RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy521
(173 letters)
>gnl|CDD|218472 pfam05158, RNA_pol_Rpc34, RNA polymerase Rpc34 subunit. Subunit
specific to RNA Pol III, the tRNA specific polymerase.
The C34 subunit of yeast RNA Pol III is part of a
subcomplex of three subunits which have no counterpart
in the other two nuclear RNA polymerases. This subunit
interacts with TFIIIB70 and is therefore participates in
Pol III recruitment.
Length = 312
Score = 162 bits (412), Expect = 7e-50
Identities = 53/153 (34%), Positives = 81/153 (52%), Gaps = 13/153 (8%)
Query: 33 FEASKKKVYMLFDLEPDRSLTGGTWYQDQDFEVEFVDVLNQQCYRFLQLKRE---KTANN 89
+A +K+YML++LEP +TGG WY D + +VEF++ L + +RF+ K
Sbjct: 136 VKAPTRKMYMLYNLEPSEEVTGGPWYTDGELDVEFINTLRRVIFRFVSQKTYVNGFGGEK 195
Query: 90 TNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTD 149
P A + T +E+ FI +LGI+ V LSEEDI+ ++ETL++DGK+E++ G
Sbjct: 196 KALPYPAGYKSYPTVEEIATFINELGITNVRLSEEDIQQLVETLVYDGKLEKVKPGAGYR 255
Query: 150 MYRAV----------SPYFAVTGLSTSPCGVCP 172
+ R GL +PCG CP
Sbjct: 256 LQRVTLQEVLQMSQKRRPLPANGLVEAPCGNCP 288
>gnl|CDD|227442 COG5111, RPC34, DNA-directed RNA polymerase III, subunit C34
[Transcription].
Length = 301
Score = 97.0 bits (241), Expect = 1e-24
Identities = 40/138 (28%), Positives = 70/138 (50%), Gaps = 5/138 (3%)
Query: 38 KKVYMLFDLEPDRSLTGGTWYQDQDFEVEFVDVLNQQCYRFLQLKREKTANNTNGPLVAQ 97
+K+YML+DL P +TGG W+ D + +VEF+ L + RFL+ N GP V
Sbjct: 142 RKIYMLYDLVPSEEITGGPWFTDNELDVEFIARLLEIIERFLEKNLFPRKNFEEGPNVFY 201
Query: 98 RLAC---ATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNIDGTDMYRAV 154
T +++ ++ ++ I V L +++ ++ + L++DGK+E++++ YRA
Sbjct: 202 APKYEDYPTLEDIMNYVRNVNILSVPLRLDNLESLADVLVYDGKVEKLHS-GPIYRYRAF 260
Query: 155 SPYFAVTGLSTSPCGVCP 172
PY A P G
Sbjct: 261 KPY-AKNQGEGEPAGNKA 277
>gnl|CDD|216147 pfam00844, Gemini_coat, Geminivirus coat protein/nuclear export
factor BR1 family. It has been shown that the 104
N-terminal amino acids of the maize streak virus coat
protein bind DNA non- specifically. This family also
includes various geminivirus movement proteins that are
nuclear export factors or shuttles. One member BR1
facilitates the export of both ds and ss DNA form the
nucleus.
Length = 244
Score = 30.3 bits (69), Expect = 0.38
Identities = 12/57 (21%), Positives = 19/57 (33%), Gaps = 2/57 (3%)
Query: 70 VLNQQCYRFLQLKREKTAN-NTNGPLVAQRLACATPKEVRKFITDLGISKVELSEED 125
V RF +KR+ ++ G VR+F LG+ + E
Sbjct: 149 VKRDLRDRF-VVKRKWKRVVSSEGDTNMVDFPGKNQLSVRRFFKWLGVKDEWKNSET 204
>gnl|CDD|224202 COG1283, NptA, Na+/phosphate symporter [Inorganic ion transport and
metabolism].
