Citrus Sinensis ID: 035446

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------6
Protein Sequence
MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKGSE
Secondary Structure (PSIPRED)
ccccccccccccccccccEEEEcccccccHHHHHHHHHHccccccccccccccEEcccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccEEEEccccHHHHHHHHHHHcccccccccccccccEEEcccc
Coil and Loop (DISEMBL)
mafdgccpdcklpgddcpliwgacnhAFHLHCILKWvnsqtpqahcpmcrrewqfkgse
Flexible Loop (DISEMBL)
MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKGSE
Low Complexity Region (SEG)
MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKGSE
Disordered region (IsUnstruct)
***DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREW******
Disordered Region (DISOPRED)
MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK***
Disordered Region (DISEMBL)
MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKGSE
Disordered Region (DISPRO)
**FDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKGSE
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	59	2.2.26 [Sep-21-2011]
Q9M9L0	84	Anaphase-promoting comple	yes	no	0.949	0.666	0.982	6e-27
Q9CPX9	84	Anaphase-promoting comple	yes	no	0.949	0.666	0.75	3e-21
Q3ZCF6	84	Anaphase-promoting comple	yes	no	0.949	0.666	0.75	3e-21
Q5R8A2	84	Anaphase-promoting comple	yes	no	0.949	0.666	0.732	1e-20
Q9NYG5	84	Anaphase-promoting comple	yes	no	0.949	0.666	0.732	1e-20
Q54L48	87	Anaphase-promoting comple	yes	no	0.983	0.666	0.711	2e-19
Q12157	165	Anaphase-promoting comple	yes	no	0.932	0.333	0.490	2e-12
Q9UT86	94	Anaphase-promoting comple	yes	no	0.983	0.617	0.482	7e-12
O13959	107	RING-box protein pip1 OS=	no	no	0.796	0.439	0.418	1e-06
Q23457	110	RING-box protein 1 OS=Cae	no	no	0.661	0.354	0.476	2e-06

>sp|Q9M9L0|APC11_ARATH Anaphase-promoting complex subunit 11 OS=Arabidopsis thaliana GN=APC11 PE=1 SV=2

 Score =  119 bits (298), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 55/56 (98%), Positives = 55/56 (98%)

Query: 1  MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
          MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQT QAHCPMCRREWQFK
Sbjct: 28 MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTSQAHCPMCRREWQFK 83

Component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin-protein ligase complex that controls progression through mitosis and the G1 phase of the cell cycle. The APC/C complex controls several key steps in the cell cycle by mediating ubiquitination and subsequent degradation of target proteins such as cyclins. The APC/C complex is required for the female gametophyte development and is involved in several aspect of development by controlling cell division and cell elongation. Involved in the control of endoreduplication. May recruit the E2 ubiquitin-conjugating enzymes to the complex.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9CPX9|APC11_MOUSE Anaphase-promoting complex subunit 11 OS=Mus musculus GN=Anapc11 PE=3 SV=1

 Score =  100 bits (249), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 42/56 (75%), Positives = 51/56 (91%)

Query: 1  MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
          MAF+GCCPDCK+PGDDCPL+WG C+H FH+HCILKW+N+Q  Q HCPMCR+EW+FK
Sbjct: 28 MAFNGCCPDCKVPGDDCPLVWGQCSHCFHMHCILKWLNAQQVQQHCPMCRQEWKFK 83

Component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle. The APC/C complex acts by mediating ubiquitination and subsequent degradation of target proteins: it mainly mediates the formation of 'Lys-11'-linked polyubiquitin chains and, to a lower extent, the formation of 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains. May recruit the E2 ubiquitin-conjugating enzymes to the complex.

Mus musculus (taxid: 10090)

>sp|Q3ZCF6|APC11_BOVIN Anaphase-promoting complex subunit 11 OS=Bos taurus GN=ANAPC11 PE=3 SV=1

 Score =  100 bits (248), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 42/56 (75%), Positives = 51/56 (91%)

Query: 1  MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
          MAF+GCCPDCK+PGDDCPL+WG C+H FH+HCILKW+N+Q  Q HCPMCR+EW+FK
Sbjct: 28 MAFNGCCPDCKVPGDDCPLVWGQCSHCFHMHCILKWLNAQQVQQHCPMCRQEWKFK 83

Component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle. The APC/C complex acts by mediating ubiquitination and subsequent degradation of target proteins: it mainly mediates the formation of 'Lys-11'-linked polyubiquitin chains and, to a lower extent, the formation of 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains. May recruit the E2 ubiquitin-conjugating enzymes to the complex.

Bos taurus (taxid: 9913)

>sp|Q5R8A2|APC11_PONAB Anaphase-promoting complex subunit 11 OS=Pongo abelii GN=ANAPC11 PE=3 SV=1

 Score = 98.2 bits (243), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 41/56 (73%), Positives = 51/56 (91%)

Query: 1  MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
          MAF+GCCPDCK+PGDDCPL+WG C+H FH+HCILKW+++Q  Q HCPMCR+EW+FK
Sbjct: 28 MAFNGCCPDCKVPGDDCPLVWGQCSHCFHMHCILKWLHAQQVQQHCPMCRQEWKFK 83

Component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle. The APC/C complex acts by mediating ubiquitination and subsequent degradation of target proteins: it mainly mediates the formation of 'Lys-11'-linked polyubiquitin chains and, to a lower extent, the formation of 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains. May recruit the E2 ubiquitin-conjugating enzymes to the complex.

Pongo abelii (taxid: 9601)

>sp|Q9NYG5|APC11_HUMAN Anaphase-promoting complex subunit 11 OS=Homo sapiens GN=ANAPC11 PE=1 SV=1

 Score = 98.2 bits (243), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 41/56 (73%), Positives = 51/56 (91%)

Query: 1  MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
          MAF+GCCPDCK+PGDDCPL+WG C+H FH+HCILKW+++Q  Q HCPMCR+EW+FK
Sbjct: 28 MAFNGCCPDCKVPGDDCPLVWGQCSHCFHMHCILKWLHAQQVQQHCPMCRQEWKFK 83

Component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle. The APC/C complex acts by mediating ubiquitination and subsequent degradation of target proteins: it mainly mediates the formation of 'Lys-11'-linked polyubiquitin chains and, to a lower extent, the formation of 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains. May recruit the E2 ubiquitin-conjugating enzymes to the complex.

Homo sapiens (taxid: 9606)

>sp|Q54L48|APC11_DICDI Anaphase-promoting complex subunit 11 OS=Dictyostelium discoideum GN=anapc11 PE=3 SV=1

 Score = 94.4 bits (233), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 42/59 (71%), Positives = 48/59 (81%), Gaps = 1/59 (1%)

Query: 1  MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKGSE 59
          MAFDGCC DCK+PGDDCP +WG CNHAFH+HCILKW+N+   Q  CPMCR EW+FK  E
Sbjct: 29 MAFDGCCVDCKIPGDDCPPVWGVCNHAFHMHCILKWLNANELQ-QCPMCRSEWRFKSDE 86

Component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin-protein ligase complex that controls progression through mitosis and the G1 phase of the cell cycle.

Dictyostelium discoideum (taxid: 44689)

>sp|Q12157|APC11_YEAST Anaphase-promoting complex subunit 11 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=APC11 PE=1 SV=1

 Score = 71.2 bits (173), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 27/55 (49%), Positives = 40/55 (72%)

Query: 2   AFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
           +++G CP CK PGD CPL+ G C+H FH HCI +W+++ T +  CPMCR+ +Q +
Sbjct: 47  SYNGTCPSCKFPGDQCPLVIGLCHHNFHDHCIYRWLDTPTSKGLCPMCRQTFQLQ 101

Probably catalytic subunit of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin-protein ligase complex that controls progression through mitosis and the G1 phase of the cell cycle. The APC/C is thought to confer substrate specificity and, in the presence of ubiquitin-conjugating E2 enzymes, it catalyzes the formation of protein-ubiquitin conjugates that are subsequently degraded by the 26S proteasome. In early mitosis, the APC/C is activated by CDC20 and targets securin PDS1, the B-type cyclin CLB5, and other anaphase inhibitory proteins for proteolysis, thereby triggering the separation of sister chromatids at the metaphase-to-anaphase transition. In late mitosis and in G1, degradation of CLB5 allows activation of the APC/C by CDH1, which is needed to destroy CDC20 and the B-type cyclin CLB2 to allow exit from mitosis and creating the low CDK state necessary for cytokinesis and for reforming prereplicative complexes in G1 prior to another round of replication. APC11 is required to recruit the ubiquitin-conjugating enzyme E2 to the APC/C.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9UT86|APC11_SCHPO Anaphase-promoting complex subunit 11 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=apc11 PE=1 SV=1

 Score = 68.9 bits (167), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 28/58 (48%), Positives = 36/58 (62%)

Query: 1  MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKGS 58
          + FDGCCP C  PGD+CP++WG C H FH HCI  W+ +   Q  CPM R+ +    S
Sbjct: 29 VPFDGCCPQCTSPGDNCPIVWGKCKHIFHAHCIQNWLATSGSQGQCPMDRQTFVVADS 86

Component of the anaphase-promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin-protein ligase complex that controls progression through mitosis and the G1 phase of the cell cycle. The APC/C is thought to confer substrate specificity and, in the presence of ubiquitin-conjugating E2 enzymes, it catalyzes the formation of protein-ubiquitin conjugates that are subsequently degraded by the 26S proteasome.

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

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

 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 23/55 (41%), Positives = 34/55 (61%), Gaps = 8/55 (14%)

Query: 7   CPDCKLPGD-----DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
           C +C+   D     +C + WG CNHAFH HCI +W+N++     CP+  REW+F+
Sbjct: 52  CIECQANTDSAAAQECTVAWGTCNHAFHFHCISRWLNTRNV---CPLDNREWEFQ 103

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 = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 20/42 (47%), Positives = 29/42 (69%), Gaps = 3/42 (7%)

Query: 15  DDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
           D+C + WG CNHAFH HCI +W+ ++     CP+  REW+F+
Sbjct: 68  DECTVAWGNCNHAFHFHCISRWLKTRQV---CPLDNREWEFQ 106

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)

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	59
449475614	229	PREDICTED: E3 ubiquitin-protein ligase h	0.966	0.248	0.982	8e-28
124365542	95	Zinc finger, RING-type [Medicago truncat	0.966	0.6	0.982	1e-26
255543044	127	ring finger, putative [Ricinus communis]	0.966	0.448	0.964	1e-26
356574062	129	PREDICTED: anaphase-promoting complex su	0.966	0.441	0.964	2e-26
359487593	81	PREDICTED: anaphase-promoting complex su	0.966	0.703	1.0	2e-26
357501427	77	Anaphase promoting complex subunit [Medi	0.966	0.740	0.982	7e-26
357467991	83	Anaphase promoting complex subunit [Medi	0.966	0.686	0.982	7e-26
388511655	84	unknown [Lotus japonicus]	0.966	0.678	0.964	2e-25
334185111	87	anaphase-promoting complex subunit 11 [A	0.949	0.643	0.982	2e-25
302595936	84	RecName: Full=Anaphase-promoting complex	0.949	0.666	0.982	2e-25

>gi|449475614|ref|XP_004154502.1| PREDICTED: E3 ubiquitin-protein ligase hrd-1-like, partial [Cucumis sativus]

 Score =  127 bits (319), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 56/57 (98%), Positives = 56/57 (98%)

Query: 1   MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG 57
           MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQT QAHCPMCRREWQFKG
Sbjct: 173 MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTSQAHCPMCRREWQFKG 229

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|124365542|gb|ABN09776.1| Zinc finger, RING-type [Medicago truncatula]

 Score =  123 bits (308), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 56/57 (98%), Positives = 56/57 (98%)

Query: 1  MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG 57
          MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQT QAHCPMCRREWQFKG
Sbjct: 39 MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTSQAHCPMCRREWQFKG 95

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255543044|ref|XP_002512585.1| ring finger, putative [Ricinus communis] gi|223548546|gb|EEF50037.1| ring finger, putative [Ricinus communis]

 Score =  123 bits (308), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 55/57 (96%), Positives = 55/57 (96%)

Query: 1   MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG 57
           MAFDGCCPDCKLPGDDCPLIWG CNHAFHLHCILKWVNSQT QAHCPMCRREWQFKG
Sbjct: 71  MAFDGCCPDCKLPGDDCPLIWGVCNHAFHLHCILKWVNSQTSQAHCPMCRREWQFKG 127

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356574062|ref|XP_003555171.1| PREDICTED: anaphase-promoting complex subunit 11-like [Glycine max]

 Score =  122 bits (307), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 55/57 (96%), Positives = 55/57 (96%)

Query: 1   MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG 57
           MAFDGCCPDCKLPGDDCPLIWG CNHAFHLHCILKWVNSQT QAHCPMCRREWQFKG
Sbjct: 73  MAFDGCCPDCKLPGDDCPLIWGVCNHAFHLHCILKWVNSQTSQAHCPMCRREWQFKG 129

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359487593|ref|XP_003633618.1| PREDICTED: anaphase-promoting complex subunit 11-like [Vitis vinifera] gi|296089855|emb|CBI39674.3| unnamed protein product [Vitis vinifera] gi|297745203|emb|CBI40283.3| unnamed protein product [Vitis vinifera]

 Score =  122 bits (307), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 57/57 (100%), Positives = 57/57 (100%)

Query: 1  MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG 57
          MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG
Sbjct: 25 MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG 81

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357501427|ref|XP_003621002.1| Anaphase promoting complex subunit [Medicago truncatula] gi|355496017|gb|AES77220.1| Anaphase promoting complex subunit [Medicago truncatula]

 Score =  121 bits (303), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 56/57 (98%), Positives = 56/57 (98%)

Query: 1  MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG 57
          MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQT QAHCPMCRREWQFKG
Sbjct: 21 MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTSQAHCPMCRREWQFKG 77

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357467991|ref|XP_003604280.1| Anaphase promoting complex subunit [Medicago truncatula] gi|355505335|gb|AES86477.1| Anaphase promoting complex subunit [Medicago truncatula]

 Score =  121 bits (303), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 56/57 (98%), Positives = 56/57 (98%)

Query: 1  MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG 57
          MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQT QAHCPMCRREWQFKG
Sbjct: 27 MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTSQAHCPMCRREWQFKG 83

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388511655|gb|AFK43889.1| unknown [Lotus japonicus]

 Score =  119 bits (299), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 55/57 (96%), Positives = 55/57 (96%)

Query: 1  MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG 57
          MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQ  QAHCPMCRREWQFKG
Sbjct: 28 MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQASQAHCPMCRREWQFKG 84

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334185111|ref|NP_187238.2| anaphase-promoting complex subunit 11 [Arabidopsis thaliana] gi|334185113|ref|NP_001189819.1| anaphase-promoting complex subunit 11 [Arabidopsis thaliana] gi|297791461|ref|XP_002863615.1| anaphase promoting complex subunit 11 [Arabidopsis lyrata subsp. lyrata] gi|297309450|gb|EFH39874.1| anaphase promoting complex subunit 11 [Arabidopsis lyrata subsp. lyrata] gi|332640788|gb|AEE74309.1| anaphase-promoting complex subunit 11 [Arabidopsis thaliana] gi|332640789|gb|AEE74310.1| anaphase-promoting complex subunit 11 [Arabidopsis thaliana]

 Score =  119 bits (299), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 55/56 (98%), Positives = 55/56 (98%)

Query: 1  MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
          MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQT QAHCPMCRREWQFK
Sbjct: 31 MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTSQAHCPMCRREWQFK 86

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302595936|sp|Q9M9L0.2|APC11_ARATH RecName: Full=Anaphase-promoting complex subunit 11; AltName: Full=Cyclosome subunit 11 gi|16197625|gb|AAL13436.1| anaphase promoting complex subunit 11 [Arabidopsis thaliana]

 Score =  119 bits (298), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 55/56 (98%), Positives = 55/56 (98%)

Query: 1  MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
          MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQT QAHCPMCRREWQFK
Sbjct: 28 MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTSQAHCPMCRREWQFK 83

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	59
UNIPROTKB|Q3ZCF6	84	ANAPC11 "Anaphase-promoting co	0.949	0.666	0.75	6.6e-26
UNIPROTKB|E2R4W0	84	ANAPC11 "Uncharacterized prote	0.949	0.666	0.75	6.6e-26
MGI|MGI:1913406	84	Anapc11 "anaphase promoting co	0.949	0.666	0.75	6.6e-26
RGD|1561880	84	Anapc11 "anaphase promoting co	0.949	0.666	0.75	6.6e-26
UNIPROTKB|Q9NYG5	84	ANAPC11 "Anaphase-promoting co	0.949	0.666	0.732	2.2e-25
UNIPROTKB|Q5R8A2	84	ANAPC11 "Anaphase-promoting co	0.949	0.666	0.732	2.2e-25
ZFIN|ZDB-GENE-061013-383	88	anapc11 "APC11 anaphase promot	0.932	0.625	0.727	1.6e-24
DICTYBASE|DDB_G0286909	87	anapc11 "anaphase promoting co	0.983	0.666	0.711	6.8e-24
UNIPROTKB|I3L933	84	ANAPC11 "Uncharacterized prote	0.881	0.619	0.730	6.1e-23
FB|FBgn0250903	85	lmgA "lemming A" [Drosophila m	0.932	0.647	0.6	3.5e-20

UNIPROTKB|Q3ZCF6 ANAPC11 "Anaphase-promoting complex subunit 11" [Bos taurus (taxid:9913)]

 Score = 293 (108.2 bits), Expect = 6.6e-26, P = 6.6e-26
 Identities = 42/56 (75%), Positives = 51/56 (91%)

Query:     1 MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
             MAF+GCCPDCK+PGDDCPL+WG C+H FH+HCILKW+N+Q  Q HCPMCR+EW+FK
Sbjct:    28 MAFNGCCPDCKVPGDDCPLVWGQCSHCFHMHCILKWLNAQQVQQHCPMCRQEWKFK 83

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

GO:0070979 "protein K11-linked ubiquitination" evidence=ISS

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0051301 "cell division" evidence=IEA

GO:0007067 "mitosis" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|E2R4W0 ANAPC11 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 293 (108.2 bits), Expect = 6.6e-26, P = 6.6e-26
 Identities = 42/56 (75%), Positives = 51/56 (91%)

Query:     1 MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
             MAF+GCCPDCK+PGDDCPL+WG C+H FH+HCILKW+N+Q  Q HCPMCR+EW+FK
Sbjct:    28 MAFNGCCPDCKVPGDDCPLVWGQCSHCFHMHCILKWLNAQQVQQHCPMCRQEWKFK 83

GO:0070979 "protein K11-linked ubiquitination" evidence=IEA

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

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

GO:0008270 "zinc ion binding" evidence=IEA

MGI|MGI:1913406 Anapc11 "anaphase promoting complex subunit 11" [Mus musculus (taxid:10090)]

 Score = 293 (108.2 bits), Expect = 6.6e-26, P = 6.6e-26
 Identities = 42/56 (75%), Positives = 51/56 (91%)

Query:     1 MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
             MAF+GCCPDCK+PGDDCPL+WG C+H FH+HCILKW+N+Q  Q HCPMCR+EW+FK
Sbjct:    28 MAFNGCCPDCKVPGDDCPLVWGQCSHCFHMHCILKWLNAQQVQQHCPMCRQEWKFK 83

GO:0003674 "molecular_function" evidence=ND

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IEA

GO:0007049 "cell cycle" evidence=IEA

GO:0007067 "mitosis" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016567 "protein ubiquitination" evidence=ISO

GO:0046872 "metal ion binding" evidence=IEA

GO:0051301 "cell division" evidence=IEA

GO:0070979 "protein K11-linked ubiquitination" evidence=ISO

RGD|1561880 Anapc11 "anaphase promoting complex subunit 11" [Rattus norvegicus (taxid:10116)]

 Score = 293 (108.2 bits), Expect = 6.6e-26, P = 6.6e-26
 Identities = 42/56 (75%), Positives = 51/56 (91%)

Query:     1 MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
             MAF+GCCPDCK+PGDDCPL+WG C+H FH+HCILKW+N+Q  Q HCPMCR+EW+FK
Sbjct:    28 MAFNGCCPDCKVPGDDCPLVWGQCSHCFHMHCILKWLNAQQVQQHCPMCRQEWKFK 83

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

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016567 "protein ubiquitination" evidence=ISO

GO:0070979 "protein K11-linked ubiquitination" evidence=IEA;ISO

UNIPROTKB|Q9NYG5 ANAPC11 "Anaphase-promoting complex subunit 11" [Homo sapiens (taxid:9606)]

 Score = 288 (106.4 bits), Expect = 2.2e-25, P = 2.2e-25
 Identities = 41/56 (73%), Positives = 51/56 (91%)

Query:     1 MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
             MAF+GCCPDCK+PGDDCPL+WG C+H FH+HCILKW+++Q  Q HCPMCR+EW+FK
Sbjct:    28 MAFNGCCPDCKVPGDDCPLVWGQCSHCFHMHCILKWLHAQQVQQHCPMCRQEWKFK 83

GO:0008270 "zinc ion binding" evidence=IEA

GO:0051301 "cell division" evidence=IEA

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

GO:0007067 "mitosis" evidence=TAS

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

GO:0070979 "protein K11-linked ubiquitination" evidence=IDA

GO:0016567 "protein ubiquitination" evidence=IDA

GO:0031145 "anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process" evidence=TAS

GO:0051436 "negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle" evidence=TAS

GO:0051437 "positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle" evidence=TAS

GO:0051439 "regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle" evidence=TAS

GO:0000075 "cell cycle checkpoint" evidence=TAS

GO:0000278 "mitotic cell cycle" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0007094 "mitotic spindle assembly checkpoint" evidence=TAS

UNIPROTKB|Q5R8A2 ANAPC11 "Anaphase-promoting complex subunit 11" [Pongo abelii (taxid:9601)]

 Score = 288 (106.4 bits), Expect = 2.2e-25, P = 2.2e-25
 Identities = 41/56 (73%), Positives = 51/56 (91%)

Query:     1 MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
             MAF+GCCPDCK+PGDDCPL+WG C+H FH+HCILKW+++Q  Q HCPMCR+EW+FK
Sbjct:    28 MAFNGCCPDCKVPGDDCPLVWGQCSHCFHMHCILKWLHAQQVQQHCPMCRQEWKFK 83

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

GO:0070979 "protein K11-linked ubiquitination" evidence=ISS

ZFIN|ZDB-GENE-061013-383 anapc11 "APC11 anaphase promoting complex subunit 11 homolog (yeast)" [Danio rerio (taxid:7955)]

 Score = 280 (103.6 bits), Expect = 1.6e-24, P = 1.6e-24
 Identities = 40/55 (72%), Positives = 49/55 (89%)

Query:     2 AFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
             +F+GCCPDCK+PGDDCPL+WG C+H FH+HCILKW+NSQ  Q  CPMCR+EW+FK
Sbjct:    29 SFNGCCPDCKVPGDDCPLVWGQCSHCFHMHCILKWLNSQQVQQQCPMCRQEWKFK 83

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0046872 "metal ion binding" evidence=IEA

DICTYBASE|DDB_G0286909 anapc11 "anaphase promoting complex subunit 11" [Dictyostelium discoideum (taxid:44689)]

 Score = 274 (101.5 bits), Expect = 6.8e-24, P = 6.8e-24
 Identities = 42/59 (71%), Positives = 48/59 (81%)

Query:     1 MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKGSE 59
             MAFDGCC DCK+PGDDCP +WG CNHAFH+HCILKW+N+   Q  CPMCR EW+FK  E
Sbjct:    29 MAFDGCCVDCKIPGDDCPPVWGVCNHAFHMHCILKWLNANELQ-QCPMCRSEWRFKSDE 86

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=ISS

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

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

GO:0051301 "cell division" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0007067 "mitosis" evidence=IEA

GO:0007049 "cell cycle" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0016567 "protein ubiquitination" evidence=IEA

UNIPROTKB|I3L933 ANAPC11 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 265 (98.3 bits), Expect = 6.1e-23, P = 6.1e-23
 Identities = 38/52 (73%), Positives = 47/52 (90%)

Query:     1 MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRRE 52
             MAF+GCCPDCK+PGDDCPL+WG C+H FH+HCILKW+++Q  Q HCPMCR+E
Sbjct:    28 MAFNGCCPDCKVPGDDCPLVWGQCSHCFHMHCILKWLHAQQVQQHCPMCRQE 79

GO:0070979 "protein K11-linked ubiquitination" evidence=IEA

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

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

GO:0008270 "zinc ion binding" evidence=IEA

FB|FBgn0250903 lmgA "lemming A" [Drosophila melanogaster (taxid:7227)]

 Score = 239 (89.2 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 33/55 (60%), Positives = 43/55 (78%)

Query:     1 MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF 55
             M+F+  CP+C LPGDDCPL+WG C+H FH+HCI+KW+N Q     CPMCR+ W+F
Sbjct:    28 MSFESTCPECALPGDDCPLVWGVCSHCFHMHCIVKWLNLQPLNKQCPMCRQSWKF 82

GO:0000090 "mitotic anaphase" evidence=NAS

GO:0005680 "anaphase-promoting complex" evidence=NAS;IPI

GO:0008270 "zinc ion binding" evidence=IEA

GO:0090302 "mitotic anaphase-promoting complex activity" evidence=IDA

GO:0045842 "positive regulation of mitotic metaphase/anaphase transition" evidence=IMP

GO:0031145 "anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process" evidence=IDA

GO:0000151 "ubiquitin ligase complex" evidence=IPI

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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)
Q9NYG5	APC11_HUMAN	No assigned EC number	0.7321	0.9491	0.6666	yes	no
Q5R8A2	APC11_PONAB	No assigned EC number	0.7321	0.9491	0.6666	yes	no
Q9M9L0	APC11_ARATH	No assigned EC number	0.9821	0.9491	0.6666	yes	no
Q3ZCF6	APC11_BOVIN	No assigned EC number	0.75	0.9491	0.6666	yes	no
Q54L48	APC11_DICDI	No assigned EC number	0.7118	0.9830	0.6666	yes	no
Q9CPX9	APC11_MOUSE	No assigned EC number	0.75	0.9491	0.6666	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00022509001 SubName- Full=Chromosome chr14 scaffold_27, whole genome shotgun sequence; (214 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	59
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	2e-24
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	3e-17
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	2e-15
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	7e-08
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	5e-05
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	1e-04

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

 Score = 85.6 bits (212), Expect = 2e-24
 Identities = 33/56 (58%), Positives = 43/56 (76%)

Query: 1  MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
          ++FDG CP CK PGDDCPL+WG C H FH+HCILKW+ ++T +  CPMCR+ + F 
Sbjct: 29 VSFDGTCPQCKFPGDDCPLVWGKCKHNFHMHCILKWLATETSKGLCPMCRQTFVFA 84

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

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

 Score = 67.5 bits (165), Expect = 3e-17
 Identities = 29/50 (58%), Positives = 37/50 (74%), Gaps = 3/50 (6%)

Query: 1  MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCR 50
            FDG CP+CK PGDDCP++WG C HAFHLHCI +W+ ++     CP+CR
Sbjct: 27 NHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRN---TCPLCR 73

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 = 62.9 bits (153), Expect = 2e-15
 Identities = 25/60 (41%), Positives = 37/60 (61%), Gaps = 6/60 (10%)

Query: 3  FDGCCPDCK---LPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKGSE 59
            G CP+C+    PGD+CP++WG CNHAFH HCI +W+++   +  CP+ R+ W      
Sbjct: 30 IMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDT---KGVCPLDRQTWVLADGG 86

Length = 88

>gnl|CDD|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

 Score = 46.2 bits (109), Expect = 7e-08
 Identities = 20/66 (30%), Positives = 27/66 (40%), Gaps = 16/66 (24%)

Query: 1    MAFDGC--CPDC---------KLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMC 49
              F G   C  C          LP   C      C + FH  C+ KW  S + +++CP+C
Sbjct: 1464 EKFSGHEECAICYSVLDMVDRSLPSKRCA----TCKNKFHTRCLYKWFAS-SARSNCPLC 1518

Query: 50   RREWQF 55
            R E  F
Sbjct: 1519 RSEITF 1524

Length = 1525

>gnl|CDD|227827 COG5540, COG5540, RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

 Score = 38.1 bits (88), Expect = 5e-05
 Identities = 11/29 (37%), Positives = 18/29 (62%), Gaps = 2/29 (6%)

Query: 24  CNHAFHLHCILKWVNSQTPQAHCPMCRRE 52
           C+H FH+ C+ KW+   + +  CP+CR  
Sbjct: 344 CDHRFHVGCVDKWLLGYSNK--CPVCRTA 370

Length = 374

>gnl|CDD|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]

 Score = 37.3 bits (86), Expect = 1e-04
 Identities = 15/33 (45%), Positives = 18/33 (54%), Gaps = 5/33 (15%)

Query: 24  CNHAFHLHCILKWVN-SQTPQAHCPMCRREWQF 55
           C H  HLHC+  W+   QT    CP+CRR   F
Sbjct: 318 CGHILHLHCLKNWLERQQT----CPICRRPVIF 346

Length = 491

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	59
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.84
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.73
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	99.73
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.68
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	99.62
PHA02929	238	N1R/p28-like protein; Provisional	99.59
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.5
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.47
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.45
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.44
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.43
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.42
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.42
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.42
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.42
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.4
PHA02926	242	zinc finger-like protein; Provisional	99.39
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	99.36
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	99.34
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.28
PF14634	44	zf-RING_5: zinc-RING finger domain	99.26
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	99.22
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	99.21
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	99.2
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	99.05
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	99.03
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	99.0
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.92
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.9
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.86
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	98.86
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.83
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.79
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.74
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.73
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.71
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.69
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.62
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.61
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.59
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.54
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	98.43
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	98.32
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	98.32
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	98.31
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	98.17
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	98.14
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.12
KOG0297	391	consensus TNF receptor-associated factor [Signal t	98.06
KOG0825	1134	consensus PHD Zn-finger protein [General function	98.06
KOG4445	368	consensus Uncharacterized conserved protein, conta	98.03
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	98.02
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	98.0
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.99
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.88
PHA02862	156	5L protein; Provisional	97.88
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	97.87
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	97.76
KOG2660	331	consensus Locus-specific chromosome binding protei	97.72
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.7
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.69
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	97.66
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.63
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.59
PHA02825	162	LAP/PHD finger-like protein; Provisional	97.57
KOG4739	233	consensus Uncharacterized protein involved in syna	97.55
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	97.35
PHA03096	284	p28-like protein; Provisional	97.32
KOG1940	276	consensus Zn-finger protein [General function pred	97.26
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	97.24
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	97.2
COG5152	259	Uncharacterized conserved protein, contains RING a	97.07
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	97.06
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	96.97
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	96.94
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	96.86
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	96.8
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	96.79
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	96.78
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	96.77
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	96.72
PF04641	260	Rtf2: Rtf2 RING-finger	96.68
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	96.57
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	96.48
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	96.46
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	96.35
KOG3039	303	consensus Uncharacterized conserved protein [Funct	96.33
KOG1001	674	consensus Helicase-like transcription factor HLTF/	96.27
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	96.24
COG5222	427	Uncharacterized conserved protein, contains RING Z	96.2
COG5175	480	MOT2 Transcriptional repressor [Transcription]	95.92
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	95.8
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	95.72
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	95.72
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	95.71
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	95.7
KOG3053	293	consensus Uncharacterized conserved protein [Funct	95.63
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	95.15
KOG4367	699	consensus Predicted Zn-finger protein [Function un	94.78
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	94.21
COG5109	396	Uncharacterized conserved protein, contains RING Z	94.04
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	93.8
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	93.57
COG5236	493	Uncharacterized conserved protein, contains RING Z	93.56
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	93.44
KOG3899	381	consensus Uncharacterized conserved protein [Funct	93.42
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	93.28
KOG0298	1394	consensus DEAD box-containing helicase-like transc	93.13
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	92.86
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	92.46
KOG3002	299	consensus Zn finger protein [General function pred	92.35
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	91.84
PF13901	202	DUF4206: Domain of unknown function (DUF4206)	91.23
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	90.47
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	90.28
KOG4718	235	consensus Non-SMC (structural maintenance of chrom	90.09
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	89.96
KOG1609	323	consensus Protein involved in mRNA turnover and st	89.75
PF06844	68	DUF1244: Protein of unknown function (DUF1244); In	89.6
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	89.45
PF04710	416	Pellino: Pellino; InterPro: IPR006800 Pellino is i	89.44
PF14569	80	zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.	89.37
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	89.35
KOG0269	839	consensus WD40 repeat-containing protein [Function	88.91
PF07191	70	zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807	88.52
KOG1829	580	consensus Uncharacterized conserved protein, conta	87.82
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	87.76
KOG3113	293	consensus Uncharacterized conserved protein [Funct	87.16
PF00628	51	PHD: PHD-finger; InterPro: IPR019787 Zinc finger (	86.76
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	85.91
PLN02189	1040	cellulose synthase	85.52
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	85.35
PF04423	54	Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IP	85.11
PLN02436	1094	cellulose synthase A	83.62
PF13771	90	zf-HC5HC2H: PHD-like zinc-binding domain	83.32
PF10497	105	zf-4CXXC_R1: Zinc-finger domain of monoamine-oxida	82.2
PF07649	30	C1_3: C1-like domain; InterPro: IPR011424 This sho	81.96
PF13832	110	zf-HC5HC2H_2: PHD-zinc-finger like domain	81.73
COG5627	275	MMS21 DNA repair protein MMS21 [DNA replication, r	80.62
PLN02638	1079	cellulose synthase A (UDP-forming), catalytic subu	80.29

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

Probab=99.84  E-value=2.5e-21  Score=99.97  Aligned_cols=57  Identities=67%  Similarity=1.749  Sum_probs=50.4

Q ss_pred             CCCCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            1 MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         1 ~~~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      ++||+.||.|..++++.+++...|+|.||..||.+|+.+++++..||+||++|.+++
T Consensus        29 ~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~k~   85 (85)
T PF12861_consen   29 MPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKFKE   85 (85)
T ss_pred             cccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeeeCC
Confidence            467888888888888999999999999999999999998655689999999998864

>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A

Probab=99.73  E-value=2.2e-18  Score=79.57  Aligned_cols=43  Identities=35%  Similarity=0.842  Sum_probs=34.8

Q ss_pred             CcccccCcCC-CCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccc
Q 035446            5 GCCPDCKLPG-DDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCR   50 (59)
Q Consensus         5 ~~C~IC~~~~-~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr   50 (59)
                      +.|+||++.. .+..++.++|+|.||.+||.+|++.+   .+||+||
T Consensus         1 d~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~---~~CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRN---NSCPVCR   44 (44)
T ss_dssp             -CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHS---SB-TTTH
T ss_pred             CCCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhC---CcCCccC
Confidence            4799999754 34566667899999999999999997   7999997

...

>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.73  E-value=5.1e-19  Score=89.57  Aligned_cols=57  Identities=75%  Similarity=1.742  Sum_probs=52.3

Q ss_pred             CCCCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            1 MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         1 ~~~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      |+||+.||-|..+.++.|+++..|.|.||..||.+|+.....+..||+||+.|.+++
T Consensus        28 m~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~~e   84 (84)
T KOG1493|consen   28 MPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQFKE   84 (84)
T ss_pred             cccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeEecC
Confidence            689999999999999999999999999999999999998776789999999998763

>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=99.68  E-value=3.6e-17  Score=82.75  Aligned_cols=44  Identities=48%  Similarity=1.417  Sum_probs=35.4

Q ss_pred             CCcccccCcCC-----------CCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccc
Q 035446            4 DGCCPDCKLPG-----------DDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCR   50 (59)
Q Consensus         4 ~~~C~IC~~~~-----------~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr   50 (59)
                      ++.|+||+++.           ++.++.++.|||.||..||.+|++.+   .+||+||
T Consensus        19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~---~~CP~CR   73 (73)
T PF12678_consen   19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN---NTCPLCR   73 (73)
T ss_dssp             CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS---SB-TTSS
T ss_pred             CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC---CcCCCCC
Confidence            56799998643           24567778999999999999999987   6999997

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 ....

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

Probab=99.62  E-value=5e-16  Score=79.28  Aligned_cols=54  Identities=46%  Similarity=1.373  Sum_probs=46.0

Q ss_pred             CCCCcccccCc---CCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccCC
Q 035446            2 AFDGCCPDCKL---PGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKGS   58 (59)
Q Consensus         2 ~~~~~C~IC~~---~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~~   58 (59)
                      +++++|+-|..   +.++.+++...|+|.||..||.+||.++   ..||++|++|.+.++
T Consensus        29 him~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk---~~CPld~q~w~~~~~   85 (88)
T COG5194          29 HIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTK---GVCPLDRQTWVLADG   85 (88)
T ss_pred             cccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhC---CCCCCCCceeEEecc
Confidence            35667777754   5678899999999999999999999997   899999999998765

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.59  E-value=1.5e-15  Score=90.74  Aligned_cols=49  Identities=33%  Similarity=0.672  Sum_probs=39.1

Q ss_pred             CCcccccCcCCCCCC------eEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            4 DGCCPDCKLPGDDCP------LIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~------~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      +..|+||++...+.+      .++++|+|.||.+||.+|++.+   .+||+||.++..
T Consensus       174 ~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~---~tCPlCR~~~~~  228 (238)
T PHA02929        174 DKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEK---NTCPVCRTPFIS  228 (238)
T ss_pred             CCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcC---CCCCCCCCEeeE
Confidence            578999997543322      3456899999999999999876   799999998764

>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=99.50  E-value=1.4e-14  Score=90.13  Aligned_cols=48  Identities=29%  Similarity=0.753  Sum_probs=39.7

Q ss_pred             cccccCcC-CCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            6 CCPDCKLP-GDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         6 ~C~IC~~~-~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      +|+||++. ..+..+..++|+|.||..||+.|+...  +..||+|++.+..
T Consensus       231 ~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~--r~~CPvCK~di~~  279 (348)
T KOG4628|consen  231 TCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT--RTFCPVCKRDIRT  279 (348)
T ss_pred             eEEEeecccccCCeeeEecCCCchhhccchhhHhhc--CccCCCCCCcCCC
Confidence            89999964 345566678999999999999999987  3579999987654

>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A

Probab=99.47  E-value=3.4e-14  Score=64.04  Aligned_cols=39  Identities=36%  Similarity=0.930  Sum_probs=31.6

Q ss_pred             ccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccc
Q 035446            7 CPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMC   49 (59)
Q Consensus         7 C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~C   49 (59)
                      |+||++...+ +++.++|||+||.+|+.+|++.+   ..||+|
T Consensus         1 C~iC~~~~~~-~~~~~~CGH~fC~~C~~~~~~~~---~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRD-PVVVTPCGHSFCKECIEKYLEKN---PKCPVC   39 (39)
T ss_dssp             ETTTTSB-SS-EEEECTTSEEEEHHHHHHHHHCT---SB-TTT
T ss_pred             CCCCCCcccC-cCEECCCCCchhHHHHHHHHHCc---CCCcCC
Confidence            7999765554 65668999999999999999985   789987

>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)

Probab=99.45  E-value=1.5e-13  Score=62.15  Aligned_cols=45  Identities=36%  Similarity=0.800  Sum_probs=35.5

Q ss_pred             cccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccc
Q 035446            6 CCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREW   53 (59)
Q Consensus         6 ~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~   53 (59)
                      .|+||++.. ..++..++|+|.||..|+.+|++..  ...||+|+..+
T Consensus         1 ~C~iC~~~~-~~~~~~~~C~H~~c~~C~~~~~~~~--~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEF-REPVVLLPCGHVFCRSCIDKWLKSG--KNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhh-hCceEecCCCChhcHHHHHHHHHhC--cCCCCCCCCcC
Confidence            589998655 3355556799999999999999873  26899999764

>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]

Probab=99.44  E-value=9.1e-14  Score=87.41  Aligned_cols=52  Identities=35%  Similarity=0.729  Sum_probs=40.8

Q ss_pred             CCCcccccCcC-CC----------CCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            3 FDGCCPDCKLP-GD----------DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         3 ~~~~C~IC~~~-~~----------~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      -|..|.||+++ ..          +.....++|||.||.+|+..|++++   .+||+||.++.+..
T Consensus       286 ~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERq---QTCPICr~p~ifd~  348 (491)
T COG5243         286 SDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ---QTCPICRRPVIFDQ  348 (491)
T ss_pred             CCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhc---cCCCcccCcccccc
Confidence            46789999854 11          1123457999999999999999998   79999999976654

>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=99.43  E-value=9.1e-14  Score=82.41  Aligned_cols=50  Identities=26%  Similarity=0.733  Sum_probs=41.1

Q ss_pred             CcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      -+|.||++..++ +++ +.|||.||+-||.+|+........||+|+..+..+
T Consensus        48 FdCNICLd~akd-PVv-TlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~   97 (230)
T KOG0823|consen   48 FDCNICLDLAKD-PVV-TLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSID   97 (230)
T ss_pred             eeeeeeccccCC-CEE-eecccceehHHHHHHHhhcCCCeeCCccccccccc
Confidence            369999876554 554 58999999999999999977667899999987654

>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A

Probab=99.42  E-value=9.4e-14  Score=63.71  Aligned_cols=41  Identities=29%  Similarity=0.668  Sum_probs=29.4

Q ss_pred             ccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCC-CCCccc
Q 035446            7 CPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQ-AHCPMC   49 (59)
Q Consensus         7 C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~-~~CP~C   49 (59)
                      ||||++.+.+ |+. ++|||+|+++||.+|++...+. ..||.|
T Consensus         1 CpiC~~~~~~-Pv~-l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKD-PVS-LPCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SS-EEE--SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCC-ccc-cCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            8999876665 444 6999999999999999876543 579987

>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A

Probab=99.42  E-value=1.2e-13  Score=65.14  Aligned_cols=46  Identities=28%  Similarity=0.698  Sum_probs=36.6

Q ss_pred             CCcccccCcCCCCCCeEecCCCCc-ccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHA-FHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~-fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      +..|+||++...+  ++.++|||. |+..|+.+|++..   ..||+||+++.
T Consensus         2 ~~~C~iC~~~~~~--~~~~pCgH~~~C~~C~~~~~~~~---~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPRD--VVLLPCGHLCFCEECAERLLKRK---KKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBSS--EEEETTCEEEEEHHHHHHHHHTT---SBBTTTTBB-S
T ss_pred             cCCCccCCccCCc--eEEeCCCChHHHHHHhHHhcccC---CCCCcCChhhc
Confidence            5689999865443  455799999 9999999999965   79999999875

...

