RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9602
(239 letters)
>gnl|CDD|188641 cd00954, NAL, N-Acetylneuraminic acid aldolase, also called
N-acetylneuraminate lyase (NAL). N-Acetylneuraminic
acid aldolase, also called N-acetylneuraminate lyase
(NAL), which catalyses the reversible aldol reaction of
N-acetyl-D-mannosamine and pyruvate to give
N-acetyl-D-neuraminic acid (D-sialic acid). It has a
widespread application as biocatalyst for the synthesis
of sialic acid and its derivatives. This enzyme has been
shown to be quite specific for pyruvate as the donor,
but flexible to a variety of D- and, to some extent,
L-hexoses and pentoses as acceptor substrates. NAL is
member of dihydrodipicolinate synthase family that
comprises several pyruvate-dependent class I aldolases.
Length = 288
Score = 99.7 bits (249), Expect = 3e-25
Identities = 40/106 (37%), Positives = 57/106 (53%), Gaps = 2/106 (1%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHA 192
VNG+TGEG ++ ERK E AK T++ +G +E ELAKHAE L A
Sbjct: 41 VNGSTGEGFLLSVEERKQIAEIVAEAAKGK-VTLIAHVGSLNLKESQELAKHAEELGYDA 99
Query: 193 VLCLPELFFTPASVEDLVDYLRDVGEAAPATPLFYYHIPMFTRVTL 238
+ + ++ S E++ DY R++ AA + P+ YHIP T V L
Sbjct: 100 ISAITPFYY-KFSFEEIKDYYREIIAAAASLPMIIYHIPALTGVNL 144
>gnl|CDD|223406 COG0329, DapA, Dihydrodipicolinate synthase/N-acetylneuraminate
lyase [Amino acid transport and metabolism / Cell
envelope biogenesis, outer membrane].
Length = 299
Score = 85.8 bits (213), Expect = 7e-20
Identities = 38/107 (35%), Positives = 54/107 (50%), Gaps = 3/107 (2%)
Query: 132 MVNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVH 191
+V GTTGE ++T ERK LEA + V+ +G E +ELAKHAE L
Sbjct: 43 VVLGTTGESPTLTLEERKEVLEAVVEAVGGRV-PVIAGVGSNSTAEAIELAKHAEKLGAD 101
Query: 192 AVLCLPELFFTPASVEDLVDYLRDVGEAAPATPLFYYHIPMFTRVTL 238
+L +P ++ S E L + + + EA P+ Y+IP T V L
Sbjct: 102 GILVVPP-YYNKPSQEGLYAHFKAIAEAVD-LPVILYNIPSRTGVDL 146
>gnl|CDD|188630 cd00408, DHDPS-like, Dihydrodipicolinate synthase family.
Dihydrodipicolinate synthase family. A member of the
class I aldolases, which use an active-site lysine which
stabilizes a reaction intermediate via Schiff base
formation, and have TIM beta/alpha barrel fold. The
dihydrodipicolinate synthase family comprises several
pyruvate-dependent class I aldolases that use the same
catalytic step to catalyze different reactions in
different pathways and includes such proteins as
N-acetylneuraminate lyase, MosA protein,
5-keto-4-deoxy-glucarate dehydratase,
trans-o-hydroxybenzylidenepyruvate hydratase-aldolase,
trans-2'-carboxybenzalpyruvate hydratase-aldolase, and
2-keto-3-deoxy- gluconate aldolase. The family is also
referred to as the N-acetylneuraminate lyase (NAL)
family.
Length = 281
Score = 84.1 bits (209), Expect = 2e-19
Identities = 36/106 (33%), Positives = 54/106 (50%), Gaps = 3/106 (2%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHA 192
V GTTGE ++T ERK +EA + V+ +G +E +ELA+HAE
Sbjct: 37 VLGTTGEAPTLTDEERKEVIEAVVEAVAG-RVPVIAGVGANSTREAIELARHAEEAGADG 95
Query: 193 VLCLPELFFTPASVEDLVDYLRDVGEAAPATPLFYYHIPMFTRVTL 238
VL +P ++ S E +V + + V + A P+ Y+IP T V L
Sbjct: 96 VLVVPP-YYNKPSQEGIVAHFKAVAD-ASDLPVILYNIPGRTGVDL 139
>gnl|CDD|188640 cd00953, KDG_aldolase, KDG (2-keto-3-deoxygluconate) aldolases
found in archaea. KDG (2-keto-3-deoxygluconate)
aldolases found in archaea. This subfamily of enzymes is
adapted for high thermostability and shows specificity
for non-phosphorylated substrates. The enzyme catalyses
the reversible aldol cleavage of 2-keto-3-dexoygluconate
to pyruvate and glyceraldehyde, the third step of a
modified non-phosphorylated Entner-Doudoroff pathway of
glucose oxidation. KDG aldolase shows no significant
sequence similarity to microbial
2-keto-3-deoxyphosphogluconate (KDPG) aldolases, and the
enzyme shows no activity with glyceraldehyde 3-phosphate
as substrate. The enzyme is a tetramer and a member of
the DHDPS family of Schiff-base-dependent class I
aldolases.
