RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 015464
(406 letters)
>gnl|CDD|215181 PLN02317, PLN02317, arogenate dehydratase.
Length = 382
Score = 655 bits (1691), Expect = 0.0
Identities = 269/366 (73%), Positives = 302/366 (82%), Gaps = 11/366 (3%)
Query: 41 WECTCVGVLAQTHRAITPVEDDRPYTPDVQSSEANERSQDSQSSGFHKDLNLLPTLVYGQ 100
W+ +C + + + +P D P P V+SS +QS FH+DL+ LP
Sbjct: 27 WQSSCAIL---SSKVRSPEGDAPPSRPAVESSGGAGLVVATQSVSFHRDLSGLP------ 77
Query: 101 IAEPLSIMELSSSPDDGTKVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVEL 160
PLSI +LS SP G+K+RVAYQG+PGAYSEAAARKAYP CE VPC+QFEAAF+AVEL
Sbjct: 78 --RPLSITDLSPSPMHGSKLRVAYQGVPGAYSEAAARKAYPNCEAVPCEQFEAAFQAVEL 135
Query: 161 WLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELKRVFS 220
WL D+AVLPIENS+GGSIHRNYDLLLRHRLHIVGEVQL V+HCLL LPGV KEELKRV S
Sbjct: 136 WLADRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEELKRVIS 195
Query: 221 HPQALAQCEMTLSNLGIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDILAEK 280
HPQALAQCE TL+ LG+VR + DDTAGAA+MVA+ G RDT A+ASA+AAE+YGLDILAE
Sbjct: 196 HPQALAQCENTLTKLGVVREAVDDTAGAAKMVAANGLRDTAAIASARAAELYGLDILAEG 255
Query: 281 IQDDDDNVTRFLILAREPIIAGTDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIE 340
IQDD DNVTRFL+LAREPII TDRP+KTSIVF+LEEGPG+LFKALAVFALRDINLTKIE
Sbjct: 256 IQDDSDNVTRFLMLAREPIIPRTDRPFKTSIVFSLEEGPGVLFKALAVFALRDINLTKIE 315
Query: 341 SRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFATFLRVLGCY 400
SRPQRKRPLRVVDDSN G+AKYFDYLFY+DFEASMADPRAQ AL HLQEFATFLRVLG Y
Sbjct: 316 SRPQRKRPLRVVDDSNSGTAKYFDYLFYVDFEASMADPRAQNALAHLQEFATFLRVLGSY 375
Query: 401 PMDTTL 406
PMD T
Sbjct: 376 PMDMTP 381
>gnl|CDD|223155 COG0077, PheA, Prephenate dehydratase [Amino acid transport and
metabolism].
Length = 279
Score = 319 bits (819), Expect = e-108
Identities = 130/284 (45%), Positives = 171/284 (60%), Gaps = 17/284 (5%)
Query: 121 RVAYQGLPGAYSEAAARKAYPK-CETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIH 179
++AY G G +SE AARK + E +PC E FKAVE D V+PIENS+ GS++
Sbjct: 4 KIAYLGPEGTFSEQAARKLFGSGAELLPCSTIEDVFKAVENGEADYGVVPIENSIEGSVN 63
Query: 180 RNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSNL--GI 237
DLL L IVGE+ L ++HCLL GV EE+K V+SHPQALAQC L G+
Sbjct: 64 ETLDLLAETDLQIVGEIVLPIHHCLLVKGGVDLEEIKTVYSHPQALAQCRKFLRAHLPGV 123
Query: 238 VRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDILAEKIQDDDDNVTRFLILARE 297
TA AA++VA + A+AS AAE+YGLDILAE I+D+ +N TRFL+L+R
Sbjct: 124 EIEYTSSTAEAAKLVAEGPDETVAAIASELAAELYGLDILAENIEDEPNNRTRFLVLSRR 183
Query: 298 PIIAGTDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNK 357
+ +D P KTS++F++ PG L+KAL VFA R INLTKIESRP +
Sbjct: 184 KPPSVSDGPEKTSLIFSVPNKPGALYKALGVFAKRGINLTKIESRPLKTGL--------- 234
Query: 358 GSAKYFDYLFYIDFEASMADPRAQFALGHLQEFATFLRVLGCYP 401
+YLF+ID E + DP + AL L+E F+++LG YP
Sbjct: 235 -----GEYLFFIDIEGHIDDPLVKEALEELKEITEFVKILGSYP 273
>gnl|CDD|237014 PRK11899, PRK11899, prephenate dehydratase; Provisional.
