RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8015
(165 letters)
>gnl|CDD|216320 pfam01135, PCMT, Protein-L-isoaspartate(D-aspartate)
O-methyltransferase (PCMT).
Length = 210
Score = 75.5 bits (186), Expect = 2e-17
Identities = 33/64 (51%), Positives = 42/64 (65%)
Query: 78 ADGRASFGDNGPYDAIHVGAAYPRYPEIFIHHLKSGGRLVIPIGDTKQQMLTIYDKFHNG 137
DGR + + PYDAIHVGAA P PE I LK GGRLVIP+G Q+L +DK ++G
Sbjct: 131 GDGRQGWPEFAPYDAIHVGAAAPEIPEALIDQLKEGGRLVIPVGPNGNQVLQQFDKRNDG 190
Query: 138 TIDI 141
++ I
Sbjct: 191 SVVI 194
>gnl|CDD|225316 COG2518, Pcm, Protein-L-isoaspartate carboxylmethyltransferase
[Posttranslational modification, protein turnover,
chaperones].
Length = 209
Score = 70.7 bits (174), Expect = 1e-15
Identities = 27/72 (37%), Positives = 35/72 (48%)
Query: 78 ADGRASFGDNGPYDAIHVGAAYPRYPEIFIHHLKSGGRLVIPIGDTKQQMLTIYDKFHNG 137
DG + + PYD I V AA P PE + LK GGRLVIP+G Q L K +G
Sbjct: 127 GDGSKGWPEEAPYDRIIVTAAAPEVPEALLDQLKPGGRLVIPVGSGPAQRLLRITKDGDG 186
Query: 138 TIDIQHWGVVQV 149
+ + V+
Sbjct: 187 NFERRDLFNVRF 198
>gnl|CDD|178974 PRK00312, pcm, protein-L-isoaspartate O-methyltransferase;
Reviewed.
Length = 212
Score = 64.5 bits (158), Expect = 3e-13
Identities = 23/56 (41%), Positives = 29/56 (51%)
Query: 78 ADGRASFGDNGPYDAIHVGAAYPRYPEIFIHHLKSGGRLVIPIGDTKQQMLTIYDK 133
DG + P+D I V AA P P + LK GG LV P+G +QQ+LT K
Sbjct: 133 GDGWKGWPAYAPFDRILVTAAAPEIPRALLEQLKEGGILVAPVGGEEQQLLTRVRK 188
>gnl|CDD|184409 PRK13942, PRK13942, protein-L-isoaspartate O-methyltransferase;
Provisional.
Length = 212
Score = 58.5 bits (142), Expect = 4e-11
Identities = 29/72 (40%), Positives = 40/72 (55%), Gaps = 2/72 (2%)
Query: 76 LIADGRASFGDNGPYDAIHVGAAYPRYPEIFIHHLKSGGRLVIPIGDTKQQMLTIYDKFH 135
++ DG + +N PYD I+V AA P P+ I LK GG +VIP+G Q+ L +K
Sbjct: 132 IVGDGTLGYEENAPYDRIYVTAAGPDIPKPLIEQLKDGGIMVIPVGSYSQE-LIRVEK-D 189
Query: 136 NGTIDIQHWGVV 147
NG I + G V
Sbjct: 190 NGKIIKKKLGEV 201
>gnl|CDD|232816 TIGR00080, pimt, protein-L-isoaspartate(D-aspartate)
O-methyltransferase. This is an all-kingdom (but not
all species) full-length ortholog enzyme for repairing
aging proteins. Among the prokaryotes, the gene name is
pcm. Among eukaryotes, pimt [Protein fate, Protein
modification and repair].
Length = 215
Score = 57.9 bits (140), Expect = 8e-11
Identities = 27/65 (41%), Positives = 36/65 (55%), Gaps = 2/65 (3%)
Query: 78 ADGRASFGDNGPYDAIHVGAAYPRYPEIFIHHLKSGGRLVIPIGDTKQQMLTIYDKFHNG 137
DG + PYD I+V AA P+ PE I LK GG LV+P+G+ Q+L +K G
Sbjct: 135 GDGTQGWEPLAPYDRIYVTAAGPKIPEALIDQLKEGGILVMPVGE-YLQVLKRAEK-RGG 192
Query: 138 TIDIQ 142
I I+
Sbjct: 193 EIIIK 197
>gnl|CDD|140001 PRK13944, PRK13944, protein-L-isoaspartate O-methyltransferase;
Provisional.
