RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 014311
(427 letters)
>gnl|CDD|215433 PLN02807, PLN02807, diaminohydroxyphosphoribosylaminopyrimidine
deaminase.
Length = 380
Score = 619 bits (1597), Expect = 0.0
Identities = 238/377 (63%), Positives = 288/377 (76%), Gaps = 3/377 (0%)
Query: 51 KSLTSTRKCRGGYRIRCGQVQNNDKDDGFYMRRCVELATKAVGSTSPNPMVGCVIVKDGK 110
+R+ +RC + DD FYMRRCVELA KA+G TSPNPMVGCVIVKDG+
Sbjct: 7 IRTAESRRFGRRTSVRC-SARAAGDDDSFYMRRCVELARKAIGCTSPNPMVGCVIVKDGR 65
Query: 111 IVGEGFHPKAGQPHAEVFALRDAGELAEGATAYVSLEPCNHYGRTPPCTEALIKAKVKKV 170
IVGEGFHPKAGQPHAEVFALRDAG+LAE ATAYVSLEPCNHYGRTPPCTEALIKAKVK+V
Sbjct: 66 IVGEGFHPKAGQPHAEVFALRDAGDLAENATAYVSLEPCNHYGRTPPCTEALIKAKVKRV 125
Query: 171 VVGMLDPNPIVNSKGLERLRDAGIDVTVGVEDELCKRLNEAFIHRIVTGKPFATLRYTLS 230
VVGM+DPNPIV SKG+ERLRDAGI+VTVGVE+ELC++LNEAFIHR++TGKPF TLRY++S
Sbjct: 126 VVGMVDPNPIVASKGIERLRDAGIEVTVGVEEELCRKLNEAFIHRMLTGKPFVTLRYSMS 185
Query: 231 VNGHVLDQLGEGVAESGGYYSQLLQEYDAIILSASSTKKYSIPASQEPDANQPFRIITVS 290
+NG +L+Q+GEG ++GGYYSQLLQEYDA+ILS++ +P SQE A QP RII
Sbjct: 186 MNGCLLNQIGEGADDAGGYYSQLLQEYDAVILSSALADADPLPLSQEAGAKQPLRIIIAR 245
Query: 291 NHASPIRIPGLSEESSSKVIVFTDGEITVEPDMGTKGIETVNLHQLNLKAVLDYCYSHGF 350
+ +SP++IP L EES++KV+V D E + EP + KG+E V L+Q+NL ++LD CY G
Sbjct: 246 SESSPLQIPSLREESAAKVLVLADKESSAEPVLRRKGVEVVVLNQINLDSILDLCYQRGL 305
Query: 351 CSVLVDLRGNYGDLEMLLKEGIEQNLLQKIVVEVLPVWNGSDGGNPHTLLNSLGKRLILK 410
CSVL+DLRGN G LE LLK+ +E LLQK+VVEVLP W+GS G + LK
Sbjct: 306 CSVLLDLRGNVGGLESLLKDALEDKLLQKVVVEVLPFWSGSQG--QSIASFGGSQSFKLK 363
Query: 411 NLQPKMSSQSIVLEGYL 427
L + S+VLEGY
Sbjct: 364 RLTSREVGGSVVLEGYF 380
>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 = 267 bits (683), Expect = 2e-86
Identities = 130/348 (37%), Positives = 189/348 (54%), Gaps = 21/348 (6%)
Query: 81 MRRCVELATKAVGSTSPNPMVGCVIVKDGKIVGEGFHPKAGQPHAEVFALRDAGELAEGA 140
M R ++LA K G+T PNP+VGCVIVK+G+IVGEG H KAG+PHAEV ALR AGE A+GA
Sbjct: 1 MNRALDLAKKGQGTTHPNPLVGCVIVKNGEIVGEGAHQKAGEPHAEVHALRQAGENAKGA 60
Query: 141 TAYVSLEPCNHYGRTPPCTEALIKAKVKKVVVGMLDPNPIVNSKGLERLRDAGIDVTVGV 200
TAYV+LEPC+H GRTPPC EA+I+A +KKVVV M DPNP+V +G ERL+ AGI+VT G+
Sbjct: 61 TAYVTLEPCSHQGRTPPCAEAIIEAGIKKVVVSMQDPNPLVAGRGAERLKQAGIEVTFGI 120
Query: 201 EDELCKRLNEAFIHRIVTGKPFATLRYTLSVNGHVLDQLGEG---VAESGGYYSQLLQEY 257
E +RLN+ F+ R+ TG P+ L+ S++G + GE +E+ +Q L+
Sbjct: 121 LKEEAERLNKGFLKRMRTGLPYVQLKLAASLDGKIATASGESKWITSEAARTDAQQLRAQ 180
Query: 258 DAIILSASSTKKYSIPA--SQEPDA-NQPFRIITVSNHASPIRIP---GLSEESSSKVIV 311
IL T K PA ++ +A QP R++ + RIP L + + I
Sbjct: 181 SDAILVGGGTVKADNPALTARLDEATEQPLRVVLDTQL----RIPEFAKLIPQIAPTWIF 236
Query: 312 FTDGEITVEPDMGTKGIETVNLHQLNLKAVLDYCYSHGFCSVLVDLRGNYGDLEMLLKEG 371
T + + + L ++ ++ V+ G SVLV+ N LL
Sbjct: 237 TTARDKKKRLEAF--EVNIFPLEKVTIREVMTQLGKRGINSVLVEGGPN------LLGSF 288
Query: 372 IEQNLLQKIVVEVLPVWNGSDGGNPHTLLNSLGKRLILKNLQPKMSSQ 419
+++ L+ ++++ + P G K N + +Q
Sbjct: 289 LDEGLVDELIIYIAPKLLGGTHAPGLCSEPGFQKMADALNFKFLEINQ 336
>gnl|CDD|223195 COG0117, RibD, Pyrimidine deaminase [Coenzyme metabolism].