Length = 279
Score = 274 bits (702), Expect = 2e-90
Identities = 126/287 (43%), Positives = 161/287 (56%), Gaps = 21/287 (7%)
Query: 121 RVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGG---S 177
R+A+QG PGA S A R A+P E +PC FE AF+AVE D A++PIENS+ G
Sbjct: 6 RIAFQGEPGANSHLACRDAFPDMEPLPCATFEDAFEAVESGEADLAMIPIENSLAGRVAD 65
Query: 178 IHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSNLGI 237
IH LL LHIVGE L + H L+ LPG EE+K V SHP AL QC + LG+
Sbjct: 66 IHH---LLPESGLHIVGEYFLPIRHQLMALPGATLEEIKTVHSHPHALGQCRKIIRALGL 122
Query: 238 VRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDILAEKIQDDDDNVTRFLILARE 297
+ A DTAGAA++VA G+ A+AS AAE+YGLDILAE I+D D N TRF++L+RE
Sbjct: 123 KPVVAADTAGAARLVAERGDPSMAALASRLAAELYGLDILAENIEDADHNTTRFVVLSRE 182
Query: 298 P-IIAGTDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSN 356
A D P T+ VF + P L+KAL FA +N+TK+ES +V
Sbjct: 183 ADWAARGDGPIVTTFVFRVRNIPAALYKALGGFATNGVNMTKLESY--------MVG--- 231
Query: 357 KGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFATFLRVLGCYPMD 403
+ FY D E D AL L+ F+ +R+LG YP
Sbjct: 232 ---GSFTATQFYADIEGHPEDRNVALALEELRFFSEEVRILGVYPAH 275
>gnl|CDD|237013 PRK11898, PRK11898, prephenate dehydratase; Provisional.
Length = 283
Score = 262 bits (671), Expect = 1e-85
Identities = 121/289 (41%), Positives = 156/289 (53%), Gaps = 23/289 (7%)
Query: 121 RVAYQGLPGAYSEAAARKAYPKC---ETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGS 177
++AY G G ++EAAA K +P E VP D AVE VD AV+PIENS+ GS
Sbjct: 3 KIAYLGPEGTFTEAAALKFFPADGEAELVPYDSIPDVLDAVEAGEVDYAVVPIENSIEGS 62
Query: 178 IHRNYDLLLRH-RLHIVGEVQLVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTL-SNL 235
++ D L L IV E+ L + LL PG + ++ V+SHPQALAQC L +L
Sbjct: 63 VNPTLDYLAHGSPLQIVAEIVLPIAQHLLVHPGHAAK-IRTVYSHPQALAQCRKWLAEHL 121
Query: 236 GIVRI-SADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDILAEKIQDDDDNVTRFLIL 294
+ A+ TA AAQ VA + A+AS AAE+YGL+ILAE IQD +N TRF +L
Sbjct: 122 PGAELEPANSTAAAAQYVAEHPDEPIAAIASELAAELYGLEILAEDIQDYPNNRTRFWLL 181
Query: 295 ARE-PIIAGTDRPYKTSIVFTL-EEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVV 352
R+ P KTS+V TL PG L+KAL+ FA R INLT+IESRP +
Sbjct: 182 GRKKPPPPLRTGGDKTSLVLTLPNNLPGALYKALSEFAWRGINLTRIESRPTKTGL---- 237
Query: 353 DDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFATFLRVLGCYP 401
G Y F+ID E + D AL L+ ++VLG YP
Sbjct: 238 -----G-----TYFFFIDVEGHIDDVLVAEALKELEALGEDVKVLGSYP 276
>gnl|CDD|216127 pfam00800, PDT, Prephenate dehydratase. This protein is involved
in Phenylalanine biosynthesis. This protein catalyzes
the decarboxylation of prephenate to phenylpyruvate.
Length = 181
Score = 247 bits (632), Expect = 3e-81
Identities = 90/181 (49%), Positives = 117/181 (64%), Gaps = 3/181 (1%)
Query: 122 VAYQGLPGAYSEAAARKAYPK-CETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHR 180
+AY G G +SE AA K + + E VPC E F+AVE D AV+PIENS+ GS++
Sbjct: 1 IAYLGPEGTFSEQAALKLFGQSVELVPCPSIEDVFEAVENGEADYAVVPIENSIEGSVNE 60
Query: 181 NYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSNL--GIV 238
DLLL L IVGEV L ++HCLL PG E++K V+SHPQALAQC L G
Sbjct: 61 TLDLLLESDLKIVGEVVLPIHHCLLARPGTDLEDIKTVYSHPQALAQCREFLEKHLPGAE 120
Query: 239 RISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDILAEKIQDDDDNVTRFLILAREP 298
R+ TA AA++VA+ G++ A+AS AAE+YGL ILAE I+D+ +N TRFL+L +EP
Sbjct: 121 RVPVSSTAAAAKIVAAEGDKGAAAIASELAAELYGLKILAENIEDNKNNTTRFLVLGKEP 180
Query: 299 I 299
Sbjct: 181 T 181
>gnl|CDD|182594 PRK10622, pheA, bifunctional chorismate mutase/prephenate
dehydratase; Provisional.
