RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13378
(272 letters)
>gnl|CDD|191217 pfam05180, zf-DNL, DNL zinc finger. The domain is named after a
short C-terminal motif of D(N/H)L. This domain is a
novel zinc-finger protein essential for protein import
into mitochondria.
Length = 66
Score = 106 bits (267), Expect = 9e-30
Identities = 44/68 (64%), Positives = 50/68 (73%), Gaps = 3/68 (4%)
Query: 116 LKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEH 175
+L +TCKVCGTR++ ISK +YEKG VIV+C GC N HLIADNL WF D K NIE
Sbjct: 1 YQLTFTCKVCGTRSTKTISKQAYEKGTVIVQCPGCKNRHLIADNLGWFGDGK---VNIED 57
Query: 176 ILAEKGEQ 183
ILAEKGE
Sbjct: 58 ILAEKGES 65
Score = 46.4 bits (111), Expect = 3e-07
Identities = 22/33 (66%), Positives = 23/33 (69%), Gaps = 3/33 (9%)
Query: 220 SHHLIADNLKWFSDLKPGVTNIEHILAEKGEQV 252
+ HLIADNL WF D K NIE ILAEKGE V
Sbjct: 37 NRHLIADNLGWFGDGK---VNIEDILAEKGESV 66
>gnl|CDD|99997 cd04946, GT1_AmsK_like, This family is most closely related to the
GT1 family of glycosyltransferases. AmsK is involved in
the biosynthesis of amylovoran, which functions as a
virulence factor. It functions as a glycosyl transferase
which transfers galactose from UDP-galactose to a
lipid-linked amylovoran-subunit precursor. The members
of this family are found mainly in bacteria and Archaea.
Length = 407
Score = 34.2 bits (79), Expect = 0.060
Identities = 31/165 (18%), Positives = 52/165 (31%), Gaps = 30/165 (18%)
Query: 25 IYHPNLNILIVENEFSVSKLCYDYGLSHS-----ELKKRANLLKFYTR----------NS 69
+ L++LI + + Y Y L + LKK + +R
Sbjct: 111 LKLKYLHLLIYNSIDGQGTVFYSYWLHETAYALALLKKEYLRKRVISRAHGYDLYEDRYP 170
Query: 70 TPGNPEPIQLEHKLKLAYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRN 129
+ P L L + C G +L ++ K IK+ + G +
Sbjct: 171 SGYIPLRRYLLSSLDAVFPCSEQGRN--YLQKRYPAYKEKIKVSY----------LGVSD 218
Query: 130 SHLISKHSYEKGVVIVKCEGCSNN---HLIADNLKWFTDLKPGVT 171
+ISK S + + IV C LI L +P +
Sbjct: 219 PGIISKPSKDDTLRIVSCSYLVPVKRVDLIIKALAALAKARPSIK 263
>gnl|CDD|217854 pfam04032, Rpr2, RNAse P Rpr2/Rpp21/SNM1 subunit domain. This
family contains a ribonuclease P subunit of humans and
yeast. Other members of the family include the probable
archaeal homologues. This family includes SNM1. It is a
subunit of RNase MRP (mitochondrial RNA processing), a
ribonucleoprotein endoribonuclease that has roles in
both mitochondrial DNA replication and nuclear 5.8S rRNA
processing. SNM1 is an RNA binding protein that binds
the MRP RNA specifically. This subunit possibly binds
the precursor tRNA.
Length = 84
Score = 30.8 bits (70), Expect = 0.17
Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 6/52 (11%)
Query: 106 EKGVIKLKHKLKLAYTCKVCGT-----RNSHLISKHSYEKGVVIVKCEGCSN 152
+K I+L +K + CK CGT N + + + V+++ C C +
Sbjct: 34 KKHRIRLPPSIKRKF-CKKCGTLLIPGVNCRVRIEKRPKNKVLVITCLKCGH 84
>gnl|CDD|226009 COG3478, COG3478, Predicted nucleic-acid-binding protein containing
a Zn-ribbon domain [General function prediction only].
Length = 68
Score = 27.5 bits (61), Expect = 1.9
Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 3/47 (6%)
Query: 83 LKLAYTCKVCGTRN---SHLISKHSYEKGVIKLKHKLKLAYTCKVCG 126
+K A+ C CG N + + + +++ + TCK CG
Sbjct: 1 MKNAFKCPKCGNTNYEEKEIAATGGGLSKIFDVQNNKFIVITCKNCG 47
>gnl|CDD|176260 cd08300, alcohol_DH_class_III, class III alcohol dehydrogenases.
Members identified as glutathione-dependent formaldehyde
dehydrogenase(FDH), a member of the zinc
dependent/medium chain alcohol dehydrogenase family.
