RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 047789
(171 letters)
>gnl|CDD|236486 PRK09369, PRK09369, UDP-N-acetylglucosamine
1-carboxyvinyltransferase; Validated.
Length = 417
Score = 179 bits (456), Expect = 3e-55
Identities = 70/141 (49%), Positives = 93/141 (65%), Gaps = 2/141 (1%)
Query: 31 ETLTITGPTQLSGHVPISGSKNSSLCLLAATLLCSNSCLLHNVPTGLSDTKTMLSILRLL 90
+ L I G LSG V ISG+KN++L +LAA+LL L NVP LSD +TM+ +LR L
Sbjct: 2 DKLVIEGGKPLSGEVTISGAKNAALPILAASLLAEEPVTLTNVPD-LSDVRTMIELLRSL 60
Query: 91 GAKIEFNERNKEILVNTDGVGRAEPCLGEMRKIRGGFFVIGPLLARFGEAVVGLPGGCDI 150
GAK+EF+ + ++ + E ++K+R V+GPLLARFGEA V LPGGC I
Sbjct: 61 GAKVEFDGNG-TVTIDASNINNTEAPYELVKKMRASILVLGPLLARFGEAKVSLPGGCAI 119
Query: 151 GERPVDLYVRGLRALGAAVEI 171
G RPVDL+++GL ALGA +EI
Sbjct: 120 GARPVDLHLKGLEALGAEIEI 140
>gnl|CDD|223837 COG0766, MurA, UDP-N-acetylglucosamine enolpyruvyl transferase
[Cell envelope biogenesis, outer membrane].
Length = 421
Score = 172 bits (438), Expect = 1e-52
Identities = 71/137 (51%), Positives = 92/137 (67%), Gaps = 2/137 (1%)
Query: 35 ITGPTQLSGHVPISGSKNSSLCLLAATLLCSNSCLLHNVPTGLSDTKTMLSILRLLGAKI 94
I G L+G V ISG+KN++L LLAATLL L NVP LSD +TML +LR LGAK+
Sbjct: 6 IEGGNPLNGEVTISGAKNAALPLLAATLLADEPVTLTNVPD-LSDVETMLELLRNLGAKV 64
Query: 95 EFNERNKEILVNTDGVGRAEPCLGEMRKIRGGFFVIGPLLARFGEAVVGLPGGCDIGERP 154
E + + E+ ++ + E +RK+R V+GPLLARFG+A V LPGGC IG RP
Sbjct: 65 ERDG-DGELEIDAPNINSTEAPYELVRKMRASILVLGPLLARFGKAKVSLPGGCAIGARP 123
Query: 155 VDLYVRGLRALGAAVEI 171
VDL+++GL ALGA +EI
Sbjct: 124 VDLHLKGLEALGAEIEI 140
>gnl|CDD|238796 cd01555, UdpNAET, UDP-N-acetylglucosamine enolpyruvyl transferase
catalyzes enolpyruvyl transfer as part of the first step
in the biosynthesis of peptidoglycan, a component of the
bacterial cell wall. The reaction is phosphoenolpyruvate
+ UDP-N-acetyl-D-glucosamine = phosphate +
UDP-N-acetyl-3-(1-carboxyvinyl)-D-glucosamine. This
enzyme is of interest as a potential target for
anti-bacterial agents. The only other known enolpyruvyl
transferase is the related
5-enolpyruvylshikimate-3-phosphate synthase.
Length = 400
Score = 169 bits (432), Expect = 7e-52
Identities = 68/131 (51%), Positives = 88/131 (67%), Gaps = 2/131 (1%)
Query: 41 LSGHVPISGSKNSSLCLLAATLLCSNSCLLHNVPTGLSDTKTMLSILRLLGAKIEFNERN 100
LSG V ISG+KN++L +LAA LL L NVP L D +TM+ +LR LGAK+EF N
Sbjct: 1 LSGEVRISGAKNAALPILAAALLTDEPVTLRNVPD-LLDVETMIELLRSLGAKVEFEGEN 59
Query: 101 KEILVNTDGVGRAEPCLGEMRKIRGGFFVIGPLLARFGEAVVGLPGGCDIGERPVDLYVR 160
++++ + E +RK+R V+GPLLARFGEA V LPGGC IG RPVDL+++
Sbjct: 60 -TLVIDASNINSTEAPYELVRKMRASILVLGPLLARFGEARVSLPGGCAIGARPVDLHLK 118
Query: 161 GLRALGAAVEI 171
GL ALGA +EI
Sbjct: 119 GLEALGAKIEI 129
>gnl|CDD|162190 TIGR01072, murA, UDP-N-acetylglucosamine 1-carboxyvinyltransferase.
