RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 007749
(591 letters)
>gnl|CDD|177973 PLN02339, PLN02339, NAD+ synthase (glutamine-hydrolysing).
Length = 700
Score = 1225 bits (3171), Expect = 0.0
Identities = 465/584 (79%), Positives = 511/584 (87%)
Query: 1 MRLLKVATCNLNNWALDFDCNLKNIKESIGRAKEAGAVIRLGPELEITGYGCEDHFLELD 60
MRLLKVATCNLN WA+DFD NLK IKESI AK AGAV R+GPELEITGYGCEDHFLELD
Sbjct: 1 MRLLKVATCNLNQWAMDFDGNLKRIKESIAEAKAAGAVYRVGPELEITGYGCEDHFLELD 60
Query: 61 TVTHAWECLKDLLLGDWTDGILCSFGMPVIKGSERYNCQVLCLNRKIIMIRPKLWLANDG 120
TVTH+WECL ++L+GD TDGILC GMPVI G RYNC+V CLNRKI++IRPK+WLANDG
Sbjct: 61 TVTHSWECLAEILVGDLTDGILCDIGMPVIHGGVRYNCRVFCLNRKILLIRPKMWLANDG 120
Query: 121 NYRELRWFTAWKQKDQLEDFQLPNEISVALKQKSVPFGYGFIQFLDTAVAAEICEELFTP 180
NYRELRWFTAWK K ++EDFQLP EI+ A QKSVPFG G++QFLDTAVAAE CEELFTP
Sbjct: 121 NYRELRWFTAWKHKKKVEDFQLPEEIAEATSQKSVPFGDGYLQFLDTAVAAETCEELFTP 180
Query: 181 IPPHADLALNGVEVFMNASGSHHQLRKLDYRIRAFISATHSRGGVYMYSNHQGCDGGRLY 240
PH DLALNGVE+ N SGSHHQLRKL+ R+ SATH GGVY+Y+N +GCDGGRLY
Sbjct: 181 QAPHIDLALNGVEIISNGSGSHHQLRKLNTRLDLIRSATHKCGGVYLYANQRGCDGGRLY 240
Query: 241 FDGCSCVVVNGDMIAQGSQFSLKDVEIVVAQVDLDAVAGFRGSISSFQEQASCKTKIPSV 300
+DGC+C+VVNG+++AQGSQFSL+DVE+V A VDLDAV FRGSISSF+EQAS K ++PSV
Sbjct: 241 YDGCACIVVNGEVVAQGSQFSLQDVEVVTACVDLDAVVSFRGSISSFREQASSKKRVPSV 300
Query: 301 AVPYNLCQPFNLKMSLSSPLKINYHSPEEEIAFGPGCWLWDYLRRSGASGFLLPLSGGAD 360
AVP+ LC PF+L + SSPLKI YHSPEEEIA GP CWLWDYLRRSGASGFLLPLSGGAD
Sbjct: 301 AVPFKLCPPFSLSLVPSSPLKIRYHSPEEEIALGPACWLWDYLRRSGASGFLLPLSGGAD 360
Query: 361 SSSVAAIVGCMCQLVVKEISNGDEQVKADAIRIGHYANGEFPTDSREFAKRIFYTVFMGS 420
SSSVAAIVG MCQLVVK I GDEQVKADA RIG+YA+GE PTDS+EFAKRIFYTV+MGS
Sbjct: 361 SSSVAAIVGSMCQLVVKAIREGDEQVKADARRIGNYADGEVPTDSKEFAKRIFYTVYMGS 420
Query: 421 ENSSQETRMLAKKLADEIGSWHLDVSIDTVVSAFLSLFQTLTGKRPCYKVDGGSNVENLG 480
ENSS+ETR AK+LADEIGS HLDV ID VVSA LSLFQTLTGKRP YKVDGGSN ENL
Sbjct: 421 ENSSEETRSRAKQLADEIGSSHLDVKIDGVVSAVLSLFQTLTGKRPRYKVDGGSNAENLA 480
Query: 481 LQNIQARIRMVLAFMLASLLPWVHNKPGFYLVLGSSNVDEGLRGYLTKYDCSSADINPIG 540
LQNIQARIRMVLAFMLASLLPWV K GF LVLGS+NVDEGLRGYLTKYDCSSADINPIG
Sbjct: 481 LQNIQARIRMVLAFMLASLLPWVRGKSGFLLVLGSANVDEGLRGYLTKYDCSSADINPIG 540
Query: 541 SISKQDLRTFLRWAATHLGYSSLAEIEAAPPTAELEPIRSNYSQ 584
ISKQDLR+FLRWAAT+LGY SLAE+EAAPPTAELEPIR +YSQ
Sbjct: 541 GISKQDLRSFLRWAATNLGYPSLAEVEAAPPTAELEPIRDDYSQ 584
>gnl|CDD|143594 cd07570, GAT_Gln-NAD-synth, Glutamine aminotransferase (GAT,
glutaminase) domain of glutamine-dependent NAD
synthetases (class 7 and 8 nitrilases).
Glutamine-dependent NAD synthetases are bifunctional
enzymes, which have an N-terminal GAT domain and a
C-terminal NAD+ synthetase domain. The GAT domain is a
glutaminase (EC 3.5.1.2) which hydrolyses L-glutamine to
L-glutamate and ammonia. The ammonia is used by the NAD+
synthetase domain in the ATP-dependent amidation of
nicotinic acid adenine dinucleotide. Glutamine
aminotransferases are categorized depending on their
active site residues into different unrelated classes.
This class of GAT domain belongs to a larger nitrilase
superfamily comprised of nitrile- or amide-hydrolyzing
enzymes and amide-condensing enzymes, which depend on a
Glu-Lys-Cys catalytic triad. This superfamily has been
classified in the literature based on global and
structure based sequence analysis into thirteen
different enzyme classes (referred to as 1-13), this
subgroup corresponds to classes 7 and 8. Members of this
superfamily generally form homomeric complexes, the
basic building block of which is a homodimer.
Mycobacterium tuberculosis glutamine-dependent NAD+
synthetase forms a homooctamer.
Length = 261
Score = 273 bits (702), Expect = 2e-88
Identities = 92/289 (31%), Positives = 132/289 (45%), Gaps = 32/289 (11%)
Query: 5 KVATCNLNNWALDFDCNLKNIKESIGRAKEAGAVIRLGPELEITGYGCEDHFLELDTVTH 64
++A LN D + N + I E+I AK GA + + PEL +TGY ED L D +
Sbjct: 1 RIALAQLNPTVGDLEGNAEKILEAIREAKAQGADLVVFPELSLTGYPPEDLLLRPDFLEA 60
Query: 65 AWECLKDLLLGDWTDGILCSFGMPVIKGSERYNCQVLCLNRKIIMIRPKLWLANDGNYRE 124
A E L++L I G+P+ + YN + N KI+ + PK L N G + E
Sbjct: 61 AEEALEELAAATADLDIAVVVGLPLRHDGKLYNAAAVLQNGKILGVVPKQLLPNYGVFDE 120
Query: 125 LRWFTAWKQKDQLEDFQLPNEISVALKQKSVPFGYGFIQFLDTAVAAEICEELFTPIPPH 184
R+FT + D L F + EICE+L+ P PP
Sbjct: 121 KRYFTPGDKPDVLF-------------------------FKGLRIGVEICEDLWVPDPPS 155
Query: 185 ADLALNGVEVFMNASGSHHQLRKLDYRIRAFISATHSRGGVYMYSNHQGCDGGRLYFDGC 244
A+LAL G ++ +N S S L K DYR S + G Y+Y N Q L FDG
Sbjct: 156 AELALAGADLILNLSASPFHLGKQDYRRELVSSRSARTGLPYVYVN-QVGGQDDLVFDGG 214
Query: 245 SCVVVN-GDMIAQGSQFSLKDVEIVVAQVDLDAVAGFRGSISSFQEQAS 292
S + N G+++A+ +F E +A VDLD + R SSF ++ +
Sbjct: 215 SFIADNDGELLAEAPRF-----EEDLADVDLDRLRSERRRNSSFLDEEA 258
>gnl|CDD|238309 cd00553, NAD_synthase, NAD+ synthase is a homodimer, which
catalyzes the final step in de novo nicotinamide adenine
dinucleotide (NAD+) biosynthesis, an amide transfer from
either ammonia or glutamine to nicotinic acid adenine
dinucleotide (NaAD). The conversion of NaAD to NAD+
occurs via an NAD-adenylate intermediate and requires
ATP and Mg2+. The intemediate is subsequently cleaved
into NAD+ and AMP. In many prokaryotes, such as E. coli
, NAD synthetase consists of a single domain and is
strictly ammonia dependent. In contrast, eukaryotes and
other prokaryotes have an additional N-terminal
amidohydrolase domain that prefer glutamine,
Interestingly, NAD+ synthases in these prokaryotes, can
also utilize ammonia as an amide source .