Length = 386
Score = 175 bits (446), Expect = 4e-51
Identities = 98/286 (34%), Positives = 143/286 (50%), Gaps = 19/286 (6%)
Query: 121 RVAYQGLPGAYSEAAARK-AYPKCETV---PCDQFEAAFKAVELWLVDKAVLPIENSVGG 176
R+A+ G G+YS AAR+ A E C +F F VE D AVLPIEN+ G
Sbjct: 105 RIAFLGPKGSYSHLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVLPIENTSSG 164
Query: 177 SIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSNLG 236
+I+ YDLL L IVGE+ L ++HC+L ++ V+SHPQ QC L+
Sbjct: 165 AINDVYDLLQHTSLSIVGEMTLPIDHCVLVSGTTDLSTIETVYSHPQPFQQCSQFLNRYP 224
Query: 237 IVRIS-ADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDILAEKIQDDDDNVTRFLILA 295
+I + TA A + VA A+ S +YGL +L + + N+TRF++LA
Sbjct: 225 HWKIEYTESTAAAMEKVAQANSPHVAALGSEAGGALYGLQVLERNLANQQQNITRFIVLA 284
Query: 296 REPIIAGTDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDS 355
R+ I P KT+++ + G L +AL V ++ +TK+ESRP P
Sbjct: 285 RKAINVSDQVPAKTTLLMATGQQAGALVEALLVLRNHNLIMTKLESRPIHGNP------- 337
Query: 356 NKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFATFLRVLGCYP 401
++ +FY+D +A++ Q AL L E L+VLGCYP
Sbjct: 338 -------WEEMFYLDVQANLRSAEMQKALKELGEITRSLKVLGCYP 376
>gnl|CDD|153177 cd04905, ACT_CM-PDT, C-terminal ACT domain of the bifunctional
chorismate mutase-prephenate dehydratase (CM-PDT) enzyme
and the prephenate dehydratase (PDT) enzyme. The
C-terminal ACT domain of the bifunctional chorismate
mutase-prephenate dehydratase (CM-PDT) enzyme and the
prephenate dehydratase (PDT) enzyme, found in plants,
fungi, bacteria, and archaea. The P-protein of E. coli
(CM-PDT, PheA) catalyzes the conversion of chorismate to
prephenate and then the decarboxylation and dehydration
to form phenylpyruvate. These are the first two steps in
the biosynthesis of L-Phe and L-Tyr via the shikimate
pathway in microorganisms and plants. The E. coli
P-protein (CM-PDT) has three domains with an N-terminal
domain with chorismate mutase activity, a middle domain
with prephenate dehydratase activity, and an ACT
regulatory C-terminal domain. The prephenate dehydratase
enzyme has a PDT and ACT domain. The ACT domain is
essential to bring about the negative allosteric
regulation by L-Phe binding. L-Phe binds with positive
cooperativity; with this binding, there is a shift in
the protein to less active tetrameric and higher
oligomeric forms from a more active dimeric form.
Members of this CD belong to the superfamily of ACT
regulatory domains.
Length = 80
Score = 119 bits (302), Expect = 1e-33
Identities = 43/94 (45%), Positives = 53/94 (56%), Gaps = 14/94 (14%)
Query: 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLF 367
KTSIVFTL PG L+ L VFA R INLTKIESRP + ++Y+F
Sbjct: 1 KTSIVFTLPNKPGALYDVLGVFAERGINLTKIESRPSKGGL--------------WEYVF 46
Query: 368 YIDFEASMADPRAQFALGHLQEFATFLRVLGCYP 401
+IDFE + DP AL L+ F++VLG YP
Sbjct: 47 FIDFEGHIEDPNVAEALEELKRLTEFVKVLGSYP 80
>gnl|CDD|153152 cd04880, ACT_AAAH-PDT-like, ACT domain of the nonheme
iron-dependent, aromatic amino acid hydroxylases (AAAH).