[Cell envelope, Biosynthesis and degradation of murein
sacculus and peptidoglycan].
Length = 416
Score = 153 bits (389), Expect = 2e-45
Identities = 71/141 (50%), Positives = 93/141 (65%), Gaps = 3/141 (2%)
Query: 31 ETLTITGPTQLSGHVPISGSKNSSLCLLAATLLCSNSCLLHNVPTGLSDTKTMLSILRLL 90
+ L + G LSG V ISG+KN++L ++AATLL L NVP LSD KT L +LR L
Sbjct: 2 DKLVVEGGKPLSGEVTISGAKNAALPIIAATLLTDEPVTLTNVPD-LSDVKTTLDLLRNL 60
Query: 91 GAKIEFNERNKEILVNTDGVGRAEPCLGEMRKIRGGFFVIGPLLARFGEAVVGLPGGCDI 150
GA++E N + +NT + E +RK+R V+GPLLARFG+AVV LPGGC I
Sbjct: 61 GARVER--DNNTLEINTPNINSTEAPYELVRKMRASILVLGPLLARFGKAVVSLPGGCAI 118
Query: 151 GERPVDLYVRGLRALGAAVEI 171
G RPVDL+++GL+ALGA + I
Sbjct: 119 GARPVDLHLKGLKALGAEIVI 139
>gnl|CDD|183779 PRK12830, PRK12830, UDP-N-acetylglucosamine
1-carboxyvinyltransferase; Reviewed.
Length = 417
Score = 136 bits (346), Expect = 4e-39
Identities = 54/141 (38%), Positives = 84/141 (59%), Gaps = 3/141 (2%)
Query: 31 ETLTITGPTQLSGHVPISGSKNSSLCLLAATLLCSNSCLLHNVPTGLSDTKTMLSILRLL 90
E + I G LSG V ISG+KNS++ L+ A +L L VP +SD +++ IL L
Sbjct: 2 EKIVINGGKPLSGEVTISGAKNSAVALIPAAILADGPVTLDGVP-DISDVHSLVDILEEL 60
Query: 91 GAKIEFNERNKEILVNTDGVGRAEPCLGEMRKIRGGFFVIGPLLARFGEAVVGLPGGCDI 150
G K++ + + ++ G+ G+++ +R ++ +G LL RF +AVVGLPGGCD+
Sbjct: 61 GGKVKRD--GDTLEIDPTGIQSMPLPNGKVKSLRASYYFMGALLGRFKKAVVGLPGGCDL 118
Query: 151 GERPVDLYVRGLRALGAAVEI 171
G RP+D +++G ALGA V
Sbjct: 119 GPRPIDQHIKGFEALGAEVTN 139
>gnl|CDD|215834 pfam00275, EPSP_synthase, EPSP synthase (3-phosphoshikimate
1-carboxyvinyltransferase).
Length = 415
Score = 96.2 bits (240), Expect = 6e-24
Identities = 47/140 (33%), Positives = 68/140 (48%), Gaps = 5/140 (3%)
Query: 35 ITGPTQLSGHVPISGSK-NSSLCLLAATLLCSNSCLLHNVPTGLSDTKTMLSILRLLGAK 93
+TG ++L+G V + GSK NS LL A L + + N+ DT+ ML LR LGA+
Sbjct: 1 VTGGSRLNGEVKVPGSKSNSHRALLLAALA-AGESTITNLLDSD-DTRLMLEALRALGAE 58
Query: 94 IEFNERNKEILVNTDGVGRAEPCLGEMRKIRGGFFVIGPLLARFGEA--VVGLPGGCDIG 151
+ + K +++ G E + + + PLL R V L G IG
Sbjct: 59 VIELDEEKTVVIVEGLGGSFEAPYELVLDLGNSGTAMRPLLGRLALQSGEVVLTGDDSIG 118
Query: 152 ERPVDLYVRGLRALGAAVEI 171
ERP+D + GLR LGA +E
Sbjct: 119 ERPIDRLLDGLRQLGAEIEY 138
>gnl|CDD|238795 cd01554, EPT-like, Enol pyruvate transferases family includes EPSP
synthases and UDP-N-acetylglucosamine enolpyruvyl
transferase. Both enzymes catalyze the reaction of
enolpyruvyl transfer.
