RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780588|ref|YP_003065001.1| acetyl-CoA carboxylase
carboxyltransferase subunit alpha [Candidatus Liberibacter asiaticus
str. psy62]
(317 letters)
>gnl|CDD|31167 COG0825, AccA, Acetyl-CoA carboxylase alpha subunit [Lipid
metabolism].
Length = 317
Score = 443 bits (1141), Expect = e-125
Identities = 179/317 (56%), Positives = 235/317 (74%), Gaps = 1/317 (0%)
Query: 1 MRHYLDFEEPISDLEAKIHELKKLSREDINEDFSEEIRELEAMVCKTLSEIYSKLTPWQK 60
M +YLDFE+PI++LEAKI ELK L+ E+ + D S+EI LE + + +IYS LTPWQ+
Sbjct: 1 MANYLDFEKPIAELEAKIDELKALA-EENDVDLSDEIERLEKRLAELTKKIYSNLTPWQR 59
Query: 61 TQVSRHPNRPHYIDYINSLFTHFISLAGDRLFGDDPAMQIGLARFHGQPVAIIGQEKGSD 120
Q++RHP+RP+ +DYI LFT F+ L GDR F DDPA+ GLARF GQPV +IG +KG D
Sbjct: 60 VQLARHPDRPYTLDYIELLFTDFVELHGDRAFADDPAIVGGLARFGGQPVVVIGHQKGRD 119
Query: 121 TKSRIKHNFGSPRPEGYRKAVRLMEMADRFKIPVISFIDTAGAYPGVDAEARGQGEAIAR 180
TK ++K NFG PRPEGYRKA+RLM++A++F +P+I+FIDT GAYPG+ AE RGQ EAIAR
Sbjct: 120 TKEKLKRNFGMPRPEGYRKALRLMKLAEKFGLPIITFIDTPGAYPGIGAEERGQSEAIAR 179
Query: 181 ATEMCLKLQVPILSIIIGEGGSGGAMGIAAANFVYMLEHAIYSVISPEGAASILWRDSSR 240
+L+VPI+SI+IGEGGSGGA+ I A+ V MLE++ YSVISPEG ASILW+D+S+
Sbjct: 180 NLREMARLKVPIISIVIGEGGSGGALAIGVADRVLMLENSTYSVISPEGCASILWKDASK 239
Query: 241 AAQAAIAMKIIATDLQDLSIIDGIIPEPIGGAHRNPAQTISSVGEIISQFLSETSTYSET 300
A +AA AMKI A DL++L IIDGIIPEP+GGAHR+P ++ + + L E E
Sbjct: 240 AKEAAEAMKITAHDLKELGIIDGIIPEPLGGAHRDPEAAAEALKNALLKELHELDKLPEE 299
Query: 301 EIREHRRQKYLNIGRNL 317
E+ R Q++ +IG
Sbjct: 300 ELLARRYQRFRSIGLFE 316
>gnl|CDD|164574 CHL00198, accA, acetyl-CoA carboxylase carboxyltransferase alpha
subunit; Provisional.
