RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|255764498|ref|YP_003065000.2| site-specific tyrosine
recombinase XerD [Candidatus Liberibacter asiaticus str. psy62]
(300 letters)
>gnl|CDD|34580 COG4974, XerD, Site-specific recombinase XerD [DNA replication,
recombination, and repair].
Length = 300
Score = 274 bits (702), Expect = 2e-74
Identities = 128/296 (43%), Positives = 179/296 (60%), Gaps = 14/296 (4%)
Query: 1 MMSSERASSINTLSAYKRDLKEMQNFLNNKEI-SLSAASTNHLISYLNHLSQRKLVTSSQ 59
+ ER S NTLS+Y+RDL++ + +L + I L+ A+ + YL L+++ L +S
Sbjct: 15 YLWIERGLSANTLSSYRRDLEDFREWLEERGITDLADATEADIREYLTELAEQGLSATSI 74
Query: 60 RRKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENP 119
R +S +R FY FL EGLR+D+P+ L+ PK LPK L ++ + LLE P
Sbjct: 75 ARALSALRSFYQFLIREGLREDDPTRLLDSPKLPKRLPKFLSEEEVEALLEA-------P 127
Query: 120 APGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSA 179
+R ++ELLYATG+RVSELV L+ ++L + + ++GKGNKERLV A
Sbjct: 128 DEDTPLGLRDRAMLELLYATGLRVSELVGLTLSDVDLRQGVVRVRGKGNKERLVPFGEEA 187
Query: 180 LHALQMY---KKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNIS 236
+ AL+ Y + + D LFP+ G L+RQ F + LK A RAGI KK IS
Sbjct: 188 VEALEKYLEEARPKLLKGKSSTD-ALFPNQRGGG-LTRQGFWKRLKDYAERAGIDKK-IS 244
Query: 237 PHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLA 292
PH +RH+FA+HLLE GADLR +Q LLGH DISTTQIYTH+ ++L+ L +HP A
Sbjct: 245 PHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVTKERLRDLYAQHHPRA 300
>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 = 230 bits (589), Expect = 3e-61
Identities = 116/285 (40%), Positives = 167/285 (58%), Gaps = 11/285 (3%)
Query: 2 MSSERASSINTLSAYKRDLKEMQNFLNNKEISLSA-ASTNHLISYLNHLSQRKLVTSSQR 60
++ ER S NTL+AY+RDL+ FL + I A + + + +L L + L S
Sbjct: 8 LAVERGLSENTLAAYRRDLERFLEFLEERGILFPADVTPDDIRRFLAELKDQGLSARSIA 67
Query: 61 RKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPA 120
RK+S +R F+ FL EGL NP++ +E PK LPK L + + LL P
Sbjct: 68 RKLSALRSFFKFLLREGLILANPAELIEPPKLKRSLPKVLTIEEVERLLAA-------PD 120
Query: 121 PGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSAL 180
+R L+ELLY+TG+RVSELV L ++L+ + ++GKGNKER+V L +A+
Sbjct: 121 GDTPLGLRDRALLELLYSTGLRVSELVGLKLSDVDLSRGLIRVRGKGNKERIVPLGETAV 180
Query: 181 HALQMY-KKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHI 239
ALQ Y + + G+ LF + + LSR+ + LK A RAGI+KK ISPH
Sbjct: 181 EALQRYLEVRRPLLLKVGDSDALFLN-QRGKRLSRRGVWKILKEYARRAGIEKK-ISPHT 238
Query: 240 IRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKL 284
+RH+FA+HLLE GADLR +Q LLGH ++TTQIYTH+ + L+++
Sbjct: 239 LRHSFATHLLENGADLRAVQELLGHASLATTQIYTHVSFEHLKEV 283
>gnl|CDD|34579 COG4973, XerC, Site-specific recombinase XerC [DNA replication,
recombination, and repair].
Length = 299
Score = 183 bits (467), Expect = 4e-47
Identities = 99/295 (33%), Positives = 153/295 (51%), Gaps = 13/295 (4%)
Query: 2 MSSERASSINTLSAYKRDLKEMQNFLNNKEI-SLSAASTNHLISYLNHLSQRKLVTSSQR 60
+ ER S +TL+ Y+R L+ + L + S + +++ +R L S
Sbjct: 17 LRVERQLSPHTLANYRRQLEALIALLAQMGLGSWQQLDPADVRAFVARSHRRGLSARSLA 76
Query: 61 RKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPA 120
R++S +R FY++L +G K NP+ + PK+ LPK L D LL+ I+ ++P
Sbjct: 77 RRLSALRSFYDWLVKQGELKANPAKGVSAPKQPRHLPKNLDVDEANRLLD---IDGDDPL 133
Query: 121 PGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSAL 180
VR L+EL+Y +G+R+SELV L ++L E + + GKGNKER V + A+
Sbjct: 134 A-----VRDRALLELMYGSGLRLSELVGLDLKHVDLDEGEVRVMGKGNKERRVPVGRKAV 188
Query: 181 HALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHII 240
AL+ + D LF S +R + R L + G+ ++ PH +
Sbjct: 189 EALEHWLA--LRGLFASEDDALFLSRLGKRISARAIQKR-LAQWGIKQGL-NSHVHPHKL 244
Query: 241 RHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLAKKE 295
RH+FA+H+LE DLR +Q LLGH ++STTQIYTHL L + HP AK++
Sbjct: 245 RHSFATHMLESSGDLRAVQELLGHANLSTTQIYTHLDFQHLASVYDAAHPRAKRK 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 = 153 bits (389), Expect = 4e-38
