RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5587
(126 letters)
>gnl|CDD|216320 pfam01135, PCMT, Protein-L-isoaspartate(D-aspartate)
O-methyltransferase (PCMT).
Length = 210
Score = 68.5 bits (168), Expect = 3e-15
Identities = 29/51 (56%), Positives = 37/51 (72%), Gaps = 1/51 (1%)
Query: 55 LIDQLRPGGRLIIPVGPEGSAQNLEQIDKNLDGTITRTPLMQVVYVPLTDK 105
LIDQL+ GGRL+IPVGP G+ Q L+Q DK DG++ L V +VPLTD+
Sbjct: 159 LIDQLKEGGRLVIPVGPNGN-QVLQQFDKRNDGSVVIKDLEGVRFVPLTDR 208
Score = 53.1 bits (128), Expect = 2e-09
Identities = 23/44 (52%), Positives = 30/44 (68%), Gaps = 1/44 (2%)
Query: 13 LIDQLRPGGRLIIPVGPEGSAQSLEQIDKNLDGTITRTPLMQLI 56
LIDQL+ GGRL+IPVGP G+ Q L+Q DK DG++ L +
Sbjct: 159 LIDQLKEGGRLVIPVGPNGN-QVLQQFDKRNDGSVVIKDLEGVR 201
>gnl|CDD|225316 COG2518, Pcm, Protein-L-isoaspartate carboxylmethyltransferase
[Posttranslational modification, protein turnover,
chaperones].
Length = 209
Score = 54.9 bits (133), Expect = 2e-10
Identities = 26/55 (47%), Positives = 33/55 (60%), Gaps = 2/55 (3%)
Query: 55 LIDQLRPGGRLIIPVGPEGSAQNLEQIDKNLDGTITRTPLMQVVYVPLTDKQHQW 109
L+DQL+PGGRL+IPVG AQ L +I K+ DG R L V +VPL +
Sbjct: 155 LLDQLKPGGRLVIPVGSGP-AQRLLRITKDGDGNFERRDLFNVRFVPLVGG-DGF 207
Score = 45.3 bits (108), Expect = 1e-06
Identities = 21/38 (55%), Positives = 26/38 (68%), Gaps = 1/38 (2%)
Query: 12 KLIDQLRPGGRLIIPVGPEGSAQSLEQIDKNLDGTITR 49
L+DQL+PGGRL+IPVG AQ L +I K+ DG R
Sbjct: 154 ALLDQLKPGGRLVIPVGSGP-AQRLLRITKDGDGNFER 190
>gnl|CDD|178974 PRK00312, pcm, protein-L-isoaspartate O-methyltransferase;
Reviewed.
Length = 212
Score = 47.1 bits (113), Expect = 2e-07
Identities = 20/50 (40%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 55 LIDQLRPGGRLIIPVGPEGSAQNLEQIDKNLDGTITRTPLMQVVYVPLTD 104
L++QL+ GG L+ PVG E Q L ++ K G R L +V +VPL
Sbjct: 161 LLEQLKEGGILVAPVGGEEQ-QLLTRVRKR-GGRFEREVLEEVRFVPLVK 208
Score = 36.3 bits (85), Expect = 0.001
Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 13 LIDQLRPGGRLIIPVGPEGSAQSLEQIDKNLDGTITRTPLMQ 54
L++QL+ GG L+ PVG E Q L ++ K G R L +
Sbjct: 161 LLEQLKEGGILVAPVGGEEQ-QLLTRVRKR-GGRFEREVLEE 200
>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 = 46.0 bits (109), Expect = 5e-07
Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 55 LIDQLRPGGRLIIPVGPEGSAQNLEQIDKNLDGTITRTPLMQVVYVPLTDKQHQW 109
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 = 40.0 bits (94), Expect = 7e-05
Identities = 21/51 (41%), Positives = 34/51 (66%), Gaps = 3/51 (5%)
Query: 55 LIDQLRPGGRLIIPVGPEGSAQNLEQIDKNLDGTITRTPLMQVVYVPLTDK 105
LI+QL+ GG ++IPVG +Q L +++K+ +G I + L +V +VPL K
Sbjct: 162 LIEQLKDGGIMVIPVG--SYSQELIRVEKD-NGKIIKKKLGEVAFVPLIGK 209
Score = 33.1 bits (76), Expect = 0.023
Identities = 10/16 (62%), Positives = 14/16 (87%)
Query: 13 LIDQLRPGGRLIIPVG 28
LI+QL+ GG ++IPVG
Sbjct: 162 LIEQLKDGGIMVIPVG 177
>gnl|CDD|140001 PRK13944, PRK13944, protein-L-isoaspartate O-methyltransferase;
Provisional.