Length = 322
Score = 307 bits (787), Expect = 4e-84
Identities = 129/313 (41%), Positives = 197/313 (62%), Gaps = 3/313 (0%)
Query: 3 HYLDFEEPISDLEAKIHELKKLS-REDINEDFSEEIRELEAMVCKTLSEIYSKLTPWQKT 61
H DF +P+++LE+++ EL KL+ + D + +++ + + EI+ LTP Q+
Sbjct: 7 HVPDFMKPLAELESQVEELSKLAPKNDKVIN--NKLKSFQRKLRILKKEIFYSLTPLQRL 64
Query: 62 QVSRHPNRPHYIDYINSLFTHFISLAGDRLFGDDPAMQIGLARFHGQPVAIIGQEKGSDT 121
+ R RP +DYI + +I L GDR DDPA+ G+ + +G+ + +G ++G +T
Sbjct: 65 HLVRQSERPTTLDYIPYILDEWIELHGDRGGSDDPALVGGIGKINGRTIVFLGHQRGRNT 124
Query: 122 KSRIKHNFGSPRPEGYRKAVRLMEMADRFKIPVISFIDTAGAYPGVDAEARGQGEAIARA 181
K + NFG P P GYRKA+RLM+ A++F +P+++FIDT GA+ GV AE GQGEAIA
Sbjct: 125 KENVLRNFGMPSPGGYRKALRLMKHANKFGLPILTFIDTPGAWAGVKAEKLGQGEAIAVN 184
Query: 182 TEMCLKLQVPILSIIIGEGGSGGAMGIAAANFVYMLEHAIYSVISPEGAASILWRDSSRA 241
+VPI+ IIGEGGSGGA+GI + + MLE+A+Y+V +PE A+ILW+DS ++
Sbjct: 185 LREMFSFEVPIICTIIGEGGSGGALGIGIGDSIMMLEYAVYTVATPEACAAILWKDSKKS 244
Query: 242 AQAAIAMKIIATDLQDLSIIDGIIPEPIGGAHRNPAQTISSVGEIISQFLSETSTYSETE 301
AA A+KI + DL+ L IID IIPEPIGGA +PA + + + + L S +E
Sbjct: 245 LDAAEALKITSEDLKVLGIIDEIIPEPIGGAQADPASASKILKKKLIRQLDFLKILSPSE 304
Query: 302 IREHRRQKYLNIG 314
++ HR +K+ +G
Sbjct: 305 LKAHRYEKFRKLG 317
>gnl|CDD|112085 pfam03255, ACCA, Acetyl co-enzyme A carboxylase carboxyltransferase
alpha subunit. Acetyl co-enzyme A carboxylase
carboxyltransferase is composed of an alpha and beta
subunit.
Length = 145
Score = 207 bits (529), Expect = 3e-54
Identities = 78/146 (53%), Positives = 104/146 (71%), Gaps = 1/146 (0%)
Query: 3 HYLDFEEPISDLEAKIHELKKLSREDINEDFSEEIRELEAMVCKTLSEIYSKLTPWQKTQ 62
L+FE+P+++LEAKI EL+KL+R++ + D S+EI LE + K EIYS LTPWQ+ Q
Sbjct: 1 VLLEFEKPLAELEAKIDELRKLARKN-DVDVSDEIHRLEKKLDKLKREIYSNLTPWQRVQ 59
Query: 63 VSRHPNRPHYIDYINSLFTHFISLAGDRLFGDDPAMQIGLARFHGQPVAIIGQEKGSDTK 122
++RHP+RP +DYI ++ FI L GDR DDPA+ GL R G+PV +IG +KG DTK
Sbjct: 60 LARHPDRPTTLDYIENILDDFIELHGDRAGADDPAIVGGLGRIDGRPVVVIGHQKGRDTK 119
Query: 123 SRIKHNFGSPRPEGYRKAVRLMEMAD 148
+ NFG P PEGYRKA+RLM+ AD
Sbjct: 120 ENLLRNFGMPAPEGYRKALRLMKHAD 145
>gnl|CDD|144579 pfam01039, Carboxyl_trans, Carboxyl transferase domain. All of the
members in this family are biotin dependent
carboxylases. The carboxyl transferase domain carries
out the following reaction; transcarboxylation from
biotin to an acceptor molecule. There are two recognized
types of carboxyl transferase. One of them uses acyl-CoA
and the other uses 2-oxoacid as the acceptor molecule of
carbon dioxide. All of the members in this family
utilize acyl-CoA as the acceptor molecule.