Identities = 79/253 (31%), Positives = 125/253 (49%), Gaps = 25/253 (9%)
Query: 33 SLSAASTNHLISYLNHLS-QRKLVTSSQRRKISVIRQFYNFLCYEGLRKDNPSDTLELPK 91
S + ++L L+ + + S+Q + +S + FY R + P+
Sbjct: 6 SPDELGEEDVRAFLTLLAVEGNVSASTQNQALSALLFFYRHTL---KRDLPWLQRIRRPR 62
Query: 92 KNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSA 151
K LP L + + LL ++ L++ LLY G+R+SE + L
Sbjct: 63 KPRKLPVVLSPEEVRRLLGALT------------GLKHRLILSLLYGCGLRLSECLRLRV 110
Query: 152 HTLNLTERTMII-QGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKT- 209
++ + + QGKG K+R V+L + L L+ Y K ++ WLFPS+ ++
Sbjct: 111 KDIDFDRGQIRVRQGKGGKDRYVMLPEALLELLRAYWKRARALGRERPWQWLFPSTRRSR 170
Query: 210 ------GHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLG 263
HLS + R LK +AGI K+ ++PH +RH+FA+HLLE G D+RTIQ LLG
Sbjct: 171 DPVERRHHLSERTLQRALKKAVEQAGIDKR-VTPHTLRHSFATHLLEAGYDIRTIQELLG 229
Query: 264 HTDISTTQIYTHL 276
H+D+ TT IYTH+
Sbjct: 230 HSDLKTTMIYTHV 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 = 131 bits (331), Expect = 3e-31
Identities = 62/154 (40%), Positives = 87/154 (56%), Gaps = 6/154 (3%)
Query: 127 VRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMII-QGKGNKERLVILSPSALHALQM 185
+R L+ELL TG+R+SEL++L ++L T+ I Q K K R V LS +AL AL+
Sbjct: 21 IRDRALVELLLLTGLRISELLSLRWSDIDLDNGTIRIPQTKTRKSRTVPLSDAALEALKE 80
Query: 186 YKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFA 245
+ + + +LF S + LSR R + RAGI+K ++PH +RH FA
Sbjct: 81 WLGDRKEAEESE---FLFVS-RRGKPLSRSTVNRAFRRAGKRAGIEKD-LTPHDLRHTFA 135
Query: 246 SHLLEGGADLRTIQILLGHTDISTTQIYTHLLPD 279
+HL E G LR IQ LLGH+ IS T YTH+ +
Sbjct: 136 THLAENGVPLRVIQKLLGHSSISMTMRYTHVAAE 169
>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 = 111 bits (278), Expect = 3e-25
Identities = 64/154 (41%), Positives = 85/154 (55%), Gaps = 5/154 (3%)
Query: 125 KRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTM-IIQGKGNKERLVILSPSALHAL 183
R++L + LL ATG+R+SEL L ++L +R + I K KER V LS AL L
Sbjct: 13 TPERLYLALLLLLATGLRISELCALRWSDIDLDKRVIHITGTKTKKERTVPLSEEALKLL 72
Query: 184 QMYKKTCSSMKMTGNDLWLFPSSTKT--GHLSRQVFARDLKALAARAGIQKKNISPHIIR 241
+ Y K G++ +LFPS LSR+ R KA RAGI K+ ++PH +R
Sbjct: 73 KEYLKKRRPAN--GDEEYLFPSRRGGPAATLSRRNVKRIFKAAGRRAGIDKEGLTPHSLR 130
Query: 242 HAFASHLLEGGADLRTIQILLGHTDISTTQIYTH 275
H FAS LL G DL +Q LLGH+ I+ T Y H
Sbjct: 131 HTFASALLNAGLDLEAVQDLLGHSSIAMTMRYAH 164
>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 = 108 bits (270), Expect = 2e-24
Identities = 62/153 (40%), Positives = 82/153 (53%), Gaps = 5/153 (3%)
Query: 125 KRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMII-QGKGNKERLVILSPSALHAL 183
R LI LL TG+RVSEL+ L ++L + T+ + + K KER V LSP L
Sbjct: 13 TAPRDRALILLLLYTGLRVSELLALRWSDIDLDKGTITVRRTKTGKERTVPLSPELAELL 72
Query: 184 QMYKKTCSSMKMTGNDLWLFPSSTKT-GHLSRQVFARDLKALAARAGIQKKNISPHIIRH 242
+ Y + D +LFPS L+R+ R LK RAGI + ++PH +RH
Sbjct: 73 REYLEL--RRPAPKPDDYLFPSRRGGPKRLTRRAVRRLLKKAGKRAGI-PERLTPHDLRH 129
Query: 243 AFASHLLEGGADLRTIQILLGHTDISTTQIYTH 275
FA+ LLE G L IQ LLGH+ ISTT+ Y H
Sbjct: 130 TFATRLLEAGVPLEVIQELLGHSSISTTERYLH 162
>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 = 94.2 bits (234), Expect = 4e-20
Identities = 65/239 (27%), Positives = 107/239 (44%), Gaps = 19/239 (7%)
Query: 45 YLNHLSQRKLVT-SSQRRKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKD 103
+L+HL + + ++ +++ + F+ + E P + ++ +P K
Sbjct: 16 FLDHLENDRGNSIRTRNARLAALHSFFRYAARE-----VPEHLPTI-QRVLAIPMKRFKR 69
Query: 104 TIANLLEQAKIEAENPAPGQ--WKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTM 161
+ L + +++A AP + W R ++ LY TG RVSE L L L
Sbjct: 70 PLVTYLTREEVQALLAAPDRRTWSGRRDRAMLLFLYNTGARVSEATGLKVDDLQLDPPAQ 129
Query: 162 I-IQGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARD 220
+ + GKG KER V L S AL+ + + + D LF + ++R
Sbjct: 130 VRLIGKGRKERTVPLWRSTAAALRAWLR---ERGLHAEDEPLFVNRRGE-PMTRFGVTYL 185
Query: 221 LKALAARAG-----IQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYT 274