ACT domain of the nonheme iron-dependent, aromatic
amino acid hydroxylases (AAAH): Phenylalanine
hydroxylases (PAH), tyrosine hydroxylases (TH) and
tryptophan hydroxylases (TPH), both peripheral (TPH1)
and neuronal (TPH2) enzymes. This family of enzymes
shares a common catalytic mechanism, in which dioxygen
is used by an active site containing a single, reduced
iron atom to hydroxylate an unactivated aromatic
substrate, concomitant with a two-electron oxidation of
tetrahydropterin (BH4) cofactor to its quinonoid
dihydropterin form. Eukaryotic AAAHs have an N-terminal
ACT (regulatory) domain, a middle catalytic domain and a
C-terminal domain which is responsible for the
oligomeric state of the enzyme forming a domain-swapped
tetrameric coiled-coil. The PAH, TH, and TPH enzymes
contain highly conserved catalytic domains but distinct
N-terminal ACT domains and differ in their mechanisms of
regulation. One commonality is that all three eukaryotic
enzymes appear to be regulated, in part, by the
phosphorylation of serine residues N-terminal of the ACT
domain. Also included in this CD are the C-terminal ACT
domains of the bifunctional chorismate mutase-prephenate
dehydratase (CM-PDT) enzyme and the prephenate
dehydratase (PDT) enzyme found in plants, fungi,
bacteria, and archaea. The P-protein of Escherichia coli
(CM-PDT) catalyzes the conversion of chorismate to
prephenate and then the decarboxylation and dehydration
to form phenylpyruvate. These are the first two steps in
the biosynthesis of L-Phe and L-Tyr via the shikimate
pathway in microorganisms and plants. The E. coli
P-protein (CM-PDT) has three domains with an N-terminal
domain with chorismate mutase activity, a middle domain
with prephenate dehydratase activity, and an ACT
regulatory C-terminal domain. The prephenate dehydratase
enzyme has a PDT and ACT domain. The ACT domain is
essential to bring about the negative allosteric
regulation by L-Phe binding. L-Phe binds with positive
cooperativity; with this binding, there is a shift in
the protein to less active tetrameric and higher
oligomeric forms from a more active dimeric form.
Members of this CD belong to the superfamily of ACT
regulatory domains.
Length = 75
Score = 101 bits (253), Expect = 2e-26
Identities = 39/89 (43%), Positives = 51/89 (57%), Gaps = 14/89 (15%)
Query: 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYI 369
S+VF+L+ PG L KAL VFA R INLTKIESRP RK ++Y F++
Sbjct: 1 SLVFSLKNKPGALAKALKVFAERGINLTKIESRPSRKGL--------------WEYEFFV 46
Query: 370 DFEASMADPRAQFALGHLQEFATFLRVLG 398
DFE + DP + AL L+ ++VLG
Sbjct: 47 DFEGHIDDPDVKEALEELKRVTEDVKVLG 75
>gnl|CDD|153176 cd04904, ACT_AAAH, ACT domain of the nonheme iron-dependent,
aromatic amino acid hydroxylases (AAAH). ACT domain of
the nonheme iron-dependent, aromatic amino acid
hydroxylases (AAAH): Phenylalanine hydroxylases (PAH),
tyrosine hydroxylases (TH) and tryptophan hydroxylases
(TPH), both peripheral (TPH1) and neuronal (TPH2)
enzymes. This family of enzymes shares a common
catalytic mechanism, in which dioxygen is used by an
active site containing a single, reduced iron atom to
hydroxylate an unactivated aromatic substrate,
concomitant with a two-electron oxidation of
tetrahydropterin (BH4) cofactor to its quinonoid
dihydropterin form. PAH catalyzes the hydroxylation of
L-Phe to L-Tyr, the first step in the catabolic
degradation of L-Phe; TH catalyses the hydroxylation of
L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting
step in the biosynthesis of catecholamines; and TPH
catalyses the hydroxylation of L-Trp to
5-hydroxytryptophan, the rate limiting step in the
biosynthesis of 5-hydroxytryptamine (serotonin) and the
first reaction in the synthesis of melatonin. Eukaryotic
AAAHs have an N-terminal ACT (regulatory) domain, a
middle catalytic domain and a C-terminal domain which is
responsible for the oligomeric state of the enzyme
forming a domain-swapped tetrameric coiled-coil. The
PAH, TH, and TPH enzymes contain highly conserved
catalytic domains but distinct N-terminal ACT domains
(this CD) and differ in their mechanisms of regulation.
One commonality is that all three eukaryotic enzymes are
regulated in part by the phosphorylation of serine
residues N-terminal of the ACT domain. Members of this
CD belong to the superfamily of ACT regulatory domains.
Length = 74
Score = 54.1 bits (131), Expect = 1e-09
Identities = 19/39 (48%), Positives = 27/39 (69%)
Query: 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKR 347
TS++F+L+E G L +AL +F +NLT IESRP R+
Sbjct: 1 TSLIFSLKEEVGALARALKLFEEFGVNLTHIESRPSRRN 39
>gnl|CDD|153203 cd04931, ACT_PAH, ACT domain of the nonheme iron-dependent aromatic
amino acid hydroxylase, phenylalanine hydroxylases
(PAH). ACT domain of the nonheme iron-dependent
aromatic amino acid hydroxylase, phenylalanine
hydroxylases (PAH). PAH catalyzes the hydroxylation of
L-Phe to L-Tyr, the first step in the catabolic
degradation of L-Phe. In PAH, an autoregulatory
sequence, N-terminal of the ACT domain, extends across
the catalytic domain active site and regulates the
enzyme by intrasteric regulation. It appears that the
activation by L-Phe induces a conformational change that
converts the enzyme to a high-affinity and high-activity
state. Modulation of activity is achieved through
inhibition by BH4 and activation by phosphorylation of
serine residues of the autoregulatory region. The
molecular basis for the cooperative activation process
is not fully understood yet. Members of this CD belong
to the superfamily of ACT regulatory domains.
