RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780514|ref|YP_003064927.1| type II restriction
endonuclease [Candidatus Liberibacter asiaticus str. psy62]
(110 letters)
>gnl|CDD|30495 COG0146, HyuB, N-methylhydantoinase B/acetone carboxylase, alpha
subunit [Amino acid transport and metabolism / Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 563
Score = 27.9 bits (62), Expect = 0.73
Identities = 16/83 (19%), Positives = 28/83 (33%), Gaps = 8/83 (9%)
Query: 3 FNEIILKNISNNYEVPKMLITELSTELFNLKTANQNFFHNTLTKKFGD-----YMSKITP 57
F E IL+ + N P I +L ++ + L ++G M ++
Sbjct: 161 FREDILRILLRNVRTPDYNIGDLKAQIAANLKGRRRV--RELIDEYGLDTVEEAMKEVIE 218
Query: 58 YLYEWVLSNTQSRRSRDGQEFEY 80
Y V + + EFE
Sbjct: 219 YAERAVRAVIRKLPDGKY-EFED 240
>gnl|CDD|32971 COG3157, Hcp, Hemolysin-coregulated protein (uncharacterized)
[Function unknown].
Length = 162
Score = 26.4 bits (58), Expect = 1.7
Identities = 13/49 (26%), Positives = 18/49 (36%), Gaps = 8/49 (16%)
Query: 47 KFGDYMSKITPYLYEWVLSNTQ--------SRRSRDGQEFEYIIYSLYN 87
F + K +P LY+ S R GQ+ EY+ L N
Sbjct: 62 TFTKPIDKASPLLYKACSSGETLKTAVLTWYRTGDAGQQEEYLTIKLTN 110
>gnl|CDD|143183 cd04982, IgV_TCR_gamma, Immunoglobulin (Ig) variable (V) domain of
T-cell receptor (TCR) gamma chain. IgV_TCR_gamma:
immunoglobulin (Ig) variable (V) domain of the gamma
chain of gamma/delta T-cell receptors (TCRs). TCRs
mediate antigen recognition by T lymphocytes, and are
heterodimers consisting of alpha and beta chains or
gamma and delta chains. Each chain contains a variable
(V) and a constant (C) region. The majority of T cells
contain alpha/beta TCRs but a small subset contain
gamma/delta TCRs. Alpha/beta TCRs recognize antigen as
peptide fragments presented by major histocompatibility
complex (MHC) molecules. Gamma/delta TCRs recognize
intact protein antigens; they recognize protein antigens
directly and without antigen processing, and MHC
independently of the bound peptide. Gamma/delta T cells
can also be stimulated by non-peptide antigens such as
small phosphate- or amine-containing compounds. The
variable domain of gamma/delta TCRs is responsible for
antigen recognition and is located at the N-terminus of
the receptor.
Length = 116
Score = 25.8 bits (57), Expect = 2.5
Identities = 7/30 (23%), Positives = 12/30 (40%), Gaps = 2/30 (6%)
Query: 71 RSRDGQEFEYIIYSLYNINTFVTHLMHKKK 100
R + GQ E ++Y + + L K
Sbjct: 36 RQKPGQALERLLY--VSSTSTQRKLSGGTK 63
>gnl|CDD|36446 KOG1232, KOG1232, KOG1232, Proteins containing the FAD binding
domain [Energy production and conversion].
Length = 511
Score = 25.6 bits (56), Expect = 3.0
Identities = 17/64 (26%), Positives = 27/64 (42%), Gaps = 1/64 (1%)
Query: 38 NFFHNTLTKKFGDYMSK-ITPYLYEWVLSNTQSRRSRDGQEFEYIIYSLYNINTFVTHLM 96
N N ++F + K + P++YEWV + S + G F Y Y+ + LM
Sbjct: 433 NLHLNIAVREFNKEIEKLLEPFVYEWVSKHKGSISAEHGIGFLKKPYLHYSKSPEEILLM 492
Query: 97 HKKK 100
K
Sbjct: 493 KDLK 496
>gnl|CDD|36455 KOG1241, KOG1241, KOG1241, Karyopherin (importin) beta 1 [Nuclear
structure, Intracellular trafficking, secretion, and
vesicular transport].