Length = 205
Score = 34.4 bits (79), Expect = 0.006
Identities = 18/48 (37%), Positives = 29/48 (60%), Gaps = 2/48 (4%)
Query: 55 LIDQLRPGGRLIIPVGPEGSAQNLEQIDKNLDGTITRTPLMQVVYVPL 102
L+ QL+ GG L+IPV EG Q L ++ K + + + + V++VPL
Sbjct: 159 LVRQLKDGGVLVIPV-EEGVGQVLYKVVKRGEK-VEKRAITYVLFVPL 204
Score = 31.3 bits (71), Expect = 0.093
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 11 SKLIDQLRPGGRLIIPVGPEGSAQSLEQIDKNLDGTITR 49
S L+ QL+ GG L+IPV EG Q L ++ K + R
Sbjct: 157 SALVRQLKDGGVLVIPV-EEGVGQVLYKVVKRGEKVEKR 194
>gnl|CDD|222177 pfam13499, EF_hand_5, EF-hand domain pair.
Length = 60
Score = 31.2 bits (71), Expect = 0.026
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 37 EQIDKNLDGTITRTPLMQLIDQLRPGGRLIIPVGPEGSAQNL-EQIDKNLDGTITR 91
+ +DK+ DG I L +L+ L G + E + +IDK+ DG I+
Sbjct: 1 KLLDKDGDGYIDVEELRKLLKAL---GLKLTDEEVEELIEADFNEIDKDGDGRISF 53
>gnl|CDD|236315 PRK08633, PRK08633, 2-acyl-glycerophospho-ethanolamine
acyltransferase; Validated.
Length = 1146
Score = 31.8 bits (73), Expect = 0.071
Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 13/54 (24%)
Query: 24 IIPVGPEGSAQSLEQIDKNLD----------GTITRTPLMQLIDQLRPGGRLII 67
+IP+ GS +SLE I K LD G ITR + + + G LI+
Sbjct: 489 VIPISSGGSKESLEFIRKALDDGEVVCIFPEGAITRNGQLN---EFKRGFELIV 539
>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 = 30.3 bits (69), Expect = 0.21
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 5/42 (11%)
Query: 11 SKLIDQLRPGGRLIIPVGPEGSAQS-LEQIDKNLDGTITRTP 51
S L+ + PGG +++PV +A S +EQ+ + G + RT
Sbjct: 262 SLLVLKSEPGGTVVVPV----TAPSVIEQLAERYGGRVIRTK 299
Score = 27.6 bits (62), Expect = 2.0
Identities = 11/42 (26%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 52 LMQLIDQLRPGGRLIIPVGPEGSAQNLEQIDKNLDGTITRTP 93
+ L+ + PGG +++PV + +EQ+ + G + RT
Sbjct: 261 VSLLVLKSEPGGTVVVPV---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 = 29.9 bits (68), Expect = 0.22
Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 3/36 (8%)
Query: 78 LEQIDKNLDGTI---TRTPLMQVVYVPLTDKQHQWP 110
LEQID L + PL+ + LT K+ P
Sbjct: 2 LEQIDVWLFLLLNGTLVHPLLDDLMPFLTGKKLSVP 37
>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 = 29.1 bits (66), Expect = 0.37
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 9 NQSKLIDQLRPGGRLIIPVGPE 30
+ +L +L PG ++P GPE
Sbjct: 9 RRRRLAAKLFPGSVAVLPAGPE 30
Score = 27.6 bits (62), Expect = 1.2
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 54 QLIDQLRPGGRLIIPVGPE 72
+L +L PG ++P GPE
Sbjct: 12 RLAAKLFPGSVAVLPAGPE 30
>gnl|CDD|238008 cd00051, EFh, EF-hand, calcium binding motif; A diverse
superfamily of calcium sensors and calcium signal
modulators; most examples in this alignment model have
2 active canonical EF hands. Ca2+ binding induces a
conformational change in the EF-hand motif, leading to
the activation or inactivation of target proteins.
