NCBI Conserved Domain Search

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Conserved domains on [gi\|117928976\|ref\|YP_873527.1\|]
hypothetical protein Acel_1769 [Acidothermus cellulolyticus 11B]

Graphical summary show options »	Show site features Horizontal zoom: ×	?



List of domain hits		?

References:

Marchler-Bauer A et al. (2009), "CDD: specific functional annotation with the Conserved Domain Database.", Nucleic Acids Res.37(D)205-10.

Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.

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of the residues that compose this conserved feature have been mapped to the query sequence.

Click on the triangle to view details about the feature, including a multiple sequence alignment of your query sequence and the protein sequences used to curate the domain model, where hash marks (#) above the aligned sequences show the location of the conserved feature residues.

The thumbnail image, if present, provides an approximate view of the feature's location in 3 dimensions. Click on the triangle for interactive 3D structure viewing options.

This image shows a graphical summary of conserved domains identified on the query sequence. The Show Concise/Full Display button at the top of the page can be used to select the desired level of detail: only top scoring hits (labeled illustration) or all hits (labeled illustration).
Domains are color coded according to superfamilies to which they have been assigned. Hits with scores that pass a domain-specific threshold (specific hits) are drawn in bright colors. Others (non-specific hits) and superfamily placeholders are drawn in pastel colors.
if a domain or superfamily has been annotated with functional sites (conserved features), they are mapped to the query sequence and indicated through sets of triangles with the same color and shade of the domain or superfamily that provides the annotation.
Mouse over the colored bars or triangles to see descriptions of the domains and features. click on the bars or triangles to view your query sequence embedded in a multiple sequence alignment of the proteins used to develop the corresponding domain model.

The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores. Click on the PssmId to view the multiple sequence alignment of the proteins used to develop the corresponding domain model.

To view your query sequence embedded in that multiple sequence alignment, click on the colored bars in the Graphical Summary portion of the search results page, or click on the triangles, if present, that represent functional sites (conserved features) mapped to the query sequence.

Concise Display shows only the best scoring domain model, in each hit category listed below except non-specific hits, for each region on the query sequence. (labeled illustration)
Full Display shows all domain models, in each hit category below, that meet or exceed the RPS-BLAST threshold for statistical significance. (labeled illustration)
Four types of hits can be shown, as available, for each region on the query sequence:

specific hits meet or exceed a domain-specific e-value threshold (illustrated example) and represent a very high confidence that the query sequence belongs to the same protein family as the sequences use to create the domain model
non-specific hits meet or exceed the RPS-BLAST threshold for statistical significance (default E-value cutoff of 0.01, or an E-value selected by user via the advanced search options)
the domain superfamily to which the specific and non-specific hits belong
multi-domain models that were computationally detected and are likely to contain multiple single domains

The CD-Search help document provides more detail about the tool and its features.

Retrieve proteins that contain one or more of the domains present in the query sequence, using the Conserved Domain Architecture Retrieval Tool (CDART).

Modify your query to search against a different database and/or use advanced search options

131037

TIGR01982

UbiB

2-polyprenylphenol 6-hydroxylase

true

false

437

5e-39

157.07

59.04

7,53,49,34,91,83,96,187,180,3,190,185,41,231,228,22,259,250,6,265,263,44

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928976  54 AEQLFDVLGELKGGAMKLGQALSVFEAAMPDDLAapyrESLTRLQENAPPLPAATVHRVLAGQLGPQWRTYFRDFEDRPA 133
TIGR01982     50 GERLRLALEELGPTFIKFGQTLSTRADLLPADIA----EELSLLQDRVPPFDFKVARKVIEAALGGPLEELFAEFEEKPL 125

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928976 134 AAASIGQVHRAVWQDGRHVAVKIQYPGAGKALLSDLTQLGRLGRVFGVLFPGLD-LKP--LLQELRARVTEELDYRLEAM 210
TIGR01982    126 AAASIAQVHRARLVDGKEVAVKVLRPGIEKTIAADIALLYRLARIVERLSPDSRrLRPteVVKEFEKTLRRELDLRREAA 205

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928976 211 SQHAFARAYLDDPDIYVPDVL--AGADRVIVSEWIDGTPLSSIIRsgtrrqRDHAGL-------LLVRFLFSGPARVGML 281
TIGR01982    206 NASELGENFKNDPGVYVPEVYwdRTSERVLTMEWIDGIPLSDIAA------LDEAGLdrkalaeNLARSFLNQVLRDGFF 279

