RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 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|178959 PRK00283, xerD, site-specific tyrosine recombinase XerD; Reviewed. Length = 299 Score = 321 bits (826), Expect = 1e-88 Identities = 124/293 (42%), Positives = 184/293 (62%), Gaps = 9/293 (3%) Query: 1 MMSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQR 60 + ER + NTLS+Y+RDL+ +L + +SL+ A+ + L ++L L++ +S Sbjct: 15 ALWVERGLAENTLSSYRRDLELFAEWLAARGLSLAEATRDDLQAFLAELAEGGYKATSSA 74 Query: 61 RKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPA 120 R++S +R+F+ FL EGLR+D+PS L+ PK LPKTL + + LL+ I+ Sbjct: 75 RRLSALRRFFQFLLREGLREDDPSALLDSPKLPRRLPKTLSEAQVEALLDAPDIDTP--- 131 Query: 121 PGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSAL 180 +R ++ELLYATG+RVSELV L+ ++L + + + GKGNKERLV L A+ Sbjct: 132 ----LGLRDRAMLELLYATGLRVSELVGLTLDDVSLRQGVVRVTGKGNKERLVPLGEEAV 187 Query: 181 HALQMYKKTCSSMKMTGNDL-WLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHI 239 +A++ Y + + G LFPS+ + G L+RQ F +K A RAGI K +SPH+ Sbjct: 188 YAIERYLERGRPALLNGRSSDALFPSA-RGGQLTRQTFWHRIKHYAKRAGIDPKKLSPHV 246 Query: 240 IRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLA 292 +RHAFA+HLL GADLR +Q LLGH+DISTTQIYTH+ ++L++L +HP A Sbjct: 247 LRHAFATHLLNHGADLRVVQELLGHSDISTTQIYTHVATERLKELHAQHHPRA 299 >gnl|CDD|162772 TIGR02225, recomb_XerD, tyrosine recombinase XerD. The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerD, one of two closely related chromosomal proteins along with XerC (TIGR02224). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and with homologs of XerD on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerD, as some apparent XerD examples score below the trusted and noise cutoff scores. XerC and XerD interact with cell division protein FtsK. Length = 291 Score = 299 bits (769), Expect = 5e-82 Identities = 126/295 (42%), Positives = 171/295 (57%), Gaps = 12/295 (4%) Query: 1 MMSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQR 60 + ER S NTL AY+RDL++ FL + I L ++ +L L + L S Sbjct: 6 YLWVERGLSQNTLEAYRRDLEKFLEFLEERGIDLEEVDRGDIVDFLAELKEAGLSARSIA 65 Query: 61 RKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPA 120 R +S +R FY FL EG+R+D+PS +E PK LPK L + + LL ++ Sbjct: 66 RALSALRSFYRFLLREGIREDDPSALIEPPKVARKLPKVLTVEEVEALLAAPDVDTPLG- 124 Query: 121 PGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSAL 180 +R ++ELLYATG+RVSELV L +NL E + ++GKGNKERLV L A+ Sbjct: 125 ------LRDRAMLELLYATGLRVSELVGLRLEDVNLDEGFVRVRGKGNKERLVPLGEEAI 178 Query: 181 HALQMYKKT---CSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISP 237 AL+ Y K K LF + + G LSRQ + LK A RAGI +K ISP Sbjct: 179 EALERYLKEARPLLLKKKVKESDALFLNR-RGGPLSRQGVWKILKEYAKRAGI-EKPISP 236 Query: 238 HIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLA 292 H +RH+FA+HLLE GADLR +Q LLGH DISTTQIYTH+ ++L+++ + +HP A Sbjct: 237 HTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVARERLKEVHKKHHPRA 291 >gnl|CDD|178942 PRK00236, xerC, site-specific tyrosine recombinase XerC; Reviewed. Length = 297 Score = 243 bits (623), Expect = 5e-65 Identities = 112/292 (38%), Positives = 155/292 (53%), Gaps = 12/292 (4%) Query: 2 MSSERASSINTLSAYKRDLKEMQNFLNNKEI-SLSAASTNHLISYLNHLSQRKLVTSSQR 60 + ER S +TL AY+RDL+ FL I SL L S+L ++ L S Sbjct: 17 LRVERGLSPHTLRAYRRDLRAFLAFLEEHGISSLQDLDAADLRSFLARRRRQGLSARSLA 76 Query: 61 RKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPA 120 R++S +R FY +L GL K NP+ L PK LPK L ++QAK + Sbjct: 77 RRLSALRSFYRWLVRRGLLKANPAAGLRAPKIPKRLPKPLD-------VDQAKRLLDAID 129 Query: 121 PGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSAL 180 +R ++ELLY +G+R+SELV L L+L T+ + GKGNKER V L +A Sbjct: 130 EDDPLALRDRAILELLYGSGLRLSELVGLDIDDLDLASGTLRVLGKGNKERTVPLGRAAR 189 Query: 181 HALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHII 240 AL+ Y + L+L + G LS +V R +K L +AG+ +I+PH + Sbjct: 190 EALEAYLALRPLFLPDDDALFL---GARGGRLSPRVVQRRVKKLGKKAGL-PSHITPHKL 245 Query: 241 RHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLA 292 RH+FA+HLLE G DLR +Q LLGH +STTQIYTH+ L ++ HP A Sbjct: 246 RHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAAHPRA 297 >gnl|CDD|162771 TIGR02224, recomb_XerC, tyrosine recombinase XerC. The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerC, one of two closely related chromosomal proteins along with XerD (TIGR02225). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and homologs of XerC on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerC, as some apparent XerC examples score in the gray zone between trusted (450) and noise (410) cutoffs, along with some XerD examples. XerC and XerD interact with cell division protein FtsK. Length = 295 Score = 238 bits (610), Expect = 1e-63 Identities = 118/296 (39%), Positives = 162/296 (54%), Gaps = 10/296 (3%) Query: 2 MSSERASSINTLSAYKRDLKEMQNFLN--NKEISLSAASTNHLISYLNHLSQRKLVTSSQ 59 + ER S +T+ AY+RDLK FL SL+ + L S+L L R L S Sbjct: 7 LRVERNYSPHTVRAYRRDLKAFLEFLEEEGGLASLAEVTAADLRSFLAELHARGLSRRSL 66 Query: 60 RRKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENP 119 RK+S +R FY FL GL K NP+ + PK+ LPK L +D + LL+ + E Sbjct: 67 ARKLSALRSFYRFLVRRGLIKANPAAGVRAPKQPKKLPKFLSEDEMEALLDAPDEDDE-- 124 Query: 120 APGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSA 179 W +R ++ELLY++G+RVSELV L L+L + ++GKGNKER+V A Sbjct: 125 ---DWLALRDRAILELLYSSGLRVSELVGLDLDDLDLDSGLVRVRGKGNKERIVPFGSYA 181 Query: 180 LHALQMYKKTCSSMKMT-GNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPH 238 ALQ Y + + LF + + G L+ + L+ L A+AG+ K + PH Sbjct: 182 KDALQAYLEARREKLLASEGQDALFLNR-RGGRLTPRGVQYRLQQLVAKAGLPKH-VHPH 239 Query: 239 IIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLAKK 294 +RH+FA+HLLE GADLR +Q LLGH +STTQIYTH+ L K+ HP AKK Sbjct: 240 ALRHSFATHLLENGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYDQAHPRAKK 295 >gnl|CDD|131303 TIGR02249, integrase_gron, integron integrase. Members of this family are integrases associated with integrons (and super-integrons), which are systems for incorporating and expressing cassettes of laterally transferred DNA. Incorporation occurs at an attI site. A super-integron, as in Vibrio sp., may include over 100 cassettes. This family belongs to the phage integrase family (pfam00589) that also includes recombinases XerC (TIGR02224) and XerD (TIGR02225), which are bacterial housekeeping proteins. Within this family of integron integrases, some are designated by class, e.g. IntI4, a class 4 integron integrase from Vibrio cholerae N16961. Length = 315 Score = 129 bits (327), Expect = 7e-31 Identities = 84/307 (27%), Positives = 136/307 (44%), Gaps = 58/307 (18%) Query: 9 SINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLS-QRKLVTSSQRRKISVIR 67 + T AY +K F N + S + + ++L+ L+ K+ S+Q + ++ + Sbjct: 15 AKRTEEAYLHWIKRFIRFHNKRHPSTMGDT--EVEAFLSDLAVDGKVAASTQNQALNALL 72 Query: 68 QFY-NFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKR 126 Y L L + P+K LP L ++ + LLE G+++ Sbjct: 73 FLYKEILKTP-LSLMERFVRAKRPRK---LPVVLTREEVRRLLEHL--------EGKYR- 119 Query: 127 VRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMII-QGKGNKERLVILSPS------- 178 L+ +LLY +GMR+ E + L ++ + I QGKG K+R V L Sbjct: 120 ----LIAKLLYGSGMRLMECLRLRIQDIDFDYGEIRIRQGKGGKDRTVTLPKELIPPLRE 175 Query: 179 ------ALHALQMYKKTCSSMKMTGND------------LWLFPSST-----KTG----- 210 A H + + +LFPS ++G Sbjct: 176 QIELARAYHEADLAEGYGGVYLPHALARKYPNAPKEWGWQYLFPSHRLSRDPESGVIRRH 235 Query: 211 HLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTT 270 H++ R ++ RAGI+K ++ H +RH+FA+HLLE GAD+RT+Q LLGH+D+ TT Sbjct: 236 HINETTIQRAVRRAVERAGIEK-PVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTT 294 Query: 271 QIYTHLL 277 QIYTH+L Sbjct: 295 QIYTHVL 301 >gnl|CDD|179273 PRK01287, xerC, site-specific tyrosine recombinase XerC; Reviewed. Length = 358 Score = 119 bits (300), Expect = 8e-28 Identities = 86/266 (32%), Positives = 131/266 (49%), Gaps = 20/266 (7%) Query: 42 LISYLNHLSQ-RK-----LVTSSQRRKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHI 95 L Y +L RK L T +QR ++S +R ++ +L NP++ LELPK+ Sbjct: 72 LERYQRYLYGYRKANGEPLSTRTQRTQLSPLRVWFRWLLKRHHILYNPAEDLELPKEEKR 131 Query: 96 LPKTLHKDTIANLLEQAKIEA--ENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHT 153 LP +L +A+ E +P + +R L+ELL++TG+R EL L + Sbjct: 132 LP--------RQILSEAETEQVLASPDLTTLQGLRDRALLELLWSTGIRRGELARLDLYD 183 Query: 154 LNLTERTMII-QGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDL-WLFPSSTKTGH 211 ++ + + + QGKGNK+R+V + AL LQ Y + D LF + G Sbjct: 184 VDASRGVVTVRQGKGNKDRVVPVGERALAWLQRYLQDVRPQLAVRPDSGALFVAMDGDG- 242 Query: 212 LSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQ 271 L+R + AGI+K + H+ RHA A+ +LE GAD R IQ +LGH + TTQ Sbjct: 243 LARNTLTNMVGRYIRAAGIEKAG-ACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQ 301 Query: 272 IYTHLLPDKLQKLVQDYHPLAKKEKK 297 IYT + LQ + HP +K + Sbjct: 302 IYTRVSIGHLQAVHASTHPAERKADE 327 >gnl|CDD|185315 PRK15417, PRK15417, integrase/recombinase; Provisional. Length = 337 Score = 95.1 bits (236), Expect = 2e-20 Identities = 84/283 (29%), Positives = 133/283 (46%), Gaps = 59/283 (20%) Query: 33 SLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFY-NFLCYEGLRKDNP-SDTLELP 90 +L ++ +S+L ++RK+ S+ R+ ++ + FY LC D P + P Sbjct: 55 TLGSSEVEAFLSWL--ANERKVSVSTHRQALAALLFFYGKVLC-----TDLPWLQEIGRP 107 Query: 91 KKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLS 150 + + LP L D + +L +E E+ R+F +LLY TGMR+SE + L Sbjct: 108 RPSRRLPVVLTPDEVVRIL--GFLEGEH---------RLF--AQLLYGTGMRISEGLQLR 154 Query: 151 AHTLNLTERTMII-QGKGNKERLVILSPSALHAL--QMYKKTCSSMKMTGND-------- 199 L+ T+I+ +GKG+K+R ++L S +L Q+ + +K Sbjct: 155 VKDLDFDHGTIIVREGKGSKDRALMLPESLAPSLREQLSRARAWWLKDQAEGRSGVALPD 214 Query: 200 ---------------LWLFPSSTKTG----------HLSRQVFARDLKALAARAGIQKKN 234 W+F T + H+ Q F R K +AGI K Sbjct: 215 ALERKYPRAGHSWPWFWVFAQHTHSTDPRSGVVRRHHMYDQTFQRAFKRAVEQAGITKP- 273 Query: 235 ISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLL 277 +PH +RH+FA+ LL G D+RT+Q LLGH+D+STT IYTH+L Sbjct: 274 ATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVL 316 >gnl|CDD|179927 PRK05084, xerS, site-specific tyrosine recombinase XerS; Reviewed. Length = 357 Score = 83.0 bits (206), Expect = 9e-17 Identities = 83/323 (25%), Positives = 135/323 (41%), Gaps = 53/323 (16%) Query: 9 SINTLSAYKRDLKEMQNFLN------------NKEISLSAAST---NHLISYLNHLSQRK 53 S TL Y L E + F N K+I LS + +++ +L +R Sbjct: 34 SPTTLYEY---LTEYRRFFNWLISEGLSDASKIKDIPLSTLENLTKKDVEAFILYLRERP 90 Query: 54 LVTS-------SQR---RKISVIRQFYNFLCYEGLRKD-------NPSDTLELPKK---- 92 L+ SQ R +S ++ + +L E +D N +EL KK Sbjct: 91 LLNGHSTKKGNSQTTINRTLSALKSLFKYLTEEAENEDGEPYFYRNVMKKIELKKKKETL 150 Query: 93 ----NHILPKTLHKDTIANLLEQAKIEAENPAPGQWKR------VRIFLLIELLYATGMR 142 +++ K D L+ E E + R +I L+ +G+R Sbjct: 151 AARAHNLKQKLFLGDEDYEFLDFIDNEYEQKLSNRALSSFKKNKERDLAIIALILGSGLR 210 Query: 143 VSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSALHALQMYKKTCSSM-KMTGNDLW 201 VSELV L LNL + T+ + KG K V ++P AL L+ Y K +S K + Sbjct: 211 VSELVNLDLSDLNLKQMTIDVTRKGGKRDSVNIAPFALPYLEEYLKIRASRYKAEKQEKA 270 Query: 202 LFPSSTKTGHLSRQVFARDLKALAAR-AGIQKKNISPHIIRHAFASHLLEGGADLRTIQI 260 LF TK ++ AR ++ + A+ + ++PH +RH A+ L + D + Sbjct: 271 LF--LTKYRGKPNRISARAIEKMVAKYSEAFGVRLTPHKLRHTLATRLYDATKDQVLVAD 328 Query: 261 LLGHTDISTTQIYTHLLPDKLQK 283 LGHT TT +YTH++ D+ ++ Sbjct: 329 QLGHTSTETTDLYTHIVNDEQKE 351 >gnl|CDD|164996 PHA02601, int, integrase; Provisional. Length = 333 Score = 72.5 bits (178), Expect = 1e-13 Identities = 57/211 (27%), Positives = 88/211 (41%), Gaps = 42/211 (19%) Query: 81 DNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATG 140 NP D + K+ L K+ I LL A + +P + L+ ++ ATG Sbjct: 154 PNPLDGIRPFKEAEPELAFLTKEEIERLL-DACDGSRSPD--------LGLIAKICLATG 204 Query: 141 MRVSELVTLSAHTLNLTE-RTMIIQGKGNKERLVILSPSALHALQMYKKTCSSMKMTGND 199 R SE TL ++ + ++ KG K R V +S ++YK Sbjct: 205 ARWSEAETLKRS--QISPYKITFVKTKGKKNRTVPISE------ELYKM----------- 245 Query: 200 LWLFPSSTKTGHL---SRQVFARDLKALAARAGIQ-KKNISPHIIRHAFASHLLEGGADL 255 + G L + + F R +K RAGI + + H++RH FASH + G ++ Sbjct: 246 -----LPKRRGRLFKDAYESFERAVK----RAGIDLPEGQATHVLRHTFASHFMMNGGNI 296 Query: 256 RTIQILLGHTDISTTQIYTHLLPDKLQKLVQ 286 +Q +LGH I T Y H PD L+ V Sbjct: 297 LVLQRILGHATIEMTMAYAHFAPDHLEDAVS 327 >gnl|CDD|182126 PRK09871, PRK09871, tyrosine recombinase; Provisional. Length = 198 Score = 61.9 bits (150), Expect = 2e-10 Identities = 53/174 (30%), Positives = 79/174 (45%), Gaps = 3/174 (1%) Query: 128 RIFLLIELLYATGMRVSELVTLSAHTLNLTE-RTMIIQGKGNKERLVILSPSALHALQMY 186 R + LI L Y GMR+SEL+ L L+L E R I + K + L A++ + Sbjct: 27 RDYCLILLAYRHGMRISELLDLHYQDLDLNEGRINIRRLKNGFSTVHPLRFDEREAVERW 86 Query: 187 KKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFAS 246 + ++ K +F S + LSRQ R ++ AG + PH++RHA Sbjct: 87 TQERANWKGADRTDAIFISRRGS-RLSRQQAYRIIRDAGIEAGTVTQT-HPHMLRHACGY 144 Query: 247 HLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLAKKEKKHYN 300 L E GAD R IQ LGH +I T YT + L + + + +K K+ Sbjct: 145 ELAERGADTRLIQDYLGHRNIRHTVRYTASNAARFAGLWERNNLINEKLKREEV 198 >gnl|CDD|182125 PRK09870, PRK09870, tyrosine recombinase; Provisional. Length = 200 Score = 51.5 bits (123), Expect = 3e-07 Identities = 52/174 (29%), Positives = 77/174 (44%), Gaps = 13/174 (7%) Query: 107 NLLEQAKIE----AENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMI 162 N L ++IE A N P R + L L + G R SE+ L ++L + + Sbjct: 11 NFLTHSEIESLLKAANTGP---HAARNYCLTLLCFIHGFRASEICRLRISDIDLKAKCIY 67 Query: 163 IQ--GKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARD 220 I KG +L+ + AL+ + +S ++ W+F S K LSRQ F Sbjct: 68 IHRLKKGFSTTHPLLN-KEIQALKNWLSIRTSYPHAESE-WVF-LSRKGNPLSRQQFYHI 124 Query: 221 LKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYT 274 + AG+ + I PH++RH+ L G D R IQ LGH +I T YT Sbjct: 125 ISTSGGNAGLSLE-IHPHMLRHSCGFALANMGIDTRLIQDYLGHRNIRHTVWYT 177 >gnl|CDD|179424 PRK02436, xerD, site-specific tyrosine recombinase XerD-like protein; Reviewed. Length = 245 Score = 43.4 bits (103), Expect = 7e-05 Identities = 63/276 (22%), Positives = 104/276 (37%), Gaps = 50/276 (18%) Query: 5 ERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKIS 64 + S N+ +Y+ DL++ + + S L Y L+ K S+Q+RKIS Sbjct: 11 SKQLSENSQKSYRYDLQQFLQLVGER------VSQEKLKLYQQSLANLKP--SAQKRKIS 62 Query: 65 VIRQFYNFLCYEGLR------KDNPSDTLELPKKNHILP-KTLHKDTIANLLEQAKIEAE 117 + QF FL +G K+ +K IL + +++T Sbjct: 63 AVNQFLYFLYQKGELDSFFKLKETAKLPESKKEKLEILDLSSFYQET------------- 109 Query: 118 NPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSP 177 P ++ L++EL G+ SE+ L ++L + + I+ G K R++ L Sbjct: 110 ---PFPEGQLIALLILEL----GLTPSEIAGLKVADIDLDFQVLTIEKAGGK-RVLTLPE 161 Query: 178 SALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISP 237 + L L+ N +LF K SRQ F LK+ I +S Sbjct: 162 ALLPFLEAIL----------NQTYLFEHKGKP--YSRQWFFNQLKSFV--KSIGYPGLSA 207 Query: 238 HIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIY 273 +R F E G + + LLG T + Y Sbjct: 208 QKLREQFILKQKEAGKSIYELARLLGLKSPVTLEKY 243 >gnl|CDD|177633 PHA03397, vlf-1, very late expression factor 1; Provisional. Length = 363 Score = 31.5 bits (72), Expect = 0.28 Identities = 39/154 (25%), Positives = 66/154 (42%), Gaps = 27/154 (17%) Query: 129 IFLLIELLYATGMRVSELVTLSAHTLNLTE-----RTMIIQGKGNKERLVIL----SPSA 179 +F +I TG+R++E ++ LN + I K K R L Sbjct: 201 VFCIIL---GTGLRITEARQITLDDLNKLIKKGEHKVNNINLKRKKSRFNYLNCIKKKPL 257 Query: 180 LHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHI 239 A ++Y+K + +K++ N SST F +D K L AG++ ++ Sbjct: 258 ELAREIYQKHPTLLKISKN------SSTP--------F-KDFKRLLEEAGVEMDRPRSNM 302 Query: 240 IRHAFASHLLEGGADLRTIQILLGHTDISTTQIY 273 IRH AS++ G L+ + L+ H +S T+ Y Sbjct: 303 IRHYLASNMYNSGVPLQKVSKLMNHESVSATRHY 336 >gnl|CDD|131316 TIGR02263, benz_CoA_red_C, benzoyl-CoA reductase, subunit C. This model describes C subunit of benzoyl-CoA reductase, a 4-subunit enzyme. Many aromatic compounds are metabolized by way of benzoyl-CoA. This enzyme acts under anaerobic conditions. Length = 380 Score = 31.1 bits (70), Expect = 0.39 Identities = 28/114 (24%), Positives = 43/114 (37%), Gaps = 18/114 (15%) Query: 14 SAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISV-------I 66 R NF ++ A N L L HLS +K+ + R I+V I Sbjct: 119 GKGARYFDLPHNFDDDLGGEFYTAELNELCEGLEHLSGKKITDDAIRASIAVFNDNRKLI 178 Query: 67 RQFYNFLCYEGLRKDNP-----SDTLELPKKNHILPKTLHKDTIANLLEQAKIE 115 + Y GLR D P +D L + ++P H +A+ L A+ + Sbjct: 179 QALY------GLRADEPWKVPSADLYLLLRAGLVIPVEEHNQMLADYLAAARKQ 226 >gnl|CDD|150989 pfam10408, Ufd2P_core, Ubiquitin elongating factor core. This is the most conserved part of the core region of Ufd2P ubiquitin elongating factor or E4, running from helix alpha-11 to alpha-38. It consists of 31 helices of variable length connected by loops of variable size forming a compact unit; the helical packing pattern of the compact unit consists of five structural repeats that resemble tandem Armadillo (ARM) repeats. This domain is involved in ubiquitination as it binds Cdc48p and escorts ubiquitinated proteins from Cdc48p to the proteasome for degradation. The core is structurally similar to the nuclear transporter protein importin-alpha. The core is associated with the U-box at the C-terminus, pfam04564, which has ligase activity. Length = 624 Score = 28.8 bits (65), Expect = 1.9 Identities = 18/71 (25%), Positives = 26/71 (36%), Gaps = 4/71 (5%) Query: 8 