RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 031854
(152 letters)
>gnl|CDD|185427 PTZ00072, PTZ00072, 40S ribosomal protein S13; Provisional.
Length = 148
Score = 239 bits (611), Expect = 1e-82
Identities = 101/120 (84%), Positives = 111/120 (92%)
Query: 4 MHSRGKGISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQV 63
M+ +GKGIS+SALPY+R PPSWLK+SS +VED ICK AKKGLTPSQIGVILRDS GI QV
Sbjct: 1 MYGKGKGISSSALPYRRKPPSWLKLSSSEVEDQICKLAKKGLTPSQIGVILRDSMGIPQV 60
Query: 64 KSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIH 123
K+VTGSKILRILK +GLAPEIPEDLY LIKKAV+IRKHLE+NRKDKDSKFRLILVESRIH
Sbjct: 61 KNVTGSKILRILKKNGLAPEIPEDLYFLIKKAVSIRKHLEKNRKDKDSKFRLILVESRIH 120
>gnl|CDD|236287 PRK08561, rps15p, 30S ribosomal protein S15P; Reviewed.
Length = 151
Score = 165 bits (420), Expect = 2e-53
Identities = 65/123 (52%), Positives = 87/123 (70%)
Query: 1 MGRMHSRGKGISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGI 60
M RMH+R +G S S P + PP W+ S +++E+ + + AK+G +PS IG+ILRD +GI
Sbjct: 1 MARMHTRRRGKSGSTRPARTEPPEWVDYSPEEIEELVVELAKQGYSPSMIGIILRDQYGI 60
Query: 61 AQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVES 120
VK +TG KI IL+ +GLAPEIPEDL +LIKKAV +RKHLE N KD +K L L+ES
Sbjct: 61 PDVKLITGKKITEILEENGLAPEIPEDLRNLIKKAVNLRKHLEENPKDLHNKRGLQLIES 120
Query: 121 RIH 123
+I
Sbjct: 121 KIR 123
>gnl|CDD|191937 pfam08069, Ribosomal_S13_N, Ribosomal S13/S15 N-terminal domain.
This domain is found at the N-terminus of ribosomal S13
and S15 proteins. This domain is also identified as
NUC021.
Length = 60
Score = 117 bits (295), Expect = 1e-35
Identities = 45/60 (75%), Positives = 50/60 (83%)
Query: 1 MGRMHSRGKGISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGI 60
M RMHSRGKGIS SA PY+RTPP WLK S ++VE+ I K AKKGLTPSQIGVILRD +GI
Sbjct: 1 MARMHSRGKGISGSARPYRRTPPEWLKYSPEEVEELIVKLAKKGLTPSQIGVILRDQYGI 60
>gnl|CDD|238213 cd00353, Ribosomal_S15p_S13e, Ribosomal protein S15
(prokaryotic)_S13 (eukaryotic) binds the central domain
of 16S rRNA and is required for assembly of the small
ribosomal subunit and for intersubunit association, thus
representing a key element in the assembly of the whole
ribosome. S15 also plays an important autoregulatory
role by binding and preventing its own mRNA from being
translated. S15 has a predominantly alpha-helical fold
that is highly structured except for the N-terminal
alpha helix.
Length = 80
Score = 72.2 bits (178), Expect = 1e-17
Identities = 26/76 (34%), Positives = 36/76 (47%), Gaps = 7/76 (9%)
Query: 70 KILRILKAHGLA----PEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIH-- 123
K ILK GLA L L ++ V + +HLE+N+KDK SK L+L+ S+
Sbjct: 1 KKQEILKEFGLAEGDTGSPEVQLALLTERIVNLTEHLEKNKKDKHSKRGLLLLVSKRRRL 60
Query: 124 -DWLATTRRQRSFHLY 138
+L R R L
Sbjct: 61 LKYLKRKDRLRYEWLI 76
>gnl|CDD|109373 pfam00312, Ribosomal_S15, Ribosomal protein S15.
