RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5230
(258 letters)
>gnl|CDD|234567 PRK00005, fmt, methionyl-tRNA formyltransferase; Reviewed.
Length = 309
Score = 141 bits (359), Expect = 1e-40
Identities = 57/153 (37%), Positives = 86/153 (56%), Gaps = 8/153 (5%)
Query: 95 ILPEDTSLTLQNKLEKLSKILIIDTIKKIEYDMTKLFFKPQSNIGESYAPLIKKNEAVLD 154
I P DT+ L +KL +L L+++T+K +E L PQ G +YAP I K EA +D
Sbjct: 155 ITPTDTAGELHDKLAELGADLLVETLKGLE--DGTLTPIPQDEEGVTYAPKISKEEARID 212
Query: 155 WSLSAKTIMRKINAFNPFPGAKTYYISYQNKKKFLKIWKAHALSIESTKKPGTILNVNFH 214
WS A + I FNP+PGA + ++ LKI +A + + PGTIL ++
Sbjct: 213 WSKPAAELENHIRGFNPWPGA---WTELDGQR--LKILEAELVEASGSGAPGTILAID-K 266
Query: 215 NGILVVCGKNVIKLLELQKNNKKKISATEFING 247
+GI+V G+ ++L +LQ KK +SA +F+NG
Sbjct: 267 DGIVVATGEGALRLTQLQPPGKKPMSAADFLNG 299
Score = 98.3 bits (246), Expect = 3e-24
Identities = 37/102 (36%), Positives = 55/102 (53%), Gaps = 11/102 (10%)
Query: 1 MKIIFAGTSISAAAILDTLYNSEHNIVLILTKPDLHSGRGMKLNFSPVKKYALKHSIKII 60
M+I+F GT A L L S H +V ++T+PD +GRG KL SPVK+ AL+H I ++
Sbjct: 1 MRIVFMGTPEFAVPSLKALLESGHEVVAVVTQPDRPAGRGKKLTPSPVKQLALEHGIPVL 60
Query: 61 QPISLKLNGKYHKIANETHKLLNKIEFDIMIVMG---ILPED 99
QP L+ E L + D+++V+ ILP+
Sbjct: 61 QPEKLR--------DPEFLAELAALNADVIVVVAYGQILPKA 94
>gnl|CDD|223301 COG0223, Fmt, Methionyl-tRNA formyltransferase [Translation,
ribosomal structure and biogenesis].
Length = 307
Score = 132 bits (335), Expect = 3e-37
Identities = 61/154 (39%), Positives = 86/154 (55%), Gaps = 8/154 (5%)
Query: 95 ILPEDTSLTLQNKLEKLSKILIIDTIKKIEYDMTKLFFKPQSNIGESYAPLIKKNEAVLD 154
I P+DT+ +L +KL +L L+++T+ ++E PQ +YAP I K + +D
Sbjct: 156 IEPDDTAGSLHDKLAELGAELLLETLPQLEAGTLTP--IPQDEEEATYAPKITKEDGRID 213
Query: 155 WSLSAKTIMRKINAFNPFPGAKTYYISYQNKKKFLKIWKAHALSIESTKKPGTILNVNFH 214
WS A I+ KI AFNP+PGA T K +KIW+A L S KPG IL +
Sbjct: 214 WSKPAAQILNKIRAFNPWPGAWTEL-----GGKRIKIWEARVLEGASNGKPGEILAAD-K 267
Query: 215 NGILVVCGKNVIKLLELQKNNKKKISATEFINGC 248
G+LV CG ++L ELQ KK +SA +F+NG
Sbjct: 268 KGLLVACGDGALRLTELQPAGKKAMSAADFLNGR 301
Score = 90.8 bits (226), Expect = 2e-21
Identities = 36/102 (35%), Positives = 56/102 (54%), Gaps = 11/102 (10%)
Query: 1 MKIIFAGTSISAAAILDTLYNSEHNIVLILTKPDLHSGRGMKLNFSPVKKYALKHSIKII 60
M+I+F GT A L+ L + H IV ++T+PD +GRG KL SPVK+ AL+ I +
Sbjct: 2 MRIVFFGTPEFAVPSLEALIEAGHEIVAVVTQPDKPAGRGKKLTPSPVKRLALELGIPVF 61
Query: 61 QPISLKLNGKYHKIANETHKLLNKIEFDIMIVMG---ILPED 99
QP L E + L ++ D+++V+ ILP++
Sbjct: 62 QPEKLN--------DPEFLEELAALDPDLIVVVAYGQILPKE 95
>gnl|CDD|217282 pfam02911, Formyl_trans_C, Formyl transferase, C-terminal domain.
