RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781220|ref|YP_003065633.1| hypothetical protein
CLIBASIA_05635 [Candidatus Liberibacter asiaticus str. psy62]
(130 letters)
>gnl|CDD|73367 cd00564, TMP_TenI, Thiamine monophosphate synthase (TMP
synthase)/TenI. TMP synthase catalyzes an important
step in the thiamine biosynthesis pathway, the
substitution of the pyrophosphate of
2-methyl-4-amino-5- hydroxymethylpyrimidine
pyrophosphate by 4-methyl-5- (beta-hydroxyethyl)
thiazole phosphate to yield thiamine phosphate. TenI is
a enzymatically inactive regulatory protein involved in
the regulation of several extracellular enzymes. This
superfamily also contains other enzymatically inactive
proteins with unknown functions..
Length = 196
Score = 31.7 bits (72), Expect = 0.060
Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 3/59 (5%)
Query: 28 IEPESNYEVEVIEKLERALKTSKKLIHFRDRTIRTHILEDLIEEVNRIIVLAKAHKRRL 86
I +++E +E ALK L+ R++ + +L+E + L + + L
Sbjct: 4 ITDRRLDGEDLLEVVEAALKGGVTLVQLREKDLSA---RELLELARALRELCRKYGVPL 59
>gnl|CDD|145623 pfam02581, TMP-TENI, Thiamine monophosphate synthase/TENI.
Thiamine monophosphate synthase (TMP) (EC:2.5.1.3)
catalyses the substitution of the pyrophosphate of
2-methyl-4-amino-5- hydroxymethylpyrimidine
pyrophosphate by 4-methyl-5-
(beta-hydroxyethyl)thiazole phosphate to yield thiamine
phosphate. This Pfam family also includes the
regulatory protein TENI.
Length = 180
Score = 29.4 bits (67), Expect = 0.30
Identities = 11/50 (22%), Positives = 25/50 (50%), Gaps = 3/50 (6%)
Query: 37 EVIEKLERALKTSKKLIHFRDRTIRTHILEDLIEEVNRIIVLAKAHKRRL 86
+++E +E ALK ++ R++ + +L+E R+ L + + L
Sbjct: 13 DLLEVVEEALKGGVTIVQLREKDLDD---RELLELAERLRALCRKYGVPL 59
>gnl|CDD|30402 COG0053, MMT1, Predicted Co/Zn/Cd cation transporters [Inorganic
ion transport and metabolism].
Length = 304
Score = 29.4 bits (66), Expect = 0.31
Identities = 18/75 (24%), Positives = 34/75 (45%), Gaps = 3/75 (4%)
Query: 18 FLSAVNPRMGIEPESNYEVEVIEKLERALKTSKKLIHFRDRTIRTHILEDLIEEVNRIIV 77
F +VN M + ++E I + ++ K + R R + I D+ EV+ +
Sbjct: 200 FKESVNELMDAALDPE-DLEKIRAIILSVPGVKGVHDLRTRKSGSRIFIDVHIEVDPDLS 258
Query: 78 LAKAHK--RRLELKI 90
L +AH+ +E +I
Sbjct: 259 LEEAHEIADEVEKRI 273
>gnl|CDD|30701 COG0352, ThiE, Thiamine monophosphate synthase [Coenzyme
metabolism].
Length = 211
Score = 28.3 bits (63), Expect = 0.66
Identities = 14/69 (20%), Positives = 28/69 (40%), Gaps = 7/69 (10%)
Query: 18 FLSAVNPRMGIEPESNYEVEVIEKLERALKTSKKLIHFRDRTIRTHILEDLIEEVNRIIV 77
L V R I V+++E +E ALK + R++ + E+ + ++
Sbjct: 7 RLYLVTDRPLIYDG----VDLLEWVEAALKGGVTAVQLREKDLSD---EEYLALAEKLRA 59
Query: 78 LAKAHKRRL 86
L + + L
Sbjct: 60 LCQKYGVPL 68
>gnl|CDD|144653 pfam01138, RNase_PH, 3' exoribonuclease family, domain 1. This
family includes 3'-5' exoribonucleases. Ribonuclease PH
contains a single copy of this domain, and removes
nucleotide residues following the -CCA terminus of tRNA.