Length = 90
Score = 47.1 bits (112), Expect = 4e-07
Identities = 20/37 (54%), Positives = 26/37 (70%)
Query: 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRK 346
S++F+L+E G L K L +F +DINLT IESRP R
Sbjct: 16 SLIFSLKEEVGALAKVLRLFEEKDINLTHIESRPSRL 52
>gnl|CDD|130335 TIGR01268, Phe4hydrox_tetr, phenylalanine-4-hydroxylase, tetrameric
form. This model describes the larger, tetrameric form
of phenylalanine-4-hydroxylase, as found in metazoans.
The enzyme irreversibly converts phenylalanine to
tryosine and is known to be the rate-limiting step in
phenylalanine catabolism in some systems. It is closely
related to metazoan tyrosine 3-monooxygenase and
tryptophan 5-monoxygenase, and more distantly to
monomeric phenylalanine-4-hydroxylases of some
Gram-negative bacteria. The member of this family from
Drosophila has been described as having both
phenylalanine-4-hydroxylase and tryptophan
5-monoxygenase activity (PMID:1371286). However, a
Drosophila member of the tryptophan 5-monoxygenase clade
has subsequently been discovered.
Length = 436
Score = 49.1 bits (117), Expect = 3e-06
Identities = 26/82 (31%), Positives = 44/82 (53%), Gaps = 15/82 (18%)
Query: 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLF 367
KTS++F+L+E G L + L +F D+NLT IESRP + P +Y F
Sbjct: 16 KTSLIFSLKEEAGALAETLKLFQAHDVNLTHIESRPSKTHP--------------GEYEF 61
Query: 368 YIDFEASMADPRAQFALGHLQE 389
+++F +D + + + HL++
Sbjct: 62 FVEF-DEASDRKLEGVIEHLRQ 82
>gnl|CDD|153201 cd04929, ACT_TPH, ACT domain of the nonheme iron-dependent aromatic
amino acid hydroxylase, tryptophan hydroxylases (TPH),
both peripheral (TPH1) and neuronal (TPH2) enzymes. ACT
domain of the nonheme iron-dependent aromatic amino acid
hydroxylase, tryptophan hydroxylases (TPH), both
peripheral (TPH1) and neuronal (TPH2) enzymes. TPH
catalyses the hydroxylation of L-Trp to
5-hydroxytryptophan, the rate limiting step in the
biosynthesis of 5-hydroxytryptamine (serotonin) and the
first reaction in the synthesis of melatonin. Very
little is known about the role of the ACT domain in TPH,
which appears to be regulated by phosphorylation but not
by its substrate or cofactor. Members of this CD belong
to the superfamily of ACT regulatory domains.
Length = 74
Score = 42.0 bits (99), Expect = 2e-05
Identities = 17/39 (43%), Positives = 25/39 (64%)
Query: 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKR 347
TS++F+L+ G L KAL +F IN+ IESR ++R
Sbjct: 1 TSVIFSLKNEVGGLAKALKLFQELGINVVHIESRKSKRR 39
>gnl|CDD|153202 cd04930, ACT_TH, ACT domain of the nonheme iron-dependent aromatic
amino acid hydroxylase, tyrosine hydroxylases (TH). ACT
domain of the nonheme iron-dependent aromatic amino acid
hydroxylase, tyrosine hydroxylases (TH). TH catalyses
the hydroxylation of L-Tyr to
3,4-dihydroxyphenylalanine, the rate limiting step in
the biosynthesis of catecholamines (dopamine,
noradrenaline and adrenaline), functioning as hormones
and neurotransmitters. The enzyme is not regulated by
its amino acid substrate, but instead by phosphorylation
at several serine residues located N-terminal of the ACT
domain, and by feedback inhibition by catecholamines at
the active site. Members of this CD belong to the
superfamily of ACT regulatory domains.
