RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780357|ref|YP_003064770.1| hypothetical protein
CLIBASIA_01210 [Candidatus Liberibacter asiaticus str. psy62]
(394 letters)
>gnl|CDD|183185 PRK11539, PRK11539, ComEC family competence protein; Provisional.
Length = 755
Score = 42.7 bits (101), Expect = 2e-04
Identities = 18/50 (36%), Positives = 29/50 (58%), Gaps = 4/50 (8%)
Query: 104 FHCIPVYGLIANILAIPILSFVVIPAGLIAILLMILSLDNIPFGVMAWGL 153
FH I + L AN+ A+P++SF+ +P L+A++L +L P W L
Sbjct: 384 FHGISLTSLPANLWAVPLVSFITVPLILLALVLHLLP----PLEQGLWFL 429
>gnl|CDD|161839 TIGR00361, ComEC_Rec2, DNA internalization-related competence
protein ComEC/Rec2. The role for this protein in
species that are not naturally transformable is unknown.
Length = 662
Score = 41.4 bits (97), Expect = 4e-04
Identities = 23/66 (34%), Positives = 38/66 (57%), Gaps = 6/66 (9%)
Query: 100 LIKHFHCIPVYGLIANILAIPILSFVVIPAGLIAILLMILSLDNIPFGVM--AWGLDIII 157
+ HFH + AN+LA+P +F ++P L A+LL+ LS FG + +W D++I
Sbjct: 312 QLYHFHGFSLISFPANMLAVPFYTFCIVPLILAAVLLLSLS---GSFGRLQGSW-FDLLI 367
Query: 158 HIAHRI 163
+A R+
Sbjct: 368 SLALRL 373
>gnl|CDD|180955 PRK07390, PRK07390, NAD(P)H-quinone oxidoreductase subunit F;
Validated.
Length = 613
Score = 33.3 bits (77), Expect = 0.10
Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 7/49 (14%)
Query: 99 FLIKHFHCIPVYGLIANILAIPILSFVVI------PAGLIAILLMILSL 141
FL++ IP+YGLI +L++P S +I PA + +L+ +L+
Sbjct: 4 FLLQTSWLIPLYGLIGALLSLP-WSPGIIRRTGPRPAAYLNLLMTLLAF 51
>gnl|CDD|162399 TIGR01525, ATPase-IB_hvy, heavy metal translocating P-type ATPase.
This alignment encompasses two equivalog models for the
copper and cadmium-type heavy metal transporting P-type
ATPases (TIGR01511 and TIGR01512) as well as those
species which score ambiguously between both models. For
more comments and references, see the files on TIGR01511
and 01512.
Length = 556
Score = 32.6 bits (75), Expect = 0.17
Identities = 11/32 (34%), Positives = 20/32 (62%)
Query: 109 VYGLIANILAIPILSFVVIPAGLIAILLMILS 140
+ L N++AIP+ + ++P L+A+LL S
Sbjct: 514 AWALGYNLVAIPLAAGGLLPLWLLAVLLHEGS 545
>gnl|CDD|178242 PLN02635, PLN02635, disproportionating enzyme.
Length = 538
Score = 28.6 bits (64), Expect = 2.7
Identities = 20/59 (33%), Positives = 25/59 (42%), Gaps = 12/59 (20%)
Query: 336 RDINTKLCNVSLLITPEILQKQGSLEITIIPPSNDNDKVKF---------IIKSAIENL 385
+D N C +LLI+ E L K G LE +P KV F +I A E L
Sbjct: 89 QDAN---CGNTLLISLEELVKDGLLEEDELPEPVPVGKVDFSAVAELKDPLIAKAAERL 144
>gnl|CDD|131015 TIGR01960, ndhF3_CO2, NAD(P)H dehydrogenase, subunit NdhF3 family.
This family represents a subfamily of NAD(P)H
dehydrogenase subunit 5, or ndhF. It is restricted to
two paralogs in each completed cyanobacterial genome, in
which several subtypes of ndhF are found. Included in
this family is NdhF3, shown to play a role in
high-affinity CO2 uptake in Synechococcus sp. PCC7002.
In all cases, neighboring genes include a paralog of
ndhD but do include other NAD(P)H dehydrogenase
subunits. Instead, genes related to C02 uptake tend to
be found nearby.