Length = 146
Score = 253 bits (649), Expect = 4e-84
Identities = 95/141 (67%), Positives = 111/141 (78%)
Query: 76 DDGFYMRRCVELATKAVGSTSPNPMVGCVIVKDGKIVGEGFHPKAGQPHAEVFALRDAGE 135
D YM R +ELA K G+TSPNP VGCVIVKDG+IVGEG+H KAG PHAEV ALR AGE
Sbjct: 5 LDERYMERALELAEKGQGTTSPNPSVGCVIVKDGEIVGEGYHEKAGGPHAEVCALRMAGE 64
Query: 136 LAEGATAYVSLEPCNHYGRTPPCTEALIKAKVKKVVVGMLDPNPIVNSKGLERLRDAGID 195
A GATAYV+LEPC+HYGRTPPC +ALIKA V +VVV MLDPNP+V GL RLR AGI+
Sbjct: 65 AARGATAYVTLEPCSHYGRTPPCADALIKAGVARVVVAMLDPNPLVAGGGLARLRAAGIE 124
Query: 196 VTVGVEDELCKRLNEAFIHRI 216
V VG+ +E ++LNE F+ R+
Sbjct: 125 VEVGILEEEAEKLNEGFLKRM 145
>gnl|CDD|182729 PRK10786, ribD, bifunctional
diaminohydroxyphosphoribosylaminopyrimidine
deaminase/5-amino-6-(5-phosphoribosylamino)uracil
reductase; Provisional.
Length = 367
Score = 214 bits (547), Expect = 7e-66
Identities = 110/238 (46%), Positives = 143/238 (60%), Gaps = 19/238 (7%)
Query: 77 DGFYMRRCVELATKAVGSTSPNPMVGCVIVKDGKIVGEGFHPKAGQPHAEVFALRDAGEL 136
D FYM R ++LA + +T PNP VGCVIVKDG+IVGEG+H +AG+PHAEV ALR AGE
Sbjct: 3 DEFYMARALKLAQRGRFTTHPNPNVGCVIVKDGEIVGEGYHQRAGEPHAEVHALRMAGEK 62
Query: 137 AEGATAYVSLEPCNHYGRTPPCTEALIKAKVKKVVVGMLDPNPIVNSKGLERLRDAGIDV 196
A+GATAYV+LEPC+H+GRTPPC +ALI A V +VV M DPNP V +GL RL+ AGIDV
Sbjct: 63 AKGATAYVTLEPCSHHGRTPPCCDALIAAGVARVVAAMQDPNPQVAGRGLYRLQQAGIDV 122
Query: 197 TVGVEDELCKRLNEAFIHRIVTGKPFATLRYTLSVNGHVLDQLGEG---VAESGGYYSQL 253
+ G+ + LN+ F+ R+ TG P+ L+ S++G GE + Q
Sbjct: 123 SHGLMMSEAEALNKGFLKRMRTGFPYIQLKLGASLDGRTAMASGESQWITSPQARRDVQR 182
Query: 254 LQEYDAIILSASSTKKYSIPAS----QEPDAN-----------QPFRIITVS-NHASP 295
L+ IL++S+T PA E DA QP RI+ S N +P
Sbjct: 183 LRAQSHAILTSSATVLADDPALTVRWSELDAQTQALYPQENLRQPVRIVIDSQNRVTP 240
>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 = 203 bits (518), Expect = 6e-65
Identities = 78/115 (67%), Positives = 92/115 (80%), Gaps = 2/115 (1%)
Query: 81 MRRCVELATKAVGSTSPNPMVGCVIVKD-GKIVGEGFHPKAGQPHAEVFALRDAGE-LAE 138
MRR +ELA K G TSPNP VGCVIV D G+IVGEG+H KAG PHAEV AL AGE LA
Sbjct: 1 MRRALELAEKGRGLTSPNPPVGCVIVDDDGEIVGEGYHRKAGGPHAEVNALASAGEKLAR 60
Query: 139 GATAYVSLEPCNHYGRTPPCTEALIKAKVKKVVVGMLDPNPIVNSKGLERLRDAG 193
GAT YV+LEPC+H+G+TPPC +A+I+A +K+VVVG+ DPNP+V KG ERLR AG
Sbjct: 61 GATLYVTLEPCSHHGKTPPCVDAIIEAGIKRVVVGVRDPNPLVAGKGAERLRAAG 115
>gnl|CDD|215887 pfam00383, dCMP_cyt_deam_1, Cytidine and deoxycytidylate deaminase
zinc-binding region.
