RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8195
(192 letters)
>gnl|CDD|182729 PRK10786, ribD, bifunctional
diaminohydroxyphosphoribosylaminopyrimidine
deaminase/5-amino-6-(5-phosphoribosylamino)uracil
reductase; Provisional.
Length = 367
Score = 211 bits (538), Expect = 6e-68
Identities = 89/191 (46%), Positives = 125/191 (65%), Gaps = 8/191 (4%)
Query: 1 MTLALQQAKLS-INSSPNPRVGCVIVKEKRIISCGYTKSPGGNHAEIDALLNA--AAQGY 57
M AL+ A+ + PNP VGCVIVK+ I+ GY + G HAE+ AL A A+G
Sbjct: 7 MARALKLAQRGRFTTHPNPNVGCVIVKDGEIVGEGYHQRAGEPHAEVHALRMAGEKAKG- 65
Query: 58 DVYNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIAINDPNPLVSGKGVAQLISAGIS 117
+T Y+TLEPCS+ G TPPC +ALI +G+ +V+ A+ DPNP V+G+G+ +L AGI
Sbjct: 66 ----ATAYVTLEPCSHHGRTPPCCDALIAAGVARVVAAMQDPNPQVAGRGLYRLQQAGID 121
Query: 118 VKQGLMQKEAYEINIGFFSRMQRGIPWVRMKIASSLDNKTSLYNNSSQWITSKESRNDSH 177
V GLM EA +N GF RM+ G P++++K+ +SLD +T++ + SQWITS ++R D
Sbjct: 122 VSHGLMMSEAEALNKGFLKRMRTGFPYIQLKLGASLDGRTAMASGESQWITSPQARRDVQ 181
Query: 178 IWRARSCAILT 188
RA+S AILT
Sbjct: 182 RLRAQSHAILT 192
>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 = 199 bits (507), Expect = 1e-63
Identities = 89/192 (46%), Positives = 125/192 (65%), Gaps = 4/192 (2%)
Query: 1 MTLALQQAKLSI-NSSPNPRVGCVIVKEKRIISCGYTKSPGGNHAEIDALLNAAAQGYDV 59
M AL AK + PNP VGCVIVK I+ G + G HAE+ AL A
Sbjct: 1 MNRALDLAKKGQGTTHPNPLVGCVIVKNGEIVGEGAHQKAGEPHAEVHALRQAGENAKG- 59
Query: 60 YNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIAINDPNPLVSGKGVAQLISAGISVK 119
+T Y+TLEPCS+ G TPPC EA+I++GIKKV++++ DPNPLV+G+G +L AGI V
Sbjct: 60 --ATAYVTLEPCSHQGRTPPCAEAIIEAGIKKVVVSMQDPNPLVAGRGAERLKQAGIEVT 117
Query: 120 QGLMQKEAYEINIGFFSRMQRGIPWVRMKIASSLDNKTSLYNNSSQWITSKESRNDSHIW 179
G++++EA +N GF RM+ G+P+V++K+A+SLD K + + S+WITS+ +R D+
Sbjct: 118 FGILKEEAERLNKGFLKRMRTGLPYVQLKLAASLDGKIATASGESKWITSEAARTDAQQL 177
Query: 180 RARSCAILTGKN 191
RA+S AIL G
Sbjct: 178 RAQSDAILVGGG 189
>gnl|CDD|223195 COG0117, RibD, Pyrimidine deaminase [Coenzyme metabolism].