Length = 115
Score = 40.5 bits (95), Expect = 2e-04
Identities = 16/41 (39%), Positives = 25/41 (60%)
Query: 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRK 346
P K +++F+L+EG L + L VF + + +ESRP RK
Sbjct: 39 PQKATLLFSLKEGFSSLSRILKVFETFEAKIHHLESRPSRK 79
>gnl|CDD|153139 cd02116, ACT, ACT domains are commonly involved in specifically
binding an amino acid or other small ligand leading to
regulation of the enzyme. Members of this CD belong to
the superfamily of ACT regulatory domains. Pairs of ACT
domains are commonly involved in specifically binding an
amino acid or other small ligand leading to regulation
of the enzyme. The ACT domain has been detected in a
number of diverse proteins; some of these proteins are
involved in amino acid and purine biosynthesis,
phenylalanine hydroxylation, regulation of bacterial
metabolism and transcription, and many remain to be
characterized. ACT domain-containing enzymes involved in
amino acid and purine synthesis are in many cases
allosteric enzymes with complex regulation enforced by
the binding of ligands. The ACT domain is commonly
involved in the binding of a small regulatory molecule,
such as the amino acids L-Ser and L-Phe in the case of
D-3-phosphoglycerate dehydrogenase and the bifunctional
chorismate mutase-prephenate dehydratase enzyme
(P-protein), respectively. Aspartokinases typically
consist of two C-terminal ACT domains in a tandem
repeat, but the second ACT domain is inserted within
the first, resulting in, what is normally the terminal
beta strand of ACT2, formed from a region N-terminal of
ACT1. ACT domain repeats have been shown to have
nonequivalent ligand-binding sites with complex
regulatory patterns such as those seen in the
bifunctional enzyme, aspartokinase-homoserine
dehydrogenase (ThrA). In other enzymes, such as
phenylalanine hydroxylases, the ACT domain appears to
function as a flexible small module providing allosteric
regulation via transmission of conformational changes,
these conformational changes are not necessarily
initiated by regulatory ligand binding at the ACT domain
itself. ACT domains are present either singularly, N- or
C-terminal, or in pairs present C-terminal or between
two catalytic domains. Unique to cyanobacteria are four
ACT domains C-terminal to an aspartokinase domain. A few
proteins are composed almost entirely of ACT domain
repeats as seen in the four ACT domain protein, the ACR
protein, found in higher plants; and the two ACT domain
protein, the glycine cleavage system transcriptional
repressor (GcvR) protein, found in some bacteria. Also
seen are single ACT domain proteins similar to the
Streptococcus pneumoniae ACT domain protein
(uncharacterized pdb structure 1ZPV) found in both
bacteria and archaea. Purportedly, the ACT domain is an
evolutionarily mobile ligand binding regulatory module
that has been fused to different enzymes at various
times.
Length = 60
Score = 37.3 bits (87), Expect = 6e-04
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRK 346
+ + + PG+L K L+V A IN+T IE R
Sbjct: 1 LTVSGPDRPGLLAKVLSVLAEAGINITSIEQRTSGD 36
>gnl|CDD|190133 pfam01842, ACT, ACT domain. This family of domains generally have
a regulatory role. ACT domains are linked to a wide
range of metabolic enzymes that are regulated by amino
acid concentration. Pairs of ACT domains bind
specifically to a particular amino acid leading to
regulation of the linked enzyme. The ACT domain is found
in: D-3-phosphoglycerate dehydrogenase EC:1.1.1.95,
which is inhibited by serine. Aspartokinase EC:2.7.2.4,
which is regulated by lysine. Acetolactate synthase
small regulatory subunit, which is inhibited by valine.
Phenylalanine-4-hydroxylase EC:1.14.16.1, which is
regulated by phenylalanine. Prephenate dehydrogenase
EC:4.2.1.51. formyltetrahydrofolate deformylase
EC:3.5.1.10, which is activated by methionine and
inhibited by glycine. GTP pyrophosphokinase EC:2.7.6.5.
Length = 66
Score = 34.6 bits (80), Expect = 0.007
Identities = 10/44 (22%), Positives = 17/44 (38%)
Query: 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVV 352
T + + + PG+L + A R IN+ I + V
Sbjct: 1 TVLEVGVPDRPGLLAEVFGALADRGINIESISQSTSGDKAGIVF 44
>gnl|CDD|130337 TIGR01270, Trp_5_monoox, tryptophan 5-monooxygenase, tetrameric.
This model describes tryptophan 5-monooxygenase, a
member of the family of tetrameric, biopterin-dependent
aromatic amino acid hydroxylases found in metazoans. It
is closely related to tetrameric
phenylalanine-4-hydroxylase and tyrosine
3-monooxygenase, and more distantly related to the
monomeric phenylalanine-4-hydroxylase found in some
Gram-negative bacteria [Energy metabolism, Amino acids
and amines].
Length = 464
Score = 36.0 bits (83), Expect = 0.035
Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 11/61 (18%)
Query: 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYI 369
SI+F+L G L KA+A+F R IN+ +ESR S G++K D L +
Sbjct: 33 SIIFSLSNVVGDLSKAIAIFQDRHINILHLESRD-----------SKDGTSKTMDVLVDV 81
Query: 370 D 370
+
Sbjct: 82 E 82
>gnl|CDD|220867 pfam10744, Med1, Mediator of RNA polymerase II transcription
subunit 1. Mediator complexes are basic necessities for
linking transcriptional regulators to RNA polymerase II.
