RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13607
(245 letters)
>gnl|CDD|235544 PRK05647, purN, phosphoribosylglycinamide formyltransferase;
Reviewed.
Length = 200
Score = 172 bits (438), Expect = 5e-54
Identities = 57/110 (51%), Positives = 75/110 (68%), Gaps = 7/110 (6%)
Query: 130 VVLCG-------EFVNRWRGKLINIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEES 182
VVL G FV+ + G++INIHP+LLP F G+H H QAL+AGV+V GCTVHFV+E
Sbjct: 84 VVLAGFMRILGPTFVSAYEGRIINIHPSLLPSFPGLHTHEQALEAGVKVHGCTVHFVDEG 143
Query: 183 VDAGAIICQESVPIYPRDTEESLSERVKSAEHKAYPRALELVATERVKLD 232
+D G II Q +VP+ DTEESL+ RV EH+ YP ++ A R+KL+
Sbjct: 144 LDTGPIIAQAAVPVLAGDTEESLAARVLEQEHRLYPLVVKWFAEGRLKLE 193
>gnl|CDD|187714 cd08645, FMT_core_GART, Phosphoribosylglycinamide formyltransferase
(GAR transformylase, GART). Phosphoribosylglycinamide
formyltransferase, also known as GAR transformylase or
GART, is an essential enzyme that catalyzes the third
step in de novo purine biosynthesis. This enzyme uses
formyl tetrahydrofolate as a formyl group donor to
produce 5'-phosphoribosyl-N-formylglycinamide. In
prokaryotes, GART is a single domain protein but in most
eukaryotes it is the C-terminal portion of a large
multifunctional protein which also contains GAR
synthetase and aminoimidazole ribonucleotide synthetase
activities.
Length = 183
Score = 166 bits (423), Expect = 5e-52
Identities = 55/102 (53%), Positives = 75/102 (73%), Gaps = 7/102 (6%)
Query: 130 VVLCG-------EFVNRWRGKLINIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEES 182
+VL G EF+ + G++INIHP+LLP F G+HAH AL+AGV+VTGCTVHFV+E
Sbjct: 82 IVLAGFMRILSPEFLEAFPGRIINIHPSLLPKFYGLHAHEAALEAGVKVTGCTVHFVDEE 141
Query: 183 VDAGAIICQESVPIYPRDTEESLSERVKSAEHKAYPRALELV 224
VD G II Q +VP+ P DT E+L+ER+ + EH+ YP A++L+
Sbjct: 142 VDTGPIIAQAAVPVLPGDTPETLAERIHALEHRLYPEAIKLL 183
>gnl|CDD|223376 COG0299, PurN, Folate-dependent phosphoribosylglycinamide
formyltransferase PurN [Nucleotide transport and
metabolism].
Length = 200
Score = 160 bits (407), Expect = 2e-49
Identities = 56/102 (54%), Positives = 78/102 (76%)
Query: 131 VLCGEFVNRWRGKLINIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIIC 190
+L EF++R+ G+++NIHP+LLP F G+HAH QAL+AGV+V+GCTVHFV E VD G II
Sbjct: 91 ILGPEFLSRFEGRILNIHPSLLPAFPGLHAHEQALEAGVKVSGCTVHFVTEGVDTGPIIA 150
Query: 191 QESVPIYPRDTEESLSERVKSAEHKAYPRALELVATERVKLD 232
Q +VP+ P DT E+L RV EH+ YP A++L+A R+K++
Sbjct: 151 QAAVPVLPGDTAETLEARVLEQEHRLYPLAVKLLAEGRLKIE 192
>gnl|CDD|161973 TIGR00639, PurN, phosphoribosylglycinamide formyltransferase,
formyltetrahydrofolate-dependent. This model describes
phosphoribosylglycinamide formyltransferase (GAR
transformylase), one of several proteins in
formyl_transf (Pfam family pfam00551). This enzyme uses
formyl tetrahydrofolate as a formyl group donor to
produce 5'-phosphoribosyl-N-formylglycinamide. PurT, a
different GAR transformylase, uses ATP and formate
rather than formyl tetrahydrofolate. Experimental proof
includes complementation of E. coli purN mutants by
orthologs from vertebrates (where it is a domain of a
multifunctional protein), Bacillus subtilis, and
Arabidopsis. No archaeal example was detected. In
phylogenetic analyses, the member from Saccharomyces
cerevisiae shows a long branch length but membership in
the family, while the formyltetrahydrofolate
deformylases form a closely related outgroup [Purines,
pyrimidines, nucleosides, and nucleotides, Purine
ribonucleotide biosynthesis].
Length = 190
Score = 140 bits (356), Expect = 7e-42
Identities = 52/100 (52%), Positives = 72/100 (72%)
Query: 131 VLCGEFVNRWRGKLINIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIIC 190
+L F++R+ G+++NIHP+LLP F G+HA QAL+AGV+ +GCTVH+V+E VD G II
Sbjct: 91 ILGPTFLSRFAGRILNIHPSLLPAFPGLHAVEQALEAGVKESGCTVHYVDEEVDTGPIIA 150
Query: 191 QESVPIYPRDTEESLSERVKSAEHKAYPRALELVATERVK 230
Q VPI P DTEE+L +R+ EH+ YP A+ A R+K
Sbjct: 151 QAKVPILPEDTEETLEQRIHKQEHRIYPLAIAWFAQGRLK 190
>gnl|CDD|144222 pfam00551, Formyl_trans_N, Formyl transferase. This family
includes the following members. Glycinamide
ribonucleotide transformylase catalyzes the third step
in de novo purine biosynthesis, the transfer of a formyl
group to 5'-phosphoribosylglycinamide.
