RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780556|ref|YP_003064969.1| hypothetical protein
CLIBASIA_02215 [Candidatus Liberibacter asiaticus str. psy62]
(120 letters)
>gnl|CDD|36212 KOG0994, KOG0994, KOG0994, Extracellular matrix glycoprotein Laminin
subunit beta [Extracellular structures].
Length = 1758
Score = 29.7 bits (66), Expect = 0.19
Identities = 17/42 (40%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 30 ESLRMVKEAKMEVLEAHKLAKEYVEQANQRVKEAEEQSNARL 71
++L MV+EAK+ EA + A+ +EQAN + E+SN L
Sbjct: 1433 QTLSMVREAKLSASEAQQSAQRALEQAN-ASRSQMEESNREL 1473
>gnl|CDD|36831 KOG1618, KOG1618, KOG1618, Predicted phosphatase [General function
prediction only].
Length = 389
Score = 29.6 bits (66), Expect = 0.20
Identities = 19/92 (20%), Positives = 39/92 (42%), Gaps = 13/92 (14%)
Query: 28 RIESLRMVKEAKMEVLEAHKLAKEYVEQANQRVKEAEEQSNARLLKGLG------MDDLV 81
+ +L V+ + +V+++H + VE +RV + S + +G G +D+L
Sbjct: 91 ELSALLGVEVSADQVIQSHSPFRLLVEYHYKRVLVVGQGSVREVAEGYGFKNVVTVDELA 150
Query: 82 RYFMNLDSQNQAFFIDTIQNKYQDEMEELSEF 113
+YF LD F D ++ + +
Sbjct: 151 KYFPLLDP-----FTDL--SRELKTTKLARDR 175
>gnl|CDD|109977 pfam00942, CBM_3, Cellulose binding domain.
Length = 83
Score = 26.1 bits (58), Expect = 2.2
Identities = 10/25 (40%), Positives = 13/25 (52%), Gaps = 2/25 (8%)
Query: 78 DDL-VRYFMNLDS-QNQAFFIDTIQ 100
DL RY+ LD + Q F+ D Q
Sbjct: 32 SDLKFRYYYTLDGNKAQGFWCDWAQ 56
>gnl|CDD|37862 KOG2651, KOG2651, KOG2651, rRNA adenine N-6-methyltransferase [RNA
processing and modification].
Length = 476
Score = 26.1 bits (57), Expect = 2.3
Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 1/52 (1%)
Query: 69 ARLLKGLGMDDLVRYFMNLDSQNQAFFIDTIQNKYQDEMEELSEFGEKVSDY 120
R+ + + SQ A F ++ K Q E+ LSE +SD+
Sbjct: 101 TRMQGIQTPSEFLENPSQS-SQLTALFRKHVRPKKQHEIRRLSELVSSISDF 151
>gnl|CDD|31731 COG1542, COG1542, Uncharacterized conserved protein [Function
unknown].
Length = 593
Score = 25.3 bits (55), Expect = 4.1
Identities = 24/87 (27%), Positives = 40/87 (45%), Gaps = 9/87 (10%)
Query: 35 VKEAKMEVLEA-HKLAKEYVEQANQRVKEAEEQSNARLLKGLGMDDLVRYFM-NLDSQNQ 92
+ E ++ +L+A KL K++ +K E++ + +DDLV + L+S
Sbjct: 282 ILEDEIRLLKAIDKLKKKHETNPAPEIKPIEKE----IKWETKIDDLVTAALYTLESFG- 336
Query: 93 AFFIDTIQNKYQDEMEELSEFGEKVSD 119
I K D L+EFGEKV +
Sbjct: 337 --LIKREVVKNGDLTYVLTEFGEKVLE 361
>gnl|CDD|30536 COG0187, GyrB, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), B subunit [DNA replication,
recombination, and repair].
Length = 635
Score = 25.5 bits (56), Expect = 4.2
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 2 RAKTLLASTLVTTAITIIGCSLVEDNRIESLR 33
R +L + + T IT +G + +D +E LR
Sbjct: 458 RLDKILKNEEIQTIITALGTGIGKDFDLEKLR 489
>gnl|CDD|35692 KOG0471, KOG0471, KOG0471, Alpha-amylase [Carbohydrate transport
and metabolism].