Polyribonucleotide nucleotidyltransferase (PNPase)
contains two tandem copies of the domain. PNPase is
involved in mRNA degradation in a 3'-5' direction. The
exosome is a 3'-5' exoribonuclease complex that is
required for 3' processing of the 5.8S rRNA. Three of
its five protein components contain a copy of this
domain. A hypothetical protein from S. pombe appears to
belong to an uncharacterized subfamily. This subfamily
is found in both eukaryotes and archaebacteria.
Length = 128
Score = 27.5 bits (62), Expect = 1.1
Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 2/60 (3%)
Query: 10 EEIEANYEFLSAVNPRMGIEPESNYEVEVIEKLERALKTSKKLIHFRDRTIR--THILED 67
E+ YE + S E+E+ ++RAL+ S L + IR +L D
Sbjct: 47 GELTVEYEEKPFASGERPEGRPSEREIELSRLIDRALRPSFPLEGYPRWEIRIDITVLSD 106
>gnl|CDD|73023 cd03264, ABC_drug_resistance_like, ABC-type multidrug transport
system, ATPase component. The biological function of
this family is not well characterized, but display ABC
domains similar to members of ABCA subfamily. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds,
like sugars, ions, peptides, and more complex organic
molecules. The nucleotide binding domain shows the
highest similarity between all members of the family.
ABC transporters are a subset of nucleotide hydrolases
that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing
proteins..
Length = 211
Score = 26.7 bits (59), Expect = 1.9
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 60 IRTHILEDLIEEVNRIIVLAKAH 82
+ THI+ED+ N++ VL K
Sbjct: 184 LSTHIVEDVESLCNQVAVLNKGK 206
>gnl|CDD|144351 pfam00718, Polyoma_coat, Polyomavirus coat protein.
Length = 296
Score = 26.6 bits (59), Expect = 1.9
Identities = 11/24 (45%), Positives = 12/24 (50%), Gaps = 6/24 (25%)
Query: 11 EIEANYEFLSAVNPRMGIEPESNY 34
EIEA +L NPRMG Y
Sbjct: 21 EIEA---YL---NPRMGQPDPEQY 38
>gnl|CDD|30058 cd01315, L-HYD_ALN, L-Hydantoinases (L-HYDs) and Allantoinase
(ALN); L-Hydantoinases are a member of the
dihydropyrimidinase family, which catalyzes the
reversible hydrolytic ring opening of dihydropyrimidines
and hydantoins (five-membered cyclic diamides used in
biotechnology). But L-HYDs differ by having an L-enantio
specificity and by lacking activity on possible natural
substrates such as dihydropyrimidines. Allantoinase
catalyzes the hydrolytic cleavage of the five-member
ring of allantoin (5-ureidohydantoin) to form allantoic
acid..
Length = 447
Score = 26.4 bits (58), Expect = 2.7
Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 5/47 (10%)
Query: 69 IEEVNRIIVLAKAHKRRLELKIFEDNEVWRLLDEARED-----CEGC 110
+E + RI++LAK RL + E L+ EAR + E C
Sbjct: 216 VEAIQRILLLAKETGCRLHIVHLSSAEAVPLIREARAEGVDVTVETC 262
>gnl|CDD|72989 cd03230, ABC_DR_subfamily_A, This family of ATP-binding proteins
belongs to a multisubunit transporter involved in drug
resistance (BcrA and DrrA), nodulation, lipid transport,
and lantibiotic immunity. In bacteria and archaea,
these transporters usually include an ATP-binding
protein and one or two integral membrane proteins.
Eukaryote systems of the ABCA subfamily display ABC
domains that are quite similar to this family. The
ATP-binding domain shows the highest similarity between
all members of the ABC transporter family. ABC
transporters are a subset of nucleotide hydrolases that
contain a signature motif, Q-loop, and H-loop/switch
region, in addition to, the Walker A motif/P-loop and
Walker B motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins..
