RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780862|ref|YP_003065275.1| NADH dehydrogenase subunit J
[Candidatus Liberibacter asiaticus str. psy62]
(199 letters)
>gnl|CDD|177129 MTH00057, ND6, NADH dehydrogenase subunit 6; Provisional.
Length = 186
Score = 127 bits (320), Expect = 3e-30
Identities = 73/178 (41%), Positives = 107/178 (60%), Gaps = 7/178 (3%)
Query: 7 FFYLFSFMAIISSFLVVTVRNPIYSVFSLIFAFVNAAGLFLLLGAEFVAMITLVVYVGAV 66
FYLF+ IIS +V++ NP++SV LI AF +A+ LF+LL EF+A+I L+VYVGA+
Sbjct: 4 LFYLFALGVIISGIMVISALNPVHSVLWLIVAFTSASALFILLEVEFIALIFLIVYVGAI 63
Query: 67 IVFFLFIIMMLDIDIEVAEPRKKRGFLGSFFIGILAAELIVCASNFMVFSAEGELSRLVF 126
+ FLF+IMML++ F IG++ L +S + S+ ++ + F
Sbjct: 64 AILFLFVIMMLNLTDLEGGGDMSNYLPAGFIIGVVF--LFEVSSGISLLSSGTKIGQWDF 121
Query: 127 -----KGNNVENIGKVLYTQYAYPLEISGFILLLSMIGAIVLMLRHRRDIKRQDISKQ 179
K +N+E +G+VLYT Y Y ++ FILL++MIGAIVL +IKRQDI Q
Sbjct: 122 PNWIEKESNIEVLGRVLYTDYYYLFILASFILLVAMIGAIVLTHDLIIEIKRQDIFIQ 179
>gnl|CDD|31181 COG0839, NuoJ, NADH:ubiquinone oxidoreductase subunit 6 (chain J)
[Energy production and conversion].
Length = 166
Score = 100 bits (250), Expect = 3e-22
Identities = 62/168 (36%), Positives = 100/168 (59%), Gaps = 2/168 (1%)
Query: 1 MVMQSLFFYLFSFMAIISSFLVVTVRNPIYSVFSLIFAFVNAAGLFLLLGAEFVAMITLV 60
M++++L FYLF+ +AI + VV +NP+YS L ++ A LF LLGAEF+ ++ ++
Sbjct: 1 MMIETLAFYLFAVLAIAFALGVVLAKNPVYSALYLALTLLSIAALFFLLGAEFLGVVQVL 60
Query: 61 VYVGAVIVFFLFIIMMLDIDIEVAEPRKKRGFLGSFFIGILAAELIVCASNFMVFSAEGE 120
VYVGAV+V FLF++MML++D RG + +G++ L++ + V S
Sbjct: 61 VYVGAVMVLFLFVVMMLNVDGAEVREEGLRGKPLAALVGLVLLALLIISV--AVVSGAFV 118
Query: 121 LSRLVFKGNNVENIGKVLYTQYAYPLEISGFILLLSMIGAIVLMLRHR 168
N++ +G VL+T Y P E++ +LL++M+GAIVL R R
Sbjct: 119 PPSNPAAIGNIKALGSVLFTDYLLPFELASVLLLVAMVGAIVLARRER 166
>gnl|CDD|177103 MTH00021, ND6, NADH dehydrogenase subunit 6; Validated.
Length = 188
Score = 98.6 bits (246), Expect = 9e-22
Identities = 56/187 (29%), Positives = 95/187 (50%), Gaps = 12/187 (6%)
Query: 11 FSFMAIISSFLVVTVRNPIYSVFSLIFAFVNAAGLFLLLGAEFVAMITLVVYVGAVIVFF 70
FS I S +V++ NP++S+F L+ FVN+A F+LLG +F+A++ L++YVGA+ + F
Sbjct: 2 FSLGIIGSGIMVISALNPVHSIFWLVVVFVNSAVFFILLGLDFLALMFLIIYVGAIAILF 61
Query: 71 LFIIMMLDIDIEVAEPRKKR--------GFLGSFFIGILAAELIVCASNFMVFSAEGELS 122
LF+IM+L++ + G + A + V +
Sbjct: 62 LFVIMLLNLTDFPPAFGGEADMTNYIPIGLIIGTLFFSEIASSWLIIGGPYVERWDLAFP 121
Query: 123 RLVFKGNNVENIGKVLYTQYAYPLEISGFILLLSMIGAIVLMLRHRRDI----KRQDISK 178
+ +N+E +G++LY Y ++ FILL++MIGAIVL ++ K+QDI
Sbjct: 122 WFLISYHNIEALGRILYITCYYLFLLASFILLVAMIGAIVLTQEPGSEVGPLSKKQDIFF 181
Query: 179 QLESNPD 185
Q+
Sbjct: 182 QISRANS 188
>gnl|CDD|177256 MTH00213, ND6, NADH dehydrogenase subunit 6; Provisional.
