RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780476|ref|YP_003064889.1| two component response
regulator [Candidatus Liberibacter asiaticus str. psy62]
(123 letters)
>gnl|CDD|29071 cd00156, REC, Signal receiver domain; originally thought to be
unique to bacteria (CheY, OmpR, NtrC, and PhoB), now
recently identified in eukaroytes ETR1 Arabidopsis
thaliana; this domain receives the signal from the
sensor partner in a two-component systems; contains a
phosphoacceptor site that is phosphorylated by histidine
kinase homologs; usually found N-terminal to a DNA
binding effector domain; forms homodimers.
Length = 113
Score = 92.6 bits (230), Expect = 3e-20
Identities = 38/115 (33%), Positives = 66/115 (57%), Gaps = 2/115 (1%)
Query: 6 MIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLEIT 65
+IV+D+ L +L R L+E GY ++ +G EAL L + KPD+I++DI + + GLE+
Sbjct: 1 LIVDDDPLIRELLRRLLEKEGYEVVEAEDGEEALALLAEEKPDLILLDIMMPGMDGLELL 60
Query: 66 KQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
++I++ +IP+I +TA D K G + Y++KP S + I+ +
Sbjct: 61 RRIRKR--GPDIPIIFLTAHGDDEDAVEALKAGADDYLTKPFSPEELLARIRALL 113
>gnl|CDD|143854 pfam00072, Response_reg, Response regulator receiver domain. This
domain receives the signal from the sensor partner in
bacterial two-component systems. It is usually found
N-terminal to a DNA binding effector domain.
Length = 111
Score = 91.9 bits (229), Expect = 4e-20
Identities = 37/113 (32%), Positives = 65/113 (57%), Gaps = 2/113 (1%)
Query: 5 VMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLEI 64
V+IV+D+ L +L R L+E GY+ + +G EALEL ++ +PD+I++DI++ + GLE+
Sbjct: 1 VLIVDDDPLIRELLRQLLEKEGYVVAEADDGEEALELLKEKRPDLILLDIRMPGMDGLEL 60
Query: 65 TKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIK 117
++I+ PVI +TA + D K G ++SKP + ++
Sbjct: 61 LRRIRRRPP--TTPVIVLTAHGDEEDAVEALKAGANDFLSKPFDPEELVAALR 111
>gnl|CDD|31127 COG0784, CheY, FOG: CheY-like receiver [Signal transduction
mechanisms].
Length = 130
Score = 79.1 bits (194), Expect = 2e-16
Identities = 40/126 (31%), Positives = 74/126 (58%), Gaps = 5/126 (3%)
Query: 1 MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNG-MEALELARQHK-PDVIIMDIQLQE 58
+V++V+D +N +L + L+E GY ++ +G EALEL R+ PD+I++DI +
Sbjct: 4 SGLRVLVVDDEPVNRRLLKRLLEDLGYEVVEAADGEEEALELLRELPQPDLILLDINMPG 63
Query: 59 ISGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLS-IFMETIK 117
+ G+E+ ++++ IPVI +TA+A + D ER G + Y++KPI L + ++
Sbjct: 64 MDGIELLRRLRAR--GPNIPVILLTAYADEADRERALAAGADDYLTKPIFLEEELLAALR 121
Query: 118 KYIGEA 123
+ + A
Sbjct: 122 RLLARA 127
>gnl|CDD|33243 COG3437, COG3437, Response regulator containing a CheY-like
receiver domain and an HD-GYP domain [Transcription /
Signal transduction mechanisms].
Length = 360
Score = 75.7 bits (186), Expect = 3e-15
Identities = 38/118 (32%), Positives = 71/118 (60%), Gaps = 1/118 (0%)
Query: 4 KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63
V++V+D N++ R L+ GY ++ NG EAL+L ++ PD++++D+++ E+ G E
Sbjct: 16 TVLLVDDEPDNLEALRQLLRMIGYRVIEAENGEEALKLLQEEPPDLVLLDVRMPEMDGAE 75
Query: 64 ITKQIKEDSEL-QEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
+ ++K S + IPVI +TA+A D +R + G + Y+SKPIS + + ++
Sbjct: 76 VLNKLKAMSPSTRRIPVILLTAYADSEDRQRALEAGADDYLSKPISPKELVARVSSHL 133
>gnl|CDD|35739 KOG0519, KOG0519, KOG0519, Sensory transduction histidine kinase
[Signal transduction mechanisms].