Length = 248
Score = 220 bits (564), Expect = 4e-68
Identities = 91/252 (36%), Positives = 117/252 (46%), Gaps = 60/252 (23%)
Query: 326 SPEEEIAFGPGCWLWDYLRRSGASGFLLPLSGGADSSSVAAIVGCMCQLVVKEISNGDEQ 385
EEI +L DYLR+SG G +L LSGG DS+ VAA+ G E
Sbjct: 1 EDLEEIINALVLFLRDYLRKSGFKGVVLGLSGGIDSALVAALAVRAL---------GREN 51
Query: 386 VKADAIRIGHYANGEFPTDSREFAKRIFYTVFMGSENSSQETRMLAKKLADEIGSWHLDV 445
V +FM S SS+ETR AK+LA+ +G H+++
Sbjct: 52 V---------------------------LALFMPSRYSSEETREDAKELAEALGIEHVNI 84
Query: 446 SIDTVVSAFLSLFQTLTGKRPCYKVDGGSNVENLGLQNIQARIRMVLAFMLASLLPWVHN 505
ID V AFL+L GGS +E+L L NIQAR+RMV+ + LA+ L
Sbjct: 85 DIDPAVEAFLALL----------GESGGSELEDLALGNIQARLRMVILYALANKL----- 129
Query: 506 KPGFYLVLGSSNVDEGLRGYLTKYDCSSADINPIGSISKQDLRTFLRWAATHLGYSSLAE 565
LVLG+ N E L GY TKY +ADINPIG + K +R R+
Sbjct: 130 ---GGLVLGTGNKSELLLGYFTKYGDGAADINPIGDLYKTQVRELARYLG------VPES 180
Query: 566 IEAAPPTAELEP 577
I PP+AEL P
Sbjct: 181 IIDKPPSAELWP 192
>gnl|CDD|223249 COG0171, NadE, NAD synthase [Coenzyme metabolism].
Length = 268
Score = 133 bits (338), Expect = 2e-35
Identities = 72/240 (30%), Positives = 103/240 (42%), Gaps = 55/240 (22%)
Query: 338 WLWDYLRRSGASGFLLPLSGGADSSSVAAIVGCMCQLVVKEISNGDEQVKADAIRIGHYA 397
+L DYL+++G G +L LSGG DS A+V + + + +
Sbjct: 15 FLRDYLKKAGFKGVVLGLSGGIDS----ALVLALAVRALGKGDS---------------- 54
Query: 398 NGEFPTDSREFAKRIFYTVFMGSENSSQETRMLAKKLADEIGSWHLDVSIDTVVSAFLSL 457
K V + + Q A+ LA+ +G + +++I V AFL
Sbjct: 55 ------------KENVLAVRLPYGYTVQADEEDAQDLAEALGIDYKEINIKPAVDAFLKK 102
Query: 458 FQTLTGKRPCYKVDGGSNVENLGLQNIQARIRMVLAFMLASLLPWVHNKPGFYLVLGSSN 517
L G +E+L L NI+AR+RMV+ + +A NK G LVLG+ N
Sbjct: 103 LLKLFL---------GIYLEDLALGNIKARLRMVILYAIA-------NKLG-GLVLGTGN 145
Query: 518 VDEGLRGYLTKYDCSSADINPIGSISKQDLRTFLRWAATHLGYSSLAEIEAAPPTAELEP 577
E GY TKY + DINPI + K + R HLG EI PPTA+L P
Sbjct: 146 KSELALGYFTKYGDGAVDINPIADLYKTQVYALAR----HLGI--PEEILKKPPTADLWP 199
>gnl|CDD|235057 PRK02628, nadE, NAD synthetase; Reviewed.
Length = 679
Score = 129 bits (328), Expect = 1e-31
Identities = 84/285 (29%), Positives = 128/285 (44%), Gaps = 35/285 (12%)
Query: 19 DC--NLKNIKESIGRAKEAGAVIRLGPELEITGYGCEDHFLE---LDTVTHAWECLKDLL 73
D N I RA + G + + PEL ++GY C+D FL+ LD V A L L+
Sbjct: 26 DPAFNAARILALARRAADDGVALAVFPELSLSGYSCDDLFLQDTLLDAVEDA---LATLV 82
Query: 74 LG--DWTDGILCSFGMPVIKGSERYNCQVLCLNRKIIMIRPKLWLANDGNYRELRWFTAW 131
D L G P+ YNC V+ +I+ + PK +L N + E RWF
Sbjct: 83 EASADLD--PLLVVGAPLRVRHRLYNCAVVIHRGRILGVVPKSYLPNYREFYEKRWFAP- 139
Query: 132 KQKDQLEDFQLPNEISVALKQKSVPFG----YGFIQFLDTAVAAEICEELFTPIPPHADL 187
E + L + VPFG + EICE+L+ PIPP +
Sbjct: 140 -------GDGARGET-IRLCGQEVPFGTDLLFEAEDLPGFVFGVEICEDLWVPIPPSSYA 191
Query: 188 ALNGVEVFMNASGSHHQLRKLDYRIRAFISATHSRG-GVYMYSNHQGCDGGR----LYFD 242
AL G V N S S+ + K DYR R +++ +R Y+Y+ G L +D
Sbjct: 192 ALAGATVLANLSASNITVGKADYR-RLLVASQSARCLAAYVYAA---AGVGESTTDLAWD 247
Query: 243 GCSCVVVNGDMIAQGSQFSLKDVEIVVAQVDLDAVAGFRGSISSF 287
G + + NG+++A+ +F ++ +++VA VDL+ + R SF
Sbjct: 248 GQTLIYENGELLAESERFP-REEQLIVADVDLERLRQERLRNGSF 291
>gnl|CDD|237577 PRK13981, PRK13981, NAD synthetase; Provisional.