Length = 205
Score = 42.1 bits (99), Expect = 3e-05
Identities = 20/50 (40%), Positives = 27/50 (54%)
Query: 79 DGRASFGDNGPYDAIHVGAAYPRYPEIFIHHLKSGGRLVIPIGDTKQQML 128
DG+ + P+DAI V AA P + LK GG LVIP+ + Q+L
Sbjct: 132 DGKRGLEKHAPFDAIIVTAAASTIPSALVRQLKDGGVLVIPVEEGVGQVL 181
>gnl|CDD|237568 PRK13943, PRK13943, protein-L-isoaspartate O-methyltransferase;
Provisional.
Length = 322
Score = 41.0 bits (96), Expect = 1e-04
Identities = 16/42 (38%), Positives = 21/42 (50%)
Query: 79 DGRASFGDNGPYDAIHVGAAYPRYPEIFIHHLKSGGRLVIPI 120
DG + PYD I V PE + LK GGR+++PI
Sbjct: 139 DGYYGVPEFAPYDVIFVTVGVDEVPETWFTQLKEGGRVIVPI 180
>gnl|CDD|234563 TIGR04364, methyltran_FxLD, methyltransferase, FxLD system.
Members of this family resemble occur regularly in the
vicinity of lantibiotic biosynthesis enzymes and their
probable target, the FxLD family of putative ribosomal
natural product precursor (TIGR04363). Members resemble
protein-L-isoaspartate O-methyltransferase (TIGR00080)
and a predicted methyltranserase, TIGR04188, of another
putative peptide modification system.
Length = 394
Score = 38.9 bits (91), Expect = 6e-04
Identities = 16/45 (35%), Positives = 23/45 (51%)
Query: 76 LIADGRASFGDNGPYDAIHVGAAYPRYPEIFIHHLKSGGRLVIPI 120
++AD A + PYD I V P ++ L GGRLV+P+
Sbjct: 137 VLADAEAGVPELAPYDRIIVTVGAWDIPPAWLDQLAPGGRLVVPL 181
>gnl|CDD|221804 pfam12847, Methyltransf_18, Methyltransferase domain. Protein in
this family function as methyltransferases.
Length = 104
Score = 35.0 bits (81), Expect = 0.004
Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 3/44 (6%)
Query: 78 ADGRASFGDNGPYDAIHVGAAYPRYPEIF---IHHLKSGGRLVI 118
D + +DA+ +G E+ LK GGRLV+
Sbjct: 58 GDAPDALDLLEGFDAVFIGGGGGDLLELLDALASLLKPGGRLVL 101
>gnl|CDD|234492 TIGR04188, methyltr_grsp, methyltransferase, ATP-grasp peptide
maturase system. Members of this protein family are
predicted SAM-dependent methyltransferases that
regularly occur in the context of a putative peptide
modification ATP-grasp enzyme (TIGR04187, related to
enzymes of microviridin maturation) and a putative
ribosomal peptide modification target (TIGR04186).
Length = 363
Score = 33.9 bits (78), Expect = 0.026
Identities = 11/45 (24%), Positives = 17/45 (37%)
Query: 77 IADGRASFGDNGPYDAIHVGAAYPRYPEIFIHHLKSGGRLVIPIG 121
DG PYD I A R P ++ + GG ++ +
Sbjct: 162 TGDGLLGHPPRAPYDRIIATCAVRRVPPAWLRQTRPGGVILTTLS 206
>gnl|CDD|132544 TIGR03505, FimV_core, FimV N-terminal domain. This region is found
at, or about 200 amino acids from, the N-terminus of
FimV from Pseudomonas aeruginosa, TspA of Neisseria
meningitidis, and related proteins. Disruption of FimV
blocks twitching motility from type IV pili; Semmler, et
al. suggest a role for this family in peptidoglycan
layer remodelling required by type IV fimbrial systems.
Most but not all members of this protein family have a
C-terminal region recognized by TIGR03504. In between is
a highly variable, often repeat-filled region rich in
the negatively charged amino acids Asp and Glu.
Length = 74
Score = 29.2 bits (66), Expect = 0.22
Identities = 9/32 (28%), Positives = 17/32 (53%), Gaps = 7/32 (21%)
Query: 103 PEIF----IHHLKSGGRLVIPIGDTKQQMLTI 130
P+ F I+ LK G L IP +++++ +
Sbjct: 30 PDAFIGGNINRLKVGQILRIP---SEEEIQAV 58
>gnl|CDD|173856 cd08491, PBP2_NikA_DppA_OppA_like_12, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 473
Score = 29.7 bits (67), Expect = 0.67
Identities = 17/37 (45%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 50 SFNINVYYYLSGGPLSSTIDPDHDYDLIADGRASFGD 86
SF VYY LS G S+ DP+ D LI A+ GD
Sbjct: 386 SFTFPVYY-LSEGSQSTFGDPELD-ALIKAAMAATGD 420
>gnl|CDD|222818 PHA01075, PHA01075, major capsid protein.