Formyltetrahydrofolate deformylase produces formate from
formyl- tetrahydrofolate. Methionyl-tRNA
formyltransferase transfers a formyl group onto the
amino terminus of the acyl moiety of the methionyl
aminoacyl-tRNA. Inclusion of the following members is
supported by PSI-blast. HOXX_BRAJA contains a related
domain of unknown function. PRTH_PORGI contains a
related domain of unknown function. Y09P_MYCTU (Q50721)
contains a related domain of unknown function.
Length = 181
Score = 128 bits (323), Expect = 5e-37
Identities = 46/91 (50%), Positives = 63/91 (69%)
Query: 131 VLCGEFVNRWRGKLINIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIIC 190
+L EF+ + GK++NIHP+LLP F+G ++AL+AG + TG TVH V+E +D G I+
Sbjct: 91 ILPPEFLQAFPGKILNIHPSLLPRFRGAAPIQRALEAGDKETGVTVHQVDEELDTGPILA 150
Query: 191 QESVPIYPRDTEESLSERVKSAEHKAYPRAL 221
Q++VPI P DT E+L RV EHKA P AL
Sbjct: 151 QKAVPILPDDTSETLYNRVAELEHKALPEAL 181
>gnl|CDD|187712 cd08369, FMT_core, Formyltransferase, catalytic core domain.
Formyltransferase, catalytic core domain. The proteins
of this superfamily contain a formyltransferase domain
that hydrolyzes the removal of a formyl group from its
substrate as part of a multistep transfer mechanism, and
this alignment model represents the catalytic core of
the formyltransferase domain. This family includes the
following known members; Glycinamide Ribonucleotide
Transformylase (GART), Formyl-FH4 Hydrolase,
Methionyl-tRNA Formyltransferase, ArnA, and
10-Formyltetrahydrofolate Dehydrogenase (FDH).
Glycinamide Ribonucleotide Transformylase (GART)
catalyzes the third step in de novo purine biosynthesis,
the transfer of a formyl group to
5'-phosphoribosylglycinamide. Formyl-FH4 Hydrolase
catalyzes the hydrolysis of 10-formyltetrahydrofolate
(formyl-FH4) to FH4 and formate. Methionyl-tRNA
Formyltransferase transfers a formyl group onto the
amino terminus of the acyl moiety of the methionyl
aminoacyl-tRNA, which plays important role in
translation initiation. ArnA is required for the
modification of lipid A with 4-amino-4-deoxy-l-arabinose
(Ara4N) that leads to resistance to cationic
antimicrobial peptides (CAMPs) and clinical
antimicrobials such as polymyxin.
10-formyltetrahydrofolate dehydrogenase (FDH) catalyzes
the conversion of 10-formyltetrahydrofolate, a precursor
for nucleotide biosynthesis, to tetrahydrofolate.
Members of this family are multidomain proteins. The
formyltransferase domain is located at the N-terminus of
FDH, Methionyl-tRNA Formyltransferase and ArnA, and at
the C-terminus of Formyl-FH4 Hydrolase. Prokaryotic
Glycinamide Ribonucleotide Transformylase (GART) is a
single domain protein while eukaryotic GART is a
trifunctional protein that catalyzes the second, third
and fifth steps in de novo purine biosynthesis.
Length = 173
Score = 100 bits (250), Expect = 2e-26
Identities = 35/90 (38%), Positives = 52/90 (57%)
Query: 134 GEFVNRWRGKLINIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIICQES 193
E + G INIHP+LLP ++G++ A+ G + TG TVH+++E +D G II QE
Sbjct: 84 PEILKLPPGGAINIHPSLLPRYRGVNPLAWAIINGEKETGVTVHYMDEGIDTGDIIAQEV 143
Query: 194 VPIYPRDTEESLSERVKSAEHKAYPRALEL 223
+PI P DT +L +R+ K AL+
Sbjct: 144 IPISPDDTAGTLYQRLIELGPKLLKEALQK 173
>gnl|CDD|177965 PLN02331, PLN02331, phosphoribosylglycinamide formyltransferase.
Length = 207
Score = 91.3 bits (227), Expect = 1e-22
Identities = 40/101 (39%), Positives = 56/101 (55%), Gaps = 5/101 (4%)
Query: 135 EFVNRWRGKLINIHPALLPLF--KGMHA---HRQALDAGVRVTGCTVHFVEESVDAGAII 189
E V + ++NIHPALLP F KG + H+ + +G R +G TVHFV+E D G I+
Sbjct: 94 ELVRAYPRSILNIHPALLPAFGGKGYYGIKVHKAVIASGARYSGPTVHFVDEHYDTGRIL 153
Query: 190 CQESVPIYPRDTEESLSERVKSAEHKAYPRALELVATERVK 230
Q VP+ DT E L+ RV EH+ Y + + ER+
Sbjct: 154 AQRVVPVLATDTPEELAARVLHEEHQLYVEVVAALCEERIV 194
>gnl|CDD|187717 cd08648, FMT_core_Formyl-FH4-Hydrolase_C, Formyltetrahydrofolate
deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase
domain. Formyl-FH4 Hydrolase catalyzes the hydrolysis
of 10-formyltetrahydrofolate (formyl-FH4) to FH4 and
formate. Formate is the substrate of
phosphoribosylglycinamide transformylase for step three
of de novo purine nucleotide synthesis. Formyl-FH4
hydrolase has been proposed to regulate the balance of
FH4 and C1-FH4 in the cell. The enzyme uses methionine
and glycine to sense the pools of C1-FH4 and FH4,
respectively. This domain belongs to the
formyltransferase (FMT) domain superfamily. Members of
this family have an N-terminal ACT domain, which is
commonly involved in specifically bind an amino acid or
other small ligand leading to regulation of the enzyme.
The N-terminal of this protein family may be responsible
for the binding of the regulators methionine and
glycine.