FDH converts formaldehyde and NAD(P) to formate and
NAD(P)H. The initial step in this process the
spontaneous formation of a S-(hydroxymethyl)glutathione
adduct from formaldehyde and glutathione, followed by
FDH-mediated oxidation (and detoxification) of the
adduct to S-formylglutathione. MDH family uses NAD(H)
as a cofactor in the interconversion of alcohols and
aldehydes or ketones. Like many zinc-dependent alcohol
dehydrogenases (ADH) of the medium chain alcohol
dehydrogenase/reductase family (MDR), these FDHs form
dimers, with 4 zinc ions per dimer. The medium chain
alcohol dehydrogenase family (MDR) have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit. Alcohol dehydrogenase in the liver
converts ethanol and NAD+ to acetaldehyde and NADH,
while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a catalytic
zinc at the active site and a structural zinc in a lobe
of the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 368
Score = 28.7 bits (65), Expect = 2.9
Identities = 20/56 (35%), Positives = 22/56 (39%), Gaps = 17/56 (30%)
Query: 164 TDLKPGVTNIEHILAEKGEQGCKGLFCLSHDIKLNTNIVRLMIETCLCHLIRETHG 219
T +KPG I E GE CK FC S +T LC IR T G
Sbjct: 76 TSVKPGDHVIPLYTPECGE--CK--FCKSG-------------KTNLCQKIRATQG 114
>gnl|CDD|239771 cd04238, AAK_NAGK-like, AAK_NAGK-like: N-Acetyl-L-glutamate kinase
(NAGK)-like . Included in this CD are the Escherichia
coli and Pseudomonas aeruginosa type NAGKs which
catalyze the phosphorylation of N-acetyl-L-glutamate
(NAG) by ATP in the second step of arginine biosynthesis
found in bacteria and photosynthetic organisms using
either the acetylated, noncyclic (NC), or
non-acetylated, cyclic (C) route of ornithine
biosynthesis. Also included in this CD is a distinct
group of uncharacterized (UC) bacterial and archeal
NAGKs. Members of this CD belong to the Amino Acid
Kinase Superfamily (AAK).
Length = 256
Score = 28.2 bits (64), Expect = 3.8
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 238 VTNIEHILAEKGEQVRRIDSNGAIELIEDEK 268
+T++ +L + G + + A ELIED
Sbjct: 178 LTDVPGVLDDPGSLISELTPKEAEELIEDGV 208
>gnl|CDD|217677 pfam03698, UPF0180, Uncharacterized protein family (UPF0180). The
members of this family are small uncharacterized
proteins.
Length = 80
Score = 26.5 bits (59), Expect = 4.3
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 236 PGVTNIEHILAEKGEQVRRIDSN 258
++NIE L EKG +V R+ +
Sbjct: 8 QSLSNIEEALKEKGYEVVRLKNE 30
>gnl|CDD|235189 PRK03988, PRK03988, translation initiation factor IF-2 subunit
beta; Validated.
Length = 138
Score = 26.8 bits (60), Expect = 7.5
Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 4/40 (10%)
Query: 111 KLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGC 150
K+ +K C CG+ ++ LI E + ++KCE C
Sbjct: 94 KIDRYVKEYVICPECGSPDTKLIK----EGRIWVLKCEAC 129
>gnl|CDD|237272 PRK13017, PRK13017, dihydroxy-acid dehydratase; Provisional.
Length = 596
Score = 27.6 bits (62), Expect = 7.6
Identities = 10/33 (30%), Positives = 19/33 (57%), Gaps = 3/33 (9%)
Query: 128 RNSHLISKHSYEKGVVIVKCEGCSNN---HLIA 157
+ S ++++ ++E +V+ G S N HLIA
Sbjct: 256 KPSDILTREAFENAIVVNSAIGGSTNAPIHLIA 288
>gnl|CDD|232809 TIGR00070, hisG, ATP phosphoribosyltransferase. Members of this
family from B. subtilis, Aquifex aeolicus, and
Synechocystis PCC6803 (and related taxa) lack the
C-terminal third of the sequence. The sole homolog from
Archaeoglobus fulgidus lacks the N-terminal 50 residues
(as reported) and is otherwise atypical of the rest of
the family. This model excludes the C-terminal extension
[Amino acid biosynthesis, Histidine family].
Length = 182
Score = 26.7 bits (60), Expect = 9.3
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 245 LAEKGEQVRRIDSNGAIEL 263
+KG V I NG++EL
Sbjct: 124 FEKKGIDVEIIKLNGSVEL 142
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 27.3 bits (61), Expect = 9.5
Identities = 19/62 (30%), Positives = 26/62 (41%), Gaps = 12/62 (19%)
Query: 8 KLQDDGYLNIDADPDSVIYHPNLNILIVENEFS-----------VSKLCYDYGLSHSELK 56
K D ++ ID +V+ N I+I FS V DYGLS +LK
Sbjct: 198 KRDPDSFIEIDRPGATVVQLRNYRIVIARPPFSDRWEITAVRPVVKLSLEDYGLS-DKLK 256
Query: 57 KR 58
+R
Sbjct: 257 ER 258
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 27.1 bits (60), Expect = 10.0
Identities = 12/65 (18%), Positives = 21/65 (32%), Gaps = 5/65 (7%)
Query: 9 LQDDGYLNIDADPDSVIYHPNLNILIVENEFSV-----SKLCYDYGLSHSELKKRANLLK 63
D + I P + I ++E S + D + E K++ L+
Sbjct: 78 FPDYAFKVIRVVPSGGGIITSTTIFVLETPREEDREIISDITLDDVIGQEEAKRKCRLIM 137
Query: 64 FYTRN 68
Y N
Sbjct: 138 EYLEN 142
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
0.319 0.137 0.419
Gapped
Lambda K H
0.267 0.0831 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,591,814
Number of extensions: 1257612
Number of successful extensions: 1003
Number of sequences better than 10.0: 1
Number of HSP's gapped: 999
Number of HSP's successfully gapped: 27
Length of query: 272
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 177
Effective length of database: 6,723,972
Effective search space: 1190143044
Effective search space used: 1190143044
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 (21.7 bits)
S2: 58 (25.9 bits)