Length = 487
Score = 88.5 bits (220), Expect = 2e-18
Identities = 48/190 (25%), Positives = 72/190 (37%), Gaps = 35/190 (18%)
Query: 100 IGLARFHGQPVAIIGQEKGSDTKSRIKHNFGSPRPEGYRKAVRLMEMADRFKIPVISFID 159
G AR G PV ++ + + G + KA R + + D F IP++ +D
Sbjct: 284 TGFARLGGIPVGVVANQP--------RVLAGVLFIDSADKAARFIRLCDAFNIPLVILVD 335
Query: 160 TAGAYPGVDAEARGQGEAIARATEMCL----KLQVPILSIIIGE--GGSGGAMGIAA--A 211
G PG D E G I + L + VP +++I + GG+ M A
Sbjct: 336 VPGFLPGTDQEYGG----ILKHGAKLLYALAEATVPKITVIPRKAYGGAYVVMDSKINGA 391
Query: 212 NFVYMLEHAIYSVISPEGAASILWRDSSRAA-------QAAIAMKIIATDLQDLSI---- 260
+ V A +V+ PEGA I +R AA +A A KI + Q
Sbjct: 392 DAVAAWPTARIAVMGPEGAVEIKFRKELAAATMRYKDLEALRAQKIAEYEEQLSPPYVAA 451
Query: 261 ----IDGIIP 266
D +I
Sbjct: 452 ARGFADLVID 461
Score = 34.9 bits (81), Expect = 0.029
Identities = 25/99 (25%), Positives = 38/99 (38%), Gaps = 6/99 (6%)
Query: 125 IKHNF-----GSPRPEGYRKAVRLMEMADRFKIPVISFIDTAGAYPGVDAEARGQGEAIA 179
+ GS P K R ME+A + P+I D+ GA E I
Sbjct: 61 VVAQDFTVWGGSLGPAHGFKITRAMELAIKEGEPLIGINDSGGARIQEGVENLRGYGLIF 120
Query: 180 RATEMCLKLQVPILSIIIGEGGSGGAMGIAAANFVYMLE 218
A +P +S++ G GGA A +F+ M++
Sbjct: 121 GANSR-ASGVIPQISLVTGPCAGGGAYSPALGDFIIMVK 158
>gnl|CDD|34408 COG4799, COG4799, Acetyl-CoA carboxylase, carboxyltransferase
component (subunits alpha and beta) [Lipid metabolism].
Length = 526
Score = 82.2 bits (203), Expect = 2e-16
Identities = 49/190 (25%), Positives = 78/190 (41%), Gaps = 27/190 (14%)
Query: 96 PAMQIGLARFHGQPVAIIGQEKGSDTKSRIKHNFGSPRPEGYRKAVRLMEMADRFKIPVI 155
+ G AR G+PV II + +H G + KA R + + D F IP++
Sbjct: 312 KNIVTGFARIDGRPVGIIANQP--------RHLGGVLDIDSADKAARFIRLCDAFNIPLV 363
Query: 156 SFIDTAGAYPGVDAEARGQGEAIARATEMCLKLQVPILSIIIGEGGSGGAMGIAA----A 211
+DT G PG D E G + A+ + VP +++I + G +
Sbjct: 364 FLVDTPGFMPGTDQEYGGIIKHGAKLLYAVAEATVPKITVITRKAYGGAYYVMGGKALGP 423
Query: 212 NFVYMLEHAIYSVISPEGAASILWR----DSSRAAQAAIAMK--IIATDLQDLS------ 259
+F Y A +V+ PEGA SIL+R + R + ++ +IA + S
Sbjct: 424 DFNYAWPTAEIAVMGPEGAVSILYRKELAAAERPEEREALLRKQLIAEYEEQFSNPYYAA 483
Query: 260 ---IIDGIIP 266
ID +I
Sbjct: 484 ERGYIDAVID 493
Score = 47.9 bits (114), Expect = 4e-06
Identities = 32/147 (21%), Positives = 55/147 (37%), Gaps = 17/147 (11%)
Query: 75 YINSLFTHFISLAGDRLFGDDPAMQIGLARFHGQPVAIIGQ---EKGSDTKSRIKHNFGS 131
+ +L H + + L GD + G+ +G+ V + KG G+
Sbjct: 60 ELGALAGHRMGGDANELPGD--GVVTGIGTINGRKVFVFANDFTVKG-----------GT 106
Query: 132 PRPEGYRKAVRLMEMADRFKIPVISFIDTAGAYPGVDAEARGQGEAIARATEMCLKLQVP 191
+K +R E+A +PVI D+ GA + I +P
Sbjct: 107 LGEMTAKKILRAQELAIENGLPVIGLNDSGGARIQEGVPSLAGYGRIFYRNAR-ASGVIP 165
Query: 192 ILSIIIGEGGSGGAMGIAAANFVYMLE 218
+S+++G GGA A +FV M+
Sbjct: 166 QISVVMGPCAGGGAYSPALTDFVIMVR 192
>gnl|CDD|35760 KOG0540, KOG0540, KOG0540, 3-Methylcrotonyl-CoA carboxylase,
non-biotin containing subunit/Acetyl-CoA carboxylase
carboxyl transferase, subunit beta [Amino acid transport
and metabolism, Lipid transport and metabolism].
