RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780961|ref|YP_003065374.1| hypothetical protein
CLIBASIA_04310 [Candidatus Liberibacter asiaticus str. psy62]
(200 letters)
>gnl|CDD|32922 COG3108, COG3108, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 185
Score = 155 bits (394), Expect = 6e-39
Identities = 69/149 (46%), Positives = 95/149 (63%), Gaps = 2/149 (1%)
Query: 54 EEVRTLKIYVVSTGSKAIVTFKRGSQYNQEGLSQLNRLLYDWHSKQSIDMDPQLFDFLWE 113
E R LK+Y + TG KA FK Y+Q LS LNRLL DW + + MDP+LFD +++
Sbjct: 35 PEPRILKLYNLHTGEKAEAEFKDNGGYDQASLSGLNRLLRDWRQNEVVRMDPRLFDLVYQ 94
Query: 114 IQQYFSVPEYIYILSGYRTQETNKMLSRRNRKIARKSQHVLGKAVDFYIPGVSLRSLYKI 173
++ + + SGYR+ TN+ML R+R +A+KS H+LG+A+DF IPGVSL L
Sbjct: 95 LKTLEGHRRPVQVTSGYRSPATNRMLRSRSRGVAKKSLHMLGQAMDFQIPGVSLWELRNA 154
Query: 174 AIRLKRGGVGYY--SKFLHIDVGRVRSWT 200
A+ ++ GGVGYY S +H+DVG VR W
Sbjct: 155 ALSMQGGGVGYYPHSNSVHMDVGPVRDWN 183
>gnl|CDD|145604 pfam02557, VanY, D-alanyl-D-alanine carboxypeptidase.
Length = 131
Score = 28.8 bits (65), Expect = 0.99
Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 12/54 (22%)
Query: 123 YIYILSGYRTQETNKML---SRRNRKI--ARK-------SQHVLGKAVDFYIPG 164
++I SGYR+ E + L + A + S+H G A+D P
Sbjct: 25 DLFIASGYRSYEYQQALYDKYVKGEGKEAALRYSAPPGYSEHQTGLAIDIGDPD 78
>gnl|CDD|37703 KOG2492, KOG2492, KOG2492, CDK5 activator-binding protein [Signal
transduction mechanisms].
Length = 552
Score = 27.3 bits (60), Expect = 2.9
Identities = 10/33 (30%), Positives = 16/33 (48%)
Query: 137 KMLSRRNRKIARKSQHVLGKAVDFYIPGVSLRS 169
++L R +R++ L + IPGV L S
Sbjct: 366 RVLEIMRRGYSREAYLELVAHIRSMIPGVGLSS 398
>gnl|CDD|36001 KOG0782, KOG0782, KOG0782, Predicted diacylglycerol kinase [Signal
transduction mechanisms].
Length = 1004
Score = 27.4 bits (60), Expect = 2.9
Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 33 LSPDLIKYHQQSSMSSDLLDQ-EEVRTLKIYVVSTGSKAIVTF 74
LS DL+K + LL Q + +L Y TG+ IV +
Sbjct: 875 LSSDLMKLQETHLNGGSLLIQGPDHCSLLHYAAKTGNGEIVKY 917
>gnl|CDD|37762 KOG2551, KOG2551, KOG2551, Phospholipase/carboxyhydrolase [Amino
acid transport and metabolism].
Length = 230
Score = 27.2 bits (60), Expect = 3.0
Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 3/61 (4%)
Query: 115 QQYFSVP--EYIYILSGYRTQETNKMLSRRNRKIARKSQHVLGKAVDFYIPGVSLRSLYK 172
Y P ++ +SG++ S R ++ S H+ G+ D +P L +
Sbjct: 129 LPYVKQPPFKFAVFISGFKFPSKKLDESAYKRPLSTPSLHIFGET-DTIVPSERSEQLAE 187
Query: 173 I 173
Sbjct: 188 S 188
>gnl|CDD|37702 KOG2491, KOG2491, KOG2491, Nuclear matrix protein [Nuclear
structure].
Length = 674
Score = 27.3 bits (60), Expect = 3.2
Identities = 14/66 (21%), Positives = 25/66 (37%), Gaps = 14/66 (21%)
Query: 100 SIDMDPQLFDFLWEIQQYFSVPEYIY--------------ILSGYRTQETNKMLSRRNRK 145
SI +D L+ W +Q YFS P +Y +L +++ + N K
Sbjct: 222 SIKVDYNLYRKFWSLQDYFSNPNSLYEKIKWKKFLKYLEEVLQVFKSYKLEDTFGESNEK 281
Query: 146 IARKSQ 151
+ +
Sbjct: 282 MEELAT 287
>gnl|CDD|48525 cd02976, NrdH, NrdH-redoxin (NrdH) family; NrdH is a small
monomeric protein with a conserved redox active CXXC
motif within a TRX fold, characterized by a glutaredoxin
(GRX)-like sequence and TRX-like activity profile. In
vitro, it displays protein disulfide reductase activity
that is dependent on TRX reductase, not glutathione
(GSH). It is part of the NrdHIEF operon, where NrdEF
codes for class Ib ribonucleotide reductase (RNR-Ib), an
efficient enzyme at low oxygen levels. Under these
conditions when GSH is mostly conjugated to spermidine,
NrdH can still function and act as a hydrogen donor for
RNR-Ib. It has been suggested that the NrdHEF system may
be the oldest RNR reducing system, capable of
functioning in a microaerophilic environment, where GSH
was not yet available. NrdH from Corynebacterium
ammoniagenes can form domain-swapped dimers, although it
is unknown if this happens in vivo. Domain-swapped
dimerization, which results in the blocking of the TRX
reductase binding site, could be a mechanism for
regulating the oxidation state of the protein..
