RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 025823
(247 letters)
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase.
Length = 260
Score = 209 bits (533), Expect = 2e-67
Identities = 75/212 (35%), Positives = 110/212 (51%), Gaps = 9/212 (4%)
Query: 1 MDGSHTRRGQP-CWFRVPKVGMIAANDGVLLRNHISRILKNHFRDKPYYVDLLDLFNEVE 59
MD S RRG+P C + + G I A D +L R L H R +P Y+ + +L N V
Sbjct: 56 MDNSDLRRGKPTCHKKFGEAGAILAGDALLSRAFQLLALLGHVRPEPKYILISELANAVG 115
Query: 60 FQTASGQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPVACALLMAGENLDKH 119
Q GQ++DL T + +L + RIV YKTA FY V ++AG + +
Sbjct: 116 AQGEVGQLMDLETEGK------DITLEEYLRIVSYKTAAL-FYASVQLGAIVAGADEEDE 168
Query: 120 VEVKDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWLVVKALELCNEEQKK 178
++ D +G+ FQ+QDD LD G E +GK VGTD+++ K + V+ ALE EEQ+K
Sbjct: 169 KDLYDFGRDLGLAFQIQDDILDLTGDTEELGKPVGTDLQEGKSTLPVLLALEGAREEQRK 228
Query: 179 LVHENYGKVDPACVAKVKELYKTLDLEGAFVE 210
L+ E Y + A+ L K L+ ++E
Sbjct: 229 LLREAYEQKLSEAAAQGVALTKALEALAEYIE 260
>gnl|CDD|173833 cd00685, Trans_IPPS_HT, Trans-Isoprenyl Diphosphate Synthases,
head-to-tail. These trans-Isoprenyl Diphosphate
Synthases (Trans_IPPS) catalyze head-to-tail (HT) (1'-4)
condensation reactions. This CD includes all-trans
(E)-isoprenyl diphosphate synthases which synthesize
various chain length (C10, C15, C20, C25, C30, C35, C40,
C45, and C50) linear isoprenyl diphosphates from
precursors, isopentenyl diphosphate (IPP) and
dimethylallyl diphosphate (DMAPP). They catalyze the
successive 1'-4 condensation of the 5-carbon IPP to
allylic substrates geranyl-, farnesyl-, or
geranylgeranyl-diphosphate. Isoprenoid chain elongation
reactions proceed via electrophilic alkylations in which
a new carbon-carbon single bond is generated through
interaction between a highly reactive electron-deficient
allylic carbocation and an electron-rich carbon-carbon
double bond. The catalytic site consists of a large
central cavity formed by mostly antiparallel alpha
helices with two aspartate-rich regions (DDXX(XX)D)
located on opposite walls. These residues mediate
binding of prenyl phosphates via bridging Mg2+ ions,
inducing proposed conformational changes that close the
active site to solvent, protecting and stabilizing
reactive carbocation intermediates. Farnesyl diphosphate
synthases produce the precursors of steroids,
cholesterol, sesquiterpenes, farnsylated proteins, heme,
and vitamin K12; and geranylgeranyl diphosphate and
longer chain synthases produce the precursors of
carotenoids, retinoids, diterpenes, geranylgeranylated
chlorophylls, ubiquinone, and archaeal ether linked
lipids. Isoprenyl diphosphate synthases are widely
distributed among archaea, bacteria, and eukareya.
Length = 259
Score = 173 bits (440), Expect = 1e-53
Identities = 68/246 (27%), Positives = 106/246 (43%), Gaps = 49/246 (19%)
Query: 1 MDGSHTRRGQPCWFRVPKVGMIAANDGVLLRNHISRILKNHFRDKPYYVDLLDLFNEVEF 60
MD S RRG+P +V A G L +L PYY L+LF+E
Sbjct: 62 MDNSDLRRGKPTVHKVFGNAT-AILAGDYLLARAFELLARLGN--PYYPRALELFSEAIL 118
Query: 61 QTASGQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPVACALLMAGENLDKHV 120
+ GQ++DL++ + + +Y RI++ KTA P+ ALL + ++
Sbjct: 119 ELVEGQLLDLLSEYDTDVTEEEY-----LRIIRLKTAALFAAAPLLGALLAGA-DEEEAE 172
Query: 121 EVKDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWLVVKALELCNEEQKKL 179
+K +G+ FQ+QDD LD FG PE +GK VG+D+ + KC+ V+ AL
Sbjct: 173 ALKRFGRNLGLAFQIQDDILDLFGDPETLGKPVGSDLREGKCTLPVLLALR--------- 223
Query: 180 VHENYGKVDPACVAKVKELYKTLDLEGAFVEYEKESYEKLTKSIEAHPTKEVQAVLKSFL 239
EL + EYE+++ E L +A P + L++
Sbjct: 224 -----------------ELAR---------EYEEKALEAL----KALPESPAREALRALA 253
Query: 240 AKIYKR 245
I +R
Sbjct: 254 DFILER 259
>gnl|CDD|173836 cd00867, Trans_IPPS, Trans-Isoprenyl Diphosphate Synthases.
Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of
class 1 isoprenoid biosynthesis enzymes which either
synthesis geranyl/farnesyl diphosphates (GPP/FPP) or
longer chained products from isoprene precursors,
isopentenyl diphosphate (IPP) and dimethylallyl
diphosphate (DMAPP), or use geranyl (C10)-, farnesyl
(C15)-, or geranylgeranyl (C20)-diphosphate as
substrate. These enzymes produce a myriad of precursors
for such end products as steroids, cholesterol,
sesquiterpenes, heme, carotenoids, retinoids,
diterpenes, ubiquinone, and archaeal ether linked
lipids; and are widely distributed among archaea,
bacteria, and eukareya. The enzymes in this family share
the same 'isoprenoid synthase fold' and include the
head-to-tail (HT) IPPS which catalyze the successive
1'-4 condensation of the 5-carbon IPP to the growing
isoprene chain to form linear, all-trans, C10-, C15-,
C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid
diphosphates. The head-to-head (HH) IPPS catalyze the
successive 1'-1 condensation of 2 farnesyl or 2
geranylgeranyl isoprenoid diphosphates. Isoprenoid chain
elongation reactions proceed via electrophilic
alkylations in which a new carbon-carbon single bond is
generated through interaction between a highly reactive
electron-deficient allylic carbocation and an
electron-rich carbon-carbon double bond. The catalytic
site consists of a large central cavity formed by mostly
antiparallel alpha helices with two aspartate-rich
regions located on opposite walls. These residues
mediate binding of prenyl phosphates via bridging Mg2+
ions, inducing proposed conformational changes that
close the active site to solvent, stabilizing reactive
carbocation intermediates. Mechanistically and
structurally distinct, cis-IPPS are not included in this
CD.
Length = 236
Score = 137 bits (347), Expect = 7e-40
Identities = 50/172 (29%), Positives = 76/172 (44%), Gaps = 13/172 (7%)
Query: 1 MDGSHTRRGQPCWFRVPKVGMIAANDGVLLRNHISRILKNHFRDKPYYVDLLDLFNEVEF 60
+D S RRG+P +A G L ++L Y L+LF E
Sbjct: 41 VDDSDLRRGKPTAHLRRFGNALAILAGDYLLARAFQLLARLG-----YPRALELFAEALR 95
Query: 61 QTASGQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPVACALLMAGENLDKHV 120
+ GQ +DL + + L +Y +YKTA L + A L + D+
Sbjct: 96 ELLEGQALDLEFERDTYETLDEY-----LEYCRYKTAGLVGLLCLLGAGLSGAD--DEQA 148
Query: 121 E-VKDILVQMGIYFQVQDDFLDCFGSPEVIGKVGTDIEDYKCSWLVVKALEL 171
E +KD +G+ FQ+ DD LD FG E +GKVG+D+ + + + V+ A E
Sbjct: 149 EALKDYGRALGLAFQLTDDLLDVFGDAEELGKVGSDLREGRITLPVILARER 200
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 120 bits (304), Expect = 1e-32
Identities = 68/250 (27%), Positives = 103/250 (41%), Gaps = 19/250 (7%)
Query: 1 MDGSHTRRGQPCWFRVPKV-GM-IAANDGVLLRNHISRILKNHFRDKPYYVDLLDLFNEV 58
MD RRG+P V G A G L +L ++ + E
Sbjct: 89 MDDDDLRRGKPT---VHAKFGEATAILAGDALLAAAFELLSKLGS---EALEAIKALAEA 142
Query: 59 EFQTASGQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPVACALLMAGENLDK 118
GQ +DL E +L + R+++ KTA V A+L AG + +
Sbjct: 143 INGLCGGQALDL----AFENK--PVTLEEYLRVIELKTAALFAAAAVLGAIL-AGADEEL 195
Query: 119 HVEVKDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWLVVKALELCNEEQK 177
++D +G+ FQ+QDD LD G E +GK VG+D+++ K + V+ ALE NE+QK
Sbjct: 196 LEALEDYGRNLGLAFQIQDDILDITGDEEELGKPVGSDLKEGKPTLPVLLALEKANEDQK 255
Query: 178 KLVHENYGKVDPACVAKVKELYKTLDLEGAFVEYEKESYEKLTKSIEAHPTKEVQAVLKS 237
L G + V + EL + K EK +++E P E + L
Sbjct: 256 LLRILLEGGGE---VEEALELLRKSGAIEYAKNLAKTYVEKAKEALEKLPDSEAKEALLE 312
