RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16878
(213 letters)
>gnl|CDD|214604 smart00295, B41, Band 4.1 homologues. Also known as
ezrin/radixin/moesin (ERM) protein domains. Present in
myosins, ezrin, radixin, moesin, protein tyrosine
phosphatases. Plasma membrane-binding domain. These
proteins play structural and regulatory roles in the
assembly and stabilization of specialized plasmamembrane
domains. Some PDZ domain containing proteins bind one or
more of this family. Now includes JAKs.
Length = 201
Score = 106 bits (268), Expect = 4e-29
Identities = 54/157 (34%), Positives = 73/157 (46%), Gaps = 14/157 (8%)
Query: 42 MENHKKHALHCTCNENT---AASDGLLLTLGYKVKHRPRPP----KIPHRY-LFCLQIKR 93
E+ + H T LTL ++VK P P + P R L LQ++
Sbjct: 45 FEDPDEDLRHWLDPAKTLLDQDVKSEPLTLYFRVKFYPPDPNQLKEDPTRLNLLYLQVRN 104
Query: 94 DLSQGLLHCNENTAALMASYIVQAECGDYVSEDYPDHTYLSSYKFVPNQT------PELE 147
D+ +G L C E A L+A+ +QAE GDY E + LS +F+P Q E
Sbjct: 105 DILEGRLPCPEEEALLLAALALQAEFGDYDEELHDLRGELSLKRFLPKQLLDSRKLKEWR 164
Query: 148 RRIMENHKKHAGQSPAAADLNLLETARRCELYGVKLH 184
RI+E HK+ G SP A L LE AR+ YGV+L
Sbjct: 165 ERIVELHKELIGLSPEEAKLKYLELARKLPTYGVELF 201
Score = 45.7 bits (109), Expect = 3e-06
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 6/55 (10%)
Query: 1 MASYIVQAECGDYVSEDYPDHTYLSSYKFVPNQT------PELERRIMENHKKHA 49
+A+ +QAE GDY E + LS +F+P Q E RI+E HK+
Sbjct: 121 LAALALQAEFGDYDEELHDLRGELSLKRFLPKQLLDSRKLKEWRERIVELHKELI 175
>gnl|CDD|215882 pfam00373, FERM_M, FERM central domain. This domain is the central
structural domain of the FERM domain.
Length = 113
Score = 94.7 bits (236), Expect = 3e-25
Identities = 42/107 (39%), Positives = 57/107 (53%), Gaps = 6/107 (5%)
Query: 84 RYLFCLQIKRDLSQGLLHCNENTAALMASYIVQAECGDYVSEDYPDHTYLSSYKFVP--- 140
R L LQ+KRD+ +G L C+E A L+A+ +QAE GDY E + F+P
Sbjct: 7 RELLYLQLKRDILEGRLPCSEEEALLLAALALQAEFGDYNPEKHSSSYLKELEYFLPSRL 66
Query: 141 ---NQTPELERRIMENHKKHAGQSPAAADLNLLETARRCELYGVKLH 184
++ ELE+RI+E HK G SPA A L L+ A+ YGV
Sbjct: 67 IKKEKSKELEKRILEAHKNLRGLSPAEAKLKYLQIAQSLPTYGVTFF 113
Score = 38.8 bits (91), Expect = 3e-04
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 6/55 (10%)
Query: 1 MASYIVQAECGDYVSEDYPDHTYLSSYKFVP------NQTPELERRIMENHKKHA 49
+A+ +QAE GDY E + F+P ++ ELE+RI+E HK
Sbjct: 33 LAALALQAEFGDYNPEKHSSSYLKELEYFLPSRLIKKEKSKELEKRILEAHKNLR 87
>gnl|CDD|241347 cd13193, FERM_C_FARP1-like, FERM, RhoGEF and pleckstrin
domain-containing protein 1 and related proteins FERM
domain. Members here include FARP1 (also called
Chondrocyte-derived ezrin-like protein; PH
domain-containing family C member 2), FARP2 (also called
FIR/FERM domain including RhoGEF; FGD1-related
Cdc42-GEF/FRG), and FRMD7(FERM domain containing 7).