Length = 83
Score = 67.0 bits (164), Expect = 1e-15
Identities = 22/68 (32%), Positives = 34/68 (50%)
Query: 66 VTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHDW 125
TG I LKA + + L ++ V +RKHLE ++KD SK LI + S+
Sbjct: 2 ATGLIISEFLKAEKDTGSVEVQIALLTERIVRLRKHLEEHKKDYHSKRGLIKMVSKRRRL 61
Query: 126 LATTRRQR 133
LA +++
Sbjct: 62 LAYLKKKD 69
>gnl|CDD|223262 COG0184, RpsO, Ribosomal protein S15P/S13E [Translation, ribosomal
structure and biogenesis].
Length = 89
Score = 62.2 bits (152), Expect = 1e-13
Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 16/80 (20%)
Query: 44 GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLE 103
S+I LRD +GI +V + +G L L ++ + +HL+
Sbjct: 1 MSLTSEIKQELRDEYGIPEVDTGSG----------------EVQLALLTERINNLTEHLK 44
Query: 104 RNRKDKDSKFRLILVESRIH 123
++KD S+ L+L+ S+
Sbjct: 45 EHKKDHHSRRGLLLLVSKRR 64
>gnl|CDD|238361 cd00677, S15_NS1_EPRS_RNA-bind, S15/NS1/EPRS_RNA-binding domain.
This short domain consists of a helix-turn-helix
structure, which can bind to several types of RNA. It is
found in the ribosomal protein S15, the influenza A
viral nonstructural protein (NSA) and in several
eukaryotic aminoacyl tRNA synthetases (aaRSs), where it
occurs as a single or a repeated unit. It is involved in
both protein-RNA interactions by binding tRNA and
protein-protein interactions in the formation of
tRNA-synthetases into multienzyme complexes. While this
domain lacks significant sequence similarity between the
subgroups in which it is found, they share similar
electrostatic surface potentials and thus are likely to
bind to RNA via the same mechanism.
Length = 46
Score = 46.0 bits (110), Expect = 7e-08
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 85 PEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIH 123
+ L ++ +++HL +N+KDK SK L L+ S+
Sbjct: 1 EVQIALLTERIRNLKEHLAKNKKDKHSKRGLDLLVSKRL 39
>gnl|CDD|239779 cd04246, AAK_AK-DapG-like, AAK_AK-DapG-like: Amino Acid Kinase
Superfamily (AAK), AK-DapG-like; this CD includes the
N-terminal catalytic aspartokinase (AK) domain of the
diaminopimelate-sensitive aspartokinase isoenzyme AKI
(DapG), a monofunctional enzymes found in Bacilli
(Bacillus subtilis 168), Clostridia, and Actinobacteria
bacterial species, as well as, the catalytic AK domain
of the lysine-sensitive aspartokinase isoenzyme AKII of
Bacillus subtilis 168, the lysine plus
threonine-sensitive aspartokinase of Corynebacterium
glutamicum, and related isoenzymes. In Bacillus
subtilis, the regulation of the diaminopimelate-lysine
biosynthetic pathway involves dual control by
diaminopimelate and lysine, effected through separate
diaminopimelate- and lysine-sensitive aspartokinase
isoenzymes. The role of the AKI isoenzyme is most likely
to provide a constant level of aspartyl-beta-phosphate
for the biosynthesis of diaminopimelate for
peptidoglycan synthesis and dipicolinate during
sporulation. The B. subtilis 168 AKII is induced by
methionine, and repressed and inhibited by lysine. In
Corynebacterium glutamicum and other various
Gram-positive bacteria, the DAP-lysine pathway is
feedback regulated by the concerted action of lysine and
threonine. Also included in this CD are the
aspartokinases of the extreme thermophile, Thermus
thermophilus HB27, the Gram-negative obligate
methylotroph, Methylophilus methylotrophus AS1, and
those single aspartokinase isoenzyme types found in
Pseudomonas, C. glutamicum, and Amycolatopsis
lactamdurans. The B. subtilis AKI is tetrameric
consisting of two alpha and two beta subunits; the alpha
(43 kD) and beta (17 kD) subunit formed by two in-phase
overlapping genes. The alpha subunit contains the AK
catalytic domain and two ACT domains. The beta subunit
contains two ACT domains. The B. subtilis 168 AKII
aspartokinase is also described as tetrameric consisting
of two alpha and two beta subunits. Some archeal
aspartokinases in this group lack recognizable ACT
domains.