Length = 239
Score = 61.8 bits (150), Expect = 1e-10
Identities = 27/51 (52%), Positives = 40/51 (78%)
Query: 27 NPIYSVFSLIFAFVNAAGLFLLLGAEFVAMITLVVYVGAVIVFFLFIIMML 77
N + SVF LI F+ ++GLF++LG EF+ +I L+VYVGA+ + FLF+IMM+
Sbjct: 22 NFLASVFWLILTFIGSSGLFIVLGMEFLGLIFLIVYVGAICIIFLFVIMMI 72
Score = 44.5 bits (105), Expect = 2e-05
Identities = 22/38 (57%), Positives = 26/38 (68%)
Query: 128 GNNVENIGKVLYTQYAYPLEISGFILLLSMIGAIVLML 165
G N+E IG VLY Y Y + FILL++MIGAIVL L
Sbjct: 196 GTNLEAIGSVLYINYYYAFILVSFILLVAMIGAIVLGL 233
>gnl|CDD|176959 CHL00016, ndhG, NADH dehydrogenase subunit 6.
Length = 182
Score = 59.1 bits (144), Expect = 8e-10
Identities = 45/168 (26%), Positives = 74/168 (44%), Gaps = 10/168 (5%)
Query: 4 QSLFFYLFSFMAIISSFLVVTVRNPIYSVFSLIFAFVNAAGLFLLLGAEFVAMITLVVYV 63
I+ S VV + NPIYS FSL V + ++LL A+FVA L++YV
Sbjct: 8 HDFLLVFLGSGLILGSLGVVLLTNPIYSAFSLGLVLVCISLFYILLNADFVAAAQLLIYV 67
Query: 64 GAVIVFFLFIIMMLDIDIEVAEPRKKRGFLGSFFIGILAAELIVCASNFMV--------F 115
GA+ V +F +M ++ E ++ G ++ L ++ +
Sbjct: 68 GAINVLIIFAVMFMN-GPEYSKDFNLWTV-GDGITSLVCTSLFFSLITTILDTSWYGIIW 125
Query: 116 SAEGELSRLVFKGNNVENIGKVLYTQYAYPLEISGFILLLSMIGAIVL 163
+ +NV+ IG L T + P E+ ILL+++IGAI +
Sbjct: 126 TTRSNQIIEQDLISNVQQIGIHLSTDFLLPFELISIILLVALIGAITV 173
>gnl|CDD|144188 pfam00499, Oxidored_q3, NADH-ubiquinone/plastoquinone
oxidoreductase chain 6.
Length = 140
Score = 51.9 bits (125), Expect = 1e-07
Identities = 41/148 (27%), Positives = 73/148 (49%), Gaps = 9/148 (6%)
Query: 16 IISSFLVVTVRNPIYSVFSLIFAFVNAAGLFLLLGAEFVAMITLVVYVGAVIVFFLFIIM 75
I+SS LV+ +NPIY SLI ++ + L LLG+ ++ +I +VYVG ++V FL+++
Sbjct: 1 ILSSLLVLFSKNPIYLGLSLILLSLSLSLLLFLLGSSWLGLILFLVYVGGILVLFLYVVS 60
Query: 76 MLDIDIEVAEPRKKRGFLGSFFIGILAAELIVCASNFMVFSAEGELSRLVFKGNNVENIG 135
+ P +K F +L L+ F + + S +NV +
Sbjct: 61 LS--------PNEKFKFKKGSKFLLLLLLLLFILLLFFLLFSNLSFSLNSISSSNVNLLS 112
Query: 136 KVLYTQYAYPLEISGFILLLSMIGAIVL 163
+LY+ + + +LL+++IG I L
Sbjct: 113 -LLYSSNSLIFILLSLLLLIALIGVIKL 139
>gnl|CDD|177120 MTH00045, ND6, NADH dehydrogenase subunit 6; Validated.