L+ AA+A + K ISPH++RH A HLL+ G D+ I + LGH + TT IY
Sbjct: 186 LRKHAAKAAATAPTLATKRISPHVLRHTTAMHLLQSGVDIVVIALWLGHASLETTNIYA 244
>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 = 92.3 bits (229), Expect = 2e-19
Identities = 64/292 (21%), Positives = 118/292 (40%), Gaps = 32/292 (10%)
Query: 1 MMSSERASSINTLSAYKRDLKEMQNFL----NNKEISLSAASTNHLISYLNHLSQ-RKLV 55
+ + +T Y+ LK ++ F+ +I+L + ++ + L + +KL
Sbjct: 26 RERVGKDKAQSTWKRYRTHLKNLREFIECTYKEIDIALLELTREFILEFKLFLRKEKKLS 85
Query: 56 TSSQRRKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIE 115
++ +S +++ + +DNP + K+ + L D + L E
Sbjct: 86 RNTAVHYLSWLKKLLKIAYRDKGLRDNPFAKFKCKKEEETDREYLTPDELQKLAET---P 142
Query: 116 AENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTL----NLTERTMIIQGKGNKER 171
++P +R +F TG+R S++ L+ + + + + K E
Sbjct: 143 CKDPRLELVRRAFLFSCF-----TGLRYSDIKKLTWEEIVEDSDGEKWIRKRRQKTKVEV 197
Query: 172 LVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQ 231
+ L AL L Y + +FP L + LK A AGI
Sbjct: 198 YIPLLDEALQILGKYP--------DEKEGLVFP------LLKNSNMNKPLKEWAKLAGI- 242
Query: 232 KKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQK 283
KK+I+ H RH FA+ L G + T+ +LGHT+I TTQ+Y + +K +
Sbjct: 243 KKHITFHCARHTFATLQLLSGGPIETVSKMLGHTNIKTTQVYARVTDEKKSE 294
>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 = 85.3 bits (211), Expect = 2e-17
Identities = 57/238 (23%), Positives = 93/238 (39%), Gaps = 15/238 (6%)
Query: 57 SSQRRKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEA 116
++ ++ V+R+F R + P L + P + I LL A
Sbjct: 59 ATWAGRLGVVRRFARHRRRADPRTEVPPADLFPRRPRRPTPYIYTDEEIQRLLAAA---L 115
Query: 117 ENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMII-QGKGNKERLVIL 175
+ P + L LL TG+R+ E + L ++L + + K K RLV L
Sbjct: 116 QLPPTSGLRPWTYRTLFGLLAVTGLRLGEALRLRLSDVDLDSGILTVRDSKFGKSRLVPL 175
Query: 176 SPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKT--GHLSRQVFARDLKALAARAGIQK- 232
S AL+ Y + + F SS + +VF + + R Q+
Sbjct: 176 HASTRAALRDYLARRDRLLPAPDSSAFFVSSRGGRLSYGGHRVFYALSREIGLRGWAQRG 235
Query: 233 KNISPHIIRHAFASHLL----EGGADL-RTIQIL---LGHTDISTTQIYTHLLPDKLQ 282
+ H +RH FA L GAD+ R + +L LGH +I+ T Y H P+ ++
Sbjct: 236 RGPRLHDLRHRFAVTRLTRWYRAGADVERKLPVLATYLGHANITDTYWYLHASPELME 293
>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 = 83.5 bits (206), Expect = 7e-17
Identities = 53/179 (29%), Positives = 73/179 (40%), Gaps = 22/179 (12%)
Query: 119 PAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERT-----MIIQGKGNKERLV 173
PA R+ L+ LLY+TG+R+SEL + L + + GKG KER V
Sbjct: 18 PAQDPEHAARLLFLLALLYSTGLRISELAAATGPDLEAFVQGGGWWLYVPVGKGGKERRV 77
Query: 174 ILSPSALHALQMYKKT--CSSMKMTGNDLWLFP-----------SSTKTGHLSRQVFARD 220
+S L AL Y++ G + L SS + + ++VF
Sbjct: 78 PVSDELLAALARYRQARGLPPEPAAGEAVPLLGRHKSAGGGGGLSSAQLYRIVKRVFGAA 137
Query: 221 LKALAARAGIQK----KNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTH 275
L A + + S H +RH ASH L G L +Q LGH I TT Y H
Sbjct: 138 ADRLQADGFEEDAAQLRAASTHWLRHTHASHDLAAGVPLEHVQDNLGHASIDTTSRYLH 196
>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 = 80.7 bits (199), Expect = 5e-16
Identities = 58/201 (28%), Positives = 86/201 (42%), Gaps = 29/201 (14%)
Query: 98 KTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLT 157
K L K+ + LLE K + + LLI LL TG+R+ E + L+ ++
Sbjct: 1 KFLTKEELKKLLEYLKKHENSFS---------KLLILLLAYTGLRIGEALALTWSDIDFE 51
Query: 158 ERTMII-----QGKGNKE----------RLVILSPSALHALQMYKKTCSSMKMTG--NDL 200
T+ I G R + L + L+ YKK + ND
Sbjct: 52 NNTITINKTWDYKTGGYIFKPPKTKSSIRTIPLDKKTIAILKEYKKEQKKYLLGEINNDD 111
Query: 201 WLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQI 260
L ++ + + LK + +AGI I+ H +RH AS LLE G ++ +
Sbjct: 112 ELVFTNKGGKISTPSTINKRLKRICKKAGI--PKITFHGLRHTHASLLLEAGVSIKYVSE 169
Query: 261 LLGHTDISTT-QIYTHLLPDK 280
LGH DISTT Y+HLLP+K
Sbjct: 170 RLGHADISTTLDTYSHLLPEK 190
>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 = 75.3 bits (185), Expect = 2e-14
