RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5588
(61 letters)
>gnl|CDD|216320 pfam01135, PCMT, Protein-L-isoaspartate(D-aspartate)
O-methyltransferase (PCMT).
Length = 210
Score = 65.9 bits (161), Expect = 2e-15
Identities = 29/52 (55%), Positives = 37/52 (71%), Gaps = 1/52 (1%)
Query: 4 ELIDQLRPGGRLIIPVGPEGSAQSLEQIDKNLDGTITRTPLMQVVYVPLTDK 55
LIDQL+ GGRL+IPVGP G+ Q L+Q DK DG++ L V +VPLTD+
Sbjct: 158 ALIDQLKEGGRLVIPVGPNGN-QVLQQFDKRNDGSVVIKDLEGVRFVPLTDR 208
>gnl|CDD|225316 COG2518, Pcm, Protein-L-isoaspartate carboxylmethyltransferase
[Posttranslational modification, protein turnover,
chaperones].
Length = 209
Score = 51.9 bits (125), Expect = 5e-10
Identities = 26/55 (47%), Positives = 33/55 (60%), Gaps = 2/55 (3%)
Query: 5 LIDQLRPGGRLIIPVGPEGSAQSLEQIDKNLDGTITRTPLMQVVYVPLTDKQHQW 59
L+DQL+PGGRL+IPVG AQ L +I K+ DG R L V +VPL +
Sbjct: 155 LLDQLKPGGRLVIPVGSGP-AQRLLRITKDGDGNFERRDLFNVRFVPLVGG-DGF 207
>gnl|CDD|178974 PRK00312, pcm, protein-L-isoaspartate O-methyltransferase;
Reviewed.
Length = 212
Score = 47.5 bits (114), Expect = 2e-08
Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 4 ELIDQLRPGGRLIIPVGPEGSAQSLEQIDKNLDGTITRTPLMQVVYVPLTD 54
L++QL+ GG L+ PVG E Q L ++ K G R L +V +VPL
Sbjct: 160 ALLEQLKEGGILVAPVGGEEQ-QLLTRVRKR-GGRFEREVLEEVRFVPLVK 208
>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 = 44.4 bits (105), Expect = 2e-07
Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 5 LIDQLRPGGRLIIPVGPEGSAQSLEQIDKNLDGTITRTPLMQVVYVPLTDKQHQW 59
LIDQL+ GG L++PVG Q L++ +K G I + V +VPL +
Sbjct: 163 LIDQLKEGGILVMPVGEY--LQVLKRAEK-RGGEIIIKDVEPVAFVPLVGGEGFQ 214
>gnl|CDD|184409 PRK13942, PRK13942, protein-L-isoaspartate O-methyltransferase;
Provisional.
Length = 212
Score = 38.5 bits (90), Expect = 4e-05
Identities = 21/51 (41%), Positives = 34/51 (66%), Gaps = 3/51 (5%)
Query: 5 LIDQLRPGGRLIIPVGPEGSAQSLEQIDKNLDGTITRTPLMQVVYVPLTDK 55
LI+QL+ GG ++IPVG +Q L +++K+ +G I + L +V +VPL K
Sbjct: 162 LIEQLKDGGIMVIPVG--SYSQELIRVEKD-NGKIIKKKLGEVAFVPLIGK 209
>gnl|CDD|140001 PRK13944, PRK13944, protein-L-isoaspartate O-methyltransferase;
Provisional.
Length = 205
Score = 33.6 bits (77), Expect = 0.002
Identities = 18/49 (36%), Positives = 29/49 (59%), Gaps = 2/49 (4%)
Query: 4 ELIDQLRPGGRLIIPVGPEGSAQSLEQIDKNLDGTITRTPLMQVVYVPL 52
L+ QL+ GG L+IPV EG Q L ++ K + + + + V++VPL
Sbjct: 158 ALVRQLKDGGVLVIPV-EEGVGQVLYKVVKRGEK-VEKRAITYVLFVPL 204
>gnl|CDD|100097 cd05805, MPG1_transferase, GTP-mannose-1-phosphate
guanyltransferase (MPG1 transferase), also known as
GDP-mannose pyrophosphorylase, is a bifunctional enzyme
with both phosphomannose isomerase (PMI) activity and
GDP-mannose phosphorylase (GMP) activity. The protein
contains an N-terminal NTP transferase domain, an
L-beta-H domain, and a C-terminal PGM-like domain that
belongs to the alpha-D-phosphohexomutase superfamily.