Length = 540
Score = 119 bits (300), Expect = 2e-28
Identities = 147/590 (24%), Positives = 211/590 (35%), Gaps = 150/590 (25%)
Query: 4 LKVATCNLNNWALDFDCNLKNIKESIGRAKEAGAVIRLGPELEITGYGCEDHFLELDTVT 63
L++A LN D N I + A +AGA + L PEL ++GY ED L +
Sbjct: 1 LRIALAQLNPTVGDIAGNAAKILAAAAEAADAGADLLLFPELFLSGYPPEDLLLRPAFLA 60
Query: 64 HAWECLKDLLLGDWTDGILCSFGMPVIKGSERYNCQVLCLNRKIIMIRPKLWLANDGNYR 123
L+ L G G P +G + YN L +++ K L N G +
Sbjct: 61 ACEAALER-LAAATAGGPAVLVGHPWREGGKLYNAAALLDGGEVLATYRKQDLPNYGVFD 119
Query: 124 ELRWFTAWKQKDQLEDFQLPNEISVALKQKSVPFGYGFIQFLDTAVAAEICEELFTPIPP 183
E R+F P ++ K V G ICE+++ P P
Sbjct: 120 EKRYFA-------------PGPEPGVVELKGVRIGV------------PICEDIWNPEPA 154
Query: 184 HADLALNGVEVFMNASGSHHQLRKLDYRIRAFISATHSRGGVYM-YSNHQGCDGGR--LY 240
LA G E+ + + S + K D R A + A G+ + Y N GG+ L
Sbjct: 155 -ETLAEAGAELLLVPNASPYHRGKPDLRE-AVLRARVRETGLPLVYLNQV---GGQDELV 209
Query: 241 FDGCSCVVVNGD--MIAQGSQFSLKDVEIVVAQVDLDAVAGFRGSISSFQEQASCKTKIP 298
FDG S V+N D + A+ F E +A VD D ++ P
Sbjct: 210 FDGAS-FVLNADGELAARLPAF-----EEQIAVVDFDRGED------GWRPLPGPIAPPP 257
Query: 299 SVAVPYNLCQPFNLKMSLSSPLKINYHSPEEEIAFGPGCW------LWDYLRRSGASGFL 352
E E + L DY+R++G G +
Sbjct: 258 ---------------------------EGEAED------YRALVLGLRDYVRKNGFPGVV 284
Query: 353 LPLSGGADSSSVAAIVGCMCQLVVKEISNGDEQVKADAIRIGHYANGEFPTDSREFAKRI 412
L LSGG DS+ VAAI V + G E+V+A
Sbjct: 285 LGLSGGIDSALVAAI-------AVDAL--GAERVRA------------------------ 311
Query: 413 FYTVFMGSENSSQETRMLAKKLADEIGSWHLDVSIDTVVSAFLSLFQTLTGKRPCYKVDG 472
V M S +S+E+ A LA +G + + I+ AF + L
Sbjct: 312 ---VMMPSRYTSEESLDDAAALAKNLGVRYDIIPIEPAFEAFEAALAPLFAGTE------ 362
Query: 473 GSNVENLGLQNIQARIRMVLAFMLASLLPWVHNKPGFYLVLGSSNVDEGLRGYLTKYDCS 532
++ +N+Q+RIR L L+ NK G LVL + N E GY T Y
Sbjct: 363 ----PDITEENLQSRIRGTLLMALS-------NKFG-SLVLTTGNKSEMAVGYATLY--- 407
Query: 533 SADIN----PIGSISKQDLRTFLRWAATHLGYSSLAE-IEAAPPTAELEP 577
D+ PI + K + RW T + E I PP+AEL P
Sbjct: 408 -GDMAGGFAPIKDVYKTLVYRLCRWRNTVSPGEVIPERIITKPPSAELRP 456
>gnl|CDD|223465 COG0388, COG0388, Predicted amidohydrolase [General function
prediction only].
Length = 274
Score = 112 bits (281), Expect = 1e-27
Identities = 72/293 (24%), Positives = 118/293 (40%), Gaps = 37/293 (12%)
Query: 2 RLLKVATCNLNNWALDFDCNLKNIKESIGRAKEAGAVIRLGPELEITGYGCED-HFLELD 60
+++VA + A D NL I I A GA + + PEL +TGY CED FLE
Sbjct: 1 SMMRVAAAQMAPKAGDPAENLARILRLIREAAARGADLVVFPELFLTGYPCEDDLFLEEA 60
Query: 61 TVTHAWECLKDL-LLGDWTDGILCSFGMPVIKGSERYNCQVLCLNR-KIIMIRPKLWLAN 118
E L+ L L + I+ G P+ + + YN L +I+ KL L +
Sbjct: 61 AAEAGEETLEFLAALAEEGGVII--VGGPLPEREKLYNNAALIDPDGEILGKYRKLHLFD 118
Query: 119 DGNYRELRWFTAWKQKDQLEDFQLPNEISVALKQKSVPFGYGFIQFLDTAVAAEICEELF 178
Y E R+FT + V F + + IC +L
Sbjct: 119 AF-YEERRFFT-------------------PGDEGVVVFETDGGK-----IGLLICYDLR 153
Query: 179 TPIPPHADLALNGVEVFMNASGSHHQLRKLDYRIRAFISATHSRGGVYM-YSNHQGCDGG 237
P LAL G E+ + + + + + A + VY+ +N G DG
Sbjct: 154 FPELARRLLALGGAELLLVPAAWPAERGLDHWEVLLRARAIEN--QVYVLAANRAGFDGA 211
Query: 238 RLYFDGCSCVVV-NGDMIAQGSQFSLKDVEIVVAQVDLDAVAGFRGSISSFQE 289
L F G S ++ +G+++A+ + + +++A +DL +A R I ++
Sbjct: 212 GLEFCGHSAIIDPDGEVLAEAGEE---EEGVLLADIDLAELAEVRRKIPVLKD 261
>gnl|CDD|217093 pfam02540, NAD_synthase, NAD synthase. NAD synthase (EC:6.3.5.1)
is involved in the de novo synthesis of NAD and is
induced by stress factors such as heat shock and glucose
limitation.
Length = 242
Score = 107 bits (268), Expect = 3e-26
Identities = 71/240 (29%), Positives = 100/240 (41%), Gaps = 64/240 (26%)
Query: 338 WLWDYLRRSGASGFLLPLSGGADSSSVAAIVGCMCQLVVKEISNGDEQVKADAIRIGHYA 397
+L DY+++SGA G +L LSGG DS A+V + + G E V A
Sbjct: 8 FLRDYVQKSGAKGVVLGLSGGIDS----AVVAYLAVKAL-----GKENVLA--------- 49
Query: 398 NGEFPTDSREFAKRIFYTVFMGSENSSQETRMLAKKLADEIGSWHLDVSIDTVVSAFLSL 457
+ M S NSS+E A LA+ +G + + I +V AF L
Sbjct: 50 ------------------LIMPSINSSEEDVQDALALAENLGINYKTIDIKPIVRAFSQL 91
Query: 458 FQTLTGKRPCYKVDGGSNVENLGLQNIQARIRMVLAFMLASLLPWVHNKPGFYLVLGSSN 517
FQ ++L N++ARIRM++ + A NK LVLG+ N
Sbjct: 92 FQ--------------PAKDDLAKGNLKARIRMIILYAHA-------NKFN-RLVLGTGN 129
Query: 518 VDEGLRGYLTKYDCSSADINPIGSISKQDLRTFLRWAATHLGYSSLAEIEAAPPTAELEP 577
E GY TKY + DI PIG + K + + L I PP+A+L P
Sbjct: 130 KSELALGYFTKYGDGACDIAPIGDLYKTQVYELAKR----LNVPE--RIIKKPPSADLWP 183
>gnl|CDD|233019 TIGR00552, nadE, NAD+ synthetase. NAD+ synthetase is a nearly
ubiquitous enzyme for the final step in the biosynthesis
of the essensial cofactor NAD. The member of this family
from Bacillus subtilis is a strictly NH(3)-dependent
NAD(+) synthetase of 272 amino acids. Proteins
consisting only of the domain modeled here may be named
as NH3-dependent NAD+ synthetase. Amidotransferase
activity may reside in a separate protein, or not be
present. Some other members of the family, such as from
Mycobacterium tuberculosis, are considerably longer,
contain an apparent amidotransferase domain, and show
glutamine-dependent as well as NH(3)-dependent activity
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Pyridine nucleotides].