Length = 786
Score = 72.8 bits (178), Expect = 2e-14
Identities = 38/118 (32%), Positives = 71/118 (60%), Gaps = 2/118 (1%)
Query: 3 KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALE-LARQHKPDVIIMDIQLQEISG 61
K+++V+DN +N K+ +++ G + +G EAL+ L H DVI MD+Q+ E+ G
Sbjct: 667 PKILLVDDNPVNRKVATGMLKKLGAEVTEVNSGQEALDKLKPPHSYDVIFMDLQMPEMDG 726
Query: 62 LEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKY 119
E T++I++ E +P++A+TA A EE + G + Y+SKP +L ++ ++++
Sbjct: 727 YEATREIRKK-ERWHLPIVALTADADPSTEEECLEVGMDGYLSKPFTLEKLVKILREF 783
>gnl|CDD|31088 COG0745, OmpR, Response regulators consisting of a CheY-like
receiver domain and a winged-helix DNA-binding domain
[Signal transduction mechanisms / Transcription].
Length = 229
Score = 68.1 bits (166), Expect = 7e-13
Identities = 31/118 (26%), Positives = 65/118 (55%), Gaps = 2/118 (1%)
Query: 3 KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
++++VED+ +L ++ +E GY +G EALE AR+ PD++++D+ L ++ GL
Sbjct: 1 MRILLVEDDPELAELLKEYLEEEGYEVDVAADGEEALEAAREQ-PDLVLLDLMLPDLDGL 59
Query: 63 EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
E+ ++++ P+I +TA + D + G + Y++KP S + ++ +
Sbjct: 60 ELCRRLRAKKGSG-PPIIVLTARDDEEDRVLGLEAGADDYLTKPFSPRELLARLRALL 116
>gnl|CDD|32386 COG2204, AtoC, Response regulator containing CheY-like receiver,
AAA-type ATPase, and DNA-binding domains [Signal
transduction mechanisms].
Length = 464
Score = 67.6 bits (165), Expect = 7e-13
Identities = 30/123 (24%), Positives = 64/123 (52%), Gaps = 8/123 (6%)
Query: 1 MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60
M+ ++++V+D+ +L +E +GY + + EALE + D++++DI++ +
Sbjct: 3 MMARILVVDDDPDIRELLEQALELAGYEVVTAESAEEALEALSESPFDLVLLDIRMPGMD 62
Query: 61 GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIR---KGGCEAYISKPISLSIFMETIK 117
GLE+ K+IK ++PVI +T GD + + G ++ KP L + ++
Sbjct: 63 GLELLKEIKSRDP--DLPVIVMTGH---GDIDTAVEALRLGAFDFLEKPFDLDRLLAIVE 117
Query: 118 KYI 120
+ +
Sbjct: 118 RAL 120
>gnl|CDD|32379 COG2197, CitB, Response regulator containing a CheY-like receiver
domain and an HTH DNA-binding domain [Signal
transduction mechanisms / Transcription].
Length = 211
Score = 65.7 bits (160), Expect = 3e-12
Identities = 38/116 (32%), Positives = 63/116 (54%), Gaps = 4/116 (3%)
Query: 4 KVMIVEDNELNMKLFRDLIETSG--YIALQTRNGMEALELARQHKPDVIIMDIQLQEISG 61
KV+IV+D+ L + R L+E + + NG EAL+LAR+ KPDV+++D+ + + G
Sbjct: 2 KVLIVDDHPLVREGLRQLLELEPDLEVVGEASNGEEALDLARELKPDVVLLDLSMPGMDG 61
Query: 62 LEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIK 117
LE KQ++ +I V+ +TA R + G + Y+ K S +E I+
Sbjct: 62 LEALKQLRA--RGPDIKVVVLTAHDDPAYVIRALRAGADGYLLKDASPEELVEAIR 115
>gnl|CDD|34367 COG4753, COG4753, Response regulator containing CheY-like receiver
domain and AraC-type DNA-binding domain [Signal
transduction mechanisms].