EF-hands tend to occur in pairs or higher copy numbers.
Length = 63
Score = 27.5 bits (62), Expect = 0.50
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 6/53 (11%)
Query: 39 IDKNLDGTITRTPLMQLIDQLRPGGRLIIPVGPEGSAQNLEQIDKNLDGTITR 91
DK+ DGTI+ L + L + E + + ++DK+ DG I
Sbjct: 9 FDKDGDGTISADELKAALKSLGE------GLSEEEIDEMIREVDKDGDGKIDF 55
>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 = 28.9 bits (65), Expect = 0.63
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 7 WGNQSKLIDQLRPGGRLIIPV 27
W +DQL PGGRL++P+
Sbjct: 161 WDIPPAWLDQLAPGGRLVVPL 181
Score = 28.5 bits (64), Expect = 0.83
Identities = 9/14 (64%), Positives = 13/14 (92%)
Query: 56 IDQLRPGGRLIIPV 69
+DQL PGGRL++P+
Sbjct: 168 LDQLAPGGRLVVPL 181
>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 = 28.1 bits (63), Expect = 1.1
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 78 LEQIDKNLDGTITRTPLMQVVYVPLTDKQHQW 109
E +++ LD + + TPL VV VP + W
Sbjct: 119 AEHLERLLDASKSTTPLSFVVIVPEWKEPPAW 150
>gnl|CDD|234369 TIGR03837, efp_adjacent_2, conserved hypothetical protein, PP_1857
family. This model describes a conserved hypothetical
protein that typically is encoded next to the gene efp
for translation elongation factor P. The function is
unknown.
Length = 371
Score = 28.0 bits (63), Expect = 1.4
Identities = 12/61 (19%), Positives = 20/61 (32%), Gaps = 4/61 (6%)
Query: 51 PLMQLIDQLRPGGR---LIIPVGP-EGSAQNLEQIDKNLDGTITRTPLMQVVYVPLTDKQ 106
L L+D L G L++P G + G + R + V +P +
Sbjct: 194 ALPALLDALAQSGSPVHLLVPEGRALAAVAAWLGDALLAAGDVHRRGALTVAVLPFVPQD 253
Query: 107 H 107
Sbjct: 254 D 254
>gnl|CDD|233634 TIGR01914, cas_Csa4, CRISPR-associated protein Cas8a2/Csa4, subtype
I-A/APERN. CRISPR loci appear to be mobile elements
with a wide host range. This model represents a protein
that tends to be found near CRISPR repeats. The species
range for this species, so far, is exclusively archaeal.
It is found so far in only four different species, and
includes two tandem genes in Pyrococcus furiosus DSM
3638. This subfamily is found in a CRISPR/Cas locus we
designate APERN, so the family is designated Csa4, for
CRISPR/Cas Subtype Protein 4 [Mobile and
extrachromosomal element functions, Other].
Length = 354
Score = 27.9 bits (62), Expect = 1.4
Identities = 12/47 (25%), Positives = 20/47 (42%)
Query: 63 GRLIIPVGPEGSAQNLEQIDKNLDGTITRTPLMQVVYVPLTDKQHQW 109
G I V + + LE+I KNL+G + V + L ++
Sbjct: 98 GANINNVNADILPKTLEKIHKNLEGKRLSKKGLVTVPLTLMPLYGKY 144
>gnl|CDD|187797 cd09666, Cas8a2_I-A, CRISPR/Cas system-associated protein Csa8a2.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Zn-finger domain containing protein, distant homologs of
Cas8 proteins; signature gene for I-A subtype; also
known as Csa4 family.