Length = 104
Score = 98.9 bits (247), Expect = 3e-25
Identities = 45/111 (40%), Positives = 63/111 (56%), Gaps = 17/111 (15%)
Query: 74 DKDDGFYMRRCVELATKAVGSTSPNPMVGCVIVK-DGKIVGEGFHPK-AGQP---HAEVF 128
+ D ++MR +E A +A + N VG VIVK DG I+ G++ + AG HAE
Sbjct: 1 MEWDEYFMRLALEAAKRA-YTPYSNFPVGAVIVKNDGGIIATGYNGENAGYDPTIHAERN 59
Query: 129 ALRDAGEL-----AEGATAYVSLEPCNHYGRTPPCTEALIKAKVKKVVVGM 174
A+R+AG L EGAT YV+LEPC C +A+I++ +KKVV G
Sbjct: 60 AIRNAGRLGEGIKLEGATLYVTLEPCGM------CRQAIIESGIKKVVFGT 104
>gnl|CDD|223663 COG0590, CumB, Cytosine/adenosine deaminases [Nucleotide transport
and metabolism / Translation, ribosomal structure and
biogenesis].
Length = 152
Score = 78.5 bits (194), Expect = 2e-17
Identities = 50/154 (32%), Positives = 72/154 (46%), Gaps = 24/154 (15%)
Query: 75 KDDGFYMRRCVELATKAV-GSTSPNPMVGCVIVK-DGKIVGEGFHP--KAGQP--HAEVF 128
+ D +MR ++ A KA P VG VIV DG+I+ G + + P HAE+
Sbjct: 6 EKDEDFMREALKEAKKAGDEGEVP---VGAVIVDADGEIIARGHNRREEDNDPTAHAEIL 62
Query: 129 ALRDAGELA-----EGATAYVSLEPCNHYGRTPPCTEALIKAKVKKVVVGMLDPNPIVNS 183
A+R A E + T YV+LEPC P C A+I A++ +VV G DP
Sbjct: 63 AIRAAAETLGNYRLKDCTLYVTLEPC------PMCAGAIIWARIDRVVYGASDPKTGAIG 116
Query: 184 KGLERLRDAG----IDVTVGVEDELCKRLNEAFI 213
L+ L+D ++V G+ +E C L F
Sbjct: 117 SLLDILKDPRLNHRVEVYGGILEEECSALLSEFF 150
>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 = 72.6 bits (179), Expect = 9e-16
Identities = 43/110 (39%), Positives = 56/110 (50%), Gaps = 22/110 (20%)
Query: 81 MRRCVELATKAV-GSTSPNPMVGCVIV-KDGKIVGEGFHPKAGQP-----HAEVFALRDA 133
MR +ELA KA+ P G VIV DGK++ G H + Q HAE+ A+R+A
Sbjct: 1 MRLAIELARKALAEGEVP---FGAVIVDDDGKVIARG-HNRVEQDGDPTAHAEIVAIRNA 56
Query: 134 GE-----LAEGATAYVSLEPCNHYGRTPPCTEALIKAKVKKVVVGMLDPN 178
L G T Y +LEPC P C AL+ A++K+VV G DP
Sbjct: 57 ARRLGSYLLSGCTLYTTLEPC------PMCAGALLWARIKRVVYGASDPK 100
>gnl|CDD|182786 PRK10860, PRK10860, tRNA-specific adenosine deaminase; Provisional.
Length = 172
Score = 65.6 bits (160), Expect = 1e-12
Identities = 42/150 (28%), Positives = 71/150 (47%), Gaps = 21/150 (14%)
Query: 76 DDGFYMRRCVELATKAVGSTSPNPMVGCVIVKDGKIVGEGFHPKAGQ----PHAEVFALR 131
++MR + LA +A P VG V+V + +++GEG++ G+ HAE+ ALR
Sbjct: 12 SHEYWMRHALTLAKRA-WDEREVP-VGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALR 69
Query: 132 DAGELAEG-----ATAYVSLEPCNHYGRTPPCTEALIKAKVKKVVVGMLDPNPIVNSKGL 186
G + + AT YV+LEPC C A++ +++ ++V G D +
Sbjct: 70 QGGLVLQNYRLLDATLYVTLEPCVM------CAGAMVHSRIGRLVFGARDAKTGAAGSLM 123
Query: 187 ERLRDAG----IDVTVGVEDELCKRLNEAF 212
+ L G +++T GV + C L F
Sbjct: 124 DVLHHPGMNHRVEITEGVLADECAALLSDF 153
>gnl|CDD|225042 COG2131, ComEB, Deoxycytidylate deaminase [Nucleotide transport and
metabolism].
