RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7778
(117 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 = 90.1 bits (224), Expect = 6e-23
Identities = 35/76 (46%), Positives = 47/76 (61%)
Query: 9 GGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68
L+YK +K +EE +VY IIEE+GN+GIW R I+ ++NL + L K LK
Sbjct: 63 NDGLVYKAVTREEAKKKATLSDEESLVYSIIEESGNEGIWTRTIKNRTNLHQSVLKKCLK 122
Query: 69 QLETKKIIKAVKSVAN 84
LE+KK IK+VKSV
Sbjct: 123 SLESKKYIKSVKSVKA 138
>gnl|CDD|227442 COG5111, RPC34, DNA-directed RNA polymerase III, subunit C34
[Transcription].
Length = 301
Score = 59.6 bits (144), Expect = 9e-12
Identities = 29/76 (38%), Positives = 45/76 (59%)
Query: 9 GGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68
G L YK + D+ E VY +I ++G +GIW++ I+ ++NL + K LK
Sbjct: 64 KGVLYYKGVLESEASPINTMDDYELTVYSLISQSGGEGIWLKTIKDRTNLHHNVVGKCLK 123
Query: 69 QLETKKIIKAVKSVAN 84
LE+K+I+K+VKSV N
Sbjct: 124 SLESKRIVKSVKSVKN 139
>gnl|CDD|163441 TIGR03729, acc_ester, putative phosphoesterase. Members of this
protein family belong to the larger family pfam00149
(calcineurin-like phosphoesterase), a family largely
defined by small motifs of metal-chelating residues. The
subfamily in this model shows a good but imperfect
co-occurrence in species with domain TIGR03715 that
defines a novel class of signal peptide typical of the
accessory secretory system.
Length = 239
Score = 29.2 bits (66), Expect = 0.35
Identities = 9/33 (27%), Positives = 19/33 (57%)
Query: 56 SNLMPTQLNKILKQLETKKIIKAVKSVANIEYL 88
+ ++ QL K L QL+ K++I V + +++
Sbjct: 148 TAIVLKQLKKQLNQLDNKQVIFVTHFVPHRDFI 180
>gnl|CDD|225310 COG2512, COG2512, Predicted membrane-associated trancriptional
regulator [Transcription].
Length = 258
Score = 28.9 bits (65), Expect = 0.46
Identities = 16/79 (20%), Positives = 35/79 (44%), Gaps = 4/79 (5%)
Query: 6 FLIGGNLLYKVKDPVTNEKLKDSDN---EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQ 62
+ + + L + + +EK + +I E G + I ++R L T
Sbjct: 168 IIYAPVIEPLLSRGDELRVLVNEYDLNEDEKEILDLIRERGGR-ITQAELRRALGLSKTT 226
Query: 63 LNKILKQLETKKIIKAVKS 81
+++IL++LE + +I+ K
Sbjct: 227 VSRILRRLEKRGLIEKEKK 245
>gnl|CDD|233379 TIGR01369, CPSaseII_lrg, carbamoyl-phosphate synthase, large
subunit. Carbamoyl-phosphate synthase (CPSase)
catalyzes the first committed step in pyrimidine,
arginine, and urea biosynthesis. In general, it is a
glutamine-dependent enzyme, EC 6.3.5.5, termed CPSase II
in eukaryotes. An exception is the mammalian
mitochondrial urea-cycle form, CPSase I, in which the
glutamine amidotransferase domain active site Cys on the
small subunit has been lost, and the enzyme is
ammonia-dependent. In both CPSase I and the closely
related, glutamine-dependent CPSase III (allosterically
activated by acetyl-glutamate) demonstrated in some
other vertebrates, the small and large chain regions are
fused in a single polypeptide chain. This model
represents the large chain of glutamine-hydrolysing
carbamoyl-phosphate synthases, or the corresponding
regions of larger, multifunctional proteins, as found in
all domains of life, and CPSase I forms are considered
exceptions within the family. In several thermophilic
species (Methanobacterium thermoautotrophicum,
Methanococcus jannaschii, Aquifex aeolicus), the large
subunit appears split, at different points, into two
separate genes [Purines, pyrimidines, nucleosides, and
nucleotides, Pyrimidine ribonucleotide biosynthesis].