Length = 536
Score = 65.4 bits (159), Expect = 2e-11
Identities = 44/172 (25%), Positives = 71/172 (41%), Gaps = 20/172 (11%)
Query: 78 SLFTHFISLAGDRLFGDDPAMQIGLARFHGQPVAIIGQEKGSDTKSRIKHNFGSPRPEGY 137
S F F GD + G AR +G+ V I+G K G E
Sbjct: 326 SRFFEFKPGYGD-------TLVTGFARLNGRTVGIVGNN--------PKFAGGVLFSESA 370
Query: 138 RKAVRLMEMADRFKIPVISFIDTAGAYPGVDAEARGQGEAIARATEMCLKLQVPILSIII 197
K R +E+ D+ IP+I + G G AEA G + A+ +VP ++II
Sbjct: 371 VKGARFIELCDQRNIPLIFLQNITGFMVGRAAEAGGIAKHGAKLVYAVACAKVPKITIIT 430
Query: 198 GEGGSGGAMGIAA----ANFVYMLEHAIYSVISPEGAASILWRDSSRAAQAA 245
G G GG + + + Y +A +V+ + AA+++++ + A A
Sbjct: 431 G-GSYGGNYAMCSRGYSGDINYAWPNARIAVMGGKQAANVIFQITLEKAVAL 481
Score = 31.9 bits (72), Expect = 0.25
Identities = 38/153 (24%), Positives = 61/153 (39%), Gaps = 27/153 (17%)
Query: 77 NSLFTHFISLAGDRLFGDDP----AMQIGLARFHGQPVAIIGQE---KGSDTKSRIKHNF 129
S F AG ++G + ++ G R +G+ +I + KG
Sbjct: 77 GSPFIELDQFAGHEMYGKEKVPSGSIVTGRGRINGRKCFVIANDFTVKG----------- 125
Query: 130 GSPRPEGYRKAVRLMEMADRFKIPVISFIDTAGAYPGVDAEARGQGEAIARATEMCLKLQ 189
GS P +K +R E+AD ++P I +D+ GA AE+ R +
Sbjct: 126 GSYYPITVKKHLRAQEIADNNRLPCIYLVDSGGARLPRQAESFADSYHFGR---IFYNQN 182
Query: 190 V------PILSIIIGEGGSGGAMGIAAANFVYM 216
V P +S+I+G +GGA A A+ M
Sbjct: 183 VMSSGNIPQISVIMGSCTAGGAYVPAMADETIM 215
>gnl|CDD|107362 cd06367, PBP1_iGluR_NMDA, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the ionotropic N-methyl-d-asparate (NMDA)
subtype of glutamate receptors. N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the ionotropic N-methyl-d-asparate (NMDA)
subtype of glutamate receptors. While this N-terminal
domain belongs to the periplasmic-binding fold type I
superfamily, the glutamate-binding domain of the iGluR
is structurally homologous to the periplasmic-binding
fold type II. The LIVBP-like domain of iGluRs is thought
to play a role in the initial assembly of iGluR
subunits, but it is not well understood how this domain
is arranged and functions in intact iGluR. The function
of the NMDA subtype receptor serves critical functions
in neuronal development, functioning, and degeneration
in the mammalian central nervous system. The functional
NMDA receptor is a heterotetramer comprising two NR1 and
two NR2 (A, B, C, and D) or NR3 (A and B) subunits. The
receptor controls a cation channel that is highly
permeable to monovalent ions and calcium and exhibits
voltage-dependent inhibition by magnesium. Dual
agonists, glutamate and glycine, are required for
efficient activation of the NMDA receptor. Among NMDA
receptor subtypes, the NR2B subunit containing receptors
appear particularly important for pain perception; thus
NR2B-selective antagonists may be useful in the
treatment of chronic pain.