FARP1 and FARP2 are members of the Dbl family guanine
nucleotide exchange factors (GEFs) which are upstream
positive regulators of Rho GTPases. FARP1 has increased
expression in differentiated chondrocytes. FARP2 is
thought to regulate neurite remodeling by mediating the
signaling pathways from membrane proteins to Rac. It is
found in brain, lung, and testis, as well as embryonic
hippocampal and cortical neurons. These members are
composed of a N-terminal FERM domain, a proline-rich
(PR) domain, Dbl-homology (DH), and two C-terminal PH
domains. Other members in this family do not contain
the DH domains such as the Human FERM domain containing
protein 7 and Caenorhabditis elegans CFRM3, both of
which have unknown functions. They contain an N-terminal
FERM domain, a PH domain, followed by a FA (FERM
adjacent) domain. The FERM domain has a cloverleaf
tripart structure (FERM_N, FERM_M, FERM_C/N, alpha-, and
C-lobe/A-lobe, B-lobe, C-lobe/F1, F2, F3). The C-lobe/F3
within the FERM domain is part of the PH domain family.
The FERM domain is found in the cytoskeletal-associated
proteins such as ezrin, moesin, radixin, 4.1R, and
merlin. These proteins provide a link between the
membrane and cytoskeleton and are involved in signal
transduction pathways. The FERM domain is also found in
protein tyrosine phosphatases (PTPs) , the tyrosine
kinases FAK and JAK, in addition to other proteins
involved in signaling. This domain is structurally
similar to the PH and PTB domains and consequently is
capable of binding to both peptides and phospholipids at
different sites.
Length = 122
Score = 92.4 bits (230), Expect = 3e-24
Identities = 31/43 (72%), Positives = 37/43 (86%)
Query: 171 ETARRCELYGVKLHPAKDHDNILLNLSVAHMGILVFQNQTKIN 213
+ ARRCELYG++LHPAKD + + LNL+VAHMGILVFQ TKIN
Sbjct: 1 DIARRCELYGIRLHPAKDREGVDLNLAVAHMGILVFQGFTKIN 43
>gnl|CDD|241343 cd13189, FERM_C_PTPN4_PTPN3_like, Protein tyrosine phosphatase
non-receptor proteins 3 and 4 (PTPN4 and PTPN3) FERM
domain C-lobe. PTPN4 (also called PTPMEG, protein
tyrosine phosphatase, megakaryocyte) is a cytoplasmic
protein-tyrosine phosphatase (PTP) thought to play a
role in cerebellar function. PTPMEG-knockout mice have
impaired memory formation and cerebellar long-term
depression. PTPN3/PTPH1 is a membrane-associated PTP
that is implicated in regulating tyrosine
phosphorylation of growth factor receptors, p97 VCP
(valosin-containing protein, or Cdc48 in Saccharomyces
cerevisiae), and HBV (Hepatitis B Virus) gene
expression; it is mutated in a subset of colon cancers.
PTPMEG and PTPN3/PTPH1 contains a N-terminal FERM
domain, a middle PDZ domain, and a C-terminal
phosphatase domain. PTP1/Tyrosine-protein phosphatase 1
from nematodes and a FERM_C repeat 1 from Tetraodon
nigroviridis also included in this cd. The FERM domain
has a cloverleaf tripart structure (FERM_N, FERM_M,
FERM_C/N, alpha-, and C-lobe/A-lobe, B-lobe, C-lobe/F1,
F2, F3). The C-lobe within the FERM domain is part of
the PH domain family. The FERM domain is found in the
cytoskeletal-associated proteins such as ezrin, moesin,
radixin, 4.1R, and merlin. These proteins provide a link
between the membrane and cytoskeleton and are involved
in signal transduction pathways. The FERM domain is also
found in protein tyrosine phosphatases (PTPs) , the
tyrosine kinases FAK and JAK, in addition to other
proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 123
Score = 73.5 bits (181), Expect = 5e-17
Identities = 32/55 (58%), Positives = 38/55 (69%)
Query: 159 GQSPAAADLNLLETARRCELYGVKLHPAKDHDNILLNLSVAHMGILVFQNQTKIN 213
GQSPA A+ N L TAR ELYGV+LH A+D N+ L + V GILVFQN +IN
Sbjct: 1 GQSPAEAEFNFLNTARTLELYGVELHSARDASNLELQVGVTSGGILVFQNGIRIN 55
>gnl|CDD|241338 cd13184, FERM_C_4_1_family, Protein 4.1 family FERM domain C-lobe.
