RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780180|ref|YP_003064593.1| S-adenosylmethionine:tRNA
ribosyltransferase-isomerase [Candidatus Liberibacter asiaticus str.
psy62]
(360 letters)
>gnl|CDD|31151 COG0809, QueA,
S-adenosylmethionine:tRNA-ribosyltransferase-isomerase
(queuine synthetase) [Translation, ribosomal structure
and biogenesis].
Length = 348
Score = 422 bits (1087), Expect = e-119
Identities = 175/360 (48%), Positives = 227/360 (63%), Gaps = 16/360 (4%)
Query: 1 MMVKEFDFDLPPSRIALRPVFPRDSARLMVVHPNLSCPLVISDHLVSDLPAFLNSNDAIV 60
M + +FDFDLP IA P PRDS+RL+V+ I DL +LN D +V
Sbjct: 1 MRLSDFDFDLPEELIAQYPAEPRDSSRLLVLDRKTG---EIEHRTFYDLIDYLNPGDLLV 57
Query: 61 FNNTKVITAQLNGVRFCHINRREKEISCTLHMRVSPNSWSVYARPSKVIKKGDILHFFSQ 120
FN+T+VI A+L F + ++ L R+ N W +PSK +K GD ++F
Sbjct: 58 FNDTRVIPARL----FGRKHESGGKVEVLLERRLDDNRWLALIKPSKRLKAGDEIYF--- 110
Query: 121 DGQSRLEATVIDKWNTGEILLVFSISGIE-LERQISLVGTIPLPPYIARKRPIDARDYVD 179
L+ATV+++ G LL F GI L + G +PLPPYI KR +D D
Sbjct: 111 --GDGLKATVLERLEHGLRLLEFDYEGIFSLLELLEKYGEMPLPPYI--KRKLDELDRDR 166
Query: 180 YQTTYAKIQGSVAAPTAGLHFTSNLLSRLISIGIKVYFVTLHVGAGTFMPVKVEDTDDHI 239
YQT YAK GSVAAPTAGLHFT LL +L + G+++ FVTLHVGAGTF PVKVE+ ++H
Sbjct: 167 YQTVYAKEPGSVAAPTAGLHFTEELLEKLKAKGVEIAFVTLHVGAGTFRPVKVENIEEHK 226
Query: 240 MHSEIGFIDAPTAQALNSVKSRGGRIVSVGTTSLRLLETATTEDGIINPWSGFTNIFITP 299
MHSE + TA A+N+ K+RGGRI++VGTTS+R LE+A E G + +SG+T+IFI P
Sbjct: 227 MHSEYYEVPQETADAINAAKARGGRIIAVGTTSVRTLESAAREAG-LKAFSGWTDIFIYP 285
Query: 300 GYRFRAVDILMSNFHLPKSTLLMLVSAFCGIEETKKMYQHAISHAYRFYSYGDTSLLFQK 359
GYRF+ VD L++NFHLPKSTLLMLVSAF G EE Y+HAI YRF+SYGD L+ +
Sbjct: 286 GYRFKVVDALITNFHLPKSTLLMLVSAFAGREELLAAYKHAIEQKYRFFSYGDAMLILRN 345
>gnl|CDD|145599 pfam02547, Queuosine_synth, Queuosine biosynthesis protein.
Queuosine (Q) biosynthesis protein, or
S-adenosylmethionine:tRNA -ribosyltransferase-isomerase,
is required for the synthesis of the queuosine precursor
(oQ). Q is a hypermodified nucleoside usually found at
the first position of the anticodon of asparagine,
aspartate, histidine, and tyrosine tRNAs.
