RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11577
(89 letters)
>gnl|CDD|176897 cd08888, SRPBCC_PITPNA-B_like, Lipid-binding SRPBCC domain of
mammalian PITPNA, -B, and related proteins (Class I
PITPs). This subgroup includes the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of
mammalian Class 1 phosphatidylinositol transfer proteins
(PITPs), PITPNA/PITPalpha and PITPNB/PITPbeta,
Drosophila vibrator, and related proteins. These are
single domain proteins belonging to the PITP family of
lipid transfer proteins, and to the SRPBCC domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. In vitro, PITPs bind phosphatidylinositol
(PtdIns), as well as phosphatidylcholine (PtdCho) but
with a lower affinity. They transfer these lipids from
one membrane compartment to another. The cellular roles
of PITPs include inositol lipid signaling, PtdIns
metabolism, and membrane trafficking. In addition,
PITPNB transfers sphingomyelin in vitro, with a low
affinity. PITPNA is found chiefly in the nucleus and
cytoplasm; it is enriched in the brain and predominantly
localized in the axons. A reduced expression of PITPNA
contributes to the neurodegenerative phenotype of the
mouse vibrator mutation. The role of PITPNA in vivo may
be to provide PtdIns for localized PI3K-dependent
signaling, thereby controlling the polarized extension
of axonal processes. PITPNA homozygous null mice die
soon after birth from complicated organ failure,
including intestinal and hepatic steatosis,
hypoglycemia, and spinocerebellar disease. PITPNB is
associated with the Golgi and ER, and is highly
expressed in the liver. Deletion of the PITPNB gene
results in embryonic lethality. The PtdIns and PtdCho
exchange activity of PITPNB is required for
COPI-mediated retrograde transport from the Golgi to the
ER. Drosophila vibrator localizes to the ER, and has an
essential role in cytokinesis during mitosis and
meiosis.
Length = 258
Score = 67.5 bits (165), Expect = 4e-15
Identities = 26/47 (55%), Positives = 32/47 (68%), Gaps = 1/47 (2%)
Query: 42 VHDLPADKLKVREVVHIDIGNDPVS-AGDYKETEDPAKFKSEKTGRG 87
VH+L ++ K EVV+IDI + DYK EDPAKF+SEKTGRG
Sbjct: 124 VHNLDPEEWKEVEVVYIDIADRSQVDPKDYKADEDPAKFQSEKTGRG 170
>gnl|CDD|176857 cd07815, SRPBCC_PITP, Lipid-binding SRPBCC domain of Class I and
Class II Phosphatidylinositol Transfer Proteins. This
family includes the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of the
phosphatidylinositol transfer protein (PITP) family of
lipid transfer proteins. This family of proteins
includes Class 1 PITPs (PITPNA/PITPalpha and
PITPNB/PITPbeta, Drosophila vibrator and related
proteins), Class IIA PITPs (PITPNM1/PITPalphaI/Nir2,
PITPNM2/PITPalphaII/Nir3, Drosophila RdgB, and related
proteins), and Class IIB PITPs (PITPNC1/RdgBbeta and
related proteins). The PITP family belongs to the SRPBCC
domain superfamily of proteins that bind hydrophobic
ligands. SRPBCC domains have a deep hydrophobic
ligand-binding pocket. In vitro, PITPs bind
phosphatidylinositol (PtdIns), as well as
phosphatidylcholine (PtdCho) but with a lower affinity.
They transfer these lipids from one membrane compartment
to another. The cellular roles of PITPs include inositol
lipid signaling, PtdIns metabolism, and membrane
trafficking. Class III PITPs, exemplified by the Sec14p
family, are found in yeast and plants but are unrelated
in sequence and structure to Class I and II PITPs and
belong to a different superfamily.