Length = 279
Score = 63.6 bits (155), Expect = 5e-12
Identities = 32/102 (31%), Positives = 51/102 (50%), Gaps = 7/102 (6%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHA 192
V GTTG G S++ E+ L+A ++ V+ Q+G +E +ELA+ A+S ++A
Sbjct: 39 VAGTTGLGPSLSFQEKLELLKA-YSDITDK---VIFQVGSLNLEESIELARAAKSFGIYA 94
Query: 193 VLCLPELFFTPASVEDLVDYLRDVGEAAPATPLFYYHIPMFT 234
+ LP +F E L+ Y D+ P F Y+ P T
Sbjct: 95 IASLPPYYFPGIPEEWLIKYFTDISS---PYPTFIYNYPKAT 133
>gnl|CDD|179749 PRK04147, PRK04147, N-acetylneuraminate lyase; Provisional.
Length = 293
Score = 58.9 bits (143), Expect = 2e-10
Identities = 38/106 (35%), Positives = 57/106 (53%), Gaps = 3/106 (2%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHA 192
V G+TGE ++T E+K LE EAK ++ Q+G E ELAK+A L A
Sbjct: 44 VGGSTGEAFLLSTEEKKQVLEIVAEEAKGK-VKLIAQVGSVNTAEAQELAKYATELGYDA 102
Query: 193 VLCLPELFFTPASVEDLVDYLRDVGEAAPATPLFYYHIPMFTRVTL 238
+ + F+ P S E++ DY R++ ++A P+ Y+IP T V L
Sbjct: 103 ISAVTP-FYYPFSFEEICDYYREIIDSA-DNPMIVYNIPALTGVNL 146
>gnl|CDD|188072 TIGR00683, nanA, N-acetylneuraminate lyase. N-acetylneuraminate
lyase is also known as N-acetylneuraminic acid aldolase,
sialic acid aldolase, or sialate lyase. It is an
intracellular enzyme. The structure of this
homotetrameric enzyme related to dihydrodipicolinate
synthase is known. In Clostridium tertium, the enzyme
appears to be in an operon with a secreted sialidase
that releases sialic acid from host
sialoglycoconjugates. In several E. coli strains,
however, this enzyme is responsible for
N-acetyl-D-neuraminic acid synthesis for capsule
production by condensing N-acetyl-D-mannosamine and
pyruvate [Cell envelope, Biosynthesis and degradation of
surface polysaccharides and lipopolysaccharides, Central
intermediary metabolism, Amino sugars].
Length = 290
Score = 55.0 bits (132), Expect = 5e-09
Identities = 31/116 (26%), Positives = 49/116 (42%), Gaps = 8/116 (6%)
Query: 129 IDQM------VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELA 182
ID+M V G+TGE ++T E+K EAK ++ Q+G +E VEL
Sbjct: 31 IDKMKVDGLYVGGSTGENFMLSTEEKKEIFRIAKDEAKDQ-IALIAQVGSVNLKEAVELG 89
Query: 183 KHAESLNVHAVLCLPELFFTPASVEDLVDYLRDVGEAAPATPLFYYHIPMFTRVTL 238
K+A L + + F+ S ++ Y + + Y IP T V +
Sbjct: 90 KYATELGYDCLSAVTP-FYYKFSFPEIKHYYDTIIAETGGLNMIVYSIPFLTGVNM 144
>gnl|CDD|201403 pfam00701, DHDPS, Dihydrodipicolinate synthetase family. This
family has a TIM barrel structure.
Length = 289
Score = 53.9 bits (130), Expect = 1e-08
Identities = 31/116 (26%), Positives = 54/116 (46%), Gaps = 8/116 (6%)
Query: 129 IDQMVN-----GTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAK 183
I++ + GTTGE +++T E + +E + EAK V+ G +E + LA+
Sbjct: 32 INKGADGLFVGGTTGESFTLSTEEHEQLIEITVDEAKGR-IPVIAGTGSNSTREAIHLAQ 90
Query: 184 HAESLNVHAVLCLPELFFTPASVEDLVDYLRDVGEAAPATPLFYYHIPMFTRVTLK 239
AE+ VL + ++ S E L + + + AA P+ Y++P T L
Sbjct: 91 LAEAAGADGVLAVTP-YYNKPSQEGLYQHFKAIA-AATDLPVILYNVPSRTGQDLT 144
>gnl|CDD|131366 TIGR02313, HpaI-NOT-DapA, 2,4-dihydroxyhept-2-ene-1,7-dioic acid
aldolase. This model represents a subset of the DapA
(dihydrodipicolinate synthase) family which has
apparently evolved a separate function. The product of
DapA, dihydrodipicolinate, results from the
non-enzymatic cyclization and dehydration of
6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is
different from the substrate of this reaction only in
the presence of the amino group. In the absence of this
amino group, and running the reaction in the opposite
direction, the reaction corresponds to the HpaI aldolase
component of the 4-hydroxyphenylacetic acid catabolism
pathway (see TIGR02311). At present, this variant of
DapA is found only in Oceanobacillus iheyensis HTE831
and Thermus thermophilus HB27. In both of these cases,
one or more other DapA genes can be found and the one
identified by this model is part of an operon for
4-hydroxyphenylacetic acid catabolism.
Length = 294
Score = 46.5 bits (110), Expect = 4e-06
Identities = 30/99 (30%), Positives = 45/99 (45%), Gaps = 2/99 (2%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHA 192
V GT+GE S+T ERK +E + + G E +EL K AE A
Sbjct: 40 VGGTSGEPGSLTLEERKQAIENAIDQIAGR-IPFAPGTGALNHDETLELTKFAEEAGADA 98
Query: 193 VLCLPELFFTPASVEDLVDYLRDVGEAAPATPLFYYHIP 231
+ + + P + E L D+ +V +A P P+ Y+IP
Sbjct: 99 AMVIVPYYNKP-NQEALYDHFAEVADAVPDFPIIIYNIP 136
>gnl|CDD|188637 cd00950, DHDPS, Dihydrodipicolinate synthase (DHDPS).