Length = 100
Score = 97.7 bits (244), Expect = 5e-26
Identities = 40/103 (38%), Positives = 57/103 (55%), Gaps = 7/103 (6%)
Query: 146 IKKNEAVLDWSLSAKTIMRKINAFNPFPGAKTYYISYQNKKKFLKIWKAHALS-IESTKK 204
I K + +DWS A+ I R I A +P+PGA Y K+ +KI KA +
Sbjct: 2 ITKEDGRIDWSQPAEEIHRLIRALSPWPGA---YTFLNGKR--VKILKAEVVEDSSGAAS 56
Query: 205 PGTILNVNFHNGILVVCGKNVIKLLELQKNNKKKISATEFING 247
PGTI++V+ G+LV CG + +LELQ KK + A +F+NG
Sbjct: 57 PGTIVSVD-KGGLLVACGDGALLILELQPEGKKAMDAADFLNG 98
>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 = 101 bits (254), Expect = 2e-25
Identities = 58/155 (37%), Positives = 85/155 (54%), Gaps = 10/155 (6%)
Query: 95 ILPEDTSLTLQNKLEKLSKILIIDTIKKIEYDMTKLFFKPQSNIGESYAPLIKKNEAVLD 154
I ED S TL +KL +L L+I+T+K++ K + +YAP I K + +D
Sbjct: 155 IEEEDNSGTLSDKLSELGAQLLIETLKELPEGKNKPEPQDAE--EATYAPKISKEQERID 212
Query: 155 WSLSAKTIMRKINAFNPFPGAKTYYISYQNKKKFLKIWKAHALSIESTK-KPGTILNVNF 213
W+ SA+ ++ KI A NP+P A + K +KI KA + + + K KPG I+ N
Sbjct: 213 WNQSAEELLNKIRALNPWPTAWL-----TFEGKNIKIHKAKVIDLSTYKAKPGEIVYHN- 266
Query: 214 HNGILVVCGKN-VIKLLELQKNNKKKISATEFING 247
GILV CGK+ ++ LL LQ KK + A +F NG
Sbjct: 267 KKGILVACGKDGILLLLSLQPPGKKVMRAEDFYNG 301
Score = 63.2 bits (154), Expect = 1e-11
Identities = 29/102 (28%), Positives = 53/102 (51%), Gaps = 11/102 (10%)
Query: 1 MKIIFAGTSISAAAILDTLYNSEHNIVLILTKPDLHSGRGMKLNFSPVKKYALKHSIKII 60
++I+F GT + +L+ L +V ++T+PD +GRG KL PVK A + I +
Sbjct: 1 LRIVFFGTPTFSLPVLEELREDNFEVVGVVTQPDKPAGRGKKLTPPPVKVLAEEKGIPVF 60
Query: 61 QPISLKLNGKYHKIANETHKLLNKIEFDIMIVMG---ILPED 99
QP + E L+ +++ D+++V+ ILP++
Sbjct: 61 QPEKQRQ--------LEELPLVRELKPDVIVVVSFGKILPKE 94
>gnl|CDD|187732 cd08704, Met_tRNA_FMT_C, C-terminal domain of Formyltransferase and
other enzymes. C-terminal domain of formyl transferase
and other proteins with diverse enzymatic activities.