Length = 408
Score = 29.6 bits (66), Expect = 0.86
Identities = 40/156 (25%), Positives = 58/156 (37%), Gaps = 27/156 (17%)
Query: 12 GAVAKYVTYLSGHSKRLDCLALTSNTKQSTTLPTFIPNSFNINVYYYLS--------GGP 63
GA+ +Y T SK D + LT+++ +S L T I N+F I + GG
Sbjct: 224 GAIGQYTT----VSKLKDIVILTTDSLKSYLLDTKIANTFQIAGIDFTDHVISFDDLGGV 279
Query: 64 LSSTIDPDHDYDLIADGRASFGDNGPY--DAIHVGAAY----PRYPEIF--IHHLKSGGR 115
T + D ++GD D I VGA + + E + +K
Sbjct: 280 FKVTKEFKLQNQDSIDFLRAYGDYQSQLGDTIPVGAVFTYDVSKLKEFTGNVEEIKPKSD 339
Query: 116 LVIPIGDTKQQMLTIYDK------FHNGTID-IQHW 144
L I D Y K F+NG D + HW
Sbjct: 340 LYAFILDINSIKYKRYTKGMLKQPFYNGEFDEVTHW 375
>gnl|CDD|234376 TIGR03863, PQQ_ABC_bind, ABC transporter, substrate binding
protein, PQQ-dependent alcohol dehydrogenase system.
Members of this protein family are putative
substrate-binding proteins of an ABC transporter family
that associates, in gene neighborhood and phylogenomic
profile, with pyrroloquinoline-quinone (PQQ)-dependent
degradation of certain alcohols, such as 2-phenylethanol
in Pseudomonas putida U [Transport and binding proteins,
Carbohydrates, organic alcohols, and acids].
Length = 347
Score = 29.2 bits (66), Expect = 0.93
Identities = 8/24 (33%), Positives = 11/24 (45%)
Query: 67 TIDPDHDYDLIADGRASFGDNGPY 90
T D+D ++AD F PY
Sbjct: 183 TQGADYDVVVVADEAGDFARYLPY 206
>gnl|CDD|225151 COG2242, CobL, Precorrin-6B methylase 2 [Coenzyme metabolism].
Length = 187
Score = 28.7 bits (65), Expect = 0.94
Identities = 19/76 (25%), Positives = 27/76 (35%), Gaps = 9/76 (11%)
Query: 90 YDAIHVG--AAYPRYPEIFIHHLKSGGRLVIPIG--DTKQQMLTIYDKFHNGTIDIQHWG 145
DAI +G E LK GGRLV +T + L ++ G +I
Sbjct: 103 PDAIFIGGGGNIEEILEAAWERLKPGGRLVANAITLETLAKALEALEQL--GGREIVQ-- 158
Query: 146 VVQVGLLYDVKAGYSM 161
VQ+ + G
Sbjct: 159 -VQISRGKPLGGGTMF 173
>gnl|CDD|197272 cd09175, PLDc_Bfil, Catalytic domain of type IIs restriction
endonuclease BfiI and similar proteins. Catalytic
domain of a novel type IIs restriction endonuclease BfiI
and similar proteins. Type II restriction endonucleases
are components of restriction modification (RM) systems
that protect bacteria and archaea against invading
foreign DNA. They usually function as homodimers or
homotetramers that cleave DNA at defined sites of 4 to 8
bp in length, and they require Mg2+, not ATP or GTP,
for catalysis. Unlike all other restriction enzymes
known to date, BfiI is unique in cleaving DNA at fixed
positions downstream of an asymmetric sequence in the
absence of Mg2+. BfiI consists of two discrete domains
with distinct functions: an N-terminal catalytic domain
with non-specific nuclease activity and dimerization
function that is more closely related to Nuc, an
EDTA-resistant nuclease from the phospholipase D (PLD)
superfamily; and a C-terminal domain that specifically
recognizes its target sequences, 5'-ACTGGG-3'. BfiI
presumably evolved through domain fusion of a DNA
recognition domain to the catalytic Nuc-like domain from
the PLD superfamily. Most PLD enzymes have two copies of
the conserved HKD motif (H-x-K-x(4)-D, where x
represents any amino acid residue) in a single
polypeptide chain and both are required for catalytic
activity. However, BfiI contains only one HKD motif per
protein chain and forms a functionally active homodimer
which has two DNA-binding surfaces located at the
C-terminal domains but only one active site, located at
the dimer interface between the two N-terminal catalytic
domains that contain the two HKD motifs from both
subunits. BfiI utilizes a single active site to cut both
DNA strands, which represents a novel mechanism for the
scission of double-stranded DNA. It uses a histidine
residue from the HKD motif in one subunit as the
nucleophile for the cleavage of the target
phosphodiester bond in both of the anti-parallel DNA
strands, while the symmetrically-related histidine
residue from the HKD motif of the opposite subunit acts
as the proton donor/acceptor during both strand-scission
events.