This subfamily is limited to bacteria and archaea. The
alpha-D-phosphohexomutases include several related
enzymes that catalyze a reversible intramolecular
phosphoryl transfer on their sugar substrates. Members
of this group appear to lack conserved residues
necessary for metal binding and catalytic activity.
Other members of this superfamily include the
phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine
mutase (PNGM), phosphoacetylglucosamine mutase (PAGM),
the bacterial phosphomannomutase ManB, the bacterial
phosphoglucosamine mutase GlmM, and the bifunctional
phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of
these enzymes has four domains with a centrally located
active site formed by four loops, one from each domain.
All four domains are included in this alignment model.
Length = 441
Score = 31.8 bits (73), Expect = 0.009
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 5/44 (11%)
Query: 1 MVVELIDQLRPGGRLIIPVGPEGSAQS-LEQIDKNLDGTITRTP 43
+V L+ + PGG +++PV +A S +EQ+ + G + RT
Sbjct: 260 LVSLLVLKSEPGGTVVVPV----TAPSVIEQLAERYGGRVIRTK 299
>gnl|CDD|239489 cd03395, PAP2_like_4, PAP2_like_4 proteins. PAP2 is a
super-family of phosphatases and haloperoxidases. This
subgroup, which is specific to bacteria, lacks
functional characterization and may act as a
membrane-associated lipid phosphatase.
Length = 177
Score = 29.5 bits (67), Expect = 0.047
Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 3/36 (8%)
Query: 28 LEQIDKNLDGTI---TRTPLMQVVYVPLTDKQHQWP 60
LEQID L + PL+ + LT K+ P
Sbjct: 2 LEQIDVWLFLLLNGTLVHPLLDDLMPFLTGKKLSVP 37
>gnl|CDD|236315 PRK08633, PRK08633, 2-acyl-glycerophospho-ethanolamine
acyltransferase; Validated.
Length = 1146
Score = 29.9 bits (68), Expect = 0.049
Identities = 15/37 (40%), Positives = 18/37 (48%), Gaps = 10/37 (27%)
Query: 16 IIPVGPEGSAQSLEQIDKNLD----------GTITRT 42
+IP+ GS +SLE I K LD G ITR
Sbjct: 489 VIPISSGGSKESLEFIRKALDDGEVVCIFPEGAITRN 525
>gnl|CDD|221479 pfam12237, PCIF1_WW, Phosphorylated CTD interacting factor 1 WW
domain. This domain family is found in bacteria and
eukaryotes, and is approximately 180 amino acids in
length. This domain is the WW domain of PCIF1. PCIF1
interacts with phosphorylated RNA polymerase II
carboxy-terminal domain (CTD). The WW domain of PCIF1
can directly and preferentially bind to the
phosphorylated CTD compared to the unphosphorylated CTD.
PCIF1 binds to the hyperphosphorylated RNAP II (RNAP
IIO) in vitro and in vivo. Double immunofluorescence
labeling in HeLa cells demonstrated that PCIF1 and
endogenous RNAP IIO are co-localized in the cell
nucleus. Thus, PCIF1 may play a role in mRNA synthesis
by modulating RNAP IIO activity.
Length = 175
Score = 29.6 bits (67), Expect = 0.061
Identities = 13/42 (30%), Positives = 19/42 (45%)
Query: 18 PVGPEGSAQSLEQIDKNLDGTITRTPLMQVVYVPLTDKQHQW 59
P E E +++ LD + + TPL VV VP + W
Sbjct: 109 PFDEELMDAMAEHLERLLDASKSTTPLSFVVIVPEWKEPPAW 150
>gnl|CDD|180140 PRK05575, cbiC, precorrin-8X methylmutase; Validated.