Dihydrodipicolinate synthase (DHDPS) is a key enzyme in
lysine biosynthesis. It catalyzes the aldol condensation
of L-aspartate-beta- semialdehyde and pyruvate to
dihydropicolinic acid via a Schiff base formation
between pyruvate and a lysine residue. The functional
enzyme is a homotetramer consisting of a dimer of
dimers. DHDPS is member of dihydrodipicolinate synthase
family that comprises several pyruvate-dependent class I
aldolases that use the same catalytic step to catalyze
different reactions in different pathways.
Length = 284
Score = 46.3 bits (111), Expect = 4e-06
Identities = 31/103 (30%), Positives = 46/103 (44%), Gaps = 11/103 (10%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHA 192
V GTTGE +++ E + +EA + EA V+ G E +EL K AE A
Sbjct: 40 VCGTTGESPTLSDEEHEAVIEA-VVEAVNGRVPVIAGTGSNNTAEAIELTKRAEKAGADA 98
Query: 193 VLCLPELFFTPA----SVEDLVDYLRDVGEAAPATPLFYYHIP 231
L + TP S E L + + + EA P+ Y++P
Sbjct: 99 ALVV-----TPYYNKPSQEGLYAHFKAIAEATDL-PVILYNVP 135
>gnl|CDD|129757 TIGR00674, dapA, dihydrodipicolinate synthase. Dihydrodipicolinate
synthase is a homotetrameric enzyme of lysine
biosynthesis. E. coli has several paralogs closely
related to dihydrodipicoline synthase (DapA), as well as
the more distant N-acetylneuraminate lyase. In
Pyrococcus horikoshii, the bidirectional best hit with
E. coli is to an uncharacterized paralog of DapA, not
DapA itself, and it is omitted from the seed. The
putative members from the Chlamydias (pathogens with a
parasitic metabolism) are easily the most divergent
members of the multiple alignment [Amino acid
biosynthesis, Aspartate family].
Length = 285
Score = 45.8 bits (109), Expect = 5e-06
Identities = 26/105 (24%), Positives = 45/105 (42%), Gaps = 3/105 (2%)
Query: 135 GTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHAVL 194
GTTGE +++ E K +E + V+ G +E + L K AE + L
Sbjct: 40 GTTGESPTLSHEEHKKVIEFVVDLVNGRV-PVIAGTGSNATEEAISLTKFAEDVGADGFL 98
Query: 195 CLPELFFTPASVEDLVDYLRDVGEAAPATPLFYYHIPMFTRVTLK 239
+ + P + E L + + + E P+ Y++P T V+L
Sbjct: 99 VVTPYYNKP-TQEGLYQHFKAIAEEV-DLPIILYNVPSRTGVSLY 141
>gnl|CDD|235107 PRK03170, PRK03170, dihydrodipicolinate synthase; Provisional.
Length = 292
Score = 42.8 bits (102), Expect = 6e-05
Identities = 18/63 (28%), Positives = 25/63 (39%), Gaps = 1/63 (1%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHA 192
V GTTGE ++T E + + A + V+ G E +EL K AE
Sbjct: 41 VVGTTGESPTLTHEEHEELIRAVVEAVN-GRVPVIAGTGSNSTAEAIELTKFAEKAGADG 99
Query: 193 VLC 195
L
Sbjct: 100 ALV 102
>gnl|CDD|188639 cd00952, CHBPH_aldolase, Trans-o-hydroxybenzylidenepyruvate
hydratase-aldolase (HBPHA) and
trans-2'-carboxybenzalpyruvate hydratase-aldolase
(CBPHA). Trans-o-hydroxybenzylidenepyruvate
hydratase-aldolase (HBPHA) and
trans-2'-carboxybenzalpyruvate hydratase-aldolase
(CBPHA). HBPHA catalyzes HBP to salicyaldehyde and
pyruvate. This reaction is part of the degradative
pathways for naphthalene and naphthalenesulfonates by
bacteria. CBPHA is homologous to HBPHA and catalyzes the
cleavage of CBP to 2-carboxylbenzaldehyde and pyruvate
during the degradation of phenanthrene. They are member
of the DHDPS family of Schiff-base-dependent class I
aldolases.
Length = 309
Score = 35.1 bits (81), Expect = 0.025
Identities = 26/102 (25%), Positives = 41/102 (40%), Gaps = 6/102 (5%)
Query: 132 MVNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCF--QEVVELAKHAESLN 189
+ GT GE ++T E K A + E G V V +G T ++ + + L
Sbjct: 47 LTMGTFGECATLTWEE-KQAFVATVVET-VAG-RVPVFVGATTLNTRDTIARTRALLDLG 103
Query: 190 VHAVLCLPELFFTPASVEDLVDYLRDVGEAAPATPLFYYHIP 231
+ ++ P V+ V + RDV EA P + Y P
Sbjct: 104 ADGTMLGRPMW-LPLDVDTAVQFYRDVAEAVPEMAIAIYANP 144
>gnl|CDD|132293 TIGR03249, KdgD, 5-dehydro-4-deoxyglucarate dehydratase.
5-dehydro-4-deoxyglucarate dehydratase not only
catalyzes the dehydration of the substrate (diol to
ketone + water), but causes the decarboxylation of the
intermediate product to yield 2-oxoglutarate
semialdehyde (2,5-dioxopentanoate). The gene for the
enzyme is usually observed in the vicinity of
transporters and dehydratases handling D-galactarate and
D-gluconate as well as aldehyde dehydrogenases which
convert the product to alpha-ketoglutarate.
