RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3963
(128 letters)
>gnl|CDD|133116 cd06906, M14_Nna1, Peptidase M14-like domain of ATP/GTP binding
proteins and cytosolic carboxypeptidases. Peptidase
M14-like domain of Nna-1 (Nervous system Nuclear protein
induced by Axotomy), also known as ATP/GTP binding
protein (AGTPBP-1) and cytosolic carboxypeptidase (CCP),
and related proteins. The Peptidase M14 family of
metallocarboxypeptidases are zinc-binding
carboxypeptidases (CPs) which hydrolyze single,
C-terminal amino acids from polypeptide chains, and have
a recognition site for the free C-terminal carboxyl
group, which is a key determinant of specificity. This
eukaryotic subgroup includes the mouse Nna1/CCP-1, and
-4 proteins, and the human Nna1/AGTPBP-1 protein.
Nna1-like proteins are active metallopeptidases that are
thought to act on cytosolic proteins such as
alpha-tubulin, to remove a C-terminal tyrosine. Nna1 is
widely expressed in the developing and adult nervous
systems, including cerebellar Purkinje and granule
neurons, miral cells of the olfactory bulb and retinal
photoreceptors. Nna1 is also induced in axotomized motor
neurons. Mutations in Nna1 cause Purkinje cell
degeneration (pcd). The Nna1 CP domain is required to
prevent the retinal photoreceptor loss and cerebellar
ataxia phenotypes of pcd mice, and a functional
zinc-binding domain is needed for Nna-1 to support
neuron survival in these mice. Nna1-like proteins from
the different phyla are highly diverse, but they all
contain a unique N-terminal conserved domain right
before the CP domain. It has been suggested that this
N-terminal domain might act as a folding domain.
Length = 278
Score = 89.5 bits (222), Expect = 8e-23
Identities = 37/66 (56%), Positives = 46/66 (69%), Gaps = 3/66 (4%)
Query: 2 LSRLLEQCALSFDPKSSHYKIERSKESTARITIWREYGVVRSYTMESTYCGFDQGSFK-- 59
L ++L A +F S + +E+SKESTAR+ +WRE GV RSYTMEST CG DQG +K
Sbjct: 199 LPKILSHIAPAFSMSSCSFVVEKSKESTARVVVWREIGVQRSYTMESTLCGCDQGKYKGL 258
Query: 60 -IGTKE 64
IGTKE
Sbjct: 259 QIGTKE 264
Score = 57.1 bits (138), Expect = 8e-11
Identities = 20/40 (50%), Positives = 32/40 (80%), Gaps = 1/40 (2%)
Query: 70 RGLIEFCTRVLKKTPYFYCDFHGHSLKKNIFLYGCSSQES 109
+GL+++ +K++P YCD+HGHS KKN+F+YGCS +E+
Sbjct: 139 KGLLQY-LAAIKRSPLVYCDYHGHSRKKNVFMYGCSIKET 177
>gnl|CDD|199859 cd06235, M14_Nna1_like_2, Peptidase M14-like domain of human
Nna1/AGTPBP-1, AGBL2 -5, and related proteins. Subgroup
of the Peptidase M14-like domain of Nna-1 (Nervous
system Nuclear protein induced by Axotomy), also known
as ATP/GTP binding protein (AGTPBP-1) and cytosolic
carboxypeptidase (CCP), and related proteins. The
Peptidase M14 family of metallocarboxypeptidases are
zinc-binding carboxypeptidases (CPs) which hydrolyze
single, C-terminal amino acids from polypeptide chains,
and have a recognition site for the free C-terminal
carboxyl group, which is a key determinant of
specificity. This eukaryotic subgroup includes the human
Nna1/AGTPBP-1 and AGBL -2, -3, -4, and -5, and the mouse
Nna1/CCP-1 and CCP -2 through -6. Nna1-like proteins are
active metallopeptidases that are thought to act on
cytosolic proteins such as alpha-tubulin, to remove a
C-terminal tyrosine. Nna1 is widely expressed in the
developing and adult nervous systems, including
cerebellar Purkinje and granule neurons, miral cells of
the olfactory bulb and retinal photoreceptors. Nna1 is
also induced in axotomized motor neurons. Mutations in
Nna1 cause Purkinje cell degeneration (pcd). The Nna1 CP
domain is required to prevent the retinal photoreceptor
loss and cerebellar ataxia phenotypes of pcd mice, and a
functional zinc-binding domain is needed for Nna-1 to
support neuron survival in these mice. Nna1-like
proteins from the different phyla are highly diverse,
but they all contain a unique N-terminal conserved
domain right before the CP domain. It has been suggested
that this N-terminal domain might act as a folding
domain.