Length = 164
Score = 64.3 bits (157), Expect = 3e-12
Identities = 43/151 (28%), Positives = 58/151 (38%), Gaps = 41/151 (27%)
Query: 94 STSPNPMVGCVIVKDGKIVGEGFHPKAGQP-----------------------------H 124
ST P VG VIVKDG+I+ G+ G P H
Sbjct: 23 STCPRRQVGAVIVKDGRIIATGY---NGAPSGEDHCIDRGCLRDKVVFVTTCGHCCRTLH 79
Query: 125 AEVFALRDA---GELAEGATAYVSLEPCNHYGRTPPCTEALIKAKVKKVVVGMLDPNPIV 181
AE A+ A G EGAT YV+ PC C + +I+A +K+VV P V
Sbjct: 80 AEQNAILQAARHGVGLEGATLYVTHFPC------SNCAKLIIQAGIKEVVYAEPYPTETV 133
Query: 182 NSKGLERLRDAGIDVTVGVEDELCKRLNEAF 212
E L +AG+ V + +R+
Sbjct: 134 APYSQELLEEAGVKVRQFPPELASERVEIMV 164
>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 = 58.7 bits (142), Expect = 5e-11
Identities = 28/89 (31%), Positives = 40/89 (44%), Gaps = 14/89 (15%)
Query: 94 STSPNPMVGCVIV--KDGKIVGEG----FHPKAGQPHAEVFALRDAGELA--EGATAYVS 145
+ N VG +V KDG VG G + HAE AL +AG +G YV+
Sbjct: 13 AKESNFQVGACLVNKKDGGKVGRGCNIENAAYSMCNHAERTALFNAGSEGDTKGQMLYVA 72
Query: 146 LEPCNHYGRTPPCTEALIKAKVKKVVVGM 174
L PC C + +I+ +K V+V +
Sbjct: 73 LSPCGA------CAQLIIELGIKDVIVVL 95
>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 = 55.0 bits (133), Expect = 2e-09
Identities = 35/106 (33%), Positives = 45/106 (42%), Gaps = 34/106 (32%)
Query: 94 STSPNPMVGCVIVKDGKIVGEGF--------------HPKAGQP-----------HAEVF 128
ST P VG VIVKD +I+ G+ + P HAE
Sbjct: 15 STCPRRQVGAVIVKDKRIISTGYNGSPSGLPHCAEVGCERDDLPSGEDQKCCRTVHAEQN 74
Query: 129 ALRDA---GELAEGATAYVSLEPCNHYGRTPPCTEALIKAKVKKVV 171
A+ A G EGAT YV+L PC C + +I+A +KKVV
Sbjct: 75 AILQAARHGVSLEGATLYVTLFPCIE------CAKLIIQAGIKKVV 114
>gnl|CDD|222894 PHA02588, cd, deoxycytidylate deaminase; Provisional.
Length = 168
Score = 50.9 bits (122), Expect = 1e-07
Identities = 41/150 (27%), Positives = 60/150 (40%), Gaps = 52/150 (34%)
Query: 101 VGCVIVKDGKIVGEGFH-PKAGQP-----------------------------------H 124
VG VI K+G+I+ G++ AG H
Sbjct: 24 VGAVIEKNGRIISTGYNGTPAGGVNCCDHANEQGWLDDEGKLKKEHRPEHSAWSSKNEIH 83
Query: 125 AE----VFALRDAGELAEGATAYVSLEPCNHYGRTPPCTEALIKAKVKKVVVGML-DPNP 179
AE +FA R G EGAT YV+ PC P C +A+ ++ +KK+V D N
Sbjct: 84 AELNAILFAAR-NGISIEGATMYVTASPC------PDCAKAIAQSGIKKLVYCEKYDRNG 136
Query: 180 IVNSKGLERLRDAGIDVTVGVEDELCKRLN 209
+ LR +GI+V + + E +LN
Sbjct: 137 P---GWDDILRKSGIEV-IQIPKEELNKLN 162
>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 = 40.6 bits (95), Expect = 3e-04
Identities = 34/116 (29%), Positives = 51/116 (43%), Gaps = 31/116 (26%)
Query: 77 DGFYMRRCVELATKAVGSTSPNPMVGCVIVKDGKIVGEGFHPK-AGQP------------ 123
D ++M + LA + ST VG IV+D +I+ G++ AG
Sbjct: 6 DQYFMAQSHLLALR---STCTRLSVGATIVRDKRIIAGGYNGSVAGGVHCIDEGCYVVDG 62
Query: 124 ------HAEVFALRDA---GELAEGATAYVSLEPCNHYGRTPPCTEALIKAKVKKV 170
HAE+ AL G EGA YV+ PC CT+++I+A +KK+
Sbjct: 63 HCVRTIHAEMNALLQCAKFGVSTEGAEIYVTHFPCLQ------CTKSIIQAGIKKI 112
>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 = 37.4 bits (87), Expect = 0.006
Identities = 21/101 (20%), Positives = 32/101 (31%), Gaps = 23/101 (22%)
Query: 113 GEGFHPKAGQPHAEVFALRDAGELAEG-------ATAYVSLEPCNHYGRTPPCTEALIKA 165
G + HAE R L + T Y S PC C E L +
Sbjct: 34 GYARNENKKSIHAEEQFFRAIESLLDFNPGTIYTITWYSSWSPCFD------CAEKLAEF 87
Query: 166 --KVKKVVVGM--------LDPNPIVNSKGLERLRDAGIDV 196
K+ V + + + + +GL L AG+ +
Sbjct: 88 LSKLPGVRLRIFVSRLYEHEERGDLYEREGLRCLARAGVKL 128
