RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780490|ref|YP_003064903.1| site-specific tyrosine
recombinase XerC [Candidatus Liberibacter asiaticus str. psy62]
(67 letters)
>gnl|CDD|34580 COG4974, XerD, Site-specific recombinase XerD [DNA replication,
recombination, and repair].
Length = 300
Score = 88.0 bits (218), Expect = 5e-19
Identities = 34/57 (59%), Positives = 44/57 (77%)
Query: 2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHP 58
+ HTLRHSFATHLL NG DLR +Q +LGH+ +STTQIYT+V +R+ ++Y Q HP
Sbjct: 242 KISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVTKERLRDLYAQHHP 298
>gnl|CDD|29499 cd00798, INT_XerDC, XerD and XerC integrases, DNA
breaking-rejoining enzymes, N- and C-terminal domains.
XerD-like integrases are involved in the site-specific
integration and excision of lysogenic bacteriophage
genomes, transposition of conjugative transposons,
termination of chromosomal replication, and stable
plasmid inheritance. They share the same fold in their
catalytic domain containing six conserved active site
residues and the overall reaction mechanism with the DNA
breaking-rejoining enzyme superfamily. In Escherichia
coli, the Xer site-specific recombination system acts to
convert dimeric chromosomes, which are formed by
homologous recombination to monomers. Two related
recombinases, XerC and XerD, bind cooperatively to a
recombination site present in the E. coli chromosome.
Each recombinase catalyzes the exchange of one pair of
DNA strand in a reaction that proceeds through a
Holliday junction intermediate. These enzymes can bridge
two different and well-separated DNA sequences called
arm- and core-sites. The C-terminal domain binds,
cleaves and re-ligates DNA strands at the core-sites,
while the N-terminal domain is largely responsible for
high-affinity binding to the arm-type sites..
Length = 284
Score = 83.7 bits (207), Expect = 9e-18
Identities = 31/52 (59%), Positives = 42/52 (80%)
Query: 2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIY 53
+ HTLRHSFATHLL NG DLR++Q +LGH+ L+TTQIYT+V+ + + E+Y
Sbjct: 233 KISPHTLRHSFATHLLENGADLRAVQELLGHASLATTQIYTHVSFEHLKEVY 284
>gnl|CDD|34579 COG4973, XerC, Site-specific recombinase XerC [DNA replication,
recombination, and repair].
Length = 299
Score = 80.0 bits (197), Expect = 1e-16
Identities = 31/58 (53%), Positives = 44/58 (75%)
Query: 6 HTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSITQK 63
H LRHSFATH+L + GDLR++Q +LGH+ LSTTQIYT+++ + + +YD HP +K
Sbjct: 242 HKLRHSFATHMLESSGDLRAVQELLGHANLSTTQIYTHLDFQHLASVYDAAHPRAKRK 299
>gnl|CDD|29514 cd01193, INT_IntI, IntI (E2) integrases, site-specific tyrosine
recombinases, DNA breaking-rejoining enzymes, N- and
C-terminal domains. This CD includes integrases which
are components of multiresistant integrons and mediate
recombination between a proximal attI site and a
secondary target called the attC (or 59-base element)
present on various mobile gene cassettes.
Integron-integrases are present in many natural
occurring mobile elements, including transposons and
conjugative plasmids. Vibrio, Shewanella, Xanthomonas
and Pseudomonas species harbor chromosomal
super-integrons. All integron-integrases carry large
inserts unlike the TnpF ermF-like proteins also seen in
this group..
Length = 242
Score = 69.1 bits (169), Expect = 3e-13
Identities = 29/41 (70%), Positives = 33/41 (80%)
Query: 4 TAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNV 44
T HTLRHSFATHLL G D+R+IQ +LGHS L TT IYT+V
Sbjct: 202 TPHTLRHSFATHLLEAGYDIRTIQELLGHSDLKTTMIYTHV 242
>gnl|CDD|144254 pfam00589, Phage_integrase, Phage integrase family. Members of
this family cleave DNA substrates by a series of
staggered cuts, during which the protein becomes
covalently linked to the DNA through a catalytic
tyrosine residue at the carboxy end of the alignment.
The catalytic site residues in CRE recombinase are
Arg-173, His-289, Arg-292 and Tyr-324.