Length = 146
Score = 177 bits (452), Expect = 1e-57
Identities = 71/142 (50%), Positives = 102/142 (71%), Gaps = 8/142 (5%)
Query: 1 MTLALQQAKL-SINSSPNPRVGCVIVKEKRIISCGYTKSPGGNHAEIDALLNA--AAQGY 57
M AL+ A+ +SPNP VGCVIVK+ I+ GY + GG HAE+ AL A AA+G
Sbjct: 10 MERALELAEKGQGTTSPNPSVGCVIVKDGEIVGEGYHEKAGGPHAEVCALRMAGEAARG- 68
Query: 58 DVYNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIAINDPNPLVSGKGVAQLISAGIS 117
+T Y+TLEPCS++G TPPC +ALIK+G+ +V++A+ DPNPLV+G G+A+L +AGI
Sbjct: 69 ----ATAYVTLEPCSHYGRTPPCADALIKAGVARVVVAMLDPNPLVAGGGLARLRAAGIE 124
Query: 118 VKQGLMQKEAYEINIGFFSRMQ 139
V+ G++++EA ++N GF RM+
Sbjct: 125 VEVGILEEEAEKLNEGFLKRMR 146
>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 = 146 bits (370), Expect = 9e-46
Identities = 57/117 (48%), Positives = 81/117 (69%), Gaps = 4/117 (3%)
Query: 1 MTLALQQAKLSIN-SSPNPRVGCVIVK-EKRIISCGYTKSPGGNHAEIDALLNAAAQGYD 58
M AL+ A+ +SPNP VGCVIV + I+ GY + GG HAE++AL A+A
Sbjct: 1 MRRALELAEKGRGLTSPNPPVGCVIVDDDGEIVGEGYHRKAGGPHAEVNAL--ASAGEKL 58
Query: 59 VYNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIAINDPNPLVSGKGVAQLISAG 115
+T+Y+TLEPCS+ G TPPC +A+I++GIK+V++ + DPNPLV+GKG +L +AG
Sbjct: 59 ARGATLYVTLEPCSHHGKTPPCVDAIIEAGIKRVVVGVRDPNPLVAGKGAERLRAAG 115
>gnl|CDD|215433 PLN02807, PLN02807, diaminohydroxyphosphoribosylaminopyrimidine
deaminase.
Length = 380
Score = 141 bits (358), Expect = 5e-41
Identities = 63/141 (44%), Positives = 96/141 (68%), Gaps = 3/141 (2%)
Query: 14 SSPNPRVGCVIVKEKRIISCGYTKSPGGNHAEIDALLNAAAQGYDVYNSTVYITLEPCSY 73
+SPNP VGCVIVK+ RI+ G+ G HAE+ AL +A G N+T Y++LEPC++
Sbjct: 50 TSPNPMVGCVIVKDGRIVGEGFHPKAGQPHAEVFALRDA---GDLAENATAYVSLEPCNH 106
Query: 74 FGYTPPCTEALIKSGIKKVIIAINDPNPLVSGKGVAQLISAGISVKQGLMQKEAYEINIG 133
+G TPPCTEALIK+ +K+V++ + DPNP+V+ KG+ +L AGI V G+ ++ ++N
Sbjct: 107 YGRTPPCTEALIKAKVKRVVVGMVDPNPIVASKGIERLRDAGIEVTVGVEEELCRKLNEA 166
Query: 134 FFSRMQRGIPWVRMKIASSLD 154
F RM G P+V ++ + S++
Sbjct: 167 FIHRMLTGKPFVTLRYSMSMN 187
>gnl|CDD|215887 pfam00383, dCMP_cyt_deam_1, Cytidine and deoxycytidylate deaminase
zinc-binding region.
Length = 104
Score = 87.8 bits (218), Expect = 5e-23
Identities = 41/102 (40%), Positives = 56/102 (54%), Gaps = 13/102 (12%)
Query: 1 MTLALQQAKLSINSSPNPRVGCVIVK-EKRIISCGYTKSPGGN----HAEIDALLNAAA- 54
M LAL+ AK + N VG VIVK + II+ GY G HAE +A+ NA
Sbjct: 8 MRLALEAAKRAYTPYSNFPVGAVIVKNDGGIIATGYNGENAGYDPTIHAERNAIRNAGRL 67
Query: 55 -QGYDVYNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIA 95
+G + +T+Y+TLEPC C +A+I+SGIKKV+
Sbjct: 68 GEGIKLEGATLYVTLEPCGM------CRQAIIESGIKKVVFG 103
>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 = 81.2 bits (201), Expect = 4e-20
Identities = 42/118 (35%), Positives = 58/118 (49%), Gaps = 33/118 (27%)
Query: 5 LQQAKLSINSS--PNPRVGCVIVKEKRIISCGYTKSPGG--------------------- 41
+ A+L+ S P +VG VIVK+KRIIS GY SP G
Sbjct: 5 MAIARLAALRSTCPRRQVGAVIVKDKRIISTGYNGSPSGLPHCAEVGCERDDLPSGEDQK 64
Query: 42 ----NHAEIDALLNAAAQGYDVYNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIA 95
HAE +A+L AA G + +T+Y+TL PC C + +I++GIKKV+ A
Sbjct: 65 CCRTVHAEQNAILQAARHGVSLEGATLYVTLFPCIE------CAKLIIQAGIKKVVYA 116
>gnl|CDD|225042 COG2131, ComEB, Deoxycytidylate deaminase [Nucleotide transport and
metabolism].
