RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17704
(412 letters)
>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 = 196 bits (502), Expect = 2e-61
Identities = 67/162 (41%), Positives = 100/162 (61%), Gaps = 7/162 (4%)
Query: 18 KHSPVIQFAQDEKLTLYRWP--MDPDLIKD----NYDIGMVVSFGHLIPSKIINAFPLGM 71
SPV + A + L + + D + +++ D+ +VV++G ++P +I++ P G
Sbjct: 44 TPSPVKELALELGLPVLQPEKLKDEEFLEELKALKPDLIVVVAYGQILPKEILDLPPYGC 103
Query: 72 INVHGSILPRWRGAAPIVHAILHGDHETGISIIRVRPKHFDRGEIVRQYRCSISPDDTAG 131
INVH S+LP++RGAAPI AIL+GD ETG++I+++ D G+I+ Q I PDDTAG
Sbjct: 104 INVHPSLLPKYRGAAPIQRAILNGDKETGVTIMKMDEG-LDTGDILAQEEVPIDPDDTAG 162
Query: 132 ELHNKLALVGGQLLLECVRDMPRCVLNAPAQPDEGATYANKI 173
EL +KLA +G LLLE + D+ LN Q + ATYA KI
Sbjct: 163 ELLDKLAELGADLLLEVLDDIEAGKLNPVPQDESEATYAPKI 204
>gnl|CDD|223301 COG0223, Fmt, Methionyl-tRNA formyltransferase [Translation,
ribosomal structure and biogenesis].
Length = 307
Score = 178 bits (455), Expect = 5e-53
Identities = 75/212 (35%), Positives = 118/212 (55%), Gaps = 8/212 (3%)
Query: 14 SKEGKHSPVIQFAQDEKLTLY-----RWPMDPDLIKD-NYDIGMVVSFGHLIPSKIINAF 67
K+ SPV + A + + ++ P + + + D+ +VV++G ++P +I++
Sbjct: 41 GKKLTPSPVKRLALELGIPVFQPEKLNDPEFLEELAALDPDLIVVVAYGQILPKEILDLP 100
Query: 68 PLGMINVHGSILPRWRGAAPIVHAILHGDHETGISIIRVRPKHFDRGEIVRQYRCSISPD 127
P G IN+H S+LPR+RGAAPI AIL+GD ETG++I+++ D G+I+ Q I PD
Sbjct: 101 PYGCINLHPSLLPRYRGAAPIQWAILNGDTETGVTIMQMDEG-LDAGDILAQREVPIEPD 159
Query: 128 DTAGELHNKLALVGGQLLLECVRDMPRCVLNAPAQPDEGATYANKIDWSYSVIDWNTMSS 187
DTAG LH+KLA +G +LLLE + + L Q +E ATYA KI IDW+ +
Sbjct: 160 DTAGSLHDKLAELGAELLLETLPQLEAGTLTPIPQDEEEATYAPKITKEDGRIDWS-KPA 218
Query: 188 VQVYNLHRALGHVYPLLAQWHGVKVKLHNISL 219
Q+ N RA + G ++K+ +
Sbjct: 219 AQILNKIRAFNPWPGAWTELGGKRIKIWEARV 250
Score = 33.4 bits (77), Expect = 0.21
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 4/56 (7%)
Query: 333 EPNPIVPELTPG-FVSFDRGSKLLRVRCVDGKSILCSQITVAGKKKMTAVDFKNGY 387
PG ++ D+ K L V C DG ++ +++ AGKK M+A DF NG
Sbjct: 249 RVLEGASNGKPGEILAADK--KGLLVACGDG-ALRLTELQPAGKKAMSAADFLNGR 301
>gnl|CDD|234567 PRK00005, fmt, methionyl-tRNA formyltransferase; Reviewed.
