Psyllid ID: psy6139

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------7
Protein Sequence
MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPEDKLAFVKSFVYDYSYSEPSVPTSYSWPKL
Secondary Structure (PSIPRED)
cEEEEEEcEEEEEEEEEEcccHHHHHHHHHHHccccccccccccEEEEcEEcccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEEEEEEEEEEEEEcccEEEEHHccccccEEEccccHHHHHHHHHHHccccccccccccccccc
Coil and Loop (DISEMBL)
MFTLKKWNAVAMWSwdvecdtcaicRVQVmgtatvypepedkLAFVKSFVYdysysepsvptsyswpkl
Flexible Loop (DISEMBL)
mftlkkwnAVAMWSWDVECDTCAICRVQVMGTATVYPEPEDKLAFVKSFVYDYSysepsvptsyswpkl
Low Complexity Region (SEG)
MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPEDKLAFVKSFVYDYSYSEPSVPTSYSWPKL
Disordered region (IsUnstruct)
**TLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPEDKLAFVKSFVYDYSY**************
Disordered Region (DISOPRED)
MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPEDKLAFVKSFVYDYSYSEPSVPTSYSWPKL
Disordered Region (DISEMBL)
MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPEDKLAFVKSFVYDYSY**************
Disordered Region (DISPRO)
MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPEDKLAFVKSFVYDYSYSEPSVPTSYS***L
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPEDKLAFVKSFVYDYSYSEPSVPTSYSWPKL
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	69	2.2.26 [Sep-21-2011]
Q9UBF6	113	RING-box protein 2 OS=Hom	yes	N/A	0.594	0.362	0.761	2e-11
Q9WTZ1	113	RING-box protein 2 OS=Mus	yes	N/A	0.594	0.362	0.761	3e-11
Q8QG64	108	RING-box protein 1 OS=Sal	N/A	N/A	0.420	0.268	0.620	4e-05
Q9W5E1	108	RING-box protein 1A OS=Dr	no	N/A	0.420	0.268	0.620	4e-05
P62878	108	E3 ubiquitin-protein liga	no	N/A	0.420	0.268	0.620	4e-05
P62877	108	E3 ubiquitin-protein liga	no	N/A	0.420	0.268	0.620	4e-05
O13959	107	RING-box protein pip1 OS=	yes	N/A	0.420	0.271	0.620	4e-05
Q23457	110	RING-box protein 1 OS=Cae	no	N/A	0.420	0.263	0.586	5e-05
P48163	572	NADP-dependent malic enzy	no	N/A	0.521	0.062	0.540	5e-05
Q8BMF3	604	NADP-dependent malic enzy	no	N/A	0.507	0.057	0.583	7e-05

>sp|Q9UBF6|RBX2_HUMAN RING-box protein 2 OS=Homo sapiens GN=RNF7 PE=1 SV=1

 Score = 67.8 bits (164), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/42 (76%), Positives = 36/42 (85%), Gaps = 1/42 (2%)

Query: 1  MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPEDK 42
          MF+LKKWNAVAMWSWDVECDTCAICRVQVM  A +  + E+K
Sbjct: 29 MFSLKKWNAVAMWSWDVECDTCAICRVQVM-DACLRCQAENK 69

Probable component of the SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins involved in cell cycle progression, signal transduction and transcription. Through the RING-type zinc finger, seems to recruit the E2 ubiquitination enzyme to the complex and brings it into close proximity to the substrate. Promotes the neddylation of CUL5 via its interaction with UBE2F. May play a role in protecting cells from apoptosis induced by redox agents.
Homo sapiens (taxid: 9606)

>sp|Q9WTZ1|RBX2_MOUSE RING-box protein 2 OS=Mus musculus GN=Rnf7 PE=2 SV=1

 Score = 67.4 bits (163), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 32/42 (76%), Positives = 36/42 (85%), Gaps = 1/42 (2%)

Query: 1  MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPEDK 42
          MF+LKKWNAVAMWSWDVECDTCAICRVQVM  A +  + E+K
Sbjct: 29 MFSLKKWNAVAMWSWDVECDTCAICRVQVM-DACLRCQAENK 69

Probable component of the SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins involved in cell cycle progression, signal transduction and transcription. Through the RING-type zinc finger, seems to recruit the E2 ubiquitination enzyme to the complex and brings it into close proximity to the substrate. Promotes the neddylation of CUL5 via its interaction with UBE2F. May play a role in protecting cells from apoptosis induced by redox agents.

Mus musculus (taxid: 10090)

>sp|Q8QG64|RBX1_SALSA RING-box protein 1 OS=Salmo salar GN=rbx1 PE=2 SV=2

 Score = 47.0 bits (110), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 18/29 (62%), Positives = 23/29 (79%)

Query: 2  FTLKKWNAVAMWSWDVECDTCAICRVQVM 30
          F +KKWNAVA+W+WD+  D CAICR  +M
Sbjct: 22 FEVKKWNAVALWAWDIVVDNCAICRNHIM 50

Component of the SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase complex, which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Through the RING-type zinc finger, seems to recruit the E2 ubiquitination enzyme, like CDC34, to the complex and brings it into close proximity to the substrate. May be required for histone H3 and histone H4 ubiquitination in response to ultraviolet and for subsequent DNA repair. Promotes the neddylation of cul1, cul2, cul4 and cul4 via its interaction with ube2m.

Salmo salar (taxid: 8030)

>sp|Q9W5E1|RBX1A_DROME RING-box protein 1A OS=Drosophila melanogaster GN=Roc1a PE=1 SV=1

 Score = 47.0 bits (110), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 18/29 (62%), Positives = 23/29 (79%)

Query: 2  FTLKKWNAVAMWSWDVECDTCAICRVQVM 30
          F +KKWNAVA+W+WD+  D CAICR  +M
Sbjct: 22 FEVKKWNAVALWAWDIVVDNCAICRNHIM 50

Component of the SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase complex, which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Through the RING-type zinc finger, seems to recruit the E2 ubiquitination enzyme to the complex and brings it into close proximity to the substrate. Required for the specific SCF-dependent proteolysis of CI, but not that of ARM, suggesting that it also participates in the selection of substrates inside the SCF complex.

Drosophila melanogaster (taxid: 7227)

>sp|P62878|RBX1_MOUSE E3 ubiquitin-protein ligase RBX1 OS=Mus musculus GN=Rbx1 PE=1 SV=1

 Score = 47.0 bits (110), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 18/29 (62%), Positives = 23/29 (79%)

Query: 2  FTLKKWNAVAMWSWDVECDTCAICRVQVM 30
          F +KKWNAVA+W+WD+  D CAICR  +M
Sbjct: 22 FEVKKWNAVALWAWDIVVDNCAICRNHIM 50

E3 ubiquitin ligase component of multiple cullin-RING-based E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins, including proteins involved in cell cycle progression, signal transduction, transcription and transcription-coupled nucleotide excision repair. The functional specificity of the E3 ubiquitin-protein ligase complexes depends on the variable substrate recognition components. As a component of the CSA complex promotes the ubiquitination of ERCC6 resulting in proteasomal degradation (By similarity). Through the RING-type zinc finger, seems to recruit the E2 ubiquitination enzyme, like CDC34, to the complex and brings it into close proximity to the substrate. Probably also stimulates CDC34 autoubiquitination. May be required for histone H3 and histone H4 ubiquitination in response to ultraviolet and for subsequent DNA repair. Promotes the neddylation of CUL1, CUL2, CUL4 and CUL4 via its interaction with UBE2M.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|P62877|RBX1_HUMAN E3 ubiquitin-protein ligase RBX1 OS=Homo sapiens GN=RBX1 PE=1 SV=1

 Score = 47.0 bits (110), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 18/29 (62%), Positives = 23/29 (79%)

Query: 2  FTLKKWNAVAMWSWDVECDTCAICRVQVM 30
          F +KKWNAVA+W+WD+  D CAICR  +M
Sbjct: 22 FEVKKWNAVALWAWDIVVDNCAICRNHIM 50

E3 ubiquitin ligase component of multiple cullin-RING-based E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins, including proteins involved in cell cycle progression, signal transduction, transcription and transcription-coupled nucleotide excision repair. The functional specificity of the E3 ubiquitin-protein ligase complexes depends on the variable substrate recognition components. As a component of the CSA complex promotes the ubiquitination of ERCC6 resulting in proteasomal degradation. Through the RING-type zinc finger, seems to recruit the E2 ubiquitination enzyme, like CDC34, to the complex and brings it into close proximity to the substrate. Probably also stimulates CDC34 autoubiquitination. May be required for histone H3 and histone H4 ubiquitination in response to ultraviolet and for subsequent DNA repair. Promotes the neddylation of CUL1, CUL2, CUL4 and CUL4 via its interaction with UBE2M.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|O13959|RBX1_SCHPO RING-box protein pip1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=pip1 PE=1 SV=2