This domain, Med1, is conserved from plants to fungi to
humans and forms part of the Med9 submodule of the
Srb/Med complex. it is one of three subunits essential
for viability of the whole organism via its role in
environmentally-directed cell-fate decisions. Med1 is
part of the tail region of the Mediator complex.
Length = 384
Score = 31.7 bits (72), Expect = 0.73
Identities = 14/62 (22%), Positives = 19/62 (30%), Gaps = 11/62 (17%)
Query: 67 PDVQSSEANERSQDSQSSGFHKDLNLLPTLVYGQIAEPLSIMELSSSPDDGTKVRVAYQG 126
VQS E + FHK+L L + +LS D A +
Sbjct: 93 DPVQSPELLSLLRAKDLDEFHKNLKGL-----------ALLDKLSGDNSDKLNCFEALRS 141
Query: 127 LP 128
L
Sbjct: 142 LE 143
>gnl|CDD|219644 pfam07922, Glyco_transf_52, Glycosyltransferase family 52. This
family features glycosyltransferases belonging to
glycosyltransferase family 52, which have alpha-2,3-
sialyltransferase (EC:4.2.99.4) and
alpha-glucosyltransferase (EC 2.4.1.-) activity. For
example, beta-galactoside alpha-2,3- sialyltransferase
expressed by Neisseria meningitidis is a member of this
family and is involved in a step of lipooligosaccharide
biosynthesis requiring sialic acid transfer; these
lipooligosaccharides are thought to be important in the
process of pathogenesis. This family includes several
bacterial lipooligosaccharide sialyltransferases similar
to the Haemophilus ducreyi LST protein. Haemophilus
ducreyi is the cause of the sexually transmitted disease
chancroid and produces a lipooligosaccharide (LOS)
containing a terminal sialyl N-acetyllactosamine
trisaccharide.
Length = 273
Score = 30.8 bits (70), Expect = 1.3
Identities = 20/74 (27%), Positives = 29/74 (39%), Gaps = 6/74 (8%)
Query: 322 LFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQ 381
FK L R I + + +SR + ++ KYFD +F A+ Q
Sbjct: 20 YFKKLKKKCERSIIIKESKSRNKLFYFKVILKIKRLLKRKYFDTVFL----ANDHSLSIQ 75
Query: 382 FALGHL--QEFATF 393
F L + EF TF
Sbjct: 76 FILSAISFNEFYTF 89
>gnl|CDD|152886 pfam12452, DUF3685, Protein of unknown function (DUF3685). This
domain family is found in bacteria and eukaryotes, and
is approximately 190 amino acids in length. There are
two completely conserved residues (L and D) that may be
functionally important.
Length = 193
Score = 30.2 bits (69), Expect = 1.3
Identities = 11/46 (23%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 196 VQLVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSNLGIVRIS 241
V+ + ++ L G P ++ L P+A+ + E+ L NL +++++
Sbjct: 8 VEELFSYLLFGEPLLIDGVLYPA-GSPEAILRLEILLENL-LIQVA 51
>gnl|CDD|153149 cd04877, ACT_TyrR, N-terminal ACT domain of the TyrR protein.
ACT_TyrR: N-terminal ACT domain of the TyrR protein. The
TyrR protein of Escherichia coli controls the expression
of a group of transcription units (TyrR regulon) whose
gene products are involved in the biosynthesis or
transport of the aromatic amino acids. Binding to
specific DNA sequences known as TyrR boxes, the TyrR
protein can either activate or repress transcription at
different sigma70 promoters. Its regulatory activity
occurs in response to intracellular levels of tyrosine,
phenylalanine and tryptophan. The TyrR protein consists
of an N-terminal region important for transcription
activation with an ATP-independent aromatic amino acid
binding site (contained within the ACT domain) and is
involved in dimerization; a central region with an ATP
binding site, an ATP-dependent aromatic amino acid
binding site and is involved in hexamerization; and a
helix turn helix DNA binding C-terminal region. In
solution, in the absence of cofactors or in the presence
of phenylalanine alone, the TyrR protein exists as a
dimer. However, in the presence of ATP and tyrosine the
TyrR protein self-aggregates to form a hexamer. Members
of this CD belong to the superfamily of ACT regulatory
domains.
Length = 74
Score = 27.2 bits (61), Expect = 3.3
Identities = 7/27 (25%), Positives = 14/27 (51%)
Query: 320 GMLFKALAVFALRDINLTKIESRPQRK 346
G+ + L + +I+L IE P+ +
Sbjct: 12 GITQEVLDLLVEHNIDLRGIEIDPKGR 38
>gnl|CDD|225982 COG3451, VirB4, Type IV secretory pathway, VirB4 components
[Intracellular trafficking and secretion].
