RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780261|ref|YP_003064674.1| 50S ribosomal protein L3 [Candidatus Liberibacter asiaticus str. psy62] (221 letters) >gnl|CDD|178784 PRK00001, rplC, 50S ribosomal protein L3; Validated. Length = 210 Score = 303 bits (778), Expect = 3e-83 Identities = 106/213 (49%), Positives = 138/213 (64%), Gaps = 4/213 (1%) Query: 1 MRSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKN 60 M G++ +K+GMT ++ +G IPVTV+ V +T++K+GY AVQ+G G+ K K Sbjct: 1 MMKGILGKKVGMTQIFTEDGESIPVTVIEAGPNVVTQVKTVEKDGYNAVQLGFGDKKEKR 60 Query: 61 VSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGF 120 V+KP G F+ V PK+ L EFRV + VG + F GQ VDVTG + GKGF Sbjct: 61 VNKPEAGHFAKAGVEPKRHLREFRV---VEEYEVGQEITVDIFEAGQKVDVTGTSKGKGF 117 Query: 121 SGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVV 180 +G +KRHNF G A+HG S SHR GS G RQ PGRVFK KKMAG MG RVTV+NLEVV Sbjct: 118 AGVIKRHNFSGGPASHGNSRSHRRPGSIGARQTPGRVFKGKKMAGHMGNERVTVQNLEVV 177 Query: 181 SVDDKRGLILVKGCVPGAKKNSWILVRDSFKSA 213 VD +R L+LVKG VPGA K ++++ + K+ Sbjct: 178 KVDAERNLLLVKGAVPGA-KGGLVIIKPAVKAK 209 >gnl|CDD|163362 TIGR03625, L3_bact, 50S ribosomal protein L3, bacterial. This model describes bacterial (and mitochondrial and chloroplast) class of ribosomal protein L3. A separate model describes the archaeal form, where both belong to Pfam family pfam00297. The name is phrased to meet the needs of bacterial genome annotation. Organellar forms typically will have transit peptides, N-terminal to the region modeled here. Length = 202 Score = 291 bits (748), Expect = 9e-80 Identities = 108/204 (52%), Positives = 139/204 (68%), Gaps = 2/204 (0%) Query: 4 GVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVSK 63 G++ +K+GMT ++ +G+ +PVTV+ + V +T++K+GY AVQ+G GE K K V+K Sbjct: 1 GLLGKKVGMTQIFTEDGKAVPVTVIEVGPNVVTQVKTVEKDGYSAVQLGFGEKKEKRVNK 60 Query: 64 PMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGA 123 P G F+ V PK+ L EFRV D + VG + F GQ VDVTG + GKGF+G Sbjct: 61 PEAGHFAKAGVEPKRHLREFRV-DDLEGYEVGDEITVDIFEAGQKVDVTGTSKGKGFAGV 119 Query: 124 MKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVD 183 MKRHNF G A+HG S SHR+ GS G RQ PGRVFK KKMAG MG RVTV+NLEVV VD Sbjct: 120 MKRHNFSGGPASHGNSKSHRAPGSIGQRQTPGRVFKGKKMAGHMGNERVTVQNLEVVKVD 179 Query: 184 DKRGLILVKGCVPGAKKNSWILVR 207 +R L+LVKG VPGA K S +L++ Sbjct: 180 AERNLLLVKGAVPGA-KGSLVLIK 202 >gnl|CDD|163363 TIGR03626, L3_arch, archaeal ribosomal protein L3. This model describes exclusively the archaeal class of ribosomal protein L3. A separate model (TIGR03625) describes the bacterial/organelle form, and both belong to Pfam family pfam00297. Eukaryotic proteins are excluded from this model. Length = 330 Score = 63.9 bits (156), Expect = 3e-11 Identities = 48/154 (31%), Positives = 63/154 (40%), Gaps = 32/154 (20%) Query: 76 PKKK--LFEFRVQKDD---------DLLPVGSVFSPS-YFTVGQLVDVTGMTIGKGFSGA 123 PKKK + E R+ +L G S S F GQLVDV +T GKGF G Sbjct: 151 PKKKPEIMEIRIGGGSVEERFEYALSIL--GKEISVSDVFKEGQLVDVIAVTKGKGFQGV 208 Query: 124 MKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVD 183 +KR L H R G+ G P RV AG+MG ++ T N ++ + Sbjct: 209 VKRWGVKLLPRKHKRRKGGRHIGTLGPWT-PSRVRWTVPQAGQMGYHQRTEYNKRILKIG 267 Query: 184 D------------KRGL-----ILVKGCVPGAKK 200 + GL +L+KG VPG K Sbjct: 268 EDGDEITPKGGFVNYGLVRNDYVLIKGSVPGPSK 301 >gnl|CDD|179795 PRK04231, rpl3p, 50S ribosomal protein L3P; Reviewed. Length = 337 Score = 53.7 bits (130), Expect = 4e-08 