 Score = 47.0 bits (110), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 18/29 (62%), Positives = 22/29 (75%)

Query: 2  FTLKKWNAVAMWSWDVECDTCAICRVQVM 30
          F +KKWNAVA+W WD+  D CAICR  +M
Sbjct: 21 FEIKKWNAVALWQWDIVVDNCAICRNHIM 49

Component of E3 ubiquitin ligase SCF complexes, which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. Seems to recruit the E2 ubiquitination enzyme, like UBC3/CDC34, to the complex and brings it into close proximity to the substrate. Component of the rik1-associated E3 ubiquitin ligase complex that shows ubiquitin ligase activity and is required for histone H3K9 methylation. H3K9me represents a specific tag for epigenetic transcriptional repression by recruiting swi6/HP1 to methylated histones which leads to transcriptional silencing within centromeric heterochromatin, telomeric regions and at the silent mating-type loci.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q23457|RBX1_CAEEL RING-box protein 1 OS=Caenorhabditis elegans GN=rbx-1 PE=1 SV=1

 Score = 46.6 bits (109), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 17/29 (58%), Positives = 24/29 (82%)

Query: 2  FTLKKWNAVAMWSWDVECDTCAICRVQVM 30
          F +KKW+AVA+W+WD++ D CAICR  +M
Sbjct: 24 FEVKKWSAVALWAWDIQVDNCAICRNHIM 52

Component of the SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase complex, which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Through the RING-type zinc finger, seems to recruit the E2 ubiquitination enzyme to the complex and brings it into close proximity to the substrate (By similarity). Essential for meiosis, mitotic chromosomal condensation and cytokinesis. Involved in histone H3 phosphorylation.

Caenorhabditis elegans (taxid: 6239)

>sp|P48163|MAOX_HUMAN NADP-dependent malic enzyme OS=Homo sapiens GN=ME1 PE=1 SV=1

 Score = 46.6 bits (109), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 20/37 (54%), Positives = 27/37 (72%), Gaps = 1/37 (2%)

Query: 32  TATVYPEPEDKLAFVKSFVYDYSYSEPSVPTSYSWPK 68
           TATVYPEP++K AFV+S +Y   Y +  +P  YSWP+
Sbjct: 526 TATVYPEPQNKEAFVRSQMYSTDYDQ-ILPDCYSWPE 561

Homo sapiens (taxid: 9606)

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 4

EC: 0

>sp|Q8BMF3|MAON_MOUSE NADP-dependent malic enzyme, mitochondrial OS=Mus musculus GN=Me3 PE=1 SV=2

 Score = 45.8 bits (107), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 21/36 (58%), Positives = 25/36 (69%), Gaps = 1/36 (2%)

Query: 33  ATVYPEPEDKLAFVKSFVYDYSYSEPSVPTSYSWPK 68
           A+ YPEP+DK AFVKS +Y   Y   S+ T YSWPK
Sbjct: 562 ASYYPEPKDKEAFVKSLIYTPDYDSFSLDT-YSWPK 596

Mus musculus (taxid: 10090)

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 4

EC: 0

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	69
351699405	498	RING-box protein 2 [Heterocephalus glabe	0.434	0.060	0.966	5e-11
322797973	61	hypothetical protein SINV_15045 [Solenop	0.536	0.606	0.837	5e-11
357623531	62	hypothetical protein KGM_11044 [Danaus p	0.449	0.5	1.0	2e-10
242025508	69	RING finger, putative [Pediculus humanus	0.492	0.492	0.911	2e-10
157104957	51	hypothetical protein AaeL_AAEL000570 [Ae	0.449	0.607	1.0	2e-10
270001542	97	hypothetical protein TcasGA2_TC000384 [T	0.594	0.422	0.785	3e-10
295293375	110	RING finger protein [Eriocheir sinensis]	0.594	0.372	0.785	4e-10
47203192	110	unnamed protein product [Tetraodon nigro	0.594	0.372	0.761	4e-10
170036860	69	conserved hypothetical protein [Culex qu	0.434	0.434	1.0	5e-10
395832912	113	PREDICTED: RING-box protein 2 [Otolemur	0.594	0.362	0.761	5e-10

>gi|351699405|gb|EHB02324.1| RING-box protein 2 [Heterocephalus glaber]

 Score = 71.6 bits (174), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 29/30 (96%), Positives = 30/30 (100%)

Query: 1   MFTLKKWNAVAMWSWDVECDTCAICRVQVM 30
           MF+LKKWNAVAMWSWDVECDTCAICRVQVM
Sbjct: 414 MFSLKKWNAVAMWSWDVECDTCAICRVQVM 443

Source: Heterocephalus glaber

Species: Heterocephalus glaber

Genus: Heterocephalus

Family: Bathyergidae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|322797973|gb|EFZ19823.1| hypothetical protein SINV_15045 [Solenopsis invicta]

 Score = 71.6 bits (174), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 31/37 (83%), Positives = 33/37 (89%)

Query: 1  MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYP 37
          MFTLKKWNAVAMWSWDVECDTCAICRVQVMG   ++ 
Sbjct: 22 MFTLKKWNAVAMWSWDVECDTCAICRVQVMGKRYIFG 58

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357623531|gb|EHJ74641.1| hypothetical protein KGM_11044 [Danaus plexippus]

 Score = 70.1 bits (170), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/31 (100%), Positives = 31/31 (100%)

Query: 1  MFTLKKWNAVAMWSWDVECDTCAICRVQVMG 31
          MFTLKKWNAVAMWSWDVECDTCAICRVQVMG
Sbjct: 22 MFTLKKWNAVAMWSWDVECDTCAICRVQVMG 52

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242025508|ref|XP_002433166.1| RING finger, putative [Pediculus humanus corporis] gi|212518707|gb|EEB20428.1| RING finger, putative [Pediculus humanus corporis]

 Score = 70.1 bits (170), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/34 (91%), Positives = 31/34 (91%)

Query: 1  MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTAT 34
          MFTLKKWNAVAMWSWDVECDTCAICRVQVM   T
Sbjct: 29 MFTLKKWNAVAMWSWDVECDTCAICRVQVMEQQT 62

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157104957|ref|XP_001648648.1| hypothetical protein AaeL_AAEL000570 [Aedes aegypti] gi|108884140|gb|EAT48365.1| AAEL000570-PA [Aedes aegypti]

 Score = 70.1 bits (170), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/31 (100%), Positives = 31/31 (100%)

Query: 1  MFTLKKWNAVAMWSWDVECDTCAICRVQVMG 31
          MFTLKKWNAVAMWSWDVECDTCAICRVQVMG
Sbjct: 20 MFTLKKWNAVAMWSWDVECDTCAICRVQVMG 50

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270001542|gb|EEZ97989.1| hypothetical protein TcasGA2_TC000384 [Tribolium castaneum]

 Score = 69.3 bits (168), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 33/42 (78%), Positives = 35/42 (83%), Gaps = 1/42 (2%)

Query: 1  MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPEDK 42
          MFTLKKWNAVAMWSWDVECDTCAICRVQVM  A +  + E K
Sbjct: 25 MFTLKKWNAVAMWSWDVECDTCAICRVQVM-DACLRCQAESK 65

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|295293375|gb|ADF87937.1| RING finger protein [Eriocheir sinensis]

 Score = 68.9 bits (167), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/42 (78%), Positives = 36/42 (85%), Gaps = 1/42 (2%)

Query: 1  MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPEDK 42
          MFTLKKWNAVAMWSWDVECDTCAICRVQVM  A +  + E+K
Sbjct: 26 MFTLKKWNAVAMWSWDVECDTCAICRVQVM-DACLRCQGENK 66

Source: Eriocheir sinensis

Species: Eriocheir sinensis

Genus: Eriocheir

Family: Varunidae

Order: Decapoda

Class: Malacostraca

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|47203192|emb|CAF94886.1| unnamed protein product [Tetraodon nigroviridis]

 Score = 68.6 bits (166), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 32/42 (76%), Positives = 36/42 (85%), Gaps = 1/42 (2%)

Query: 1  MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPEDK 42
          MF+LKKWNAVAMWSWDVECDTCAICRVQVM  A +  + E+K
Sbjct: 26 MFSLKKWNAVAMWSWDVECDTCAICRVQVM-DACLRCQAENK 66

Source: Tetraodon nigroviridis

Species: Tetraodon nigroviridis

Genus: Tetraodon

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|170036860|ref|XP_001846279.1| conserved hypothetical protein [Culex quinquefasciatus] gi|167879814|gb|EDS43197.1| conserved hypothetical protein [Culex quinquefasciatus]

 Score = 68.6 bits (166), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 30/30 (100%), Positives = 30/30 (100%)

