RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254781219|ref|YP_003065632.1| hypothetical protein
CLIBASIA_05630 [Candidatus Liberibacter asiaticus str. psy62]
(200 letters)
>gnl|CDD|131269 TIGR02214, spoVD_pbp, stage V sporulation protein D. This model
describes the spoVD subfamily of homologs of the cell
division protein FtsI, a penicillin binding protein.
This subfamily is restricted to Bacillus subtilis and
related Gram-positive species with known or suspected
endospore formation capability. In these species, the
functional equivalent of FtsI is desginated PBP-2B, a
paralog of spoVD.
Length = 636
Score = 29.0 bits (65), Expect = 0.88
Identities = 12/46 (26%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 79 HFIEGLIESERSKITEKFKPLAVAKVVSDELLHDKLNKILKKSVRN 124
H ++ + +S+ + + + F+P +VVS E KL L+ V
Sbjct: 430 HIMKEISDSQNNAVDQTFEPEVKRQVVSKE-TTQKLRLALETVVSK 474
>gnl|CDD|179818 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A'';
Validated.
Length = 383
Score = 27.9 bits (63), Expect = 1.9
Identities = 11/47 (23%), Positives = 25/47 (53%)
Query: 81 IEGLIESERSKITEKFKPLAVAKVVSDELLHDKLNKILKKSVRNYSR 127
+E +E ++ +K K K+ +L +++ +I+++ VR Y R
Sbjct: 7 LEEKLEDASLELPQKLKEELREKLEERKLTEEEVEEIIEEVVREYLR 53
>gnl|CDD|149191 pfam07976, Phe_hydrox_dim, Phenol hydroxylase, C-terminal
dimerization domain. Phenol hydroxylase acts a
homodimer, to hydroxylates phenol to catechol or similar
product. The enzyme is comprised of three domains. The
first two domains from the active site. The third
domain, this domain, is involved in forming the
dimerization interface. The domain adopts a
thioredoxin-like fold.
Length = 169
Score = 27.6 bits (62), Expect = 2.3
Identities = 9/32 (28%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 21 LDKWCEALYSPESYSNTY-REQKLRDKIIELR 51
LD E L SP+S + + D +I++
Sbjct: 80 LDALAEYLESPDSPLRRFTPKGADIDSVIDVL 111
>gnl|CDD|183266 PRK11663, PRK11663, regulatory protein UhpC; Provisional.
Length = 434
Score = 27.4 bits (61), Expect = 2.7
Identities = 9/19 (47%), Positives = 14/19 (73%), Gaps = 1/19 (5%)
Query: 73 ITYSLSHFIEGLIESERSK 91
ITY +S F+ G++ S+RS
Sbjct: 69 ITYGVSKFVSGIV-SDRSN 86
>gnl|CDD|150993 pfam10412, TrwB_AAD_bind, Type IV secretion-system coupling protein
DNA-binding domain. The plasmid conjugative coupling
protein TrwB forms hexamers from six structurally very
similar protomers. This hexamer contains a central
channel running from the cytosolic pole (made up by the
AADs) to the membrane pole ending at the transmembrane
pore shaped by 12 transmembrane helices, rendering an
overall mushroom-like structure. The TrwB_AAD (all-alpha
domain) domain appears to be the DNA-binding domain of
the structure. TrwB, a basic integral inner-membrane
nucleoside-triphosphate-binding protein, is the
structural prototype for the type IV secretion system
coupling proteins, a family of proteins essential for
macromolecular transport between cells and export.
Length = 386
Score = 26.8 bits (60), Expect = 4.0
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 147 YLEDFYKEIKHTFGNPADALSPHISELADEIHT 179
++E FY+ NP DA SP+ S +E T
Sbjct: 55 FVERFYRPGGDIILNPLDARSPNWS-PFNECET 86
>gnl|CDD|132392 TIGR03349, IV_VI_DotU, type IV / VI secretion system protein, DotU
family. At least two families of proteins, often
encoded by adjacent genes, show sequence similarity due
to homology between type IV secretion systems and type
VI secretion systems. One is the IcmF family
(TIGR03348). The other is the family described by this
model. Members include DotU from the Legionella
pneumophila type IV secretion system. Many of the
members of this protein family from type VI secretion
systems have an additional C-terminal domain with
OmpA/MotB homology.
Length = 183
Score = 26.5 bits (59), Expect = 4.5
Identities = 12/64 (18%), Positives = 20/64 (31%), Gaps = 18/64 (28%)
Query: 124 NYSRDSGHLNRDVI----------FHSRYALI----RYLED----FYKEIKHTFGNPADA 165
+ D++ F +Y + LE Y+ ++ G A
Sbjct: 92 ERLLADPAEHLDLLELYYLCLSLGFEGKYRVEEDGREQLEALRDRLYRLLRGARGPVPPA 151
Query: 166 LSPH 169
LSPH
Sbjct: 152 LSPH 155
>gnl|CDD|185541 PTZ00292, PTZ00292, ribokinase; Provisional.