Identities = 44/155 (28%), Positives = 59/155 (38%), Gaps = 20/155 (12%)
Query: 131 LLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSALHALQMYKKTC 190
+ L TG R E + L A + R + K K R V +S L+ +
Sbjct: 20 DVAILCLDTGARWGEALGLKAEDI-QEGRVTFWKTKSGKSRTVPISERVAAMLKRRRMR- 77
Query: 191 SSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLE 250
LFP L + F K K + HI+RH FASH +
Sbjct: 78 ---------GGLFPD------LYYESFRHIWKRAKIEL---PKGQATHILRHTFASHFMM 119
Query: 251 GGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLV 285
G ++ T+Q +LGH I T Y HL PD L V
Sbjct: 120 NGGNIATLQHILGHATIEMTMRYAHLAPDHLDDAV 154
>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 = 71.8 bits (176), Expect = 2e-13
Identities = 54/210 (25%), Positives = 82/210 (39%), Gaps = 41/210 (19%)
Query: 96 LPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLN 155
LP+ L + + LL A + P +R LL LL G+R E+ L ++
Sbjct: 1 LPRALPWEDVERLL--ASCDRSTPVG---RRDYAILL--LLARLGLRAGEVAALRLDDID 53
Query: 156 LTERTMII-QGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSR 214
T+ + QGKG + + L AL Y L +T SR
Sbjct: 54 WRTGTIRVRQGKGGRVTRLPLPAEVGAALADY-------------LRDGRPATD----SR 96
Query: 215 QVFARDL----------------KALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTI 258
+VF R + RAGI + H++RH+ A+ LL GA L+ I
Sbjct: 97 RVFLRMRAPFRPFAGHSAVSNIVRRALRRAGISPRRGGAHLLRHSLATRLLRAGAPLKEI 156
Query: 259 QILLGHTDISTTQIYTHLLPDKLQKLVQDY 288
+LGH +T IY + D L+ + +
Sbjct: 157 GDVLGHRSPDSTAIYAKVDVDALRAIALPW 186
>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 = 70.4 bits (172), Expect = 6e-13
Identities = 52/148 (35%), Positives = 78/148 (52%), Gaps = 4/148 (2%)
Query: 128 RIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQG-KGNKERLVILSPSALHALQMY 186
R + L+ L++ G+RVSE L ++L R + I+ KG L L AL+ +
Sbjct: 25 RDYCLMLLMFRHGLRVSEACGLKLSDIDLESRQIYIRRLKGGFSTTHPLRDDELEALKNW 84
Query: 187 KKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFAS 246
+ + + +D W+F S + G LSRQ + ++ L A+AG+ K + PH++RHA
Sbjct: 85 LEIRAWKGLPDSD-WIFLSR-RGGPLSRQQVYKLIRRLGAQAGLSIK-VHPHMLRHACGY 141
Query: 247 HLLEGGADLRTIQILLGHTDISTTQIYT 274
L GAD R IQ LGH +I T IYT
Sbjct: 142 ALANQGADTRLIQDYLGHRNIRHTVIYT 169
>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 = 70.3 bits (172), Expect = 6e-13
Identities = 49/232 (21%), Positives = 84/232 (36%), Gaps = 26/232 (11%)
Query: 41 HLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKT- 99
L+ L + R + ++ RR ++Q + + GL + NP+ L
Sbjct: 120 DLLDVLRRIEARGALETA-RRVRQRLKQVFRYAIARGLIEANPAADLRGADGAPKKQHDR 178
Query: 100 -LHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTE 158
L D + L+ + +P L ++LL TG+R EL ++L
Sbjct: 179 ALSPDELPEFLQALDAASGSP--------VTRLALKLLLLTGVRPGELRGARWSEIDLEN 230
Query: 159 RTMIIQG---KGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTK-TGHLSR 214
I K + V LS AL L+ ++ ++G+ ++FPS LS
Sbjct: 231 ALWTIPAERMKTRRPHRVPLSDQALALLEELRE------LSGHSEYVFPSRRDRGKPLSE 284
Query: 215 QVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTD 266
+ LK + +PH +R + L E G I+ L H
Sbjct: 285 NTLNKALKRM-----GYLGEWTPHGLRRTARTWLNELGFPPDVIERQLAHVL 331
>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 = 68.8 bits (168), Expect = 2e-12
Identities = 42/153 (27%), Positives = 66/153 (43%), Gaps = 15/153 (9%)
Query: 133 IELLYATGMRVSELVTLSAHTLNLTERTMII---QGKGNKERLVILSPSALHALQMYKKT 189
+ TG+R SE++ L ++L R + KG + V L+ AL L+
Sbjct: 27 VLFALNTGLRRSEILGLEWSQVDLDNRVAWVRPATSKGGRAIRVPLNDEALQVLK----- 81
Query: 190 CSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLL 249
K + W+F G R + RAGI + H +RH +AS L+
Sbjct: 82 --RQKAGAHKPWVFA---GAGGDPRIDSKTAWRQALQRAGIS--DFRWHDLRHTWASWLV 134
Query: 250 EGGADLRTIQILLGHTDISTTQIYTHLLPDKLQ 282
+ G L +Q LLGH+ + + Y HL P+ L+
Sbjct: 135 QSGVPLYVLQELLGHSSLQMVRRYAHLSPEHLR 167
>gnl|CDD|145844 pfam02899, Phage_integr_N, Phage integrase, N-terminal SAM-like
domain.