Length = 1050
Score = 27.3 bits (61), Expect = 2.3
Identities = 20/99 (20%), Positives = 40/99 (40%), Gaps = 8/99 (8%)
Query: 13 LYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLET 72
L+K+K+ V E+ + ++ +++ A G I + ++ K+ K+L
Sbjct: 458 LHKIKNIVDLEEELEEVKLTELDPELLRRAKKLGFSDAQIARLIGVTEAEVRKLRKELGI 517
Query: 73 KKIIKAVKSVA-------NIEYLT-EGTVNAMVLPSRKK 103
+ K V + A Y T EG + + +KK
Sbjct: 518 MPVYKRVDTCAAEFEAQTPYLYSTYEGERDDVPFTDKKK 556
>gnl|CDD|131948 TIGR02902, spore_lonB, ATP-dependent protease LonB. Members of
this protein are LonB, a paralog of the ATP-dependent
protease La (LonA, TIGR00763). LonB proteins are found
strictly, and almost universally, in endospore-forming
bacteria. This protease was shown, in Bacillus subtilis,
to be expressed specifically in the forespore, during
sporulation, under control of sigma(F). The lonB gene,
despite location immediately upstream of lonA, was shown
to be monocistronic. LonB appears able to act on
sigma(H) for post-translation control, but lonB mutation
did not produce an obvious sporulation defect under the
conditions tested. Note that additional paralogs of LonA
and LonB occur in the Clostridium lineage and this model
selects only one per species as the protein that
corresponds to LonB in B. subtilis [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Cellular processes, Sporulation and germination].
Length = 531
Score = 26.7 bits (59), Expect = 3.1
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 58 LMPTQLNKILKQLETKKI 75
L P Q+NK+LK LE +K+
Sbjct: 187 LHPVQMNKLLKVLEDRKV 204
>gnl|CDD|223439 COG0362, Gnd, 6-phosphogluconate dehydrogenase [Carbohydrate
transport and metabolism].
Length = 473
Score = 26.4 bits (59), Expect = 4.2
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 24 KLKDSDNEEKVVYKIIEEAGNKG 46
+ KD + + +V KI+++AG KG
Sbjct: 240 RKKDEEGGKPLVDKILDKAGQKG 262
>gnl|CDD|236834 PRK11067, PRK11067, outer membrane protein assembly factor YaeT;
Provisional.
Length = 803
Score = 26.2 bits (58), Expect = 4.5
Identities = 12/38 (31%), Positives = 22/38 (57%), Gaps = 3/38 (7%)
Query: 20 VTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSN 57
T ++ D+D K+ + +AGN+ ++R IRF+ N
Sbjct: 323 QTQPEINDADKTVKLHVNV--DAGNR-FYVRKIRFEGN 357
>gnl|CDD|205590 pfam13412, HTH_24, Winged helix-turn-helix DNA-binding.
Length = 48
Score = 24.3 bits (54), Expect = 5.5
Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 36 YKIIEE-AGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIK 77
KI+ N I R++ + L +N+ LK+LE + +IK
Sbjct: 6 LKILRLLQENPRISQRELAERLGLSLGTVNRRLKRLEEEGLIK 48
>gnl|CDD|225107 COG2197, CitB, Response regulator containing a CheY-like receiver
domain and an HTH DNA-binding domain [Signal
transduction mechanisms / Transcription].
Length = 211
Score = 25.7 bits (57), Expect = 6.1
Identities = 9/49 (18%), Positives = 20/49 (40%), Gaps = 1/49 (2%)
Query: 66 ILKQLETKKIIKAVKSVANIE-YLTEGTVNAMVLPSRKKREERQDRGVL 113
+LK +++++A+++VA YL + E +L
Sbjct: 101 LLKDASPEELVEAIRAVAAGGTYLPPDIARKLAGLLPSSSAEAPLAELL 149
>gnl|CDD|236363 PRK09029, PRK09029, O-succinylbenzoic acid--CoA ligase;
Provisional.