Length = 204
Score = 27.4 bits (61), Expect = 0.34
Identities = 13/32 (40%), Positives = 21/32 (65%), Gaps = 2/32 (6%)
Query: 4 ELIDQLRPGGRLII--PVGPEGSAQSLEQIDK 33
ELI + + + II PVG G+A+S E+++K
Sbjct: 144 ELIKEGKANPKFIIAVPVGFVGAAESKEELEK 175
>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 = 27.3 bits (61), Expect = 0.34
Identities = 9/14 (64%), Positives = 13/14 (92%)
Query: 6 IDQLRPGGRLIIPV 19
+DQL PGGRL++P+
Sbjct: 168 LDQLAPGGRLVVPL 181
>gnl|CDD|237568 PRK13943, PRK13943, protein-L-isoaspartate O-methyltransferase;
Provisional.
Length = 322
Score = 27.5 bits (61), Expect = 0.37
Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 4/36 (11%)
Query: 6 IDQLRPGGRLIIPVGPEGSAQS----LEQIDKNLDG 37
QL+ GGR+I+P+ + S + ++ D L G
Sbjct: 167 FTQLKEGGRVIVPINLKLSRRQPAFLFKKKDPYLVG 202
>gnl|CDD|198079 smart01011, AMP_N, Aminopeptidase P, N-terminal domain. This
domain is structurally very similar to the creatinase
N-terminal domain. However, little or no sequence
similarity exists between the two families.
Length = 135
Score = 26.8 bits (60), Expect = 0.55
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 5 LIDQLRPGGRLIIPVGPE 22
L +L PG ++P GPE
Sbjct: 13 LAAKLFPGSVAVLPAGPE 30
>gnl|CDD|219318 pfam07167, PhaC_N, Poly-beta-hydroxybutyrate polymerase (PhaC)
N-terminus. This family represents the N-terminal
region of the bacterial poly-beta-hydroxybutyrate
polymerase (PhaC). Polyhydroxyalkanoic acids (PHAs) are
carbon and energy reserve polymers produced in some
bacteria when carbon sources are plentiful and another
nutrient, such as nitrogen, phosphate, oxygen, or
sulfur, becomes limiting. PHAs composed of monomeric
units ranging from 3 to 14 carbons exist in nature. When
the carbon source is exhausted, PHA is utilised by the
bacterium. PhaC links D-(-)-3-hydroxybutyrl-CoA to an
existing PHA molecule by the formation of an ester bond.
This family appears to be a partial segment of an
alpha/beta hydrolase domain.
Length = 172
Score = 26.0 bits (58), Expect = 1.1
Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 5/36 (13%)
Query: 30 QIDKNLDGT----ITRTPLMQVV-YVPLTDKQHQWP 60
++ KNL T + R L +++ Y P T+K H+ P
Sbjct: 111 EVGKNLATTPGKVVFRNDLFELIQYKPTTEKVHKRP 146
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 25.4 bits (56), Expect = 1.6
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 2 VVELIDQLRPGGRLIIPVGPEGS 24
+V++I Q + GR I+ VGP G+
Sbjct: 54 IVKMIKQGKMAGRGILIVGPPGT 76
>gnl|CDD|100086 cd03084, phosphohexomutase, The alpha-D-phosphohexomutase
superfamily includes several related enzymes that
catalyze a reversible intramolecular phosphoryl transfer
on their sugar substrates. Members of this family
include the phosphoglucomutases (PGM1 and PGM2),
phosphoglucosamine mutase (PNGM),
phosphoacetylglucosamine mutase (PAGM), the bacterial
phosphomannomutase ManB, the bacterial
phosphoglucosamine mutase GlmM, and the bifunctional
phosphomannomutase/phosphoglucomutase (PMM/PGM). These
enzymes play important and diverse roles in carbohydrate
metabolism in organisms from bacteria to humans. Each of
these enzymes has four domains with a centrally located
active site formed by four loops, one from each domain.
All four domains are included in this alignment model.
Length = 355
Score = 25.4 bits (56), Expect = 1.6
Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 3/43 (6%)
Query: 1 MVVELIDQLRPGGRLIIPVGPEGSAQSLEQIDKNLDGTITRTP 43
+ VEL P G ++ V S+ +L+++ K L + RT
Sbjct: 207 LAVELFLTFNPRGGVVKTVV---SSGALDKVAKKLGIKVIRTK 246
>gnl|CDD|218491 pfam05195, AMP_N, Aminopeptidase P, N-terminal domain. This
domain is structurally very similar to the creatinase
N-terminal domain (pfam01321). However, little or no
sequence similarity exists between the two families.