Length = 258
Score = 62.6 bits (153), Expect = 7e-13
Identities = 18/59 (30%), Positives = 35/59 (59%)
Query: 2 LSRLLEQCALSFDPKSSHYKIERSKESTARITIWREYGVVRSYTMESTYCGFDQGSFKI 60
+LL + F S +K+++ KE TAR+ +W+E + SYT+E+++ G+ +G+
Sbjct: 179 FPKLLSKLCPYFSFSSCSFKVQKDKEGTARVALWKELKIPNSYTLETSFGGYQKGNRAG 237
Score = 58.7 bits (143), Expect = 2e-11
Identities = 15/38 (39%), Positives = 23/38 (60%)
Query: 81 KKTPYFYCDFHGHSLKKNIFLYGCSSQESWLSSDKCRV 118
++ + D HGHS KKN F+YGC + + L+ K R+
Sbjct: 141 ERNIILFIDLHGHSRKKNSFMYGCENSDDPLNYYKERL 178
>gnl|CDD|133117 cd06907, M14_AGBL2-3_like, Peptidase M14-like domain of ATP/GTP
binding protein AGBL-2 and AGBL-3, and related proteins.
Peptidase M14-like domain of ATP/GTP binding
protein_like (AGBL)-2, and related proteins. The
Peptidase M14 family of metallocarboxypeptidases are
zinc-binding carboxypeptidases (CPs) which hydrolyze
single, C-terminal amino acids from polypeptide chains,
and have a recognition site for the free C-terminal
carboxyl group, which is a key determinant of
specificity. This subgroup includes the human AGBL-2,
and -3, and the mouse cytosolic carboxypeptidase
(CCPs)-2, and -3. ATP/GTP binding protein
(AGTPBP-1/Nna1)-like proteins are active
metallopeptidases that are thought to act on cytosolic
proteins such as alpha-tubulin, to remove a C-terminal
tyrosine. Mutations in AGTPBP-1/Nna1 cause Purkinje cell
degeneration (pcd). AGTPBP-1/Nna1 however does not
belong to this subgroup. AGTPBP-1/Nna1-like proteins
from the different phyla are highly diverse, but they
all contain a unique N-terminal conserved domain right
before the CP domain. It has been suggested that this
N-terminal domain might act as a folding domain.
Length = 261
Score = 58.5 bits (142), Expect = 2e-11
Identities = 27/82 (32%), Positives = 46/82 (56%), Gaps = 11/82 (13%)
Query: 4 RLLEQCALS-FDPKSSHYKIERSKESTARITIWREYGVVRSYTMESTYCGFDQGSFKIGT 62
++ + A F +S +K+++SKE T R+ +WR G++ S+TME+T+CG G + GT
Sbjct: 182 LMMSKNAPDKFSFRSCKFKVQKSKEGTGRVVMWRL-GILNSFTMEATFCGSTLGR-RKGT 239
Query: 63 K------ESM--KIVRGLIEFC 76
ESM L+++C
Sbjct: 240 HFTTSDLESMGYHFCDTLLDYC 261
Score = 47.4 bits (113), Expect = 2e-07
Identities = 16/30 (53%), Positives = 20/30 (66%), Gaps = 3/30 (10%)
Query: 86 FYCDFHGHSLKKNIFLYGCSSQ---ESWLS 112
YCD HGHS K N+F+YGC ++ E WL
Sbjct: 147 LYCDLHGHSRKNNVFMYGCENKLNPEKWLH 176
>gnl|CDD|199841 cd03856, M14_Nna1_like, Peptidase M14-like domain of ATP/GTP
binding proteins, cytosolic carboxypeptidases and
related proteins. Peptidase M14-like domain of Nna-1
(Nervous system Nuclear protein induced by Axotomy),
also known as ATP/GTP binding protein (AGTPBP-1) and
cytosolic carboxypeptidase (CCP), and related proteins.
