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)