>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 = 37.0 bits (86), Expect = 0.009
Identities = 38/183 (20%), Positives = 74/183 (40%), Gaps = 26/183 (14%)
Query: 219 GKPFATLRYTLSVNGHVLDQLGEGVAESGGYYSQLLQEYDA---IILSASSTKKYSIPA- 274
G+P+ L+Y +S++G + GE + + + + A IL S T P
Sbjct: 1 GRPYVILKYAMSLDGKIATASGESSWITSEEARRDVHQLRAQSDAILVGSGTVLADDPRL 60
Query: 275 ----SQEPDANQPFRIITVSNHASPIRIPGLSEESSSKVIVFTDGEITVE-----PDMGT 325
+ + P R++ S P L+++ + V T E D
Sbjct: 61 TVRWVELDELRNPVRVVLDSQLRVPPTARLLNDD--APTWVATTEPADEEKVKELEDF-- 116
Query: 326 KGIETVNLHQ--LNLKAVLDYCYSHGFCSVLVDLRGNYGDLEMLLKEGIEQNLLQKIVVE 383
G+E + L ++LK +++ Y G SV+V+ G L +++ L+ +++V
Sbjct: 117 -GVEVLVLETKRVDLKKLMEILYEEGINSVMVEGGGT------LNGSLLKEGLVDELIVY 169
Query: 384 VLP 386
+ P
Sbjct: 170 IAP 172
>gnl|CDD|238431 cd00851, MTH1175, This uncharacterized conserved protein belongs to
a family of iron-molybdenum cluster-binding proteins
that includes NifX, NifB, and NifY, all of which are
involved in the synthesis of an iron-molybdenum cofactor
(FeMo-co) that binds the active site of the
dinitrogenase enzyme. This domain is a predicted
small-molecule-binding domain (SMBD) with an alpha/beta
fold that is present either as a stand-alone domain
(e.g. NifX and NifY) or fused to another conserved
domain (e.g. NifB) however, its function is still
undetermined.The SCOP database suggests that this domain
is most similar to structures within the ribonuclease H
superfamily. This conserved domain is represented in
two of the three major divisions of life (bacteria and
archaea).
Length = 103
Score = 30.3 bits (69), Expect = 0.47
Identities = 17/53 (32%), Positives = 21/53 (39%), Gaps = 8/53 (15%)
Query: 149 CNHYGRTPPCTEALIKAKVKKVVVGMLDPNPIVNSKGLERLRDAGIDVTVGVE 201
G E L V V+VG + P L +LR+AGI V G E
Sbjct: 48 TGGAGGKAA--EFLADEGVDVVIVGGIGPRA------LNKLRNAGIKVYKGAE 92
>gnl|CDD|233277 TIGR01116, ATPase-IIA1_Ca, sarco/endoplasmic reticulum
calcium-translocating P-type ATPase. This model
describes the P-type ATPase responsible for
translocating calcium ions across the endoplasmic
reticulum membrane of eukaryotes , and is of particular
importance in the sarcoplasmic reticulum of skeletal and
cardiac muscle in vertebrates. These pumps transfer Ca2+
from the cytoplasm to the lumen of the endoplasmic
reticulum. In humans and mice, at least, there are
multiple isoforms of the SERCA pump with overlapping but
not redundant functions. Defects in SERCA isoforms are
associated with diseases in humans. The calcium P-type
ATPases have been characterized as Type IIA based on a
phylogenetic analysis which distinguishes this group
from the Type IIB PMCA calcium pump modelled by
TIGR01517. A separate analysis divides Type IIA into
sub-types, SERCA and PMR1 the latter of which is
modelled by TIGR01522 [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 917
Score = 32.1 bits (73), Expect = 0.61
Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 11/66 (16%)
Query: 171 VVGMLDPNPIVNSKGLERLRDAGIDVTV------GVEDELCKRL-----NEAFIHRIVTG 219
VVGMLDP + +E+ R AGI V + + +C+R+ +E + TG
Sbjct: 531 VVGMLDPPRPEVADAIEKCRTAGIRVIMITGDNKETAEAICRRIGIFSPDEDVTFKSFTG 590
Query: 220 KPFATL 225
+ F +
Sbjct: 591 REFDEM 596
>gnl|CDD|217119 pfam02579, Nitro_FeMo-Co, Dinitrogenase iron-molybdenum cofactor.