Length = 161
Score = 28.2 bits (63), Expect = 1.6
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 101 RYPEIFIHHLKSGGRLVIPIGDTKQQMLT 129
R+ +F H+ GG++V G + Q L+
Sbjct: 50 RFYPVFTEHIHKGGKVVAIFGGSTSQRLS 78
>gnl|CDD|234757 PRK00421, murC, UDP-N-acetylmuramate--L-alanine ligase;
Provisional.
Length = 461
Score = 28.2 bits (64), Expect = 2.3
Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 19/56 (33%)
Query: 68 IDPDH-DYDLIADGRASFGDNGPYDAIHVGAAYPRYPEIFIHHLKSGGRLVIPIGD 122
ID DH DY +GD ++ + A+ + F H+L G LV D
Sbjct: 183 IDADHLDY---------YGD---FEDLK--DAF----QEFAHNLPFYGALVACGDD 220
>gnl|CDD|225983 COG3452, COG3452, Predicted periplasmic ligand-binding sensor
domain [Signal transduction mechanisms].
Length = 297
Score = 27.9 bits (62), Expect = 2.3
Identities = 8/25 (32%), Positives = 9/25 (36%)
Query: 65 SSTIDPDHDYDLIADGRASFGDNGP 89
S I P D + DG G G
Sbjct: 200 VSLISPGLDIRVAIDGLDLIGGQGR 224
>gnl|CDD|102061 PRK05922, PRK05922, type III secretion system ATPase; Validated.
Length = 434
Score = 27.2 bits (60), Expect = 4.8
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 81 RASFGDNGPYDAIHVGAAYPRYPEIFIHHLKS 112
RA D G A++ YP +P+IF +LKS
Sbjct: 293 RAGNNDKGSITALYAILHYPNHPDIFTDYLKS 324
>gnl|CDD|201880 pfam01596, Methyltransf_3, O-methyltransferase. Members of this
family are O-methyltransferases. The family includes
catechol o-methyltransferase, caffeoyl-CoA
O-methyltransferase and a family of bacterial
O-methyltransferases that may be involved in antibiotic
production.
Length = 204
Score = 26.5 bits (59), Expect = 7.0
Identities = 15/47 (31%), Positives = 21/47 (44%), Gaps = 8/47 (17%)
Query: 75 DLIADGRASFGDNGPYDAIHVGA---AYPRYPEIFIHHLKSGGRLVI 118
+L+ D G +D I V A YP Y E + +K GG + I
Sbjct: 111 ELVKDKP-----LGEFDFIFVDADKSNYPNYYERLLELVKVGGLIAI 152
>gnl|CDD|226607 COG4122, COG4122, Predicted O-methyltransferase [General function
prediction only].
Length = 219
Score = 26.1 bits (58), Expect = 7.8
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 87 NGPYDAIHVGAA---YPRYPEIFIHHLKSGGRLVI 118
+G +D + + A YP Y E + L+ GG +V
Sbjct: 130 DGSFDLVFIDADKADYPEYLERALPLLRPGGLIVA 164
>gnl|CDD|215754 pfam00153, Mito_carr, Mitochondrial carrier protein.
Length = 96
Score = 25.3 bits (56), Expect = 8.3
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 1 MLIVFVSGSVSGAVAKYVTY 20
L ++G ++GA+A VTY
Sbjct: 5 FLASLLAGGIAGAIAATVTY 24
>gnl|CDD|223570 COG0496, SurE, Predicted acid phosphatase [General function
prediction only].
Length = 252
Score = 26.0 bits (58), Expect = 9.5
Identities = 10/44 (22%), Positives = 19/44 (43%), Gaps = 4/44 (9%)
Query: 56 YYYLSGGPLSSTIDPDHDYDLIADGRAS----FGDNGPYDAIHV 95
YY++ G L+ + D+ + +G S D Y+A+
Sbjct: 203 YYWIGPGGLAEDAEEGTDFHAVREGYISITPLQLDLTAYEALES 246
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
0.321 0.140 0.428
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,647,876
Number of extensions: 792891
Number of successful extensions: 635
Number of sequences better than 10.0: 1
Number of HSP's gapped: 634
Number of HSP's successfully gapped: 32
Length of query: 165
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 75
Effective length of database: 6,945,742
Effective search space: 520930650
Effective search space used: 520930650
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.0 bits)