Length = 475
Score = 63.0 bits (153), Expect = 2e-11
Identities = 39/125 (31%), Positives = 66/125 (52%), Gaps = 11/125 (8%)
Query: 4 KVMIVEDNELNMKLFRDLIETSGY---IALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60
KV+IV+D L + + LI+ + NG EALEL ++ +PD++I DI + +
Sbjct: 3 KVLIVDDEPLIREGLKSLIDWEALGIEVVGTAANGKEALELIQETQPDIVITDINMPGMD 62
Query: 61 GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKG---GCEAYISKPISLSIFMETIK 117
GL++ K IKE S + I ++ + + E +K G + Y+ KP+ + E +K
Sbjct: 63 GLDLIKAIKEQS--PDTEFIILSGY---DEFEYAKKAMKLGVKDYLLKPVDKAELEEALK 117
Query: 118 KYIGE 122
K IG+
Sbjct: 118 KIIGK 122
>gnl|CDD|32383 COG2201, CheB, Chemotaxis response regulator containing a CheY-like
receiver domain and a methylesterase domain [Cell
motility and secretion / Signal transduction
mechanisms].
Length = 350
Score = 62.6 bits (152), Expect = 3e-11
Identities = 32/107 (29%), Positives = 62/107 (57%), Gaps = 7/107 (6%)
Query: 4 KVMIVEDNELNMKLFRDLIETSG--YIALQTRNGMEALELARQHKPDVIIMDIQLQEISG 61
+V++V+D+ L K+ D++ + + RNG EA++ ++ KPDVI +D+++ + G
Sbjct: 3 RVLVVDDSALMRKVISDILNSDPDIEVVGTARNGREAIDKVKKLKPDVITLDVEMPVMDG 62
Query: 62 LEITKQIKEDSELQEIPVIAVTAFAMKGDEERIR--KGGCEAYISKP 106
LE ++I L+ +PVI V++ +G E + + G +I+KP
Sbjct: 63 LEALRKIM---RLRPLPVIMVSSLTEEGAEATLEALELGAVDFIAKP 106
>gnl|CDD|33501 COG3706, PleD, Response regulator containing a CheY-like receiver
domain and a GGDEF domain [Signal transduction
mechanisms].
Length = 435
Score = 59.9 bits (145), Expect = 2e-10
Identities = 28/109 (25%), Positives = 64/109 (58%), Gaps = 6/109 (5%)
Query: 3 KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
KK+++V+D+ + R +++ G+ ++ +G EAL + PD++++D + ++ GL
Sbjct: 133 KKILVVDDDATQRERLRRILQVEGFRVVEATDGEEALLQLAELPPDLVLLDANMPDMDGL 192
Query: 63 EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKG---GCEAYISKPIS 108
E+ ++++ ++IP+I +++ K D+E + + G YI+KPI
Sbjct: 193 ELCTRLRQLERTRDIPIILLSS---KDDDELVVRAFELGVNDYITKPIE 238
Score = 43.8 bits (103), Expect = 1e-05
Identities = 22/92 (23%), Positives = 42/92 (45%), Gaps = 4/92 (4%)
Query: 27 YIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLEITKQIKEDSELQEIPVIAVTAFA 86
+ G+ AL + HKPD ++D+ + + G E+ +++K + V+ VTA
Sbjct: 13 KEVATAKKGLIALAILLDHKPDYKLLDVMMPGMDGFELCRRLKAEPA----TVVMVTALD 68
Query: 87 MKGDEERIRKGGCEAYISKPISLSIFMETIKK 118
R K G + +++KP++ S K
Sbjct: 69 DSAPRVRGLKAGADDFLTKPVNDSQLFLRAKS 100
>gnl|CDD|164540 CHL00148, orf27, Ycf27; Reviewed.
