RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6804
(207 letters)
>gnl|CDD|238613 cd01286, deoxycytidylate_deaminase, Deoxycytidylate deaminase
domain. Deoxycytidylate deaminase catalyzes the
deamination of dCMP to dUMP, providing the nucleotide
substrate for thymidylate synthase. The enzyme binds
Zn++, which is required for catalytic activity. The
activity of the enzyme is allosterically regulated by
the ratio of dCTP to dTTP not only in eukaryotic cells
but also in T-even phage-infected Escherichia coli, with
dCTP acting as an activator and dTTP as an inhibitor.
Length = 131
Score = 144 bits (366), Expect = 1e-44
Identities = 53/125 (42%), Positives = 67/125 (53%), Gaps = 10/125 (8%)
Query: 92 HEYFMASAFLVAKRSKDPVTRVGAVIVNEDNKIVGTGYNGMPIGCSDDEFPW----DKNT 147
EYFMA A L A RS P +VGAVIV D +I+ TGYNG P G D +
Sbjct: 1 DEYFMAIARLAALRSTCPRRQVGAVIVK-DKRIISTGYNGSPSGLPHCAEVGCERDDLPS 59
Query: 148 HDELDMC---HAEMNAILN--KNSADTKRCKLYTSLFPCNECAKVIIQSGIKEVIYMCDK 202
++ C HAE NAIL ++ + LY +LFPC ECAK+IIQ+GIK+V+Y
Sbjct: 60 GEDQKCCRTVHAEQNAILQAARHGVSLEGATLYVTLFPCIECAKLIIQAGIKKVVYAEPY 119
Query: 203 QMSYK 207
Sbjct: 120 DDDDP 124
Score = 69.6 bits (171), Expect = 2e-15
Identities = 24/62 (38%), Positives = 35/62 (56%), Gaps = 5/62 (8%)
Query: 1 MNAILN--KNSADTKRCKLYTSLFPCNECAKVIIQSGIKEVIYMCDKHKQKPATIASKRM 58
NAIL ++ + LY +LFPC ECAK+IIQ+GIK+V+Y P A+ +
Sbjct: 73 QNAILQAARHGVSLEGATLYVTLFPCIECAKLIIQAGIKKVVYAEPYDDDDP---AAAEL 129
Query: 59 FD 60
+
Sbjct: 130 LE 131
>gnl|CDD|225042 COG2131, ComEB, Deoxycytidylate deaminase [Nucleotide transport and
metabolism].
Length = 164
Score = 122 bits (309), Expect = 1e-35
Identities = 53/125 (42%), Positives = 64/125 (51%), Gaps = 11/125 (8%)
Query: 91 WHEYFMASAFLVAKRSKDPVTRVGAVIVNEDNKIVGTGYNGMPIGCSDDEFPW----DKN 146
W EYFMA A LVA RS P +VGAVIV D +I+ TGYNG P G
Sbjct: 8 WDEYFMAIAELVALRSTCPRRQVGAVIVK-DGRIIATGYNGAPSGEDHCIDRGCLRDKVV 66
Query: 147 THDELDMC----HAEMNAILN--KNSADTKRCKLYTSLFPCNECAKVIIQSGIKEVIYMC 200
C HAE NAIL ++ + LY + FPC+ CAK+IIQ+GIKEV+Y
Sbjct: 67 FVTTCGHCCRTLHAEQNAILQAARHGVGLEGATLYVTHFPCSNCAKLIIQAGIKEVVYAE 126
Query: 201 DKQMS 205
Sbjct: 127 PYPTE 131
Score = 55.9 bits (135), Expect = 4e-10
Identities = 25/66 (37%), Positives = 37/66 (56%), Gaps = 3/66 (4%)
Query: 1 MNAILN--KNSADTKRCKLYTSLFPCNECAKVIIQSGIKEVIYMCDKHKQKPATIASKRM 58
NAIL ++ + LY + FPC+ CAK+IIQ+GIKEV+Y + A S+ +
Sbjct: 82 QNAILQAARHGVGLEGATLYVTHFPCSNCAKLIIQAGIKEVVYAEPYPTETVAPY-SQEL 140
Query: 59 FDAAKV 64
+ A V
Sbjct: 141 LEEAGV 146
>gnl|CDD|215887 pfam00383, dCMP_cyt_deam_1, Cytidine and deoxycytidylate deaminase
zinc-binding region.