Length = 162
Score = 38.0 bits (89), Expect = 0.002
Identities = 43/166 (25%), Positives = 69/166 (41%), Gaps = 8/166 (4%)
Query: 8 FYLFSFMAIISSFLVVTVRNPIYSVFSLIFAFVNAAGLFLLLGAEFVAMITLVVYVGAVI 67
FYLF + + S LV +P YS L+ ++ L LLG F+A++ L++Y+G ++
Sbjct: 3 FYLFLILMLFGSTLVFYSLSPYYSALGLVLVSLSGCLLLSLLGLSFLALLLLLIYMGGML 62
Query: 68 VFFLFIIMMLDIDIEVAEPRKKRGFLGSFFIGILAAELIVCASNFMVFSAEGELSRLVFK 127
V F++ AE LG + L L V S E +
Sbjct: 63 VVFVY------SSALSAERYPSVSNLGEVLVLSLLLSLWVFISFDNFL--ELSNNNWSLV 114
Query: 128 GNNVENIGKVLYTQYAYPLEISGFILLLSMIGAIVLMLRHRRDIKR 173
+ LY L + GFILL++++ A+V+ H R
Sbjct: 115 SLSDLVGSSELYNSGGLYLLLGGFILLVALVVALVISFGHEYSSLR 160
>gnl|CDD|177257 MTH00214, ND6, NADH dehydrogenase subunit 6; Provisional.
Length = 168
Score = 35.0 bits (81), Expect = 0.013
Identities = 15/71 (21%), Positives = 33/71 (46%)
Query: 7 FFYLFSFMAIISSFLVVTVRNPIYSVFSLIFAFVNAAGLFLLLGAEFVAMITLVVYVGAV 66
F +L F ++ +V + +P + L+ + L L G F+ +I ++Y+G +
Sbjct: 4 FVFLLMFGFLLGLMMVASSPSPYFGALGLVLLALLGCFLLLSHGNSFLGLILFLIYLGGM 63
Query: 67 IVFFLFIIMML 77
+V F + +
Sbjct: 64 LVVFSYSAALA 74
>gnl|CDD|177176 MTH00115, ND6, NADH dehydrogenase subunit 6; Provisional.
Length = 174
Score = 35.1 bits (82), Expect = 0.013
Identities = 20/64 (31%), Positives = 35/64 (54%)
Query: 7 FFYLFSFMAIISSFLVVTVRNPIYSVFSLIFAFVNAAGLFLLLGAEFVAMITLVVYVGAV 66
F +L ++ V + +P Y V SL+ A V G+ + LG FV+++ +VY+G +
Sbjct: 4 FVFLLGVCFVLGVVGVASNPSPYYGVVSLVLASVFGCGVLVSLGGSFVSLVLFLVYLGGM 63
Query: 67 IVFF 70
+V F
Sbjct: 64 LVVF 67
>gnl|CDD|31751 COG1563, COG1563, Predicted subunit of the Multisubunit Na+/H+
antiporter [Inorganic ion transport and metabolism].
Length = 87
Score = 31.4 bits (71), Expect = 0.18
Identities = 17/69 (24%), Positives = 33/69 (47%)
Query: 6 LFFYLFSFMAIISSFLVVTVRNPIYSVFSLIFAFVNAAGLFLLLGAEFVAMITLVVYVGA 65
L YL + + ++S+ L + R+ + +V + + AA L+ LL A VA+ +V G
Sbjct: 10 LIEYLITILLLLSALLAIFQRDLLNAVIASGVLSLLAALLYTLLLAPDVALTEALVGAGL 69
Query: 66 VIVFFLFII 74
+ +
Sbjct: 70 STAVYAIAL 78
>gnl|CDD|37045 KOG1834, KOG1834, KOG1834, Calsyntenin [Extracellular structures].
