RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781115|ref|YP_003065528.1| poly(A) polymerase protein [Candidatus Liberibacter asiaticus str. psy62] (416 letters) >gnl|CDD|30962 COG0617, PcnB, tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]. Length = 412 Score = 219 bits (560), Expect = 9e-58 Identities = 113/410 (27%), Positives = 184/410 (44%), Gaps = 16/410 (3%) Query: 9 WFHDSDLINILSLLNKGEDKSCIVGGAVRDSLMNLSVQDIDIATTILPDRVMRIFSKTRY 68 + + +LS L + ++ +VGGAVRD L+ +D+DIAT P+ V ++F TR Sbjct: 5 KDLSPNALKVLSKLKEAGYEAYLVGGAVRDLLLGRPPKDVDIATNATPEEVKKLFRNTR- 63 Query: 69 KVIPTSISYGTIKIICRKKYFDITTLRSD-LITDGRYAKVVFTRDWKADSLRRDFTINAL 127 P +GT+ + + ++TT R + +GR VVF + D RRDFTINAL Sbjct: 64 ---PVGRKFGTVTVPFNGEIIEVTTFRKEGYGYNGRPLPVVFPGTLEEDLKRRDFTINAL 120 Query: 128 -YADQQGKVIDYVGGLNDLRNRTIKFIGDAHHRILEDYLRILRFFRFFAHYGEKNIDSDG 186 Y + G++ID GGL DL NR ++ IGDA R ED LRILR RF A G I+ + Sbjct: 121 AYDPEDGEIIDPFGGLKDLENRVLRHIGDASERFREDPLRILRAARFAARLGFT-IEPET 179 Query: 187 LVASIKAKKGLKILSSERIWSEINKLLEAKNPLNAIVHMYNGGIFKEIF--LDVQEISLD 244 A L +S ER+W E+ KLL + NP A+ + G K +F LD Sbjct: 180 EEAIRLMAPLLAKISRERLWDELKKLLLSPNPREALQLLREYGALKILFPELDKLFGVPK 239 Query: 245 QLSQVIEAEQVFEWKIDSLLRFIVLISWQDKKSILSMAKKFSLPREIRYFLISFFNCNFN 304 L + E E + D LL + + + ++ + I + Sbjct: 240 LLLALREIELLLHNT-DELLLALAALLPAFLLAAATLPLLLRKGKTIAKKRRELKHDEAA 298 Query: 305 QKTLS--IPEIKKLFYLYGDKVMIAKLK--IFLALHYNNLTHQDTCFILQVLSDIIHWKK 360 K ++ + + + YL K ++ +++ A T + +L++L+ + Sbjct: 299 AKAVNDLLKRLLRPNYLGYLKRLVEEVREIWHEAGELLPRTGKRARKLLRLLAFRAALEL 358 Query: 361 PLFPLTGDDVVKYGIPPGKKVGNILVHCKQEWINSSFQLSQEDLHHLLRK 410 + + G PG K+G IL +++ + + +E L L + Sbjct: 359 LILGRDLGEA--AGYKPGPKLGEILQLLEEKPLKGVIKNLKEALIERLER 406 >gnl|CDD|37370 KOG2159, KOG2159, KOG2159, tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]. Length = 416 Score = 151 bits (383), Expect = 3e-37 Identities = 107/396 (27%), Positives = 172/396 (43%), Gaps = 41/396 (10%) Query: 31 IVGGAVRDSLMNLSVQDIDIATTILPDRVMRIFSKTRYKVIPTS----ISYGTIKI-ICR 85 + GG VRD L+ +DIDIATT + ++ +F + +V + G IK Sbjct: 33 LAGGWVRDLLLGREPKDIDIATTAMSGQMKEMFQSAQIRVGKKFPICHVIMGPIKSKHLE 92 Query: 86 KKYFDITTLRSDLITDGRYA----KVVFTRDWK--ADSLRRDFTINAL-YADQQGKVIDY 138 F ITTLR D + R A + + D ++LRRDFTIN+L + G V DY Sbjct: 93 TATFRITTLRIDFVNLRREAYTETSIPYVTDGTRDENALRRDFTINSLFFNPFDGTVEDY 152 Query: 139 VGGLNDLRNRTIKFIGDAHHRILEDYLRILRFFRFFAHYG--EKNIDSDGLVASIKAKKG 196 GGL DL+N+ ++ + A LED LRILR RF A G + L A + Sbjct: 153 TGGLEDLKNKKVRTVLHAKQTFLEDPLRILRGIRFAARLGFTIDEESKETLEAIKENVAL 212 Query: 197 LKILSSERIWSEINKLLEAKNPLNAIVHMYNGGIFKEIFLDVQEISLDQLSQVIEAEQVF 256 L +S ERI EINK+L + ++ ++ F+ IFL ++ SL++ + F Sbjct: 213 LAKISRERIGVEINKMLVGNSAEASLRLLWRLFGFEYIFLPIEA-SLEEFQGFNRRDG-F 270 Query: 257 