Length = 250
Score = 97.8 bits (244), Expect = 7e-23
Identities = 63/240 (26%), Positives = 95/240 (39%), Gaps = 61/240 (25%)
Query: 338 WLWDYLRRSGASGFLLPLSGGADSSSVAAIVGCMCQLVVKEISNGDEQVKADAIRIGHYA 397
+L Y+++SGA G +L LSGG DS+ VAA+ C EQ
Sbjct: 12 FLRGYVQKSGAKGVVLGLSGGIDSAVVAAL----CVEA------LGEQN----------- 50
Query: 398 NGEFPTDSREFAKRIFYTVFMGSENSSQETRMLAKKLADEIGSWHLDVSIDTVVSAFLSL 457
A + ++V E Q+ LA+ L G + ++ I + ++F +
Sbjct: 51 ----------HALLLPHSVQT-PEQDVQDALALAEPL----GINYKNIDIAPIAASFQAQ 95
Query: 458 FQTLTGKRPCYKVDGGSNVENLGLQNIQARIRMVLAFMLASLLPWVHNKPGFYLVLGSSN 517
+T + G N++AR+RM + +A NK LVLG+ N
Sbjct: 96 TETGDELSD-FLAKG----------NLKARLRMAALYAIA-------NKHN-LLVLGTGN 136
Query: 518 VDEGLRGYLTKYDCSSADINPIGSISKQDLRTFLRWAATHLGYSSLAEIEAAPPTAELEP 577
E + GY TKY DI PIG + K + + L I PPTA+L
Sbjct: 137 KSELMLGYFTKYGDGGCDIAPIGDLFKTQVYELAKR----LNVPE--RIIEKPPTADLFD 190
>gnl|CDD|184435 PRK13980, PRK13980, NAD synthetase; Provisional.
Length = 265
Score = 89.9 bits (224), Expect = 4e-20
Identities = 70/235 (29%), Positives = 97/235 (41%), Gaps = 65/235 (27%)
Query: 341 DYLRRSGASGFLLPLSGGADSSSVAAIVGCMCQLVVKEISNGDEQVKADAIRIGHYANGE 400
+ + ++GA G +L LSGG DS+ VA L VK + G E V A
Sbjct: 23 EEVEKAGAKGVVLGLSGGIDSAVVAY-------LAVKAL--GKENVLA------------ 61
Query: 401 FPTDSREFAKRIFYTVFMGSENSSQETRMLAKKLADEIGSWHLDVSIDTVVSAFLSLFQT 460
+ M S S E A+ +A+++G + + I +V AF S
Sbjct: 62 ---------------LLMPSSVSPPEDLEDAELVAEDLGIEYKVIEITPIVDAFFSAIPD 106
Query: 461 LTGKRPCYKVDGGSNVENLGLQNIQARIRMVLAFMLASLLPWVHNKPGFYLVLGSSNVDE 520
R +G NI AR RMVL + A+ LVLG+ N E
Sbjct: 107 ADRLR-------------VG--NIMARTRMVLLYDYANREN--------RLVLGTGNKSE 143
Query: 521 GLRGYLTKYDCSSADINPIGSISKQDLRTFLRWAATHLGYSSLAEIEAAPPTAEL 575
L GY TKY + D+NPIG + K +R A HLG +I PP+A+L
Sbjct: 144 LLLGYFTKYGDGAVDLNPIGDLYKTQVREL----ARHLGVPE--DIIEKPPSADL 192
>gnl|CDD|216124 pfam00795, CN_hydrolase, Carbon-nitrogen hydrolase. This family
contains hydrolases that break carbon-nitrogen bonds.
The family includes: Nitrilase EC:3.5.5.1, Aliphatic
amidase EC:3.5.1.4, Biotidinase EC:3.5.1.12,
Beta-ureidopropionase EC:3.5.1.6. Nitrilase-related
proteins generally have a conserved E-K-C catalytic
triad, and are multimeric alpha-beta-beta-alpha sandwich
proteins.
Length = 172
Score = 83.9 bits (208), Expect = 7e-19
Identities = 51/202 (25%), Positives = 68/202 (33%), Gaps = 36/202 (17%)
Query: 5 KVATCNLNNWALDFDCNLKNIKESIGRAKEAGAVIRLGPELEITGYGCEDHFLELDTVTH 64
KVA L A D + NL+ + E I A GA + + PEL I GY E +
Sbjct: 1 KVALVQLPPSAFDLEANLQKLLELIEEAARQGADLVVLPELFIPGYA--HGATEYLELAE 58
Query: 65 A--WECLKDL--LLGDWTDGILCSFGMPVIKGSERYNCQVLCLNRKIIMIRPKLWLANDG 120
A E L+ L L GI G+P G YN VL ++ G
Sbjct: 59 AIPGETLQFLSALARKN--GITVVAGIPEKDGGGLYNTLVLIDPDGELL----------G 106
Query: 121 NYRELRWFT--AWKQKDQLEDFQLPNEISVALKQKSVPFGYGFIQFLDTAVAAEICEELF 178
YR+ W ++ + P G + IC E+
Sbjct: 107 KYRKRHLVPVGEWVERPLFGPGGATFPVF------DTPVG---------KLGLLICYEIR 151
Query: 179 TPIPPHADLALNGVEVFMNASG 200
P LAL G E+ N S
Sbjct: 152 FPELARM-LALKGAEILANPSA 172
>gnl|CDD|143610 cd07586, nitrilase_8, Uncharacterized subgroup of the nitrilase
superfamily (putative class 13 nitrilases). The
nitrilase superfamily is comprised of nitrile- or
amide-hydrolyzing enzymes and amide-condensing enzymes,
which depend on a Glu-Lys-Cys catalytic triad. This
superfamily has been classified in the literature based
on global and structure based sequence analysis into
thirteen different enzyme classes (referred to as 1-13).
Class 13 represents proteins that at the time were
difficult to place in a distinct similarity group; this
subgroup represents either a new class or one that was
included previously in class 13. Members of this
superfamily generally form homomeric complexes, the
basic building block of which is a homodimer.
Length = 269
Score = 65.0 bits (159), Expect = 1e-11
Identities = 65/268 (24%), Positives = 109/268 (40%), Gaps = 40/268 (14%)
Query: 17 DFDCNLKNIKESIGRAKEAGAVIRLGPELEITGYGCEDHFLELDTVTHAWECLKDLLLGD 76
D + NL+ E I A+E GA + + PEL +TGY D E+ L +
Sbjct: 13 DVEENLEKHLEIIETARERGADLVVFPELSLTGYNLGDLVYEVAMHADDPRLQA---LAE 69
Query: 77 WTDGILCSFGM-PVIKGSERYNCQVLCLNRKIIMIRPKLWLANDGNYRELRWFTAWKQKD 135
+ GI FG + YN + +++ + K++L G + E R+F
Sbjct: 70 ASGGICVVFGFVEEGRDGRFYNSAAYLEDGRVVHVHRKVYLPTYGLFEEGRYFAP---GS 126
Query: 136 QLEDFQLPNEISVALKQKSVPFGYGFIQFLDTAVAAEICEELFTPIPPHADLALNGVEVF 195
L F +F V ICE+ + P P+ LAL+G +V
Sbjct: 127 HLRAFD--------------------TRFGRAGVL--ICEDAWHPSLPYL-LALDGADVI 163
Query: 196 --MNASGSHHQLRKLDYRI--RAFISATHSRGGVYM-YSNHQGCDGGRLYFDGCSCVV-V 249
S + D + GVY+ ++N G + G +YF G S VV
Sbjct: 164 FIPANSPARGVGGDFDNEENWETLLKFYAMMNGVYVVFANRVGVEDG-VYFWGGSRVVDP 222
Query: 250 NGDMIAQGSQFSLKDVEIVVAQVDLDAV 277
+G+++A+ F + +++VA++D A+
Sbjct: 223 DGEVVAEAPLF---EEDLLVAELDRSAI 247
>gnl|CDD|143587 cd07197, nitrilase, Nitrilase superfamily, including nitrile- or
amide-hydrolyzing enzymes and amide-condensing enzymes.
This superfamily (also known as the C-N hydrolase
superfamily) contains hydrolases that break
carbon-nitrogen bonds; it includes nitrilases, cyanide
dihydratases, aliphatic amidases, N-terminal amidases,
beta-ureidopropionases, biotinidases, pantotheinase,
N-carbamyl-D-amino acid amidohydrolases, the glutaminase
domain of glutamine-dependent NAD+ synthetase,
apolipoprotein N-acyltransferases, and
N-carbamoylputrescine amidohydrolases, among others.