Query: 1  MFTLKKWNAVAMWSWDVECDTCAICRVQVM 30
          MFTLKKWNAVAMWSWDVECDTCAICRVQVM
Sbjct: 21 MFTLKKWNAVAMWSWDVECDTCAICRVQVM 50

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|395832912|ref|XP_003789495.1| PREDICTED: RING-box protein 2 [Otolemur garnettii]

 Score = 68.6 bits (166), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 32/42 (76%), Positives = 36/42 (85%), Gaps = 1/42 (2%)

Query: 1  MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPEDK 42
          MF+LKKWNAVAMWSWDVECDTCAICRVQVM  A +  + E+K
Sbjct: 29 MFSLKKWNAVAMWSWDVECDTCAICRVQVM-DACLRCQAENK 69

Source: Otolemur garnettii

Species: Otolemur garnettii

Genus: Otolemur

Family: Galagidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	69
UNIPROTKB|F1NSF0	114	RNF7 "Uncharacterized protein"	0.594	0.359	0.761	5.6e-13
UNIPROTKB|Q0P5F4	113	RNF7 "Ring finger protein 7" [	0.594	0.362	0.761	5.6e-13
UNIPROTKB|E2QUL6	113	RNF7 "Uncharacterized protein"	0.594	0.362	0.761	5.6e-13
UNIPROTKB|Q9UBF6	113	RNF7 "RING-box protein 2" [Hom	0.594	0.362	0.761	5.6e-13
MGI|MGI:1337096	113	Rnf7 "ring finger protein 7" [	0.594	0.362	0.761	5.6e-13
RGD|1311048	113	Rnf7 "ring finger protein 7" [	0.594	0.362	0.761	5.6e-13
ZFIN|ZDB-GENE-050220-12	113	rnf7 "ring finger protein 7" [	0.594	0.362	0.761	5.6e-13
FB|FBgn0044020	113	Roc2 "Roc2" [Drosophila melano	0.434	0.265	0.966	1.2e-12
UNIPROTKB|I3LR41	90	RNF7 "Uncharacterized protein"	0.420	0.322	0.931	5e-12
WB|WBGene00019993	112	rbx-2 [Caenorhabditis elegans	0.420	0.258	0.793	2.5e-10

UNIPROTKB|F1NSF0 RNF7 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 171 (65.3 bits), Expect = 5.6e-13, P = 5.6e-13
 Identities = 32/42 (76%), Positives = 36/42 (85%)

Query:     1 MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPEDK 42
             MF+LKKWNAVAMWSWDVECDTCAICRVQVM  A +  + E+K
Sbjct:    30 MFSLKKWNAVAMWSWDVECDTCAICRVQVMD-ACLRCQAENK 70

GO:0008270 "zinc ion binding" evidence=IEA

GO:0019788 "NEDD8 ligase activity" evidence=IEA

GO:0045116 "protein neddylation" evidence=IEA

UNIPROTKB|Q0P5F4 RNF7 "Ring finger protein 7" [Bos taurus (taxid:9913)]

 Score = 171 (65.3 bits), Expect = 5.6e-13, P = 5.6e-13
 Identities = 32/42 (76%), Positives = 36/42 (85%)

Query:     1 MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPEDK 42
             MF+LKKWNAVAMWSWDVECDTCAICRVQVM  A +  + E+K
Sbjct:    29 MFSLKKWNAVAMWSWDVECDTCAICRVQVMD-ACLRCQAENK 69

GO:0045116 "protein neddylation" evidence=IEA

GO:0019788 "NEDD8 ligase activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|E2QUL6 RNF7 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 171 (65.3 bits), Expect = 5.6e-13, P = 5.6e-13
 Identities = 32/42 (76%), Positives = 36/42 (85%)

Query:     1 MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPEDK 42
             MF+LKKWNAVAMWSWDVECDTCAICRVQVM  A +  + E+K
Sbjct:    29 MFSLKKWNAVAMWSWDVECDTCAICRVQVMD-ACLRCQAENK 69

GO:0045116 "protein neddylation" evidence=IEA

GO:0019788 "NEDD8 ligase activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|Q9UBF6 RNF7 "RING-box protein 2" [Homo sapiens (taxid:9606)]

 Score = 171 (65.3 bits), Expect = 5.6e-13, P = 5.6e-13
 Identities = 32/42 (76%), Positives = 36/42 (85%)

Query:     1 MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPEDK 42
             MF+LKKWNAVAMWSWDVECDTCAICRVQVM  A +  + E+K
Sbjct:    29 MFSLKKWNAVAMWSWDVECDTCAICRVQVMD-ACLRCQAENK 69

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA;NAS

GO:0016567 "protein ubiquitination" evidence=IEA

GO:0019788 "NEDD8 ligase activity" evidence=IDA

GO:0005634 "nucleus" evidence=IDA;NAS

GO:0045116 "protein neddylation" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0051775 "response to redox state" evidence=TAS

GO:0031466 "Cul5-RING ubiquitin ligase complex" evidence=IDA

GO:0005507 "copper ion binding" evidence=TAS

GO:0043066 "negative regulation of apoptotic process" evidence=TAS

GO:0008631 "intrinsic apoptotic signaling pathway in response to oxidative stress" evidence=TAS

GO:0005730 "nucleolus" evidence=IDA

MGI|MGI:1337096 Rnf7 "ring finger protein 7" [Mus musculus (taxid:10090)]

 Score = 171 (65.3 bits), Expect = 5.6e-13, P = 5.6e-13
 Identities = 32/42 (76%), Positives = 36/42 (85%)

Query:     1 MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPEDK 42
             MF+LKKWNAVAMWSWDVECDTCAICRVQVM  A +  + E+K
Sbjct:    29 MFSLKKWNAVAMWSWDVECDTCAICRVQVMD-ACLRCQAENK 69

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0006919 "activation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IDA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008631 "intrinsic apoptotic signaling pathway in response to oxidative stress" evidence=IDA

GO:0008637 "apoptotic mitochondrial changes" evidence=IDA

GO:0019788 "NEDD8 ligase activity" evidence=ISO

GO:0031466 "Cul5-RING ubiquitin ligase complex" evidence=ISO

GO:0043066 "negative regulation of apoptotic process" evidence=IDA

GO:0045116 "protein neddylation" evidence=ISO

GO:0046872 "metal ion binding" evidence=IEA

RGD|1311048 Rnf7 "ring finger protein 7" [Rattus norvegicus (taxid:10116)]

 Score = 171 (65.3 bits), Expect = 5.6e-13, P = 5.6e-13
 Identities = 32/42 (76%), Positives = 36/42 (85%)

Query:     1 MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPEDK 42
             MF+LKKWNAVAMWSWDVECDTCAICRVQVM  A +  + E+K
Sbjct:    29 MFSLKKWNAVAMWSWDVECDTCAICRVQVMD-ACLRCQAENK 69

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0006919 "activation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=ISO

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008631 "intrinsic apoptotic signaling pathway in response to oxidative stress" evidence=ISO

GO:0008637 "apoptotic mitochondrial changes" evidence=ISO

GO:0019788 "NEDD8 ligase activity" evidence=IEA;ISO

GO:0031466 "Cul5-RING ubiquitin ligase complex" evidence=ISO

GO:0043066 "negative regulation of apoptotic process" evidence=ISO

GO:0045116 "protein neddylation" evidence=IEA;ISO

GO:0005730 "nucleolus" evidence=ISO

ZFIN|ZDB-GENE-050220-12 rnf7 "ring finger protein 7" [Danio rerio (taxid:7955)]

 Score = 171 (65.3 bits), Expect = 5.6e-13, P = 5.6e-13
 Identities = 32/42 (76%), Positives = 36/42 (85%)

Query:     1 MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPEDK 42
             MF+LKKWNAVAMWSWDVECDTCAICRVQVM  A +  + E+K
Sbjct:    29 MFSLKKWNAVAMWSWDVECDTCAICRVQVMD-ACLRCQAENK 69

GO:0008270 "zinc ion binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

FB|FBgn0044020 Roc2 "Roc2" [Drosophila melanogaster (taxid:7227)]

 Score = 168 (64.2 bits), Expect = 1.2e-12, P = 1.2e-12
 Identities = 29/30 (96%), Positives = 29/30 (96%)

Query:     1 MFTLKKWNAVAMWSWDVECDTCAICRVQVM 30
             MFTLKKWNAVAMWSWDVECD CAICRVQVM
Sbjct:    24 MFTLKKWNAVAMWSWDVECDICAICRVQVM 53

GO:0004842 "ubiquitin-protein ligase activity" evidence=ISS;IDA

GO:0019005 "SCF ubiquitin ligase complex" evidence=NAS

GO:0016567 "protein ubiquitination" evidence=IDA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|I3LR41 RNF7 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 162 (62.1 bits), Expect = 5.0e-12, P = 5.0e-12
 Identities = 27/29 (93%), Positives = 29/29 (100%)