Proteins found in this family include methionyl-tRNA
formyltransferase, ArnA, and 10-formyltetrahydrofolate
dehydrogenase. Methionyl-tRNA formyltransferases
constitute the majority of the family and also
demonstrate greater sequence diversity. Although most
proteins with formyltransferase activity contain the
C-terminal domain, some formyltransferases ( for
example, prokaryotic glycinamide ribonucleotide
transformylase (GART)) only have the core catalytic
domain, indicating that the C-terminal domain is not a
requirement for catalytic activity and may be involved
in substrate binding. For example, the C-terminal domain
of methionyl-tRNA formyltransferase is involved in the
tRNA binding.
Length = 87
Score = 94.5 bits (236), Expect = 5e-25
Identities = 41/92 (44%), Positives = 52/92 (56%), Gaps = 6/92 (6%)
Query: 150 EAVLDWSLSAKTIMRKINAFNPFPGAKTYYISYQNKKKFLKIWKAHALSIESTKKPGTIL 209
E +DWS SA+ I I A NP+PGA T K+ LKI KA L PGTIL
Sbjct: 2 EGRIDWSKSAEEIHNLIRALNPWPGAYTT---LNGKR--LKILKAEVLEESGEAAPGTIL 56
Query: 210 NVNFHNGILVVCGKNVIKLLELQKNNKKKISA 241
V+ G+LV CG +++LELQ KK++SA
Sbjct: 57 AVD-KKGLLVACGDGALEILELQPEGKKRMSA 87
>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 = 96.0 bits (240), Expect = 2e-24
Identities = 36/102 (35%), Positives = 57/102 (55%), Gaps = 11/102 (10%)
Query: 1 MKIIFAGTSISAAAILDTLYNSEHNIVLILTKPDLHSGRGMKLNFSPVKKYALKHSIKII 60
M+I+F GT A L+ L S H +V ++T+PD GRG KL SPVK+ AL+ + ++
Sbjct: 1 MRIVFMGTPDFAVPSLEALLKSGHEVVAVVTQPDKPRGRGKKLTPSPVKELALELGLPVL 60
Query: 61 QPISLKLNGKYHKIANETHKLLNKIEFDIMIVM---GILPED 99
QP LK E + L ++ D+++V+ ILP++
Sbjct: 61 QPEKLK--------DEEFLEELKALKPDLIVVVAYGQILPKE 94
Score = 45.5 bits (109), Expect = 6e-06
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 95 ILPEDTSLTLQNKLEKLSKILIIDTIKKIEYDMTKLFFKPQSNIGESYAPLI 146
I P+DT+ L +KL +L L+++ + IE KL PQ +YAP I
Sbjct: 155 IDPDDTAGELLDKLAELGADLLLEVLDDIEA--GKLNPVPQDESEATYAPKI 204
>gnl|CDD|236156 PRK08125, PRK08125, bifunctional UDP-glucuronic acid
decarboxylase/UDP-4-amino-4-deoxy-L-arabinose
formyltransferase; Validated.
Length = 660
Score = 65.8 bits (161), Expect = 3e-12
Identities = 39/142 (27%), Positives = 71/142 (50%), Gaps = 11/142 (7%)
Query: 95 ILPEDTSLTLQNKLEKLSKILIIDTIKKIEYDMTKLFFKPQSNIGESYAPLIKKNEAVLD 154
I P+DT+LTL +KL ++ L+ T+ I+ + PQ +Y + ++D
Sbjct: 152 IAPDDTALTLHHKLCHAARQLLEQTLPAIK--HGNIPEIPQDESQATYFGRRTPADGLID 209
Query: 155 WSLSAKTIMRKINAF-NPFPGAKTYYISYQNKKKFLKIWKAHALSIESTKKPGTILNVNF 213
W A T+ + A +P+PGA SY ++KF +W + L S +PGT+L+V
Sbjct: 210 WHKPASTLHNLVRAVTDPWPGA----FSYVGEQKFT-VWSSRVLPDASGAQPGTVLSV-- 262
Query: 214 HNGILVVCGKNVIKLLELQKNN 235
+ + CG+ ++++ Q +
Sbjct: 263 -APLRIACGEGALEIVTGQAGD 283
>gnl|CDD|187730 cd08702, Arna_FMT_C, C-terminal subdomain of the formyltransferase
domain on ArnA, which modifies lipid A with
4-amino-4-deoxy-l-arabinose. Domain found in ArnA with
similarity to the C-terminal domain of
Formyltransferase. 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 domain of ArnA is a dehydrogenase domain that
catalyzes the oxidative decarboxylation of
UDP-glucuronic acid (UDP-GlcUA) to UDP-4-keto-arabinose
(UDP-Ara4O) and the N-terminal domain is a
formyltransferase domain that 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
C-terminal subdomain of the formyltransferase domain,
downstream of the N-terminal subdomain containing the
catalytic center. ArnA forms a hexameric structure (a
dimer of trimers), in which the dehydrogenase domains
are arranged at the center with the transformylase
domains on the outside of the complex.