Query: 238 FLAKIYKRQK 247
I KR+
Sbjct: 313 LADFIIKRKY 322
>gnl|CDD|173830 cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynthesis enzymes,
Class 1. Superfamily of trans-isoprenyl diphosphate
synthases (IPPS) and class I terpene cyclases which
either synthesis geranyl/farnesyl diphosphates (GPP/FPP)
or longer chained products from isoprene precursors,
isopentenyl diphosphate (IPP) and dimethylallyl
diphosphate (DMAPP), or use geranyl (C10)-, farnesyl
(C15)-, or geranylgeranyl (C20)-diphosphate as
substrate. These enzymes produce a myriad of precursors
for such end products as steroids, cholesterol,
sesquiterpenes, heme, carotenoids, retinoids, and
diterpenes; and are widely distributed among archaea,
bacteria, and eukaryota.The enzymes in this superfamily
share the same 'isoprenoid synthase fold' and include
several subgroups. The head-to-tail (HT) IPPS catalyze
the successive 1'-4 condensation of the 5-carbon IPP to
the growing isoprene chain to form linear, all-trans,
C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or
C50-isoprenoid diphosphates. Cyclic monoterpenes,
diterpenes, and sesquiterpenes, are formed from their
respective linear isoprenoid diphosphates by class I
terpene cyclases. The head-to-head (HH) IPPS catalyze
the successive 1'-1 condensation of 2 farnesyl or 2
geranylgeranyl isoprenoid diphosphates. Cyclization of
these 30- and 40-carbon linear forms are catalyzed by
class II cyclases. Both the isoprenoid chain elongation
reactions and the class I terpene cyclization reactions
proceed via electrophilic alkylations in which a new
carbon-carbon single bond is generated through
interaction between a highly reactive electron-deficient
allylic carbocation and an electron-rich carbon-carbon
double bond. The catalytic site consists of a large
central cavity formed by mostly antiparallel alpha
helices with two aspartate-rich regions located on
opposite walls. These residues mediate binding of prenyl
phosphates via bridging Mg2+ ions, inducing proposed
conformational changes that close the active site to
solvent, stabilizing reactive carbocation intermediates.
Generally, the enzymes in this family exhibit an
all-trans reaction pathway, an exception, is the
cis-trans terpene cyclase, trichodiene synthase.
Mechanistically and structurally distinct, class II
terpene cyclases and cis-IPPS are not included in this
CD.
Length = 243
Score = 94.9 bits (236), Expect = 1e-23
Identities = 54/246 (21%), Positives = 91/246 (36%), Gaps = 37/246 (15%)
Query: 1 MDGSHTRRGQPCWFRVPKV--GMIAANDGVLLRNHISRILKNHFRDKPYYVDLLDLFNEV 58
+D S TRRG P + A G LL L + L++ E
Sbjct: 33 VDDSGTRRGLPTAHLAVAIDGLPEAILAGDLLLADAFEELAREGS-----PEALEILAEA 87
Query: 59 EFQTASGQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPVACALLMAGENLDK 118
GQ++DL E L +Y +YKTA L + A L GE +
Sbjct: 88 LLDLLEGQLLDLKWRREYVPTLEEY-----LEYCRYKTAGLVGALCLLGAGLSGGE-AEL 141
Query: 119 HVEVKDILVQMGIYFQVQDDFLDCFGSPEVIGKVGTDIEDYKCSWLVVKALELCNEEQKK 178
++ + +G+ FQ+ +D LD G E + KC+ V+ ALE +
Sbjct: 142 LEALRKLGRALGLAFQLTNDLLDYEGDAE--------RGEGKCTLPVLYALEYGVPAEDL 193
Query: 179 LVHENYGKVDPACVAKVKELYKTLDLEGAFVEYEKESYEKLTKSIEAHPTKEVQAVLKSF 238
L+ E G ++ + + +E+ ++L + I + P +V L +
Sbjct: 194 LLVEKSGSLE--------------EALEELAKLAEEALKELNELILSLP--DVPRALLAL 237
Query: 239 LAKIYK 244
+Y+
Sbjct: 238 ALNLYR 243
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional.