Query:     1 MFTLKKWNAVAMWSWDVECDTCAICRVQV 29
             MF+LKKWNAVAMWSWDVECDTCAICRVQ+
Sbjct:    29 MFSLKKWNAVAMWSWDVECDTCAICRVQM 57

GO:0045116 "protein neddylation" evidence=IEA

GO:0019788 "NEDD8 ligase activity" evidence=IEA

WB|WBGene00019993 rbx-2 [Caenorhabditis elegans (taxid:6239)]

 Score = 146 (56.5 bits), Expect = 2.5e-10, P = 2.5e-10
 Identities = 23/29 (79%), Positives = 27/29 (93%)

Query:     2 FTLKKWNAVAMWSWDVECDTCAICRVQVM 30
             F LKKWNA+A+W+WDVECDTCAICRV +M
Sbjct:    30 FVLKKWNALAVWAWDVECDTCAICRVHLM 58

GO:0008270 "zinc ion binding" evidence=IEA

GO:0004842 "ubiquitin-protein ligase activity" evidence=IEA

GO:0005680 "anaphase-promoting complex" evidence=IEA

GO:0040039 "inductive cell migration" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0008406 "gonad development" evidence=IMP

GO:0016477 "cell migration" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O13959	RBX1_SCHPO	No assigned EC number	0.6206	0.4202	0.2710	yes	N/A
Q54K33	RBX1_DICDI	No assigned EC number	0.5862	0.4202	0.2788	yes	N/A
Q9WTZ1	RBX2_MOUSE	No assigned EC number	0.7619	0.5942	0.3628	yes	N/A
Q08273	RBX1_YEAST	No assigned EC number	0.6206	0.4202	0.2396	yes	N/A
Q9UBF6	RBX2_HUMAN	No assigned EC number	0.7619	0.5942	0.3628	yes	N/A
Q9M2B0	RBX1B_ARATH	No assigned EC number	0.6206	0.4202	0.2521	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	69
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	1e-12
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	1e-10
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	2e-05

>gnl|CDD|221705 pfam12678, zf-rbx1, RING-H2 zinc finger

 Score = 55.9 bits (135), Expect = 1e-12
 Identities = 22/41 (53%), Positives = 25/41 (60%)

Query: 1  MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPED 41
             +KKWNAVA+WSWD+E D CAICR    GT      P D
Sbjct: 1  RVEIKKWNAVALWSWDIEDDVCAICRNHFDGTCPECKSPGD 41

There are 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding. The protein, of which this domain is the conserved region, participates in diverse functions relevant to chromosome metabolism and cell cycle control. Length = 73

>gnl|CDD|227521 COG5194, APC11, Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]

 Score = 51.4 bits (123), Expect = 1e-10
 Identities = 19/31 (61%), Positives = 24/31 (77%)

Query: 2  FTLKKWNAVAMWSWDVECDTCAICRVQVMGT 32
            +KKW+AVA+WSWD+  D CAICR  +MGT
Sbjct: 3  VKIKKWHAVALWSWDIPIDVCAICRNHIMGT 33

Length = 88

>gnl|CDD|193335 pfam12861, zf-Apc11, Anaphase-promoting complex subunit 11 RING-H2 finger

 Score = 37.8 bits (88), Expect = 2e-05
 Identities = 17/31 (54%), Positives = 20/31 (64%), Gaps = 1/31 (3%)

Query: 3  TLKKWNAVAMWSWDV-ECDTCAICRVQVMGT 32
           +K+WNAVA W+WD    D C ICRV   GT
Sbjct: 4  KIKEWNAVATWTWDTPSDDVCGICRVSFDGT 34

Apc11 is one of the subunits of the anaphase-promoting complex or cyclosome. The APC subunits are cullin family proteins with ubiquitin ligase activity. Polyubiquitination marks proteins for degradation by the 26S proteasome and is carried out by a cascade of enzymes that includes ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and ubiquitin ligases (E3s). Apc11 acts as an E3 enzyme and is responsible for recruiting E2s to the APC and for mediating the subsequent transfer of ubiquitin to APC substrates in vivo. In Saccharomyces cerevisiae this RING-H2 finger protein defines the minimal ubiquitin ligase activity of the APC, and the integrity of the RING-H2 finger is essential for budding yeast cell viability. Length = 85

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	69
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.84
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	99.82
KOG1493|consensus	84		99.81
KOG2930|consensus	114		99.58
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.55
KOG1257|consensus	582		98.7
PLN03129	581	NADP-dependent malic enzyme; Provisional	87.38
PRK13529	563	malate dehydrogenase; Provisional	86.05
PF12907	40	zf-met2: Zinc-binding	82.94

>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger

Probab=99.84  E-value=3.6e-22  Score=122.66  Aligned_cols=62  Identities=31%  Similarity=0.664  Sum_probs=56.3

Q ss_pred             CEEEEEEEeEEEeEeec-CCCeeccccchhhccCCCCCCCCchhhHHhhhcccccCCCCCCCccccC
Q psy6139           1 MFTLKKWNAVAMWSWDV-ECDTCAICRVQVMGTATVYPEPEDKLAFVKSFVYDYSYSEPSVPTSYSW   66 (69)
Q Consensus         1 ~~~i~~~~~v~~W~W~~-~~d~CaICr~~~~g~a~~~p~P~D~~~~V~~~~Y~~~Y~~s~lp~~y~w   66 (69)
                      +|+||+||+|+.|+||+ .+|+|||||++|+|.|+.|..|||.|++|.++ .++.|+   +..++.|
T Consensus         2 kv~i~~w~~va~W~Wd~~~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~-C~H~FH---~hCI~kW   64 (85)
T PF12861_consen    2 KVKIKEWHAVATWKWDVANDDVCGICRMPFDGCCPDCKFPGDDCPLVWGK-CSHNFH---MHCILKW   64 (85)
T ss_pred             eeEEEEEEEEEEEEEecCCCCceeeEecccccCCCCccCCCCCCceeecc-CccHHH---HHHHHHH
Confidence            68999999999999997 59999999999999999999999999999998 888886   5565555

>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]

Probab=99.82  E-value=1.4e-21  Score=119.51  Aligned_cols=62  Identities=39%  Similarity=0.820  Sum_probs=55.3

Q ss_pred             CEEEEEEEeEEEeEeecCCCeeccccchhhccCCCCCC---CCchhhHHhhhcccccCCCCCCCccccC
Q psy6139           1 MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPE---PEDKLAFVKSFVYDYSYSEPSVPTSYSW   66 (69)
Q Consensus         1 ~~~i~~~~~v~~W~W~~~~d~CaICr~~~~g~a~~~p~---P~D~~~~V~~~~Y~~~Y~~s~lp~~y~w   66 (69)
                      +||||+||+|+.|+||+..|+||||||+|+|+|+.|..   |+|.|+.+.|. .++.|+   ...+|.|
T Consensus         2 kvkIkkw~aVa~Wswdi~id~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~-CnHaFH---~HCI~rW   66 (88)
T COG5194           2 KVKIKKWHAVALWSWDIPIDVCAICRNHIMGTCPECQFGMTPGDECPVVWGV-CNHAFH---DHCIYRW   66 (88)
T ss_pred             ceEeeeEeEEEEEecccccchhhhhhccccCcCcccccCCCCCCcceEEEEe-cchHHH---HHHHHHH
Confidence            69999999999999999999999999999999999999   99999999886 677775   4455555

>KOG1493|consensus

Probab=99.81  E-value=2e-20  Score=113.64  Aligned_cols=55  Identities=29%  Similarity=0.595  Sum_probs=51.3

Q ss_pred             CEEEEEEEeEEEeEeecCCCeeccccchhhccCCCCCCCCchhhHHhhhcccccCC
Q psy6139           1 MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPEDKLAFVKSFVYDYSYS   56 (69)
Q Consensus         1 ~~~i~~~~~v~~W~W~~~~d~CaICr~~~~g~a~~~p~P~D~~~~V~~~~Y~~~Y~   56 (69)
                      +||||++|+++.|+|+..+|+|||||.+|+|.|+.|+.|||.|++|.| ...+.|+
T Consensus         2 kvki~~~h~~a~wtW~~~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G-~C~h~fh   56 (84)
T KOG1493|consen    2 KVKIKRYHAVAWWTWDAPDETCGICRMPFDGCCPDCKLPGDDCPLVWG-YCLHAFH   56 (84)
T ss_pred             ceEEEEEEEEEEEEEcCCCCccceEecccCCcCCCCcCCCCCCccHHH-HHHHHHH
Confidence            689999999999999999999999999999999999999999999999 4666664

>KOG2930|consensus

Probab=99.58  E-value=3.8e-16  Score=99.51  Aligned_cols=38  Identities=50%  Similarity=1.067  Sum_probs=36.1