Length = 92
Score = 59.9 bits (146), Expect = 6e-12
Identities = 26/82 (31%), Positives = 45/82 (54%), Gaps = 8/82 (9%)
Query: 153 LDWSLSAKTIMRKINAFN-PFPGAKTYYISYQNKKKFLKIWKAHALSIESTKK-PGTILN 210
+DW +SA+ I + A P+PGA T+ +K +KIWKA + PG +L+
Sbjct: 5 IDWRMSAREIYNLVRAVTKPYPGAFTFV---GGQK--IKIWKARPVDDAFYNGEPGKVLS 59
Query: 211 VNFHNGILVVCGKNVIKLLELQ 232
V+ + ++V CG +++LE +
Sbjct: 60 VD-GDPLIVACGDGALEILEAE 80
>gnl|CDD|215159 PLN02285, PLN02285, methionyl-tRNA formyltransferase.
Length = 334
Score = 54.7 bits (132), Expect = 1e-08
Identities = 34/157 (21%), Positives = 63/157 (40%), Gaps = 6/157 (3%)
Query: 97 PEDTSLTLQNKLEKLSKILIIDTIKKIEYDMTKLFFKPQSNIGESYAPLIKKNEAVLDWS 156
+ + L L +L L++ + + K PQ + ++AP I E+ L +
Sbjct: 172 EDIKAPELLPLLFELGTKLLLRELPSVLDGSAKDKATPQDDSKATHAPKISPEESWLSFD 231
Query: 157 LSAKTIMRKINAFNPFPGAKTYYI-----SYQNKKKFLKIWKAHALSIESTKKPGTILNV 211
A+ + K+ AF +PG + + + + LKI +
Sbjct: 232 EEARVLHNKVRAFAGWPGTRAKFQLVDDGDGEREVLELKIITTRVCEAGGEQTGSADAVT 291
Query: 212 NFHNGILVVCGKN-VIKLLELQKNNKKKISATEFING 247
+ +LV CG +++LE+Q KK + A +F NG
Sbjct: 292 FKKDSLLVPCGGGTWLEVLEVQPPGKKVMKAKDFWNG 328
Score = 43.9 bits (104), Expect = 3e-05
Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 6/58 (10%)
Query: 2 KIIFAGTSISAAAILDTLY------NSEHNIVLILTKPDLHSGRGMKLNFSPVKKYAL 53
+++F GT AA +LD L +S + ++T+P GRG KL SPV + AL
Sbjct: 8 RLVFLGTPEVAATVLDALLDASQAPDSAFEVAAVVTQPPARRGRGRKLMPSPVAQLAL 65
>gnl|CDD|187728 cd08700, FMT_C_OzmH_like, C-terminal subdomain of the
Formyltransferase-like domain found in OzmH-like
proteins. Domain found in OzmH-like proteins with
similarity to the C-terminal domain of
Formyltransferase. OzmH is one of the proteins involved
in the synthesis of Oxazolomycin (OZM), which is a
hybrid peptide-polyketide antibiotic that exhibits
potent antitumor and antiviral activities. OzmH 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
phosphopantetheine (PP)-binding domain, which may
function as an acyl carrier. It shows sequence
similarity with other peptide-polyketide biosynthesis
proteins.