Length = 134
Score = 25.2 bits (56), Expect = 1.7
Identities = 7/18 (38%), Positives = 9/18 (50%)
Query: 5 LIDQLRPGGRLIIPVGPE 22
L+ L P I+P PE
Sbjct: 13 LLALLPPNSAAILPGAPE 30
>gnl|CDD|102471 PRK06628, PRK06628, lipid A biosynthesis lauroyl acyltransferase;
Provisional.
Length = 290
Score = 25.3 bits (55), Expect = 1.8
Identities = 12/24 (50%), Positives = 18/24 (75%), Gaps = 1/24 (4%)
Query: 2 VVELIDQLRPGGRL-IIPVGPEGS 24
V +L+++ R G +L +IP GPEGS
Sbjct: 152 VNKLVNESRAGDKLRLIPKGPEGS 175
>gnl|CDD|233596 TIGR01846, type_I_sec_HlyB, type I secretion system ABC
transporter, HlyB family. Type I protein secretion is a
system in some Gram-negative bacteria to export proteins
(often proteases) across both inner and outer membranes
to the extracellular medium. This is one of three
proteins of the type I secretion apparatus. Targeted
proteins are not cleaved at the N-terminus, but rather
carry signals located toward the extreme C-terminus to
direct type I secretion [Protein fate, Protein and
peptide secretion and trafficking].
Length = 694
Score = 25.1 bits (55), Expect = 2.2
Identities = 14/41 (34%), Positives = 17/41 (41%), Gaps = 12/41 (29%)
Query: 11 PGGRLIIPVGPEGSAQSLEQIDKNLDGTITRTPLMQVVYVP 51
G I VGP GS +S T T L+Q +Y P
Sbjct: 481 KPGEFIGIVGPSGSGKS------------TLTKLLQRLYTP 509
>gnl|CDD|234266 TIGR03571, lucif_BA3436, luciferase-type oxidoreductase, BA3436
family. This family is a distinct subgroup among
members of the luciferase monooxygenase domain family.
The larger family contains both FMN-binding enzymes
(luciferase, alkane monooxygenase) and F420-binding
enzymes (methylenetetrahydromethanopterin reductase,
secondary alcohol dehydrogenase, glucose-6-phosphate
dehydrogenase). Although some members of the domain
family bind coenzyme F420 rather than FMN, members of
this family are from species that lack the genes for
F420 biosynthesis. A crystal structure, but not
function, is known (but unpublished) for the member from
Bacillus cereus, PDB|2B81 [Unknown function, Enzymes of
unknown specificity].
Length = 298
Score = 24.9 bits (55), Expect = 2.4
Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 10/55 (18%)
Query: 8 QLRPGGRLI-------IPVGPEGSA-QSLEQIDKNLDGTIT--RTPLMQVVYVPL 52
+L G L+ IP+ GSA QSLE I +N+DG +T R P Q +
Sbjct: 160 ELDGGLDLLPKPTSGRIPLLATGSAQQSLEWIARNMDGWMTYPRPPETQRARIDE 214
>gnl|CDD|222673 pfam14315, DUF4380, Domain of unknown function (DUF4380). This
family of proteins is found in bacteria, archaea and
eukaryotes. Proteins in this family are typically
between 288 and 372 amino acids in length. There are two
completely conserved residues (G and E) that may be
functionally important.
Length = 274
Score = 25.0 bits (55), Expect = 2.4
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 8 QLRPGGRLIIPVGPEGS 24
+L PGGR+ +P+ P G
Sbjct: 145 RLAPGGRVFVPLAPAGD 161
>gnl|CDD|224157 COG1236, YSH1, Predicted exonuclease of the beta-lactamase fold
involved in RNA processing [Translation, ribosomal
structure and biogenesis].
Length = 427
Score = 24.7 bits (54), Expect = 3.7
Identities = 10/27 (37%), Positives = 14/27 (51%), Gaps = 1/27 (3%)
Query: 3 VELIDQ-LRPGGRLIIPVGPEGSAQSL 28
+E + L GG ++IP G AQ L
Sbjct: 206 IESVKAALERGGTVLIPAFALGRAQEL 232
>gnl|CDD|225854 COG3317, NlpB, Uncharacterized lipoprotein [Cell envelope
biogenesis, outer membrane].