Length = 173
Score = 26.1 bits (58), Expect = 3.0
Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 10/60 (16%)
Query: 24 PRMGIEPESNYEV-EVIEKLERALKTSKKLIHFRDRTIRTHILEDLIEEVNRIIVLAKAH 82
P G++PES E E++ +L++ KT + +HILE+ +R+ +L
Sbjct: 122 PTSGLDPESRREFWELLRELKKEGKTI---------LLSSHILEEAERLCDRVAILNNGR 172
>gnl|CDD|114218 pfam05482, Serendipity_A, Serendipity locus alpha protein (SRY-A).
The Drosophila serendipity alpha (sry alpha) gene is
specifically transcribed at the blastoderm stage, from
nuclear cycle 11 to the onset of gastrulation, in all
somatic nuclei. SRY-A is required for the
cellularisation of the embryo and is involved in the
localisation of the actin filaments just prior to and
during plasma membrane invagination.
Length = 549
Score = 25.6 bits (56), Expect = 4.5
Identities = 18/71 (25%), Positives = 25/71 (35%), Gaps = 11/71 (15%)
Query: 18 FLSAVNPRMGIEPESNYEVEVI-----------EKLERALKTSKKLIHFRDRTIRTHILE 66
L V PR E N +VE I +LER + L R H L+
Sbjct: 46 HLPEVAPRWEAEGGINIDVETIFLCLTQVVTCITQLERTINIEGTLAAGATPMTRLHFLD 105
Query: 67 DLIEEVNRIIV 77
+ + R+ V
Sbjct: 106 RIDWCLRRLQV 116
>gnl|CDD|72984 cd03225, ABC_cobalt_CbiO_domain1, Domain I of the ABC component of
a cobalt transport family found in bacteria, archaea,
and eukaryota. The transition metal cobalt is an
essential component of many enzymes and must be
transported into cells in appropriate amounts when
needed. This ABC transport system of the CbiMNQO family
is involved in cobalt transport in association with the
cobalamin (vitamin B12) biosynthetic pathways. Most of
cobalt (Cbi) transport systems possess a separate CbiN
component, the cobalt-binding periplasmic protein, and
they are encoded by the conserved gene cluster cbiMNQO.
Both the CbiM and CbiQ proteins are integral cytoplasmic
membrane proteins, and the CbiO protein has the linker
peptide and the Walker A and B motifs commonly found in
the ATPase components of the ABC-type transport
systems..
Length = 211
Score = 25.5 bits (56), Expect = 4.8
Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 8/66 (12%)
Query: 21 AVNPRMGI--EPESNYEVEVIEKLERALKTSKKLIHFRDRTI--RTHILEDLIEEVNRII 76
A++P + + EP + + +L LK K +TI TH L+ L+E +R+I
Sbjct: 150 AMDPDILLLDEPTAGLDPAGRRELLELLKKLKA----EGKTIIIVTHDLDLLLELADRVI 205
Query: 77 VLAKAH 82
VL
Sbjct: 206 VLEDGK 211
>gnl|CDD|36487 KOG1273, KOG1273, KOG1273, WD40 repeat protein [General function
prediction only].
Length = 405
Score = 25.3 bits (55), Expect = 5.3
Identities = 11/36 (30%), Positives = 22/36 (61%)
Query: 36 VEVIEKLERALKTSKKLIHFRDRTIRTHILEDLIEE 71
V+ I+++ + K +I+ DR IRT+ + D+ +E
Sbjct: 196 VQAIKQIIVSRKGRFLIINTSDRVIRTYEISDIDDE 231
>gnl|CDD|31761 COG1573, COG1573, Uracil-DNA glycosylase [DNA replication,
recombination, and repair].