Length = 100
Score = 49.2 bits (118), Expect = 6e-08
Identities = 24/104 (23%), Positives = 37/104 (35%), Gaps = 22/104 (21%)
Query: 151 AVLDWSLSAKTIMRKINA--FNPFPGAKTYYISYQNKKKFLKIW---------KAHALSI 199
VLD++ A + + A F Y N KI KA L++
Sbjct: 3 GVLDFTRPAAELSALVRALDFGG----------YWNPLCVAKILLADRVLLVGKAEVLAV 52
Query: 200 ESTKKPGTILNVNFHNGILVVCGKNVIKLLELQKNNKKKISATE 243
S PGT+L V+ +G V G ++L L + +
Sbjct: 53 SSGGAPGTVLAVD-ADGWTVATGDGAVRLSGLTDLDGAAVDLAA 95
>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 = 39.9 bits (94), Expect = 3e-04
Identities = 18/106 (16%), Positives = 38/106 (35%), Gaps = 23/106 (21%)
Query: 2 KIIFAGTSISAAAILDTLYNSEHNIVLILTKPDLHSGRGMKLNFSPVKKYALKHSIKI-I 60
+I+F G + L+ + + +V ++T D S S + +
Sbjct: 1 RIVFIGCVEFSLIALEAILEAGGEVVGVITLDDSSSNN---------------DSDYLDL 45
Query: 61 QPISLKLNGKYHKIAN----ETHKLLNKIEFDIMIVMG---ILPED 99
+ K Y+K + E + + + DI+ V G +L +
Sbjct: 46 DSFARKNGIPYYKFTDINDEEIIEWIKEANPDIIFVFGWSQLLKPE 91
>gnl|CDD|187727 cd08370, FMT_C_like, Carboxy-terminal domain of Formyltransferase
and similar domains. This family represents the
C-terminal domain of formyltransferase and similar
proteins. This domain is found in a variety of enzymes
with formyl transferase and alkyladenine DNA glycosylase
activities. The proteins with formyltransferase function
include methionyl-tRNA formyltransferase, ArnA,
10-formyltetrahydrofolate dehydrogenase and HypX
proteins. Although most proteins with formyl transferase
activity contain this C-terminal domain, prokaryotic
glycinamide ribonucleotide transformylase (GART), a
single domain protein, only contains the core catalytic
domain. Thus, the C-terminal domain is not required for
formyl transferase catalytic activity and may be
involved in substrate binding. Some members of this
family have shown nucleic acid binding capacity. The
C-terminal domain of methionyl-tRNA formyltransferase is
involved in tRNA binding. Alkyladenine DNA glycosylase
is a distant member of this family with very low
sequence similarity to other members. It catalyzes the
first step in base excision repair (BER) by cleaving
damaged DNA bases within double-stranded DNA to produce
an abasic site and shows ability to bind to DNA.
Length = 73
Score = 35.9 bits (83), Expect = 0.002
Identities = 18/78 (23%), Positives = 36/78 (46%), Gaps = 9/78 (11%)
Query: 157 LSAKTIMRKINAFNPFPGAKTYYISYQNKKKFLKIWKAHALSIESTKK--PGTILNVNFH 214
L A+++ R I A P+ GA+ + + +++ +A + + + G IL V++
Sbjct: 1 LDAESLERTIRAL-PYQGARL-----EIDGERVRLLEAEVVDDVTNEARHSGKILFVDY- 53
Query: 215 NGILVVCGKNVIKLLELQ 232
I V G + + LQ
Sbjct: 54 QCITVATGDGALLITALQ 71
>gnl|CDD|187729 cd08701, FMT_C_HypX, C-terminal subdomain of the
Formyltransferase-like domain found in HypX-like
proteins. Domain found in HypX-like proteins with
similarity to the C-terminal domain of
Formyltransferase. HypX is involved in the maturation
process of active [NiFe] hydrogenase. [NiFe]
hydrogenases function in H2 metabolism in a variety of
microorganisms, enabling them to use H2 as a source of
reducing equivalents under aerobic and anaerobic
conditions. [NiFe] hydrogenases consist of a large and a
small subunit. The large subunit contains the [NiFe]
active site but is synthesized as a precursor without
the [NiFe] active site. This precursor undergoes a
complex post-translational maturation process that
requires the presence of a number of accessory proteins.
