RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780765|ref|YP_003065178.1| 3-deoxy-manno-octulosonate cytidylyltransferase [Candidatus Liberibacter asiaticus str. psy62] (268 letters) >gnl|CDD|180091 PRK05450, PRK05450, 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional. Length = 245 Score = 305 bits (784), Expect = 9e-84 Identities = 119/249 (47%), Positives = 148/249 (59%), Gaps = 15/249 (6%) Query: 9 KVLVIIPARLNSMRFPKKILADINGLPMILHTAIRARKANIGRVIVAVDDTKINEIVLQA 68 K L+IIPAR S R P K LADI G PMI+ RA KA RV+VA DD +I + V Sbjct: 2 KFLIIIPARYASTRLPGKPLADIGGKPMIVRVYERASKAGADRVVVATDDERIADAVEAF 61 Query: 69 GFESVMTHTSHQSGSDRIFEALNIIDSDKKSQIIVNMQADIPNIEPEILASVLLPLQNPI 128 G E VMT H SG+DRI EA + I+VN+Q D P I PEI+ V PL NP Sbjct: 62 GGEVVMTSPDHPSGTDRIAEAAAKLGLADD-DIVVNVQGDEPLIPPEIIDQVAEPLANPE 120 Query: 129 VDIGTLGTRIHGSTDPDDPNIVKIVVASPSENGCFRALYFTRTKTPHG--------TGPF 180 D+ TL IH + + +PN+VK+V+ + +G RALYF+R P+G P Sbjct: 121 ADMATLAVPIHDAEEAFNPNVVKVVLDA---DG--RALYFSRAPIPYGRDAFADSAPTPV 175 Query: 181 YQHLGIYAYRREALKRFTQLSPSVLEQRESLEQLRALEARMRIDVKIVQSNAM-SVDTTN 239 Y+H+GIYAYRR L+RF L PS LE+ ESLEQLRALE RI V +V+ VDT Sbjct: 176 YRHIGIYAYRRGFLRRFVSLPPSPLEKIESLEQLRALENGYRIHVVVVEEAPSIGVDTPE 235 Query: 240 DLEKVRTLI 248 DLE+VR L+ Sbjct: 236 DLERVRALL 244 >gnl|CDD|184007 PRK13368, PRK13368, 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional. Length = 238 Score = 217 bits (555), Expect = 2e-57 Identities = 103/243 (42%), Positives = 143/243 (58%), Gaps = 15/243 (6%) Query: 9 KVLVIIPARLNSMRFPKKILADINGLPMILHTAIRARKA-NIGRVIVAVDDTKINEIVLQ 67 KV+V+IPAR S R P K L DI G PMI H RA +A + V VA DD +I + V Sbjct: 2 KVVVVIPARYGSSRLPGKPLLDILGKPMIQHVYERAAQAAGVEEVYVATDDQRIEDAVEA 61 Query: 68 AGFESVMTHTSHQSGSDRIFEALNIIDSDKKSQIIVNMQADIPNIEPE-ILASVLLPLQN 126 G + VMT H SG+DR+ E + I++D I +N+Q D P I P I + L + Sbjct: 62 FGGKVVMTSDDHLSGTDRLAEVMLKIEAD----IYINVQGDEPMIRPRDIDTLIQPMLDD 117 Query: 127 PIVDIGTLGTRIHGSTDPDDPNIVKIVVASPSENGCFRALYFTRTKTPHG-TGPF---YQ 182 P +++ TL I + + PN+VK+VV +NG ALYF+R+ P G + Sbjct: 118 PSINVATLCAPISTEEEFESPNVVKVVV---DKNG--DALYFSRSPIPSRRDGESARYLK 172 Query: 183 HLGIYAYRREALKRFTQLSPSVLEQRESLEQLRALEARMRIDVKIVQSNAMSVDTTNDLE 242 H+GIYA+RR+ L++F+QL + LEQ ESLEQLRALE +I + V + ++ VDT DLE Sbjct: 173 HVGIYAFRRDVLQQFSQLPETPLEQIESLEQLRALEHGEKIRMVEVAATSIGVDTPEDLE 232 Query: 243 KVR 245 +VR Sbjct: 233 RVR 235 >gnl|CDD|129558 TIGR00466, kdsB, 3-deoxy-D-manno-octulosonate cytidylyltransferase. Length = 238 Score = 181 bits (460), Expect = 2e-46 Identities = 92/244 (37%), Positives = 126/244 (51%), Gaps = 18/244 (7%) Query: 11 LVIIPARLNSMRFPKKILADINGLPMILHTAIRARKANIGRVIVAVDDTKINEIVLQAGF 70 +VIIPARL S R P K L DI G PMI+H A A ++ R IVA DD + + + G Sbjct: 1 MVIIPARLASSRLPGKPLEDIFGKPMIVHVAENANESGADRCIVATDDESVAQTCQKFGI 60 Query: 71 ESVMTHTSHQSGSDRIFEALNIIDSDKKSQIIVNMQADIPNIEPEILASVLLPLQNPIVD 130 E MT H SG++R+ E + + + K + IVN+Q D P I EI+ V L V Sbjct: 61 EVCMTSKHHNSGTERLAEVVEKL-ALKDDERIVNLQGDEPFIPKEIIRQVADNLATKNVP 119 Query: 131 IGTLGTRIHGSTDPDDPNIVKIVVASPSENGCFRALYFTRTKTPH-----------GTGP 179 + L +IH + + +PN VK+V+ S ALYF+R+ P Sbjct: 120 MAALAVKIHDAEEAFNPNAVKVVLDSQG-----YALYFSRSLIPFDRDFFAKRQTPVGDN 174 Query: 180 