Length = 83
Score = 64.6 bits (158), Expect = 3e-11
Identities = 29/75 (38%), Positives = 43/75 (57%)
Query: 3 SSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRK 62
S ER S NT+ AY+RDLK FL +SL +T+ + ++L L + L +S R+
Sbjct: 9 SLERGLSPNTVRAYRRDLKAFLKFLAEGGLSLDQLTTDDVRAFLAELLREGLSAASLARR 68
Query: 63 ISVIRQFYNFLCYEG 77
+S +R F+ FL EG
Sbjct: 69 LSALRSFFQFLKREG 83
>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 = 62.6 bits (152), Expect = 1e-10
Identities = 43/185 (23%), Positives = 76/185 (41%), Gaps = 23/185 (12%)
Query: 125 KRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGK------------------ 166
++E L+ TGMR+ EL+ L ++ + + I G
Sbjct: 19 NNQLYADILEFLFLTGMRIGELLALQEKDIDFENKLINIDGTLDSHTGKEENGYKDTPKT 78
Query: 167 GNKERLVILSPSALHALQMYKKTCSSMKMT---GNDLWLFPSSTKTGHLSRQVFARDLKA 223
+ R + LS A+ ++ + K K + +LF + + ++ L
Sbjct: 79 KSSIRTISLSERAVEIIKRFIKRNKFDKFNPDYKDSDFLFTNKKGNPLDLGPINSKILSK 138
Query: 224 LAARAGIQ-KKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTT-QIYTHLLPDKL 281
G Q KK+++ HI RH S L E G L+ I +GH+D TT +IY+H+
Sbjct: 139 FLKDLGSQSKKHVTTHIFRHTHISFLAEEGVPLKAIMDRVGHSDGKTTLRIYSHVTEKMK 198
Query: 282 QKLVQ 286
++V+
Sbjct: 199 DEIVK 203
>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 = 60.7 bits (147), Expect = 4e-10
Identities = 57/286 (19%), Positives = 94/286 (32%), Gaps = 38/286 (13%)
Query: 11 NTLSAYKRDLKEMQNFL---NNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIR 67
NT AY D + + + S + + YL L+ S+ R++S +
Sbjct: 2 NTRKAYLSDWRRFAAWCQAHGRTPLPASPET---VTLYLTDLADSLAP-STISRRLSALS 57
Query: 68 QFYNFLCYEGLRKDNP-SDTLELPKKNHILPK----TLHKDTIANLLEQAKIEAENPAPG 122
Q + L ++ PK + + + L
Sbjct: 58 QLHRRSGLPSPADSPLVRLVLRGIRREEARPKRQALAILPEDLDKLRSLLDESDTL---- 113
Query: 123 QWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMII----QGKGNKERL--VILS 176
+ +R L+ L +A +R SELV L L T+ ++ + K ++ L + L
Sbjct: 114 --RDLRDLALLLLGFAGLLRRSELVRLRWEDLTFTDGGGLLVTLRRSKTDQSGLGVLKLI 171
Query: 177 PSALH----ALQMYKKTCSSMKMTGNDLWLFPSSTKTG-----HLSRQVFARDLKALAAR 227
P AL+ + + K LF + G LS R LK LA
Sbjct: 172 PPLTTCPVRALERWLEAARIPKG-----PLFRRIDRWGVLGPGALSDNSLNRILKRLAEA 226
Query: 228 AGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIY 273
AG++ + S H +R FA+ G L I Y
Sbjct: 227 AGLRSGSWSGHSLRRGFATEAARAGYSLLEIMRQGRWRSPKMVSRY 272
>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 = 60.4 bits (146), Expect = 5e-10
Identities = 64/278 (23%), Positives = 117/278 (42%), Gaps = 32/278 (11%)
Query: 9 SINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQ 68
S NT+S+Y R + +Q FLN KE++ +L+ Y +L Q + ++ I +
Sbjct: 11 SKNTVSSYLRTV--VQYFLNGKELT-----KPNLLEYKGYL-QENFKAQTVNLRLQGINK 62
Query: 69 FYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVR 128
+ F+ + L+ +++ +K L + L K +
Sbjct: 63 YLEFIGWHDLK----LKFVKVQQKA-FLENVISDADYKFLKTALKADGNE---------E 108
Query: 129 IFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSALHALQMYKK 188
+ ++ L ATG RVSEL+ + + I KG K R + + + + K
Sbjct: 109 WYFVVWFLAATGARVSELIHIKVEHVQTGY--ADIYSKGGKIRRLYIPKNLRVEALKWLK 166
Query: 189 TCSSMKMTGNDLWLFPSSTKTGH-LSRQVFARDLKALAARAGIQKKNISPHIIRHAFASH 247
+ + ++L + G ++ + A+ LK AA+ + + + PH RH FA +
Sbjct: 167 ---ELNLDSGYIFL----NRFGKPITARGIAQQLKNYAAKYKMNPRVVYPHSFRHLFAKN 219
Query: 248 LLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLV 285
L DL + L+GH I TT+IY + Q++V
Sbjct: 220 FLAKYNDLALLADLMGHESIETTRIYLRKTATEQQRIV 257
>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 = 57.5 bits (139), Expect = 5e-09
Identities = 40/150 (26%), Positives = 65/150 (43%), Gaps = 9/150 (6%)
Query: 125 KRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSALHALQ 184