Length = 408
Score = 73.0 bits (179), Expect = 1e-15
Identities = 33/134 (24%), Positives = 52/134 (38%), Gaps = 12/134 (8%)
Query: 41 LSGHVPISGSKNSSLCLLAATLLCSNSCLLHNVPTGLSDTKTMLSILRLLGAKIEFNERN 100
L G + + G K+ S L L ++N+ G D + + +LR LG +IE +
Sbjct: 1 LHGIIRVPGDKSISHRSLIFASLAEGETKVYNILRG-EDVLSTMQVLRDLGVEIEDKDGV 59
Query: 101 KEILVNTDGVGRAEPCL-----GEMRKIRGGFFVIGPLLARFGEAVVGLPGGCDIGERPV 155
I G P IR + G L E V L G + +RP+
Sbjct: 60 ITIQGV-GMAGLKAPQNALNLGNSGTAIR---LISGVLAGADFE--VELFGDDSLSKRPM 113
Query: 156 DLYVRGLRALGAAV 169
D L+ +GA++
Sbjct: 114 DRVTLPLKKMGASI 127
>gnl|CDD|238797 cd01556, EPSP_synthase, EPSP synthase domain. 3-phosphoshikimate
1-carboxyvinyltransferase
(5-enolpyruvylshikimate-3-phosphate synthase) (EC
2.5.1.19) catalyses the reaction between
shikimate-3-phosphate (S3P) and phosphoenolpyruvate
(PEP) to form 5-enolpyruvylshkimate-3-phosphate (EPSP),
an intermediate in the shikimate pathway leading to
aromatic amino acid biosynthesis. The reaction is
phosphoenolpyruvate + 3-phosphoshikimate = phosphate +
5-O-(1-carboxyvinyl)-3-phosphoshikimate. It is found in
bacteria and plants but not animals. The enzyme is the
target of the widely used herbicide glyphosate, which
has been shown to occupy the active site. In bacteria
and plants, it is a single domain protein, while in
fungi, the domain is found as part of a multidomain
protein with functions that are all part of the
shikimate pathway.
Length = 409
Score = 52.2 bits (126), Expect = 2e-08
Identities = 44/139 (31%), Positives = 59/139 (42%), Gaps = 21/139 (15%)
Query: 41 LSGHVPISGSKNSSL-CLLAATLLCSNSCLLHNVPTGLSDTKTMLSILRLLGAKIEFNER 99
LSG + + GSK+ S LL A L + N+ DT L LR LGAKIE E
Sbjct: 1 LSGEITVPGSKSISHRALLLA-ALAEGESRIENLLDS-DDTLATLEALRALGAKIE--EE 56
Query: 100 NKEILVNTDGVGRAEPC----LGE----MRKIRGGFFVIGPLLARFGEAVVGLPGGCDIG 151
+ + G P G MR + G L + G++V L G +
Sbjct: 57 GGTVEIVGGGGLGLPPEAVLDCGNSGTTMR------LLTGLLALQGGDSV--LTGDESLR 108
Query: 152 ERPVDLYVRGLRALGAAVE 170
+RP+ V LR LGA +E
Sbjct: 109 KRPMGRLVDALRQLGAEIE 127
>gnl|CDD|235037 PRK02427, PRK02427, 3-phosphoshikimate 1-carboxyvinyltransferase;
Provisional.