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.42  E-value=2e-13  Score=79.46  Aligned_cols=51  Identities=29%  Similarity=0.670  Sum_probs=38.9

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCC-------------CCCCCcccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQT-------------PQAHCPMCRREWQFK   56 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~-------------~~~~CP~Cr~~~~~~   56 (59)
                      +..|+||++...+ +++ ++|||+||+.||.+|+....             ....||+||+++...
T Consensus        18 ~~~CpICld~~~d-PVv-T~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~   81 (193)
T PLN03208         18 DFDCNICLDQVRD-PVV-TLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEA   81 (193)
T ss_pred             ccCCccCCCcCCC-cEE-cCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChh
Confidence            4689999876554 444 69999999999999986421             135799999988654

>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=99.42  E-value=9.8e-14  Score=79.79  Aligned_cols=49  Identities=27%  Similarity=0.561  Sum_probs=41.3

Q ss_pred             CcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      ..|||||+.+.+...+.+.|||+||..||...++..   ..||+|++.+..+
T Consensus       132 ~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~---~~CP~C~kkIt~k  180 (187)
T KOG0320|consen  132 YKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNT---NKCPTCRKKITHK  180 (187)
T ss_pred             cCCCceecchhhccccccccchhHHHHHHHHHHHhC---CCCCCcccccchh
Confidence            469999987766655668999999999999999987   7999999876654

>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]

Probab=99.40  E-value=2e-13  Score=83.09  Aligned_cols=48  Identities=31%  Similarity=0.751  Sum_probs=39.8

Q ss_pred             CcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      ..|.+|+++.... .. ++|||.||+.||..|...+   ..||+||..+..++
T Consensus       240 ~kC~LCLe~~~~p-Sa-TpCGHiFCWsCI~~w~~ek---~eCPlCR~~~~psk  287 (293)
T KOG0317|consen  240 RKCSLCLENRSNP-SA-TPCGHIFCWSCILEWCSEK---AECPLCREKFQPSK  287 (293)
T ss_pred             CceEEEecCCCCC-Cc-CcCcchHHHHHHHHHHccc---cCCCcccccCCCcc
Confidence            5699998765543 33 6999999999999999987   67999999887654

>PHA02926 zinc finger-like protein; Provisional

Probab=99.39  E-value=4.4e-13  Score=79.49  Aligned_cols=54  Identities=24%  Similarity=0.569  Sum_probs=39.8

Q ss_pred             CCCCcccccCcCCCC-------CCeEecCCCCcccHHHHHHHHHhCC---CCCCCccccccccc
Q 035446            2 AFDGCCPDCKLPGDD-------CPLIWGACNHAFHLHCILKWVNSQT---PQAHCPMCRREWQF   55 (59)
Q Consensus         2 ~~~~~C~IC~~~~~~-------~~~~~~~C~H~fh~~Ci~~w~~~~~---~~~~CP~Cr~~~~~   55 (59)
                      +-|..|+||++...+       ..-++.+|+|.||..||.+|.+...   ....||+||..+.+
T Consensus       168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~  231 (242)
T PHA02926        168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRN  231 (242)
T ss_pred             cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeee
Confidence            347899999864211       1234579999999999999998642   13579999998765

>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]

Probab=99.36  E-value=4.7e-13  Score=71.25  Aligned_cols=41  Identities=44%  Similarity=1.305  Sum_probs=36.3

Q ss_pred             CCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccCC
Q 035446           15 DDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKGS   58 (59)
Q Consensus        15 ~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~~   58 (59)
                      ++..++...|+|.||..||.+|+++.   ..||++.++|.+++.
T Consensus        72 ~EC~VaWG~CNHaFH~hCisrWlktr---~vCPLdn~eW~~qr~  112 (114)
T KOG2930|consen   72 EECTVAWGVCNHAFHFHCISRWLKTR---NVCPLDNKEWVFQRY  112 (114)
T ss_pred             CceEEEeeecchHHHHHHHHHHHhhc---CcCCCcCcceeEeec
Confidence            35577888999999999999999997   899999999998753

>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.34  E-value=1.4e-12  Score=59.01  Aligned_cols=41  Identities=39%  Similarity=1.049  Sum_probs=32.5

Q ss_pred             ccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccc
Q 035446            7 CPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMC   49 (59)
Q Consensus         7 C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~C   49 (59)
                      |+||++...+ +..+++|||.||..||.+|++.. ....||+|
T Consensus         1 C~iC~~~~~~-~~~~~~C~H~fC~~C~~~~~~~~-~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFED-PVILLPCGHSFCRDCLRKWLENS-GSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSS-EEEETTTSEEEEHHHHHHHHHHT-SSSBTTTT
T ss_pred             CCcCCccccC-CCEEecCCCcchHHHHHHHHHhc-CCccCCcC
Confidence            7899876554 34468999999999999999952 23689987

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. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....

>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=99.28  E-value=2.8e-12  Score=79.05  Aligned_cols=49  Identities=29%  Similarity=0.602  Sum_probs=39.2

Q ss_pred             CcccccCcC-CCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            5 GCCPDCKLP-GDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         5 ~~C~IC~~~-~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      ..|+||+.. .+...+..++|.|.||..|+++|+...+  ..||+||.++..
T Consensus       324 veCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~--~~CPvCrt~iPP  373 (374)
T COG5540         324 VECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYS--NKCPVCRTAIPP  373 (374)
T ss_pred             ceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhc--ccCCccCCCCCC
Confidence            479999953 3334466789999999999999998653  689999998754

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=99.26  E-value=6.6e-12  Score=57.87  Aligned_cols=43  Identities=26%  Similarity=0.611  Sum_probs=34.0

Q ss_pred             cccccCcCC-CCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccc
Q 035446            6 CCPDCKLPG-DDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRR   51 (59)
Q Consensus         6 ~C~IC~~~~-~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~   51 (59)
                      .|+||.+.. ++.+..+++|||+||..|+.++...   ...||+||+
T Consensus         1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~---~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGK---SVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcccCCHHHHHHHHhhcCC---CCCCcCCCC
Confidence            489998655 3445667899999999999999822   268999985

>smart00504 Ubox Modified RING finger domain

Probab=99.22  E-value=2.2e-11  Score=59.26  Aligned_cols=48  Identities=21%  Similarity=0.344  Sum_probs=39.3

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      +..||||.+...+ +++ ++|||+|+++||.+|++.+   ..||+|+.++..+
T Consensus         1 ~~~Cpi~~~~~~~-Pv~-~~~G~v~~~~~i~~~~~~~---~~cP~~~~~~~~~   48 (63)
T smart00504        1 EFLCPISLEVMKD-PVI-LPSGQTYERRAIEKWLLSH---GTDPVTGQPLTHE   48 (63)
T ss_pred             CcCCcCCCCcCCC-CEE-CCCCCEEeHHHHHHHHHHC---CCCCCCcCCCChh
Confidence            3579999876555 544 6999999999999999885   7899999988654

Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.

>smart00184 RING Ring finger

Probab=99.21  E-value=2.1e-11  Score=53.32  Aligned_cols=39  Identities=36%  Similarity=0.858  Sum_probs=30.0

Q ss_pred             ccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccc
Q 035446            7 CPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMC   49 (59)
Q Consensus         7 C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~C   49 (59)
                      |+||++...  ....++|+|.||..|+..|++..  ...||+|
T Consensus         1 C~iC~~~~~--~~~~~~C~H~~c~~C~~~~~~~~--~~~CP~C   39 (39)
T smart00184        1 CPICLEELK--DPVVLPCGHTFCRSCIRKWLKSG--NNTCPIC   39 (39)
T ss_pred             CCcCccCCC--CcEEecCCChHHHHHHHHHHHhC--cCCCCCC
Confidence            789976532  34446999999999999999833  2679987

E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)

>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=99.20  E-value=6.9e-12  Score=81.69  Aligned_cols=48  Identities=29%  Similarity=0.574  Sum_probs=38.4

Q ss_pred             CCCcccccCcCCCCC---CeEecCCCCcccHHHHHHHHHhCCCCCCCccccccc
Q 035446            3 FDGCCPDCKLPGDDC---PLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREW   53 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~---~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~   53 (59)
                      .++.|+||++.....   ...+++|+|.||..|+.+|+++.   ++||.||..+
T Consensus       290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~---qtCP~CR~~~  340 (543)
T KOG0802|consen  290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQ---QTCPTCRTVL  340 (543)
T ss_pred             cCCeeeeechhhccccccccceeecccchHHHHHHHHHHHh---CcCCcchhhh
Confidence            478999998654331   23447999999999999999997   7999999843

>TIGR00599 rad18 DNA repair protein rad18

Probab=99.05  E-value=1.7e-10  Score=73.21  Aligned_cols=47  Identities=36%  Similarity=0.641  Sum_probs=38.4

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      +..|+||++.+.. ++ +++|||.||..||..|+...   ..||+|+.++..
T Consensus        26 ~l~C~IC~d~~~~-Pv-itpCgH~FCs~CI~~~l~~~---~~CP~Cr~~~~~   72 (397)
T TIGR00599        26 SLRCHICKDFFDV-PV-LTSCSHTFCSLCIRRCLSNQ---PKCPLCRAEDQE   72 (397)
T ss_pred             ccCCCcCchhhhC-cc-CCCCCCchhHHHHHHHHhCC---CCCCCCCCcccc
Confidence            4689999876554 33 36999999999999999875   689999998764

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A

Probab=99.03  E-value=3.6e-10  Score=52.01  Aligned_cols=41  Identities=29%  Similarity=0.682  Sum_probs=22.5

Q ss_pred             ccccCcCC-CCCCeEecCCCCcccHHHHHHHHHhCC-CCCCCc
Q 035446            7 CPDCKLPG-DDCPLIWGACNHAFHLHCILKWVNSQT-PQAHCP   47 (59)
Q Consensus         7 C~IC~~~~-~~~~~~~~~C~H~fh~~Ci~~w~~~~~-~~~~CP   47 (59)
                      ||||++.. ++.+..+++|||+|+++||+++++.+. ....||
T Consensus         1 CpIc~e~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKEFSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCccccccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence            89998732 234445578999999999999999752 234676

>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=99.00  E-value=4.2e-10  Score=72.80  Aligned_cols=52  Identities=35%  Similarity=0.731  Sum_probs=39.8

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCC--CCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQT--PQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~--~~~~CP~Cr~~~~~~~   57 (59)
                      +..||||+++..- + +++.|||+||..||-++|....  +...||+||..+..++
T Consensus       186 ~~~CPICL~~~~~-p-~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kd  239 (513)
T KOG2164|consen  186 DMQCPICLEPPSV-P-VRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKD  239 (513)
T ss_pred             CCcCCcccCCCCc-c-cccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccc
Confidence            6789999875443 2 3357999999999999987752  2357999999887654

>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins

Probab=98.92  E-value=2.6e-09  Score=50.33  Aligned_cols=44  Identities=25%  Similarity=0.762  Sum_probs=32.3

Q ss_pred             cccccCcCCCCCCeEecCCC-----CcccHHHHHHHHHhCCCCCCCcccc
Q 035446            6 CCPDCKLPGDDCPLIWGACN-----HAFHLHCILKWVNSQTPQAHCPMCR   50 (59)
Q Consensus         6 ~C~IC~~~~~~~~~~~~~C~-----H~fh~~Ci~~w~~~~~~~~~CP~Cr   50 (59)
                      .|-||++..++......+|.     |.+|..|+.+|+..+. ..+||+|+
T Consensus         1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~-~~~C~iC~   49 (49)
T smart00744        1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESG-NKTCEICK   49 (49)
T ss_pred             CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcC-CCcCCCCC
Confidence            48899863333333456885     8999999999998863 35899984

Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class

>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.90  E-value=9.6e-10  Score=66.55  Aligned_cols=50  Identities=32%  Similarity=0.664  Sum_probs=38.2

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHH-HHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILK-WVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~-w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      |-.|+||+++... + +.++|||+||..||.. |-..+.  ..||+||+....++
T Consensus       215 d~kC~lC~e~~~~-p-s~t~CgHlFC~~Cl~~~~t~~k~--~~CplCRak~~pk~  265 (271)
T COG5574         215 DYKCFLCLEEPEV-P-SCTPCGHLFCLSCLLISWTKKKY--EFCPLCRAKVYPKK  265 (271)
T ss_pred             ccceeeeecccCC-c-ccccccchhhHHHHHHHHHhhcc--ccCchhhhhccchh
Confidence            4569999875544 3 3369999999999999 766652  46999999876654

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.86  E-value=3.4e-09  Score=65.53  Aligned_cols=52  Identities=23%  Similarity=0.549  Sum_probs=36.7

Q ss_pred             CCcccccCcC--CCCCC-eEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKLP--GDDCP-LIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~--~~~~~-~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      +..||+|+..  ..... ..+..|||.||..|+...+....  ..||.|+.++...+
T Consensus         3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~--~~CP~C~~~lrk~~   57 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGS--GSCPECDTPLRKNN   57 (309)
T ss_pred             CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCC--CCCCCCCCccchhh
Confidence            4579999853  22221 12237999999999999776543  68999998876543

All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.86  E-value=1.5e-09  Score=68.82  Aligned_cols=50  Identities=30%  Similarity=0.744  Sum_probs=37.7

Q ss_pred             CCCCCcccccCc--CCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccc
Q 035446            1 MAFDGCCPDCKL--PGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCR   50 (59)
Q Consensus         1 ~~~~~~C~IC~~--~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr   50 (59)
                      ||....|.||.+  +.+...-.+..|||+||..|+.+|++....+..||+|+
T Consensus         1 mpi~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~   52 (465)
T KOG0827|consen    1 MPIMAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQ   52 (465)
T ss_pred             CCccceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCcee
Confidence            678889999953  22222222346999999999999999875556899998

>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.83  E-value=6.1e-10  Score=67.93  Aligned_cols=52  Identities=31%  Similarity=0.675  Sum_probs=38.7

Q ss_pred             CCcccccCcCCC----C----CCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            4 DGCCPDCKLPGD----D----CPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         4 ~~~C~IC~~~~~----~----~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      |..|+||-...+    +    ..+..++|+|+||..||..|-...+ .++||.|++.++.+
T Consensus       224 d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGK-kqtCPYCKekVdl~  283 (328)
T KOG1734|consen  224 DSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGK-KQTCPYCKEKVDLK  283 (328)
T ss_pred             cchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecC-CCCCchHHHHhhHh
Confidence            567999963211    1    1344679999999999999987654 36999999987754

>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A

Probab=98.79  E-value=1.2e-09  Score=54.86  Aligned_cols=53  Identities=25%  Similarity=0.561  Sum_probs=25.4

Q ss_pred             CCcccccCcCCC---CCCeE-e--cCCCCcccHHHHHHHHHhCCC--------CCCCcccccccccc
Q 035446            4 DGCCPDCKLPGD---DCPLI-W--GACNHAFHLHCILKWVNSQTP--------QAHCPMCRREWQFK   56 (59)
Q Consensus         4 ~~~C~IC~~~~~---~~~~~-~--~~C~H~fh~~Ci~~w~~~~~~--------~~~CP~Cr~~~~~~   56 (59)
                      +..|+||.....   +.+.+ -  ..|+..||..||.+|+.....        ...||.|++++..+
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~~   68 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISWS   68 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEGG
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeEe
Confidence            568999974322   22222 2  379999999999999985321        13599999988765

>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.74  E-value=4.1e-09  Score=61.79  Aligned_cols=42  Identities=26%  Similarity=0.590  Sum_probs=35.0

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCR   50 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr   50 (59)
                      +..|+||++.+...  .+++|+|+||..|+..++. .  ...||.||
T Consensus        13 ~~~C~iC~~~~~~p--~~l~C~H~~c~~C~~~~~~-~--~~~Cp~cr   54 (386)
T KOG2177|consen   13 ELTCPICLEYFREP--VLLPCGHNFCRACLTRSWE-G--PLSCPVCR   54 (386)
T ss_pred             cccChhhHHHhhcC--ccccccchHhHHHHHHhcC-C--CcCCcccC
Confidence            56899998766654  4579999999999999998 2  37899999

>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.73  E-value=6.6e-09  Score=67.63  Aligned_cols=48  Identities=35%  Similarity=0.926  Sum_probs=36.3

Q ss_pred             CcccccCcCCC------CC---------CeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            5 GCCPDCKLPGD------DC---------PLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         5 ~~C~IC~~~~~------~~---------~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      ..|+||+.+.+      +.         ...+++|.|.||..|+.+|+.+.+  ..||+||.++.
T Consensus       572 ~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~yk--l~CPvCR~pLP  634 (636)
T KOG0828|consen  572 NDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYK--LICPVCRCPLP  634 (636)
T ss_pred             ccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhc--ccCCccCCCCC
Confidence            57999985422      11         123469999999999999999652  58999999875

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=98.71  E-value=4.9e-09  Score=67.29  Aligned_cols=45  Identities=38%  Similarity=0.849  Sum_probs=35.3

Q ss_pred             CcccccCcCCC--CCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            5 GCCPDCKLPGD--DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         5 ~~C~IC~~~~~--~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      .+||||++..+  ...++...|.|+||-.|+.+|...     +||+||.-..
T Consensus       176 PTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~~-----scpvcR~~q~  222 (493)
T KOG0804|consen  176 PTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWDS-----SCPVCRYCQS  222 (493)
T ss_pred             CCcchhHhhcCccccceeeeecccccchHHHhhcccC-----cChhhhhhcC
Confidence            47999996444  334566799999999999999764     6999997544

>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=98.69  E-value=7.9e-09  Score=71.31  Aligned_cols=50  Identities=30%  Similarity=0.729  Sum_probs=36.8

Q ss_pred             CcccccCc-----CCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            5 GCCPDCKL-----PGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         5 ~~C~IC~~-----~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      +.|+||..     +..-.......|.|.||..|+.+|+++. ++++||+||..+.+
T Consensus      1470 eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss-~~s~CPlCRseitf 1524 (1525)
T COG5219        1470 EECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASS-ARSNCPLCRSEITF 1524 (1525)
T ss_pred             chhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhc-CCCCCCcccccccc
Confidence            57999952     1111122235899999999999999985 45799999988765

>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis

Probab=98.62  E-value=3e-08  Score=49.89  Aligned_cols=53  Identities=19%  Similarity=0.327  Sum_probs=37.1

Q ss_pred             CCCCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            1 MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         1 ~~~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      +|-+..|||+.+...+ |++ +++||+|.+.+|.+|++.+  ...||+++.++...+
T Consensus         1 iP~~f~CpIt~~lM~d-PVi-~~~G~tyer~~I~~~l~~~--~~~~P~t~~~l~~~~   53 (73)
T PF04564_consen    1 IPDEFLCPITGELMRD-PVI-LPSGHTYERSAIERWLEQN--GGTDPFTRQPLSESD   53 (73)
T ss_dssp             SSGGGB-TTTSSB-SS-EEE-ETTSEEEEHHHHHHHHCTT--SSB-TTT-SB-SGGG
T ss_pred             CCcccCCcCcCcHhhC-cee-CCcCCEEcHHHHHHHHHcC--CCCCCCCCCcCCccc
Confidence            3556789999765554 444 5899999999999999983  279999999877643

Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....

>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B

Probab=98.61  E-value=7.2e-09  Score=51.18  Aligned_cols=47  Identities=26%  Similarity=0.554  Sum_probs=22.9

Q ss_pred             CcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      ..|++|.+... .|+.+..|.|+||..||.+-+.     ..||+|+.+.-.++
T Consensus         8 LrCs~C~~~l~-~pv~l~~CeH~fCs~Ci~~~~~-----~~CPvC~~Paw~qD   54 (65)
T PF14835_consen    8 LRCSICFDILK-EPVCLGGCEHIFCSSCIRDCIG-----SECPVCHTPAWIQD   54 (65)
T ss_dssp             TS-SSS-S--S-S-B---SSS--B-TTTGGGGTT-----TB-SSS--B-S-SS
T ss_pred             cCCcHHHHHhc-CCceeccCccHHHHHHhHHhcC-----CCCCCcCChHHHHH
Confidence            46999965544 4666689999999999977443     35999998865544

>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]

Probab=98.59  E-value=2.3e-08  Score=61.84  Aligned_cols=46  Identities=28%  Similarity=0.556  Sum_probs=36.5

Q ss_pred             CcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      ..|-||...+. .+. .++|||.||.-||...|.++   ..||+||.+..+
T Consensus        26 lrC~IC~~~i~-ip~-~TtCgHtFCslCIR~hL~~q---p~CP~Cr~~~~e   71 (391)
T COG5432          26 LRCRICDCRIS-IPC-ETTCGHTFCSLCIRRHLGTQ---PFCPVCREDPCE   71 (391)
T ss_pred             HHhhhhhheee-cce-ecccccchhHHHHHHHhcCC---CCCccccccHHh
Confidence            46899955443 333 46999999999999999997   899999987543

>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]

Probab=98.54  E-value=2.4e-08  Score=62.73  Aligned_cols=47  Identities=28%  Similarity=0.515  Sum_probs=37.9

Q ss_pred             CcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      ..|-||.+++.- +++ ++|+|.||.-||..+|..+   ..||.|+.++...
T Consensus        24 LRC~IC~eyf~i-p~i-tpCsHtfCSlCIR~~L~~~---p~CP~C~~~~~Es   70 (442)
T KOG0287|consen   24 LRCGICFEYFNI-PMI-TPCSHTFCSLCIRKFLSYK---PQCPTCCVTVTES   70 (442)
T ss_pred             HHHhHHHHHhcC-cee-ccccchHHHHHHHHHhccC---CCCCceecccchh
Confidence            369999766554 443 5899999999999999987   7999999877643

>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]

Probab=98.43  E-value=6.7e-08  Score=64.84  Aligned_cols=49  Identities=20%  Similarity=0.539  Sum_probs=38.8

Q ss_pred             CcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      ..||+|.....+.  +++.|+|.||..|+..-+.+..  ..||.|...|..-+
T Consensus       644 LkCs~Cn~R~Kd~--vI~kC~H~FC~~Cvq~r~etRq--RKCP~Cn~aFganD  692 (698)
T KOG0978|consen  644 LKCSVCNTRWKDA--VITKCGHVFCEECVQTRYETRQ--RKCPKCNAAFGAND  692 (698)
T ss_pred             eeCCCccCchhhH--HHHhcchHHHHHHHHHHHHHhc--CCCCCCCCCCCccc
Confidence            4799996443443  3369999999999999998874  78999999987644

>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.32  E-value=3.1e-07  Score=56.76  Aligned_cols=48  Identities=25%  Similarity=0.502  Sum_probs=37.3

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      +..|+||+.. ...| +.+.|+|.||..||........  ..|++||.++..
T Consensus         7 ~~eC~IC~nt-~n~P-v~l~C~HkFCyiCiKGsy~ndk--~~CavCR~pids   54 (324)
T KOG0824|consen    7 KKECLICYNT-GNCP-VNLYCFHKFCYICIKGSYKNDK--KTCAVCRFPIDS   54 (324)
T ss_pred             CCcceeeecc-CCcC-ccccccchhhhhhhcchhhcCC--CCCceecCCCCc
Confidence            5689999643 2234 4579999999999999887763  679999998764

>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.32  E-value=4.1e-07  Score=57.17  Aligned_cols=53  Identities=32%  Similarity=0.649  Sum_probs=38.6

Q ss_pred             CCcccccCcCCCCCC------eEecCCCCcccHHHHHHHHHhCCC----CCCCcccccccccc
Q 035446            4 DGCCPDCKLPGDDCP------LIWGACNHAFHLHCILKWVNSQTP----QAHCPMCRREWQFK   56 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~------~~~~~C~H~fh~~Ci~~w~~~~~~----~~~CP~Cr~~~~~~   56 (59)
                      +..|.||++...+.+      -.+++|.|.||..||..|-...+.    ...||.||....+.
T Consensus       161 ~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v  223 (344)
T KOG1039|consen  161 EKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFV  223 (344)
T ss_pred             cccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccc
Confidence            678999986433322      123689999999999999855431    36899999876653

>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.31  E-value=5.3e-07  Score=57.69  Aligned_cols=49  Identities=27%  Similarity=0.736  Sum_probs=37.8

Q ss_pred             CCCcccccCcC---CCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccc
Q 035446            3 FDGCCPDCKLP---GDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRRE   52 (59)
Q Consensus         3 ~~~~C~IC~~~---~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~   52 (59)
                      ...+||||++.   ..+.-++.+.|||.|-.+||++|+. +.....||.|...
T Consensus         3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~-k~~~~~cp~c~~k   54 (463)
T KOG1645|consen    3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG-KKTKMQCPLCSGK   54 (463)
T ss_pred             ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHh-hhhhhhCcccCCh
Confidence            44689999853   2344566789999999999999996 4444689999764

>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C

Probab=98.17  E-value=1.3e-06  Score=42.28  Aligned_cols=44  Identities=27%  Similarity=0.605  Sum_probs=28.6

Q ss_pred             CCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcc
Q 035446            3 FDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPM   48 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~   48 (59)
                      .+..|||-+.++.+ |+....|+|+|-++.|.+|++++ ....||+
T Consensus        10 ~~~~CPiT~~~~~~-PV~s~~C~H~fek~aI~~~i~~~-~~~~CPv   53 (57)
T PF11789_consen   10 ISLKCPITLQPFED-PVKSKKCGHTFEKEAILQYIQRN-GSKRCPV   53 (57)
T ss_dssp             --SB-TTTSSB-SS-EEEESSS--EEEHHHHHHHCTTT-S-EE-SC
T ss_pred             eccCCCCcCChhhC-CcCcCCCCCeecHHHHHHHHHhc-CCCCCCC
Confidence            35679999776554 66667999999999999999543 2357998

>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.14  E-value=3.3e-06  Score=50.89  Aligned_cols=53  Identities=23%  Similarity=0.485  Sum_probs=41.2

Q ss_pred             CCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCC-----CCCCccccccccc
Q 035446            3 FDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTP-----QAHCPMCRREWQF   55 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~-----~~~CP~Cr~~~~~   55 (59)
                      |+..|..|..+..+...+.+.|.|.||++|+++|...-..     ...||-|..++..
T Consensus        49 Y~pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFP  106 (299)
T KOG3970|consen   49 YNPNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFP  106 (299)
T ss_pred             CCCCCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCC
Confidence            5678999976666666667899999999999999875321     2479999987654

>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.12  E-value=2e-07  Score=58.64  Aligned_cols=50  Identities=30%  Similarity=0.586  Sum_probs=38.5

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      +..|+||+...... +....|.|.||.+||...++..  +..||.||+.+..+
T Consensus        43 ~v~c~icl~llk~t-mttkeClhrfc~~ci~~a~r~g--n~ecptcRk~l~Sk   92 (381)
T KOG0311|consen   43 QVICPICLSLLKKT-MTTKECLHRFCFDCIWKALRSG--NNECPTCRKKLVSK   92 (381)
T ss_pred             hhccHHHHHHHHhh-cccHHHHHHHHHHHHHHHHHhc--CCCCchHHhhcccc
Confidence            56799998644432 3336999999999999998876  37999999876543

>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]

Probab=98.06  E-value=2.3e-06  Score=54.50  Aligned_cols=49  Identities=31%  Similarity=0.666  Sum_probs=38.2

Q ss_pred             CCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            3 FDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      .+..|++|.....+ ++..+.|||.||..|+..|+..+   ..||.|+.....
T Consensus        20 ~~l~C~~C~~vl~~-p~~~~~cgh~fC~~C~~~~~~~~---~~cp~~~~~~~~   68 (391)
T KOG0297|consen   20 ENLLCPICMSVLRD-PVQTTTCGHRFCAGCLLESLSNH---QKCPVCRQELTQ   68 (391)
T ss_pred             ccccCccccccccC-CCCCCCCCCcccccccchhhccC---cCCcccccccch
Confidence            45789999754444 33335999999999999999985   789999886654

>KOG0825 consensus PHD Zn-finger protein [General function prediction only]

Probab=98.06  E-value=6.5e-07  Score=61.16  Aligned_cols=48  Identities=25%  Similarity=0.509  Sum_probs=35.4

Q ss_pred             CcccccCcC-CCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            5 GCCPDCKLP-GDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         5 ~~C~IC~~~-~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      ..|++|+.. .+........|+|.||..||..|.+..   .+||+||..|..
T Consensus       124 ~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~a---qTCPiDR~EF~~  172 (1134)
T KOG0825|consen  124 NQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCA---QTCPVDRGEFGE  172 (1134)
T ss_pred             hhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhc---ccCchhhhhhhe
Confidence            457788632 222222334899999999999999987   799999987653

>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]

Probab=98.03  E-value=1.5e-06  Score=54.03  Aligned_cols=54  Identities=24%  Similarity=0.624  Sum_probs=38.9

Q ss_pred             CCcccccCcCCCCC-CeEecCCCCcccHHHHHHHHHhC--------------------CCCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGDDC-PLIWGACNHAFHLHCILKWVNSQ--------------------TPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~~~-~~~~~~C~H~fh~~Ci~~w~~~~--------------------~~~~~CP~Cr~~~~~~~   57 (59)
                      ...|.||+.-+.+. .+..+.|.|.||..|+.+++..-                    .....||+||..+..+.
T Consensus       115 ~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~  189 (368)
T KOG4445|consen  115 NGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEE  189 (368)
T ss_pred             CCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccccc
Confidence            46899998644433 36678999999999998876420                    01247999999887643

>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.02  E-value=7.2e-06  Score=50.34  Aligned_cols=50  Identities=28%  Similarity=0.627  Sum_probs=37.4

Q ss_pred             CCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            3 FDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      .+.+|++|.++ ...|-+..+|+|+||.-||..-..... ..+||.|..+..
T Consensus       238 ~~~~C~~Cg~~-PtiP~~~~~C~HiyCY~Ci~ts~~~~a-sf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  238 SDTECPVCGEP-PTIPHVIGKCGHIYCYYCIATSRLWDA-SFTCPLCGENVE  287 (298)
T ss_pred             CCceeeccCCC-CCCCeeeccccceeehhhhhhhhcchh-hcccCccCCCCc
Confidence            46789999543 334556678999999999998766431 258999998766

>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.00  E-value=1.3e-06  Score=42.00  Aligned_cols=48  Identities=23%  Similarity=0.515  Sum_probs=34.2

Q ss_pred             CCCcccccCcCCCCCCeEecCCCCc-ccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            3 FDGCCPDCKLPGDDCPLIWGACNHA-FHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~C~H~-fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      .++.|.||.+..-+..  +-.|||. .|.+|-.+-++..  ...||+||+++.
T Consensus         6 ~~dECTICye~pvdsV--lYtCGHMCmCy~Cg~rl~~~~--~g~CPiCRapi~   54 (62)
T KOG4172|consen    6 WSDECTICYEHPVDSV--LYTCGHMCMCYACGLRLKKAL--HGCCPICRAPIK   54 (62)
T ss_pred             cccceeeeccCcchHH--HHHcchHHhHHHHHHHHHHcc--CCcCcchhhHHH
Confidence            4688999976333322  3489995 7899977766643  278999999864

>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]

Probab=97.99  E-value=2.9e-06  Score=54.64  Aligned_cols=48  Identities=27%  Similarity=0.670  Sum_probs=36.9

Q ss_pred             CcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      +.|-||-+...+..+  -+|||..|..|+..|.....+ ..||.||-++.-
T Consensus       370 eLCKICaendKdvkI--EPCGHLlCt~CLa~WQ~sd~g-q~CPFCRcEIKG  417 (563)
T KOG1785|consen  370 ELCKICAENDKDVKI--EPCGHLLCTSCLAAWQDSDEG-QTCPFCRCEIKG  417 (563)
T ss_pred             HHHHHhhccCCCccc--ccccchHHHHHHHhhcccCCC-CCCCceeeEecc
Confidence            358899665555444  499999999999999876533 689999987653

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=97.88  E-value=5.6e-06  Score=53.15  Aligned_cols=47  Identities=28%  Similarity=0.610  Sum_probs=34.8

Q ss_pred             CCcccccCcC--CCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccc
Q 035446            4 DGCCPDCKLP--GDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRR   51 (59)
Q Consensus         4 ~~~C~IC~~~--~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~   51 (59)
                      +..|..|-+.  ..+.....++|.|+||..|+...+.++. ..+||.||+
T Consensus       365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~-~rsCP~Crk  413 (518)
T KOG1941|consen  365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNG-TRSCPNCRK  413 (518)
T ss_pred             hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCC-CCCCccHHH
Confidence            4568888642  2233445579999999999999997754 368999994

>PHA02862 5L protein; Provisional

Probab=97.88  E-value=1.6e-05  Score=44.87  Aligned_cols=50  Identities=22%  Similarity=0.642  Sum_probs=36.6

Q ss_pred             CCcccccCcCCCCCCeEecCCC-----CcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGDDCPLIWGACN-----HAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~-----H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      ++.|=||.+..++. .  -+|.     -.-|.+|+.+|+... ....|++|+.++..+.
T Consensus         2 ~diCWIC~~~~~e~-~--~PC~C~GS~K~VHq~CL~~WIn~S-~k~~CeLCkteY~Ik~   56 (156)
T PHA02862          2 SDICWICNDVCDER-N--NFCGCNEEYKVVHIKCMQLWINYS-KKKECNLCKTKYNIKK   56 (156)
T ss_pred             CCEEEEecCcCCCC-c--ccccccCcchhHHHHHHHHHHhcC-CCcCccCCCCeEEEEE
Confidence            56799998654432 2  3554     478999999999764 4578999999887643

>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1

Probab=97.87  E-value=5.3e-06  Score=43.60  Aligned_cols=32  Identities=25%  Similarity=0.508  Sum_probs=27.0

Q ss_pred             CCCcccccCcCCCCCCeEecCCCCcccHHHHH
Q 035446            3 FDGCCPDCKLPGDDCPLIWGACNHAFHLHCIL   34 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~   34 (59)
                      .+..|++|..+......+..+|||.||..|+.
T Consensus        77 ~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   77 ESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence            45789999877776778888999999999975

Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].