Length = 352
Score = 27.9 bits (62), Expect = 1.4
Identities = 12/47 (25%), Positives = 20/47 (42%)
Query: 63 GRLIIPVGPEGSAQNLEQIDKNLDGTITRTPLMQVVYVPLTDKQHQW 109
G I V + + LE+I KNL+G + V + L ++
Sbjct: 98 GANINNVNADILPKTLEKIHKNLEGKRLSKKGLVTVPLTLMPLYGKY 144
>gnl|CDD|218092 pfam04452, Methyltrans_RNA, RNA methyltransferase. RNA
methyltransferases modify nucleotides during ribosomal
RNA maturation in a site-specific manner. The
Escherichia coli member is specific for U1498
methylation.
Length = 224
Score = 27.6 bits (62), Expect = 1.8
Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 9/61 (14%)
Query: 21 GRLIIPV--GPEGSAQSLEQIDKNL------DGTITRTPLMQLIDQLRPGGRLIIPVGPE 72
GR +P P + LE++D+ + + PL +L+ L GG++++ +GPE
Sbjct: 125 GRTRLPEVLPPISFKELLEELDEADKLILYEEEAKSLGPLSELLASL-KGGKVLLIIGPE 183
Query: 73 G 73
G
Sbjct: 184 G 184
>gnl|CDD|237568 PRK13943, PRK13943, protein-L-isoaspartate O-methyltransferase;
Provisional.
Length = 322
Score = 27.5 bits (61), Expect = 1.8
Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 4/36 (11%)
Query: 56 IDQLRPGGRLIIPVGPEGSAQN----LEQIDKNLDG 87
QL+ GGR+I+P+ + S + ++ D L G
Sbjct: 167 FTQLKEGGRVIVPINLKLSRRQPAFLFKKKDPYLVG 202
Score = 27.5 bits (61), Expect = 1.9
Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 4/36 (11%)
Query: 14 IDQLRPGGRLIIPVGPEGSAQS----LEQIDKNLDG 45
QL+ GGR+I+P+ + S + ++ D L G
Sbjct: 167 FTQLKEGGRVIVPINLKLSRRQPAFLFKKKDPYLVG 202
>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 = 26.8 bits (60), Expect = 2.1
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 9 NQSKLIDQLRPGGRLIIPVGPE 30
+++L+ L P I+P PE
Sbjct: 9 RRARLLALLPPNSAAILPGAPE 30
Score = 26.4 bits (59), Expect = 3.6
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 54 QLIDQLRPGGRLIIPVGPE 72
+L+ L P I+P PE
Sbjct: 12 RLLALLPPNSAAILPGAPE 30
>gnl|CDD|237898 PRK15068, PRK15068, tRNA mo(5)U34 methyltransferase; Provisional.
Length = 322
Score = 27.5 bits (62), Expect = 2.1
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 52 LMQLIDQLRPGGRLII 67
L QL DQL PGG L++
Sbjct: 209 LKQLKDQLVPGGELVL 224
>gnl|CDD|220563 pfam10093, DUF2331, Uncharacterized protein conserved in bacteria
(DUF2331). Members of this family of hypothetical
bacterial proteins have no known function.
Length = 373
Score = 27.6 bits (62), Expect = 2.1
Identities = 9/61 (14%), Positives = 20/61 (32%), Gaps = 4/61 (6%)
Query: 51 PLMQLIDQLRPGGR---LIIPVGPE-GSAQNLEQIDKNLDGTITRTPLMQVVYVPLTDKQ 106
L L+D + L++P G + ++ G + + V +P +
Sbjct: 195 ALPALLDAWADSDQPVHLLVPEGRALNALAAWLGVEALAAGAQHQRGNLTVHVLPFVPQD 254
Query: 107 H 107
Sbjct: 255 D 255
>gnl|CDD|236959 PRK11713, PRK11713, 16S ribosomal RNA methyltransferase RsmE;
Provisional.