Length = 458
Score = 26.0 bits (58), Expect = 6.1
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 58 LMPTQLNKILKQLETKKIIKAV 79
L+PTQL ++L +KAV
Sbjct: 224 LVPTQLWRLLDNRSEPLSLKAV 245
>gnl|CDD|183831 PRK12933, secD, preprotein translocase subunit SecD; Reviewed.
Length = 604
Score = 25.8 bits (57), Expect = 7.8
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 73 KKIIKAVKSVANIEYLTEGTVNAMVLPSRKKR 104
K +I A S+A E G+VNA VL + R
Sbjct: 275 KNVIGATASLAFYEVKESGSVNAKVLKDKNGR 306
>gnl|CDD|165206 PHA02875, PHA02875, ankyrin repeat protein; Provisional.
Length = 413
Score = 25.3 bits (55), Expect = 8.6
Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 2/80 (2%)
Query: 6 FLIGGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNK 65
L+ + VK P +L D+ E V K +EE + G + D+ +K + P L
Sbjct: 53 LLMKHGAIPDVKYPDIESELHDAVEEGDV--KAVEELLDLGKFADDVFYKDGMTPLHLAT 110
Query: 66 ILKQLETKKIIKAVKSVANI 85
ILK+L+ K++ A + +I
Sbjct: 111 ILKKLDIMKLLIARGADPDI 130
>gnl|CDD|226405 COG3888, COG3888, Predicted transcriptional regulator
[Transcription].
Length = 321
Score = 25.2 bits (55), Expect = 9.4
Identities = 11/44 (25%), Positives = 24/44 (54%)
Query: 34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIK 77
+ + ++ AG +GI +I L + +++ L +LE + I+K
Sbjct: 8 KLIRELKRAGPEGIDQTEIEELMGLSKSTVSEALSELEKQGIVK 51
>gnl|CDD|240146 cd05015, SIS_PGI_1, Phosphoglucose isomerase (PGI) contains two
SIS (Sugar ISomerase) domains. This classification is
based on the alignment of the first SIS domain. PGI is
a multifunctional enzyme which as an intracellular
dimer catalyzes the reversible isomerization of glucose
6-phosphate to fructose 6-phosphate. As an
extracellular protein, PGI also has functions
equivalent to neuroleukin (NLK), autocrine motility
factor (AMF), and maturation factor (MF). Evidence
suggests that PGI, NLK, AMF, and MF are closely related
or identical. NLK is a neurotrophic growth factor that
promotes regeneration and survival of neurons. The
dimeric form of NLK has isomerase function, whereas its
monomeric form carries out neurotrophic activity. AMF
is a cytokine that stimulates cell migration and
metastasis. MF mediates the differentiation of human
myeloid leukemic HL-60 cells to terminal monocytic
cells.
Length = 158
Score = 24.8 bits (55), Expect = 9.8
Identities = 11/34 (32%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 50 RDIRFKSNLMPTQLNKILKQLETKK--IIKAVKS 81
+ F SN+ P L ++LK+L+ + I KS
Sbjct: 50 LRLHFVSNVDPDDLAELLKKLDPETTLFIVISKS 83
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
0.316 0.135 0.367
Gapped
Lambda K H
0.267 0.0723 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,821,184
Number of extensions: 501359
Number of successful extensions: 649
Number of sequences better than 10.0: 1
Number of HSP's gapped: 649
Number of HSP's successfully gapped: 51
Length of query: 117
Length of database: 10,937,602
Length adjustment: 80
Effective length of query: 37
Effective length of database: 7,389,282
Effective search space: 273403434
Effective search space used: 273403434
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 (21.6 bits)
S2: 53 (24.2 bits)