The protein 4.1 family includes four well-defined
members: erythroid protein 4.1 (4.1R), the bestknown and
characterized member, 4.1G (general), 4.1N (neuronal),
and 4.1 B (brain). The less well understood 4.1O/FRMD3
is not a true member of this family and is not included
in this hierarchy. Besides three highly conserved
domains, FERM, SAB (spectrin and actin binding domain)
and CTD (C-terminal domain), the proteins from this
family contain several unique domains: U1, U2 and U3.
FERM domains like other members of the FERM domain
superfamily have a cloverleaf architecture with three
distinct lobes (FERM_N, FERM_M, FERM_C/N, alpha-, and
C-lobe/A-lobe, B-lobe, C-lobe/F1, F2, F3). The C-lobe/F3
within the FERM domain is part of the PH domain family.
The brain is a particularly rich source of protein 4.1
isoforms. The various 4.1R, 4.1G, 4.1N, and 4.1B mRNAs
are all expressed in distinct patterns within the brain.
It is likely that 4.1 proteins play important functional
roles in the brain including motor coordination and
spatial learning, postmitotic differentiation, and
synaptic architecture and function. In addition they are
found in nonerythroid, nonneuronal cells where they may
play a general structural role in nuclear architecture
and/or may interact with splicing factors. The FERM C
domain is the third structural domain within the FERM
domain. The FERM domain is found in the
cytoskeletal-associated proteins such as ezrin, moesin,
radixin, 4.1R, and merlin. These proteins provide a link
between the membrane and cytoskeleton and are involved
in signal transduction pathways. The FERM domain is also
found in protein tyrosine phosphatases (PTPs) , the
tyrosine kinases FAK and JAK, in addition to other
proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 113
Score = 73.1 bits (180), Expect = 6e-17
Identities = 27/55 (49%), Positives = 40/55 (72%)
Query: 159 GQSPAAADLNLLETARRCELYGVKLHPAKDHDNILLNLSVAHMGILVFQNQTKIN 213
GQ+PA A+L+ LE A++ LYGV LHPAKD + + + L V GILV++++ +IN
Sbjct: 1 GQTPAEAELHFLENAKKLALYGVDLHPAKDSEGVDIMLGVCAGGILVYRDRLRIN 55
>gnl|CDD|241340 cd13186, FERM_C_NBL4_NBL5, Novel band 4.1-like protein 4 and 5 FERM
(NBL4 and 5) domain C-lobe. NBL4 (also called
Erythrocyte protein band 4.1-like 4; Epb4 1l4) plays a
role the beta-catenin/Tcf signaling pathway and is
thought to be involved in establishing the cell polarity
or proliferation. NBL4 may be also involved in adhesion,
in cell motility and/or in cell-to-cell communication.
No role for NBL5 has been proposed to date. Both NBL4
and NBL5 contain a N-terminal FERM domain which has a
cloverleaf tripart structure (FERM_N, FERM_M, FERM_C/N,
alpha-, and C-lobe/A-lobe, B-lobe, C-lobe/F1, F2, F3).