Length = 533
Score = 29.5 bits (67), Expect = 0.93
Identities = 12/41 (29%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 105 KEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINNI 145
+E++ ++ +SK LSEE+ R E + +E I +I
Sbjct: 380 EEIKLYLAR--LSKEGLSEEESRRWAEIIDAAINLEHIGDI 418
>gnl|CDD|215345 PLN02641, PLN02641, anthranilate phosphoribosyltransferase.
Length = 343
Score = 29.3 bits (66), Expect = 0.98
Identities = 13/39 (33%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 104 PKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQI 142
R+ I L I +L+EE+ L+ LL D QI
Sbjct: 1 IASFRQLIESL-IQGTDLTEEEAEAALDFLLDDADEAQI 38
>gnl|CDD|227754 COG5467, COG5467, Uncharacterized conserved protein [Function
unknown].
Length = 104
Score = 28.3 bits (63), Expect = 1.0
Identities = 25/104 (24%), Positives = 39/104 (37%), Gaps = 25/104 (24%)
Query: 59 QDQDFEVEFVDVLNQQCYRFLQLKREKTANNTNGPLVAQRLACATPKE------------ 106
++Q FE +F L+++ L+ K N G A L + +
Sbjct: 7 REQGFERKFA--LDEE----LRFKATARRNKLLGLWAAGLLGKSDAEAYAREVVASDFEE 60
Query: 107 ------VRKFITDLGISKVELSEEDIRTILETLLFDGKIEQINN 144
RK DL + V +E +IR + LL IEQI +
Sbjct: 61 AGDEDVFRKVREDLDAAGVSTTEGEIRMKMAELLAQA-IEQIKS 103
>gnl|CDD|223251 COG0173, AspS, Aspartyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 585
Score = 29.1 bits (66), Expect = 1.3
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 7/45 (15%)
Query: 76 YRFLQLKREKTANNTNGPLVAQRLACATPKEVRKFITDLGISKVE 120
YR+L L+R + N +L K +R F+ D G ++E
Sbjct: 127 YRYLDLRRPEMQKN-------LKLRSKVTKAIRNFLDDQGFLEIE 164
>gnl|CDD|178810 PRK00034, gatC, aspartyl/glutamyl-tRNA amidotransferase subunit C;
Reviewed.
Length = 95
Score = 27.5 bits (62), Expect = 1.7
Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 8/51 (15%)
Query: 103 TPKEVRKFITDLGISKVELSEEDIRTILETL---LFDGKIEQINNIDGTDM 150
T +EV+ + L +++ELSEE++ L L +EQ+N +D +
Sbjct: 4 TREEVKH-LAKL--ARLELSEEELEKFAGQLNKIL--DFVEQLNEVDTEGV 49
>gnl|CDD|233418 TIGR01448, recD_rel, helicase, putative, RecD/TraA family. This
model describes a family similar to RecD, the
exodeoxyribonuclease V alpha chain of TIGR01447. Members
of this family, however, are not found in a context of
RecB and RecC and are longer by about 200 amino acids at
the amino end. Chlamydia muridarum has both a member of
this family and a RecD [Unknown function, Enzymes of
unknown specificity].
Length = 720
Score = 28.6 bits (64), Expect = 2.1
Identities = 20/105 (19%), Positives = 37/105 (35%), Gaps = 13/105 (12%)
Query: 40 VYMLFDLEPDRSLTGGTWYQDQDFEVEFVDVLNQQCYRFLQLKREKTANNTNGPLVAQRL 99
VY L + G T+ F + V +LN Q +E+ + +RL
Sbjct: 216 VYSLQQACTE---EGHTYLPRNRFIKQVVHLLNVQ-------PQERLLVPE--AVELERL 263
Query: 100 ACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGK-IEQIN 143
++ + + + +E+ I + + LL I IN
Sbjct: 264 YLDEEPKLAAEDGRIYLPSLFRAEKQIASHIRRLLATSPAIGAIN 308
>gnl|CDD|176800 cd08966, EcFpg-like_N, N-terminal domain of Escherichia coli
Fpg1/MutM and related bacterial DNA glycosylases. This
family contains the N-terminal domain of Escherichia
coli Fpg1/MutM and related bacterial DNA glycosylases.
