RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780138|ref|YP_003064551.1| ABC transporter [Candidatus
Liberibacter asiaticus str. psy62]
(373 letters)
>gnl|CDD|31110 COG0767, Ttg2B, ABC-type transport system involved in resistance to
organic solvents, permease component [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 267
Score = 220 bits (562), Expect = 6e-58
Identities = 102/260 (39%), Positives = 148/260 (56%), Gaps = 7/260 (2%)
Query: 114 IGKKIVKFINDSCSQAHILGLVISNTGEFCASSYKFKGFLLSLIRQMYYVGVSGVPVVIL 173
+GK ++K + LG G ++ L+RQ+Y+VGV +P+V L
Sbjct: 15 LGKALLKTLRS-------LGRAFLFLGNALRGLFREPFRPRELVRQLYFVGVGSLPIVAL 67
Query: 174 ISFVTGAVIAQQGAFQLSQFGAEIFSIDLMSILQLREIGVLLTAVMIAGRSGSAIVAEIG 233
S GAV+A QG QL FGAE FS L+++ LRE+G +LTA+++AGR GSAI AEIG
Sbjct: 68 TSLFVGAVLALQGYTQLRDFGAEDFSGFLVALSLLRELGPVLTALVVAGRVGSAITAEIG 127
Query: 234 SMKINEEIDAIRTMGLDFVRILISPRIWALIISLPLLTILANFSAIIGASIVIWKYYDIP 293
+M+I EEIDA+ MG+D + L++PR+ A +I LPLLT LA+ + I+G +V I
Sbjct: 128 AMRITEEIDALEVMGIDPISRLVAPRVLAGVIVLPLLTALADAAGILGGYLVAVFLLGIS 187
Query: 294 FAVFFSRFHSTATLANIFTGLIKAPFMACAIGIVAMKEGFAVGVHSNSLGKKVTTCVVQS 353
F SR + ++ GLIKAP IG++ G+ VG +G+ T VV S
Sbjct: 188 PGAFLSRLQTFVGPEDVLIGLIKAPVFGVIIGLIGCYYGYTVGGGPEGVGRATTRSVVTS 247
Query: 354 ISIVIIIDSLFAIFYFAIGI 373
I +VI++D + F +GI
Sbjct: 248 ILVVIVLDFVLTALMFGVGI 267
>gnl|CDD|145511 pfam02405, DUF140, Domain of unknown function DUF140. This domain
has no known function nor do any of the proteins that
possess it. The aligned region is approximately 150
amino acids long.
Length = 215
Score = 219 bits (561), Expect = 9e-58
Identities = 86/213 (40%), Positives = 131/213 (61%)
Query: 156 LIRQMYYVGVSGVPVVILISFVTGAVIAQQGAFQLSQFGAEIFSIDLMSILQLREIGVLL 215
++RQ+Y+VGV +P+V L +F GAV+A QGA+QL QFGAE F L+++ +RE+G +L
Sbjct: 3 ILRQIYFVGVGSLPIVALTAFFIGAVLALQGAYQLRQFGAESFVGALVALSLVRELGPVL 62
Query: 216 TAVMIAGRSGSAIVAEIGSMKINEEIDAIRTMGLDFVRILISPRIWALIISLPLLTILAN 275
TA+++AGR GSAI AE+G+M++ EEIDA+ MG+D +R L+ PR+ A +I+LPLLTI+A+
Sbjct: 63 TALLVAGRVGSAITAELGTMRVTEEIDALEVMGIDPIRYLVLPRVLAGVIALPLLTIIAD 122
Query: 276 FSAIIGASIVIWKYYDIPFAVFFSRFHSTATLANIFTGLIKAPFMACAIGIVAMKEGFAV 335
I+G +V I F F S ++ GLIKA I ++ G
Sbjct: 123 LVGILGGYLVAVVVLGISPGAFLHSFQSFVDPTDVLVGLIKAVVFGLIIALIGCYYGLTA 182
Query: 336 GVHSNSLGKKVTTCVVQSISIVIIIDSLFAIFY 368
+ +G+ T VV SI +I++D + +
Sbjct: 183 KGGAEGVGRATTRAVVTSIVAIIVLDFVLTALF 215
>gnl|CDD|132914 cd07043, STAS_anti-anti-sigma_factors, Sulphate Transporter and
Anti-Sigma factor antagonist) domain of anti-anti-sigma
factors, key regulators of anti-sigma factors by
phosphorylation. Anti-anti-sigma factors play an
important role in the regulation of several sigma
factors and their corresponding anti-sigma factors.