Length = 796
Score = 29.7 bits (67), Expect = 3.8
Identities = 8/82 (9%), Positives = 21/82 (25%), Gaps = 5/82 (6%)
Query: 274 LDILAEKIQDDDDNVTRFLILAREPIIAGTDRPYKTSIVFTLEEGPGMLFKA-LAVFAL- 331
+ ++ + L+ T R + G + +++
Sbjct: 195 VLEFLAELINGGYLQPVPLVGGLLDDALETSRVVFGKDGIEIRTPKGEKYALLISIKEYP 254
Query: 332 ---RDINLTKIESRPQRKRPLR 350
R I L + + P +
Sbjct: 255 WSTRFITLDALLALPFEFIITQ 276
>gnl|CDD|223394 COG0317, SpoT, Guanosine polyphosphate
pyrophosphohydrolases/synthetases [Signal transduction
mechanisms / Transcription].
Length = 701
Score = 28.8 bits (65), Expect = 5.7
Identities = 9/49 (18%), Positives = 17/49 (34%)
Query: 301 AGTDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPL 349
+ Y I + G+L V A IN+ + +R + +
Sbjct: 620 PEYGQVYPVDIEIRAYDRSGLLRDVSQVLANEKINVLGVNTRSDKDQFA 668
>gnl|CDD|214497 smart00062, PBPb, Bacterial periplasmic substrate-binding proteins.
bacterial proteins, eukaryotic ones are in PBPe.
Length = 219
Score = 28.4 bits (64), Expect = 5.8
Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 7/62 (11%)
Query: 112 SSPDDGTKVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVE-----LWLVDKA 166
S +D +VA G +E +K YP+ + V D A A++ + D
Sbjct: 99 KSLEDLKGKKVAVV--AGTTAEELLKKLYPEAKIVSYDSNAEALAALKAGRADAAVADAP 156
Query: 167 VL 168
+L
Sbjct: 157 LL 158
>gnl|CDD|238078 cd00134, PBPb, Bacterial periplasmic transport systems use
membrane-bound complexes and substrate-bound,
membrane-associated, periplasmic binding proteins (PBPs)
to transport a wide variety of substrates, such as,
amino acids, peptides, sugars, vitamins and inorganic
ions. PBPs have two cell-membrane translocation
functions: bind substrate, and interact with the
membrane bound complex. A diverse group of periplasmic
transport receptors for lysine/arginine/ornithine (LAO),
glutamine, histidine, sulfate, phosphate, molybdate, and
methanol are included in the PBPb CD.
Length = 218
Score = 28.1 bits (63), Expect = 6.2
Identities = 18/65 (27%), Positives = 27/65 (41%), Gaps = 7/65 (10%)
Query: 109 ELSSSPDDGTKVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVE-----LWLV 163
S D +VA Q G+ +E +KA P+ + V D A A+E +V
Sbjct: 95 SPIKSVKDLKGKKVAVQ--KGSTAEKYLKKALPEAKVVSYDDNAEALAALENGRADAVIV 152
Query: 164 DKAVL 168
D+ L
Sbjct: 153 DEIAL 157
>gnl|CDD|236879 PRK11195, PRK11195, lysophospholipid transporter LplT; Provisional.
Length = 393
Score = 28.3 bits (64), Expect = 8.2
Identities = 11/64 (17%), Positives = 17/64 (26%), Gaps = 12/64 (18%)
Query: 321 MLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRA 380
L LA I Q P+ ++ D F+ D
Sbjct: 160 ALIYLLAALFNLFIPRLGARRPGQSWNPIALLRD------------FFHACRVLWRDKLG 207
Query: 381 QFAL 384
+F+L
Sbjct: 208 RFSL 211
>gnl|CDD|236115 PRK07854, PRK07854, enoyl-CoA hydratase; Provisional.
Length = 243
Score = 27.7 bits (62), Expect = 9.8
Identities = 18/44 (40%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 235 LGIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDILA 278
LG +++A+ A A M IG A A AAEI GL LA
Sbjct: 152 LGAEKLTAE-QALATGMANRIGTLAD---AQAWAAEIAGLAPLA 191
>gnl|CDD|150144 pfam09371, Tex_N, Tex-like protein N-terminal domain. This
presumed domain is found at the N-terminus of Bordetella
pertussis tex. This protein defines a novel family of
prokaryotic transcriptional accessory factors.
Length = 193
Score = 27.4 bits (62), Expect = 10.0
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 263 VASAQAAEIYGLDILAEKIQDDDDNVTR 290
VA + A DILAE+I +D + +
Sbjct: 143 VADVEEALEGARDILAERISEDAELRKK 170
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
0.320 0.137 0.407
Gapped
Lambda K H
0.267 0.0720 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,835,297
Number of extensions: 2054565
Number of successful extensions: 1551
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1530
Number of HSP's successfully gapped: 34
Length of query: 406
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 307
Effective length of database: 6,546,556
Effective search space: 2009792692
Effective search space used: 2009792692
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: 60 (26.9 bits)