RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780161|ref|YP_003064574.1| phytoene synthase protein [Candidatus Liberibacter asiaticus str. psy62] (299 letters) >gnl|CDD|178239 PLN02632, PLN02632, phytoene synthase. Length = 334 Score = 37.0 bits (86), Expect = 0.006 Identities = 34/130 (26%), Positives = 53/130 (40%), Gaps = 9/130 (6%) Query: 98 PFSVELLSIVRQYDLPNQYFLDMIEAHFFDSYNDSIFDCKQFEH-YAFRISSR--LIHLA 154 L V ++ L Q F DMIE D S ++ + Y + ++ L+ + Sbjct: 123 MLDAALADTVSKFPLDIQPFRDMIEGMRMD-LVKSRYENFDELYLYCYYVAGTVGLMSVP 181 Query: 155 TMILDSERYSASLRVIKYAGIAQFIG-QLICQLPI---HYHRGQLYFPLDILGAVGLDRE 210 M + E AS + A +A I QL L RG++Y P D L GL E Sbjct: 182 VMGIAPE-SKASTESVYNAALALGIANQLTNILRDVGEDARRGRVYLPQDELAQFGLTDE 240 Query: 211 SFLSGQNSDR 220 +G+ +D+ Sbjct: 241 DIFAGKVTDK 250 >gnl|CDD|163278 TIGR03465, HpnD, squalene synthase HpnD. The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have been characterized as squalene synthases (farnesyl-pyrophosphate ligases). Often, these genes appear in tandem with the HpnC gene which appears to have resulted from an ancient gene duplication event. Presumably these proteins form a heteromeric complex, but this has not yet been experimentally demonstrated. Length = 266 Score = 36.1 bits (84), Expect = 0.012 Identities = 43/191 (22%), Positives = 77/191 (40%), Gaps = 14/191 (7%) Query: 36 YLACLLSPPLYRISLSFLYYFHTELMRVRDTARNPITRDMRLQWWKDIFESSTKGLIAES 95 Y L PP R +++ LY F E+ + D +P +L WW+ + G Sbjct: 9 YYGMRLLPPERRRAMTALYAFCREVDDIVDEDSDPEVAQAKLAWWRAEIDRLYAG---AP 65 Query: 96 ISPFSVELLSIVRQYDLPNQYFLDMIEAHFFDSYNDSIFDCKQFEHYAFRISSRLIHLAT 155 P + L R++DLP + FL++I+ D D + + Y R++ + L+ Sbjct: 66 SHPVARALADPARRFDLPQEDFLEVIDGMEMDLEQTRYPDFAELDLYCDRVAGAVGRLSA 125 Query: 156 MIL-----DSERYSASLRVIKYAGIAQFIGQLICQLPIHYHRGQLYFPLDILGAVGLDRE 210 I + Y+ L G A + ++ + RG++Y P + L G+ Sbjct: 126 RIFGATDARTLEYAHHL------GRALQLTNILRDVGEDARRGRIYLPAEELQRFGVPAA 179 Query: 211 SFLSGQNSDRI 221 L G+ S + Sbjct: 180 DILEGRYSPAL 190 >gnl|CDD|163277 TIGR03464, HpnC, squalene synthase HpnC. This family of genes are members of a superfamily (pfam00494) of phytoene and squalene synthases which catalyze the head-t0-head condensation of polyisoprene pyrophosphates. The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have been characterized as squalene synthases (farnesyl-pyrophosphate ligases). Often, these genes appear in tandem with the HpnD gene which appears to have resulted from an ancient gene duplication event. Presumably these proteins form a heteromeric complex, but this has not yet been experimentally demonstrated. Length = 266 Score = 35.0 bits (81), Expect = 0.022 Identities = 34/138 (24%), Positives = 53/138 (38%), Gaps = 39/138 (28%) Query: 98 PFSVELLSIVRQYDLPNQYFLDMIEAHFFDSYNDSIFDCKQFEHYAFRISSRLIHLATM- 156 P V L V+++ LP + FLD+++A FR + AT Sbjct: 69 PVFVALARTVQRHGLPIEPFLDLLDA--------------------FRQDVVVTRYATWA 108 Query: 157 -ILDSERYSAS------LRVIKYAGIAQF-IGQLIC---QLPIH-------YHRGQLYFP 198 +LD RYSA+ L + + + IC QL Y +G++Y P Sbjct: 109 ELLDYCRYSANPVGRLVLDLYGASDPENVALSDAICTALQLINFWQDVGVDYRKGRVYLP 