A single FERM_C repeat 2 from Tetraodon nigroviridis
also included in this cdThe C-lobe is a member of the PH
superfamily. The FERM domain is found in the
cytoskeletal-associated proteins such as ezrin, moesin,
radixin, 4.1R, and merlin. These proteins provide a link
between the membrane and cytoskeleton and are involved
in signal transduction pathways. The FERM domain is also
found in protein tyrosine phosphatases (PTPs) , the
tyrosine kinases FAK and JAK, in addition to other
proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 111
Score = 58.0 bits (141), Expect = 3e-11
Identities = 25/52 (48%), Positives = 33/52 (63%)
Query: 161 SPAAADLNLLETARRCELYGVKLHPAKDHDNILLNLSVAHMGILVFQNQTKI 212
+PA A+LN L A+ E+YGV LHP K D L + GILV++N+TKI
Sbjct: 1 TPAEAELNYLNKAKWLEMYGVDLHPVKGEDGNEYFLGLTPTGILVYENKTKI 52
>gnl|CDD|241346 cd13192, FERM_C_FRMD3_FRMD5, FERM domain-containing protein 3 and 5
FERM (FRMD3 and 5) domain C-lobe. FRMD3 (also called
Band 4.1-like protein 4O/4.1O though it is not a true
member of that family) is a novel putative tumor
suppressor gene that is implicated in the origin and
progression of lung cancer. In humans there are 5
isoforms that are produced by alternative splicing. Less
is known about FRMD5, though there are 2 isoforms of the
human protein are produced by alternative splicing. Both
FRMD3 and FRMD5 contain a N-terminal FERM domain,
followed by a FERM adjacent (FA) domain, and 4.1 protein
C-terminal domain (CTD). The FERM domain has a
cloverleaf tripart structure (FERM_N, FERM_M, FERM_C/N,
alpha-, and C-lobe/A-lobe, B-lobe, C-lobe/F1, F2, F3).
The C-lobe/F3 within the FERM domain is part of the PH
domain family. The FERM domain is found in the
cytoskeletal-associated proteins such as ezrin, moesin,
radixin, 4.1R, and merlin. These proteins provide a link
between the membrane and cytoskeleton and are involved
in signal transduction pathways. The FERM domain is also
found in protein tyrosine phosphatases (PTPs) , the
tyrosine kinases FAK and JAK, in addition to other
proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 105
Score = 49.3 bits (118), Expect = 3e-08
Identities = 21/48 (43%), Positives = 26/48 (54%)
Query: 165 ADLNLLETARRCELYGVKLHPAKDHDNILLNLSVAHMGILVFQNQTKI 212
A+LN L A E YGV HP KDH L L H G++VFQ ++
Sbjct: 1 AELNFLRKAHTLETYGVDPHPVKDHYGTQLYLGFTHTGVVVFQGGKRV 48
>gnl|CDD|241349 cd13195, FERM_C_MYLIP_IDOL, The E3 ubiquitin ligase myosin
regulatory light chain-interacting protein (MYLIP; also
called inducible degrader of the LDL receptor, IDOL)
FERM domain C-lobe. MYLIP/IDOL is a regulator of the
LDL receptor (LDLR) pathway via the nuclear receptor
liver X receptor (LXR). In response to cellular
cholesterol loading, the activation of LXR leads to the
induction of MYLIP expression. MYLIP stimulates
ubiquitination of the LDLR on its cytoplasmic tail,
directing its degradation. The LXR-MYLIP-LDLR pathway
provides a complementary pathway to sterol regulatory
element-binding proteins for the feedback inhibition of
cholesterol uptake. MYLIP has an N-terminal FERM domain
and in some cases a C-terminal RING domain. The FERM
domain has a cloverleaf tripart structure (FERM_N,
FERM_M, FERM_C/N, alpha-, and C-lobe/A-lobe, B-lobe,
C-lobe/F1, F2, F3). The C-lobe/F3 within the FERM domain
is part of the PH domain family. The FERM domain is
found in the cytoskeletal-associated proteins such as
ezrin, moesin, radixin, 4.1R, and merlin. These proteins
provide a link between the membrane and cytoskeleton and
are involved in signal transduction pathways. The FERM
domain is also found in protein tyrosine phosphatases
(PTPs) , the tyrosine kinases FAK and JAK, in addition
to other proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 131
Score = 38.4 bits (90), Expect = 6e-04
Identities = 13/48 (27%), Positives = 21/48 (43%)
Query: 159 GQSPAAADLNLLETARRCELYGVKLHPAKDHDNILLNLSVAHMGILVF 206
G SP+ A+ L+ E YGV+ + + L + V GI +
Sbjct: 1 GMSPSTAEYLFLKEVSELENYGVETFHVRTIEGQKLVIGVGPDGIRIC 48
>gnl|CDD|220216 pfam09380, FERM_C, FERM C-terminal PH-like domain.
