RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4101
(82 letters)
>gnl|CDD|235000 PRK02106, PRK02106, choline dehydrogenase; Validated.
Length = 560
Score = 86.4 bits (215), Expect = 1e-21
Identities = 35/62 (56%), Positives = 49/62 (79%), Gaps = 2/62 (3%)
Query: 13 VILSAGTIGSPQILMISGIGPKDHLQDMGIPVIHDLR-VGDNLQDHVGMAGLTFLVDKPV 71
VILSAG I SPQ+L +SGIGP +HL+++GIPV+HDL VG+NLQDH+ + + + +PV
Sbjct: 254 VILSAGAINSPQLLQLSGIGPAEHLKELGIPVVHDLPGVGENLQDHLEVY-IQYECKQPV 312
Query: 72 SI 73
S+
Sbjct: 313 SL 314
>gnl|CDD|233581 TIGR01810, betA, choline dehydrogenase. Choline dehydrogenase
catalyzes the conversion of exogenously supplied choline
into the intermediate glycine betaine aldehyde, as part
of a two-step oxidative reaction leading to the
formation of osmoprotectant betaine. This enzymatic
system can be found in both gram-positive and
gram-negative bacteria. As in Escherichia coli ,
Staphylococcus xylosus , and Sinorhizobium meliloti,
this enzyme is found associated in a transciptionally
co-induced gene cluster with betaine aldehyde
dehydrogenase, the second catalytic enzyme in this
reaction. Other gram-positive organisms have been shown
to employ a different enzymatic system, utlizing a
soluable choline oxidase or type III alcohol
dehydrogenase instead of choline dehydrogenase. This
enzyme is a member of the GMC oxidoreductase family
(pfam00732 and pfam05199), sharing a common
evoluntionary origin and enzymatic reaction with alcohol
dehydrogenase. Outgrouping from this model, Caulobacter
crescentus shares sequence homology with choline
dehydrogenase, yet other genes participating in this
enzymatic reaction have not currently been identified
[Cellular processes, Adaptations to atypical
conditions].
Length = 532
Score = 73.0 bits (179), Expect = 6e-17
Identities = 32/73 (43%), Positives = 44/73 (60%), Gaps = 2/73 (2%)
Query: 2 GMLRHRPQASNVILSAGTIGSPQILMISGIGPKDHLQDMGIPVIHDLR-VGDNLQDHVGM 60
G H VILSAG I SPQ+L +SGIG +HL+++GI L VG+NLQDH+ +
Sbjct: 236 GRKEHTEANKEVILSAGAINSPQLLQLSGIGDAEHLRELGIEPRIHLPGVGENLQDHLEV 295
Query: 61 AGLTFLVDKPVSI 73
+ +PVS+
Sbjct: 296 Y-VQHACKQPVSL 307
>gnl|CDD|225186 COG2303, BetA, Choline dehydrogenase and related flavoproteins
[Amino acid transport and metabolism].
Length = 542
Score = 71.7 bits (176), Expect = 2e-16
Identities = 30/64 (46%), Positives = 43/64 (67%), Gaps = 2/64 (3%)
Query: 10 ASNVILSAGTIGSPQILMISGIGPKDHLQDMGIPVIHDLR-VGDNLQDHVGMAGLTFLVD 68
A V+L+AG I SP++L++SGIGP DHL + GI V+ L VG NLQDH+ + + F
Sbjct: 255 AREVVLAAGAINSPKLLLLSGIGPADHLLEHGIDVVGRLPGVGQNLQDHLEI-YVAFEAT 313
Query: 69 KPVS 72
+P +
Sbjct: 314 EPTN 317
>gnl|CDD|215420 PLN02785, PLN02785, Protein HOTHEAD.
Length = 587
Score = 62.5 bits (152), Expect = 3e-13
Identities = 26/51 (50%), Positives = 35/51 (68%), Gaps = 1/51 (1%)
Query: 7 RPQASNVILSAGTIGSPQILMISGIGPKDHLQDMGIPVI-HDLRVGDNLQD 56
+ S +ILSAG IGSPQ+L++SGIGPK L+ IPV+ H+ VG + D
Sbjct: 276 NNKGSEIILSAGAIGSPQMLLLSGIGPKKELKKHKIPVVLHNEHVGKGMAD 326
>gnl|CDD|234421 TIGR03970, Rv0697, dehydrogenase, Rv0697 family. This model
describes a set of dehydrogenases belonging to the
glucose-methanol-choline oxidoreductase (GMC
oxidoreductase) family. Members of the present family
are restricted to Actinobacterial genome contexts
containing also members of families TIGR03962 and
TIGR03969 (the mycofactocin system), and are proposed to
be uniform in function.