These enzymes depend on a Glu-Lys-Cys catalytic triad,
and work through a thiol acylenzyme intermediate.
Members of this superfamily generally form homomeric
complexes, the basic building block of which is a
homodimer. These oligomers include dimers, tetramers,
hexamers, octamers, tetradecamers, octadecamers, as well
as variable length helical arrangements and
homo-oligomeric spirals. These proteins have roles in
vitamin and co-enzyme metabolism, in detoxifying small
molecules, in the synthesis of signaling molecules, and
in the post-translational modification of proteins. They
are used industrially, as biocatalysts in the fine
chemical and pharmaceutical industry, in cyanide
remediation, and in the treatment of toxic effluent.
This superfamily has been classified previously in the
literature, based on global and structure-based sequence
analysis, into thirteen different enzyme classes
(referred to as 1-13). This hierarchy includes those
thirteen classes and a few additional subfamilies. A
putative distant relative, the plasmid-borne TraB
family, has not been included in the hierarchy.
Length = 253
Score = 59.3 bits (144), Expect = 9e-10
Identities = 78/300 (26%), Positives = 119/300 (39%), Gaps = 67/300 (22%)
Query: 6 VATCNLNNWALDFDCNLKNIKESIGRAKEAGAVIRLGPELEITGYGCEDHFLELDTVTHA 65
+A L D + NL I A E GA + + PEL +TGY E +LD A
Sbjct: 1 IAAVQLAPKIGDVEANLAKALRLIKEAAEQGADLIVLPELFLTGYSFESAKEDLD---LA 57
Query: 66 WECLKDLLLGDWTD---------GILCSFGMPVIKGSERYNCQVLCL-NRKIIMIRPKLW 115
E L G + GI G+ G + YN V+ + +II K+
Sbjct: 58 EE-----LDGPTLEALAELAKELGIYIVAGIAEKDGDKLYNTAVVIDPDGEIIGKYRKIH 112
Query: 116 LANDGNYRELRWFTAWKQKDQLEDFQLPNEISVALKQKSVPFGYGFIQFLDTAVAAEICE 175
L + G E R+F+ +E V P G + IC
Sbjct: 113 LFDFG---ERRYFSP------------GDEFPVF----DTPGGK---------IGLLICY 144
Query: 176 ELFTPIPPHA-DLALNGVEVFMNAS----GSHHQLRKLDYRIRAFISATHSRGGVY-MYS 229
+L P A +LAL G ++ + + L R RA + GVY + +
Sbjct: 145 DLR--FPELARELALKGADIILVPAAWPTARREHWELLL-RARAIEN------GVYVVAA 195
Query: 230 NHQGCDGGRLYFDGCSCVVV-NGDMIAQGSQFSLKDVEIVVAQVDLDAVAGFRGSISSFQ 288
N G +GG L F G S +V +G+++A+ S ++ I+VA++DLD + R S +
Sbjct: 196 NRVGEEGG-LEFAGGSMIVDPDGEVLAEAS----EEEGILVAELDLDELREARKRWSYLR 250
>gnl|CDD|234831 PRK00768, nadE, NAD synthetase; Reviewed.
Length = 268
Score = 45.1 bits (108), Expect = 4e-05
Identities = 27/72 (37%), Positives = 39/72 (54%), Gaps = 15/72 (20%)
Query: 327 PEEEI----AFGPGCWLWDYLRRSGASGFLLPLSGGADSSSVAAIVGCMCQLVVKEI--S 380
PEEEI F L DYL++SG +L +SGG DS+ + G + QL V+E+
Sbjct: 18 PEEEIRRRVDF-----LKDYLKKSGLKSLVLGISGGQDST----LAGRLAQLAVEELRAE 68
Query: 381 NGDEQVKADAIR 392
GD+ + A+R
Sbjct: 69 TGDDDYQFIAVR 80
Score = 43.2 bits (103), Expect = 2e-04
Identities = 30/101 (29%), Positives = 45/101 (44%), Gaps = 28/101 (27%)
Query: 483 NIQARIRMVLAFMLASLLPWVHNKPGFYLVLGSSNVDEGLRGYLTKYDCSSADINPIGSI 542
NI+AR RM+ + +A LV+G+ + E + G+ TK+ ADI P+ +
Sbjct: 134 NIKARERMIAQYAIAGA----TG----GLVVGTDHAAEAVTGFFTKFGDGGADILPLFGL 185
Query: 543 SKQDLRTFLRWAATHLGYSSLAEIEAAP-------PTAELE 576
+K+ R L LG AP PTA+LE
Sbjct: 186 NKRQGRALLA----ALG---------APEHLYEKVPTADLE 213
>gnl|CDD|179150 PRK00876, nadE, NAD synthetase; Reviewed.
Length = 326
Score = 44.2 bits (105), Expect = 1e-04
Identities = 61/271 (22%), Positives = 97/271 (35%), Gaps = 92/271 (33%)
Query: 343 LRRSGASGFLLPLSGGADSSSVAAIVGCMCQLVVKEISNGDEQVKADAIRIGHYANGEFP 402
LRR G +L LSGG DSS AA L V+ + G E+V
Sbjct: 31 LRRRGV---VLGLSGGIDSSVTAA-------LCVRAL--GKERV---------------- 62
Query: 403 TDSREFAKRIFYTVFMGSENSSQETRMLAKKLADEIGSWHLDVSIDTVVSAF-------- 454
Y + M +SS E+ L +++A+ +G ++ I + A
Sbjct: 63 -----------YGLLMPERDSSPESLRLGREVAEHLGVEYVVEDITPALEALGCYRRRDE 111
Query: 455 ---------------------------LSLF----QTLTGKRPCYKVDGGSNVENLGLQN 483
L++F Q G+ ++ + ++ + N
Sbjct: 112 AIRRVVPEYGPGWKSKIVLPNLLDGDGLNVFSLVVQDPDGEVTRKRLPANAYLQIVAATN 171
Query: 484 IQARIRMVLAFMLASLLPWVHNKPGFYLVLGSSNVDEGLRGYLTKYDCSSADINPIGSIS 543
+ R R ++ + A L N Y V G+ N E +G+ K +AD+ PI +
Sbjct: 172 FKQRTRKMVEYYHADRL----N----YAVAGTPNRLEYDQGFFVKNGDGAADLKPIAHLY 223
Query: 544 KQDLRTFLRWAATHLGYSSLAEIEAAPPTAE 574
K T + A HLG EI PPT +
Sbjct: 224 K----TQVYALAEHLGVP--EEIRRRPPTTD 248
>gnl|CDD|143609 cd07585, nitrilase_7, Uncharacterized subgroup of the nitrilase
superfamily (putative class 13 nitrilases). The
nitrilase superfamily is comprised of nitrile- or
amide-hydrolyzing enzymes and amide-condensing enzymes,
which depend on a Glu-Lys-Cys catalytic triad. This
superfamily has been classified in the literature based
on global and structure based sequence analysis into
thirteen different enzyme classes (referred to as 1-13).
Class 13 represents proteins that at the time were
difficult to place in a distinct similarity group; this
subgroup represents either a new class or one that was
included previously in class 13. Members of this
superfamily generally form homomeric complexes, the
basic building block of which is a homodimer.