Length = 170
Score = 63.9 bits (156), Expect = 9e-12
Identities = 26/45 (57%), Positives = 32/45 (71%)
Query: 4 TAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKR 48
T H LRH+FATHL NG LR IQ +LGHS +S T YT+V ++R
Sbjct: 126 TPHDLRHTFATHLAENGVPLRVIQKLLGHSSISMTMRYTHVAAER 170
>gnl|CDD|29506 cd01185, INT_Tn4399, Tn4399 and related integrases, DNA
breaking-rejoining enzymes, integrase/recombinases, N-
and C-terminal domains. This CD includes various
bacterial integrases, including cLV25, a Bacteroides
fragilis chromosomal transfer factor integrase similar
to the Bacteroides mobilizable transposon, Tn4399,
integrase..
Length = 299
Score = 58.0 bits (140), Expect = 6e-10
Identities = 18/41 (43%), Positives = 27/41 (65%)
Query: 4 TAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNV 44
T H RH+FAT L +GG + ++ +LGH+ + TTQ+Y V
Sbjct: 247 TFHCARHTFATLQLLSGGPIETVSKMLGHTNIKTTQVYARV 287
>gnl|CDD|29498 cd00797, HP1_INT_C, Phage HP1 integrase, C-terminal catalytic
domain. Bacteriophage HP1 and related integrases are
found in eubacteria, plasmids and temperate
bacteriophages of the P2 family. They belong to the DNA
breaking-rejoining enzyme superfamily, which includes
tyrosine recombinases and type IB topoisomerases. These
enzymes share the same fold in their C-terminal
catalytic domain containing six conserved active site
residues and the overall reaction mechanism. The HP1
recombinase controls phage replication by site-specific
recombination between the HP1 genome and the chromosomal
DNA. It is a heterobifunctional DNA-binding protein,
which recognizes two different DNA sequence motifs (type
I and type II binding sites). The C-terminal catalytic
domain of the HP1 integrase binds to the type I site,
while the less conserved N-terminal domain is largely
responsible for binding to the type II site..
Length = 158
Score = 54.5 bits (131), Expect = 6e-09
Identities = 17/36 (47%), Positives = 26/36 (72%)
Query: 6 HTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIY 41
H LRH+FA+H + NGG++ ++Q ILGH+ + T Y
Sbjct: 107 HILRHTFASHFMMNGGNIATLQHILGHATIEMTMRY 142
>gnl|CDD|29503 cd01182, INT_REC_C, DNA breaking-rejoining enzymes,
intergrase/recombinases, C-terminal catalytic domain.
The tyrosine recombinase/integrase family share the same
catalytic domain containing six conserved active site
residues. The best-studied members of this diverse
family include the bacteriophage lambda integrase, the
bacteriophage P1 Cre recombinase, the yeast Flp
recombinase and the bacterial XerD/C recombinases. Their
overall reaction mechanism is essentially identical and
involves cleavage of a single strand of a DNA duplex by
nucleophilic attack of a conserved tyrosine to give a 3'
phosphotyrosyl protein-DNA adduct. In the second
rejoining step, a terminal 5' hydroxyl attacks the
covalent adduct to release the enzyme and generate
duplex DNA. Many intergrase/recombinases also have
N-terminal domains, which show little sequence or
structure similarity..
Length = 162
Score = 54.5 bits (130), Expect = 7e-09
Identities = 22/39 (56%), Positives = 26/39 (66%)
Query: 4 TAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYT 42
T H LRH+FAT LL G L IQ +LGHS +STT+ Y
Sbjct: 123 TPHDLRHTFATRLLEAGVPLEVIQELLGHSSISTTERYL 161
>gnl|CDD|29511 cd01190, INT_SG5, INT_SG5, DNA breaking-rejoining enzymes,
integrase/recombinases subgroup 5, N- and C-terminal
domains. The CD contains mainly predicted bacterial
integrase/recombinases..
Length = 260
Score = 53.0 bits (127), Expect = 2e-08
Identities = 20/55 (36%), Positives = 28/55 (50%)
Query: 4 TAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHP 58
+ H LRH+ A HLL +G D+ I LGH+ L TT IY + + + P
Sbjct: 206 SPHVLRHTTAMHLLQSGVDIVVIALWLGHASLETTNIYAEADLEMKRRALAKATP 260
>gnl|CDD|29495 cd00397, DNA_BRE_C, DNA breaking-rejoining enzymes, C-terminal
catalytic domain. The DNA breaking-rejoining enzyme
superfamily includes type IB topoisomerases and tyrosine
recombinases that share the same fold in their catalytic
domain containing six conserved active site residues.
