RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780131|ref|YP_003064544.1| DNA ligase, NAD-dependent
[Candidatus Liberibacter asiaticus str. psy62]
(119 letters)
>gnl|CDD|30621 COG0272, Lig, NAD-dependent DNA ligase (contains BRCT domain type
II) [DNA replication, recombination, and repair].
Length = 667
Score = 56.7 bits (137), Expect = 2e-09
Identities = 25/66 (37%), Positives = 34/66 (51%)
Query: 53 SLSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDH 112
+ S EA E+E L ++ H YY LD P +D YD++ L L+E+ PEL D
Sbjct: 1 AWSMAEAQEEIEELRELLNKHDYRYYVLDAPSVSDAEYDQLYRELQELEEKHPELITPDS 60
Query: 113 PWNTVG 118
P VG
Sbjct: 61 PTQRVG 66
>gnl|CDD|145016 pfam01653, DNA_ligase_aden, NAD-dependent DNA ligase adenylation
domain. DNA ligases catalyse the crucial step of
joining the breaks in duplex DNA during DNA replication,
repair and recombination, utilising either ATP or NAD(+)
as a cofactor. This domain is the catalytic adenylation
domain. The NAD+ group is covalently attached to this
domain at the lysine in the KXDG motif of this domain.
This enzyme- adenylate intermediate is an important
feature of the proposed catalytic mechanism.
Length = 315
Score = 53.5 bits (129), Expect = 1e-08
Identities = 26/61 (42%), Positives = 34/61 (55%)
Query: 58 EAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTV 117
EA E+ L ++ + YY LD+P D YDR+ RL AL+E+FPEL D P V
Sbjct: 2 EAQQEIARLRELIRQYDYHYYVLDNPEVPDAEYDRLYRRLQALEEKFPELITPDSPTQRV 61
Query: 118 G 118
G
Sbjct: 62 G 62
>gnl|CDD|29013 cd00114, LIGANc, NAD+ dependent DNA ligase adenylation domain. DNA
ligases catalyze the crucial step of joining the breaks
in duplex DNA during DNA replication, repair and
recombination, utilizing either ATP or NAD(+) as a
cofactor, but using the same basic reaction mechanism.
The enzyme reacts with the cofactor to form a
phosphoamide-linked AMP with the amino group of a
conserved Lysine in the KXDG motif, and subsequently
transfers it to the DNA substrate to yield adenylated
DNA. This alignment contains members of the NAD+
dependent subfamily only..
Length = 307
Score = 51.4 bits (123), Expect = 6e-08
Identities = 22/57 (38%), Positives = 30/57 (52%)
Query: 62 EVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVG 118
+ L ++ H YY LD+P +D YDR+ L AL+E+ PEL D P VG
Sbjct: 2 RIAELRELLNKHDYRYYVLDEPSVSDAEYDRLYRELRALEEEHPELKTPDSPTQRVG 58
>gnl|CDD|144194 pfam00508, PPV_E2_N, E2 (early) protein, N terminal.
Length = 201
Score = 27.8 bits (63), Expect = 0.78
Identities = 13/18 (72%), Positives = 16/18 (88%)
Query: 94 SERLDALQEQFPELFDED 111
SERLDALQEQ EL+++D
Sbjct: 4 SERLDALQEQLLELYEKD 21
>gnl|CDD|143504 cd06831, PLPDE_III_ODC_like_AZI, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme Ornithine Decarboxylase-like
Antizyme Inhibitor. Antizyme inhibitor (AZI) is
homologous to the fold type III PLP-dependent enzyme ODC
but does not retain any decarboxylase activity. Like
ODC, AZI is presumed to exist as a homodimer. Antizyme
is a regulatory protein that binds directly to the ODC
monomer to block its active site, leading to its
degradation by the 26S proteasome. AZI binds to Antizyme
with a higher affinity than ODC, preventing the
formation of the Antizyme-ODC complex. Thus, AZI blocks
the ability of Antizyme to promote ODC degradation,
which leads to increased ODC enzymatic activity and
polyamine levels. AZI also prevents the degradation of
other proteins regulated by Antizyme, such as cyclin D1.
Length = 394
Score = 26.7 bits (59), Expect = 1.5
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 4/37 (10%)
Query: 73 HQKWYYRLDDPLFTDGLYDRVSERLDALQEQ--FPEL 107
H+K Y+ D+PLFT L+ + LD + E PEL
Sbjct: 314 HKK--YKEDEPLFTSSLWGPSCDELDQIVESCLLPEL 348
>gnl|CDD|31304 COG1107, COG1107, Archaea-specific RecJ-like exonuclease, contains
DnaJ-type Zn finger domain [DNA replication,
recombination, and repair].
