RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3051
(111 letters)
>gnl|CDD|215475 PLN02880, PLN02880, tyrosine decarboxylase.
Length = 490
Score = 119 bits (299), Expect = 5e-33
Identities = 50/109 (45%), Positives = 71/109 (65%), Gaps = 2/109 (1%)
Query: 1 MNSEEFREFGKAAIDFIADYHDTVRQRQVLPSVQPGYLASLVPGEMPEEGEDWRHIMRDM 60
M++E+ RE G +DFIADY+ ++ VL VQPGYL L+P P + E ++ D+
Sbjct: 10 MDAEQLRECGHRMVDFIADYYKSIENFPVLSQVQPGYLRELLPDSAPNQPETLDQVLDDV 69
Query: 61 NTVIMPGITHWQSPHFHAFYPSASSFPSILGELLSTGLGVLSFTW--SP 107
I+PG+THWQSP++ A+YPS SS LGE+LS GL ++ F+W SP
Sbjct: 70 QAKILPGVTHWQSPNYFAYYPSNSSVAGFLGEMLSAGLNIVGFSWITSP 118
>gnl|CDD|178200 PLN02590, PLN02590, probable tyrosine decarboxylase.
Length = 539
Score = 108 bits (271), Expect = 5e-29
Identities = 51/109 (46%), Positives = 70/109 (64%), Gaps = 4/109 (3%)
Query: 1 MNSEEFREFGKAAIDFIADYH----DTVRQRQVLPSVQPGYLASLVPGEMPEEGEDWRHI 56
M+SE RE G +DFIADY+ D+ + VL VQPGYL ++P PE E + +
Sbjct: 54 MDSELLREQGHIMVDFIADYYKNLQDSPQDFPVLSQVQPGYLRDMLPDSAPERPESLKEL 113
Query: 57 MRDMNTVIMPGITHWQSPHFHAFYPSASSFPSILGELLSTGLGVLSFTW 105
+ D++ IMPGITHWQSP + A+Y S++S LGE+L+ GL V+ FTW
Sbjct: 114 LDDVSKKIMPGITHWQSPSYFAYYASSTSVAGFLGEMLNAGLSVVGFTW 162
>gnl|CDD|215836 pfam00282, Pyridoxal_deC, Pyridoxal-dependent decarboxylase
conserved domain.
Length = 373
Score = 93.2 bits (232), Expect = 7e-24
Identities = 32/71 (45%), Positives = 46/71 (64%)
Query: 35 PGYLASLVPGEMPEEGEDWRHIMRDMNTVIMPGITHWQSPHFHAFYPSASSFPSILGELL 94
PGYL L+P P E I+ D+ IMPG+T W SP+FHA++P+ +S+PS+LG++L
Sbjct: 1 PGYLRPLLPEAAPIIPEPLLDILGDIRKNIMPGVTTWHSPNFHAYFPAGNSYPSLLGDML 60
Query: 95 STGLGVLSFTW 105
S + FTW
Sbjct: 61 SDAINCNGFTW 71
>gnl|CDD|223154 COG0076, GadB, Glutamate decarboxylase and related PLP-dependent
proteins [Amino acid transport and metabolism].
Length = 460
Score = 44.3 bits (105), Expect = 2e-06
Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 3/97 (3%)
Query: 14 IDFIADYHDTVRQRQVLPSVQPGYLASLVPGEMPEEGEDWRHIMRDMN-TVIMPGITHWQ 72
ID + D +R S+ P + A PE+GE ++ ++ +I +
Sbjct: 1 IDGLIDKDMLNSKRYSGDSLSPLFGALSDSRMAPEKGEPLEEVLDELAELLIKDELYLDG 60
Query: 73 SPHFHAFYPSASSFPSILGELLSTGL--GVLSFTWSP 107
P + + P + ELL + L + SP
Sbjct: 61 HPRANLAGFCPTRVPPVAAELLVSALNKNLGDPDESP 97
>gnl|CDD|99743 cd06450, DOPA_deC_like, DOPA decarboxylase family. This family
belongs to pyridoxal phosphate (PLP)-dependent aspartate
aminotransferase superfamily (fold I). The major groups
in this CD correspond to DOPA/tyrosine decarboxylase
(DDC), histidine decarboxylase (HDC), and glutamate
decarboxylase (GDC). DDC is active as a dimer and
catalyzes the decarboxylation of tyrosine. GDC catalyzes
the decarboxylation of glutamate and HDC catalyzes the
decarboxylation of histidine.