Length = 218
Score = 257 bits (658), Expect = 5e-69
Identities = 100/233 (42%), Positives = 131/233 (56%), Gaps = 16/233 (6%)
Query: 1 MMVKEFDFDLPPSRIALRPVFPRDSARLMVVHPNLSCPLVISDHLVSDLPAFLNSNDAIV 60
M + +FD++LP IA P PRDS+RL+V+ I SDLP +L D +V
Sbjct: 1 MKLSDFDYELPEELIAQYPAEPRDSSRLLVLDRETG---EIEHRRFSDLPDYLRPGDLLV 57
Query: 61 FNNTKVITAQLNGVRFCHINRREKEISCTLHMRVSPNSWSVYARPSKVIKKGDILHFFSQ 120
FN+T+VI A+L G + ++ L + W +PSK +K GD L F
Sbjct: 58 FNDTRVIPARLFGRKET-----GGKVEVLLLRPLDDGRWLALVKPSKKLKPGDTLEF--- 109
Query: 121 DGQSRLEATVIDKWNTGEILLVFSISGIE-LERQISLVGTIPLPPYIARKRPIDARDYVD 179
L+A V+++ G L+ F G E L + G IPLPPYI KRP + D
Sbjct: 110 --GDGLKAEVLERLEEGGRLVRFQFEGGEDLLELLERYGHIPLPPYI--KRPDEEEDRER 165
Query: 180 YQTTYAKIQGSVAAPTAGLHFTSNLLSRLISIGIKVYFVTLHVGAGTFMPVKV 232
YQT YAK GSVAAPTAGLHFT LL RL + G+++ FVTLHVGAGTF+PV+V
Sbjct: 166 YQTVYAKKPGSVAAPTAGLHFTPELLERLKAKGVEIAFVTLHVGAGTFLPVRV 218
>gnl|CDD|145901 pfam02996, Prefoldin, Prefoldin subunit. This family comprises of
several prefoldin subunits. The biogenesis of the
cytoskeletal proteins actin and tubulin involves
interaction of nascent chains of each of the two
proteins with the oligomeric protein prefoldin (PFD) and
their subsequent transfer to the cytosolic chaperonin
CCT (chaperonin containing TCP-1). Electron microscopy
shows that eukaryotic PFD, which has a similar structure
to its archaeal counterpart, interacts with unfolded
actin along the tips of its projecting arms. In its
PFD-bound state, actin seems to acquire a conformation
similar to that adopted when it is bound to CCT.
Length = 120
Score = 31.5 bits (72), Expect = 0.40
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 218 VTLHVGAGTFMPVKVEDTDDHIMH 241
V + +GAG F+ +V DTD ++
Sbjct: 41 VLVPLGAGLFVKGEVIDTDKVLVD 64
>gnl|CDD|38799 KOG3592, KOG3592, KOG3592, Microtubule-associated proteins
[Cytoskeleton].
Length = 934
Score = 29.7 bits (66), Expect = 1.2
Identities = 13/31 (41%), Positives = 16/31 (51%)
Query: 17 LRPVFPRDSARLMVVHPNLSCPLVISDHLVS 47
L PV D A L P+ S PLV S+H +
Sbjct: 546 LDPVELTDEAELKPPTPDPSAPLVPSEHDII 576
>gnl|CDD|29840 cd00584, Prefoldin_alpha, Prefoldin alpha subunit; Prefoldin is a
hexameric molecular chaperone complex, found in both
eukaryotes and archaea, that binds and stabilizes newly
synthesized polypeptides allowing them to fold
correctly. The complex contains two alpha and four beta
subunits, the two subunits being evolutionarily related.
In archaea, there is usually only one gene for each
subunit while in eukaryotes there two or more paralogous
genes encoding each subunit adding heterogeneity to the
structure of the hexamer. The structure of the complex
consists of a double beta barrel assembly with six
protruding coiled-coils..
Length = 129
Score = 29.4 bits (66), Expect = 1.5
Identities = 11/43 (25%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 222 VGAGTFMPVKVEDTDDHIMHSEIG---FIDAPTAQALNSVKSR 261
+GAG F+ KV+DTD ++ +G +++ +A+ + +
Sbjct: 55 LGAGVFVKAKVKDTDKVLVD--LGTGYYVEKDLEEAIEFLDKK 95
>gnl|CDD|119347 cd06555, ASCH_PF0470_like, ASC-1 homology domain, subfamily similar
to Pyrococcus furiosus Pf0470. The ASCH domain, a small
beta-barrel domain found in all three kingdoms of life,
resembles the RNA-binding PUA domain and may also
interact with RNA. ASCH has been proposed to function as
an RNA-binding domain during coactivation,
RNA-processing and the regulation of prokaryotic
translation..