Length = 234
Score = 26.8 bits (60), Expect = 3.2
Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 7/55 (12%)
Query: 21 GRLIIPV--GPEGSAQSLEQIDKNLDGTITRTPLMQLIDQLRPGGRLIIPVGPEG 73
GR IP P + LE++ + L+ GG++++ +GPEG
Sbjct: 139 GRTRIPEVRPPISLKEFLEELLPADLKAGLK-----LVLHPEAGGKVLLLIGPEG 188
>gnl|CDD|180140 PRK05575, cbiC, precorrin-8X methylmutase; Validated.
Length = 204
Score = 26.7 bits (59), Expect = 3.3
Identities = 12/34 (35%), Positives = 22/34 (64%), Gaps = 2/34 (5%)
Query: 52 LMQLIDQLRPGGRLII--PVGPEGSAQNLEQIDK 83
L +LI + + + II PVG G+A++ E+++K
Sbjct: 142 LKELIKEGKANPKFIIAVPVGFVGAAESKEELEK 175
>gnl|CDD|102471 PRK06628, PRK06628, lipid A biosynthesis lauroyl acyltransferase;
Provisional.
Length = 290
Score = 26.8 bits (59), Expect = 3.5
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 8/49 (16%)
Query: 11 SKLIDQLRPGGRL-IIPVGPEGSAQSLEQIDKNLDGTITRTPLMQLIDQ 58
+KL+++ R G +L +IP GPEGS + I + ++ L+DQ
Sbjct: 153 NKLVNESRAGDKLRLIPKGPEGSRALVRAIKE-------SESIVMLVDQ 194
>gnl|CDD|235100 PRK03031, rnpA, ribonuclease P; Reviewed.
Length = 122
Score = 26.1 bits (58), Expect = 4.0
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 49 RTPLMQLIDQLRPGGRLIIPVGPEGSAQNLEQ 80
R L QL+ ++ PG L+I V P + N EQ
Sbjct: 72 RAALRQLLPRIAPGWDLVIIVKPTAAECNYEQ 103
>gnl|CDD|220076 pfam08937, DUF1863, MTH538 TIR-like domain (DUF1863). This
domain adopts the flavodoxin fold, that is, five
parallel beta-strands and four helical segments. The
structure is a three-layer sandwich with alpha-1 and
alpha-4 on one side of the beta-sheet, and alpha-2 and
alpha-3 on the other side. Probable role in signal
transduction as a phosphorylation-independent
conformational switch protein. This domain is similar
to the TIR domain.
Length = 122
Score = 25.7 bits (57), Expect = 4.4
Identities = 17/73 (23%), Positives = 23/73 (31%), Gaps = 7/73 (9%)
Query: 5 SF-WGNQSKLIDQLRPGGRLIIPVGPEGSAQSLEQIDKNLDGTITRT---PLMQLI-DQL 59
SF + DQLR D N I R + + I DQ+
Sbjct: 6 SFHHEDDVWRYDQLR--NLGANEGINGAENIDFGFFDVNDWEPIKRPNDAYIKRWIRDQI 63
Query: 60 RPGGRLIIPVGPE 72
+ I+ VG E
Sbjct: 64 KGSSVTIVLVGEE 76
>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 = 4.5
Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 5/36 (13%)
Query: 80 QIDKNLDGT----ITRTPLMQVV-YVPLTDKQHQWP 110
++ KNL T + R L +++ Y P T+K H+ P
Sbjct: 111 EVGKNLATTPGKVVFRNDLFELIQYKPTTEKVHKRP 146
>gnl|CDD|237126 PRK12520, PRK12520, RNA polymerase sigma factor; Provisional.
