RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780753|ref|YP_003065166.1| peptide chain release factor 2 [Candidatus Liberibacter asiaticus str. psy62] (355 letters) >gnl|CDD|179072 PRK00578, prfB, peptide chain release factor 2; Validated. Length = 367 Score = 554 bits (1431), Expect = e-159 Identities = 206/352 (58%), Positives = 250/352 (71%) Query: 1 MKLSRQLNCLGGLFDWDNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFIK 60 L +L + G+ D D +RL L + EDP W + A+ + +E L + ++ Sbjct: 10 KDLDEKLENIRGVLDVDALKERLEELEAEAEDPDFWNDQERAQKVTKELSSLKAKLDTLE 69 Query: 61 EIQDRLCDNLILLELALEEDDCSILQETSDNLQRIKLEVEYKQFESLLSGEADSNDAYLE 120 E++ RL D LLELA EEDD L E L+ ++ ++ + E LLSGE D+N+A L Sbjct: 70 ELRQRLDDLEELLELAEEEDDEETLAEAEAELKALEKKLAALELERLLSGEYDANNAILT 129 Query: 121 VHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLLIKGPNAYGW 180 +HAGAGGTE+QDWA+MLLRMY RWAE+ FK E L+ +GEEAGIKSAT IKGP AYG+ Sbjct: 130 IHAGAGGTEAQDWASMLLRMYLRWAERHGFKVEVLDYSEGEEAGIKSATFKIKGPYAYGY 189 Query: 181 LKGEQGVHRLVRISPYDSNSRRHTSFSSIWVYPVVDDSIEIEISESDCRIDTYRASGAGG 240 LK E GVHRLVRISP+DS RRHTSF+S+ VYP VDD+IEIEI+ D RIDTYR+SGAGG Sbjct: 190 LKSETGVHRLVRISPFDSAGRRHTSFASVEVYPEVDDTIEIEINPKDLRIDTYRSSGAGG 249 Query: 241 QHVNTTDSAVRITHIPTGVVVQCQQERSQHKNKAQAWNMLRAKLYELELQKREEIANIGE 300 QHVN TDSAVRITHIPTG+VVQCQ ERSQH+NKA A ML+AKLYELEL+KR + + Sbjct: 250 QHVNKTDSAVRITHIPTGIVVQCQNERSQHQNKASAMKMLKAKLYELELEKRAAEKDALK 309 Query: 301 SSKTEIGWGRQIRSYVLQPYQMVKDLRTNIEKTSPSDVLDGDLDDFMKATLA 352 K EIGWG QIRSYVL PYQMVKDLRT E + VLDGDLD F++A L Sbjct: 310 GEKKEIGWGSQIRSYVLHPYQMVKDLRTGYETGNTQAVLDGDLDGFIEAYLR 361 >gnl|CDD|168914 PRK07342, PRK07342, peptide chain release factor 2; Provisional. Length = 339 Score = 548 bits (1413), Expect = e-157 Identities = 226/324 (69%), Positives = 277/324 (85%) Query: 29 KTEDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLELALEEDDCSILQET 88 K EDP LW + EA+ LMRERQ LD++I+ I ++ L DN+ L+ + EE D SI+++ Sbjct: 2 KAEDPSLWNDAQEAQKLMRERQQLDDSINGINHLEQTLNDNIELIAMGEEEGDKSIVEDA 61 Query: 89 SDNLQRIKLEVEYKQFESLLSGEADSNDAYLEVHAGAGGTESQDWANMLLRMYTRWAEKR 148 ++ +K E++ +Q ++LLSGEAD+ND YLEVHAGAGGTESQDWA+MLLRMYTRWAE++ Sbjct: 62 EKTIRDLKDEIDRRQIDALLSGEADANDTYLEVHAGAGGTESQDWASMLLRMYTRWAERQ 121 Query: 149 KFKTEALEIHDGEEAGIKSATLLIKGPNAYGWLKGEQGVHRLVRISPYDSNSRRHTSFSS 208 K E LE+HDGEEAGIKSAT+L+KG NAYGWLK E GVHRLVRISPYDSN+RRHTSF+S Sbjct: 122 GRKVEVLEVHDGEEAGIKSATILVKGHNAYGWLKTESGVHRLVRISPYDSNARRHTSFAS 