Length = 109
Score = 29.5 bits (67), Expect = 1.7
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 109 IKKGDILHFFSQDGQSRLEATVID 132
IK GD + F D +L V+D
Sbjct: 32 IKVGDKILFNDLDTGQQLLVKVVD 55
>gnl|CDD|31916 COG1730, GIM5, Predicted prefoldin, molecular chaperone implicated
in de novo protein folding [Posttranslational
modification, protein turnover, chaperones].
Length = 145
Score = 29.1 bits (65), Expect = 1.9
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 218 VTLHVGAGTFMPVKVEDTDDHIMH 241
V + VGAG F+ KV+D D I+
Sbjct: 58 VLVPVGAGLFVKAKVKDMDKVIVS 81
>gnl|CDD|37262 KOG2051, KOG2051, KOG2051, Nonsense-mediated mRNA decay 2 protein
[RNA processing and modification].
Length = 1128
Score = 27.7 bits (61), Expect = 5.5
Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 2/52 (3%)
Query: 8 FDLPPSRIALRPVFPRDSARLMVVHPNLSCPLVISDHLVSDLPAFLNSNDAI 59
F +P +R+ L P + R A L P+++ LV L + + L+ I
Sbjct: 468 FVVPRTRLDLLPYYSRLVATLSKCMPDVATELV--TMLRKEFRSHLHKKAQI 517
>gnl|CDD|176216 cd08254, hydroxyacyl_CoA_DH, 6-hydroxycyclohex-1-ene-1-carboxyl-CoA
dehydrogenase, N-benzyl-3-pyrrolidinol dehydrogenase,
and other MDR family members. This group contains
enzymes of the zinc-dependent alcohol dehydrogenase
family, including members (aka MDR) identified as
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase and
N-benzyl-3-pyrrolidinol dehydrogenase.
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase
catalyzes the conversion of
6-Hydroxycyclohex-1-enecarbonyl-CoA and NAD+ to
6-Ketoxycyclohex-1-ene-1-carboxyl-CoA,NADH, and H+. This
group displays the characteristic catalytic and
structural zinc sites of the zinc-dependent alcohol
dehydrogenases. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 338
Score = 27.6 bits (62), Expect = 5.5
Identities = 11/25 (44%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 251 TAQALNSVKSRGGRIVSVGTTSLRL 275
A +VK GGRIV VG +L
Sbjct: 246 FEDAQKAVK-PGGRIVVVGLGRDKL 269
>gnl|CDD|37265 KOG2054, KOG2054, KOG2054, Nucleolar RNA-associated protein (NRAP)
[Function unknown].
Length = 1121
Score = 26.9 bits (59), Expect = 9.3
Identities = 24/103 (23%), Positives = 38/103 (36%), Gaps = 11/103 (10%)
Query: 229 PVKVEDTDDHIMHSEIGFIDAPTAQAL--NSVKSRGGRIVSVGTTSLRLLETATTEDGII 286
+ D + FID+ L N S ++ +L LL++ +
Sbjct: 384 SPSLPALADFHEGQLVTFIDSSGHLNLCANMTASTYEQVQEEARLTLMLLDSRADD---- 439
Query: 287 NPWSGFTNIFITPGYRFRAVD-ILMSNFHLPKSTLLMLVSAFC 328
GF+ IF+T FRA D +L + L+S FC
Sbjct: 440 ----GFSLIFMTKIPVFRAYDHVLHLSPLSRLQAAEHLLSGFC 478
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
0.323 0.138 0.409
Gapped
Lambda K H
0.267 0.0758 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,420,236
Number of extensions: 233039
Number of successful extensions: 532
Number of sequences better than 10.0: 1
Number of HSP's gapped: 521
Number of HSP's successfully gapped: 12
Length of query: 360
Length of database: 6,263,737
Length adjustment: 95
Effective length of query: 265
Effective length of database: 4,210,882
Effective search space: 1115883730
Effective search space used: 1115883730
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 58 (26.1 bits)