Length = 191
Score = 26.2 bits (58), Expect = 4.7
Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 3/43 (6%)
Query: 12 KLIDQLRPGGRLIIPVGPEGSAQSLEQIDKNL---DGTITRTP 51
K+ID +R G R + + QS + + L DG P
Sbjct: 64 KIIDAIRSGRREVRLSLDDADEQSDDDLFDALFAADGHYREPP 106
>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 = 26.1 bits (58), Expect = 5.0
Identities = 9/27 (33%), Positives = 13/27 (48%), Gaps = 5/27 (18%)
Query: 6 FWGNQSKLIDQLRPGGRLIIPVGPEGS 32
W +L PGGR+ +P+ P G
Sbjct: 140 LWFLT-----RLAPGGRVFVPLAPAGD 161
Score = 25.8 bits (57), Expect = 6.9
Identities = 8/25 (32%), Positives = 14/25 (56%)
Query: 58 QLRPGGRLIIPVGPEGSAQNLEQID 82
+L PGGR+ +P+ P G ++
Sbjct: 145 RLAPGGRVFVPLAPAGDHPLSRRLV 169
>gnl|CDD|238935 cd01976, Nitrogenase_MoFe_alpha, Nitrogenase_MoFe_alpha_II:
Nitrogenase MoFe protein, beta subunit. A group of
proteins similar to the alpha subunit of the MoFe
protein of the molybdenum (Mo-) nitrogenase. The
nitrogenase enzyme catalyzes the ATP-dependent reduction
of dinitrogen to ammonia. The Mo-nitrogenase is the most
widespread and best characterized of these systems.
Mo-nitrogenase consists of the MoFe protein (component
1) and the Fe protein (component 2). MoFe is an
alpha2beta2 tetramer. Each alphabeta pair of MoFe
contains one P-cluster (at the alphabeta interface) and,
one molecule of iron molybdenum cofactor (FeMoco)
contained within the alpha subunit. The Fe protein
contains a single [4Fe-4S] cluster. Electrons are
transferred from the [4Fe-4S] cluster of the Fe protein
to the P-cluster of the MoFe and in turn to FeMoCo, the
site of substrate reduction.
Length = 421
Score = 26.1 bits (58), Expect = 5.2
Identities = 17/58 (29%), Positives = 25/58 (43%), Gaps = 13/58 (22%)
Query: 27 VGPEGSAQSLEQIDKNLDGTITR---------TPLMQ-LIDQLRP---GGRLIIPVGP 71
GP A+SL +I D IT P M+ +I + RP G +++ VG
Sbjct: 252 FGPTKIAESLRKIAAYFDDEITAKTEEVIAEYKPAMEAVIAKYRPRLEGKTVMLYVGG 309
>gnl|CDD|149213 pfam08003, Methyltransf_9, Protein of unknown function (DUF1698).
This family contains many hypothetical proteins. It also
includes two putative methyltransferase proteins.
Length = 315
Score = 26.2 bits (58), Expect = 5.4
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 52 LMQLIDQLRPGGRLII 67
L+QL DQL GG L++
Sbjct: 202 LLQLKDQLVKGGELVL 217
>gnl|CDD|234247 TIGR03533, L3_gln_methyl, protein-(glutamine-N5) methyltransferase,
ribosomal protein L3-specific. Members of this protein
family methylate ribosomal protein L3 on a glutamine
side chain. This family is related to HemK, a
protein-glutamine methyltranferase for peptide chain
release factors [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 284
Score = 25.9 bits (58), Expect = 5.4
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 44 DG-TITRTPLMQLIDQLRPGGRLIIPVGPEGSAQNLEQ 80
DG + R L + D L G L++ VG S + LE+
Sbjct: 225 DGLDLVRRILAEAADHLNENGVLVVEVG--NSMEALEE 260
>gnl|CDD|185053 PRK15098, PRK15098, beta-D-glucoside glucohydrolase; Provisional.
Length = 765
Score = 26.2 bits (58), Expect = 6.1
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 10/61 (16%)
Query: 14 IDQLRPGGRLIIPVGPEGSAQSL-EQIDKNLDG----TITRTPLMQLIDQLRPGGRLIIP 68
I QLR +I VGP+ +++ E I G T+TR + + DQ+ RL IP
Sbjct: 51 IGQLR-----LISVGPDNPKEAIREMIKAGQVGAIFNTVTRQDIRAMQDQVMQLSRLKIP 105
Query: 69 V 69
+
Sbjct: 106 L 106
>gnl|CDD|200397 TIGR04146, GGGPS_Afulg, phosphoglycerol
geranylgeranyltransferase. This enzyme, known also as
GGGP synthase and GGGPS, catalyzes the stereospecific
first step in the biosynthesis of the characteristic
membrane diether lipids of archaea. Interestingly, the
closest homologs outside this family are not the
functionally equivalent enzymes of other archaea, but
rather functionally distinct bacterial enzymes.