Length = 239
Score = 30.9 bits (71), Expect = 0.18
Identities = 11/36 (30%), Positives = 18/36 (50%)
Query: 43 KGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAH 78
LT Q G++ D HG A++ + +IL L+
Sbjct: 91 ISLTGWQAGILTDDHHGNARIIDIDPKRILEALEEG 126
>gnl|CDD|225293 COG2445, COG2445, Uncharacterized conserved protein [Function
unknown].
Length = 138
Score = 30.0 bits (68), Expect = 0.28
Identities = 16/53 (30%), Positives = 22/53 (41%), Gaps = 5/53 (9%)
Query: 50 IGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHL 102
IG +L G+ T + IL G+ IPE+ +KK V R L
Sbjct: 51 IGNMLISKFGLRDPG--TYDDCIDILVEEGV---IPEEEAEELKKMVGFRNIL 98
>gnl|CDD|239794 cd04261, AAK_AKii-LysC-BS, AAK_AKii-LysC-BS: Amino Acid Kinase
Superfamily (AAK), AKii; this CD includes the N-terminal
catalytic aspartokinase (AK) domain of the
lysine-sensitive aspartokinase isoenzyme AKII of
Bacillus subtilis 168, and the lysine plus
threonine-sensitive aspartokinase of Corynebacterium
glutamicum, and related sequences. In B. subtilis 168,
the regulation of the diaminopimelate (Dap)-lysine
biosynthetic pathway involves dual control by Dap and
lysine, effected through separate Dap- and
lysine-sensitive aspartokinase isoenzymes. The B.
subtilis 168 AKII is induced by methionine, and
repressed and inhibited by lysine. Although
Corynebacterium glutamicum is known to contain a single
aspartokinase isoenzyme type, both the succinylase and
dehydrogenase variant pathways of DAP-lysine synthesis
operate simultaneously in this organism. In this
organism and other various Gram-positive bacteria, the
DAP-lysine pathway is feedback regulated by the
concerted action of lysine and theronine. Also included
in this CD are the aspartokinases of the extreme
thermophile, Thermus thermophilus HB27, the
Gram-negative obligate methylotroph, Methylophilus
methylotrophus AS1, and those single aspartokinases
found in Pseudomons, C. glutamicum, and Amycolatopsis
lactamdurans. B. subtilis 168 AKII, and the C.
glutamicum, Streptomyces clavuligerus and A.
lactamdurans aspartokinases are described as tetramers
consisting of two alpha and two beta subunits; the alpha
(44 kD) and beta (18 kD) subunits formed by two in-phase
overlapping polypeptides.
Length = 239
Score = 29.0 bits (66), Expect = 0.86
Identities = 9/39 (23%), Positives = 18/39 (46%)
Query: 43 KGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLA 81
LT Q G++ HG A++ + +I +L+ +
Sbjct: 91 ISLTGWQAGILTDGHHGKARIIDIDPDRIRELLEEGDVV 129
>gnl|CDD|235843 PRK06635, PRK06635, aspartate kinase; Reviewed.
Length = 404
Score = 28.9 bits (66), Expect = 0.99
Identities = 10/36 (27%), Positives = 17/36 (47%)
Query: 43 KGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAH 78
+ T Q G+I +HG A++ + S+I L
Sbjct: 93 RSFTGWQAGIITDSAHGKARITDIDPSRIREALDEG 128
>gnl|CDD|216680 pfam01752, Peptidase_M9, Collagenase. This family of enzymes break
down collagens.
Length = 296
Score = 28.6 bits (64), Expect = 1.1
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 4/34 (11%)
Query: 94 KAVAIRKHLERNRKDKDSKFRLILVESRIHDWLA 127
+A+R LE + +D S +LV SR + A
Sbjct: 247 GYLAVRFMLENHNRDVLS----LLVHSRYGNSFA 276
>gnl|CDD|183984 PRK13340, PRK13340, alanine racemase; Reviewed.