Length = 299
Score = 39.8 bits (93), Expect = 6e-04
Identities = 54/203 (26%), Positives = 80/203 (39%), Gaps = 41/203 (20%)
Query: 1 MDGSHTRRGQP-CWFRVPKVGMIAANDGVLLRNHISRILKNHFRDKPYYVDLLDLFNEVE 59
MD RRG P C + + I A D L+ IL + P D + E
Sbjct: 89 MDDDDLRRGLPTCHVKFGEANAILAGDA--LQTLAFSILSD--APMPEVSDRDRISMISE 144
Query: 60 FQTASG-------QMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPVACALLMA 112
+ASG Q +DL E + + L RI ++KT V L A
Sbjct: 145 LASASGIAGMCGGQALDL------EAEGKQVPLDALERIHRHKTGAL-IRAAVRLGALSA 197
Query: 113 GEN-------LDKHVEVKDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWL 164
G+ LD++ E +G+ FQVQDD LD G +GK G D + K ++
Sbjct: 198 GDKGRRALPVLDRYAE------SIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYP 251
Query: 165 VV--------KALELCNEEQKKL 179
+ KA +L ++ ++ L
Sbjct: 252 ALLGLEQARKKARDLIDDARQSL 274
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 35.5 bits (82), Expect = 0.017
Identities = 37/156 (23%), Positives = 67/156 (42%), Gaps = 7/156 (4%)
Query: 94 YKTAYYSFYLPVACALLMAGENLDKHVEVKDILVQMGIYFQVQDDFLDCFGSPEVIGK-V 152
YKTA A ALL + + H + +G+ FQ+ DD LD S E +GK +
Sbjct: 173 YKTASLIAASCKAAALL-SDADEKDHNDFYLYGKHLGLAFQIIDDVLDITSSTESLGKPI 231
Query: 153 GTDIEDYKCSWLVVKALELCNEEQKKLVHENYGKVDPACVAKVKELYK-TLDLEGAFVEY 211
G+D+++ + V+ AL N + KL+ + + +++ ++ K T +E A +
Sbjct: 232 GSDLKNGNLTAPVLFALTQ-NSKLAKLIEREF--CETKDISQALQIIKETNGIEKAK-DL 287
Query: 212 EKESYEKLTKSIEAHPTKEVQAVLKSFLAKIYKRQK 247
E + + ++ P + L I R
Sbjct: 288 ALEHMQAAIQCLKFLPPSSAKDSLIEIANFIINRLN 323
>gnl|CDD|131796 TIGR02749, prenyl_cyano, solanesyl diphosphate synthase. Members
of this family all are from cyanobacteria or
plastid-containing eukaryotes. A member from Arabidopsis
(where both plastoquinone and ubiquinone contain the
C(45) prenyl moiety) was characterized by heterologous
expression as a solanesyl diphosphate synthase
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Menaquinone and ubiquinone].
Length = 322
Score = 35.1 bits (81), Expect = 0.022
Identities = 19/44 (43%), Positives = 26/44 (59%), Gaps = 1/44 (2%)
Query: 128 QMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWLVVKALE 170
+G+ FQV DD LD GS E +GK G+D+ + V+ ALE
Sbjct: 205 HLGLAFQVVDDILDFTGSTEQLGKPAGSDLMKGNLTAPVLFALE 248
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 34.0 bits (78), Expect = 0.058
Identities = 26/94 (27%), Positives = 46/94 (48%), Gaps = 2/94 (2%)
Query: 90 RIVQYKTAYYSFYLPVACALLMAGENLDKHVEVKDILVQMGIYFQVQDDFLDCFGSPEVI 149
R++ KTA F C+ ++AG ++ ++D +G FQ+ DD LD E +
Sbjct: 165 RVIYSKTARL-FEAAAQCSGILAGCTPEQEKGLQDYGRYLGTAFQLIDDLLDYSADGETL 223
Query: 150 GK-VGTDIEDYKCSWLVVKALELCNEEQKKLVHE 182
GK VG D+ + K + ++ A+ EQ ++
Sbjct: 224 GKNVGDDLNEGKPTLPLLHAMHHGTPEQAAMIRT 257
>gnl|CDD|218791 pfam05879, RHD3, Root hair defective 3 GTP-binding protein (RHD3).
