RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|255764512|ref|YP_003065529.2| preprotein tranlocase protein
[Candidatus Liberibacter asiaticus str. psy62]
(108 letters)
>gnl|CDD|145709 pfam02699, YajC, Preprotein translocase subunit. See.
Length = 83
Score = 92.5 bits (231), Expect = 2e-20
Identities = 33/83 (39%), Positives = 56/83 (67%), Gaps = 1/83 (1%)
Query: 19 SPLEMAGLFFVLAVVWYFLLIRPQRQQLQRRAEMLRNLRRGDSIVTAAGIVGKVVRVIDD 78
S L ++ ++YFLLIRPQ+++ + EML +L++GD +VT GI GK+V+ +DD
Sbjct: 1 SGLSSLLPLVLIFAIFYFLLIRPQQKRQKEHKEMLSSLKKGDEVVTIGGIHGKIVK-VDD 59
Query: 79 LELEVEIAENVRVRVVRSFVSEV 101
+ +EIA+ V+V+V +S ++ V
Sbjct: 60 DTVVLEIADGVKVKVDKSAIARV 82
>gnl|CDD|32047 COG1862, YajC, Preprotein translocase subunit YajC [Intracellular
trafficking and secretion].
Length = 97
Score = 84.5 bits (209), Expect = 5e-18
Identities = 29/94 (30%), Positives = 56/94 (59%), Gaps = 1/94 (1%)
Query: 15 TSATSPLEMAGLFFVLAVVWYFLLIRPQRQQLQRRAEMLRNLRRGDSIVTAAGIVGKVVR 74
S L + ++ ++YFL+IRPQR++++ E+L +L++GD +VT GIVG V +
Sbjct: 3 MQGGSGLVLLLPLVLIFAIFYFLIIRPQRKRMKEHQELLNSLKKGDEVVTIGGIVGTVTK 62
Query: 75 VIDDLELEVEIAENVRVRVVRSFVSEVQSKSEPV 108
V DD +E+E+ + +++ + ++ V K +
Sbjct: 63 VGDD-TVEIELGDGTKIKFEKEAIATVLEKGDLK 95
>gnl|CDD|32283 COG2100, COG2100, Predicted Fe-S oxidoreductase [General function
prediction only].
Length = 414
Score = 27.2 bits (60), Expect = 0.90
Identities = 16/72 (22%), Positives = 35/72 (48%), Gaps = 12/72 (16%)
Query: 37 LLIRPQRQQLQRRAEMLRNLRRGDSI---VTAAGIV---------GKVVRVIDDLELEVE 84
L+++P + R + + +RG+ + V G + +V+ VI+ E +
Sbjct: 333 LILKPGEFGMHPRPRLPKPFKRGEVVKAEVVLPGRLKGEMLAVARDRVIAVINSNEGALL 392
Query: 85 IAENVRVRVVRS 96
+ + V+VR+VR+
Sbjct: 393 VGDRVKVRIVRT 404
>gnl|CDD|30878 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 26.7 bits (59), Expect = 1.5
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 56 LRRGDSIVTAAGIVGKVVRVIDDLELEVEIAENVRVRVVRSFVSEVQS 103
L++GD IV A G G+V ++DDL ++ A V +SEV +
Sbjct: 208 LKKGDIIV-AGGEYGRVRTMVDDLGKPIKEAG-PSKPVEILGLSEVPA 253
>gnl|CDD|28760 cd03118, alpha_CA_V, Carbonic anhydrase alpha, CA isozyme V_like
subgroup. Carbonic anhydrases (CAs) are zinc-containing
enzymes that catalyze the reversible hydration of carbon
dioxide in a two-step mechanism: a nucleophilic attack
of a zinc-bound hydroxide ion on carbon dioxide,
followed by the regeneration of the active site by
ionization of the zinc-bound water molecule and removal
of a proton from the active site. They are ubiquitous
enzymes involved in fundamental processes like
photosynthesis, respiration, pH homeostasis and ion
transport. Most alpha CAs are monomeric enzymes. The
zinc ion is complexed by three histidines. This
vertebrate subgroup comprises isozyme V. CA V is the
mitochondrial isozyme, which may play a role in
gluconeogenesis and ureagenesis and possibly also in
lipogenesis..