181 Query: 209 IWVYPVVDDSIEIEISESDCRIDTYRASGAGGQHVNTTDSAVRITHIPTGVVVQCQQERS 268 IWVYPV+DD+IE++++ESD RIDTYR+SGAGGQHVNTTDSAVRITHIPTG+VVQCQQERS Sbjct: 182 IWVYPVIDDNIEVDVNESDVRIDTYRSSGAGGQHVNTTDSAVRITHIPTGIVVQCQQERS 241 Query: 269 QHKNKAQAWNMLRAKLYELELQKREEIANIGESSKTEIGWGRQIRSYVLQPYQMVKDLRT 328 QHKN+A+AW+MLRA+LYE EL+KREE N +SKT+IGWG QIRSYVLQPYQ+VKDLRT Sbjct: 242 QHKNRAKAWSMLRARLYEEELKKREEATNAAAASKTDIGWGHQIRSYVLQPYQLVKDLRT 301 Query: 329 NIEKTSPSDVLDGDLDDFMKATLA 352 +E T+P DVLDGDL++FM+A LA Sbjct: 302 GVESTNPQDVLDGDLNEFMEAALA 325 >gnl|CDD|161667 TIGR00020, prfB, peptide chain release factor 2. In many but not all taxa, there is a conserved real translational frameshift at a TGA codon. RF-2 helps terminate translation at TGA codons and can therefore regulate its own production by readthrough when RF-2 is insufficient. There is a Pfam model called "RF-1" for the superfamily of RF-1, RF-2, mitochondrial, RF-H, etc. Length = 364 Score = 458 bits (1180), Expect = e-130 Identities = 200/354 (56%), Positives = 255/354 (72%), Gaps = 4/354 (1%) Query: 3 LSRQLNCLGGLFDWDNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFIKEI 62 L+ +L+ + G D + RL L + EDP+ W + A+ +++ER L+ + ++E+ Sbjct: 12 LTSRLDTVRGSLDPEKKKARLEELEKEMEDPNFWNDQERAQAVIKERSSLEAVLDTLEEL 71 Query: 63 QDRLCDNLILLELALEEDDCSILQETSDNLQRIKLEVEYKQFE--SLLSGEADSNDAYLE 120 ++ L D LLELA+EEDD E L+ LE + + E ++LSGE D+N+AYL Sbjct: 72 KNSLEDLSELLELAVEEDDEETFNELDAELK--ALEKKLAELELRTMLSGEYDANNAYLT 129 Query: 121 VHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLLIKGPNAYGW 180 + AGAGGTE+QDWA+ML RMY RWAE+R FK E ++ +GEEAGIKS T+LIKGP AYG+ Sbjct: 130 IQAGAGGTEAQDWASMLYRMYLRWAERRGFKVEIIDYSEGEEAGIKSVTILIKGPYAYGY 189 Query: 181 LKGEQGVHRLVRISPYDSNSRRHTSFSSIWVYPVVDDSIEIEISESDCRIDTYRASGAGG 240 LK EQGVHRLVRISP+D+N RRHTSF+S++V P VDD I+IEI D RIDTYRASGAGG Sbjct: 190 LKSEQGVHRLVRISPFDANGRRHTSFASVFVMPEVDDDIDIEIKPEDLRIDTYRASGAGG 249 Query: 241 QHVNTTDSAVRITHIPTGVVVQCQQERSQHKNKAQAWNMLRAKLYELELQKREEIANIGE 300 QHVN TDSAVRITHIPTG+VVQCQ +RSQHKNK A +L+AKLYELE++K + + E Sbjct: 250 QHVNKTDSAVRITHIPTGIVVQCQNDRSQHKNKDSAMKVLKAKLYELEMEKEQAEKDAKE 309 Query: 301 SSKTEIGWGRQIRSYVLQPYQMVKDLRTNIEKTSPSDVLDGDLDDFMKATLAIK 354 K+EIGWG QIRSYVL PY MVKDLRT E + VLDGD+D F++A L K Sbjct: 310 GEKSEIGWGSQIRSYVLHPYSMVKDLRTGYETGNVQAVLDGDIDQFIEAYLKWK 363 >gnl|CDD|180152 PRK05589, PRK05589, peptide chain release factor 2; Provisional. Length = 325 Score = 360 bits (925), Expect = e-100 Identities = 162/322 (50%), Positives = 228/322 (70%), Gaps = 3/322 (0%) Query: 31 EDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLELALEEDDCSILQETSD 90 ++P+ W ++ EA+ + E ++L + + +++R+ D +L E+ EEDD +E Sbjct: 2 QEPNFWNDIKEAQEITSEEKYLKDKLDKYNHLRNRIEDIEVLCEMMSEEDDEMK-KEIIS 60 Query: 91 NLQRIKLEVEYKQFESLLSGEADSNDAYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKF 150 ++ IK E++ + E+LLSGE D N+A L +H+G GGT++QDW MLLRMYTRWAEK+ + Sbjct: 61 EVKNIKEEIDRFKIETLLSGEYDRNNAILTLHSGVGGTDAQDWTEMLLRMYTRWAEKKGY 120 Query: 151 KTEALEIHDGEEAGIKSATLLIKGPNAYGWLKGEQGVHRLVRISPYDSNSRRHTSFSSIW 210 K E +++ +G+EAGIKS TL I G AYG+LK E+G+HRLVRISP+++N +R TSF+S+ Sbjct: 121 KVEIIDLLEGDEAGIKSVTLKITGEFAYGYLKAEKGIHRLVRISPFNANGKRQTSFASVE 180 Query: 211 VYPVVDDSIEIEISESDCRIDTYRASGAGGQHVNTTDSAVRITHIPTGVVVQCQQERSQH 270 V P + D +IEI D +IDTYRA GAGGQHVN T+SAVRITHIPTG+VVQCQ ERSQH Sbjct: 181 VLPELTDDQDIEIRSEDLKIDTYRAGGAGGQHVNKTESAVRITHIPTGIVVQCQNERSQH 240 Query: 271 KNKAQAWNMLRAKLYEL-ELQKREEIANIGESSKTEIGWGRQIRSYVLQPYQMVKDLRTN 329 NK A ML++KL EL E +E+I ++ K ++GWG QIRSYV PY +VKD RT Sbjct: 241 SNKETAMKMLKSKLVELKERAHKEKIEDLTGELK-DMGWGSQIRSYVFHPYNLVKDHRTG 299 Query: 330 IEKTSPSDVLDGDLDDFMKATL 351 +E ++ V+DGD+D+F+ L Sbjct: 300 VETSNVDSVMDGDIDNFITQYL 321 >gnl|CDD|136970 PRK08787, PRK08787, peptide chain release factor 2; Provisional. Length = 313 Score = 338 bits (868), Expect = 1e-93 Identities = 164/300 (54%), Positives = 217/300 (72%), Gaps = 1/300 (0%) Query: 52 LDNAISFIKEIQDRLCDNLILLELALEEDDCSILQETSDNLQRIKLEVEYKQFESLLSGE 111 L+ + I ++ L D LL+LA E D +L + + VE +F+ + SG+ Sbjct: 2 LEKTVIGIADVLSGLADAGELLDLAESEQDEDTALAVIADLDKYQAHVEKLEFQRMFSGQ 61 Query: 112 ADSNDAYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLL 171 D +A++++ AGAGGTE+QDWA +LLRMY RWAE R +KTE +E+ GE AGIKSAT+ Sbjct: 62 MDGANAFVDIQAGAGGTEAQDWAEILLRMYLRWAESRGWKTELMEVSGGEVAGIKSATVR 121 Query: 172 IKGPNAYGWLKGEQGVHRLVRISPYDSNSRRHTSFSSIWVYPVVDDSIEIEISESDCRID 231 I+G AYGWLK E GVHRLVR SP+DS++RRHTSF+S++V P VDD+IEI+I+ +D R D Sbjct: 122 IEGEYAYGWLKTEIGVHRLVRKSPFDSDNRRHTSFTSVFVSPEVDDNIEIDINPADLRTD 181 Query: 232 TYRASGAGGQHVNTTDSAVRITHIPTGVVVQCQQERSQHKNKAQAWNMLRAKLYELELQK 291 YR+SGAGGQHVN T+SAVRITHIPT VV CQ RSQH+N+ A ML AKLYELE+QK Sbjct: 182 VYRSSGAGGQHVNKTESAVRITHIPTNTVVACQTGRSQHQNRDNAMKMLAAKLYELEVQK 241 Query: 292 REEIANIGESSKTEIGWGRQIRSYVLQPYQMVKDLRTNIEKTSPSDVLDGDLDDFMKATL 351 R + E++K++IGWG