It belongs to the FpgNei_N, [N-terminal domain of Fpg
(formamidopyrimidine-DNA glycosylase, MutM)_Nei
(endonuclease VIII)] domain superfamily. DNA
glycosylases maintain genome integrity by recognizing
base lesions created by ionizing radiation, alkylating
or oxidizing agents, and endogenous reactive oxygen
species. They initiate the base-excision repair process,
which is completed with the help of enzymes such as
phosphodiesterases, AP endonucleases, DNA polymerases
and DNA ligases. DNA glycosylases cleave the N-glycosyl
bond between the sugar and the damaged base, creating an
AP (apurinic/apyrimidinic) site. Most FpgNei DNA
glycosylases use their N-terminal proline residue as the
key catalytic nucleophile, and the reaction proceeds via
a Schiff base intermediate. Escherichia coli Fpg mainly
recognizes and excises damaged purines such as
8-oxo-7,8-dihydroguanine (8-oxoG) and
2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG). It
is bifunctional, having both a DNA glycosylase
(recognition activity) and a AP lyase activity. In
addition to this EcFpg-like_N domain, enzymes belonging
to this family contain a helix-two turn-helix (H2TH)
domain and a zinc-finger motif, which also contribute
residues to the active site.
Length = 120
Score = 27.1 bits (61), Expect = 3.0
Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 11/57 (19%)
Query: 11 YMLFDLEPDRSL------TGGTWYQDQDFEASKKKVYMLFDLEPDRSLTGGTWYQDQ 61
Y+LF+L+ L TG D E +K +++F+L+ R L + D
Sbjct: 59 YLLFELDDGLVLVIHLGMTGRLLVVPPD-EPPEKHDHVIFELDDGREL----RFNDP 110
>gnl|CDD|100087 cd03085, PGM1, Phosphoglucomutase 1 (PGM1) catalyzes the
bidirectional interconversion of glucose-1-phosphate
(G-1-P) and glucose-6-phosphate (G-6-P) via a glucose
1,6-diphosphate intermediate, an important metabolic
step in prokaryotes and eukaryotes. In one direction,
G-1-P produced from sucrose catabolism is converted to
G-6-P, the first intermediate in glycolysis. In the
other direction, conversion of G-6-P to G-1-P generates
a substrate for synthesis of UDP-glucose which is
required for synthesis of a variety of cellular
constituents including cell wall polymers and
glycoproteins. The PGM1 family also includes a
non-enzymatic PGM-related protein (PGM-RP) thought to
play a structural role in eukaryotes, as well as
pp63/parafusin, a phosphoglycoprotein that plays an
important role in calcium-regulated exocytosis in
ciliated protozoans. PGM1 belongs to the
alpha-D-phosphohexomutase superfamily which includes
several related enzymes that catalyze a reversible
intramolecular phosphoryl transfer on their sugar
substrates. Other members of this superfamily include
phosphoglucosamine mutase (PNGM),
phosphoacetylglucosamine mutase (PAGM), the bacterial
phosphomannomutase ManB, the bacterial
phosphoglucosamine mutase GlmM, and the bifunctional
phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of
these enzymes has four domains with a centrally located
active site formed by four loops, one from each domain.
All four domains are included in this alignment model.
Length = 548
Score = 27.6 bits (62), Expect = 3.6
Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 30 DQDFEASKK--KVYMLFDLEPDRSLTGGTWYQDQDFEVEFVD 69
D+ +E +KK + + D + D S G T + + F VE +D
Sbjct: 140 DKIYEITKKITEYKIADDPDVDLSKIGVTKFGGKPFTVEVID 181
>gnl|CDD|148766 pfam07345, DUF1476, Domain of unknown function (DUF1476). This
family consists of several hypothetical bacterial
proteins of around 100 residues in length. Members of
this family are found in Bradyrhizobium, Rhizobium,
Brucella and Caulobacter species. The function of this
family is unknown.