Length = 345
Score = 31.4 bits (72), Expect = 0.057
Identities = 9/31 (29%), Positives = 17/31 (54%)
Query: 76 FHAFYPSASSFPSILGELLSTGLGVLSFTWS 106
F A + + P++L E+L++ + FTW
Sbjct: 1 FLAGFVTTMDPPALLLEMLTSAKNAIDFTWD 31
>gnl|CDD|233256 TIGR01063, gyrA, DNA gyrase, A subunit. This model describes the
common type II DNA topoisomerase (DNA gyrase). Two
apparently independently arising families, one in the
Proteobacteria and one in Gram-positive lineages, are
both designated toposisomerase IV [DNA metabolism, DNA
replication, recombination, and repair].
Length = 800
Score = 29.6 bits (67), Expect = 0.31
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 7 REFGKAAIDFIADYHDTVRQRQVLPSVQPGYLA 39
R+ K +DF+ +Y + ++ VLPS P L
Sbjct: 129 RDIDKETVDFVPNYDGSEQEPTVLPSRFPNLLV 161
>gnl|CDD|226729 COG4279, COG4279, Uncharacterized conserved protein [Function
unknown].
Length = 266
Score = 27.8 bits (62), Expect = 1.2
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 34 QPGYLASLVPGEMPEEGED 52
+ Y A L+ GEMPE ED
Sbjct: 88 KANYAAKLLSGEMPESIED 106
>gnl|CDD|240478 cd12898, SPRY_PRY_TRIM76, PRY/SPRY domain in tripartite
motif-containing protein 76 (TRIM76), also called
cardiomyopathy-associated protein 5. This domain,
consisting of the distinct N-terminal PRY subdomain
followed by the SPRY subdomain, is found at the
C-terminus of TRIM76, a Class I TRIM protein. TRIM76
(also known as cardiomyopathy-associated protein 5 or
CMYA5 or myospryn or SPRYD2) is a muscle-specific
member of the TRIM superfamily, but lacks the RING
domain. It has been suggested that TRIM76 is involved
in two distinct processes, protein kinase A signaling
and vesicular trafficking. It has also been implicated
in Duchenne muscular dystrophy and cardiac disease;
gene polymorphism of TRIM76 is associated with left
ventricular wall thickness in patients with
hypertension while its interactions with M-band titin
and calpain 3 link it to tibial and limb-girdle
muscular dystrophies.
Length = 171
Score = 27.5 bits (61), Expect = 1.2
Identities = 14/40 (35%), Positives = 16/40 (40%), Gaps = 7/40 (17%)
Query: 55 HIMRDMNTVIMPGITHWQSPHFHAFYPSASSFPSILGELL 94
I D TVI SP + PS+LGELL
Sbjct: 16 EISADRTTVIYCHEAPEGSPTD-------TECPSVLGELL 48
>gnl|CDD|219860 pfam08486, SpoIID, Stage II sporulation protein. This domain is
found in the stage II sporulation protein SpoIID.
SpoIID is necessary for membrane migration as well as
for some of the earlier steps in engulfment during
bacterial endospore formation. The domain is also found
in amidase enhancer proteins. Amidases, like SpoIID,
are cell wall hydrolases.
Length = 95
Score = 26.3 bits (59), Expect = 1.7
Identities = 6/11 (54%), Positives = 7/11 (63%)
Query: 37 YLASLVPGEMP 47
YL +V EMP
Sbjct: 19 YLKGVVAAEMP 29
>gnl|CDD|184752 PRK14573, PRK14573, bifunctional D-alanyl-alanine synthetase
A/UDP-N-acetylmuramate--L-alanine ligase; Provisional.
Length = 809
Score = 27.1 bits (60), Expect = 1.9
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 6/51 (11%)
Query: 48 EEGEDWRHIMRDMNTVIMPGITHWQSPHFHAFYPSASSFPSILGELLSTGL 98
EEG W + +MN + PG+T SP AF ++ I+ +L+ GL
Sbjct: 743 EEGNFW---LSEMNPI--PGMTE-ASPFLTAFVRKGWTYEQIVHQLIIDGL 787
>gnl|CDD|130134 TIGR01062, parC_Gneg, DNA topoisomerase IV, A subunit,
proteobacterial. Operationally, topoisomerase IV is a
type II topoisomerase required for the decatenation of
chromosome segregation. Not every bacterium has both a
topo II and a topo IV. The topo IV families of the
Gram-positive bacteria and the Gram-negative bacteria
appear not to represent a single clade among the type II
topoisomerases, and are represented by separate models
for this reason [DNA metabolism, DNA replication,
recombination, and repair].