Length = 362
Score = 32.3 bits (74), Expect = 0.18
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 247 AMKIIATDLQDLSIIDGIIPEPIGGAHRNPAQTISSVGEIISQFLSETSTYSET 300
A+ I+A + L G +PEP + + SS G+ +++FL + ET
Sbjct: 264 AVAIVARAAESLLRDKGALPEPPVNCYDTANKRESS-GQYLARFLMNVTFDGET 316
>gnl|CDD|39429 KOG4228, KOG4228, KOG4228, Protein tyrosine phosphatase [Signal
transduction mechanisms].
Length = 1087
Score = 29.6 bits (66), Expect = 1.2
Identities = 24/88 (27%), Positives = 36/88 (40%), Gaps = 12/88 (13%)
Query: 6 DFEEPISDLEAKIHELKKLSREDINEDFSEEIRELEA-------MVCKTLSEIYSK---- 54
D E P S L +LK++ + EE + L + M+C L E SK
Sbjct: 801 DTEVPASTLAPYSQKLKRIDPPENKTGLEEEFKTLNSCKPRTRMMICGNLPENKSKNRQV 860
Query: 55 -LTPWQKTQVSRHPNRPHYIDYINSLFT 81
+ P+ + +V P DYIN+ F
Sbjct: 861 NILPYDRNRVILIPTHGESSDYINASFI 888
>gnl|CDD|48241 cd03345, eu_TyrOH, Eukaryotic tyrosine hydroxylase (TyrOH); a
member of the biopterin-dependent aromatic amino acid
hydroxylase family of non-heme, iron(II)-dependent
enzymes that also includes prokaryotic and eukaryotic
phenylalanine-4-hydroxylase (PheOH) and eukaryotic
tryptophan hydroxylase (TrpOH). TyrOH catalyzes the
conversion of tyrosine to L-dihydroxyphenylalanine
(L-DOPA), the rate-limiting step in the biosynthesis of
the catecholamines dopamine, noradrenaline, and
adrenaline..
Length = 298
Score = 29.1 bits (65), Expect = 1.5
Identities = 17/49 (34%), Positives = 22/49 (44%), Gaps = 5/49 (10%)
Query: 58 WQKTQVSRHPNRPHYI---DYINSLFTHFISLAGDRLFGDDPAMQIGLA 103
+Q TQ RH + P + D + L H LA D F + IGLA
Sbjct: 144 FQCTQYIRHASSPMHSPEPDCCHELLGHVPMLA-DPTFA-QFSQDIGLA 190
>gnl|CDD|31120 COG0777, AccD, Acetyl-CoA carboxylase beta subunit [Lipid
metabolism].
Length = 294
Score = 28.7 bits (64), Expect = 2.0
Identities = 19/71 (26%), Positives = 31/71 (43%), Gaps = 8/71 (11%)
Query: 93 GDDPAMQIGLARFHGQPVAIIGQEKGSDTKSRIKHNFGSPRPEGYRKAVRLMEMADRFKI 152
G D A+ G +G PV + + + + + GS E K R +E A K+
Sbjct: 107 GLDDAVVTGEGTINGLPVVLAVMD-----FAFMGGSMGSVVGE---KITRAIERAIEDKL 158
Query: 153 PVISFIDTAGA 163
P++ F + GA
Sbjct: 159 PLVLFSASGGA 169
>gnl|CDD|143508 cd06841, PLPDE_III_MccE_like, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme MccE. This subfamily is composed
of uncharacterized proteins with similarity to
Escherichia coli MccE, a hypothetical protein that is
homologous to eukaryotic ornithine decarboxylase (ODC)
and diaminopimelate decarboxylase (DapDC). ODC and DapDC
are fold type III PLP-dependent enzymes that contain an
N-terminal PLP-binding TIM-barrel domain and a
C-terminal beta-sandwich domain, similar to bacterial
alanine racemases. ODC participates in the formation of
putrescine by catalyzing the decarboxylation of
ornithine, the first step in polyamine biosynthesis.
DapDC participates in the last step of lysine
biosynthesis, the conversion of
meso-2,6-diaminoheptanedioate to L-lysine. Most members
of this subfamily share the same domain architecture as
ODC and DapDC. A few members, including Escherichia coli
MccE, contain an additional acetyltransferase domain at
the C-terminus.