Length = 90
Score = 36.1 bits (84), Expect = 0.001
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 188 DHDNILLNLSVAHMGILVFQNQTKIN 213
D L L V+ GILV+++ KIN
Sbjct: 1 DKKGTDLWLGVSAKGILVYEDNNKIN 26
>gnl|CDD|241342 cd13188, FERM_C_PTPN14_PTPN21, Protein tyrosine phosphatase
non-receptor proteins 14 and 21 (PTPN14 and 21) FERM
domain. This CD contains PTP members: pez/PTPN14 and
PTPN21. A number of mutations in Pez have been shown to
be associated with breast and colorectal cancer. The
PTPN protein family belong to larger family of PTPs.
PTPs are known to be signaling molecules that regulate a
variety of cellular processes including cell growth,
differentiation, mitotic cycle, and oncogenic
transformation. The members are composed of a N-terminal
FERM domain and a C-terminal PTP catalytic domain. The
FERM domain has a cloverleaf tripart structure (FERM_N,
FERM_M, FERM_C/N, alpha-, and C-lobe/A-lobe, B-lobe,
C-lobe/F1, F2, F3). The C-lobe/F3 within the FERM domain
is part of the PH domain family. Like most other ERM
members they have a phosphoinositide-binding site in
their FERM domain. The FERM C domain is the third
structural domain within the FERM domain. The FERM
domain is found in the cytoskeletal-associated proteins
such as ezrin, moesin, radixin, 4.1R, and merlin. These
proteins provide a link between the membrane and
cytoskeleton and are involved in signal transduction
pathways. The FERM domain is also found in protein
tyrosine phosphatases (PTPs) , the tyrosine kinases FAK
and JAK, in addition to other proteins involved in
signaling. This domain is structurally similar to the PH
and PTB domains and consequently is capable of binding
to both peptides and phospholipids at different sites.
Length = 111
Score = 33.4 bits (77), Expect = 0.023
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 159 GQSPAAADLNLLETARRCELYGVKLHPAKDHDNILLNLSVAHMGILV 205
G SPA A+L ++ + + YG + +PAKD+ + + + GI V
Sbjct: 1 GLSPAEAELLYIQEVEQLDGYGEESYPAKDNQGNDIFIGASFEGIFV 47
>gnl|CDD|184966 PRK15004, PRK15004, alpha-ribazole phosphatase; Provisional.
Length = 199
Score = 29.2 bits (66), Expect = 1.3
Identities = 9/32 (28%), Positives = 19/32 (59%), Gaps = 3/32 (9%)
Query: 173 ARRCELYGVKLHPAKDHDNILLNLSVAHMGIL 204
++R E + +L + + N+L+ V+H G+L
Sbjct: 125 SQRVERFIARLSAFQHYQNLLI---VSHQGVL 153
>gnl|CDD|193540 cd05664, M20_Acy1_like6, M20 Peptidase Aminoacylase 1 subfamily.
Peptidase M20 family, Uncharacterized subfamily of
proteins predicted as putative amidohydrolases or
hippurate hydrolases. These are a class of zinc binding
homodimeric enzymes involved in the hydrolysis of
N-acetylated proteins. N-terminal acetylation of
proteins is a widespread and highly conserved process
that is involved in the protection and stability of
proteins. Several types of aminoacylases can be
distinguished on the basis of substrate specificity.