Length = 296
Score = 33.9 bits (78), Expect = 0.046
Identities = 25/87 (28%), Positives = 39/87 (44%), Gaps = 3/87 (3%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGTCFQEVVELAKHAESLNVHA 192
G TGE S+T AE + +E ++ AK V +GG + +E+A+ AE
Sbjct: 45 AAGGTGEFFSLTPAEYEQVVEIAVSTAKG-KVPVYTGVGGN-TSDAIEIARLAEKAGADG 102
Query: 193 VLCLPELFFTPASVEDLVDYLRDVGEA 219
L LP + E L ++ V E+
Sbjct: 103 YLLLPP-YLINGEQEGLYAHVEAVCES 128
>gnl|CDD|221028 pfam11208, DUF2992, Protein of unknown function (DUF2992). This
bacterial family of proteins has no known function.
However, the cis-regulatory yjdF motif, just upstream
from the gene encoding the proteins for this family, is
a small non-coding RNA, Rfam:RF01764. The yjdF motif is
found in many Firmicutes, including Bacillus subtilis.
In most cases, it resides in potential 5' UTRs of
homologues of the yjdF gene whose function is unknown.
However, in Streptococcus thermophilus, a yjdF RNA motif
is associated with an operon whose protein products
synthesise nicotinamide adenine dinucleotide (NAD+).
Also, the S. thermophilus yjdF RNA lacks typical yjdF
motif consensus features downstream of and including the
P4 stem. Thus, if yjdF RNAs are riboswitch aptamers, the
S. thermophilus RNAs might sense a distinct compound
that structurally resembles the ligand bound by other
yjdF RNAs. On the ohter hand, perhaps these RNAs have an
alternative solution forming a similar binding site, as
is observed with some SAM riboswitches.
Length = 132
Score = 31.5 bits (72), Expect = 0.14
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 4/63 (6%)
Query: 19 RQNSAEEEAEKAAQ-TIAQRARRGGHDRSKRFTQTRKVDNHHNSRPAASQIRRKKKRKRR 77
Q A +E +K T AQ+A + H+R+K Q +K + + R+ K++K++
Sbjct: 70 LQRQAAKEVKKPGISTKAQQALKLEHERNK---QEKKKRSKEKKEEEKERKRQLKQQKKK 126
Query: 78 RKR 80
K
Sbjct: 127 AKH 129
>gnl|CDD|237964 PRK15426, PRK15426, putative diguanylate cyclase YedQ; Provisional.
Length = 570
Score = 32.3 bits (74), Expect = 0.24
Identities = 19/79 (24%), Positives = 31/79 (39%), Gaps = 15/79 (18%)
Query: 80 RLRNAHGEVVMIDP---SDLPKRAKWTIIITAGLLLLTCMLLVGITLRMAPIIDQMVNGT 136
RL + G +V + +I +T L T MLL I+ +I +MV+
Sbjct: 333 RLDHFDGVLVRVHTLREGVRGDFGSISIALTLLWALFTAMLL--ISWY---VIRRMVS-- 385
Query: 137 TGEGVSMTTAERKLNLEAW 155
+M + L +AW
Sbjct: 386 -----NMFVLQSSLQWQAW 399
>gnl|CDD|163674 cd03174, DRE_TIM_metallolyase, DRE-TIM metallolyase superfamily.
The DRE-TIM metallolyase superfamily includes
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 265
Score = 31.3 bits (72), Expect = 0.33
Identities = 27/91 (29%), Positives = 35/91 (38%), Gaps = 13/91 (14%)
Query: 143 MTTAERKLNLEAWMTEAKTHGFTVMVQI-----GGTCFQEVVELAKHAESLNVHAVLCLP 197
+ E N E + AK G V + T + V+E+AK E + L
Sbjct: 108 KSREEDLENAEEAIEAAKEAGLEVEGSLEDAFGCKTDPEYVLEVAKALEEAGAD-EISLK 166
Query: 198 ---ELFFTPASVEDLVDYLRDVGEAAPATPL 225
L TP V +LV LR EA P PL
Sbjct: 167 DTVGLA-TPEEVAELVKALR---EALPDVPL 193
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 30.0 bits (68), Expect = 0.99
Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 195 CLPELFFTPASVEDLVDYLRDVGEA 219
CLP LFF + ++LVD L + EA
Sbjct: 176 CLP-LFFRAPTDDELVDVLESIAEA 199
>gnl|CDD|180317 PRK05942, PRK05942, aspartate aminotransferase; Provisional.
Length = 394
Score = 29.3 bits (66), Expect = 1.6
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 175 FQEVVELAKHAESLNVHAVLCLPELFF 201
F+E+V A+ E + VH LC EL F
Sbjct: 192 FEEIVAFARKYEIMLVHD-LCYAELAF 217
>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho;
Provisional.
Length = 672
Score = 29.5 bits (67), Expect = 1.7
Identities = 11/75 (14%), Positives = 21/75 (28%), Gaps = 1/75 (1%)
Query: 12 TTGGGSGRQNSAEEEAEKAAQTIAQRARRGGHDRSKRFTQTRKVDNHHNSRPAASQIRRK 71
G + + + +R R D + + D + R +
Sbjct: 206 RDRREQGDRREERGRRDGGDRRGRRRRRDRR-DARGDDNREDRGDRDGDDGEGRGGRRGR 264
Query: 72 KKRKRRRKRLRNAHG 86
+ R R R+ R G
Sbjct: 265 RFRDRDRRGRRGGDG 279
>gnl|CDD|216747 pfam01865, PhoU_div, Protein of unknown function DUF47. This
family includes prokaryotic proteins of unknown
function, as well as a protein annotated as the pit
accessory protein from Sinorhizobium meliloti. However,
the function of this protein is also unknown (Pit stands
for Phosphate transport). It is probably distantly
related to pfam01895 (personal obs:Yeats C).