FYQHLGIYAYRREALKRFTQLSPSVLEQRESLEQLRALEARMRIDVKIVQS-NAMSVDTT 238 +H+GIY YR ++ + P VLE+ E LEQLR L +I VKI Q ++ VDT Sbjct: 175 LLRHIGIYGYRAGFIEEYVAWKPCVLEEIEKLEQLRVLYYGEKIHVKIAQEVPSVGVDTQ 234 Query: 239 NDLE 242 DLE Sbjct: 235 EDLE 238 >gnl|CDD|178505 PLN02917, PLN02917, CMP-KDO synthetase. Length = 293 Score = 144 bits (364), Expect = 2e-35 Identities = 96/251 (38%), Positives = 133/251 (52%), Gaps = 17/251 (6%) Query: 7 KEKVLVIIPARLNSMRFPKKILADINGLPMILHTAIRARKA-NIGRVIVAVDDTKINEIV 65 + +V+ IIPAR S RF K L I G PMI T RA+ A + ++VA DD +I E Sbjct: 45 RSRVVGIIPARFASSRFEGKPLVHILGKPMIQRTWERAKLATTLDHIVVATDDERIAECC 104 Query: 66 LQAGFESVMTHTSHQSGSDRIFEALNIIDSDKKSQIIVNMQADIPNIEPEILASVLLPLQ 125 G + +MT S ++G++R EAL ++ KK I+VN+Q D P IEPEI+ V+ LQ Sbjct: 105 RGFGADVIMTSESCRNGTERCNEALKKLE--KKYDIVVNIQGDEPLIEPEIIDGVVKALQ 162 Query: 126 -NPIVDIGTLGTRIHGSTDPDDPNIVKIVVASPSENGCFRALYFTRTKTPHGTG------ 178 P T T + D DPN VK VV G A+YF+R P+ Sbjct: 163 AAPDAVFSTAVTSLK-PEDASDPNRVKCVV---DNQG--YAIYFSRGLIPYNKSGKVNPQ 216 Query: 179 -PFYQHLGIYAYRREALKRFTQLSPSVLEQRESLEQLRALEARMRIDVKIVQSNAMSVDT 237 P+ HLGI +Y + LK + +L P+ L+ E LEQL+ LE ++ V V A VDT Sbjct: 217 FPYLLHLGIQSYDAKFLKIYPELPPTPLQLEEDLEQLKVLENGYKMKVIKVDHEAHGVDT 276 Query: 238 TNDLEKVRTLI 248 D+EK+ L+ Sbjct: 277 PEDVEKIEALM 287 >gnl|CDD|163336 TIGR03584, PseF, pseudaminic acid CMP-transferase. The sequences in this family include the pfam02348 (cytidyltransferase) domain and are homologous to the NeuA protein responsible for the transfer of CMP to neuraminic acid. According to, this gene is responsible for the transfer of CMP to the structurally related sugar, pseudaminic acid which is observed as a component of sugar modifications of flagellin in Campylobacter species. This gene is commonly observed in apparent operons with other genes responsible for the biosynthesis of pseudaminic acid and as a component of flagellar and exopolysaccharide biosynthesis loci. Length = 222 Score = 44.2 bits (105), Expect = 3e-05 Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 1/60 (1%) Query: 11 LVIIPARLNSMRFPKKILADINGLPMILHTAIRARKANI-GRVIVAVDDTKINEIVLQAG 69 + IIPAR S R P+K + G PMI ++ A + + +V+V+ DD +I E+ G Sbjct: 1 IAIIPARGGSKRIPRKNIKPFCGKPMIAYSIEAALNSGLFDKVVVSTDDEEIAEVAKSYG 60 >gnl|CDD|184642 PRK14353, glmU, bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional. Length = 446 Score = 32.5 bits (75), Expect = 0.13 Identities = 34/144 (23%), Positives = 48/144 (33%), Gaps = 39/144 (27%) Query: 21 MRFPK-KILADINGLPMILHTAIRARKANIGRVIVAVDDTKINEIVLQAGFESVMTHTSH 79 M+ K+L + G PM+ H A RV V V+ G E+V + Sbjct: 19 MKSSLPKVLHPVAGRPMLAHVLAAAASLGPSRVAV----------VVGPGAEAVAAAAAK 68 Query: 80 QSGSDRIF----------------EALNIIDSDKKSQIIVNMQADIPNIEPEILASVLLP 123 + IF EAL D ++ + D P I E LA + Sbjct: 69 IAPDAEIFVQKERLGTAHAVLAAREALAGGYGD-----VLVLYGDTPLITAETLARLRER 123 Query: 124 LQNPIVDIGTLGTRIHGSTDPDDP 147 L + D+ LG R DP Sbjct: 124 LADG-ADVVVLGFR------AADP 140 >gnl|CDD|131935 TIGR02889, spore_YpeB, germination protein YpeB. Members of this family are YpeB, a protein usually encoded with the putative spore-cortex-lytic enzyme SleB and required, together with SleB, for normal germination. This