HypX has been shown to be involved in this maturation
process and have been proposed to participate in the
generation and transport of the CO and CN ligands.
However, HypX is not present in all
hydrogen-metabolizing bacteria. Furthermore, hypX
deletion mutants have a reduced but detectable level of
hydrogenase activity. Thus, HypX might not be the
determining factor in the maturation process. Members of
this group have an N-terminal formyl transferase domain
and a C-terminal enoyl-CoA hydratase/isomerase domain.
Length = 96
Score = 34.6 bits (80), Expect = 0.008
Identities = 24/80 (30%), Positives = 34/80 (42%), Gaps = 22/80 (27%)
Query: 152 VLDWSL-SAKTIMRKINAFNPFPGAK------TYYISYQNKKKFLKIWKAH-ALSIESTK 203
+DW SA+ I+RKI A + PG Y ++ AH ++
Sbjct: 4 RIDWEKDSAEEILRKIRAADSQPGVLDELFGTEVY-----------LFGAHPEEALPDAG 52
Query: 204 KPGTILNVNFHNG-ILVVCG 222
KPGTIL +G +LV G
Sbjct: 53 KPGTILAQ--RDGAVLVATG 70
>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 = 33.8 bits (78), Expect = 0.044
Identities = 19/101 (18%), Positives = 37/101 (36%), Gaps = 20/101 (19%)
Query: 3 IIFAGTSISAAAILDTLYNSE-HNIVLILTKPDLHSGRGMKLNFSPVKKYALKHSIKIIQ 61
I+ G+ +L L + E H IV ++T PD + A
Sbjct: 1 IVILGSGNIGQRVLKALLSKEGHEIVGVVTHPD------------SPRGTAQLSLE---- 44
Query: 62 PISLKLNGKYHKIANETHKLLNKIEFDIMIVMG---ILPED 99
+ K+ + E +LL + D+++ + I+P +
Sbjct: 45 LVGGKVYLDSNINTPELLELLKEFAPDLIVSINFRQIIPPE 85
>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 = 32.3 bits (74), Expect = 0.16
Identities = 14/66 (21%), Positives = 24/66 (36%), Gaps = 3/66 (4%)
Query: 1 MKIIFAGTSISAAAILDTLYNSEHNIVLILTKPDLHSGRGMKLNFSPVKKYALKHSIKII 60
MK + L+ L + +V + T D G + F V + A +H I +
Sbjct: 1 MKAVVFAYHEVGYRCLEALLAAGFEVVAVFTHTDNP---GENIWFGSVAQLAREHGIPVF 57
Query: 61 QPISLK 66
P +
Sbjct: 58 TPDDIN 63
>gnl|CDD|178532 PLN02946, PLN02946, cysteine-tRNA ligase.
Length = 557
Score = 31.1 bits (70), Expect = 0.70
Identities = 29/107 (27%), Positives = 45/107 (42%), Gaps = 12/107 (11%)
Query: 21 NSEHNIVLILTKPDLHSGRGMKLNFSPVKKYALKHSIKIIQPISLKLNGKYHKIANETHK 80
N H+ + DLH+ PV AL +K I + GK + E+
Sbjct: 408 NKFHDEFVTSMSDDLHT---------PVALAALSEPLKTINDLLHTRKGKKQEKRLESLA 458
Query: 81 LLNKIEFDIMIVMGILPEDTSLTLQNKLEKL---SKILIIDTIKKIE 124
L K D++ V+G++P S LQ EK +K+ ++KIE
Sbjct: 459 ALEKKIRDVLSVLGLMPTSYSEALQQLREKALRRAKLTEEQVLQKIE 505
>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 = 28.5 bits (64), Expect = 3.0
Identities = 15/58 (25%), Positives = 22/58 (37%), Gaps = 4/58 (6%)
Query: 1 MKIIF--AGTSISAAAILDTLYNSEHN--IVLILTKPDLHSGRGMKLNFSPVKKYALK 54
MKI +GT + A+LD L H IV ++T D +G +
Sbjct: 1 MKIAVLISGTGSNLQALLDALRKGGHEVEIVAVVTNKDKAAGLERAEQAGIPVEVFEH 58
>gnl|CDD|216721 pfam01820, Dala_Dala_lig_N, D-ala D-ala ligase N-terminus. This
family represents the N-terminal region of the
D-alanine--D-alanine ligase enzyme EC:6.3.2.4 which is
thought to be involved in substrate binding. D-Alanine
is one of the central molecules of the cross-linking
step of peptidoglycan assembly. There are three enzymes
involved in the D-alanine branch of peptidoglycan
biosynthesis: the pyridoxal phosphate-dependent
D-alanine racemase (Alr), the ATP-dependent
D-alanine:D-alanine ligase (Ddl), and the ATP-dependent
D-alanine:D-alanine-adding enzyme (MurF).