This family consists of several eukaryotic root hair
defective 3 like GTP-binding proteins. It has been
speculated that the RHD3 protein is a member of a novel
class of GTP-binding proteins that is widespread in
eukaryotes and required for regulated cell enlargement.
The family also contains the homologous yeast synthetic
enhancement of YOP1 (SEY1) protein which is involved in
membrane trafficking.
Length = 743
Score = 33.9 bits (78), Expect = 0.081
Identities = 16/56 (28%), Positives = 25/56 (44%)
Query: 190 ACVAKVKELYKTLDLEGAFVEYEKESYEKLTKSIEAHPTKEVQAVLKSFLAKIYKR 245
CV K E ++L +E A + KL K I+AH + + LK + K+
Sbjct: 378 KCVEKFDEECESLAIEQATWSNSDKIRLKLEKDIDAHSARLRKEELKELTNRYEKK 433
>gnl|CDD|234689 PRK00216, ubiE, ubiquinone/menaquinone biosynthesis
methyltransferase; Reviewed.
Length = 239
Score = 30.1 bits (69), Expect = 0.78
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 213 KESYEKLTKSIEAHPTKEVQA 233
E+Y L +SI A P +E A
Sbjct: 190 AEAYSYLAESIRAFPDQEELA 210
>gnl|CDD|239663 cd03692, mtIF2_IVc, mtIF2_IVc: this family represents the C2
subdomain of domain IV of mitochondrial translation
initiation factor 2 (mtIF2) which adopts a beta-barrel
fold displaying a high degree of structural similarity
with domain II of the translation elongation factor
EF-Tu. The C-terminal part of mtIF2 contains the entire
fMet-tRNAfmet binding site of IF-2 and is resistant to
proteolysis. This C-terminal portion consists of two
domains, IF2 C1 and IF2 C2. IF2 C2 been shown to
contain all molecular determinants necessary and
sufficient for the recognition and binding of
fMet-tRNAfMet. Like IF2 from certain prokaryotes such
as Thermus thermophilus, mtIF2lacks domain II which is
thought to be involved in binding of E.coli IF-2 to
30S subunits.
Length = 84
Score = 28.2 bits (64), Expect = 1.2
Identities = 13/30 (43%), Positives = 18/30 (60%), Gaps = 3/30 (10%)
Query: 14 FRVPKVGMIAA---NDGVLLRNHISRILKN 40
F++ KVG IA DG + RN R+L+N
Sbjct: 9 FKISKVGNIAGCYVTDGKIKRNAKVRVLRN 38
>gnl|CDD|178478 PLN02890, PLN02890, geranyl diphosphate synthase.
Length = 422
Score = 29.9 bits (67), Expect = 1.3
Identities = 47/183 (25%), Positives = 80/183 (43%), Gaps = 16/183 (8%)
Query: 64 SGQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPVACALLMAGENLDKHVEVK 123
+G+ + + ++ E + S+ + + YKTA A A+L AG+ + V
Sbjct: 241 TGETMQITSSRE-----QRRSMDYYMQKTYYKTASLISNSCKAVAIL-AGQTAEVAVLAF 294
Query: 124 DILVQMGIYFQVQDDFLDCFGSPEVIGKVG-TDIEDYKCSWLVVKALELCNEEQKKLVHE 182
+ +G+ FQ+ DD LD G+ +GK +DI V+ A L E+ + E
Sbjct: 295 EYGRNLGLAFQLIDDVLDFTGTSASLGKGSLSDIRHG-----VITAPILFAMEEFPQLRE 349
Query: 183 --NYGKVDPACVAKVKE-LYKTLDLEGAFVEYEKESYEKLTKSIEAHPTKEVQAVLKSFL 239
+ G +PA V E L K+ ++ E +E +IE+ P + + VL S
Sbjct: 350 VVDRGFDNPANVDIALEYLGKSRGIQRT-RELAREHANLAAAAIESLPETDDEDVLTSRR 408
Query: 240 AKI 242
A I
Sbjct: 409 ALI 411
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 29.4 bits (67), Expect = 1.7
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 3/30 (10%)
Query: 14 FRVPKVGMIAA---NDGVLLRNHISRILKN 40
F+V KVG IA +G + RN R+L++
Sbjct: 662 FKVSKVGTIAGCMVTEGKIKRNAKVRVLRD 691
>gnl|CDD|132237 TIGR03193, 4hydroxCoAred, 4-hydroxybenzoyl-CoA reductase, gamma
subunit. 4-hydroxybenzoyl-CoA reductase converts
4-hydroxybenzoyl-CoA to benzoyl-CoA, a common
intermediate in the degradation of aromatic compounds.
