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)