>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A

Probab=97.76  E-value=1.2e-05  Score=37.46  Aligned_cols=42  Identities=19%  Similarity=0.642  Sum_probs=25.7

Q ss_pred             ccccCcCCCCCCeEecCCCC-----cccHHHHHHHHHhCCCCCCCccc
Q 035446            7 CPDCKLPGDDCPLIWGACNH-----AFHLHCILKWVNSQTPQAHCPMC   49 (59)
Q Consensus         7 C~IC~~~~~~~~~~~~~C~H-----~fh~~Ci~~w~~~~~~~~~CP~C   49 (59)
                      |-||++..++......+|+-     ..|.+||.+|+..+. ...|++|
T Consensus         1 CrIC~~~~~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~~~-~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDEPLISPCRCKGSMKYVHRSCLERWIRESG-NRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS-EE-SSS-SSCCGSEECCHHHHHHHHHT--SB-TTT
T ss_pred             CeEeCCcCCCCCceecccccCCCcchhHHHHHHHHHHhcC-CCcCCCC
Confidence            56888544433333357763     679999999999743 3578887

>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]

Probab=97.72  E-value=7.2e-06  Score=51.22  Aligned_cols=46  Identities=26%  Similarity=0.483  Sum_probs=35.5

Q ss_pred             CcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      .+|.+|...+-+.. .+.-|-|.||+.||.+.+...   ..||.|...+.
T Consensus        16 itC~LC~GYliDAT-TI~eCLHTFCkSCivk~l~~~---~~CP~C~i~ih   61 (331)
T KOG2660|consen   16 ITCRLCGGYLIDAT-TITECLHTFCKSCIVKYLEES---KYCPTCDIVIH   61 (331)
T ss_pred             eehhhccceeecch-hHHHHHHHHHHHHHHHHHHHh---ccCCccceecc
Confidence            57888965443332 235999999999999999996   79999987554

>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.70  E-value=3.1e-05  Score=48.85  Aligned_cols=45  Identities=22%  Similarity=0.495  Sum_probs=33.6

Q ss_pred             CcccccCcCCCCCCeEecCCCCc-ccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHA-FHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~-fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      ..|-||+....+  +++++|.|. .|..|.+...-..   +.||+||+++.
T Consensus       291 keCVIClse~rd--t~vLPCRHLCLCs~Ca~~Lr~q~---n~CPICRqpi~  336 (349)
T KOG4265|consen  291 KECVICLSESRD--TVVLPCRHLCLCSGCAKSLRYQT---NNCPICRQPIE  336 (349)
T ss_pred             CeeEEEecCCcc--eEEecchhhehhHhHHHHHHHhh---cCCCccccchH
Confidence            469999865554  344799995 8999988765333   68999999875

>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]

Probab=97.69  E-value=4e-05  Score=55.93  Aligned_cols=52  Identities=27%  Similarity=0.574  Sum_probs=39.6

Q ss_pred             CCCcccccCc-CCCCCCeEecCCCCcccHHHHHHHHHhCCC-------CCCCcccccccc
Q 035446            3 FDGCCPDCKL-PGDDCPLIWGACNHAFHLHCILKWVNSQTP-------QAHCPMCRREWQ   54 (59)
Q Consensus         3 ~~~~C~IC~~-~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~-------~~~CP~Cr~~~~   54 (59)
                      .|+.|.||.. .....|...+.|+|.||.+|...-+++...       --.||+|..+++
T Consensus      3485 ~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3485 ADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred             cCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence            3677999973 445556677899999999999988877542       137999998765

>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B

Probab=97.66  E-value=4.7e-05  Score=35.70  Aligned_cols=46  Identities=24%  Similarity=0.572  Sum_probs=22.1

Q ss_pred             ccccCcCCC--CCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            7 CPDCKLPGD--DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         7 C~IC~~~~~--~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      ||+|.++.+  +.....-.|++..++.|..+-++..  ...||-||++++
T Consensus         1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~--~g~CPgCr~~Y~   48 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENE--GGRCPGCREPYK   48 (48)
T ss_dssp             -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS---SB-TTT--B--
T ss_pred             CCCcccccccCCCccccCcCCCcHHHHHHHHHHhcc--CCCCCCCCCCCC
Confidence            688875443  3333434788999999988877643  278999999863

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=97.63  E-value=2.3e-05  Score=52.11  Aligned_cols=53  Identities=28%  Similarity=0.578  Sum_probs=38.7

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCC--CCCCccccccccccCC
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTP--QAHCPMCRREWQFKGS   58 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~--~~~CP~Cr~~~~~~~~   58 (59)
                      +..|-+|.++.++...  ..|.|.||+.||.++...-..  +.+||.|...+....+
T Consensus       536 ~~~C~lc~d~aed~i~--s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDls  590 (791)
T KOG1002|consen  536 EVECGLCHDPAEDYIE--SSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLS  590 (791)
T ss_pred             ceeecccCChhhhhHh--hhhhHHHHHHHHHHHHHhhhcccCCCCcccccccccccc
Confidence            3568899766555333  599999999999988765322  3689999987766543

>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.59  E-value=4.3e-05  Score=49.02  Aligned_cols=46  Identities=28%  Similarity=0.713  Sum_probs=35.0

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      +-.|.||..-... ++. ++|||.|+..||.+-+...   ..||.||.++.
T Consensus        84 ef~c~vc~~~l~~-pv~-tpcghs~c~~Cl~r~ld~~---~~cp~Cr~~l~  129 (398)
T KOG4159|consen   84 EFECCVCSRALYP-PVV-TPCGHSFCLECLDRSLDQE---TECPLCRDELV  129 (398)
T ss_pred             hhhhhhhHhhcCC-Ccc-ccccccccHHHHHHHhccC---CCCcccccccc
Confidence            4578899543333 444 5999999999999976654   78999998875

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=97.57  E-value=0.00011  Score=41.99  Aligned_cols=49  Identities=31%  Similarity=0.744  Sum_probs=35.5

Q ss_pred             CCcccccCcCCCCCCeEecCCC--C---cccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACN--H---AFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~--H---~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      +..|=||.+..+. ..  .+|.  .   .-|.+|+++|+..+. ...|++|+.++...
T Consensus         8 ~~~CRIC~~~~~~-~~--~PC~CkGs~k~VH~sCL~rWi~~s~-~~~CeiC~~~Y~i~   61 (162)
T PHA02825          8 DKCCWICKDEYDV-VT--NYCNCKNENKIVHKECLEEWINTSK-NKSCKICNGPYNIK   61 (162)
T ss_pred             CCeeEecCCCCCC-cc--CCcccCCCchHHHHHHHHHHHhcCC-CCcccccCCeEEEE
Confidence            5679999755332 22  2554  4   569999999999753 46899999988765

>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]

Probab=97.55  E-value=5e-05  Score=45.71  Aligned_cols=47  Identities=23%  Similarity=0.576  Sum_probs=34.2

Q ss_pred             cccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            6 CCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         6 ~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      .|..|.......+..++.|+|+||..|...-.     ...||+|++++....
T Consensus         5 hCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~-----~~~C~lCkk~ir~i~   51 (233)
T KOG4739|consen    5 HCNKCFRFPSQDPFFLTACRHVFCEPCLKASS-----PDVCPLCKKSIRIIQ   51 (233)
T ss_pred             EeccccccCCCCceeeeechhhhhhhhcccCC-----ccccccccceeeeee
Confidence            47777644446677889999999999975421     248999999866543

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=97.35  E-value=0.00011  Score=35.35  Aligned_cols=34  Identities=21%  Similarity=0.457  Sum_probs=27.1

Q ss_pred             ecCCCCcccHHHHHHHHHhCCCCCCCccccccccccCCC
Q 035446           21 WGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKGSE   59 (59)
Q Consensus        21 ~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~~~   59 (59)
                      +++|+|..+..|...+--     +.||.|.+++...+.+
T Consensus        22 ~~pCgH~I~~~~f~~~rY-----ngCPfC~~~~~~~~~~   55 (55)
T PF14447_consen   22 VLPCGHLICDNCFPGERY-----NGCPFCGTPFEFDDPF   55 (55)
T ss_pred             cccccceeeccccChhhc-----cCCCCCCCcccCCCCC
Confidence            369999999999877532     4699999999887653

>PHA03096 p28-like protein; Provisional

Probab=97.32  E-value=0.00014  Score=44.93  Aligned_cols=47  Identities=23%  Similarity=0.374  Sum_probs=31.1

Q ss_pred             CcccccCcCCCC------CCeEecCCCCcccHHHHHHHHHhCCCCCCCccccc
Q 035446            5 GCCPDCKLPGDD------CPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRR   51 (59)
Q Consensus         5 ~~C~IC~~~~~~------~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~   51 (59)
                      ..|.||++....      .--.+..|.|.|+..|+..|........+||.||.
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~  231 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR  231 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence            368999853211      11234699999999999999887544345555544

>KOG1940 consensus Zn-finger protein [General function prediction only]

Probab=97.26  E-value=0.00023  Score=43.87  Aligned_cols=46  Identities=24%  Similarity=0.415  Sum_probs=34.9

Q ss_pred             CCCcccccCcC--CCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccc
Q 035446            3 FDGCCPDCKLP--GDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRR   51 (59)
Q Consensus         3 ~~~~C~IC~~~--~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~   51 (59)
                      .+..||||.+.  .....+..++|||..|..|+......+   .+||+|.+
T Consensus       157 ~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~---y~CP~C~~  204 (276)
T KOG1940|consen  157 SEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEG---YTCPICSK  204 (276)
T ss_pred             ccCCCchhHHHhccccccCCccCcccchHHHHHHHHhccC---CCCCcccc
Confidence            34569999752  222333447999999999999988776   79999987

>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.24  E-value=0.00025  Score=45.37  Aligned_cols=47  Identities=21%  Similarity=0.505  Sum_probs=36.3

Q ss_pred             CCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            3 FDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      .|..||||.-  .....+..+|+|.-|..||.+-+.+.   ..|=.|+..+.
T Consensus       421 Ed~lCpICyA--~pi~Avf~PC~H~SC~~CI~qHlmN~---k~CFfCktTv~  467 (489)
T KOG4692|consen  421 EDNLCPICYA--GPINAVFAPCSHRSCYGCITQHLMNC---KRCFFCKTTVI  467 (489)
T ss_pred             ccccCcceec--ccchhhccCCCCchHHHHHHHHHhcC---CeeeEecceee
Confidence            4678999942  22223346999999999999999987   68999988665

>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]

Probab=97.20  E-value=0.00025  Score=49.09  Aligned_cols=47  Identities=32%  Similarity=0.624  Sum_probs=33.2

Q ss_pred             CcccccCcCCC--CCCeEecCCCCcccHHHHHHHHHhCCC----CCCCccccc
Q 035446            5 GCCPDCKLPGD--DCPLIWGACNHAFHLHCILKWVNSQTP----QAHCPMCRR   51 (59)
Q Consensus         5 ~~C~IC~~~~~--~~~~~~~~C~H~fh~~Ci~~w~~~~~~----~~~CP~Cr~   51 (59)
                      ..|.||.+...  .....-..|.|+||..||.+|.+....    .-.||.|..
T Consensus       192 yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs  244 (950)
T KOG1952|consen  192 YECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS  244 (950)
T ss_pred             eEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence            46999986433  333344578899999999999876321    136999984

>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]

Probab=97.07  E-value=0.00022  Score=42.45  Aligned_cols=43  Identities=23%  Similarity=0.624  Sum_probs=33.0

Q ss_pred             cccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccc
Q 035446            6 CCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREW   53 (59)
Q Consensus         6 ~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~   53 (59)
                      .|.||...+.. |++ +.|||.||..|...-++..   ..|-+|.+..
T Consensus       198 ~C~iCKkdy~s-pvv-t~CGH~FC~~Cai~~y~kg---~~C~~Cgk~t  240 (259)
T COG5152         198 LCGICKKDYES-PVV-TECGHSFCSLCAIRKYQKG---DECGVCGKAT  240 (259)
T ss_pred             eehhchhhccc-hhh-hhcchhHHHHHHHHHhccC---Ccceecchhh
Confidence            68999755444 444 5999999999988877765   7899997653

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=97.06  E-value=0.00033  Score=48.50  Aligned_cols=41  Identities=32%  Similarity=0.829  Sum_probs=30.8

Q ss_pred             CcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccc
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRRE   52 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~   52 (59)
                      ..|..|... -+.|.+--.|||+||.+|+.    .+  ...||-|+..
T Consensus       841 skCs~C~~~-LdlP~VhF~CgHsyHqhC~e----~~--~~~CP~C~~e  881 (933)
T KOG2114|consen  841 SKCSACEGT-LDLPFVHFLCGHSYHQHCLE----DK--EDKCPKCLPE  881 (933)
T ss_pred             eeecccCCc-cccceeeeecccHHHHHhhc----cC--cccCCccchh
Confidence            469999433 44577778999999999998    22  2689999863

>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.97  E-value=0.00027  Score=43.93  Aligned_cols=44  Identities=25%  Similarity=0.484  Sum_probs=34.5

Q ss_pred             cccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            6 CCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         6 ~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      .|-||..++.. +|+ +.|+|.||..|...-++..   ..|++|.+...
T Consensus       243 ~c~icr~~f~~-pVv-t~c~h~fc~~ca~~~~qk~---~~c~vC~~~t~  286 (313)
T KOG1813|consen  243 KCFICRKYFYR-PVV-TKCGHYFCEVCALKPYQKG---EKCYVCSQQTH  286 (313)
T ss_pred             ccccccccccc-chh-hcCCceeehhhhccccccC---Ccceecccccc
Confidence            59999766555 343 5999999999998887775   68999987643

>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.94  E-value=0.00062  Score=44.02  Aligned_cols=46  Identities=20%  Similarity=0.328  Sum_probs=32.9

Q ss_pred             CcccccCcCCC-CCCeEecCCCCcccHHHHHHHHHhCCC-----CCCCcccc
Q 035446            5 GCCPDCKLPGD-DCPLIWGACNHAFHLHCILKWVNSQTP-----QAHCPMCR   50 (59)
Q Consensus         5 ~~C~IC~~~~~-~~~~~~~~C~H~fh~~Ci~~w~~~~~~-----~~~CP~Cr   50 (59)
                      -.|.||++... ..-+..++|+|+||+.|+..++.....     ...||-+.
T Consensus       185 f~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~  236 (445)
T KOG1814|consen  185 FDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPK  236 (445)
T ss_pred             ccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCC
Confidence            36999985433 345666899999999999999875421     23677654

>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.86  E-value=0.00072  Score=42.88  Aligned_cols=46  Identities=22%  Similarity=0.532  Sum_probs=32.2

Q ss_pred             CCCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            2 AFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         2 ~~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      +..+.|.||++...+  .+..+|||.-+  |..-....    ..||+||+.+..
T Consensus       303 ~~p~lcVVcl~e~~~--~~fvpcGh~cc--ct~cs~~l----~~CPvCR~rI~~  348 (355)
T KOG1571|consen  303 PQPDLCVVCLDEPKS--AVFVPCGHVCC--CTLCSKHL----PQCPVCRQRIRL  348 (355)
T ss_pred             CCCCceEEecCCccc--eeeecCCcEEE--chHHHhhC----CCCchhHHHHHH
Confidence            346789999876555  33459999977  66554443    469999987643

>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.80  E-value=0.00062  Score=47.27  Aligned_cols=35  Identities=29%  Similarity=0.605  Sum_probs=28.5

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHH
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVN   38 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~   38 (59)
                      ++.|.+|..+....+..+-+|||.||++||.+-..
T Consensus       817 ~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~~v~  851 (911)
T KOG2034|consen  817 QDSCDHCGRPLLIKPFYVFPCGHCFHRDCLIRHVL  851 (911)
T ss_pred             ccchHHhcchhhcCcceeeeccchHHHHHHHHHHH
Confidence            57899998766666767789999999999988643

>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]

Probab=96.79  E-value=0.00072  Score=46.77  Aligned_cols=40  Identities=28%  Similarity=0.742  Sum_probs=30.0

Q ss_pred             cccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcc
Q 035446            6 CCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPM   48 (59)
Q Consensus         6 ~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~   48 (59)
                      .|+||-........+...|+|+.|.+|...|++++   ..||.
T Consensus      1030 ~C~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~~g---d~Cps 1069 (1081)
T KOG0309|consen 1030 QCAICHLAVRGSSNFCGTCGHVGHTSCMMEWFRTG---DVCPS 1069 (1081)
T ss_pred             eeeeEeeEeeccchhhccccccccHHHHHHHHhcC---CcCCC
Confidence            46666544444455567999999999999999997   67773

>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length

Probab=96.78  E-value=0.00056  Score=38.21  Aligned_cols=36  Identities=17%  Similarity=0.292  Sum_probs=25.0

Q ss_pred             CCcccccCcCCCC-CCeEecCCC------CcccHHHHHHHHHh
Q 035446            4 DGCCPDCKLPGDD-CPLIWGACN------HAFHLHCILKWVNS   39 (59)
Q Consensus         4 ~~~C~IC~~~~~~-~~~~~~~C~------H~fh~~Ci~~w~~~   39 (59)
                      ...|.||++.... ..++..++|      |.||.+|+.+|-+.
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~   68 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRRE   68 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHhh
Confidence            4579999864333 333334665      78999999999543

The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.

>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.77  E-value=0.0012  Score=38.79  Aligned_cols=37  Identities=27%  Similarity=0.667  Sum_probs=29.0

Q ss_pred             cCCCCcccHHHHHHHHHhCCC--------CCCCccccccccccCC
Q 035446           22 GACNHAFHLHCILKWVNSQTP--------QAHCPMCRREWQFKGS   58 (59)
Q Consensus        22 ~~C~H~fh~~Ci~~w~~~~~~--------~~~CP~Cr~~~~~~~~   58 (59)
                      ..||..||.-|+..|++.--.        -..||.|..++..+-+
T Consensus       188 ~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKmS  232 (234)
T KOG3268|consen  188 IQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKMS  232 (234)
T ss_pred             cccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeecc
Confidence            489999999999999974211        1369999999887654

>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.72  E-value=0.0016  Score=39.82  Aligned_cols=49  Identities=22%  Similarity=0.425  Sum_probs=35.6

Q ss_pred             CcccccCcCCC----CCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            5 GCCPDCKLPGD----DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         5 ~~C~IC~~~~~----~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      ..|-||-++++    +.....+.|||.|+..|+..-+....  ..||.||.+...
T Consensus         4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~--i~cpfcR~~~~~   56 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSR--ILCPFCRETTEI   56 (296)
T ss_pred             CceeecCccccccCcccCCcccccCceehHhHHHHHhcCce--eeccCCCCcccC
Confidence            46889964332    22233468999999999999887763  578999998644

>PF04641 Rtf2: Rtf2 RING-finger

Probab=96.68  E-value=0.0023  Score=38.88  Aligned_cols=49  Identities=14%  Similarity=0.317  Sum_probs=36.0

Q ss_pred             CcccccCcCCC--CCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            5 GCCPDCKLPGD--DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         5 ~~C~IC~~~~~--~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      -.|||....+.  ...+.+.+|||+|-..+|.+.- ..   ..||+|..+|...+
T Consensus       114 ~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~---~~Cp~c~~~f~~~D  164 (260)
T PF04641_consen  114 FICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KS---KKCPVCGKPFTEED  164 (260)
T ss_pred             eECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-cc---ccccccCCccccCC
Confidence            35888875433  2345667999999999999973 22   57999999987543

>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]

Probab=96.57  E-value=0.0025  Score=40.27  Aligned_cols=48  Identities=23%  Similarity=0.508  Sum_probs=35.7

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      ...||+|+.... .+.++..-|-+||..|+-+++.+.   ..||+=..+...
T Consensus       300 ~~~CpvClk~r~-Nptvl~vSGyVfCY~Ci~~Yv~~~---~~CPVT~~p~~v  347 (357)
T KOG0826|consen  300 REVCPVCLKKRQ-NPTVLEVSGYVFCYPCIFSYVVNY---GHCPVTGYPASV  347 (357)
T ss_pred             cccChhHHhccC-CCceEEecceEEeHHHHHHHHHhc---CCCCccCCcchH
Confidence            467999964333 344445679999999999999976   789987665543

>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO)

Probab=96.48  E-value=0.0035  Score=28.53  Aligned_cols=26  Identities=31%  Similarity=0.847  Sum_probs=16.3

Q ss_pred             CCCCcccHHHHHHHHHhCCCCCCCccc
Q 035446           23 ACNHAFHLHCILKWVNSQTPQAHCPMC   49 (59)
Q Consensus        23 ~C~H~fh~~Ci~~w~~~~~~~~~CP~C   49 (59)
                      .|+=.+|..|+..+++..+. ..||.|
T Consensus        18 ~C~~r~H~~C~~~y~r~~~~-~~CP~C   43 (43)
T PF08746_consen   18 DCNVRLHDDCFKKYFRHRSN-PKCPNC   43 (43)
T ss_dssp             -S--EE-HHHHHHHTTT-SS--B-TTT
T ss_pred             ccCchHHHHHHHHHHhcCCC-CCCcCC
Confidence            58889999999999988642 379987

; PDB: 3NW0_A 2CT0_A.

>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.46  E-value=0.0034  Score=40.39  Aligned_cols=51  Identities=22%  Similarity=0.427  Sum_probs=38.5

Q ss_pred             cccccCc-CCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            6 CCPDCKL-PGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         6 ~C~IC~~-~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      .|||=.+ -.++.|...+.|||+..++-|.+..+++.....||.|-......
T Consensus       336 ~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~~~~  387 (394)
T KOG2817|consen  336 ICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQLAS  387 (394)
T ss_pred             ecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCcccCHH
Confidence            5788764 34566667789999999999999888765446799997655443

>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans

Probab=96.35  E-value=0.0049  Score=39.33  Aligned_cols=30  Identities=30%  Similarity=0.812  Sum_probs=23.3

Q ss_pred             CcccHHHHHHHHHhCCC----------CCCCccccccccc
Q 035446           26 HAFHLHCILKWVNSQTP----------QAHCPMCRREWQF   55 (59)
Q Consensus        26 H~fh~~Ci~~w~~~~~~----------~~~CP~Cr~~~~~   55 (59)
                      -..|.+|+.+|+...+.          +..||.||+++-.
T Consensus       313 PmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCi  352 (358)
T PF10272_consen  313 PMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCI  352 (358)
T ss_pred             chHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCccccee
Confidence            45689999999987652          2479999998754

They are purported to be transmembrane protein-precursors but their function is unknown.

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.33  E-value=0.0056  Score=37.64  Aligned_cols=50  Identities=12%  Similarity=0.179  Sum_probs=38.0

Q ss_pred             CcccccCcCCC--CCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            5 GCCPDCKLPGD--DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         5 ~~C~IC~~~~~--~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      -.||++.+...  ..-.++.++||+|..+|.++.+...   ..+|++-+++..++
T Consensus       222 yiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D---~v~pv~d~plkdrd  273 (303)
T KOG3039|consen  222 YICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKD---MVDPVTDKPLKDRD  273 (303)
T ss_pred             eecccchhhhcCccceEEeccCCcEeeHHHHHHhcccc---ccccCCCCcCcccc
Confidence            36999975332  2223456999999999999998876   78999998877554

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=96.27  E-value=0.0014  Score=44.52  Aligned_cols=47  Identities=28%  Similarity=0.600  Sum_probs=35.5

Q ss_pred             CcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      ..|+||++ .+  ..+.+.|+|.|+.+|+...++.... ..||+||..+..
T Consensus       455 ~~c~ic~~-~~--~~~it~c~h~~c~~c~~~~i~~~~~-~~~~~cr~~l~~  501 (674)
T KOG1001|consen  455 HWCHICCD-LD--SFFITRCGHDFCVECLKKSIQQSEN-APCPLCRNVLKE  501 (674)
T ss_pred             cccccccc-cc--cceeecccchHHHHHHHhccccccC-CCCcHHHHHHHH
Confidence            57999977 22  2334699999999999998887542 369999986543

>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.24  E-value=0.0005  Score=42.91  Aligned_cols=42  Identities=26%  Similarity=0.651  Sum_probs=29.7

Q ss_pred             CCcccccCcCCCCCCeEecCCCC-cccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNH-AFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H-~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      +..|.||++-..+.  +.+.||| +-|.+|-.+       ...||+||+.+.
T Consensus       300 ~~LC~ICmDaP~DC--vfLeCGHmVtCt~CGkr-------m~eCPICRqyi~  342 (350)
T KOG4275|consen  300 RRLCAICMDAPRDC--VFLECGHMVTCTKCGKR-------MNECPICRQYIV  342 (350)
T ss_pred             HHHHHHHhcCCcce--EEeecCcEEeehhhccc-------cccCchHHHHHH
Confidence            45699997644444  4469999 568888544       257999998654

>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=96.20  E-value=0.0035  Score=39.58  Aligned_cols=44  Identities=30%  Similarity=0.551  Sum_probs=32.7

Q ss_pred             CcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccc
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRR   51 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~   51 (59)
                      ..|+.|... -..++...-|+|.|+.+||...|....  ..||.|.+
T Consensus       275 LkCplc~~L-lrnp~kT~cC~~~fc~eci~~al~dsD--f~CpnC~r  318 (427)
T COG5222         275 LKCPLCHCL-LRNPMKTPCCGHTFCDECIGTALLDSD--FKCPNCSR  318 (427)
T ss_pred             ccCcchhhh-hhCcccCccccchHHHHHHhhhhhhcc--ccCCCccc
Confidence            568888532 223444458999999999999887653  78999976

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=95.92  E-value=0.0082  Score=38.51  Aligned_cols=52  Identities=25%  Similarity=0.557  Sum_probs=35.2

Q ss_pred             CCcccccCcCCC--CCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGD--DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~--~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      |+-||.|+++.+  +.-...-+||-..|.-|...--+.-  +..||-||+.+..++
T Consensus        14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~l--ngrcpacrr~y~den   67 (480)
T COG5175          14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNL--NGRCPACRRKYDDEN   67 (480)
T ss_pred             cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhc--cCCChHhhhhccccc
Confidence            456999997543  2233334899888888866544432  368999999876554

>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0

Probab=95.80  E-value=0.014  Score=32.76  Aligned_cols=52  Identities=15%  Similarity=0.370  Sum_probs=36.5

Q ss_pred             cccccCcCCCCCCeE--ecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            6 CCPDCKLPGDDCPLI--WGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         6 ~C~IC~~~~~~~~~~--~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      .|.||.+...+....  --=||-..|..|-...|+.......||+|+..+....
T Consensus        82 eCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~  135 (140)
T PF05290_consen   82 ECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSS  135 (140)
T ss_pred             eccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence            699997532221111  0258999999998888877666689999999887654

>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=95.72  E-value=0.0034  Score=29.37  Aligned_cols=30  Identities=23%  Similarity=0.731  Sum_probs=21.6

Q ss_pred             CCC-CcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446           23 ACN-HAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus        23 ~C~-H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      .|+ |..|..|+...+...   ..||+|..++..
T Consensus        17 ~C~dHYLCl~CLt~ml~~s---~~C~iC~~~LPt   47 (50)
T PF03854_consen   17 KCSDHYLCLNCLTLMLSRS---DRCPICGKPLPT   47 (50)
T ss_dssp             E-SS-EEEHHHHHHT-SSS---SEETTTTEE---
T ss_pred             eecchhHHHHHHHHHhccc---cCCCcccCcCcc
Confidence            565 999999999999886   799999988754

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. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.

>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]

Probab=95.72  E-value=0.013  Score=36.51  Aligned_cols=47  Identities=28%  Similarity=0.634  Sum_probs=34.1

Q ss_pred             cccccCcC--CC-CCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            6 CCPDCKLP--GD-DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         6 ~C~IC~~~--~~-~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      .||+|...  .. +....+-+|+|..|.+|++.-+..+.  ..||.|...+.
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~--~~CpeC~~iLR   51 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGP--AQCPECMVILR   51 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCC--CCCCcccchhh
Confidence            58999732  11 22233349999999999999988874  68999977543

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=95.71  E-value=0.018  Score=27.57  Aligned_cols=43  Identities=23%  Similarity=0.526  Sum_probs=30.4

Q ss_pred             CcccccCcCC--CCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcc--cccccc
Q 035446            5 GCCPDCKLPG--DDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPM--CRREWQ   54 (59)
Q Consensus         5 ~~C~IC~~~~--~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~--Cr~~~~   54 (59)
                      ..|++|.+.+  ++..++-..|+-.+|++|-+.   .    ..|-.  |..++.
T Consensus         6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~---~----g~C~~~~c~~~~~   52 (54)
T PF14446_consen    6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK---A----GGCINYSCGTGFE   52 (54)
T ss_pred             ccChhhCCcccCCCCEEECCCCCCcccHHHHhh---C----CceEeccCCCCcc
Confidence            5699998765  566677789999999999543   2    35655  655543

>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function

Probab=95.70  E-value=0.029  Score=32.31  Aligned_cols=36  Identities=22%  Similarity=0.484  Sum_probs=20.6

Q ss_pred             CCcccccCcCCCCCCeEe----------cCCCC-cccHHHHHHHHHh
Q 035446            4 DGCCPDCKLPGDDCPLIW----------GACNH-AFHLHCILKWVNS   39 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~----------~~C~H-~fh~~Ci~~w~~~   39 (59)
                      |.+||||++..-..++++          --|+- .-|.-||+++.+.
T Consensus         2 d~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka   48 (162)
T PF07800_consen    2 DVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKA   48 (162)
T ss_pred             CccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHHH
Confidence            678999987433221110          12332 3467799998653

The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.63  E-value=0.0063  Score=37.48  Aligned_cols=51  Identities=25%  Similarity=0.733  Sum_probs=34.2

Q ss_pred             CCcccccCcCCCCCCeE--ecCCC-----CcccHHHHHHHHHhCCC-----CCCCcccccccc
Q 035446            4 DGCCPDCKLPGDDCPLI--WGACN-----HAFHLHCILKWVNSQTP-----QAHCPMCRREWQ   54 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~--~~~C~-----H~fh~~Ci~~w~~~~~~-----~~~CP~Cr~~~~   54 (59)
                      |..|=||+...++....  +-||.     |..|.+|+..|+..+..     ...||.|+.++.
T Consensus        20 eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYi   82 (293)
T KOG3053|consen   20 ERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYI   82 (293)
T ss_pred             ceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhe
Confidence            45699997433333221  12553     88999999999987543     237999998764

>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]

Probab=95.15  E-value=0.018  Score=40.51  Aligned_cols=53  Identities=26%  Similarity=0.730  Sum_probs=38.3

Q ss_pred             CCcccccCc-CCCCCCeEecCCCC-----cccHHHHHHHHHhCCCCCCCccccccccccCC
Q 035446            4 DGCCPDCKL-PGDDCPLIWGACNH-----AFHLHCILKWVNSQTPQAHCPMCRREWQFKGS   58 (59)
Q Consensus         4 ~~~C~IC~~-~~~~~~~~~~~C~H-----~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~~   58 (59)
                      +.+|-||.. ...+.|.. -||..     ..|++|+.+|+.-+ +...|-+|..++.+++.
T Consensus        12 ~~~CRICr~e~~~d~pLf-hPCKC~GSIkYiH~eCL~eW~~~s-~~~kCdiChy~~~Fk~I   70 (1175)
T COG5183          12 KRSCRICRTEDIRDDPLF-HPCKCSGSIKYIHRECLMEWMECS-GTKKCDICHYEYKFKDI   70 (1175)
T ss_pred             chhceeecCCCCCCCcCc-ccccccchhHHHHHHHHHHHHhcC-CCcceeeecceeeeeee
Confidence            367999984 33344443 36653     58999999999864 34689999999988763

>KOG4367 consensus Predicted Zn-finger protein [Function unknown]

Probab=94.78  E-value=0.016  Score=38.39  Aligned_cols=37  Identities=24%  Similarity=0.442  Sum_probs=28.0

Q ss_pred             CCCCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHh
Q 035446            1 MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNS   39 (59)
Q Consensus         1 ~~~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~   39 (59)
                      |..|..|+||..++.+ |++ ++|+|+.|..|...-+.+
T Consensus         1 meeelkc~vc~~f~~e-pii-l~c~h~lc~~ca~~~~~~   37 (699)
T KOG4367|consen    1 MEEELKCPVCGSFYRE-PII-LPCSHNLCQACARNILVQ   37 (699)
T ss_pred             CcccccCceehhhccC-ceE-eecccHHHHHHHHhhccc
Confidence            5567889999655554 554 599999999998876543

>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]

Probab=94.21  E-value=0.023  Score=36.07  Aligned_cols=29  Identities=31%  Similarity=0.735  Sum_probs=21.4

Q ss_pred             ecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446           21 WGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus        21 ~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      +.+|.|+||.+|...     ...+.||.|..++.
T Consensus       106 mIPCkHvFCl~CAr~-----~~dK~Cp~C~d~Vq  134 (389)
T KOG2932|consen  106 MIPCKHVFCLECARS-----DSDKICPLCDDRVQ  134 (389)
T ss_pred             ccccchhhhhhhhhc-----CccccCcCcccHHH
Confidence            359999999999644     11368999987653

>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=94.04  E-value=0.046  Score=34.80  Aligned_cols=48  Identities=21%  Similarity=0.381  Sum_probs=35.8

Q ss_pred             cccccCc-CCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccc
Q 035446            6 CCPDCKL-PGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREW   53 (59)
Q Consensus         6 ~C~IC~~-~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~   53 (59)
                      .||+=.+ -.++.|...+.|||+.-.+-+++..+++.....||.|-..-
T Consensus       338 iCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~~~  386 (396)
T COG5109         338 ICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCPEMS  386 (396)
T ss_pred             eccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCCcch
Confidence            4666543 34566777789999999999999888776556899996543

>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]

Probab=93.80  E-value=0.036  Score=34.15  Aligned_cols=46  Identities=28%  Similarity=0.663  Sum_probs=32.5

Q ss_pred             CCcccccCcC--CC-CCCeEecC-CCCcccHHHHHHHHHhCCCCCCCc--cccc
Q 035446            4 DGCCPDCKLP--GD-DCPLIWGA-CNHAFHLHCILKWVNSQTPQAHCP--MCRR   51 (59)
Q Consensus         4 ~~~C~IC~~~--~~-~~~~~~~~-C~H~fh~~Ci~~w~~~~~~~~~CP--~Cr~   51 (59)
                      |..||||...  .. +..+.+-| |.|..|.+|+++-+..+.  ..||  -|.+
T Consensus        10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~Gp--AqCP~~gC~k   61 (314)
T COG5220          10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGP--AQCPYKGCGK   61 (314)
T ss_pred             cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCC--CCCCCccHHH
Confidence            5689999743  22 22233334 999999999999998864  6799  6654

>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=93.57  E-value=0.038  Score=35.51  Aligned_cols=37  Identities=16%  Similarity=0.312  Sum_probs=26.2

Q ss_pred             CCcccccC-cCC-CCCCeEecCCCCcccHHHHHHHHHhC
Q 035446            4 DGCCPDCK-LPG-DDCPLIWGACNHAFHLHCILKWVNSQ   40 (59)
Q Consensus         4 ~~~C~IC~-~~~-~~~~~~~~~C~H~fh~~Ci~~w~~~~   40 (59)
                      ..+|.||. +.. .+.......|+|.||.+|+.+.++.+
T Consensus       146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~  184 (384)
T KOG1812|consen  146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVK  184 (384)
T ss_pred             cccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhh
Confidence            35799997 322 21222246899999999999998865

>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=93.56  E-value=0.073  Score=34.41  Aligned_cols=46  Identities=24%  Similarity=0.493  Sum_probs=31.6

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHH--HHhCCCCCCCcccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKW--VNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w--~~~~~~~~~CP~Cr~~~~   54 (59)
                      +..|.||-....  -..+++|+|..|-.|.-+.  |-..   ..||+||..+.
T Consensus        61 n~~C~ICA~~~T--Ys~~~PC~H~~CH~Ca~RlRALY~~---K~C~~CrTE~e  108 (493)
T COG5236          61 NMNCQICAGSTT--YSARYPCGHQICHACAVRLRALYMQ---KGCPLCRTETE  108 (493)
T ss_pred             cceeEEecCCce--EEEeccCCchHHHHHHHHHHHHHhc---cCCCccccccc
Confidence            356888854322  2345799999999997653  2232   57999998775

>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]

Probab=93.44  E-value=0.012  Score=40.34  Aligned_cols=50  Identities=22%  Similarity=0.444  Sum_probs=37.4

Q ss_pred             CCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            3 FDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      .+..|+||.....+.  .++.|.|.|+..|+..-+....+...||+|+....
T Consensus        20 k~lEc~ic~~~~~~p--~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~e   69 (684)
T KOG4362|consen   20 KILECPICLEHVKEP--SLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIE   69 (684)
T ss_pred             hhccCCceeEEeecc--chhhhhHHHHhhhhhceeeccCccccchhhhhhhh
Confidence            467899998655543  34699999999999887766544468999986543

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.42  E-value=0.064  Score=33.89  Aligned_cols=33  Identities=21%  Similarity=0.684  Sum_probs=24.2

Q ss_pred             CCCcccHHHHHHHHHhCCC----------CCCCcccccccccc
Q 035446           24 CNHAFHLHCILKWVNSQTP----------QAHCPMCRREWQFK   56 (59)
Q Consensus        24 C~H~fh~~Ci~~w~~~~~~----------~~~CP~Cr~~~~~~   56 (59)
                      |.-..|.+|+.+|+...+.          ..+||+||+.+-..
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~  367 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIR  367 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEe
Confidence            4457889999999865432          35899999977543

>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines

Probab=93.28  E-value=0.053  Score=22.16  Aligned_cols=23  Identities=22%  Similarity=0.595  Sum_probs=9.4

Q ss_pred             cccccCcCCCCCCeEecCCCCcc
Q 035446            6 CCPDCKLPGDDCPLIWGACNHAF   28 (59)
Q Consensus         6 ~C~IC~~~~~~~~~~~~~C~H~f   28 (59)
                      .||-|..........-..|||.|
T Consensus         2 ~CP~C~~~V~~~~~~Cp~CG~~F   24 (26)
T PF10571_consen    2 TCPECGAEVPESAKFCPHCGYDF   24 (26)
T ss_pred             cCCCCcCCchhhcCcCCCCCCCC
Confidence            45666433222222223455554

Several members are annotated as putative helicases.

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]

Probab=93.13  E-value=0.027  Score=40.98  Aligned_cols=43  Identities=21%  Similarity=0.519  Sum_probs=33.4

Q ss_pred             cccccCcCCC-CCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccc
Q 035446            6 CCPDCKLPGD-DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREW   53 (59)
Q Consensus         6 ~C~IC~~~~~-~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~   53 (59)
                      .|+||++... ...+.  .|||.++..|+..|+..+   ..||+|....
T Consensus      1155 ~c~ic~dil~~~~~I~--~cgh~~c~~c~~~~l~~~---s~~~~~ksi~ 1198 (1394)
T KOG0298|consen 1155 VCEICLDILRNQGGIA--GCGHEPCCRCDELWLYAS---SRCPICKSIK 1198 (1394)
T ss_pred             chHHHHHHHHhcCCee--eechhHhhhHHHHHHHHh---ccCcchhhhh
Confidence            6888875433 33443  899999999999999997   7899997543

>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=92.86  E-value=0.097  Score=34.06  Aligned_cols=36  Identities=25%  Similarity=0.453  Sum_probs=28.6

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhC
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQ   40 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~   40 (59)
                      +..|-||.+.... .++.+.|+|.|+..|...++.++
T Consensus        70 ~~~c~ic~~~~~~-~~~~~~c~H~~c~~cw~~yl~~k  105 (444)
T KOG1815|consen   70 DVQCGICVESYDG-EIIGLGCGHPFCPPCWTGYLGTK  105 (444)
T ss_pred             cccCCcccCCCcc-hhhhcCCCcHHHHHHHHHHhhhe
Confidence            4679999765444 45567999999999999999875

>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=92.46  E-value=0.026  Score=36.69  Aligned_cols=48  Identities=25%  Similarity=0.442  Sum_probs=34.0

Q ss_pred             CcccccCcCCCC--CCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            5 GCCPDCKLPGDD--CPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         5 ~~C~IC~~~~~~--~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      ..++||......  ..+....|||.+|.++|.+|+.+.   ..+|.|++.+..
T Consensus       197 ~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~---~kl~~~~rel~~  246 (465)
T KOG0827|consen  197 GSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATK---RKLPSCRRELPK  246 (465)
T ss_pred             hhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHH---HHhHHHHhhhhh
Confidence            456777532111  112234899999999999999986   689999987764

>KOG3002 consensus Zn finger protein [General function prediction only]

Probab=92.35  E-value=0.18  Score=31.64  Aligned_cols=41  Identities=32%  Similarity=0.638  Sum_probs=29.5

Q ss_pred             CcccccCcCCCCCCeEecCC--CCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            5 GCCPDCKLPGDDCPLIWGAC--NHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C--~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      ..||||..+... |+.  .|  ||..|..|-.+   ..   ..||.||.++.
T Consensus        49 leCPvC~~~l~~-Pi~--QC~nGHlaCssC~~~---~~---~~CP~Cr~~~g   91 (299)
T KOG3002|consen   49 LDCPVCFNPLSP-PIF--QCDNGHLACSSCRTK---VS---NKCPTCRLPIG   91 (299)
T ss_pred             ccCchhhccCcc-cce--ecCCCcEehhhhhhh---hc---ccCCccccccc
Confidence            479999765554 554  56  69999988653   22   67999998876

>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=91.84  E-value=0.099  Score=31.09  Aligned_cols=38  Identities=24%  Similarity=0.598  Sum_probs=25.8

Q ss_pred             ccccCcCCCCCCeEecCCCC-cccHHHHHHHHHhCCCCCCCccccccc
Q 035446            7 CPDCKLPGDDCPLIWGACNH-AFHLHCILKWVNSQTPQAHCPMCRREW   53 (59)
Q Consensus         7 C~IC~~~~~~~~~~~~~C~H-~fh~~Ci~~w~~~~~~~~~CP~Cr~~~   53 (59)
                      |-.|.+  .+..++++||.| .+|..|-..       -..||+|+.+.
T Consensus       161 Cr~C~~--~~~~VlllPCrHl~lC~~C~~~-------~~~CPiC~~~~  199 (207)
T KOG1100|consen  161 CRKCGE--REATVLLLPCRHLCLCGICDES-------LRICPICRSPK  199 (207)
T ss_pred             ceecCc--CCceEEeecccceEeccccccc-------CccCCCCcChh
Confidence            666633  233467789997 688888533       15799998764

>PF13901 DUF4206: Domain of unknown function (DUF4206)

Probab=91.23  E-value=0.14  Score=30.23  Aligned_cols=38  Identities=32%  Similarity=0.710  Sum_probs=26.6

Q ss_pred             cccccCc-----CCCC-CCeEecCCCCcccHHHHHHHHHhCCCCCCCccccc
Q 035446            6 CCPDCKL-----PGDD-CPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRR   51 (59)
Q Consensus         6 ~C~IC~~-----~~~~-~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~   51 (59)
                      .|.+|..     |++. ..+.-..|+-+||+.|..+        ..||-|.+
T Consensus       154 iCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~--------~~CpkC~R  197 (202)
T PF13901_consen  154 ICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRK--------KSCPKCAR  197 (202)
T ss_pred             CCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCC--------CCCCCcHh
Confidence            5777752     3333 4555678999999999762        46999965

>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3

Probab=90.47  E-value=0.37  Score=20.17  Aligned_cols=37  Identities=24%  Similarity=0.604  Sum_probs=22.4

Q ss_pred             ccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            7 CPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         7 C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      |+.|..+..+.......=+..||.+|           ..|..|+.++.
T Consensus         2 C~~C~~~i~~~~~~~~~~~~~~H~~C-----------f~C~~C~~~L~   38 (39)
T smart00132        2 CAGCGKPIRGGELVLRALGKVWHPEC-----------FKCSKCGKPLG   38 (39)
T ss_pred             ccccCCcccCCcEEEEeCCccccccC-----------CCCcccCCcCc
Confidence            67786554443122223467899877           46778877653

Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]

Probab=90.28  E-value=0.082  Score=36.96  Aligned_cols=39  Identities=18%  Similarity=0.396  Sum_probs=28.2

Q ss_pred             CCCCcccccCcCCC-----CCCeEecCCCCcccHHHHHHHHHhC
Q 035446            2 AFDGCCPDCKLPGD-----DCPLIWGACNHAFHLHCILKWVNSQ   40 (59)
Q Consensus         2 ~~~~~C~IC~~~~~-----~~~~~~~~C~H~fh~~Ci~~w~~~~   40 (59)
                      ++++.|.-|.++..     -..++...|+|.||..|+..-..++
T Consensus       782 ~~e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~  825 (846)
T KOG2066|consen  782 SVEERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRN  825 (846)
T ss_pred             eehhhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhc
Confidence            45678888976432     1234557999999999998877664

>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]

Probab=90.09  E-value=0.18  Score=30.49  Aligned_cols=45  Identities=27%  Similarity=0.657  Sum_probs=31.4

Q ss_pred             cccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            6 CCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         6 ~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      .|.+|..- .-..+...+|+=.+|..|+..++++.   ..||.|..-|.
T Consensus       183 ~Cn~Ch~L-vIqg~rCg~c~i~~h~~c~qty~q~~---~~cphc~d~w~  227 (235)
T KOG4718|consen  183 NCNLCHCL-VIQGIRCGSCNIQYHRGCIQTYLQRR---DICPHCGDLWT  227 (235)
T ss_pred             HHhHhHHH-hheeeccCcccchhhhHHHHHHhccc---CcCCchhcccC
Confidence            57777532 11123345778889999999999985   78999965443

>smart00249 PHD PHD zinc finger

Probab=89.96  E-value=0.25  Score=21.43  Aligned_cols=31  Identities=23%  Similarity=0.488  Sum_probs=20.7

Q ss_pred             cccccCcCC-CCCCeEecCCCCcccHHHHHHH
Q 035446            6 CCPDCKLPG-DDCPLIWGACNHAFHLHCILKW   36 (59)
Q Consensus         6 ~C~IC~~~~-~~~~~~~~~C~H~fh~~Ci~~w   36 (59)
                      .|.+|.... .+..+.-..|+..||..|+..-
T Consensus         1 ~C~~C~~~~~~~~~i~C~~C~~~~H~~C~~~~   32 (47)
T smart00249        1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPP   32 (47)
T ss_pred             CcccCCCcCCCCCEEECCCCCchhhhhhCCCc
Confidence            477886432 3334444588999999998653

The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the

>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]

Probab=89.75  E-value=0.21  Score=30.39  Aligned_cols=50  Identities=20%  Similarity=0.579  Sum_probs=32.6

Q ss_pred             CcccccCcCCCCCC--eEecCCC-----CcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            5 GCCPDCKLPGDDCP--LIWGACN-----HAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         5 ~~C~IC~~~~~~~~--~~~~~C~-----H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      ..|=||........  ....+|.     ...|+.|+..|+..+. ...|.+|...+..
T Consensus        79 ~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~-~~~CeiC~~~~~~  135 (323)
T KOG1609|consen   79 PICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKG-NITCEICKSFFIN  135 (323)
T ss_pred             CcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhcccc-Ceeeeccccccee
Confidence            46888875332111  2234564     5679999999998643 3689999876543

>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length

Probab=89.60  E-value=0.28  Score=24.39  Aligned_cols=13  Identities=31%  Similarity=0.876  Sum_probs=9.4

Q ss_pred             cccHHHHHHHHHh
Q 035446           27 AFHLHCILKWVNS   39 (59)
Q Consensus        27 ~fh~~Ci~~w~~~   39 (59)
                      -||+.||.+|+..
T Consensus        11 gFCRNCLskWy~~   23 (68)
T PF06844_consen   11 GFCRNCLSKWYRE   23 (68)
T ss_dssp             S--HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            3999999999875

The function of this family is unknown.; PDB: 2O35_A 3FYB_B.