Length = 342
Score = 24.3 bits (53), Expect = 4.1
Identities = 9/36 (25%), Positives = 16/36 (44%)
Query: 26 QSLEQIDKNLDGTITRTPLMQVVYVPLTDKQHQWPG 61
+L+++ + + V Y PL+D Q PG
Sbjct: 253 AALDKVGFTVTDRNRSQGVYAVTYAPLSDSDWQKPG 288
>gnl|CDD|146172 pfam03393, Pneumo_matrix, Pneumovirus matrix protein.
Length = 252
Score = 24.5 bits (53), Expect = 4.2
Identities = 8/33 (24%), Positives = 16/33 (48%)
Query: 9 LRPGGRLIIPVGPEGSAQSLEQIDKNLDGTITR 41
++P + I+ +G +S+ + N T TR
Sbjct: 216 IKPQSQFIVDLGAYLEKESIYYVTTNWKHTATR 248
>gnl|CDD|238500 cd01018, ZntC, Metal binding protein ZntC. These proteins are
predicted to function as initial receptors in ABC
transport of metal ions. They belong to the TroA
superfamily of helical backbone metal receptor proteins
that share a distinct fold and ligand binding mechanism.
They are comprised of two globular subdomains connected
by a long alpha helix and bind their specific ligands in
the cleft between these domains. In addition, many of
these proteins possess a metal-binding histidine-rich
motif (repetitive HDH sequence).
Length = 266
Score = 24.2 bits (53), Expect = 4.5
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 4 ELIDQLRPGGRLIIPVGPEGSAQSLEQIDKNLDGTITRT-PL 44
LID + G ++ V P+ S +S E I + + + PL
Sbjct: 208 RLIDLAKEKGVRVVFVQPQFSTKSAEAIAREIGAKVVTIDPL 249
>gnl|CDD|235100 PRK03031, rnpA, ribonuclease P; Reviewed.
Length = 122
Score = 23.8 bits (52), Expect = 5.7
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 4 ELIDQLRPGGRLIIPVGPEGSAQSLEQ 30
+L+ ++ PG L+I V P + + EQ
Sbjct: 77 QLLPRIAPGWDLVIIVKPTAAECNYEQ 103
>gnl|CDD|233551 TIGR01734, D-ala-DACP-lig, D-alanine--poly(phosphoribitol) ligase,
subunit 1. This model represents the enzyme (also
called D-alanine-D-alanyl carrier protein ligase) which
activates D-alanine as an adenylate via the reaction
D-ala + ATP -> D-ala-AMP + PPi, and further catalyzes
the condensation of the amino acid adenylate with the
D-alanyl carrier protein (D-ala-ACP). The D-alanine is
then further transferred to teichoic acid in the
biosynthesis of lipoteichoic acid (LTA) and wall
teichoic acid (WTA) in gram positive bacteria, both
polysacchatides [Cell envelope, Biosynthesis and
degradation of murein sacculus and peptidoglycan].
Length = 502
Score = 23.9 bits (52), Expect = 5.9
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 7 DQLRPGGRLIIPVGPEGSAQSLEQIDKNLDGTITRTPLMQVVYVPLTDKQHQ 58
QL GRL + G LE I+ NL + + + V VP +K H+
Sbjct: 387 GQLFYQGRLDFQIKLHGYRIELEDIEFNLRQS---SYIESAVVVPKYNKDHK 435
>gnl|CDD|237898 PRK15068, PRK15068, tRNA mo(5)U34 methyltransferase; Provisional.
Length = 322
Score = 23.7 bits (52), Expect = 7.5
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 1 MVVELIDQLRPGGRLII 17
+ +L DQL PGG L++
Sbjct: 208 HLKQLKDQLVPGGELVL 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
0.317 0.140 0.418
Gapped
Lambda K H
0.267 0.0766 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,138,025
Number of extensions: 219223
Number of successful extensions: 317
Number of sequences better than 10.0: 1
Number of HSP's gapped: 313
Number of HSP's successfully gapped: 30
Length of query: 61
Length of database: 10,937,602
Length adjustment: 32
Effective length of query: 29
Effective length of database: 9,518,274
Effective search space: 276029946
Effective search space used: 276029946
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: 53 (24.1 bits)