Length = 104
Score = 102 bits (256), Expect = 2e-28
Identities = 45/118 (38%), Positives = 55/118 (46%), Gaps = 20/118 (16%)
Query: 89 LEWHEYFMASAFLVAKRS--KDPVTRVGAVIVNEDNKIVGTGYNGMPIGCSDDEFPWDKN 146
+EW EYFM A AKR+ VGAVIV D I+ TGYNG G
Sbjct: 1 MEWDEYFMRLALEAAKRAYTPYSNFPVGAVIVKNDGGIIATGYNGENAGYD--------P 52
Query: 147 THDELDMCHAEMNAILNKNSA----DTKRCKLYTSLFPCNECAKVIIQSGIKEVIYMC 200
T HAE NAI N + LY +L PC C + II+SGIK+V++
Sbjct: 53 T------IHAERNAIRNAGRLGEGIKLEGATLYVTLEPCGMCRQAIIESGIKKVVFGT 104
Score = 50.4 bits (121), Expect = 1e-08
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 1 MNAILNKNSA----DTKRCKLYTSLFPCNECAKVIIQSGIKEVIYMC 43
NAI N + LY +L PC C + II+SGIK+V++
Sbjct: 58 RNAIRNAGRLGEGIKLEGATLYVTLEPCGMCRQAIIESGIKKVVFGT 104
>gnl|CDD|238406 cd00786, cytidine_deaminase-like, Cytidine and deoxycytidylate
deaminase zinc-binding region. The family contains
cytidine deaminases, nucleoside deaminases,
deoxycytidylate deaminases and riboflavin deaminases.
Also included are the apoBec family of mRNA editing
enzymes. All members are Zn dependent. The zinc ion in
the active site plays a central role in the proposed
catalytic mechanism, activating a water molecule to form
a hydroxide ion that performs a nucleophilic attack on
the substrate.
Length = 96
Score = 86.8 bits (215), Expect = 2e-22
Identities = 33/110 (30%), Positives = 51/110 (46%), Gaps = 16/110 (14%)
Query: 93 EYFMASAFLVAKRSKDPVTRVGAVIVNEDNKIVGTGYNGMPIGCSDDEFPWDKNTHDELD 152
+ +A L +K+ +VGA +VN+ + GC+ + +
Sbjct: 2 TEALKAADLGY--AKESNFQVGACLVNKK------DGGKVGRGCNIENAAYSM------- 46
Query: 153 MCHAEMNAILNKNS-ADTKRCKLYTSLFPCNECAKVIIQSGIKEVIYMCD 201
HAE A+ N S DTK LY +L PC CA++II+ GIK+VI +
Sbjct: 47 CNHAERTALFNAGSEGDTKGQMLYVALSPCGACAQLIIELGIKDVIVVLT 96
Score = 57.2 bits (138), Expect = 4e-11
Identities = 20/45 (44%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 1 MNAILNKNS-ADTKRCKLYTSLFPCNECAKVIIQSGIKEVIYMCD 44
A+ N S DTK LY +L PC CA++II+ GIK+VI +
Sbjct: 52 RTALFNAGSEGDTKGQMLYVALSPCGACAQLIIELGIKDVIVVLT 96
>gnl|CDD|131622 TIGR02571, ComEB, ComE operon protein 2. This protein is found in
the ComE operon for "late competence" as characterized
in B. subtilis. Proteins in this family contain homology
to a cytidine/deoxycytidine deaminase domain family
(pfam00383), and may carry out this activity.