>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=89.45  E-value=0.19  Score=23.27  Aligned_cols=38  Identities=21%  Similarity=0.515  Sum_probs=24.4

Q ss_pred             ccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            7 CPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         7 C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      |+.|..+..+..+.+..=+..||.+|           ..|-.|++++..
T Consensus         1 C~~C~~~I~~~~~~~~~~~~~~H~~C-----------f~C~~C~~~l~~   38 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIKAMGKFWHPEC-----------FKCSKCGKPLND   38 (58)
T ss_dssp             BTTTSSBESSSSEEEEETTEEEETTT-----------SBETTTTCBTTT
T ss_pred             CCCCCCCccCcEEEEEeCCcEEEccc-----------cccCCCCCccCC
Confidence            56676554444444335677888877           468888877654

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 entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....

>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ]

Probab=89.44  E-value=0.11  Score=33.87  Aligned_cols=34  Identities=24%  Similarity=0.691  Sum_probs=0.0

Q ss_pred             CCCeEecCCCCcccHHHHHHHHHhCC---CCCCCcccccc
Q 035446           16 DCPLIWGACNHAFHLHCILKWVNSQT---PQAHCPMCRRE   52 (59)
Q Consensus        16 ~~~~~~~~C~H~fh~~Ci~~w~~~~~---~~~~CP~Cr~~   52 (59)
                      ..|.+-+.|||++-.   ..|-....   ....||+||..
T Consensus       301 ~qP~VYl~CGHVhG~---h~Wg~~~~~~~~~r~CPlCr~~  337 (416)
T PF04710_consen  301 RQPWVYLNCGHVHGY---HNWGQDSDRDPRSRTCPLCRQV  337 (416)
T ss_dssp             ----------------------------------------
T ss_pred             cCceeeccccceeee---cccccccccccccccCCCcccc
Confidence            446667899998774   45654322   13689999975

; PDB: 3EGB_B 3EGA_A.

>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A

Probab=89.37  E-value=0.77  Score=23.58  Aligned_cols=50  Identities=14%  Similarity=0.307  Sum_probs=20.2

Q ss_pred             CcccccCcCC-----CCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            5 GCCPDCKLPG-----DDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         5 ~~C~IC~~~~-----~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      ..|.||-+..     .+.-++...|+--.++.|.+-=.+..  +..||.|+.++...
T Consensus        10 qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg--~q~CpqCkt~ykr~   64 (80)
T PF14569_consen   10 QICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEG--NQVCPQCKTRYKRH   64 (80)
T ss_dssp             -B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS---SB-TTT--B----
T ss_pred             cccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcC--cccccccCCCcccc
Confidence            4699996432     23334455777888999987655444  57899999887653

>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=89.35  E-value=0.99  Score=20.94  Aligned_cols=46  Identities=22%  Similarity=0.473  Sum_probs=19.2

Q ss_pred             CcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCC--CCCCCcccccc
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQT--PQAHCPMCRRE   52 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~--~~~~CP~Cr~~   52 (59)
                      ..|||-.... ..|+....|.|.-+.+ +..|+....  ..-.||+|.++
T Consensus         3 L~CPls~~~i-~~P~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    3 LRCPLSFQRI-RIPVRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             SB-TTTSSB--SSEEEETT--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred             eeCCCCCCEE-EeCccCCcCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence            4677775433 3467777999985433 333443321  12479999864

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 entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.

>KOG0269 consensus WD40 repeat-containing protein [Function unknown]

Probab=88.91  E-value=0.41  Score=33.61  Aligned_cols=36  Identities=19%  Similarity=0.371  Sum_probs=26.4

Q ss_pred             cccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCC
Q 035446            6 CCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQT   41 (59)
Q Consensus         6 ~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~   41 (59)
                      .|.+|.....+..+-...|||.-|.+++.+|+...+
T Consensus       781 ~CtVC~~vi~G~~~~c~~C~H~gH~sh~~sw~~~~s  816 (839)
T KOG0269|consen  781 KCTVCDLVIRGVDVWCQVCGHGGHDSHLKSWFFKAS  816 (839)
T ss_pred             CceeecceeeeeEeecccccccccHHHHHHHHhcCC
Confidence            577775444443344458999999999999999873

>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length

Probab=88.52  E-value=0.0061  Score=30.62  Aligned_cols=42  Identities=24%  Similarity=0.646  Sum_probs=20.8

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      |..||.|..+.     .... ++.+|..|-..+...    ..||-|.+++..
T Consensus         1 e~~CP~C~~~L-----~~~~-~~~~C~~C~~~~~~~----a~CPdC~~~Le~   42 (70)
T PF07191_consen    1 ENTCPKCQQEL-----EWQG-GHYHCEACQKDYKKE----AFCPDCGQPLEV   42 (70)
T ss_dssp             --B-SSS-SBE-----EEET-TEEEETTT--EEEEE----EE-TTT-SB-EE
T ss_pred             CCcCCCCCCcc-----EEeC-CEEECccccccceec----ccCCCcccHHHH
Confidence            46799996432     2222 677777776654433    579999988754

Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.

>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]

Probab=87.82  E-value=0.2  Score=33.97  Aligned_cols=43  Identities=26%  Similarity=0.651  Sum_probs=27.2

Q ss_pred             cccccC-----cCC-CCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            6 CCPDCK-----LPG-DDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         6 ~C~IC~-----~~~-~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      .|.+|.     .++ .+.......|+++||..|+..    .+  ..||.|-+...
T Consensus       513 iCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r----~s--~~CPrC~R~q~  561 (580)
T KOG1829|consen  513 ICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRR----KS--PCCPRCERRQK  561 (580)
T ss_pred             eeeeccCCCcccccccccceeHHHHHHHHHHHHHhc----cC--CCCCchHHHHH
Confidence            466663     133 333444568999999999754    22  44999966433

>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=87.76  E-value=0.17  Score=29.59  Aligned_cols=26  Identities=19%  Similarity=0.289  Sum_probs=20.3

Q ss_pred             CcccccCcCCC-CCCeEecCCCCcccH
Q 035446            5 GCCPDCKLPGD-DCPLIWGACNHAFHL   30 (59)
Q Consensus         5 ~~C~IC~~~~~-~~~~~~~~C~H~fh~   30 (59)
                      ..|.||+++.. ...|..++|-.+||+
T Consensus       178 GECvICLEdL~~GdtIARLPCLCIYHK  204 (205)
T KOG0801|consen  178 GECVICLEDLEAGDTIARLPCLCIYHK  204 (205)
T ss_pred             CcEEEEhhhccCCCceeccceEEEeec
Confidence            57999997543 457788999999986

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.16  E-value=0.7  Score=28.72  Aligned_cols=47  Identities=17%  Similarity=0.298  Sum_probs=31.5

Q ss_pred             cccccCcCCC--CCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            6 CCPDCKLPGD--DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         6 ~C~IC~~~~~--~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      .|||=..+..  ..-.++..|||+|-..-+.+.-.     ..|++|...+...+
T Consensus       113 iCPvtgleMng~~~F~~l~~CGcV~SerAlKeika-----s~C~~C~a~y~~~d  161 (293)
T KOG3113|consen  113 ICPVTGLEMNGKYRFCALRCCGCVFSERALKEIKA-----SVCHVCGAAYQEDD  161 (293)
T ss_pred             ecccccceecceEEEEEEeccceeccHHHHHHhhh-----ccccccCCcccccC
Confidence            4665542222  22345679999999888877532     57999999877653

>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=86.76  E-value=0.28  Score=22.34  Aligned_cols=46  Identities=26%  Similarity=0.576  Sum_probs=28.7

Q ss_pred             cccccCcCCC-CCCeEecCCCCcccHHHHHHHHHhCC---CCCCCccccc
Q 035446            6 CCPDCKLPGD-DCPLIWGACNHAFHLHCILKWVNSQT---PQAHCPMCRR   51 (59)
Q Consensus         6 ~C~IC~~~~~-~~~~~~~~C~H~fh~~Ci~~w~~~~~---~~~~CP~Cr~   51 (59)
                      .|.||..... +..+.-..|+-.||..|+..-.....   ..-.||.|+.
T Consensus         1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~   50 (51)
T PF00628_consen    1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP   50 (51)
T ss_dssp             EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred             eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence            3788975333 33455568899999999876543211   1246887753

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 entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....

>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=85.91  E-value=0.5  Score=30.50  Aligned_cols=36  Identities=28%  Similarity=0.718  Sum_probs=24.4

Q ss_pred             CcccccCcC---CCCCCeEecCCCCcccHHHHHHHHHhC
Q 035446            5 GCCPDCKLP---GDDCPLIWGACNHAFHLHCILKWVNSQ   40 (59)
Q Consensus         5 ~~C~IC~~~---~~~~~~~~~~C~H~fh~~Ci~~w~~~~   40 (59)
                      ..||.|...   ..+..-..-.|||.|+..|...|...+
T Consensus       307 r~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~  345 (384)
T KOG1812|consen  307 RQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHN  345 (384)
T ss_pred             CcCcccceeeeecCCcceEEeeccccchhhcCcchhhCC
Confidence            368999632   222322223599999999999998765

>PLN02189 cellulose synthase

Probab=85.52  E-value=0.95  Score=32.80  Aligned_cols=49  Identities=14%  Similarity=0.349  Sum_probs=33.2

Q ss_pred             CcccccCcCCC----CC-CeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            5 GCCPDCKLPGD----DC-PLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         5 ~~C~IC~~~~~----~~-~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      ..|.||.+..+    +. -++.-.|+--.|+.|.+-  +.+.+++.||.|+..+..
T Consensus        35 ~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyey--er~eg~q~CpqCkt~Y~r   88 (1040)
T PLN02189         35 QVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEY--ERREGTQNCPQCKTRYKR   88 (1040)
T ss_pred             ccccccccccCcCCCCCEEEeeccCCCccccchhhh--hhhcCCccCcccCCchhh
Confidence            47999975422    22 234445888899999844  333446899999998874

>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=85.35  E-value=0.35  Score=33.62  Aligned_cols=37  Identities=30%  Similarity=0.463  Sum_probs=25.5

Q ss_pred             CcccccCc-CC-C-CCCeEecCCCCcccHHHHHHHHHhCCCCCCCc
Q 035446            5 GCCPDCKL-PG-D-DCPLIWGACNHAFHLHCILKWVNSQTPQAHCP   47 (59)
Q Consensus         5 ~~C~IC~~-~~-~-~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP   47 (59)
                      ..|+||+. ++ . -.++. +.|||..|+.|+..-..     .+||
T Consensus        12 l~c~ic~n~f~~~~~~Pvs-l~cghtic~~c~~~lyn-----~scp   51 (861)
T KOG3161|consen   12 LLCDICLNLFVVQRLEPVS-LQCGHTICGHCVQLLYN-----ASCP   51 (861)
T ss_pred             hhchHHHHHHHHHhcCccc-ccccchHHHHHHHhHhh-----ccCC
Confidence            46999963 21 1 23443 69999999999988654     3588

>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association

Probab=85.11  E-value=0.47  Score=22.16  Aligned_cols=12  Identities=33%  Similarity=0.891  Sum_probs=6.4

Q ss_pred             CCCccccccccc
Q 035446           44 AHCPMCRREWQF   55 (59)
Q Consensus        44 ~~CP~Cr~~~~~   55 (59)
                      ..||+|.+++..
T Consensus        21 ~~CPlC~r~l~~   32 (54)
T PF04423_consen   21 GCCPLCGRPLDE   32 (54)
T ss_dssp             EE-TTT--EE-H
T ss_pred             CcCCCCCCCCCH
Confidence            389999998864

The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.

>PLN02436 cellulose synthase A

Probab=83.62  E-value=1.3  Score=32.33  Aligned_cols=49  Identities=14%  Similarity=0.370  Sum_probs=33.0

Q ss_pred             CcccccCcCCC-----CCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            5 GCCPDCKLPGD-----DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         5 ~~C~IC~~~~~-----~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      ..|.||-+...     +.-++.-.|+--.|+.|.+-  +.+.+++.||.|+..+..
T Consensus        37 ~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyey--er~eg~~~Cpqckt~Y~r   90 (1094)
T PLN02436         37 QTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEY--ERREGNQACPQCKTRYKR   90 (1094)
T ss_pred             ccccccccccCcCCCCCEEEeeccCCCccccchhhh--hhhcCCccCcccCCchhh
Confidence            37999975422     22344446777899999844  333446899999998874

>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain

Probab=83.32  E-value=0.89  Score=22.97  Aligned_cols=33  Identities=27%  Similarity=0.454  Sum_probs=22.0

Q ss_pred             CCCcccccCcC-CCCCCeEecCCCCcccHHHHHH
Q 035446            3 FDGCCPDCKLP-GDDCPLIWGACNHAFHLHCILK   35 (59)
Q Consensus         3 ~~~~C~IC~~~-~~~~~~~~~~C~H~fh~~Ci~~   35 (59)
                      ....|.+|... +....-....|.-.||..|...
T Consensus        35 ~~~~C~~C~~~~Ga~i~C~~~~C~~~fH~~CA~~   68 (90)
T PF13771_consen   35 RKLKCSICKKKGGACIGCSHPGCSRSFHVPCARK   68 (90)
T ss_pred             hCCCCcCCCCCCCeEEEEeCCCCCcEEChHHHcc
Confidence            35679999655 3222223457889999999765

>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression

Probab=82.20  E-value=3.8  Score=21.88  Aligned_cols=27  Identities=26%  Similarity=0.594  Sum_probs=19.8

Q ss_pred             CCcccHHHHHHHHHhCC------CCCCCccccc
Q 035446           25 NHAFHLHCILKWVNSQT------PQAHCPMCRR   51 (59)
Q Consensus        25 ~H~fh~~Ci~~w~~~~~------~~~~CP~Cr~   51 (59)
                      .=.||..||..++....      ..-.||.||.
T Consensus        37 ~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg   69 (105)
T PF10497_consen   37 RGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG   69 (105)
T ss_pred             cceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence            66799999999876531      1246999986

This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].

>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines

Probab=81.96  E-value=1.2  Score=18.28  Aligned_cols=28  Identities=25%  Similarity=0.552  Sum_probs=10.3

Q ss_pred             cccccCcCCCC-CCeEecCCCCcccHHHH
Q 035446            6 CCPDCKLPGDD-CPLIWGACNHAFHLHCI   33 (59)
Q Consensus         6 ~C~IC~~~~~~-~~~~~~~C~H~fh~~Ci   33 (59)
                      .|.+|..+... ....-..|.-.+|.+|+
T Consensus         2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~Ca   30 (30)
T PF07649_consen    2 RCDACGKPIDGGWFYRCSECDFDLHEECA   30 (30)
T ss_dssp             --TTTS----S--EEE-TTT-----HHHH
T ss_pred             cCCcCCCcCCCCceEECccCCCccChhcC
Confidence            47778655444 44455688888888885

The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.

>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain

Probab=81.73  E-value=2.5  Score=22.14  Aligned_cols=31  Identities=26%  Similarity=0.462  Sum_probs=20.4

Q ss_pred             CCcccccCcCCCCCCeEe--cCCCCcccHHHHHH
Q 035446            4 DGCCPDCKLPGDDCPLIW--GACNHAFHLHCILK   35 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~--~~C~H~fh~~Ci~~   35 (59)
                      ...|.||... .+..+.-  ..|...||..|...
T Consensus        55 ~~~C~iC~~~-~G~~i~C~~~~C~~~fH~~CA~~   87 (110)
T PF13832_consen   55 KLKCSICGKS-GGACIKCSHPGCSTAFHPTCARK   87 (110)
T ss_pred             CCcCcCCCCC-CceeEEcCCCCCCcCCCHHHHHH
Confidence            5689999654 2222222  24888999999866

>COG5627 MMS21 DNA repair protein MMS21 [DNA replication, recombination, and repair]

Probab=80.62  E-value=0.77  Score=28.29  Aligned_cols=44  Identities=25%  Similarity=0.441  Sum_probs=31.9

Q ss_pred             CCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcc
Q 035446            3 FDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPM   48 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~   48 (59)
                      ++.+|||=+.+... |+....|+|.|-++-|...++..- ...||.
T Consensus       188 ~~nrCpitl~p~~~-pils~kcnh~~e~D~I~~~lq~~~-trvcp~  231 (275)
T COG5627         188 LSNRCPITLNPDFY-PILSSKCNHKPEMDLINKKLQVEC-TRVCPR  231 (275)
T ss_pred             hcccCCcccCcchh-HHHHhhhcccccHHHHHHHhcCCc-eeecch
Confidence            46789998766443 566679999999999999988431 145663

>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit

Probab=80.29  E-value=2  Score=31.35  Aligned_cols=49  Identities=14%  Similarity=0.370  Sum_probs=33.4

Q ss_pred             CcccccCcCCC-----CCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            5 GCCPDCKLPGD-----DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         5 ~~C~IC~~~~~-----~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      ..|.||-+...     +.-++.-.|+--.|+.|.+-  +++.+++.||.|+..+..
T Consensus        18 qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEY--Er~eG~q~CPqCktrYkr   71 (1079)
T PLN02638         18 QVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEY--ERKDGNQSCPQCKTKYKR   71 (1079)
T ss_pred             ceeeecccccCcCCCCCEEEEeccCCCccccchhhh--hhhcCCccCCccCCchhh
Confidence            37999975422     22344557777799999843  334456899999998873

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	59
2lgv_A	100	Rbx1 Length = 100		3e-07
4a0k_B	117	Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp		3e-07
1u6g_B	108	Crystal Structure Of The Cand1-Cul1-Roc1 Complex Le		3e-07
3dpl_R	106	Structural Insights Into Nedd8 Activation Of Cullin		4e-07
4a0c_D	98	Structure Of The Cand1-Cul4b-Rbx1 Complex Length =		4e-07
3dqv_R	106	Structural Insights Into Nedd8 Activation Of Cullin		4e-07
1ldj_B	90	Structure Of The Cul1-rbx1-skp1-f Boxskp2 Scf Ubiqu		5e-07
2ecl_A	81	Solution Structure Of The Ring Domain Of The Human		4e-04

>pdb|2LGV|A Chain A, Rbx1 Length = 100

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 19/44 (43%), Positives = 29/44 (65%), Gaps = 3/44 (6%)
Query: 13 PGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
            ++C + WG CNHAFH HCI +W+ ++     CP+  REW+F+
Sbjct: 56 TSEECTVAWGVCNHAFHFHCISRWLKTRQV---CPLDNREWEFQ 96

>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 = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 19/44 (43%), Positives = 29/44 (65%), Gaps = 3/44 (6%)
Query: 13  PGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
             ++C + WG CNHAFH HCI +W+ ++     CP+  REW+F+
Sbjct: 73  TSEECTVAWGVCNHAFHFHCISRWLKTRQV---CPLDNREWEFQ 113

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

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 19/44 (43%), Positives = 29/44 (65%), Gaps = 3/44 (6%)
Query: 13  PGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
             ++C + WG CNHAFH HCI +W+ ++     CP+  REW+F+
Sbjct: 64  TSEECTVAWGVCNHAFHFHCISRWLKTRQV---CPLDNREWEFQ 104

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 19/44 (43%), Positives = 29/44 (65%), Gaps = 3/44 (6%)
Query: 13  PGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
             ++C + WG CNHAFH HCI +W+ ++     CP+  REW+F+
Sbjct: 62  TSEECTVAWGVCNHAFHFHCISRWLKTRQV---CPLDNREWEFQ 102

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 19/44 (43%), Positives = 29/44 (65%), Gaps = 3/44 (6%)
Query: 13 PGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
            ++C + WG CNHAFH HCI +W+ ++     CP+  REW+F+
Sbjct: 54 TSEECTVAWGVCNHAFHFHCISRWLKTRQV---CPLDNREWEFQ 94

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 19/44 (43%), Positives = 29/44 (65%), Gaps = 3/44 (6%)
Query: 13  PGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
             ++C + WG CNHAFH HCI +W+ ++     CP+  REW+F+
Sbjct: 62  TSEECTVAWGVCNHAFHFHCISRWLKTRQV---CPLDNREWEFQ 102

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 19/44 (43%), Positives = 29/44 (65%), Gaps = 3/44 (6%)
Query: 13 PGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
            ++C + WG CNHAFH HCI +W+ ++     CP+  REW+F+
Sbjct: 46 TSEECTVAWGVCNHAFHFHCISRWLKTRQV---CPLDNREWEFQ 86

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

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 16/42 (38%), Positives = 26/42 (61%), Gaps = 3/42 (7%)
Query: 15 DDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
          +DC ++WG CNH+FH  C+  WV        CP+C+++W  +
Sbjct: 39 EDCVVVWGECNHSFHNCCMSLWVKQNN---RCPLCQQDWVVQ 77

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	59
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	2e-13
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	9e-12
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	2e-11
3nw0_A	238	Non-structural maintenance of chromosomes element	4e-07
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	1e-05
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	2e-05
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	3e-05
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	7e-05
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	1e-04
2ect_A	78	Ring finger protein 126; metal binding protein, st	2e-04
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	2e-04
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	2e-04
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	3e-04
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	3e-04
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	4e-04
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	4e-04

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

 Score = 57.6 bits (139), Expect = 2e-13
 Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 5/58 (8%)

Query: 1  MAFDGCCPDCKLPG--DDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
          +     C  C+     +DC ++WG CNH+FH  C+  WV        CP+C+++W  +
Sbjct: 23 VQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNN---RCPLCQQDWVVQ 77

>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 = 54.1 bits (129), Expect = 9e-12
 Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 3/56 (5%)

Query: 1   MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
           +  +          ++C + WG CNHAFH HCI +W+ +   +  CP+  REW+F+
Sbjct: 50  LCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT---RQVCPLDNREWEFQ 102

>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 = 53.3 bits (127), Expect = 2e-11
 Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 3/56 (5%)

Query: 1   MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
           +  +          ++C + WG CNHAFH HCI +W+ +   +  CP+  REW+F+
Sbjct: 61  LCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT---RQVCPLDNREWEFQ 113

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens} Length = 238

 Score = 43.2 bits (101), Expect = 4e-07
 Identities = 14/51 (27%), Positives = 18/51 (35%), Gaps = 8/51 (15%)

Query: 6   CCPDCK---LPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREW 53
            C  C    + G  C      C    HL C+ K+  S   +  CP C   W
Sbjct: 182 ICNICHSLLIQGQSCE----TCGIRMHLPCVAKYFQSN-AEPRCPHCNDYW 227

>2y1n_A E3 ubiquitin-protein ligase; ligase-transferase complex, ubiquitin ring E3 ligase; HET: PTR; 2.00A {Homo sapiens} PDB: 2y1m_A* 4a4c_A* 4a4b_A* 1fbv_A* 3vgo_A 4a49_A* 2k4d_A 2ldr_A* Length = 389

 Score = 39.0 bits (90), Expect = 1e-05
 Identities = 10/29 (34%), Positives = 12/29 (41%), Gaps = 2/29 (6%)

Query: 24  CNHAFHLHCILKWVNSQTPQAHCPMCRRE 52
           C H     C+  W  S+     CP CR E
Sbjct: 350 CGHLMCTSCLTSWQESEGQG--CPFCRCE 376

>1v87_A Deltex protein 2; ring-H2 domain, zinc-binding domain, notch signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.44.1.1 Length = 114

 Score = 37.9 bits (87), Expect = 2e-05
 Identities = 15/50 (30%), Positives = 20/50 (40%), Gaps = 2/50 (4%)

Query: 9  DCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAH--CPMCRREWQFK 56
          D K  G         C+HAFHL C+L    +        CP C+  +  K
Sbjct: 46 DSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK 95

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 74

 Score = 36.8 bits (85), Expect = 3e-05
 Identities = 10/30 (33%), Positives = 13/30 (43%), Gaps = 1/30 (3%)

Query: 24 CNHAFHLHCILKWVNSQTPQAHCPMCRREW 53
          C    HL C+ K+  S   +  CP C   W
Sbjct: 34 CGIRMHLPCVAKYFQSN-AEPRCPHCNDYW 62

>1x4j_A Ring finger protein 38; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 75

 Score = 35.4 bits (82), Expect = 7e-05
 Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 3/29 (10%)

Query: 24 CNHAFHLHCILKWVNSQTPQAHCPMCRRE 52
          CNH FH  C+ KW+ +      CP+CR +
Sbjct: 44 CNHEFHAKCVDKWLKA---NRTCPICRAD 69

>2l0b_A E3 ubiquitin-protein ligase praja-1; zinc finger, NESG, structural genomics, PSI-2, protein struc initiative; NMR {Homo sapiens} Length = 91

 Score = 35.4 bits (82), Expect = 1e-04
 Identities = 10/29 (34%), Positives = 14/29 (48%), Gaps = 3/29 (10%)

Query: 24 CNHAFHLHCILKWVNSQTPQAHCPMCRRE 52
          C+H FH  C+  W+        CP+CR  
Sbjct: 61 CHHYFHKPCVSIWLQK---SGTCPVCRCM 86

>2ect_A Ring finger protein 126; metal binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 78

 Score = 34.3 bits (79), Expect = 2e-04
 Identities = 12/29 (41%), Positives = 16/29 (55%), Gaps = 3/29 (10%)

Query: 24 CNHAFHLHCILKWVNSQTPQAHCPMCRRE 52
          CNH FH  CI+ W+        CP+CR+ 
Sbjct: 36 CNHLFHDSCIVPWLEQHD---SCPVCRKS 61

>2ep4_A Ring finger protein 24; zinc binding, ubiquitin, E3 enzyme, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 74

 Score = 34.4 bits (79), Expect = 2e-04
 Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 3/29 (10%)

Query: 24 CNHAFHLHCILKWVNSQTPQAHCPMCRRE 52
          C HAFH  C++KW+     +  CP+C   
Sbjct: 36 CKHAFHRKCLIKWLEV---RKVCPLCNMP 61

>2kiz_A E3 ubiquitin-protein ligase arkadia; ring-H2 finger, E3 ligase, Zn binding domain, metal zinc, zinc-finger, metal binding protein; NMR {Homo sapiens} Length = 69

 Score = 33.9 bits (78), Expect = 2e-04
 Identities = 10/29 (34%), Positives = 16/29 (55%), Gaps = 3/29 (10%)

Query: 24 CNHAFHLHCILKWVNSQTPQAHCPMCRRE 52
          C H FH  C+ +W+ +      CP+CR +
Sbjct: 35 CMHLFHQVCVDQWLIT---NKKCPICRVD 60

>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid herpesvirus 1} SCOP: g.44.1.1 Length = 68

 Score = 33.9 bits (78), Expect = 3e-04
 Identities = 10/29 (34%), Positives = 14/29 (48%), Gaps = 3/29 (10%)

Query: 24 CNHAFHLHCILKWVNSQTPQAHCPMCRRE 52
          C HAF   CI +W+        CP+C+  
Sbjct: 24 CLHAFCYVCITRWIRQNP---TCPLCKVP 49

>2ecn_A Ring finger protein 141; RNF141, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 70

 Score = 33.9 bits (78), Expect = 3e-04
 Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 3/29 (10%)

Query: 24 CNHAFHLHCILKWVNSQTPQAHCPMCRRE 52
          C H+F   CI KW +      +CP+CR +
Sbjct: 32 CAHSFCQKCIDKWSDR---HRNCPICRLQ 57

>1iym_A EL5; ring-H2 finger, ubiquitin ligase, DNA binding protein; NMR {Oryza sativa} SCOP: g.44.1.1 Length = 55

 Score = 33.3 bits (77), Expect = 4e-04
 Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 3/29 (10%)

Query: 23 ACNHAFHLHCILKWVNSQTPQAHCPMCRR 51
           C H FH  C+  W+ S    + CP+CR 
Sbjct: 26 RCGHGFHAECVDMWLGS---HSTCPLCRL 51

>3k1l_B Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A {Drosophila melanogaster} Length = 381

 Score = 35.2 bits (80), Expect = 4e-04
 Identities = 12/61 (19%), Positives = 20/61 (32%), Gaps = 11/61 (18%)

Query: 7   CPDCKLPGDDCPLIW---GACNHAFHLHCILKWVNSQT--------PQAHCPMCRREWQF 55
           C   +L G + PL+      C    H  C+ +W  +              CP C+ +   
Sbjct: 314 CFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLST 373

Query: 56  K 56
            
Sbjct: 374 S 374

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	59
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.79
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.76
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.72
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.72
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.71
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.71
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.71
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.7
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.7
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.69
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.68
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.68
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.68
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.68
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.67
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.67
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.66
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.63
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.63
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.63
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.62
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.62
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.61
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.59
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.59
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.58
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.58
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.58
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.58
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.56
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.56
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.56
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.55
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.55
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.55
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.53
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.52
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.51
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.51
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.51
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.51
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.5
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.49
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.48
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.46
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.44
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.43
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.42
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.42
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.4
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.38
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.38
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.37
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.36
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	99.34
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.31
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.29
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.28
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.28
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.23
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	99.19
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	99.18
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	99.13
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	99.07
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	99.05
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	99.05
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.99
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.94
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.91
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.85
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.8
3nw0_A	238	Non-structural maintenance of chromosomes element	98.68
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	97.34
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	96.5
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	96.49
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	95.97
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	95.21
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	95.13
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	94.39
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	94.16
1weu_A	91	Inhibitor of growth family, member 4; structural g	93.91
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	93.81
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	93.77
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	93.46
2yt5_A	66	Metal-response element-binding transcription facto	93.36
1wev_A	88	Riken cDNA 1110020M19; structural genomics, PHD do	93.13
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	93.12
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	92.78
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	92.56
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	92.25
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	92.15
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	91.88
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	91.64
3c6w_A	59	P28ING5, inhibitor of growth protein 5; chromatin,	90.53
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	90.48
1we9_A	64	PHD finger family protein; structural genomics, PH	90.29
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	90.13
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	90.05
2vnf_A	60	ING 4, P29ING4, inhibitor of growth protein 4; ace	89.73
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	89.67
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	89.34
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	89.08
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	89.05
3o7a_A	52	PHD finger protein 13 variant; PHF13, zinc finger,	89.03
3shb_A	77	E3 ubiquitin-protein ligase UHRF1; unmodified hist	88.84
1wem_A	76	Death associated transcription factor 1; structura	88.67
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	88.64
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	88.16
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	87.18
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	87.14
3i2d_A	371	E3 SUMO-protein ligase SIZ1; signal transduction,	86.84
2o35_A	105	Hypothetical protein DUF1244; helix bundle, struct	86.81
3fyb_A	104	Protein of unknown function (DUF1244); hydrocar de	86.74
2g6q_A	62	Inhibitor of growth protein 2; protein-peptide com	86.59
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	86.45
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	86.34
3asl_A	70	E3 ubiquitin-protein ligase UHRF1; histone reader	86.34
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	86.26
2e6s_A	77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	86.26
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	86.03
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	85.95
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	85.61
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	85.46
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	85.22
4fo9_A	360	E3 SUMO-protein ligase PIAS2; E3 ligase, pinit dom	85.18
1z60_A	59	TFIIH basal transcription factor complex P44 subun	84.6
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	84.18
2gmg_A	105	Hypothetical protein PF0610; winged-helix like pro	83.27
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	82.77
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	82.26
3ask_A	226	E3 ubiquitin-protein ligase UHRF1; histone reader	82.09
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	81.5
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	81.2
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	80.89
3a1b_A	159	DNA (cytosine-5)-methyltransferase 3A, histone H3;	80.82
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	80.53
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	80.43

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

Probab=99.79  E-value=1e-19  Score=92.44  Aligned_cols=51  Identities=35%  Similarity=1.090  Sum_probs=40.9

Q ss_pred             CCcccccCcCCC-------------CCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGD-------------DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~-------------~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      ++.|+||++.+.             +.++++++|+|.||.+||.+|++.+   .+||+||+++.+++
T Consensus        15 ~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~---~~CP~CR~~~~~~~   78 (81)
T 2ecl_A           15 CDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQN---NRCPLCQQDWVVQR   78 (81)
T ss_dssp             CSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTC---CBCTTTCCBCCEEE
T ss_pred             CCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhC---CCCCCcCCCcchhh
Confidence            567888876443             2255666799999999999999987   79999999988764

>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=99.76  E-value=5.9e-19  Score=93.85  Aligned_cols=52  Identities=40%  Similarity=1.084  Sum_probs=42.6

Q ss_pred             CCcccccCcCCC----------------CCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccCC
Q 035446            4 DGCCPDCKLPGD----------------DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKGS   58 (59)
Q Consensus         4 ~~~C~IC~~~~~----------------~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~~   58 (59)
                      +++|+||++.+.                +.+++.++|+|.||..||.+|++.+   .+||+||++|.+++.
T Consensus        37 ~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~---~~CP~Cr~~~~~~~~  104 (106)
T 3dpl_R           37 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTR---QVCPLDNREWEFQKY  104 (106)
T ss_dssp             SCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTC---SBCSSSCSBCCEEEC
T ss_pred             CCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHcC---CcCcCCCCcceeecC
Confidence            578999986433                2256778999999999999999986   799999999887653

>2ecm_A Ring finger and CHY zinc finger domain- containing protein 1; RCHY1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2jrj_A

Probab=99.72  E-value=8.4e-18  Score=79.31  Aligned_cols=49  Identities=20%  Similarity=0.394  Sum_probs=40.8

Q ss_pred             CCCcccccCcCCC--CCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            3 FDGCCPDCKLPGD--DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         3 ~~~~C~IC~~~~~--~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      .+..|+||++...  +..++.++|+|.||..||.+|++..   ..||+||+++.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEG---YRCPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHT---CCCTTSCCSSC
T ss_pred             CCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcC---CcCCCCCCcCC
Confidence            3578999987543  3456778999999999999999987   78999999864

>1v87_A Deltex protein 2; ring-H2 domain, zinc-binding domain, notch signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.44.1.1

Probab=99.72  E-value=6.8e-18  Score=89.65  Aligned_cols=55  Identities=25%  Similarity=0.436  Sum_probs=41.0

Q ss_pred             CCcccccCcCCCC----------------CCeEecCCCCcccHHHHHHHHHhCC--CCCCCccccccccccCC
Q 035446            4 DGCCPDCKLPGDD----------------CPLIWGACNHAFHLHCILKWVNSQT--PQAHCPMCRREWQFKGS   58 (59)
Q Consensus         4 ~~~C~IC~~~~~~----------------~~~~~~~C~H~fh~~Ci~~w~~~~~--~~~~CP~Cr~~~~~~~~   58 (59)
                      +..|+||++.+..                ..+.+++|+|.||..||.+|+....  ...+||+||+.+..+.+
T Consensus        25 ~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~~g   97 (114)
T 1v87_A           25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKTG   97 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCSS
T ss_pred             CCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCCCC
Confidence            5789999865432                2334689999999999999996421  13689999998876543

>2kiz_A E3 ubiquitin-protein ligase arkadia; ring-H2 finger, E3 ligase, Zn binding domain, metal zinc, zinc-finger, metal binding protein; NMR {Homo sapiens}

Probab=99.71  E-value=2.7e-17  Score=80.73  Aligned_cols=50  Identities=24%  Similarity=0.593  Sum_probs=41.4

Q ss_pred             CCcccccCcCCC-CCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            4 DGCCPDCKLPGD-DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         4 ~~~C~IC~~~~~-~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      +..|+||++.+. ...++.++|+|.||..||.+|++.+   .+||+||+++...
T Consensus        14 ~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~---~~CP~Cr~~~~~~   64 (69)
T 2kiz_A           14 EEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITN---KKCPICRVDIEAQ   64 (69)
T ss_dssp             CCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHC---SBCTTTCSBSCSC
T ss_pred             CCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcC---CCCcCcCccccCc
Confidence            567999987543 3456668999999999999999986   6899999988764

>1iym_A EL5; ring-H2 finger, ubiquitin ligase, DNA binding protein; NMR {Oryza sativa} SCOP: g.44.1.1

Probab=99.71  E-value=7.5e-18  Score=79.56  Aligned_cols=50  Identities=28%  Similarity=0.621  Sum_probs=38.7

Q ss_pred             CCCCcccccCcCCCC-CCeEecC-CCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            2 AFDGCCPDCKLPGDD-CPLIWGA-CNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         2 ~~~~~C~IC~~~~~~-~~~~~~~-C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      ..+..|+||++.... ..+..++ |+|.||..||.+|++.+   .+||+||+++.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~---~~CP~Cr~~~~   54 (55)
T 1iym_A            3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSH---STCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTC---CSCSSSCCCSC
T ss_pred             CCCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcC---CcCcCCCCEeE
Confidence            345789999865432 2333455 99999999999999875   78999999875

>2ep4_A Ring finger protein 24; zinc binding, ubiquitin, E3 enzyme, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=1.6e-17  Score=82.51  Aligned_cols=50  Identities=28%  Similarity=0.629  Sum_probs=40.9

Q ss_pred             CCCcccccCcCCC-CCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            3 FDGCCPDCKLPGD-DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         3 ~~~~C~IC~~~~~-~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      .+..|+||++.+. ...+..++|+|.||..||.+|++.+   ..||+||+++..
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~---~~CP~Cr~~~~~   64 (74)
T 2ep4_A           14 LHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVR---KVCPLCNMPVLQ   64 (74)
T ss_dssp             CSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHC---SBCTTTCCBCSS
T ss_pred             CCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcC---CcCCCcCccccc
Confidence            4678999997543 3445567999999999999999987   689999998764

>1x4j_A Ring finger protein 38; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=6.6e-18  Score=84.24  Aligned_cols=51  Identities=29%  Similarity=0.640  Sum_probs=41.3

Q ss_pred             CCcccccCcCCC-CCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGD-DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~-~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      +..|+||++.+. ...+..++|+|.||..||.+|++.+   ..||+||+++....
T Consensus        23 ~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~~---~~CP~Cr~~~~~~~   74 (75)
T 1x4j_A           23 QTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKAN---RTCPICRADSGPSS   74 (75)
T ss_dssp             CCEETTTTEECCBTCEEEEETTTEEEETTHHHHHHHHC---SSCTTTCCCCCCCC
T ss_pred             CCCCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHcC---CcCcCcCCcCCCCC
Confidence            467999996543 3345567999999999999999986   78999999887654