Length = 309
Score = 173 bits (442), Expect = 3e-51
Identities = 69/188 (36%), Positives = 110/188 (58%), Gaps = 16/188 (8%)
Query: 20 SPVIQFAQDEKLTLYRWPMDPDLIKD----------NYDIGMVVSFGHLIPSKIINAFPL 69
SPV Q A + + + + P+ ++D N D+ +VV++G ++P +++ L
Sbjct: 46 SPVKQLALEHGIPVLQ----PEKLRDPEFLAELAALNADVIVVVAYGQILPKAVLDIPRL 101
Query: 70 GMINVHGSILPRWRGAAPIVHAILHGDHETGISIIRVRPKHFDRGEIVRQYRCSISPDDT 129
G IN+H S+LPRWRGAAPI AI+ GD ETG++I+++ D G+++ + I+P DT
Sbjct: 102 GCINLHASLLPRWRGAAPIQRAIIAGDAETGVTIMQMDEG-LDTGDMLLKAEVPITPTDT 160
Query: 130 AGELHNKLALVGGQLLLECVRDMPRCVLNAPAQPDEGATYANKIDWSYSVIDWNTMSSVQ 189
AGELH+KLA +G LL+E ++ + L Q +EG TYA KI + IDW+ + +
Sbjct: 161 AGELHDKLAELGADLLVETLKGLEDGTLTPIPQDEEGVTYAPKISKEEARIDWS-KPAAE 219
Query: 190 VYNLHRAL 197
+ N R
Sbjct: 220 LENHIRGF 227
Score = 30.9 bits (71), Expect = 1.0
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 357 VRCVDGKSILCSQITVAGKKKMTAVDFKNG 386
V +G ++ +Q+ GKK M+A DF NG
Sbjct: 271 VATGEG-ALRLTQLQPPGKKPMSAADFLNG 299
>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 = 169 bits (431), Expect = 1e-49
Identities = 79/236 (33%), Positives = 123/236 (52%), Gaps = 23/236 (9%)
Query: 5 LISKLEVVSSKEGKHSPVIQFAQDEKL-TLYRWPMDPDLIKDNYDIGMVVSFGHLIPSKI 63
++V++ ++G I Q EK L P + + D+ +VVSFG ++P +
Sbjct: 44 TPPPVKVLAEEKG-----IPVFQPEKQRQLEELP---LVRELKPDVIVVVSFGKILPKEF 95
Query: 64 INAFPLGMINVHGSILPRWRGAAPIVHAILHGDHETGISIIRVRPKHFDRGEIVRQYRCS 123
++ FP G INVH S+LPRWRG API AIL+GD +TG++I+++ PK D G+I++Q
Sbjct: 96 LDLFPYGCINVHPSLLPRWRGGAPIQRAILNGDKKTGVTIMQMVPK-MDAGDILKQETFP 154
Query: 124 ISPDDTAGELHNKLALVGGQLLLECVRDMPRCVLNAPAQPDEGATYANKIDWSYSVIDWN 183
I +D +G L +KL+ +G QLL+E ++++P Q E ATYA KI IDWN
Sbjct: 155 IEEEDNSGTLSDKLSELGAQLLIETLKELPEGKNKPEPQDAEEATYAPKISKEQERIDWN 214
Query: 184 TMSSVQVYNLHRALGHVYPLLAQWHGVKVKL--HNISLDTKLRSDALLRPNTSHVP 237
S+ ++ N RAL W + NI + ++ + P
Sbjct: 215 -QSAEELLNKIRALN-------PWPTAWLTFEGKNIKI---HKAKVIDLSTYKAKP 259
Score = 29.7 bits (67), Expect = 2.9
Identities = 14/47 (29%), Positives = 18/47 (38%), Gaps = 3/47 (6%)
Query: 343 PGFVSFDRGSKLLRVRCVDGKSILC-SQITVAGKKKMTAVDFKNGYL 388
PG + + +L IL + GKK M A DF NG
Sbjct: 259 PGEIVYHNKKGILVACG--KDGILLLLSLQPPGKKVMRAEDFYNGSR 303
>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 = 106 bits (267), Expect = 3e-27
Identities = 40/116 (34%), Positives = 68/116 (58%), Gaps = 5/116 (4%)
Query: 38 MDPDLIKD----NYDIGMVVSFGHLIPSKIINAFPLGMINVHGSILPRWRGAAPIVHAIL 93
D +L D+ ++ + ++P + + AFP ++N+H S+LPR+RGAAPI A+
Sbjct: 67 FDSELADSLAALAPDLIVLAGYMRILPPEFLQAFPGKILNIHPSLLPRFRGAAPIQRALE 126
Query: 94 HGDHETGISIIRVRPKHFDRGEIVRQYRCSISPDDTAGELHNKLALVGGQLLLECV 149
GD ETG+++ +V + D G I+ Q I PDDT+ L+N++A + + L E +
Sbjct: 127 AGDKETGVTVHQVD-EELDTGPILAQKAVPILPDDTSETLYNRVAELEHKALPEAL 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 = 105 bits (265), Expect = 4e-27
Identities = 41/100 (41%), Positives = 65/100 (65%), Gaps = 1/100 (1%)
Query: 48 DIGMVVSFGHLIPSKIINAFPLGMINVHGSILPRWRGAAPIVHAILHGDHETGISIIRVR 107
D+ + ++F +IP +I+ P G IN+H S+LPR+RG P+ AI++G+ ETG+++ +
Sbjct: 71 DLIVSINFRQIIPPEILKLPPGGAINIHPSLLPRYRGVNPLAWAIINGEKETGVTVHYMD 130
Query: 108 PKHFDRGEIVRQYRCSISPDDTAGELHNKLALVGGQLLLE 147
D G+I+ Q ISPDDTAG L+ +L +G +LL E
Sbjct: 131 EG-IDTGDIIAQEVIPISPDDTAGTLYQRLIELGPKLLKE 169
>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 = 96.6 bits (241), Expect = 2e-23
Identities = 46/132 (34%), Positives = 71/132 (53%), Gaps = 8/132 (6%)
Query: 38 MDPDLIKDNYDIGMVVSFGHLIPSKIINAFPLGMINVHGSILPRWRGAAPIVHAILHGDH 97
+ PDLI Y + H+I I+ LG N+HGS+LP++RG AP+ A+++G+
Sbjct: 74 LKPDLIFSFY-------YRHMISEDILEIARLGAFNLHGSLLPKYRGRAPLNWALINGET 126
Query: 98 ETGISIIRVRPKHFDRGEIVRQYRCSISPDDTAGELHNKLALVGGQLLLECVRDMPRCVL 157
ETG+++ R+ K D G IV Q + I PDDTA L +KL + +LL + +
Sbjct: 127 ETGVTLHRMTKK-PDAGAIVDQEKVPILPDDTAKSLFHKLCVAARRLLARTLPALKAGKA 185
Query: 158 NAPAQPDEGATY 169
Q + A+Y
Sbjct: 186 RERPQDETQASY 197
>gnl|CDD|236156 PRK08125, PRK08125, bifunctional UDP-glucuronic acid
decarboxylase/UDP-4-amino-4-deoxy-L-arabinose
formyltransferase; Validated.