Length = 406
Score = 28.1 bits (63), Expect = 2.1
Identities = 10/44 (22%), Positives = 18/44 (40%), Gaps = 3/44 (6%)
Query: 23 PSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDS---HGIAQV 63
+WL+IS NI S++ +++ HGI +
Sbjct: 40 NAWLEISPGAFRHNIKTLRSLLANKSKVCAVMKADAYGHGIELL 83
>gnl|CDD|189017 cd09610, M3B_PepF_5, Peptidase family M3B Oligopeptidase F (PepF).
Peptidase family M3B Oligopeptidase F (PepF;
Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
includes oligoendopeptidase F from Lactococcus lactis.
This enzyme hydrolyzes peptides containing between 7 and
17 amino acids with fairly broad specificity. The PepF
gene is duplicated in L. lactis on the plasmid that
bears it, while a shortened second copy is found in
Bacillus subtilis. Most bacterial PepFs are cytoplasmic
endopeptidases; however, the PepF Bacillus
amyloliquefaciens oligopeptidase is a secreted protein
and may facilitate the process of sporulation.
Specifically, the yjbG gene encoding the homolog of the
PepF1 and PepF2 oligoendopeptidases of Lactococcus
lactis has been identified in Bacillus subtilis as an
inhibitor of sporulation initiation when over expressed
from a multicopy plasmid.
Length = 472
Score = 28.0 bits (63), Expect = 2.3
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 106 RKDKDSKFRLILVESRIHDWLATTRRQRSFH 136
+ D + RL L+ +I D AT RQ +F
Sbjct: 318 ERLSDPEERLALLAGKIEDIFATVFRQIAFT 348
>gnl|CDD|224302 COG1384, LysS, Lysyl-tRNA synthetase (class I) [Translation,
ribosomal structure and biogenesis].
Length = 521
Score = 28.1 bits (63), Expect = 2.3
Identities = 16/68 (23%), Positives = 24/68 (35%), Gaps = 7/68 (10%)
Query: 60 IAQVKSVTGSKILRILKAHGLA---PEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLI 116
+ Q+ + IL IL L P+ EDL I+ A L +K KF ++
Sbjct: 375 LVQIANAEEEDILEILIRRYLPDADPDTIEDLDERIEYA---INWLRDYAPEK-VKFSIL 430
Query: 117 LVESRIHD 124
Sbjct: 431 EKPPEAEL 438
>gnl|CDD|239767 cd04234, AAK_AK, AAK_AK: Amino Acid Kinase Superfamily (AAK),
Aspartokinase (AK); this CD includes the N-terminal
catalytic domain of aspartokinase
(4-L-aspartate-4-phosphotransferase;). AK is the first
enzyme in the biosynthetic pathway of the aspartate
family of amino acids (lysine, threonine, methionine,
and isoleucine) and the bacterial cell wall component,
meso-diaminopimelate. It also catalyzes the conversion
of aspartate and ATP to aspartylphosphate and ADP. One
mechanism for the regulation of this pathway is by the
production of several isoenzymes of aspartokinase with
different repressors and allosteric inhibitors. Pairs of
ACT domains are proposed to specifically bind amino
acids leading to allosteric regulation of the enzyme. In
Escherichia coli, three different aspartokinase
isoenzymes are regulated specifically by lysine,
methionine, and threonine. AK-HSDHI (ThrA) and AK-HSDHII
(MetL) are bifunctional enzymes that consist of an
N-terminal AK and a C-terminal homoserine dehydrogenase
(HSDH). ThrA and MetL are involved in threonine and
methionine biosynthesis, respectively. The third
isoenzyme, AKIII (LysC), is monofunctional and is
involved in lysine synthesis. The three Bacillus
subtilis isoenzymes, AKI (DapG), AKII (LysC), and AKIII
(YclM), are feedback-inhibited by meso-diaminopimelate,
lysine, and lysine plus threonine, respectively. The E.
