RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17229
(131 letters)
>gnl|CDD|215399 PLN02748, PLN02748, tRNA dimethylallyltransferase.
Length = 468
Score = 46.4 bits (110), Expect = 7e-07
Identities = 28/74 (37%), Positives = 41/74 (55%), Gaps = 7/74 (9%)
Query: 24 IDDILQRNKVPIIVGGTNYYIESLLWTILLDNKTNINEQGEFTLY-----DIDKMRNLEH 78
I++IL RN +P+IVGGTNYYI++L+ LLD+ E F + +D L
Sbjct: 104 IEEILSRNGLPVIVGGTNYYIQALVSPFLLDDMAEETEDCTFVVASVLDEHMDVESGL-- 161
Query: 79 GRDVLEGLWKLDKE 92
G D + ++L KE
Sbjct: 162 GNDDEDHGYELLKE 175
>gnl|CDD|234626 PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase;
Reviewed.
Length = 307
Score = 45.5 bits (109), Expect = 1e-06
Identities = 16/25 (64%), Positives = 20/25 (80%)
Query: 24 IDDILQRNKVPIIVGGTNYYIESLL 48
I DIL R K+PI+VGGT YI++LL
Sbjct: 86 IADILARGKLPILVGGTGLYIKALL 110
>gnl|CDD|223401 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase
[Translation, ribosomal structure and biogenesis].
Length = 308
Score = 43.8 bits (104), Expect = 4e-06
Identities = 16/25 (64%), Positives = 21/25 (84%)
Query: 24 IDDILQRNKVPIIVGGTNYYIESLL 48
IDDIL R K+PI+VGGT Y+++LL
Sbjct: 85 IDDILARGKLPILVGGTGLYLKALL 109
>gnl|CDD|216659 pfam01715, IPPT, IPP transferase. This is a family of IPP
transferases EC:2.5.1.8 also known as tRNA
delta(2)-isopentenylpyrophosphate transferase. These
enzymes modify both cytoplasmic and mitochondrial tRNAs
at A(37) to give isopentenyl A(37).
Length = 253
Score = 41.5 bits (98), Expect = 3e-05
Identities = 12/25 (48%), Positives = 18/25 (72%)
Query: 24 IDDILQRNKVPIIVGGTNYYIESLL 48
I +I R K+P++VGGT Y ++LL
Sbjct: 49 IAEIRARGKIPLLVGGTGLYFKALL 73
>gnl|CDD|213512 TIGR00174, miaA, tRNA dimethylallyltransferase. Alternate names
include delta(2)-isopentenylpyrophosphate transferase,
IPP transferase, 2-methylthio-N6-isopentyladenosine tRNA
modification enzyme. Catalyzes the first step in the
modification of an adenosine near the anticodon to
2-methylthio-N6-isopentyladenosine. Understanding of
substrate specificity has changed [Protein synthesis,
tRNA and rRNA base modification].
Length = 287
Score = 37.4 bits (87), Expect = 8e-04
Identities = 13/25 (52%), Positives = 19/25 (76%)
Query: 24 IDDILQRNKVPIIVGGTNYYIESLL 48
I DI R K+P++VGGT Y+++LL
Sbjct: 81 IADITARGKIPLLVGGTGLYLKALL 105
>gnl|CDD|177823 PLN02165, PLN02165, adenylate isopentenyltransferase.
Length = 334
Score = 36.7 bits (85), Expect = 0.001
Identities = 12/25 (48%), Positives = 18/25 (72%)
Query: 24 IDDILQRNKVPIIVGGTNYYIESLL 48
I +I R K+PI+ GG+N +I +LL
Sbjct: 126 ISEITSRQKLPIVAGGSNSFIHALL 150
>gnl|CDD|215451 PLN02840, PLN02840, tRNA dimethylallyltransferase.
Length = 421
Score = 32.1 bits (73), Expect = 0.054
Identities = 17/32 (53%), Positives = 20/32 (62%), Gaps = 5/32 (15%)
Query: 20 RASQIDDILQRNKVPIIVGGTNYYIESLLWTI 51
RA+Q DIL R +VPI+ GGT Y L W I
Sbjct: 101 RATQ--DILNRGRVPIVAGGTGLY---LRWYI 127
>gnl|CDD|202102 pfam02056, Glyco_hydro_4, Family 4 glycosyl hydrolase.
Length = 183
Score = 29.3 bits (66), Expect = 0.46
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 3/43 (6%)
Query: 32 KVPIIVGGTNYYIESLLWTILLDNKTNINEQGEFTLYDIDKMR 74
K+ II GG+ ++LL + + E LYDID+ R
Sbjct: 1 KIVIIGGGSTITPKNLLGDLDHTEELPGRE---LALYDIDEER 40
>gnl|CDD|111162 pfam02238, COX7a, Cytochrome c oxidase subunit VIIa. Cytochrome
c oxidase, a 13 sub-unit complex, is the terminal
oxidase in the mitochondrial electron transport chain.
This family is composed of the heart and liver isoforms
of cytochrome c oxidase subunit VIIa.
