RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780202|ref|YP_003064615.1| hypothetical protein
CLIBASIA_00435 [Candidatus Liberibacter asiaticus str. psy62]
(211 letters)
>gnl|CDD|30947 COG0602, NrdG, Organic radical activating enzymes
[Posttranslational modification, protein turnover,
chaperones].
Length = 212
Score = 138 bits (349), Expect = 1e-33
Identities = 74/227 (32%), Positives = 99/227 (43%), Gaps = 31/227 (13%)
Query: 1 MKLYSIKEIFLTLQGEGGHAGRVAVFCRFSGCNLWSGREQDRLSAQCRFCDTD-FVGIQG 59
Y I EIF ++QGEG + GR +VF RF+GCNL C CDT
Sbjct: 1 QMKYRIVEIFDSIQGEGKNIGRPSVFVRFAGCNLR-----------CPGCDTKYTWDFNY 49
Query: 60 TKGGRYNVDQLADLIEEQWITGEKEGRYCVLTGGEPLLQVDV-PLIQALNKRGFEIAVET 118
K G AD I + + R LTGGEPLLQ ++ L++ L + GF IA+ET
Sbjct: 50 GKPGT---PMSADEILADIKSLGYKARGVSLTGGEPLLQPNLLELLELLKRLGFRIALET 106
Query: 119 NGTIEPP--QGIDWICVSPKAG------CDLKIKGGQELKLVFPQVNVSPEN------YI 164
NGTI ID + VSPK+ D + G +K V+ +V + +
Sbjct: 107 NGTIPVWTGYTIDELTVSPKSDKSLLSAIDEVLVDGDFIKFVYAKVLADRGSANQRVLRL 166
Query: 165 GFDFERFSLQPMDGPFLEENTNLAISYCFQNPKWRLSVQTHKFIGIR 211
+ L P L++ L RLS QTHK +GI
Sbjct: 167 AESLKPVVLVPQPISRLDKLVKLCARLAI-RLNVRLSPQTHKLLGIN 212
>gnl|CDD|146602 pfam04055, Radical_SAM, Radical SAM superfamily. Radical SAM
proteins catalyse diverse reactions, including unusual
methylations, isomerisation, sulphur insertion, ring
formation, anaerobic oxidation and protein radical
formation.
Length = 165
Score = 48.7 bits (116), Expect = 1e-06
Identities = 33/123 (26%), Positives = 55/123 (44%), Gaps = 28/123 (22%)
Query: 31 GCNLWSGREQDRLSAQCRFCDTDFVGIQGTKGGRYNVDQLADLIEEQWITGEKEGRYCVL 90
GCNL +C +C + +G KG + +++ + +E G +L
Sbjct: 6 GCNL-----------RCTYCAFPSIRARG-KGRELSPEEILEEAKELARLG---VEVVIL 50
Query: 91 TGGEPLLQVDVP-----LIQALNKRGFEIAVETNGTIEPPQ--------GIDWICVSPKA 137
TGGEPLL D+ L++ G I +ETNGT+ + G+D + +S ++
Sbjct: 51 TGGEPLLLPDLVELLERLLKLEELEGIRITLETNGTLLDEELLEELKEAGLDRVSISLQS 110
Query: 138 GCD 140
G D
Sbjct: 111 GDD 113
>gnl|CDD|31373 COG1180, PflA, Pyruvate-formate lyase-activating enzyme
[Posttranslational modification, protein turnover,
chaperones].
Length = 260
Score = 41.4 bits (97), Expect = 2e-04
Identities = 26/107 (24%), Positives = 44/107 (41%), Gaps = 20/107 (18%)
Query: 22 RVAVFCRFSGCNLWSGREQDRLSAQCRFCDT-DFVGIQGTKGGRYNVDQLADLIEEQWIT 80
R++VF GCNL +C +C + G ++
Sbjct: 37 RLSVF--LQGCNL-----------RCPYCQNPEISQRGREVSGEEVSPEVLVDKAFY--- 80
Query: 81 GEKEGRYCVLTGGEPLLQVD--VPLIQALNKRGFEIAVETNGTIEPP 125
+ G +GGEP LQ + + L++A +RG +A++TNG + P
Sbjct: 81 -SESGGGVTFSGGEPTLQAEFALDLLRAAKERGLHVALDTNGFLPPE 126
>gnl|CDD|100105 cd01335, Radical_SAM, Radical SAM superfamily. Enzymes of this
family generate radicals by combining a 4Fe-4S cluster
and S-adenosylmethionine (SAM) in close proximity. They
are characterized by a conserved CxxxCxxC motif, which
coordinates the conserved iron-sulfur cluster.