QIR+YVL + +KDLRT IE++ VLDGDLD+F++A+L Sbjct: 242 RNAEKDALEATKSDIGWGSQIRNYVLDQSR-IKDLRTGIERSDTQKVLDGDLDEFVEASL 300 >gnl|CDD|75726 PRK06746, PRK06746, peptide chain release factor 2; Provisional. Length = 326 Score = 309 bits (793), Expect = 5e-85 Identities = 165/317 (52%), Positives = 214/317 (67%) Query: 35 LWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLELALEEDDCSILQETSDNLQR 94 W + A+ ++ E L + + +++ + + I EL EE D + +E ++ Sbjct: 6 FWDDQQGAQAVINEANALKDMVGKFRQLDETFENLEITHELLKEEYDEDLHEELESEVKG 65 Query: 95 IKLEVEYKQFESLLSGEADSNDAYLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEA 154 + E+ + + LLS D N+A LE+H GAGGTESQDW +MLLRMYTRWAEKR FK E Sbjct: 66 LIQEMNEYELQLLLSDPYDKNNAILELHPGAGGTESQDWGSMLLRMYTRWAEKRGFKVET 125 Query: 155 LEIHDGEEAGIKSATLLIKGPNAYGWLKGEQGVHRLVRISPYDSNSRRHTSFSSIWVYPV 214 ++ G+EAGIKS TLLIKG NAYG+LK E+GVHRLVRISP+DS+ RRHTSF S V P Sbjct: 126 VDYLPGDEAGIKSVTLLIKGHNAYGYLKAEKGVHRLVRISPFDSSGRRHTSFVSCEVVPE 185 Query: 215 VDDSIEIEISESDCRIDTYRASGAGGQHVNTTDSAVRITHIPTGVVVQCQQERSQHKNKA 274 +D +EIE+ D +IDTYRASGAGGQHVNTTDSAVRITH PT VV CQ ERSQ KN+ Sbjct: 186 FNDEVEIEVRTEDLKIDTYRASGAGGQHVNTTDSAVRITHTPTNTVVTCQSERSQIKNRE 245 Query: 275 QAWNMLRAKLYELELQKREEIANIGESSKTEIGWGRQIRSYVLQPYQMVKDLRTNIEKTS 334 A ML+AKLY+ +L++++ + + EIGWG QIRSYV PY +VKD RTN E + Sbjct: 246 HAMKMLKAKLYQKKLEEQQAELDEIRGEQKEIGWGSQIRSYVFHPYSLVKDHRTNTEVGN 305 Query: 335 PSDVLDGDLDDFMKATL 351 V+DG++D F+ A L Sbjct: 306 VQAVMDGEIDPFIDAYL 322 >gnl|CDD|179074 PRK00591, prfA, peptide chain release factor 1; Validated. Length = 359 Score = 270 bits (694), Expect = 3e-73 Identities = 132/341 (38%), Positives = 195/341 (57%), Gaps = 13/341 (3%) Query: 17 DNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLD---NAISFIKEIQDRLCDNLILL 73 + +R L DP + + + L +E L+ A K+ Q+ L + +L Sbjct: 9 EALEERYEELEALLSDPEVISDQKRFRKLSKEYAELEPIVEAYREYKQAQEDLEEAKEML 68 Query: 74 ELALEEDDCSILQETSDNLQRIKLEVEYKQFESLL--SGEADSNDAYLEVHAGAGGTESQ 131 E + + + +E L+ E+E ++ + LL D + LE+ AG GG E+ Sbjct: 69 EEESDPEMREMAKEELKELEERLEELE-EELKILLLPKDPNDDKNVILEIRAGTGGDEAA 127 Query: 132 DWANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLLIKGPNAYGWLKGEQGVHRLV 191 +A L RMY+R+AE++ +K E L +GE G K I G Y LK E GVHR+ Sbjct: 128 LFAGDLFRMYSRYAERQGWKVEILSASEGELGGYKEVIAEISGDGVYSKLKFESGVHRVQ 187 Query: 192 RISPYDSNSRRHTSFSSIWVYPVVDDSIEIEISESDCRIDTYRASGAGGQHVNTTDSAVR 251 R+ +S R HTS +++ V P ++ +E+EI+ D RIDT+R+SGAGGQHVNTTDSAVR Sbjct: 