Length = 214
Score = 28.8 bits (65), Expect = 1.8
Identities = 11/45 (24%), Positives = 20/45 (44%)
Query: 176 QEVVELAKHAESLNVHAVLCLPELFFTPASVEDLVDYLRDVGEAA 220
+E+ EL + A+ + L L F P DL++ + + A
Sbjct: 47 KEISELEREADEIKREIRLNLTSGAFLPVDRGDLLELIESQDKIA 91
>gnl|CDD|178038 PLN02417, PLN02417, dihydrodipicolinate synthase.
Length = 280
Score = 28.8 bits (65), Expect = 2.1
Identities = 23/102 (22%), Positives = 40/102 (39%), Gaps = 11/102 (10%)
Query: 133 VNGTTGEGVSMTTAERKLNLEAWMTEAKTHGFTVMVQIGGT---CFQEVVELAKHAESLN 189
V GTTGEG M+ E + + + + IG T +E + + ++
Sbjct: 41 VGGTTGEGQLMSWDEHIMLIGHTVNCFG----GKIKVIGNTGSNSTREAIHATEQGFAVG 96
Query: 190 VHAVLCLPELFFTPASVEDLVDYLRDVGEAAPATPLFYYHIP 231
+HA L + + S E L+ + V P Y++P
Sbjct: 97 MHAALHINPYYGKT-SQEGLIKHFETV---LDMGPTIIYNVP 134
>gnl|CDD|223727 COG0654, UbiH, 2-polyprenyl-6-methoxyphenol hydroxylase and related
FAD-dependent oxidoreductases [Coenzyme metabolism /
Energy production and conversion].
Length = 387
Score = 28.9 bits (65), Expect = 2.1
Identities = 15/71 (21%), Positives = 25/71 (35%), Gaps = 2/71 (2%)
Query: 15 GGSGRQNSAEEEAEKAAQTIAQRARRGGHDRS-KRFTQTRKVDNHHNSRPAASQIRRKKK 73
G G N A E+A A+ +A R G + + R+ + + + R
Sbjct: 294 AGQGA-NLALEDAAALAEALAAAPRPGADAAALAAYEARRRPRAEAIQKLSRALGRLFSA 352
Query: 74 RKRRRKRLRNA 84
+ LRN
Sbjct: 353 DGPFARFLRNL 363
>gnl|CDD|176954 CHL00011, ndhD, NADH dehydrogenase subunit 4.
Length = 498
Score = 28.8 bits (65), Expect = 2.6
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 114 TCMLLVGITLRM 125
TCMLL GI L+M
Sbjct: 245 TCMLLAGILLKM 256
>gnl|CDD|217970 pfam04220, YihI, Der GTPase activator (YihI). YihI activates the
GTPase activity of Der, a 50S ribosomal subunit
stability factor. The stimulation is specific to Der as
YihI does not stimulate the GTPase activity of Era or
ObgE. The interaction of YihI with Der requires only
the C-terminal 78 amino acids of YihI. A yihI deletion
mutant is viable and shows a shorter lag period, but
the same post-lag growth rate as a wild-type strain.
yihI is expressed during the lag period. Overexpression
of yihI inhibits cell growth and biogenesis of the 50S
ribosomal subunit. YihI is an unusual, highly
hydrophilic protein with an uneven distribution of
charged residues, resulting in an N-terminal region
with high pI and a C-terminal region with low pI.
Length = 169
Score = 28.1 bits (63), Expect = 3.1
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 9/53 (16%)
Query: 39 RRGGHDRSKRFTQTRKVDNHHNSRPAASQIRRKKKRKRRRKRL----RNAHGE 87
R+ G + K + +K R Q R++KRK++RK L R+
Sbjct: 1 RKSGKNGPKLAPKGKKKT-----RYELDQEARERKRKKKRKGLKSGSRHNEES 48
>gnl|CDD|236916 PRK11492, hyfE, hydrogenase 4 membrane subunit; Provisional.
Length = 216
Score = 28.4 bits (64), Expect = 3.2
Identities = 10/54 (18%), Positives = 23/54 (42%), Gaps = 7/54 (12%)
Query: 79 KRLRNAHGEVVMIDPSDLPKRAKWTIIITAGLLLLTCMLLVGITLRMAPIIDQM 132
++L + E + P +I++ A ++LL ++ + L MA +
Sbjct: 81 RKLGDNIEEEPVFGP-------AMSILLAALIVLLCAFVVQPVKLPMALGLKPA 127
>gnl|CDD|224490 COG1574, COG1574, Predicted metal-dependent hydrolase with the
TIM-barrel fold [General function prediction only].
Length = 535
Score = 28.5 bits (64), Expect = 3.7
Identities = 10/35 (28%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 72 KKRKRRRKRLRNAHGEVVMIDPSDLPKRAKWTIII 106
KK + R R H E ++ P + + AK +I
Sbjct: 359 KKNGLKGLRHRIEHAE--LVSPDQIERFAKLGVIA 391
>gnl|CDD|149438 pfam08374, Protocadherin, Protocadherin. The structure of
protocadherins is similar to that of classic cadherins
(pfam00028), but particularly on the cytoplasmic domains
they also have some unique features. They are expressed
in a variety of organisms and are found in high
concentrations in the brain where they seem to be
localised mainly at cell-cell contact sites. Their
expression seems to be developmentally regulated.