Length = 196
Score = 89.5 bits (223), Expect = 5e-22
Identities = 36/99 (36%), Positives = 57/99 (57%)
Query: 131 VLCGEFVNRWRGKLINIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIIC 190
+L +FV R+ ++INIH + LP FKG + QA + GV++ G T H+V E +D G II
Sbjct: 88 ILSPDFVERYPNRIINIHHSFLPAFKGAKPYHQAFERGVKLIGATAHYVTEELDEGPIIE 147
Query: 191 QESVPIYPRDTEESLSERVKSAEHKAYPRALELVATERV 229
Q+ + RD+ E L + + E + RA++ +RV
Sbjct: 148 QDVERVSHRDSVEDLVRKGRDIEKQVLARAVKWHLEDRV 186
>gnl|CDD|178422 PLN02828, PLN02828, formyltetrahydrofolate deformylase.
Length = 268
Score = 83.6 bits (207), Expect = 3e-19
Identities = 38/99 (38%), Positives = 56/99 (56%)
Query: 131 VLCGEFVNRWRGKLINIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIIC 190
+L G F+ + +INIH LLP FKG + +QA DAGV++ G T HFV E +DAG II
Sbjct: 159 ILSGNFLKGYGKDIINIHHGLLPSFKGGNPSKQAFDAGVKLIGATSHFVTEELDAGPIIE 218
Query: 191 QESVPIYPRDTEESLSERVKSAEHKAYPRALELVATERV 229
Q + RD S ++ ++ E + +A++ RV
Sbjct: 219 QMVERVSHRDNLRSFVQKSENLEKQCLAKAIKSYCELRV 257
>gnl|CDD|223859 COG0788, PurU, Formyltetrahydrofolate hydrolase [Nucleotide
transport and metabolism].
Length = 287
Score = 81.9 bits (203), Expect = 2e-18
Identities = 34/99 (34%), Positives = 54/99 (54%)
Query: 131 VLCGEFVNRWRGKLINIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIIC 190
+L +FV R+ GK+INIH + LP F G + + QA + GV++ G T H+V +D G II
Sbjct: 178 ILSPDFVERFPGKIINIHHSFLPAFIGANPYHQAYERGVKLIGATAHYVTADLDEGPIIE 237
Query: 191 QESVPIYPRDTEESLSERVKSAEHKAYPRALELVATERV 229
Q+ + + + E L + E RA++ +RV
Sbjct: 238 QDVIRVDHAYSVEDLVRAGRDVEKLVLARAVKAHLEDRV 276
>gnl|CDD|233074 TIGR00655, PurU, formyltetrahydrofolate deformylase. This model
describes formyltetrahydrofolate deformylases. The
enzyme is a homohexamer. Sequences from a related enzyme
formyl tetrahydrofolate-specific enzyme,
phosphoribosylglycinamide formyltransferase, serve as an
outgroup for phylogenetic analysis. Putative members of
this family, scoring below the trusted cutoff, include a
sequence from Rhodobacter capsulatus that lacks an
otherwise conserved C-terminal region [Purines,
pyrimidines, nucleosides, and nucleotides, Purine
ribonucleotide biosynthesis].
Length = 280
Score = 75.5 bits (186), Expect = 3e-16
Identities = 36/99 (36%), Positives = 56/99 (56%)
Query: 131 VLCGEFVNRWRGKLINIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIIC 190
+L +FV R+ K+INIH + LP F G + +++A + GV++ G T H+V E +D G II
Sbjct: 172 ILSPDFVKRYPNKIINIHHSFLPAFIGANPYQRAYERGVKIIGATAHYVTEELDEGPIIE 231
Query: 191 QESVPIYPRDTEESLSERVKSAEHKAYPRALELVATERV 229
Q+ V + D E L + E RA++L +RV
Sbjct: 232 QDVVRVDHTDNVEDLIRAGRDIEKVVLARAVKLHLEDRV 270
>gnl|CDD|187721 cd08653, FMT_core_like_3, Formyl transferase catalytic core domain
found in a group of proteins with unknown functions.
Formyl transferase catalytic core domain found in a
group of proteins with unknown functions. Formyl
transferase catalyzes the transfer of one-carbon groups,
specifically the formyl- or hydroxymethyl- group. This
domain contains a Rossmann fold and it is the catalytic
domain of the enzyme.
Length = 152
Score = 68.0 bits (167), Expect = 2e-14
Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 1/79 (1%)
Query: 145 INIHPALLPLFKGMHAHRQALDAG-VRVTGCTVHFVEESVDAGAIICQESVPIYPRDTEE 203
+N+H +LP ++G+H AL G G TVH V+ +D G ++ Q P+ DT
Sbjct: 72 LNLHGGILPDYRGVHTGFWALANGDPDNVGVTVHLVDAGIDTGDVLAQARPPLAAGDTLL 131
Query: 204 SLSERVKSAEHKAYPRALE 222
SL R+ A + A+
Sbjct: 132 SLYLRLYRAGVELMVEAIA 150
>gnl|CDD|235676 PRK06027, purU, formyltetrahydrofolate deformylase; Reviewed.
Length = 286
Score = 68.2 bits (168), Expect = 2e-13
Identities = 37/99 (37%), Positives = 56/99 (56%)
Query: 131 VLCGEFVNRWRGKLINIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIIC 190
+L +FV R+ G++INIH + LP FKG + QA + GV++ G T H+V +D G II
Sbjct: 177 ILSPDFVARFPGRIINIHHSFLPAFKGAKPYHQAYERGVKLIGATAHYVTADLDEGPIIE 236
Query: 191 QESVPIYPRDTEESLSERVKSAEHKAYPRALELVATERV 229
Q+ + + RDT E L + E + RA+ +RV
Sbjct: 237 QDVIRVDHRDTAEDLVRAGRDVEKQVLARAVRWHLEDRV 275
>gnl|CDD|187715 cd08646, FMT_core_Met-tRNA-FMT_N, Methionyl-tRNA formyltransferase,
N-terminal hydrolase domain. Methionyl-tRNA
formyltransferase (Met-tRNA-FMT), N-terminal
formyltransferase domain. Met-tRNA-FMT transfers a
formyl group from N-10 formyltetrahydrofolate to the
amino terminal end of a methionyl-aminoacyl-tRNA acyl
moiety, yielding formyl-Met-tRNA. Formyl-Met-tRNA plays
essential role in protein translation initiation by
forming complex with IF2. The formyl group plays a dual
role in the initiator identity of N-formylmethionyl-tRNA
by promoting its recognition by IF2 and by impairing its
binding to EFTU-GTP. The N-terminal domain contains a
Rossmann fold and it is the catalytic domain of the
enzyme.