Length = 164
Score = 79.0 bits (195), Expect = 8e-19
Identities = 46/158 (29%), Positives = 70/158 (44%), Gaps = 34/158 (21%)
Query: 3 LALQQAKLSINSS--PNPRVGCVIVKEKRIISCGYTKSPGGN------------------ 42
+ A+L S P +VG VIVK+ RII+ GY +P G
Sbjct: 11 YFMAIAELVALRSTCPRRQVGAVIVKDGRIIATGYNGAPSGEDHCIDRGCLRDKVVFVTT 70
Query: 43 --------HAEIDALLNAAAQGYDVYNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVII 94
HAE +A+L AA G + +T+Y+T PCS C + +I++GIK+V+
Sbjct: 71 CGHCCRTLHAEQNAILQAARHGVGLEGATLYVTHFPCS------NCAKLIIQAGIKEVVY 124
Query: 95 AINDPNPLVSGKGVAQLISAGISVKQGLMQKEAYEINI 132
A P V+ L AG+ V+Q + + + I
Sbjct: 125 AEPYPTETVAPYSQELLEEAGVKVRQFPPELASERVEI 162
>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 = 73.8 bits (182), Expect = 2e-17
Identities = 35/107 (32%), Positives = 55/107 (51%), Gaps = 14/107 (13%)
Query: 1 MTLALQQAKLSINSSPNPRVGCVIV-KEKRIISCGYTKSPGGN----HAEIDALLNAAAQ 55
M LA++ A+ ++ P G VIV + ++I+ G+ + HAEI A+ NAA +
Sbjct: 1 MRLAIELARKALAEGEVP-FGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARR 59
Query: 56 --GYDVYNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIAINDPN 100
Y + T+Y TLEPC C AL+ + IK+V+ +DP
Sbjct: 60 LGSYLLSGCTLYTTLEPCPM------CAGALLWARIKRVVYGASDPK 100
>gnl|CDD|224896 COG1985, RibD, Pyrimidine reductase, riboflavin biosynthesis
[Coenzyme metabolism].
Length = 218
Score = 75.8 bits (187), Expect = 3e-17
Identities = 26/50 (52%), Positives = 34/50 (68%)
Query: 140 RGIPWVRMKIASSLDNKTSLYNNSSQWITSKESRNDSHIWRARSCAILTG 189
RG P+V +K+A SLD K + + SS+WIT +E+R D H RA S AIL G
Sbjct: 1 RGRPFVTLKLAMSLDGKIATASGSSKWITGEEARADVHELRAESDAILVG 50
>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 = 66.4 bits (162), Expect = 1e-14
Identities = 33/102 (32%), Positives = 47/102 (46%), Gaps = 13/102 (12%)
Query: 1 MTLALQQAKLSINSSPNPRVGCVIVKEK------RIISCGYTKSPGGNHAEIDALLNAAA 54
MT AL+ A L N +VG +V +K R + NHAE AL NA +
Sbjct: 1 MTEALKAADLGYAKESNFQVGACLVNKKDGGKVGRGCNIENAAYSMCNHAERTALFNAGS 60
Query: 55 QGYDVYNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIAI 96
+G D +Y+ L PC C + +I+ GIK VI+ +
Sbjct: 61 EG-DTKGQMLYVALSPCGA------CAQLIIELGIKDVIVVL 95
>gnl|CDD|223663 COG0590, CumB, Cytosine/adenosine deaminases [Nucleotide transport
and metabolism / Translation, ribosomal structure and
biogenesis].
Length = 152
Score = 65.4 bits (160), Expect = 7e-14
Identities = 44/153 (28%), Positives = 65/153 (42%), Gaps = 32/153 (20%)
Query: 1 MTLALQQAKLS--INSSPNPRVGCVIVKEKRIISCGYTKSPGGN----------HAEIDA 48
M AL++AK + P VG VIV I + G N HAEI A
Sbjct: 12 MREALKEAKKAGDEGEVP---VGAVIVDADGEII-----ARGHNRREEDNDPTAHAEILA 63
Query: 49 LLNAAAQG--YDVYNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIAINDPNPLVSGK 106
+ AA Y + + T+Y+TLEPC P C A+I + I +V+ +DP G
Sbjct: 64 IRAAAETLGNYRLKDCTLYVTLEPC------PMCAGAIIWARIDRVVYGASDPKTGAIGS 117
Query: 107 GVAQLISAG----ISVKQGLMQKEAYEINIGFF 135
+ L + V G++++E + FF
Sbjct: 118 LLDILKDPRLNHRVEVYGGILEEECSALLSEFF 150
>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 = 57.2 bits (138), Expect = 8e-11
Identities = 33/100 (33%), Positives = 48/100 (48%), Gaps = 25/100 (25%)
Query: 20 VGCVIVKEKRIISCGYTKSPGGN-------------------HAEIDALLNAAAQGYDVY 60
VG IV++KRII+ GY S G HAE++ALL A G
Sbjct: 27 VGATIVRDKRIIAGGYNGSVAGGVHCIDEGCYVVDGHCVRTIHAEMNALLQCAKFGVSTE 86
Query: 61 NSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIAINDPN 100
+ +Y+T PC CT+++I++GIKK+ A + N
Sbjct: 87 GAEIYVTHFPCL------QCTKSIIQAGIKKIYYAQDYHN 120
>gnl|CDD|222894 PHA02588, cd, deoxycytidylate deaminase; Provisional.