Mechanistically, they share the transfer of a single
electron from the iron-sulfur cluster to SAM, which
leads to its reductive cleavage to methionine and a
5'-deoxyadenosyl radical, which, in turn, abstracts a
hydrogen from the appropriately positioned carbon atom.
Depending on the enzyme, SAM is consumed during this
process or it is restored and reused. Radical SAM
enzymes catalyze steps in metabolism, DNA repair, the
biosynthesis of vitamins and coenzymes, and the
biosynthesis of many antibiotics. Examples are biotin
synthase (BioB), lipoyl synthase (LipA), pyruvate
formate-lyase (PFL), coproporphyrinogen oxidase (HemN),
lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide
reductase (ARR), and MoaA, an enzyme of the
biosynthesis of molybdopterin..
Length = 204
Score = 39.6 bits (92), Expect = 6e-04
Identities = 33/117 (28%), Positives = 43/117 (36%), Gaps = 30/117 (25%)
Query: 31 GCNLWSGREQDRLSAQCRFCDTDFVGIQGTKGGRYNVDQLADLIEEQWITGEKEG--RYC 88
GCNL C FC GR + KE
Sbjct: 6 GCNL-----------NCGFC------SNPASKGRGPESPPEIEEILDIVLEAKERGVEVV 48
Query: 89 VLTGGEPLLQVDVP--LIQAL-NKRGFEIAVETNGTIE--------PPQGIDWICVS 134
+LTGGEPLL ++ L + GFEI++ETNGT+ G+D + VS
Sbjct: 49 ILTGGEPLLYPELAELLRRLKKELPGFEISIETNGTLLTEELLKELKELGLDGVGVS 105
>gnl|CDD|32721 COG2896, MoaA, Molybdenum cofactor biosynthesis enzyme [Coenzyme
metabolism].
Length = 322
Score = 37.9 bits (88), Expect = 0.002
Identities = 23/83 (27%), Positives = 43/83 (51%), Gaps = 5/83 (6%)
Query: 41 DRLSAQCRFCDTDFVGIQGTKGGRYNVDQLADLIEEQWITGEKEGRYCVLTGGEPLLQVD 100
DR + +C +C + K +++++ L+ G ++ R LTGGEPLL+ D
Sbjct: 19 DRCNFRCTYCMPEGPLAFLPKEELLSLEEIRRLVRAFAELGVEKVR---LTGGEPLLRKD 75
Query: 101 VP-LIQALNKRG-FEIAVETNGT 121
+ +I L + G ++++ TNG
Sbjct: 76 LDEIIARLARLGIRDLSLTTNGV 98
>gnl|CDD|31698 COG1509, KamA, Lysine 2,3-aminomutase [Amino acid transport and
metabolism].
Length = 369
Score = 31.8 bits (72), Expect = 0.15
Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 6/58 (10%)
Query: 41 DRLSAQCRFC-DTDFVGIQGTKGGRYNVDQLADLIEEQWITGEKEGRYCVLTGGEPLL 97
+ CR+C FVG + D+ D +I E R +L+GG+PL
Sbjct: 119 GVCAVYCRYCFRRRFVGQDNQGFNKEEWDKALD-----YIAAHPEIREVLLSGGDPLS 171
>gnl|CDD|30881 COG0535, COG0535, Predicted Fe-S oxidoreductases [General function
prediction only].
Length = 347
Score = 30.0 bits (66), Expect = 0.54
Identities = 27/103 (26%), Positives = 47/103 (45%), Gaps = 15/103 (14%)
Query: 42 RLSAQCRFCDTDFVGIQGTKGGRYNVDQLADLIEEQWITGEKEGRYCVLTGGEPLLQVDV 101
R + C+ C + G + ++ +I+E GE + TGGEPLL+ D+
Sbjct: 28 RCNLACKHC---YAEAGKKLPGELSTEEDLRVIDELAELGEIP--VVIFTGGEPLLRPDL 82
Query: 102 PLI--QALNKRGFEIAVETNGTIEPPQ--------GIDWICVS 134
I A K G +++ TNGT+ + G+D++ +S
Sbjct: 83 LEIVEYARKKGGIRVSLSTNGTLLTEEVLEKLKEAGLDYVSIS 125
>gnl|CDD|31645 COG1456, CdhE, CO dehydrogenase/acetyl-CoA synthase gamma subunit
(corrinoid Fe-S protein) [Energy production and
conversion].