168 Query: 199 LDILGAVGLDRESFLSGQ 216 D L G+ E +G+ Sbjct: 169 RDDLARFGVSEEDLAAGR 186 >gnl|CDD|180546 PRK06370, PRK06370, mercuric reductase; Validated. Length = 463 Score = 30.2 bits (69), Expect = 0.68 Identities = 17/53 (32%), Positives = 22/53 (41%), Gaps = 15/53 (28%) Query: 130 NDSIF---DCKQ---FEHYA---FRISSRLIHLATMILDSERYSASLRVIKYA 173 N I+ DC F H A RI +A +LD R S R++ YA Sbjct: 301 NPGIYAAGDCNGRGAFTHTAYNDARI------VAANLLDGGRRKVSDRIVPYA 347 >gnl|CDD|163472 TIGR03760, ICE_TraI_Pfluor, integrating conjugative element relaxase, PFL_4751 family. Members of this protein family are the TraI putative relaxases required for transfer by a subclass of integrating conjugative elements (ICE) as found in Pseudomonas fluorescens Pf-5, and understood from study of two related ICE, SXT and R391. This model represents the N-terminal domain. Note that no homology is detected to the similarly named TraI relaxase of the F plasmid. Length = 218 Score = 28.4 bits (64), Expect = 2.3 Identities = 7/31 (22%), Positives = 14/31 (45%) Query: 169 VIKYAGIAQFIGQLICQLPIHYHRGQLYFPL 199 + YA + +G+L + + GQ + P Sbjct: 107 AVFYAALLHDLGKLAVDIEVELQDGQRWHPW 137 >gnl|CDD|185492 PTZ00166, PTZ00166, DNA polymerase delta catalytic subunit; Provisional. Length = 1054 Score = 28.1 bits (63), Expect = 3.0 Identities = 15/39 (38%), Positives = 18/39 (46%), Gaps = 3/39 (7%) Query: 12 KEEKIFSR--DSLFVLRNLRDIDYDRYLACLLSPPLYRI 48 K + R D L+VL N ID YL + PL RI Sbjct: 886 KGAPQYERAEDPLYVLENNIPIDTQYYLDQ-IKNPLLRI 923 >gnl|CDD|178063 PLN02444, PLN02444, HMP-P synthase. Length = 642 Score = 27.6 bits (61), Expect = 3.6 Identities = 10/21 (47%), Positives = 14/21 (66%) Query: 252 PAFIPVSITESVLKHAQNHGF 272 P F + ITE V K+A+ HG+ Sbjct: 573 PKFCSMKITEDVRKYAEEHGY 593 >gnl|CDD|185191 PRK15291, PRK15291, fimbrial protein StgD; Provisional. Length = 355 Score = 27.4 bits (60), Expect = 4.3 Identities = 14/40 (35%), Positives = 21/40 (52%) Query: 35 RYLACLLSPPLYRISLSFLYYFHTELMRVRDTARNPITRD 74 R L L S Y++ S L +F + V TAR+P++ D Sbjct: 57 RDLETLTSSESYKVGCSCLTHFSSTFREVYYTARSPLSID 96 >gnl|CDD|149890 pfam08963, DUF1878, Protein of unknown function (DUF1878). This domain is found in a set of hypothetical bacterial proteins. Length = 113 Score = 26.2 bits (58), Expect = 9.3 Identities = 11/30 (36%), Positives = 15/30 (50%), Gaps = 5/30 (16%) Query: 175 IAQFIGQLICQLPIH-----YHRGQLYFPL 199 +A F GQL +L +H H L+ PL Sbjct: 72 LALFAGQLNEKLEVHETIFALHAQGLFKPL 101 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 0.328 0.141 0.423 Gapped Lambda K H 0.267 0.0729 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 4,936,526 Number of extensions: 320137 Number of successful extensions: 776 Number of sequences better than 10.0: 1 Number of HSP's gapped: 773 Number of HSP's successfully gapped: 19 Length of query: 299 Length of database: 5,994,473 Length adjustment: 93 Effective length of query: 206 Effective length of database: 3,984,929 Effective search space: 820895374 Effective search space used: 820895374 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 57 (25.7 bits)