Length = 660
Score = 101 bits (254), Expect = 3e-23
Identities = 55/165 (33%), Positives = 92/165 (55%), Gaps = 9/165 (5%)
Query: 38 MDPDLIKDNYDIGMVVSFGHLIPSKIINAFPLGMINVHGSILPRWRGAAPIVHAILHGDH 97
+ PD+I Y + +L+ +I+ P G N+HGS+LP++RG AP+ +++G+
Sbjct: 74 LAPDVIFSFY-------YRNLLSDEILQLAPAGAFNLHGSLLPKYRGRAPLNWVLVNGET 126
Query: 98 ETGISIIRVRPKHFDRGEIVRQYRCSISPDDTAGELHNKLALVGGQLLLECVRDMPRCVL 157
ETG+++ R+ K D G IV Q R +I+PDDTA LH+KL QLL + + + +
Sbjct: 127 ETGVTLHRM-VKRADAGAIVAQQRVAIAPDDTALTLHHKLCHAARQLLEQTLPAIKHGNI 185
Query: 158 NAPAQPDEGATYANKIDWSYSVIDWNTMSSVQVYNLHRALGHVYP 202
Q + ATY + + +IDW+ + ++NL RA+ +P
Sbjct: 186 PEIPQDESQATYFGRRTPADGLIDWH-KPASTLHNLVRAVTDPWP 229
>gnl|CDD|215159 PLN02285, PLN02285, methionyl-tRNA formyltransferase.
Length = 334
Score = 98.2 bits (245), Expect = 6e-23
Identities = 55/174 (31%), Positives = 88/174 (50%), Gaps = 19/174 (10%)
Query: 48 DIGMVVSFGHLIPSKIINAFPLGMINVHGSILPRWRGAAPIVHAILHGDHETGISII-RV 106
D+ + ++G+++P K ++ LG +N+H S+LP +RGAAP+ A+ G +ETG+S+ V
Sbjct: 95 DLCITAAYGNILPQKFLDIPKLGTVNIHPSLLPLYRGAAPVQRALQDGVNETGVSVAFTV 154
Query: 107 RPKHFDRGEIVRQYRCSISPDDTAGELHNKLALVGGQLLLECVRDMP-----RCVLNAPA 161
R D G ++ Q R + D A EL L +G +LLL R++P A
Sbjct: 155 RA--LDAGPVIAQERVEVDEDIKAPELLPLLFELGTKLLL---RELPSVLDGSAKDKATP 209
Query: 162 QPDEGATYANKIDWSYSVIDWNTMSSVQVYNLHRALGHVYPLLAQWHGVKVKLH 215
Q D AT+A KI S + ++ + ++N RA A W G + K
Sbjct: 210 QDDSKATHAPKISPEESWLSFD-EEARVLHNKVRA-------FAGWPGTRAKFQ 255
Score = 35.4 bits (82), Expect = 0.046
Identities = 17/47 (36%), Positives = 23/47 (48%), Gaps = 2/47 (4%)
Query: 344 GFVSFDRGSKLLRVRCVDGKSILCSQITVAGKKKMTAVDFKNGYLGK 390
V+F + S L V C G + ++ GKK M A DF NG G+
Sbjct: 288 DAVTFKKDS--LLVPCGGGTWLEVLEVQPPGKKVMKAKDFWNGLRGQ 332
>gnl|CDD|235902 PRK06988, PRK06988, putative formyltransferase; Provisional.