Length = 251
Score = 67.0 bits (164), Expect = 4e-15
Identities = 27/46 (58%), Positives = 34/46 (73%)
Query: 42 VHDLPADKLKVREVVHIDIGNDPVSAGDYKETEDPAKFKSEKTGRG 87
H+L A++L R+VV IDI ND V++ DYK EDP FKS+KTGRG
Sbjct: 123 AHNLSAEQLAQRKVVVIDIANDSVASKDYKPEEDPKLFKSKKTGRG 168
>gnl|CDD|111058 pfam02121, IP_trans, Phosphatidylinositol transfer protein. Along
with the structurally unrelated Sec14p family (found in
pfam00650), this family can bind/exchange one molecule
of phosphatidylinositol (PI) or phosphatidylcholine (PC)
and thus aids their transfer between different membrane
compartments. There are three sub-families - all share
an N-terminal PITP-like domain, whose sequence is highly
conserved. It is described as consisting of three
regions. The N-terminal region is thought to bind the
lipid and contains two helices and an eight-stranded,
mostly antiparallel beta-sheet. An intervening loop
region, which is thought to play a role in
protein-protein interactions, separates this from the
C-terminal region, which exhibits the greatest sequence
variation and may be involved in membrane binding. PITP
alpha has a 16-fold greater affinity for PI than PC.
Together with PITP beta, it is expressed ubiquitously in
all tissues.
Length = 254
Score = 58.3 bits (141), Expect = 8e-12
Identities = 24/46 (52%), Positives = 28/46 (60%)
Query: 42 VHDLPADKLKVREVVHIDIGNDPVSAGDYKETEDPAKFKSEKTGRG 87
V +L K R + +IDI D VS+GDYK EDP F S KTGRG
Sbjct: 125 VFNLSPKDWKTRIIDYIDIVRDQVSSGDYKAEEDPKLFHSVKTGRG 170
>gnl|CDD|176899 cd08890, SRPBCC_PITPNC1_like, Lipid-binding SRPBCC domain of
mammalian PITPNC1,and related proteins (Class IIB
PITPs). This subgroup includes the N-terminal SRPBCC
(START/RHO_alpha_C /PITP /Bet_v1/CoxG/CalC) domain of
mammalian Class IIB phosphatidylinositol transfer
protein (PITP), PITPNC1/RdgBbeta, and related proteins.
These are metazoan proteins belonging to the PITP family
of lipid transfer proteins, and to the SRPBCC domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. In vitro, PITPs bind phosphatidylinositol
(PtdIns), as well as phosphatidylcholine (PtdCho) but
with a lower affinity. They transfer these lipids from
one membrane compartment to another. The cellular roles
of PITPs include inositol lipid signaling, PtdIns
metabolism, and membrane trafficking. Mammalian PITPNC1
contains an amino-terminal SRPBCC PITP-like domain and a
short carboxyl-terminal domain. It is a cytoplasmic
protein, and is ubiquitously expressed. It can transfer
phosphatidylinositol (PtdIns) in vitro with a similar
ability to other PITPs.
Length = 250
Score = 54.8 bits (132), Expect = 1e-10
Identities = 24/44 (54%), Positives = 27/44 (61%)
Query: 44 DLPADKLKVREVVHIDIGNDPVSAGDYKETEDPAKFKSEKTGRG 87
L +L REV H+DI D + YKE EDP FKSEKTGRG
Sbjct: 124 FLSEAELSEREVCHLDIAYDEIPEKYYKEEEDPKYFKSEKTGRG 167
>gnl|CDD|176898 cd08889, SRPBCC_PITPNM1-2_like, Lipid-binding SRPBCC domain of
mammalian PITPNM1-2 and related proteins (Class IIA
PITPs). This subgroup includes an N-terminal SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of
mammalian Class II phosphatidylinositol transfer protein
(PITPs), PITPNM1/PITPalphaI/Nir2 (PYK2 N-terminal
domain-interacting receptor2) and
PITPNM2/PITPalphaII/Nir3), Drosophila RdgB, and related
proteins. These are membrane associated multidomain
proteins belonging to the PITP family of lipid transfer
proteins, and to the SRPBCC domain superfamily of
proteins that bind hydrophobic ligands. SRPBCC domains
have a deep hydrophobic ligand-binding pocket. In vitro,
PITPs bind phosphatidylinositol (PtdIns), as well as
phosphatidylcholine (PtdCho) but with a lower affinity.