                        250       260
                 ....*....|....*....|....*...
gi 117928976 282 HADPHPGNYRLLDDGRLAVLDFGAVNRL 309
TIGR01982    280 HADLHPGNIFVLKDGKIIALDFGIVGRL 307

cl09925

142329

PKc_like

Protein Kinases, catalytic domain

-1

111949

pfam03109

ABC1

ABC1 family

false

117

2e-28

121.93

98.29

1,115,1,115

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928976 116 QLGPQWRTYFRDFEDRPAAAASIGQVHRAVWQDGRHVAVKIQYPGAGKALLSDLTQLGRLGRVFGVLFPGLDLKPLLQEL 195
pfam03109      2 ELGAPVEEVFAEFDEEPIAAASIAQVHRAVLKDGEEVAVKVQRPGVKKRIRSDLKLLKFLAKILKKFFPGFDLDWLVDEF 81

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 117928976 196 RARVTEELDYRLEAMSQHAFARAYLDDPDIYVPDV 230
pfam03109     82 RKSLPQELDFLREAANAEKFRENFADLPWVYVPKV 116

cl09925

142329

PKc_like

Protein Kinases, catalytic domain

-1

135177

PRK04750

ubiB

putative ubiquinone biosynthesis protein UbiB; Reviewed

false

540

2e-23

105.39

45.74

10,69,67,18,91,85,57,148,143,36,184,180,6,190,188,43,233,233,20,253,256,6,265,262,2,267,268,22,289,294,20

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928976  70 KLGQALSVFEAAMPDDLAapyrESLTRLQENAPPLPAATVHRVLAGQLGPQWRTYFRDFEDRPAAAASIGQVHRAVWQD- 148
PRK04750      68 KFGQMLSTRRDLFPPDIA----DELALLQDRVPPFDGALARAIIEKALGGPVEEWFDDFDIEPLASASIAQVHTARLKDn 143

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928976 149 GRHVAVKIQYPGAGKALLSDLTQLGRLGRVFGVLFP-GLDLKP--LLQELRARVTEELDYRLEAMSQHAFARAYLDDPDI 225
PRK04750     144 GREVVVKVLRPDILPVIDADLALMRRLARWVERLLPdGRRLKPreVVAEFEKTLHDELDLMREAANASQLRRNFEDSDLL 223

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928976 226 YVPDVLAG--ADRVIVSEWIDGTPLSSIIR---SGTRRQrdhaglLL----VRFLFSGPARVGMLHADPHPGN----YRL 292
PRK04750     224 YVPEVYWDycSETVLVMERMYGIPVSDVAAlraAGTDMK------LLaergVEVFFTQVFRDGFFHADMHPGNifvsYDH 297

                        250
                 ....*....|....*..
gi 117928976 293 LDDGRLAVLDFGAVNRL 309
PRK04750     298 PENPRYIALDFGIVGSL 314

cl09925

142329

PKc_like

Protein Kinases, catalytic domain

-1

88612

cd05120

APH_ChoK_like

Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). The family is composed of APH, ChoK, ethanolamine kinase (ETNK), macrolide 2'-phosphotransferase (MPH2'), an unusual homoserine kinase, and uncharacterized proteins with similarity to the N-terminal domain of acyl-CoA dehydrogenase 10 (ACAD10). The members of this family catalyze the transfer of the gamma-phosphoryl group from ATP (or CTP) to small molecule substrates such as aminoglycosides, macrolides, choline, ethanolamine, and homoserine. Phosphorylation of the antibiotics, aminoglycosides and macrolides, leads to their inactivation and to bacterial antibiotic resistance. Phosphorylation of choline, ethanolamine, and homoserine serves as precursors to the synthesis of important biological compounds, such as the major phospholipids, phosphatidylcholine and phosphatidylethanolamine and the amino acids, threonine, methionine, and isoleucine.

Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/...

false

155

0.001

39.27

63.23

4,203,36,30,234,66,33,268,99,10,279,109,25

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928976 204 DYRLEAMSQHAFARAYLDDPDIYVPDVLAGaDRVIVSEWIDGTPLSSIIRSGTRRQRDHAGLLLvRFLFSGPARVgMLHA 283
cd05120       37 DREREVAILQLLARKGLPVPKVLASGESDG-WSYLLMEWIEGETLDEVSEEEKEDIAEQLAELL-AKLHQLPLLV-LCHG 113