Length = 735
Score = 27.2 bits (60), Expect = 2.2
Identities = 9/33 (27%), Positives = 18/33 (54%)
Query: 8 EFGKAAIDFIADYHDTVRQRQVLPSVQPGYLAS 40
E G+ +DF ++ T+ + +LP+ P L +
Sbjct: 131 ELGQGTVDFRPNFDGTLLEPVILPARLPNILLN 163
>gnl|CDD|185265 PRK15367, PRK15367, type III secretion system protein SsaD;
Provisional.
Length = 395
Score = 26.8 bits (59), Expect = 2.8
Identities = 20/82 (24%), Positives = 34/82 (41%), Gaps = 17/82 (20%)
Query: 33 VQPGYLASLVPGEMPEE---------GEDWRHIMRDMNTVIMPGITHWQSPHFHAFYPSA 83
++ GY + V E P + WR + + + PG+ HWQ H H
Sbjct: 211 IKMGYPHAEVSSEGPGSVLIHDDIQMDQQWRKVQPLLADI--PGLLHWQISHSH-----Q 263
Query: 84 SSFPSILGELLSTGL-GVLSFT 104
S I+ ++ GL G+++ T
Sbjct: 264 SQGDDIISAIIENGLVGLVNVT 285
>gnl|CDD|216055 pfam00674, DUP, DUP family. This family consists of several
yeast proteins of unknown functions. Swiss-prot
annotates these as belonging to the DUP family. Several
members of this family contain an internal duplication
of this region.
Length = 108
Score = 25.3 bits (56), Expect = 4.9
Identities = 10/33 (30%), Positives = 18/33 (54%), Gaps = 5/33 (15%)
Query: 49 EGEDWRHIMRDMNT-VIMPGITHWQSPHFHAFY 80
+G++W I +MN + + W +P+F FY
Sbjct: 58 DGKEWDTIAYNMNQYLFEHKL--WNTPYF--FY 86
>gnl|CDD|163355 TIGR03612, RutA, pyrimidine utilization protein A. This protein is
observed in operons extremely similar to that
characterized in E. coli K-12 responsible for the import
and catabolism of pyrimidines, primarily uracil. This
protein is a member of the luciferase family defined by
pfam00296 and is likely a FMN-dependent monoxygenase
[Unknown function, Enzymes of unknown specificity].
Length = 355
Score = 25.9 bits (57), Expect = 5.2
Identities = 11/42 (26%), Positives = 16/42 (38%), Gaps = 12/42 (28%)
Query: 68 ITHWQSP------------HFHAFYPSASSFPSILGELLSTG 97
+T WQ P +F Y + + +L EL TG
Sbjct: 117 VTGWQKPEYSQMGLWPGDEYFADRYEYLAEYVQVLRELWETG 158
>gnl|CDD|235681 PRK06039, ileS, isoleucyl-tRNA synthetase; Reviewed.
Length = 975
Score = 25.9 bits (58), Expect = 5.4
Identities = 9/24 (37%), Positives = 11/24 (45%), Gaps = 2/24 (8%)
Query: 2 NSEEFREFGKAAIDFIADYHDTVR 25
N E F + A DFI + D R
Sbjct: 536 NKEWFEKHFPA--DFIVEGIDQTR 557
>gnl|CDD|220046 pfam08863, YolD, YolD-like protein. Members of this family are
functionally uncharacterized. However it has been
predicted that thes proteins are functionally
equivalent to the UmuD subunit of polymerase V from
gram-negative bacteria.
Length = 92
Score = 24.8 bits (55), Expect = 5.7
Identities = 8/27 (29%), Positives = 13/27 (48%)
Query: 46 MPEEGEDWRHIMRDMNTVIMPGITHWQ 72
+PE E R +++ N V P + Q
Sbjct: 1 LPEHFESLREYIKEQNKVEKPELDEDQ 27
>gnl|CDD|234570 PRK00009, PRK00009, phosphoenolpyruvate carboxylase; Reviewed.