Length = 379
Score = 28.4 bits (64), Expect = 2.4
Identities = 11/34 (32%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 134 PEGYRKAVR-LMEMADRFKIPVISFIDTAGAYPG 166
PE Y A + L+E+ DR + ++D G +P
Sbjct: 182 PEAYSAAAKKLIELLDRLFGLELEYLDLGGGFPA 215
>gnl|CDD|37294 KOG2083, KOG2083, KOG2083, Na+/K+ symporter [Inorganic ion
transport and metabolism].
Length = 643
Score = 27.6 bits (61), Expect = 4.3
Identities = 21/86 (24%), Positives = 35/86 (40%), Gaps = 6/86 (6%)
Query: 164 YPGVDAEARGQGEAIARATEMCLKLQVPILSIIIGEGGSGGAMGIAAANFVYMLEHAI-- 221
YP + A+G G+ L + I IGE + +NF ++L +A+
Sbjct: 351 YPSILFFAKGYGKNKEPLRGYLLTFLTAVSFIAIGE---LNIIAPIISNF-FLLSYALIN 406
Query: 222 YSVISPEGAASILWRDSSRAAQAAIA 247
+S A S WR S + A ++
Sbjct: 407 FSCFHASLAISEGWRPSFKFYNAWVS 432
>gnl|CDD|144523 pfam00956, NAP, Nucleosome assembly protein (NAP). NAP proteins
are involved in moving histones into the nucleus,
nucleosome assembly and chromatin fluidity. They affect
the transcription of many genes.
Length = 237
Score = 27.7 bits (62), Expect = 4.8
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 17 KIHELKKLSRE--DINEDFSEEIRELEAMVCKTLSEIYSK 54
++ LK L +E ++ F EE+ ELE K +Y K
Sbjct: 3 RVEALKALQKELDELEAKFQEEVLELERKYDKLYQPLYDK 42
>gnl|CDD|35863 KOG0644, KOG0644, KOG0644, Uncharacterized conserved protein,
contains WD40 repeat and BROMO domains [General function
prediction only].
Length = 1113
Score = 27.4 bits (60), Expect = 5.6
Identities = 15/77 (19%), Positives = 26/77 (33%), Gaps = 2/77 (2%)
Query: 6 DFEEPISDLEAKIHELKKLSREDINEDFSEEIRELEAMVCKTLSEIYSKLTPWQKTQVSR 65
F D EA+ HE ++L+ F +L ++V ++ W
Sbjct: 330 RFLTGSRDGEARNHEFEQLAWRSNLLIFVTRSSDLSSIVVTARNDHRLC--VWNLYTGQL 387
Query: 66 HPNRPHYIDYINSLFTH 82
N + D + L H
Sbjct: 388 LHNLMGHSDEVYVLDVH 404
>gnl|CDD|36182 KOG0964, KOG0964, KOG0964, Structural maintenance of chromosome
protein 3 (sister chromatid cohesion complex Cohesin,
subunit SMC3) [Cell cycle control, cell division,
chromosome partitioning].
Length = 1200
Score = 27.3 bits (60), Expect = 5.9
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 8/61 (13%)
Query: 4 YLDFEEPISDLEAKIHELKKLSREDINEDFSE-EIRELEAM------VCKTLSEIYSKLT 56
+++F E L+ + EL + S++ I E + + R+ EA+ V K SE++S+L
Sbjct: 979 FVNFSEQRESLKKRQEELDR-SKDSILELITVLDQRKYEAIDLTFKQVKKNFSEVFSRLV 1037
Query: 57 P 57
P
Sbjct: 1038 P 1038
>gnl|CDD|39024 KOG3820, KOG3820, KOG3820, Aromatic amino acid hydroxylase [Amino
acid transport and metabolism].
Length = 461
Score = 27.2 bits (60), Expect = 6.0
Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 5/49 (10%)
Query: 58 WQKTQVSRHPNRPHYI---DYINSLFTHFISLAGDRLFGDDPAMQIGLA 103
+ TQ RH + P Y D + L H + L D F + +IGLA
Sbjct: 269 FHCTQYIRHHSSPFYTPEPDTCHELLGH-VPLFADPSFA-QFSQEIGLA 315
>gnl|CDD|132932 cd07021, Clp_protease_NfeD_like, Nodulation formation efficiency D
(NfeD) is a membrane-bound ClpP-class protease.