Length = 240
Score = 53.2 bits (128), Expect = 2e-08
Identities = 29/106 (27%), Positives = 61/106 (57%), Gaps = 3/106 (2%)
Query: 3 KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
+K+++V+D K+ + GY + +G EAL+L R+ +PD++I+D+ + ++ G
Sbjct: 7 EKILVVDDEAYIRKILETRLSIIGYEVITASDGEEALKLFRKEQPDLVILDVMMPKLDGY 66
Query: 63 EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPIS 108
+ ++I+++S ++P+I +TA D + G + Y+ KP S
Sbjct: 67 GVCQEIRKES---DVPIIMLTALGDVSDRITGLELGADDYVVKPFS 109
>gnl|CDD|33728 COG3947, COG3947, Response regulator containing CheY-like receiver
and SARP domains [Signal transduction mechanisms].
Length = 361
Score = 51.9 bits (124), Expect = 5e-08
Identities = 26/105 (24%), Positives = 59/105 (56%), Gaps = 4/105 (3%)
Query: 4 KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63
+++IV+D+ +KL ++ +G+ + +EAL+L KPD+I +DI + ++G+E
Sbjct: 2 RIIIVDDDAAIVKLLSVILSRAGHEVRSCSHPVEALDLLEVFKPDLIFLDIVMPYMNGIE 61
Query: 64 ITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPIS 108
+Q+++ +P+I +++ A D+ + Y+ KP++
Sbjct: 62 FAEQVRD--IESAVPIIFISSHAEYADDS--FGMNLDDYLPKPVT 102
>gnl|CDD|34204 COG4566, TtrR, Response regulator [Signal transduction mechanisms].
Length = 202
Score = 51.0 bits (122), Expect = 7e-08
Identities = 26/116 (22%), Positives = 56/116 (48%), Gaps = 2/116 (1%)
Query: 5 VMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLEI 64
V +V+D+E L+E++G+ + E L A +P +++D+++ +SGLE+
Sbjct: 7 VHVVDDDESVRDALAFLLESAGFQVKCFASAEEFLAAAPLDRPGCLLLDVRMPGMSGLEL 66
Query: 65 TKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
++ E +PVI +T + K G ++ KP S ++ +++ +
Sbjct: 67 QDRLAE--RGIRLPVIFLTGHGDIPMAVQAMKAGAVDFLEKPFSEQDLLDAVERAL 120
>gnl|CDD|33502 COG3707, AmiR, Response regulator with putative antiterminator
output domain [Signal transduction mechanisms].
Length = 194
Score = 50.2 bits (120), Expect = 1e-07
Identities = 34/117 (29%), Positives = 64/117 (54%), Gaps = 4/117 (3%)
Query: 1 MLKKVMIVEDNELNMKLFRDLIETSGYIAL-QTRNGMEALELARQHKPDVIIMDIQLQEI 59
ML +V++ +D L R+ + +GY + + +G+EA+E+ + +PDV+I+DI E+
Sbjct: 4 MLLRVLVADDEALTRMDIREGLLEAGYQRVGEAADGLEAVEVCERLQPDVVILDI---EM 60
Query: 60 SGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETI 116
+I + + SE P++A+TA++ E + G AYI KP+ S + +
Sbjct: 61 PRRDIIEALLLASENVARPIVALTAYSDPALIEAAIEAGVMAYIVKPLDESRLLPIL 117
>gnl|CDD|34203 COG4565, CitB, Response regulator of citrate/malate metabolism
[Transcription / Signal transduction mechanisms].
Length = 224
Score = 48.7 bits (116), Expect = 4e-07
Identities = 28/121 (23%), Positives = 61/121 (50%), Gaps = 10/121 (8%)
Query: 4 KVMIVEDNELNMKLFRDLIETSGY--IALQTRNGMEALELARQHKPDVIIMDIQLQEISG 61
V+I+ED+ + ++ R ++ + EA + + KPD+I++DI + + +G
Sbjct: 2 NVLIIEDDPMVAEIHRRYVKQIPGFSVVGTAGTLEEAKMIIEEFKPDLILLDIYMPDGNG 61
Query: 62 LEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRK---GGCEAYISKPISLSIFMETIKK 118
+E+ +++ S+ + VI +TA + D E I++ G Y+ KP + + + +
Sbjct: 62 IELLPELR--SQHYPVDVIVITAAS---DMETIKEALRYGVVDYLIKPFTFERLQQALTR 116
Query: 119 Y 119
Y
Sbjct: 117 Y 117
>gnl|CDD|34205 COG4567, COG4567, Response regulator consisting of a CheY-like
receiver domain and a Fis-type HTH domain [Signal
transduction mechanisms / Transcription].