Length = 236
Score = 26.1 bits (57), Expect = 2.2
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 30 LAVVWYFLLIRPQRQQLQRRAEMLRNLRRGDSIV 63
LAV+ FL + + LQ+ + L +R D++V
Sbjct: 117 LAVIGVFLKLGAHHEGLQKLVDALPEVRHKDTVV 150
>gnl|CDD|173935 cd08176, LPO, Lactadehyde:propanediol oxidoreductase (LPO)
catalyzes the interconversion between L-lactaldehyde
and L-1,2-propanediol in Escherichia coli and other
enterobacteria. Lactadehyde:propanediol oxidoreductase
(LPO) is a member of the group III iron-activated
dehydrogenases which catalyze the interconversion
between L-lactaldehyde and L-1,2-propanediol in
Escherichia coli and other enterobacteria. L-Fucose and
L-rhamnose is used by Escherichia coli through an
inducible pathway mediated by the fucose regulon
comprising four linked oeprons fucO, fucA, fucPIK, and
fucR. The fucA-encoded aldolase catalyzes the formation
of dihydroxyacetone phosphate and L-lactaldehyde. Under
anaerobic conditions, with NADH as a cofactor,
lactaldehyde is converted by a fucO-encoded
Lactadehyde:propanediol oxidoreductase (LPO) to
L-1,2-propanediol, which is excreted as a fermentation
product. In mutant strains, E. coli adapted to grow on
L-1,2-propanediol, FucO catalyzes the oxidation of the
polyol to L-lactaldehyde. FucO is induced regardless of
the respiratory conditions of the culture, remains
fully active in the absence of oxygen. In the presence
of oxygen, this enzyme becomes oxidatively inactivated
by a metal-catalyzed oxidation mechanism. FucO is an
iron-dependent metalloenzyme that is inactivated by
other metals, such as zinc, copper, or cadmium. This
enzyme can also reduces glycol aldehyde with similar
efficiency. Beside L-1,2-propanediol, the enzyme is
also able to oxidize methanol as alternative
substrates.
Length = 377
Score = 25.6 bits (57), Expect = 3.2
Identities = 11/34 (32%), Positives = 18/34 (52%), Gaps = 5/34 (14%)
Query: 62 IVT-----AAGIVGKVVRVIDDLELEVEIAENVR 90
IVT G+V KV V+D+ ++ I + V+
Sbjct: 33 IVTDKGLVKIGVVEKVTDVLDEAGIDYVIYDGVK 66
>gnl|CDD|176214 cd08252, AL_MDR, Arginate lyase and other MDR family members. This
group contains a structure identified as an arginate
lyase. Other members are identified quinone reductases,
alginate lyases, and other proteins related to the
zinc-dependent dehydrogenases/reductases. QOR catalyzes
the conversion of a quinone and NAD(P)H to a
hydroquinone and NAD(P+. Quinones are cyclic diones
derived from aromatic compounds. Membrane bound QOR acts
in the respiratory chains of bacteria and mitochondria,
while soluble QOR acts to protect from toxic quinones
(e.g. DT-diaphorase) or as a soluble eye-lens protein in
some vertebrates (e.g. zeta-crystalin). QOR reduces
quinones through a semi-quinone intermediate via a
NAD(P)H-dependent single electron transfer. QOR is a
member of the medium chain dehydrogenase/reductase
family, but lacks the zinc-binding sites of the
prototypical alcohol dehydrogenases of this group.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 336
Score = 25.2 bits (56), Expect = 4.0
Identities = 17/89 (19%), Positives = 30/89 (33%), Gaps = 28/89 (31%)
Query: 13 AITSATSPLEMAGLFF-VLAVVWYFLLIRP---------QRQQLQRRAEML--------- 53
I PL++ L + W F+ R Q + L A++L
Sbjct: 246 LIVDPQEPLDLGPLKSKSASFHWEFMFTRSMFQTPDMIEQHEILNEVADLLDAGKLKTTL 305
Query: 54 ---------RNLRRGDSIVTAAGIVGKVV 73
NLR +++ + +GK+V
Sbjct: 306 TETLGPINAENLREAHALLESGKTIGKIV 334
>gnl|CDD|146989 pfam04612, GspM, General secretion pathway, M protein. This is a
family of membrane proteins involved in the secretion
of a number of molecules in Gram-negative bacteria. The
precise function of these proteins is unknown, though
in Vibrio cholerae, the EpsM protein interacts with the
EpsL protein, and also forms homodimers.
Length = 159
Score = 25.3 bits (56), Expect = 4.1
Identities = 9/36 (25%), Positives = 15/36 (41%)
Query: 23 MAGLFFVLAVVWYFLLIRPQRQQLQRRAEMLRNLRR 58
+L V+ Y L +P Q+ R L+ R+
Sbjct: 20 AVLGAVLLLVLLYLGLWQPLSQRRARAQRRLQAARQ 55
>gnl|CDD|110924 pfam01972, SDH_sah, Serine dehydrogenase proteinase. This family
of archaebacterial proteins, formerly known as DUF114,
has been found to be a serine dehydrogenase proteinase
distantly related to ClpP proteinases that belong to
the serine proteinase superfamily. The family has a
catalytic triad of Ser, Asp, His residues, which shows
an altered residue ordering compared with the ClpP
proteinases but similar to that of the carboxypeptidase
clan.