Length = 715
Score = 26.0 bits (57), Expect = 2.5
Identities = 21/63 (33%), Positives = 29/63 (46%), Gaps = 9/63 (14%)
Query: 57 GEAMIEVEYLVKIA--LHHQKWYYR-------LDDPLFTDGLYDRVSERLDALQEQFPEL 107
E + E L KIA + ++ +Y R + D L T G DR E +D L EQ E
Sbjct: 525 AERGYDREDLEKIALAVDYEAFYLRFMDGRGIIADILGTTGDADRHRELVDHLYEQAKEA 584
Query: 108 FDE 110
+E
Sbjct: 585 VEE 587
>gnl|CDD|143492 cd06818, PLPDE_III_cryptic_DSD, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme Bacterial Cryptic D-Serine
Dehydratase. This subfamily is composed of Burkholderia
cepacia cryptic D-serine dehydratase (cryptic DSD),
which is also called D-serine deaminase, and similar
bacterial proteins. Members of this subfamily are fold
type III PLP-dependent enzymes with similarity to
bacterial alanine racemase (AR), which contains an
N-terminal PLP-binding TIM-barrel domain and a
C-terminal beta-sandwich domain. AR exists as dimers
with active sites that lie at the interface between the
TIM barrel domain of one subunit and the beta-sandwich
domain of the other subunit. Based on similarity, it is
possible cryptic DSDs may also form dimers. Cryptic DSDs
are distinct from the ubiquitous bacterial DSDs coded by
the dsdA gene, mammalian L-serine dehydratases (LSD) and
mammalian serine racemase (SerRac), which are fold type
II PLP-dependent enzymes. At present, the enzymatic and
biochemical properties of cryptic DSDs are still poorly
understood. Typically, DSDs catalyze the dehydration of
D-serine to aminoacrylate, which is rapidly hydrolyzed
to pyruvate and ammonia.
Length = 382
Score = 26.1 bits (58), Expect = 2.6
Identities = 9/32 (28%), Positives = 14/32 (43%), Gaps = 3/32 (9%)
Query: 77 YYRLDDPLFTDG---LYDRVSERLDALQEQFP 105
+ + + T G +D V+E L AL P
Sbjct: 202 LFPDRELILTAGGSAWFDLVAEALAALALDGP 233
>gnl|CDD|37310 KOG2099, KOG2099, KOG2099, Glycogen phosphorylase [Carbohydrate
transport and metabolism].
Length = 843
Score = 26.1 bits (57), Expect = 2.7
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 8 FRSSKFENEHN-ITPAQWKKLLTLEAKFLPNKRALESWLDKAKKVTSLSK 56
KF+N+ N ITP +W L L ++ E W+ ++T L K
Sbjct: 476 LEPEKFQNKTNGITPRRWLLLCNPGLADLITEKIGEEWITDLDQLTKLRK 525
>gnl|CDD|176946 CHL00001, rpoB, RNA polymerase beta subunit.
Length = 1070
Score = 26.0 bits (58), Expect = 2.8
Identities = 15/64 (23%), Positives = 28/64 (43%), Gaps = 16/64 (25%)
Query: 41 LESWLDKAKKVTSLSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDAL 100
S+L+ +K SK A++E +Q++ DP+F++ L L
Sbjct: 204 FLSFLNDKEKKKIGSKENAILEF---------YQQFACVGGDPVFSESLC-------KEL 247
Query: 101 QEQF 104
Q++F
Sbjct: 248 QKKF 251
>gnl|CDD|33492 COG3696, COG3696, Putative silver efflux pump [Inorganic ion
transport and metabolism].
Length = 1027
Score = 25.6 bits (56), Expect = 3.0
Identities = 14/28 (50%), Positives = 16/28 (57%), Gaps = 5/28 (17%)
Query: 84 LFTDG--LY---DRVSERLDALQEQFPE 106
+F DG LY RV ERL +Q Q PE
Sbjct: 96 IFKDGTDLYWARQRVLERLSQVQSQLPE 123
>gnl|CDD|145808 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain.
Transcription of the anti-viral guanylate-binding
protein (GBP) is induced by interferon-gamma during
macrophage induction. This family contains GBP1 and
GPB2, both GTPases capable of binding GTP, GDP and GMP.
Length = 297
Score = 25.7 bits (57), Expect = 3.3
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 12 KFENEHNITPAQWKKLLTLEAKFLPNKRALESWLDKAKKVTSLSKGEAMIEVE 64
K E ++N P + K + +FL +K A+E + + + +L+ E IE E
Sbjct: 159 KLEAKYNQVPRKGVKAEEVLQEFLNSKEAVEEAILQTDQ--ALTAKEKAIEAE 209
>gnl|CDD|36524 KOG1310, KOG1310, KOG1310, WD40 repeat protein [General function
prediction only].