Length = 103
Score = 26.5 bits (59), Expect = 3.7
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 107 VRKFITDLGISKVELSEEDIRTILETLL 134
+RK DL + VE+SE +IR ++ LL
Sbjct: 69 LRKVRGDLAAAGVEISEAEIRAKMDELL 96
>gnl|CDD|181334 PRK08263, PRK08263, short chain dehydrogenase; Provisional.
Length = 275
Score = 27.3 bits (61), Expect = 4.5
Identities = 16/70 (22%), Positives = 29/70 (41%), Gaps = 25/70 (35%)
Query: 120 ELSEEDIRTILETLLF-----------------DGKIEQINNIDG------TDMYRAVSP 156
E++E + R ++T F G I QI++I G + +Y A
Sbjct: 95 EVTESEARAQIDTNFFGALWVTQAVLPYLREQRSGHIIQISSIGGISAFPMSGIYHASK- 153
Query: 157 YFAVTGLSTS 166
+A+ G+S +
Sbjct: 154 -WALEGMSEA 162
>gnl|CDD|226512 COG4025, COG4025, Predicted membrane protein [Function unknown].
Length = 284
Score = 27.1 bits (60), Expect = 5.3
Identities = 8/41 (19%), Positives = 15/41 (36%), Gaps = 1/41 (2%)
Query: 91 NGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTILE 131
N P + +L PK L + + S + ++E
Sbjct: 23 NLPWIVVKLLKEGPKRSAMKTEQL-LRTIGESASKVEKVME 62
>gnl|CDD|216321 pfam01136, Peptidase_U32, Peptidase family U32.
Length = 232
Score = 26.9 bits (60), Expect = 6.0
Identities = 11/29 (37%), Positives = 18/29 (62%), Gaps = 4/29 (13%)
Query: 109 KFITDLGISKV----ELSEEDIRTILETL 133
+F+ +LG +V ELS ++I+ I E L
Sbjct: 54 RFLAELGAKRVVLARELSLDEIKEIAEKL 82
>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 576
Score = 27.0 bits (60), Expect = 6.1
Identities = 7/11 (63%), Positives = 8/11 (72%)
Query: 162 GLSTSPCGVCP 172
GL+ PC VCP
Sbjct: 67 GLTAEPCNVCP 77
>gnl|CDD|221358 pfam11985, DUF3486, Protein of unknown function (DUF3486). This
family of proteins is functionally uncharacterized. This
protein is found in bacteria and viruses. Proteins in
this family are about 190 amino acids in length.
Length = 179
Score = 26.5 bits (59), Expect = 6.8
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 117 SKVELSEEDIRTILETLLFDGKIEQ 141
SKV+L ++R L+ L +G Q
Sbjct: 5 SKVDLLPPEVRQWLDRRLREGGFTQ 29
>gnl|CDD|189012 cd09605, M3A, Peptidase M3A family includes Thimet oligopeptidase,
dipeptidyl carboxypeptidase and mitochondrial
intermediate peptidase. The peptidase M3-like family,
also called neurolysin-like family, is part of the
"zincins" metallopeptidases, and includes M3, M2 and M32
families of metallopeptidases. The M3 family is
subdivided into two subfamilies: the widespread M3A,
which comprises a number of high-molecular mass endo-
and exopeptidases from bacteria, archaea, protozoa,
fungi, plants and animals, and the small M3B, whose
members are enzymes primarily from bacteria. Well-known
mammalian/eukaryotic M3A endopeptidases are the thimet
oligopeptidase (TOP; endopeptidase 3.4.24.15),
neurolysin (alias endopeptidase 3.4.24.16), and the
mitochondrial intermediate peptidase. The first two are
intracellular oligopeptidases, which act only on
relatively short substrates of less than 20 amino acid
residues, while the latter cleaves N-terminal
octapeptides from proteins during their import into the
mitochondria. The M3A subfamily also contains several
bacterial endopeptidases, collectively called
oligopeptidases A, as well as a large number of
bacterial carboxypeptidases, called dipeptidyl
peptidases (Dcp; Dcp II; peptidyl dipeptidase; EC
3.4.15.5). The peptidases in the M3 family contain the
HEXXH motif that forms the active site in conjunction
with a C-terminally-located Glutamic acid (Glu) residue.