Length = 168
Score = 55.5 bits (134), Expect = 5e-10
Identities = 34/111 (30%), Positives = 48/111 (43%), Gaps = 42/111 (37%)
Query: 19 RVGCVIVKEKRIISCGYTKSPGGN------------------------------------ 42
+VG VI K RIIS GY +P G
Sbjct: 23 KVGAVIEKNGRIISTGYNGTPAGGVNCCDHANEQGWLDDEGKLKKEHRPEHSAWSSKNEI 82
Query: 43 HAEIDALLNAAAQGYDVYNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVI 93
HAE++A+L AA G + +T+Y+T PC P C +A+ +SGIKK++
Sbjct: 83 HAELNAILFAARNGISIEGATMYVTASPC------PDCAKAIAQSGIKKLV 127
>gnl|CDD|182786 PRK10860, PRK10860, tRNA-specific adenosine deaminase; Provisional.
Length = 172
Score = 54.4 bits (131), Expect = 1e-09
Identities = 44/150 (29%), Positives = 70/150 (46%), Gaps = 18/150 (12%)
Query: 1 MTLALQQAKLSINSSPNPRVGCVIVKEKRIISCGYTKSPGGN----HAEIDALLN--AAA 54
M AL AK + + P VG V+V R+I G+ + G + HAEI AL
Sbjct: 17 MRHALTLAKRAWDEREVP-VGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVL 75
Query: 55 QGYDVYNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIAINDPNPLVSGKGVAQLISA 114
Q Y + ++T+Y+TLEPC C A++ S I +++ D +G + L
Sbjct: 76 QNYRLLDATLYVTLEPCVM------CAGAMVHSRIGRLVFGARDAKTGAAGSLMDVLHHP 129
Query: 115 G----ISVKQGLMQKEAYEINIGFFSRMQR 140
G + + +G++ E + FF RM+R
Sbjct: 130 GMNHRVEITEGVLADECAALLSDFF-RMRR 158
>gnl|CDD|216753 pfam01872, RibD_C, RibD C-terminal domain. The function of this
domain is not known, but it is thought to be involved in
riboflavin biosynthesis. This domain is found in the C
terminus of RibD/RibG, in combination with pfam00383, as
well as in isolation in some archaebacterial proteins.
This family appears to be related to pfam00186.
Length = 201
Score = 53.9 bits (130), Expect = 3e-09
Identities = 24/50 (48%), Positives = 31/50 (62%)
Query: 143 PWVRMKIASSLDNKTSLYNNSSQWITSKESRNDSHIWRARSCAILTGKNI 192
P+V +K A SLD K + SSQWIT +E+R D H RA + AIL G+
Sbjct: 1 PYVILKFAMSLDGKIAAAGGSSQWITGEEARADVHQLRAEADAILVGRGT 50
>gnl|CDD|129330 TIGR00227, ribD_Cterm, riboflavin-specific deaminase C-terminal
domain. Eubacterial riboflavin-specific deaminases have
a zinc-binding domain recognized by the dCMP_cyt_deam
model toward the N-terminus and this domain toward the
C-terminus. Yeast HTP reductase, a
riboflavin-biosynthetic enzyme, and several archaeal
proteins believed related to riboflavin biosynthesis
consist only of this domain and lack the dCMP_cyt_deam
domain.