coli lysine-sensitive AK is described as a homodimer,
whereas, the B. subtilis lysine-sensitive AK is
described as a heterodimeric complex of alpha- and beta-
subunits that are formed from two in-frame overlapping
genes. A single AK enzyme type has been described in
Pseudomonas, Amycolatopsis, and Corynebacterium. The
fungal aspartate pathway is regulated at the AK step,
with L-Thr being an allosteric inhibitor of the
Saccharomyces cerevisiae AK (Hom3). At least two
distinct AK isoenzymes can occur in higher plants, one
is a monofunctional lysine-sensitive isoenzyme, which is
involved in the overall regulation of the pathway and
can be synergistically inhibited by
S-adenosylmethionine. The other isoenzyme is a
bifunctional, threonine-sensitive AK-HSDH protein. Also
included in this CD is the catalytic domain of the
Methylomicrobium alcaliphilum ectoine AK, the first
enzyme of the ectoine biosynthetic pathway, found in
this bacterium, and several other
halophilic/halotolerant bacteria.
Length = 227
Score = 27.4 bits (62), Expect = 2.6
Identities = 9/35 (25%), Positives = 18/35 (51%)
Query: 45 LTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHG 79
L Q G+ D+HG A++ ++ ++ +L G
Sbjct: 79 LDARQAGITTDDNHGAARIIEISYERLKELLAEIG 113
>gnl|CDD|180393 PRK06087, PRK06087, short chain acyl-CoA synthetase; Reviewed.
Length = 547
Score = 27.8 bits (62), Expect = 2.7
Identities = 19/79 (24%), Positives = 33/79 (41%), Gaps = 13/79 (16%)
Query: 28 ISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKI--LRILKAHGLAPEIP 85
ISS++VED + + K + D+ +A G + +LKA + +
Sbjct: 443 ISSREVEDILLQHPK-----------IHDACVVAMPDERLGERSCAYVVLKAPHHSLTLE 491
Query: 86 EDLYHLIKKAVAIRKHLER 104
E + +K VA K+ E
Sbjct: 492 EVVAFFSRKRVAKYKYPEH 510
>gnl|CDD|239793 cd04260, AAK_AKi-DapG-BS, AAK_AKi-DapG-BS: Amino Acid Kinase
Superfamily (AAK), AKi-DapG; this CD includes the
N-terminal catalytic aspartokinase (AK) domain of the
diaminopimelate-sensitive aspartokinase isoenzyme AKI
(DapG), a monofunctional class enzyme found in Bacilli
(Bacillus subtilis 168), Clostridia, and Actinobacteria
bacterial species. In Bacillus subtilis, the regulation
of the diaminopimelate-lysine biosynthetic pathway
involves dual control by diaminopimelate and lysine,
effected through separate diaminopimelate- and
lysine-sensitive aspartokinase isoenzymes. AKI activity
is invariant during the exponential and stationary
phases of growth and is not altered by addition of amino
acids to the growth medium. The role of this isoenzyme
is most likely to provide a constant level of
aspartyl-beta-phosphate for the biosynthesis of
diaminopimelate for peptidoglycan synthesis and
dipicolinate during sporulation. The B. subtilis AKI is
tetrameric consisting of two alpha and two beta
subunits; the alpha (43 kD) and beta (17 kD) subunit
formed by two in-phase overlapping genes. The alpha
subunit contains the AK catalytic domain and two ACT
domains. The beta subunit contains two ACT domains.
Length = 244
Score = 27.0 bits (60), Expect = 3.8
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 45 LTPSQIGVILRDSHGIAQVKSVTGSKILRILKAH 78
LT +Q G++ D++ A++ V KIL LK
Sbjct: 98 LTGAQAGILTDDNYSNAKIIKVNPKKILSALKEG 131
>gnl|CDD|232878 TIGR00216, ispH_lytB, (E)-4-hydroxy-3-methyl-but-2-enyl
pyrophosphate reductase (IPP and DMAPP forming). The
IspH protein (previously designated LytB) has now been
recognized as the last enzyme in the biosynthesis of
isopentenyl diphosphate (IPP) and dimethylallyl
diphosphate (DMAPP). Escherichia coli LytB protein had
been found to regulate the activity of RelA (guanosine
3',5'-bispyrophosphate synthetase I), which in turn
controls the level of a regulatory metabolite. It is
involved in penicillin tolerance and the stringent
response [Biosynthesis of cofactors, prosthetic groups,
and carriers, Other].