Length = 151
Score = 81.4 bits (201), Expect = 9e-20
Identities = 47/122 (38%), Positives = 65/122 (53%), Gaps = 16/122 (13%)
Query: 89 LEWHEYFMASAFLVAKRSKDPVTRVGAVIVNEDNKIVGTGYNGMPIG---CSDDEFPWDK 145
++W +YFMA + L+A RS VGA IV D +I+ GYNG G C D+
Sbjct: 3 IKWDQYFMAQSHLLALRSTCTRLSVGATIV-RDKRIIAGGYNGSVAGGVHCIDE------ 55
Query: 146 NTHDELDMC----HAEMNAILN--KNSADTKRCKLYTSLFPCNECAKVIIQSGIKEVIYM 199
+ C HAEMNA+L K T+ ++Y + FPC +C K IIQ+GIK++ Y
Sbjct: 56 GCYVVDGHCVRTIHAEMNALLQCAKFGVSTEGAEIYVTHFPCLQCTKSIIQAGIKKIYYA 115
Query: 200 CD 201
D
Sbjct: 116 QD 117
Score = 47.9 bits (114), Expect = 3e-07
Identities = 21/48 (43%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 1 MNAILN--KNSADTKRCKLYTSLFPCNECAKVIIQSGIKEVIYMCDKH 46
MNA+L K T+ ++Y + FPC +C K IIQ+GIK++ Y D H
Sbjct: 72 MNALLQCAKFGVSTEGAEIYVTHFPCLQCTKSIIQAGIKKIYYAQDYH 119
>gnl|CDD|222894 PHA02588, cd, deoxycytidylate deaminase; Provisional.
Length = 168
Score = 80.6 bits (199), Expect = 3e-19
Identities = 46/128 (35%), Positives = 67/128 (52%), Gaps = 22/128 (17%)
Query: 95 FMASAFLVAKRSKDPVTRVGAVIVNEDNKIVGTGYNGMPIG---CSD--DEFPWDKNT-- 147
++ A+LV++ SK +VGAVI + +I+ TGYNG P G C D +E W +
Sbjct: 6 YLQIAYLVSQESKCVSWKVGAVIEK-NGRIISTGYNGTPAGGVNCCDHANEQGWLDDEGK 64
Query: 148 --------HDELDMC---HAEMNAIL--NKNSADTKRCKLYTSLFPCNECAKVIIQSGIK 194
H HAE+NAIL +N + +Y + PC +CAK I QSGIK
Sbjct: 65 LKKEHRPEHSAWSSKNEIHAELNAILFAARNGISIEGATMYVTASPCPDCAKAIAQSGIK 124
Query: 195 EVIYMCDK 202
+++Y C+K
Sbjct: 125 KLVY-CEK 131
Score = 45.5 bits (108), Expect = 2e-06
Identities = 20/53 (37%), Positives = 32/53 (60%), Gaps = 3/53 (5%)
Query: 1 MNAIL--NKNSADTKRCKLYTSLFPCNECAKVIIQSGIKEVIYMCDKHKQKPA 51
+NAIL +N + +Y + PC +CAK I QSGIK+++Y C+K+ +
Sbjct: 86 LNAILFAARNGISIEGATMYVTASPCPDCAKAIAQSGIKKLVY-CEKYDRNGP 137
>gnl|CDD|223663 COG0590, CumB, Cytosine/adenosine deaminases [Nucleotide transport
and metabolism / Translation, ribosomal structure and
biogenesis].
Length = 152
Score = 68.9 bits (169), Expect = 5e-15
Identities = 39/119 (32%), Positives = 52/119 (43%), Gaps = 25/119 (21%)
Query: 88 VLEWHEYFMASAFLVAKRSKD----PVTRVGAVIVNEDNKIVGTGYNGMPIGCSDDEFPW 143
+ E E FM A AK++ D PV GAVIV+ D +I+ G+N
Sbjct: 4 LSEKDEDFMREALKEAKKAGDEGEVPV---GAVIVDADGEIIARGHN------------- 47
Query: 144 DKNTHDELDMCHAEMNAILN----KNSADTKRCKLYTSLFPCNECAKVIIQSGIKEVIY 198
+ D HAE+ AI + K C LY +L PC CA II + I V+Y
Sbjct: 48 -RREEDNDPTAHAEILAIRAAAETLGNYRLKDCTLYVTLEPCPMCAGAIIWARIDRVVY 105
Score = 36.1 bits (84), Expect = 0.004
Identities = 14/31 (45%), Positives = 17/31 (54%)
Query: 11 DTKRCKLYTSLFPCNECAKVIIQSGIKEVIY 41
K C LY +L PC CA II + I V+Y
Sbjct: 75 RLKDCTLYVTLEPCPMCAGAIIWARIDRVVY 105
>gnl|CDD|238612 cd01285, nucleoside_deaminase, Nucleoside deaminases include
adenosine, guanine and cytosine deaminases. These
enzymes are Zn dependent and catalyze the deamination of
nucleosides. The zinc ion in the active site plays a
central role in the proposed catalytic mechanism,
activating a water molecule to form a hydroxide ion that
performs a nucleophilic attack on the substrate. The
functional enzyme is a homodimer. Cytosine deaminase
catalyzes the deamination of cytosine to uracil and
ammonia and is a member of the pyrimidine salvage
pathway. Cytosine deaminase is found in bacteria and
fungi but is not present in mammals; for this reason,
the enzyme is currently of interest for antimicrobial
drug design and gene therapy applications against
tumors. Some members of this family are tRNA-specific
adenosine deaminases that generate inosine at the first
position of their anticodon (position 34) of specific
tRNAs; this modification is thought to enlarge the codon
recognition capacity during protein synthesis. Other
members of the family are guanine deaminases which
deaminate guanine to xanthine as part of the utilization
of guanine as a nitrogen source.