EWKIDSLLRFIVLISWQDKKSILSM-AKKFSLPREI----RYFLISFFNCNFNQKTLSIP 311 + SLL + D+ L + L ++ R+ + + + L Sbjct: 271 SNEPLSLLANLDKSLAPDEPCHLRLKLSILELLKKFIDQPRFPTVPAVSSSAPLSKLQDV 330 Query: 312 EIKKLFYLYGDKVMIAKLKIFLALHY---NNLTHQDTCFILQVLSDIIHWKKPLFPLTGD 368 EI K K+ ++ L N L ++ ++ W P FP++ + Sbjct: 331 EIPK-------KIEKDHDRLRQLLVSQEKNELDNE----------TLLDWSVPDFPISIN 373 Query: 369 DVVKYGIPPGKKVGNILVHCKQEWINSSFQLSQEDL 404 D+ G G +G +L + + W +S F ++ L Sbjct: 374 DLAIEGTSKGSIIGALLRYLQAPWSDSVFTSLKDSL 409 >gnl|CDD|143388 cd05398, NT_ClassII-CCAase, Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes. CCA-adding enzymes add the sequence [cytidine(C)-cytidine-adenosine (A)], one nucleotide at a time, onto the 3' end of tRNA, in a template-independent reaction. This Class II group is comprised mainly of eubacterial and eukaryotic enzymes and includes Bacillus stearothermophilus CCAase, Escherichia coli poly(A) polymerase I, human mitochondrial CCAase, and Saccharomyces cerevisiae CCAase (CCA1). CCA-adding enzymes have a single catalytic pocket, which recognizes both ATP and CTP substrates. Included in this subgroup are CC- and A-adding enzymes from various ancient species of bacteria such as Aquifex aeolicus; these enzymes collaborate to add CCA to tRNAs. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These carboxylate residues are fairly well conserved in this family. Escherichia coli CCAase is related to this group but has not been included in this alignment as this enzyme lacks the N-terminal helix conserved in the remainder of the NT superfamily. Length = 139 Score = 126 bits (320), Expect = 8e-30 Identities = 54/139 (38%), Positives = 74/139 (53%), Gaps = 7/139 (5%) Query: 14 DLINILSLLNKGEDKSC-IVGGAVRDSLMNLSVQDIDIATT-ILPDRVMRIFSKTRYKVI 71 +L+ +L L K +VGGAVRD L+ +DIDIAT P+ +F K +V+ Sbjct: 3 ELLKLLRELKKALGYEAYLVGGAVRDLLLGRPPKDIDIATDADGPEFAEALFKKIGGRVV 62 Query: 72 PTSISYGTIKIICRKKYFDITTLRSDLITD--GRYAKVVFTRDWKADSLRRDFTINALYA 129 +GT ++ D+ TLR++ TD R V FT + D LRRDFTINA+ Sbjct: 63 GLGEEFGTATVVINGLTIDVATLRTETYTDPGRRPPVVGFTIE--EDLLRRDFTINAMAY 120 Query: 130 D-QQGKVIDYVGGLNDLRN 147 D G++ID GGL DL N Sbjct: 121 DLDDGELIDPFGGLKDLEN 139 >gnl|CDD|110721 pfam01743, PolyA_pol, Poly A polymerase head domain. This family includes nucleic acid independent RNA polymerases, such as Poly(A) polymerase, which adds the poly (A) tail to mRNA EC:2.7.7.19. This family also includes the tRNA nucleotidyltransferase that adds the CCA to the 3' of the tRNA EC:2.7.7.25. Length = 126 Score = 123 bits (311), Expect = 8e-29 Identities = 44/125 (35%), Positives = 66/125 (52%), Gaps = 3/125 (2%) Query: 30 CIVGGAVRDSLMNLSVQDIDIATTILPDRVMRIFSKTRYKVIPTSISYGTIKIICRKKYF 89 +VGGAVRD L+ +D+DIAT P++V +F + + +GTI ++ + Sbjct: 2 YLVGGAVRDLLLGRPPKDVDIATDAGPEQVATLFRNRIIVHLESGKEFGTIHVLFGNQIL 61 Query: 90 DITTLRSDLITDGRYAK--VVFTRDWKADSLRRDFTINALYAD-QQGKVIDYVGGLNDLR 146 ++ T R++ FT + D RRDFTINAL D G+VID GG+ DL+ Sbjct: 62 EVATFRTESDESDFRNPKSEEFTGTLEEDLKRRDFTINALAYDPNDGEVIDPFGGIKDLK 121 Query: 147 NRTIK 151 N I+ Sbjct: 122 NGVIR 126 >gnl|CDD|35731 KOG0511, KOG0511, KOG0511, Ankyrin repeat protein [General function prediction only]. Length = 516 Score = 30.0 bits (67), Expect = 1.1 Identities = 24/138 (17%), Positives = 45/138 (32%), Gaps = 4/138 (2%) Query: 189 ASIKAKKGLKILSSERIWSEINKLLEAKNPLNAIVHMYN--GGIFKEIFLDVQEISLDQL 246 A+ A K L S + + + + A + + K+++L+ DQ Sbjct: 160 ANFDAHKFLLEARSSNYFPKDVMFYVQGHEIEAHRVILSAFSPFLKQLYLNTNAEWKDQY 219 Query: 247 SQVIEAEQVFEWKIDSLLRFIVLISWQDKKSILSMAKKFSLPREIRYFLISFFNCNFNQK 306 + ++ E F + L I +D I + + S + I LI + Sbjct: 220 NALLSIEVKFS--KEKLSLEISKDRMEDLSRICKVCQCESTQKIIEKELIHQRYAEYKTH 277 Query: 307 TLSIPEIKKLFYLYGDKV 324 K F L G + Sbjct: 278 RDLDNSPMKRFSLQGAYI 295 >gnl|CDD|119402 cd00490, Met_repressor_MetJ, Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. MetJ forms sufficiently strong interactions with the sugar-phosphate backbone to accomodate sequence variation in natural operators. However, it is very sensitive to particular base changes in the operator. MetJ exists as a homodimer.. Length = 103 Score = 29.9 bits (67), Expect = 1.3 Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 4/58 (6%) Query: 174 FAHYGEKNIDSDGLVASIKAKKGLKILSSERIWSEINKLLEAKNP---LNAIVHMYNG 228 +A +G+K+ + SI K LKIL+ ER ++N L A N A +H + G Sbjct: 11 YAEHGKKSEQVKKITVSIPLKV-LKILTDERTRRQVNNLRHATNSELLCEAFLHAFTG 67 >gnl|CDD|32874 COG3060, MetJ, Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]. Length = 105 Score = 28.5 bits (63), Expect = 3.2 Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 4/58 (6%) Query: 174 FAHYGEKNIDSDGLVASIKAKKGLKILSSERIWSEINKLLEAKNP---LNAIVHMYNG 228 +A +G+K+ + SI K LKIL+ ER ++N L A N A +H + G Sbjct: 12 YAEHGKKSEQVKKITVSIPLKV-LKILTDERTRRQVNNLRHATNSELLCEAFLHAFTG 68 >gnl|CDD|114400 pfam05674, DUF816, Baculovirus protein of unknown function (DUF816). This family includes proteins that are about 200 amino acids in length. The proteins are all from baculoviruses. This family includes ORF107 from Orgyia pseudotsugata multicapsid polyhedrosis virus (OpMNPV) and a variety of other numbered ORF proteins, such as ORF52, ORF140. The function of these proteins is unknown. Length = 171 Score = 28.5 bits (64), Expect = 3.8 Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 3/40 (7%) Query: 54 ILPDRVMRIFSKTR--YKVIPTSISYGTIK-IICRKKYFD 90 +LP+ V+ I R Y PT +Y IK + + KY D Sbjct: 25 MLPENVLAIIKTARDEYFQNPTDKNYENIKKLFSQTKYVD 64 >gnl|CDD|31842 COG1656, COG1656, Uncharacterized