Nodulation formation efficiency D (NfeD; stomatin operon
partner protein, STOPP; DUF107) is a member of
membrane-anchored ClpP-class proteases. Currently, more
than 300 NfeD homologs have been identified - all of
which are bacterial or archaeal in origin. Majority of
these genomes have been shown to possess operons
containing a homologous NfeD/stomatin gene pair, causing
NfeD to be previously named STOPP (stomatin operon
partner protein). NfeD homologs can be divided into two
groups: long and short forms. Long-form homologs have a
putative ClpP-class serine protease domain while the
short form homologs do not. Downstream from the
ClpP-class domain is the so-called NfeD or DUF107
domain. N-terminal region of the NfeD homolog PH1510
(1510-N or PH1510-N) from Pyrococcus horikoshii has been
shown to possess serine protease activity and has a
Ser-Lys catalytic dyad, preferentially cleaving
hydrophobic substrates. Difference in oligomeric form
and catalytic residues between 1510-N (forming a dimer)
and ClpP (forming a tetradecamer) shows a possible
functional difference: 1510-N is likely to have a
regulatory function while ClpP is involved in protein
quality control.
Length = 178
Score = 27.2 bits (61), Expect = 6.4
Identities = 7/29 (24%), Positives = 16/29 (55%), Gaps = 4/29 (13%)
Query: 140 AVRLMEMADRFKIPVISFIDT----AGAY 164
A+ ++++ IP I++++ AGA
Sbjct: 47 ALEIVDLILNSPIPTIAYVNDRAASAGAL 75
>gnl|CDD|37259 KOG2048, KOG2048, KOG2048, WD40 repeat protein [General function
prediction only].
Length = 691
Score = 27.2 bits (60), Expect = 6.4
Identities = 15/57 (26%), Positives = 23/57 (40%), Gaps = 6/57 (10%)
Query: 232 SILWRDSSRAAQAAIAMKIIATDLQDLSIIDGIIPEPIGGA----HRNPAQTISSVG 284
S+ W + R + ++ I DL L + GGA NP TI ++G
Sbjct: 74 SLAWAEGGRLFSSGLSGSITEWDLHTLKQK--YNIDSNGGAIWSIAINPENTILAIG 128
>gnl|CDD|48024 cd03460, 1,2-CTD, Catechol 1,2 dioxygenase (1,2-CTD) catalyzes an
intradiol cleavage reaction of catechol to form
cis,cis-muconate. 1,2-CTDs is homodimers with one
catalytic non-heme ferric ion per monomer. They belong
to the aromatic dioxygenase family, a family of
mononuclear non-heme iron intradiol-cleaving enzymes
that catalyze the oxygenation of catecholates to
aliphatic acids via the cleavage of aromatic rings..
Length = 282
Score = 27.2 bits (60), Expect = 7.2
Identities = 18/79 (22%), Positives = 25/79 (31%), Gaps = 11/79 (13%)
Query: 61 TQVSRHPNRPHYIDYINSLFTHF-----ISLAGDRLFGDDPAMQ-----IGLARFHGQPV 110
+ RH NRP +I + S H I++ GD DD A I
Sbjct: 202 NALGRHGNRPAHIHFFVSAPGHRKLTTQINIEGDPYIWDDFAFATREGLIPEVVEVEDAA 261
Query: 111 AIIGQEKGSDTKSRIKHNF 129
A+ I +F
Sbjct: 262 ALKQYGLDGPFA-EIAFDF 279
>gnl|CDD|133370 cd04170, EF-G_bact, Elongation factor G (EF-G) subfamily.