Length = 216
Score = 53.5 bits (129), Expect = 5e-09
Identities = 25/51 (49%), Positives = 32/51 (62%)
Query: 141 GIPWVRMKIASSLDNKTSLYNNSSQWITSKESRNDSHIWRARSCAILTGKN 191
G P+V +K A SLD K + + S WITS+E+R D H RA+S AIL G
Sbjct: 1 GRPYVILKYAMSLDGKIATASGESSWITSEEARRDVHQLRAQSDAILVGSG 51
>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 = 36.2 bits (84), Expect = 0.002
Identities = 16/67 (23%), Positives = 25/67 (37%), Gaps = 10/67 (14%)
Query: 19 RVGCVIVKEK-RIISCGY----TKSPGGNHAEIDALLNAAAQGYDVYNSTVYITLEPCSY 73
VG ++ + RI + G AE A+ A ++G Y T ++ E
Sbjct: 19 TVGAALLTKDGRIFT-GVNVENASYGLTLCAERTAIGKAVSEGLRRYLVTWAVSDEG--- 74
Query: 74 FGYTPPC 80
G PC
Sbjct: 75 -GVWSPC 80
>gnl|CDD|206603 pfam14437, MafB19-deam, MafB19-like deaminase. A member of the
nucleic acid/nucleotide deaminase superfamily prototyped
by Neisseria MafB19. Members of this family are present
in a wide phyletic range of bacteria and are predicted
to function as toxins in bacterial polymorphic toxin
systems.
Length = 143
Score = 30.1 bits (68), Expect = 0.35
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 5/54 (9%)
Query: 43 HAEIDALLNAAAQGYDVYNS-TVYITLEPCSYF-GYTPPCTEALIKSGIKKVII 94
HAE A+ A G S T+Y+ + C Y G P E K G+K + +
Sbjct: 79 HAEAGAIQQAYDAGMTGGKSMTMYVDRDVCGYCGGDIPSMAE---KLGLKSLTV 129
>gnl|CDD|222755 pfam14440, XOO_2897-deam, Xanthomonas XOO_2897-like deaminase. A
member of the nucleic acid/nucleotide deaminase
superfamily prototyped by Xanthomonas XOO_2897. Members
of this family are present in a wide phyletic range of
bacteria and are predicted to function as toxins in
bacterial polymorphic toxin systems. The Xanthomonas
XOO_2897 lack an immunity protein and is predicted to
be deployed against its eukaryotic host.
Length = 117
Score = 29.8 bits (67), Expect = 0.40
Identities = 20/50 (40%), Positives = 21/50 (42%), Gaps = 4/50 (8%)
Query: 36 TKSPGGNHAEIDALLNAAAQGYDVYNST-VYITLEPCSYFGYTPPCTEAL 84
KS GG HAE L A G +Y LEPCS GY C L
Sbjct: 39 AKSGGGPHAERTLLDQLRAHGVPPDQILELYTELEPCSEPGY---CARML 85
>gnl|CDD|223661 COG0588, GpmA, Phosphoglycerate mutase 1 [Carbohydrate transport
and metabolism].
Length = 230
Score = 29.9 bits (68), Expect = 0.66
Identities = 11/39 (28%), Positives = 23/39 (58%), Gaps = 5/39 (12%)
Query: 104 SGKGVAQLISAGISVKQGLMQKEAYEINIGFFSRMQRGI 142
+ KG+++ +AG L+++E E +I + S ++R I
Sbjct: 29 TEKGISEAKAAGK-----LLKEEGLEFDIAYTSVLKRAI 62
>gnl|CDD|233193 TIGR00929, VirB4_CagE, type IV secretion/conjugal transfer ATPase,
VirB4 family. Type IV secretion systems are found in
Gram-negative pathogens. They export proteins, DNA, or
complexes in different systems and are related to
plasmid conjugation systems. This model represents
related ATPases that include VirB4 in Agrobacterium
tumefaciens (DNA export) CagE in Helicobacter pylori
(protein export) and plasmid TraB (conjugation).