The best-studied members of this diverse superfamily
include human topoisomerase I, the bacteriophage lambda
integrase, the bacteriophage P1 Cre recombinase, the
yeast Flp recombinase and the bacterial XerD/C
recombinases. Their overall reaction mechanism is
essentially identical and involves cleavage of a single
strand of a DNA duplex by nucleophilic attack of a
conserved tyrosine to give a 3' phosphotyrosyl
protein-DNA adduct. In the second rejoining step, a
terminal 5' hydroxyl attacks the covalent adduct to
release the enzyme and generate duplex DNA. The enzymes
differ in that topoisomerases cleave and then rejoin the
same 5' and 3' termini, whereas a site-specific
recombinase transfers a 5' hydroxyl generated by
recombinase cleavage to a new 3' phosphate partner
located in a different duplex region. Many DNA
breaking-rejoining enzymes also have N-terminal domains,
which show little sequence or structure similarity..
Length = 164
Score = 53.1 bits (127), Expect = 2e-08
Identities = 19/39 (48%), Positives = 28/39 (71%)
Query: 4 TAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYT 42
T H+LRH+FA+ LL+ G DL ++Q +LGHS ++ T Y
Sbjct: 125 TPHSLRHTFASALLNAGLDLEAVQDLLGHSSIAMTMRYA 163
>gnl|CDD|29509 cd01188, INT_pAE1, pAE1 and related integrases, DNA
breaking-rejoining enzymes, integrase/recombinases,
C-terminal domain. This CD includes various bacterial
integrases, including the predicted integrase of the
deletion-prone region of plasmid pAE1 of Alcaligenes
eutrophus H1..
Length = 188
Score = 51.0 bits (122), Expect = 6e-08
Identities = 21/48 (43%), Positives = 26/48 (54%)
Query: 5 AHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEI 52
AH LRHS AT LL G L+ I +LGH +T IY V+ + I
Sbjct: 135 AHLLRHSLATRLLRAGAPLKEIGDVLGHRSPDSTAIYAKVDVDALRAI 182
>gnl|CDD|29504 cd01183, INT_SG1_C, INT_SG1, DNA breaking-rejoining enzymes,
integrase/recombinases subgroup 1, C-terminal catalytic
domain. The CD contains mainly predicted
integrase/recombinase and site-specific XerD
recombinases. The members of this CD are found
predominantly in proteobacteria. These proteins have not
been biochemically characerised as yet..
Length = 196
Score = 45.0 bits (106), Expect = 4e-06
Identities = 16/39 (41%), Positives = 23/39 (58%)
Query: 4 TAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYT 42
+ H LRH+ A+H L+ G L +Q LGH+ + TT Y
Sbjct: 157 STHWLRHTHASHDLAAGVPLEHVQDNLGHASIDTTSRYL 195
>gnl|CDD|29510 cd01189, INT_phiLC3_C, phiLC3 phage and phage-related integrases,
site-specific recombinases, DNA breaking-rejoining
enzymes, C-terminal catalytic domain. This CD includes
various bacterial (mainly gram positive) and phage
integrases, including those similar to Lactococcus phage
phiLC3, TPW22, Tuc2009, BK5-T, A2, bIL285, bIL286,
bIL311, ul36 and phi g1e; Staphylococcus aureus phage
phi13 and phi42; Oenococcus oeni phage fOg44;
Streptococcus thermophilus phage O1205 and Sfi21; and
Streptococcus pyogenes phage T12 and T270..
Length = 191
Score = 42.5 bits (100), Expect = 2e-05
Identities = 16/46 (34%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 4 TAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTT-QIYTNVNSKR 48
T H LRH+ A+ LL G ++ + LGH+ +STT Y+++ ++
Sbjct: 145 TFHGLRHTHASLLLEAGVSIKYVSERLGHADISTTLDTYSHLLPEK 190
>gnl|CDD|29513 cd01192, INT_P22_C, P22-like integrases, site-specific
recombinases, DNA breaking-rejoining enzymes, C-terminal
catalytic domain. This CD includes various bacterial and
phage integrases, including those similar to phage
P22-like integrases, DLP12 and APSE-1..
Length = 177
Score = 42.2 bits (99), Expect = 3e-05
Identities = 15/36 (41%), Positives = 23/36 (63%)
Query: 6 HTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIY 41
H LRH++A+ L+ +G L +Q +LGHS L + Y
Sbjct: 123 HDLRHTWASWLVQSGVPLYVLQELLGHSSLQMVRRY 158
>gnl|CDD|29518 cd01197, INT_FimBE_C, FimB and FimE and related proteins, DNA
breaking-rejoining enzymes, integrase/recombinases,
catalytic domain. This CD includes those proteins
similar to E.coli FimE and FimB regulatory proteins and
Proteus mirabilis MrpI..