Length = 204
Score = 63.2 bits (155), Expect = 3e-12
Identities = 28/67 (41%), Positives = 41/67 (61%), Gaps = 6/67 (8%)
Query: 145 INIHPALLPLFKGMHA---HRQALDAGVRVTGCTVHFVEESVDAGAIICQESVPIYPRDT 201
IN+HP+LLP ++G A R A+ G + TG T+ ++E +D G I+ QE VPI P DT
Sbjct: 104 INVHPSLLPKYRG--AAPIQR-AILNGDKETGVTIMKMDEGLDTGDILAQEEVPIDPDDT 160
Query: 202 EESLSER 208
L ++
Sbjct: 161 AGELLDK 167
>gnl|CDD|237266 PRK13011, PRK13011, formyltetrahydrofolate deformylase; Reviewed.
Length = 286
Score = 64.6 bits (158), Expect = 3e-12
Identities = 33/99 (33%), Positives = 50/99 (50%)
Query: 131 VLCGEFVNRWRGKLINIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIIC 190
VL E + G+ INIH + LP FKG + QA + GV++ G T H+V + +D G II
Sbjct: 177 VLSPELCRKLAGRAINIHHSFLPGFKGAKPYHQAYERGVKLIGATAHYVTDDLDEGPIIE 236
Query: 191 QESVPIYPRDTEESLSERVKSAEHKAYPRALELVATERV 229
Q+ + + E L + + E RA++ RV
Sbjct: 237 QDVERVDHAYSPEDLVAKGRDVECLTLARAVKAHIERRV 275
>gnl|CDD|215159 PLN02285, PLN02285, methionyl-tRNA formyltransferase.
Length = 334
Score = 64.3 bits (157), Expect = 5e-12
Identities = 35/114 (30%), Positives = 53/114 (46%), Gaps = 18/114 (15%)
Query: 145 INIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIICQESVPIYPRDTEES 204
+NIHP+LLPL++G ++AL GV TG +V F ++DAG +I QE V +
Sbjct: 119 VNIHPSLLPLYRGAAPVQRALQDGVNETGVSVAFTVRALDAGPVIAQERVEVDEDIKAPE 178
Query: 205 LSERV-----------------KSAEHKAYPRALELVATERVKLDLDSGKLDFN 241
L + SA+ KA P+ + AT K+ + L F+
Sbjct: 179 LLPLLFELGTKLLLRELPSVLDGSAKDKATPQD-DSKATHAPKISPEESWLSFD 231
>gnl|CDD|139334 PRK13010, purU, formyltetrahydrofolate deformylase; Reviewed.
Length = 289
Score = 63.7 bits (155), Expect = 5e-12
Identities = 33/99 (33%), Positives = 49/99 (49%)
Query: 131 VLCGEFVNRWRGKLINIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIIC 190
VL + + G+ INIH + LP FKG + QA GV++ G T HFV + +D G II
Sbjct: 181 VLSDDLSRKLSGRAINIHHSFLPGFKGARPYHQAHARGVKLIGATAHFVTDDLDEGPIIE 240
Query: 191 QESVPIYPRDTEESLSERVKSAEHKAYPRALELVATERV 229
Q+ + + E L + + E RA++ RV
Sbjct: 241 QDVERVDHSYSPEDLVAKGRDVECLTLARAVKAFIEHRV 279
>gnl|CDD|223301 COG0223, Fmt, Methionyl-tRNA formyltransferase [Translation,
ribosomal structure and biogenesis].
Length = 307
Score = 61.5 bits (150), Expect = 4e-11
Identities = 30/99 (30%), Positives = 49/99 (49%)
Query: 132 LCGEFVNRWRGKLINIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIICQ 191
L E ++ IN+HP+LLP ++G + A+ G TG T+ ++E +DAG I+ Q
Sbjct: 92 LPKEILDLPPYGCINLHPSLLPRYRGAAPIQWAILNGDTETGVTIMQMDEGLDAGDILAQ 151
Query: 192 ESVPIYPRDTEESLSERVKSAEHKAYPRALELVATERVK 230
VPI P DT SL +++ + L + +
Sbjct: 152 REVPIEPDDTAGSLHDKLAELGAELLLETLPQLEAGTLT 190
>gnl|CDD|232983 TIGR00460, fmt, methionyl-tRNA formyltransferase. The top-scoring
characterized proteins other than methionyl-tRNA
formyltransferase (fmt) itself are
formyltetrahydrofolate dehydrogenases. The mitochondrial
methionyl-tRNA formyltransferases are so divergent that,
in a multiple alignment of bacterial fmt, mitochondrial
fmt, and formyltetrahydrofolate dehydrogenases, the
mitochondrial fmt appears the most different. However,
because both bacterial and mitochondrial fmt are
included in the seed alignment, all credible fmt
sequences score higher than any non-fmt sequence. This
enzyme modifies Met on initiator tRNA to f-Met [Protein
synthesis, tRNA aminoacylation].