Length = 545
Score = 25.4 bits (55), Expect = 4.3
Identities = 11/50 (22%), Positives = 21/50 (42%), Gaps = 7/50 (14%)
Query: 76 GMDDLVRYFMNLDSQNQAFFIDTIQNKYQDEM------EELSEFGEKVSD 119
+ + +R F L+ F ID ++ + E + + GEK+ D
Sbjct: 193 AIKEWLRDFW-LEKGVDGFRIDAVKGYAGENFKNMWPDEPVFDVGEKLQD 241
>gnl|CDD|146587 pfam04029, 2-ph_phosp, 2-phosphosulpholactate phosphatase. Thought
to catalyse 2-phosphosulpholactate = sulpholactate +
phosphate. Probable magnesium cofactor. Involved in the
second step of coenzyme M biosynthesis. Inhibited by
vanadate in Methanococcus jannaschii. Also known as the
ComB family.
Length = 231
Score = 25.2 bits (56), Expect = 4.7
Identities = 13/59 (22%), Positives = 27/59 (45%)
Query: 33 RMVKEAKMEVLEAHKLAKEYVEQANQRVKEAEEQSNARLLKGLGMDDLVRYFMNLDSQN 91
++ + E+ + + A Q N ++ S+ R LK LG++D + + LD +
Sbjct: 160 LLLGLGEEELNDEARAALALYRQENDLLELLRNSSHGRRLKALGLEDDLEFCAQLDILD 218
>gnl|CDD|145014 pfam01650, Peptidase_C13, Peptidase C13 family. Members of this
family are asparaginyl peptidases. The blood fluke
parasite Schistosoma mansoni has at least five Clan CA
cysteine peptidases in its digestive tract including
cathepsins B (2 isoforms), C, F and L. All have been
recombinantly expressed as active enzymes, albeit in
various stages of activation. In addition, a Clan CD
peptidase, termed asparaginyl endopeptidase or
'legumain' has been identified. This has formerly been
characterized as a 'haemoglobinase', but this term is
probably incorrect. Two cDNAs have been described for
Schistosoma mansoni legumain; one encodes an active
enzyme whereas the active site cysteine residue encoded
by the second cDNA is substituted by an asparagine
residue. Both forms have been recombinantly expressed.
Length = 258
Score = 24.9 bits (55), Expect = 4.9
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 40 MEVLEAHKLAKEYVEQANQRVKEAEEQSN 68
ME + H L+KE +EQ + VK S+
Sbjct: 210 MEDSDDHDLSKETLEQQFELVKNRTTGSH 238
>gnl|CDD|48129 cd03202, GST_C_etherase_LigE, GST_C family, Beta etherase LigE
subfamily; composed of proteins similar to Sphingomonas
paucimobilis beta etherase, LigE, a GST-like protein
that catalyzes the cleavage of the beta-aryl ether
linkages present in low-moleculer weight lignins using
GSH as the hydrogen donor. This reaction is an essential
step in the degradation of lignin, a complex phenolic
polymer that is the most abundant aromatic material in
the biosphere. The beta etherase activity of LigE is
enantioselective and it complements the activity of the
other GST family beta etherase, LigF. The GST fold
contains an N-terminal thioredoxin-fold domain and a
C-terminal alpha helical domain, with an active site
located in a cleft between the two domains..
Length = 124
Score = 24.8 bits (54), Expect = 5.2
Identities = 13/47 (27%), Positives = 23/47 (48%)
Query: 64 EEQSNARLLKGLGMDDLVRYFMNLDSQNQAFFIDTIQNKYQDEMEEL 110
E SN L+ GL + LD +QA+F + + ++ +EE+
Sbjct: 6 ERWSNTTLVPGLFPLIVPDIHDLLDPPDQAYFRQSREKRFGRSLEEV 52
>gnl|CDD|143803 pfam00012, HSP70, Hsp70 protein. Hsp70 chaperones help to fold
many proteins. Hsp70 assisted folding involves repeated
cycles of substrate binding and release. Hsp70 activity
is ATP dependent. Hsp70 proteins are made up of two
regions: the amino terminus is the ATPase domain and the
carboxyl terminus is the substrate binding region.