The Peptidase M14 family of metallocarboxypeptidases are
zinc-binding carboxypeptidases (CPs) which hydrolyze
single, C-terminal amino acids from polypeptide chains,
and have a recognition site for the free C-terminal
carboxyl group, which is a key determinant of
specificity. This subfamily includes the human AGTPBP-1
and AGBL -2, -3, -4, and -5, and the mouse Nna1/CCP-1
and CCP -2 through -6. Nna1-like proteins are active
metallopeptidases that are thought to act on cytosolic
proteins such as alpha-tubulin, to remove a C-terminal
tyrosine. Nna1 is widely expressed in the developing and
adult nervous systems, including cerebellar Purkinje and
granule neurons, miral cells of the olfactory bulb and
retinal photoreceptors. Nna1 is also induced in
axotomized motor neurons. Mutations in Nna1 cause
Purkinje cell degeneration (pcd). The Nna1 CP domain is
required to prevent the retinal photoreceptor loss and
cerebellar ataxia phenotypes of pcd mice, and a
functional zinc-binding domain is needed for Nna-1 to
support neuron survival in these mice. Nna1-like
proteins from the different phyla are highly diverse,
but they all contain a characteristic N-terminal
conserved domain right before the CP domain. It has been
suggested that this N-terminal domain might act as a
folding domain.
Length = 258
Score = 44.2 bits (104), Expect = 3e-06
Identities = 11/40 (27%), Positives = 15/40 (37%), Gaps = 1/40 (2%)
Query: 69 VRGLIEFCTRVLKKTPYFYCDFHGHSLKKNIFLYGCSSQE 108
VR + F DFHG K ++F GC +
Sbjct: 139 VRDKMTS-IVQGGGKIVFAVDFHGTFRKHDVFYTGCDDHD 177
Score = 43.4 bits (102), Expect = 6e-06
Identities = 15/62 (24%), Positives = 21/62 (33%), Gaps = 12/62 (19%)
Query: 9 CALSFDPKSSHYKIERSKES-----TARITIWREYGVVRSYTMESTYCGFDQGSFKIGTK 63
S+ +K E S A+ + Y V S T E DQG +IG +
Sbjct: 193 AETSWV-----FKTENKSASSPDRGIAKQYVADHYKV-HSVTYEVGDNTNDQGK-QIGRQ 245
Query: 64 ES 65
Sbjct: 246 LI 247
>gnl|CDD|199860 cd06236, M14_AGBL5_like, Peptidase M14-like domain of ATP/GTP
binding protein (AGBL)-5 and related proteins.
Peptidase M14-like domain of ATP/GTP binding
protein_like (AGBL)-5, and related proteins. The
Peptidase M14 family of metallocarboxypeptidases are
zinc-binding carboxypeptidases (CPs) which hydrolyze
single, C-terminal amino acids from polypeptide chains,
and have a recognition site for the free C-terminal
carboxyl group, which is a key determinant of
specificity. This eukaryotic subgroup includes the human
AGBL5 and the mouse cytosolic carboxypeptidase (CCP)-5.
ATP/GTP binding protein (AGTPBP-1/Nna1)-like proteins
are active metallopeptidases that are thought to act on
cytosolic proteins such as alpha-tubulin, to remove a
C-terminal tyrosine. Mutations in AGTPBP-1/Nna1 cause
Purkinje cell degeneration (pcd). AGTPBP-1/Nna1 however
does not belong to this subgroup. AGTPBP-1/Nna1-like
proteins from the different phyla are highly diverse,
but they all contain a unique N-terminal conserved
domain right before the CP domain. It has been suggested
that this N-terminal domain might act as a folding
domain.