188 RVPATESQGRIHTSAATVAVLPEAEE-VEVEINPKDLRIDTFRSSGAGGQHVNTTDSAVR 246 Query: 252 ITHIPTGVVVQCQQERSQHKNKAQAWNMLRAKLYELELQKREEIANIGESSKTEIGWG-R 310 ITH+PTG+VV+CQ ERSQHKNKA+A +LRA+LY+ E QK + A + K+++G G R Sbjct: 247 ITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAERQKAQ--AEEAATRKSQVGSGDR 304 Query: 311 --QIRSYVLQPYQMVKDLRTNIEKTSPSDVLDGDLDDFMKA 349 +IR+Y P V D R N+ +V++GDLD+ + A Sbjct: 305 SERIRTYNF-PQGRVTDHRINLTLYKLDEVMEGDLDELIDA 344 >gnl|CDD|129130 TIGR00019, prfA, peptide chain release factor 1. This model describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognize and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cutoff for this model. RF-1 does not have a translational frameshift. Length = 360 Score = 258 bits (660), Expect = 2e-69 Identities = 129/343 (37%), Positives = 202/343 (58%), Gaps = 12/343 (3%) Query: 17 DNAVQRLSFLNTKTEDPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRLCDNLILLELA 76 ++ ++R L DP + + + + L +E L+ I + +++ + Sbjct: 10 ESLLERYEELEALLSDPEVISDQDKLRKLSKEYSQLEE-IVDCYREYQQAQEDIKEAKEI 68 Query: 77 LEEDDCSILQETSDNLQRIKLEVE--YKQFESLL--SGEADSNDAYLEVHAGAGGTESQD 132 LEE D + + + L+ ++ ++E +Q + LL D + LE+ AG GG E+ Sbjct: 69 LEESDPEMREMAKEELEELEEKIEELEEQLKVLLLPKDPNDEKNVILEIRAGTGGDEAAI 128 Query: 133 WANMLLRMYTRWAEKRKFKTEALEIHDGEEAGIKSATLLIKGPNAYGWLKGEQGVHRLVR 192 +A L RMY+R+AE + +K E L ++ E G K IKG Y LK E GVHR+ R Sbjct: 129 FAGDLFRMYSRYAESKGWKVEILSANETELGGYKEVIAEIKGDGVYSRLKFESGVHRVQR 188 Query: 193 ISPYDSNSRRHTSFSSIWVYPVVDDSIEIEISESDCRIDTYRASGAGGQHVNTTDSAVRI 252 + +S R HTS +++ V P +++ +E++I+ +D RIDT+R+SGAGGQHVNTTDSAVRI Sbjct: 189 VPVTESQGRIHTSAATVAVMPELEE-VEVDINPADLRIDTFRSSGAGGQHVNTTDSAVRI 247 Query: 253 THIPTGVVVQCQQERSQHKNKAQAWNMLRAKLYELELQKREEIANIGESSKTEIGWG--- 309 TH+PTG+VV+CQ ERSQHKNK +A +LRA+LYE E +K++ A + K+++G G Sbjct: 248 THLPTGIVVECQDERSQHKNKDKAMKVLRARLYEAEQEKQQ--AAQASTRKSQVGSGDRS 305 Query: 310 RQIRSYVLQPYQMVKDLRTNIEKTSPSDVLDGDLDDFMKATLA 352 +IR+Y P V D R N+ +VL+GDLD+ ++A +A Sbjct: 306 ERIRTYNF-PQNRVTDHRINLTLYKLDEVLEGDLDELIEALIA 347 >gnl|CDD|132116 TIGR03072, release_prfH, putative peptide chain release factor H. Members of this protein family are bacterial proteins homologous to peptide chain release factors 1 (RF-1, product of the prfA gene), and 2 (RF-2, product of the prfB gene). The member from Escherichia coli K-12, designated prfH, appears to be a pseudogene. This class I release factor is always