Length = 435
Score = 49.8 bits (120), Expect = 1e-07
Identities = 47/148 (31%), Positives = 65/148 (43%), Gaps = 22/148 (14%)
Query: 32 TLTITGPTQLSGHVPISGSKNSSL-CLLAATLLCSNSCLLHNVPTGLSDTKTMLSILRLL 90
L I P+ LSG V + GSK+ S LL A L + N+ DT L+ LR L
Sbjct: 4 MLLIIPPSPLSGTVRVPGSKSISHRALLLA-ALAEGETTITNLLRS-EDTLATLNALRAL 61
Query: 91 GAKIEFNERNKEILVNTDGVGRAEPC----LGE----MRKIRGGFFVIGPLLARFGEAVV 142
G +I E ++ ++ G G EP G MR + G LLA VV
Sbjct: 62 GVEI---EDDEVVVEGVGGGGLKEPEDVLDCGNSGTTMR------LLTG-LLALQPGEVV 111
Query: 143 GLPGGCDIGERPVDLYVRGLRALGAAVE 170
L G + +RP+ + LR +GA +E
Sbjct: 112 -LTGDESLRKRPMGRLLDPLRQMGAKIE 138
>gnl|CDD|223206 COG0128, AroA, 5-enolpyruvylshikimate-3-phosphate synthase [Amino
acid transport and metabolism].
Length = 428
Score = 48.4 bits (116), Expect = 4e-07
Identities = 41/141 (29%), Positives = 56/141 (39%), Gaps = 18/141 (12%)
Query: 38 PTQLSGHVPISGSKNSSLCLLAATLLCSNSCLLHNVPTGLSDTKTMLSILRLLGAKIEFN 97
P+ L G V GSK+ S L L + N+ DT L LR LGA+IE
Sbjct: 10 PSPLRGTVRAPGSKSISHRALLLAALAEGESTITNLLDS-EDTLATLEALRALGARIE-- 66
Query: 98 ERNKEILVNTDGVGRAEPC----LGE----MRKIRGGFFVIGPLLARFGEAVVGLPGGCD 149
+ ++V G EP G +R + G LLA L G
Sbjct: 67 KEGDTLVVRGTGGELKEPPAVLDCGNSGTTLR------LLTG-LLALGSPGETVLTGDES 119
Query: 150 IGERPVDLYVRGLRALGAAVE 170
+ +RP+ V LR LGA ++
Sbjct: 120 LRKRPMGPLVDALRQLGAKID 140
Score = 27.6 bits (62), Expect = 3.9
Identities = 25/97 (25%), Positives = 38/97 (39%), Gaps = 18/97 (18%)
Query: 84 LSILRLLGAKIEFNERNKEILVNTDGVGRAEPCLGEMRKIRG--------GFFVIGPLLA 135
+ LR LGAKI+ E + + G G +I G ++ PLLA
Sbjct: 129 VDALRQLGAKIDGREGEGYLPLTIKG-----GLKGGEVEIDGPVSSQQVSSLLLLAPLLA 183
Query: 136 RFGEAVVGLPGGCDIGERP-VDLYVRGLRALGAAVEI 171
+V G + +P +D + L+A G VE
Sbjct: 184 EGTTIIV----GGVLESKPYIDHTLDMLKAFGVEVEN 216
>gnl|CDD|233373 TIGR01356, aroA, 3-phosphoshikimate 1-carboxyvinyltransferase.
This model represents
3-phosphoshikimate-1-carboxyvinyltransferase (aroA),
which catalyzes the sixth of seven steps in the
shikimate pathway of the biosynthesis of chorimate.
Chorismate is last common precursor of all three
aromatic amino acids. Sequences scoring between the
trusted and noise cutoffs include fragmentary and
aberrant sequences in which generally well-conserved
motifs are missing or altererd, but no example of a
protein known to have a different function [Amino acid
biosynthesis, Aromatic amino acid family].
Length = 409
Score = 44.2 bits (105), Expect = 1e-05
Identities = 41/136 (30%), Positives = 57/136 (41%), Gaps = 21/136 (15%)
Query: 43 GHVPISGSKNSSLCLLAATLLCSNSCLLHNVPTGLSDTKTMLSILRLLGAKIEFNERNKE 102
G + GSK+ + L L + N+ DT L LR LGAKIE + +
Sbjct: 1 GEIRAPGSKSITHRALILAALAEGETRVRNLLRSE-DTLATLDALRALGAKIE--DGGEV 57
Query: 103 ILVNTDGVGRAEPC----LGE----MRKIRGGFFVIGPLLARFGEAVVGLPGGCDIGERP 154
++ +GVG EP LG R + G +LA VV L G + +RP
Sbjct: 58 AVI--EGVGGKEPQAELDLGNSGTTAR------LLTG-VLALADGEVV-LTGDESLRKRP 107
Query: 155 VDLYVRGLRALGAAVE 170
+ V LR LGA +
Sbjct: 108 MGRLVDALRQLGAEIS 123
Score = 27.6 bits (62), Expect = 3.4
Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 5/43 (11%)
Query: 57 LLAATLLCSNSCLLHNVPTGLSDTKT---MLSILRLLGAKIEF 96
LAA + L N+ G++ T+ ++ +L +GA IE
Sbjct: 230 FLAAAAITGGRVTLENL--GINPTQGDKAIIIVLEEMGADIEV 270
>gnl|CDD|177972 PLN02338, PLN02338, 3-phosphoshikimate 1-carboxyvinyltransferase.