Length = 56
Score = 26.6 bits (59), Expect = 1.0
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 25 DDILQRNKVPIIVGGTNYYIESLLW 49
DD L R +P+ +GGT Y++ L
Sbjct: 26 DDKLYRVTMPLTLGGTAYFLIGLGI 50
>gnl|CDD|133425 cd05197, GH4_glycoside_hydrolases, Glycoside Hydrases Family 4.
Glycoside hydrolases cleave glycosidic bonds to release
smaller sugars from oligo- or polysaccharides. Some
bacteria simultaneously translocate and phosphorylate
disaccharides via the phosphoenolpyruvate-dependent
phosphotransferase system (PEP-PTS). After
translocation, these phospho-disaccharides may be
hydrolyzed by GH4 glycoside hydrolases. Other organisms
(such as archaea and Thermotoga maritima) lack the
PEP-PTS system, but have several enzymes normally
associated with the PEP-PTS operon. GH4 family members
include 6-phospho-beta-glucosidases,
6-phospho-alpha-glucosidases,
alpha-glucosidases/alpha-glucuronidases (only from
Thermotoga), and alpha-galactosidases. They require two
cofactors, NAD+ and a divalent metal (Mn2+, Ni2+, Mg2+),
for activity. Some also require reducing conditions. GH4
glycoside hydrolases are part of the NAD(P)-binding
Rossmann fold superfamily, which includes a wide variety
of protein families including the NAD(P)-binding domains
of alcohol dehydrogenases, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate
dehydrogenases, formate/glycerate dehydrogenases,
siroheme synthases, 6-phosphogluconate dehydrogenases,
aminoacid dehydrogenases, repressor rex, and NAD-binding
potassium channel domains, among others.
Length = 425
Score = 28.3 bits (63), Expect = 1.4
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 8/77 (10%)
Query: 32 KVPIIVGGTNYYIESLLWTILLDNKTNINEQGEFTLYDIDKMRNLEHGRDVLEGLWKLDK 91
K+ II GG+++ E L + LL + E TLYDID+ R D++ + K
Sbjct: 2 KIAIIGGGSSFTPE--LVSGLLKTPEEL-PISEVTLYDIDEER-----LDIILTIAKRYV 53
Query: 92 EEKDDLFKVHDTDKIDE 108
EE K T +++
Sbjct: 54 EEVGADIKFEKTMDLED 70
>gnl|CDD|173191 PRK14729, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase;
Provisional.
Length = 300
Score = 27.9 bits (62), Expect = 1.6
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 24 IDDILQRNKVPIIVGGTNYYIESL 47
I ++ Q+ K+PI VGG+ +Y + L
Sbjct: 85 IKELRQQKKIPIFVGGSAFYFKHL 108
>gnl|CDD|224980 COG2069, CdhD, CO dehydrogenase/acetyl-CoA synthase delta subunit
(corrinoid Fe-S protein) [Energy production and
conversion].
Length = 403
Score = 27.9 bits (62), Expect = 1.7
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 21 ASQIDDILQRNKVPIIVGGT 40
A ++D+LQ VPII+GG+
Sbjct: 188 AKTLEDVLQAVDVPIIIGGS 207
>gnl|CDD|131219 TIGR02164, torA, trimethylamine-N-oxide reductase TorA. This very
narrowly defined family represents TorA, part of a
family of related molybdoenzymes that include biotin
sulfoxide reductases, dimethyl sulfoxide reductases, and
at least two different subfamilies of
trimethylamine-N-oxide reductases. A single enzyme from
the larger family may have more than one activity. TorA
typically is located in the periplasm, has a Tat
(twin-arginine translocation)-dependent signal sequence,
and is encoded in a torCAD operon.
Length = 822
Score = 27.9 bits (62), Expect = 1.9
Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 6/47 (12%)
Query: 33 VPIIVGGTNYYIESLLWTILLDNKTNINEQGEFTLYDIDKMRNLEHG 79
+P ++G T Y + W ++L+N I L+ D ++NL+ G
Sbjct: 188 LPYVLGSTEVYAQGTSWPLILENSDTI------VLWANDPVKNLQVG 228
>gnl|CDD|178259 PLN02653, PLN02653, GDP-mannose 4,6-dehydratase.
Length = 340
Score = 27.0 bits (60), Expect = 3.1
Identities = 11/39 (28%), Positives = 21/39 (53%)
Query: 62 QGEFTLYDIDKMRNLEHGRDVLEGLWKLDKEEKDDLFKV 100
Q + L ++D R+ D +E +W + ++EK D + V
Sbjct: 218 QKKLFLGNLDASRDWGFAGDYVEAMWLMLQQEKPDDYVV 256
>gnl|CDD|151298 pfam10849, DUF2654, Protein of unknown function (DUF2654). Some
members in this family of proteins are annotated as
a-gt.4 however currently no function is known.
Length = 70
Score = 25.8 bits (57), Expect = 3.3
Identities = 8/34 (23%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 68 YDIDKMRNL---EHGRDVLEGLWKLDKEEKDDLF 98
Y I K+R++ ++LE +W+ +++ D+
Sbjct: 37 YAIKKLRDIYKQPLNDELLETMWETSRQQILDMI 70
>gnl|CDD|184165 PRK13585, PRK13585,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Provisional.