Length = 202
Score = 25.0 bits (54), Expect = 6.2
Identities = 10/27 (37%), Positives = 13/27 (48%)
Query: 95 EVWRLLDEAREDCEGCENCSEHPDQEH 121
E LL+E RE+ E C C D+
Sbjct: 5 EAAELLEELREEIEACRRCPLLKDRTP 31
>gnl|CDD|37251 KOG2040, KOG2040, KOG2040, Glycine dehydrogenase (decarboxylating)
[Amino acid transport and metabolism].
Length = 1001
Score = 24.9 bits (54), Expect = 6.2
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 77 VLAKAHKRRLELKIFEDNEVWRLLDE 102
VL +A KR++ L++ ED + LDE
Sbjct: 438 VLDRAAKRQINLRLVEDGTIGVSLDE 463
>gnl|CDD|63887 cd03556, L-fucose_isomerase, L-fucose isomerase (FucIase); FucIase
converts L-fucose, an aldohexose, to its ketose form,
which prepares it for aldol cleavage (similar to the
isomerization of glucose during glycolysis). L-fucose
(or 6-deoxy-L-galactose) is found in blood group
determinants as well as in various oligo- and
polysaccharides, and glycosides in mammals, bacteria and
plants..
Length = 584
Score = 25.0 bits (54), Expect = 6.2
Identities = 12/41 (29%), Positives = 25/41 (60%)
Query: 84 RRLELKIFEDNEVWRLLDEAREDCEGCENCSEHPDQEHKED 124
RR++ +I++ E + L +E+C+ E+ +E DQ+ +E
Sbjct: 209 RRMDEEIYDPEEYEKALAWTKENCKEGEDENEKNDQKKREQ 249
>gnl|CDD|34199 COG4555, NatA, ABC-type Na+ transport system, ATPase component
[Energy production and conversion / Inorganic ion
transport and metabolism].
Length = 245
Score = 24.9 bits (54), Expect = 6.8
Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 8/58 (13%)
Query: 29 EPESNYEVEVIEKLE---RALKTSKKLIHFRDRTIRTHILEDLIEEVNRIIVLAKAHK 83
EP S ++ K + LK + + F +HI++++ +R+IVL K
Sbjct: 159 EPTSGLDIRTRRKFHDFIKQLKNEGRAVIFS-----SHIMQEVEALCDRVIVLHKGEV 211
>gnl|CDD|36198 KOG0980, KOG0980, KOG0980, Actin-binding protein
SLA2/Huntingtin-interacting protein Hip1 [Cytoskeleton].
Length = 980
Score = 25.0 bits (54), Expect = 7.1
Identities = 16/44 (36%), Positives = 19/44 (43%), Gaps = 3/44 (6%)
Query: 65 LEDLIEEVNRIIVLAKAHKRRLELKIFEDNEVWRLLDEAREDCE 108
LE+L EE R I + LE E E R E RE+ E
Sbjct: 349 LENLKEEARRRIEQYENQLLALEG---ELQEQQREAQENREEQE 389
>gnl|CDD|31326 COG1131, CcmA, ABC-type multidrug transport system, ATPase
component [Defense mechanisms].