Length = 443
Score = 42.0 bits (99), Expect = 6e-05
Identities = 46/155 (29%), Positives = 66/155 (42%), Gaps = 22/155 (14%)
Query: 30 AETLTITGPTQLSGHVPISGSKN-SSLCLLAATLLCSNSCLLHNVPTGLSDTKTMLSILR 88
AE +T+ ++SG V + GSK+ S+ LL A L + ++ N+ D + ML L+
Sbjct: 1 AEEITLQPIKEISGTVKLPGSKSLSNRILLLAAL-SEGTTVVDNLLDS-DDIRYMLGALK 58
Query: 89 LLGAKIEFNERNKEILVN---------TDGVGRAEPCLGE----MRKIRGGFFVIGPLLA 135
LG +E + N +V D E LG MR + G
Sbjct: 59 TLGLNVEEDSENNRAVVEGCGGKFPVSGDSKEDVELFLGNAGTAMRPLTAAVTAAG---- 114
Query: 136 RFGEAVVGLPGGCDIGERPVDLYVRGLRALGAAVE 170
G A L G + ERP+ V GL+ LGA VE
Sbjct: 115 --GNASYVLDGVPRMRERPIGDLVDGLKQLGADVE 147
>gnl|CDD|237003 PRK11860, PRK11860, bifunctional 3-phosphoshikimate
1-carboxyvinyltransferase/cytidine monophosphate kinase;
Provisional.
Length = 661
Score = 33.9 bits (78), Expect = 0.028
Identities = 43/145 (29%), Positives = 61/145 (42%), Gaps = 35/145 (24%)
Query: 42 SGHVPISGSKNSS--LCLLAATLLCSNSCLLHNVPTGLSDTKTMLSILRLLGAKIEFNER 99
G V + GSK+ S + LLAA L + + ++ DT+ ML LR LG +E
Sbjct: 16 GGTVRLPGSKSISNRVLLLAA--LSEGTTTVRDL-LDSDDTRVMLDALRALGCGVEQLGD 72
Query: 100 NKEILVNTDGVG------RAEPCLGE----MRKIRGGFFVIGPLLARFGEAVVG----LP 145
I G+G +A+ LG MR PL A A++G L
Sbjct: 73 TYRI----TGLGGQFPVKQADLFLGNAGTAMR----------PLTAAL--ALLGGEYELS 116
Query: 146 GGCDIGERPVDLYVRGLRALGAAVE 170
G + ERP+ V LR LG ++
Sbjct: 117 GVPRMHERPIGDLVDALRQLGCDID 141
>gnl|CDD|237820 PRK14806, PRK14806, bifunctional cyclohexadienyl dehydrogenase/
3-phosphoshikimate 1-carboxyvinyltransferase;
Provisional.
Length = 735
Score = 31.5 bits (72), Expect = 0.21
Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 6/76 (7%)
Query: 28 REAETLTITGPTQLSG-HVPISGSKNSSLCLLAATLLCSNS-CLLHNVPTGLSDTKT-ML 84
E T+++ G +L+ + + +S+ L A + S L +V G++ T+T ++
Sbjct: 511 VEGNTISVEGGGKLTATDIEVPADISSAAFFLVAASIAEGSELTLEHV--GINPTRTGVI 568
Query: 85 SILRLLGAKIE-FNER 99
IL+L+GA I NER
Sbjct: 569 DILKLMGADITLENER 584
>gnl|CDD|240547 cd13142, MATE_like_12, Uncharacterized subfamily of the multidrug
and toxic compound extrusion (MATE) proteins. The
integral membrane proteins from the MATE family are
involved in exporting metabolites across the cell
membrane and are responsible for multidrug resistance
(MDR) in many bacteria and animals. A number of family
members are involved in the synthesis of peptidoglycan
components in bacteria.