Length = 308
Score = 37.0 bits (86), Expect = 0.001
Identities = 11/35 (31%), Positives = 18/35 (51%)
Query: 69 VRGLIEFCTRVLKKTPYFYCDFHGHSLKKNIFLYG 103
+ L+ + + FY D HGH+ K+ F+YG
Sbjct: 154 AKALLLYLHEHFESGLAFYIDLHGHASKRGCFIYG 188
Score = 30.4 bits (69), Expect = 0.20
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 25 SKESTARITIWREYGVVRSYTMESTY 50
SKE + R+ I++ G++ SYT+E Y
Sbjct: 236 SKEGSGRVAIYKATGIIHSYTLECNY 261
>gnl|CDD|133118 cd06908, M14_AGBL4_like, Peptidase M14-like domain of ATP/GTP
binding protein AGBL-4 and related proteins. Peptidase
M14-like domain of ATP/GTP binding protein_like
(AGBL)-4, and related proteins. The Peptidase M14 family
of metallocarboxypeptidases are zinc-binding
carboxypeptidases (CPs) which hydrolyze single,
C-terminal amino acids from polypeptide chains, and have
a recognition site for the free C-terminal carboxyl
group, which is a key determinant of specificity. This
eukaryotic subgroup includes the human AGBL4 and the
mouse cytosolic carboxypeptidase (CCP)-6. ATP/GTP
binding protein (AGTPBP-1/Nna1)-like proteins are active
metallopeptidases that are thought to act on cytosolic
proteins such as alpha-tubulin, to remove a C-terminal
tyrosine. Mutations in AGTPBP-1/Nna1 cause Purkinje cell
degeneration (pcd). AGTPBP-1/Nna1 however does not
belong to this subgroup. AGTPBP-1/Nna1-like proteins
from the different phyla are highly diverse, but they
all contain a unique N-terminal conserved domain right
before the CP domain. It has been suggested that this
N-terminal domain might act as a folding domain.
Length = 261
Score = 31.2 bits (71), Expect = 0.092
Identities = 10/18 (55%), Positives = 11/18 (61%)
Query: 86 FYCDFHGHSLKKNIFLYG 103
FY D H HS N F+YG
Sbjct: 146 FYIDLHAHSSLMNCFIYG 163
>gnl|CDD|215816 pfam00246, Peptidase_M14, Zinc carboxypeptidase.
Length = 277
Score = 28.5 bits (64), Expect = 0.81
Identities = 9/40 (22%), Positives = 15/40 (37%), Gaps = 4/40 (10%)
Query: 69 VRGLIEFCTRVLKKTPYFYCDFHGHSLKKNIFLYGCSSQE 108
R + +F + Y D HG+S + YG +
Sbjct: 154 TRAVADF---IRSYKFKLYIDLHGYSQLIL-YPYGYTYSS 189
>gnl|CDD|239652 cd03680, MM_CoA_mutase_ICM_like, Coenzyme
B12-dependent-methylmalonyl coenzyme A (CoA) mutase
(MCM) family, isobutyryl-CoA mutase (ICM)-like
subfamily; contains archaeal and bacterial proteins
similar to the large subunit of Streptomyces
cinnamonensis coenzyme B12-dependent ICM. ICM from S.
cinnamonensis is comprised of a large and a small
subunit. The holoenzyme appears to be an alpha2beta2
heterotetramer with up to 2 molecules of coenzyme B12
bound. The small subunit binds coenzyme B12. ICM
catalyzes the reversible rearrangement of n-butyryl-CoA
to isobutyryl-CoA, intermediates in fatty acid and
valine catabolism, which in S. cinnamonensis can be
converted to methylmalonyl-CoA and used in polyketide
synthesis.
Length = 538
Score = 27.6 bits (62), Expect = 1.8
Identities = 7/28 (25%), Positives = 16/28 (57%)
Query: 55 QGSFKIGTKESMKIVRGLIEFCTRVLKK 82
Q + + S+++V +IE+C + + K
Sbjct: 194 QKEWIFPPEPSVRLVTDIIEYCAKNVPK 221
>gnl|CDD|188902 cd09503, SAM_tumor-p63,p73, SAM domain of tumor-p63,p73 proteins.
