RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8360
(152 letters)
>gnl|CDD|177755 PLN00152, PLN00152, DNA-directed RNA polymerase; Provisional.
Length = 130
Score = 134 bits (338), Expect = 2e-41
Identities = 55/69 (79%), Positives = 62/69 (89%)
Query: 83 RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDW 142
+YERAR+LGTRALQI+M APVMVELEGETDPL+IAMKEL+ RKIP IRRYLPD SYEDW
Sbjct: 62 KYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYEDW 121
Query: 143 GIDELKIID 151
G+DEL + D
Sbjct: 122 GVDELIVED 130
>gnl|CDD|179220 PRK01099, rpoK, DNA-directed RNA polymerase subunit K; Provisional.
Length = 62
Score = 84.6 bits (210), Expect = 9e-23
Identities = 28/54 (51%), Positives = 41/54 (75%)
Query: 83 RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPD 136
R+ERAR++G RALQI+M APV++++ TDPL IA +E K +PI ++R LP+
Sbjct: 9 RFERARIIGARALQISMGAPVLIDIPESTDPLDIAEEEFKRGVLPITVKRPLPN 62
>gnl|CDD|201652 pfam01192, RNA_pol_Rpb6, RNA polymerase Rpb6. Rpb6 is an essential
subunit in the eukaryotic polymerases Pol I, II and III.
This family also contains the bacterial equivalent to
Rpb6, the omega subunit. Rpb6 and omega are structurally
conserved and both function in polymerase assembly.
Length = 57
Score = 60.7 bits (148), Expect = 2e-13
Identities = 21/48 (43%), Positives = 31/48 (64%)
Query: 83 RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIII 130
RYE AR++ RA Q++ AP +V+ E E P+ IA++E+ KIP I
Sbjct: 10 RYELARIIAKRAKQLSYGAPPLVDEESEIKPVVIALEEIADGKIPPEI 57
>gnl|CDD|224672 COG1758, RpoZ, DNA-directed RNA polymerase, subunit K/omega
[Transcription].
Length = 74
Score = 60.0 bits (146), Expect = 6e-13
Identities = 24/59 (40%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 83 RYERARVLGTRALQIAMCAPVMVELEGE-TDPLQIAMKELKARKIPIIIRRYLPDNSYE 140
RYE V RA Q+A AP +V+ E P+ IA++E+ KIPI I R L +S +
Sbjct: 16 RYELVVVAAKRARQLAAGAPPLVDDEENKDKPVVIALREIAEGKIPIEILRELLIHSLQ 74
>gnl|CDD|192849 pfam11840, DUF3360, Protein of unknown function (DUF3360). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 489 to 517 amino acids in
length.
Length = 491
Score = 27.4 bits (61), Expect = 3.7
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 8/31 (25%)
Query: 18 LGWAFTLLLD--------ENAPTPSKANKWM 40
GWA T+LLD E + T S A++W+
Sbjct: 435 FGWALTMLLDNLGLIGDKERSATLSFADRWV 465
>gnl|CDD|214886 smart00888, EF1_GNE, EF-1 guanine nucleotide exchange domain.
Translation elongation factors are responsible for two
main processes during protein synthesis on the ribosome.
EF1A (or EF-Tu) is responsible for the selection and
binding of the cognate aminoacyl-tRNA to the A-site
(acceptor site) of the ribosome. EF2 (or EF-G) is
responsible for the translocation of the peptidyl-tRNA
from the A-site to the P-site (peptidyl-tRNA site) of
the ribosome, thereby freeing the A-site for the next
aminoacyl-tRNA to bind. Elongation factors are
responsible for achieving accuracy of translation and
both EF1A and EF2 are remarkably conserved throughout
evolution. Elongation factor EF1B (also known as EF-Ts
or EF-1beta/gamma/delta) is a nucleotide exchange factor
that is required to regenerate EF1A from its inactive
form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is
then ready to interact with a new aminoacyl-tRNA to
begin the cycle again. EF1B is more complex in
eukaryotes than in bacteria, and can consist of three
subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or
EF-1gamma) and EF1B-beta (or EF-1delta). This entry
represents the guanine nucleotide exchange domain of the
beta (EF-1beta, also known as EF1B-alpha) and delta
(EF-1delta, also known as EF1B-beta) chains of EF1B
proteins from eukaryotes and archaea. The beta and delta
chains have exchange activity, which mainly resides in
their homologous guanine nucleotide exchange domains,
found in the C-terminal region of the peptides. Their
N-terminal regions may be involved in interactions with
the gamma chain (EF-1gamma).
