RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6193
(122 letters)
>gnl|CDD|225147 COG2238, RPS19A, Ribosomal protein S19E (S16A) [Translation,
ribosomal structure and biogenesis].
Length = 147
Score = 28.1 bits (63), Expect = 0.97
Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 4/49 (8%)
Query: 69 RKKQELLSKTGQWINK---GMNSTPQGDAIMRKIEADMMFEDKRPKLER 114
RK + L K G + K G TP+G +++ +I ++ E + P+LE+
Sbjct: 99 RKVLQQLEKAG-LVEKTPKGRVLTPKGRSLLDRIATEIKEELEEPELEK 146
>gnl|CDD|219368 pfam07299, FBP, Fibronectin-binding protein (FBP). This family
consists of several bacterial fibronectin-binding
proteins which are thought to be involved in virulence
in Listeria species.
Length = 208
Score = 28.0 bits (63), Expect = 1.2
Identities = 8/39 (20%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 12 AQTNADIIPDLSHLTLEERQIIESVMMRQKQEE-ERELE 49
A I+ L+ E++++++ ++ + + E E+ LE
Sbjct: 35 ALAIEKILDLFPELSPEQKELLDKLLTVRTRAEAEKFLE 73
>gnl|CDD|131094 TIGR02039, CysD, sulfate adenylyltransferase, small subunit.
Metabolic assimilation of sulfur from inorganic sulfate,
requires sulfate activation by coupling to a nucleoside,
for the production of high-energy nucleoside
phosphosulfates. This pathway appears to be similar in
all prokaryotic organisms. Activation is first achieved
through sulfation of sulfate with ATP by sulfate
adenylyltransferase (ATP sulfurylase) to produce
5'-phosphosulfate (APS), coupled by GTP hydrolysis.
Subsequently, APS is phosphorylated by an APS kinase to
produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS). In
Escherichia coli, ATP sulfurylase is a heterodimer
composed of two subunits encoded by cysD and cysN, with
APS kinase encoded by cysC. These genes are located in a
unidirectionally transcribed gene cluster, and have been
shown to be required for the synthesis of
sulfur-containing amino acids. Homologous to this E.coli
activation pathway are nodPQH gene products found among
members of the Rhizobiaceae family. These gene products
have been shown to exhibit ATP sulfurase and APS kinase
activity, yet are involved in Nod factor sulfation, and
sulfation of other macromolecules [Central intermediary
metabolism, Sulfur metabolism].
Length = 294
Score = 27.4 bits (61), Expect = 1.9
Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 6/44 (13%)
Query: 6 GMVTSMAQTNADIIPDLSHLTLEERQ------IIESVMMRQKQE 43
G + S A T +II + + ERQ + M +K+E
Sbjct: 248 GAIESDAATVEEIIAETAAARTSERQGRAIDRDQAASMEDKKRE 291
>gnl|CDD|233517 TIGR01662, HAD-SF-IIIA, HAD-superfamily hydrolase, subfamily IIIA.
This subfamily falls within the Haloacid Dehalogenase
(HAD) superfamily of aspartate-nucleophile hydrolases.
The Class III subfamilies are characterized by the lack
of any domains located between either between the first
and second conserved catalytic motifs (as in the Class I
subfamilies, TIGR01493, TIGR01509, TIGR01488 and
TIGR01494) or between the second and third conserved
catalytic motifs (as in the Class II subfamilies,
TIGR01460 and TIGR01484) of the superfamily domain. The
IIIA subfamily contains five major clades:
histidinol-phosphatase (TIGR01261) and
histidinol-phosphatase-related protein (TIGR00213) which
together form a subfamily (TIGR01656), DNA
3'-phosphatase (TIGR01663, TIGR01664), YqeG (TIGR01668)
and YrbI (TIGR01670). In the case of histidinol
phosphatase and PNK-3'-phosphatase, this model
represents a domain of a bifunctional system. In the
histidinol phosphatase HisB, a C-terminal domain is an
imidazoleglycerol-phosphate dehydratase which catalyzes
a related step in histidine biosynthesis. In
PNK-3'-phosphatase, N- and C-terminal domains constitute
the polynucleotide kinase and DNA-binding components of
the enzyme [Unknown function, Enzymes of unknown
specificity].
Length = 132
Score = 27.0 bits (60), Expect = 2.1
Identities = 11/51 (21%), Positives = 19/51 (37%), Gaps = 9/51 (17%)
Query: 57 VYLMVIWVCILCRKKQELLSKTGQWINKGMN-STPQ-----GDAIMRKIEA 101
V + +++ C CRK K N P+ GD + ++A
Sbjct: 72 VPIDILYACPHCRKP---KPGMFLEALKRFNEIDPEESVYVGDQDLTDLQA 119
>gnl|CDD|188764 cd09378, LIM2_Lmx1a_Lmx1b, The second LIM domain of Lmx1a and
Lmx1b. The second LIM domain of Lmx1a and Lmx1b: Lmx1a
and Lmx1b belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs such as the pituitary gland and the pancreas.