A single zinc ion is ligated by the side-chains of the
two Histidine (His) residues, and the more C-terminal
Glu. Most of the peptidases are synthesized without
signal peptides or propeptides, and function
intracellularly. The structure of neurolysin shows
similarities to those of angiotensin-converting enzyme
(ACE; peptidyl-dipeptidase A) peptidase unit 2 belonging
to peptidase family M2. ACE is an enzyme responsible for
cleavage of dipeptides from the C-termini of proteins,
notably converting angiotensin I to angiotensin II in
mammals. There are similarities to the thermostable
carboxypeptidases from Pyrococcus furiosus
carboxypeptidase (PfuCP), and Thermus aquaticus (TaqCP),
belonging to peptidase family M32. Little is known about
function of this family, including carboxypeptidases Taq
and Pfu.
Length = 590
Score = 26.7 bits (60), Expect = 7.2
Identities = 9/48 (18%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 96 AQRLACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQIN 143
++A TP+ V F+ DL +E+++ + +G +++
Sbjct: 199 EDKMA-KTPEAVLDFLEDLAEKAKPRAEKELAELQAFKKKEGGDDELQ 245
>gnl|CDD|223793 COG0721, GatC, Asp-tRNAAsn/Glu-tRNAGln amidotransferase C subunit
[Translation, ribosomal structure and biogenesis].
Length = 96
Score = 25.6 bits (57), Expect = 7.7
Identities = 11/36 (30%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 116 ISKVELSEEDIRTILETL-LFDGKIEQINNIDGTDM 150
++++ELSEE++ L G +EQ+N +D +
Sbjct: 14 LARLELSEEELEKFATQLEDILGYVEQLNEVDTEGV 49
>gnl|CDD|131883 TIGR02836, spore_IV_A, stage IV sporulation protein A. A
comparative genome analysis of all sequenced genomes of
shows a number of proteins conserved strictly among the
endospore-forming subset of the Firmicutes. This
protein, a member of this panel, is designated stage IV
sporulation protein A. It acts in the mother cell
compartment and plays a role in spore coat morphogenesis
[Cellular processes, Sporulation and germination].
Length = 492
Score = 26.3 bits (58), Expect = 9.0
Identities = 14/55 (25%), Positives = 26/55 (47%)
Query: 89 NTNGPLVAQRLACATPKEVRKFITDLGISKVELSEEDIRTILETLLFDGKIEQIN 143
N+ P + A E + + L + + E DI ++LE +L++ I +IN
Sbjct: 188 NSTHPYHPETEALRQELEEKYDVPVLAMDVESMRESDILSVLEEVLYEFPILEIN 242
>gnl|CDD|216794 pfam01930, Cas_Cas4, Domain of unknown function DUF83. This domain
has no known function. The domain contains three
conserved cysteines at its C terminus.
Length = 162
Score = 26.0 bits (58), Expect = 9.3
Identities = 10/27 (37%), Positives = 17/27 (62%), Gaps = 3/27 (11%)
Query: 118 KVELSEEDIRTILETLLFDGKIEQINN 144
+VEL+EED + E + +IE+I +
Sbjct: 115 EVELTEEDREELEEAI---KEIEEIIS 138
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
0.318 0.136 0.401
Gapped
Lambda K H
0.267 0.0849 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,808,615
Number of extensions: 800341
Number of successful extensions: 840
Number of sequences better than 10.0: 1
Number of HSP's gapped: 836
Number of HSP's successfully gapped: 37
Length of query: 173
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 83
Effective length of database: 6,945,742
Effective search space: 576496586
Effective search space used: 576496586
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (24.7 bits)