Length = 182
Score = 44.6 bits (105), Expect = 7e-06
Identities = 25/105 (23%), Positives = 57/105 (54%), Gaps = 4/105 (3%)
Query: 3 KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
K +++V+D+ ++ +E G+ + + EAL AR P ++D++L + SGL
Sbjct: 10 KSLLLVDDDTPFLRTLARAMERRGFAVVTAESVEEALAAARTAPPAYAVVDLKLGDGSGL 69
Query: 63 EITKQIKEDSELQEIPVIAVTAFA-MKGDEERIRKGGCEAYISKP 106
+ + ++E ++ ++ +T +A + E ++ G C+ Y++KP
Sbjct: 70 AVIEALRE--RRADMRIVVLTGYASIATAVEAVKLGACD-YLAKP 111
>gnl|CDD|33090 COG3279, LytT, Response regulator of the LytR/AlgR family
[Transcription / Signal transduction mechanisms].
Length = 244
Score = 42.3 bits (99), Expect = 4e-05
Identities = 33/120 (27%), Positives = 61/120 (50%), Gaps = 8/120 (6%)
Query: 4 KVMIVEDNELNMKLFRDLIETS--GYIALQTRNGMEALELARQHKPDVIIMDIQLQEISG 61
KV+IV+D L + R ++ I + NG EAL+L + +PD++ +DI + +I+G
Sbjct: 3 KVLIVDDEPLAREELRRILNEIPDIEIVGEAENGEEALQLLQGLRPDLVFLDIAMPDING 62
Query: 62 LEITKQIKE-DSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
+E+ +I++ D + V A +A+ E Y+ KPIS +T+++
Sbjct: 63 IELAARIRKGDPRPAIVFVTAHDEYAVAAFEVEA-----LDYLLKPISEERLAKTLERLR 117
>gnl|CDD|145766 pfam02782, FGGY_C, FGGY family of carbohydrate kinases, C-terminal
domain. This domain adopts a ribonuclease H-like fold
and is structurally related to the N-terminal domain.
Length = 193
Score = 30.7 bits (70), Expect = 0.090
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 4/37 (10%)
Query: 17 LFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMD 53
L+R ++E +ALQ R +EAL D II
Sbjct: 119 LYRAILEG---LALQLRQILEALA-ELGAPIDRIIAS 151
>gnl|CDD|176521 cd08579, GDPD_memb_like, Glycerophosphodiester phosphodiesterase
domain of uncharacterized bacterial
glycerophosphodiester phosphodiesterases. This
subfamily corresponds to the glycerophosphodiester
phosphodiesterase domain (GDPD) present in
uncharacterized bacterial glycerophosphodiester
phosphodiesterases. In addition to a C-terminal GDPD
domain, most members in this family have an N-terminus
that functions as a membrane anchor.
Length = 220
Score = 29.1 bits (66), Expect = 0.36
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 26 GYIALQTRNGMEALELARQHKPDVIIMDIQL 56
G + N +EALE A + KPD + +D+Q
Sbjct: 6 GVSSNGVENTLEALEAAIKAKPDYVEIDVQE 36
>gnl|CDD|153436 cd07967, OBF_DNA_ligase_III, The Oligonucleotide/oligosaccharide
binding (OB)-fold domain of ATP-dependent DNA ligase III
is a DNA-binding module that is part of the catalytic
core unit. ATP-dependent polynucleotide ligases
catalyze phosphodiester bond formation using nicked
nucleic acid substrates with the high energy nucleotide
of ATP as a cofactor in a three step reaction mechanism.
DNA ligases play a vital role in the diverse processes
of DNA replication, recombination and repair.