Length = 313
Score = 60.9 bits (148), Expect = 7e-11
Identities = 27/82 (32%), Positives = 48/82 (58%)
Query: 131 VLCGEFVNRWRGKLINIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIIC 190
+L EF++ + IN+HP+LLP ++G ++A+ G + TG T+ + +DAG I+
Sbjct: 90 ILPKEFLDLFPYGCINVHPSLLPRWRGGAPIQRAILNGDKKTGVTIMQMVPKMDAGDILK 149
Query: 191 QESVPIYPRDTEESLSERVKSA 212
QE+ PI D +LS+++
Sbjct: 150 QETFPIEEEDNSGTLSDKLSEL 171
>gnl|CDD|187720 cd08651, FMT_core_like_4, Formyl transferase catalytic core domain
found in a group of proteins with unknown functions.
Formyl transferase catalytic core domain found in a
group of proteins with unknown functions. Formyl
transferase catalyzes the transfer of one-carbon groups,
specifically the formyl- or hydroxymethyl- group. This
domain contains a Rossmann fold and it is the catalytic
domain of the enzyme.
Length = 180
Score = 56.5 bits (137), Expect = 6e-10
Identities = 24/80 (30%), Positives = 39/80 (48%)
Query: 145 INIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIICQESVPIYPRDTEES 204
I HP LP +G A+ G++ T T +++E D+G I+ QE PI DT S
Sbjct: 101 IGFHPTKLPKNRGRAPIPWAILLGLKETASTFFWMDEGADSGDILSQEPFPIDKDDTANS 160
Query: 205 LSERVKSAEHKAYPRALELV 224
L +++ A + + L +
Sbjct: 161 LYDKIMEAAKQQIDKFLPRL 180
>gnl|CDD|187724 cd08822, FMT_core_like_2, Formyl transferase catalytic core domain
found in a group of proteins with unknown functions.
Formyl transferase catalytic core domain found in a
group of proteins with unknown functions. Formyl
transferase catalyzes the transfer of one-carbon groups,
specifically the formyl- or hydroxymethyl- group. This
domain contains a Rossmann fold and it is the catalytic
domain of the enzyme.
Length = 192
Score = 55.5 bits (134), Expect = 2e-09
Identities = 24/71 (33%), Positives = 34/71 (47%)
Query: 139 RWRGKLINIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIICQESVPIYP 198
R R I HP+LLP +G A + +TG TV+ +++ VD G I Q+ + P
Sbjct: 86 RARLGAIGYHPSLLPRHRGRDAVEWTIRMRDPITGGTVYHLDDGVDGGPIAAQDWCHVRP 145
Query: 199 RDTEESLSERV 209
DT L R
Sbjct: 146 GDTAAELWRRA 156
>gnl|CDD|234567 PRK00005, fmt, methionyl-tRNA formyltransferase; Reviewed.
Length = 309
Score = 56.7 bits (138), Expect = 2e-09
Identities = 25/67 (37%), Positives = 39/67 (58%), Gaps = 6/67 (8%)
Query: 145 INIHPALLPLFKGMHA---HRQALDAGVRVTGCTVHFVEESVDAGAIICQESVPIYPRDT 201
IN+H +LLP ++G A R A+ AG TG T+ ++E +D G ++ + VPI P DT
Sbjct: 104 INLHASLLPRWRG--AAPIQR-AIIAGDAETGVTIMQMDEGLDTGDMLLKAEVPITPTDT 160
Query: 202 EESLSER 208
L ++
Sbjct: 161 AGELHDK 167
>gnl|CDD|187713 cd08644, FMT_core_ArnA_N, ArnA, N-terminal formyltransferase
domain. ArnA_N: ArnA is a bifunctional enzyme required
for the modification of lipid A with
4-amino-4-deoxy-L-arabinose (Ara4N) that leads to
resistance to cationic antimicrobial peptides (CAMPs)
and clinical antimicrobials such as polymyxin. The
C-terminal dehydrogenase domain of ArnA catalyzes the
oxidative decarboxylation of UDP-glucuronic acid
(UDP-GlcUA) to UDP-4-keto-arabinose (UDP-Ara4O), while
the N-terminal formyltransferase domain of ArnA
catalyzes the addition of a formyl group to
UDP-4-amino-4-deoxy-L-arabinose (UDP-L-Ara4N) to form
UDP-L-4-formamido-arabinose (UDP-L-Ara4FN). This domain
family represents the catalytic core of the N-terminal
formyltransferase domain. The formyltransferase also
contains a smaller C-terminal domain the may be
involved in substrate binding. ArnA forms a hexameric
structure, in which the dehydrogenase domains are
arranged at the center of the particle with the
transformylase domains on the outside of the particle.
Length = 203
Score = 55.0 bits (133), Expect = 2e-09
Identities = 31/76 (40%), Positives = 43/76 (56%)
Query: 146 NIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIICQESVPIYPRDTEESL 205
N+H +LLP ++G AL G TG T+H + + DAGAI+ QE VPI P DT +SL
Sbjct: 102 NLHGSLLPKYRGRAPLNWALINGETETGVTLHRMTKKPDAGAIVDQEKVPILPDDTAKSL 161
Query: 206 SERVKSAEHKAYPRAL 221
++ A + R L
Sbjct: 162 FHKLCVAARRLLARTL 177
>gnl|CDD|235902 PRK06988, PRK06988, putative formyltransferase; Provisional.
Length = 312
Score = 55.5 bits (134), Expect = 4e-09
Identities = 36/99 (36%), Positives = 51/99 (51%), Gaps = 4/99 (4%)
Query: 141 RGKLINIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIICQESVPIYPRD 200
RG N+H +LLP ++G A+ G TG T+H + DAGAI+ Q +VPI P D
Sbjct: 100 RGAY-NMHGSLLPKYRGRVPVNWAVLNGETETGATLHEMVAKPDAGAIVDQTAVPILPDD 158
Query: 201 TEESLSERVKSAEHKAYPRAL-ELVATE--RVKLDLDSG 236
T + ++V A + R L L+A E + DL G
Sbjct: 159 TAAQVFDKVTVAAEQTLWRVLPALLAGEAPHLPNDLAQG 197
>gnl|CDD|187718 cd08649, FMT_core_NRPS_like, N-terminal formyl transferase
catalytic core domain of NRPS_like proteins, one of the
proteins involved in the synthesis of Oxazolomycin.
