RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780391|ref|YP_003064804.1| DNA polymerase III subunit chi
[Candidatus Liberibacter asiaticus str. psy62]
(141 letters)
>gnl|CDD|146811 pfam04364, DNA_pol3_chi, DNA polymerase III chi subunit, HolC. The
DNA polymerase III holoenzyme (EC:2.7.7.7) is the
polymerase responsible for the replication of the
Escherichia coli chromosome. The holoenzyme is composed
of the DNA polymerase III core, the sliding clamp, and
the DnaX clamp loading complex. The DnaX complex
contains either either the tau or gamma product of gene
dnax, complexed to delta.delta' and to chi psi. Chi
forms a 1:1 heterodimer with psi. The chi psi complex
functions by increasing the affinity of tau and gamma
for delta.delta' allowing a functional clamp-loading
complex to form at physiological subunit concentrations.
Psi is responsible for the interaction with DnaX
(gamma/tau), but psi is insoluble unless it is in a
complex with chi.
Length = 136
Score = 98.0 bits (245), Expect = 9e-22
Identities = 40/140 (28%), Positives = 65/140 (46%), Gaps = 8/140 (5%)
Query: 1 MRTLLFYRFKNDWEYNLL-VLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPH 59
M + FY D L L + +G RV V+C E ++L+E LWT++ D FLPH
Sbjct: 1 MTRVDFYHLTRDPLEALACRLAEKALRQGWRVLVRCEDEEQAEALDELLWTFRPDSFLPH 60
Query: 60 GVDVGDEGDFSSFQPVLLTISSLNANTS-TIRFLVDEASMHIGDVDYYEKVVFIINTDDQ 118
G+ ++ QPVLL N N + +D A +E+V+ ++ DD
Sbjct: 61 GL---AGEGPAAGQPVLLGWDGENPNGHADVLINLDGAVP--EFASRFERVIEFVDGDDA 115
Query: 119 GSLEWGRAHWRSLKNSGYAP 138
+ + R W++ + +GY
Sbjct: 116 -AKQAARERWKAYRAAGYEL 134
>gnl|CDD|32751 COG2927, HolC, DNA polymerase III, chi subunit [DNA replication,
recombination, and repair].
Length = 144
Score = 78.8 bits (194), Expect = 5e-16
Identities = 34/140 (24%), Positives = 64/140 (45%), Gaps = 8/140 (5%)
Query: 1 MRTLLFYRFKND-WEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPH 59
M+ FY L + + G RV +QC E ++L+E+LWT+ + F+PH
Sbjct: 1 MKEATFYLLSESTLLAAACRLAEKAWRSGWRVLIQCEDEAQAEALDEHLWTFSAESFIPH 60
Query: 60 GVDVGDEGDFSSFQPVLLTISSLNANTSTIRFLVDEASMHIGDVDYYEKVVFIIN--TDD 117
+ G+ QP+L+ N N++ + L++ A YE V + + D+
Sbjct: 61 NLA-GEPPPAG--QPILIAWPGGNPNSARVDLLINLAD--EFPDFAYEFVTRVFDFVPDE 115
Query: 118 QGSLEWGRAHWRSLKNSGYA 137
+ L+ R W++ + +G+
Sbjct: 116 EALLQLARERWKAYRGAGFQ 135
>gnl|CDD|35738 KOG0518, KOG0518, KOG0518, Actin-binding cytoskeleton protein,
filamin [Cytoskeleton].
Length = 1113
Score = 30.3 bits (68), Expect = 0.19
Identities = 12/56 (21%), Positives = 16/56 (28%), Gaps = 6/56 (10%)
Query: 51 WKKDGFLPHGVDV-GDEGDFSSFQPVLLTISSLNANTSTIRFLVDEASMHIGDVDY 105
K G LP V V G +L T + F+ E + V
Sbjct: 287 ASKAGLLPLEVAVCGGRVPVEPVM-----AVALGDGTYNVSFVPSEDGPYTISVRI 337
>gnl|CDD|37636 KOG2425, KOG2425, KOG2425, Nuclear protein involved in cell
morphogenesis and cell surface growth [General function
prediction only].
Length = 599
Score = 28.2 bits (62), Expect = 0.92
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 35 CGSERVRDSLNEYLWTWKKDGFLP 58
C E+ +S Y W+K +LP
Sbjct: 216 CLWEKANESFVSYFTVWEKARYLP 239
>gnl|CDD|113574 pfam04808, CTV_P23, Citrus tristeza virus (CTV) P23 protein. This
family consists of protein P23 from the citrus tristeza
virus, which is a member of the Closteroviridae. CTV
viruses produce more positive than negative RNA strands,
and P23 controls this asymmetrical RNA accumulation.
Amino acids 42-180 are essential for function and are
thought to contain RNA-binding and zinc finger domains.