found as the downstream gene of a two-gene operon. Length = 200 Score = 114 bits (286), Expect = 4e-26 Identities = 61/180 (33%), Positives = 88/180 (48%), Gaps = 6/180 (3%) Query: 118 YLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEALEIHDGEEAG-IKSATLLIKGPN 176 L++ + G E L TR A R + E LE GE G ++SA + + G Sbjct: 2 LLQLSSAQGPAECCLAVAKALERLTREAAARGVRVEVLEQEPGEVPGTLRSALVSLDGEA 61 Query: 177 AYGWLKGEQGVHRLVRISPYDSNSRRHTSFSSIWVYPVVDDSIEIEISESDCRIDTYRAS 236 A +G + SPY + RR W V S E +E + R +T R+S Sbjct: 62 AAALADRWEGTLLWICPSPYRPHHRRKN-----WFIGVQRFSASEEATEDEIRFETLRSS 116 Query: 237 GAGGQHVNTTDSAVRITHIPTGVVVQCQQERSQHKNKAQAWNMLRAKLYELELQKREEIA 296 G GGQHVN T+SAVR TH+ +G+ V+ Q ERSQH NK A +L +L +L+ ++ + Sbjct: 117 GPGGQHVNKTESAVRATHLASGISVKVQSERSQHANKRLATLLLAVRLADLQQEQAAALR 176 >gnl|CDD|181271 PRK08179, prfH, peptide chain release factor-like protein; Reviewed. Length = 200 Score = 105 bits (263), Expect = 2e-23 Identities = 54/174 (31%), Positives = 83/174 (47%), Gaps = 6/174 (3%) Query: 118 YLEVHAGAGGTESQDWANMLLRMYTRWAEKRKFKTEALEIHDGEEAG-IKSATLLIKGPN 176 L++ + G E L + A ++ + LE G ++SA + + G N Sbjct: 3 LLQLSSAQGPAECCLAVAKALERLLKEAARQGVRVTVLETETGRYPDTLRSALVSLDGDN 62 Query: 177 AYGWLKGEQGVHRLVRISPYDSNSRRHTSFSSIWVYPVVDDSIEIEISESDCRIDTYRAS 236 A + G + + SPY + R F I + S + E + R +T R+S Sbjct: 63 AEALAESWCGTIQWICPSPYRPHHGRKNWFVGIGRF-----SADEEEQSDEIRFETLRSS 117 Query: 237 GAGGQHVNTTDSAVRITHIPTGVVVQCQQERSQHKNKAQAWNMLRAKLYELELQ 290 G GGQHVN TDSAVR TH+ +G+ V+ Q ERSQH NK A ++ KL + + + Sbjct: 118 GPGGQHVNKTDSAVRATHLASGISVKVQSERSQHANKRLARLLIAWKLEQQQQE 171 >gnl|CDD|181730 PRK09256, PRK09256, hypothetical protein; Provisional. Length = 138 Score = 54.8 bits (133), Expect = 3e-08 Identities = 27/93 (29%), Positives = 38/93 (40%), Gaps = 32/93 (34%) Query: 221 IEISESDCRIDTYRASGAGGQHVNTTDSAV-------------------------RITHI 255 + I E++ RASG GGQ+VN +AV RIT Sbjct: 8 LVIPENELEWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHRIT-- 65 Query: 256 PTGV-VVQCQQERSQHKNKAQAWNMLRAKLYEL 287 GV V++ Q+ RSQ +N+ A +L L Sbjct: 66 KDGVIVIKAQEFRSQERNREDA----LERLVAL 94 >gnl|CDD|163484 TIGR03772, anch_rpt_subst, anchored repeat ABC transporter, substrate-binding protein. Members of this protein family are ABC transporter permease subunits as identified by pfam00950, but additionally contain the Actinobacterial insert domain described by TIGR03769. Some homologs (lacking the insert) have