This family contains several NIF (B, Y and X) proteins
which are iron-molybdenum cofactors (FeMo-co) in the
dinitrogenase enzyme which catalyzes the reduction of
dinitrogen to ammonium. Dinitrogenase is a
hetero-tetrameric (alpha(2)beta(2)) enzyme which
contains the iron-molybdenum cofactor (FeMo-co) at its
active site.
Length = 94
Score = 29.5 bits (67), Expect = 0.88
Identities = 18/81 (22%), Positives = 26/81 (32%), Gaps = 6/81 (7%)
Query: 124 HAEVFALRDAGELAEGATAYVSLEPCNHYGRTPPCTEALIKAKVKKVVVGMLDPNPIVNS 183
A FA+ + + G + L V V+VG + PN
Sbjct: 11 RAPYFAIYEVDDGGVEVVENREPACDEGGGGGGKLAQLLALEGVDAVIVGGIGPNA---- 66
Query: 184 KGLERLRDAGIDVTVGVEDEL 204
L +L AGI V G +
Sbjct: 67 --LAKLEAAGIKVYKGAGGTV 85
>gnl|CDD|197227 cd09129, PLDc_unchar2_1, Putative catalytic domain, repeat 1, of
uncharacterized phospholipase D-like proteins. Putative
catalytic domain, repeat 1, of uncharacterized
phospholipase D (PLD, EC 3.1.4.4)-like proteins. PLD
enzymes hydrolyze phospholipid phosphodiester bonds to
yield phosphatidic acid and a free polar head group.
They can also catalyze transphosphatidylation of
phospholipids to acceptor alcohols. Members of this
subfamily contain two HKD motifs (H-x-K-x(4)-D, where x
represents any amino acid residue) that characterizes
the PLD superfamily. The two motifs may be part of the
active site and may be involved in phosphatidyl group
transfer.
Length = 196
Score = 30.7 bits (70), Expect = 1.2
Identities = 15/47 (31%), Positives = 27/47 (57%), Gaps = 9/47 (19%)
Query: 159 TEALIKAKVK----KVVVGMLDPNPIV----NSKGLERLRDAGIDVT 197
T+ALI+ K + +VV + DP ++ L++L++AGI+V
Sbjct: 42 TDALIEKKKENPDLPIVV-ITDPINTFYGSHDNPHLKKLKEAGIEVV 87
>gnl|CDD|224350 COG1433, COG1433, Uncharacterized conserved protein [Function
unknown].
Length = 121
Score = 28.8 bits (65), Expect = 2.0
Identities = 13/54 (24%), Positives = 18/54 (33%), Gaps = 6/54 (11%)
Query: 151 HYGRTPPCTEALIKAKVKKVVVGMLDPNPIVNSKGLERLRDAGIDVTVGVEDEL 204
G E L+ V V+ + PN L+ AGI V V +
Sbjct: 50 EKGAGIRIAELLVDEGVDVVIASNIGPNAY------NALKAAGIKVYVAPGGTV 97
>gnl|CDD|176675 cd07252, BphC1-RGP6_N_like, N-terminal domain of
2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC
1.13.11.39) 1 from Rhodococcus globerulus P6
(BphC1-RGP6) and similar proteins. This subfamily
contains the N-terminal, non-catalytic, domain of
BphC1-RGP6 and similar proteins. BphC catalyzes the
extradiol ring cleavage reaction of
2,3-dihydroxybiphenyl, the third step in the
polychlorinated biphenyls (PCBs) degradation pathway
(bph pathway). This subfamily of BphCs belongs to the
type I extradiol dioxygenase family, which require a
metal in the active site in its catalytic mechanism.
Polychlorinated biphenyl degrading bacteria demonstrate
a multiplicity of 2,3-dihydroxybiphenyl
1,2-dioxygenases. For example, three types of BphC
enzymes have been found in Rhodococcus globerulus
(BphC1-RGP6 - BphC3-RGP6), all three enzymes are type I
extradiol dioxygenases. BphC1-RGP6 has an internal
duplication, it is a two-domain dioxygenase which forms
octamers, and has Fe(II) at the catalytic site. Its
N-terminal repeat is represented in this subfamily.
BphC2-RGP6 and BphC3-RGP6 are one-domain dioxygenases,
they belong to a different family, the
ED_TypeI_classII_C (C-terminal domain of type I, class
II extradiol dioxygenases) family.