Length = 221
Score = 25.8 bits (57), Expect = 6.1
Identities = 10/35 (28%), Positives = 19/35 (54%), Gaps = 4/35 (11%)
Query: 43 LDGT--ITRTPLMQLIDQLRPGGRLII--PVGPEG 73
L GT +T+ + +L+D ++ G ++ P GP
Sbjct: 34 LSGTQNVTKENVAELLDMVKEYGLPLVVEPAGPSA 68
>gnl|CDD|213908 TIGR04295, B12_rSAM_oligo, B12-binding domain/radical SAM domain
protein, rhizo-twelve system. A variety of bacteria,
including multiple species of Bradyrhizobium,
Mesorhizobium, and Methylobacterium, have a typically
twelve-gene cassette (hence the designation
rhizo-twelve) for the biosynthesis of some unknown
oligosaccaride. This family is a B12-binding
domain/radical SAM domain protein found in roughly have
of these cassettes, but nowhere else.
Length = 422
Score = 25.9 bits (57), Expect = 6.3
Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 1/27 (3%)
Query: 49 RTPLMQLIDQLRPGGRLIIPVGPEGSA 75
R P M + LR G ++ VGP S
Sbjct: 88 RVP-MATLRALRETGGTLVAVGPHAST 113
>gnl|CDD|218172 pfam04609, MCR_C, Methyl-coenzyme M reductase operon protein C.
Methyl coenzyme M reductase (MCR) catalyzes the final
step in methanogenesis. MCR is composed of three
subunits, alpha (pfam02249), beta (pfam02241) and gamma
(pfam02240). Genes encoding the beta (mcrB) and gamma
(mcrG) subunits are separated by two open reading frames
coding for two proteins C and D. The function of
proteins C and D (this family) is unknown. This family
nowalso includes family MtrC_related,.
Length = 268
Score = 25.9 bits (57), Expect = 6.4
Identities = 14/49 (28%), Positives = 20/49 (40%), Gaps = 5/49 (10%)
Query: 71 PEGSAQNLEQIDKNLDGTITRTPLM--QVVYVPLTDKQHQWPGRSHEVC 117
PE +E+ K L GT PL ++ V + +H P H C
Sbjct: 45 PEEDLDIIEEKAKELLGTFAEAPLAGTEIAVVAPSLGRHHLP---HPAC 90
>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 = 25.8 bits (57), Expect = 7.5
Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 8/64 (12%)
Query: 36 LEQIDKNLDGTITRTP----LMQLIDQLRPGGRLIIPVGPEGSAQNLEQIDKNLDGTITR 91
L QI +G + P L +LID + G ++ V P+ S ++ E I + + +
Sbjct: 189 LTQIPIEEEG---KEPSPADLKRLIDLAKEKGVRVVFVQPQFSTKSAEAIAREIGAKVVT 245
Query: 92 T-PL 94
PL
Sbjct: 246 IDPL 249
>gnl|CDD|223225 COG0147, TrpE, Anthranilate/para-aminobenzoate synthases component
I [Amino acid transport and metabolism / Coenzyme
metabolism].
Length = 462
Score = 25.8 bits (57), Expect = 7.8
Identities = 9/23 (39%), Positives = 14/23 (60%), Gaps = 3/23 (13%)
Query: 45 GTITRTP---LMQLIDQLRPGGR 64
GT+T P M++I++L P R
Sbjct: 368 GTVTGAPKVRAMEIIEELEPSPR 390
>gnl|CDD|162284 TIGR01282, nifD, nitrogenase molybdenum-iron protein alpha chain.
Nitrogenase consists of alpha (NifD) and beta (NifK)
subunits of the molybdenum-iron protein and an
ATP-binding iron-sulfur protein (NifH). This model
describes a large clade of NifD proteins, but excludes a
lineage that contains putative NifD and NifD homologs
from species with vanadium-dependent nitrogenases
[Central intermediary metabolism, Nitrogen fixation].