Mouse Lmx1a is expressed in multiple tissues, including
the roof plate of the neural tube, the developing
brain, the otic vesicles, the notochord, and the
pancreas. In mouse, mutations in Lmx1a result in
failure of the roof plate to develop. Lmx1a may act
upstream of other roof plate markers such as MafB,
Gdf7, Bmp6, and Bmp7. Further characterization of these
mice reveals numerous defects including disorganized
cerebellum, hippocampus, and cortex; altered
pigmentation; female sterility, skeletal defects, and
behavioral abnormalities. In the mouse, Lmx1b
functions in the developing limbs and eyes, the
kidneys, the brain, and in cranial mesenchyme. The
disruption of Lmx1b gene results kidney and limb
defects. In the brain, Lmx1b is important for
generation of mesencephalic dopamine neurons and the
differentiation of serotonergic neurons. In the mouse
eye, Lmx1b regulates anterior segment (cornea, iris,
ciliary body, trabecular meshwork, and lens)
development. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 55
Score = 25.5 bits (56), Expect = 2.8
Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 4/40 (10%)
Query: 50 IMRSACQVYLMVIWVCILC----RKKQELLSKTGQWINKG 85
+MR+ VY + + C +C +K E + K GQ + K
Sbjct: 14 VMRALENVYHLRCFCCCVCERQLQKGDEFVLKEGQLLCKS 53
>gnl|CDD|240371 PTZ00343, PTZ00343, triose or hexose phosphate/phosphate
translocator; Provisional.
Length = 350
Score = 26.6 bits (59), Expect = 4.2
Identities = 16/72 (22%), Positives = 27/72 (37%), Gaps = 4/72 (5%)
Query: 22 LSHLTLEERQIIESVMMRQKQEEERELEIMRSACQVYLMVIWVCILCRKKQELLSKTGQW 81
LS+L R I M+ K E L +A +Y+++ + L L + +W
Sbjct: 201 LSNLGSSLRSIFAKKTMKNKSEIGENL----TASNIYMLLTLIASLISLPLVLFFEGKKW 256
Query: 82 INKGMNSTPQGD 93
+ N T
Sbjct: 257 VPVWTNYTANMT 268
>gnl|CDD|233879 TIGR02468, sucrsPsyn_pln, sucrose phosphate synthase/possible
sucrose phosphate phosphatase, plant. Members of this
family are sucrose-phosphate synthases of plants. This
enzyme is known to exist in multigene families in
several species of both monocots and dicots. The
N-terminal domain is the glucosyltransferase domain.
Members of this family also have a variable linker
region and a C-terminal domain that resembles sucrose
phosphate phosphatase (SPP) (EC 3.1.3.24) (see
TIGR01485), the next and final enzyme of sucrose
biosynthesis. The SPP-like domain likely serves a
binding and not a catalytic function, as the reported
SPP is always encoded by a distinct protein.
Length = 1050
Score = 25.9 bits (57), Expect = 7.7
Identities = 23/74 (31%), Positives = 32/74 (43%), Gaps = 12/74 (16%)
Query: 30 RQIIESVMMRQKQEEERELEIMRSACQVYLMVIWVCILCRKKQELLSKTGQWINKGMNST 89
R +++V R QE LE M C IW L RKK++L + Q + K
Sbjct: 59 RTWVKAVATRSPQERNTRLENM---C----WRIWN--LARKKKQLEWEEAQRLAKRRLER 109
Query: 90 PQGDAIMRKIEADM 103
+G R+ ADM
Sbjct: 110 ERGR---REATADM 120
>gnl|CDD|206107 pfam13936, HTH_38, Helix-turn-helix domain. This
helix-turn-helix domain is often found in transferases
and is likely to be DNA-binding.
Length = 44
Score = 23.5 bits (52), Expect = 9.0
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 23 SHLTLEERQIIE 34
HLTLEER+ IE
Sbjct: 3 KHLTLEEREEIE 14
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 0.130 0.371
Gapped
Lambda K H
0.267 0.0885 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,885,466
Number of extensions: 488699
Number of successful extensions: 504
Number of sequences better than 10.0: 1
Number of HSP's gapped: 501
Number of HSP's successfully gapped: 20
Length of query: 122
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 38
Effective length of database: 7,211,866
Effective search space: 274050908
Effective search space used: 274050908
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: 53 (23.9 bits)