been described as transporters of manganese or of chelated iron. Members of this family typically are found along with an ATP-binding cassette protein, a permease, and an LPXTG-anchored protein with two or three copies of the TIGR03769 insert that occurs just once in this protein family. Length = 479 Score = 30.2 bits (68), Expect = 0.92 Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 13/35 (37%) Query: 32 DPHLWQNVIEAKMLMRERQHLDNAISFIKEIQDRL 66 DPHLW NV NAI++++ I+D+L Sbjct: 310 DPHLWHNV-------------KNAIAYVEVIRDKL 331 >gnl|CDD|184331 PRK13795, PRK13795, hypothetical protein; Provisional. Length = 636 Score = 28.0 bits (63), Expect = 3.6 Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 20/59 (33%) Query: 36 WQNVIEAKMLMRERQHLD----NAISFIKEIQDRLC-----------DNLILLELALEE 79 ++ IEA R+HL+ A++FI+ + ++ D+L++L+LA E Sbjct: 213 LEDAIEAN-----RKHLEEKEKEAVNFIRGVAEKYNLPVSVSFSGGKDSLVVLDLAREA 266 >gnl|CDD|162983 TIGR02712, urea_carbox, urea carboxylase. Members of this family are ATP-dependent urea carboxylase, including characterized members from Oleomonas sagaranensis (alpha class Proteobacterium) and yeasts such as Saccharomyces cerevisiae. The allophanate hydrolase domain of the yeast enzyme is not included in this model and is represented by an adjacent gene in Oleomonas sagaranensis. The fusion of urea carboxylase and allophanate hydrolase is designated urea amidolyase. The enzyme from Oleomonas sagaranensis was shown to be highly active on acetamide and formamide as well as urea. Length = 1201 Score = 28.1 bits (63), Expect = 3.8 Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 5/45 (11%) Query: 94 RIKLEVE-----YKQFESLLSGEADSNDAYLEVHAGAGGTESQDW 133 R K+ VE +++ L+ ADS +A+ E GA E W Sbjct: 1062 RFKVRVEETVFDLAEYQRFLADNADSIEAFKERQQGAFEAERARW 1106 >gnl|CDD|172808 PRK14332, PRK14332, (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional. Length = 449 Score = 27.6 bits (61), Expect = 4.4 Identities = 17/39 (43%), Positives = 23/39 (58%), Gaps = 1/39 (2%) Query: 141 YTRWAEK-RKFKTEALEIHDGEEAGIKSATLLIKGPNAY 178 YTR E+ R K+ EI D +E GI+ TLL + N+Y Sbjct: 175 YTRGRERSRDPKSIVREIQDLQEKGIRQVTLLGQNVNSY 213 >gnl|CDD|151997 pfam11561, Saw1, Single strand annealing-weakened 1. This family of yeast proteins is involved in single-strand-annealing, or SSA. SSA entails multiple steps: end resection and ssDNA formation; annealing of complementary ssDNAs; removal of 