Length = 286
Score = 24.8 bits (54), Expect = 4.9
Identities = 11/36 (30%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 23 MAGLFFVLAVVWYFLLIRPQRQQLQRRAEMLRNLRR 58
++ LF+ L ++++L+I PQ + Q LR +R
Sbjct: 10 LSSLFWFL--LFFYLIIAPQMKMRQLIMARLRCIRE 43
>gnl|CDD|132877 cd07180, RNaseH_typeII_Archaea_like, Archaeal ribonuclease HII.
Ribonuclease (RNase) H is classified into two families,
type I (prokaryotic RNase HI, eukaryotic RNase H1 and
viral RNase H) and type II (prokaryotic RNase HII and
HIII, archaeal RNase HII and eukaryotic RNase H2/HII).
RNase H endonucleolytically hydrolyzes an RNA strand
when it is annealed to a complementary DNA strand in the
presence of divalent cations, in DNA replication or
repair. Some archaeal RNase HII show broad divalent
cation specificity. It is proposed that three of the
four acidic residues at the active site are involved in
metal binding and the fourth one involved in the
catalytic process in archaea. Most archaeal genomes
contain multiple RNase H genes. Despite a lack of
evidence for homology from sequence comparisons, type I
and type II RNase H share a common fold and similar
steric configurations of the four acidic active-site
residues, suggesting identical or very similar catalytic
mechanisms. It appears that type I and type II RNases H
also have overlapping functions in cells, as
over-expression of Escherichia coli RNase HII can
complement an RNase HI deletion phenotype in E. coli.
Length = 204
Score = 24.5 bits (54), Expect = 5.9
Identities = 10/23 (43%), Positives = 16/23 (69%), Gaps = 2/23 (8%)
Query: 62 IVTAAGIVGKVVR--VIDDLELE 82
+V+AA I+ KV R I++L+ E
Sbjct: 139 VVSAASIIAKVERDREIEELKEE 161
>gnl|CDD|173650 cd05094, PTKc_TrkC, Catalytic domain of the Protein Tyrosine
Kinase, Tropomyosin Related Kinase C. Protein Tyrosine
Kinase (PTK) family; Tropomyosin Related Kinase C
(TrkC); catalytic (c) domain. The PTKc family is part
of a larger superfamily that includes the catalytic
domains of other kinases such as protein
serine/threonine kinases, RIO kinases, and
phosphoinositide 3-kinase (PI3K). PTKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
tyrosine (tyr) residues in protein substrates. TrkC is
a member of the Trk subfamily of proteins, which are
receptor tyr kinases (RTKs) containing an extracellular
region with arrays of leucine-rich motifs flanked by
two cysteine-rich clusters followed by two
immunoglobulin-like domains, a transmembrane segment,
and an intracellular catalytic domain. Binding of TrkC
to its ligand, neurotrophin 3 (NT3), results in
receptor oligomerization and activation of the
catalytic domain. TrkC is broadly expressed in the
nervous system and in some non-neural tissues including
the developing heart. NT3/TrkC signaling plays an
important role in the innervation of the cardiac
conducting system and the development of smooth muscle
cells. Mice deficient with NT3 and TrkC have multiple
heart defects. NT3/TrkC signaling is also critical for
the development and maintenance of enteric neurons that
are important for the control of gut peristalsis.
Length = 291
Score = 24.6 bits (53), Expect = 6.4
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 43 RQQLQRRAEMLRNLRRGDSIVTAAGIVG 70
R+ QR AE+L NL+ + IV G+ G
Sbjct: 51 RKDFQREAELLTNLQH-EHIVKFYGVCG 77
>gnl|CDD|173769 cd08229, STKc_Nek7, Catalytic domain of the Protein
Serine/Threonine Kinase, Never In Mitosis gene A-related
kinase 7. Serine/Threonine Kinases (STKs), Never In
Mitosis gene A (NIMA)-related kinase 7 (Nek7) subfamily,
catalytic (c) domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The Nek7 subfamily is
one of a family of 11 different Neks (Nek1-11) that are
involved in cell cycle control. The Nek family is part
of a larger superfamily that includes the catalytic
domains of other protein STKs, protein tyrosine kinases,
RIO kinases, aminoglycoside phosphotransferase, choline
kinase, and phosphoinositide 3-kinase. Nek7 is required
for mitotic spindle formation and cytokinesis. It is
enriched in the centrosome and is critical for
microtubule nucleation. Nek7 is activated by Nek9 during
mitosis, and may regulate the p70 ribosomal S6 kinase.