R +LL + TG+R+S+++ L + ER I + K K + + L+P L
Sbjct: 22 HSERNYLLFLIGINTGLRISDILALKVKDVRGDERISIKEKKTGKRKRIYLNPILKEELL 81
Query: 185 MYKKTCSSMKMTGNDLWLFPS-STKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHA 243
Y K + N+ +LF S ++RQ R LK A + GI NI H +R
Sbjct: 82 YYIK-----DLEENE-YLFQSRKGGNRPITRQQAYRILKKAAEQVGI--DNIGTHTLRKT 133
Query: 244 FASHLLEGGADLRTIQILLGHTDISTTQIY 273
F H + D+ + + H+ + T Y
Sbjct: 134 FGYHYYKQTKDIALLMEIFNHSSPAITLRY 163
>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 = 54.1 bits (130), Expect = 4e-08
Identities = 51/227 (22%), Positives = 92/227 (40%), Gaps = 27/227 (11%)
Query: 58 SQRRKISVIRQFYNFLCYEG--LRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIE 115
+ RR+++++ + E NP + + P + L ++ LL E
Sbjct: 1 TVRRELALLSHLFTVARKEWGLDVLTNPVELVRKPPVGKGRDRRLTEEEEERLLRAFGEE 60
Query: 116 AENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERT-MIIQGKGNKERLVI 174
+P R+ ++I L T MR E+++L ++L +R + K R V
Sbjct: 61 EGSP--------RLPVIILLALETAMRRGEILSLRWEQVDLKKRVAHLPDTKNGTSRDVP 112
Query: 175 LSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKN 234
LS A+ LQM + +D +FP ++ + + RAG+ ++
Sbjct: 113 LSKRAVALLQM-------LPKVPDDGPVFPITSDS-------VDAAFRRAKERAGL--ED 156
Query: 235 ISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKL 281
+ H +RH S L E G + + + GH D + YTHL + L
Sbjct: 157 LHFHDLRHEATSRLFEKGLSIMEVASISGHRDWRMLKRYTHLSAEDL 203
>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 = 53.0 bits (127), Expect = 1e-07
Identities = 51/206 (24%), Positives = 79/206 (38%), Gaps = 42/206 (20%)
Query: 97 PKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNL 156
P +D A L+E A+ Q + L E TG+R SEL+ L+ ++L
Sbjct: 1 PDPFTRDEFAALIEAAR------VCQQEQN-----LWEFAVFTGLRPSELIALAWEDVDL 49
Query: 157 TERTMII-------QGKGNKE----RLVILSPSALHALQMYKK----------------T 189
T+ + K K R V L+P AL AL+ K
Sbjct: 50 ERGTVYVRRALVRGIFKVPKTKAGTRDVDLNPPALAALKEQAKLTRLSRPHQITVLEREY 109
Query: 190 CSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLL 249
+ K G ++ P + + + RAGI+ +N P+ +RH FAS +L
Sbjct: 110 GRTEKQKGTFVFHDPKTGEPWTYAVASRKSFWDPALKRAGIRYRN--PYQMRHTFASWML 167
Query: 250 EGGADLRTIQILLGHTDISTTQIYTH 275
GA+ I +GH S ++ H
Sbjct: 168 TAGANPAFIADQMGHK--SAEMVFKH 191
>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 = 52.3 bits (125), Expect = 2e-07
Identities = 42/165 (25%), Positives = 71/165 (43%), Gaps = 9/165 (5%)
Query: 132 LIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSALHALQMYKKTCS 191
+I L TG+R EL+ L +NL + T+ ++ NK L P ++++
Sbjct: 22 VIVGLAKTGIRRGELINLDRRDVNLDKPTLYLKPASNKRSNRTLFP--DLETELFRWLAI 79
Query: 192 SMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQK------KNISPHIIRHAFA 245
+ T LF T+ G R++ + +A R G + +N +PH RH F
Sbjct: 80 RPRTTSPADALF-IGTQDGWGCRRLVYEMVTGMARRHGEHRPWGDLEENFTPHCFRHFFT 138
Query: 246 SHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHP 290
+ L G D +Q L G + YTH+ D+L++ + P
Sbjct: 139 TWLRRRGGDRGVVQELRGDSRDEAIDTYTHIWGDELREAYLKHIP 183
>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 = 50.3 bits (120), Expect = 7e-07
Identities = 38/164 (23%), Positives = 68/164 (41%), Gaps = 16/164 (9%)
Query: 126 RVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGN----------KERLVIL 175
+R L LLY TG+R+ E + L ++L E + + + + +ER + +
Sbjct: 15 NLRDKFLFALLYETGLRIGEALGLRIEDIDLAENQIWLVPREDNANGARAKSGRERRIPV 74
Query: 176 SPSALHALQMYKKTCSSMKMTGND-LWLFPSSTKTGHLSRQVFARDL-KALAARAGIQKK 233
S + Y ++ +D +++ G DL + L + GI
Sbjct: 75 SQYLIDLYVDYVTEIYYLEELESDYVFVNVKGGNQGKPLNYTDVYDLVRRLKKKTGI--- 131
Query: 234 NISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTT-QIYTHL 276
+ +PH+ RH A+ L+ G + + LGH + TT Y HL
Sbjct: 132 DFTPHMFRHTHATELIRAGWSIEVVADRLGHAHVQTTLNTYGHL 175