Q ss_pred             CEEEEEEEeEEEeEeecCCCeeccccchhhccCCCCCC
Q psy6139           1 MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPE   38 (69)
Q Consensus         1 ~~~i~~~~~v~~W~W~~~~d~CaICr~~~~g~a~~~p~   38 (69)
                      ||+||||++||.|+||+..|+||||||+++++|..|.-
T Consensus        28 rF~lKKWnAvAlWaWDi~vDnCAICRnHIMd~CieCQa   65 (114)
T KOG2930|consen   28 RFELKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQA   65 (114)
T ss_pred             ceEEeeeeeeeeeeeeeeechhHHHHHHHHHHHHhhcc
Confidence            69999999999999999999999999999999999853

>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.55  E-value=1.5e-15  Score=89.89  Aligned_cols=55  Identities=38%  Similarity=0.765  Sum_probs=47.6

Q ss_pred             CEEEEEEEeEEEeEeecCCCeeccccchhhccCCCCCCCCchhhHHhhhcccccCC
Q psy6139           1 MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPEDKLAFVKSFVYDYSYS   56 (69)
Q Consensus         1 ~~~i~~~~~v~~W~W~~~~d~CaICr~~~~g~a~~~p~P~D~~~~V~~~~Y~~~Y~   56 (69)
                      ||+||+|++|+.|+|++.+|.||||+++|++.++.+..|++.++++.+. ..+.|+
T Consensus         1 ~~~i~~~~~v~~~~~~~~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~-C~H~FH   55 (73)
T PF12678_consen    1 KFKIKKWNAVALWSWDIADDNCAICREPLEDPCPECQAPQDECPIVWGP-CGHIFH   55 (73)
T ss_dssp             SEEEEEEEEEEEEEESSCCSBETTTTSBTTSTTCCHHHCTTTS-EEEET-TSEEEE
T ss_pred             CeEEEEEEEEEEEeecCcCCcccccChhhhChhhhhcCCccccceEecc-cCCCEE
Confidence            7999999999999999999999999999999999999999888876554 455543

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....

>KOG1257|consensus

Probab=98.70  E-value=9.1e-09  Score=79.84  Aligned_cols=39  Identities=44%  Similarity=0.867  Sum_probs=37.1

Q ss_pred             hccCCCCCCCCchhhHHhhhcccccCCCCCCCccccCCCC
Q psy6139          30 MGTATVYPEPEDKLAFVKSFVYDYSYSEPSVPTSYSWPKL   69 (69)
Q Consensus        30 ~g~a~~~p~P~D~~~~V~~~~Y~~~Y~~s~lp~~y~wp~~   69 (69)
                      +|+|+.+|+|+|+++|++++||+++|+ +++|++|+||.+
T Consensus       540 ~glA~~~p~P~d~~~~~~~~~y~~~Y~-~~~~~~y~~p~~  578 (582)
T KOG1257|consen  540 EGLATRYPEPKDKEKFIEESMYNPEYR-NSLPDTYDWPVE  578 (582)
T ss_pred             cCccccCCCcccHHHHHHhccCCcccc-ccccccccCccc
Confidence            799999999999999999999999998 899999999963

>PLN03129 NADP-dependent malic enzyme; Provisional

Probab=87.38  E-value=0.4  Score=38.18  Aligned_cols=34  Identities=32%  Similarity=0.524  Sum_probs=28.2

Q ss_pred             ccccchh-hccCCCCCCCCchhhHHhhhcccccCC
Q psy6139          23 AICRVQV-MGTATVYPEPEDKLAFVKSFVYDYSYS   56 (69)
Q Consensus        23 aICr~~~-~g~a~~~p~P~D~~~~V~~~~Y~~~Y~   56 (69)
                      |+.+..+ +|+|...++|+|..++|+++||+++|.
T Consensus       544 aVa~~A~~~G~A~~~~~~~~~~~~i~~~mw~P~Y~  578 (581)
T PLN03129        544 AVAAKAYEEGLATRLPRPEDLVEYAESCMYSPVYR  578 (581)
T ss_pred             HHHHHHHHcCCCCCCCCHHHHHHHHHHcCcCCCCC
Confidence            3445555 478888889999999999999999996

>PRK13529 malate dehydrogenase; Provisional

Probab=86.05  E-value=0.44  Score=37.79  Aligned_cols=32  Identities=16%  Similarity=0.277  Sum_probs=25.7

Q ss_pred             cccchh-hccCCCCCCCCchhhHHhhhcccccCC
Q psy6139          24 ICRVQV-MGTATVYPEPEDKLAFVKSFVYDYSYS   56 (69)
Q Consensus        24 ICr~~~-~g~a~~~p~P~D~~~~V~~~~Y~~~Y~   56 (69)
                      +.+.++ +|+|.. +.|+|..+||+++||+++|.
T Consensus       526 Va~~A~~~GlA~~-~~~~~~~~~i~~~~w~P~Y~  558 (563)
T PRK13529        526 VAKAAIEEGLARE-TSDEDLEQAIEDNMWQPEYR  558 (563)
T ss_pred             HHHHHHHhCCCCC-CCHHHHHHHHHhcCcCCCCc
Confidence            344444 467875 78999999999999999996

>PF12907 zf-met2: Zinc-binding

Probab=82.94  E-value=0.38  Score=25.71  Aligned_cols=14  Identities=43%  Similarity=0.861  Sum_probs=12.0

Q ss_pred             eeccccchhhccCC
Q psy6139          21 TCAICRVQVMGTAT   34 (69)
Q Consensus        21 ~CaICr~~~~g~a~   34 (69)
                      .|.|||+.|+.++.
T Consensus         3 ~C~iC~qtF~~t~~   16 (40)
T PF12907_consen    3 ICKICRQTFMQTTN   16 (40)
T ss_pred             CcHHhhHHHHhcCC
Confidence            69999999988764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	69
4a0k_B	117	Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp		2e-06
3dpl_R	106	Structural Insights Into Nedd8 Activation Of Cullin		3e-06
1u6g_B	108	Crystal Structure Of The Cand1-Cul1-Roc1 Complex Le		3e-06
4a0c_D	98	Structure Of The Cand1-Cul4b-Rbx1 Complex Length =		3e-06
2ecl_A	81	Solution Structure Of The Ring Domain Of The Human		4e-06
2aw5_A	575	Crystal Structure Of A Human Malic Enzyme Length =		4e-06
1ldj_B	90	Structure Of The Cul1-rbx1-skp1-f Boxskp2 Scf Ubiqu		4e-06
3dqv_R	106	Structural Insights Into Nedd8 Activation Of Cullin		1e-05
1gq2_A	555	Malic Enzyme From Pigeon Liver Length = 555		2e-04
1llq_A	605	Crystal Structure Of Malic Enzyme From Ascaris Suum		4e-04

>pdb|4A0K|B Chain B, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic Site Containing Dna-Duplex Length = 117

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 18/29 (62%), Positives = 23/29 (79%)
Query: 2  FTLKKWNAVAMWSWDVECDTCAICRVQVM 30
          F +KKWNAVA+W+WD+  D CAICR  +M
Sbjct: 31 FEVKKWNAVALWAWDIVVDNCAICRNHIM 59

>pdb|3DPL|R Chain R, Structural Insights Into Nedd8 Activation Of Cullin-Ring Ligases: Conformational Control Of Conjugation. Length = 106

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 18/29 (62%), Positives = 23/29 (79%)
Query: 2  FTLKKWNAVAMWSWDVECDTCAICRVQVM 30
          F +KKWNAVA+W+WD+  D CAICR  +M
Sbjct: 20 FEVKKWNAVALWAWDIVVDNCAICRNHIM 48

>pdb|1U6G|B Chain B, Crystal Structure Of The Cand1-Cul1-Roc1 Complex Length = 108

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 18/29 (62%), Positives = 23/29 (79%)
Query: 2  FTLKKWNAVAMWSWDVECDTCAICRVQVM 30
          F +KKWNAVA+W+WD+  D CAICR  +M
Sbjct: 22 FEVKKWNAVALWAWDIVVDNCAICRNHIM 50

>pdb|4A0C|D Chain D, Structure Of The Cand1-Cul4b-Rbx1 Complex Length = 98

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 18/29 (62%), Positives = 23/29 (79%)
Query: 2  FTLKKWNAVAMWSWDVECDTCAICRVQVM 30
          F +KKWNAVA+W+WD+  D CAICR  +M
Sbjct: 12 FEVKKWNAVALWAWDIVVDNCAICRNHIM 40

>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring-Box Protein 2 Length = 81

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 22/31 (70%), Positives = 25/31 (80%), Gaps = 1/31 (3%)
Query: 12 MWSWDVECDTCAICRVQVMGTATVYPEPEDK 42
          MWSWDVECDTCAICRVQVM  A +  + E+K
Sbjct: 8  MWSWDVECDTCAICRVQVM-DACLRCQAENK 37