Length = 785
Score = 28.8 bits (65), Expect = 2.0
Identities = 17/64 (26%), Positives = 24/64 (37%), Gaps = 6/64 (9%)
Query: 23 VIVKEKRIISCGYTKSPGGNHAEIDALLNAAAQGYDVYNSTVYITLEPCSYFGYTPPCTE 82
V+ K +I + G A ID D+Y + +Y+TLE Y P
Sbjct: 73 HTVRRKIVIDYPDPEFKNGFAAAIDEEWRRKFASSDLYENDLYLTLE------YKPDSIG 126
Query: 83 ALIK 86
L K
Sbjct: 127 VLEK 130
>gnl|CDD|239311 cd03013, PRX5_like, Peroxiredoxin (PRX) family, PRX5-like
subfamily; members are similar to the human protein,
PRX5, a homodimeric TRX peroxidase, widely expressed in
tissues and found cellularly in mitochondria,
peroxisomes and the cytosol. The cellular location of
PRX5 suggests that it may have an important antioxidant
role in organelles that are major sources of reactive
oxygen species (ROS), as well as a role in the control
of signal transduction. PRX5 has been shown to reduce
hydrogen peroxide, alkyl hydroperoxides and
peroxynitrite. As with all other PRXs, the N-terminal
peroxidatic cysteine of PRX5 is oxidized into a
sulfenic acid intermediate upon reaction with
peroxides. Human PRX5 is able to resolve this
intermediate by forming an intramolecular disulfide
bond with its C-terminal cysteine (the resolving
cysteine), which can then be reduced by TRX, just like
an atypical 2-cys PRX. This resolving cysteine,
however, is not conserved in other members of the
subfamily. In such cases, it is assumed that the
oxidized cysteine is directly resolved by an external
small-molecule or protein reductant, typical of a 1-cys
PRX. In the case of the H. influenza PRX5 hybrid, the
resolving glutaredoxin domain is on the same protein
chain as PRX. PRX5 homodimers show an A-type interface,
similar to atypical 2-cys PRXs.
Length = 155
Score = 27.9 bits (63), Expect = 2.3
Identities = 10/36 (27%), Positives = 17/36 (47%), Gaps = 12/36 (33%)
Query: 76 YTPPCTE-----------ALIKSGIKKVI-IAINDP 99
+TP C+ L G+ +VI +++NDP
Sbjct: 41 FTPTCSAQHLPGYVENADELKAKGVDEVICVSVNDP 76
>gnl|CDD|197200 cd00138, PLDc_SF, Catalytic domain of phospholipase D superfamily
proteins. Catalytic domain of phospholipase D (PLD)
superfamily proteins. The PLD superfamily is composed
of a large and diverse group of proteins including
plant, mammalian and bacterial PLDs, bacterial
cardiolipin (CL) synthases, bacterial
phosphatidylserine synthases (PSS), eukaryotic
phosphatidylglycerophosphate (PGP) synthase, eukaryotic
tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some
bacterial endonucleases (Nuc and BfiI), among others.
PLD enzymes hydrolyze phospholipid phosphodiester bonds
to yield phosphatidic acid and a free polar head group.
They can also catalyze the transphosphatidylation of
phospholipids to acceptor alcohols. The majority of
members in this superfamily contain a short conserved
sequence motif (H-x-K-x(4)-D, where x represents any
amino acid residue), called the HKD signature motif.
There are varying expanded forms of this motif in
different family members. Some members contain variant
HKD motifs. Most PLD enzymes are monomeric proteins
with two HKD motif-containing domains. Two HKD motifs
from two domains form a single active site. Some PLD
enzymes have only one copy of the HKD motif per subunit
but form a functionally active dimer, which has a
single active site at the dimer interface containing
the two HKD motifs from both subunits. Different PLD
enzymes may have evolved through domain fusion of a
common catalytic core with separate substrate
recognition domains. Despite their various catalytic
functions and a very broad range of substrate
specificities, the diverse group of PLD enzymes can
bind to a phosphodiester moiety. Most of them are
active as bi-lobed monomers or dimers, and may possess
similar core structures for catalytic activity. They
are generally thought to utilize a common two-step
ping-pong catalytic mechanism, involving an
enzyme-substrate intermediate, to cleave phosphodiester
bonds. The two histidine residues from the two HKD
motifs play key roles in the catalysis. Upon substrate
binding, a histidine from one HKD motif could function
as the nucleophile, attacking the phosphodiester bond
to create a covalent phosphohistidine intermediate,
while the other histidine residue from the second HKD
motif could serve as a general acid, stabilizing the
leaving group.
Length = 119
Score = 27.1 bits (60), Expect = 3.5
Identities = 16/63 (25%), Positives = 27/63 (42%), Gaps = 3/63 (4%)
Query: 27 EKRIISCGYTKSPGGNHAEIDALLNAAAQGYDVYNSTVYITLEPCSYFGYTPPCTEALIK 86
++ I S + ALL AA +G DV + I P + + EAL++
Sbjct: 11 KESIFIATPNFSFNSADRLLKALLAAAERGVDVR---LIIDKPPNAAGSLSAALLEALLR 67
Query: 87 SGI 89
+G+
Sbjct: 68 AGV 70
>gnl|CDD|133047 cd06425, M1P_guanylylT_B_like_N, N-terminal domain of the
M1P-guanylyltransferase B-isoform like proteins.