Length = 109
Score = 60.3 bits (147), Expect = 3e-12
Identities = 34/112 (30%), Positives = 50/112 (44%), Gaps = 27/112 (24%)
Query: 96 MASAFLVAKRSKD----PVTRVGAVIVNEDNKIVGTGYNGMPIGCSDDEFPWDKNTHDEL 151
M A +A+++ P GAVIV++D K++ G+N +
Sbjct: 1 MRLAIELARKALAEGEVPF---GAVIVDDDGKVIARGHN---------------RVEQDG 42
Query: 152 D-MCHAEMNAILN----KNSADTKRCKLYTSLFPCNECAKVIIQSGIKEVIY 198
D HAE+ AI N S C LYT+L PC CA ++ + IK V+Y
Sbjct: 43 DPTAHAEIVAIRNAARRLGSYLLSGCTLYTTLEPCPMCAGALLWARIKRVVY 94
Score = 36.4 bits (85), Expect = 0.002
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 13 KRCKLYTSLFPCNECAKVIIQSGIKEVIYMCDKHK 47
C LYT+L PC CA ++ + IK V+Y K
Sbjct: 66 SGCTLYTTLEPCPMCAGALLWARIKRVVYGASDPK 100
>gnl|CDD|223195 COG0117, RibD, Pyrimidine deaminase [Coenzyme metabolism].
Length = 146
Score = 60.7 bits (148), Expect = 4e-12
Identities = 33/122 (27%), Positives = 51/122 (41%), Gaps = 30/122 (24%)
Query: 90 EWHEYFMASAFLVAKRSKDPVT---RVGAVIVNEDNKIVGTGYNGMPIGCSDDEFPWDKN 146
E E +M A +A++ + + VG VIV D +IVG GY
Sbjct: 4 ELDERYMERALELAEKGQGTTSPNPSVGCVIVK-DGEIVGEGY----------------- 45
Query: 147 THDELDMCHAEMNAILNKNSADTKRCKLYTSLFPCNE------CAKVIIQSGIKEVIY-M 199
H++ HAE+ A L + Y +L PC+ CA +I++G+ V+ M
Sbjct: 46 -HEKAGGPHAEVCA-LRMAGEAARGATAYVTLEPCSHYGRTPPCADALIKAGVARVVVAM 103
Query: 200 CD 201
D
Sbjct: 104 LD 105
Score = 30.7 bits (70), Expect = 0.25
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 7/35 (20%)
Query: 17 LYTSLFPCNE------CAKVIIQSGIKEVIY-MCD 44
Y +L PC+ CA +I++G+ V+ M D
Sbjct: 71 AYVTLEPCSHYGRTPPCADALIKAGVARVVVAMLD 105
>gnl|CDD|238611 cd01284, Riboflavin_deaminase-reductase, Riboflavin-specific
deaminase. Riboflavin biosynthesis protein RibD
(Diaminohydroxyphosphoribosylaminopyrimidine deaminase)
catalyzes the deamination of
2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone
5'-phosphate, which is an intermediate step in the
biosynthesis of riboflavin.The ribG gene of Bacillus
subtilis and the ribD gene of E. coli are bifunctional
and contain this deaminase domain and a reductase domain
which catalyzes the subsequent reduction of the ribosyl
side chain.