Upon dephosphorylation they bind the anti-sigma factor
and induce the release of the sigma factor from the
anti-sigma factor. In a feedback mechanism the
anti-anti-sigma factor can be inactivated via
phosphorylation by the anti-sigma factor. Well studied
examples from Bacillus subtilis are SpoIIAA (regulating
sigmaF and sigmaC which play an important role in
sporulation) and RsbV (regulating sigmaB involved in
the general stress response). The STAS domain is also
found in the C- terminal region of sulphate
transporters and stressosomes.
Length = 99
Score = 32.1 bits (74), Expect = 0.25
Identities = 17/88 (19%), Positives = 38/88 (43%), Gaps = 5/88 (5%)
Query: 3 ENGITVFRFAGNWKSPEISEIADDVVMAINKSIQSDSAIVDLSAITEIDTIGAELIMYF- 61
G+ V R +G + E+ + + + + + ++DLS +T ID+ G +++
Sbjct: 6 RGGVLVVRLSGELDAATAPELREALEELLAEGPRR--LVLDLSGVTFIDSSGLGVLLGAY 63
Query: 62 --MEKYHGKIKLQGVSTHIEQLFSLISF 87
G++ L VS + ++ L
Sbjct: 64 KRARAAGGRLVLVNVSPAVRRVLELTGL 91
>gnl|CDD|37454 KOG2243, KOG2243, KOG2243, Ca2+ release channel (ryanodine receptor)
[Signal transduction mechanisms].
Length = 5019
Score = 29.7 bits (66), Expect = 1.3
Identities = 16/56 (28%), Positives = 32/56 (57%), Gaps = 7/56 (12%)
Query: 55 AELIMYFMEKYHGKIKLQGVSTHIEQLFSLISFTHRKKIKNQKPQ-----RSFFYN 105
AE ++ + E + G+I++ G + IE+++ IS + R + +KPQ R F ++
Sbjct: 4153 AESVLNYFEPFLGRIEIMGGAKKIERVYFEISESSRTQW--EKPQVKESKRQFIFD 4206
>gnl|CDD|145083 pfam01740, STAS, STAS domain. The STAS (after Sulphate
Transporter and AntiSigma factor antagonist) domain is
found in the C terminal region of Sulphate transporters
and bacterial antisigma factor antagonists. It has been
suggested that this domain may have a general NTP
binding function.
Length = 106
Score = 28.3 bits (64), Expect = 3.8
Identities = 17/90 (18%), Positives = 34/90 (37%), Gaps = 10/90 (11%)
Query: 4 NGITVFRFAGNWKSPEISEIADDVVMAINKSIQSDSA---IVDLSAITEIDTIGAELIMY 60
GI + R G P A+ + ++I+ I+DLS + ID+ G ++
Sbjct: 8 PGILILRLDG----PLDFANAEAFRERLLRAIEEGEIRHVILDLSGVPFIDSSGLGALLE 63
Query: 61 FMEKYH---GKIKLQGVSTHIEQLFSLISF 87
++ ++ L G S + +
Sbjct: 64 LYKELRRRGVELVLVGPSPEVRRTLEKTGL 93
>gnl|CDD|30407 COG0058, GlgP, Glucan phosphorylase [Carbohydrate transport and
metabolism].
Length = 750
Score = 27.9 bits (62), Expect = 4.4
Identities = 34/157 (21%), Positives = 52/157 (33%), Gaps = 30/157 (19%)
Query: 4 NGITVFRFAGNWKSPEISEIADDVVMAINKSIQSDSAIVDLSAITEIDTIGAELIMYFME 63
NGIT R W +P +AD + I +D I+D D ELI
Sbjct: 410 NGITPRR----WLAPANPGLADLLDEKIGDEWLNDLDILDELLWFADDKAFRELIAEI-- 463
Query: 64 KYHGKIKL-------QGVSTHIEQLF------------SLISFTH----RKKIKNQKPQR 100
K K +L G+ LF L++ + +K R
Sbjct: 464 KRENKKRLAEEIADRTGIEVDPNALFDGQARRIHEYKRQLLNLLDIERLYRILKEDWVPR 523
Query: 101 SFFYNSFK-NLHYHIGKKIVKFINDSCSQAHILGLVI 136
+ K + + K+I+K IND + V+
Sbjct: 524 VQIIFAGKAHPADYAAKEIIKLINDVADVINNKLKVV 560
>gnl|CDD|132915 cd06586, TPP_enzyme_PYR, Pyrimidine (PYR) binding domain of
thiamine pyrophosphate (TPP)-dependent enzymes.