Length = 120
Score = 28.7 bits (65), Expect = 2.3
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 186 LERLRDAGIDVTVGVEDELCKR 207
RLR AG+ V G + +R
Sbjct: 75 AARLRAAGVAVEEGSAELAAER 96
>gnl|CDD|240650 cd12173, PGDH_4, Phosphoglycerate dehydrogenases, NAD-binding and
catalytic domains. Phosphoglycerate dehydrogenases
(PGDHs) catalyze the initial step in the biosynthesis of
L-serine from D-3-phosphoglycerate. PGDHs come in 3
distinct structural forms, with this first group being
related to 2-hydroxy acid dehydrogenases, sharing
structural similarity to formate and glycerate
dehydrogenases. PGDH in E. coli and Mycobacterium
tuberculosis form tetramers, with subunits containing a
Rossmann-fold NAD binding domain. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence.
Length = 304
Score = 30.1 bits (69), Expect = 2.3
Identities = 19/46 (41%), Positives = 28/46 (60%), Gaps = 8/46 (17%)
Query: 169 KVVVGMLDPNPIVNSKGLERLRDAGIDVTVGV---EDELCKRLNEA 211
KV+V DP ++ +GLE LR+AGI+V V E+EL + +A
Sbjct: 1 KVLV--TDP---IDEEGLELLREAGIEVDVAPGLSEEELLAIIADA 41
>gnl|CDD|201390 pfam00682, HMGL-like, HMGL-like. This family contains a diverse
set of enzymes. These include various aldolases and a
region of pyruvate carboxylase.
Length = 236
Score = 29.6 bits (67), Expect = 2.4
Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 6/61 (9%)
Query: 157 PCTEALIKAKVKKVVVGMLDPNPIVNSKGLERLRDAGIDVTVGVEDELCKRLNEAFIHRI 216
++ K K+ K + D +E R AGIDV +G ED R + AF+ +
Sbjct: 88 ATSDLHRKYKLNKDREEVAD----RAVAAVEAARSAGIDVELGCEDA--GRTDLAFLIEV 141
Query: 217 V 217
V
Sbjct: 142 V 142
>gnl|CDD|215932 pfam00465, Fe-ADH, Iron-containing alcohol dehydrogenase.
Length = 323
Score = 29.9 bits (68), Expect = 2.8
Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 153 GRTPPCTEALIKAKVKKVVVGMLDPNPIVNS--KGLERLRDAGIDVTVGV 200
G ++L +A ++ VV ++PNP + + R+ G DV + V
Sbjct: 36 GLLDKVLDSLEEAGIEVVVFDGVEPNPTLEEVDEAAAAAREEGADVIIAV 85
>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 = 29.6 bits (67), Expect = 3.1
Identities = 10/37 (27%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 160 EALIKAKVKKVVVGMLDPNPIVNSKGLERLRDAGIDV 196
E LI V +++ +D + + L++ AGI V
Sbjct: 49 EDLIAQGVDGIIISPVDSAALTPA--LKKANAAGIPV 83
>gnl|CDD|237356 PRK13347, PRK13347, coproporphyrinogen III oxidase; Provisional.
Length = 453
Score = 29.6 bits (67), Expect = 4.0
Identities = 21/79 (26%), Positives = 32/79 (40%), Gaps = 15/79 (18%)
Query: 129 ALRDAGELAEGATAYVSLEPCNHYGRTPPCTEALIKAKVKKVVVGMLDPNPIVN------ 182
ALRDA + A A V ++P T +AL + G+ D +P V
Sbjct: 128 ALRDAFDFAPEAEIAVEIDPRTV---TAEMLQALAALGFNRASFGVQDFDPQVQKAINRI 184
Query: 183 ------SKGLERLRDAGID 195
++ +E LR AG +
Sbjct: 185 QPEEMVARAVELLRAAGFE 203
>gnl|CDD|240642 cd12165, 2-Hacid_dh_6, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 314
Score = 28.7 bits (65), Expect = 5.1
Identities = 27/104 (25%), Positives = 40/104 (38%), Gaps = 29/104 (27%)
Query: 110 KIVGEGFHPKAGQPHAEVFALRDAGE-LAEGATAYVSLEPCNHYGRTPPCTEALIKA--- 165
+++G PK + V L D E L + V+L P T LI A
Sbjct: 162 RVIGVSRSPKEDEGADFVGTLSDLDEALEQADVVVVAL-PLTKQ------TRGLIGAAEL 214
Query: 166 ---KVKKVVVGMLDPN----PIVNSKGL-ERLRD-----AGIDV 196
K ++V N P+V+ + L E L++ A IDV
Sbjct: 215 AAMKPGAILV-----NVGRGPVVDEEALYEALKERPIAGAAIDV 253
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 28.8 bits (65), Expect = 5.1
Identities = 27/182 (14%), Positives = 59/182 (32%), Gaps = 25/182 (13%)
Query: 258 DAIILSASSTKK--------YSIPASQEPDANQPFRIITVSNHASPIRIPGLSEESSSKV 309
DA+ILS +K + A+ + + + A P ++ +
Sbjct: 25 DAVILSTRKVRKGGLFGKKFVEVTAAIDEEEVAAASAEEEAKKALEPADPAKLPATAEPL 84
Query: 310 IVFTDGEITVEPD--MGTKGIETVNLHQ--LNLKAVLDYCYSHGFCSVLVDLRGNYGD-- 363
+ E P + L + L+ +L+ + + R G
Sbjct: 85 ELPAPLEEPAAPAAQAAEPLLPEAELRKELSALRELLE----RLLAGLALQRRDPEGAKL 140
Query: 364 LEMLLKEGIEQNLLQKIVVEVLPVWNGSDGGNPHTLLNSLGKRLILKNLQPKMSSQSIVL 423
LE LL+ G+ + L ++++ ++ + + L + + L K I+
Sbjct: 141 LERLLEAGVSEELARELLEKLP------EDLDAEDAWRWL-REALEGMLPVKPEEDPILE 193
Query: 424 EG 425
G
Sbjct: 194 RG 195
>gnl|CDD|223766 COG0694, COG0694, Thioredoxin-like proteins and domains
[Posttranslational modification, protein turnover,
chaperones].