Length = 115
Score = 58.0 bits (141), Expect = 3e-11
Identities = 29/92 (31%), Positives = 42/92 (45%), Gaps = 24/92 (26%)
Query: 113 VGAVIVNEDNKIVGTGYNGMPIGCSDDEFPWDKNTHDELDMCHAEMNAILNKNSADTKRC 172
VG VIV++D +IVG GY H + HAE+NA+ + +
Sbjct: 21 VGCVIVDDDGEIVGEGY------------------HRKAGGPHAEVNALASAGEKLARGA 62
Query: 173 KLYTSLFPCNE------CAKVIIQSGIKEVIY 198
LY +L PC+ C II++GIK V+
Sbjct: 63 TLYVTLEPCSHHGKTPPCVDAIIEAGIKRVVV 94
Score = 33.4 bits (77), Expect = 0.022
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 6/33 (18%)
Query: 15 CKLYTSLFPCNE------CAKVIIQSGIKEVIY 41
LY +L PC+ C II++GIK V+
Sbjct: 62 ATLYVTLEPCSHHGKTPPCVDAIIEAGIKRVVV 94
>gnl|CDD|182786 PRK10860, PRK10860, tRNA-specific adenosine deaminase; Provisional.
Length = 172
Score = 53.3 bits (128), Expect = 4e-09
Identities = 39/118 (33%), Positives = 57/118 (48%), Gaps = 32/118 (27%)
Query: 92 HEYFMASAFLVAKRSKD----PVTRVGAVIVNEDNKIVGTGYNGMPIGCSDDEFPWDKNT 147
HEY+M A +AKR+ D PV GAV+V+ +N+++G G+N PIG
Sbjct: 13 HEYWMRHALTLAKRAWDEREVPV---GAVLVH-NNRVIGEGWN-RPIG-----------R 56
Query: 148 HDELDMCHAEMNAIL-------NKNSADTKRCKLYTSLFPCNECAKVIIQSGIKEVIY 198
HD HAE+ A+ N D LY +L PC CA ++ S I +++
Sbjct: 57 HDP--TAHAEIMALRQGGLVLQNYRLLDAT---LYVTLEPCVMCAGAMVHSRIGRLVF 109
Score = 28.2 bits (63), Expect = 2.0
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 17 LYTSLFPCNECAKVIIQSGIKEVIY 41
LY +L PC CA ++ S I +++
Sbjct: 85 LYVTLEPCVMCAGAMVHSRIGRLVF 109
>gnl|CDD|232920 TIGR00326, eubact_ribD, riboflavin biosynthesis protein RibD. This
model describes the ribD protein as found in Escherichia
coli. The N-terminal domain includes the conserved
zinc-binding site region captured in the model
dCMP_cyt_deam and shared by proteins such as cytosine
deaminase, mammalian apolipoprotein B mRNA editing
protein, blasticidin-S deaminase, and Bacillus subtilis
competence protein comEB. The C-terminal domain is
homologous to the full length of yeast HTP reductase, a
protein required for riboflavin biosynthesis. A number
of archaeal proteins believed related to riboflavin
biosynthesis contain only this C-terminal domain and are
not found as full-length matches to this model
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Riboflavin, FMN, and FAD].
Length = 344
Score = 49.4 bits (118), Expect = 3e-07
Identities = 35/116 (30%), Positives = 53/116 (45%), Gaps = 30/116 (25%)
Query: 96 MASAFLVAKRSK---DPVTRVGAVIVNEDNKIVGTGYNGMPIGCSDDEFPWDKNTHDELD 152
M A +AK+ + P VG VIV ++ +IVG G H +
Sbjct: 1 MNRALDLAKKGQGTTHPNPLVGCVIV-KNGEIVGEGA------------------HQKAG 41
Query: 153 MCHAEMNAILNKNSADTKRCKLYTSLFPCNE------CAKVIIQSGIKEVIY-MCD 201
HAE++A L + + K Y +L PC+ CA+ II++GIK+V+ M D
Sbjct: 42 EPHAEVHA-LRQAGENAKGATAYVTLEPCSHQGRTPPCAEAIIEAGIKKVVVSMQD 96
Score = 35.6 bits (82), Expect = 0.011
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 7/46 (15%)
Query: 10 ADTKRCKLYTSLFPCNE------CAKVIIQSGIKEVIY-MCDKHKQ 48
+ K Y +L PC+ CA+ II++GIK+V+ M D +
Sbjct: 55 ENAKGATAYVTLEPCSHQGRTPPCAEAIIEAGIKKVVVSMQDPNPL 100
>gnl|CDD|238610 cd01283, cytidine_deaminase, Cytidine deaminase zinc-binding
domain. These enzymes are Zn dependent. The zinc ion in
the active site plays a central role in the proposed
catalytic mechanism, activating a water molecule to form
a hydroxide ion that performs a nucleophilic attack on
the substrate. Cytidine deaminases catalyze the
deamination of cytidine to uridine and are important in
the pyrimadine salvage pathway in many cell types, from
bacteria to humans. This family also includes the
apoBec proteins, which are a mammal specific expansion
of RNA editing enzymes, and the closely related
phorbolins, and the AID (activation-induced) enzymes.