Length = 444
Score = 27.9 bits (63), Expect = 2.6
Identities = 16/46 (34%), Positives = 19/46 (41%), Gaps = 3/46 (6%)
Query: 126 GFFVIGPLLARFGEAVVGLPGGCDIGERPVDLYVRGLRALGAAVEI 171
GF V+ L+A FG VV G IG R + L L A
Sbjct: 256 GFTVMTALVAGFGTVVVAAYG---IGNRIISLVFLPAFGLARATST 298
>gnl|CDD|226914 COG4539, COG4539, Predicted membrane protein [Function unknown].
Length = 180
Score = 27.5 bits (61), Expect = 3.2
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 61 TLLCSNSCLLHNVPTGLSDTKTMLSILRLLG 91
T+L S + LLH GLS++K +S LL
Sbjct: 30 TILLSGAVLLHRPVIGLSNSKLQISPALLLS 60
>gnl|CDD|235521 PRK05590, PRK05590, hypothetical protein; Provisional.
Length = 166
Score = 27.2 bits (61), Expect = 3.7
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 94 IEFNERNKEILVNTDGVGRAEPC 116
I + + +VN + VGR +PC
Sbjct: 129 IHKEWKKSKTVVNENKVGRNDPC 151
>gnl|CDD|113341 pfam04566, RNA_pol_Rpb2_4, RNA polymerase Rpb2, domain 4. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). Domain 4,
is also known as the external 2 domain.
Length = 63
Score = 25.7 bits (57), Expect = 4.4
Identities = 9/20 (45%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 94 IEFNERNKEILVNTDGVGRA 113
+ N R +EI +NTD GR
Sbjct: 36 VVRNIRQREIRINTDA-GRI 54
>gnl|CDD|130387 TIGR01320, mal_quin_oxido, malate:quinone-oxidoreductase. This
membrane-associated enzyme is an alternative to the
better-known NAD-dependent malate dehydrogenase as part
of the TCA cycle. The reduction of a quinone rather than
NAD+ makes the reaction essentially irreversible in the
direction of malate oxidation to oxaloacetate. Both
forms of malate dehydrogenase are active in E. coli;
disruption of this form causes less phenotypic change.
In some bacteria, this form is the only or the more
important malate dehydrogenase [Energy metabolism, TCA
cycle].
Length = 483
Score = 27.5 bits (61), Expect = 4.5
Identities = 17/68 (25%), Positives = 24/68 (35%), Gaps = 9/68 (13%)
Query: 80 TKTMLSILRLLGAKIEFNERNKEILVNTDGVGRAEPC---LGEMRKIRGGFFVIG----- 131
TK +L L G I F + + +DG G R + F +G
Sbjct: 181 TKQLLGYLVQNGTTIRFGHEVRNLKRQSDGSWTVTVKNTRTGGKRTLNTRFVFVGAGGGA 240
Query: 132 -PLLARFG 138
PLL + G
Sbjct: 241 LPLLQKSG 248
>gnl|CDD|219600 pfam07833, Cu_amine_oxidN1, Copper amine oxidase N-terminal domain.
Copper amine oxidases catalyze the oxidative
deamination of primary amines to the corresponding
aldehydes, while reducing molecular oxygen to hydrogen
peroxide. These enzymes are dimers of identical
subunits, each comprising four domains. The N-terminal
domain, which is absent in some amine oxidases, consists
of a five-stranded antiparallel beta sheet twisted
around an alpha helix. The D1 domains from the two
subunits comprise the 'stalk' of the mushroom-shaped
dimer, and interact with each other but do not pack
tightly against each other.
Length = 93
Score = 26.0 bits (58), Expect = 5.2
Identities = 8/33 (24%), Positives = 17/33 (51%), Gaps = 3/33 (9%)
Query: 81 KTMLS---ILRLLGAKIEFNERNKEILVNTDGV 110
+T++ I LGAK+ ++ + K + + G
Sbjct: 4 RTLVPLRAIAEALGAKVSWDGKTKTVTITKGGK 36
>gnl|CDD|183244 PRK11629, lolD, lipoprotein transporter ATP-binding subunit;
Provisional.