Length = 73
Score = 26.3 bits (58), Expect = 6.1
Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 101 IDMDPQLFDFLWEIQQYFSVPEYIY---ILSGYRTQETNKML 139
+D DP+ + L ++ Y SVP + LSG+R + +L
Sbjct: 32 VDEDPEALEELKKLNGYRSVPVVVIGDEHLSGFRPDKLRALL 73
>gnl|CDD|147498 pfam05343, Peptidase_M42, M42 glutamyl aminopeptidase. These
peptidases are found in Archaea and Bacteria. The
example in Lactococcus lactis, PepA, aids growth on
milk. Pyrococcus horikoshii contain a thermostable
de-blocking aminopeptidase member of this family used
commercially for N-terminal protein sequencing.
Length = 292
Score = 26.0 bits (58), Expect = 7.1
Identities = 8/30 (26%), Positives = 15/30 (50%)
Query: 103 MDPQLFDFLWEIQQYFSVPEYIYILSGYRT 132
P+L FL E+ + ++P + + G T
Sbjct: 221 YHPKLRKFLLELAKKNNIPYQVEVYPGGGT 250
>gnl|CDD|133086 cd06228, Peptidase_M14-like_3, A functionally uncharacterized
subgroup of the M14 family of metallocarboxypeptidases
(MCPs). The M14 family are zinc-binding
carboxypeptidases (CPs) which hydrolyze single,
C-terminal amino acids from polypeptide chains, and have
a recognition site for the free C-terminal carboxyl
group, which is a key determinant of specificity. Two
major subfamilies of the M14 family, defined based on
sequence and structural homology, are the A/B and N/E
subfamilies. Enzymes belonging to the A/B subfamily are
normally synthesized as inactive precursors containing
preceding signal peptide, followed by an N-terminal
pro-region linked to the enzyme; these proenzymes are
called procarboxypeptidases. The A/B enzymes can be
further divided based on their substrate specificity;
Carboxypeptidase A-like (CPA-like) enzymes favor
hydrophobic residues while carboxypeptidase B-like
(CPB-like) enzymes only cleave the basic residues lysine
or arginine. The A forms have slightly different
specificities, with Carboxypeptidase A1 (CPA1)
preferring aliphatic and small aromatic residues, and
CPA2 preferring the bulky aromatic side chains. Enzymes
belonging to the N/E subfamily enzymes are not produced
as inactive precursors and instead rely on their
substrate specificity and subcellular
compartmentalization to prevent inappropriate cleavages.
They contain an extra C-terminal transthyretin-like
domain, thought to be involved in folding or formation
of oligomers. MCPs can also be classified based on
their involvement in specific physiological processes;
the pancreatic MCPs participate only in alimentary
digestion and include carboxypeptidase A and B (A/B
subfamily), while others, namely regulatory MCPs or the
N/E subfamily, are involved in more selective reactions,
mainly in non-digestive tissues and fluids, acting on
blood coagulation/fibrinolysis, inflammation and local
anaphylaxis, pro-hormone and neuropeptide processing,
cellular response and others. Another MCP subfamily,
is that of succinylglutamate desuccinylase
/aspartoacylase, which hydrolyzes N-acetyl-L-aspartate
(NAA), and deficiency in which is the established cause
of Canavan disease. Another subfamily (referred to as
subfamily C) includes an exceptional type of activity in
the MCP family, that of dipeptidyl-peptidase activity of
gamma-glutamyl-(L)-meso-diaminopimelate peptidase I
which is involved in bacterial cell wall metabolism.
Length = 332
Score = 25.9 bits (57), Expect = 8.0
Identities = 8/12 (66%), Positives = 10/12 (83%)
Query: 108 FDFLWEIQQYFS 119
FDFLW+ Q+YF
Sbjct: 130 FDFLWDFQKYFD 141
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
0.323 0.137 0.403
Gapped
Lambda K H
0.267 0.0798 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,432,974
Number of extensions: 121372
Number of successful extensions: 328
Number of sequences better than 10.0: 1
Number of HSP's gapped: 326
Number of HSP's successfully gapped: 18
Length of query: 200
Length of database: 6,263,737
Length adjustment: 89
Effective length of query: 111
Effective length of database: 4,340,536
Effective search space: 481799496
Effective search space used: 481799496
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (24.8 bits)