Length = 952
Score = 28.5 bits (63), Expect = 1.2
Identities = 13/44 (29%), Positives = 25/44 (56%)
Query: 150 GFILLLSMIGAIVLMLRHRRDIKRQDISKQLESNPDNSIVMVKV 193
GF++ + ++G + + HRR +RQ K E + D+S + + V
Sbjct: 838 GFLVFMVVLGVLRIRDAHRRRRRRQKRQKDGEMDWDDSALTITV 881
>gnl|CDD|34870 COG5273, COG5273, Uncharacterized protein containing DHHC-type Zn
finger [General function prediction only].
Length = 309
Score = 27.3 bits (60), Expect = 2.9
Identities = 15/80 (18%), Positives = 29/80 (36%), Gaps = 6/80 (7%)
Query: 7 FFYLFSFMAIISSFLVVTV------RNPIYSVFSLIFAFVNAAGLFLLLGAEFVAMITLV 60
FFY F I+ + +V+ + + G LL F+ L+
Sbjct: 154 FFYQFLLYTILVALVVLLSTAYYIAGIFSIRHDTSLAICFLIFGCSLLGVVFFIITTLLL 213
Query: 61 VYVGAVIVFFLFIIMMLDID 80
+++ +I+ L I + I
Sbjct: 214 LFLIYLILNNLTTIEFIQIS 233
>gnl|CDD|176167 cd08478, PBP2_CrgA, The C-terminal substrate binding domain of
LysR-type transcriptional regulator CrgA, contains the
type 2 periplasmic binding domain. This CD represents
the substrate binding domain of LysR-type
transcriptional regulator (LTTR) CrgA. The LTTRs are
acting as both auto-repressors and activators of target
promoters, controlling operons involved in a wide
variety of cellular processes such as amino acid
biosynthesis, CO2 fixation, antibiotic resistance,
degradation of aromatic compounds, nodule formation of
nitrogen-fixing bacteria, and synthesis of virulence
factors, to name a few. In contrast to the tetrameric
form of other LTTRs, CrgA from Neisseria meningitides
assembles into an octameric ring, which can bind up to
four 63-bp DNA oligonucleotides. Phylogenetic cluster
analysis further showed that the CrgA-like regulators
form a subclass of the LTTRs that function as octamers.
The CrgA is an auto-repressor of its own gene and
activates the expression of the mdaB gene which coding
for an NADPH-quinone reductase and that its action is
increased by MBL (alpha-methylene-gamma-butyrolactone),
an inducer of NADPH-quinone oxidoreductase. The
structural topology of this substrate-binding domain 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.
Length = 199
Score = 27.3 bits (61), Expect = 3.1
Identities = 19/52 (36%), Positives = 21/52 (40%), Gaps = 6/52 (11%)
Query: 106 IVCASNFMVFS--AEGELSRLVFKGNNV---ENIGKVLYTQYAYPLEISGFI 152
I C S+FM AEG L L F + I V Y A L I FI
Sbjct: 146 IACLSDFMTDKDIAEGRLIPL-FAEQTSDVRQPINAVYYRNTALSLRIRCFI 196
>gnl|CDD|35387 KOG0165, KOG0165, KOG0165, Microtubule-associated protein Asp
[Cytoskeleton].
Length = 1023
Score = 26.2 bits (57), Expect = 6.3
Identities = 10/41 (24%), Positives = 19/41 (46%)
Query: 159 GAIVLMLRHRRDIKRQDISKQLESNPDNSIVMVKVKSGKGI 199
A V++ +H R +S + S P V ++++S I
Sbjct: 217 KAAVVLQKHLMHKLRAFLSAKHFSQPTMLKVYLQIRSSVII 257
>gnl|CDD|37277 KOG2066, KOG2066, KOG2066, Vacuolar assembly/sorting protein VPS41
[Intracellular trafficking, secretion, and vesicular
transport].