They transfer these lipids from one membrane compartment
to another. The cellular roles of PITPs include inositol
lipid signaling, PtdIns metabolism, and membrane
trafficking. Ablation of the mouse gene encoding PITPNM1
results in early embryonic death. PITPNM1 is localized
chiefly to the Golgi apparatus, and under certain
conditions translocates to the lipid droplets. Targeting
to the latter is dependent on a specific threonine
residue within the SRPBCC domain. PITPNM1 plays a part
in Golgi-mediated transport. It regulates diacylglycerol
(DAG) production at the trans-Golgi network (TGN) via
the CDP-choline pathway. Drosophila RdgB, the founding
member of the PITP family, is implicated in the visual
and olfactory transduction. RdgB is required for
maintenance of ultra structure in photoreceptors and for
sensory transduction. The mouse PITPNM1 gene rescues the
phenotype of Drosophila rdgB mutant flies. In addition
to the SRPBCC domain, PITPNM1 and -2 contain a
Rho-inhibitory domain (Rid), six hydrophobic stretches,
a DDHD calcium binding region, and a C-terminal tyrosine
kinase Pyk2-binding / HAD-like phosphohydrolase domain.
PITPNM1 has a role in regulating cell morphogenesis
through its Rho inhibitory domain (Rid). This
SRPBCC_PITPNM1-2_like domain model includes the first 52
residues of the 224 residues Rid (Rho-inhibitory
domain).
Length = 260
Score = 53.2 bits (128), Expect = 5e-10
Identities = 23/46 (50%), Positives = 28/46 (60%)
Query: 42 VHDLPADKLKVREVVHIDIGNDPVSAGDYKETEDPAKFKSEKTGRG 87
V +L +L+ R + IDI DPV DYK EDP + SEKTGRG
Sbjct: 125 VFNLSPAELRQRIIDFIDIVKDPVPGSDYKAEEDPKLYVSEKTGRG 170
>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated.
Length = 330
Score = 29.1 bits (66), Expect = 0.23
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 7 EKRKKSDEEEEKKKEEEEEEGAGEFG 32
+ ++ +EEEE+++E EEE A G
Sbjct: 301 AEEEEEEEEEEEEEEPSEEEAAAGLG 326
Score = 26.8 bits (60), Expect = 1.4
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 7 EKRKKSDEEEEKKKEEEEEEGAGE 30
++ +EEEE+++EE EE A
Sbjct: 300 AAEEEEEEEEEEEEEEPSEEEAAA 323
Score = 24.8 bits (55), Expect = 7.4
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 11 KSDEEEEKKKEEEEEEGAGE 30
+ EEEE+++EEEEEE E
Sbjct: 299 AAAEEEEEEEEEEEEEEPSE 318
Score = 24.4 bits (54), Expect = 9.4
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 10 KKSDEEEEKKKEEEEEEGAGEFGPEEL 36
++EEEE+++EEEEEE + E L
Sbjct: 299 AAAEEEEEEEEEEEEEEPSEEEAAAGL 325
>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230;
Provisional.
Length = 2849
Score = 29.2 bits (65), Expect = 0.24
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 13 DEEEEKKKEEEEEEGAGEFGPEELPGFG 40
DE+E++ ++EE++ E EE+ GF
Sbjct: 157 DEDEDEDDDDEEDDEEEEEEEEEIKGFD 184
Score = 26.2 bits (57), Expect = 3.1
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 4 DKWEKRKKSDEEEEKKKEEEEEEGAGEFGPEELPGFG 40
D ++ + D+EE+ ++EEEEEE F E+ G
Sbjct: 156 DDEDEDEDDDDEEDDEEEEEEEEEIKGFDDEDEEDEG 192
>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein. This
protein is covalently attached to the terminii of
replicating DNA in vivo.