Length = 598
Score = 24.9 bits (55), Expect = 5.8
Identities = 22/67 (32%), Positives = 32/67 (47%), Gaps = 11/67 (16%)
Query: 9 STLVTTAITIIGCSLVEDNRIESLRMVKEA---------KMEVLEAHKLAKEYVEQANQR 59
T ITI S + D+ IE RMVK+A + E +EA A+EYV +
Sbjct: 486 GTGKEQKITITNSSGLSDDEIE--RMVKDAEEYAAEDKKRKERIEAKNEAEEYVYSLEKS 543
Query: 60 VKEAEEQ 66
+KE ++
Sbjct: 544 LKEEGDK 550
>gnl|CDD|37327 KOG2116, KOG2116, KOG2116, Protein involved in plasmid
maintenance/nuclear protein involved in lipid metabolism
[Cell motility, Lipid transport and metabolism].
Length = 738
Score = 24.6 bits (53), Expect = 6.4
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 85 MNLDSQNQAFFIDTIQNKYQDEMEELS 111
M L +AFF++ ++ +D +EL
Sbjct: 74 MKLGDSGEAFFVEETEDDVEDVPDELL 100
>gnl|CDD|185706 cd07895, Adenylation_mRNA_capping, Adenylation domain of
GTP-dependent mRNA capping enzymes. RNA capping
enzymes transfer GMP from GTP to the 5'-diphosphate end
of nascent mRNAs to form a G(5')ppp(5')RNA cap
structure. The RNA cap is found only in eukarya. RNA
capping is chemically analogous to the first two steps
of polynucleotide ligation. ATP-dependent
polynucleotide ligases catalyze phosphodiester bond
formation of nicked nucleic acid substrates using the
high energy nucleotide of ATP as a cofactor in a three
step reaction mechanism. Structural studies reveal a
shared structure for DNA ligases and capping enzymes,
with a common catalytic core composed of an adenylation
or nucleotidyltransferase domain and a C-terminal
OB-fold domain containing conserved sequence motifs.
The adenylation domain binds ATP and contains many
active site residues.
Length = 215
Score = 24.5 bits (54), Expect = 6.4
Identities = 5/17 (29%), Positives = 10/17 (58%)
Query: 81 VRYFMNLDSQNQAFFID 97
VRY + + + + + ID
Sbjct: 52 VRYLLLITGRGEVYLID 68
>gnl|CDD|177069 CHL00149, odpA, pyruvate dehydrogenase E1 component alpha subunit;
Reviewed.
Length = 341
Score = 24.4 bits (53), Expect = 6.9
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 40 MEVLEAHKLAKEYVEQANQ 58
M+VL ++AKE VE+A Q
Sbjct: 229 MDVLAVREVAKEAVERARQ 247
>gnl|CDD|177000 CHL00060, atpB, ATP synthase CF1 beta subunit.
Length = 494
Score = 24.2 bits (53), Expect = 7.6
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 65 EQSNARLLKGLGMDDLVRYFMNLDSQNQAFFIDTI 99
E AR+ GL + YF +++ Q+ FID I
Sbjct: 237 EPPGARMRVGLTALTMAEYFRDVNKQDVLLFIDNI 271
>gnl|CDD|36143 KOG0925, KOG0925, KOG0925, mRNA splicing factor ATP-dependent RNA
helicase [RNA processing and modification].
Length = 699
Score = 24.1 bits (52), Expect = 9.0
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 48 LAKEYVEQANQRVKEAEEQSNARLLKGLGMDDLVRY-FMN 86
KE Q + + S LK LG+DDLV + FM+
Sbjct: 389 FEKEMQPQTYPEILRSNLSSTVLQLKKLGIDDLVHFDFMD 428
>gnl|CDD|107325 cd06330, PBP1_Arsenic_SBP_like, Periplasmic solute-binding domain
of active transport proteins. Periplasmic
solute-binding domain of active transport proteins found
in bacteria and Archaea that is predicted to be involved
in the efflux of toxic compounds. Members of this
subgroup include proteins from Herminiimonas
arsenicoxydans, which is resistant to arsenic and
various heavy metals such as cadmium and zinc. Moreover,
they show significant sequence similarity to the cluster
of AmiC and active transport systems for short-chain
amides and urea (FmdDEF), and thus are likely to exhibit
a ligand-binding mode similar to that of the amide
sensor protein AmiC from Pseudomonas aeruginosa.