Length = 312
Score = 97.1 bits (242), Expect = 1e-22
Identities = 57/173 (32%), Positives = 87/173 (50%), Gaps = 29/173 (16%)
Query: 40 PDLIKDNYDIGMVVSFGHLIPSKIINAFPLGMINVHGSILPRWRGAAPIVHAILHGDHET 99
PD I Y + H+IP ++ P G N+HGS+LP++RG P+ A+L+G+ ET
Sbjct: 78 PDFIFSFY-------YRHMIPVDLLALAPRGAYNMHGSLLPKYRGRVPVNWAVLNGETET 130
Query: 100 GISIIRVRPKHFDRGEIVRQYRCSISPDDTAGELHNKLALVGGQLLLECVRDMPRCVL-N 158
G ++ + K D G IV Q I PDDTA ++ +K+ + Q L R +P +
Sbjct: 131 GATLHEMVAKP-DAGAIVDQTAVPILPDDTAAQVFDKVTVAAEQTLW---RVLPALLAGE 186
Query: 159 APAQPD---EGATYANK------IDWSYSVIDWNTMSSVQVYNLHRALGHVYP 202
AP P+ +G+ + + IDW + + QVYNL RA+ YP
Sbjct: 187 APHLPNDLAQGSYFGGRKPEDGRIDW--------SKPAAQVYNLIRAVAPPYP 231
>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 = 78.6 bits (194), Expect = 3e-17
Identities = 40/120 (33%), Positives = 62/120 (51%), Gaps = 6/120 (5%)
Query: 28 DEKLTLYRWPMDPDLIKDNYDIGMVVSFGHLIPSKIINAFPLGMINVHGSILPRWRGAAP 87
+ K L W D +V +F + IP I++ PLG N+H +LP +RG P
Sbjct: 58 NLKEQLAEWLRALAA-----DTVVVFTFPYRIPQHILDLPPLGFYNLHPGLLPAYRGPDP 112
Query: 88 IVHAILHGDHETGISIIRVRPKHFDRGEIVRQYRCSISPDDTAGELHNKLALVGGQLLLE 147
+ I + + ET I++ ++ + DRG IV + I PDDT G L ++LA++ LL E
Sbjct: 113 LFWQIRNQEQETAITVHKMTAE-IDRGPIVLEQFTPIHPDDTYGLLCSRLAMLAVGLLEE 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 = 73.5 bits (181), Expect = 2e-15
Identities = 37/109 (33%), Positives = 56/109 (51%), Gaps = 2/109 (1%)
Query: 42 LIKD-NYDIGMVVSFGHLIPSKIINAFPLGMINVHGSILPRWRGAAPIVHAILHGDHETG 100
IK+ N DI V + L+ +I+ LG+I H + LP+ RG API AIL G ET
Sbjct: 70 WIKEANPDIIFVFGWSQLLKPEILAIPRLGVIGFHPTKLPKNRGRAPIPWAILLGLKETA 129
Query: 101 ISIIRVRPKHFDRGEIVRQYRCSISPDDTAGELHNKLALVGGQLLLECV 149
+ + + D G+I+ Q I DDTA L++K+ Q + + +
Sbjct: 130 STFFWM-DEGADSGDILSQEPFPIDKDDTANSLYDKIMEAAKQQIDKFL 177
>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 = 70.9 bits (174), Expect = 3e-14
Identities = 45/117 (38%), Positives = 62/117 (52%), Gaps = 12/117 (10%)
Query: 59 IPSKIINAFPLGMINVHGSILPRWRGAAPIVHAILHGDHETGISIIRVRPKHFDRGEIVR 118
IP ++I+A G I H SILPR RGA+ I ++HGD + G +I D G I+
Sbjct: 90 IPMEVIDAPKHGSIIYHPSILPRHRGASAINWTLIHGDKKAGFTIFWA-DDGLDTGPILL 148
Query: 119 QYRCSISPDDTAGELHNK-LALVGGQLLLECVR-----DMPRCVLNAPAQPDEGATY 169
Q C + P+DT L+N+ L G + ++E VR PR QP+EGATY
Sbjct: 149 QKECDVLPNDTVDTLYNRFLYPEGIKAMVEAVRLIAEGKAPRIP-----QPEEGATY 200
>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 = 69.2 bits (170), Expect = 4e-14
Identities = 32/113 (28%), Positives = 58/113 (51%), Gaps = 10/113 (8%)
Query: 40 PDLIKDNYDIGMVVSFGHLIPSKIINAFPLGMINVHGSILPRWRGAAPIVHAILHGDHE- 98
PD++ V +I ++ PLG++N+HG ILP +RG A+ +GD +
Sbjct: 48 PDVV--------SVYGCGIIKDALLAIPPLGVLNLHGGILPDYRGVHTGFWALANGDPDN 99
Query: 99 TGISIIRVRPKHFDRGEIVRQYRCSISPDDTAGELHNKLALVGGQLLLECVRD 151
G+++ V D G+++ Q R ++ DT L+ +L G +L++E + D
Sbjct: 100 VGVTVHLVDAG-IDTGDVLAQARPPLAAGDTLLSLYLRLYRAGVELMVEAIAD 151
>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 = 64.3 bits (158), Expect = 3e-12
Identities = 36/160 (22%), Positives = 68/160 (42%), Gaps = 26/160 (16%)
Query: 11 VVSSKEGKHSPVIQFAQDE---------KLTLYRWPMDPDLIK--DNYDIGMVVSFG--H 57
V+S+ + ++ A+ K R D L++ Y + ++V G
Sbjct: 32 VISNNPD--AYGLERAKKAGIPTFVINRKDFPSREEFDEALLELLKEYKVDLIVLAGFMR 89
Query: 58 LIPSKIINAFPLGMINVHGSILPRWRGAAPIVHAILHGDHETGISIIRVRPKHF-----D 112
++ + + AFP +IN+H S+LP++ G A+ G TG ++ HF D
Sbjct: 90 ILSPEFLEAFPGRIINIHPSLLPKFYGLHAHEAALEAGVKVTGCTV------HFVDEEVD 143
Query: 113 RGEIVRQYRCSISPDDTAGELHNKLALVGGQLLLECVRDM 152
G I+ Q + P DT L ++ + +L E ++ +
Sbjct: 144 TGPIIAQAAVPVLPGDTPETLAERIHALEHRLYPEAIKLL 183
>gnl|CDD|223376 COG0299, PurN, Folate-dependent phosphoribosylglycinamide
formyltransferase PurN [Nucleotide transport and
metabolism].
