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)