Length = 487
Score = 59.5 bits (144), Expect = 4e-12
Identities = 22/48 (45%), Positives = 31/48 (64%)
Query: 10 ASNVILSAGTIGSPQILMISGIGPKDHLQDMGIPVIHDLRVGDNLQDH 57
A V+L AG + S +L++SGIGP + L+ GI V+ DL VG + DH
Sbjct: 244 ADRVVLCAGAVESAHLLLLSGIGPAEQLRAAGIAVVLDLPVGSDFVDH 291
>gnl|CDD|216089 pfam00732, GMC_oxred_N, GMC oxidoreductase. This family of
proteins bind FAD as a cofactor.
Length = 218
Score = 46.9 bits (112), Expect = 6e-08
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 12/57 (21%)
Query: 1 MGMLRHRPQASNVILSAGTIGSPQILMISGIGPKDHLQDMGIPVIHDLRVGDNLQDH 57
G+ R A V+++AG + +P +L+ SG+G H VG NLQ H
Sbjct: 172 GGIKRLITAAKEVVVAAGALNTPPLLLRSGLGKNPH------------PVGKNLQLH 216
>gnl|CDD|131515 TIGR02462, pyranose_ox, pyranose oxidase. Pyranose oxidase (also
called glucose 2-oxidase) converts D-glucose and
molecular oxygen to 2-dehydro-D-glucose and hydrogen
peroxide. Peroxide production is believed to be
important to the wood rot fungi in which this enzyme is
found for lignin degradation.
Length = 544
Score = 27.5 bits (61), Expect = 0.76
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 10 ASNVILSAGTIGSPQILMISGIGP 33
A +L+ G + +PQIL+ SG G
Sbjct: 268 ADVYVLACGAVHNPQILVNSGFGQ 291
>gnl|CDD|234040 TIGR02867, spore_II_P, stage II sporulation protein P. Stage II
sporulation protein P is a protein of the endospore
formation program in a number of lineages in the
Firmicutes (low-GC Gram-positive bacteria). It is
expressed in the mother cell compartment, under control
of Sigma-E. SpoIIP, along with SpoIIM and SpoIID, is
one of three major proteins involved in engulfment of
the forespore by the mother cell. This protein family
is named for the single member in Bacillus subtilis,
although most sporulating bacteria have two members
[Cellular processes, Sporulation and germination].
Length = 196
Score = 26.1 bits (58), Expect = 1.7
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 34 KDHLQDMGIPVIHDLRVGDNL 54
L++ GI VIHD V D L
Sbjct: 40 AKELEEKGIGVIHDKTVHDGL 60
>gnl|CDD|238929 cd01967, Nitrogenase_MoFe_alpha_like, Nitrogenase_MoFe_alpha_like:
Nitrogenase MoFe protein, alpha subunit_like. The
nitrogenase enzyme catalyzes the ATP-dependent reduction
of dinitrogen to ammonia. Three genetically distinct
types of nitrogenase systems are known to exist: a
molybdenum-dependent nitrogenase (Mo-nitrogenase), a
vanadium dependent nitrogenase (V-nitrogenase), and an
iron-only nitrogenase (Fe-nitrogenase). These
nitrogenase systems consist of component 1 (MoFe
protein, VFe protein or, FeFe protein respectively) and,
component 2 (Fe protein). This group contains the alpha
subunit of component 1 of all three different forms. The
most widespread and best characterized of these systems
is the Mo-nitrogenase. MoFe is an alpha2beta2 tetramer,
the alternative nitrogenases are alpha2beta2delta2
hexamers having alpha and beta subunits similar to the
alpha and beta subunits of MoFe. The role of the delta
subunit is unknown. For MoFe, each alphabeta pair of
subunits contains one P-cluster (located at the
alphabeta interface) and, one molecule of iron
molybdenum cofactor (FeMoco) contained within the alpha
subunit. The Fe protein is a homodimer which contains, a
single [4Fe-4S] cluster from which electrons are
transferred to the P-cluster of the MoFe and in turn,
to FeMoCo the site of substrate reduction. The
V-nitrogenase requires an iron-vanadium cofactor
(FeVco), the iron only-nitrogenase an iron only cofactor
(FeFeco). These cofactors are analogous to the FeMoco.
The V-nitrogenase has P clusters identical to those of
MoFe. In addition to N2, nitrogenase also catalyzes the
reduction of a variety of other substrates such as
acetylene The V-nitrogenase differs from the Mo-
nitrogenase in that it produces free hydrazine, as a
minor product during dinitrogen reduction and, ethane
as a minor product during acetylene reduction.