Length = 859
Score = 25.3 bits (55), Expect = 3.8
Identities = 12/29 (41%), Positives = 13/29 (44%), Gaps = 1/29 (3%)
Query: 42 NTLTKKFGDYMSKITPYLYEWVLSNTQSR 70
+L K F YM PYL LSN Q
Sbjct: 626 ESLGKGFAKYMPAFKPYLLM-GLSNFQEY 653
>gnl|CDD|147760 pfam05783, DLIC, Dynein light intermediate chain (DLIC). This
family consists of several eukaryotic dynein light
intermediate chain proteins. The light intermediate
chains (LICs) of cytoplasmic dynein consist of multiple
isoforms, which undergo post-translational modification
to produce a large number of species. DLIC1 is known to
be involved in assembly, organisation, and function of
centrosomes and mitotic spindles when bound to
pericentrin. DLIC2 is a subunit of cytoplasmic dynein 2
that may play a role in maintaining Golgi organisation
by binding cytoplasmic dynein 2 to its Golgi-associated
cargo.
Length = 490
Score = 25.2 bits (55), Expect = 4.0
Identities = 13/40 (32%), Positives = 19/40 (47%)
Query: 38 NFFHNTLTKKFGDYMSKITPYLYEWVLSNTQSRRSRDGQE 77
NFF++ L+KK G S +NTQ + GQ+
Sbjct: 422 NFFNSLLSKKTGSPGSPGGGGSPAGTGTNTQGTAKKSGQK 461
>gnl|CDD|173954 cd08195, DHQS, Dehydroquinate synthase (DHQS) catalyzes the
conversion of DAHP to DHQ in shikimate pathway for
aromatic compounds synthesis. Dehydroquinate synthase
(DHQS) catalyzes the conversion of
3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to
dehydroquinate (DHQ) in the second step of the shikimate
pathway. This pathway, which involves seven sequential
enzymatic steps in the conversion of erythrose
4-phosphate and phosphoenolpyruvate into chorismate for
subsequent synthesis of aromatic compounds, is found in
bacteria, microbial eukaryotes, and plants, but not in
mammals. Therefore, enzymes of this pathway are
attractive targets for the development of non-toxic
antimicrobial compounds, herbicides and anti-parasitic
agents. The activity of DHQS requires nicotinamide
adenine dinucleotide (NAD) as cofactor. A single active
site in DHQS catalyzes five sequential reactions
involving alcohol oxidation, phosphate elimination,
carbonyl reduction, ring opening, and intramolecular
aldol condensation. The binding of substrates and
ligands induces domain conformational changes. In some
fungi and protozoa, this domain is fused with the other
four domains in shikimate pathway and forms a
penta-domain AROM protein, which catalyzes steps 2-6 in
the shikimate pathway.
Length = 345
Score = 25.1 bits (56), Expect = 4.6
Identities = 8/25 (32%), Positives = 14/25 (56%)
Query: 59 LYEWVLSNTQSRRSRDGQEFEYIIY 83
L+EW+ N ++ + D + E II
Sbjct: 186 LFEWLEENKEAILALDPEALEEIIA 210
>gnl|CDD|39472 KOG4271, KOG4271, KOG4271, Rho-GTPase activating protein [Signal
transduction mechanisms].
Length = 1100
Score = 24.7 bits (53), Expect = 5.4
Identities = 11/58 (18%), Positives = 20/58 (34%)
Query: 43 TLTKKFGDYMSKITPYLYEWVLSNTQSRRSRDGQEFEYIIYSLYNINTFVTHLMHKKK 100
T KF +S+ P W + + R D + + + F H+ K+
Sbjct: 53 TAKDKFETLVSQAVPLHTYWNQVSAKIDRHPDYMNYVTLEGTRKAFEMFERHISELKE 110
>gnl|CDD|37037 KOG1826, KOG1826, KOG1826, Ras GTPase activating protein
RasGAP/neurofibromin [Defense mechanisms].
Length = 2724
Score = 24.2 bits (52), Expect = 8.6
Identities = 19/74 (25%), Positives = 28/74 (37%), Gaps = 9/74 (12%)
Query: 3 FNEIILKNISNN-YEVPKMLITELSTELFNLKTANQNFFHNT--LTKKFGDYMSKITPYL 59
FN + LK +E P E ELF F++ ++ Y+S T L
Sbjct: 1873 FNPVSLKIYFQVLHENPPHYKLEFLEELF------SGKFNSVYEISHLCLVYVSPWTGVL 1926
Query: 60 YEWVLSNTQSRRSR 73
E+ SN +R
Sbjct: 1927 VEFTKSNDDEKRLI 1940
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
0.319 0.132 0.375
Gapped
Lambda K H
0.267 0.0626 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,235,726
Number of extensions: 55506
Number of successful extensions: 144
Number of sequences better than 10.0: 1
Number of HSP's gapped: 143
Number of HSP's successfully gapped: 20
Length of query: 110
Length of database: 6,263,737
Length adjustment: 76
Effective length of query: 34
Effective length of database: 4,621,453
Effective search space: 157129402
Effective search space used: 157129402
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 (21.8 bits)
S2: 51 (23.6 bits)