Length = 110
Score = 26.8 bits (60), Expect = 5.4
Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 9/43 (20%)
Query: 1 MKI--IFAGTS-------ISAAAILDTLYNSEHNIVLILTKPD 34
M+I +F G S SA A+L L + ++ I D
Sbjct: 1 MRIAVLFGGRSSEHEVSLKSARAVLKALDKEGYEVIPIDIDKD 43
>gnl|CDD|113093 pfam04310, MukB, MukB N-terminal. This family represents the
N-terminal region of MukB, one of a group of bacterial
proteins essential for the movement of nucleoids from
mid-cell towards the cell quarters (i.e. chromosome
partitioning). The structure of the N-terminal domain
consists of an antiparallel six-stranded beta sheet
surrounded by one helix on one side and by five helices
on the other side. It contains an exposed Walker A loop
in an unexpected helix-loop-helix motif (in other
proteins, Walker A motifs generally adopt a P loop
conformation as part of a strand-loop-helix motif
embedded in a conserved topology of alternating helices
and (parallel) beta strands).
Length = 227
Score = 27.7 bits (61), Expect = 5.5
Identities = 23/75 (30%), Positives = 34/75 (45%), Gaps = 3/75 (4%)
Query: 14 AILDTLYNSEHNIVLILTKPDLHSGRGMKLNFSPVKKYALKHSIKIIQPISLKLNGKYHK 73
A LDT+ NS H +L K +GR K++ P L +K ++ LN K+ +
Sbjct: 88 AALDTI-NSRHQRLLFAVKLQQVAGRDKKVDIKPFAIQGLPMHVKPTDLLTETLNDKHAR 146
Query: 74 I--ANETHKLLNKIE 86
+ NE L IE
Sbjct: 147 VLPINELKDALEAIE 161
>gnl|CDD|214840 smart00829, PKS_ER, Enoylreductase. Enoylreductase in Polyketide
synthases.
Length = 287
Score = 27.7 bits (63), Expect = 5.8
Identities = 5/15 (33%), Positives = 10/15 (66%)
Query: 88 DIMIVMGILPEDTSL 102
D++I +G+ P + L
Sbjct: 12 DVLIALGLYPGEAVL 26
>gnl|CDD|102370 PRK06425, PRK06425, histidinol-phosphate aminotransferase;
Validated.
Length = 332
Score = 27.1 bits (60), Expect = 9.8
Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 15/82 (18%)
Query: 44 NFSPVKKYALKHSIKIIQPISLKLNGKYHKIANETHKLLNKIEFDIMIVMG-------IL 96
NF+ K YA H I+I +L N + N ++LN FD++ ++ ++
Sbjct: 88 NFNEYKGYAFTHGIRIS---ALPFN-----LINNNPEILNNYNFDLIFIVSPDNPLGNLI 139
Query: 97 PEDTSLTLQNKLEKLSKILIID 118
D+ LT+ K +L ID
Sbjct: 140 SRDSLLTISEICRKKGALLFID 161
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 0.136 0.384
Gapped
Lambda K H
0.267 0.0902 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,844,357
Number of extensions: 1226154
Number of successful extensions: 1196
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1173
Number of HSP's successfully gapped: 53
Length of query: 258
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 163
Effective length of database: 6,723,972
Effective search space: 1096007436
Effective search space used: 1096007436
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 (25.8 bits)