Length = 200
Score = 60.3 bits (147), Expect = 1e-10
Identities = 28/108 (25%), Positives = 48/108 (44%), Gaps = 15/108 (13%)
Query: 38 MDPDLIK--DNYDIGMVVSFG--HLIPSKIINAFPLGMINVHGSILPRWRGAAPIVHAIL 93
D L++ D Y +VV G ++ + ++ F ++N+H S+LP + G A+
Sbjct: 67 FDRALVEALDEYGPDLVVLAGYMRILGPEFLSRFEGRILNIHPSLLPAFPGLHAHEQALE 126
Query: 94 HGDHETGISIIRVRPKHF-----DRGEIVRQYRCSISPDDTAGELHNK 136
G +G ++ HF D G I+ Q + P DTA L +
Sbjct: 127 AGVKVSGCTV------HFVTEGVDTGPIIAQAAVPVLPGDTAETLEAR 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 = 57.8 bits (140), Expect = 5e-10
Identities = 31/110 (28%), Positives = 49/110 (44%), Gaps = 1/110 (0%)
Query: 42 LIKDNYDIGMVVSFGHLIPSKIINAFPLGMINVHGSILPRWRGAAPIVHAILHGDHETGI 101
L DI + V + ++P I+ N+H + LP +RG HAIL+GD + G
Sbjct: 65 LENKGVDILISVQYHWILPGSILEKAKEIAFNLHNAPLPEYRGCNQFSHAILNGDDQFGT 124
Query: 102 SIIRVRPKHFDRGEIVRQYRCSISPDDTAGELHNKLALVGGQLLLECVRD 151
+I + + D G+I+ + R I D T L+ L E + D
Sbjct: 125 TIHWM-AEGIDSGDIIFEKRFPIPSDCTVISLYILAHYAAIALFGEHITD 173
>gnl|CDD|235544 PRK05647, purN, phosphoribosylglycinamide formyltransferase;
Reviewed.
Length = 200
Score = 53.6 bits (130), Expect = 2e-08
Identities = 25/97 (25%), Positives = 40/97 (41%), Gaps = 13/97 (13%)
Query: 45 DNYDIGMVVSFGH--LIPSKIINAFPLGMINVHGSILPRWRGAAPIVHAILHGDHETGIS 102
D Y +VV G ++ ++A+ +IN+H S+LP + G A+ G G +
Sbjct: 77 DAYQPDLVVLAGFMRILGPTFVSAYEGRIINIHPSLLPSFPGLHTHEQALEAGVKVHGCT 136
Query: 103 IIRVRPKHF-----DRGEIVRQYRCSISPDDTAGELH 134
+ HF D G I+ Q + DT L
Sbjct: 137 V------HFVDEGLDTGPIIAQAAVPVLAGDTEESLA 167
>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 = 52.8 bits (127), Expect = 4e-08
Identities = 42/115 (36%), Positives = 56/115 (48%), Gaps = 5/115 (4%)
Query: 59 IPSKIINAFPLGMINVHGSILPRWRGAAPIVHAILHGDHETGISIIRVRPKHFDRGEIVR 118
I +K LG I H S+LPR RG + I D TG ++ + D G I
Sbjct: 79 ISAKTRARARLGAIGYHPSLLPRHRGRDAVEWTIRMRDPITGGTVYHLDDG-VDGGPIAA 137
Query: 119 QYRCSISPDDTAGELHNK-LALVGGQLLLECVRDMPRCVLNAPAQP-DEG-ATYA 170
Q C + P DTA EL + LA +G +LL + + + R N PAQP DE AT+
Sbjct: 138 QDWCHVRPGDTAAELWRRALAPMGVKLLTQVIDALLRGG-NLPAQPQDERLATWE 191
>gnl|CDD|177965 PLN02331, PLN02331, phosphoribosylglycinamide formyltransferase.