SAM (sterile alpha motif) domain of p63, p73
transcriptional factors is a putative protein-protein
interaction domain and lipid-binding domain. p63 and
p73 are homologs to the tumor suppressor p53. They have
a C-terminal SAM domain in their longest spliced alpha
forms, while p53 doesn't have it. p63 or p73 knockout
mice show significant developmental abnormalities but
no increased cancer susceptibility, suggesting that p63
and p73 play a role in regulation of normal
development. It was shown that SAM domain of p73 is
able to bind some membrane lipids. The structural
rearrangements in SAM are necessary to accomplish the
binding. No evidence for homooligomerization through
SAM domains was found for p63/p73 subfamily. It was
suggested that the partner proteins should be either
more distantly related SAM-containing domain proteins
or proteins without the SAM domain.
Length = 65
Score = 25.7 bits (57), Expect = 2.5
Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 6/32 (18%)
Query: 44 YTMESTYCGFDQGSFKIGTKESMKIVRGLIEF 75
+T+E D + KI + KI +GL+E+
Sbjct: 37 FTLE------DLAAMKIPEQHRNKIWKGLLEY 62
>gnl|CDD|163683 cd07945, DRE_TIM_CMS, Leptospira interrogans citramalate synthase
(CMS) and related proteins, N-terminal catalytic TIM
barrel domain. Citramalate synthase (CMS) catalyzes the
conversion of pyruvate and acetyl-CoA to (R)-citramalate
in the first dedicated step of the citramalate pathway.
Citramalate is only found in Leptospira interrogans and
a few other microorganisms. This family belongs to the
DRE-TIM metallolyase superfamily. DRE-TIM metallolyases
include 2-isopropylmalate synthase (IPMS),
alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 280
Score = 27.0 bits (60), Expect = 3.2
Identities = 6/21 (28%), Positives = 12/21 (57%)
Query: 73 IEFCTRVLKKTPYFYCDFHGH 93
+ + ++K+ P + DFH H
Sbjct: 179 YTYISDMVKRYPNLHFDFHAH 199
>gnl|CDD|235550 PRK05660, PRK05660, HemN family oxidoreductase; Provisional.
Length = 378
Score = 26.8 bits (60), Expect = 4.0
Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 5/27 (18%)
Query: 73 IEFCTRVLKKTPYFYCDFHGHSLKKNI 99
I +C + K PY CDF+ H+LK +
Sbjct: 13 IPWCVQ---KCPY--CDFNSHALKGEV 34
>gnl|CDD|222725 pfam14386, DUF4417, Domain of unknown function (DUF4417). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria and viruses.
Proteins in this family are typically between 220 and
340 amino acids in length. There is a single completely
conserved residue G that may be functionally important.
Length = 200
Score = 26.1 bits (58), Expect = 5.2
Identities = 21/69 (30%), Positives = 30/69 (43%), Gaps = 16/69 (23%)
Query: 35 WREYGV-----VRSYTMES-TYC--GFDQGS-------FKIGTKESMKIVR-GLIEFCTR 78
W+E G+ VR ES +C G +GS +I KE+ ++ R GL E R
Sbjct: 106 WQEQGINVIPTVRWSDKESFDFCFDGIPKGSIVAISTYGQIKNKENKELFRLGLEEMIER 165
Query: 79 VLKKTPYFY 87
+ K Y
Sbjct: 166 LEPKRIIVY 174
>gnl|CDD|216353 pfam01190, Pollen_Ole_e_I, Pollen proteins Ole e I like.
Length = 95
Score = 25.1 bits (55), Expect = 6.1
Identities = 8/42 (19%), Positives = 12/42 (28%)
Query: 56 GSFKIGTKESMKIVRGLIEFCTRVLKKTPYFYCDFHGHSLKK 97
G FK+ + L C L +P C +
Sbjct: 50 GYFKVELPGDPSSLTHLESACRAKLVSSPDSACSAPTNGNGT 91
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
0.323 0.136 0.421
Gapped
Lambda K H
0.267 0.0734 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,140,981
Number of extensions: 497986
Number of successful extensions: 330
Number of sequences better than 10.0: 1
Number of HSP's gapped: 328
Number of HSP's successfully gapped: 21
Length of query: 128
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 42
Effective length of database: 7,123,158
Effective search space: 299172636
Effective search space used: 299172636
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.2 bits)