This family represents the N-terminal formyl transferase
catalytic core domain present in a subgroup of
non-ribosomal peptide synthetases. In Streptomyces albus
a member of this family has been shown to be involved in
the synthesis of oxazolomycin (OZM). OZM is a hybrid
peptide-polyketide antibiotic and exhibits potent
antitumor and antiviral activities. It is a multi-domain
protein consisting of a formyl transferase domain, a
Flavin-utilizing monoxygenase domain, a LuxE domain
functioning as an acyl protein synthetase and a
pp-binding domain, which may function as an acyl
carrier. It shows sequence similarity with other
peptide-polyketide biosynthesis proteins.
Length = 166
Score = 49.9 bits (120), Expect = 9e-08
Identities = 30/71 (42%), Positives = 36/71 (50%)
Query: 135 EFVNRWRGKLINIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIICQESV 194
E + R IN H LP + G++A AL AG G T H +EE VDAG I+ Q
Sbjct: 77 EVLALPRKGAINFHDGPLPRYAGLNATSWALLAGETRHGVTWHRIEEGVDAGDILVQRPF 136
Query: 195 PIYPRDTEESL 205
I P DT SL
Sbjct: 137 DIAPDDTALSL 147
>gnl|CDD|187725 cd08823, FMT_core_like_5, Formyl transferase catalytic core domain
found in a group of proteins with unknown functions.
Formyl transferase catalytic core domain found in a
group of proteins with unknown functions. Formyl
transferase catalyzes the transfer of one-carbon groups,
specifically the formyl- or hydroxymethyl- group. This
domain contains a Rossmann fold and it is the catalytic
domain of the enzyme.
Length = 177
Score = 49.4 bits (118), Expect = 2e-07
Identities = 21/65 (32%), Positives = 33/65 (50%)
Query: 145 INIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIICQESVPIYPRDTEES 204
N+HP LLP ++G + + T TVH + +D G I+ ++ PI+P DT
Sbjct: 97 YNLHPGLLPAYRGPDPLFWQIRNQEQETAITVHKMTAEIDRGPIVLEQFTPIHPDDTYGL 156
Query: 205 LSERV 209
L R+
Sbjct: 157 LCSRL 161
>gnl|CDD|236156 PRK08125, PRK08125, bifunctional UDP-glucuronic acid
decarboxylase/UDP-4-amino-4-deoxy-L-arabinose
formyltransferase; Validated.
Length = 660
Score = 49.6 bits (119), Expect = 6e-07
Identities = 25/67 (37%), Positives = 37/67 (55%)
Query: 146 NIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIICQESVPIYPRDTEESL 205
N+H +LLP ++G L G TG T+H + + DAGAI+ Q+ V I P DT +L
Sbjct: 102 NLHGSLLPKYRGRAPLNWVLVNGETETGVTLHRMVKRADAGAIVAQQRVAIAPDDTALTL 161
Query: 206 SERVKSA 212
++ A
Sbjct: 162 HHKLCHA 168
>gnl|CDD|187722 cd08820, FMT_core_like_6, Formyl transferase catalytic core domain
found in a group of proteins with unknown functions.
Formyl transferase catalytic core domain found in a
group of proteins with unknown functions. Formyl
transferase catalyzes the transfer of one-carbon groups,
specifically the formyl- or hydroxymethyl- group. This
domain contains a Rossmann fold and it is the catalytic
domain of the enzyme.
Length = 173
Score = 46.3 bits (110), Expect = 2e-06
Identities = 21/61 (34%), Positives = 33/61 (54%)
Query: 145 INIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIICQESVPIYPRDTEES 204
N+H A LP ++G + A+ G G T+H++ E +D+G II ++ PI T S
Sbjct: 95 FNLHNAPLPEYRGCNQFSHAILNGDDQFGTTIHWMAEGIDSGDIIFEKRFPIPSDCTVIS 154
Query: 205 L 205
L
Sbjct: 155 L 155
>gnl|CDD|187716 cd08647, FMT_core_FDH_N, 10-formyltetrahydrofolate dehydrogenase
(FDH), N-terminal hydrolase domain. This family
represents the N-terminal hydrolase domain of the
bifunctional protein 10-formyltetrahydrofolate
dehydrogenase (FDH). This domain contains a
10-formyl-tetrahydrofolate (10-formyl-THF) binding site
and shares sequence homology and structural topology
with other enzymes utilizing this substrate. This domain
functions as a hydrolase, catalyzing the conversion of
10-formyl-THF, a precursor for nucleotide biosynthesis,
to tetrahydrofolate (THF). The overall FDH reaction
mechanism is a coupling of two sequential reactions, a
hydrolase and a formyl dehydrogenase, bridged by a
substrate transfer step. The N-terminal hydrolase
domain removes the formyl group from 10-formyl-THF and
the C-terminal NADP-dependent dehydrogenase domain then
reduces the formyl group to carbon dioxide. The two
catalytic domains are connected by a third intermediate
linker domain that transfers the formyl group,
covalently attached to the sulfhydryl group of the
phosphopantetheine arm, from the N-terminal domain to
the C-terminal domain.