Length = 88
Score = 25.6 bits (57), Expect = 6.0
Identities = 13/31 (41%), Positives = 21/31 (67%), Gaps = 3/31 (9%)
Query: 91 GTRALQIAMCAPVMVELEGETDPLQIAMKEL 121
G +ALQI + V+ + EG TD L+ A++E+
Sbjct: 47 GLKALQIYV---VVEDDEGGTDELEEAIEEV 74
>gnl|CDD|239997 cd04625, CBS_pair_12, The CBS domain, named after human CBS, is a
small domain originally identified in cystathionine
beta-synthase and is subsequently found in a wide range
of different proteins. CBS domains usually occur in
tandem repeats. They associate to form a so-called
Bateman domain or a CBS pair based on crystallographic
studies in bacteria. The CBS pair was used as a basis
for this cd hierarchy since the human CBS proteins can
adopt the typical core structure and form an
intramolecular CBS pair. The interface between the two
CBS domains forms a cleft that is a potential ligand
binding site. The CBS pair coexists with a variety of
other functional domains and this has been used to help
in its classification here. It has been proposed that
the CBS domain may play a regulatory role, although its
exact function is unknown. Mutations of conserved
residues within this domain are associated with a
variety of human hereditary diseases, including
congenital myotonia, idiopathic generalized epilepsy,
hypercalciuric nephrolithiasis, and classic Bartter
syndrome (CLC chloride channel family members),
Wolff-Parkinson-White syndrome (gamma 2 subunit of
AMP-activated protein kinase), retinitis pigmentosa (IMP
dehydrogenase-1), and homocystinuria (cystathionine
beta-synthase).
Length = 112
Score = 25.4 bits (56), Expect = 8.0
Identities = 11/43 (25%), Positives = 19/43 (44%)
Query: 87 ARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPII 129
A VL T I P++ + D ++ M E R +P++
Sbjct: 53 AGVLDTTVRAIMNPEPIVASPDDSIDEVRRLMVERHLRYLPVL 95
>gnl|CDD|226980 COG4633, COG4633, Plastocyanin domain containing protein [General
function prediction only].
Length = 272
Score = 26.1 bits (57), Expect = 8.0
Identities = 18/77 (23%), Positives = 29/77 (37%), Gaps = 14/77 (18%)
Query: 27 DENAPTPS-------KANKWMGDLNLILGIKGERALVLILNHYMKVKSKNQIKNNNKLNI 79
D N TP+ K K D + G + L L ++ K K+QI I
Sbjct: 25 DHNGYTPNGLQTEQFKPIKQPLDGKSAVTCNGLGLIGLELWWFLLKKPKSQIAFAPN-GI 83
Query: 80 KQIR------YERARVL 90
++I Y +R++
Sbjct: 84 QEISITVDGGYIPSRIV 100
>gnl|CDD|188995 cd06456, M3A_DCP, Peptidase family M3 dipeptidyl carboxypeptidase
(DCP). Peptidase family M3 dipeptidyl carboxypeptidase
(DCP; Dcp II; peptidyl dipeptidase; EC 3.4.15.5). This
metal-binding M3A family also includes oligopeptidase A
(OpdA; EC 3.4.24.70) enzyme. DCP cleaves dipeptides off
the C-termini of various peptides and proteins, the
smallest substrate being N-blocked tripeptides and
unblocked tetrapeptides. DCP from E. coli is inhibited
by the anti-hypertensive drug captopril, an inhibitor of
the mammalian angiotensin converting enzyme (ACE, also
called peptidyl dipeptidase A). Oligopeptidase A (OpdA)
may play a specific role in the degradation of signal
peptides after they are released from precursor forms of
secreted proteins. It can also cleave N-acetyl-L-Ala.
Length = 654
Score = 25.9 bits (58), Expect = 9.7
Identities = 9/26 (34%), Positives = 17/26 (65%), Gaps = 3/26 (11%)
Query: 69 NQIKNNNKLNIKQI---RYERARVLG 91
N + +N+ I++I R E+A++LG
Sbjct: 227 NGGEFDNRPIIEEILALRAEKAKLLG 252
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
0.321 0.137 0.417
Gapped
Lambda K H
0.267 0.0827 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,850,977
Number of extensions: 708929
Number of successful extensions: 749
Number of sequences better than 10.0: 1
Number of HSP's gapped: 748
Number of HSP's successfully gapped: 20
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 (24.8 bits)