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=3.3e-17  Score=81.23  Aligned_cols=50  Identities=24%  Similarity=0.360  Sum_probs=41.5

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      +..|+||++...+ ++.+++|||.||..||.+|++..   ..||+||+++...+
T Consensus        15 ~~~C~IC~~~~~~-p~~~~~CgH~fC~~Ci~~~~~~~---~~CP~Cr~~~~~~~   64 (72)
T 2djb_A           15 YILCSICKGYLID-ATTITECLHTFCKSCIVRHFYYS---NRCPKCNIVVHQTQ   64 (72)
T ss_dssp             GGSCTTTSSCCSS-CEECSSSCCEECHHHHHHHHHHC---SSCTTTCCCCCSSC
T ss_pred             CCCCCCCChHHHC-cCEECCCCCHHHHHHHHHHHHcC---CcCCCcCcccCccc
Confidence            4689999876554 56656999999999999999885   78999999887654

>2ect_A Ring finger protein 126; metal binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.69  E-value=2.1e-17  Score=82.78  Aligned_cols=51  Identities=31%  Similarity=0.687  Sum_probs=41.8

Q ss_pred             CCcccccCcCCC-CCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGD-DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~-~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      +..|+||++.+. ...+..++|+|.||..||.+|++.+   ..||+||+++..++
T Consensus        15 ~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~---~~CP~Cr~~~~~~~   66 (78)
T 2ect_A           15 GLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQH---DSCPVCRKSLTGQN   66 (78)
T ss_dssp             SCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTT---CSCTTTCCCCCCSC
T ss_pred             CCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcC---CcCcCcCCccCCcc
Confidence            568999987544 3455667999999999999999876   78999999887654

>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus}

Probab=99.68  E-value=2e-17  Score=81.33  Aligned_cols=51  Identities=24%  Similarity=0.553  Sum_probs=41.4

Q ss_pred             CCcccccCcCCC-----CCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGD-----DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~-----~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      +..|+||++...     +..++.++|||.||..||.+|++.+   ..||+||+++...+
T Consensus        10 ~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~~~~~~   65 (71)
T 3ng2_A           10 TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA---NTCPTCRKKINHKR   65 (71)
T ss_dssp             CCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHC---SBCTTTCCBCCCCS
T ss_pred             CCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcC---CCCCCCCCccChhh
Confidence            567999986432     2344668999999999999999987   79999999987654

>2l0b_A E3 ubiquitin-protein ligase praja-1; zinc finger, NESG, structural genomics, PSI-2, protein struc initiative; NMR {Homo sapiens}

Probab=99.68  E-value=2.5e-17  Score=84.98  Aligned_cols=49  Identities=29%  Similarity=0.655  Sum_probs=39.3

Q ss_pred             CCcccccCcCCC-CCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            4 DGCCPDCKLPGD-DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         4 ~~~C~IC~~~~~-~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      +..|+||++.+. +..+..++|+|.||..||.+|++.+   .+||+||+++..
T Consensus        40 ~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~~---~~CP~Cr~~~~~   89 (91)
T 2l0b_A           40 EMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKS---GTCPVCRCMFPP   89 (91)
T ss_dssp             CSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTTT---CBCTTTCCBSSC
T ss_pred             CCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHcC---CcCcCcCccCCC
Confidence            457999986443 3345557899999999999999876   799999998754

>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=99.68  E-value=2.5e-18  Score=92.83  Aligned_cols=51  Identities=41%  Similarity=1.118  Sum_probs=0.5

Q ss_pred             CCcccccCcCCC----------------CCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGD----------------DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~----------------~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      ++.|+||++.+.                +.+++.++|+|.||..||.+|++.+   .+||+||++|.+++
T Consensus        48 ~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~---~~CP~Cr~~~~~~k  114 (117)
T 4a0k_B           48 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTR---QVCPLDNREWEFQK  114 (117)
T ss_dssp             C---------------------------------------------------------------------
T ss_pred             CCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcC---CcCCCCCCeeeeec
Confidence            578999986433                2245557999999999999999986   79999999998765

>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=2e-17  Score=80.84  Aligned_cols=49  Identities=22%  Similarity=0.561  Sum_probs=39.5

Q ss_pred             CCcccccCcCCC-----CCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            4 DGCCPDCKLPGD-----DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         4 ~~~C~IC~~~~~-----~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      +..|+||++...     ...++.++|||.||..||.+|++.+   ..||+||+++..
T Consensus        15 ~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~~~~   68 (69)
T 2ea6_A           15 TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA---NTCPTCRKKINH   68 (69)
T ss_dssp             CCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHHC---SSCTTTCCCCCC
T ss_pred             CCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHcC---CCCCCCCCccCc
Confidence            568999986432     2334668999999999999999986   799999998764

>2ct2_A Tripartite motif protein 32; zinc-finger protein HT2A, TAT- interacting protein, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=2.1e-16  Score=80.31  Aligned_cols=54  Identities=20%  Similarity=0.386  Sum_probs=41.8

Q ss_pred             CCcccccCcCCCC--CCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGDD--CPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~~--~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      +..|+||++.+.+  ...+.++|||.||..||.+|++.......||+||+++...+
T Consensus        15 ~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   70 (88)
T 2ct2_A           15 VLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRITS   70 (88)
T ss_dssp             CCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCSS
T ss_pred             CCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccchh
Confidence            4689999865443  22455799999999999999998533468999999887643

>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding; HET: SUC; 1.50A {Homo sapiens}

Probab=99.67  E-value=3.3e-17  Score=79.02  Aligned_cols=51  Identities=24%  Similarity=0.534  Sum_probs=40.9

Q ss_pred             CCcccccCcCCC-----CCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGD-----DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~-----~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      +..|+||++...     ...++.++|||.||..||.+|++.+   ..||+||+++..++
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~~~~~~   58 (64)
T 2xeu_A            3 MVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA---NTCPTCRKKINHKR   58 (64)
T ss_dssp             CCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHHC---SBCTTTCCBCTTTC
T ss_pred             CCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHcC---CCCCCCCccCCccc
Confidence            568999986432     2344567999999999999999986   79999999887653

>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid herpesvirus 1} SCOP: g.44.1.1

Probab=99.66  E-value=9.8e-17  Score=78.46  Aligned_cols=49  Identities=27%  Similarity=0.644  Sum_probs=40.7

Q ss_pred             CCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            3 FDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      .+..|+||++...+ +.+.++|||.||..|+.+|++.+   ..||+||+++..
T Consensus         4 ~~~~C~IC~~~~~~-~~~~~~C~H~fc~~Ci~~~~~~~---~~CP~Cr~~~~~   52 (68)
T 1chc_A            4 VAERCPICLEDPSN-YSMALPCLHAFCYVCITRWIRQN---PTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCS-CEEETTTTEEESTTHHHHHHHHS---CSTTTTCCCCCC
T ss_pred             CCCCCeeCCccccC-CcEecCCCCeeHHHHHHHHHhCc---CcCcCCChhhHh
Confidence            45789999876554 44568999999999999999886   799999998753

>2ecn_A Ring finger protein 141; RNF141, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=5.3e-17  Score=79.87  Aligned_cols=48  Identities=29%  Similarity=0.654  Sum_probs=39.8

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      +..|+||++...+   +.++|+|.||..||.+|+...   ..||+||+++...+
T Consensus        15 ~~~C~IC~~~~~~---~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~~~~~~   62 (70)
T 2ecn_A           15 EEECCICMDGRAD---LILPCAHSFCQKCIDKWSDRH---RNCPICRLQMTGAN   62 (70)
T ss_dssp             CCCCSSSCCSCCS---EEETTTEEECHHHHHHSSCCC---SSCHHHHHCTTCCC
T ss_pred             CCCCeeCCcCccC---cccCCCCcccHHHHHHHHHCc---CcCCCcCCcccCCC
Confidence            4689999876655   457999999999999999864   79999999887543

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=2.2e-16  Score=78.03  Aligned_cols=53  Identities=25%  Similarity=0.525  Sum_probs=41.4

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccCC
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKGS   58 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~~   58 (59)
                      +..|+||++...+ ++. ++|||.||..||.+|++.......||+||+++..++.
T Consensus        20 ~~~C~IC~~~~~~-~~~-~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~   72 (73)
T 2ysl_A           20 EVICPICLDILQK-PVT-IDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNAI   72 (73)
T ss_dssp             CCBCTTTCSBCSS-EEE-CTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCCC
T ss_pred             CCEeccCCcccCC-eEE-cCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCcccC
Confidence            5689999876554 343 5999999999999999743334689999999887653

>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=3.5e-16  Score=79.55  Aligned_cols=52  Identities=29%  Similarity=0.807  Sum_probs=40.8

Q ss_pred             CCcccccCcCCC-CCCeEecCCC-----CcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGD-DCPLIWGACN-----HAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~-~~~~~~~~C~-----H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      +..|.||++.++ +.++ +++|+     |.||.+||.+|+..+. ..+||+||.++.++.
T Consensus        15 ~~~C~IC~~~~~~~~~l-~~pC~C~Gs~h~fH~~Cl~~Wl~~~~-~~~CplCr~~~~~~~   72 (80)
T 2d8s_A           15 QDICRICHCEGDDESPL-ITPCHCTGSLHFVHQACLQQWIKSSD-TRCCELCKYEFIMET   72 (80)
T ss_dssp             SCCCSSSCCCCCSSSCE-ECSSSCCSSSCCEETTHHHHHHHHHC-CSBCSSSCCBCCCCC
T ss_pred             CCCCeEcCccccCCCee-EeccccCCcCCeeCHHHHHHHHhhCC-CCCCCCCCCeeecCc
Confidence            568999996544 3344 57996     9999999999999852 258999999987654

>1g25_A CDK-activating kinase assembly factor MAT1; ring finger (C3HC4), metal binding protein; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=99.62  E-value=2.9e-16  Score=76.38  Aligned_cols=52  Identities=23%  Similarity=0.507  Sum_probs=39.8

Q ss_pred             CCcccccCc-CCCCC--CeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKL-PGDDC--PLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~-~~~~~--~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      +..|+||++ ...+.  ..+.++|||+||..||.+|+...  ...||+||+++...+
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~--~~~CP~Cr~~~~~~~   57 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRG--AGNCPECGTPLRKSN   57 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTT--SSSCTTTCCCCSSCC
T ss_pred             CCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcC--CCcCCCCCCcccccc
Confidence            568999987 33322  23457999999999999998764  268999999887654

>3lrq_A E3 ubiquitin-protein ligase TRIM37; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; HET: MSE; 2.29A {Homo sapiens}

Probab=99.62  E-value=3.8e-16  Score=81.70  Aligned_cols=51  Identities=27%  Similarity=0.568  Sum_probs=41.2

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      +..|+||++.+.+ ++..++|||.||..||.+|+....  ..||+||.++...+
T Consensus        22 ~~~C~IC~~~~~~-p~~~~~CgH~FC~~Ci~~~~~~~~--~~CP~Cr~~~~~~~   72 (100)
T 3lrq_A           22 VFRCFICMEKLRD-ARLCPHCSKLCCFSCIRRWLTEQR--AQCPHCRAPLQLRE   72 (100)
T ss_dssp             HTBCTTTCSBCSS-EEECTTTCCEEEHHHHHHHHHHTC--SBCTTTCCBCCGGG
T ss_pred             CCCCccCCccccC-ccccCCCCChhhHHHHHHHHHHCc--CCCCCCCCcCCHHH
Confidence            4689999876554 554479999999999999999863  58999999886543

>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=7.1e-16  Score=75.17  Aligned_cols=50  Identities=22%  Similarity=0.468  Sum_probs=39.3

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      +..|+||++...+ ++. ++|||.||..||.+|++..  ...||+||+++..++
T Consensus        15 ~~~C~IC~~~~~~-p~~-~~CgH~fC~~Ci~~~~~~~--~~~CP~Cr~~~~~~~   64 (66)
T 2ecy_A           15 KYKCEKCHLVLCS-PKQ-TECGHRFCESCMAALLSSS--SPKCTACQESIVKDK   64 (66)
T ss_dssp             CEECTTTCCEESS-CCC-CSSSCCCCHHHHHHHHTTS--SCCCTTTCCCCCTTT
T ss_pred             CCCCCCCChHhcC-eeE-CCCCCHHHHHHHHHHHHhC--cCCCCCCCcCCChhh
Confidence            4679999865544 333 5999999999999999643  268999999987654

>4ayc_A E3 ubiquitin-protein ligase RNF8; DNA damage, K63 chains; HET: CPQ; 1.90A {Homo sapiens} PDB: 4epo_C

Probab=99.59  E-value=4.2e-16  Score=85.38  Aligned_cols=47  Identities=26%  Similarity=0.605  Sum_probs=38.7

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      +..|+||++...+ ++ .++|||.||..||.+|+..+   ..||+||+++..
T Consensus        53 ~~~C~iC~~~~~~-~~-~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~~~~   99 (138)
T 4ayc_A           53 ELQCIICSEYFIE-AV-TLNCAHSFCSYCINEWMKRK---IECPICRKDIKS   99 (138)
T ss_dssp             HSBCTTTCSBCSS-EE-EETTSCEEEHHHHHHHTTTC---SBCTTTCCBCCC
T ss_pred             cCCCcccCcccCC-ce-ECCCCCCccHHHHHHHHHcC---CcCCCCCCcCCC
Confidence            3579999876654 33 46999999999999999876   789999998764

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=2.8e-15  Score=75.56  Aligned_cols=46  Identities=22%  Similarity=0.481  Sum_probs=38.3

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      +..|+||++...+ ++ +++|||.||..||.+|++..   ..||+||+++.
T Consensus        15 ~~~C~IC~~~~~~-p~-~~~CgH~fC~~Ci~~~~~~~---~~CP~Cr~~~~   60 (81)
T 2csy_A           15 PFRCFICRQAFQN-PV-VTKCRHYFCESCALEHFRAT---PRCYICDQPTG   60 (81)
T ss_dssp             CSBCSSSCSBCCS-EE-ECTTSCEEEHHHHHHHHHHC---SBCSSSCCBCC
T ss_pred             CCCCcCCCchhcC-ee-EccCCCHhHHHHHHHHHHCC---CcCCCcCcccc
Confidence            4579999876554 44 47999999999999999875   78999999875

>2d8t_A Dactylidin, ring finger protein 146; RNF146, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.58  E-value=3.7e-16  Score=77.19  Aligned_cols=48  Identities=23%  Similarity=0.410  Sum_probs=39.0

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      +..|+||++...+ ++ .++|||.||..||.+|+...   ..||+||+.+...
T Consensus        15 ~~~C~IC~~~~~~-~~-~~~CgH~fC~~Ci~~~~~~~---~~CP~Cr~~~~~~   62 (71)
T 2d8t_A           15 VPECAICLQTCVH-PV-SLPCKHVFCYLCVKGASWLG---KRCALCRQEIPED   62 (71)
T ss_dssp             CCBCSSSSSBCSS-EE-EETTTEEEEHHHHHHCTTCS---SBCSSSCCBCCHH
T ss_pred             CCCCccCCcccCC-CE-EccCCCHHHHHHHHHHHHCC---CcCcCcCchhCHh
Confidence            4679999876554 33 35899999999999999876   7899999987643

>1t1h_A Gspef-atpub14, armadillo repeat containing protein; ubiquitin ligase, E3 ligase, U-BOX,; NMR {Arabidopsis thaliana} SCOP: g.44.1.2

Probab=99.58  E-value=1.5e-15  Score=75.92  Aligned_cols=51  Identities=20%  Similarity=0.350  Sum_probs=40.7

Q ss_pred             CCCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            2 AFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         2 ~~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      +.+..|+||++...+ ++. ++|||+||+.||.+|+..+  ...||+||+++...
T Consensus         6 ~~~~~C~IC~~~~~~-Pv~-~~CgH~fc~~Ci~~~~~~~--~~~CP~C~~~~~~~   56 (78)
T 1t1h_A            6 PEYFRCPISLELMKD-PVI-VSTGQTYERSSIQKWLDAG--HKTCPKSQETLLHA   56 (78)
T ss_dssp             SSSSSCTTTSCCCSS-EEE-ETTTEEEEHHHHHHHHTTT--CCBCTTTCCBCSSC
T ss_pred             cccCCCCCccccccC-CEE-cCCCCeecHHHHHHHHHHC--cCCCCCCcCCCChh
Confidence            446789999876554 444 5999999999999999863  27899999988654

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens}

Probab=99.58  E-value=1.1e-15  Score=79.56  Aligned_cols=49  Identities=22%  Similarity=0.377  Sum_probs=40.0

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      +..|+||++...+ ++.+++|||.||..||.+|+..+   ..||+||.++...
T Consensus        22 ~~~C~IC~~~~~~-p~~~~~CgH~fC~~Ci~~~~~~~---~~CP~Cr~~~~~~   70 (99)
T 2y43_A           22 LLRCGICFEYFNI-AMIIPQCSHNYCSLCIRKFLSYK---TQCPTCCVTVTEP   70 (99)
T ss_dssp             HTBCTTTCSBCSS-EEECTTTCCEEEHHHHHHHHTTC---CBCTTTCCBCCGG
T ss_pred             CCCcccCChhhCC-cCEECCCCCHhhHHHHHHHHHCC---CCCCCCCCcCChh
Confidence            3679999876554 55545999999999999999875   7999999987753

>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens}

Probab=99.58  E-value=1.3e-15  Score=75.78  Aligned_cols=50  Identities=20%  Similarity=0.397  Sum_probs=39.3

Q ss_pred             CCcccccCcCCCCCCeEecC-CCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGA-CNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~-C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      +..|+||++.+.+ ++. ++ |||.||..||.+|++... ...||+||+++...
T Consensus        15 ~~~C~IC~~~~~~-p~~-~~~CgH~fC~~Ci~~~~~~~~-~~~CP~Cr~~~~~~   65 (74)
T 2yur_A           15 ELLCLICKDIMTD-AVV-IPCCGNSYCDECIRTALLESD-EHTCPTCHQNDVSP   65 (74)
T ss_dssp             GGSCSSSCCCCTT-CEE-CSSSCCEECTTHHHHHHHHSS-SSCCSSSCCSSCCT
T ss_pred             CCCCcCCChHHhC-CeE-cCCCCCHHHHHHHHHHHHhcC-CCcCCCCCCcCCCc
Confidence            5689999876554 555 57 999999999999998752 25899999976543

>2ckl_A Polycomb group ring finger protein 4; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_B 2h0d_A

Probab=99.56  E-value=2.5e-15  Score=79.21  Aligned_cols=49  Identities=22%  Similarity=0.438  Sum_probs=40.5

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      +..|+||++...+ ++.+++|||+||..||.+|+..+   ..||+||..+...
T Consensus        15 ~~~C~IC~~~~~~-p~~~~~CgH~fC~~Ci~~~~~~~---~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           15 HLMCVLCGGYFID-ATTIIECLHSFCKTCIVRYLETS---KYCPICDVQVHKT   63 (108)
T ss_dssp             GTBCTTTSSBCSS-EEEETTTCCEEEHHHHHHHHTSC---SBCTTTCCBSCSS
T ss_pred             cCCCccCChHHhC-cCEeCCCCChhhHHHHHHHHHhC---CcCcCCCcccccc
Confidence            5689999876554 55556999999999999999876   7899999987653

>1e4u_A Transcriptional repressor NOT4; gene regulation, transcriptional control; NMR {Homo sapiens} SCOP: g.44.1.1 PDB: 1ur6_B

Probab=99.56  E-value=4e-15  Score=75.26  Aligned_cols=52  Identities=19%  Similarity=0.394  Sum_probs=38.7

Q ss_pred             CCcccccCcCCCCC--CeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGDDC--PLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~~~--~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      +.+||||+++....  .+..++|||+||..|+.+++...  ...||+||+++....
T Consensus        11 ~~~CpICle~~~~~d~~~~p~~CGH~fC~~Cl~~~~~~~--~~~CP~CR~~~~~~~   64 (78)
T 1e4u_A           11 PVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDE--NGLCPACRKPYPEDP   64 (78)
T ss_dssp             CCBCTTTCCBCCTTTTTCCSSTTSCCCCHHHHHHHTTSS--CSBCTTTCCBCSSCS
T ss_pred             CCcCCccCccCccccccccccCCCCCcCHHHHHHHHhcC--CCCCCCCCCccCCCc
Confidence            46899999876432  22222499999999999998653  368999999887543

>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=5.1e-15  Score=71.44  Aligned_cols=44  Identities=30%  Similarity=0.648  Sum_probs=35.0

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMC   49 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~C   49 (59)
                      +..|+||++...+ ++. ++|||.||..||.+|++.......||+|
T Consensus        20 ~~~C~IC~~~~~~-p~~-~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           20 EVICPICLDILQK-PVT-IDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCBCTTTCSBCSS-CEE-CTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             CCCCCcCCchhCC-eEE-eCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            5689999876554 444 5999999999999999864334689998

>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.55  E-value=5.8e-15  Score=74.25  Aligned_cols=51  Identities=31%  Similarity=0.690  Sum_probs=40.2

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCC---CCCCCcccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQT---PQAHCPMCRREWQFK   56 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~---~~~~CP~Cr~~~~~~   56 (59)
                      +..|+||++...+ ++ .++|||.||..||.+|+....   ....||+||.++...
T Consensus        19 ~~~C~IC~~~~~~-p~-~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecw_A           19 EVTCPICLELLKE-PV-SADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFG   72 (85)
T ss_dssp             TTSCTTTCSCCSS-CE-ECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTT
T ss_pred             CCCCcCCChhhCc-ce-eCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHH
Confidence            5689999876554 44 369999999999999999831   136899999988754

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=99.55  E-value=1.5e-15  Score=81.49  Aligned_cols=50  Identities=24%  Similarity=0.588  Sum_probs=40.3

Q ss_pred             CCcccccCcCCCC-----CCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            4 DGCCPDCKLPGDD-----CPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         4 ~~~C~IC~~~~~~-----~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      +..|+||++...+     ..++.++|||+||..||.+|++.+   ..||+||+.+...
T Consensus         7 ~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~~~~~   61 (133)
T 4ap4_A            7 TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA---NTCPTCRKKINHK   61 (133)
T ss_dssp             SCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTC---SBCTTTCCBCTTT
T ss_pred             CCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhC---CCCCCCCCcCccc
Confidence            5689999865332     234567999999999999999886   6999999988754

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

Probab=99.55  E-value=4e-15  Score=74.79  Aligned_cols=52  Identities=23%  Similarity=0.537  Sum_probs=40.8

Q ss_pred             CcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccCC
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKGS   58 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~~   58 (59)
                      ..|+||.+.+.. ......|+|.||..||.+|+++.. ..+||+||++|..+..
T Consensus        16 ~~C~IC~~~i~~-g~~C~~C~h~fH~~Ci~kWl~~~~-~~~CP~Cr~~w~~~~~   67 (74)
T 2ct0_A           16 KICNICHSLLIQ-GQSCETCGIRMHLPCVAKYFQSNA-EPRCPHCNDYWPHEIP   67 (74)
T ss_dssp             CBCSSSCCBCSS-SEECSSSCCEECHHHHHHHSTTCS-SCCCTTTCSCCCSCCC
T ss_pred             CcCcchhhHccc-CCccCCCCchhhHHHHHHHHHhcC-CCCCCCCcCcCCCCCC
Confidence            679999865443 233349999999999999998753 3689999999987654

>2ecv_A Tripartite motif-containing protein 5; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=1e-14  Score=73.33  Aligned_cols=52  Identities=27%  Similarity=0.583  Sum_probs=40.2

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhC---CCCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQ---TPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~---~~~~~CP~Cr~~~~~~~   57 (59)
                      +..|+||++...+ ++. ++|||.||..||.+|+...   .....||+||..+...+
T Consensus        19 ~~~C~IC~~~~~~-p~~-~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~   73 (85)
T 2ecv_A           19 EVTCPICLELLTQ-PLS-LDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPEN   73 (85)
T ss_dssp             CCCCTTTCSCCSS-CBC-CSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSS
T ss_pred             CCCCCCCCcccCC-cee-CCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHh
Confidence            5689999876554 333 5999999999999999871   12378999999887543

>1jm7_A BRCA1, breast cancer type 1 susceptibility protein; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=99.52  E-value=7.7e-15  Score=77.32  Aligned_cols=51  Identities=27%  Similarity=0.658  Sum_probs=40.2

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      +..|+||++...+ ++. ++|||.||..||.+|+..+.+...||+||.++...
T Consensus        21 ~~~C~IC~~~~~~-p~~-~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   71 (112)
T 1jm7_A           21 ILECPICLELIKE-PVS-TKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR   71 (112)
T ss_dssp             HTSCSSSCCCCSS-CCB-CTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTT
T ss_pred             CCCCcccChhhcC-eEE-CCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHh
Confidence            3579999876554 333 59999999999999999764345899999987754

>2ecj_A Tripartite motif-containing protein 39; TRIM39, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=1.6e-14  Score=68.44  Aligned_cols=44  Identities=27%  Similarity=0.684  Sum_probs=34.1

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMC   49 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~C   49 (59)
                      +..|+||++...+. +. ++|||.||..||.+|+........||+|
T Consensus        15 ~~~C~IC~~~~~~p-~~-~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           15 EASCSVCLEYLKEP-VI-IECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCBCSSSCCBCSSC-CC-CSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             CCCCccCCcccCcc-Ee-CCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            56899998765553 33 6999999999999997652234789998

>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing, mRNA splicing; NMR {Homo sapiens}

Probab=99.51  E-value=1.3e-14  Score=74.46  Aligned_cols=49  Identities=20%  Similarity=0.398  Sum_probs=38.5

Q ss_pred             CCCcccccCcCCCCCCeEecC-CCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            3 FDGCCPDCKLPGDDCPLIWGA-CNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~-C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      .+..|+||++.+.+ ++. ++ |||+||..||.+|+.... ...||+||.++.
T Consensus        12 ~~~~C~IC~~~~~~-p~~-~~~CgH~fC~~Ci~~~~~~~~-~~~CP~Cr~~~~   61 (92)
T 3ztg_A           12 DELLCLICKDIMTD-AVV-IPCCGNSYCDECIRTALLESD-EHTCPTCHQNDV   61 (92)
T ss_dssp             TTTEETTTTEECSS-CEE-CTTTCCEECHHHHHHHHHHCT-TCCCTTTCCSSC
T ss_pred             cCCCCCCCChhhcC-ceE-CCCCCCHHHHHHHHHHHHhcC-CCcCcCCCCcCC
Confidence            35689999865554 554 57 999999999999998642 258999999873

>2egp_A Tripartite motif-containing protein 34; ZF-C3HC4 domain, tripartite motif protein 34, interferon- responsive finger protein 1; NMR {Homo sapiens}

Probab=99.51  E-value=1.7e-15  Score=75.72  Aligned_cols=52  Identities=25%  Similarity=0.537  Sum_probs=39.9

Q ss_pred             CCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhC----CCCCCCcccccccccc
Q 035446            3 FDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQ----TPQAHCPMCRREWQFK   56 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~----~~~~~CP~Cr~~~~~~   56 (59)
                      .+..|+||++...+ ++. ++|||.||..||.+|+...    .....||+||.++...
T Consensus        11 ~~~~C~IC~~~~~~-p~~-l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~   66 (79)
T 2egp_A           11 EEVTCPICLELLTE-PLS-LDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFE   66 (79)
T ss_dssp             CCCEETTTTEECSS-CCC-CSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSS
T ss_pred             cCCCCcCCCcccCC-eeE-CCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHh
Confidence            35689999876554 333 5999999999999999863    1136899999988654

>2ckl_B Ubiquitin ligase protein RING2; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_C 2h0d_B

Probab=99.51  E-value=1.5e-14  Score=80.88  Aligned_cols=48  Identities=27%  Similarity=0.558  Sum_probs=39.2

Q ss_pred             CcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      ..|+||++...+ ++.+++|||.||..||.+|+...  ...||+||.++..
T Consensus        55 ~~C~IC~~~~~~-p~~~~~CgH~fC~~Ci~~~~~~~--~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           55 LMCPICLDMLKN-TMTTKECLHRFCADCIITALRSG--NKECPTCRKKLVS  102 (165)
T ss_dssp             HBCTTTSSBCSS-EEEETTTCCEEEHHHHHHHHHTT--CCBCTTTCCBCCS
T ss_pred             CCCcccChHhhC-cCEeCCCCChhHHHHHHHHHHhC--cCCCCCCCCcCCC
Confidence            379999876554 55556999999999999999973  2789999998753

>3fl2_A E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA damage, DNA repair, ring finger domain, metal binding, DNA replication; 1.75A {Homo sapiens}

Probab=99.50  E-value=1.1e-14  Score=78.32  Aligned_cols=48  Identities=23%  Similarity=0.433  Sum_probs=38.6

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      +..|+||++...+ ++. ++|||.||..||.+|+..+  ...||+||+++..
T Consensus        52 ~~~C~IC~~~~~~-p~~-~~CgH~fC~~Ci~~~~~~~--~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           52 TFQCICCQELVFR-PIT-TVCQHNVCKDCLDRSFRAQ--VFSCPACRYDLGR   99 (124)
T ss_dssp             HTBCTTTSSBCSS-EEE-CTTSCEEEHHHHHHHHHTT--CCBCTTTCCBCCT
T ss_pred             CCCCCcCChHHcC-cEE-eeCCCcccHHHHHHHHhHC--cCCCCCCCccCCC
Confidence            3579999876554 443 5999999999999999854  2589999998865

>3hct_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 3hcu_A 2eci_A 2jmd_A

Probab=99.49  E-value=2.5e-14  Score=76.50  Aligned_cols=49  Identities=22%  Similarity=0.474  Sum_probs=39.5

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      +..|+||++...+ ++. ++|||.||..||.+|+....  ..||+||.++...
T Consensus        18 ~~~C~IC~~~~~~-p~~-~~CgH~fC~~Ci~~~~~~~~--~~CP~Cr~~~~~~   66 (118)
T 3hct_A           18 KYECPICLMALRE-AVQ-TPCGHRFCKACIIKSIRDAG--HKCPVDNEILLEN   66 (118)
T ss_dssp             GGBCTTTCSBCSS-EEE-CTTSCEEEHHHHHHHHHHHC--SBCTTTCCBCCGG
T ss_pred             CCCCCcCChhhcC-eEE-CCcCChhhHHHHHHHHhhCC--CCCCCCCCCcCHH
Confidence            4689999876554 343 69999999999999998862  4899999988754

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=99.48  E-value=1.4e-14  Score=77.71  Aligned_cols=51  Identities=24%  Similarity=0.553  Sum_probs=40.1

Q ss_pred             CCcccccCcCCC-----CCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGD-----DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~-----~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      +..|+||++...     ....+.++|||.||..||.+|++..   .+||+||+++..++
T Consensus        72 ~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~~~~~~  127 (133)
T 4ap4_A           72 TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA---NTCPTCRKKINHKR  127 (133)
T ss_dssp             SCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHC---SBCTTTCCBCCGGG
T ss_pred             CCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcC---CCCCCCCCcCChhc
Confidence            457999975432     2234567999999999999999987   79999999887653

>1rmd_A RAG1; V(D)J recombination, antibody, MAD, ring finger, zinc binuclear cluster, zinc finger, DNA-binding protein; 2.10A {Mus musculus} SCOP: g.37.1.1 g.44.1.1

Probab=99.46  E-value=2.9e-14  Score=75.88  Aligned_cols=50  Identities=28%  Similarity=0.540  Sum_probs=39.9

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      +..|+||++...+ ++. ++|||.||..||.+|+....  ..||+||.++...+
T Consensus        23 ~~~C~IC~~~~~~-p~~-~~CgH~fC~~Ci~~~~~~~~--~~CP~Cr~~~~~~~   72 (116)
T 1rmd_A           23 SISCQICEHILAD-PVE-TSCKHLFCRICILRCLKVMG--SYCPSCRYPCFPTD   72 (116)
T ss_dssp             HTBCTTTCSBCSS-EEE-CTTSCEEEHHHHHHHHHHTC--SBCTTTCCBCCGGG
T ss_pred             CCCCCCCCcHhcC-cEE-cCCCCcccHHHHHHHHhHCc--CcCCCCCCCCCHhh
Confidence            3579999876554 444 69999999999999999842  68999999887543

>2vje_A E3 ubiquitin-protein ligase MDM2; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_A* 2hdp_A

Probab=99.44  E-value=5.8e-14  Score=68.43  Aligned_cols=48  Identities=23%  Similarity=0.445  Sum_probs=37.8

Q ss_pred             CCcccccCcCCCCCCeEecCCCCc-ccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHA-FHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~-fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      +..|+||++...+..+..++|||. |+.+|+.+|++.+   ..||+||+++.
T Consensus         8 ~~~C~IC~~~~~~~~~~~~pCgH~~~C~~C~~~~~~~~---~~CPiCR~~i~   56 (64)
T 2vje_A            8 IEPCVICQGRPKNGCIVHGKTGHLMACFTCAKKLKKRN---KPCPVCRQPIQ   56 (64)
T ss_dssp             GSCCTTTSSSCSCEEEEETTEEEEEECHHHHHHHHHTT---CCCTTTCCCCC
T ss_pred             cCCCCcCCCCCCCEEEECCCCCChhhHHHHHHHHHHcC---CcCCCcCcchh
Confidence            568999987555432223499999 8999999999875   68999999875

>1z6u_A NP95-like ring finger protein isoform B; structural genomics consortium, ligase, ubiquitin-protein ligase, cell cycle regulation, SGC; 2.10A {Homo sapiens}

Probab=99.43  E-value=6.9e-14  Score=77.74  Aligned_cols=49  Identities=22%  Similarity=0.475  Sum_probs=39.4

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      +..|+||++...+ ++. ++|||.||..||.+|+...  ...||+||.++...
T Consensus        78 ~~~C~IC~~~~~~-pv~-~~CgH~fC~~Ci~~~~~~~--~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           78 SFMCVCCQELVYQ-PVT-TECFHNVCKDCLQRSFKAQ--VFSCPACRHDLGQN  126 (150)
T ss_dssp             HTBCTTTSSBCSS-EEE-CTTSCEEEHHHHHHHHHTT--CCBCTTTCCBCCTT
T ss_pred             CCEeecCChhhcC-CEE-cCCCCchhHHHHHHHHHhC--CCcCCCCCccCCCC
Confidence            3579999876554 444 6999999999999999875  25899999988754

>2vje_B MDM4 protein; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_B*

Probab=99.42  E-value=7.3e-14  Score=67.89  Aligned_cols=49  Identities=29%  Similarity=0.595  Sum_probs=38.8

Q ss_pred             CCCcccccCcCCCCCCeEecCCCCc-ccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            3 FDGCCPDCKLPGDDCPLIWGACNHA-FHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~C~H~-fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      .+..|+||++...+..++.++|||. |+.+|+.+|++.+   ..||+||+++.
T Consensus         6 ~~~~C~IC~~~~~~~~~~~~pCgH~~~C~~C~~~~~~~~---~~CPiCR~~i~   55 (63)
T 2vje_B            6 LLKPCSLCEKRPRDGNIIHGRTGHLVTCFHCARRLKKAG---ASCPICKKEIQ   55 (63)
T ss_dssp             GGSBCTTTSSSBSCEEEEETTEEEEEECHHHHHHHHHTT---CBCTTTCCBCC
T ss_pred             cCCCCcccCCcCCCeEEEecCCCCHhHHHHHHHHHHHhC---CcCCCcCchhh
Confidence            3568999987544433444599998 9999999999775   68999999875

>2kr4_A Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ring, E3 ligase, UBL conjugation pathway; NMR {Mus musculus}

Probab=99.42  E-value=1.9e-13  Score=69.77  Aligned_cols=50  Identities=14%  Similarity=0.030  Sum_probs=40.8

Q ss_pred             CCCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            2 AFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         2 ~~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      +.+..||||++...+ |+. ++|||+|++.||.+|+...   .+||+|+.++...
T Consensus        12 p~~~~CpI~~~~m~d-PV~-~~cGhtf~r~~I~~~l~~~---~~cP~~~~~l~~~   61 (85)
T 2kr4_A           12 PDEFRDPLMDTLMTD-PVR-LPSGTVMDRSIILRHLLNS---PTDPFNRQMLTES   61 (85)
T ss_dssp             CTTTBCTTTCSBCSS-EEE-CTTSCEEEHHHHHHHHHHC---SBCTTTCCBCCGG
T ss_pred             chheECcccCchhcC-CeE-CCCCCEECHHHHHHHHhcC---CCCCCCcCCCChH
Confidence            446789999876555 444 5899999999999999975   7999999988654

>3knv_A TNF receptor-associated factor 2; cross-brace, alternative splicing, apoptosis, cytoplasm, metal-binding, UBL conjugation, zinc, zinc-finger; 1.90A {Homo sapiens}

Probab=99.40  E-value=7.7e-14  Score=76.94  Aligned_cols=48  Identities=21%  Similarity=0.544  Sum_probs=38.0

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      +..|+||++...+ ++. ++|||.||..||.+|+....  ..||+||.++.+
T Consensus        31 ~~~C~IC~~~~~~-pv~-~~CgH~FC~~Ci~~~~~~~~--~~CP~Cr~~~~~   78 (141)
T 3knv_A           31 KYLCSACRNVLRR-PFQ-AQCGHRYCSFCLASILSSGP--QNCAACVHEGIY   78 (141)
T ss_dssp             GGBCTTTCSBCSS-EEE-CTTSCEEEHHHHHHHGGGSC--EECHHHHHTTCC
T ss_pred             CcCCCCCChhhcC-cEE-CCCCCccCHHHHHHHHhcCC--CCCCCCCCcccc
Confidence            4689999876554 344 69999999999999998652  489999997643

>1jm7_B BARD1, BRCA1-associated ring domain protein 1; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=99.38  E-value=8.7e-14  Score=74.26  Aligned_cols=47  Identities=23%  Similarity=0.587  Sum_probs=37.6

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      +..|+||++.+.+ ++.+.+|||+||..||.+|+.     ..||+||.++...
T Consensus        22 ~~~C~IC~~~~~~-pv~~~~CgH~fC~~Ci~~~~~-----~~CP~Cr~~~~~~   68 (117)
T 1jm7_B           22 LLRCSRCTNILRE-PVCLGGCEHIFCSNCVSDCIG-----TGCPVCYTPAWIQ   68 (117)
T ss_dssp             TTSCSSSCSCCSS-CBCCCSSSCCBCTTTGGGGTT-----TBCSSSCCBCSCS
T ss_pred             CCCCCCCChHhhC-ccEeCCCCCHHHHHHHHHHhc-----CCCcCCCCcCccc
Confidence            4689999866544 555349999999999999987     4699999988654

>3l11_A E3 ubiquitin-protein ligase RNF168; E3 ligase, ring domain, DNA damage, chromatin regulator, CHR protein, DNA repair, metal-binding, nucleus; 2.12A {Homo sapiens}

Probab=99.38  E-value=2.7e-14  Score=75.89  Aligned_cols=48  Identities=27%  Similarity=0.520  Sum_probs=38.1

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      +..|+||++...+ ++. ++|||.||..||.+|+...  ...||+||..+..
T Consensus        15 ~~~C~iC~~~~~~-p~~-~~CgH~fC~~Ci~~~~~~~--~~~CP~Cr~~~~~   62 (115)
T 3l11_A           15 ECQCGICMEILVE-PVT-LPCNHTLCKPCFQSTVEKA--SLCCPFCRRRVSS   62 (115)
T ss_dssp             HHBCTTTCSBCSS-CEE-CTTSCEECHHHHCCCCCTT--TSBCTTTCCBCHH
T ss_pred             CCCCccCCcccCc-eeE-cCCCCHHhHHHHHHHHhHC--cCCCCCCCcccCc
Confidence            3579999866554 444 5999999999999999764  2689999998753

>2kre_A Ubiquitin conjugation factor E4 B; U-box domain, E3 ubiquitin ligase, E4 polyubiquitin chain EL factor, phosphoprotein, UBL conjugation pathway; NMR {Homo sapiens} PDB: 3l1x_A 3l1z_B

Probab=99.37  E-value=3.3e-13  Score=70.81  Aligned_cols=50  Identities=14%  Similarity=0.036  Sum_probs=40.4