Length = 467
Score = 29.1 bits (65), Expect = 0.80
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 51 DTDFVGIQ-GTKGGRYNVDQLADLIEEQWITGEKEGRYCVLTGGEPLLQVDV 101
DT + + GG+ +++ DLIEE I + R V+ G LQ D+
Sbjct: 386 DTGGLAVDVSVAGGQLTGEKVKDLIEETGIEDKVNHRVLVIPGLAARLQGDI 437
>gnl|CDD|39417 KOG4216, KOG4216, KOG4216, Steroid hormone nuclear receptor
[Transcription].
Length = 479
Score = 29.2 bits (65), Expect = 0.83
Identities = 15/63 (23%), Positives = 26/63 (41%)
Query: 87 YCVLTGGEPLLQVDVPLIQALNKRGFEIAVETNGTIEPPQGIDWICVSPKAGCDLKIKGG 146
YC T GE V + + L + + +ET +E I W + + + KG
Sbjct: 221 YCSFTNGETSPTVSMAELDHLAQNIIKSHLETQYLLEELHQITWQTFDQEEIENYQNKGR 280
Query: 147 QEL 149
+E+
Sbjct: 281 EEM 283
>gnl|CDD|37025 KOG1814, KOG1814, KOG1814, Predicted E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 445
Score = 28.5 bits (63), Expect = 1.4
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 25 VFCRFSGCNLWSGREQDRLSAQCRFCDTDF 54
V+C + C L ++ R A C C+ F
Sbjct: 274 VYCPRACCQLPVKQDPGRALAICSKCNFAF 303
>gnl|CDD|176115 cd08423, PBP2_LTTR_like_6, The C-terminal substrate binding domain
of an uncharacterized LysR-type transcriptional
regulator, contains the type 2 periplasmic binding fold.
LysR-transcriptional regulators comprise the largest
family of prokaryotic transcription factor. Homologs of
some of LTTRs with similar domain organizations are also
found in the archaea and eukaryotic organisms. The LTTRs
are composed of two functional domains joined by a
linker helix involved in oligomerization: an N-terminal
HTH (helix-turn-helix) domain, which is responsible for
the DNA-binding specificity, and a C-terminal
substrate-binding domain, which is structurally
homologous to the type 2 periplasmic binding proteins.
As also observed in the periplasmic binding proteins,
the C-terminal domain of the bacterial transcriptional
repressor undergoes a conformational change upon
substrate binding which in turn changes the DNA binding
affinity of the repressor. The genes controlled by the
LTTRs have diverse functional roles including amino acid
biosynthesis, CO2 fixation, antibiotic resistance,
degradation of aromatic compounds, nodule formation of
nitrogen-fixing bacteria, and synthesis of virulence
factors, to a name a few. This substrate-binding domain
shows significant homology to the type 2 periplasmic
binding proteins (PBP2), which are responsible for the
uptake of a variety of substrates such as phosphate,
sulfate, polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 200
Score = 28.3 bits (64), Expect = 1.7
Identities = 20/60 (33%), Positives = 24/60 (40%), Gaps = 15/60 (25%)
Query: 63 GRYNVDQLADLIEEQWITGEKEGRYCVLTGGEPLLQVDVPLIQALNKRGFE--IAVETNG 120
GR V LADL +E WI G G C L++A GF IA E +
Sbjct: 91 GREEVA-LADLADEPWIAGC-PGSPCHRW-----------LVRACRAAGFTPRIAHEADD 137
>gnl|CDD|29617 cd01570, NAPRTase_A, Nicotinate phosphoribosyltransferase
(NAPRTase), subgroup A. Nicotinate
phosphoribosyltransferase catalyses the formation of
NAMN and PPi from 5-phosphoribosy -1-pyrophosphate
(PRPP) and nicotinic acid, this is the first, and also
rate limiting, reaction in the NAD salvage synthesis.
This salvage pathway serves to recycle NAD degradation
products. This subgroup is present in bacteria and
eukaryota (except funghi)..
Length = 327
Score = 28.2 bits (63), Expect = 1.9
Identities = 19/60 (31%), Positives = 25/60 (41%), Gaps = 9/60 (15%)
Query: 67 VDQLADLIEEQWITGEKEGRYCVLTGGEPLLQVDVPLIQA-------LNKRGFEIAVETN 119
+D L I EG V+ EPLL V+ PLI+A LN F+ + T
Sbjct: 77 LDYLRGFRFTGTIYAIPEGE--VVFPNEPLLTVEGPLIEAQLLETLLLNLINFQTLIATK 134
>gnl|CDD|73175 COG1964, COG1964, Predicted Fe-S oxidoreductases [General function
prediction only].