>pdb|2AW5|A Chain A, Crystal Structure Of A Human Malic Enzyme Length = 575

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 20/37 (54%), Positives = 27/37 (72%), Gaps = 1/37 (2%)
Query: 32  TATVYPEPEDKLAFVKSFVYDYSYSEPSVPTSYSWPK 68
           TATVYPEP++K AFV+S +Y   Y +  +P  YSWP+
Sbjct: 537 TATVYPEPQNKEAFVRSQMYSTDYDQ-ILPDCYSWPE 572

>pdb|1LDJ|B Chain B, Structure Of The Cul1-rbx1-skp1-f Boxskp2 Scf Ubiquitin Ligase Complex Length = 90

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 18/29 (62%), Positives = 23/29 (79%)
Query: 2  FTLKKWNAVAMWSWDVECDTCAICRVQVM 30
          F +KKWNAVA+W+WD+  D CAICR  +M
Sbjct: 4  FEVKKWNAVALWAWDIVVDNCAICRNHIM 32

>pdb|3DQV|R Chain R, Structural Insights Into Nedd8 Activation Of Cullin-Ring Ligases: Conformational Control Of Conjugation Length = 106

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 17/28 (60%), Positives = 22/28 (78%)
Query: 2  FTLKKWNAVAMWSWDVECDTCAICRVQV 29
          F +KKWNAVA+W+WD+  D CAICR  +
Sbjct: 20 FEVKKWNAVALWAWDIVVDNCAICRNHI 47

>pdb|1GQ2|A Chain A, Malic Enzyme From Pigeon Liver Length = 555

Iteration: 1
 Score = 40.4 bits (93), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 18/37 (48%), Positives = 25/37 (67%), Gaps = 1/37 (2%)
Query: 32  TATVYPEPEDKLAFVKSFVYDYSYSEPSVPTSYSWPK 68
           TA+ YP+PED  AF++S VY   Y+   V  SY+WP+
Sbjct: 514 TASTYPQPEDLEAFIRSQVYSTDYN-CFVADSYTWPE 549

>pdb|1LLQ|A Chain A, Crystal Structure Of Malic Enzyme From Ascaris Suum Complexed With Nicotinamide Adenine Dinucleotide Length = 605

Iteration: 1
 Score = 40.0 bits (92), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 16/38 (42%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 31  GTATVYPEPEDKLAFVKSFVYDYSYSEPSVPTSYSWPK 68
           GTA +YP+PED   +V++ VY+  Y E  +  +Y WP+
Sbjct: 550 GTANLYPQPEDLEKYVRAQVYNTEYEE-LINATYDWPE 586

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	69
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	1e-11
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	8e-11
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	4e-10
1gq2_A	555	Malic enzyme; oxidoreductase, pigeon liver, NADP-d	2e-09
1pj3_A	564	NAD-dependent malic enzyme, mitochondrial; oxidati	7e-09
1o0s_A	605	NAD-ME, NAD-dependent malic enzyme; oxidoreductase	8e-09

>4a0k_B E3 ubiquitin-protein ligase RBX1; ligase-DNA-binding protein-DNA complex, DNA-binding protein- complex; HET: DNA 3DR; 5.93A {Mus musculus} Length = 117

 Score = 54.5 bits (130), Expect = 1e-11
 Identities = 18/40 (45%), Positives = 24/40 (60%)

Query: 1  MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPE 40
           F +KKWNAVA+W+WD+  D CAICR  +M         +
Sbjct: 30 RFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQ 69

>2ecl_A Ring-box protein 2; RNF7, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 81

 Score = 51.4 bits (123), Expect = 8e-11
 Identities = 19/29 (65%), Positives = 20/29 (68%)

Query: 7  WNAVAMWSWDVECDTCAICRVQVMGTATV 35
            +  MWSWDVECDTCAICRVQVM     
Sbjct: 3  SGSSGMWSWDVECDTCAICRVQVMDACLR 31

>3dpl_R Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} SCOP: g.44.1.1 PDB: 3dqv_R 3rtr_B 1u6g_B 2hye_D* 4a0c_D 4a0l_F* 1ldj_B 1ldk_C 2lgv_A Length = 106

 Score = 50.2 bits (119), Expect = 4e-10
 Identities = 18/39 (46%), Positives = 23/39 (58%)

Query: 1  MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEP 39
           F +KKWNAVA+W+WD+  D CAICR  +M         
Sbjct: 19 RFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQAN 57

>1gq2_A Malic enzyme; oxidoreductase, pigeon liver, NADP-dependent, NAD-NADP selectivity, decarboxylase, malate, Mn2+; HET: NAP; 2.5A {Columba livia} SCOP: c.2.1.7 c.58.1.3 PDB: 2aw5_A Length = 555

 Score = 50.0 bits (120), Expect = 2e-09
 Identities = 18/38 (47%), Positives = 24/38 (63%), Gaps = 1/38 (2%)

Query: 31  GTATVYPEPEDKLAFVKSFVYDYSYSEPSVPTSYSWPK 68
            TA+ YP+PED  AF++S VY   Y    V  SY+WP+
Sbjct: 513 NTASTYPQPEDLEAFIRSQVYSTDY-NCFVADSYTWPE 549

>1pj3_A NAD-dependent malic enzyme, mitochondrial; oxidative decarboxylase, oxidoreductase; HET: NAD; 2.10A {Homo sapiens} SCOP: c.2.1.7 c.58.1.3 PDB: 1pj2_A* 1do8_A* 1pj4_A* 1qr6_A* 1efl_A* 1pjl_A* 1efk_A* 1gz4_A* 1gz3_A* Length = 564

 Score = 48.9 bits (117), Expect = 7e-09
 Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 1/38 (2%)

Query: 31  GTATVYPEPEDKLAFVKSFVYDYSYSEPSVPTSYSWPK 68
             A  YPEPEDK  +VK   +   Y +  +P  Y WP+
Sbjct: 518 KMAFRYPEPEDKAKYVKERTWRSEY-DSLLPDVYEWPE 554

>1o0s_A NAD-ME, NAD-dependent malic enzyme; oxidoreductase, oxidative decarboxylase, rossmann fold, MAla dehydrogenase; HET: NAI; 2.00A {Ascaris suum} SCOP: c.2.1.7 c.58.1.3 PDB: 1llq_A* Length = 605

 Score = 48.6 bits (116), Expect = 8e-09
 Identities = 16/38 (42%), Positives = 25/38 (65%), Gaps = 1/38 (2%)

Query: 31  GTATVYPEPEDKLAFVKSFVYDYSYSEPSVPTSYSWPK 68
           GTA +YP+PED   +V++ VY+  Y E  +  +Y WP+
Sbjct: 550 GTANLYPQPEDLEKYVRAQVYNTEY-EELINATYDWPE 586

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	69
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.46
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.42
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	98.67
1gq2_A	555	Malic enzyme; oxidoreductase, pigeon liver, NADP-d	97.19
1pj3_A	564	NAD-dependent malic enzyme, mitochondrial; oxidati	97.08
1o0s_A	605	NAD-ME, NAD-dependent malic enzyme; oxidoreductase	97.07
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	86.11

>4a0k_B E3 ubiquitin-protein ligase RBX1; ligase-DNA-binding protein-DNA complex, DNA-binding protein- complex; HET: DNA 3DR; 5.93A {Mus musculus}

Probab=99.46  E-value=2.7e-14  Score=90.45  Aligned_cols=55  Identities=33%  Similarity=0.755  Sum_probs=18.5

Q ss_pred             CEEEEEEEeEEEeEeecCCCeeccccchhhccCCCCCCC-----CchhhHHhhhcccccCC
Q psy6139           1 MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEP-----EDKLAFVKSFVYDYSYS   56 (69)
Q Consensus         1 ~~~i~~~~~v~~W~W~~~~d~CaICr~~~~g~a~~~p~P-----~D~~~~V~~~~Y~~~Y~   56 (69)
                      ||+||+|++|+.|+||+.+|+|+||++.|++.|+.|..+     ++.+..+... ..+.|+
T Consensus        30 r~~ikkw~ava~w~wd~~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~-C~H~FH   89 (117)
T 4a0k_B           30 RFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFH   89 (117)
T ss_dssp             SEEEEEEEEEEEEEECCCC------------------------------------------
T ss_pred             ceEEEEEEEEEEEeecCCCCcCeECChhhcCcChhhhcccccccccccccccCC-cCceEc
Confidence            699999999999999999999999999999999999874     7777665443 455554

>3dpl_R Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} SCOP: g.44.1.1 PDB: 3dqv_R 3rtr_B 4f52_B 1u6g_B 2hye_D* 4a0c_D 4a0l_F* 1ldj_B 1ldk_C 2lgv_A