Q ss_pred             CCCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            2 AFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         2 ~~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      +.+..||||++...+ |+. ++|||+|++.||.+|+...   .+||+||.++...
T Consensus        27 p~~~~CpI~~~~m~d-PV~-~~cGhtf~r~~I~~~l~~~---~~cP~~~~~l~~~   76 (100)
T 2kre_A           27 PDEFRDPLMDTLMTD-PVR-LPSGTIMDRSIILRHLLNS---PTDPFNRQTLTES   76 (100)
T ss_dssp             STTTBCTTTCSBCSS-EEE-ETTTEEEEHHHHHHHTTSC---SBCSSSCCBCCTT
T ss_pred             cHhhCCcCccCcccC-CeE-CCCCCEEchHHHHHHHHcC---CCCCCCCCCCChh
Confidence            346789999876555 444 4799999999999999864   7999999988754

>1wgm_A Ubiquitin conjugation factor E4A; ubiquitinating enzyme, KIAA0126, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.2

Probab=99.36  E-value=4.8e-13  Score=69.99  Aligned_cols=50  Identities=14%  Similarity=0.052  Sum_probs=40.8

Q ss_pred             CCCCcccccCcCCCCCCeEecCCC-CcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            2 AFDGCCPDCKLPGDDCPLIWGACN-HAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         2 ~~~~~C~IC~~~~~~~~~~~~~C~-H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      +.+..||||++...+ |++ ++|| |+|++.||.+|+...   .+||+||.++...
T Consensus        20 p~~~~CpI~~~~m~d-PV~-~~cG~htf~r~cI~~~l~~~---~~cP~~~~~l~~~   70 (98)
T 1wgm_A           20 CDEFLDPIMSTLMCD-PVV-LPSSRVTVDRSTIARHLLSD---QTDPFNRSPLTMD   70 (98)
T ss_dssp             CTTTBCTTTCSBCSS-EEE-CTTTCCEEEHHHHHHHTTTS---CBCTTTCSBCCTT
T ss_pred             cHhcCCcCccccccC-CeE-CCCCCeEECHHHHHHHHHhC---CCCCCCCCCCChh
Confidence            446789999876555 444 5899 999999999999875   7899999988754

>3hcs_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.20A {Homo sapiens}

Probab=99.34  E-value=9.4e-13  Score=73.80  Aligned_cols=49  Identities=22%  Similarity=0.474  Sum_probs=39.7

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      +..|+||++...+ ++. ++|||+||..||.+|+..+.  ..||+||.++...
T Consensus        18 ~~~C~IC~~~~~~-pv~-~~CgH~fC~~Ci~~~~~~~~--~~CP~Cr~~~~~~   66 (170)
T 3hcs_A           18 KYECPICLMALRE-AVQ-TPCGHRFCKACIIKSIRDAG--HKCPVDNEILLEN   66 (170)
T ss_dssp             GGBCTTTCSBCSS-EEE-CTTSCEEEHHHHHHHHHHHC--SBCTTTCCBCCGG
T ss_pred             CCCCCCCChhhcC-cEE-CCCCCHHHHHHHHHHHHhCC--CCCCCCccCcchh
Confidence            4689999876554 444 69999999999999998752  4899999988754

>2yu4_A E3 SUMO-protein ligase NSE2; SP-ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.31  E-value=3.6e-12  Score=65.96  Aligned_cols=51  Identities=24%  Similarity=0.488  Sum_probs=38.3

Q ss_pred             CCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhC---CCCCCCcc--cccc-cc
Q 035446            3 FDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQ---TPQAHCPM--CRRE-WQ   54 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~---~~~~~CP~--Cr~~-~~   54 (59)
                      .+..||||++.+.+ |+.+..|||+|++.||.+|+..+   ....+||+  |+.. +.
T Consensus         6 ~~~~CPI~~~~~~d-PV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~   62 (94)
T 2yu4_A            6 SGFTCPITKEEMKK-PVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIR   62 (94)
T ss_dssp             SCCBCTTTCSBCSS-EEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBC
T ss_pred             cEeECcCcCchhcC-CEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccC
Confidence            45789999876655 55543599999999999999874   12358999  9865 44

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=99.29  E-value=2.1e-12  Score=76.01  Aligned_cols=51  Identities=12%  Similarity=0.018  Sum_probs=40.5

Q ss_pred             CCCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            2 AFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         2 ~~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      +.+..||||++...+ |++ ++|||+|++.||.+|+..+.  .+||+||.++...
T Consensus       206 ~~~~~c~i~~~~~~d-Pv~-~~~gh~f~~~~i~~~~~~~~--~~cP~~~~~~~~~  256 (281)
T 2c2l_A          206 PDYLCGKISFELMRE-PCI-TPSGITYDRKDIEEHLQRVG--HFNPVTRSPLTQE  256 (281)
T ss_dssp             CSTTBCTTTCSBCSS-EEE-CSSCCEEETTHHHHHHHHTC--SSCTTTCCCCCGG
T ss_pred             CcccCCcCcCCHhcC-CeE-CCCCCEECHHHHHHHHHHCC--CCCcCCCCCCchh
Confidence            446789999876555 444 58999999999999998752  4599999988654

>2y1n_A E3 ubiquitin-protein ligase; ligase-transferase complex, ubiquitin ring E3 ligase; HET: PTR; 2.00A {Homo sapiens} PDB: 2y1m_A* 4a4c_A* 4a4b_A* 1fbv_A* 3vgo_A 4a49_A* 2k4d_A 2ldr_A*

Probab=99.28  E-value=2.6e-12  Score=80.37  Aligned_cols=48  Identities=27%  Similarity=0.633  Sum_probs=38.3

Q ss_pred             CcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      ..|+||++...+  .+.++|||.||..|+.+|+...  ...||+||+++...
T Consensus       333 ~~C~ICle~~~~--pv~lpCGH~FC~~Ci~~wl~~~--~~~CP~CR~~i~~~  380 (389)
T 2y1n_A          333 QLCKICAENDKD--VKIEPCGHLMCTSCLTSWQESE--GQGCPFCRCEIKGT  380 (389)
T ss_dssp             SBCTTTSSSBCC--EEEETTCCEECHHHHHHHHHHT--CSBCTTTCCBCCEE
T ss_pred             CCCCccCcCCCC--eEEeCCCChhhHHHHHHHHhcC--CCCCCCCCCccCCc
Confidence            589999876544  3446999999999999999843  26899999987653

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=99.28  E-value=6.4e-13  Score=63.07  Aligned_cols=46  Identities=22%  Similarity=0.576  Sum_probs=36.0

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      +..|+||++.+.+ ++ .++|||+||..||.+|   .   ..||+||+++....
T Consensus         6 ~~~C~IC~~~~~~-p~-~l~CgH~fC~~Ci~~~---~---~~CP~Cr~~~~~~~   51 (56)
T 1bor_A            6 FLRCQQCQAEAKC-PK-LLPCLHTLCSGCLEAS---G---MQCPICQAPWPLGA   51 (56)
T ss_dssp             CSSCSSSCSSCBC-CS-CSTTSCCSBTTTCSSS---S---SSCSSCCSSSSCCS
T ss_pred             CCCceEeCCccCC-eE-EcCCCCcccHHHHccC---C---CCCCcCCcEeecCC
Confidence            4679999876554 33 3699999999999873   2   68999999987654

>4ic3_A E3 ubiquitin-protein ligase XIAP; ring domain, zinc-finger, E3 ligase; 1.78A {Homo sapiens} PDB: 4ic2_A

Probab=99.23  E-value=2.1e-12  Score=64.27  Aligned_cols=43  Identities=23%  Similarity=0.493  Sum_probs=34.1

Q ss_pred             CCcccccCcCCCCCCeEecCCCCc-ccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHA-FHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~-fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      +..|+||++...+ + +.++|||. ||..|+.+|       ..||+||+++..
T Consensus        24 ~~~C~iC~~~~~~-~-~~~pCgH~~~C~~C~~~~-------~~CP~Cr~~i~~   67 (74)
T 4ic3_A           24 EKLCKICMDRNIA-I-VFVPCGHLVTCKQCAEAV-------DKCPMCYTVITF   67 (74)
T ss_dssp             HTBCTTTSSSBCC-E-EEETTCCBCCCHHHHTTC-------SBCTTTCCBCSE
T ss_pred             CCCCCCCCCCCCC-E-EEcCCCChhHHHHhhhcC-------ccCCCcCcCccC
Confidence            4679999865444 3 34699999 999999988       479999998764

>3htk_C E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-ring, ring, ATP-binding, chromosomal protein, coiled coil, DNA damage; 2.31A {Saccharomyces cerevisiae}

Probab=99.19  E-value=1.1e-11  Score=74.36  Aligned_cols=52  Identities=27%  Similarity=0.577  Sum_probs=41.1

Q ss_pred             CCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcc--cccccccc
Q 035446            3 FDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPM--CRREWQFK   56 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~--Cr~~~~~~   56 (59)
                      .+..||||++.+.+ |+....|||+|++.||.+|++.+ +...||+  |++.+...
T Consensus       180 ~el~CPIcl~~f~D-PVts~~CGHsFcR~cI~~~~~~~-~~~~CPvtGCr~~l~~~  233 (267)
T 3htk_C          180 IELTCPITCKPYEA-PLISRKCNHVFDRDGIQNYLQGY-TTRDCPQAACSQVVSMR  233 (267)
T ss_dssp             CCSBCTTTSSBCSS-EEEESSSCCEEEHHHHHHHSTTC-SCEECSGGGCSCEECGG
T ss_pred             eeeECcCccCcccC-CeeeCCCCCcccHHHHHHHHHhC-CCCCCCcccccCcCchh
Confidence            45789999876655 56556999999999999999864 2357999  99987654

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=99.18  E-value=1.9e-11  Score=59.02  Aligned_cols=50  Identities=18%  Similarity=0.497  Sum_probs=37.1

Q ss_pred             CCcccccCcCCCCCCeEecCCC--C---cccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACN--H---AFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~--H---~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      +..|.||++..++ +. .++|.  +   .||.+||.+|+..+. +.+||+|+.++.++
T Consensus         6 ~~~CrIC~~~~~~-~l-~~PC~C~gs~~~~H~~Cl~~W~~~~~-~~~C~~C~~~~~~r   60 (60)
T 1vyx_A            6 VPVCWICNEELGN-ER-FRACGCTGELENVHRSCLSTWLTISR-NTACQICGVVYNTR   60 (60)
T ss_dssp             CCEETTTTEECSC-CC-CCSCCCSSGGGSCCHHHHHHHHHHHT-CSBCTTTCCBCCCC
T ss_pred             CCEeEEeecCCCC-ce-ecCcCCCCchhhhHHHHHHHHHHhCC-CCccCCCCCeeecC
Confidence            4579999865333 33 35765  4   999999999998642 36899999988753

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C

Probab=99.13  E-value=3.8e-11  Score=68.63  Aligned_cols=51  Identities=12%  Similarity=0.004  Sum_probs=40.6

Q ss_pred             CCCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            2 AFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         2 ~~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      |.+..||||++...+ |++ ++|||+|++.||..|+..+.  .+||+|+.++...
T Consensus       104 p~~f~CPI~~elm~D-PV~-~~~Ghtfer~~I~~~l~~~~--~tcP~t~~~l~~~  154 (179)
T 2f42_A          104 PDYLCGKISFELMRE-PCI-TPSGITYDRKDIEEHLQRVG--HFDPVTRSPLTQD  154 (179)
T ss_dssp             CGGGBCTTTCSBCSS-EEE-CTTSCEEEHHHHHHHHHHTC--SBCTTTCCBCCGG
T ss_pred             cHhhcccCccccCCC-CeE-CCCCCEECHHHHHHHHHhCC--CCCCCCcCCCChh
Confidence            445789999876665 554 59999999999999998752  3799999988654

>1wim_A KIAA0161 protein; ring finger domain, UBCM4-interacting protein 4, UIP4, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=99.07  E-value=5.6e-11  Score=61.19  Aligned_cols=49  Identities=18%  Similarity=0.409  Sum_probs=36.4

Q ss_pred             CCcccccCcCCCCCCe-EecCCCCcccHHHHHHHHHhC----C-CCCCCcc--cccc
Q 035446            4 DGCCPDCKLPGDDCPL-IWGACNHAFHLHCILKWVNSQ----T-PQAHCPM--CRRE   52 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~-~~~~C~H~fh~~Ci~~w~~~~----~-~~~~CP~--Cr~~   52 (59)
                      +.+|+||++....... .+.+|||.||.+|+.++++.+    . ....||.  |+..
T Consensus         5 ~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            5 SSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             BCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            4689999876554333 334799999999999999752    1 1247999  9987

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.05  E-value=1.7e-10  Score=57.31  Aligned_cols=42  Identities=24%  Similarity=0.504  Sum_probs=32.5

Q ss_pred             CcccccCcCCCCCCeEecCCCCc-ccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHA-FHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~-fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      ..|+||++...+.  +.++|||. ||..|+.+    .   ..||+||+++..
T Consensus        26 ~~C~IC~~~~~~~--~~~pCgH~~~C~~C~~~----~---~~CP~Cr~~i~~   68 (75)
T 2ecg_A           26 KLCKICMDRNIAI--VFVPCGHLVTCKQCAEA----V---DKCPMCYTVITF   68 (75)
T ss_dssp             HSCSSSCSSCCCB--CCSSSCCCCBCHHHHHH----C---SBCTTTCCBCCC
T ss_pred             CCCCcCCCCCCCE--EEecCCCHHHHHHHhhC----C---CCCccCCceecC
Confidence            4799998765543  33699999 99999953    2   589999998764

>3k1l_B Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A {Drosophila melanogaster}

Probab=99.05  E-value=4.1e-11  Score=74.40  Aligned_cols=51  Identities=24%  Similarity=0.539  Sum_probs=36.4

Q ss_pred             CcccccCcCCCC---CCeE---ecCCCCcccHHHHHHHHHhCCC--------CCCCccccccccc
Q 035446            5 GCCPDCKLPGDD---CPLI---WGACNHAFHLHCILKWVNSQTP--------QAHCPMCRREWQF   55 (59)
Q Consensus         5 ~~C~IC~~~~~~---~~~~---~~~C~H~fh~~Ci~~w~~~~~~--------~~~CP~Cr~~~~~   55 (59)
                      ..|+||+....+   .+..   .+.|+|.||..||.+|+++...        ...||+||+++..
T Consensus       309 ~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~  373 (381)
T 3k1l_B          309 LRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLST  373 (381)
T ss_dssp             CSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEG
T ss_pred             ccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCc
Confidence            479999854332   2211   3489999999999999986321        1369999998764

>2yho_A E3 ubiquitin-protein ligase mylip; ligase, E2 ligase-E3 ligase complex, ring zinc-finger, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 2yhn_A

Probab=98.99  E-value=9e-11  Score=59.12  Aligned_cols=43  Identities=21%  Similarity=0.485  Sum_probs=33.3

Q ss_pred             CCcccccCcCCCCCCeEecCCCCc-ccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHA-FHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~-fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      +..|+||++...+  .+.++|||. ||..|+..|       ..||+||.++..
T Consensus        18 ~~~C~IC~~~~~~--~v~~pCgH~~~C~~C~~~~-------~~CP~Cr~~i~~   61 (79)
T 2yho_A           18 AMLCMVCCEEEIN--STFCPCGHTVCCESCAAQL-------QSCPVCRSRVEH   61 (79)
T ss_dssp             HTBCTTTSSSBCC--EEEETTCBCCBCHHHHTTC-------SBCTTTCCBCCE
T ss_pred             CCEeEEeCcccCc--EEEECCCCHHHHHHHHHhc-------CcCCCCCchhhC
Confidence            4579999865443  345699999 999999875       379999997653

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.94  E-value=4.3e-10  Score=55.22  Aligned_cols=43  Identities=26%  Similarity=0.490  Sum_probs=33.4

Q ss_pred             CCcccccCcCCCCCCeEecCCCCc-ccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHA-FHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~-fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      +..|+||++...+  +++++|||. ||..|+..    .   ..||+||+++..
T Consensus        15 ~~~C~IC~~~~~~--~v~~pCgH~~~C~~C~~~----~---~~CP~CR~~i~~   58 (68)
T 2ea5_A           15 SKDCVVCQNGTVN--WVLLPCRHTCLCDGCVKY----F---QQCPMCRQFVQE   58 (68)
T ss_dssp             SSCCSSSSSSCCC--CEETTTTBCCSCTTHHHH----C---SSCTTTCCCCCC
T ss_pred             CCCCCCcCcCCCC--EEEECCCChhhhHHHHhc----C---CCCCCCCcchhc
Confidence            4679999865443  455799999 99999983    2   589999998753

>2bay_A PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin ligase, E3 ligase; 1.50A {Saccharomyces cerevisiae} SCOP: g.44.1.2 PDB: 1n87_A

Probab=98.91  E-value=1.2e-09  Score=52.64  Aligned_cols=50  Identities=10%  Similarity=0.173  Sum_probs=39.8

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      ...|||+++...+ +++..++||+|.+++|.+|++.+   .+||+.+.++...+
T Consensus         3 ~~~CpIs~~~m~d-PV~~~~sG~~yer~~I~~~l~~~---~~cP~t~~~L~~~~   52 (61)
T 2bay_A            3 HMLCAISGKVPRR-PVLSPKSRTIFEKSLLEQYVKDT---GNDPITNEPLSIEE   52 (61)
T ss_dssp             -CCCTTTCSCCSS-EEEETTTTEEEEHHHHHHHHHHH---SBCTTTCCBCCGGG
T ss_pred             eEEecCCCCCCCC-CEEeCCCCcEEcHHHHHHHHHhC---CCCcCCcCCCChhh
Confidence            3579999876554 55544899999999999999986   67999999887654

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=98.85  E-value=2.5e-09  Score=56.15  Aligned_cols=47  Identities=26%  Similarity=0.480  Sum_probs=35.8

Q ss_pred             cccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            6 CCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         6 ~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      -|++|..+.... ..+.+|+|+||.+|+..|.++..  .+||.|+.++..
T Consensus         3 fC~~C~~Pi~iy-gRmIPCkHvFCydCa~~~~~~~~--k~Cp~C~~~V~r   49 (101)
T 3vk6_A            3 FCDKCGLPIKVY-GRMIPCKHVFCYDCAILHEKKGD--KMCPGCSDPVQR   49 (101)
T ss_dssp             BCTTTCSBCSEE-EEEETTCCEEEHHHHHHHHHTTC--CBCTTTCCBCSE
T ss_pred             ecCccCCCeEEE-eeeccccccHHHHHHHHHHhccC--CCCcCcCCeeee
Confidence            478886554432 23469999999999999987653  789999998764

>3t6p_A Baculoviral IAP repeat-containing protein 2; ring, BIR, CARD, UBA, apoptosis, ubiquitin ligase, SMAC/ ubiquitin, caspase, IAP family, SMAC mimetic; 1.90A {Homo sapiens} PDB: 1qbh_A 2l9m_A 3eb5_A 3eb6_A 4auq_B

Probab=98.80  E-value=7e-10  Score=68.46  Aligned_cols=43  Identities=21%  Similarity=0.488  Sum_probs=34.1

Q ss_pred             CCcccccCcCCCCCCeEecCCCCc-ccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHA-FHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~-fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      +..|+||++...+ + +.++|||. ||..|+..|       ..||+||.++..
T Consensus       295 ~~~C~IC~~~~~~-~-v~lpCgH~~fC~~C~~~~-------~~CP~CR~~i~~  338 (345)
T 3t6p_A          295 ERTCKVCMDKEVS-V-VFIPCGHLVVCQECAPSL-------RKCPICRGIIKG  338 (345)
T ss_dssp             TCBCTTTSSSBCC-E-EEETTCCEEECTTTGGGC-------SBCTTTCCBCCE
T ss_pred             CCCCCccCCcCCc-e-EEcCCCChhHhHHHHhcC-------CcCCCCCCCccC
Confidence            4689999875543 3 34699999 999999987       479999998763

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens}

Probab=98.68  E-value=2.5e-08  Score=58.90  Aligned_cols=52  Identities=23%  Similarity=0.537  Sum_probs=39.4

Q ss_pred             CcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccCC
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKGS   58 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~~   58 (59)
                      ..|.||.+.... ......|+|.||..|+.+|+++.. ...||.|+.+|..+..
T Consensus       181 ~~C~iC~~iv~~-g~~C~~C~~~~H~~C~~~~~~~~~-~~~CP~C~~~W~~~~~  232 (238)
T 3nw0_A          181 KICNICHSLLIQ-GQSCETCGIRMHLPCVAKYFQSNA-EPRCPHCNDYWPHEIP  232 (238)
T ss_dssp             CBCTTTCSBCSS-CEECSSSCCEECHHHHHHHTTTCS-SCBCTTTCCBCCSCCC
T ss_pred             CcCcchhhHHhC-CcccCccChHHHHHHHHHHHHhCC-CCCCCCCCCCCCCCCC
Confidence            469999754433 334446999999999999998742 3589999999987653

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=97.34  E-value=0.00025  Score=36.27  Aligned_cols=34  Identities=15%  Similarity=0.263  Sum_probs=25.4

Q ss_pred             CCCcccccCcC-CCCCCeEecCCCCcccHHHHHHH
Q 035446            3 FDGCCPDCKLP-GDDCPLIWGACNHAFHLHCILKW   36 (59)
Q Consensus         3 ~~~~C~IC~~~-~~~~~~~~~~C~H~fh~~Ci~~w   36 (59)
                      .+..|+||.+. ..+....-+.|+|+||..|+..+
T Consensus         2 ee~~C~~C~~~~~~~av~~C~~C~~~~C~~Cl~~~   36 (101)
T 2jun_A            2 EKVLCQFCDQDPAQDAVKTCVTCEVSYCDECLKAT   36 (101)
T ss_dssp             CCCBCTTCCSSSCCBCCEEETTTTEEECHHHHHHH
T ss_pred             CCCCCcCCCCCCCCCceEECCcCChHHhHHHCHHH
Confidence            46789999753 34433434799999999999983

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=96.49  E-value=0.003  Score=30.50  Aligned_cols=50  Identities=22%  Similarity=0.348  Sum_probs=34.7

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCC-CCCCCccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQT-PQAHCPMCRREWQF   55 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~-~~~~CP~Cr~~~~~   55 (59)
                      +..|.||.+.  +..+.-..|...||..|+...+.... +.=.||.|+.....
T Consensus        12 ~~~C~vC~~~--~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~~p   62 (66)
T 2lri_C           12 GARCGVCGDG--TDVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDVTP   62 (66)
T ss_dssp             TCCCTTTSCC--TTCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCCCC
T ss_pred             CCCcCCCCCC--CeEEECCCCCCceecccCCCccCcCCCCCEECccccCCCcc
Confidence            3569999643  23555678999999999987765532 12479999875443

>1wil_A KIAA1045 protein; ring finger domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: g.50.1.3

Probab=95.97  E-value=0.0082  Score=30.55  Aligned_cols=35  Identities=20%  Similarity=0.459  Sum_probs=24.4

Q ss_pred             CCCCcccccCcCCCCCCeEecCCCCcccHHHHHHH
Q 035446            2 AFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKW   36 (59)
Q Consensus         2 ~~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w   36 (59)
                      +-|+.|.||.....+...---.|+-+||..|+.+-
T Consensus        13 ~~D~~C~VC~~~t~~~l~pCRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           13 VNDEMCDVCEVWTAESLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTTCCCCSSCCSSCSSSSSCCCHHHHHHH
T ss_pred             CCCcccCccccccccceeccccccccccHhhcccc
Confidence            45788999963333322222478999999999995

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=95.21  E-value=0.0043  Score=30.28  Aligned_cols=51  Identities=24%  Similarity=0.542  Sum_probs=33.9

Q ss_pred             cccccCcCCCC-CCeEecCCCCcccHHHHHHHHHhCC-CCCCCcccccccccc
Q 035446            6 CCPDCKLPGDD-CPLIWGACNHAFHLHCILKWVNSQT-PQAHCPMCRREWQFK   56 (59)
Q Consensus         6 ~C~IC~~~~~~-~~~~~~~C~H~fh~~Ci~~w~~~~~-~~~~CP~Cr~~~~~~   56 (59)
                      .|+||....++ ..+.-..|.-.||..|+.--..... +.-.||.|+..+...
T Consensus        20 ~C~~C~~~~~~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~k~   72 (75)
T 2k16_A           20 ICPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIKKD   72 (75)
T ss_dssp             CBTTTTBCCSSCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHCSC
T ss_pred             CCCCCCCCCCCCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchhhc
Confidence            59999754433 3455568889999999975433211 235799998776543

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=95.13  E-value=0.013  Score=26.41  Aligned_cols=46  Identities=33%  Similarity=0.748  Sum_probs=30.3

Q ss_pred             cccccCcCC-CCCCeEecCCCCcccHHHHHHHHHhC-CCCCCCccccc
Q 035446            6 CCPDCKLPG-DDCPLIWGACNHAFHLHCILKWVNSQ-TPQAHCPMCRR   51 (59)
Q Consensus         6 ~C~IC~~~~-~~~~~~~~~C~H~fh~~Ci~~w~~~~-~~~~~CP~Cr~   51 (59)
                      .|.||.... .+..+.-..|...||..|+..-+... .+.-.||.|+.
T Consensus         2 ~C~vC~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGEDDKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCCCEEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            588997543 23455566889999999997533321 12246999975

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=94.39  E-value=0.019  Score=27.07  Aligned_cols=47  Identities=21%  Similarity=0.586  Sum_probs=31.8

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhC-CCCCCCcccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQ-TPQAHCPMCRRE   52 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~-~~~~~CP~Cr~~   52 (59)
                      +..|.+|...  ...+.-..|.-.||..|+..-+... .+.-.||.|+..
T Consensus        11 ~~~C~vC~~~--g~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~~   58 (61)
T 2l5u_A           11 QDYCEVCQQG--GEIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEKE   58 (61)
T ss_dssp             CSSCTTTSCC--SSEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGGG
T ss_pred             CCCCccCCCC--CcEEECCCCChhhhhhccCCCCCCCCCCceECcccccc
Confidence            4679999653  3345556888999999998754332 123479999763

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=94.16  E-value=0.087  Score=28.93  Aligned_cols=47  Identities=28%  Similarity=0.556  Sum_probs=32.0

Q ss_pred             CCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHH--------hCCCCCCCccccc
Q 035446            3 FDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVN--------SQTPQAHCPMCRR   51 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~--------~~~~~~~CP~Cr~   51 (59)
                      .++.|.+|.+..  ..+.-..|.-+||..||..-+.        ...+.=.||+|+.
T Consensus        62 ~~d~C~vC~~GG--~LlcCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~  116 (142)
T 2lbm_A           62 MDEQCRWCAEGG--NLICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHP  116 (142)
T ss_dssp             CBCSCSSSCCCS--SEEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCC
T ss_pred             CCCeecccCCCC--cEEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccC
Confidence            467799995432  2344458889999999997553        1233457999974

>1weu_A Inhibitor of growth family, member 4; structural genomics, PHD domain, ING1-like protein, DNA binding protein, NPPSFA; NMR {Mus musculus} SCOP: g.50.1.2

Probab=93.91  E-value=0.015  Score=29.71  Aligned_cols=47  Identities=21%  Similarity=0.467  Sum_probs=29.0

Q ss_pred             cccccCcCCCCCCeEecC--CC-CcccHHHHHHHHHhC-CCCCCCccccccccc
Q 035446            6 CCPDCKLPGDDCPLIWGA--CN-HAFHLHCILKWVNSQ-TPQAHCPMCRREWQF   55 (59)
Q Consensus         6 ~C~IC~~~~~~~~~~~~~--C~-H~fh~~Ci~~w~~~~-~~~~~CP~Cr~~~~~   55 (59)
                      .| ||........+.--.  |. ..||..|+.  +... .+.-.||.|+.....
T Consensus        38 yC-iC~~~~~g~MI~CD~~dC~~~WfH~~CVg--l~~~p~g~W~Cp~C~~~~~k   88 (91)
T 1weu_A           38 YC-LCHQVSYGEMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQESGP   88 (91)
T ss_dssp             CS-TTCCBCCSCCCCCSCSSCSCCCCCSTTTT--CSSCCCSSCCCTTTCCCCSS
T ss_pred             EE-ECCCCCCCCEeEecCCCCCCCCEecccCC--cCcCCCCCEECcCccCcCCc
Confidence            46 887644444444445  55 689999997  3221 123589999876443

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=93.81  E-value=0.014  Score=30.35  Aligned_cols=36  Identities=25%  Similarity=0.501  Sum_probs=25.9

Q ss_pred             CCCcccccCcCCC-CCCeEecCCCCcccHHHHHHHHH
Q 035446            3 FDGCCPDCKLPGD-DCPLIWGACNHAFHLHCILKWVN   38 (59)
Q Consensus         3 ~~~~C~IC~~~~~-~~~~~~~~C~H~fh~~Ci~~w~~   38 (59)
                      -++.|.||....+ +..+.-..|+..||..|+...+.
T Consensus         6 ~~~~C~~C~~~g~~~~ll~C~~C~~~~H~~Cl~~~~~   42 (111)
T 2ysm_A            6 SGANCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAVT   42 (111)
T ss_dssp             CCSCBTTTCCCCCTTTSEECSSSCCEECTTTTTCCCC
T ss_pred             CCCCCcCCCCCCCCcCCeECCCCCCCcChHHhCCccc
Confidence            3678999975543 22355578999999999987654

>1wen_A Inhibitor of growth family, member 4; ING1-like protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.50.1.2 PDB: 1wes_A

Probab=93.77  E-value=0.016  Score=28.29  Aligned_cols=48  Identities=21%  Similarity=0.449  Sum_probs=29.1

Q ss_pred             CcccccCcCCCCCCeEecC--CC-CcccHHHHHHHHHhC-CCCCCCccccccccc
Q 035446            5 GCCPDCKLPGDDCPLIWGA--CN-HAFHLHCILKWVNSQ-TPQAHCPMCRREWQF   55 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~--C~-H~fh~~Ci~~w~~~~-~~~~~CP~Cr~~~~~   55 (59)
                      ..| ||........+.--.  |. ..||..|+.  +... .+.-.||.|+..-..
T Consensus        17 ~~C-~C~~~~~g~MI~CD~~~C~~~wfH~~Cvg--l~~~p~g~w~Cp~C~~~~~k   68 (71)
T 1wen_A           17 TYC-LCHQVSYGEMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQESGP   68 (71)
T ss_dssp             CCS-TTCCCSCSSEECCSCSSCSCCCEETTTTT--CSSCCSSCCCCTTTSSCSSS
T ss_pred             CEE-ECCCCCCCCEeEeeCCCCCCccEecccCC--cCcCCCCCEECCCCCccccc
Confidence            346 787543443333334  65 689999997  3322 124589999876443

>1weo_A Cellulose synthase, catalytic subunit (IRX3); structure genomics, ring-finger, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: g.44.1.1

Probab=93.46  E-value=0.28  Score=25.08  Aligned_cols=49  Identities=16%  Similarity=0.322  Sum_probs=34.7

Q ss_pred             CcccccCcCC-----CCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            5 GCCPDCKLPG-----DDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         5 ~~C~IC~~~~-----~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      ..|.||-+..     .+.-++...|+-..|+.|.+-=.+..  +..||.|+.++..
T Consensus        17 qiCqiCGD~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG--~q~CpqCktrYkr   70 (93)
T 1weo_A           17 QFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREG--TQNCPQCKTRYKR   70 (93)
T ss_dssp             CBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTS--CSSCTTTCCCCCC
T ss_pred             CccccccCccccCCCCCEEEeeeccCChhhHHHHHHHHhcc--CccccccCCcccc
Confidence            4799996532     12334445778889999998755544  5789999998863

>2yt5_A Metal-response element-binding transcription factor 2; zinc-regulated factor 1, ZIRF1, metal-response element DNA-binding protein M96; NMR {Mus musculus}

Probab=93.36  E-value=0.0056  Score=29.11  Aligned_cols=51  Identities=20%  Similarity=0.423  Sum_probs=33.1

Q ss_pred             CCcccccCcCC---CCCCeEecCCCCcccHHHHHHHHHh----CCCCCCCcccccccc
Q 035446            4 DGCCPDCKLPG---DDCPLIWGACNHAFHLHCILKWVNS----QTPQAHCPMCRREWQ   54 (59)
Q Consensus         4 ~~~C~IC~~~~---~~~~~~~~~C~H~fh~~Ci~~w~~~----~~~~~~CP~Cr~~~~   54 (59)
                      +..|.||....   ....+.-..|.-.||..|+..-+..    ..+.-.||.|.....
T Consensus         6 ~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~~~   63 (66)
T 2yt5_A            6 SGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFATT   63 (66)
T ss_dssp             CCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHTTS
T ss_pred             CCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCccc
Confidence            56799997532   2334455688899999998754321    222357999976533

>1wev_A Riken cDNA 1110020M19; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: g.50.1.2

Probab=93.13  E-value=0.0057  Score=30.96  Aligned_cols=52  Identities=17%  Similarity=0.321  Sum_probs=34.1

Q ss_pred             CCcccccCcCCC---CCCeEecCCCCcccHHHHHHHHHh-----CCCCCCCccccccccc
Q 035446            4 DGCCPDCKLPGD---DCPLIWGACNHAFHLHCILKWVNS-----QTPQAHCPMCRREWQF   55 (59)
Q Consensus         4 ~~~C~IC~~~~~---~~~~~~~~C~H~fh~~Ci~~w~~~-----~~~~~~CP~Cr~~~~~   55 (59)
                      +..|.||.....   ...+.--.|...||..|+..-+..     ..+.=.|+.|+.....
T Consensus        16 ~~~C~vC~~~~~~~~~~ll~CD~C~~~yH~~Cl~Ppl~~~~~~~p~g~W~C~~C~~~~~~   75 (88)
T 1wev_A           16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMKR   75 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHCC
T ss_pred             CCcCCCCCCCCCCCCCceEECCCCCCeEcCccCCCcccccccCCCCCCeeCccccchhhh
Confidence            457999975422   334455688999999999865432     2223579999765443

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=93.12  E-value=0.36  Score=25.03  Aligned_cols=32  Identities=16%  Similarity=0.238  Sum_probs=22.9

Q ss_pred             CCCcccccCcCC-------CCCCeEecCCCCcccHHHHH
Q 035446            3 FDGCCPDCKLPG-------DDCPLIWGACNHAFHLHCIL   34 (59)
Q Consensus         3 ~~~~C~IC~~~~-------~~~~~~~~~C~H~fh~~Ci~   34 (59)
                      -...|.+|+...       .+..+.-..|+..||..|+.
T Consensus         4 p~~~C~~C~~~~~~~~~g~~~~Ll~C~~C~~~~H~~Cl~   42 (112)
T 3v43_A            4 PIPICSFCLGTKEQNREKKPEELISCADCGNSGHPSCLK   42 (112)
T ss_dssp             CCSSBTTTCCCTTCCTTSCCCCCEECTTTCCEECHHHHT
T ss_pred             cCccccccCCchhhCcCCCchhceEhhhcCCCCCCchhc
Confidence            356799997431       23455567899999999995

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=92.78  E-value=0.0063  Score=28.55  Aligned_cols=50  Identities=20%  Similarity=0.543  Sum_probs=33.5

Q ss_pred             CCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhC-CCCCCCcccccccc
Q 035446            3 FDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQ-TPQAHCPMCRREWQ   54 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~-~~~~~CP~Cr~~~~   54 (59)
                      -+..|.+|...  +..+.-..|.-.||..|+..-+... .+.-.||.|+....
T Consensus         4 ~~~~C~vC~~~--g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~~   54 (60)
T 2puy_A            4 HEDFCSVCRKS--GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQML   54 (60)
T ss_dssp             CCSSCTTTCCC--SSCEECSSSSCEECGGGSSSCCSSCCCSCCCCHHHHHHHH
T ss_pred             CCCCCcCCCCC--CcEEEcCCCCcCEECCcCCCCcCCCCCCceEChhccChhh
Confidence            35789999653  3455566889999999998544321 12347999976543

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=92.56  E-value=0.035  Score=28.22  Aligned_cols=50  Identities=24%  Similarity=0.569  Sum_probs=33.2

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhC-CCCCCCccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQ-TPQAHCPMCRREWQF   55 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~-~~~~~CP~Cr~~~~~   55 (59)
                      +..|.+|....  ..+.-..|.-.||..|+..-+... .+.-.||.|+..-..
T Consensus        25 ~~~C~vC~~~g--~LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~~~~   75 (88)
T 1fp0_A           25 ATICRVCQKPG--DLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDL   75 (88)
T ss_dssp             SSCCSSSCSSS--CCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCSS
T ss_pred             CCcCcCcCCCC--CEEECCCCCCceecccCCCCCCCCcCCCcCCccccCCCcc
Confidence            46799996432  345556888899999997655432 123479999865443

>3ql9_A Transcriptional regulator ATRX; zinc finger, transcription, lysine trimethylation, protein, histone-binding protein, transcription-structural complex; HET: M3L; 0.93A {Homo sapiens} PDB: 3qla_A* 3qlc_A 3qln_A 2jm1_A

Probab=92.25  E-value=0.35  Score=26.11  Aligned_cols=47  Identities=26%  Similarity=0.523  Sum_probs=30.3

Q ss_pred             CCCcccccCcCCCCCCeEecCCCCcccHHHHHHH-----H-Hh--CCCCCCCccccc
Q 035446            3 FDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKW-----V-NS--QTPQAHCPMCRR   51 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w-----~-~~--~~~~~~CP~Cr~   51 (59)
                      .++.|.||.+. .+ .+.-..|-.+||..||..-     + +.  ..+.=.|++|+.
T Consensus        56 ~~~~C~vC~dG-G~-LlcCd~Cpr~Fc~~Cl~~~lg~~~l~~i~~~~~~W~C~~C~~  110 (129)
T 3ql9_A           56 MDEQCRWCAEG-GN-LICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHP  110 (129)
T ss_dssp             CBSSCTTTCCC-SE-EEECSSSSCEEEHHHHHHHTCHHHHHHHTCTTSCCCCTTTCC
T ss_pred             CCCcCeecCCC-Ce-eEecCCCchhhhHHHhCCCcchhHHHHhccCCCCeEcCCcCC
Confidence            45679999532 22 3334578899999999974     2 22  222357999965

>3o36_A Transcription intermediary factor 1-alpha; TRIM24, PHD finger, bromodomain, H4K16 acetylation, breast C transcription-protein binding complex; HET: ALY; 1.70A {Homo sapiens} PDB: 3o33_A* 3o34_A* 3o35_A* 3o37_A

Probab=92.15  E-value=0.023  Score=31.86  Aligned_cols=49  Identities=22%  Similarity=0.450  Sum_probs=33.4

Q ss_pred             CCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhC-CCCCCCccccccc
Q 035446            3 FDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQ-TPQAHCPMCRREW   53 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~-~~~~~CP~Cr~~~   53 (59)
                      -++.|.+|...  +..+.-..|.-.||..|+..-+... .+.-.||.|+..-
T Consensus         3 ~~~~C~~C~~~--g~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   52 (184)
T 3o36_A            3 NEDWCAVCQNG--GELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLS   52 (184)
T ss_dssp             SCSSCTTTCCC--SSCEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCccccCCCC--CeeeecCCCCcccCccccCCCCCCCCCCCEECccccCcc
Confidence            35779999643  2355556899999999987655432 1234799998754

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=91.88  E-value=0.019  Score=29.01  Aligned_cols=52  Identities=23%  Similarity=0.309  Sum_probs=33.0

Q ss_pred             CCcccccCcCC---CCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            4 DGCCPDCKLPG---DDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         4 ~~~C~IC~~~~---~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      +..|.||....   .+..+.-..|.-.||..|+..-+ ...+.-.||.|......+
T Consensus        25 ~~~C~vC~~~~s~~~~~ll~CD~C~~~fH~~Cl~p~~-vP~g~W~C~~C~~~~~~~   79 (88)
T 2l43_A           25 DAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPY-IPEGQWLCRHCLQSRARP   79 (88)
T ss_dssp             CCCCSSCCSSSSCSEEEEEECSSSCCCCCHHHHTCSS-CCSSCCCCHHHHHHTTSC
T ss_pred             CCcCCcCCCCCCCCCCCEEECCCCCchhhcccCCCCc-cCCCceECccccCccchh
Confidence            46799997532   12334445788899999997532 222234799998755444

>1mm2_A MI2-beta; PHD, zinc finger, protein scaffold, DNA binding protein; NMR {Homo sapiens} SCOP: g.50.1.2 PDB: 2l75_A* 1mm3_A

Probab=91.64  E-value=0.025  Score=26.65  Aligned_cols=47  Identities=23%  Similarity=0.476  Sum_probs=30.9