Length = 466
Score = 25.8 bits (57), Expect = 8.1
Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 13/57 (22%)
Query: 27 VGPEGSAQSLEQIDKNLDGTITR---------TPLMQ-LIDQLRP---GGRLIIPVG 70
GP A+SL +I + D I P + +I + RP G +++ VG
Sbjct: 287 FGPTKIAESLRKIAEFFDDEIKEKAEEVIAKYQPAVDAVIAKYRPRLEGKTVMLYVG 343
>gnl|CDD|222415 pfam13847, Methyltransf_31, Methyltransferase domain. This family
appears to be have methyltransferase activity.
Length = 151
Score = 25.5 bits (56), Expect = 8.3
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 52 LMQLIDQLRPGGRLII--PVGPEGSAQNLEQIDKNLDGTI 89
L ++I L+PGG LI+ PV LE +++ G +
Sbjct: 95 LEEIIRVLKPGGVLIVSDPVLLSELPALLEDLERLYAGVL 134
>gnl|CDD|227265 COG4928, COG4928, Predicted P-loop ATPase [General function
prediction only].
Length = 646
Score = 25.9 bits (57), Expect = 8.8
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 4 RSFWGNQSKLIDQLRPGGRLIIPVGPEGSAQS 35
WGN I +L P G L++ G G+ +S
Sbjct: 35 SGGWGNGKSSICKLAPRGILVVASGEWGTGKS 66
>gnl|CDD|223677 COG0604, Qor, NADPH:quinone reductase and related Zn-dependent
oxidoreductases [Energy production and conversion /
General function prediction only].
Length = 326
Score = 25.4 bits (56), Expect = 9.0
Identities = 8/28 (28%), Positives = 11/28 (39%)
Query: 46 TITRTPLMQLIDQLRPGGRLIIPVGPEG 73
T+ + L PGGRL+ G
Sbjct: 218 TVGGDTFAASLAALAPGGRLVSIGALSG 245
>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 = 25.3 bits (56), Expect = 9.6
Identities = 26/123 (21%), Positives = 45/123 (36%), Gaps = 31/123 (25%)
Query: 4 RSFWGNQSKLID----QLRPGGRLI-------IPVGPEGSA-QSLEQIDKNLDGTITRTP 51
R+ I +L G L+ IP+ GSA QSLE I +N+DG +T
Sbjct: 144 RAALREPFPSIRSSLGELDGGLDLLPKPTSGRIPLLATGSAQQSLEWIARNMDGWMT--- 200
Query: 52 LMQLIDQLRPGGRLIIPVGPEGSAQNLEQIDKNLDGTITRTPLMQVVYVPLTDKQHQWPG 111
P PE +++ + + + P Q +++ L++ + P
Sbjct: 201 ---------------YPRPPETQRARIDEWREAVASGGFK-PFGQSMHLDLSEDPDEPPT 244
Query: 112 RSH 114
Sbjct: 245 PIR 247
>gnl|CDD|224157 COG1236, YSH1, Predicted exonuclease of the beta-lactamase fold
involved in RNA processing [Translation, ribosomal
structure and biogenesis].
Length = 427
Score = 25.5 bits (56), Expect = 9.8
Identities = 10/36 (27%), Positives = 15/36 (41%), Gaps = 2/36 (5%)
Query: 3 SRSFWGNQSK--LIDQLRPGGRLIIPVGPEGSAQSL 36
+R + + L GG ++IP G AQ L
Sbjct: 197 NRDEVERRFIESVKAALERGGTVLIPAFALGRAQEL 232
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
0.319 0.139 0.426
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: 6,395,274
Number of extensions: 556804
Number of successful extensions: 700
Number of sequences better than 10.0: 1
Number of HSP's gapped: 694
Number of HSP's successfully gapped: 70
Length of query: 126
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 41
Effective length of database: 7,167,512
Effective search space: 293867992
Effective search space used: 293867992
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 (21.7 bits)
S2: 53 (24.1 bits)