Length = 180
Score = 41.9 bits (98), Expect = 4e-05
Identities = 19/53 (35%), Positives = 27/53 (50%)
Query: 1 MSTTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIY 53
+ H LRH+ L + G D R IQ LGH + T IYT N+ R + ++
Sbjct: 128 IKVHPHMLRHACGYALANQGADTRLIQDYLGHRNIRHTVIYTASNAARFLNLW 180
>gnl|CDD|29520 cd01199, INT_Tn1545_C, Tn1545-related conjugative transposon
integrases, site-specific recombinases, DNA
breaking-rejoining enzymes, C-terminal catalytic domain.
This CD includes bacterial (gram positive) and phage
integrases, including those similar to Tn1545, Tn5252,
and Tn5276 conjugative transposon integrases and
Lactobacillus phage phi adh integrase..
Length = 205
Score = 40.7 bits (95), Expect = 1e-04
Identities = 19/50 (38%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 4 TAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTT-QIYTNVNSKRMMEI 52
T H RH+ + L G L++I +GHS TT +IY++V K EI
Sbjct: 152 TTHIFRHTHISFLAEEGVPLKAIMDRVGHSDGKTTLRIYSHVTEKMKDEI 201
>gnl|CDD|29517 cd01196, INT_VanD, VanD integrase, IntD, and related integrases,
DNA breaking-rejoining enzymes, integrase/recombinases,
N- and C-terminal domains. This CD includes various
bacterial integrases including those similar to IntD, a
putative integrase-like protein, a component of the vanD
glycopeptide resistance cluster in Enterococcus faecium
BM4339. Members of this CD are predominantly bacterial
in origin..
Length = 263
Score = 39.6 bits (92), Expect = 2e-04
Identities = 16/50 (32%), Positives = 26/50 (52%)
Query: 6 HTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQ 55
H+ RH FA + L+ DL + ++GH + TT+IY + I D+
Sbjct: 210 HSFRHLFAKNFLAKYNDLALLADLMGHESIETTRIYLRKTATEQQRIVDK 259
>gnl|CDD|29519 cd01198, INT_ASSRA_C, Archaeal site-specific recombinase A (ASSRA),
DNA breaking-rejoining enzymes, integrase/recombinases,
C-terminal catalytic domain. Members of this CD are
archael in origin. No biochemical characterization is
available for the proteins of this subgroup at this
point..
Length = 186
Score = 39.6 bits (92), Expect = 2e-04
Identities = 20/58 (34%), Positives = 27/58 (46%)
Query: 4 TAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSIT 61
T H RH F T L GGD +Q + G SR YT++ + E Y + PS+
Sbjct: 129 TPHCFRHFFTTWLRRRGGDRGVVQELRGDSRDEAIDTYTHIWGDELREAYLKHIPSLG 186
>gnl|CDD|29516 cd01195, INT_Tn544B_C, Tn544B and related transposases, DNA
breaking-rejoining enzymes, integrase/recombinases,
catalytic domain. This CD includes various bacterial
transposases similar to TnpB from transposon Tn554..
Length = 195
Score = 38.5 bits (89), Expect = 4e-04
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 5 AHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNV 44
AH RH+ AT +++NG + IQ LGH T Y ++
Sbjct: 147 AHAFRHTVATRMINNGMPIHIIQKFLGHESPEMTSRYAHI 186
>gnl|CDD|29515 cd01194, INT_Tn554A_C, Tn544A and related transposases, DNA
breaking-rejoining enzymes, integrase/recombinases,
C-terminal catalytic domain. This CD includes various
bacterial transposases similar to TnpA from transposon
Tn554..
Length = 186
Score = 34.9 bits (80), Expect = 0.005
Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 4 TAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTT-QIYTNVNSKRMMEIY 53
T H RH+ AT L+ G + + LGH+ + TT Y +++ + + +
Sbjct: 134 TPHMFRHTHATELIRAGWSIEVVADRLGHAHVQTTLNTYGHLSEEDIRREF 184
>gnl|CDD|29505 cd01184, INT_SG2_C, INT_SG2, DNA breaking-rejoining enzymes,
integrase/recombinases subgroup 2, C-terminal catalytic
domain. The CD contains mainly predicted
integrase/recombinases and phage-related integrases.
