RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy548
(84 letters)
>gnl|CDD|177755 PLN00152, PLN00152, DNA-directed RNA polymerase; Provisional.
Length = 130
Score = 125 bits (315), Expect = 6e-39
Identities = 55/71 (77%), Positives = 63/71 (88%)
Query: 13 IKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYE 72
+ +YERAR+LGTRALQI+M APVMVELEGETDPL+IAMKEL+ RKIP IRRYLPD SYE
Sbjct: 60 MTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYLPDGSYE 119
Query: 73 DWGIDELKIID 83
DWG+DEL + D
Sbjct: 120 DWGVDELIVED 130
>gnl|CDD|179220 PRK01099, rpoK, DNA-directed RNA polymerase subunit K;
Provisional.
Length = 62
Score = 74.2 bits (183), Expect = 1e-19
Identities = 28/54 (51%), Positives = 41/54 (75%)
Query: 15 RYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPD 68
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 = 55.4 bits (134), Expect = 3e-12
Identities = 21/55 (38%), Positives = 34/55 (61%)
Query: 8 IITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIII 62
+ + + RYE AR++ RA Q++ AP +V+ E E P+ IA++E+ KIP I
Sbjct: 3 LTSKYLNRYELARIIAKRAKQLSYGAPPLVDEESEIKPVVIALEEIADGKIPPEI 57
>gnl|CDD|224672 COG1758, RpoZ, DNA-directed RNA polymerase, subunit K/omega
[Transcription].
Length = 74
Score = 52.3 bits (126), Expect = 7e-11
Identities = 24/59 (40%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 15 RYERARVLGTRALQIAMCAPVMVELEGE-TDPLQIAMKELKARKIPIIIRRYLPDNSYE 72
RYE V RA Q+A AP +V+ E P+ IA++E+ KIPI I R L +S +
Sbjct: 16 RYELVVVAAKRARQLAAGAPPLVDDEENKDKPVVIALREIAEGKIPIEILRELLIHSLQ 74
>gnl|CDD|181057 PRK07608, PRK07608, ubiquinone biosynthesis hydroxylase family
protein; Provisional.
Length = 388
Score = 25.7 bits (57), Expect = 2.9
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 12 VIKRYERARVLGTRALQIA 30
+++RYERAR ALQ+A
Sbjct: 328 LLRRYERARREDILALQVA 346
>gnl|CDD|206741 cd09914, RocCOR, Ras of complex proteins (Roc) C-terminal of Roc
(COR) domain family. RocCOR (or Roco) protein family is
characterized by a superdomain containing a Ras-like
GTPase domain, called Roc (Ras of complex proteins), and
a characteristic second domain called COR (C-terminal of
Roc). A kinase domain and diverse regulatory domains are
also often found in Roco proteins. Their functions are
diverse; in Dictyostelium discoideum, which encodes 11
Roco proteins, they are involved in cell division,
chemotaxis and development, while in human, where 4 Roco
proteins (LRRK1, LRRK2, DAPK1, and MFHAS1) are encoded,
these proteins are involved in epilepsy and cancer.
Mutations in LRRK2 (leucine-rich repeat kinase 2) are
known to cause familial Parkinson's disease.
Length = 161
Score = 25.4 bits (56), Expect = 3.1
Identities = 13/39 (33%), Positives = 15/39 (38%), Gaps = 1/39 (2%)
Query: 42 ETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELK 80
E+ I K L K P II + GI ELK
Sbjct: 118 ESCDEDILKKALNK-KFPAIINDIHFVSCKNGKGIAELK 155
>gnl|CDD|214009 cd12810, Esterase_713_like-3, Uncharacterized enzymes similar to
novel bacterial esterase that cleaves esters on
halogenated cyclic compounds. This family contains
uncharacterized proteins similar to a novel bacterial
esterase (Alcaligenes esterase 713) with the alpha/beta
hydrolase fold but does not contain the GXSXXG
pentapeptide around the active site serine residue as
commonly seen in other enzymes of this class. Esterase
713 shows negligible sequence homology to other esterase
and lipase enzymes. It is active as a dimer and cleaves
esters on halogenated cyclic compounds though its
natural substrate is unknown.
Length = 328
Score = 25.6 bits (57), Expect = 3.4
Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 34 PVMVELEGETDPLQIAMKE-LKARKIPIIIR--RYLPDNSYEDWGIDE 78
P G P+ + +++ LK KIPI+I +PD + G+D
Sbjct: 220 PPPPSAFGPLGPVGVPLEDFLKLTKIPIVIYFGDNIPDGPSDIPGLDF 267
>gnl|CDD|149769 pfam08813, Phage_tail_3, Phage tail protein. This family of
proteins include phage tail proteins. They probably
include bacterial Ig-like domains related to pfam02368.
Which also includes a number of phage tail invasin
proteins.
Length = 165
Score = 25.1 bits (55), Expect = 4.0
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 45 PLQIAMKELKARKIPIIIRRYLPDNS 70
P A+K RK +++R LP+
Sbjct: 101 PFYAALKSADDRKQVVVLRATLPNGD 126
>gnl|CDD|99867 cd06114, EcCS_like, Escherichia coli (Ec) citrate synthase (CS)
GltA_like. CS catalyzes the condensation of acetyl
coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate
and coenzyme A (CoA), the first step in the citric acid
cycle (TCA or Krebs cycle). The overall CS reaction is
thought to proceed through three partial reactions and
involves both closed and open conformational forms of
the enzyme: a) the carbanion or equivalent is generated
from AcCoA by base abstraction of a proton, b) the
nucleophilic attack of this carbanion on OAA to generate
citryl-CoA, and c) the hydrolysis of citryl-CoA to
produce citrate and CoA. There are two types of CSs:
type I CS and type II CSs. Type I CSs are found in
eukarya, gram-positive bacteria, archaea, and in some
gram-negative bacteria and are homodimers with both
subunits participating in the active site. Type II CSs
are unique to gram-negative bacteria and are
homohexamers of identical subunits (approximated as a
trimer of dimers). Some type II CSs including EcCS are
strongly and specifically inhibited by NADH through an
allosteric mechanism. Included in this group is an
NADH-insensitive type II Acetobacter acetii CS which has
retained many of the residues used by EcCS for NADH
binding.
Length = 400
Score = 24.8 bits (55), Expect = 6.1
Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 7/41 (17%)
Query: 12 VIKRYE-RARVLGTRALQIAMCAPVMVELEGETDPLQIAMK 51
V K Y+ RA++L C V+ EL + L+IAM+
Sbjct: 292 VYKNYDPRAKILKK------TCDEVLAELGKDDPLLEIAME 326
>gnl|CDD|215487 PLN02900, PLN02900, alanyl-tRNA synthetase.
Length = 936
Score = 25.0 bits (55), Expect = 6.9
Identities = 11/34 (32%), Positives = 15/34 (44%), Gaps = 8/34 (23%)
Query: 33 APVMVELEGETDPLQIAMKELKARKIPI--IIRR 64
V+VEL G+ P E+K + I II
Sbjct: 353 VEVVVELSGDVFP------EVKKNEKRITEIIAE 380
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
0.326 0.143 0.414
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: 4,670,508
Number of extensions: 393033
Number of successful extensions: 617
Number of sequences better than 10.0: 1
Number of HSP's gapped: 616
Number of HSP's successfully gapped: 22
Length of query: 84
Length of database: 10,937,602
Length adjustment: 52
Effective length of query: 32
Effective length of database: 8,631,194
Effective search space: 276198208
Effective search space used: 276198208
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.0 bits)