Length = 223
Score = 27.9 bits (62), Expect = 3.7
Identities = 11/57 (19%), Positives = 23/57 (40%)
Query: 38 ARRGGHDRSKRFTQTRKVDNHHNSRPAASQIRRKKKRKRRRKRLRNAHGEVVMIDPS 94
R K+ Q K + P ++KKK+ +++K ++ V ++ S
Sbjct: 60 VRYCRQAERKKGYQAGKKETEDWFSPNQENKQKKKKKDKKKKSPKSLLLNFVTVEES 116
>gnl|CDD|235141 PRK03620, PRK03620, 5-dehydro-4-deoxyglucarate dehydratase;
Provisional.
Length = 303
Score = 28.2 bits (64), Expect = 4.1
Identities = 12/41 (29%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 179 VELAKHAESLNVHAVLCLPELFFTPASVEDLVDYLRDVGEA 219
+E A+ AE +L LP + T A E L ++ V ++
Sbjct: 91 IEYAQAAERAGADGILLLPP-YLTEAPQEGLAAHVEAVCKS 130
>gnl|CDD|143594 cd07570, GAT_Gln-NAD-synth, Glutamine aminotransferase (GAT,
glutaminase) domain of glutamine-dependent NAD
synthetases (class 7 and 8 nitrilases).
Glutamine-dependent NAD synthetases are bifunctional
enzymes, which have an N-terminal GAT domain and a
C-terminal NAD+ synthetase domain. The GAT domain is a
glutaminase (EC 3.5.1.2) which hydrolyses L-glutamine to
L-glutamate and ammonia. The ammonia is used by the NAD+
synthetase domain in the ATP-dependent amidation of
nicotinic acid adenine dinucleotide. Glutamine
aminotransferases are categorized depending on their
active site residues into different unrelated classes.
This class of GAT domain belongs to a larger nitrilase
superfamily comprised of nitrile- or amide-hydrolyzing
enzymes and amide-condensing enzymes, which depend on a
Glu-Lys-Cys catalytic triad. This superfamily has been
classified in the literature based on global and
structure based sequence analysis into thirteen
different enzyme classes (referred to as 1-13), this
subgroup corresponds to classes 7 and 8. Members of this
superfamily generally form homomeric complexes, the
basic building block of which is a homodimer.
Mycobacterium tuberculosis glutamine-dependent NAD+
synthetase forms a homooctamer.
Length = 261
Score = 27.8 bits (63), Expect = 4.1
Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 176 QEVVELAKHAESLNVHAVLCLPELFFTPASVEDLV---DYLRDVGEA 219
++++E + A++ ++ PEL T EDL+ D+L EA
Sbjct: 19 EKILEAIREAKAQGAD-LVVFPELSLTGYPPEDLLLRPDFLEAAEEA 64
>gnl|CDD|218269 pfam04794, YdjC, YdjC-like protein. Family of YdjC-like proteins.
This region is possibly involved in the the cleavage of
cellobiose-phosphate.
Length = 261
Score = 28.0 bits (63), Expect = 4.2
Identities = 15/49 (30%), Positives = 19/49 (38%), Gaps = 4/49 (8%)
Query: 165 TVMVQIGGTCFQEVVELAKHAESLNV--HAVLCLPELFFTPASVEDLVD 211
++MV F+ LAK L V H L + P V LVD
Sbjct: 33 SLMV--NMPAFEHAAALAKRNPDLGVGLHLTLTAGKPLLPPTEVPSLVD 79
>gnl|CDD|221821 pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 38-associated
hydrophilic C-term. This domain is a hydrophilic
region found at the C-terminus of plant and metazoan
pre-mRNA-splicing factor 38 proteins. The function is
not known.
Length = 97
Score = 26.7 bits (59), Expect = 4.6
Identities = 15/64 (23%), Positives = 24/64 (37%), Gaps = 6/64 (9%)
Query: 17 SGRQNSAEEEAEKAAQTIAQRARRGGHDRSKRFTQTRKVDNHHNSRPAASQIRRKKKRKR 76
+ +EE + A+ R RR R++R + R + RR + R R
Sbjct: 15 ESEEEEDDEEIRRKAERDVDRGRRSPRRRTRR---RSRRRKRSRKR---RRRRRDRDRAR 68
Query: 77 RRKR 80
R R
Sbjct: 69 YRDR 72
>gnl|CDD|222466 pfam13945, NST1, Splicing factor, salt tolerance regulator. NST1
is a family of proteins that seem to be involved,
directly or indirectly, in the salt sensitivity of some
cellular functions in yeast. These proteins also
interact with the splicing factor Msl1p.
Length = 189
Score = 27.6 bits (61), Expect = 4.6
Identities = 10/46 (21%), Positives = 20/46 (43%)
Query: 41 GGHDRSKRFTQTRKVDNHHNSRPAASQIRRKKKRKRRRKRLRNAHG 86
H ++ +Q + + +S + KKK+K+R K +H
Sbjct: 4 ETHKYAQPHSQQNTDELNTVIHNDSSSSKSKKKKKKRSKATSPSHN 49
>gnl|CDD|234707 PRK00270, rpsU, 30S ribosomal protein S21; Reviewed.