>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 = 48.5 bits (115), Expect = 2e-06
Identities = 42/166 (25%), Positives = 63/166 (37%), Gaps = 17/166 (10%)
Query: 135 LLYATGMRVSELVTLSAHTL--------NLTERTMIIQGKGNKERLVILSPSALHALQMY 186
++ TGMR+S+L+TL + L I + K + + I AL
Sbjct: 28 IVQETGMRISDLLTLKKNCLLEDKDGDFFYKYYQCIWKTKIKEHIIPISKKVALLIKVRE 87
Query: 187 KKTCSSMKMTGNDL-WLFPS---STKTGHLSRQVFARDLKALAARAGIQKKN-----ISP 237
KT N +LFP K ++Q F +L LA I K+
Sbjct: 88 DKTKELSTEDNNPSEYLFPRYDGKPKGQPTNKQAFRGELNKLAYEKNIVDKSGEIYHFHA 147
Query: 238 HIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQK 283
H RH A+ ++ G + IQ LGH T Y H+ + L+
Sbjct: 148 HAFRHTVATRMINNGMPIHIIQKFLGHESPEMTSRYAHIFDETLKN 193
>gnl|CDD|29501 cd00800, INT_Lambda_C, Lambda integrase, C-terminal catalytic
domain. Lambda-type integrases catalyze site-specific
integration and excision of temperate bacteriophages and
other mobile genetic elements to and from the bacterial
host chromosome. They belong to the superfamily of DNA
breaking-rejoining enzymes, which share the same fold in
their catalytic domain and the overall reaction
mechanism. The phage lambda integrase 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 = 162
Score = 46.4 bits (110), Expect = 1e-05
Identities = 36/157 (22%), Positives = 62/157 (39%), Gaps = 15/157 (9%)
Query: 120 APGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSA 179
A W R ++L TG RV +++ + ++ + I Q K + + LSPS
Sbjct: 16 ADAPWLRC----AMDLALLTGQRVGDVLRMKWSDID-DDGLHIEQSKTGAKLAIPLSPSL 70
Query: 180 LHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISP-- 237
++ + + +L + +S + +R + AG++ P
Sbjct: 71 REVIERCRDLSRV-----SSPYLVHTRPGGKQVSAKTLSRAFRKARKAAGVKWGGDPPTF 125
Query: 238 HIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYT 274
H IR A A+ E + Q LLGH D T+IY
Sbjct: 126 HDIR-AKAASDYEEQG--KDAQALLGHKDEKMTKIYR 159
>gnl|CDD|30927 COG0582, XerC, Integrase [DNA replication, recombination, and
repair].
Length = 309
Score = 46.1 bits (106), Expect = 1e-05
Identities = 73/250 (29%), Positives = 106/250 (42%), Gaps = 26/250 (10%)
Query: 52 RKLVTSSQRRKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQ 111
+ T ++ +++ +R F+ +L G E PK+ LPK L + + LLE
Sbjct: 81 LRESTLTRVFRLAALRGFFAYLDNPGAPLKAL---REKPKRRKKLPKALTAEEVEALLEA 137
Query: 112 AKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQG---KGN 168
+ L L+ TG+RVSEL+ L ++L T+ I+G KG
Sbjct: 138 LDRYRDAL-----------RLALLILLTGLRVSELLGLRWSDIDLENGTIWIRGTKTKGR 186
Query: 169 KERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARA 228
KER V LS AL AL+ Y + +LF S + L A+A
Sbjct: 187 KERRVPLSEQALEALKKYLL------IRRPREYLFLSLRGPRLSRSALTINRLLRARAKA 240
Query: 229 GIQKK--NISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQ 286
+ I+PH +RH FA+ LL GG D R IQ LLGH ++TTQ + D+ K
Sbjct: 241 AKEAGIRKITPHGLRHTFATLLLAGG-DERVIQKLLGHASLNTTQTVYYHASDERLKEAA 299
Query: 287 DYHPLAKKEK 296
K
Sbjct: 300 LKLLELLLIK 309
>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 = 38.0 bits (88), Expect = 0.004
Identities = 37/150 (24%), Positives = 58/150 (38%), Gaps = 26/150 (17%)
Query: 139 TGMRVSELVTLSAHTLNLTERTMII----QGKGNK------ERLVILSPSALHA--LQMY 186
TG RV+E+ L + + I + R + + P + L
Sbjct: 36 TGARVNEIAQLQVDDIREEDGVPCIDITNDDEDQSLKNAASRRTIPVHPELIELGFLDYV 95
Query: 187 KKTCSSMKMTGNDLWLFP--SSTKTGHLSRQV---FARDLKALAARAGIQKKNISPHIIR 241
+ + + G+ LFP + KTG V F+R LK L G++ K S H R
Sbjct: 96 E----ARRAAGHKR-LFPDLPAGKTGGYGSAVSKWFSRYLKKL----GLKDKGKSFHSFR 146
Query: 242 HAFASHLLEGGADLRTIQILLGHTDISTTQ 271
H F + L G I ++GH + +TT
Sbjct: 147 HTFITELRNAGVSRELIAAIMGHEEGTTTF 176
>gnl|CDD|143912 pfam00141, peroxidase, Peroxidase.