Length = 207
Score = 46.2 bits (110), Expect = 8e-06
Identities = 29/97 (29%), Positives = 49/97 (50%), Gaps = 6/97 (6%)
Query: 58 LIPSKIINAFPLGMINVHGSILPRWRGAAPI---VHA--ILHGDHETGISIIRVRPKHFD 112
LIP +++ A+P ++N+H ++LP + G VH I G +G ++ V +H+D
Sbjct: 90 LIPVELVRAYPRSILNIHPALLPAFGGKGYYGIKVHKAVIASGARYSGPTVHFVD-EHYD 148
Query: 113 RGEIVRQYRCSISPDDTAGELHNKLALVGGQLLLECV 149
G I+ Q + DT EL ++ QL +E V
Sbjct: 149 TGRILAQRVVPVLATDTPEELAARVLHEEHQLYVEVV 185
>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 = 44.9 bits (107), Expect = 1e-05
Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 58 LIPSKIINAFPLGMINVHGSILPRWRGAAPIVHAILHGDHETGISIIRVRPKHFDRGEIV 117
++PS+++ G IN H LPR+ G A+L G+ G++ R+ D G+I+
Sbjct: 73 ILPSEVLALPRKGAINFHDGPLPRYAGLNATSWALLAGETRHGVTWHRIEEG-VDAGDIL 131
Query: 118 RQYRCSISPDDTA 130
Q I+PDDTA
Sbjct: 132 VQRPFDIAPDDTA 144
>gnl|CDD|236058 PRK07579, PRK07579, hypothetical protein; Provisional.
Length = 245
Score = 44.9 bits (106), Expect = 3e-05
Identities = 27/112 (24%), Positives = 52/112 (46%), Gaps = 4/112 (3%)
Query: 41 DLIKDNYDIGMVVSFGHLIPSKIINAFPLGMINVHGSILPRWRGAAPIVHAILHGDHETG 100
I + YD+ + P+K++N + IN+H P RG P V +I++ + G
Sbjct: 60 AEIVERYDLVLSFHCKQRFPAKLVNG--VRCINIHPGFNPYNRGWFPQVFSIIN-GLKIG 116
Query: 101 ISIIRVRPKHFDRGEIVRQYRCSISPDDTAGELHNKLALVGGQLLLECVRDM 152
+I + D G I+ Q I D++G ++ ++ + +L+LE +
Sbjct: 117 ATI-HEMDEQLDHGPIIAQREVEIESWDSSGSVYARVMDIERELVLEHFDAI 167
>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 = 43.5 bits (103), Expect = 5e-05
Identities = 26/106 (24%), Positives = 50/106 (47%), Gaps = 15/106 (14%)
Query: 38 MDPDLIK--DNYDIGMVVSFGHL--IPSKIINAFPLGMINVHGSILPRWRGAAPIVHAIL 93
D +I+ +++ +VV G + + ++ F ++N+H S+LP + G + A+
Sbjct: 67 FDQAIIEELRAHEVDLVVLAGFMRILGPTFLSRFAGRILNIHPSLLPAFPGLHAVEQALE 126
Query: 94 HGDHETGISIIRVRPKHF-----DRGEIVRQYRCSISPDDTAGELH 134
G E+G ++ H+ D G I+ Q + I P+DT L
Sbjct: 127 AGVKESGCTV------HYVDEEVDTGPIIAQAKVPILPEDTEETLE 166
>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 = 39.9 bits (94), Expect = 2e-04
Identities = 12/23 (52%), Positives = 16/23 (69%), Gaps = 1/23 (4%)
Query: 180 IDWNTMSSVQVYNLHRALGHVYP 202
IDW MS+ ++YNL RA+ YP
Sbjct: 5 IDWR-MSAREIYNLVRAVTKPYP 26
>gnl|CDD|217282 pfam02911, Formyl_trans_C, Formyl transferase, C-terminal domain.
Length = 100
Score = 36.5 bits (85), Expect = 0.003
Identities = 21/46 (45%), Positives = 26/46 (56%), Gaps = 4/46 (8%)
Query: 343 PG-FVSFDRGSKLLRVRCVDGKSILCSQITVAGKKKMTAVDFKNGY 387
PG VS D+G L V C DG ++L ++ GKK M A DF NG
Sbjct: 57 PGTIVSVDKGG--LLVACGDG-ALLILELQPEGKKAMDAADFLNGA 99
Score = 32.6 bits (75), Expect = 0.082
Identities = 11/37 (29%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 180 IDWNTMSSVQVYNLHRALGHVYP-LLAQWHGVKVKLH 215
IDW+ + +++ L RAL +P +G +VK+
Sbjct: 9 IDWS-QPAEEIHRLIRALS-PWPGAYTFLNGKRVKIL 43
>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 = 37.4 bits (87), Expect = 0.009
Identities = 25/99 (25%), Positives = 41/99 (41%), Gaps = 13/99 (13%)
Query: 45 DNYDIGMVV--SFGHLIPSKIINAFPLGMINVHGSILPRWRGAAPIVHAILHGDHETGIS 102
Y + +VV + ++ + +P +IN+H S LP + GA P A +E G+
Sbjct: 157 KQYQVDLVVLAKYMQILSPDFVKRYPNKIINIHHSFLPAFIGANPYQRA-----YERGVK 211
Query: 103 IIRVRPKHF-----DRGEIVRQYRCSISPDDTAGELHNK 136
II H+ D G I+ Q + D +L
Sbjct: 212 IIGA-TAHYVTEELDEGPIIEQDVVRVDHTDNVEDLIRA 249
>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 = 32.5 bits (75), Expect = 0.054
Identities = 12/41 (29%), Positives = 24/41 (58%), Gaps = 3/41 (7%)
Query: 180 IDWNTMSSVQVYNLHRALGHVYP-LLAQWHGVKVKLHNISL 219
IDW+ S+ +++NL RAL + +P +G ++K+ +
Sbjct: 5 IDWS-KSAEEIHNLIRAL-NPWPGAYTTLNGKRLKILKAEV 43
Score = 27.1 bits (61), Expect = 5.8
Identities = 11/38 (28%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 343 PGFVSFDRGSKLLRVRCVDGKSILCSQITVAGKKKMTA 380
++ D+ L V C DG ++ ++ GKK+M+A
Sbjct: 53 GTILAVDKKG--LLVACGDG-ALEILELQPEGKKRMSA 87
>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 = 33.3 bits (77), Expect = 0.15
Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 11/78 (14%)
Query: 64 INAFPLGMINVHGSILPRWRGAAPIVHAILHGDHETGISIIRVRPKHF-----DRGEIVR 118
+ +P +IN+H S LP ++GA P H E G+ +I H+ D G I+
Sbjct: 94 VERYPNRIINIHHSFLPAFKGAKP-----YHQAFERGVKLIGA-TAHYVTEELDEGPIIE 147
Query: 119 QYRCSISPDDTAGELHNK 136
Q +S D+ +L K
Sbjct: 148 QDVERVSHRDSVEDLVRK 165
>gnl|CDD|139334 PRK13010, purU, formyltetrahydrofolate deformylase; Reviewed.