Length = 209
Score = 27.0 bits (59), Expect = 1.7
Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 15/71 (21%)
Query: 25 YEKGKRVSVQCGSERVRDSL-------------NEYLWTWKKDGFLP--HGVDVGDEGDF 69
Y K ++++V +ER + L Y + LP + VDVGD D
Sbjct: 129 YTKERQLAVDLAAEREKTRLARRHPMRSPEETPEHYKFGMTAKAMLPEINAVDVGDNEDT 188
Query: 70 SSFQPVLLTIS 80
SS PV L++S
Sbjct: 189 SSEYPVSLSVS 199
>gnl|CDD|146921 pfam04523, Herpes_U30, Herpes virus tegument protein U30. This
family is named after the human herpesvirus protein, but
has been characterized in cytomegalovirus as UL47.
Cytomegalovirus UL47 is a component of the tegument,
which is a protein layer surrounding the viral capsid.
UL47 co-precipitates with UL48 and UL69 tegument
proteins, and the major capsid protein UL86. A
UL47-containing complex is thought to be involved in the
release of viral DNA from the disassembling virus
particle.
Length = 883
Score = 25.4 bits (56), Expect = 5.3
Identities = 8/24 (33%), Positives = 10/24 (41%)
Query: 1 MRTLLFYRFKNDWEYNLLVLLQDE 24
MR+ L+ K W L L E
Sbjct: 459 MRSYLYIDAKRKWGDILFPLTAPE 482
>gnl|CDD|31489 COG1298, FlhA, Flagellar biosynthesis pathway, component FlhA [Cell
motility and secretion / Intracellular trafficking and
secretion].
Length = 696
Score = 25.2 bits (55), Expect = 6.1
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 68 DFSSFQPVLL--TISSLNANTSTIRFLVDEASMHIGDV 103
DFSSF +LL T+ L N ++ R ++ G V
Sbjct: 69 DFSSFPTLLLITTLLRLGLNVASTRVILSHGHEAAGKV 106
>gnl|CDD|73263 cd01379, MYSc_type_III, Myosin motor domain, type III myosins.
Myosin III has been shown to play a role in the vision
process in insects and in hearing in mammals. Myosin
III, an unconventional myosin, does not form dimers.
This catalytic (head) domain has ATPase activity and
belongs to the larger group of P-loop NTPases. Myosins
are actin-dependent molecular motors that play important
roles in muscle contraction, cell motility, and
organelle transport. The head domain is a molecular
motor, which utilizes ATP hydrolysis to generate
directed movement toward the plus end along actin
filaments. A cyclical interaction between myosin and
actin provides the driving force. Rates of ATP
hydrolysis and consequently the speed of movement along
actin filaments vary widely, from about 0.04 micrometer
per second for myosin I to 4.5 micrometer per second for
myosin II in skeletal muscle. Myosin II moves in
discrete steps about 5-10 nm long and generates 1-5
piconewtons of force. Upon ATP binding, the myosin head
dissociates from an actin filament. ATP hydrolysis
causes the head to pivot and associate with a new actin
subunit. The release of Pi causes the head to pivot and
move the filament (power stroke). Release of ADP
completes the cycle..
Length = 653
Score = 25.0 bits (54), Expect = 7.3
Identities = 9/48 (18%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 29 KRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVL 76
+++ + +E+++ N++++ W++ +L GVD ++ +P+L
Sbjct: 392 EQLCINIANEQIQYYFNQHIFAWEQQEYLNEGVDA-RLVEYEDNRPLL 438
>gnl|CDD|107208 cd06447, D-Ser-dehyd, D-Serine dehydratase is a pyridoxal phosphate
(PLP)-dependent enzyme which catalyzes the conversion of
L- or D-serine to pyruvate and ammonia. D-serine
dehydratase serves as a detoxifying enzyme in most E.
coli strains where D-serine is a competitive antagonist
of beta-alanine in the biosynthetic pathway to
pentothenate and coenzyme A. D-serine dehydratase is
different from other pyridoxal-5'-phosphate-dependent
enzymes in that it catalyzes alpha, beta-elimination
reactions on amino acids..
Length = 404
Score = 25.0 bits (55), Expect = 7.6
Identities = 10/22 (45%), Positives = 12/22 (54%), Gaps = 1/22 (4%)
Query: 51 WKKDGFLPHGVDVGD-EGDFSS 71
WKKD GV V + E D+S
Sbjct: 171 WKKDKLRSKGVTVVEYETDYSK 192
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.320 0.138 0.431
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,784,972
Number of extensions: 83972
Number of successful extensions: 195
Number of sequences better than 10.0: 1
Number of HSP's gapped: 191
Number of HSP's successfully gapped: 15
Length of query: 141
Length of database: 6,263,737
Length adjustment: 84
Effective length of query: 57
Effective length of database: 4,448,581
Effective search space: 253569117
Effective search space used: 253569117
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: 52 (23.8 bits)