Length = 112
Score = 34.6 bits (80), Expect = 0.009
Identities = 26/113 (23%), Positives = 37/113 (32%), Gaps = 25/113 (22%)
Query: 97 ASAFLVAKRSKDPVTRVGAVIVNEDNKIVGTGYNGMPIGCSDDEFPWDKNTHDELDMCHA 156
A+ F A S V GA ++ +D +I TG N E T A
Sbjct: 7 AAEFAYAPYSNFTV---GAALLTKDGRIF-TGVN--------VENASYGLT------LCA 48
Query: 157 EMNAILNKNSADTKRCK--LYTS-----LFPCNECAKVIIQSGIKEVIYMCDK 202
E AI S +R S PC C +V+ + + + D
Sbjct: 49 ERTAIGKAVSEGLRRYLVTWAVSDEGGVWSPCGACRQVLAEFLPSRLYIIIDN 101
>gnl|CDD|219747 pfam08210, APOBEC_N, APOBEC-like N-terminal domain. A mechanism of
generating protein diversity is mRNA editing. Members of
this family are C-to-U editing enzymes. The N-terminal
domain of APOBEC-1 like proteins is the catalytic
domain, while the C-terminal domain is a pseudocatalyitc
domain. More specifically, the catalytic domain is a
zinc dependent deaminases domain and is essential for
cytidine deamination.APOBEC-3 like members contain two
copies of this domain. RNA editing by APOBEC-1 requires
homodimerisation and this complex interacts with RNA
binding proteins to from the editosome (and references
therein). This family also includes the functionally
homologous activation induced deaminase (AID), which is
essential for the development of antibody diversity in B
lymphocytes, and the sea lamprey PmCDA1 and PmCDA2,
which are predicted to play an AID-like role in the
adaptive immune response of jawless vertebrates.
Divergent members of this family are present in various
eukaryotes such as Nematostella, C. elegans, Micromonas
and Emiliania, and prokaryotes such as Wolbachia and
Pseudomonas brassicacearum.
Length = 176
Score = 33.9 bits (78), Expect = 0.024
Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 11/59 (18%)
Query: 153 MCHAE---MNAILNKNSADTKRC---KLYTSLFPCNECAKVIIQ-----SGIKEVIYMC 200
HAE AI + + Y+S PC +CA+ + + G++ I++
Sbjct: 43 SIHAEEQFFRAIESLLDFNPGTIYTITWYSSWSPCFDCAEKLAEFLSKLPGVRLRIFVS 101
Score = 29.3 bits (66), Expect = 0.95
Identities = 8/32 (25%), Positives = 17/32 (53%), Gaps = 5/32 (15%)
Query: 17 LYTSLFPCNECAKVIIQ-----SGIKEVIYMC 43
Y+S PC +CA+ + + G++ I++
Sbjct: 70 WYSSWSPCFDCAEKLAEFLSKLPGVRLRIFVS 101
>gnl|CDD|212774 cd11840, SH3_Intersectin_5, Fifth Src homology 3 domain (or SH3E)
of Intersectin. Intersectins (ITSNs) are adaptor
proteins that function in exo- and endocytosis, actin
cytoskeletal reorganization, and signal transduction.
They are essential for initiating clathrin-coated pit
formation. They bind to many proteins through their
multidomain structure and facilitate the assembly of
multimeric complexes. Vertebrates contain two ITSN
proteins, ITSN1 and ITSN2, which exist in alternatively
spliced short and long isoforms. The short isoforms
contain two Eps15 homology domains (EH1 and EH2), a
coiled-coil region and five SH3 domains (SH3A-E), while
the long isoforms, in addition, contain RhoGEF (also
called Dbl-homologous or DH), Pleckstrin homology (PH)
and C2 domains. ITSN1 and ITSN2 are both widely
expressed, with variations depending on tissue type and
stage of development. The fifth SH3 domain (or SH3E) of
ITSN1 has been shown to bind many protein partners
including SGIP1, Sos1, dynamin1/2, CIN85, c-Cbl, SHIP2,
N-WASP, and synaptojanin-1, among others. SH3 domains
are protein interaction domains that bind to
proline-rich ligands with moderate affinity and
selectivity, preferentially to PxxP motifs. They play
versatile and diverse roles in the cell including the
regulation of enzymes, changing the subcellular
localization of signaling pathway components, and
mediating the formation of multiprotein complex
assemblies.