Length = 261
Score = 40.8 bits (96), Expect = 0.001
Identities = 64/271 (23%), Positives = 98/271 (36%), Gaps = 42/271 (15%)
Query: 17 DFDCNLKNIKESIGRAKEAGAVIRLGPELEITGYGCEDH-FLELDTVT-HAWECLKDLLL 74
D NL I +A GA + PE+ ITGY E + + + L DL
Sbjct: 13 DKARNLAVIARWTRKAAAQGAELVCFPEMCITGYTHVRALSREAEVPDGPSTQALSDLAR 72
Query: 75 GDWTDGILCSFGMPVIKGSERYNCQVLCLNRKIIMIRPKLWLANDGNYRELRWFTAWKQK 134
G+ G+ G YN ++CL ++ KL L RE + A
Sbjct: 73 ---RYGLTILAGLIEKAGDRPYNTYLVCLPDGLVHRYRKLHLFR----REHPYIAA---G 122
Query: 135 DQLEDFQLPNEISVALKQKSVPFGYGFIQFLDTAVAAEICEELFTPIPPHADLALNGVEV 194
D+ F P IC + P A AL G E+
Sbjct: 123 DEYPVFATP----------------------GVRFGILICYDNHFPENVRA-TALLGAEI 159
Query: 195 -FM-NASGSHHQLRKLDYRIRAFISATHSRGGVYMYSNHQGCDGGRLYFDGCSCVV-VNG 251
F +A+ + ++ +R + + G N G DGG + F G + ++ G
Sbjct: 160 LFAPHATPGTTSPKGREWWMRWLPARAYDNGVFVAACNGVGRDGGEV-FPGGAMILDPYG 218
Query: 252 DMIAQGSQFSLKDVEIVVAQVDLDAVAGFRG 282
++A+ S D +VVA +DLD + RG
Sbjct: 219 RVLAE--TTSGGD-GMVVADLDLDLINTVRG 246
>gnl|CDD|143600 cd07576, R-amidase_like, Pseudomonas sp. MCI3434 R-amidase and
related proteins (putative class 13 nitrilases).
Pseudomonas sp. MCI3434 R-amidase hydrolyzes
(R,S)-piperazine-2-tert-butylcarboxamide to form
(R)-piperazine-2-carboxylic acid. It does so with strict
R-stereoselectively. Its preferred substrates are
carboxamide compounds which have the amino or imino
group connected to their beta- or gamma-carbon. This
subgroup belongs to a larger nitrilase superfamily
comprised of nitrile- or amide-hydrolyzing enzymes and
amide-condensing enzymes, which depend on a Glu-Lys-Cys
catalytic triad. This superfamily has been classified in
the literature based on global and structure based
sequence analysis into thirteen different enzyme classes
(referred to as 1-13), class 13 represents proteins that
at the time were difficult to place in a distinct
similarity group. It has been suggested that this
subgroup represents a new class. Members of the
nitrilase superfamily generally form homomeric
complexes, the basic building block of which is a
homodimer. Native R-amidase however appears to be a
monomer.
Length = 254
Score = 35.6 bits (83), Expect = 0.045
Identities = 64/275 (23%), Positives = 95/275 (34%), Gaps = 69/275 (25%)
Query: 21 NLKNIKESIGRAKEAGAVIRLGPELEITGYGCEDHFLELDTVTHAWECLKDLLLGDWTD- 79
NL + E+ RA AGA + + PEL +TGY D V E L
Sbjct: 17 NLARLDEAAARAAAAGADLLVFPELFLTGYNIGDA------VARLAEPADGPALQALRAI 70
Query: 80 ----GILCSFGMPVIKGSERYNCQVLCLNRKIIMIRPKLWLANDG----NYRELRWFTAW 131
GI G P G YN VL + DG NYR+ F
Sbjct: 71 ARRHGIAIVVGYPERAGGAVYNAAVL--------------IDEDGTVLANYRKTHLFGDS 116
Query: 132 KQKDQLEDFQLPNEISVALKQKSVPFGYGFIQFLDTAVAAEICEEL-FTPIPPHA-DLAL 189
++ F + V V G V IC ++ F P LAL
Sbjct: 117 ERA----AFTPGDRFPV------VELR-GL------RVGLLICYDVEF---PELVRALAL 156
Query: 190 NGVEVFM----NASGSHHQLRKLDYRIRAFISATHSRGGVYM-YSNHQGCDGGRLYFDGC 244
G ++ + R L RAF + +++ Y+N G L + G
Sbjct: 157 AGADLVLVPTALMEPYGFVARTL-VPARAFEN------QIFVAYANRCG-AEDGLTYVGL 208
Query: 245 SCVVV-NGDMIAQGSQFSLKDVEIVVAQVDLDAVA 278
S + +G ++A+ + ++VA +D A+A
Sbjct: 209 SSIAGPDGTVLARAG----RGEALLVADLDPAALA 239
>gnl|CDD|185554 PTZ00323, PTZ00323, NAD+ synthase; Provisional.
Length = 294
Score = 35.5 bits (82), Expect = 0.052
Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 7/43 (16%)
Query: 332 AFGPGCW-------LWDYLRRSGASGFLLPLSGGADSSSVAAI 367
AF P W L +Y+RR G G + +SGG DS+ V A+
Sbjct: 23 AFNPAAWIEKKCAKLNEYMRRCGLKGCVTSVSGGIDSAVVLAL 65
>gnl|CDD|236038 PRK07521, flgK, flagellar hook-associated protein FlgK; Validated.
Length = 483
Score = 35.3 bits (82), Expect = 0.095
Identities = 20/62 (32%), Positives = 26/62 (41%), Gaps = 12/62 (19%)
Query: 236 GGRLYFDGCSCVVVNGD----MIAQGS---QFSLKDVEIVVAQVDLDAVAGFRGSISSFQ 288
G +Y DG V + G +A GS L+D Q LD +A RG I+ F
Sbjct: 249 GNAVYIDG---VPLTGGSGVMPLAGGSLAALLQLRDEIAPTYQAQLDEIA--RGLITRFA 303
Query: 289 EQ 290
E
Sbjct: 304 ES 305
>gnl|CDD|143607 cd07583, nitrilase_5, Uncharacterized subgroup of the nitrilase
superfamily (putative class 13 nitrilases). The
nitrilase superfamily is comprised of nitrile- or
amide-hydrolyzing enzymes and amide-condensing enzymes,
which depend on a Glu-Lys-Cys catalytic triad. This
superfamily has been classified in the literature based
on global and structure based sequence analysis into
thirteen different enzyme classes (referred to as 1-13).
Class 13 represents proteins that at the time were
difficult to place in a distinct similarity group; this
subgroup represents either a new class or one that was
included previously in class 13. Members of this
superfamily generally form homomeric complexes, the
basic building block of which is a homodimer.
Length = 253
Score = 34.4 bits (80), Expect = 0.11
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 6/57 (10%)
Query: 233 GCDGGRLYFDGCSCVV-VNGDMIAQGSQFSLKDVEIVVAQVDLDAVAGFRGSISSFQ 288
G DGG + G S V+ G+++A+ + + EI+ A++DL+ VA R I F+
Sbjct: 199 GTDGGNEFG-GHSMVIDPWGEVLAEAGE----EEEILTAEIDLEEVAEVRKKIPVFK 250
>gnl|CDD|233454 TIGR01536, asn_synth_AEB, asparagine synthase
(glutamine-hydrolyzing). This model describes the
glutamine-hydrolysing asparagine synthase. A poorly
conserved C-terminal extension was removed from the
model. Bacterial members of the family tend to have a
long, poorly conserved insert lacking from archaeal and
eukaryotic sequences. Multiple isozymes have been
demonstrated, such as in Bacillus subtilis. Long-branch
members of the phylogenetic tree (which typically were
also second or third candidate members from their
genomes) were removed from the seed alignment and score
below trusted cutoff [Amino acid biosynthesis, Aspartate
family].