                         90       100
                 ....*....|....*....|.
gi 117928976 284 DPHPGNYRLLDDGRLAVLDFG 304
cd05120      114 DLHPGNILVDDGKILGIIDWE 134

cl09925

142329

PKc_like

Protein Kinases, catalytic domain

-1

88274

cd05144

RIO2_C

RIO kinase family; RIO2, C-terminal catalytic domain. The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). RIO kinases are atypical protein serine kinases containing a kinase catalytic signature, but otherwise show very little sequence similarity to typical PKs. Serine kinases catalyze the transfer of the gamma-phosphoryl group from ATP to serine residues in protein substrates. The RIO catalytic domain is truncated compared to the catalytic domains of typical PKs, with deletions of the loops responsible for substrate binding. RIO2 is present in archaea and eukaryotes. It contains an N-terminal winged helix (wHTH) domain and a C-terminal RIO kinase catalytic domain. The wHTH domain is primarily seen in DNA-binding proteins, although some wHTH domains may be involved in RNA recognition. RIO2 is essential for survival and is necessary for rRNA cleavage during 40S ribosomal subunit maturation. The biological substrates of RIO2 are still unknown.

RIO kinase family; RIO2, C-terminal catalytic domain. The RIO kinase catalytic domain...

false

true

false

198

0.007

37.42

46.97

3,205,76,13,219,89,52,275,141,28

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928976 206 RLEAMSQHAFARAyLDDPDIYVPDVLAGADRVIVSEWIDGTPLSSIIRSGTRRQRDHAGLLLVRFLfsgpARVGMLHADP 285
cd05144       77 RLAAQKEFAALKA-LYEEGFPVPKPIDWNRHAVVMEYIDGVELYRVRVLEDPEEVLDEILEEIVKA----YKHGIIHGDL 151

                         90
                 ....*....|....*...
gi 117928976 286 HPGNYRLLDDGRLAVLDF 303
cd05144      152 SEFNILVDDDEKIYIIDW 169

cl09925

142329

PKc_like

Protein Kinases, catalytic domain

-1

31005

COG0661

AarF

Predicted unusual protein kinase [General function prediction only]

false

true

false

517

3e-69

257.57

85.88

10,0,3,38,38,42,38,80,80,105,185,188,46,231,236,26,257,263,93,350,358,12,362,372,14,378,386,14,392,402,45

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928976   1 MGSMADIPRGTVARTARLARLPLSAAGRTAVGIGKRLT-GRPAEEVIGEFQRRTAEQLFDVLGELKGGAMKLGQALSvfe 79
COG0661        4 LYAVSRLPRIIRVRLRYLLGRLLRLTGRLALLLRLLSWlGKSKLASSEELREKRAERLRLALEELGPTFIKLGQILS--- 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928976  80 aAMPDDLAAPYRESLTRLQENAPPLPAATVHRVLAGQLGPQWRTYFRDFEDRPAAAASIGQVHRAVWQDGRHVAVKIQYP 159
COG0661       81 -TRPDLVPPEYAEELAKLQDRVPPFPFEEAERIIEEELGRPIEELFSEFEPEPIASASIAQVHRAVLKSGEEVAVKVQRP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928976 160 GAGKALLSDLTQLGRLGRVFGVLFPG---LDLKPLLQELRARVTEELDYRLEAMSQHAFARAYLDDPDIYVPDVL--AGA 234
COG0661      160 GIRERIEADLKLLRRLARLIKRLPPGgrrLDLVEVVDEFEKRLREELDYRREAANAERFRENFKDDPDVYVPKVYweYTT 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928976 235 DRVIVSEWIDGTPLSSIIRSGTR-RQRDHAGLLLVRFLFSGPARVGMLHADPHPGNYRLLDDGRLAVLDFGAVNRLPGGF 313
COG0661      240 RRVLTMEWIDGIKISDIAALKSAgIDRKELAELLVRAFLRQLLRDGFFHADPHPGNILVRSDGRIVLLDFGIVGRLDPKF 319

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117928976 314 PPIIGRLLSLALREEPDAVLEGLREEGFVRARRSVDP--HDLLAYLNPFLD--PVRYPVFHFTRRWLreQASRIGDPRTP 389
COG0661      320 RRYLAELLLAFLNRDYDRVAELHVELGYVPPDTDRDPlaAAIRAVLEPIYGkpLEEISFGEILDKLF--EVARRFPMRLP 397

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|
gi 117928976 390 SGA--LARQLNLPPSYLLIHRVWMGSIGILCQLDAAGPFRAEIERWLPGL 437
COG0661      398 PELvlLQRTLLLVEGVGRQLDPRFNLWAVAQPLLAKWLKKQLSPKLLREL 447

-1