ATP-dependent ligases are present in many organisms such
as viruses, bacteriohages, eukarya, archaea and
bacteria. There are three classes of ATP-dependent DNA
ligases in eukaryotic cells (I, III and IV). DNA ligase
III is not found in lower eukaryotes and is present both
in the nucleus and mitochondria. It has several
isoforms; two splice forms, III-alpha and III-beta,
differ in their carboxy-terminal sequences. DNA ligase
III-beta is believed to play a role in homologous
recombination during meiotic prophase. DNA ligase
III-alpha interacts with X-ray Cross Complementing
factor 1 (XRCC1) and functions in single nucleotide Base
Excision Repair (BER). The mitochondrial form of DNA
ligase III originates from the nucleolus and is involved
in the mitochondrial DNA repair pathway. This isoform is
expressed by a second start site on the DNA ligase III
gene. DNA ligases have a highly modular architecture
consisting of a unique arrangement of two or more
discrete domains. The adenylation and C-terminal
oligouncleotide/oligosaccharide binding (OB)-fold
domains comprise a catalytic core unit that is common to
most members of the ATP-dependent DNA ligase family. The
catalytic core unit contains six conserved sequence
motifs (I, III, IIIa, IV, V and VI) that define this
family of related nucleotidyltransferases. The OB-fold
domain contacts the nicked DNA substrate and is required
for the ATP-dependent DNA ligase nucleotidylation step.
The RxDK motif (motif VI), which is essential for ATP
hydrolysis, is located in the OB-fold domain.
Length = 139
Score = 28.1 bits (63), Expect = 0.71
Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 3/31 (9%)
Query: 39 LELARQHKPDVIIMDI---QLQEISGLEITK 66
L+ + PD I+ D + EI+G E +K
Sbjct: 76 LKCNKSLVPDFIVKDPKKAPVWEITGAEFSK 106
>gnl|CDD|145645 pfam02606, LpxK, Tetraacyldisaccharide-1-P 4'-kinase. This family
consists of tetraacyldisaccharide-1-P 4'-kinase also
known as Lipid-A 4'-kinase or Lipid A biosynthesis
protein LpxK, EC:2.7.1.130. This enzyme catalyses the
reaction: ATP + 2,3-bis(3-hydroxytetradecanoyl)-D
-glucosaminyl-(beta-D-1,6)-2,
3-bis(3-hydroxytetradecanoyl)-D-glu cosam inyl
beta-phosphate <=> ADP +
2,3,2',3'-tetrakis(3-hydroxytetradecanoyl)-D-
glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate.
This enzyme is involved in the synthesis of lipid A
portion of the bacterial lipopolysaccharide layer (LPS).
The family contains a P-loop motif at the N terminus.
Length = 318
Score = 27.5 bits (62), Expect = 0.96
Identities = 8/16 (50%), Positives = 9/16 (56%)
Query: 38 ALELARQHKPDVIIMD 53
A L H DVII+D
Sbjct: 119 ARALLEAHGADVIILD 134
>gnl|CDD|144163 pfam00465, Fe-ADH, Iron-containing alcohol dehydrogenase.
Length = 312
Score = 27.6 bits (62), Expect = 1.00
Identities = 8/16 (50%), Positives = 9/16 (56%)
Query: 36 MEALELARQHKPDVII 51
EA AR+ DVII
Sbjct: 69 DEAAAAAREEGADVII 84
>gnl|CDD|113680 pfam04916, Phospholip_B, Phospholipase B. Phospholipase B (PLB)
catalyses the hydrolytic cleavage of both acylester
bonds of glycerophospholipids. This family of PLB
enzymes has been identified in mammals, flies and
nematodes but not in yeast. In Drosophila this protein
was named LAMA for laminin ancestor since it is
expressed in the neuronal and glial precursors that
surround the lamina.
Length = 563
Score = 26.7 bits (59), Expect = 1.7
Identities = 8/26 (30%), Positives = 12/26 (46%)
Query: 22 IETSGYIALQTRNGMEALELARQHKP 47
I +SG ++T G L L + P
Sbjct: 284 ITSSGLAVIETTIGNYNLTLLKNVVP 309
>gnl|CDD|173937 cd08178, AAD_C, C-terminal alcohol dehydrogenase domain of the
acetaldehyde dehydrogenase-alcohol dehydrogenase
bifunctional two-domain protein (AAD). Alcohol
dehydrogenase domain located on the C-terminal of a
bifunctional two-domain protein. The N-terminal of the
protein contains an acetaldehyde-CoA dehydrogenase
domain. This protein is involved in pyruvate
metabolism. Pyruvate is converted to acetyl-CoA and
formate by pyruvate formate-lysase (PFL). Under
anaerobic condition, acetyl-CoA is reduced to
acetaldehyde and ethanol by this two-domain protein.