Length = 911
Score = 25.9 bits (58), Expect = 5.9
Identities = 10/22 (45%), Positives = 14/22 (63%), Gaps = 2/22 (9%)
Query: 39 ASLVPGEMPEEGEDWRHIMRDM 60
ASL+P PE +WR IM ++
Sbjct: 668 ASLLP--PPEPKPEWREIMDEL 687
>gnl|CDD|176463 cd01359, Argininosuccinate_lyase, Argininosuccinate lyase
(argininosuccinase, ASAL). This group contains ASAL and
related proteins. It is a member of the Lyase class I
family. Members of this family for the most part
catalyze similar beta-elimination reactions in which a
C-N or C-O bond is cleaved with the release of fumarate
as one of the products. These proteins are active as
tetramers. The four active sites of the homotetrameric
enzyme are each formed by residues from three different
subunits. ASAL is a cytosolic enzyme which catalyzes the
reversible breakdown of argininosuccinate to arginine
and fumarate during arginine biosynthesis. In ureotelic
species ASAL also catalyzes a reaction involved in the
production of urea. Included in this group are the major
soluble avian eye lens proteins from duck, delta 1 and
delta 2 crystallin. Of these two isoforms only delta 2
has retained ASAL activity. These crystallins may have
evolved by, gene recruitment of ASAL followed by gene
duplication. In humans, mutations in ASAL result in the
autosomal recessive disorder argininosuccinic aciduria.
Length = 435
Score = 25.6 bits (57), Expect = 7.1
Identities = 7/10 (70%), Positives = 7/10 (70%)
Query: 63 VIMPGITHWQ 72
IMPG TH Q
Sbjct: 127 TIMPGYTHLQ 136
>gnl|CDD|173301 PRK14840, PRK14840, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 250
Score = 25.2 bits (55), Expect = 7.9
Identities = 18/62 (29%), Positives = 24/62 (38%), Gaps = 14/62 (22%)
Query: 54 RHIMRDMNTVIMPGITHWQSPH--------FHAFYPSASSFPSILGELLSTGLGVLS-FT 104
RH+ +IM G W H Y A S P I+ L G+ VL+ F
Sbjct: 20 RHV-----AIIMDGNRRWYRKHEQFCQKRAISGHYYGAKSLPQIVDTALHLGIEVLTLFA 74
Query: 105 WS 106
+S
Sbjct: 75 FS 76
>gnl|CDD|238111 cd00187, TOP4c, DNA Topoisomerase, subtype IIA; domain A';
bacterial DNA topoisomerase IV (C subunit, ParC),
bacterial DNA gyrases (A subunit, GyrA),mammalian DNA
toposiomerases II. DNA topoisomerases are essential
enzymes that regulate the conformational changes in DNA
topology by catalysing the concerted breakage and
rejoining of DNA strands during normal cellular growth.
Length = 445
Score = 25.2 bits (56), Expect = 9.7
Identities = 7/30 (23%), Positives = 14/30 (46%)
Query: 6 FREFGKAAIDFIADYHDTVRQRQVLPSVQP 35
+ +DF+ +Y + +VLP + P
Sbjct: 106 LPDIDDPTVDFVPNYDGQEVEPEVLPPIFP 135
>gnl|CDD|238278 cd00498, Hsp33, Heat shock protein 33 (Hsp33): Cytosolic protein
that acts as a molecular chaperone under oxidative
conditions. In normal (reducing) cytosolic conditions,
four conserved Cys residues are coordinated by a Zn ion.
Under oxidative stress (such as heat shock), the Cys
are reversibly oxidized to disulfide bonds, which causes
the chaperone activity to be turned on. Hsp33 is
homodimeric in its functional form.
Length = 275
Score = 24.9 bits (55), Expect = 9.7
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 36 GYLASLVPGEMPEEGEDWRHIMRDMNTV 63
G L ++PG E+ + W +++ M TV
Sbjct: 170 GLLLQVLPGADEEDIDAWEKVIKLMPTV 197
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 0.136 0.434
Gapped
Lambda K H
0.267 0.0793 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,921,844
Number of extensions: 505117
Number of successful extensions: 592
Number of sequences better than 10.0: 1
Number of HSP's gapped: 590
Number of HSP's successfully gapped: 32
Length of query: 111
Length of database: 10,937,602
Length adjustment: 75
Effective length of query: 36
Effective length of database: 7,611,052
Effective search space: 273997872
Effective search space used: 273997872
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 (24.1 bits)