Probab=99.42  E-value=4.7e-14  Score=87.53  Aligned_cols=47  Identities=38%  Similarity=0.848  Sum_probs=39.4

Q ss_pred             CEEEEEEEeEEEeEeecCCCeeccccchhhccCCCCC-----CCCchhhHHh
Q psy6139           1 MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYP-----EPEDKLAFVK   47 (69)
Q Consensus         1 ~~~i~~~~~v~~W~W~~~~d~CaICr~~~~g~a~~~p-----~P~D~~~~V~   47 (69)
                      ||+||+|++|+.|+|++.+|+|+||++.|++.|+.|.     .|++.+..+.
T Consensus        19 r~~ik~~~~v~~w~~d~~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~   70 (106)
T 3dpl_R           19 RFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAW   70 (106)
T ss_dssp             SEEEEEEEEEEEEEESSCSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEE
T ss_pred             ceeEEEEEEeeEeecCCCCCCCccCChhHhCcCchhhccccccCCccceEee
Confidence            7999999999999999999999999999999999887     4666665443

>2ecl_A Ring-box protein 2; RNF7, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.67  E-value=1.3e-09  Score=63.61  Aligned_cols=34  Identities=56%  Similarity=1.055  Sum_probs=31.4

Q ss_pred             EEEeEEEeEeecCCCeeccccchhhccCCCCCCC
Q psy6139           6 KWNAVAMWSWDVECDTCAICRVQVMGTATVYPEP   39 (69)
Q Consensus         6 ~~~~v~~W~W~~~~d~CaICr~~~~g~a~~~p~P   39 (69)
                      ++++|+.|+|+++++.|+||++.|++.|+.|.++
T Consensus         2 ~~~~~~~w~~~~~~~~C~IC~~~~~~~C~iC~~~   35 (81)
T 2ecl_A            2 SSGSSGMWSWDVECDTCAICRVQVMDACLRCQAE   35 (81)
T ss_dssp             CCCCCCCCCCSCCCSCBTTTTBCTTSCCTTHHHH
T ss_pred             CcceeEEeeecCCCCCCcccChhhhccCcccccc
Confidence            5799999999999999999999999999988664

>1gq2_A Malic enzyme; oxidoreductase, pigeon liver, NADP-dependent, NAD-NADP selectivity, decarboxylase, malate, Mn2+; HET: NAP; 2.5A {Columba livia} SCOP: c.2.1.7 c.58.1.3 PDB: 2aw5_A

Probab=97.19  E-value=0.00029  Score=54.12  Aligned_cols=39  Identities=46%  Similarity=0.820  Sum_probs=35.5

Q ss_pred             hccCCCCCCCCchhhHHhhhcccccCCCCCCCccccCCCC
Q psy6139          30 MGTATVYPEPEDKLAFVKSFVYDYSYSEPSVPTSYSWPKL   69 (69)
Q Consensus        30 ~g~a~~~p~P~D~~~~V~~~~Y~~~Y~~s~lp~~y~wp~~   69 (69)
                      +|+|...++|+|..+||+++||+++|+ ++.+.+|+||+.
T Consensus       512 ~GvA~~~~~~~d~~~~i~~~~~~P~Y~-~~~~~~~~~p~~  550 (555)
T 1gq2_A          512 NNTASTYPQPEDLEAFIRSQVYSTDYN-CFVADSYTWPEE  550 (555)
T ss_dssp             TTCCCCSSCCSSHHHHHHTTSCCCSCC-CCSCCCCCCCSS
T ss_pred             cCCCCCCCChHHHHHHHHHhccCCCCC-CccccccCCCcc
Confidence            578888899999999999999999997 799999999963

>1pj3_A NAD-dependent malic enzyme, mitochondrial; oxidative decarboxylase, oxidoreductase; HET: NAD; 2.10A {Homo sapiens} SCOP: c.2.1.7 c.58.1.3 PDB: 1pj2_A* 1do8_A* 1pj4_A* 1qr6_A* 1efl_A* 1pjl_A* 1efk_A* 1gz4_A* 1gz3_A*

Probab=97.08  E-value=0.00042  Score=53.32  Aligned_cols=39  Identities=38%  Similarity=0.731  Sum_probs=34.7

Q ss_pred             hccCCCCCCCCchhhHHhhhcccccCCCCCCCccccCCCC
Q psy6139          30 MGTATVYPEPEDKLAFVKSFVYDYSYSEPSVPTSYSWPKL   69 (69)
Q Consensus        30 ~g~a~~~p~P~D~~~~V~~~~Y~~~Y~~s~lp~~y~wp~~   69 (69)
                      +|+|...++|+|..+||+++||++.|. ++.+..|+||+.
T Consensus       517 ~GvA~~~~~~~d~~~~i~~~~~~p~Y~-~~~~~~~~~p~~  555 (564)
T 1pj3_A          517 NKMAFRYPEPEDKAKYVKERTWRSEYD-SLLPDVYEWPES  555 (564)
T ss_dssp             TTCCCCSSCCSSHHHHHHHTCCCCSCC-CCCCCCCCCC--
T ss_pred             cCCCCCCCChHHHHHHHHHHhhCCCCC-CccccccCCCcc
Confidence            578888899999999999999999997 899999999963

>1o0s_A NAD-ME, NAD-dependent malic enzyme; oxidoreductase, oxidative decarboxylase, rossmann fold, MAla dehydrogenase; HET: NAI; 2.00A {Ascaris suum} SCOP: c.2.1.7 c.58.1.3 PDB: 1llq_A*

Probab=97.07  E-value=0.00037  Score=54.00  Aligned_cols=38  Identities=39%  Similarity=0.892  Sum_probs=35.1

Q ss_pred             hccCCCCCCCCchhhHHhhhcccccCCCCCCCccccCCC
Q psy6139          30 MGTATVYPEPEDKLAFVKSFVYDYSYSEPSVPTSYSWPK   68 (69)
Q Consensus        30 ~g~a~~~p~P~D~~~~V~~~~Y~~~Y~~s~lp~~y~wp~   68 (69)
                      +|+|...++|+|..+||+++||+++|+ ++.+.+|+||+
T Consensus       549 ~GvA~~~~~~~d~~~~i~~~~w~P~Y~-~~~~~~~~~p~  586 (605)
T 1o0s_A          549 NGTANLYPQPEDLEKYVRAQVYNTEYE-ELINATYDWPE  586 (605)
T ss_dssp             TTCBCSSSCCSCHHHHHHHHSCCCSCC-CCSCCCBCCCG
T ss_pred             cCCCCCCCChHHHHHHHHHhccCCCCC-cccccccCCCc
Confidence            578888899999999999999999997 79999999995

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=86.11  E-value=0.16  Score=29.16  Aligned_cols=13  Identities=23%  Similarity=0.741  Sum_probs=11.3

Q ss_pred             CCCeeccccchhh
Q psy6139          18 ECDTCAICRVQVM   30 (69)
Q Consensus        18 ~~d~CaICr~~~~   30 (69)
                      ..+.|+||++.|+
T Consensus        14 ~i~~C~IC~~~i~   26 (74)
T 2ct0_A           14 AVKICNICHSLLI   26 (74)
T ss_dssp             SSCBCSSSCCBCS
T ss_pred             CCCcCcchhhHcc
Confidence            4689999999996

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	69
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	2e-10
d1gq2a1	298	c.2.1.7 (A:280-580) Mitochondrial NAD(P)-dependent	7e-09
d1o0sa1	308	c.2.1.7 (A:296-603) Mitochondrial NAD(P)-dependent	1e-08
d1pj3a1	294	c.2.1.7 (A:280-573) Mitochondrial NAD(P)-dependent	7e-08

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.4 bits (117), Expect = 2e-10
 Identities = 18/41 (43%), Positives = 24/41 (58%)

Query: 2  FTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEPEDK 42
          F +KKWNAVA+W+WD+  D CAICR  +M         +  
Sbjct: 4  FEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQAS 44

>d1gq2a1 c.2.1.7 (A:280-580) Mitochondrial NAD(P)-dependent malic enzyme {Domestic pigeon (Columba livia) [TaxId: 8932]} Length = 298

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Aminoacid dehydrogenase-like, C-terminal domain
domain: Mitochondrial NAD(P)-dependent malic enzyme
species: Domestic pigeon (Columba livia) [TaxId: 8932]

 Score = 47.7 bits (113), Expect = 7e-09
 Identities = 18/38 (47%), Positives = 24/38 (63%), Gaps = 1/38 (2%)

Query: 31  GTATVYPEPEDKLAFVKSFVYDYSYSEPSVPTSYSWPK 68
            TA+ YP+PED  AF++S VY   Y    V  SY+WP+
Sbjct: 256 NTASTYPQPEDLEAFIRSQVYSTDY-NCFVADSYTWPE 292