Length = 326
Score = 26.2 bits (58), Expect = 5.4
Identities = 18/65 (27%), Positives = 23/65 (35%), Gaps = 7/65 (10%)
Query: 53 KFAKENGLKTVTEVCPKPKDITYSLSH----FIEGLI--ESERSKIT-EKFKPLAVAKVV 105
K AKE G TV P PK + ++ E E + IT + A
Sbjct: 167 KEAKERGCYTVFNPAPAPKLAEVEIIKPFLKYVSLFCVNEVEAALITGMEVTDTESAFKA 226
Query: 106 SDELL 110
S EL
Sbjct: 227 SKELQ 231
>gnl|CDD|161904 TIGR00507, aroE, shikimate 5-dehydrogenase. This model finds
proteins from prokaryotes and functionally equivalent
domains from larger, multifunctional proteins of fungi
and plants. Below the trusted cutoff of 180, but above
the noise cutoff of 20, are the putative shikimate
dehydrogenases of Thermotoga maritima and Mycobacterium
tuberculosis, and uncharacterized paralogs of shikimate
dehydrogenase from E. coli and H. influenzae. The
related enzyme quinate 5-dehydrogenase scores below the
noise cutoff. A neighbor-joining tree, constructed with
quinate 5-dehydrogenases as the outgroup, shows the
Clamydial homolog as clustering among the shikimate
dehydrogenases, although the sequence is unusual in the
degree of sequence divergence and the presence of an
additional N-terminal domain.
Length = 270
Score = 26.2 bits (58), Expect = 5.8
Identities = 10/50 (20%), Positives = 15/50 (30%), Gaps = 3/50 (6%)
Query: 131 HLNRDVIFHSRYALIRYLEDFYKEIKHTFGNPADALSPH---ISELADEI 177
L + + + LED A+ SP + DEI
Sbjct: 25 QLGLEGPYIAFLVPPDDLEDALSGFFALGFKGANVTSPFKEEAFQFLDEI 74
>gnl|CDD|181535 PRK08673, PRK08673, 3-deoxy-7-phosphoheptulonate synthase;
Reviewed.
Length = 335
Score = 26.0 bits (58), Expect = 6.1
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 6/37 (16%)
Query: 30 SPESYSNTYREQKLRDKIIELRRKFAKENGLKTVTEV 66
SP S+ Q L ++ ++L + +E GL VTEV
Sbjct: 134 SPYSF------QGLGEEGLKLLAEAREETGLPIVTEV 164
>gnl|CDD|179436 PRK02507, PRK02507, proton extrusion protein PcxA; Provisional.
Length = 422
Score = 26.1 bits (58), Expect = 7.1
Identities = 10/26 (38%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 40 EQKLRDKIIELRRKFAKE--NGLKTV 63
E+KL++K EL + E N +K V
Sbjct: 278 EEKLKEKAEELAEEARYESLNAIKNV 303
>gnl|CDD|150362 pfam09674, DUF2400, Protein of unknown function (DUF2400). Members
of this uncharacterized protein family are found
sporadically, so far only among spirochetes, epsilon and
delta proteobacteria, and Bacteroides. The function is
unknown and its gene neighbourhoods show little
conservation.
Length = 230
Score = 25.6 bits (57), Expect = 8.5
Identities = 14/63 (22%), Positives = 24/63 (38%), Gaps = 4/63 (6%)
Query: 38 YREQKLRDK---IIELRRKFAKENGLKTV-TEVCPKPKDITYSLSHFIEGLIESERSKIT 93
YR Q D I L+R + + L+ + + K + ++S FI+ E
Sbjct: 69 YRFQNSEDLAALFIALKRIYEEHGSLEDLFLKAYQKSGTLQEAISAFIKAFFELNHPSRG 128
Query: 94 EKF 96
K
Sbjct: 129 YKH 131
>gnl|CDD|179065 PRK00558, uvrC, excinuclease ABC subunit C; Validated.
Length = 598
Score = 25.5 bits (57), Expect = 9.9
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 116 KILKKSVRNYSRDSGHLNR 134
K LK VR+Y R S +
Sbjct: 34 KNLKNRVRSYFRKSHDSPK 52
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.318 0.135 0.387
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,295,084
Number of extensions: 208644
Number of successful extensions: 529
Number of sequences better than 10.0: 1
Number of HSP's gapped: 529
Number of HSP's successfully gapped: 35
Length of query: 200
Length of database: 5,994,473
Length adjustment: 89
Effective length of query: 111
Effective length of database: 4,071,361
Effective search space: 451921071
Effective search space used: 451921071
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 (21.7 bits)
S2: 55 (24.9 bits)