This protein family represents the gamma chain of this
three-subunit enzyme.
Length = 148
Score = 28.3 bits (63), Expect = 2.3
Identities = 13/28 (46%), Positives = 15/28 (53%), Gaps = 2/28 (7%)
Query: 5 HTRRGQPCWFRVPKVGMIAANDGVLLRN 32
H R G C F P GMI A + +L RN
Sbjct: 90 HERLGTQCGFCTP--GMIMAAEALLRRN 115
>gnl|CDD|215656 pfam00012, HSP70, Hsp70 protein. Hsp70 chaperones help to fold
many proteins. Hsp70 assisted folding involves repeated
cycles of substrate binding and release. Hsp70 activity
is ATP dependent. Hsp70 proteins are made up of two
regions: the amino terminus is the ATPase domain and the
carboxyl terminus is the substrate binding region.
Length = 598
Score = 28.7 bits (65), Expect = 2.9
Identities = 12/62 (19%), Positives = 24/62 (38%), Gaps = 2/62 (3%)
Query: 175 EQKKLVHENYGKVDPACVAKVKELYKTLDLEGAFVEYEKESYEKLTKSIEAHPTKEVQAV 234
+K + E K+ A KV+E L+ +KE E T+ ++ + +
Sbjct: 539 SLEKSLKEEGDKLPEADKKKVEE--AIEWLKEELEGEDKEEIEAKTEELQKVVQPIGERM 596
Query: 235 LK 236
+
Sbjct: 597 YQ 598
>gnl|CDD|236760 PRK10792, PRK10792, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 285
Score = 28.0 bits (63), Expect = 5.2
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 10/34 (29%)
Query: 104 PVACALLMAG----------ENLDKHVEVKDILV 127
P++ LL+AG +NL HV D+LV
Sbjct: 174 PMSLELLLAGCTVTVCHRFTKNLRHHVRNADLLV 207
>gnl|CDD|131795 TIGR02748, GerC3_HepT, heptaprenyl diphosphate synthase component
II. Members of this family are component II of the
heterodimeric heptaprenyl diphosphate synthase. The
trusted cutoff was set such that all members identified
are encoded near to a recognizable gene for component I
(in Pfam family pfam07307). This enzyme acts in
menaquinone-7 isoprenoid side chain biosynthesis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Menaquinone and ubiquinone].
Length = 319
Score = 27.8 bits (62), Expect = 5.3
Identities = 27/89 (30%), Positives = 42/89 (47%), Gaps = 10/89 (11%)
Query: 74 IEGEKDLSKYSLPLH---RRIVQYKTAYYSFYLPVACAL--LMAGENLDKHVEVKDILVQ 128
IE KD + L RRI + KTA + +C L + +G N ++
Sbjct: 146 IEQIKDKYNFDQNLRTYLRRI-KRKTA---LLIAASCQLGAIASGANEAIVKKLYWFGYY 201
Query: 129 MGIYFQVQDDFLDCFGSPEVIGK-VGTDI 156
+G+ +Q+ DD LD G+ E +GK G D+
Sbjct: 202 VGMSYQITDDILDFVGTEEELGKPAGGDL 230
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 27.9 bits (63), Expect = 5.6
Identities = 11/30 (36%), Positives = 19/30 (63%), Gaps = 3/30 (10%)
Query: 14 FRVPKVGMIAA---NDGVLLRNHISRILKN 40
F++PKVG IA +GV+ R R++++
Sbjct: 422 FKLPKVGAIAGCMVTEGVIKRGAPVRVVRD 451
>gnl|CDD|215382 PLN02712, PLN02712, arogenate dehydrogenase.