Length = 758
Score = 25.1 bits (54), Expect = 4.3
Identities = 11/40 (27%), Positives = 14/40 (35%)
Query: 73 HQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDEDH 112
QK ++RL L Y ALQ FP +
Sbjct: 444 IQKAHFRLARALNELTRYLEALSCHWALQMSFPTDVARQN 483
>gnl|CDD|35731 KOG0511, KOG0511, KOG0511, Ankyrin repeat protein [General function
prediction only].
Length = 516
Score = 25.0 bits (54), Expect = 4.7
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 4 FDRVFRSSKFENEHNITPAQWKKLLTLEAKFLPNKRALE 42
F + + N + Q+ LL++E KF K +LE
Sbjct: 200 FSPFLKQ-LYLNTNAEWKDQYNALLSIEVKFSKEKLSLE 237
>gnl|CDD|107272 cd06277, PBP1_LacI_like_1, Ligand-binding domain of uncharacterized
DNA-binding regulatory proteins that are members of the
LacI-GalR family of bacterial transcription repressors.
This group includes the ligand-binding domain of
uncharacterized DNA-binding regulatory proteins that are
members of the LacI-GalR family of bacterial
transcription repressors. The LacI-GalR family
repressors are composed of two functional domains: an
N-terminal HTH (helix-turn-helix) domain, which is
responsible for the DNA-binding specificity, and a
C-terminal ligand-binding domain, which is homologous to
the sugar-binding domain of ABC-type transport systems
that contain the type I periplasmic binding protein-like
fold. As also observed in the periplasmic binding
proteins, the C-terminal domain of the bacterial
transcription repressor undergoes a conformational
change upon ligand binding which in turn changes the DNA
binding affinity of the repressor.
Length = 268
Score = 24.9 bits (55), Expect = 4.8
Identities = 12/49 (24%), Positives = 21/49 (42%), Gaps = 3/49 (6%)
Query: 63 VEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELFDED 111
EYL I H+K + + DPL++ +R AL + ++
Sbjct: 110 TEYL--IEKGHRKIGF-VGDPLYSPSFEERYEGYKKALLDHGIPFNEDY 155
>gnl|CDD|63864 cd04395, RhoGAP_ARHGAP21, RhoGAP_ARHGAP21: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain of
ArhGAP21-like proteins. ArhGAP21 is a multi-domain
protein, containing RhoGAP, PH and PDZ domains, and is
believed to play a role in the organization of the
cell-cell junction complex. It has been shown to
function as a GAP of Cdc42 and RhoA, and to interact
with alpha-catenin and Arf6. Small GTPases cluster into
distinct families, and all act as molecular switches,
active in their GTP-bound form but inactive when
GDP-bound. The Rho family of GTPases activates effectors
involved in a wide variety of developmental processes,
including regulation of cytoskeleton formation, cell
proliferation and the JNK signaling pathway. GTPases
generally have a low intrinsic GTPase hydrolytic
activity but there are family-specific groups of GAPs
that enhance the rate of GTP hydrolysis by several
orders of magnitude..
Length = 196
Score = 24.9 bits (54), Expect = 6.0
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 12/55 (21%)
Query: 75 KWYYR-LDDPLFTDGLY------DRVS---ERLDALQEQFPELFDEDHPWNTVGY 119
K ++R L +PLFT+ LY +R+ ERL L+ L DH + T+ +
Sbjct: 81 KSFFRKLPEPLFTNELYPDFIEANRIEDPVERLKELRRLIHSL--PDHHYETLKH 133
>gnl|CDD|35737 KOG0517, KOG0517, KOG0517, Beta-spectrin [Cytoskeleton].
Length = 2473
Score = 24.6 bits (53), Expect = 6.3
Identities = 19/88 (21%), Positives = 37/88 (42%), Gaps = 14/88 (15%)
Query: 34 FLPNKRALESWLDKAKKV-------TSLSKGEAMIEVEYLVKIALH-HQKWYYRLDD--- 82
FL + ++WL+ + L++ E +++ ++ + +Q+ Y R+
Sbjct: 1062 FLRDLDDFQAWLESTQTQVASEEGPVDLAEAEQLLKQHAALREEIDGYQEDYQRMRALGE 1121
Query: 83 ---PLFTDGLYDRVSERLDALQEQFPEL 107
TD Y + ERL AL + EL
Sbjct: 1122 TVADGQTDPQYLFLRERLQALGTGWEEL 1149
>gnl|CDD|63853 cd04384, RhoGAP_CdGAP, RhoGAP_CdGAP: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain of
CdGAP-like proteins; CdGAP contains an N-terminal RhoGAP
domain and a C-terminal proline-rich region, and it is
active on both Cdc42 and Rac1 but not RhoA. CdGAP is
recruited to focal adhesions via the interaction with
the scaffold protein actopaxin (alpha-parvin). Small
GTPases cluster into distinct families, and all act as
molecular switches, active in their GTP-bound form but
inactive when GDP-bound. The Rho family of GTPases
activates effectors involved in a wide variety of
developmental processes, including regulation of
cytoskeleton formation, cell proliferation and the JNK
signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude..