Length = 293
Score = 24.5 bits (53), Expect = 8.2
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 9/59 (15%)
Query: 23 NPRMGIEPESNYEV-EVIEKLERALKTSKKLIHFRDRTIRTHILEDLIEEVNRIIVLAK 80
P G++PES E+ E++ +L + + L THILE+ E +R+I+L
Sbjct: 162 EPTSGLDPESRREIWELLRELAKEGGVTILLS--------THILEEAEELCDRVIILND 212
>gnl|CDD|33811 COG4053, COG4053, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 244
Score = 24.6 bits (53), Expect = 8.8
Identities = 26/100 (26%), Positives = 39/100 (39%), Gaps = 29/100 (29%)
Query: 37 EVIEKLERALKT--SKKLIHF-------RDRTIRTHILEDLIEEVNRIIVLAKAHKRRLE 87
++ E +E+ +K SK I D I + + E+L+E+VN+ I
Sbjct: 23 KLNELVEKEIKKLLSKLGIKATLSNITGDDIVITSFVEENLLEKVNKAIF---------- 72
Query: 88 LKIFEDNEVWRLLDEAREDCEGCENCSEHPDQEHKEDYYA 127
EV R E +D G SE PD + YA
Sbjct: 73 -------EVLRKYAEGFDDLRG---ISEDPDGAGEGLSYA 102
>gnl|CDD|73385 cd04723, HisA_HisF, Phosphoribosylformimino-5-aminoimidazole
carboxamide ribonucleotide (ProFAR) isomerase (HisA) and
the cyclase subunit of imidazoleglycerol phosphate
synthase (HisF). The ProFAR isomerase catalyzes the
fourth step in histidine biosynthesis, an isomerisation
of the aminoaldose moiety of ProFAR to the aminoketose
of PRFAR
(N-(5'-phospho-D-1'-ribulosylformimino)-5-amino-1-(5''-
phospho-ribosyl)-4-imidazolecarboxamide). In bacteria
and archaea, ProFAR isomerase is encoded by the HisA
gene. The Imidazole glycerol phosphate synthase (IGPS)
catalyzes the fifth step of histidine biosynthesis, the
formation of the imidazole ring. IGPS converts
N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4-
carboxamide ribonucleotide (PRFAR) to imidazole glycerol
phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide)
ribonucleotide (AICAR). This conversion involves two
tightly coupled reactions in distinct active sites of
IGPS. The two catalytic domains can be fused, like in
fungi and plants, or peformed by a heterodimer
(HisH-glutaminase and HisF-cyclase), like in bacteria..
Length = 233
Score = 24.4 bits (53), Expect = 9.8
Identities = 10/53 (18%), Positives = 19/53 (35%), Gaps = 1/53 (1%)
Query: 59 TIRTHILEDLIEEVNRI-IVLAKAHKRRLELKIFEDNEVWRLLDEAREDCEGC 110
T+ + ED + + +VL+ + LK + LL + E
Sbjct: 110 TLPSDDDEDRLAALGEQRLVLSLDFRGGQLLKPTDFIGPEELLRRLAKWPEEL 162
>gnl|CDD|143508 cd06841, PLPDE_III_MccE_like, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme MccE. This subfamily is composed
of uncharacterized proteins with similarity to
Escherichia coli MccE, a hypothetical protein that is
homologous to eukaryotic ornithine decarboxylase (ODC)
and diaminopimelate decarboxylase (DapDC). ODC and DapDC
are fold type III PLP-dependent enzymes that contain an
N-terminal PLP-binding TIM-barrel domain and a
C-terminal beta-sandwich domain, similar to bacterial
alanine racemases. ODC participates in the formation of
putrescine by catalyzing the decarboxylation of
ornithine, the first step in polyamine biosynthesis.
DapDC participates in the last step of lysine
biosynthesis, the conversion of
meso-2,6-diaminoheptanedioate to L-lysine. Most members
of this subfamily share the same domain architecture as
ODC and DapDC. A few members, including Escherichia coli
MccE, contain an additional acetyltransferase domain at
the C-terminus.
Length = 379
Score = 24.1 bits (53), Expect = 9.9
Identities = 11/45 (24%), Positives = 22/45 (48%), Gaps = 2/45 (4%)
Query: 46 LKTSKKLIHFRDRTIRTHILEDLIEEVNRIIVLAKAHKRRLELKI 90
K+ ++L + +I D +E+ RI+ +AK R ++ I
Sbjct: 87 YKSKEELEKALEEGALINI--DSFDELERILEIAKELGRVAKVGI 129
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
0.317 0.135 0.385
Gapped
Lambda K H
0.267 0.0594 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,641,620
Number of extensions: 81325
Number of successful extensions: 343
Number of sequences better than 10.0: 1
Number of HSP's gapped: 342
Number of HSP's successfully gapped: 63
Length of query: 130
Length of database: 6,263,737
Length adjustment: 83
Effective length of query: 47
Effective length of database: 4,470,190
Effective search space: 210098930
Effective search space used: 210098930
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.1 bits)