GDP-mannose pyrophosphorylase (GTP:
alpha-d-mannose-1-phosphate guanyltransferase)
catalyzes the formation of GDP-d-mannose from GTP and
alpha-d-mannose-1-Phosphate. It contains an N-terminal
catalytic domain and a C-terminal Lefthanded-beta-Helix
fold domain. GDP-d-mannose is the activated form of
mannose for formation of cell wall lipoarabinomannan
and various mannose-containing glycolipids and
polysaccharides. The function of GDP-mannose
pyrophosphorylase is essential for cell wall integrity,
morphogenesis and viability. Repression of GDP-mannose
pyrophosphorylase in yeast leads to phenotypes, such as
cell lysis, defective cell wall, and failure of
polarized growth and cell separation.
Length = 233
Score = 27.2 bits (61), Expect = 4.9
Identities = 9/16 (56%), Positives = 15/16 (93%)
Query: 82 EALIKSGIKKVIIAIN 97
EAL K+G+K++I+A+N
Sbjct: 39 EALAKAGVKEIILAVN 54
>gnl|CDD|224605 COG1691, COG1691, NCAIR mutase (PurE)-related proteins [General
function prediction only].
Length = 254
Score = 27.4 bits (61), Expect = 5.1
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 93 IIAINDPNPLVSGKGVAQLISAGIS 117
+AI DPN G ++SAG S
Sbjct: 104 TLAIKDPNYEPKKGGKVGVLSAGTS 128
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 27.3 bits (61), Expect = 5.4
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 82 EALIKSGIKKVII 94
EA ++GIKKVII
Sbjct: 556 EAAAEAGIKKVII 568
>gnl|CDD|235340 PRK05086, PRK05086, malate dehydrogenase; Provisional.
Length = 312
Score = 27.3 bits (61), Expect = 5.7
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 98 DPNPLVSGKGVAQLISAGISVKQGLMQKEAYEINIG 133
DP P + G V LISAG++ K G+ + + + +N G
Sbjct: 62 DPTPALEGADVV-LISAGVARKPGMDRSDLFNVNAG 96
>gnl|CDD|234883 PRK00979, PRK00979, tetrahydromethanopterin S-methyltransferase
subunit H; Provisional.
Length = 308
Score = 26.8 bits (60), Expect = 6.8
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 82 EALIKSGIKKVII-AINDPNPLVSGKGVAQLISAGISVKQGLMQK 125
EAL +S IK I+ A + +P V G+ + L G +G++
Sbjct: 140 EALKESDIKAAIVLAFDPMDPSVEGR-LKMLEEGGKGQDKGMLPL 183
>gnl|CDD|222241 pfam13583, Reprolysin_4, Metallo-peptidase family M12B
Reprolysin-like. This zinc-binding metallo-peptidase
has the characteristic binding motif HExxGHxxGxxH of
Reprolysin-like peptidases of family M12B.
Length = 195
Score = 26.6 bits (59), Expect = 7.1
Identities = 13/55 (23%), Positives = 21/55 (38%), Gaps = 3/55 (5%)
Query: 31 ISCGYTKSPGGNHAEIDALLNAA-AQGYDVYNSTVYITLEPCSY--FGYTPPCTE 82
Y GG+ ++ A +N A+ +VY V I+L YT +
Sbjct: 11 ADYSYYSIFGGSVDKVKAFINNVVARLNEVYGRNVGISLTLIGDERLIYTTSSAD 65
>gnl|CDD|107249 cd01536, PBP1_ABC_sugar_binding_like, Periplasmic sugar-binding
domain of active transport systems that are members of
the type I periplasmic binding protein (PBP1)
superfamily. Periplasmic sugar-binding domain of active
transport systems that are members of the type I
periplasmic binding protein (PBP1) superfamily. The
members of this family function as the primary receptors
for chemotaxis and transport of many sugar based solutes
in bacteria and archaea. The sugar binding domain is
also homologous to the ligand-binding domain of
eukaryotic receptors such as glutamate receptor (GluR)
and DNA-binding transcriptional repressors such as LacI
and GalR. Moreover, this periplasmic binding domain,
also known as Venus flytrap domain, undergoes transition
from an open to a closed conformational state upon the
binding of ligands such as lactose, ribose, fructose,
xylose, arabinose, galactose/glucose, and other sugars.
This family also includes the periplasmic binding domain
of autoinducer-2 (AI-2) receptors such as LsrB and LuxP
which are highly homologous to periplasmic
pentose/hexose sugar-binding proteins.