Length = 241
Score = 26.8 bits (60), Expect = 3.5
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 10 LDTATGGVVCRASQIDDILQRNKVPIIVGG 39
LD A G A I+ I++ VP+ +GG
Sbjct: 54 LDGAFEGERKNAEAIEKIIEAVGVPVQLGG 83
>gnl|CDD|232948 TIGR00381, cdhD, CO dehydrogenase/acetyl-CoA synthase, delta
subunit. This is the small subunit of a heterodimer
which catalyzes the reaction CO + H2O + Acceptor = CO2 +
Reduced acceptor and is involved in the synthesis of
acetyl-CoA from CO2 and H2 [Energy metabolism,
Chemoautotrophy].
Length = 389
Score = 26.8 bits (59), Expect = 4.3
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 21 ASQIDDILQRNKVPIIVGGT 40
A ++D+LQ VPI++GG+
Sbjct: 177 AKVLEDVLQAVDVPIVIGGS 196
>gnl|CDD|215741 pfam00135, COesterase, Carboxylesterase family.
Length = 510
Score = 26.5 bits (59), Expect = 4.3
Identities = 9/32 (28%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 31 NKVPIIVGGTNYYIESLLWTILLDNKTNINEQ 62
NKVP+++G T+ E LL+ + +
Sbjct: 302 NKVPLLIGVTSD--EGLLFLAYVLPDPTELSE 331
>gnl|CDD|183660 PRK12660, PRK12660, putative monovalent cation/H+ antiporter
subunit C; Reviewed.
Length = 114
Score = 25.5 bits (56), Expect = 5.7
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 98 FKVHDTDKIDELEGEND 114
+KV D+I+ L GE+D
Sbjct: 96 YKVTKEDEIEGLRGEDD 112
>gnl|CDD|212526 cd10002, HDAC10_HDAC6-dom1, Histone deacetylase 6, domain 1 and
histone deacetylase 10. Histone deacetylases 6 and 10
are class IIb Zn-dependent enzymes that catalyze
hydrolysis of N(6)-acetyl-lysine of a histone to yield a
deacetylated histone (EC 3.5.1.98). Histone
acetylation/deacetylation process is important for
mediation of transcriptional regulation of many genes.
HDACs usually act via association with DNA binding
proteins to target specific chromatin regions. HDAC6 is
the only histone deacetylase with internal duplication
of two catalytic domains which appear to function
independently of each other, and also has a C-terminal
ubiquitin-binding domain. It is located in the cytoplasm
and associates with microtubule motor complex,
functioning as the tubulin deacetylase and regulating
microtubule-dependent cell motility. HDAC10 has an
N-terminal deacetylase domain and a C-terminal
pseudo-repeat that shares significant similarity with
its catalytic domain. It is located in the nucleus and
cytoplasm, and is involved in regulation of
melanogenesis. It transcriptionally down-regulates
thioredoxin-interacting protein (TXNIP), leading to
altered reactive oxygen species (ROS) signaling in human
gastric cancer cells. Known interaction partners of
HDAC6 are alpha tubulin (substrate) and ubiquitin-like
modifier FAT10 (also known as Ubiquitin D or UBD) while
interaction partners of HDAC10 are Pax3, KAP1, hsc70 and
HDAC3 proteins.
Length = 336
Score = 25.7 bits (57), Expect = 7.6
Identities = 10/46 (21%), Positives = 20/46 (43%), Gaps = 6/46 (13%)
Query: 84 EGLWKLDKE------EKDDLFKVHDTDKIDELEGENDKRDNKREDL 123
+GL + + E+D++ VH + ID ++ + E L
Sbjct: 24 DGLLERCVKIPAREAEEDEILLVHSQEYIDLVKSTETMEKEELESL 69
>gnl|CDD|221336 pfam11951, Fungal_trans_2, Fungal specific transcription factor
domain. This family of are likely to be transcription
factors. This protein is found in fungi. Proteins in
this family are typically between 454 to 826 amino acids
in length. This protein is found associated with
pfam00172.
Length = 381
Score = 25.9 bits (57), Expect = 8.9
Identities = 12/37 (32%), Positives = 16/37 (43%), Gaps = 2/37 (5%)
Query: 66 TLYDIDKMRNLEHGRDVLEGLWKL--DKEEKDDLFKV 100
L + N+ R+VLE +WK EE D V
Sbjct: 334 KLERRSGLGNVRRAREVLEEVWKRRDLGEESVDWRDV 370
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.317 0.140 0.413
Gapped
Lambda K H
0.267 0.0790 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,805,773
Number of extensions: 613889
Number of successful extensions: 713
Number of sequences better than 10.0: 1
Number of HSP's gapped: 713
Number of HSP's successfully gapped: 47
Length of query: 131
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 45
Effective length of database: 7,123,158
Effective search space: 320542110
Effective search space used: 320542110
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 (21.6 bits)
S2: 53 (24.1 bits)