conserved protein [Function unknown]. Length = 165 Score = 28.0 bits (62), Expect = 5.2 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 5/61 (8%) Query: 144 DLRNRTIKFIGDAHHRILEDYLRILRFFRFFAHYGEKNIDSDGLVASIKAKKGLKILSSE 203 +KF+ DA L R LR + Y + +SD + I K+G +L+ + Sbjct: 1 PSPMGEMKFVVDAM---LGKLARWLRLLGYDTVYS--SNESDDEIILIAKKEGRILLTRD 55 Query: 204 R 204 R Sbjct: 56 R 56 >gnl|CDD|145980 pfam03122, Herpes_MCP, Herpes virus major capsid protein. This family represents the major capsid protein (MCP) of herpes viruses. The capsid shell consists of 150 MCP hexamers and 12 MCP pentamers. One pentamer is found at each of the 12 apices of the icosahedral shell, and the hexamers form the edges and 20 faces. Length = 1352 Score = 27.6 bits (62), Expect = 7.3 Identities = 10/35 (28%), Positives = 19/35 (54%), Gaps = 1/35 (2%) Query: 374 GIPPGKKVGNILV-HCKQEWINSSFQLSQEDLHHL 407 G PP K+ + + ++ I+++F+LS L L Sbjct: 95 GHPPSKQTTYYVTKYIEKHPISAAFELSAAALELL 129 >gnl|CDD|48072 cd01968, Nitrogenase_NifE_I, Nitrogenase_NifE_I: a subgroup of the NifE subunit of the NifEN complex: NifE forms an alpha2beta2 tetramer with NifN. NifE and NifN are structurally homologous to nitrogenase MoFe protein alpha and beta subunits respectively. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of the MoFe protein. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to the NifEN complex where it is further processed to FeMoco. The NifEN bound precursor of FeMoco has been identified as a molybdenum-free, iron- and sulfur- containing analog of FeMoco. It has been suggested that this NifEN bound precursor also acts as a cofactor precursor in nitrogenase systems which require a cofactor other than FeMoco: i.e. iron-vanadium cofactor (FeVco) or iron only cofactor (FeFeco).. Length = 410 Score = 27.1 bits (60), Expect = 8.9 Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 5/59 (8%) Query: 276 KSILSMAKKFSLPREIRYFLISFFNCNFNQKTLSIPEIKKLFYLYGDKVMIAKLKIFLA 334 KS++ +A+K I Y +SF+ + S+ I +L GD+ +I + + +A Sbjct: 215 KSMIYLARKMEEKYGIPYIEVSFY--GIRDTSKSLRNIAELL---GDEELIERTEELIA 268 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.325 0.141 0.420 Gapped Lambda K H 0.267 0.0713 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 5,176,450 Number of extensions: 285572 Number of successful extensions: 826 Number of sequences better than 10.0: 1 Number of HSP's gapped: 814 Number of HSP's successfully gapped: 23 Length of query: 416 Length of database: 6,263,737 Length adjustment: 96 Effective length of query: 320 Effective length of database: 4,189,273 Effective search space: 1340567360 Effective search space used: 1340567360 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 59 (26.5 bits)