Length = 548
Score = 28.5 bits (64), Expect = 0.41
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 12 SDEEEEKKKEEEEEEGAGEFGPE 34
+EE +++EEEEEE F E
Sbjct: 311 EEEEVPEEEEEEEEEEERTFEEE 333
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 28.0 bits (62), Expect = 0.59
Identities = 15/33 (45%), Positives = 22/33 (66%)
Query: 4 DKWEKRKKSDEEEEKKKEEEEEEGAGEFGPEEL 36
D E+ ++ +EEEE+++EEEEEE E E L
Sbjct: 862 DSEEEEEEEEEEEEEEEEEEEEEEEEEENEEPL 894
Score = 26.5 bits (58), Expect = 2.2
Identities = 13/30 (43%), Positives = 20/30 (66%)
Query: 7 EKRKKSDEEEEKKKEEEEEEGAGEFGPEEL 36
E+ ++ +EEEE+++EEEEEE P L
Sbjct: 867 EEEEEEEEEEEEEEEEEEEEEEENEEPLSL 896
Score = 26.1 bits (57), Expect = 2.7
Identities = 11/23 (47%), Positives = 18/23 (78%)
Query: 4 DKWEKRKKSDEEEEKKKEEEEEE 26
D + ++ +EEEE+++EEEEEE
Sbjct: 859 DGGDSEEEEEEEEEEEEEEEEEE 881
Score = 25.3 bits (55), Expect = 4.6
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 10 KKSDEEEEKKKEEEEEEGAGEFGPEELP 37
++ +EEEE+++EEEEEE E E P
Sbjct: 866 EEEEEEEEEEEEEEEEEEEEEEEENEEP 893
>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein. This
family includes the radial spoke head proteins RSP4 and
RSP6 from Chlamydomonas reinhardtii, and several
eukaryotic homologues, including mammalian RSHL1, the
protein product of a familial ciliary dyskinesia
candidate gene.
Length = 481
Score = 27.7 bits (62), Expect = 0.65
Identities = 17/45 (37%), Positives = 23/45 (51%)
Query: 5 KWEKRKKSDEEEEKKKEEEEEEGAGEFGPEELPGFGLVHDLPADK 49
W ++ DEEEE++ EEEEEE PE G L+ + D
Sbjct: 340 TWVNPEQKDEEEEQEDEEEEEEEEEPEEPEPEEGPPLLTPISEDA 384
>gnl|CDD|240285 PTZ00135, PTZ00135, 60S acidic ribosomal protein P0; Provisional.
Length = 310
Score = 27.7 bits (62), Expect = 0.67
Identities = 8/23 (34%), Positives = 10/23 (43%)
Query: 10 KKSDEEEEKKKEEEEEEGAGEFG 32
+ +EEEEEE FG
Sbjct: 285 AAAAAAAAPAEEEEEEEDDMGFG 307
>gnl|CDD|151656 pfam11214, Med2, Mediator complex subunit 2. This family of
mediator complex subunit 2 proteins is conserved in
fungi. Cyclin-dependent kinase CDK8 or Srb10 interacts
with and phosphorylates Med2. Post-translational
modifications of Mediator subunits are important for
regulation of gene expression.
Length = 99
Score = 26.6 bits (59), Expect = 1.1
Identities = 13/19 (68%), Positives = 16/19 (84%)
Query: 7 EKRKKSDEEEEKKKEEEEE 25
E +KK +EEE KKKEEEE+
Sbjct: 80 ENKKKQEEEERKKKEEEEK 98
Score = 24.3 bits (53), Expect = 6.3
Identities = 12/19 (63%), Positives = 16/19 (84%)
Query: 8 KRKKSDEEEEKKKEEEEEE 26
+ KK EEEE+KK+EEEE+
Sbjct: 80 ENKKKQEEEERKKKEEEEK 98
>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed.
Length = 106
Score = 26.5 bits (59), Expect = 1.3
Identities = 14/26 (53%), Positives = 18/26 (69%)
Query: 7 EKRKKSDEEEEKKKEEEEEEGAGEFG 32
+ KK +EEEE++KEE EEE A G
Sbjct: 77 AEEKKEEEEEEEEKEESEEEAAAGLG 102
>gnl|CDD|206063 pfam13892, DBINO, DNA-binding domain. DBINO is a DNA-binding
domain found on global transcription activator SNF2L1
proteins and chromatin re-modelling proteins.
Length = 140
Score = 26.5 bits (59), Expect = 1.4
Identities = 12/29 (41%), Positives = 16/29 (55%), Gaps = 4/29 (13%)
Query: 2 KYDKWE----KRKKSDEEEEKKKEEEEEE 26
K +K E KR + + E+ KKEEE E
Sbjct: 80 KNEKEERELRKRAEKEALEQAKKEEELRE 108
>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional.
Length = 292
Score = 26.3 bits (59), Expect = 2.1
Identities = 12/27 (44%), Positives = 20/27 (74%)
Query: 1 MKYDKWEKRKKSDEEEEKKKEEEEEEG 27
+K ++ E+R++ EE E+K EE +EEG
Sbjct: 39 LKAEEIEERREVREEAEEKYEEAKEEG 65
>gnl|CDD|219141 pfam06697, DUF1191, Protein of unknown function (DUF1191). This
family contains hypothetical plant proteins of unknown
function.