Length = 53
Score = 29.7 bits (67), Expect = 0.15
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 141 FPWDKNTHDELDMCHAEMNAILNKNSADTKRCKL--YTSLFPCN 182
FP+ DEL ++ +L+K+ D R +L T LFP N
Sbjct: 6 FPYTAQNEDELSFQKGDIINVLSKDDPDWWRGELNGQTGLFPSN 49
>gnl|CDD|133024 cd04181, NTP_transferase, NTP_transferases catalyze the transfer of
nucleotides onto phosphosugars. Nucleotidyltransferases
transfer nucleotides onto phosphosugars. The enzyme
family includes Alpha-D-Glucose-1-Phosphate
Cytidylyltransferase, Mannose-1-phosphate
guanyltransferase, and Glucose-1-phosphate
thymidylyltransferase. The products are activated sugars
that are precursors for synthesis of lipopolysaccharide,
glycolipids and polysaccharides.
Length = 217
Score = 29.1 bits (66), Expect = 1.3
Identities = 11/40 (27%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 87 DVLEWHEYFMASAFLVAKRSKDPVTRVGAVIVNEDNKIVG 126
++L +H A A + K +DP +R G V +++D ++
Sbjct: 114 ELLRFHREKGADATIAVKEVEDP-SRYGVVELDDDGRVTR 152
>gnl|CDD|133065 cd06915, NTP_transferase_WcbM_like, WcbM_like is a subfamily of
nucleotidyl transferases. WcbM protein of Burkholderia
mallei is involved in the biosynthesis, export or
translocation of capsule. It is a subfamily of
nucleotidyl transferases that transfer nucleotides onto
phosphosugars.
Length = 223
Score = 29.1 bits (66), Expect = 1.5
Identities = 10/40 (25%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 87 DVLEWHEYFMASAFLVAKRSKDPVTRVGAVIVNEDNKIVG 126
+L A A + +R D +R G V V+ D +++
Sbjct: 114 ALLAALRASGADATMALRRVPD-ASRYGNVTVDGDGRVIA 152
>gnl|CDD|206605 pfam14439, Bd3614-deam, Bd3614-like deaminase. A member of the
nucleic acid/nucleotide deaminase superfamily prototyped
by Bdellovibrio Bd3614. They are typified by a distinct
N-terminal globular domain. The Bdellovibrio version
occurs in a predicted operon with a 23S rRNA
G2445-modifying methylase suggesting that it might be
involved in RNA editing.
Length = 113
Score = 27.9 bits (62), Expect = 1.8
Identities = 15/62 (24%), Positives = 27/62 (43%), Gaps = 9/62 (14%)
Query: 146 NTHDELDMCHAEMNAILNKNSADTKR-----CKLYTSLFPCNECAKVIIQ----SGIKEV 196
NT+ + HAE+N + +R +L +L C CA ++ G ++V
Sbjct: 27 NTNAKNKTLHAEVNLLQPLLRETARRPIPPGARLLVTLQCCKMCAALVCAACDDPGQRKV 86
Query: 197 IY 198
+Y
Sbjct: 87 VY 88
>gnl|CDD|147282 pfam05020, zf-NPL4, NPL4 family, putative zinc binding region. The
HRD4 gene was identical to NPL4, a gene previously
implicated in nuclear transport. Using a diverse set of
substrates and direct ubiquitination assays, analysis
revealed that HRD4/NPL4 is required for a poorly
characterized step in ER-associated degradation after
ubiquitination of target proteins but before their
recognition by the 26S proteasome. This region of the
protein contains possibly two zinc binding motifs
(Bateman A pers. obs.). Npl4p physically associates with
Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex.
The Cdc48-Ufd1-Npl4 complex functions in the recognition
of several polyubiquitin-tagged proteins and facilitates
their presentation to the 26S proteasome for processive
degradation or even more specific processing.