3' single-stranded non-homologous tails; gap fill-in synthesis; and ligation. Saw1 in combination with Slx4 catalyses the 3' non-homologous tail removal during recombination. Saw1 interacts physically with Rad1/Rad10, Msh2/Msh3, and Rad52 proteins, and works by targeting Rad1/Rad10 to Rad52-coated recombination intermediates. Length = 208 Score = 27.5 bits (61), Expect = 5.3 Identities = 13/47 (27%), Positives = 23/47 (48%), Gaps = 2/47 (4%) Query: 57 SFIKEIQDRLCDNLILLELALEEDDCSILQETSDNLQRIKLEVEYKQ 103 S + EI+ L IL EL L + D +IL+ + + K +++ Sbjct: 63 SLLDEIRRDLLL--ILYELKLNQGDQTILRTLNIDDVERKCKMKVPV 107 >gnl|CDD|166155 PLN02514, PLN02514, cinnamyl-alcohol dehydrogenase. Length = 357 Score = 27.5 bits (61), Expect = 6.1 Identities = 13/40 (32%), Positives = 17/40 (42%), Gaps = 6/40 (15%) Query: 300 ESSKTEIGWGRQIRSYVLQPYQMVKDLRTNIEKTSPSDVL 339 E+ K GW + S L PY + KT P DV+ Sbjct: 5 EAEKKTTGWAARDPSGHLSPYTY------TLRKTGPEDVV 38 >gnl|CDD|177929 PLN02292, PLN02292, ferric-chelate reductase. Length = 702 Score = 26.8 bits (59), Expect = 8.5 Identities = 25/104 (24%), Positives = 40/104 (38%), Gaps = 13/104 (12%) Query: 172 IKGPNAYGWLKGEQGVHRLV-----------RISPYDSNSRRHTSFSSIWVYPVVDDSIE 220 I GPN++ WL L+ I P D NS ++T +Y +V SI Sbjct: 542 ILGPNSWLWLAAILSSSFLIFIIIIAIITRYHIYPIDQNSNKYTLAYKSLIYLLV-ISIS 600 Query: 221 IEISESDCRIDTYRASGAG-GQHVNTTDSAVRITHIPTGVVVQC 263 + + + + + Q V+ DS I P ++VQ Sbjct: 601 VVATSTAAMLWNKKKYYKKSSQQVDNVDSPREIESSPQQLLVQR 644 >gnl|CDD|178860 PRK00095, mutL, DNA mismatch repair protein; Reviewed. Length = 617 Score = 26.7 bits (60), Expect = 9.8 Identities = 14/31 (45%), Positives = 19/31 (61%) Query: 70 LILLELALEEDDCSILQETSDNLQRIKLEVE 100 LI L L L ED+ L+E + L R+ LE+E Sbjct: 482 LIPLVLELSEDEADRLEEHKELLARLGLELE 512 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 0.316 0.132 0.385 Gapped Lambda K H 0.267 0.0615 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 5,636,012 Number of extensions: 350465 Number of successful extensions: 689 Number of sequences better than 10.0: 1 Number of HSP's gapped: 680 Number of HSP's successfully gapped: 28 Length of query: 355 Length of database: 5,994,473 Length adjustment: 94 Effective length of query: 261 Effective length of database: 3,963,321 Effective search space: 1034426781 Effective search space used: 1034426781 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 (21.6 bits) S2: 58 (26.4 bits)