Length = 289
Score = 30.9 bits (70), Expect = 1.0
Identities = 19/53 (35%), Positives = 25/53 (47%), Gaps = 11/53 (20%)
Query: 72 INVHGSILPRWRGAAPIVHAILHGDHETGISIIRVRPKHF-----DRGEIVRQ 119
IN+H S LP ++GA P H H G+ +I HF D G I+ Q
Sbjct: 195 INIHHSFLPGFKGARP-----YHQAHARGVKLIGA-TAHFVTDDLDEGPIIEQ 241
>gnl|CDD|187723 cd08821, FMT_core_like_1, 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 = 211
Score = 30.0 bits (68), Expect = 1.5
Identities = 22/65 (33%), Positives = 34/65 (52%), Gaps = 6/65 (9%)
Query: 55 FGH---LIPSKIINAFPLGMINVHGSILPRWRGAAPIVHAILHGDHETGISIIRVRPKHF 111
F H +IP +I F + H + LP RG +P+ + I+ G +ET IS +++ K
Sbjct: 50 FPHWSWIIPKEIFENFEC--VVFHMTDLPYGRGGSPLQNLIVRGHYETKISALKME-KGL 106
Query: 112 DRGEI 116
D G I
Sbjct: 107 DTGPI 111
>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 = 28.8 bits (65), Expect = 2.2
Identities = 16/70 (22%), Positives = 24/70 (34%), Gaps = 18/70 (25%)
Query: 51 MVVSFGHLIPSKIINAFPLGMINVHG--------------SILPRWRGAAPIVHAILHGD 96
+++ G L+P +I+A L + ILP W H I HG
Sbjct: 31 LILILGILLPLGLIDAEALSYDRIIAFAQSWIGKLFLLVLIILPLWHAM----HRIHHGL 86
Query: 97 HETGISIIRV 106
H+ I
Sbjct: 87 HDLKIHRGPA 96
>gnl|CDD|216345 pfam01176, eIF-1a, Translation initiation factor 1A / IF-1. This
family includes both the eukaryotic translation factor
eIF-1A and the bacterial translation initiation factor
IF-1.
Length = 65
Score = 27.1 bits (61), Expect = 3.1
Identities = 7/28 (25%), Positives = 11/28 (39%), Gaps = 3/28 (10%)
Query: 350 RGSKLLRVRCVDGKSILCSQITVAGKKK 377
G+ V DG L + GK++
Sbjct: 13 LGNGRFEVELEDGHERLAH---IPGKRR 37
>gnl|CDD|215560 PLN03076, PLN03076, ARF guanine nucleotide exchange factor (ARF-GEF);
Provisional.
Length = 1780
Score = 29.8 bits (67), Expect = 3.8
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 189 QVYNLHRA---LGHVYPLLAQWHGVKVKLHNISLDTKLRS 225
++YN++R + L H V H I+ DT LRS
Sbjct: 1581 EIYNMYRPRLSAKNTLVLFDALHTVASHAHKINSDTALRS 1620
>gnl|CDD|178422 PLN02828, PLN02828, formyltetrahydrofolate deformylase.
Length = 268
Score = 28.9 bits (65), Expect = 4.7
Identities = 21/94 (22%), Positives = 40/94 (42%), Gaps = 12/94 (12%)
Query: 41 DLIKDNYDIGMVVSFGHLIPSKIINAFPLGMINVHGSILPRWRGAAPIVHAILHGDHETG 100
+L+K D ++ + ++ + + +IN+H +LP ++G P A + G
Sbjct: 143 ELVKGT-DFLVLARYMQILSGNFLKGYGKDIINIHHGLLPSFKGGNPSKQA-----FDAG 196
Query: 101 ISIIRVRPKHF-----DRGEIVRQYRCSISPDDT 129
+ +I HF D G I+ Q +S D
Sbjct: 197 VKLIGA-TSHFVTEELDAGPIIEQMVERVSHRDN 229
>gnl|CDD|223859 COG0788, PurU, Formyltetrahydrofolate hydrolase [Nucleotide
transport and metabolism].