Length = 177
Score = 27.9 bits (63), Expect = 3.7
Identities = 10/25 (40%), Positives = 14/25 (56%), Gaps = 1/25 (4%)
Query: 132 LIELLYATGMRVSELVTLS-AHTLN 155
L + G+ +LV LS AHTL+
Sbjct: 126 LRDRFARKGLTAEDLVALSGAHTLD 150
>gnl|CDD|34064 COG4342, COG4342, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 291
Score = 27.3 bits (60), Expect = 5.0
Identities = 22/106 (20%), Positives = 41/106 (38%), Gaps = 8/106 (7%)
Query: 45 YLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRKDNPSDTLELP-KKNHILPKTLHKD 103
YL+ L++ + + R F FL G+ + ++ L P K L+
Sbjct: 63 YLSALNRPIGSVREKDKYQKAYRLFIKFLTSRGIISEEFAEKLRKPLKVKKSNGVDLYIP 122
Query: 104 TIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTL 149
+ + ++ E R +L+ LL +G R+SE V +
Sbjct: 123 SDEEIRATEELAREY-------SERAYLVYLLLLFSGARLSEAVAV 161
>gnl|CDD|35744 KOG0524, KOG0524, KOG0524, Pyruvate dehydrogenase E1, beta subunit
[Energy production and conversion].
Length = 359
Score = 26.8 bits (59), Expect = 6.8
Identities = 20/80 (25%), Positives = 29/80 (36%), Gaps = 10/80 (12%)
Query: 109 LEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGN 168
L +A I ENP +FL ELLY + E L L + + +G
Sbjct: 188 LLKAAIRDENPV--------VFLENELLYGLSFEIPEEALSKDFVLPLGKAKIEREGT-- 237
Query: 169 KERLVILSPSALHALQMYKK 188
+V S H L+ +
Sbjct: 238 HITIVTYSRMVGHCLEAAET 257
>gnl|CDD|132780 cd06870, PX_CISK, The phosphoinositide binding Phox Homology
Domain of Cytokine-Independent Survival Kinase. The PX
domain is a phosphoinositide (PI) binding module
present in many proteins with diverse functions.
Cytokine-independent survival kinase (CISK), also
called Serum- and Glucocorticoid-induced Kinase 3
(SGK3), plays a role in cell growth and survival. It is
expressed in most tissues and is most abundant in the
embryo and adult heart and spleen. It was originally
discovered in a screen for antiapoptotic genes. It
phosphorylates and inhibits the proapoptotic proteins,
Bad and FKHRL1. CISK/SGK3 also regulates many
transporters, ion channels, and receptors. It plays a
critical role in hair follicle morphogenesis and hair
cycling. N-terminal to a catalytic kinase domain, CISK
contains a PX domain which binds highly phosphorylated
PIs, directs membrane localization, and regulates the
enzyme's activity.
Length = 109
Score = 27.0 bits (60), Expect = 6.9
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 53 KLVTSSQRRKISVIRQFYNFL-CYEGLRKDNPSDTLELPKK 92
K+V S R V R++ F YE L+K P+ L++P K
Sbjct: 24 KVVVSVGRSSWFVFRRYAEFDKLYESLKKQFPASNLKIPGK 64
>gnl|CDD|31331 COG1136, SalX, ABC-type antimicrobial peptide transport system,
ATPase component [Defense mechanisms].
Length = 226
Score = 26.7 bits (59), Expect = 7.7
Identities = 18/70 (25%), Positives = 28/70 (40%), Gaps = 6/70 (8%)
Query: 46 LNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTI 105
L LS+++L +R+KI + Q +N L + +ELP K
Sbjct: 69 LTKLSEKEL-AKLRRKKIGFVFQNFNLLPDL-----TVLENVELPLLIAGKSAGRRKRAA 122
Query: 106 ANLLEQAKIE 115
LLE +E
Sbjct: 123 EELLEVLGLE 132
>gnl|CDD|38059 KOG2848, KOG2848, KOG2848, 1-acyl-sn-glycerol-3-phosphate
acyltransferase [Lipid transport and metabolism].
Length = 276
Score = 26.4 bits (58), Expect = 8.9
Identities = 12/49 (24%), Positives = 19/49 (38%)
Query: 182 ALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGI 230
A+ K MK +W+FP T+ F + LA +A +
Sbjct: 148 AIDTLDKCAERMKKENRKVWVFPEGTRNKEGRLLPFKKGAFHLAVQAQV 196
>gnl|CDD|147197 pfam04906, Tweety, Tweety. The tweety (tty) gene has not been
characterized at the protein level. However, it is
thought to form a membrane protein with five potential
membrane-spanning regions. A number of potential
functions have been suggested in.
Length = 406
Score = 26.5 bits (59), Expect = 9.4
Identities = 8/27 (29%), Positives = 14/27 (51%)
Query: 8 SSINTLSAYKRDLKEMQNFLNNKEISL 34
++ K+DL +Q LN+ E +L
Sbjct: 305 FAVPLFPTAKKDLLGIQGDLNSTERNL 331
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
0.318 0.131 0.369
Gapped
Lambda K H
0.267 0.0711 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,383,086
Number of extensions: 168647
Number of successful extensions: 472
Number of sequences better than 10.0: 1
Number of HSP's gapped: 429
Number of HSP's successfully gapped: 45
Length of query: 300
Length of database: 6,263,737
Length adjustment: 93
Effective length of query: 207
Effective length of database: 4,254,100
Effective search space: 880598700
Effective search space used: 880598700
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (25.8 bits)