Length = 475
Score = 27.9 bits (62), Expect = 2.3
Identities = 12/33 (36%), Positives = 21/33 (63%), Gaps = 2/33 (6%)
Query: 90 LTGGEPLLQVDVP-LIQALNKRGFE-IAVETNG 120
TGGEP L+ D+ +I+ + G++ + + TNG
Sbjct: 116 FTGGEPTLRDDLIEIIKIAREEGYDHVQLNTNG 148
>gnl|CDD|163647 cd07404, MPP_MS158, Microscilla MS158 and related proteins,
metallophosphatase domain. MS158 is an uncharacterized
Microscilla protein with a metallophosphatase domain.
Microscilla proteins MS152, and MS153 are also included
in this family. The domain present in members of this
family belongs to the metallophosphatase (MPP)
superfamily. MPPs are functionally diverse, but all
share a conserved domain with an active site consisting
of two metal ions (usually manganese, iron, or zinc)
coordinated with octahedral geometry by a cage of
histidine, aspartate, and asparagine residues. The MPP
superfamily includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and
acid sphingomyelinases (ASMases). The conserved domain
is a double beta-sheet sandwich with a di-metal active
site made up of residues located at the C-terminal side
of the sheets. This domain is thought to allow for
productive metal coordination.
Length = 166
Score = 27.3 bits (61), Expect = 3.0
Identities = 10/31 (32%), Positives = 11/31 (35%), Gaps = 1/31 (3%)
Query: 26 FCRFSGCNLWSGREQDRLSAQCRFCDTDFVG 56
+ R G LWS A R DF G
Sbjct: 68 YVRIIGTTLWSDISLFGE-AAARMRMNDFRG 97
>gnl|CDD|99911 cd05569, PTS_IIB_fructose, PTS_IIB_fructose: subunit IIB of enzyme
II (EII) of the fructose-specific
phosphoenolpyruvate:carbohydrate phosphotransferase
system (PTS). In this system, EII (also referred to as
FruAB) is a fructose-specific permease made up of two
proteins (FruA and FruB) each containing 3 domains. The
FruA protein contains two tandem nonidentical IIB
domains and a C-terminal IIC transmembrane domain. Both
IIB domains of FruA are included in this alignment. The
FruB protein (also referred to as diphosphoryl transfer
protein) contains a IIA domain, a domain of unknown
function, and an Hpr-like domain called FPr
(fructose-inducible HPr). This familiy also includes the
IIB domains of several fructose-like PTS permeases
including the Frv permease encoded by the frvABXR
operon, the Frw permease encoded by the frwACBD operon,
the Frx permease encoded by the hrsA gene, and the Fry
permease encoded by the fryABC (ypdDGH) operon. FruAB
takes up exogenous fructose, releasing the 1-phosphate
ester in to the cytoplasm in preparation for metabolism
primarily via glycolysis. The IIB domain fold includes a
central four-stranded parallel open twisted beta-sheet
flanked by alpha-helices on both sides. The seven major
PTS systems with this IIB fold include fructose,
chitobiose/lichenan, ascorbate, lactose, galactitol,
mannitol, and a sensory system with similarity to the
bacterial bgl system..
Length = 96
Score = 26.3 bits (59), Expect = 5.9
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 103 LIQALNKRGFEIAVETNGTI 122
L +A K G+EI VET G++
Sbjct: 21 LEKAAKKLGWEIKVETQGSL 40
>gnl|CDD|144342 pfam00702, Hydrolase, haloacid dehalogenase-like hydrolase. This
family are structurally different from the alpha/ beta
hydrolase family (pfam00561). This family includes
L-2-haloacid dehalogenase, epoxide hydrolases and
phosphatases. The structure of the family consists of
two domains. One is an inserted four helix bundle, which
is the least well conserved region of the alignment,
between residues 16 and 96 of (S)-2-haloacid
dehalogenase from Pseudomonas sp. CBS3. The rest of the
fold is composed of the core alpha/beta domain.
Length = 190
Score = 26.1 bits (57), Expect = 7.4
Identities = 8/26 (30%), Positives = 15/26 (57%)
Query: 101 VPLIQALNKRGFEIAVETNGTIEPPQ 126
++AL +RG ++A+ TNG +
Sbjct: 103 REALKALKERGIKVAILTNGDRANAE 128
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
0.322 0.142 0.450
Gapped
Lambda K H
0.267 0.0623 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,695,135
Number of extensions: 138523
Number of successful extensions: 277
Number of sequences better than 10.0: 1
Number of HSP's gapped: 270
Number of HSP's successfully gapped: 20
Length of query: 211
Length of database: 6,263,737
Length adjustment: 90
Effective length of query: 121
Effective length of database: 4,318,927
Effective search space: 522590167
Effective search space used: 522590167
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 (21.9 bits)
S2: 55 (25.2 bits)