAETDMNNSVIPLLEAFCLDLGRNHKIEFDEFSKDWERAW 99
Query: 178 MEKYERIQFGDISWIVP 194
+ + +QFG WI P
Sbjct: 100 KDNFHPVQFGKRFWICP 116
>gnl|CDD|178165 PLN02550, PLN02550, threonine dehydratase.
Length = 591
Score = 28.0 bits (62), Expect = 5.3
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 2/72 (2%)
Query: 78 AKLNSSTLKHKVIIHYTGNNPKKRLNAAFLIGCYAIIYLKFTPNEI-YKALQANNKVPFI 136
AKL L VI GN+ + +A +GC A+I + T EI +++++ +
Sbjct: 149 AKLPKEQLDKGVICSSAGNHAQGVALSAQRLGCDAVIAMPVTTPEIKWQSVE-RLGATVV 207
Query: 137 AFQDASDENSKY 148
D+ DE Y
Sbjct: 208 LVGDSYDEAQAY 219
>gnl|CDD|118177 pfam09644, Mg296, Mg296 protein. This protein of 129 residues is
expressed in bacteria. It consists of three identical
chains of five alpha helices. Two copies of each chain
associate into a complex of six units of possible
biological significance but of unknown function.
Length = 121
Score = 26.8 bits (59), Expect = 5.9
Identities = 10/37 (27%), Positives = 19/37 (51%)
Query: 156 FNAVFKARQHNLFDFDDFDVDEMEKYERIQFGDISWI 192
FN + QH ++D D D+ + +E+ D+ +I
Sbjct: 27 FNLCLEREQHTRIIYEDDDYDDQDFFEKPMLSDLFFI 63
>gnl|CDD|184989 PRK15029, PRK15029, arginine decarboxylase; Provisional.
Length = 755
Score = 27.5 bits (61), Expect = 6.6
Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 5/56 (8%)
Query: 85 LKHKVIIHYTGNNPKKRLNAAFLIGCYAIIYLKFTPNEIYKALQANNKVPFIAFQD 140
L + NNP RLN A+ + + TP E Y A+ NN V ++ ++
Sbjct: 634 LGDTMFAWLKENNPGARLNEAY----SGLPVAEITPREAYNAIVDNN-VELVSIEN 684
>gnl|CDD|224390 COG1473, AbgB, Metal-dependent
amidase/aminoacylase/carboxypeptidase [General function
prediction only].
Length = 392
Score = 27.2 bits (61), Expect = 7.5
Identities = 8/41 (19%), Positives = 13/41 (31%)
Query: 186 FGDISWIVPNKLLAFSGPNTTEQNTCYHPPEFYLDKVSIPI 226
FG VP + H P+F D+ ++
Sbjct: 336 FGYYLEKVPGAFFFLGTGSADGGTYPLHHPKFDFDEAALAT 376
>gnl|CDD|241517 cd13363, PH_PLC_delta, Phospholipase C-delta (PLC-delta) pleckstrin
homology (PH) domain. The PLC-delta (PLCdelta) consists
of three family members, delta 1, 2, and 3. PLC-delta1
is the most well studied. PLC-delta is activated by high
calcium levels generated by other PLC family members,
and functions as a calcium amplifier within the cell.
PLC-delta consists of an N-terminal PH domain, a EF hand
domain, a catalytic domain split into X and Y halves,
and a C-terminal C2 domain. The PH domain binds PIP2 and
promotes activation of the catalytic core as well as
tethering the enzyme to the plasma membrane. The C2
domain has been shown to mediate calcium-dependent
phospholipid binding as well. The PH and C2 domains
operate in concert as a "tether and fix" apparatus
necessary for processive catalysis by the enzyme. Its
leucine-rich nuclear export signal (NES) in its EF hand
motif, as well as a Nuclear localization signal within
its linker region allow PLC-delta 1 to actively
translocate into and out of the nucleus. PLCs (EC
3.1.4.3) play a role in the initiation of cellular
activation, proliferation, differentiation and
apoptosis. They are central to inositol lipid signalling
pathways, facilitating intracellular Ca2+ release and
protein kinase C (PKC) activation. Specificaly, PLCs
catalyze the cleavage of
phosphatidylinositol-4,5-bisphosphate (PIP2) and result
in the release of 1,2-diacylglycerol (DAG) and inositol
1,4,5-triphosphate (IP3). These products trigger the
activation of protein kinase C (PKC) and the release of
Ca2+ from intracellular stores. There are fourteen kinds
of mammalian phospholipase C proteins which are are
classified into six isotypes (beta, gamma, delta,
epsilon, zeta, eta). PH domains have diverse functions,
but in general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 117
Score = 26.1 bits (58), Expect = 7.6
Identities = 12/23 (52%), Positives = 13/23 (56%), Gaps = 2/23 (8%)
Query: 147 KYTLELLE--CFNAVFKARQHNL 167
KY E E CF VFK R+ NL
Sbjct: 64 KYAEEFPEDRCFTIVFKGRRKNL 86
>gnl|CDD|216875 pfam02102, Peptidase_M35, Deuterolysin metalloprotease (M35)
family.
Length = 352
Score = 27.2 bits (60), Expect = 8.0
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 49 DETHVYLNFFGDFGPICLSTLYR 71
+ T V+LNFF D P+ +LYR
Sbjct: 53 EVTFVHLNFFRDAAPVKKVSLYR 75
>gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional.
Length = 895
Score = 27.2 bits (60), Expect = 9.6
Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 15/66 (22%)
Query: 112 AIIYLKFTPNEIYKALQANNKVPFIAFQDASDENSKYTLELLECFNAVFKARQHNLFDFD 171
AI LK + +A + VP + + AS + T + L FN DFD
Sbjct: 734 AIGDLK----RLREAFDKSG-VPAMIRKSASQAMTSLTRKYLFEFN----------LDFD 778
Query: 172 DFDVDE 177
D DVD+
Sbjct: 779 DIDVDQ 784
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
0.323 0.140 0.432
Gapped
Lambda K H
0.267 0.0736 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,567,747
Number of extensions: 1064017
Number of successful extensions: 920
Number of sequences better than 10.0: 1
Number of HSP's gapped: 920
Number of HSP's successfully gapped: 24
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 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 57 (25.7 bits)