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhC-CCCCCCcccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQ-TPQAHCPMCRRE   52 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~-~~~~~CP~Cr~~   52 (59)
                      +..|.||...  ...+.-..|...||..|+..-+... .+.-.||.|+..
T Consensus         9 ~~~C~vC~~~--g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~   56 (61)
T 1mm2_A            9 MEFCRVCKDG--GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCP   56 (61)
T ss_dssp             CSSCTTTCCC--SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTT
T ss_pred             CCcCCCCCCC--CCEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCc
Confidence            4679999643  2344445788999999998544331 112479999764

>3c6w_A P28ING5, inhibitor of growth protein 5; chromatin, PHD, ING, epigenetics, alternative splicing, metal-binding, phosphoprotein, zinc; HET: M3L; 1.75A {Homo sapiens} PDB: 2pnx_A*

Probab=90.53  E-value=0.015  Score=27.29  Aligned_cols=43  Identities=21%  Similarity=0.522  Sum_probs=26.3

Q ss_pred             cccccCcCCCCCCeEecC--CC-CcccHHHHHHHHHhC-CCCCCCccccc
Q 035446            6 CCPDCKLPGDDCPLIWGA--CN-HAFHLHCILKWVNSQ-TPQAHCPMCRR   51 (59)
Q Consensus         6 ~C~IC~~~~~~~~~~~~~--C~-H~fh~~Ci~~w~~~~-~~~~~CP~Cr~   51 (59)
                      .| ||..+..+..+.--.  |. ..||..|+.  +... .+.-.||.|++
T Consensus        11 yC-~C~~~~~g~mi~CD~~~C~~~wfH~~Cvg--l~~~p~~~w~Cp~C~~   57 (59)
T 3c6w_A           11 YC-LCHQVSYGEMIGCDNPDCPIEWFHFACVD--LTTKPKGKWFCPRCVQ   57 (59)
T ss_dssp             ET-TTTEECCSEEEECSCTTCSSCEEETGGGT--CSSCCSSCCCCHHHHC
T ss_pred             EE-ECCCCCCCCeeEeeCCCCCCCCEecccCC--cccCCCCCEECcCccC
Confidence            35 887543443444445  66 699999998  3322 12357999865

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=90.48  E-value=0.028  Score=26.81  Aligned_cols=47  Identities=21%  Similarity=0.486  Sum_probs=31.7

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhC-CCCCCCcccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQ-TPQAHCPMCRRE   52 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~-~~~~~CP~Cr~~   52 (59)
                      +..|.||...  ...+.-..|.-.||..|+..-+... .+.-.||.|...
T Consensus         8 ~~~C~vC~~~--g~ll~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~~   55 (66)
T 1xwh_A            8 EDECAVCRDG--GELICCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQA   55 (66)
T ss_dssp             CCSBSSSSCC--SSCEECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHHT
T ss_pred             CCCCccCCCC--CCEEEcCCCChhhcccccCCCcCcCCCCCeECccccCc
Confidence            5679999643  2355556888999999997543321 122469999764

>1we9_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=90.29  E-value=0.098  Score=24.50  Aligned_cols=50  Identities=22%  Similarity=0.419  Sum_probs=32.6

Q ss_pred             CCcccccCcCCC--CCCeEecCCCCcccHHHHHHHHHhC--CCCCCCccccccc
Q 035446            4 DGCCPDCKLPGD--DCPLIWGACNHAFHLHCILKWVNSQ--TPQAHCPMCRREW   53 (59)
Q Consensus         4 ~~~C~IC~~~~~--~~~~~~~~C~H~fh~~Ci~~w~~~~--~~~~~CP~Cr~~~   53 (59)
                      +..|+||..+.+  ...|.-..|...||..|+.--....  .....||.|+..-
T Consensus         6 ~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k~   59 (64)
T 1we9_A            6 SGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKS   59 (64)
T ss_dssp             CCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTTT
T ss_pred             CCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcCcC
Confidence            356999976542  3345556888999999986532211  1236899997653

>2vpb_A Hpygo1, pygopus homolog 1; gene regulation, WNT signaling pathway, WNT signaling complex, chromosomal rearrangement, signaling protein; 1.59A {Homo sapiens} PDB: 2vpd_A 2yyr_A* 2dx8_A* 2vp7_A 2vpg_A* 2vpe_A*

Probab=90.13  E-value=0.29  Score=23.26  Aligned_cols=32  Identities=19%  Similarity=0.302  Sum_probs=22.0

Q ss_pred             CCcccccCcCCC--CCCeEec-CCCCcccHHHHHH
Q 035446            4 DGCCPDCKLPGD--DCPLIWG-ACNHAFHLHCILK   35 (59)
Q Consensus         4 ~~~C~IC~~~~~--~~~~~~~-~C~H~fh~~Ci~~   35 (59)
                      ...|++|..+..  ...+.-. .|.-.||..|+.-
T Consensus         8 ~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cvgl   42 (65)
T 2vpb_A            8 VYPCGICTNEVNDDQDAILCEASCQKWFHRICTGM   42 (65)
T ss_dssp             -CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHHTC
T ss_pred             cCcCccCCCccCCCCCeEecccCccccCchhccCC
Confidence            357999986543  2344555 7889999999743

>3o70_A PHD finger protein 13; PHF13, structural genomics consortium, SGC, structural genom type zinc finger, protein binding, zinc ION binding; 1.85A {Homo sapiens}

Probab=90.05  E-value=0.023  Score=27.42  Aligned_cols=45  Identities=22%  Similarity=0.397  Sum_probs=28.7

Q ss_pred             cccccCcCCCC-CCeEecCCCCcccHHHHHHHHHhCCCCCCCccccc
Q 035446            6 CCPDCKLPGDD-CPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRR   51 (59)
Q Consensus         6 ~C~IC~~~~~~-~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~   51 (59)
                      .| ||..+.++ ..|.-..|.-.||..|+.--.........||.|+.
T Consensus        21 ~C-iC~~~~~~~~MIqCd~C~~WfH~~Cvgi~~~~~~~~~~C~~C~~   66 (68)
T 3o70_A           21 TC-FCMKPFAGRPMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCRD   66 (68)
T ss_dssp             CS-TTCCCCTTCCEEECTTTCCEEETTTTTCCTTSCCSSCCCHHHHT
T ss_pred             Ee-ECCCcCCCCCEEECCCCCccccccccCcCcccCCCcEECCCCCC
Confidence            46 88654443 34556678999999998643221112357998865

>2vnf_A ING 4, P29ING4, inhibitor of growth protein 4; acetylation, alternative splicing, anti-oncogene, cell cycle, coiled C nucleus, zinc, zinc-finger, ING4; HET: M3L; 1.76A {Homo sapiens} SCOP: g.50.1.2 PDB: 2k1j_A 2jmq_A 2qic_A*

Probab=89.73  E-value=0.019  Score=27.04  Aligned_cols=43  Identities=21%  Similarity=0.545  Sum_probs=25.8

Q ss_pred             cccccCcCCCCCCeEecC--CC-CcccHHHHHHHHHhC-CCCCCCccccc
Q 035446            6 CCPDCKLPGDDCPLIWGA--CN-HAFHLHCILKWVNSQ-TPQAHCPMCRR   51 (59)
Q Consensus         6 ~C~IC~~~~~~~~~~~~~--C~-H~fh~~Ci~~w~~~~-~~~~~CP~Cr~   51 (59)
                      .| ||.....+..+.--.  |. ..||..|+.  +... .+.-.||.|++
T Consensus        12 ~C-~C~~~~~g~mi~CD~cdC~~~wfH~~Cvg--l~~~p~g~w~C~~C~~   58 (60)
T 2vnf_A           12 YC-LCHQVSYGEMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQ   58 (60)
T ss_dssp             ET-TTTEECCSEEEECSCTTCSSCEEETGGGT--CSSCCSSCCCCHHHHC
T ss_pred             EE-ECCCcCCCCEEEeCCCCCCCceEehhcCC--CCcCCCCCEECcCccC
Confidence            35 887543443343345  55 689999997  3332 12357998865

>1wyh_A SLIM 2, skeletal muscle LIM-protein 2; structural genomics, riken structural genomics/proteomics initiative, RSGI, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=89.67  E-value=0.56  Score=21.81  Aligned_cols=41  Identities=17%  Similarity=0.297  Sum_probs=26.5

Q ss_pred             CCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            3 FDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      +...|+.|..+......++..=+..||.+|           ..|-.|+.++.
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~C-----------F~C~~C~~~L~   44 (72)
T 1wyh_A            4 GSSGCSACGETVMPGSRKLEYGGQTWHEHC-----------FLCSGCEQPLG   44 (72)
T ss_dssp             CCCBCSSSCCBCCSSSCEECSTTCCEETTT-----------CBCTTTCCBTT
T ss_pred             cCCCCccCCCccccCccEEEECccccCccc-----------CeECCCCCcCC
Confidence            456788897665532122335578899877           46777877664

>3m62_A Ubiquitin conjugation factor E4; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} PDB: 3m63_A* 2qiz_A 2qj0_A

Probab=89.34  E-value=0.5  Score=32.97  Aligned_cols=50  Identities=16%  Similarity=0.060  Sum_probs=37.5

Q ss_pred             CCCCcccccCcCCCCCCeEecCCC-CcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            2 AFDGCCPDCKLPGDDCPLIWGACN-HAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         2 ~~~~~C~IC~~~~~~~~~~~~~C~-H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      |-+-.|||=++...+ |++ ++-| +.|-+..|.+|+.++   .+||.=|.++...
T Consensus       889 P~~F~cPIs~~lM~D-PVi-lpsG~~TydR~~I~~wl~~~---~tdP~Tr~~L~~~  939 (968)
T 3m62_A          889 PDEFLDPLMYTIMKD-PVI-LPASKMNIDRSTIKAHLLSD---STDPFNRMPLKLE  939 (968)
T ss_dssp             CGGGBCTTTCSBCSS-EEE-CTTTCCEEEHHHHHHHHTTC---CBCTTTCCBCCGG
T ss_pred             cHHhCCcchhhHHhC-CeE-cCCCCEEECHHHHHHHHhcC---CCCCCCCCCCCcc
Confidence            344568888655444 554 4766 699999999999875   7999999887653

>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain, TGF-beta, epigenetics, methylation, K9ME3, K14AC, transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB: 3u5m_A* 3u5o_A* 3u5p_A*

Probab=89.08  E-value=0.031  Score=31.98  Aligned_cols=47  Identities=28%  Similarity=0.537  Sum_probs=31.7

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhC-CCCCCCcccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQ-TPQAHCPMCRRE   52 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~-~~~~~CP~Cr~~   52 (59)
                      ++.|.+|....  ..+.-..|...||..|+..-+... .+.-.||.|+..
T Consensus         7 ~~~C~~C~~~g--~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~   54 (207)
T 3u5n_A            7 EDWCAVCQNGG--DLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDI   54 (207)
T ss_dssp             CSSBTTTCCCE--EEEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCS
T ss_pred             CCCCCCCCCCC--ceEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCc
Confidence            56799996432  244456888999999987655432 122479999864

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=89.05  E-value=0.39  Score=23.19  Aligned_cols=48  Identities=25%  Similarity=0.373  Sum_probs=30.8

Q ss_pred             CCcccccCcCC---CCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccc
Q 035446            4 DGCCPDCKLPG---DDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRRE   52 (59)
Q Consensus         4 ~~~C~IC~~~~---~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~   52 (59)
                      +..|.||....   .+..+.-..|.-.||..|+..-. ...+.=.||.|+..
T Consensus        16 ~~~C~vC~~~~s~~~~~ll~CD~C~~~~H~~Cl~~~~-vP~g~W~C~~C~~~   66 (71)
T 2ku3_A           16 DAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPY-IPEGQWLCRHCLQS   66 (71)
T ss_dssp             SCSCSSSCCCCCCSSSCEEECSSSCCEEEHHHHTCSS-CCSSCCCCHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCEEECCCCCCccccccCCCCc-CCCCCcCCccCcCc
Confidence            56799997542   23344456888999999987532 12223478888653

>3o7a_A PHD finger protein 13 variant; PHF13, zinc finger, PHD domain, nuclear protein, structural structural genomics consortium, SGC, protein binding; HET: M3L; 1.67A {Homo sapiens}

Probab=89.03  E-value=0.058  Score=24.46  Aligned_cols=49  Identities=20%  Similarity=0.292  Sum_probs=29.9

Q ss_pred             CCCcccccCcCCCC-CCeEecCCCCcccHHHHHHHHHhCCCCCCCccccc
Q 035446            3 FDGCCPDCKLPGDD-CPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRR   51 (59)
Q Consensus         3 ~~~~C~IC~~~~~~-~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~   51 (59)
                      +|..=-||..+.++ ..+.-..|+--||..|+.--.........||.|+.
T Consensus         2 ~d~~~C~C~~~~~~~~MI~Cd~C~~W~H~~Cvgi~~~~~~~~~~C~~C~~   51 (52)
T 3o7a_A            2 WDLVTCFCMKPFAGRPMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCRD   51 (52)
T ss_dssp             TTCBCSTTCCBCTTCCEEECTTTCCEEETTTTTCCGGGCCSSCCCHHHHT
T ss_pred             CcCeEEEeCCcCCCCCEEEcCCCCccccccccCCCcccCCCcEECcCCCC
Confidence            34443477654333 44555678899999998643322222467998865

>3shb_A E3 ubiquitin-protein ligase UHRF1; unmodified histone, methylation, UHRF1, PHD, ligase-NUCL protein complex; 1.80A {Homo sapiens}

Probab=88.84  E-value=0.028  Score=27.83  Aligned_cols=46  Identities=33%  Similarity=0.643  Sum_probs=27.0

Q ss_pred             cccccCcCCC-CCCeEecCCCCcccHHHHHHHHHhCCC-C-CCCccccc
Q 035446            6 CCPDCKLPGD-DCPLIWGACNHAFHLHCILKWVNSQTP-Q-AHCPMCRR   51 (59)
Q Consensus         6 ~C~IC~~~~~-~~~~~~~~C~H~fh~~Ci~~w~~~~~~-~-~~CP~Cr~   51 (59)
                      .|.||....+ +..+.-..|...||..|+..-+..... . =.||.|+.
T Consensus        28 ~C~vC~~~~d~~~ll~CD~C~~~yH~~Cl~PpL~~~P~g~~W~C~~C~~   76 (77)
T 3shb_A           28 ACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN   76 (77)
T ss_dssp             SBTTTCCCSCGGGEEECTTTCCEEETTTSSSCCSSCCSSSCCCCTTTC-
T ss_pred             cCCccCCCCCCcceeEeCCCCCccCcccCCCcccCCCCCCceECcCccc
Confidence            3555543222 223444578899999999865543221 2 37998875

>1wem_A Death associated transcription factor 1; structural genomics, PHD domain, death inducer- obliterator 1(DIO-1); NMR {Mus musculus} SCOP: g.50.1.2

Probab=88.67  E-value=0.12  Score=25.11  Aligned_cols=48  Identities=21%  Similarity=0.416  Sum_probs=29.8

Q ss_pred             cccccCcCCC-CCCeEecCCCCcccHHHHHHHHHh------CCCCCCCcccccccc
Q 035446            6 CCPDCKLPGD-DCPLIWGACNHAFHLHCILKWVNS------QTPQAHCPMCRREWQ   54 (59)
Q Consensus         6 ~C~IC~~~~~-~~~~~~~~C~H~fh~~Ci~~w~~~------~~~~~~CP~Cr~~~~   54 (59)
                      .| ||..+.. ...|.-..|.-.||..|+.--...      ......||.|+....
T Consensus        18 ~C-~C~~~~~~~~MI~Cd~C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~~~~~   72 (76)
T 1wem_A           18 YC-ICRQPHNNRFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILSG   72 (76)
T ss_dssp             CS-TTCCCCCSSCEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHSC
T ss_pred             EE-ECCCccCCCCEEEeCCCCCcEeCeEEccchhhhhhccCCCCeEECcCCcCccC
Confidence            46 7865544 234555688999999998532211      112378999986543

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=88.64  E-value=0.057  Score=27.65  Aligned_cols=45  Identities=18%  Similarity=0.356  Sum_probs=28.6

Q ss_pred             cccccCcCCC-CCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccc
Q 035446            6 CCPDCKLPGD-DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRR   51 (59)
Q Consensus         6 ~C~IC~~~~~-~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~   51 (59)
                      .| ||....+ +..+.-..|.-.||..|+..-.......-.||.|+.
T Consensus        30 rC-iC~~~~~~~~mi~Cd~C~~w~H~~C~~~~~~~~p~~w~C~~C~~   75 (98)
T 2lv9_A           30 RC-ICGFTHDDGYMICCDKCSVWQHIDCMGIDRQHIPDTYLCERCQP   75 (98)
T ss_dssp             CC-TTSCCSCSSCEEEBTTTCBEEETTTTTCCTTSCCSSBCCTTTSS
T ss_pred             Ee-ECCCccCCCcEEEcCCCCCcCcCcCCCCCccCCCCCEECCCCcC
Confidence            36 7865433 334555688899999998653322212358999974

>1wep_A PHF8; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: g.50.1.2

Probab=88.16  E-value=0.57  Score=22.80  Aligned_cols=47  Identities=26%  Similarity=0.552  Sum_probs=30.2

Q ss_pred             cccccCcCC--CCCCeEecCCCCcccHHHHHHHHHhC--CCCCCCccccccc
Q 035446            6 CCPDCKLPG--DDCPLIWGACNHAFHLHCILKWVNSQ--TPQAHCPMCRREW   53 (59)
Q Consensus         6 ~C~IC~~~~--~~~~~~~~~C~H~fh~~Ci~~w~~~~--~~~~~CP~Cr~~~   53 (59)
                      .| ||..+.  +...|.-..|.-.||..|+.--....  .....||.|+...
T Consensus        14 ~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~   64 (79)
T 1wep_A           14 YC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             EE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCccccc
Confidence            35 887554  33455666889999999986432211  1236899998753

>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens}

Probab=87.18  E-value=0.15  Score=28.86  Aligned_cols=48  Identities=25%  Similarity=0.573  Sum_probs=31.7

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhC-CCCCCCccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQ-TPQAHCPMCRREW   53 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~-~~~~~CP~Cr~~~   53 (59)
                      ++.|.+|....  ..+....|.-.||..|+..-+... .+.-.||.|+..-
T Consensus         2 ~~~C~~C~~~g--~ll~Cd~C~~~~H~~Cl~p~l~~~p~g~W~C~~C~~~~   50 (189)
T 2ro1_A            2 ATICRVCQKPG--DLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   50 (189)
T ss_dssp             CCCBTTTCCCS--SCCCCTTTCCBCCSTTSTTCCSSCCCTTCCTTTTSCSC
T ss_pred             CCcCccCCCCC--ceeECCCCCchhccccCCCCcccCCCCCCCCcCccCCC
Confidence            56799996432  234446788999999997544321 2234799998653

>2cs3_A Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.3

Probab=87.14  E-value=0.72  Score=23.28  Aligned_cols=36  Identities=22%  Similarity=0.448  Sum_probs=25.3

Q ss_pred             CcccccCcCCCCCCeEec--CCCCcccHHHHHHHHHhC
Q 035446            5 GCCPDCKLPGDDCPLIWG--ACNHAFHLHCILKWVNSQ   40 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~--~C~H~fh~~Ci~~w~~~~   40 (59)
                      ..|.+|.+..++.-.+.-  .=+|.||.-|-...++.+
T Consensus        16 l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sIk~q   53 (93)
T 2cs3_A           16 LCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKAQ   53 (93)
T ss_dssp             CCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHHH
T ss_pred             eEeecchhhhccCceeeCCCccCCeeeccccHHHHHhc
Confidence            569999876665444311  126999999999998764

>3i2d_A E3 SUMO-protein ligase SIZ1; signal transduction, replication, ring E3, PIAS, ubiquitin, UBC9, metal-binding, nucleus; 2.60A {Saccharomyces cerevisiae}

Probab=86.84  E-value=1.3  Score=27.85  Aligned_cols=51  Identities=22%  Similarity=0.350  Sum_probs=32.7

Q ss_pred             CcccccCcCCCCCCeEecCCCCc--ccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHA--FHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~--fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      ..||+=.... ..|+....|.|.  |-..=+.+..... ..-.||+|.+.+.+.+
T Consensus       250 L~CPlS~~ri-~~PvRg~~C~HlQCFDl~sfL~~~~~~-~~W~CPIC~k~~~~~d  302 (371)
T 3i2d_A          250 LQCPISYTRM-KYPSKSINCKHLQCFDALWFLHSQLQI-PTWQCPVCQIDIALEN  302 (371)
T ss_dssp             SBCTTTSSBC-SSEEEETTCCSSCCEEHHHHHHHHHHS-CCCBCTTTCCBCCGGG
T ss_pred             ecCCCccccc-cccCcCCcCCCcceECHHHHHHHhhcC-CceeCCCCCcccCHHH
Confidence            4577664332 346667799998  6655555544432 2358999999876654

>2o35_A Hypothetical protein DUF1244; helix bundle, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.12A {Sinorhizobium meliloti} SCOP: a.293.1.1

Probab=86.81  E-value=0.35  Score=25.20  Aligned_cols=12  Identities=25%  Similarity=0.869  Sum_probs=11.1

Q ss_pred             ccHHHHHHHHHh
Q 035446           28 FHLHCILKWVNS   39 (59)
Q Consensus        28 fh~~Ci~~w~~~   39 (59)
                      ||+.||.+|+..
T Consensus        43 FCRNCLskWy~~   54 (105)
T 2o35_A           43 FCRNCLSNWYRE   54 (105)
T ss_dssp             CCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999999999975

>3fyb_A Protein of unknown function (DUF1244); hydrocar degrading, structural genomics, PSI-2; HET: PEG; 1.80A {Alcanivorax borkumensis SK2}

Probab=86.74  E-value=0.36  Score=25.14  Aligned_cols=12  Identities=33%  Similarity=0.971  Sum_probs=11.1

Q ss_pred             ccHHHHHHHHHh
Q 035446           28 FHLHCILKWVNS   39 (59)
Q Consensus        28 fh~~Ci~~w~~~   39 (59)
                      ||+.||.+|+..
T Consensus        42 FCRNCLskWy~~   53 (104)
T 3fyb_A           42 FCRNCLAKWLME   53 (104)
T ss_dssp             CCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999999999974

>2g6q_A Inhibitor of growth protein 2; protein-peptide complex, gene regulation, apoptosis; HET: M3L; 2.00A {Mus musculus}

Probab=86.59  E-value=0.042  Score=26.04  Aligned_cols=44  Identities=23%  Similarity=0.514  Sum_probs=26.3

Q ss_pred             cccccCcCCCCCCeEecC--CC-CcccHHHHHHHHHhC-CCCCCCcccccc
Q 035446            6 CCPDCKLPGDDCPLIWGA--CN-HAFHLHCILKWVNSQ-TPQAHCPMCRRE   52 (59)
Q Consensus         6 ~C~IC~~~~~~~~~~~~~--C~-H~fh~~Ci~~w~~~~-~~~~~CP~Cr~~   52 (59)
                      .| ||........+.--.  |. ..||..|+.-  ... .+.-.||.|+..
T Consensus        13 yC-~C~~~~~g~MI~CD~c~C~~~WfH~~Cvgl--~~~p~~~w~Cp~C~~~   60 (62)
T 2g6q_A           13 YC-LCNQVSYGEMIGCDNEQCPIEWFHFSCVSL--TYKPKGKWYCPKCRGD   60 (62)
T ss_dssp             ET-TTTEECCSEEEECSCTTCSSCEEETGGGTC--SSCCSSCCCCHHHHTC
T ss_pred             EE-ECCCCCCCCeeeeeCCCCCcccEecccCCc--CcCCCCCEECcCcccC
Confidence            35 886543333444445  54 7999999972  221 123579999753

>1x68_A FHL5 protein; four-and-A-half LIM protein 5, zinc finger domain, AN actin- interacting protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=86.45  E-value=0.62  Score=22.04  Aligned_cols=41  Identities=17%  Similarity=0.334  Sum_probs=26.2

Q ss_pred             CCCcccccCcCCCC--CCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            3 FDGCCPDCKLPGDD--CPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         3 ~~~~C~IC~~~~~~--~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      +...|+.|..+..+  ....+..=+..||.+|           ..|-.|+.++.
T Consensus         4 ~~~~C~~C~~~I~~~g~~~~~~a~~~~wH~~C-----------F~C~~C~~~L~   46 (76)
T 1x68_A            4 GSSGCVACSKPISGLTGAKFICFQDSQWHSEC-----------FNCGKCSVSLV   46 (76)
T ss_dssp             CCCCCTTTCCCCCTTTTCCEEEETTEEEEGGG-----------CBCTTTCCBCS
T ss_pred             cCCCCccCCCcccCCCCceeEEECCcccCccc-----------CChhhCCCcCC
Confidence            45679999765553  1122234577899888           46777777664

>2kwj_A Zinc finger protein DPF3; acetyl-lysine, transcription regulation, nucleus, metal BIND protein; HET: ALY; NMR {Homo sapiens} PDB: 2kwk_A 2kwn_A* 2kwo_A*

Probab=86.34  E-value=0.34  Score=25.25  Aligned_cols=33  Identities=15%  Similarity=0.241  Sum_probs=23.1

Q ss_pred             CCcccccCcCC--------CCCCeEecCCCCcccHHHHHHH
Q 035446            4 DGCCPDCKLPG--------DDCPLIWGACNHAFHLHCILKW   36 (59)
Q Consensus         4 ~~~C~IC~~~~--------~~~~~~~~~C~H~fh~~Ci~~w   36 (59)
                      +..|.||+...        .+..+.-..|+..||..|+...
T Consensus         1 ~~~C~~C~~~~~~n~k~g~~~~Li~C~~C~~~~H~~Cl~~~   41 (114)
T 2kwj_A            1 GSYCDFCLGGSNMNKKSGRPEELVSCADCGRSGHPTCLQFT   41 (114)
T ss_dssp             CCCCSSSCCBTTBCTTTCCCCCCEECSSSCCEECTTTTTCC
T ss_pred             CCcCccCCCCccccccCCCCCCCeEeCCCCCccchhhCCCh
Confidence            35799997432        1234555689999999998754

>3asl_A E3 ubiquitin-protein ligase UHRF1; histone reader module, epigenetic regulation, LI binding protein complex; 1.41A {Homo sapiens} PDB: 3sou_A 3sow_A* 3sox_A 3zvy_A 2lgg_A 2lgk_A* 2lgl_A 3t6r_A 3zvz_B

Probab=86.34  E-value=0.073  Score=25.73  Aligned_cols=47  Identities=30%  Similarity=0.619  Sum_probs=27.8

Q ss_pred             cccccCcCC-CCCCeEecCCCCcccHHHHHHHHHhC-CC-CCCCcccccc
Q 035446            6 CCPDCKLPG-DDCPLIWGACNHAFHLHCILKWVNSQ-TP-QAHCPMCRRE   52 (59)
Q Consensus         6 ~C~IC~~~~-~~~~~~~~~C~H~fh~~Ci~~w~~~~-~~-~~~CP~Cr~~   52 (59)
                      .|.||.... .+..+.-..|...||..|+..-+... .+ .=.||.|+..
T Consensus        20 ~C~~C~~~~~~~~ll~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~~   69 (70)
T 3asl_A           20 ACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND   69 (70)
T ss_dssp             SBTTTCCCSCGGGEEECTTTCCEEEGGGSSSCCSSCCSSSCCCCTTTSCC
T ss_pred             CCcCCCCcCCCCCEEEcCCCCCceecccCCCCcCCCCCCCCcCCcCccCc
Confidence            355665322 22334445788999999998544332 11 2479999753

>2xb1_A Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro; fusion protein, signal transduction, transcription, metal BI WNT proteins; 1.90A {Homo sapiens}

Probab=86.26  E-value=0.26  Score=25.49  Aligned_cols=51  Identities=18%  Similarity=0.353  Sum_probs=31.4

Q ss_pred             CcccccCcCC--CCCCeEec-CCCCcccHHHHHHHHH-------hCCCCCCCccccccccc
Q 035446            5 GCCPDCKLPG--DDCPLIWG-ACNHAFHLHCILKWVN-------SQTPQAHCPMCRREWQF   55 (59)
Q Consensus         5 ~~C~IC~~~~--~~~~~~~~-~C~H~fh~~Ci~~w~~-------~~~~~~~CP~Cr~~~~~   55 (59)
                      ..|+||..+.  +...+.-- .|.-.||..|+.--..       .......||.|+.....
T Consensus         4 ~~C~iC~~p~~~~~~mi~Cdd~C~~WfH~~CVglt~~~~~~i~~~~~~~~~Cp~C~~~~~~   64 (105)
T 2xb1_A            4 YPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTKEG   64 (105)
T ss_dssp             CBCTTTCSBCCTTSCEEECTTTTCCEEEGGGTTCCHHHHHHHHHCTTEEECCHHHHHTTTT
T ss_pred             CCCCCCCCccCCCCCEEEecCCcccccccccCCcCHHHHHhhccCCCCCEECccccCcCCC
Confidence            4799998653  23334443 7889999999753211       01112579999875443

>2e6s_A E3 ubiquitin-protein ligase UHRF2; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=86.26  E-value=0.1  Score=25.68  Aligned_cols=47  Identities=23%  Similarity=0.537  Sum_probs=29.3

Q ss_pred             CcccccCcCC-CCCCeEecCCCCcccHHHHHHHHHhCC-C-CCCCccccc
Q 035446            5 GCCPDCKLPG-DDCPLIWGACNHAFHLHCILKWVNSQT-P-QAHCPMCRR   51 (59)
Q Consensus         5 ~~C~IC~~~~-~~~~~~~~~C~H~fh~~Ci~~w~~~~~-~-~~~CP~Cr~   51 (59)
                      ..|.||.... .+..+.-..|...||..|+..-+.... + .=.||.|..
T Consensus        27 c~C~vC~~~~~~~~ll~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~   76 (77)
T 2e6s_A           27 CSCRVCGGKHEPNMQLLCDECNVAYHIYCLNPPLDKVPEEEYWYCPSCKT   76 (77)
T ss_dssp             SSCSSSCCCCCSTTEEECSSSCCEEETTSSSSCCSSCCCSSCCCCTTTCC
T ss_pred             CCCcCcCCcCCCCCEEEcCCCCccccccccCCCccCCCCCCCcCCcCccC
Confidence            3677886432 233444568889999999985443321 1 236888864

>1x63_A Skeletal muscle LIM-protein 1; LIM domain, four and A half LIM domains protein 1, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=86.03  E-value=1.2  Score=21.19  Aligned_cols=41  Identities=15%  Similarity=0.212  Sum_probs=25.3

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      ...|+.|.........++..=+..||.+|           ..|-.|++++..
T Consensus        15 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~C-----------F~C~~C~~~L~~   55 (82)
T 1x63_A           15 SPKCKGCFKAIVAGDQNVEYKGTVWHKDC-----------FTCSNCKQVIGT   55 (82)
T ss_dssp             SCBCSSSCCBCCSSSCEEECSSCEEETTT-----------CCCSSSCCCCTT
T ss_pred             CCcCccCCcccccCceEEEECcccccccc-----------CchhhCCCccCC
Confidence            45788887655422222234578899877           467788776643

>1x61_A Thyroid receptor interacting protein 6; LIM domain, OPA-interacting protein 1, zyxin related protein 1 (ZRP-1), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=85.95  E-value=0.88  Score=21.12  Aligned_cols=41  Identities=22%  Similarity=0.342  Sum_probs=24.3

Q ss_pred             CCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            3 FDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      +...|+.|..+.......+..=+..||.+|           ..|-.|+.++.
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~C-----------F~C~~C~~~L~   44 (72)
T 1x61_A            4 GSSGCGGCGEDVVGDGAGVVALDRVFHVGC-----------FVCSTCRAQLR   44 (72)
T ss_dssp             CCCCCSSSCSCCCSSSCCEECSSSEECTTT-----------CBCSSSCCBCT
T ss_pred             CCCCCccCCCccCCCceEEEECCCeEcccC-----------CcccccCCcCC
Confidence            345788887554431111124467888877           46777777663

>1x4k_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=85.61  E-value=0.56  Score=21.80  Aligned_cols=41  Identities=17%  Similarity=0.277  Sum_probs=25.3

Q ss_pred             CCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            3 FDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      +...|+.|..+......++..=+..||.+|           ..|-.|+.++.
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~C-----------F~C~~C~~~L~   44 (72)
T 1x4k_A            4 GSSGCQECKKTIMPGTRKMEYKGSSWHETC-----------FICHRCQQPIG   44 (72)
T ss_dssp             CCCCBSSSCCCCCSSSCEEEETTEEEETTT-----------TCCSSSCCCCC
T ss_pred             cCCCCccCCCcccCCceEEEECcCeecccC-----------CcccccCCccC
Confidence            456788897655532212224567888877           46777777654

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=85.46  E-value=0.24  Score=22.64  Aligned_cols=46  Identities=22%  Similarity=0.598  Sum_probs=30.4

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhC-CCCCCCccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQ-TPQAHCPMCRR   51 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~-~~~~~CP~Cr~   51 (59)
                      +..|.+|...  ...+.-..|.-.||..|+..-+... .+.-.||.|..
T Consensus         9 ~~~C~vC~~~--g~ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            9 EDFCSVCRKS--GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             CCSCSSSCCS--SCCEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCccCCCC--CeEEEcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            5679999653  2355556889999999997544322 11236888854

>2kgg_A Histone demethylase jarid1A; PHD finger, histone modification, leukemia, alternative splicing, chromatin regulator, developmental protein; NMR {Homo sapiens} PDB: 2kgi_A* 3gl6_A*

Probab=85.22  E-value=0.19  Score=22.68  Aligned_cols=45  Identities=20%  Similarity=0.405  Sum_probs=26.4

Q ss_pred             cccccCcCCCC--CCeEec-CCCCcccHHHHHHHHHh-CCCCCCCcccc
Q 035446            6 CCPDCKLPGDD--CPLIWG-ACNHAFHLHCILKWVNS-QTPQAHCPMCR   50 (59)
Q Consensus         6 ~C~IC~~~~~~--~~~~~~-~C~H~fh~~Ci~~w~~~-~~~~~~CP~Cr   50 (59)
                      .|.+|..+.++  ..+.-. .|.-.||..|+.--... ......||.|+
T Consensus         4 ~cc~C~~p~~~~~~mI~Cd~~C~~WfH~~Cvgl~~~~~~~~~~~C~~C~   52 (52)
T 2kgg_A            4 AAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA   52 (52)
T ss_dssp             SCTTCCCCCCTTCCEEECTTTTCCEEETTTTTCCHHHHHHSCCCCSCC-
T ss_pred             cCCCCcCccCCCCcEEEeCCCCCccCcccccCCCccccCCCCEECCCCC
Confidence            46788765432  234444 68889999997642221 00236899885

>4fo9_A E3 SUMO-protein ligase PIAS2; E3 ligase, pinit domain, SP-ring domain, structural GE consortium, SGC; 2.39A {Homo sapiens} PDB: 2asq_B

Probab=85.18  E-value=1.7  Score=27.18  Aligned_cols=51  Identities=24%  Similarity=0.459  Sum_probs=33.2

Q ss_pred             CcccccCcCCCCCCeEecCCCCc--ccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHA--FHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~--fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      ..||+=.... ..|+....|.|.  |-..=+.+..... +.-.||+|.+.+.+++
T Consensus       216 L~CPlS~~ri-~~P~Rg~~C~HlqCFDl~sfL~~~~~~-~~W~CPiC~k~~~~~d  268 (360)
T 4fo9_A          216 LMCPLGKMRL-TIPCRAVTCTHLQCFDAALYLQMNEKK-PTWICPVCDKKAAYES  268 (360)
T ss_dssp             SBCTTTCSBC-SSEEEETTCCCCCCEEHHHHHHHHHHS-CCCBCTTTCSBCCGGG
T ss_pred             eeCCCcccee-ccCCcCCCCCCCccCCHHHHHHHHhhC-CCeECCCCCcccCHHH
Confidence            4576664333 346667799998  6665555554443 2358999999887654

>1z60_A TFIIH basal transcription factor complex P44 subunit; basic transcription factor, zinc binding protein, ring finger; NMR {Homo sapiens} SCOP: g.49.1.2

Probab=84.60  E-value=0.45  Score=22.38  Aligned_cols=41  Identities=24%  Similarity=0.551  Sum_probs=25.4

Q ss_pred             cccccCcCCCCCC-eEecCCCCcccHHHHHHHHHhCCCCCCCccc
Q 035446            6 CCPDCKLPGDDCP-LIWGACNHAFHLHCILKWVNSQTPQAHCPMC   49 (59)
Q Consensus         6 ~C~IC~~~~~~~~-~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~C   49 (59)
                      .|-.|...+.+.. ..-..|++.|+.+|=.---++   -..||.|
T Consensus        17 ~C~~C~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~---Lh~CPgC   58 (59)
T 1z60_A           17 FCYGCQGELKDQHVYVCAVCQNVFCVDCDVFVHDS---LHSCPGC   58 (59)
T ss_dssp             EETTTTEECTTSEEECCTTTTCCBCHHHHHTTTTT---SCSSSTT
T ss_pred             cccccCcccCCCccEECCccCcCcccchhHHHHhh---ccCCcCC
Confidence            4777865443322 345689999999994332222   2479887

>1x4l_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=84.18  E-value=1.1  Score=20.87  Aligned_cols=40  Identities=20%  Similarity=0.428  Sum_probs=25.7

Q ss_pred             CCCcccccCcCCCC---CCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            3 FDGCCPDCKLPGDD---CPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         3 ~~~~C~IC~~~~~~---~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      +...|+.|..+..+   ..++ ..=+..||.+|           ..|-.|+.++.
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~~-~a~~~~wH~~C-----------F~C~~C~~~L~   46 (72)
T 1x4l_A            4 GSSGCAGCTNPISGLGGTKYI-SFEERQWHNDC-----------FNCKKCSLSLV   46 (72)
T ss_dssp             CSCSBTTTTBCCCCSSSCSCE-ECSSCEECTTT-----------CBCSSSCCBCT
T ss_pred             CCCCCcCCCccccCCCCcceE-EECCcccCccc-----------CEeccCCCcCC
Confidence            34678889765543   1222 24578899877           46777877664

>2gmg_A Hypothetical protein PF0610; winged-helix like protein with metal binding site, structura genomics, PSI, protein structure initiative; NMR {Pyrococcus furiosus} SCOP: a.4.5.82

Probab=83.27  E-value=0.56  Score=24.55  Aligned_cols=27  Identities=26%  Similarity=0.719  Sum_probs=17.4

Q ss_pred             ecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446           21 WGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus        21 ~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      ...||+.|.        ........||.|++.+..
T Consensus        70 C~~CG~~F~--------~~~~kPsrCP~CkSe~Ie   96 (105)
T 2gmg_A           70 CRKCGFVFK--------AEINIPSRCPKCKSEWIE   96 (105)
T ss_dssp             BTTTCCBCC--------CCSSCCSSCSSSCCCCBC
T ss_pred             hhhCcCeec--------ccCCCCCCCcCCCCCccC
Confidence            458999991        111123689999987654

>2ri7_A Nucleosome-remodeling factor subunit BPTF; zinc finger, alpha-helical bundle, dimethyl-lysine, bromodom chromatin regulator, metal-binding, nucleus; HET: MLY; 1.45A {Homo sapiens} PDB: 2fsa_A* 2f6n_A 2f6j_A* 3qzv_A* 3uv2_A* 3qzt_A* 3qzs_A* 2fui_A 2fuu_A*

Probab=82.77  E-value=0.3  Score=26.88  Aligned_cols=47  Identities=23%  Similarity=0.501  Sum_probs=29.8

Q ss_pred             CcccccCcCCC--CCCeEecCCCCcccHHHHHHHHHh--CCCCCCCcccccc
Q 035446            5 GCCPDCKLPGD--DCPLIWGACNHAFHLHCILKWVNS--QTPQAHCPMCRRE   52 (59)
Q Consensus         5 ~~C~IC~~~~~--~~~~~~~~C~H~fh~~Ci~~w~~~--~~~~~~CP~Cr~~   52 (59)
                      ..| +|..+.+  +..+.-..|.-.||..|+.--...  ....-.||.|+..
T Consensus         9 ~~C-~C~~~~~~~~~mi~Cd~C~~WfH~~Cv~~~~~~~~~~~~~~C~~C~~~   59 (174)
T 2ri7_A            9 LYC-ICKTPEDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQST   59 (174)
T ss_dssp             EET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCHHHHTTCSSCCCHHHHHH
T ss_pred             cEe-eCCCCCCCCCCEeECCCCCchhChhhcCCchhhccCccCeecCCCcch
Confidence            358 9975432  334555688899999998532221  1223689999863