Aminoacylase 1 (ACY1) breaks down cytosolic aliphatic
N-acyl-alpha-amino acids (except L-aspartate),
especially N-acetyl-methionine and acetyl-glutamate into
L-amino acids and an acyl group. However, ACY1 can also
catalyze the reverse reaction, the synthesis of
acetylated amino acids. ACY1 may also play a role in
xenobiotic bioactivation as well as in the inter-organ
processing of amino acid-conjugated xenobiotic
derivatives (S-substituted-N-acetyl-L-cysteine).
Length = 398
Score = 29.0 bits (66), Expect = 2.1
Identities = 12/46 (26%), Positives = 17/46 (36%), Gaps = 1/46 (2%)
Query: 114 IVQAECGDYVSEDYPDHTYLSSYKFVPNQTPELERRIMENHKKHAG 159
IV+AE + P+ T S N P L R+ + G
Sbjct: 273 IVRAEAAAAGAPREPEITVTDSTPATVN-DPALTARVRAAFRAVFG 317
Score = 28.2 bits (64), Expect = 3.7
Identities = 11/44 (25%), Positives = 16/44 (36%), Gaps = 1/44 (2%)
Query: 5 IVQAECGDYVSEDYPDHTYLSSYKFVPNQTPELERRIMENHKKH 48
IV+AE + P+ T S N P L R+ +
Sbjct: 273 IVRAEAAAAGAPREPEITVTDSTPATVN-DPALTARVRAAFRAV 315
>gnl|CDD|130078 TIGR01005, eps_transp_fam, exopolysaccharide transport protein
family. The model describes the exopolysaccharide
transport protein family in bacteria. The transport
protein is part of a large genetic locus which is
associated with exopolysaccharide (EPS) biosynthesis.
Detailed molecular characterization and gene fusion
analysis revealed atleast seven gene products are
involved in the overall regulation, which among other
things, include exopolysaccharide biosynthesis, property
of conferring virulence and exopolysaccharide export
[Transport and binding proteins, Carbohydrates, organic
alcohols, and acids].
Length = 754
Score = 28.0 bits (62), Expect = 4.8
Identities = 11/52 (21%), Positives = 21/52 (40%)
Query: 93 RDLSQGLLHCNENTAALMASYIVQAECGDYVSEDYPDHTYLSSYKFVPNQTP 144
R +QG+ N + + + + Y+ YPD ++ + P TP
Sbjct: 697 RADAQGISRLNGEVTGVFLNMLDPNDEVKYIESGYPDLYRVTPIGYEPPGTP 748
>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
Provisional.
Length = 378
Score = 27.6 bits (61), Expect = 5.3
Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 2/47 (4%)
Query: 30 VPNQTPELERRIMENHKKHALHCTCNENTAASDGLLLTLGYKVKHRP 76
+P + +L + +E + +L+ C++ +AAS LL LG+ H P
Sbjct: 332 IPGEFDKLRKNYLERREWSSLYVICDDASAAS--LLCKLGFNAVHHP 376
>gnl|CDD|241233 cd00836, FERM_C-lobe, FERM domain C-lobe. The FERM domain has a
cloverleaf tripart structure (FERM_N, FERM_M, FERM_C/N,
alpha-, and C-lobe/A-lobe, B-lobe, C-lobe/F1, F2, F3).
The C-lobe/F3 within the FERM domain is part of the PH
domain family. The FERM domain is found in the
cytoskeletal-associated proteins such as ezrin, moesin,
radixin, 4.1R, and merlin. These proteins provide a link
between the membrane and cytoskeleton and are involved
in signal transduction pathways. The FERM domain is also
found in protein tyrosine phosphatases (PTPs), the
tyrosine kinases FAK and JAK, in addition to other
proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 91
Score = 26.2 bits (58), Expect = 5.6
Identities = 11/33 (33%), Positives = 14/33 (42%), Gaps = 1/33 (3%)
Query: 180 GVKLHPAKDHD-NILLNLSVAHMGILVFQNQTK 211
GV+ KD L L V+ GI V + T
Sbjct: 1 GVEFFDVKDKSGGSELILGVSLEGISVLDDNTG 33
>gnl|CDD|211799 TIGR03247, glucar-dehydr, glucarate dehydratase. Glucarate
dehydratase converts D-glucarate (and L-idarate, a
stereoisomer) to 5-dehydro-4-deoxyglucarate which is
subsequently acted on by GarL, tartronate semialdehyde
reductase and glycerate kinase (, GenProp0716). The E.
coli enzyme has been well-characterized.