Length = 280
Score = 26.9 bits (60), Expect = 4.1
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 7/37 (18%)
Query: 52 VILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDL 88
L D +A +V I++AHG+ PE+ E+L
Sbjct: 55 FFLEDLDEVAAGDTV-------IIRAHGVPPEVREEL 84
>gnl|CDD|233192 TIGR00928, purB, adenylosuccinate lyase. This family consists of
adenylosuccinate lyase, the enzyme that catalyzes step 8
in the purine biosynthesis pathway for de novo synthesis
of IMP and also the final reaction in the two-step
sequence from IMP to AMP [Purines, pyrimidines,
nucleosides, and nucleotides, Purine ribonucleotide
biosynthesis].
Length = 435
Score = 26.9 bits (60), Expect = 4.3
Identities = 23/97 (23%), Positives = 45/97 (46%), Gaps = 14/97 (14%)
Query: 11 ISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSK 70
+ +SA+P+KR P I ++V + + L+P+ V L + +T S
Sbjct: 266 VGSSAMPHKRNP-----IDFENVCGL-ARVIRSVLSPALENVPLWHE------RDLTDSS 313
Query: 71 ILRIL--KAHGLAPEIPEDLYHLIKKAVAIRKHLERN 105
+ RI+ + LA + + ++KK V +++ RN
Sbjct: 314 VERIILPDSFILADIMLKTTLKVVKKLVVNPENILRN 350
>gnl|CDD|129871 TIGR00789, flhB_rel, flhB C-terminus-related protein. This model
describes a short protein (80-93 residues) homologous
to the C-terminus of the flagellar biosynthetic protein
FlhB. It is found so far only in species that also have
FlhB. In a phylogenetic tree based on alignment of both
this family and the homologous region of FlhB and its
homologs, the members of this family form a
monophyletic set [Unknown function, General].
Length = 82
Score = 25.5 bits (56), Expect = 5.1
Identities = 23/87 (26%), Positives = 35/87 (40%), Gaps = 20/87 (22%)
Query: 9 KGISASALPYKRTPPSWLKISSQ---DVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKS 65
K A AL Y K+ + +V + I + AKK HGI V+
Sbjct: 1 KIKKAVALSYDTGKDKAPKVVASGVGEVAERIIEIAKK--------------HGIPIVED 46
Query: 66 VTGSKILRILKAHGLAPEIPEDLYHLI 92
++ +L L EIPE+LY ++
Sbjct: 47 PD---LVDVLLKLDLDDEIPEELYEVV 70
>gnl|CDD|225166 COG2257, COG2257, Uncharacterized homolog of the cytoplasmic domain
of flagellar protein FhlB [Function unknown].
Length = 92
Score = 25.8 bits (57), Expect = 5.2
Identities = 20/96 (20%), Positives = 38/96 (39%), Gaps = 20/96 (20%)
Query: 13 ASALPYKRTPPSWLKISSQ---DVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGS 69
A AL Y K+ + ++ + I + AK+ HG+ +
Sbjct: 10 AVALAYDEGKDKAPKVVASGKGEIAEKIIEKAKE--------------HGVPIQEDPL-- 53
Query: 70 KILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLERN 105
++ +L L EIPE+LY ++ + A ++ N
Sbjct: 54 -LVELLLKLELGDEIPEELYEVVAEIFAFIYEVDNN 88
>gnl|CDD|224805 COG1893, ApbA, Ketopantoate reductase [Coenzyme metabolism].
Length = 307
Score = 26.5 bits (59), Expect = 6.0
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 70 KILRILKAHGLA-PEIPEDLYHLIKKAVAIRK 100
++R+ K HGLA P + LY L+K A R
Sbjct: 274 AVVRLAKKHGLATPVN-DTLYALLKAKEAERG 304
>gnl|CDD|236188 PRK08210, PRK08210, aspartate kinase I; Reviewed.