Length = 287
Score = 28.7 bits (65), Expect = 5.7
Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 11/53 (20%)
Query: 72 INVHGSILPRWRGAAPIVHAILHGDHETGISIIRVRPKHF-----DRGEIVRQ 119
IN+H S LP + GA P H +E G+ +I H+ D G I+ Q
Sbjct: 192 INIHHSFLPAFIGANP-----YHQAYERGVKLIGA-TAHYVTADLDEGPIIEQ 238
>gnl|CDD|237266 PRK13011, PRK13011, formyltetrahydrofolate deformylase; Reviewed.
Length = 286
Score = 28.4 bits (64), Expect = 6.4
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 11/53 (20%)
Query: 72 INVHGSILPRWRGAAPIVHAILHGDHETGISIIRVRPKHF-----DRGEIVRQ 119
IN+H S LP ++GA P H +E G+ +I H+ D G I+ Q
Sbjct: 191 INIHHSFLPGFKGAKP-----YHQAYERGVKLIGA-TAHYVTDDLDEGPIIEQ 237
>gnl|CDD|215397 PLN02744, PLN02744, dihydrolipoyllysine-residue acetyltransferase
component of pyruvate dehydrogenase complex.
Length = 539
Score = 28.7 bits (64), Expect = 7.3
Identities = 10/46 (21%), Positives = 16/46 (34%)
Query: 305 SGDTSSKPPSETKEPPERSKEPTDRLTEEPNPIVPELTPGFVSFDR 350
S + P PP +E ++ P P + + S DR
Sbjct: 203 SSSAAPAAPKAKPSPPPPKEEEVEKPASSPEPKASKPSAPPSSGDR 248
>gnl|CDD|133315 cd04115, Rab33B_Rab33A, Rab GTPase family 33 includes Rab33A and
Rab33B. Rab33B/Rab33A subfamily. Rab33B is ubiquitously
expressed in mouse tissues and cells, where it is
localized to the medial Golgi cisternae. It colocalizes
with alpha-mannose II. Together with the other cisternal
Rabs, Rab6A and Rab6A', it is believed to regulate the
Golgi response to stress and is likely a molecular
target in stress-activated signaling pathways. Rab33A
(previously known as S10) is expressed primarily in the
brain and immune system cells. In humans, it is located
on the X chromosome at Xq26 and its expression is
down-regulated in tuberculosis patients. Experimental
evidence suggests that Rab33A is a novel CD8+ T cell
factor that likely plays a role in tuberculosis disease
processes. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation of
the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 170
Score = 27.8 bits (62), Expect = 7.7
Identities = 11/32 (34%), Positives = 14/32 (43%)
Query: 286 TSHVPRDQHSQLTSALSFLSGDTSSKPPSETK 317
VP D + A S +TS+K PSE
Sbjct: 124 QIQVPTDLAQRFADAHSMPLFETSAKDPSEND 155
>gnl|CDD|115269 pfam06599, DUF1139, Protein of unknown function (DUF1139). This
family consists of several hypothetical Fijivirus
proteins of unknown function.
Length = 309
Score = 27.9 bits (62), Expect = 9.2
Identities = 14/45 (31%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 337 IVPELTPGFV--SFD-RGSKLLRVRCVDGKSILCSQITVAGKKKM 378
I PEL F+ +F + S+LL+V + S++ + + GKK +
Sbjct: 168 IAPELRICFMFRAFKLKPSQLLQVSRILSGSLMFPGLNLIGKKSL 212
>gnl|CDD|215490 PLN02903, PLN02903, aminoacyl-tRNA ligase.
Length = 652
Score = 28.2 bits (63), Expect = 9.8
Identities = 20/106 (18%), Positives = 33/106 (31%), Gaps = 18/106 (16%)
Query: 280 TLLRPNTSHVPRDQHSQLTSALSFLSGDTSSKPPSETKEPPERSKEPTDRLTEEPNPIVP 339
TL N H P+ + T+ LS S ++ + + +LT
Sbjct: 7 TLFSLNPYHAPKPLARKRTTLLSTSS---AASSAATVIPVVSAVDSMSSQLT-------- 55
Query: 340 ELTPGFVSFDRGSKLLRVRCVDGKSILCSQITVAGKKKMTAVDFKN 385
+ S L V V + LC V + M + F +
Sbjct: 56 -----WPSRSHLCGALSVNDVGSRVTLCGW--VDLHRDMGGLTFLD 94
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 0.134 0.402
Gapped
Lambda K H
0.267 0.0608 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,553,182
Number of extensions: 1962888
Number of successful extensions: 1639
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1607
Number of HSP's successfully gapped: 52
Length of query: 412
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 313
Effective length of database: 6,546,556
Effective search space: 2049072028
Effective search space used: 2049072028
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 (27.2 bits)