RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781063|ref|YP_003065476.1| hypothetical protein
CLIBASIA_04825 [Candidatus Liberibacter asiaticus str. psy62]
(129 letters)
>gnl|CDD|32334 COG2151, PaaD, Predicted metal-sulfur cluster biosynthetic enzyme
[General function prediction only].
Length = 111
Score = 119 bits (300), Expect = 2e-28
Identities = 52/107 (48%), Positives = 73/107 (68%), Gaps = 1/107 (0%)
Query: 24 IPPEDLERISNDIIAALKTVYDPEIPCDIFELGLIYKIDVEN-DYMVKILMTLTAPGCPV 82
I E ++ DI+ ALKTV DPEI DI +LGL+Y++D+++ D +VK+ MTLT+PGCP+
Sbjct: 5 IEEEAIKVTLEDILEALKTVIDPEIGIDIVDLGLVYEVDIDDVDGLVKVKMTLTSPGCPL 64
Query: 83 AGDMPKWIENAVGAVEGISGVEVSITFDPPWTPDLMSEEAQIATGYY 129
A + +E A+ + G+ VEV +T PPWTPD MSEEA+ A G
Sbjct: 65 AEVIADQVEAALEEIPGVEDVEVELTLSPPWTPDRMSEEARRALGIT 111
>gnl|CDD|110847 pfam01883, DUF59, Domain of unknown function DUF59. This family
includes prokaryotic proteins of unknown function. The
family also includes PhaH from Pseudomonas putida. PhaH
forms a complex with PhaF, PhaG, and PhaI, which
hydroxylates phenylacetic acid to 2-hydroxyphenylacetic
acid. So members of this family may all be components of
ring hydroxylating complexes.
Length = 76
Score = 91.1 bits (227), Expect = 7e-20
Identities = 34/73 (46%), Positives = 51/73 (69%)
Query: 35 DIIAALKTVYDPEIPCDIFELGLIYKIDVENDYMVKILMTLTAPGCPVAGDMPKWIENAV 94
I+ ALKTV DPE+P DI +LGL+Y++D+++D VK+ MTLT PGCP+A + + A+
Sbjct: 4 AILEALKTVIDPELPVDIVDLGLVYEVDIDDDGNVKVKMTLTTPGCPLADLIALDVREAL 63
Query: 95 GAVEGISGVEVSI 107
+ G+ VEV +
Sbjct: 64 LELPGVEDVEVEL 76
>gnl|CDD|29471 cd00371, HMA, Heavy-metal-associated domain (HMA) is a conserved
domain of approximately 30 amino acid residues found in
a number of proteins that transport or detoxify heavy
metals, for example, the CPx-type heavy metal ATPases
and copper chaperones. HMA domain contains two cysteine
residues that are important in binding and transfer of
metal ions, such as copper, cadmium, cobalt and zinc. In
the case of copper, stoichiometry of binding is one Cu+
ion per binding domain. Repeats of the HMA domain in
copper chaperone has been associated with Menkes/Wilson
disease due to binding of multiple copper ions..
Length = 63
Score = 30.6 bits (69), Expect = 0.12
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 8/46 (17%)
Query: 90 IENAVGAVEGISGVEVS-------ITFDPPWTPDLMSEEAQIATGY 128
IE A+ + G+ VEV + +DP +P+ + EA GY
Sbjct: 16 IEKALEKLPGVESVEVDLETGKATVEYDPEVSPEEL-LEAIEDAGY 60
>gnl|CDD|38591 KOG3381, KOG3381, KOG3381, Uncharacterized conserved protein
[Function unknown].
Length = 161
Score = 29.5 bits (66), Expect = 0.26
Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 12/73 (16%)
Query: 19 SPESTIPPEDLERISNDIIAALKTVYDPEIPCDIFELGLIYKIDVE--------NDYMVK 70
E ED E I + I + + DPE P + +L ++ + VE + V+
Sbjct: 26 EDELLPDSEDAEEIFDLI----RDIRDPEHPLTLEQLNVVSEEGVEVDDPNVGDEESYVR 81
Query: 71 ILMTLTAPGCPVA 83
I T T P C +A
Sbjct: 82 ITFTPTIPHCSMA 94
>gnl|CDD|32952 COG3138, AstA, Arginine/ornithine N-succinyltransferase beta
subunit [Amino acid transport and metabolism].
Length = 336
Score = 28.3 bits (63), Expect = 0.67
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 95 GAVEGISGVEVSITFDPPW 113
G V GIS +E ++ + P+
Sbjct: 68 GTVVGISAIEAAVGLNDPF 86
>gnl|CDD|34313 COG4697, COG4697, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 319
Score = 27.6 bits (61), Expect = 1.1
Identities = 18/97 (18%), Positives = 30/97 (30%), Gaps = 10/97 (10%)
Query: 22 STIPPEDLERISNDIIAALKTVYDPEIPCDIFELGLIYKIDVENDYMVKILMTLTAPGCP 81
S+ P E IS+ L DP +P E G I+ + ++ + +
Sbjct: 168 SSNPAEKGRDISDKATFGLLLRIDPGVPQIDTESGAIFGMALDGEGLYI----------G 217
Query: 82 VAGDMPKWIENAVGAVEGISGVEVSITFDPPWTPDLM 118
+G + G V V P P +
Sbjct: 218 ASGANHTGVYRYRAGDGGGFAVPVPELGREPRFPRRI 254
>gnl|CDD|37623 KOG2412, KOG2412, KOG2412, Nuclear-export-signal (NES)-containing
protein/polyadenylated-RNA export factor [RNA
processing and modification].