Length = 203
Score = 43.2 bits (102), Expect = 4e-05
Identities = 27/93 (29%), Positives = 46/93 (49%), Gaps = 1/93 (1%)
Query: 135 EFVNRWRGKLINIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIICQESV 194
E ++ + I HP++LP +G A L G + G T+ + ++ +D G I+ Q+
Sbjct: 93 EVIDAPKHGSIIYHPSILPRHRGASAINWTLIHGDKKAGFTIFWADDGLDTGPILLQKEC 152
Query: 195 PIYPRDTEESLSERVKSAEH-KAYPRALELVAT 226
+ P DT ++L R E KA A+ L+A
Sbjct: 153 DVLPNDTVDTLYNRFLYPEGIKAMVEAVRLIAE 185
>gnl|CDD|236058 PRK07579, PRK07579, hypothetical protein; Provisional.
Length = 245
Score = 42.6 bits (100), Expect = 6e-05
Identities = 24/69 (34%), Positives = 36/69 (52%), Gaps = 1/69 (1%)
Query: 145 INIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIICQESVPIYPRDTEES 204
INIHP P +G ++ G+++ G T+H ++E +D G II Q V I D+ S
Sbjct: 89 INIHPGFNPYNRGWFPQVFSIINGLKI-GATIHEMDEQLDHGPIIAQREVEIESWDSSGS 147
Query: 205 LSERVKSAE 213
+ RV E
Sbjct: 148 VYARVMDIE 156
>gnl|CDD|222478 pfam13966, zf-RVT, zinc-binding in reverse transcriptase. This
domain would appear to be a zinc-binding region of a
putative reverse transcriptase.
Length = 86
Score = 28.7 bits (65), Expect = 0.83
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 12 DDRCRRCKEKAETIQHITSGCS 33
+RC C ++ ET H+ CS
Sbjct: 59 PNRCVLCGQEEETRDHLFFHCS 80
>gnl|CDD|129992 TIGR00914, 2A0601, heavy metal efflux pump, CzcA family. This
model represents a family of H+/heavy metal cation
antiporters. This family is one of several subfamilies
within the scope of Pfam model pfam00873 [Cellular
processes, Detoxification, Transport and binding
proteins, Cations and iron carrying compounds].
Length = 1051
Score = 30.1 bits (68), Expect = 1.3
Identities = 29/111 (26%), Positives = 38/111 (34%), Gaps = 35/111 (31%)
Query: 86 YDRTIMTDKTIPNNRPDIVVHDKERRMALLVDIAIPNTHNMESTVVLCGEFVNRWRGKLI 145
YDR+ + D I V ALLV +V+ F+ R LI
Sbjct: 330 YDRSQLVDAAIAT------VKKNLLEGALLV-------------IVILFLFLGNIRAALI 370
Query: 146 NIHPALLPL-----FKGMHAHR--------QALDAGVRVTGCTVHFVEESV 183
++PL F GM ALD G+ V G V VE +
Sbjct: 371 AA--TVIPLSLLITFIGMVFQGISANLMSLGALDFGLIVDGAVV-IVENAH 418
>gnl|CDD|222883 PHA02572, nrdA, ribonucleoside-diphosphate reductase subunit alpha;
Provisional.
Length = 753
Score = 28.9 bits (65), Expect = 2.7
Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 52 HQNISSNLKLID-EKTPYYKYEPPPVIETAKYTV---YYDRTIMT 92
+Q +++ L + K Y ++EPP I+ V YD I++
Sbjct: 75 YQYVAARLLMFALRKQVYGQFEPPSFIDHISKCVNEGKYDPEILS 119
>gnl|CDD|236086 PRK07742, PRK07742, phosphate butyryltransferase; Validated.
Length = 299
Score = 28.5 bits (64), Expect = 3.1
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 9/53 (16%)
Query: 176 VHFVEESVDAGAIICQESVPIYPRDTEESLSERVKSAEHKAYPRALELVATER 228
V+F + V GA+I PI L+ R SAE K Y AL + +
Sbjct: 256 VYFADAKV--GAMIAGAKAPI-------VLTSRADSAETKLYSLALAVCTASK 299
>gnl|CDD|144386 pfam00765, Autoind_synth, Autoinducer synthetase.
Length = 182
Score = 28.1 bits (63), Expect = 3.6
Identities = 20/59 (33%), Positives = 27/59 (45%), Gaps = 9/59 (15%)
Query: 114 LLVDIAIPNTHNM-ESTVVLCGEFV--NRWRGKLINIHPALLPLFKGMHAHRQALDAGV 169
DI++P + N ES+ FV R RG L N+ P L LF M + A +G
Sbjct: 78 YFDDISLPESGNYIESSRF----FVDKARARGLLGNLAPISLMLFLSMINY--ARASGY 130
>gnl|CDD|238307 cd00547, QFR_TypeD_subunitD, Quinol:fumarate reductase (QFR) Type D
subfamily, 13kD hydrophobic subunit D; QFR couples the
reduction of fumarate to succinate to the oxidation of
quinol to quinone, the opposite reaction to that
catalyzed by the related protein, succinate:quinine
oxidoreductase (SQR). QFRs oxidize low potential quinols
such as menaquinol and are involved in anaerobic
respiration with fumarate as the terminal electron
acceptor. SQR and QFR share a common subunit
arrangement, composed of a flavoprotein catalytic
subunit, an iron-sulfur protein and one or two
hydrophobic transmembrane subunits. Members of this
subfamily are classified as Type D as they contain two
transmembrane subunits (C and D) and no heme groups.
The structural arrangement allows efficient electron
transfer between the catalytic subunit, through
iron-sulfur centers, and the transmembrane subunit
containing the electron donor (quinol). The quinone
binding site resides in the transmembrane subunits.