Length = 846
Score = 26.0 bits (57), Expect = 7.2
Identities = 15/41 (36%), Positives = 24/41 (58%), Gaps = 3/41 (7%)
Query: 147 EISGFILLLSMIG---AIVLMLRHRRDIKRQDISKQLESNP 184
+I I+LL ++ AI L+L +R I ++ +QLE NP
Sbjct: 548 QIKDQIVLLMLLDSKKAIDLLLDNRDSISPSEVVEQLEDNP 588
>gnl|CDD|29942 cd00949, FBP_aldolase_I_bact, Fructose-1.6-bisphosphate aldolase
found in gram +/- bacteria. The enzyme catalyzes the
cleavage of fructose 1,6-bisphosphate to glyceraldehyde
3-phosphate and dihydroxyacetone phosphate (DHAP). The
enzyme is member of the class I aldolase family, which
utilizes covalent catalysis through a Schiff base formed
between a lysine residue of the enzyme and ketose
substrates..
Length = 292
Score = 26.0 bits (57), Expect = 7.9
Identities = 24/94 (25%), Positives = 41/94 (43%), Gaps = 6/94 (6%)
Query: 103 AELIVCASNFMVFSAEGELSRLVFKGNNVENIGKVLYTQYAYPLEI--SGFILLLSMIGA 160
EL++ A VF G R V K N + I V+ Q+ +I G + ++
Sbjct: 122 DELLMRAKEKGVF---GTKMRSVIKEANPKGIAAVVDQQFELAKQILSHGLVPIIEPEVD 178
Query: 161 IVLMLRHR-RDIKRQDISKQLESNPDNSIVMVKV 193
I + + I + +I K L+ P+ VM+K+
Sbjct: 179 IHSADKAKCEAILKAEILKHLDKLPEGQQVMLKL 212
>gnl|CDD|145271 pfam01997, Translin, Translin family. Members of this family
include Translin that interacts with DNA and forms a
ring around the DNA. This family also includes
Translin-associated protein X, which was found to
interact with translin with yeast two-hybrid screen.
Length = 186
Score = 25.6 bits (57), Expect = 8.8
Identities = 16/69 (23%), Positives = 26/69 (37%), Gaps = 12/69 (17%)
Query: 114 VFSAEGELSRLVFKGNNVENIGKVLYTQYAYPLEISGFI----LLLSMIGAIVLMLRHRR 169
+F GEL R + ++ Y PLEI F+ ++ LR +
Sbjct: 113 LFDLTGELMRFA-----LNSVTL---GDYERPLEILEFMEELYAGFRLLNLKNDGLRKKL 164
Query: 170 DIKRQDISK 178
D+ R + K
Sbjct: 165 DVLRYSLEK 173
>gnl|CDD|39167 KOG3964, KOG3964, KOG3964, Phosphatidylglycerolphosphate synthase
[Lipid transport and metabolism].
Length = 469
Score = 25.7 bits (56), Expect = 8.8
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 88 KKRGFLGSFFIGILAAELIVCASN 111
++R FL S ++G L EL+ C SN
Sbjct: 52 QRRIFLASLYLGKLERELVDCLSN 75
>gnl|CDD|35427 KOG0206, KOG0206, KOG0206, P-type ATPase [General function prediction
only].
Length = 1151
Score = 25.6 bits (56), Expect = 9.9
Identities = 14/81 (17%), Positives = 33/81 (40%), Gaps = 2/81 (2%)
Query: 1 MVMQSLFFYLFSFMAIISSFLVVTVRNPIYS-VFSLIFAFVNAAGLFLLLGAEFVA-MIT 58
+ +++ ++ + + I S L+ V IYS + I G+ L + +
Sbjct: 997 IALETSYWTWINHIVIWGSILLWFVFLFIYSELTPAISTPDPFYGVAEHLLSSPSFWLTL 1056
Query: 59 LVVYVGAVIVFFLFIIMMLDI 79
L+ V A++ F++ +
Sbjct: 1057 LLTVVAALLPDFVYKSLQRTF 1077
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
0.333 0.147 0.408
Gapped
Lambda K H
0.267 0.0657 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,374,076
Number of extensions: 134594
Number of successful extensions: 977
Number of sequences better than 10.0: 1
Number of HSP's gapped: 934
Number of HSP's successfully gapped: 273
Length of query: 199
Length of database: 6,263,737
Length adjustment: 89
Effective length of query: 110
Effective length of database: 4,340,536
Effective search space: 477458960
Effective search space used: 477458960
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)
S2: 55 (25.1 bits)