>d1o0sa1 c.2.1.7 (A:296-603) Mitochondrial NAD(P)-dependent malic enzyme {Pig roundworm (Ascaris suum) [TaxId: 6253]} Length = 308

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Aminoacid dehydrogenase-like, C-terminal domain
domain: Mitochondrial NAD(P)-dependent malic enzyme
species: Pig roundworm (Ascaris suum) [TaxId: 6253]

 Score = 46.9 bits (111), Expect = 1e-08
 Identities = 16/38 (42%), Positives = 25/38 (65%), Gaps = 1/38 (2%)

Query: 31  GTATVYPEPEDKLAFVKSFVYDYSYSEPSVPTSYSWPK 68
           GTA +YP+PED   +V++ VY+  Y E  +  +Y WP+
Sbjct: 255 GTANLYPQPEDLEKYVRAQVYNTEY-EELINATYDWPE 291

>d1pj3a1 c.2.1.7 (A:280-573) Mitochondrial NAD(P)-dependent malic enzyme {Human (Homo sapiens) [TaxId: 9606]} Length = 294

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Aminoacid dehydrogenase-like, C-terminal domain
domain: Mitochondrial NAD(P)-dependent malic enzyme
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.0 bits (106), Expect = 7e-08
 Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 1/37 (2%)

Query: 31  GTATVYPEPEDKLAFVKSFVYDYSYSEPSVPTSYSWP 67
             A  YPEPEDK  +VK   +   Y +  +P  Y WP
Sbjct: 259 KMAFRYPEPEDKAKYVKERTWRSEY-DSLLPDVYEWP 294

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	69
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.21
d1gq2a1	298	Mitochondrial NAD(P)-dependent malic enzyme {Domes	98.58
d1o0sa1	308	Mitochondrial NAD(P)-dependent malic enzyme {Pig r	98.4
d1pj3a1	294	Mitochondrial NAD(P)-dependent malic enzyme {Human	98.31
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	90.25

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.21  E-value=2.1e-12  Score=75.81  Aligned_cols=39  Identities=46%  Similarity=1.014  Sum_probs=35.7

Q ss_pred             CEEEEEEEeEEEeEeecCCCeeccccchhhccCCCCCCC
Q psy6139           1 MFTLKKWNAVAMWSWDVECDTCAICRVQVMGTATVYPEP   39 (69)
Q Consensus         1 ~~~i~~~~~v~~W~W~~~~d~CaICr~~~~g~a~~~p~P   39 (69)
                      ||+||+||+|+.|+||+.+|.|+||++.++..+..+..+
T Consensus         3 ~~~ik~~~av~~w~~d~~~d~C~IC~~~~~~~~~~~~~~   41 (88)
T d3dplr1           3 RFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQAN   41 (88)
T ss_dssp             SEEEEEEEEEEEEEESSCSCCCSSSCSCTTSCCTTHHHH
T ss_pred             ceEEeeEEEEEEEeecCCCCcCEEccchhhCcccccccc
Confidence            699999999999999999999999999999988876544

>d1gq2a1 c.2.1.7 (A:280-580) Mitochondrial NAD(P)-dependent malic enzyme {Domestic pigeon (Columba livia) [TaxId: 8932]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Aminoacid dehydrogenase-like, C-terminal domain
domain: Mitochondrial NAD(P)-dependent malic enzyme
species: Domestic pigeon (Columba livia) [TaxId: 8932]

Probab=98.58  E-value=1.6e-08  Score=70.71  Aligned_cols=46  Identities=41%  Similarity=0.720  Sum_probs=40.5

Q ss_pred             ccccchh-hccCCCCCCCCchhhHHhhhcccccCCCCCCCccccCCCC
Q psy6139          23 AICRVQV-MGTATVYPEPEDKLAFVKSFVYDYSYSEPSVPTSYSWPKL   69 (69)
Q Consensus        23 aICr~~~-~g~a~~~p~P~D~~~~V~~~~Y~~~Y~~s~lp~~y~wp~~   69 (69)
                      ++++..+ +|+|...++|+|.++||+++||+++|+ +++|++|+||++
T Consensus       247 aVa~~A~~~GvA~~~~~~~dl~~~i~~~~w~P~Y~-~~~~~~y~~~~~  293 (298)
T d1gq2a1         247 RIAKEAYRNNTASTYPQPEDLEAFIRSQVYSTDYN-CFVADSYTWPEE  293 (298)
T ss_dssp             HHHHHHHHTTCCCCSSCCSSHHHHHHTTSCCCSCC-CCSCCCCCCCSS
T ss_pred             HHHHHHHHcCCCCCCCChHHHHHHHHHhcCCCccc-CcCCccccCchh
Confidence            4455555 789999999999999999999999998 899999999974

>d1o0sa1 c.2.1.7 (A:296-603) Mitochondrial NAD(P)-dependent malic enzyme {Pig roundworm (Ascaris suum) [TaxId: 6253]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Aminoacid dehydrogenase-like, C-terminal domain
domain: Mitochondrial NAD(P)-dependent malic enzyme
species: Pig roundworm (Ascaris suum) [TaxId: 6253]

Probab=98.40  E-value=7.4e-08  Score=67.61  Aligned_cols=45  Identities=33%  Similarity=0.750  Sum_probs=39.3

Q ss_pred             cccchh-hccCCCCCCCCchhhHHhhhcccccCCCCCCCccccCCCC
Q psy6139          24 ICRVQV-MGTATVYPEPEDKLAFVKSFVYDYSYSEPSVPTSYSWPKL   69 (69)
Q Consensus        24 ICr~~~-~g~a~~~p~P~D~~~~V~~~~Y~~~Y~~s~lp~~y~wp~~   69 (69)
                      +.+..+ +|+|...++|+|.++||++.||+++|. +++|++|+||++
T Consensus       247 Va~~A~~~GvA~~~~~~~dl~~~i~~~mw~p~Y~-~~~~~~~~~~~~  292 (308)
T d1o0sa1         247 MAKYCYKNGTANLYPQPEDLEKYVRAQVYNTEYE-ELINATYDWPEQ  292 (308)
T ss_dssp             HHHHHHHTTCBCSSSCCSCHHHHHHHHSCCCSCC-CCSCCCBCCCGG
T ss_pred             HHHHHHHcCCCCCCCChHHHHHHHHHhCCCCCCc-ccccccccchhh
Confidence            344444 789999999999999999999999997 899999999964

>d1pj3a1 c.2.1.7 (A:280-573) Mitochondrial NAD(P)-dependent malic enzyme {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Aminoacid dehydrogenase-like, C-terminal domain
domain: Mitochondrial NAD(P)-dependent malic enzyme
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.31  E-value=2e-07  Score=64.96  Aligned_cols=43  Identities=35%  Similarity=0.664  Sum_probs=37.8

Q ss_pred             cccchh-hccCCCCCCCCchhhHHhhhcccccCCCCCCCccccCC
Q psy6139          24 ICRVQV-MGTATVYPEPEDKLAFVKSFVYDYSYSEPSVPTSYSWP   67 (69)
Q Consensus        24 ICr~~~-~g~a~~~p~P~D~~~~V~~~~Y~~~Y~~s~lp~~y~wp   67 (69)
                      .++..+ +|+|...+.|+|..++|+++||+++|+ +++|++|+||
T Consensus       251 Va~~A~~~g~A~~~~~~~~~~~~i~~~~w~p~Y~-~~~p~~~~~~  294 (294)
T d1pj3a1         251 VTEYLYANKMAFRYPEPEDKAKYVKERTWRSEYD-SLLPDVYEWP  294 (294)
T ss_dssp             HHHHHHHTTCCCCSSCCSSHHHHHHHTCCCCSCC-CCCCCCCCCC
T ss_pred             HHHHHHHcCCCCCCCChHHHHHHHHHhcCCCccC-ccCCCCCCCC
Confidence            344444 678999999999999999999999998 8999999998

>d1rutx4 g.39.1.3 (X:114-146) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.25  E-value=0.013  Score=28.12  Aligned_cols=25  Identities=24%  Similarity=0.705  Sum_probs=20.0

Q ss_pred             eeccccchhhccCCCCCCCCchhhHHhhhcccc
Q psy6139          21 TCAICRVQVMGTATVYPEPEDKLAFVKSFVYDY   53 (69)
Q Consensus        21 ~CaICr~~~~g~a~~~p~P~D~~~~V~~~~Y~~   53 (69)
                      +|++|||.|        .|||.=.||-+.+|--
T Consensus         1 tC~tC~n~L--------VPGDRFHyvNG~lfCE   25 (33)
T d1rutx4           1 TCSTCRNRL--------VPGDRFHYINGSLFCE   25 (33)
T ss_dssp             BCTTTCCBC--------CTTCEEEEETTEEEEG
T ss_pred             Ccccccccc--------cCCceeEEecCEEEEe
Confidence            599999876        6899888888887743