Acetyl-CoA is first converted into an enzyme-bound
thiohemiacetal by the N-terminal acetaldehyde
dehydrogenase domain. The enzyme-bound thiohemiacetal
is subsequently reduced by the C-terminal
NAD+-dependent alcohol dehydrogenase domain. In E.
coli, this protein is called AdhE and was shown
pyruvate formate-lysase (PFL) deactivase activity,
which is involved in the inactivation of PFL, a key
enzyme in anaerobic metabolism. In Escherichia coli and
Entamoeba histolytica, this enzyme forms homopolymeric
peptides composed of more than 20 protomers associated
in a helical rod-like structure.
Length = 398
Score = 26.8 bits (60), Expect = 1.7
Identities = 8/16 (50%), Positives = 9/16 (56%)
Query: 36 MEALELARQHKPDVII 51
+ LEL KPD II
Sbjct: 68 RKGLELMNSFKPDTII 83
>gnl|CDD|35947 KOG0728, KOG0728, KOG0728, 26S proteasome regulatory complex,
ATPase RPT6 [Posttranslational modification, protein
turnover, chaperones].
Length = 404
Score = 26.1 bits (57), Expect = 2.9
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 27 YIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLEITKQIKEDSELQ 75
YI +R E +AR+H P +I MD ++ I + DSE+Q
Sbjct: 221 YIGEGSRMVRELFVMAREHAPSIIFMD-EIDSIGSSRVESGSGGDSEVQ 268
>gnl|CDD|30371 COG0021, TktA, Transketolase [Carbohydrate transport and
metabolism].
Length = 663
Score = 25.9 bits (57), Expect = 3.2
Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 4/38 (10%)
Query: 14 NMKLFR--DLIETSG--YIALQTRNGMEALELARQHKP 47
N+ + R D ET+ AL+ ++G AL L RQ+ P
Sbjct: 487 NLSVIRPADANETAAAWKYALERKDGPTALILTRQNLP 524
>gnl|CDD|30537 COG0188, GyrA, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), A subunit [DNA replication,
recombination, and repair].
Length = 804
Score = 25.6 bits (56), Expect = 4.1
Identities = 11/26 (42%), Positives = 19/26 (73%)
Query: 51 IMDIQLQEISGLEITKQIKEDSELQE 76
I+D++L+ ++GLE K KE EL++
Sbjct: 423 ILDLRLRRLTGLEEEKIEKELKELEK 448
>gnl|CDD|35958 KOG0739, KOG0739, KOG0739, AAA+-type ATPase [Posttranslational
modification, protein turnover, chaperones].
Length = 439
Score = 24.9 bits (54), Expect = 5.8
Identities = 7/15 (46%), Positives = 12/15 (80%)
Query: 39 LELARQHKPDVIIMD 53
E+AR++KP +I +D
Sbjct: 218 FEMARENKPSIIFID 232
>gnl|CDD|163654 cd07411, MPP_SoxB_N, Thermus thermophilus SoxB and related
proteins, N-terminal metallophosphatase domain. SoxB
(sulfur oxidation protein B) is a periplasmic
thiosulfohydrolase and an essential component of the
sulfur oxidation pathway in archaea and bacteria. SoxB
has a dinuclear manganese cluster and is thought to
catalyze the release of sulfate from a protein-bound
cysteine S-thiosulfonate. SoxB is expressed from the
sox (sulfur oxidation) gene cluster, which encodes 15
other sox genes, and has two domains, an N-terminal
metallophosphatase domain and a C-terminal
5'-nucleotidase domain. SoxB binds the SoxYZ complex
and is thought to function as a sulfate-thiohydrolase.