Length = 406
Score = 26.0 bits (58), Expect = 2.0
Identities = 12/28 (42%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 26 LMISGIGPKDHLQDMGIPV--IHDLRVG 51
L++SGI K Q +GIP +H R G
Sbjct: 358 LILSGIKEKYVAQKLGIPFLDLHSERNG 385
>gnl|CDD|236579 PRK09585, anmK, anhydro-N-acetylmuramic acid kinase; Reviewed.
Length = 365
Score = 25.9 bits (58), Expect = 2.5
Identities = 13/51 (25%), Positives = 18/51 (35%), Gaps = 18/51 (35%)
Query: 4 LRHRPQASNVILSAGT--IGSPQILMISGIGPKDHLQDMGIPVIHDLRVGD 52
+RHRP T IG ++ + GI V+ D R D
Sbjct: 101 VRHRPGE------GFTLQIGDGALIA----------ELTGITVVADFRRRD 135
>gnl|CDD|188930 cd09531, SAM_CS047, SAM domain of CS047 subfamily. SAM (sterile
alpha motif) domain of CS047 subfamily is a putative
protein-protein interaction domain. Proteins of this
subfamily have a SAM domain at the N-terminus. SAM is a
widespread domain in signaling and regulatory proteins.
In many cases SAM mediates
homodimerization/oligomerization. The exact function of
proteins belonging to this group is unknown.
Length = 65
Score = 24.6 bits (54), Expect = 3.8
Identities = 7/14 (50%), Positives = 11/14 (78%)
Query: 34 KDHLQDMGIPVIHD 47
K+ L++MGI V+ D
Sbjct: 40 KEILKEMGITVMGD 53
>gnl|CDD|235118 PRK03348, PRK03348, DNA polymerase IV; Provisional.
Length = 454
Score = 25.3 bits (56), Expect = 4.0
Identities = 10/22 (45%), Positives = 13/22 (59%), Gaps = 2/22 (9%)
Query: 30 GIGP--KDHLQDMGIPVIHDLR 49
GIGP ++ L +GI I DL
Sbjct: 187 GIGPVTEEKLHRLGIETIGDLA 208
>gnl|CDD|219415 pfam07454, SpoIIP, Stage II sporulation protein P (SpoIIP). This
family contains the bacterial stage II sporulation
protein P (SpoIIP) (approximately 350 residues long). It
has been shown that a block in polar cytokinesis in
Bacillus subtilis is mediated partly by transcription of
spoIID, spoIIM and spoIIP. This inhibition of polar
division is involved in the locking in of asymmetry
after the formation of a polar septum during
sporulation. Engulfment in Bacillus subtilis is mediated
by two complementary systems: the first includes the
proteins SpoIID, SpoIIM and SpoIIP (DMP) which carry out
the engulfment, and the second includes the
SpoIIQ-SpoIIIAGH (Q-AH) zipper, that recruits other
proteins to the septum in a second-phase of the
engulfment. The course of events follows as the
incorporation firstly of SpoIIB into the septum during
division to serve directly or indirectly as a landmark
for localising SpoIIM and then SpoIIP and SpoIID to the
septum. SpoIIP and SpoIID interact together to form part
of the DMP complex. SpoIIP itself has been identified as
an autolysin with peptidoglycan hydrolase activity.
Length = 258
Score = 25.3 bits (56), Expect = 4.3
Identities = 9/19 (47%), Positives = 10/19 (52%)
Query: 34 KDHLQDMGIPVIHDLRVGD 52
L+ GI VIHD V D
Sbjct: 107 AQELEKYGIGVIHDKTVHD 125
>gnl|CDD|132882 cd07025, Peptidase_S66, LD-Carboxypeptidase, a serine protease,
includes microcin C7 self immunity protein.
LD-carboxypeptidase (Muramoyltetrapeptide
carboxypeptidase; EC 3.4.17.13; Merops family S66;
initially described as Carboxypeptidase II) family also
includes the microcin c7 self-immunity protein (MccF) as
well as uncharacterized proteins including hypothetical
proteins. LD-carboxypeptidase hydrolyzes the amide bond
that links the dibasic amino acids to C-terminal
D-amino acids. The physiological substrates of
LD-carboxypeptidase are tetrapeptide fragments (such as
UDP-MurNAc-tetrapeptides) that are produced when
bacterial cell walls are degraded; they contain an
L-configured residue (L-lysine or meso-diaminopimelic
acid residue) as the penultimate residue and D-alanine
as the ultimate residue. A possible role of
LD-carboxypeptidase is in peptidoglycan recycling
whereby the resulting tripeptide (precursor for murein
synthesis) can be reconverted into peptidoglycan by
attachment of preformed D-Ala-D-Ala dipeptides. Some
enzymes possessing LD-carboxypeptidase activity also act
as LD-transpeptidase by replacing the terminal D-Ala
with another D-amino acid. MccF contributes to
self-immunity towards microcin C7 (MccC7), a ribosomally
encoded peptide antibiotic that contains a
phosphoramidate linkage to adenosine monophosphate at
its C-terminus. Its possible biological role is to
defend producer cells against exogenous microcin from
re-entering after having been exported. It is suggested
that MccF is involved in microcin degradation or
sequestration in the periplasm.