Length = 267
Score = 24.6 bits (53), Expect = 6.5
Identities = 11/38 (28%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 33 VW-YFLLIRPQRQQLQRRAEMLRNLRRGDSIVTAAGIV 69
VW YF+ + + + R M R+++ + +TA G+V
Sbjct: 108 VWKYFVQLCSALEHMHSRRVMHRDIKPANVFITATGVV 145
>gnl|CDD|132878 cd07181, RNaseH_typeII_eukaryota_like, Eukaryotic Ribonuclease HII;
putative role in Okazaki fragment removal during
replication. Ribonuclease (RNase) HII
endonucleolytically hydrolyzes an RNA strand when it is
annealed to a complementary DNA strand in the presence
of divalent cations, in DNA replication and repair.
RNase H is classified into two families, type I
(prokaryotic RNase HI, eukaryotic RNase H1 and viral
RNase H) and type II (prokaryotic RNase HII and HIII,
and eukaryotic RNase H2/HII). The enzyme can be found in
bacteria, archaea, and eukaryotes. Most prokaryotic and
eukaryotic genomes contain multiple RNase H genes.
Despite a lack of evidence for homology from sequence
comparisons, type I and type II RNase H share a common
fold and similar steric configurations of the four
acidic active-site residues, suggesting identical or
very similar catalytic mechanisms. Eukaryotic RNase HII
is a type II RNase H that is active during replication
and is believed to play a role in removal of Okazaki
fragment primers and single ribonucleotides in DNA-DNA
duplexes. Eukaryotic RNase HII is functional when it
forms a complex with two other accessory proteins. It is
speculated that the two accessory subunits are required
for correct folding of the catalytic subunit of RNase
HII. It appears that type I and type II RNases H also
have overlapping functions in cells, as over-expression
of Escherichia coli RNase HII can complement an RNase HI
deletion phenotype in E. coli.
Length = 216
Score = 24.5 bits (54), Expect = 7.3
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 62 IVTAAGIVGKVVR 74
IV+AA IV KV R
Sbjct: 145 IVSAASIVAKVTR 157
>gnl|CDD|39694 KOG4494, KOG4494, KOG4494, Cell surface ATP diphosphohydrolase
Apyrase [Nucleotide transport and metabolism].
Length = 352
Score = 24.2 bits (52), Expect = 7.3
Identities = 11/80 (13%), Positives = 31/80 (38%), Gaps = 4/80 (5%)
Query: 27 FFVLAVVWYFLLIRPQRQQLQRRAEMLRNLRRGDSIVTAAGIVGKVVRVIDDLELEVEIA 86
FV A+++Y + R+ E + + GI ++ +I DL+ + +
Sbjct: 16 GFVTAILFYSG---SHFNKSGRQEEHIAHANLYSPKKFDDGIEYRIA-LIADLDTDSKDG 71
Query: 87 ENVRVRVVRSFVSEVQSKSE 106
+ + + + +++
Sbjct: 72 KTWKSYLKKGYLTVSADHKH 91
>gnl|CDD|143978 pfam00223, PsaA_PsaB, Photosystem I psaA/psaB protein.
Length = 682
Score = 24.3 bits (53), Expect = 7.6
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 6 YAQSDAPAITSATSPLEMAGLFFVLA-VVWYF 36
+A S + I S S L + GL F+ A VW F
Sbjct: 588 WANS-SQVINSYGSLLSVYGLMFLGAHFVWAF 618
>gnl|CDD|145017 pfam01654, Bac_Ubq_Cox, Bacterial Cytochrome Ubiquinol Oxidase.
This family are the alternative oxidases found in many
bacteria which oxidize ubiquinol and reduce oxygen as
part of the electron transport chain. This family is the
subunit I of the oxidase E. coli has two copies of the
oxidase, bo and bd', both of which are represented here
In some nitrogen fixing bacteria, e.g. Klebsiella
pneumoniae this oxidase is responsible for removing
oxygen in microaerobic conditions, making the oxidase
required for nitrogen fixation. This subunit binds a
single b-haem, through ligands at His186 and Met393
(using SW:P11026 numbering). In addition His19 is a
ligand for the haem b found in subunit II.
Length = 430
Score = 24.0 bits (53), Expect = 9.2
Identities = 13/44 (29%), Positives = 19/44 (43%)
Query: 1 MFTTVYAQSDAPAITSATSPLEMAGLFFVLAVVWYFLLIRPQRQ 44
+ T A S A S + L+ VL V +LL+R R+
Sbjct: 383 LLRTADAVSPVSAGQVLFSLIGFTLLYAVLFVAEVYLLLRYARK 426
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.324 0.135 0.368
Gapped
Lambda K H
0.267 0.0748 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,199,201
Number of extensions: 58268
Number of successful extensions: 340
Number of sequences better than 10.0: 1
Number of HSP's gapped: 337
Number of HSP's successfully gapped: 39
Length of query: 108
Length of database: 6,263,737
Length adjustment: 75
Effective length of query: 33
Effective length of database: 4,643,062
Effective search space: 153221046
Effective search space used: 153221046
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (23.4 bits)