Length = 233
Score = 26.7 bits (59), Expect = 5.6
Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 6/81 (7%)
Query: 21 RTQTTQIREAETLTITGPTQLSGHVP--ISGSKNSSLCLLAATLLCSNSCLLHNVPTGLS 78
+ R E L G + H P +SG + + + A L+ + +L + PTG
Sbjct: 118 KPAEINSRALEMLAAVGLEHRANHRPSELSGGERQRVAI-ARALVNNPRLVLADEPTGNL 176
Query: 79 DTKTMLSILRLLGAKIEFNER 99
D + SI +LLG E N
Sbjct: 177 DARNADSIFQLLG---ELNRL 194
>gnl|CDD|131957 TIGR02911, sulfite_red_B, sulfite reductase, subunit B. Members of
this protein family include the B subunit, one of three
subunits, of the anaerobic sulfite reductase of
Salmonella, and close homologs from various Clostridum
species, where the three-gene neighborhood is preserved.
Two such gene clusters are found in Clostridium
perfringens, but it may be that these sets of genes
correspond to the distinct assimilatory and
dissimilatory forms as seen in Clostridium pasteurianum
[Central intermediary metabolism, Sulfur metabolism].
Length = 261
Score = 26.7 bits (59), Expect = 5.9
Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 5/36 (13%)
Query: 125 GGFFVIGPLLARFGEAVVGLPGGCDIGERPVDLYVR 160
G FF + L ++GEA + + IGE +DL +R
Sbjct: 34 GQFFEVS--LPKYGEAPISV---SGIGEGYIDLTIR 64
>gnl|CDD|235972 PRK07225, PRK07225, DNA-directed RNA polymerase subunit B';
Validated.
Length = 605
Score = 26.8 bits (60), Expect = 6.1
Identities = 8/20 (40%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 94 IEFNERNKEILVNTDGVGRA 113
+ + E E+++NTD GRA
Sbjct: 42 VSYKEETNEVIINTDA-GRA 60
>gnl|CDD|218805 pfam05910, DUF868, Plant protein of unknown function (DUF868).
This family consists of several hypothetical proteins
from Arabidopsis thaliana and Oryza sativa. The function
of this family is unknown.
Length = 271
Score = 26.6 bits (59), Expect = 7.7
Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 88 RLLGAKIEFNERNK--EILVNTDGVGRAEPCL 117
R+ K F+++ K EI++ D G +P L
Sbjct: 144 RVFSTKARFSDQGKEHEIVIECDTEGLKDPEL 175
>gnl|CDD|240044 cd04688, Nudix_Hydrolase_29, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent cation,
such as Mg2+ or Mn2+, for their activity and contain a
highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. Substrates of
nudix hydrolases include intact and oxidatively damaged
nucleoside triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the
nucleotide pools and to maintain cell viability, thereby
serving as surveillance & "house-cleaning" enzymes.
Substrate specificity is used to define families within
the superfamily. Differences in substrate specificity
are determined by the N-terminal extension or by
residues in variable loop regions. Mechanistically,
substrate hydrolysis occurs by a nucleophilic
substitution reaction, with variation in the numbers and
roles of divalent cations required.
Length = 126
Score = 25.7 bits (57), Expect = 8.4
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 88 RLLGAKIEFNERNKEILV 105
R G IEF E ++E L+
Sbjct: 26 RPPGGGIEFGESSEEALI 43
>gnl|CDD|182732 PRK10789, PRK10789, putative multidrug transporter
membrane\ATP-binding components; Provisional.
Length = 569
Score = 26.6 bits (59), Expect = 9.3
Identities = 10/30 (33%), Positives = 14/30 (46%)
Query: 10 FNSPQTQKPQIRTQTTQIREAETLTITGPT 39
F PQT P + ++ + L I GPT
Sbjct: 321 FTYPQTDHPALENVNFTLKPGQMLGICGPT 350
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.138 0.404
Gapped
Lambda K H
0.267 0.0771 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,481,320
Number of extensions: 767173
Number of successful extensions: 687
Number of sequences better than 10.0: 1
Number of HSP's gapped: 661
Number of HSP's successfully gapped: 34
Length of query: 171
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 81
Effective length of database: 6,945,742
Effective search space: 562605102
Effective search space used: 562605102
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (24.9 bits)