SoxB is closely related to the UshA, YchR, and CpdB
proteins, all of which have the same two-domain
architecture. The N-terminal metallophosphatase domain
belongs to a large superfamily of distantly related
metallophosphatases (MPPs) that includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). MPPs are functionally
diverse, but all share a conserved domain with an active
site consisting of two metal ions (usually manganese,
iron, or zinc) coordinated with octahedral geometry by a
cage of histidine, aspartate, and asparagine residues.
The conserved domain is a double beta-sheet sandwich
with a di-metal active site made up of residues located
at the C-terminal side of the sheets. This domain is
thought to allow for productive metal coordination.
Length = 264
Score = 24.9 bits (55), Expect = 5.8
Identities = 8/41 (19%), Positives = 18/41 (43%), Gaps = 6/41 (14%)
Query: 40 ELARQHKPDVIIMDIQLQEISGLEITKQIKEDSELQEIPVI 80
+L R+ DV+++ +S + ++ + I VI
Sbjct: 177 KLRREEGVDVVVL------LSHNGLPVDVELAERVPGIDVI 211
>gnl|CDD|147744 pfam05758, Ycf1, Ycf1. The chloroplast genomes of most higher
plants contain two giant open reading frames designated
ycf1 and ycf2. Although the function of Ycf1 is unknown,
it is known to be an essential gene.
Length = 832
Score = 24.6 bits (54), Expect = 6.7
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 106 PISLSIFMETIKKYI 120
P SLS F E I++ I
Sbjct: 352 PPSLSTFGEMIERKI 366
>gnl|CDD|163616 cd00840, MPP_Mre11_N, Mre11 nuclease, N-terminal
metallophosphatase domain. Mre11 (also known as SbcD
in Escherichia coli) is a subunit of the MRX protein
complex. This complex includes: Mre11, Rad50, and
Xrs2/Nbs1, and plays a vital role in several nuclear
processes including DNA double-strand break repair,
telomere length maintenance, cell cycle checkpoint
control, and meiotic recombination, in eukaryotes.
During double-strand break repair, the MRX complex is
required to hold the two ends of a broken chromosome
together. In vitro studies show that Mre11 has 3'-5'
exonuclease activity on dsDNA templates and
endonuclease activity on dsDNA and ssDNA templates. In
addition to the N-terminal phosphatase domain, the
eukaryotic MRE11 members of this family have a
C-terminal DNA binding domain (not included in this
alignment model). MRE11-like proteins are found in
prokaryotes and archaea was well as in eukaryotes.
Mre11 belongs to the metallophosphatase (MPP)
superfamily. MPPs are functionally diverse, but all
share a conserved domain with an active site consisting
of two metal ions (usually manganese, iron, or zinc)
coordinated with octahedral geometry by a cage of
histidine, aspartate, and asparagine residues. The MPP
superfamily includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and
acid sphingomyelinases (ASMases). The conserved domain
is a double beta-sheet sandwich with a di-metal active
site made up of residues located at the C-terminal side
of the sheets. This domain is thought to allow for
productive metal coordination.
Length = 223
Score = 24.6 bits (54), Expect = 6.7
Identities = 6/16 (37%), Positives = 11/16 (68%)
Query: 37 EALELARQHKPDVIIM 52
E +ELA + K D +++
Sbjct: 32 EIVELAIEEKVDFVLI 47
>gnl|CDD|31415 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 24.4 bits (53), Expect = 7.5
Identities = 15/49 (30%), Positives = 21/49 (42%), Gaps = 1/49 (2%)
Query: 27 YIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLEITKQIKEDSELQ 75
YI R E ELAR+ P +I +D ++ I D E+Q
Sbjct: 225 YIGEGARLVRELFELAREKAPSIIFID-EIDAIGAKRFDSGTSGDREVQ 272
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
0.318 0.136 0.360
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,385,570
Number of extensions: 66262
Number of successful extensions: 327
Number of sequences better than 10.0: 1
Number of HSP's gapped: 308
Number of HSP's successfully gapped: 63
Length of query: 123
Length of database: 6,263,737
Length adjustment: 82
Effective length of query: 41
Effective length of database: 4,491,799
Effective search space: 184163759
Effective search space used: 184163759
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (23.4 bits)