Length = 64
Score = 26.0 bits (58), Expect = 5.0
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 7/42 (16%)
Query: 44 DRSKRFTQTRKVDNHHNSRPAASQIRRKKK---RKRRRKRLR 82
+++ + R+ +P S+ R++KK RKRRRK+L
Sbjct: 24 EKAGILRELRR--REFYEKP--SEKRKRKKAAARKRRRKKLA 61
>gnl|CDD|111727 pfam02873, MurB_C, UDP-N-acetylenolpyruvoylglucosamine reductase,
C-terminal domain. Members of this family are
UDP-N-acetylenolpyruvoylglucosamine reductase enzymes
EC:1.1.1.158. This enzyme is involved in the
biosynthesis of peptidoglycan.
Length = 103
Score = 26.5 bits (59), Expect = 5.0
Identities = 6/27 (22%), Positives = 14/27 (51%), Gaps = 1/27 (3%)
Query: 159 AKTHGFTVMVQIGGTCFQEVVELAKHA 185
++ H ++ G ++VV+L +H
Sbjct: 58 SEKHA-NFIINTGNATAEDVVDLIRHV 83
>gnl|CDD|224310 COG1392, COG1392, Phosphate transport regulator (distant homolog of
PhoU) [Inorganic ion transport and metabolism].
Length = 217
Score = 27.6 bits (62), Expect = 5.2
Identities = 10/38 (26%), Positives = 20/38 (52%)
Query: 176 QEVVELAKHAESLNVHAVLCLPELFFTPASVEDLVDYL 213
+E+ +L A+ + L L + FF P ED+++ +
Sbjct: 49 KEIKDLEHEADEIKREIRLELYKGFFLPFDREDILELI 86
>gnl|CDD|215581 PLN03109, PLN03109, ETHYLENE-INSENSITIVE3-like3 protein;
Provisional.
Length = 599
Score = 27.9 bits (62), Expect = 5.6
Identities = 12/61 (19%), Positives = 22/61 (36%), Gaps = 4/61 (6%)
Query: 44 DRSKRFTQTRKVDNHHNSRPAASQIRRKKKRKRRRKRLR----NAHGEVVMIDPSDLPKR 99
+ + + + ++ + + KK RKR+R R R EV P +
Sbjct: 343 NLQPVAQEPERARDDAPNQVVPDKEKTKKPRKRKRPRGRSTVAEQEVEVTQEHPPAESRN 402
Query: 100 A 100
A
Sbjct: 403 A 403
>gnl|CDD|214451 MTH00182, COX1, cytochrome c oxidase subunit I; Provisional.
Length = 525
Score = 27.9 bits (62), Expect = 5.8
Identities = 13/23 (56%), Positives = 18/23 (78%), Gaps = 1/23 (4%)
Query: 102 WTIIITAGLLLLTCMLLVG-ITL 123
W+I+ITA LLLL+ +L G IT+
Sbjct: 188 WSILITAFLLLLSLPVLAGAITM 210
>gnl|CDD|226657 COG4194, COG4194, Predicted membrane protein [General function
prediction only].
Length = 350
Score = 27.4 bits (61), Expect = 6.3
Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 1/47 (2%)
Query: 76 RRRKRLRNAHGEVVMIDPSDLPKRAKWTIIITAGLLLLTCMLLVGIT 122
+K A +V+ID S L K L ++ L++GI
Sbjct: 97 GWKKEWLIAKVRIVVIDTS-LGKLKFPWTWFLVILGIIIFTLVIGIV 142
>gnl|CDD|189038 cd09868, PIN_XPG, PIN domain of Xeroderma pigmentosum
complementation group G (XPG) nuclease, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. The Xeroderma pigmentosum
complementation group G (XPG) nuclease plays a central
role in nucleotide excision repair (NER) in cleaving DNA
bubble structures or loops. XPG is a member of the
structure-specific, 5' nuclease family that catalyzes
hydrolysis of DNA duplex-containing nucleic acid
structures during DNA replication, repair, and
recombination. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region (I
domain). In XPG PIN domains, this arch region can be
quite variable and extensive (400 - 800 residues) in
length and is required for NER activity and for
efficient processing of bubble substrates. Inserted
within the PIN domain of these 5' nucleases is a H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA binding. Nucleases within this group
also have a carboxylate-rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+).
Length = 249
Score = 27.2 bits (61), Expect = 7.5
Identities = 11/53 (20%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 32 QTIAQRARRGGHDRSKRFTQTRKVDNHHNSRPAASQIRRKKKRKRRRKRLRNA 84
+T+A+R ++ R K +K + ASQ+++ + +++++ R+A
Sbjct: 86 RTLAKRRQQ----REKAEINAKKTAE----KLLASQLKKSAVKSQQQQQERDA 130
>gnl|CDD|221272 pfam11857, DUF3377, Domain of unknown function (DUF3377). This
domain is functionally uncharacterized. This domain is
found in eukaryotes. This presumed domain is about 70
amino acids in length.
Length = 74
Score = 25.7 bits (57), Expect = 7.7
Identities = 11/48 (22%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 76 RRRKRLRNAHGEVVMIDPSDLPKRAKWTIIITAGLLLLTCMLLVGITL 123
RR R R ++++ ++P + L+LL C+L++ T+
Sbjct: 5 ERRDRGRPEDDVDIVVEVDEVPGTVN-AAAVVIPLVLLLCILVLLYTI 51
>gnl|CDD|225365 COG2807, CynX, Cyanate permease [Inorganic ion transport and
metabolism].