family is retricted to endospore-forming species in the Firmicutes lineage of bacteria, and found in all such species to date except Clostridium perfringens. The matching phenotypes of mutants in SleB (called a lytic transglycosylase) and YpeB suggests that YpeB is necessary to allow SleB to function. Length = 435 Score = 28.5 bits (64), Expect = 1.9 Identities = 14/62 (22%), Positives = 24/62 (38%), Gaps = 6/62 (9%) Query: 176 GTGPFYQHLGIYAY---RREALKRFTQLSPSVLEQRESL-EQLRALEARMRIDVKIVQSN 231 T F +G + Y ++A + LS + +L Q LE ++R IV Sbjct: 97 KTSKFLSQVGDFTYTLSVKDAEGK--SLSDKEYKTLTTLYNQAVKLENQLRKVQNIVMQG 154 Query: 232 AM 233 + Sbjct: 155 GV 156 >gnl|CDD|184034 PRK13405, bchH, magnesium chelatase subunit H; Provisional. Length = 1209 Score = 27.7 bits (62), Expect = 3.0 Identities = 18/72 (25%), Positives = 27/72 (37%), Gaps = 12/72 (16%) Query: 191 REALKRFTQLSPSVLEQRESLEQLRALEARMRIDVKIVQSNAMSVDTTND---------L 241 + +L+R+ L P E+R L L +A V + + + L Sbjct: 678 KASLERWRGLPPDATEERAELAALIQAQAA---AVDLAPAEPAWEEEAGARIAKLWAALL 734 Query: 242 EKVRTLIPHDHH 253 E TLIPH H Sbjct: 735 ELEYTLIPHGLH 746 >gnl|CDD|178905 PRK00155, ispD, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase; Reviewed. Length = 227 Score = 27.4 bits (62), Expect = 3.6 Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 12/63 (19%) Query: 7 KEKVLVIIPA-----RLNSMRFPKKILADINGLPMILHTAIRARKAN--IGRVIVAV--D 57 V IIPA R+ + R K + G P++ HT + A A+ I +IV V D Sbjct: 1 MMMVYAIIPAAGKGSRMGADR--PKQYLPLGGKPILEHT-LEAFLAHPRIDEIIVVVPPD 57 Query: 58 DTK 60 D Sbjct: 58 DRP 60 >gnl|CDD|132513 TIGR03473, HpnK, hopanoid biosynthesis associated protein HpnK. The sequences represented by this model are members of the pfam04794 "YdjC-like" family of uncharacterized proteins. The member of this clade from Acidithiobacillus ferrooxidans ATCC 23270 (AFE_0976) is found in the same locus as squalene-hopene cyclase (SHC, TIGR01507) and other genes associated with the biosynthesis of hopanoid natural products. Similarly, in Ralstonia eutropha JMP134 (Reut_B4902) this gene is adjacent to HpnAB, IspH and HpnH (TIGR03470), although SHC itself is elsewhere in the genome. Notably, this gene (here named HpnK) and three others form a conserved set (HpnIJKL) which occur in a subset of all genomes containing the SHC enzyme. This relationship was discerned using the method of partial phylogenetic profiling. This group includes Zymomonas mobilis, the organism where the initial hopanoid biosynthesis locus was described consisting of the genes HpnA-E and SHC (HpnF). Continuing past SHC are found a phosphorylase enzyme (ZMO0873, i.e. HpnG, TIGR03468) and a radical SAM enzyme (ZMO0874), HpnH. Although discontinuous in Z. mobilis, we continue the gene symbol sequence with HpnIJKL. Length = 283 Score = 27.4 bits (61), Expect = 4.1 Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 4/43 (9%) Query: 51 RVIVAVDD----TKINEIVLQAGFESVMTHTSHQSGSDRIFEA 89 R+IV DD ++NE V +A + ++T S G+ +A Sbjct: 3 RLIVTADDFGLSLEVNEAVEKAHRDGILTAASLMVGAPAAEDA 45 >gnl|CDD|172940 PRK14465, PRK14465, ribosomal RNA large subunit methyltransferase N; Provisional. Length = 342 Score = 27.2 bits (60), Expect = 4.4 Identities = 14/34 (41%), Positives = 17/34 (50%) Query: 185 GIYAYRREALKRFTQLSPSVLEQRESLEQLRALE 218 G+Y R E +FT S V E+ E L L LE Sbjct: 35 GLYVNRYETWDQFTTFSKEVKEKLEELCSLTELE 68 >gnl|CDD|184643 PRK14354, glmU, bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional. Length = 458 Score = 27.1 bits (61), Expect = 4.6 Identities = 10/31 (32%), Positives = 17/31 (54%) Query: 26 KILADINGLPMILHTAIRARKANIGRVIVAV 56 K+L + G PM+ H +KA I +++ V Sbjct: 22 KVLHKVCGKPMVEHVVDSVKKAGIDKIVTVV 52 >gnl|CDD|180612 PRK06543, PRK06543, nicotinate-nucleotide pyrophosphorylase; Provisional. Length = 281 Score = 27.1 bits (60), Expect = 5.0 Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 3/50 (6%) Query: 28 LADINGLPMILHTAIRARKANIG---RVIVAVDDTKINEIVLQAGFESVM 74 LA + + L A+R +A +G V V VD E VL AG +++M Sbjct: 169 LAALAAQGLDLTEALRHVRAQLGHTTHVEVEVDRLDQIEPVLAAGVDTIM 218 >gnl|CDD|152291 pfam11855, DUF3375, Protein of unknown function (DUF3375). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 479 to 499 amino acids in length. Length = 471 Score = 26.6 bits (59), Expect = 7.1 Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 1/29 (3%) Query: 192 EALKRFTQLSPSVLEQRESLEQLRALEAR 220 E+L+RF S + LE R ++ LR E+ Sbjct: 302 ESLRRFVD-SQTWLENRRVMQLLREAESL 329 >gnl|CDD|152494 pfam12059, DUF3540, Protein of unknown function (DUF3540). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 212 to 238 amino acids in length. This protein has a conserved SCL sequence motif. Length = 195 Score = 26.6 bits (59), Expect = 8.0 Identities = 7/30 (23%), Positives = 12/30 (40%) Query: 195 KRFTQLSPSVLEQRESLEQLRALEARMRID 224 R TQ + + E +Q+RA + Sbjct: 138 DRLTQRAKNSFRTVEGTDQVRAGNLDQTAE 167 >gnl|CDD|162797 TIGR02290, M3_fam_3, oligoendopeptidase, pepF/M3 family. The M3 family of metallopeptidases contains several distinct clades. Oligoendopeptidase F as characterized in Lactococcus, the functionally equivalent oligoendopeptidase B of group B Streptococcus, and closely related sequences are described by TIGR00181. The present family is quite similar but forms a distinct clade, and a number of species have one member of each. A greater sequence difference separates members of TIGR02289, probable oligoendopeptidases of the M3 family that probably should not be designated PepF. Length = 587 Score = 26.1 bits (58), Expect = 8.8 Identities = 10/33 (30%), Positives = 16/33 (48%), Gaps = 2/33 (6%) Query: 184 LGIYAYRREALKRFTQLSPSVLEQ--RESLEQL 214 LG+YA RE + F ++L + E+L Sbjct: 524 LGLYAKYREEGESFVPKYIALLRDTGSMTPEEL 556 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 0.320 0.136 0.383 Gapped Lambda K H 0.267 0.0780 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 4,429,852 Number of extensions: 289125 Number of successful extensions: 670 Number of sequences better than 10.0: 1 Number of HSP's gapped: 655 Number of HSP's successfully gapped: 29 Length of query: 268 Length of database: 5,994,473 Length adjustment: 92 Effective length of query: 176 Effective length of database: 4,006,537 Effective search space: 705150512 Effective search space used: 705150512 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 56 (25.3 bits)