Length = 346
Score = 24.1 bits (53), Expect = 9.2
Identities = 10/43 (23%), Positives = 14/43 (32%), Gaps = 2/43 (4%)
Query: 50 KEYVEQANQRVKEAEEQSNARLLKGLGMDDLVRY--FMNLDSQ 90
VE+A A + A L+GL + D Q
Sbjct: 294 AAAVEKAGATDGGAPPEQIAAALEGLSFETPGGPITMRAADHQ 336
>gnl|CDD|173833 cd00685, Trans_IPPS_HT, Trans-Isoprenyl Diphosphate Synthases,
head-to-tail. These trans-Isoprenyl Diphosphate
Synthases (Trans_IPPS) catalyze head-to-tail (HT) (1'-4)
condensation reactions. This CD includes all-trans
(E)-isoprenyl diphosphate synthases which synthesize
various chain length (C10, C15, C20, C25, C30, C35, C40,
C45, and C50) linear isoprenyl diphosphates from
precursors, isopentenyl diphosphate (IPP) and
dimethylallyl diphosphate (DMAPP). They catalyze the
successive 1'-4 condensation of the 5-carbon IPP to
allylic substrates geranyl-, farnesyl-, or
geranylgeranyl-diphosphate. Isoprenoid chain elongation
reactions proceed via electrophilic alkylations in which
a new carbon-carbon single bond is generated through
interaction between a highly reactive electron-deficient
allylic carbocation and an electron-rich carbon-carbon
double bond. The catalytic site consists of a large
central cavity formed by mostly antiparallel alpha
helices with two aspartate-rich regions (DDXX(XX)D)
located on opposite walls. These residues mediate
binding of prenyl phosphates via bridging Mg2+ ions,
inducing proposed conformational changes that close the
active site to solvent, protecting and stabilizing
reactive carbocation intermediates. Farnesyl diphosphate
synthases produce the precursors of steroids,
cholesterol, sesquiterpenes, farnsylated proteins, heme,
and vitamin K12; and geranylgeranyl diphosphate and
longer chain synthases produce the precursors of
carotenoids, retinoids, diterpenes, geranylgeranylated
chlorophylls, ubiquinone, and archaeal ether linked
lipids. Isoprenyl diphosphate synthases are widely
distributed among archaea, bacteria, and eukareya.
Length = 259
Score = 24.0 bits (53), Expect = 9.9
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 47 KLAKEYVEQANQRVKEAEEQSNARLLKGL 75
+LA+EY E+A + +K E L+ L
Sbjct: 224 ELAREYEEKALEALKALPESPAREALRAL 252
>gnl|CDD|147308 pfam05059, Orbi_VP4, Orbivirus VP4 core protein. Orbiviruses are
double stranded RNA retroviruses of which the bluetongue
virus is a member. The core of bluetongue virus (BTV) is
a multienzyme complex composed of two major proteins
(VP7 and VP3) and three minor proteins (VP1, VP4 and
VP6) in addition to the viral genome. VP4 has been shown
to perform all RNA capping activities and has both
methyltransferase type 1 and type 2 activities
associated with it.
Length = 642
Score = 23.9 bits (52), Expect = 10.0
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 27 NRIESLRMVKEAKMEVLE 44
NR + LR + EAK EV+E
Sbjct: 581 NREQKLRDLSEAKAEVIE 598
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
0.314 0.129 0.334
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,217,809
Number of extensions: 54255
Number of successful extensions: 265
Number of sequences better than 10.0: 1
Number of HSP's gapped: 262
Number of HSP's successfully gapped: 53
Length of query: 120
Length of database: 6,263,737
Length adjustment: 82
Effective length of query: 38
Effective length of database: 4,491,799
Effective search space: 170688362
Effective search space used: 170688362
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: 51 (23.4 bits)