Length = 278
Score = 26.3 bits (58), Expect = 2.3
Identities = 13/39 (33%), Positives = 15/39 (38%)
Query: 8 KRKKSDEEEEKKKEEEEEEGAGEFGPEELPGFGLVHDLP 46
KRKK EE E++ EE E G P P
Sbjct: 240 KRKKRREEMERRAEEGEALRVSMVGRSRAPSATGTRTQP 278
>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P. This model
represents the L12P protein of the large (50S) subunit
of the archaeal ribosome.
Length = 105
Score = 25.4 bits (56), Expect = 3.0
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 7 EKRKKSDEEEEKKKEEEEEEGAGEFG 32
E+ ++ +EEEE+++EE EEE G
Sbjct: 76 EEEEEEEEEEEEEEEESEEEAMAGLG 101
>gnl|CDD|234306 TIGR03674, fen_arch, flap structure-specific endonuclease.
Endonuclease that cleaves the 5'-overhanging flap
structure that is generated by displacement synthesis
when DNA polymerase encounters the 5'-end of a
downstream Okazaki fragment. Has 5'-endo-/exonuclease
and 5'-pseudo-Y-endonuclease activities. Cleaves the
junction between single and double-stranded regions of
flap DNA.
Length = 338
Score = 25.7 bits (57), Expect = 3.2
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 1 MKYDKWEKRKKSDEEEEKKKEEEEEEG 27
+K + E+R++ EE E+K EE E+G
Sbjct: 86 LKAETLEERREIREEAEEKWEEALEKG 112
>gnl|CDD|185582 PTZ00373, PTZ00373, 60S Acidic ribosomal protein P2; Provisional.
Length = 112
Score = 25.3 bits (55), Expect = 4.1
Identities = 11/17 (64%), Positives = 14/17 (82%)
Query: 10 KKSDEEEEKKKEEEEEE 26
K ++EEKK+EEEEEE
Sbjct: 87 KAEAKKEEKKEEEEEEE 103
>gnl|CDD|237682 PRK14343, PRK14343, lipoate-protein ligase B; Provisional.
Length = 235
Score = 25.5 bits (56), Expect = 4.2
Identities = 11/26 (42%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 32 GPEELPGFGLVHDLPADKLKVREVVH 57
GP ++ + L+ DL KL VRE+V
Sbjct: 89 GPGQVVAYLLL-DLRRRKLMVRELVT 113
>gnl|CDD|227446 COG5116, RPN2, 26S proteasome regulatory complex component
[Posttranslational modification, protein turnover,
chaperones].
Length = 926
Score = 25.3 bits (55), Expect = 5.1
Identities = 8/32 (25%), Positives = 14/32 (43%)
Query: 5 KWEKRKKSDEEEEKKKEEEEEEGAGEFGPEEL 36
K + ++K ++E K E E GE +
Sbjct: 798 KQKPKEKGPNDKEIKIESPSVETEGERCTIKQ 829
>gnl|CDD|162338 TIGR01398, FlhA, flagellar biosynthesis protein FlhA. This model
describes flagellar biosynthesis protein FlhA, one of a
large number of genes associated with the biosynthesis
of functional bacterial flagella. Homologs of many such
proteins, including FlhA, function in type III protein
secretion systems. A separate model describes InvA
(Salmonella enterica), LcrD (Yersinia enterocolitica),
HrcV (Xanthomonas), etc., all of which score below the
noise cutoff for this model [Cellular processes,
Chemotaxis and motility].
Length = 678
Score = 25.3 bits (56), Expect = 5.7
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 13 DEEEEKKKEEEEEEGAGEFG 32
EEE KK+ EE E+ A +G
Sbjct: 159 TEEEAKKRREELEQEADFYG 178
>gnl|CDD|189037 cd09867, PIN_FEN1, PIN domain of Flap Endonuclease-1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. Flap endonuclease-1 (FEN1) is
involved in multiple DNA metabolic pathways, including
DNA replication processes (5' flap DNA endonuclease
activity and double stranded DNA 5'-exonuclease
activity) and DNA repair processes (long-patch base
excision repair) in eukaryotes and archaea. Interaction
between FEN1 and PCNA (Proliferating cell nuclear
antigen) is an essential prerequisite to FEN1's DNA
replication functionality and stimulates FEN1 nuclease
activity by 10-50 fold. FEN1 belongs to the
FEN1-EXO1-like family of structure-specific, 5'
nucleases. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region (I
domain) of variable length (approximately 45 residues in
FEN1 PIN domains) and a H3TH (helix-3-turn-helix)
domain, an atypical helix-hairpin-helix-2-like region.