Length = 93
Score = 27.3 bits (61), Expect = 5.3
Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 366 MLLKEGIEQNLLQKI--VVEVLPVWNGSDGGNP 396
+ LK GIE+ L ++I V EV V + G +
Sbjct: 61 VTLKNGIERQLKEEIPEVKEVEQVTEHARGEHS 93
>gnl|CDD|223321 COG0243, BisC, Anaerobic dehydrogenases, typically
selenocysteine-containing [Energy production and
conversion].
Length = 765
Score = 29.0 bits (65), Expect = 5.5
Identities = 14/48 (29%), Positives = 16/48 (33%), Gaps = 3/48 (6%)
Query: 85 VELATKAVGSTSPNPMVGC---VIVKDGKIVGEGFHPKAGQPHAEVFA 129
K V + P VGC V VKDGK+V P
Sbjct: 34 GTPKAKEVKTICPGCGVGCGIRVHVKDGKVVRITIEGDPDHPINRGRL 81
>gnl|CDD|217329 pfam03033, Glyco_transf_28, Glycosyltransferase family 28
N-terminal domain. The glycosyltransferase family 28
includes monogalactosyldiacylglycerol synthase (EC
2.4.1.46) and UDP-N-acetylglucosamine transferase (EC
2.4.1.-). This N-terminal domain contains the acceptor
binding site and likely membrane association site. This
family also contains a large number of proteins that
probably have quite distinct activities.
Length = 136
Score = 27.7 bits (62), Expect = 5.7
Identities = 14/78 (17%), Positives = 24/78 (30%), Gaps = 13/78 (16%)
Query: 187 ERLRDAGIDVTVGVEDELCKRLNEAFI-HRIVTGKPFAT------------LRYTLSVNG 233
LR G +V +G L + + EA + + G R
Sbjct: 20 WALRRRGHEVRLGTPPGLEEFVEEAGLPFVPIGGDGLRRKSLKNLKEPLEGGRALRQAKE 79
Query: 234 HVLDQLGEGVAESGGYYS 251
+ + + V GGY +
Sbjct: 80 ILKEFKPDLVIGFGGYVA 97
>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 = 27.5 bits (61), Expect = 6.3
Identities = 10/32 (31%), Positives = 13/32 (40%), Gaps = 6/32 (18%)
Query: 124 HAEVFAL------RDAGELAEGATAYVSLEPC 149
HAEV L + GA V+L+ C
Sbjct: 36 HAEVNLLQPLLRETARRPIPPGARLLVTLQCC 67
>gnl|CDD|236978 PRK11778, PRK11778, putative inner membrane peptidase; Provisional.
Length = 330
Score = 28.6 bits (65), Expect = 6.5
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 186 LERLRDAGIDVTVGV 200
L+RLRDAGI +TV V
Sbjct: 147 LQRLRDAGIPLTVAV 161
>gnl|CDD|224149 COG1228, HutI, Imidazolonepropionase and related amidohydrolases
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 406
Score = 28.5 bits (64), Expect = 7.3
Identities = 15/48 (31%), Positives = 20/48 (41%), Gaps = 2/48 (4%)
Query: 82 RRCVELATKAVGSTSPNPMV--GCVIVKDGKIVGEGFHPKAGQPHAEV 127
LAT A ++ G V+++DGKIV G AEV
Sbjct: 7 ANIAMLATLAGRGLPGLGIIEDGAVLIEDGKIVAVGPEEIDIPAGAEV 54
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 0.136 0.401
Gapped
Lambda K H
0.267 0.0626 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,636,432
Number of extensions: 2125963
Number of successful extensions: 2149
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2122
Number of HSP's successfully gapped: 39
Length of query: 427
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 327
Effective length of database: 6,502,202
Effective search space: 2126220054
Effective search space used: 2126220054
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 (21.7 bits)
S2: 60 (27.1 bits)