SSINTLSAYKRDLKEMQNFLNNKEISLSAAST-NHLISYLNHLSQRKLVTSSQ---RRKI 63 I R+LK +Q+ L E S + L L LS KL Q + Sbjct: 184 PLIEEYKRLLRELKRLQDSLEELEQSRPNWAQLKRLEKQLEILSAEKLSLEGQLLDPSLL 243 Query: 64 SVIRQFYNFLC 74 + QF +F+ Sbjct: 244 QRLLQFLSFVA 254 >gnl|CDD|163247 TIGR03396, PC_PLC, phospholipase C, phosphocholine-specific, Pseudomonas-type. Members of this protein family are bacterial, phosphatidylcholine-hydrolyzing phospholipase C enzymes, with a characteristic domain architecture as found in hemolytyic (PlcH) and nonhemolytic (PlcN) secreted enzymes of Pseudomonas aeruginosa. PlcH hydrolyzes phosphatidylcholine to diacylglycerol and phosphocholine, but unlike PlcN can also hydrolyze sphingomyelin to ceramide ((N-acylsphingosine)) and phosphocholine. Members of this family share the twin-arginine signal sequence for Sec-independent transport across the plasma membrane. PlcH is secreted as a heterodimer with a small chaperone, PlcR, encoded immediately downstream. Length = 690 Score = 28.1 bits (63), Expect = 2.8 Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 6/35 (17%) Query: 207 TKTGHLSRQVFARD----LKALAARAGIQKKNISP 237 +K G ++ QVF D L+ L R G+++ NISP Sbjct: 401 SKGGWVNSQVF--DHTSVLRFLEKRFGVREPNISP 433 >gnl|CDD|118291 pfam09759, Atx10homo_assoc, Spinocerebellar ataxia type 10 protein domain. This is the conserved C-terminal 100 residues of Ataxin-10. Ataxin-10 belongs to the family of armadillo repeat proteins and in solution it tends to form homotrimeric complexes, which associate via a tip-to-tip association in a horseshoe-shaped contact with the concave sides of the molecules facing each other. This domain may represent the homo-association site since that is located near the C-terminus of Ataxin-10. The protein does not contain a signal sequence for secretion or any subcellular compartment confirming its cytoplasmic localisation, specifically to the olivocerebellar region. Length = 102 Score = 26.4 bits (59), Expect = 8.7 Identities = 13/63 (20%), Positives = 22/63 (34%), Gaps = 16/63 (25%) Query: 62 KISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAP 121 K ++R L Y+ K+ EL +A +L +I+ NP Sbjct: 3 KRELVR-LIANLTYK--NKEVQDKVREL-------------GGLALILSNTRIDDNNPFI 46 Query: 122 GQW 124 +W Sbjct: 47 KEW 49 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.318 0.131 0.369 Gapped Lambda K H 0.267 0.0721 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 4,679,871 Number of extensions: 289047 Number of successful extensions: 628 Number of sequences better than 10.0: 1 Number of HSP's gapped: 607 Number of HSP's successfully gapped: 32 Length of query: 300 Length of database: 5,994,473 Length adjustment: 93 Effective length of query: 207 Effective length of database: 3,984,929 Effective search space: 824880303 Effective search space used: 824880303 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)