Length = 115
Score = 27.3 bits (61), Expect = 4.1
Identities = 15/55 (27%), Positives = 19/55 (34%), Gaps = 10/55 (18%)
Query: 136 FVNRWRGKLINIHPALLPLFKGMHAHRQALDAGVRVTGCTVHFVEESVDAGAIIC 190
F W GKL + +LP++ MH L V AG II
Sbjct: 53 FAQSWIGKLFLLVLIILPMWHAMHRIHHGLH----------DLKIHHVPAGKIIF 97
>gnl|CDD|111228 pfam02313, Fumarate_red_D, Fumarate reductase subunit D. Fumarate
reductase is a membrane-bound flavoenzyme consisting of
four subunits, A-B. A and B comprise the
membrane-extrinsic catalytic domain and C and D link the
catalytic centres to the electron-transport chain. This
family consists of the 13kD hydrophobic subunit D.
Length = 118
Score = 26.9 bits (60), Expect = 4.6
Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 6/52 (11%)
Query: 112 MALLVDIAIP----NTHNMESTVVLCGEFVNRWRGKLINIHPALLPLFKGMH 159
+ L++ I +P + + ++ F W GKL + +LPL+ MH
Sbjct: 31 LILILGILLPLGLIDAEALSYDRII--AFAQSWIGKLFLLVLIILPLWHAMH 80
>gnl|CDD|225082 COG2171, DapD, Tetrahydrodipicolinate N-succinyltransferase [Amino
acid transport and metabolism].
Length = 271
Score = 27.7 bits (62), Expect = 5.8
Identities = 14/47 (29%), Positives = 15/47 (31%), Gaps = 9/47 (19%)
Query: 168 GVRV-TGCTVHFVEESVDAGAIICQESVPIYPRDTEESLSERVKSAE 213
GV V GC V AG I Q IY R V +
Sbjct: 200 GVIVGDGCVV-------AAGVFITQ-DTKIYDRVAGRVAGSVVVAGT 238
>gnl|CDD|100041 cd03350, LbH_THP_succinylT,
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP)
N-succinyltransferase (also called THP
succinyltransferase): THDP N-succinyltransferase
catalyzes the conversion of tetrahydrodipicolinate and
succinyl-CoA to N-succinyltetrahydrodipicolinate and
CoA. It is the committed step in the succinylase pathway
by which bacteria synthesize L-lysine and
meso-diaminopimelate, a component of peptidoglycan. The
enzyme is homotrimeric and each subunit contains an
N-terminal region with alpha helices and hairpin loops,
as well as a C-terminal region with a left-handed
parallel alpha-helix (LbH) structural motif encoded by
hexapeptide repeat motifs.
Length = 139
Score = 27.0 bits (60), Expect = 6.2
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 171 VTGCTVHFVEESVDAGAIICQESVPIYPRDTEESLSERV 209
V G V + +V A ++ +S PIY R+T E RV
Sbjct: 91 VEGVIVG--KGAVLAAGVVLTQSTPIYDRETGEIYYGRV 127
>gnl|CDD|129593 TIGR00502, nagB, glucosamine-6-phosphate isomerase. The set of
proteins recognized by This model includes a closely
related pair from Bacillus subtilis, one of which is
uncharacterized but included as a member of the
orthologous set [Central intermediary metabolism, Amino
sugars].
Length = 259
Score = 27.5 bits (61), Expect = 6.4
Identities = 10/43 (23%), Positives = 16/43 (37%), Gaps = 1/43 (2%)
Query: 19 KEKAETIQHITSGC-SAMSQTEYLHRHNQVAAIIHQNISSNLK 60
+KA +Q G + M L H + +N + LK
Sbjct: 206 HQKALALQKAVEGGVNHMWTISALQLHKHAIVVCDENATQELK 248
>gnl|CDD|226220 COG3696, COG3696, Putative silver efflux pump [Inorganic ion
transport and metabolism].
Length = 1027
Score = 27.6 bits (62), Expect = 6.7
Identities = 20/84 (23%), Positives = 30/84 (35%), Gaps = 26/84 (30%)
Query: 81 KYTVYYDRTIMTDKTIPNNRPDIVVHDKERRMALLVDIAIPNTHNMESTVVLCGEFVNRW 140
K YDR+ + DK I V ++LV +++ F+ +
Sbjct: 318 KIVTTYDRSELIDKAIDT------VSKTLIEGSVLV-------------IIVLALFLGNF 358
Query: 141 RGKLINIHPALLPL-----FKGMH 159
R LI I LPL F M+
Sbjct: 359 RSALIVI--ISLPLSLLIAFIVMN 380
>gnl|CDD|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A'';
Provisional.
Length = 858
Score = 27.6 bits (61), Expect = 7.5
Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 3/47 (6%)
Query: 190 CQESVPIYPRDTEESLSERVKSAEHKAYPRALELVATERVKLDLDSG 236
CQE++ + S+ + EH YP + E LD ++G
Sbjct: 203 CQEAIDLREYL---PASDYGEIEEHAVYPVQGTVGLPETFPLDEETG 246
>gnl|CDD|214472 smart00017, OSTEO, Osteopontin. Osteopontin is an acidic
phosphorylated glycoprotein of about 40 Kd which is
abundant in the mineral matrix of bones and which binds
tightly to hydroxyapatite. It is suggested that
osteopontin might function as a cell attachment factor
and could play a key role in the adhesion of osteoclasts
to the mineral matrix of bone.
Length = 287
Score = 26.9 bits (59), Expect = 9.1
Identities = 16/43 (37%), Positives = 21/43 (48%)
Query: 197 YPRDTEESLSERVKSAEHKAYPRALELVATERVKLDLDSGKLD 239
YP TEE L+ V+S E P+A+ + V D DS D
Sbjct: 159 YPDATEEDLTSHVESEELDDAPKAIPVAQRLNVPSDWDSAGKD 201
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 0.398
Gapped
Lambda K H
0.267 0.0563 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,359,297
Number of extensions: 1147343
Number of successful extensions: 1016
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1009
Number of HSP's successfully gapped: 51
Length of query: 245
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 151
Effective length of database: 6,768,326
Effective search space: 1022017226
Effective search space used: 1022017226
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: 58 (26.5 bits)