Length = 395
Score = 27.2 bits (61), Expect = 8.7
Identities = 12/42 (28%), Positives = 22/42 (52%), Gaps = 8/42 (19%)
Query: 110 LLLLTCMLLVGITLR-----MAPIIDQMVNGTTGEGVSMTTA 146
LLLL ++L+ LR + P++D++ G+S + A
Sbjct: 11 LLLLAGIVLIAFNLRPAITSVGPLLDEIRQDL---GLSFSVA 49
>gnl|CDD|214431 MTH00142, COX1, cytochrome c oxidase subunit I; Provisional.
Length = 511
Score = 27.4 bits (61), Expect = 8.8
Identities = 12/23 (52%), Positives = 17/23 (73%), Gaps = 1/23 (4%)
Query: 102 WTIIITAGLLLLTCMLLVG-ITL 123
W++ ITA LLLL+ +L G IT+
Sbjct: 184 WSVKITAILLLLSLPVLAGAITM 206
>gnl|CDD|221516 pfam12299, DUF3627, Protein of unknown function (DUF3627). This
domain family is found in bacteria and viruses, and is
approximately 90 amino acids in length. The family is
found in association with pfam02498.
Length = 89
Score = 25.7 bits (57), Expect = 9.3
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 68 IRRKKKRKRRRKRLRNAHGEVVM 90
IR +K+ RRRKR E++
Sbjct: 39 IRGQKRYVRRRKRKLKNDMEIIY 61
>gnl|CDD|233727 TIGR02101, IpaC_SipC, type III secretion target, IpaC/SipC family.
This model represents a family of proteins associated
with bacterial type III secretion systems, which are
injection machines for virulence factors into host cell
cytoplasm. Characterized members of this protein family
are known to be secreted and are described as invasins,
including IpaC from Shigella flexneri and SipC from
Salmonella typhimurium (GB:AAA75170.1). Members may be
referred to as invasins, pathogenicity island effectors,
and cell invasion proteins [Cellular processes,
Pathogenesis].
Length = 317
Score = 26.8 bits (59), Expect = 9.8
Identities = 10/40 (25%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 15 GGSGRQNSAEEEAEKAAQTIAQR-ARRGGHDRSKRFTQTR 53
G SG+ + +EEAE+ + R A ++ + +T+
Sbjct: 253 GASGQYAATQEEAEQQISQSSSRTASTASNETREASRKTK 292
>gnl|CDD|238833 cd01663, Cyt_c_Oxidase_I, Cytochrome C oxidase subunit I.
Cytochrome c oxidase (CcO), the terminal oxidase in the
respiratory chains of eukaryotes and most bacteria, is a
multi-chain transmembrane protein located in the inner
membrane of mitochondria and the cell membrane of
prokaryotes. It catalyzes the reduction of O2 and
simultaneously pumps protons across the membrane. The
number of subunits varies from three to five in bacteria
and up to 13 in mammalian mitochondria. Only subunits I
and II are essential for function, but subunit III,
which is also conserved, may play a role in assembly or
oxygen delivery to the active site. Subunits I, II, and
III of mammalian CcO are encoded within the
mitochondrial genome and the remaining 10 subunits are
encoded within the nuclear genome. Subunit I contains a
heme-copper binuclear center (the active site where O2
is reduced to water) formed by a high-spin heme (heme
a3) and a copper ion (CuB). It also contains a low-spin
heme (heme a), believed to participate in the transfer
of electrons to the binuclear center. For every
reduction of an O2 molecule, eight protons are taken
from the inside aqueous compartment and four electrons
are taken from cytochrome c on the opposite side of the
membrane. The four electrons and four of the protons
are used in the reduction of O2; the four remaining
protons are pumped across the membrane. This charge
separation of four charges contributes to the
electrochemical gradient used for ATP synthesis. Two
proton channels, the D-pathway and K-pathway, leading to
the binuclear center have been identified in subunit I.
A well-defined pathway for the transfer of pumped
protons beyond the binuclear center has not been
identified. Electrons are transferred from cytochrome c
(the electron donor) to heme a via the CuA binuclear
site in subunit II, and directly from heme a to the
binuclear center.
Length = 488
Score = 27.1 bits (61), Expect = 9.8
Identities = 12/23 (52%), Positives = 18/23 (78%), Gaps = 1/23 (4%)
Query: 102 WTIIITAGLLLLTCMLLVG-ITL 123
W+++ITA LLLL+ +L G IT+
Sbjct: 177 WSVLITAFLLLLSLPVLAGAITM 199
>gnl|CDD|221324 pfam11933, DUF3451, Domain of unknown function (DUF3451). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 199 to 238 amino acids in length. This domain is
found associated with pfam06512, pfam00520. This domain
has a conserved ADD sequence motif.
Length = 222
Score = 26.7 bits (59), Expect = 9.8
Identities = 9/45 (20%), Positives = 17/45 (37%), Gaps = 3/45 (6%)
Query: 59 HNSRPAASQIRRKKKRKRRRKRLRNAHGE---VVMIDPSDLPKRA 100
+S A + R K K+ + + G+ + +D KR
Sbjct: 6 LSSESAKERRNRNDKNKKEEHSIGSEEGDSEKEPKSESADGRKRC 50
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
0.320 0.132 0.382
Gapped
Lambda K H
0.267 0.0772 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,210,199
Number of extensions: 1159107
Number of successful extensions: 2460
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2407
Number of HSP's successfully gapped: 110
Length of query: 239
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 145
Effective length of database: 6,768,326
Effective search space: 981407270
Effective search space used: 981407270
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: 57 (25.7 bits)