Length = 195
Score = 24.1 bits (52), Expect = 9.2
Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 75 KWYYR-LDDPLFTDGLYDRVSERLDA 99
K Y+R L +PL T LY++ SE + A
Sbjct: 80 KLYFRELPNPLLTYQLYEKFSEAVSA 105
>gnl|CDD|176897 cd08888, SRPBCC_PITPNA-B_like, Lipid-binding SRPBCC domain of
mammalian PITPNA, -B, and related proteins (Class I
PITPs). This subgroup includes the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of
mammalian Class 1 phosphatidylinositol transfer proteins
(PITPs), PITPNA/PITPalpha and PITPNB/PITPbeta,
Drosophila vibrator, and related proteins. These are
single domain proteins belonging to the PITP family of
lipid transfer proteins, and to the SRPBCC domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. In vitro, PITPs bind phosphatidylinositol
(PtdIns), as well as phosphatidylcholine (PtdCho) but
with a lower affinity. They transfer these lipids from
one membrane compartment to another. The cellular roles
of PITPs include inositol lipid signaling, PtdIns
metabolism, and membrane trafficking. In addition,
PITPNB transfers sphingomyelin in vitro, with a low
affinity. PITPNA is found chiefly in the nucleus and
cytoplasm; it is enriched in the brain and predominantly
localized in the axons. A reduced expression of PITPNA
contributes to the neurodegenerative phenotype of the
mouse vibrator mutation. The role of PITPNA in vivo may
be to provide PtdIns for localized PI3K-dependent
signaling, thereby controlling the polarized extension
of axonal processes. PITPNA homozygous null mice die
soon after birth from complicated organ failure,
including intestinal and hepatic steatosis,
hypoglycemia, and spinocerebellar disease. PITPNB is
associated with the Golgi and ER, and is highly
expressed in the liver. Deletion of the PITPNB gene
results in embryonic lethality. The PtdIns and PtdCho
exchange activity of PITPNB is required for
COPI-mediated retrograde transport from the Golgi to the
ER. Drosophila vibrator localizes to the ER, and has an
essential role in cytokinesis during mitosis and
meiosis.
Length = 258
Score = 24.3 bits (53), Expect = 9.3
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 12 KFENEHNITPAQWKK 26
EN HN+ P +WK+
Sbjct: 120 TQENVHNLDPEEWKE 134
>gnl|CDD|144275 pfam00620, RhoGAP, RhoGAP domain. GTPase activator proteins
towards Rho/Rac/Cdc42-like small GTPases.
Length = 152
Score = 24.1 bits (53), Expect = 9.3
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 10/38 (26%)
Query: 75 KWYYR-LDDPLFTDGLYDRV---------SERLDALQE 102
K + R L +PL T LY+ ER++AL+E
Sbjct: 61 KLFLRELPEPLLTFELYEEFLEAAKSEDEEERIEALRE 98
>gnl|CDD|37255 KOG2044, KOG2044, KOG2044, 5'-3' exonuclease HKE1/RAT1
[Replication, recombination and repair, RNA processing
and modification].
Length = 931
Score = 24.2 bits (52), Expect = 9.3
Identities = 12/39 (30%), Positives = 19/39 (48%)
Query: 6 RVFRSSKFENEHNITPAQWKKLLTLEAKFLPNKRALESW 44
R FR++K E + ++ E KFLP K E++
Sbjct: 117 RRFRAAKEAAEKEAEIERLREEFEAEGKFLPPKVKKETF 155
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
0.319 0.136 0.420
Gapped
Lambda K H
0.267 0.0811 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,547,230
Number of extensions: 72336
Number of successful extensions: 266
Number of sequences better than 10.0: 1
Number of HSP's gapped: 266
Number of HSP's successfully gapped: 36
Length of query: 119
Length of database: 6,263,737
Length adjustment: 81
Effective length of query: 38
Effective length of database: 4,513,408
Effective search space: 171509504
Effective search space used: 171509504
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: 51 (23.3 bits)