Length = 267
Score = 26.9 bits (60), Expect = 7.2
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 82 EALIKSGIKKVIIAINDPNPLVSGKGVAQLISAGISV 118
E LI G+ +II+ D L + + +AGI V
Sbjct: 49 EDLIAQGVDGIIISPVDSAALT--PALKKANAAGIPV 83
>gnl|CDD|218734 pfam05758, Ycf1, Ycf1. The chloroplast genomes of most higher
plants contain two giant open reading frames designated
ycf1 and ycf2. Although the function of Ycf1 is unknown,
it is known to be an essential gene.
Length = 832
Score = 27.3 bits (61), Expect = 7.2
Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 7/43 (16%)
Query: 134 FFSRMQRGIPWVRMKIASSLDNKTSLYNNSSQWITSKESRNDS 176
F ++R I SS D LYN+ W+ + E + D+
Sbjct: 358 FGEMIERKISLFTTSKLSSDD----LYNH---WVYTNEKKKDN 393
>gnl|CDD|239398 cd03124, alpha_CA_prokaryotic_like, Carbonic anhydrase alpha,
prokaryotic-like subfamily. Carbonic anhydrases (CAs)
are zinc-containing enzymes that catalyze the reversible
hydration of carbon dioxide in a two-step mechanism: a
nucleophilic attack of a zinc-bound hydroxide ion on
carbon dioxide, followed by the regeneration of the
active site by ionization of the zinc-bound water
molecule and removal of a proton from the active site.
They are ubiquitous enzymes involved in fundamental
processes like photosynthesis, respiration, pH
homeostasis and ion transport. Most alpha CAs are
monomeric enzymes. The zinc ion is complexed by three
histidines. This sub-family includes bacterial carbonic
anhydrase alpha, as well as plant enzymes such as
tobacco nectarin III and yam dioscorin and, carbonic
anhydrases from molluscs, such as nacrein, which are
part of the organic matrix layer in shells. Other
members of this family may be involved in maintaining pH
balance, in facilitating transport of carbon dioxide or
carbonic acid, or in sensing carbon dioxide levels in
the environment. Dioscorin is the major storage protein
of yam tubers and may play a role as an antioxidant.
Tobacco Nectarin may play a role in the maintenace of pH
and oxidative balance in nectar. Mollusc nacrein may
participate in calcium carbonate crystal formation of
the nacreous layer. This subfamily also includes three
alpha carbonic anhydrases from Chlamydomonas reinhardtii
(CAH 1-3). CAHs1-2 are localized in the periplasmic
space. CAH1 faciliates the movement of carbon dioxide
across the plasma membrane when the medium is alkaline.
CAH3 is localized to the thylakoid lumen and provides
CO2 to Rubisco.
Length = 216
Score = 26.5 bits (59), Expect = 7.5
Identities = 8/16 (50%), Positives = 10/16 (62%), Gaps = 5/16 (31%)
Query: 72 SYFGY-----TPPCTE 82
SY+ Y TPPC+E
Sbjct: 158 SYYRYEGSLTTPPCSE 173
>gnl|CDD|181670 PRK09140, PRK09140, 2-dehydro-3-deoxy-6-phosphogalactonate
aldolase; Reviewed.
Length = 206
Score = 26.3 bits (59), Expect = 9.0
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 10/51 (19%)
Query: 75 GYTP----PCTEALIKSGIKKVIIAINDPNPLVSGKGVAQ------LISAG 115
G TP ALI++G + + I +N P+P S + + LI AG
Sbjct: 18 GITPDEALAHVGALIEAGFRAIEIPLNSPDPFDSIAALVKALGDRALIGAG 68
>gnl|CDD|219069 pfam06512, Na_trans_assoc, Sodium ion transport-associated.
Members of this family contain a region found
exclusively in eukaryotic sodium channels or their
subunits, many of which are voltage-gated. Members very
often also contain between one and four copies of
pfam00520 and, less often, one copy of pfam00612.
Length = 230
Score = 26.6 bits (59), Expect = 9.4
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 135 FSRMQRGIPWVRMKIAS 151
+R+QRGI WV+ I
Sbjct: 11 IARIQRGINWVKRNIRD 27
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
0.317 0.132 0.389
Gapped
Lambda K H
0.267 0.0650 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,507,196
Number of extensions: 860108
Number of successful extensions: 829
Number of sequences better than 10.0: 1
Number of HSP's gapped: 802
Number of HSP's successfully gapped: 49
Length of query: 192
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 100
Effective length of database: 6,857,034
Effective search space: 685703400
Effective search space used: 685703400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (25.5 bits)