Thiamine pyrophosphate (TPP) family, pyrimidine (PYR)
binding domain; found in many key metabolic enzymes
which use TPP (also known as thiamine diphosphate) as a
cofactor. TPP binds in the cleft formed by a PYR domain
and a PP domain. The PYR domain, binds the
aminopyrimidine ring of TPP, the PP domain binds the
diphosphate residue. A polar interaction between the
conserved glutamate of the PYR domain and the N1' of the
TPP aminopyrimidine ring is shared by most TPP-dependent
enzymes, and participates in the activation of TPP. The
PYR and PP domains have a common fold, but do not share
strong sequence conservation. The PP domain is not
included in this group. Most TPP-dependent enzymes have
the PYR and PP domains on the same subunit although
these domains can be alternatively arranged in the
primary structure. In the case of 2-oxoisovalerate
dehydrogenase (2OXO), sulfopyruvate decarboxylase
(ComDE), and the E1 component of human pyruvate
dehydrogenase complex (E1- PDHc) the PYR and PP domains
appear on different subunits. TPP-dependent enzymes are
multisubunit proteins, the smallest catalytic unit being
a dimer-of-active sites. For many of these enzymes the
active sites lie between PP and PYR domains on different
subunits. However, for the homodimeric enzymes
1-deoxy-D-xylulose 5-phosphate synthase (DXS) and
Desulfovibrio africanus pyruvate:ferredoxin
oxidoreductase (PFOR), each active site lies at the
interface of the PYR and PP domains from the same
subunit.
Length = 154
Score = 27.3 bits (61), Expect = 6.8
Identities = 12/46 (26%), Positives = 16/46 (34%), Gaps = 3/46 (6%)
Query: 152 FLLSLIRQMYYVGVSGVPVVILI---SFVTGAVIAQQGAFQLSQFG 194
LL+ I + +PVV LI A Q F L +
Sbjct: 70 GLLNAINGLADAAAEHLPVVFLIGARGISAQAKQTFQSMFDLGMYR 115
>gnl|CDD|99996 cd04300, GT1_Glycogen_Phosphorylase, This is a family of
oligosaccharide phosphorylases. It includes yeast and
mammalian glycogen phosphorylases, plant starch/glucan
phosphorylase, as well as the maltodextrin
phosphorylases of bacteria. The members of this family
catalyze the breakdown of oligosaccharides into
glucose-1-phosphate units. They are important allosteric
enzymes in carbohydrate metabolism. The allosteric
control mechanisms of yeast and mammalian members of
this family are different from that of bacterial
members. The members of this family belong to the GT-B
structural superfamily of glycoslytransferases, which
have characteristic N- and C-terminal domains each
containing a typical Rossmann fold. The two domains have
high structural homology despite minimal sequence
homology. The large cleft that separates the two
domains includes the catalytic center and permits a high
degree of flexibility..
Length = 797
Score = 27.0 bits (61), Expect = 8.6
Identities = 6/13 (46%), Positives = 9/13 (69%)
Query: 112 YHIGKKIVKFIND 124
Y++ K I+K IN
Sbjct: 582 YYMAKLIIKLINA 594
>gnl|CDD|132839 cd07200, cPLA2_Grp-IVA, Group IVA cytosolic phospholipase A2;
catalytic domain; Ca-dependent. Group IVA cPLA2, an 85
kDa protein, consists of two domains: the regulatory C2
domain and the alpha/beta hydrolase PLA2 domain. Group
IVA cPLA2 is also referred to as cPLA2-alpha. The
catalytic domain of cytosolic phospholipase A2 (cPLA2;
EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of
phospholipids to release arachidonic acid. At the active
site, cPLA2 contains a serine nucleophile through which
the catalytic mechanism is initiated. The active site is
partially covered by a solvent-accessible flexible lid.
cPLA2 displays interfacial activation as it exists in
both "closed lid" and "open lid" forms. Movement of the
cPLA2 lid possibly exposes a greater hydrophobic surface
and the active site. cPLA2 belongs to the alpha-beta
hydrolase family which is identified by a characteristic
nucleophile elbow with a consensus sequence of
Sm-X-Nu-Sm (Sm = small residue, X = any residue and Nu =
nucleophile). Calcium is required for cPLA2 to bind with
membranes or phospholipids. A calcium-dependent
phospholipid binding domain resides in the N-terminal
region of cPLA2; it is homologous to the C2 domain
superfamily which is not included in this hierarchy.
Includes PLA2G4A from chicken, human, and frog.
Length = 505
Score = 27.0 bits (60), Expect = 9.3
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 208 LREIGVLLTAVMIAGRSGSA 227
L + GVL A +AG SGS
Sbjct: 68 LYDSGVLDCATYVAGLSGST 87
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
0.327 0.140 0.401
Gapped
Lambda K H
0.267 0.0719 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,428,234
Number of extensions: 243813
Number of successful extensions: 950
Number of sequences better than 10.0: 1
Number of HSP's gapped: 944
Number of HSP's successfully gapped: 73
Length of query: 373
Length of database: 6,263,737
Length adjustment: 95
Effective length of query: 278
Effective length of database: 4,210,882
Effective search space: 1170625196
Effective search space used: 1170625196
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 58 (26.1 bits)