Some have N-terminal domains, which show little sequence
similarity to each other. Members of this subgroup are
predominantly found in proteobacteria..
Length = 181
Score = 32.6 bits (74), Expect = 0.026
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 4 TAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQ 39
+ H+ RH+F T L + G I +I+GH +TT
Sbjct: 141 SFHSFRHTFITELRNAGVSRELIAAIMGHEEGTTTF 176
>gnl|CDD|29500 cd00799, INT_Cre, Cre recombinase, C-terminal catalytic domain.
Cre-like recombinases belong to the superfamily of DNA
breaking-rejoining enzymes, which share the same fold in
their catalytic domain and the overall reaction
mechanism. The bacteriophage P1 Cre recombinase
maintains the circular phage replicon in a monomeric
state by catalyzing a site-specific recombination
between two loxP sites. The catalytic core domain of
Cre recombinase is linked to a more divergent helical
N-terminal domain, which interacts primarily with the
DNA major groove proximal to the crossover region..
Length = 287
Score = 32.2 bits (73), Expect = 0.032
Identities = 10/38 (26%), Positives = 12/38 (31%)
Query: 4 TAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIY 41
+ H+LR FAT G L I Y
Sbjct: 235 SGHSLRRGFATEAARAGYSLLEIMRQGRWRSPKMVSRY 272
>gnl|CDD|29507 cd01186, INT_SG3_C, INT_SG3, DNA breaking-rejoining enzymes,
integrase/recombinases subgroup 3, catalytic domain. The
CD contains various predicted bacterial and phage
integrase/recombinase sequences for which not much
experimental characterization is available..
Length = 180
Score = 31.3 bits (71), Expect = 0.065
Identities = 14/50 (28%), Positives = 21/50 (42%)
Query: 6 HTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQ 55
HTLR +F H D+ + I HS + T Y +N + + D
Sbjct: 128 HTLRKTFGYHYYKQTKDIALLMEIFNHSSPAITLRYIGINQDEIDKQLDN 177
>gnl|CDD|29508 cd01187, INT_SG4, INT_SG4, DNA breaking-rejoining enzymes,
integrase/recombinases subgroup 4, N- and C-terminal
domains. The CD contains mainly predicted bacterial
integrase/recombinases for which not much biochemical
characterization is available..
Length = 299
Score = 29.1 bits (65), Expect = 0.31
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 8/44 (18%)
Query: 6 HTLRHSFATHLLS----NGGD----LRSIQSILGHSRLSTTQIY 41
H LRH FA L+ G D L + + LGH+ ++ T Y
Sbjct: 241 HDLRHRFAVTRLTRWYRAGADVERKLPVLATYLGHANITDTYWY 284
>gnl|CDD|29502 cd00801, INT_P4, Bacteriophage P4 integrase. P4-like integrases are
found in temperate bacteriophages, integrative plasmids,
pathogenicity and symbiosis islands, and other mobile
genetic elements. They share the same fold in their
catalytic domain and the overall reaction mechanism with
the superfamily of DNA breaking-rejoining enzymes. The
P4 integrase mediates integrative and excisive
site-specific recombination between two sites, called
attachment sites, located on the phage genome and the
bacterial chromosome. The phage attachment site is often
found adjacent to the integrase gene, while the host
attachment sites are typically situated near tRNA
genes..
Length = 357
Score = 28.7 bits (64), Expect = 0.40
Identities = 10/30 (33%), Positives = 12/30 (40%)
Query: 4 TAHTLRHSFATHLLSNGGDLRSIQSILGHS 33
T H LR + T L G I+ L H
Sbjct: 301 TPHGLRRTARTWLNELGFPPDVIERQLAHV 330
>gnl|CDD|29497 cd00796, INT_Rci, Rci recombinase, C-terminal catalytic domain.
Rci enzymes are found in IncI1 incompatibility group
plasmids such as R64. These recombinases belong to the
superfamily of DNA breaking-rejoining enzymes, which
share the same fold in their catalytic domain and the
overall reaction mechanism. The R64 Rci recombinase
mediates site specific recombination at the highly
mobile DNA segments called shufflon located in the
C-terminal region of the pilV gene, which determines the
recipient specificity in liquid mating. This gene
encodes a thin pilus component that recognizes
recipient's receptors required for liquid mating. The
recombination occurs between any of the seven inverted
repeats that separate four DNA segments of the shufflon.