Length = 591
Score = 26.2 bits (57), Expect = 2.4
Identities = 7/42 (16%), Positives = 11/42 (26%)
Query: 1 MKQKNPDTENNIADKIALSPESTIPPEDLERISNDIIAALKT 42
+ D I++ PE DL + L
Sbjct: 1 EGIPLEEPCPKSVDGISIDPEPNWNFPDLVAEIASVEKKLNG 42
>gnl|CDD|31518 COG1327, COG1327, Predicted transcriptional regulator, consists of
a Zn-ribbon and ATP-cone domains [Transcription].
Length = 156
Score = 26.0 bits (57), Expect = 3.0
Identities = 6/28 (21%), Positives = 13/28 (46%)
Query: 24 IPPEDLERISNDIIAALKTVYDPEIPCD 51
+ E +E + I L++ + E+P
Sbjct: 79 VSSEQIEEAVSHIERQLRSSGEREVPSK 106
>gnl|CDD|37186 KOG1975, KOG1975, KOG1975, mRNA cap methyltransferase [RNA
processing and modification].
Length = 389
Score = 25.7 bits (56), Expect = 3.7
Identities = 13/29 (44%), Positives = 16/29 (55%)
Query: 79 GCPVAGDMPKWIENAVGAVEGISGVEVSI 107
GC GD+ KW + +G GI EVSI
Sbjct: 125 GCGKGGDLLKWDKAGIGEYIGIDIAEVSI 153
>gnl|CDD|145557 pfam02479, Herpes_IE68, Herpesvirus immediate early protein. This
regulatory protein is expressed from an immediate early
gene in the cell cycle of herpesvirus. The protein is
known by various names including IE-68, US1, ICP22 and
IR4.
Length = 132
Score = 25.4 bits (56), Expect = 4.2
Identities = 11/41 (26%), Positives = 12/41 (29%), Gaps = 11/41 (26%)
Query: 77 APGCPVAGDMPKWIENAVGAVEGISGVEVSITFDPPWTPDL 117
G P A + GA PPW PDL
Sbjct: 3 EYGPPSAPAGLRSYSRGPGAFCA-----------PPWRPDL 32
>gnl|CDD|173858 cd08493, PBP2_DppA_like, The substrate-binding component of an
ABC-type dipeptide import system contains the type 2
periplasmic binding fold. This family represents the
substrate-binding domain of an ATP-binding cassette
(ABC)-type dipeptide import system. The DppA binds
dipeptides and some tripeptides and is involved in
chemotaxis toward dipeptides, whereas the OppA binds
peptides of a wide range of lengths (2-35 amino acid
residues) and plays a role in recycling of cell wall
peptides, which precludes any involvement in chemotaxis.
Most of other periplasmic binding proteins are
comprised of only two globular subdomains corresponding
to domains I and III of the dipeptide/oligopeptide
binding proteins. The structural topology of these
domains is most similar to that of 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. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 482
Score = 24.8 bits (55), Expect = 7.3
Identities = 10/28 (35%), Positives = 14/28 (50%), Gaps = 2/28 (7%)
Query: 51 DIFELGLIYKIDVENDYMVKILMTLTAP 78
+ LI ++ +DY VK TLT P
Sbjct: 109 SMGLGSLIKSVEAVDDYTVKF--TLTRP 134
>gnl|CDD|144525 pfam00958, GMP_synt_C, GMP synthase C terminal domain. GMP
synthetase is a glutamine amidotransferase from the de
novo purine biosynthetic pathway. This family is the
C-terminal domain specific to the GMP synthases
EC:6.3.5.2. In prokaryotes this domain mediates
dimerization. Eukaryotic GMP synthases are monomers.
This domain in eukaryotes includes several large
insertions that may form globular domains.
Length = 93
Score = 24.3 bits (54), Expect = 9.7
Identities = 12/26 (46%), Positives = 14/26 (53%), Gaps = 4/26 (15%)
Query: 24 IPPEDLERISNDIIAALK----TVYD 45
+P E LERISN I + VYD
Sbjct: 57 LPYEVLERISNRITNEVPGVNRVVYD 82
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 0.136 0.404
Gapped
Lambda K H
0.267 0.0732 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,671,057
Number of extensions: 82021
Number of successful extensions: 186
Number of sequences better than 10.0: 1
Number of HSP's gapped: 185
Number of HSP's successfully gapped: 18
Length of query: 129
Length of database: 6,263,737
Length adjustment: 83
Effective length of query: 46
Effective length of database: 4,470,190
Effective search space: 205628740
Effective search space used: 205628740
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: 42 (21.9 bits)
S2: 52 (23.8 bits)