Both the H3TH domain (not included here) and the helical
arch/clamp region are involved in DNA binding. Nucleases
within this group also have a carboxylate-rich active
site that is involved in binding essential divalent
metal ion cofactors (Mg2+/Mn2+). FEN1 has a C-terminal
extension containing residues forming the consensus
PIP-box - Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1
to PCNA.
Length = 261
Score = 25.2 bits (56), Expect = 5.8
Identities = 13/27 (48%), Positives = 19/27 (70%)
Query: 1 MKYDKWEKRKKSDEEEEKKKEEEEEEG 27
+K + EKR++ EE E+K EE +EEG
Sbjct: 87 LKSGELEKRRERREEAEEKLEEAKEEG 113
>gnl|CDD|224530 COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthase beta subunit
[Energy production and conversion].
Length = 470
Score = 25.2 bits (55), Expect = 6.1
Identities = 15/32 (46%), Positives = 20/32 (62%)
Query: 10 KKSDEEEEKKKEEEEEEGAGEFGPEELPGFGL 41
++ EEEE+++EEEEEE A P E P G
Sbjct: 399 ERWAEEEEEEEEEEEEEAAEAEAPMEEPVPGF 430
>gnl|CDD|221342 pfam11960, DUF3474, Domain of unknown function (DUF3474). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria and eukaryotes. This domain
is typically between 126 to 140 amino acids in length.
This domain is found associated with pfam00487.
Length = 135
Score = 24.6 bits (54), Expect = 6.3
Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 14 EEEEKKKEEEEEEGAGEFGPEELPGFGL 41
EEEE++ +EEE EF P P F L
Sbjct: 74 EEEEEENGNDEEEE-EEFDPGAPPPFKL 100
>gnl|CDD|235302 PRK04456, PRK04456, acetyl-CoA decarbonylase/synthase complex
subunit beta; Reviewed.
Length = 463
Score = 25.0 bits (55), Expect = 7.1
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 7 EKRKKSDEEEEKKKEEEEEEGAGEFGPEELPGFGL 41
E+ +EEEE+++EEEEEE E P L
Sbjct: 400 ERWAAEEEEEEEEEEEEEEEPVAEVMMMPAPEMQL 434
>gnl|CDD|176227 cd08266, Zn_ADH_like1, Alcohol dehydrogenases of the MDR family.
This group contains proteins related to the
zinc-dependent alcohol dehydrogenases. However, while
the group has structural zinc site characteristic of
these enzymes, it lacks the consensus site for a
catalytic zinc. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. 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 has 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.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 342
Score = 24.5 bits (54), Expect = 8.7
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 8/45 (17%)
Query: 46 PADKL-KVREVVHIDIGNDPVSAGDYKETEDPAKFKSEKTGRGVD 89
DKL + +E +G D V DY++ + + + RGVD
Sbjct: 200 SEDKLERAKE-----LGADYVI--DYRKEDFVREVRELTGKRGVD 237
>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207). This
family is found in eukaryotes; it has several conserved
tryptophan residues. The function is not known.
Length = 261
Score = 24.3 bits (53), Expect = 9.6
Identities = 4/24 (16%), Positives = 16/24 (66%)
Query: 2 KYDKWEKRKKSDEEEEKKKEEEEE 25
+ +WE +K +++++++E ++
Sbjct: 183 RLQEWELKKLKQQQQKREEERRKQ 206
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
0.304 0.132 0.374
Gapped
Lambda K H
0.267 0.0709 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,813,385
Number of extensions: 417975
Number of successful extensions: 1845
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1525
Number of HSP's successfully gapped: 270
Length of query: 89
Length of database: 10,937,602
Length adjustment: 57
Effective length of query: 32
Effective length of database: 8,409,424
Effective search space: 269101568
Effective search space used: 269101568
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.8 bits)
S2: 53 (24.2 bits)