Length = 667
Score = 28.0 bits (62), Expect = 5.8
Identities = 19/86 (22%), Positives = 35/86 (40%), Gaps = 7/86 (8%)
Query: 165 VVKALELCNEEQKKLVHENYGKVDPACVAKVKELYKTLDLEGAFVEYEKESYEKLTKSIE 224
VV+ NEE+K V N+ + A + L + +G +YE + +++ +
Sbjct: 309 VVRKQLFGNEEKKVHVQPNHAENHTYGAAFLSSL-DMMRFQGVAQKYEYNA--QVSGCVN 365
Query: 225 AHPTKEVQAV----LKSFLAKIYKRQ 246
++ V FLAK +Q
Sbjct: 366 DGSKLKIAIVGFGNFGQFLAKTMVKQ 391
>gnl|CDD|215462 PLN02857, PLN02857, octaprenyl-diphosphate synthase.
Length = 416
Score = 27.9 bits (62), Expect = 5.9
Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 129 MGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWLVVKALE 170
+G+ FQV DD LD S E +GK G+D+ + V+ ALE
Sbjct: 300 LGLAFQVVDDILDFTQSTEQLGKPAGSDLAKGNLTAPVIFALE 342
>gnl|CDD|198400 cd10453, GIY-YIG_RE_Cfr42I, Catalytic GIY-YIG domain of type II
restriction enzyme R.Cfr42I and similar proteins. This
family corresponds to the catalytic GIY-YIG domain of
GGCGCC-specific type II restriction endonucleases
R.Cfr42I and similar proteins. R.Cfr42I is encoded on
plasmid pET21b(+) in the Citrobacter freundii RFL42
strain. This enzyme recognizes the palindromic
5'-CCGC/GG-3' target and cuts between Cyt4 and Gua5 on
each strand of the restriction site to generate
3'-staggered ends. It is an isoschizomer of R.Eco29kI.
Unlike R.Eco29kI, R.Cfr42I is functional as a
homotetramer, binding and cleaving two cognate DNA
molecules in a cooperative manner. Members in this
family are single-domain proteins sharing sequence
similarities with the catalytic domain of GIY-YIG
endonucleases, such as homing endonuclease I-TevI.
However, they utilize loop insertions and terminal
extensions instead of the separate DNA-binding domain to
interact with the target site 5'-CCGC/GG-3'. A divalent
metal-ion cofactor is required for their catalysis.
Length = 156
Score = 27.0 bits (60), Expect = 6.5
Identities = 8/12 (66%), Positives = 10/12 (83%)
Query: 155 DIEDYKCSWLVV 166
DIED+ C +LVV
Sbjct: 108 DIEDFYCRFLVV 119
>gnl|CDD|201071 pfam00194, Carb_anhydrase, Eukaryotic-type carbonic anhydrase.
Length = 238
Score = 27.3 bits (61), Expect = 7.6
Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 4/62 (6%)
Query: 179 LVHENYGKVDPACVAKVKELYKTLDLEGAFVEY--EKESYEKLTKSIEAHPTKEVQAVLK 236
LVH N K A+ + L + G FV+ E +K+ ++++ TK A
Sbjct: 98 LVHWNSTKYGSYKEAQSQP--DGLAVLGVFVKVGPENPGLQKVVDALDSIKTKGKSATFT 155
Query: 237 SF 238
+F
Sbjct: 156 NF 157
>gnl|CDD|216540 pfam01509, TruB_N, TruB family pseudouridylate synthase (N terminal
domain). Members of this family are involved in
modifying bases in RNA molecules. They carry out the
conversion of uracil bases to pseudouridine. This family
includes TruB, a pseudouridylate synthase that
specifically converts uracil 55 to pseudouridine in most
tRNAs. This family also includes Cbf5p that modifies
rRNA.
Length = 149
Score = 26.7 bits (60), Expect = 8.3
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 11/46 (23%)
Query: 201 TLDLEGAFVEYEKESYEKLTKSIEAHPTKE-VQAVLKSFLAKIYKR 245
TLD EG E + + H T+E ++ VL SF +I +
Sbjct: 56 TLDAEG----------EIVEEPPVDHITEEKIEEVLASFTGEIEQV 91
>gnl|CDD|233645 TIGR01934, MenG_MenH_UbiE, ubiquinone/menaquinone biosynthesis
methyltransferases. This model represents a family of
methyltransferases involved in the biosynthesis of
menaquinone and ubiqinone. Some members such as the UbiE
enzyme from E. coli are believed to act in both
pathways, while others may act in only the menaquinone
pathway. These methyltransferases are members of the
UbiE/CoQ family of methyltransferases (pfam01209) which
also contains ubiquinone methyltransferases and other
methyltransferases. Members of this clade include a wide
distribution of bacteria and eukaryotes, but no archaea.