Length = 466
Score = 34.2 bits (79), Expect = 0.17
Identities = 20/102 (19%), Positives = 34/102 (33%), Gaps = 37/102 (36%)
Query: 355 LSGGADSSSVAAIVGCMCQLVVKEISNGDEQVKADAIRIGHYANGEFPTDSREFAKRIFY 414
LSGG DSS VAAI + + +
Sbjct: 259 LSGGLDSSLVAAI--------------ARREAPRGPVHT--------------------F 284
Query: 415 TVFMGSENSSQETRMLAKKLADEIGSWH--LDVSIDTVVSAF 454
++ E+ A+K+AD +G+ H + S++ + A
Sbjct: 285 SIGFEGSPDFDESPY-ARKVADHLGTEHHEVLFSVEEGLDAL 325
>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM1 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 84
Score = 30.0 bits (68), Expect = 0.71
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 151 KQKSVPFGYGFIQFLDTAVAAEICEELF-TPIP 182
K P GY F++F D A A +L PIP
Sbjct: 36 KLTGGPAGYCFVEFADEATAERCLHKLNGKPIP 68
>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM2 of TDP-43 (also termed
TARDBP), a ubiquitously expressed pathogenic protein
whose normal function and abnormal aggregation are
directly linked to the genetic disease cystic fibrosis,
and two neurodegenerative disorders: frontotemporal
lobar degeneration (FTLD) and amyotrophic lateral
sclerosis (ALS). TDP-43 binds both DNA and RNA, and has
been implicated in transcriptional repression, pre-mRNA
splicing and translational regulation. TDP-43 is a
dimeric protein with two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
glycine-rich domain. The RRMs are responsible for DNA
and RNA binding; they bind to TAR DNA and RNA sequences
with UG-repeats. The glycine-rich domain can interact
with the hnRNP family proteins to form the hnRNP-rich
complex involved in splicing inhibition. It is also
essential for the cystic fibrosis transmembrane
conductance regulator (CFTR) exon 9-skipping activity. .
Length = 71
Score = 29.5 bits (67), Expect = 0.75
Identities = 13/40 (32%), Positives = 17/40 (42%), Gaps = 10/40 (25%)
Query: 156 PF-GYGFIQFLDTAVAAEICEELFTPIPPHADLALNGVEV 194
PF + F+ F D VA +C E D + GV V
Sbjct: 35 PFRAFAFVTFADPEVAQSLCGE---------DHIIKGVSV 65
>gnl|CDD|238949 cd01991, Asn_Synthase_B_C, The C-terminal domain of Asparagine
Synthase B. This domain is always found associated
n-terminal amidotransferase domain. Family members that
contain this domain catalyse the conversion of aspartate
to asparagine. Asparagine synthetase B catalyzes the
assembly of asparagine from aspartate, Mg(2+)ATP, and
glutamine. The three-dimensional architecture of the
N-terminal domain of asparagine synthetase B is similar
to that observed for glutamine
phosphoribosylpyrophosphate amidotransferase while the
molecular motif of the C-domain is reminiscent to that
observed for GMP synthetase .
Length = 269
Score = 31.2 bits (71), Expect = 1.2
Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 15/60 (25%)
Query: 353 LPLSGGADSSSVAAIVGCMCQLVVKEISNGDEQVKADAIRIGHYANGEFPTDSREFAKRI 412
+ LSGG DSS VAA+ +L E VK +I G +D RE+A+R+
Sbjct: 20 VLLSGGLDSSLVAAL---AARL-------LPEPVKTFSIGF-----GFEGSDEREYARRV 64
>gnl|CDD|143593 cd07569, DCase, N-carbamyl-D-amino acid amidohydrolase (DCase,
class 6 nitrilases). DCase hydrolyses
N-carbamyl-D-amino acids to produce D-amino acids. It is
an important biocatalyst in the pharmaceutical industry,
producing useful D-amino acids for example in the
preparation of beta-lactam antibiotics. This subgroup
belongs to a larger nitrilase superfamily comprised of
nitrile- or amide-hydrolyzing enzymes and
amide-condensing enzymes, which depend on a Glu-Lys-Cys
catalytic triad. This superfamily has been classified in
the literature based on global and structure based
sequence analysis into thirteen different enzyme classes
(referred to as 1-13), this subgroup corresponds to
class 6. Members of this superfamily generally form
homomeric complexes, the basic building block of which
is a homodimer. Agrobacterium radiobacter DCase forms a
tetramer (dimer of dimers). Some DCases may form
trimers.
Length = 302
Score = 31.5 bits (72), Expect = 1.2
Identities = 17/46 (36%), Positives = 29/46 (63%), Gaps = 4/46 (8%)
Query: 243 GCSCVVV-NGDMIAQGSQFSLKDVEIVVAQVDLDAVAGFRGSISSF 287
G SC+V G+++AQ + +L+D E++VA DLD R ++ +F
Sbjct: 246 GGSCIVAPTGEIVAQAT--TLED-EVIVADCDLDLCREGRETVFNF 288
>gnl|CDD|107331 cd06336, PBP1_ABC_ligand_binding_like_3, Type I periplasmic
ligand-binding domain of uncharacterized ABC (ATPase
Binding Cassette)-type active transport systems that are
predicted to be involved in transport of amino acids,
peptides, or inorganic ions. This group includes the
type I periplasmic ligand-binding domain of
uncharacterized ABC (ATPase Binding Cassette)-type
active transport systems that are predicted to be
involved in transport of amino acids, peptides, or
inorganic ions. Members of this group are
sequence-similar to members of the family of ABC-type
hydrophobic amino acid transporters (HAAT), such as
leucine-isoleucine-valine-binding protein (LIVBP);
however their ligand specificity has not been determined
experimentally.
Length = 347
Score = 31.1 bits (71), Expect = 1.8
Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 5/66 (7%)
Query: 350 GFLLPLSGGADSSSVAAIVGCMCQLVVKEIS-NGDEQVKADA--IRIGHYANGEFPTDSR 406
GF PLSG A + + + G QL +EI+ G +V + I Y + P ++
Sbjct: 3 GFSGPLSGPAAAWGLPGLRG--VQLAAEEINAAGGIKVGGKKYKVEIVSYDDKYDPAEAA 60
Query: 407 EFAKRI 412
A+R+
Sbjct: 61 ANARRL 66
>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding
protein 19 (RBM19 or RBD-1) and similar proteins. This
subfamily corresponds to the RRM5 of RBM19 and RRM4 of
MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1),
is a nucleolar protein conserved in eukaryotes involved
in ribosome biogenesis by processing rRNA and is
essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 82
Score = 28.3 bits (64), Expect = 2.3
Identities = 8/27 (29%), Positives = 13/27 (48%)
Query: 151 KQKSVPFGYGFIQFLDTAVAAEICEEL 177
K + GYGF++F A + + L
Sbjct: 41 PGKLLSMGYGFVEFKSKEAAQKALKRL 67
>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43) and similar
proteins. This subfamily corresponds to the RRM1 in
tRNA selenocysteine-associated protein 1 (SECp43), yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8, and similar proteins. SECp43 is an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. Yeast proteins, NGR1 and NAM8, show
high sequence similarity with SECp43. NGR1 is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA). It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains three RRMs, two of which are followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the C-terminus which also
harbors a methionine-rich region. NAM8 is a putative
RNA-binding protein that acts as a suppressor of
mitochondrial splicing deficiencies when overexpressed
in yeast. It may be a non-essential component of the
mitochondrial splicing machinery. NAM8 also contains
three RRMs. .
Length = 81
Score = 28.0 bits (63), Expect = 3.0
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 151 KQKSVPFGYGFIQFLDTAVAAEICEELF-TPIP 182
KQ GYGF++F A + + L PIP
Sbjct: 35 KQTGKSAGYGFVEFATHEAAEQALQSLNGKPIP 67
>gnl|CDD|185431 PTZ00077, PTZ00077, asparagine synthetase-like protein;
Provisional.