Translocation is mediated by EF-G (also called
translocase). The structure of EF-G closely resembles
that of the complex between EF-Tu and tRNA. This is an
example of molecular mimicry; a protein domain evolved
so that it mimics the shape of a tRNA molecule. EF-G in
the GTP form binds to the ribosome, primarily through
the interaction of its EF-Tu-like domain with the 50S
subunit. The binding of EF-G to the ribosome in this
manner stimulates the GTPase activity of EF-G. On GTP
hydrolysis, EF-G undergoes a conformational change that
forces its arm deeper into the A site on the 30S
subunit. To accommodate this domain, the peptidyl-tRNA
in the A site moves to the P site, carrying the mRNA and
the deacylated tRNA with it. The ribosome may be
prepared for these rearrangements by the initial binding
of EF-G as well. The dissociation of EF-G leaves the
ribosome ready to accept the next aminoacyl-tRNA into
the A site. This group contains only bacterial members.
Length = 268
Score = 26.7 bits (60), Expect = 7.9
Identities = 19/55 (34%), Positives = 24/55 (43%), Gaps = 10/55 (18%)
Query: 142 RLMEMADRFKIPVISFI---DTAGA-YPGVDAEARGQGEAIARATEMCLKLQVPI 192
+L E AD IP I FI D A + A + EA R + LQ+PI
Sbjct: 107 KLWEFADEAGIPRIIFINKMDRERADFDKTLAALQ---EAFGRP---VVPLQLPI 155
>gnl|CDD|144031 pfam00291, PALP, Pyridoxal-phosphate dependent enzyme. Members of
this family are all pyridoxal-phosphate dependent
enzymes. This family includes: serine dehydratase
EC:4.2.1.13 P20132, threonine dehydratase EC:4.2.1.16,
tryptophan synthase beta chain EC:4.2.1.20, threonine
synthase EC:4.2.99.2, cysteine synthase EC:4.2.99.8,
cystathionine beta-synthase EC:4.2.1.22,
1-aminocyclopropane-1-carboxylate deaminase EC:4.1.99.4.
Length = 251
Score = 26.9 bits (60), Expect = 8.3
Identities = 23/92 (25%), Positives = 35/92 (38%), Gaps = 18/92 (19%)
Query: 181 ATEMCLKLQVPILSIIIGEGGSGGAMGIAAANFVYMLEHAIYSVISPEGAASILWRDSSR 240
E+ +L ++++ GG G A GIA VI E A S
Sbjct: 154 GLEILEQLGGVPDAVVVPVGGGGLAAGIARG---LKELGPGIRVIGVEPAVS-------- 202
Query: 241 AAQAAIAMKIIATDLQDLSIIDGIIPEPIGGA 272
+A AM+++A +GI+ EP A
Sbjct: 203 DEEALEAMRLLARR-------EGILVEPSSAA 227
>gnl|CDD|35676 KOG0455, KOG0455, KOG0455, Homoserine dehydrogenase [Amino acid
transport and metabolism].
Length = 364
Score = 26.9 bits (59), Expect = 8.4
Identities = 11/32 (34%), Positives = 15/32 (46%)
Query: 90 RLFGDDPAMQIGLARFHGQPVAIIGQEKGSDT 121
RL G D + I R+ QP+ I G G+
Sbjct: 316 RLRGSDNIISIYTKRYKTQPLVIQGAGAGAAV 347
>gnl|CDD|144444 pfam00850, Hist_deacetyl, Histone deacetylase domain. Histones can
be reversibly acetylated on several lysine residues.
Regulation of transcription is caused in part by this
mechanism. Histone deacetylases catalyse the removal of
the acetyl group. Histone deacetylases are related to
other proteins.
Length = 302
Score = 26.8 bits (60), Expect = 8.6
Identities = 11/26 (42%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 134 PEGYRKAVR-LMEMADRFKIPVISFI 158
EGY + R L+E+AD + PV+S +
Sbjct: 256 TEGYAERTRLLLELADEYGGPVVSVL 281
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.319 0.135 0.389
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,889,340
Number of extensions: 210829
Number of successful extensions: 760
Number of sequences better than 10.0: 1
Number of HSP's gapped: 748
Number of HSP's successfully gapped: 45
Length of query: 317
Length of database: 6,263,737
Length adjustment: 94
Effective length of query: 223
Effective length of database: 4,232,491
Effective search space: 943845493
Effective search space used: 943845493
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 (21.7 bits)
S2: 57 (25.7 bits)