Length = 403
Score = 26.4 bits (59), Expect = 6.4
Identities = 11/34 (32%), Positives = 17/34 (50%)
Query: 45 LTPSQIGVILRDSHGIAQVKSVTGSKILRILKAH 78
LT Q G+I D+ A++ V +IL L+
Sbjct: 100 LTGGQAGIITDDNFTNAKIIEVNPDRILEALEEG 133
>gnl|CDD|220640 pfam10234, Cluap1, Clusterin-associated protein-1. This protein is
conserved from worms to humans. The protein of 413 amino
acids contains a central coiled-coil domain, possibly
the region that binds to clusterin. Cluap1 expression is
highest in the nucleus and gradually increases during
late S to G2/M phases of the cell cycle and returns to
the basal level in the G0/G1 phases. In addition, it is
upregulated in colon cancer tissues compared to
corresponding non-cancerous mucosa. It thus plays a
crucial role in the life of the cell.
Length = 269
Score = 26.1 bits (58), Expect = 7.2
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 68 GSKILRILKAHGLAPEIPED---LYHLIKKAVAIRKHLER 104
GSKI + A LA EI E LY L+ K + +R+ ++
Sbjct: 115 GSKISDLKAARQLASEITERGAALYDLLGKELDLRESRQK 154
>gnl|CDD|238801 cd01567, NAPRTase_PncB, Nicotinate phosphoribosyltransferase
(NAPRTase) family. Nicotinate phosphoribosyltransferase
catalyses the formation of NAMN and PPi from
5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic
acid, this is the first, and also rate limiting,
reaction in the NAD salvage synthesis. This salvage
pathway serves to recycle NAD degradation products.
Length = 343
Score = 26.5 bits (59), Expect = 7.3
Identities = 12/30 (40%), Positives = 15/30 (50%), Gaps = 3/30 (10%)
Query: 87 DLYHLIKKAVAIRKHLERNRKDKDSKFRLI 116
D LIKK RKHL+ D + K +I
Sbjct: 273 DPVELIKKV---RKHLDELGIDLNKKKIII 299
>gnl|CDD|237783 PRK14667, uvrC, excinuclease ABC subunit C; Provisional.
Length = 567
Score = 26.2 bits (58), Expect = 7.9
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 89 YHLIKKAVAIRKHLER--NRKDKDSKFRLILVESRIHDWLAT 128
Y I KA I+ L + + + D K R I ES +W+ T
Sbjct: 28 YIYIGKAKNIKNRLLQHYKQSETDPKERAIFSESSSLEWIIT 69
>gnl|CDD|185635 PTZ00456, PTZ00456, acyl-CoA dehydrogenase; Provisional.
Length = 622
Score = 26.4 bits (58), Expect = 9.0
Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 5/80 (6%)
Query: 53 ILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVA-IRKHLERNRKDKDS 111
ILRD+ + TG + L + L+ + ++ K+ +R HL
Sbjct: 452 ILRDARIGTLYEGTTGIQALDFIGRKVLSLKGGNEVARFGKRVSKLVRAHLFSRGALGQY 511
Query: 112 KFRLILVESRIHDW-LATTR 130
RL L++ + W LATTR
Sbjct: 512 ARRLWLLQKQ---WRLATTR 528
>gnl|CDD|222706 pfam14356, DUF4403, Domain of unknown function (DUF4403). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 455 and 518 amino
acids in length. There is a single completely conserved
residue W that may be functionally important.
Length = 425
Score = 26.1 bits (58), Expect = 9.0
Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 8/55 (14%)
Query: 16 LPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSK 70
+ + PP+WL++ Q + + +T +G+ A+ ++VTG K
Sbjct: 182 ILLSKPPPAWLRVKPQRILATPLRLDNNAIT-LTLGI-------KARTRTVTGPK 228
>gnl|CDD|143499 cd06826, PLPDE_III_AR2, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme, Alanine Racemase 2. This
subfamily is composed of bacterial alanine racemases
(EC 5.1.1.1) with similarity to Yersinia pestis and
Vibrio cholerae alanine racemase (AR) 2. ARs catalyze
the interconversion between L- and D-alanine, an
essential component of the peptidoglycan layer of
bacterial cell walls. These proteins are similar to
other bacterial ARs and are fold type III PLP-dependent
enzymes containing contains an N-terminal PLP-binding
TIM-barrel domain and a C-terminal beta-sandwich
domain. They exist as homodimers with active sites that
lie at the interface between the TIM barrel domain of
one subunit and the beta-sandwich domain of the other
subunit. Homodimer formation and the presence of the
PLP cofactor are required for catalytic activity.