Length = 586
Score = 30.1 bits (68), Expect = 3.6
Identities = 18/37 (48%), Positives = 20/37 (54%), Gaps = 7/37 (18%)
Query: 351 FLLPLSGGADSSSVAAIVGCMCQLVVKEISNGDEQVK 387
F L LSGG DSS VAAI V K I NG+ +
Sbjct: 240 FGLFLSGGLDSSIVAAI-------VAKLIKNGEIDLS 269
>gnl|CDD|143604 cd07580, nitrilase_2, Uncharacterized subgroup of the nitrilase
superfamily (putative class 13 nitrilases). The
nitrilase superfamily is comprised of nitrile- or
amide-hydrolyzing enzymes and amide-condensing enzymes,
which depend on a Glu-Lys-Cys catalytic triad. This
superfamily has been classified in the literature based
on global and structure based sequence analysis into
thirteen different enzyme classes (referred to as 1-13).
Class 13 represents proteins that at the time were
difficult to place in a distinct similarity group; this
subgroup represents either a new class or one that was
included previously in class 13. Members of this
superfamily generally form homomeric complexes, the
basic building block of which is a homodimer.
Length = 268
Score = 29.6 bits (67), Expect = 3.7
Identities = 35/131 (26%), Positives = 45/131 (34%), Gaps = 12/131 (9%)
Query: 5 KVATCNLNNWALDFDCNLKNIKESIGRAKEAGAVIRLGPELEITGYGCEDHFLELDTVTH 64
+VA + D D NL E I A +AGA + + PEL TGY E +
Sbjct: 1 RVACVQFDPRVGDLDANLARSIELIREAADAGANLVVLPELANTGYVFES---RDEAFAL 57
Query: 65 AWECLKDLLLGDWTD-----GILCSFGMPVIKGSERYNCQVLCLNRKIIMIRPKLWLAND 119
A E W + G+ G G YN VL +I K L N+
Sbjct: 58 AEEVPDGASTRAWAELAAELGLYIVAGFAERDGDRLYNSAVLVGPDGVIGTYRKAHLWNE 117
Query: 120 GNYRELRWFTA 130
E F
Sbjct: 118 ----EKLLFEP 124
>gnl|CDD|143597 cd07573, CPA, N-carbamoylputrescine amidohydrolase (CPA) (class
11 nitrilases). CPA (EC 3.5.1.53, also known as
N-carbamoylputrescine amidase and carbamoylputrescine
hydrolase) converts N-carbamoylputrescine to
putrescine, a step in polyamine biosynthesis in plants
and bacteria. This subgroup includes Arabidopsis
thaliana CPA, also known as nitrilase-like 1 (NLP1),
and Pseudomonas aeruginosa AguB. This subgroup belongs
to a larger nitrilase superfamily comprised of nitrile-
or amide-hydrolyzing enzymes and amide-condensing
enzymes, which depend on a Glu-Lys-Cys catalytic triad.
This superfamily has been classified in the literature
based on global and structure based sequence analysis
into thirteen different enzyme classes (referred to as
1-13), this subgroup corresponds to class 11. Members
of this superfamily generally form homomeric complexes,
the basic building block of which is a homodimer; P.
aeruginosa AugB is a homohexamer, Arabidopsis thaliana
NLP1 is a homooctomer.
Length = 284
Score = 29.8 bits (68), Expect = 3.8
Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 4/47 (8%)
Query: 14 WALDFDCNLKNIKESIGRAKEAGAVIRLGPELEITGYGC----EDHF 56
+ D + NL +E + A GA I EL T Y C ED+F
Sbjct: 10 CSEDPEANLAKAEELVREAAAQGAQIVCLQELFETPYFCQEEDEDYF 56
Score = 28.7 bits (65), Expect = 7.7
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 4/52 (7%)
Query: 231 HQGCDGGRLYFDGCSCVV-VNGDMIAQGSQFSLKDVEIVVAQVDLDAVAGFR 281
+G G + F G S + G+++AQ S+ + EI+VA+ DLD + R
Sbjct: 217 VEGDPGSGITFYGSSFIADPFGEILAQASR---DEEEILVAEFDLDEIEEVR 265
>gnl|CDD|183745 PRK12787, fliX, flagellar assembly regulator FliX; Reviewed.
Length = 138
Score = 28.4 bits (64), Expect = 4.7
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 344 RRSGASGFLLPLSGGADSSSVAAIVG 369
RR+G+SGF LP + + A+
Sbjct: 19 RRTGSSGFSLPDESASGAGEARAVSA 44
>gnl|CDD|143606 cd07582, nitrilase_4, Uncharacterized subgroup of the nitrilase
superfamily (putative class 13 nitrilases). The
nitrilase superfamily is comprised of nitrile- or
amide-hydrolyzing enzymes and amide-condensing enzymes,
which depend on a Glu-Lys-Cys catalytic triad. This
superfamily has been classified in the literature based
on global and structure based sequence analysis into
thirteen different enzyme classes (referred to as 1-13).
Class 13 represents proteins that at the time were
difficult to place in a distinct similarity group; this
subgroup represents either a new class or one that was
included previously in class 13. Members of this
superfamily generally form homomeric complexes, the
basic building block of which is a homodimer.
Length = 294
Score = 29.2 bits (66), Expect = 5.4
Identities = 28/135 (20%), Positives = 46/135 (34%), Gaps = 24/135 (17%)
Query: 157 FGYGFIQFL---DTAV---AAEICEELFTPIPPHADLALNGVEVFMNASGSHHQ----LR 206
+GYG DT + CEE P LA+NG EV + +S
Sbjct: 150 YGYGLDALFPVADTEIGNLGCLACEEGLYPEVARG-LAMNGAEVLLRSSSEVPSVELDPW 208
Query: 207 KLDYRIRA-----FISATHSRGGVYMYSNHQGCDGGRLYFDGCSCVVVNGDMIAQGSQFS 261
++ R RA ++ + +S G GG + D V+
Sbjct: 209 EIANRARALENLAYVVSANSGGIYGSPYPADSFGGGSMIVDYKGRVLAEAGYGPGSM--- 265
Query: 262 LKDVEIVVAQVDLDA 276
+ A++D++A
Sbjct: 266 -----VAGAEIDIEA 275
>gnl|CDD|224315 COG1397, DraG, ADP-ribosylglycohydrolase [Posttranslational
modification, protein turnover, chaperones].
Length = 314
Score = 29.3 bits (66), Expect = 5.5
Identities = 11/56 (19%), Positives = 21/56 (37%), Gaps = 8/56 (14%)
Query: 358 GADSSSVAAIVGCMCQLVVKEISNGDEQVKADAIRIGHYANGEFPTDSREFAKRIF 413
G D+ ++AAI G + G+E + + + + D E A +
Sbjct: 266 GGDTDTIAAITGAIAG-----AYYGEEAIPQQLLA---ELDEDLIGDLAELAYALA 313
>gnl|CDD|216090 pfam00733, Asn_synthase, Asparagine synthase. This family is
always found associated with pfam00310. Members of this
family catalyze the conversion of aspartate to
asparagine.
Length = 195
Score = 28.7 bits (65), Expect = 6.2
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 355 LSGGADSSSVAAI 367
LSGG DSS +AA+
Sbjct: 24 LSGGLDSSLIAAL 36
>gnl|CDD|225467 COG2915, COG2915, Uncharacterized protein involved in purine
metabolism [General function prediction only].
Length = 207
Score = 28.5 bits (64), Expect = 8.7
Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 3/52 (5%)
Query: 442 HLDVSIDTVVSAFLSLFQ-TLTGKRPCYKVDGGSNVENLGLQNIQARIRMVL 492
H D+ +T++S S++ ++ P +V G L +QA+IR +L
Sbjct: 120 HFDLQSETMLSTLASIYVDVISPLGPRIQVTGSPAY--LQQPQVQAKIRALL 169
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 0.137 0.425
Gapped
Lambda K H
0.267 0.0703 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 30,349,968
Number of extensions: 2979005
Number of successful extensions: 2426
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2393
Number of HSP's successfully gapped: 49
Length of query: 591
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 489
Effective length of database: 6,413,494
Effective search space: 3136198566
Effective search space used: 3136198566
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 (21.9 bits)
S2: 62 (27.7 bits)