Identities = 48/154 (31%), Positives = 63/154 (40%), Gaps = 32/154 (20%) Query: 76 PKKK--LFEFRVQKDD---------DLLPVGSVFSPS-YFTVGQLVDVTGMTIGKGFSGA 123 PKKK + E R+ +LL G S S F GQLVDV +T GKGF G Sbjct: 156 PKKKPEIMEIRIGGGSVEERLEYAKELL--GKEISISDVFKEGQLVDVIAVTKGKGFQGV 213 Query: 124 MKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVD 183 +KR L H R G+ G P RV AG+MG ++ T N ++ + Sbjct: 214 VKRWGVKLLPRKHKRRGGSRHIGTLGPWN-PSRVMWTVPQAGQMGFHQRTEYNKRILKIG 272 Query: 184 D-----------------KRGLILVKGCVPGAKK 200 D + +L+KG VPG K Sbjct: 273 DDGDEITPKGGFLHYGLVRNDYVLIKGSVPGPAK 306 >gnl|CDD|185447 PTZ00103, PTZ00103, 60S ribosomal protein L3; Provisional. Length = 390 Score = 33.9 bits (78), Expect = 0.030 Identities = 47/190 (24%), Positives = 64/190 (33%), Gaps = 63/190 (33%) Query: 43 KNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSY 102 K M +QV G K V K L E V PV SVF Sbjct: 174 KAHVMEIQVNGGSVAEK--------------VDFAKSLLEKEV-------PVDSVFQQ-- 210 Query: 103 FTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGC--RQDPGRVFKN 160 +++DV G+T G GF G +KR +G T +HR C P RV Sbjct: 211 ---NEMIDVIGVTKGHGFEGVVKR--WG---VTRLPRKTHRGLRKVACIGAWHPARVQYT 262 Query: 161 KKMAGRMGGNRVTVKNLEVVSV---DDKRG---------------------------LIL 190 AG+ G + T N ++ + +D ++ Sbjct: 263 VPRAGQHGYHHRTELNKKIYRIGVAEDPNNATTEADLTEKTITPMGGFPHYGTVRNDFLM 322 Query: 191 VKGCVPGAKK 200 +KGCV G KK Sbjct: 323 LKGCVVGPKK 332 >gnl|CDD|162117 TIGR00932, 2a37, transporter, monovalent cation:proton antiporter-2 (CPA2) family. Length = 273 Score = 28.4 bits (64), Expect = 1.4 Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 1/31 (3%) Query: 81 FEFRVQKDDDLLPVGSVFSPSYF-TVGQLVD 110 E+R + + DL P+G V P +F +VG VD Sbjct: 243 SEYRHKLESDLEPIGGVLLPLFFISVGMSVD 273 >gnl|CDD|129656 TIGR00565, trpE_proteo, anthranilate synthase component I, proteobacterial subset. This enzyme resembles some other chorismate-binding enzymes, including para-aminobenzoate synthase (pabB) and isochorismate synthase. There is a fairly deep split between two sets, seen in the pattern of gaps as well as in amino acid sequence differences. This group includes proteobacteria such as E. coli and Helicobacter pylori but also the gram-positive organism Corynebacterium glutamicum. The second group includes eukaryotes, archaea, and most other bacterial lineages; sequences from the second group may resemble pabB more closely than other trpE from this group. Length = 498 Score = 27.9 bits (62), Expect = 2.0 Identities = 18/53 (33%), Positives = 23/53 (43%), Gaps = 10/53 (18%) Query: 12 MTCVYNIEGRRI-----PVTVL----HLDNCQVVVHRTLDKNGYMAVQVGAGE 55 M +Y EG+R V L LD C +V+ +NG VQ GAG Sbjct: 418 MQLIYQAEGQRRGSYGGAVGYLTSHGDLDTC-IVIRSAFVENGIATVQAGAGI 469 >gnl|CDD|163551 TIGR03839, termin_org_P1, adhesin P1. Members of this protein family are the major adhesin of the Mycoplasma terminal organelle. The protein is called adhesin P1, cytadhesin P1, P140, attachment protein, and MgPa, with locus names MG191 in Mycoplasma genitalium and MPN141 in M. pneumoniae. A conserved C-terminal region is shared by additional paralogs in M. pneumoniae and M. gallisepticum, as well as by the member of this family. Length = 1425 Score = 27.8 bits (61), Expect = 2.0 Identities = 19/73 (26%), Positives = 23/73 (31%) Query: 45 GYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFT 104 + V A RG F S S F+ D D V S + + Sbjct: 949 TWGEVNGLYNTALNITYYNLTRGDFGSNTPSTPGIGFKPEQNNDSDATLVSSGLNWTPQD 