Length = 441
Score = 27.1 bits (60), Expect = 8.6
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 181 VKLHPAKDHDNILLNLSVAH 200
+++ P HD++LLNLS AH
Sbjct: 9 MRVIPVAGHDSMLLNLSGAH 28
>gnl|CDD|193556 cd05681, M20_dipept_like_4, Uncharacterized M20 Dipeptidases.
Peptidase M20 family, unknown dipeptidase-like subfamily
3 (inferred by homology to be dipeptidases). M20
dipeptidases include a large variety of bacterial
enzymes including cytosolic nonspecific dipeptidase
(CNDP), Xaa-methyl-His dipeptidase (anserinase),and
canosinase. These dipeptidases have been shown to act on
a wide range of dipeptides, but not larger peptides. For
example, anserinase mainly catalyzes the hydrolysis of
N-alpha-acetylhistidine while carnosinase degrades
beta-alanyl-L-histidine.
Length = 430
Score = 26.8 bits (60), Expect = 8.9
Identities = 18/66 (27%), Positives = 29/66 (43%), Gaps = 21/66 (31%)
Query: 139 VPNQTPE----LERRIMENH-------KKHAGQSPAAADLN------LLETARRCELYG- 180
VP+Q PE L R ++ + G+ PA DL+ L+TA++ +YG
Sbjct: 311 VPDQDPEEVLDLLRAHLDKNGFSDIEVTYLLGEPPARTDLDAPLVQAALDTAKK--VYGT 368
Query: 181 -VKLHP 185
+ P
Sbjct: 369 DPVVLP 374
>gnl|CDD|99827 cd05784, DNA_polB_II_exo, DEDDy 3'-5' exonuclease domain of
Escherichia coli DNA polymerase II and similar bacterial
family-B DNA polymerases. The 3'-5' exonuclease domain
of Escherichia coli DNA polymerase II (Pol II) and
similar bacterial proteins. Pol II is a family-B DNA
polymerase. Family-B DNA polymerases contain an
N-terminal DEDDy DnaQ-like exonuclease domain in the
same polypeptide chain as the polymerase domain, similar
to family-A DNA polymerases. This exonuclease domain
contains three sequence motifs termed ExoI, ExoII and
ExoIII, with a specific YX(3)D pattern at ExoIII. These
motifs are clustered around the active site and are
involved in metal binding and catalysis. The exonuclease
domain has a fundamental role in the proofreading
activity of polII. It contains a beta hairpin structure
that plays an important role in active site switching in
the event of a nucleotide misincorporation. Pol II is
involved in a variety of cellular activities, such as
the repair of DNA damaged by UV irradiation or
oxidation. It plays a pivotal role in
replication-restart, a process that bypasses DNA damage
in an error-free manner. Pol II is also involved in
lagging strand synthesis.
Length = 193
Score = 26.4 bits (59), Expect = 9.7
Identities = 9/27 (33%), Positives = 13/27 (48%), Gaps = 2/27 (7%)
Query: 166 DLNLLETARRCELYGVKLHPAKDHDNI 192
DL LL RR E +G+ L + +
Sbjct: 79 DLRLL--QRRAEAHGLPLRLGRGGSPL 103
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 0.134 0.407
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,549,603
Number of extensions: 943648
Number of successful extensions: 734
Number of sequences better than 10.0: 1
Number of HSP's gapped: 730
Number of HSP's successfully gapped: 24
Length of query: 213
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 120
Effective length of database: 6,812,680
Effective search space: 817521600
Effective search space used: 817521600
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 (21.8 bits)
S2: 57 (25.7 bits)