Length = 606
Score = 28.5 bits (64), Expect = 2.8
Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 7/49 (14%)
Query: 99 FLIKHFHCIPVYGLIANILAIPILSFVVI------PAGLIAILLMILSL 141
L++ +P YGLI +L++P S + PAG +L+ ++
Sbjct: 4 SLLETSWLVPFYGLIGALLSLP-WSPGITRQTGPRPAGYFNLLMTFVAF 51
>gnl|CDD|148126 pfam06325, PrmA, Ribosomal protein L11 methyltransferase (PrmA).
This family consists of several Ribosomal protein L11
methyltransferase (EC:2.1.1.-) sequences.
Length = 294
Score = 27.6 bits (62), Expect = 5.9
Identities = 13/60 (21%), Positives = 21/60 (35%), Gaps = 14/60 (23%)
Query: 81 LNEIRANIGTYGSASASIFLIKHFHCIPVYGLIANILAIPILSFV------VIPAGLIAI 134
LN + A + Y ++ANILA P++ V P G + +
Sbjct: 205 LNGVEAQLEVYLPGDLPE--------GKADVVVANILADPLIELAPDIYALVKPGGYLIL 256
>gnl|CDD|161838 TIGR00360, ComEC_N-term, ComEC/Rec2-related protein. The related
model ComEC_Rec2 (TIGR00361) describes a set of proteins
of ~ 700-800 residues, one each from a number of
different species, of which most can become competent
for natural transformation with exogenous DNA. The
best-studied examples are ComEC from Bacillus subtilis
and Rec-2 from Haemophilus influenzae, where the protein
appears to form part of the DNA import structure. This
model represents a region found in full-length
ComEC/Rec2 and shorter homologs of unknown function from
large number of additional bacterial species, most of
which are not known to become competent for
transformation (an exception is Helicobacter pylori).
Length = 171
Score = 27.3 bits (61), Expect = 6.5
Identities = 12/29 (41%), Positives = 21/29 (72%)
Query: 100 LIKHFHCIPVYGLIANILAIPILSFVVIP 128
L+ FH + ++AN+LAIP+ SF+++P
Sbjct: 142 LLYLFHGLSPISVLANLLAIPLYSFLLLP 170
>gnl|CDD|129873 TIGR00791, gntP, gluconate transporter. This family includes known
gluconate transporters of E. coli and Bacillus species
as well as an idonate transporter from E. coli.
Length = 440
Score = 26.9 bits (60), Expect = 8.7
Identities = 19/60 (31%), Positives = 28/60 (46%), Gaps = 4/60 (6%)
Query: 105 HCIPVYGLIANILAI----PILSFVVIPAGLIAILLMILSLDNIPFGVMAWGLDIIIHIA 160
C G IA IL I V+I +G+ + ++S NI +MAW + I+ IA
Sbjct: 292 SCGSAIGSIAMILLIIGGGGAFKQVLIDSGVGDYIAELMSGMNISPILMAWLIAAILRIA 351
>gnl|CDD|162101 TIGR00911, 2A0308, L-type amino acid transporter.
Length = 501
Score = 27.0 bits (60), Expect = 8.9
Identities = 25/115 (21%), Positives = 51/115 (44%), Gaps = 11/115 (9%)
Query: 113 IANILAIPILSFVVI-----------PAGLIAILLMILSLDNIPFGVMAWGLDIIIHIAH 161
IA I+++PI++F+ + P L+A L + + GVM+W + ++ ++
Sbjct: 270 IAIIISMPIVTFIYVLTNIAYFTVLSPEELLASLAVAVDFGERLLGVMSWAMPALVGLSC 329
Query: 162 RISVAHNEFCIGRIPETSFVTIVVEFLLMVFCKTNIRHIGSIMIGITIIILFTFP 216
SV + F R+ + LL + + + S++I T+ +L F
Sbjct: 330 FGSVNGSLFSSSRLFFVGGREGHLPSLLSMIHVKRLTPLPSLLIVCTLTLLMLFS 384
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
0.325 0.141 0.425
Gapped
Lambda K H
0.267 0.0680 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 6,439,016
Number of extensions: 420374
Number of successful extensions: 1247
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1246
Number of HSP's successfully gapped: 41
Length of query: 394
Length of database: 5,994,473
Length adjustment: 95
Effective length of query: 299
Effective length of database: 3,941,713
Effective search space: 1178572187
Effective search space used: 1178572187
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (26.2 bits)