An outgroup for this clade is provided by the
phosphatidylethanolamine methyltransferase (EC 2.1.1.17)
from Rhodobacter sphaeroides. Note that a number of
non-orthologous genes which are members of pfam03737
have been erroneously annotated as MenG
methyltransferases [Biosynthesis of cofactors,
prosthetic groups, and carriers, Menaquinone and
ubiquinone].
Length = 223
Score = 26.8 bits (60), Expect = 8.3
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 206 GAFVEYEKESYEKLTKSIEAHPTKEVQA 233
G + E+Y L +SI A P++E A
Sbjct: 168 GGLISKNAEAYTYLPESIRAFPSQEELA 195
>gnl|CDD|227427 COG5096, COG5096, Vesicle coat complex, various subunits
[Intracellular trafficking and secretion].
Length = 757
Score = 27.4 bits (61), Expect = 8.8
Identities = 9/29 (31%), Positives = 16/29 (55%), Gaps = 3/29 (10%)
Query: 165 VVKALELCNEEQKKLVH---ENYGKVDPA 190
V+K + + E K+L++ E Y K+ P
Sbjct: 60 VIKNVATRDVELKRLLYLYLERYAKLKPE 88
>gnl|CDD|132771 cd06861, PX_Vps5p, The phosphoinositide binding Phox Homology
domain of yeast sorting nexin Vps5p. The PX domain is a
phosphoinositide (PI) binding module present in many
proteins with diverse functions. Sorting nexins (SNXs)
make up the largest group among PX domain containing
proteins. They are involved in regulating membrane
traffic and protein sorting in the endosomal system. The
PX domain of SNXs binds PIs and targets the protein to
PI-enriched membranes. SNXs differ from each other in
PI-binding specificity and affinity, and the presence of
other protein-protein interaction domains, which help
determine subcellular localization and specific function
in the endocytic pathway. Vsp5p is the yeast counterpart
of human SNX1 and is part of the retromer complex, which
functions in the endosome-to-Golgi retrieval of vacuolar
protein sorting receptor Vps10p, the Golgi-resident
membrane protein A-ALP, and endopeptidase Kex2. The PX
domain of Vps5p binds phosphatidylinositol-3-phosphate
(PI3P). Similar to SNX1, Vps5p contains a
Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane
curvature, C-terminal to the PX domain. Both domains
have been shown to determine the specific
membrane-targeting of SNX1.
Length = 112
Score = 26.2 bits (58), Expect = 9.4
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 208 FVEYEKESYEKLTKSIEAHPTKEVQAVLKSFL 239
FVE + + EK+ + I HP + + FL
Sbjct: 78 FVEQRRAALEKMLRKIANHPVLQKDPDFRLFL 109
>gnl|CDD|238397 cd00774, GlyRS-like_core, Glycyl-tRNA synthetase (GlyRS)-like
class II core catalytic domain. GlyRS functions as a
homodimer in eukaryotes, archaea and some bacteria and
as a heterotetramer in the remainder of prokaryotes. It
is responsible for the attachment of glycine to the 3'
OH group of ribose of the appropriate tRNA. This domain
is primarily responsible for ATP binding and
hydrolysis. This alignment contains only sequences from
the GlyRS form which homodimerizes. The heterotetramer
glyQ is in a different family of class II aaRS. Class
II assignment is based upon its structure and the
presence of three characteristic sequence motifs. This
domain is also found at the N-terminus of the accessory
subunit of mitochondrial polymerase gamma (Pol gamma
b). Pol gamma b stimulates processive DNA synthesis and
is functional as a homodimer, which can associate with
the catalytic subunit Pol gamma alpha to form a
heterotrimer. Despite significant both structural and
sequence similarity with GlyRS, Pol gamma b lacks
conservation of several class II functional residues.
Length = 254
Score = 26.8 bits (60), Expect = 10.0
Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 3/42 (7%)
Query: 27 GVLLRNHISRILKNHF---RDKPYYVDLLDLFNEVEFQTASG 65
GV L+N+I + F + +D + E+ F+T+ G
Sbjct: 31 GVELKNNIKSAWRKSFVLEEEDMLEIDSPIITPELMFKTSIG 72
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
0.321 0.138 0.409
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,676,710
Number of extensions: 1216615
Number of successful extensions: 1182
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1161
Number of HSP's successfully gapped: 51
Length of query: 247
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 153
Effective length of database: 6,768,326
Effective search space: 1035553878
Effective search space used: 1035553878
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.0 bits)