The segments can be inverted independently or in groups,
resulting in a complex DNA rearrangement. The catalytic
domain of Rci is linked to a variable N-terminal domain,
whose function is unknown..
Length = 206
Score = 28.3 bits (63), Expect = 0.45
Identities = 12/38 (31%), Positives = 17/38 (44%)
Query: 6 HTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTN 43
H LRH + L G + + SI GH + YT+
Sbjct: 160 HDLRHEATSRLFEKGLSIMEVASISGHRDWRMLKRYTH 197
>gnl|CDD|30927 COG0582, XerC, Integrase [DNA replication, recombination, and
repair].
Length = 309
Score = 28.4 bits (60), Expect = 0.48
Identities = 24/50 (48%), Positives = 30/50 (60%), Gaps = 1/50 (2%)
Query: 2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMME 51
T H LRH+FAT LL GGD R IQ +LGH+ L+TTQ S ++
Sbjct: 248 KITPHGLRHTFATLLL-AGGDERVIQKLLGHASLNTTQTVYYHASDERLK 296
>gnl|CDD|145902 pfam03000, NPH3, NPH3 family. Phototropism of Arabidopsis thaliana
seedlings in response to a blue light source is
initiated by nonphototropic hypocotyl 1 (NPH1), a
light-activated serine-threonine protein kinase.
Mutations in NPH3 disrupt early signaling occurring
downstream of the NPH1 photoreceptor. The NPH3 gene
encodes a NPH1-interacting protein. NPH3 is a member of
a large protein family, apparently specific to higher
plants, and may function as an adapter or scaffold
protein to bring together the enzymatic components of a
NPH1-activated phosphorelay.
Length = 246
Score = 27.5 bits (62), Expect = 0.86
Identities = 10/41 (24%), Positives = 22/41 (53%), Gaps = 6/41 (14%)
Query: 26 IQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSITQKDKK 66
+++ +R S +Y R ++IY + HP +++ +KK
Sbjct: 196 AEALPDSARPSHDGLY------RAIDIYLKAHPGLSESEKK 230
>gnl|CDD|29512 cd01191, INT_phiCTX_C, phiCTX phage and phage-related integrases,
site-specific recombinases, DNA breaking-rejoining
enzymes, C-terminal catalytic domain. This CD includes
various phage and bacterial integrases, including those
similar to phage integrases: Bordetella and Pseudomonas
phiCTX; E. coli Rac, Qin, and Shiga toxin 2 933W; and
Salmonella typhimurium LT2 Gifsy-2 and Fels-1; and a
putative pore-forming cytotoxin integrase from Vibrio
parahaemolyticus O3:K6..
Length = 196
Score = 27.2 bits (60), Expect = 1.1
Identities = 10/34 (29%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 8 LRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIY 41
+RH+FA+ +L+ G + I +GH S ++
Sbjct: 158 MRHTFASWMLTAGANPAFIADQMGHK--SAEMVF 189
>gnl|CDD|31403 COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope
biogenesis, outer membrane].
Length = 291
Score = 25.1 bits (55), Expect = 4.2
Identities = 6/16 (37%), Positives = 12/16 (75%)
Query: 45 NSKRMMEIYDQTHPSI 60
K+M+E+Y++T S+
Sbjct: 141 CLKQMIELYEETGGSV 156
>gnl|CDD|145244 pfam01964, ThiC, ThiC family. ThiC is found within the thiamine
biosynthesis operon. ThiC is involved in pyrimidine
biosynthesis. The precise catalytic function of ThiC is
still not known. ThiC participates in the formation of
4-Amino-5-hydroxymethyl-2-methylpyrimidine from AIR, an
intermediate in the de novo pyrimidine biosynthesis.
Length = 421
Score = 24.3 bits (54), Expect = 8.4
Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 3/28 (10%)
Query: 17 LSNGGDLRSI-QSILGHSRLS--TTQIY 41
LS GGDL I ++IL +S + T IY
Sbjct: 96 LSTGGDLDEIRRAILENSPVPVGTVPIY 123
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
0.314 0.124 0.341
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 673,660
Number of extensions: 22898
Number of successful extensions: 70
Number of sequences better than 10.0: 1
Number of HSP's gapped: 70
Number of HSP's successfully gapped: 33
Length of query: 67
Length of database: 6,263,737
Length adjustment: 38
Effective length of query: 29
Effective length of database: 5,442,595
Effective search space: 157835255
Effective search space used: 157835255
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (23.3 bits)