Length = 365
Score = 26.2 bits (58), Expect = 9.4
Identities = 17/44 (38%), Positives = 28/44 (63%), Gaps = 5/44 (11%)
Query: 24 SWLKISSQDVEDNICKFAKKGLTP-SQIGVILR-DS--HGIAQV 63
+WL+IS+ E+NI K KK L +++ +++ D+ HGIA V
Sbjct: 2 AWLEISTGAFENNI-KLLKKLLGGNTKLCAVMKADAYGHGIALV 44
>gnl|CDD|223422 COG0345, ProC, Pyrroline-5-carboxylate reductase [Amino acid
transport and metabolism].
Length = 266
Score = 26.0 bits (58), Expect = 9.4
Identities = 11/48 (22%), Positives = 19/48 (39%), Gaps = 6/48 (12%)
Query: 46 TPSQIGVILRDSHGIAQVKSVTGS---KILRILKAHGLAPEIPEDLYH 90
TP+ +G I+ +V+ + +L A G E+ E L
Sbjct: 119 TPALVG---AGVTAISANANVSEEDKAFVEALLSAVGKVVEVEESLMD 163
>gnl|CDD|223953 COG1022, FAA1, Long-chain acyl-CoA synthetases (AMP-forming) [Lipid
metabolism].
Length = 613
Score = 26.1 bits (58), Expect = 9.4
Identities = 16/84 (19%), Positives = 28/84 (33%), Gaps = 4/84 (4%)
Query: 45 LTPSQIGVILRDSH--GIAQVKSVTGSKILRILKAH--GLAPEIPEDLYHLIKKAVAIRK 100
TP Q+ IL +S I +L +L+ + + DL +A A+
Sbjct: 104 STPEQLAYILNESESKVIFVENQELLDLVLPVLEDCPKVVDLIVIIDLVREAVEAKALVL 163
Query: 101 HLERNRKDKDSKFRLILVESRIHD 124
+ + +E RI
Sbjct: 164 EVFPDEGISLFLIDSAGLEGRIAP 187
>gnl|CDD|220767 pfam10459, Peptidase_S46, Peptidase S46. Dipeptidyl-peptidase 7
(DPP-7) is the best characterized member of this family.
It is a serine peptidase that is located on the cell
surface and is predicted to have two N-terminal
transmembrane domains.
Length = 696
Score = 26.0 bits (58), Expect = 9.5
Identities = 9/20 (45%), Positives = 14/20 (70%), Gaps = 2/20 (10%)
Query: 17 PYKRTPPSWLKISSQDVEDN 36
PYK P +LK+S+Q V++
Sbjct: 223 PYK--PKHFLKVSAQGVKEG 240
>gnl|CDD|225831 COG3294, COG3294, HD supefamily hydrolase [General function
prediction only].
Length = 269
Score = 25.9 bits (57), Expect = 9.6
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 47 PSQIGVILRDSHGIAQVKSVTGSKILR 73
P +I V +++ G+ QV+ V G KI R
Sbjct: 216 PVRIEVEMQNEAGVFQVEEVLGEKIHR 242
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 0.135 0.406
Gapped
Lambda K H
0.267 0.0762 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,802,135
Number of extensions: 700272
Number of successful extensions: 801
Number of sequences better than 10.0: 1
Number of HSP's gapped: 799
Number of HSP's successfully gapped: 50
Length of query: 152
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 64
Effective length of database: 7,034,450
Effective search space: 450204800
Effective search space used: 450204800
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: 55 (24.9 bits)