Length = 282
Score = 25.2 bits (56), Expect = 4.3
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 34 KDHLQDMGIPVIHDLRVG 51
K+ L D+GIPV++ L +G
Sbjct: 250 KEVLGDLGIPVLYGLPIG 267
>gnl|CDD|216847 pfam02016, Peptidase_S66, LD-carboxypeptidase.
Muramoyl-tetrapeptide carboxypeptidase hydrolyses a
peptide bond between a di-basic amino acid and the
C-terminal D-alanine in the tetrapeptide moiety in
peptidoglycan. This cleaves the bond between an L- and a
D-amino acid. The function of this activity is in murein
recycling. This family also includes the microcin c7
self-immunity protein. This family corresponds to Merops
family S66.
Length = 281
Score = 25.2 bits (56), Expect = 4.4
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 34 KDHLQDMGIPVIHDLRVG 51
++ L D+GIPV++ L G
Sbjct: 247 EEVLGDLGIPVLYGLPFG 264
>gnl|CDD|215079 PLN00151, PLN00151, potassium transporter; Provisional.
Length = 852
Score = 25.1 bits (55), Expect = 4.8
Identities = 6/25 (24%), Positives = 12/25 (48%)
Query: 29 SGIGPKDHLQDMGIPVIHDLRVGDN 53
I P + +G+P++ D R+
Sbjct: 728 VLIAPNGSVYSLGVPLLADYRLTSK 752
>gnl|CDD|176454 cd01700, PolY_Pol_V_umuC, umuC subunit of DNA Polymerase V. umuC
subunit of Pol V. Pol V is a bacterial translesion
synthesis (TLS) polymerase that consists of the
heterotrimer of one umuC and two umuD subunits.
Translesion synthesis is a process that allows the
bypass of a variety of DNA lesions. TLS polymerases
lack proofreading activity and have low fidelity and low
processivity. They use damaged DNA as templates and
insert nucleotides opposite the lesions. Pol V, RecA,
single stranded DNA-binding protein, beta sliding clamp,
and gamma clamp loading complex are responsible for
inducing the SOS response in bacteria to repair
UV-induced DNA damage.
Length = 344
Score = 24.8 bits (55), Expect = 5.0
Identities = 9/22 (40%), Positives = 10/22 (45%), Gaps = 2/22 (9%)
Query: 30 GIGPK--DHLQDMGIPVIHDLR 49
GIG + L MGI DL
Sbjct: 183 GIGRRTAKKLNAMGIHTAGDLA 204
>gnl|CDD|234789 PRK00549, PRK00549, competence damage-inducible protein A;
Provisional.
Length = 414
Score = 24.7 bits (55), Expect = 6.4
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 35 DHLQDMGIPVIHDLRVGDN 53
+ L ++GI V H VGDN
Sbjct: 27 EKLAELGIDVYHQTVVGDN 45
>gnl|CDD|114761 pfam06057, VirJ, Bacterial virulence protein (VirJ). This family
consists of several bacterial VirJ virulence proteins.
VirJ is thought to be involved in the type IV secretion
system. It is thought that the substrate proteins
localised to the periplasm may associate with the pilus
in a manner that is mediated by VirJ, and suggest a
two-step process for type IV secretion in
Agrobacterium.
Length = 192
Score = 24.2 bits (53), Expect = 9.4
Identities = 5/11 (45%), Positives = 7/11 (63%)
Query: 35 DHLQDMGIPVI 45
LQ G+PV+
Sbjct: 23 SALQKQGVPVV 33
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.323 0.141 0.408
Gapped
Lambda K H
0.267 0.0736 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,167,101
Number of extensions: 337568
Number of successful extensions: 345
Number of sequences better than 10.0: 1
Number of HSP's gapped: 341
Number of HSP's successfully gapped: 30
Length of query: 82
Length of database: 10,937,602
Length adjustment: 51
Effective length of query: 31
Effective length of database: 8,675,548
Effective search space: 268941988
Effective search space used: 268941988
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 (21.9 bits)
S2: 53 (24.2 bits)