1008 Query: 105 VGQLVDVTGMTIG 117 VG LV TG G Sbjct: 1009 VGNLVVSTGTQQG 1021 >gnl|CDD|183059 PRK11253, ldcA, L,D-carboxypeptidase A; Provisional. Length = 305 Score = 27.6 bits (62), Expect = 2.4 Identities = 18/47 (38%), Positives = 21/47 (44%), Gaps = 5/47 (10%) Query: 84 RVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFG 130 Q+DD LL VG S FT QL + FSG M +FG Sbjct: 93 ARQQDDPLLIVGH----SDFTAIQLA-LLAQANVITFSGPMLAADFG 134 >gnl|CDD|130373 TIGR01306, GMP_reduct_2, guanosine monophosphate reductase, bacterial. A deep split separates two families of GMP reductase. The other (TIGR01305) is found in eukaryotic and some proteobacterial lineages, including E. coli, while this family is found in a variety of bacterial lineages. Length = 321 Score = 27.6 bits (61), Expect = 2.5 Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 12/80 (15%) Query: 32 NCQVVVHRT----LDKNGYMAVQVGAGEAKVKNVSKPM--RGFFSSVNVSPKKKLFEFRV 85 N Q ++ L +NGY + E K M RG F+S++V K +EF Sbjct: 41 NMQTIIDEKLAEQLAENGYFYIMHRFDEESRIPFIKDMQERGLFASISVGVKACEYEFVT 100 Query: 86 QKDDDLLPVGSVFSPSYFTV 105 Q ++ L +P Y T+ Sbjct: 101 QLAEEAL------TPEYITI 114 >gnl|CDD|163300 TIGR03508, decahem_SO, decaheme c-type cytochrome, DmsE family. Members of this family are small, decaheme c-type cytochromes, related DmsE of Shewanella oneidensis MR-1, which has been shown to be part of an anaerobic dimethyl sulfoxide reductase. Length = 258 Score = 27.8 bits (62), Expect = 2.6 Identities = 10/27 (37%), Positives = 13/27 (48%) Query: 52 GAGEAKVKNVSKPMRGFFSSVNVSPKK 78 G G VK +PM F S N+ +K Sbjct: 42 GPGGKHVKGGGEPMITFGSFSNLPAEK 68 >gnl|CDD|179377 PRK02135, PRK02135, hypothetical protein; Provisional. Length = 201 Score = 27.5 bits (62), Expect = 2.7 Identities = 9/19 (47%), Positives = 13/19 (68%) Query: 28 LHLDNCQVVVHRTLDKNGY 46 LH D+C ++H LD+ GY Sbjct: 181 LHADHCITLIHNELDRRGY 199 >gnl|CDD|178849 PRK00082, hrcA, heat-inducible transcription repressor; Provisional. Length = 339 Score = 26.7 bits (60), Expect = 4.7 Identities = 7/23 (30%), Positives = 14/23 (60%), Gaps = 1/23 (4%) Query: 170 NRVTVKNLEVVSVDDKRGL-ILV 191 + +K++E+V + R L +LV Sbjct: 132 SDSRLKHIELVPLSPHRALAVLV 154 >gnl|CDD|151320 pfam10871, DUF2748, Protein of unknown function (DUF2748). This is a bacterial family of proteins with unknown function. Length = 452 Score = 26.9 bits (59), Expect = 4.7 Identities = 11/30 (36%), Positives = 17/30 (56%) Query: 54 GEAKVKNVSKPMRGFFSSVNVSPKKKLFEF 83 GE +++ KP FFS + + KKL+ F Sbjct: 412 GENYMRDFKKPKSNFFSKILIFRIKKLWPF 441 >gnl|CDD|179633 PRK03699, PRK03699, putative transporter; Provisional. Length = 394 Score = 26.8 bits (60), Expect = 5.0 Identities = 10/17 (58%), Positives = 11/17 (64%) Query: 101 SYFTVGQLVDVTGMTIG 117 SY G LV VTGM +G Sbjct: 15 SYALTGALVIVTGMVMG 31 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 0.321 0.137 0.405 Gapped Lambda K H 0.267 0.0499 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 3,530,432 Number of extensions: 217591 Number of successful extensions: 362 Number of sequences better than 10.0: 1 Number of HSP's gapped: 356 Number of HSP's successfully gapped: 18 Length of query: 221 Length of database: 5,994,473 Length adjustment: 90 Effective length of query: 131 Effective length of database: 4,049,753 Effective search space: 530517643 Effective search space used: 530517643 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: 55 (25.5 bits)