Length = 147
Score = 27.7 bits (62), Expect = 2.6
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 128 GYNGMPIGCSDDEFPWDKNTHDELDMCHAEMNAILNKNSADTKRCKLYTSLFP 180
G GM CS E PWD+ E + H +A L K ++ T + + +S P
Sbjct: 30 GDKGMCEYCSPLE-PWDEEYLKEHKIKHMSFHAYLRKLNSATNKKESGSSYIP 81
>gnl|CDD|185745 cd09004, GH43_bXyl, Glycosyl hydrolase family 43, includes mostly
1,4-beta-xylanases. This glycosyl hydrolase family 43
(GH43) includes enzymes that have been characterized
with xylan-digesting beta-xylosidase (EC 3.2.1.37) and
xylanase (endo-alpha-L-arabinanase) activities. These
are all inverting enzymes (i.e. they invert the
stereochemistry of the anomeric carbon atom of the
substrate) that have an aspartate as the catalytic
general base, a glutamate as the catalytic general acid
and another aspartate that is responsible for pKa
modulation and orienting the catalytic acid. A common
structural feature of GH43 enzymes is a 5-bladed
beta-propeller domain that contains the catalytic acid
and catalytic base. A long V-shaped groove, partially
enclosed at one end, forms a single extended
substrate-binding surface across the face of the
propeller.
Length = 275
Score = 28.0 bits (63), Expect = 3.2
Identities = 11/51 (21%), Positives = 19/51 (37%), Gaps = 12/51 (23%)
Query: 94 YFMAS-----------AFLVAKRSKDPVTRVGAVIV-NEDNKIVGTGYNGM 132
Y M S A+ +A P R G +I+ + G G++ +
Sbjct: 181 YLMWSEGGWTDPDYHVAYAMADSPLGPFERPGNIILQQDPGIATGPGHHSV 231
>gnl|CDD|235073 PRK02813, PRK02813, putative aminopeptidase 2; Provisional.
Length = 428
Score = 27.8 bits (63), Expect = 4.5
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 149 DELDMCHAEMNAILNKNSADTK 170
D L CHA + A+L S T
Sbjct: 234 DNLSSCHAGLEALLAAASDATN 255
>gnl|CDD|180142 PRK05578, PRK05578, cytidine deaminase; Validated.
Length = 131
Score = 26.4 bits (59), Expect = 7.8
Identities = 13/43 (30%), Positives = 24/43 (55%), Gaps = 4/43 (9%)
Query: 90 EWHEYFMASAFLVAKRSKDPVTR--VGAVIVNEDNKIVGTGYN 130
+W E A A ++++ P ++ VGA ++ +D +I TG N
Sbjct: 2 DWKELIEA-AIEASEKAYAPYSKFPVGAALLTDDGRIY-TGCN 42
>gnl|CDD|224169 COG1249, Lpd, Pyruvate/2-oxoglutarate dehydrogenase complex,
dihydrolipoamide dehydrogenase (E3) component, and
related enzymes [Energy production and conversion].
Length = 454
Score = 26.8 bits (60), Expect = 8.4
Identities = 10/41 (24%), Positives = 15/41 (36%), Gaps = 1/41 (2%)
Query: 52 TIASKRMFDAAKV-HYWSEMDKMNGVQNGSPHKRVDDVLEW 91
I SK + AA+V K G+ P + +L
Sbjct: 48 CIPSKALLHAAEVIEEARHAAKEYGISAEVPKIDFEKLLAR 88
>gnl|CDD|234703 PRK00258, aroE, shikimate 5-dehydrogenase; Reviewed.
Length = 278
Score = 26.7 bits (60), Expect = 9.1
Identities = 7/18 (38%), Positives = 12/18 (66%), Gaps = 2/18 (11%)
Query: 112 RVGAV--IVNEDNKIVGT 127
+GAV +V ED +++G
Sbjct: 85 LIGAVNTLVLEDGRLIGD 102
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 0.132 0.411
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,831,339
Number of extensions: 866730
Number of successful extensions: 775
Number of sequences better than 10.0: 1
Number of HSP's gapped: 745
Number of HSP's successfully gapped: 45
Length of query: 207
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 115
Effective length of database: 6,857,034
Effective search space: 788558910
Effective search space used: 788558910
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)