>3f6q_B LIM and senescent cell antigen-like-containing domain protein 1; ILK, integrin-linked kinase, pinch, ankyrin repeat, ANK, IPP; 1.60A {Homo sapiens} PDB: 2kbx_B 3ixe_B

Probab=82.26  E-value=1.2  Score=20.44  Aligned_cols=41  Identities=20%  Similarity=0.427  Sum_probs=25.7

Q ss_pred             CCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            3 FDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      ....|+.|.........++..=+..||.+|           ..|-.|.+++.
T Consensus        10 ~~~~C~~C~~~i~~~e~~~~~~~~~~H~~C-----------F~C~~C~~~L~   50 (72)
T 3f6q_B           10 ASATCERCKGGFAPAEKIVNSNGELYHEQC-----------FVCAQCFQQFP   50 (72)
T ss_dssp             TTCBCTTTCCBCCTTCEEEEETTEEEETTT-----------SSCTTTCCCCG
T ss_pred             CCccchhcCccccCCceEEEeCcCeeCcCC-----------CcccCCCCCCC
Confidence            346799997655533322224467889877           45777877664

>3ask_A E3 ubiquitin-protein ligase UHRF1; histone reader modules, epigenetic regulation, trimethylaion of lysine residue, ligase-DNA binding protein; HET: M3L; 2.90A {Homo sapiens}

Probab=82.09  E-value=0.28  Score=28.85  Aligned_cols=47  Identities=30%  Similarity=0.610  Sum_probs=26.9

Q ss_pred             cccccCcCC-CCCCeEecCCCCcccHHHHHHHHHhCC-C-CCCCcccccc
Q 035446            6 CCPDCKLPG-DDCPLIWGACNHAFHLHCILKWVNSQT-P-QAHCPMCRRE   52 (59)
Q Consensus         6 ~C~IC~~~~-~~~~~~~~~C~H~fh~~Ci~~w~~~~~-~-~~~CP~Cr~~   52 (59)
                      .|.+|.... .+..+.-..|...||..|+..-+.... + .=.||.|+..
T Consensus       176 ~C~vC~~~~~~~~lL~CD~C~~~yH~~CL~PPL~~vP~G~~W~Cp~C~~~  225 (226)
T 3ask_A          176 ACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND  225 (226)
T ss_dssp             SCSSSCCCCC--CCEECSSSCCEECSCC--CCCCSCCSSSCCCCGGGC--
T ss_pred             CCcCCCCCCCCCCeEEcCCCCcceeCccCCCCcccCCCCCCCCCcCCcCc
Confidence            577886432 234555568999999999986544321 1 2369999753

>2d8z_A Four and A half LIM domains 2; skeletal muscle LIM-protein 3, LIM-domain protein DRAL, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=81.50  E-value=1.5  Score=20.20  Aligned_cols=39  Identities=23%  Similarity=0.524  Sum_probs=24.9

Q ss_pred             CCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            3 FDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      +...|+.|..+..+..+  ..=+..||.+|           ..|-.|++++.
T Consensus         4 ~~~~C~~C~~~I~~~~~--~a~~~~~H~~C-----------F~C~~C~~~L~   42 (70)
T 2d8z_A            4 GSSGCVQCKKPITTGGV--TYREQPWHKEC-----------FVCTACRKQLS   42 (70)
T ss_dssp             CCCBCSSSCCBCCSSEE--ESSSSEEETTT-----------SBCSSSCCBCT
T ss_pred             CCCCCcccCCeeccceE--EECccccCCCC-----------CccCCCCCcCC
Confidence            34578888765544332  34577888877           46777777654

>1wig_A KIAA1808 protein; LIM domain, zinc finger, metal-binding protein, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=81.20  E-value=1.7  Score=20.45  Aligned_cols=39  Identities=23%  Similarity=0.432  Sum_probs=24.9

Q ss_pred             CCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            3 FDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      +...|+-|..+..+..+  ..=+..||.+|           ..|-.|..++.
T Consensus         4 ~~~~C~~C~~~I~~~~v--~a~~~~wH~~C-----------F~C~~C~~~L~   42 (73)
T 1wig_A            4 GSSGCDSCEKYITGRVL--EAGEKHYHPSC-----------ALCVRCGQMFA   42 (73)
T ss_dssp             SCCSCSSSCCCCSSCCB--CCSSCCBCTTT-----------SCCSSSCCCCC
T ss_pred             CcCCcccCCCEecCeeE--EeCCCCCCCCc-----------CEeCCCCCCCC
Confidence            34578888765554333  35577888877           45777776654

>1x64_A Alpha-actinin-2 associated LIM protein; LIM domain, PDZ and LIM domain 3, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3

Probab=80.89  E-value=2.7  Score=20.33  Aligned_cols=37  Identities=19%  Similarity=0.326  Sum_probs=24.8

Q ss_pred             CcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      ..|+.|.....+..+  ..-+..||.+|           ..|-.|+..+.
T Consensus        26 ~~C~~C~~~I~~~~~--~a~~~~~H~~C-----------F~C~~C~~~L~   62 (89)
T 1x64_A           26 PLCDKCGSGIVGAVV--KARDKYRHPEC-----------FVCADCNLNLK   62 (89)
T ss_dssp             CBCTTTCCBCCSCCE--ESSSCEECTTT-----------CCCSSSCCCTT
T ss_pred             CCcccCCCEecccEE--EECCceECccC-----------CEecCCCCCCC
Confidence            468888765554333  25578899887           46777877664

>3a1b_A DNA (cytosine-5)-methyltransferase 3A, histone H3; zinc-finger, histone binding, chromosomal protein, DNA damag repair, DNA-binding, methylation; HET: DNA; 2.29A {Homo sapiens} PDB: 3a1a_A*

Probab=80.82  E-value=1.2  Score=24.86  Aligned_cols=35  Identities=23%  Similarity=0.513  Sum_probs=23.1

Q ss_pred             CCCcccccCcCCCCCCeEec--CCCCcccHHHHHHHHHh
Q 035446            3 FDGCCPDCKLPGDDCPLIWG--ACNHAFHLHCILKWVNS   39 (59)
Q Consensus         3 ~~~~C~IC~~~~~~~~~~~~--~C~H~fh~~Ci~~w~~~   39 (59)
                      ++..|.||-+. . ..+.-.  .|...||..||...+..
T Consensus        78 ~~~yC~wC~~G-g-~l~~Cdn~~C~r~FC~~CI~~nvG~  114 (159)
T 3a1b_A           78 YQSYCTICCGG-R-EVLMCGNNNCCRCFCVECVDLLVGP  114 (159)
T ss_dssp             SBSSCTTTSCC-S-EEEECSSTTTCCEEEHHHHHHHTCT
T ss_pred             CcceeeEecCC-C-eEEeeCCCCCCCchhHHHHHHhcCH
Confidence            45678888432 2 222222  68899999999998643

>1x62_A C-terminal LIM domain protein 1; PDZ and LIM domain protein 1, LIM domain protein CLP-36, contractIle protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=80.53  E-value=2.1  Score=20.30  Aligned_cols=38  Identities=16%  Similarity=0.259  Sum_probs=24.7

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      ...|+.|.....+..+  ..-+..||.+|           ..|-.|+.++.
T Consensus        15 ~~~C~~C~~~I~~~~~--~a~~~~~H~~C-----------F~C~~C~~~L~   52 (79)
T 1x62_A           15 LPMCDKCGTGIVGVFV--KLRDRHRHPEC-----------YVCTDCGTNLK   52 (79)
T ss_dssp             CCCCSSSCCCCCSSCE--ECSSCEECTTT-----------TSCSSSCCCHH
T ss_pred             CCccccCCCCccCcEE--EECcceeCcCc-----------CeeCCCCCCCC
Confidence            3568889766554433  35578899887           35777766543

>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain, leukemia, apoptosis, chromati regulator, DNA-binding, isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A* 3lqj_A* 2kyu_A

Probab=80.43  E-value=0.6  Score=26.47  Aligned_cols=49  Identities=22%  Similarity=0.418  Sum_probs=30.7

Q ss_pred             CcccccCcCCCC-----CCeEecCCCCcccHHHHHHH------HHhC--CCCCCCccccccc
Q 035446            5 GCCPDCKLPGDD-----CPLIWGACNHAFHLHCILKW------VNSQ--TPQAHCPMCRREW   53 (59)
Q Consensus         5 ~~C~IC~~~~~~-----~~~~~~~C~H~fh~~Ci~~w------~~~~--~~~~~CP~Cr~~~   53 (59)
                      ..||||..+..+     ..+.-..|...||..|+.--      +...  .....||.|+..-
T Consensus         3 ~~CpiC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~~   64 (183)
T 3lqh_A            3 NFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERH   64 (183)
T ss_dssp             CBCTTTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCSS
T ss_pred             CcCCCCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCCC
Confidence            469999754332     24555688999999997431      1100  0026899998753

---

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	59
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	3e-07
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	7e-05
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	0.001
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	0.002
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	0.004
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	0.004

>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 = 40.9 bits (95), Expect = 3e-07
 Identities = 19/51 (37%), Positives = 29/51 (56%), Gaps = 3/51 (5%)

Query: 6  CCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK 56
                   ++C + WG CNHAFH HCI +W+ +   +  CP+  REW+F+
Sbjct: 39 QANQASATSEECTVAWGVCNHAFHFHCISRWLKT---RQVCPLDNREWEFQ 86

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 114

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.4 bits (80), Expect = 7e-05
 Identities = 15/50 (30%), Positives = 20/50 (40%), Gaps = 2/50 (4%)

Query: 9  DCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAH--CPMCRREWQFK 56
          D K  G         C+HAFHL C+L    +        CP C+  +  K
Sbjct: 46 DSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK 95

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 31.6 bits (71), Expect = 0.001
 Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 2/46 (4%)

Query: 7  CPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRRE 52
          CP C     +       C+H F   C+LK +N +   + CP+C+ +
Sbjct: 24 CPICLELIKEPVST--KCDHIFCKFCMLKLLNQKKGPSQCPLCKND 67

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 30.7 bits (69), Expect = 0.002
 Identities = 13/47 (27%), Positives = 16/47 (34%), Gaps = 4/47 (8%)

Query: 6  CCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRRE 52
           C  C     D  +    C H     C+  W  S+     CP CR E
Sbjct: 25 LCKICAENDKDVKIE--PCGHLMCTSCLTSWQESEGQG--CPFCRCE 67

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]} Length = 55

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

 Score = 29.8 bits (67), Expect = 0.004
 Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 3/29 (10%)

Query: 24 CNHAFHLHCILKWVNSQTPQAHCPMCRRE 52
          C H FH  C+  W+ S    + CP+CR  
Sbjct: 27 CGHGFHAECVDMWLGS---HSTCPLCRLT 52

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]} Length = 68

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

 Score = 29.5 bits (66), Expect = 0.004
 Identities = 10/31 (32%), Positives = 15/31 (48%), Gaps = 3/31 (9%)

Query: 24 CNHAFHLHCILKWVNSQTPQAHCPMCRREWQ 54
          C HAF   CI +W+        CP+C+   +
Sbjct: 24 CLHAFCYVCITRWIRQ---NPTCPLCKVPVE 51

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	59
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.78
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.77
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.75
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.75
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.74
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.72
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.67
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.65
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.62
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.61
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.55
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.49
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.47
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.47
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.45
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.22
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.89
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	96.25
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	95.81
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	95.52
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	94.96
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	94.76
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	94.76
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	94.28
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	93.31
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	92.26
d1wesa_	71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	91.96
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	91.02
d2pnxa1	51	Inhibitor of growth protein 4, Ing4 {Homo sapiens	90.78
d2o35a1	79	Hypothetical protein SMc04008 {Rhizobium meliloti	89.19
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	88.09
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	82.29

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

Probab=99.78  E-value=7.8e-20  Score=86.37  Aligned_cols=49  Identities=27%  Similarity=0.628  Sum_probs=38.8

Q ss_pred             CCCcccccCcCCC--CCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            3 FDGCCPDCKLPGD--DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         3 ~~~~C~IC~~~~~--~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      -+..|+||++++.  +....++.|+|.||..||.+|++++   .+||+||+++.
T Consensus         4 d~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~---~~CP~CR~~i~   54 (55)
T d1iyma_           4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSH---STCPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTC---CSCSSSCCCSC
T ss_pred             CCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhC---CcCCCCCCEeE
Confidence            3467999997544  2334445799999999999999886   78999999864

>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=99.77  E-value=1.6e-19  Score=92.00  Aligned_cols=51  Identities=41%  Similarity=1.118  Sum_probs=41.3

Q ss_pred             CCcccccCcCCC----------------CCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGD----------------DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~----------------~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      ++.|+||++...                ...+..++|||.||.+||.+|++.+   .+||+||++|.+++
T Consensus        21 ~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~---~~CP~CR~~~~~~~   87 (88)
T d3dplr1          21 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTR---QVCPLDNREWEFQK   87 (88)
T ss_dssp             SCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTC---SBCSSSCSBCCEEE
T ss_pred             CCcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHHC---CcCCCCCCcccccc
Confidence            567999975322                1245678999999999999999987   78999999998864

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.75  E-value=1.3e-18  Score=91.59  Aligned_cols=55  Identities=25%  Similarity=0.410  Sum_probs=41.9

Q ss_pred             CCCcccccCcCCC----------------CCCeEecCCCCcccHHHHHHHHHhCC--CCCCCccccccccccC
Q 035446            3 FDGCCPDCKLPGD----------------DCPLIWGACNHAFHLHCILKWVNSQT--PQAHCPMCRREWQFKG   57 (59)
Q Consensus         3 ~~~~C~IC~~~~~----------------~~~~~~~~C~H~fh~~Ci~~w~~~~~--~~~~CP~Cr~~~~~~~   57 (59)
                      .++.|+||++...                ...+.+++|+|.||..||.+|++...  .+.+||+||+.|..+.
T Consensus        24 ~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~~   96 (114)
T d1v87a_          24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKT   96 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCS
T ss_pred             ccccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhccCc
Confidence            4678999985321                23456789999999999999998753  2357999999887654

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

Probab=99.75  E-value=5.5e-19  Score=86.28  Aligned_cols=47  Identities=28%  Similarity=0.690  Sum_probs=40.0

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~   54 (59)
                      .+.|+||++...+ +++.++|||.||..||.+|++.+   .+||+||+++.
T Consensus         5 ~d~C~IC~~~~~~-~~~~~~C~H~Fc~~Ci~~w~~~~---~~CP~CR~~i~   51 (68)
T d1chca_           5 AERCPICLEDPSN-YSMALPCLHAFCYVCITRWIRQN---PTCPLCKVPVE   51 (68)
T ss_dssp             CCCCSSCCSCCCS-CEEETTTTEEESTTHHHHHHHHS---CSTTTTCCCCC
T ss_pred             CCCCccCCcCccC-CcEEeCCCCcCcHHHHHHHHHhC---CcCCCCCcchH
Confidence            3679999876654 45668999999999999999986   78999999875

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=1.2e-18  Score=84.41  Aligned_cols=52  Identities=23%  Similarity=0.542  Sum_probs=40.6

Q ss_pred             CCcccccCcC---CCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKLP---GDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~---~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      +..||||++.   ..+..+++++|||.||.+||.+|+...+  ..||+||+++...+
T Consensus         3 d~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~--~~CP~CR~~i~~~~   57 (65)
T d1g25a_           3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGA--GNCPECGTPLRKSN   57 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTS--SSCTTTCCCCSSCC
T ss_pred             CCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCc--CCCCCCCcCccccc
Confidence            5789999853   2344556679999999999999997653  57999999886543

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=9.8e-19  Score=81.63  Aligned_cols=48  Identities=23%  Similarity=0.534  Sum_probs=37.8

Q ss_pred             cccccCcCCC--CCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccc
Q 035446            6 CCPDCKLPGD--DCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQF   55 (59)
Q Consensus         6 ~C~IC~~~~~--~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~   55 (59)
                      .||||++.++  +..+..++|||.||.+||.+|++.++  .+||+||+++..
T Consensus         2 eCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~--~~CP~CR~~~~~   51 (52)
T d1ur6b_           2 ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDEN--GLCPACRKPYPE   51 (52)
T ss_dssp             EETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSC--CBCTTTCCBCSC
T ss_pred             CCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcC--CCCCccCCcCCC
Confidence            6999996543  23344568999999999999998753  579999998864

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=5.7e-17  Score=81.02  Aligned_cols=48  Identities=27%  Similarity=0.632  Sum_probs=38.7

Q ss_pred             CcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      ..|+||++...+  .++++|||.||..||.+|+..+.  ..||+||..+...
T Consensus        24 ~~C~IC~~~~~~--~~~~~CgH~fC~~Ci~~wl~~~~--~~CP~Cr~~i~~~   71 (79)
T d1fbva4          24 QLCKICAENDKD--VKIEPCGHLMCTSCLTSWQESEG--QGCPFCRCEIKGT   71 (79)
T ss_dssp             TBCTTTSSSBCC--EECSSSCCEECHHHHHHHHHTTC--CSCTTTCCCCCCC
T ss_pred             CCCccCCCcCCC--eEEeCCCCeeeHHHHHHHHHHCc--CcCCCCCcCccCC
Confidence            469999876554  34579999999999999998652  6799999988754

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.65  E-value=3.9e-17  Score=77.06  Aligned_cols=48  Identities=10%  Similarity=0.201  Sum_probs=40.7

Q ss_pred             cccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            6 CCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         6 ~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      .|+||++...+ ++....|||+|+++||.+|++.+   .+||+||+++..++
T Consensus         2 ~C~Ic~~~~~~-Pv~~~~cGh~fc~~cI~~~l~~~---~~CP~c~~~l~~~d   49 (56)
T d2baya1           2 LCAISGKVPRR-PVLSPKSRTIFEKSLLEQYVKDT---GNDPITNEPLSIEE   49 (56)
T ss_dssp             CCTTTCSCCSS-EEEETTTTEEEEHHHHHHHHHHH---SBCTTTCCBCCGGG
T ss_pred             CCccCCchHHh-cCccCCCCCcccHHHHHHHHhhc---cCCCccCCcCCHHh
Confidence            69999876554 66666899999999999999987   78999999987654

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.62  E-value=1.2e-16  Score=81.11  Aligned_cols=49  Identities=29%  Similarity=0.548  Sum_probs=39.7

Q ss_pred             CcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      ..|+||++...+ ++. ++|||.||+.||.+|++.+.  ..||+||.++...+
T Consensus        24 l~C~IC~~~~~~-pv~-~~CgH~FC~~Ci~~~~~~~~--~~CP~Cr~p~~~~~   72 (86)
T d1rmda2          24 ISCQICEHILAD-PVE-TSCKHLFCRICILRCLKVMG--SYCPSCRYPCFPTD   72 (86)
T ss_dssp             TBCTTTCSBCSS-EEE-CTTSCEEEHHHHHHHHHHTC--SBCTTTCCBCCGGG
T ss_pred             cCCccCCcchhc-cee-cCCCChhhHHHHHHHHhhCC--CcCcccCCCCChhh
Confidence            479999876654 443 69999999999999998753  57999999887554

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=1.8e-16  Score=82.23  Aligned_cols=51  Identities=27%  Similarity=0.686  Sum_probs=40.5

Q ss_pred             CcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      ..|+||++...+ |+. ++|||+||..||.+|++.......||+||+++...+
T Consensus        22 l~CpIC~~~~~~-pv~-~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   72 (103)
T d1jm7a_          22 LECPICLELIKE-PVS-TKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS   72 (103)
T ss_dssp             TSCSSSCCCCSS-CCB-CTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTT
T ss_pred             cCCCccCchhCC-eEE-cCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhh
Confidence            579999876654 443 689999999999999987644458999999886543

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

Probab=99.55  E-value=1.3e-15  Score=72.40  Aligned_cols=51  Identities=14%  Similarity=0.348  Sum_probs=37.0

Q ss_pred             CcccccCcCCCCCCeE---ecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            5 GCCPDCKLPGDDCPLI---WGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~---~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      ..|+||++..++..+.   ...|+|.||..||.+|+..+. +.+||+||++|..+
T Consensus         7 ~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~-~~~CP~Cr~~~~~k   60 (60)
T d1vyxa_           7 PVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISR-NTACQICGVVYNTR   60 (60)
T ss_dssp             CEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHT-CSBCTTTCCBCCCC
T ss_pred             CCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCC-CCCCcccCCeeecC
Confidence            5799998654433222   223469999999999997642 36899999998764

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=1.7e-15  Score=77.70  Aligned_cols=48  Identities=23%  Similarity=0.575  Sum_probs=37.9

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      +..|+||++.+.+ ++.+++|||.||..||.+|+.     ..||.||.++...+
T Consensus        22 ~l~C~IC~~~~~~-pv~~~~CgH~fC~~Ci~~~~~-----~~CP~Cr~~~~~~~   69 (97)
T d1jm7b_          22 LLRCSRCTNILRE-PVCLGGCEHIFCSNCVSDCIG-----TGCPVCYTPAWIQD   69 (97)
T ss_dssp             TTSCSSSCSCCSS-CBCCCSSSCCBCTTTGGGGTT-----TBCSSSCCBCSCSS
T ss_pred             cCCCccCCchhhc-CceeCCCCCchhHHHHHHHHh-----ccccccCCcCchhh
Confidence            4589999876554 555568999999999999984     35999999876543

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: E3 ubiquitin ligase PUB14
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.47  E-value=2.6e-14  Score=70.76  Aligned_cols=52  Identities=19%  Similarity=0.344  Sum_probs=41.7

Q ss_pred             CCCCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            1 MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         1 ~~~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      +|.+..|+||++...+ ++. ++|||+|++.||.+|++.+.  ..||.|+.++...
T Consensus         5 iP~~l~CpIc~~~m~d-PV~-~~cgh~fc~~ci~~~~~~~~--~~cP~~~~~l~~~   56 (78)
T d1t1ha_           5 FPEYFRCPISLELMKD-PVI-VSTGQTYERSSIQKWLDAGH--KTCPKSQETLLHA   56 (78)
T ss_dssp             CSSSSSCTTTSCCCSS-EEE-ETTTEEEEHHHHHHHHTTTC--CBCTTTCCBCSSC
T ss_pred             CCccCCCcCcCchhhC-ceE-ccCCCcchHHHHHHHHHHCC--CCCCcccccCCcc
Confidence            4567899999866555 454 59999999999999998752  6799999987654

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.47  E-value=1.8e-14  Score=71.70  Aligned_cols=52  Identities=12%  Similarity=0.034  Sum_probs=41.9

Q ss_pred             CCCCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            1 MAFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         1 ~~~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      +|-+..||||++...+ |+. ++|||+|++.||.+|+....  ..||.||.++...
T Consensus         4 iP~~l~CpIc~~l~~d-Pv~-~~cGhtfc~~ci~~~l~~~~--~~cP~c~~~l~~~   55 (80)
T d2c2la2           4 IPDYLCGKISFELMRE-PCI-TPSGITYDRKDIEEHLQRVG--HFNPVTRSPLTQE   55 (80)
T ss_dssp             CCSTTBCTTTCSBCSS-EEE-CSSCCEEETTHHHHHHHHTC--SSCTTTCCCCCGG
T ss_pred             CCccccCcCcCchhhh-hcc-cCCcCeecHHHHHHHHhcCC--ccCCCcccccccc
Confidence            4567889999866555 443 69999999999999998753  5799999987654

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.45  E-value=4.6e-15  Score=69.92  Aligned_cols=45  Identities=22%  Similarity=0.648  Sum_probs=35.4

Q ss_pred             CcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      ..|+||++...+ ++. ++|||+||..||.+|      ...||+||+++....
T Consensus         7 l~C~IC~~~~~~-p~~-lpCgH~fC~~Ci~~~------~~~CP~Cr~~~~~~~   51 (56)
T d1bora_           7 LRCQQCQAEAKC-PKL-LPCLHTLCSGCLEAS------GMQCPICQAPWPLGA   51 (56)
T ss_dssp             SSCSSSCSSCBC-CSC-STTSCCSBTTTCSSS------SSSCSSCCSSSSCCS
T ss_pred             CCCcccCcccCC-CEE-ecCCCHHhHHHHHcC------CCcCcCCCCcccCCC
Confidence            489999876654 333 699999999999764      268999999987654

>d1wgma_ g.44.1.2 (A:) Ubiquitin conjugation factor E4A {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Ubiquitin conjugation factor E4A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.22  E-value=6.5e-12  Score=64.45  Aligned_cols=52  Identities=13%  Similarity=0.059  Sum_probs=39.8

Q ss_pred             CCCCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCCCCCCCccccccccccC
Q 035446            2 AFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFKG   57 (59)
Q Consensus         2 ~~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~~   57 (59)
                      |-+..||||+....+ |+++..|+|.|++.||.+|+..+   ..||+|++++...+
T Consensus        20 P~~f~CPI~~~lm~d-PV~~~~~~~ty~r~~I~~~l~~~---~~~P~~~~~l~~~~   71 (98)
T d1wgma_          20 CDEFLDPIMSTLMCD-PVVLPSSRVTVDRSTIARHLLSD---QTDPFNRSPLTMDQ   71 (98)
T ss_dssp             CTTTBCTTTCSBCSS-EEECTTTCCEEEHHHHHHHTTTS---CBCTTTCSBCCTTT
T ss_pred             cHHhCCcCchhHHHH-HHhcccccchhhHHHHHHHHHhc---CCcccccccccchh
Confidence            446789999765554 55533445699999999999876   78999999887643

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.89  E-value=2.6e-10  Score=57.47  Aligned_cols=47  Identities=17%  Similarity=0.323  Sum_probs=33.9

Q ss_pred             CCcccccCcCCC-CCCeEecCCCCcccHHHHHHHHHhCC-----CCCCCcccc
Q 035446            4 DGCCPDCKLPGD-DCPLIWGACNHAFHLHCILKWVNSQT-----PQAHCPMCR   50 (59)
Q Consensus         4 ~~~C~IC~~~~~-~~~~~~~~C~H~fh~~Ci~~w~~~~~-----~~~~CP~Cr   50 (59)
                      ...|+||++... +..+.+++|+|.||.+|+.+|++.+.     ....||.|+
T Consensus         5 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~   57 (94)
T d1wima_           5 SSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAA   57 (94)
T ss_dssp             BCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTT
T ss_pred             CCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCC
Confidence            357999986544 33445578999999999999997531     123699864

>d1f62a_ g.50.1.2 (A:) Williams-Beuren syndrome transcription factor, WSTF {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Williams-Beuren syndrome transcription factor, WSTF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.25  E-value=0.0014  Score=28.67  Aligned_cols=46  Identities=30%  Similarity=0.735  Sum_probs=31.2

Q ss_pred             cccccCcCCC-CCCeEecCCCCcccHHHHHHHHHhCC-CCCCCccccc
Q 035446            6 CCPDCKLPGD-DCPLIWGACNHAFHLHCILKWVNSQT-PQAHCPMCRR   51 (59)
Q Consensus         6 ~C~IC~~~~~-~~~~~~~~C~H~fh~~Ci~~w~~~~~-~~~~CP~Cr~   51 (59)
                      .|.||....+ +..+.-..|...||..|+..-+.... +.-.||.|+.
T Consensus         2 ~C~vC~~~~~~~~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDDKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCCCEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            5889975433 33455668999999999987654321 1247999975

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Nuclear corepressor KAP-1 (TIF-1beta)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.81  E-value=0.0015  Score=30.56  Aligned_cols=52  Identities=19%  Similarity=0.462  Sum_probs=32.3

Q ss_pred             CCCcccccCc-CCCCCCeEecCCCCcccHHHHHHHHHhCC-CCCCCcccccccc
Q 035446            3 FDGCCPDCKL-PGDDCPLIWGACNHAFHLHCILKWVNSQT-PQAHCPMCRREWQ   54 (59)
Q Consensus         3 ~~~~C~IC~~-~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~-~~~~CP~Cr~~~~   54 (59)
                      +|+.|.+|.. ...+..+.-..|...||..|+...+.... +.-.||.|+....
T Consensus         3 ~Dd~c~~C~~C~~~~~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~   56 (70)
T d1fp0a1           3 LDDSATICRVCQKPGDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPD   56 (70)
T ss_dssp             SSSSSSCCSSSCSSSCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCS
T ss_pred             cCCCCCCCCCCCCcCEEEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcCc
Confidence            4555555532 11233555678999999999987654331 1246999976543

>d1wila_ g.50.1.3 (A:) Hypothetical protein KIAA1045 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: variant PHD-like domain
domain: Hypothetical protein KIAA1045
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.52  E-value=0.0075  Score=29.35  Aligned_cols=35  Identities=20%  Similarity=0.459  Sum_probs=24.2

Q ss_pred             CCCCcccccCcCCCCCCeEecCCCCcccHHHHHHH
Q 035446            2 AFDGCCPDCKLPGDDCPLIWGACNHAFHLHCILKW   36 (59)
Q Consensus         2 ~~~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w   36 (59)
                      .-|..|.||.....+...----|+-+||..|+.+-
T Consensus        13 ~~D~mC~vC~v~t~~~l~pCRvCtRv~H~~CL~r~   47 (89)
T d1wila_          13 VNDEMCDVCEVWTAESLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTTCCCCSSCCSSCSSSSSCCCHHHHHHH
T ss_pred             CcCccccccCcccccceecceeecchhhHHHHHHh
Confidence            34788999954433332222368899999999986

>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Sumoylation ligase E3, SIZ1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=94.96  E-value=0.0048  Score=29.22  Aligned_cols=48  Identities=19%  Similarity=0.328  Sum_probs=28.9

Q ss_pred             cccccCcCCCCCCeEec---CCCCcccHHHHHHHH----H--hCCCCCCCcccccccc
Q 035446            6 CCPDCKLPGDDCPLIWG---ACNHAFHLHCILKWV----N--SQTPQAHCPMCRREWQ   54 (59)
Q Consensus         6 ~C~IC~~~~~~~~~~~~---~C~H~fh~~Ci~~w~----~--~~~~~~~CP~Cr~~~~   54 (59)
                      .| ||....+....+..   .|...||..|+.---    .  .......||.|+..-.
T Consensus        18 ~C-~C~~~~~~~~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~~~   74 (78)
T d1wewa_          18 RC-VCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTSG   74 (78)
T ss_dssp             CC-SSCCCCCCSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCCS
T ss_pred             Ee-ECCCccCCCcEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCcCC
Confidence            47 89765544444444   499999999984210    0  0001268999976543

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At5g26210
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=94.76  E-value=0.0025  Score=29.05  Aligned_cols=50  Identities=22%  Similarity=0.392  Sum_probs=32.3

Q ss_pred             CCcccccCcCCCCC--CeEecCCCCcccHHHHHHHHHh--CCCCCCCccccccc
Q 035446            4 DGCCPDCKLPGDDC--PLIWGACNHAFHLHCILKWVNS--QTPQAHCPMCRREW   53 (59)
Q Consensus         4 ~~~C~IC~~~~~~~--~~~~~~C~H~fh~~Ci~~w~~~--~~~~~~CP~Cr~~~   53 (59)
                      +..|.+|....++.  .|.-..|+..||..|+..-...  ......||.|+..-
T Consensus         6 ~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~~   59 (64)
T d1we9a_           6 SGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKS   59 (64)
T ss_dssp             CCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTTT
T ss_pred             CCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCcC
Confidence            56899997543332  3456689999999998632111  11235899998653

>d1wepa_ g.50.1.2 (A:) PHD finger protein 8 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 8
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.76  E-value=0.056  Score=25.35  Aligned_cols=49  Identities=22%  Similarity=0.408  Sum_probs=30.1

Q ss_pred             cccccCcCCC--CCCeEecCCCCcccHHHHHHH--HHhCCCCCCCcccccccc
Q 035446            6 CCPDCKLPGD--DCPLIWGACNHAFHLHCILKW--VNSQTPQAHCPMCRREWQ   54 (59)
Q Consensus         6 ~C~IC~~~~~--~~~~~~~~C~H~fh~~Ci~~w--~~~~~~~~~CP~Cr~~~~   54 (59)
                      .+-||....+  +..|.--.|.-.||..|+.--  .........||.|+....
T Consensus        13 v~CiC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~g   65 (79)
T d1wepa_          13 VYCLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFG   65 (79)
T ss_dssp             CCSTTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSC
T ss_pred             eEeECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCcC
Confidence            3448975433  224556788999999998532  111112368999987543

>d1weva_ g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 22
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.28  E-value=0.0061  Score=29.30  Aligned_cols=50  Identities=20%  Similarity=0.367  Sum_probs=30.6

Q ss_pred             CCcccccCcCCC---CCCeEecCCCCcccHHHHHHH-----HHhCCCCCCCccccccc
Q 035446            4 DGCCPDCKLPGD---DCPLIWGACNHAFHLHCILKW-----VNSQTPQAHCPMCRREW   53 (59)
Q Consensus         4 ~~~C~IC~~~~~---~~~~~~~~C~H~fh~~Ci~~w-----~~~~~~~~~CP~Cr~~~   53 (59)
                      +..|.||.....   ...+.--.|...||..|+...     .......-.||.|....
T Consensus        16 ~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~~   73 (88)
T d1weva_          16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQM   73 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHH
T ss_pred             cCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCchH
Confidence            356999974322   223445688899999997632     12211124799997543

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Mi2-beta (CHD4)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.31  E-value=0.0041  Score=28.17  Aligned_cols=47  Identities=23%  Similarity=0.473  Sum_probs=30.8

Q ss_pred             CCcccccCcCCCCCCeEecCCCCcccHHHHHHHHHhCC-CCCCCcccccc
Q 035446            4 DGCCPDCKLPGDDCPLIWGACNHAFHLHCILKWVNSQT-PQAHCPMCRRE   52 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~-~~~~CP~Cr~~   52 (59)
                      ++.|.+|.+.  ...+.-..|.-.||..|+...+.... ..-.||.|+..
T Consensus         9 ~~~C~~C~~~--g~lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~   56 (61)
T d1mm2a_           9 MEFCRVCKDG--GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCP   56 (61)
T ss_dssp             CSSCTTTCCC--SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTT
T ss_pred             cCCCcCCCCC--CeEEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCc
Confidence            3568888543  23455568899999999875544321 13479999754

>d1weoa_ g.44.1.1 (A:) Cellulose synthase A catalytic subunit 7, IRX3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Cellulose synthase A catalytic subunit 7, IRX3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=92.26  E-value=0.25  Score=23.90  Aligned_cols=50  Identities=16%  Similarity=0.302  Sum_probs=34.6

Q ss_pred             CcccccCcCC-----CCCCeEecCCCCcccHHHHHHHHHhCCCCCCCcccccccccc
Q 035446            5 GCCPDCKLPG-----DDCPLIWGACNHAFHLHCILKWVNSQTPQAHCPMCRREWQFK   56 (59)
Q Consensus         5 ~~C~IC~~~~-----~~~~~~~~~C~H~fh~~Ci~~w~~~~~~~~~CP~Cr~~~~~~   56 (59)
                      ..|.||-+..     .+.-++.-.|+--.|+.|.+-=.+..  +..||.|+.++..-
T Consensus        17 q~CqiCGd~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG--~q~CpqCkt~Ykr~   71 (93)
T d1weoa_          17 QFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREG--TQNCPQCKTRYKRL   71 (93)
T ss_dssp             CBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTS--CSSCTTTCCCCCCC
T ss_pred             chhhhcccccccCCCCCEEEEecccCCccchHHHHHHHhcc--CccCcccCChhhhh
Confidence            5799997532     22334445677889999987655544  47899999988653

>d1wesa_ g.50.1.2 (A:) PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD Inhibitor of growth protein 2, Ing2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.96  E-value=0.025  Score=26.33  Aligned_cols=44  Identities=20%  Similarity=0.427  Sum_probs=24.8

Q ss_pred             ccccCcCCCCCCeEe--cCCC-CcccHHHHHHHHHhC-CCCCCCcccccc
Q 035446            7 CPDCKLPGDDCPLIW--GACN-HAFHLHCILKWVNSQ-TPQAHCPMCRRE   52 (59)
Q Consensus         7 C~IC~~~~~~~~~~~--~~C~-H~fh~~Ci~~w~~~~-~~~~~CP~Cr~~   52 (59)
                      +-||.....+..+..  -.|. ..||..|+.  +... ...-.||.|+..
T Consensus        18 ~CiC~~~~~~~~i~c~~~~C~~~wfH~~Cvg--l~~~p~~~w~C~~C~~~   65 (71)
T d1wesa_          18 YCLCNQVSYGEMIGCDNEQCPIEWFHFSCVS--LTYKPKGKWYCPKCRGD   65 (71)
T ss_dssp             CSTTCCCCCSSEECCSCTTCSCCCEETTTTT--CSSCCSSCCCCTTTSSC
T ss_pred             EEEeCCCCCCCEEEEECCCCCCcCccCccCC--CCcCCCCcEECcCCccc
Confidence            338975544332222  1343 479999984  2221 123589999764

>d1wema_ g.50.1.2 (A:) Death associated transcription factor 1, Datf1 (DIO-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Death associated transcription factor 1, Datf1 (DIO-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.02  E-value=0.16  Score=23.21  Aligned_cols=47  Identities=21%  Similarity=0.537  Sum_probs=28.1

Q ss_pred             cccccCcCCCC-CCeEecCCCCcccHHHHH------HHHHhCCCCCCCccccccc
Q 035446            6 CCPDCKLPGDD-CPLIWGACNHAFHLHCIL------KWVNSQTPQAHCPMCRREW   53 (59)
Q Consensus         6 ~C~IC~~~~~~-~~~~~~~C~H~fh~~Ci~------~w~~~~~~~~~CP~Cr~~~   53 (59)
                      .| ||....++ ..+.--.|.-.||..|+.      .........-.||.|+..-
T Consensus        18 ~C-iC~~~~~~~~mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~~   71 (76)
T d1wema_          18 YC-ICRQPHNNRFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILS   71 (76)
T ss_dssp             CS-TTCCCCCSSCEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHS
T ss_pred             EE-ECCCccCCCeEEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcCcC
Confidence            46 78654333 344556788999999982      1111111236899997543

>d2pnxa1 g.50.1.2 (A:195-245) Inhibitor of growth protein 4, Ing4 {Homo sapiens [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Inhibitor of growth protein 4, Ing4
species: Homo sapiens [TaxId: 9606]

Probab=90.78  E-value=0.0071  Score=26.54  Aligned_cols=43  Identities=21%  Similarity=0.486  Sum_probs=23.8

Q ss_pred             cccccCcCCCCCCeEecC--C-CCcccHHHHHHHHHhC-CCCCCCccccc
Q 035446            6 CCPDCKLPGDDCPLIWGA--C-NHAFHLHCILKWVNSQ-TPQAHCPMCRR   51 (59)
Q Consensus         6 ~C~IC~~~~~~~~~~~~~--C-~H~fh~~Ci~~w~~~~-~~~~~CP~Cr~   51 (59)
                      -| ||..+.++..+....  | .-.||..|+.-  ... .+.-.||.|++
T Consensus         4 yC-~C~~~~~~~mi~Cd~~~C~~~WfH~~Cvgl--~~~p~~~w~C~~C~~   50 (51)
T d2pnxa1           4 YC-LCHQVSYGEMIGCDNPDCSIEWFHFACVGL--TTKPRGKWFCPRCSQ   50 (51)
T ss_dssp             ET-TTTEECCSEEEECSCTTCSSCEEEGGGGTC--SSCCSSCCCCHHHHC
T ss_pred             EE-EcCCCCCCCEEEEecCCCCCCCEeCCccCC--CcCCCCcEECcCCCC
Confidence            36 786554444333222  3 45699999852  221 12347988875

>d2o35a1 a.293.1.1 (A:2-80) Hypothetical protein SMc04008 {Rhizobium meliloti [TaxId: 382]}

class: All alpha proteins
fold: SMc04008-like
superfamily: SMc04008-like
family: SMc04008-like
domain: Hypothetical protein SMc04008
species: Rhizobium meliloti [TaxId: 382]

Probab=89.19  E-value=0.1  Score=24.82  Aligned_cols=13  Identities=23%  Similarity=0.815  Sum_probs=11.4

Q ss_pred             cccHHHHHHHHHh
Q 035446           27 AFHLHCILKWVNS   39 (59)
Q Consensus        27 ~fh~~Ci~~w~~~   39 (59)
                      -||+.||.+|+..
T Consensus        39 GFCRNCLskWy~~   51 (79)
T d2o35a1          39 GFCRNCLSNWYRE   51 (79)
T ss_dssp             SCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            3999999999965

>d2cs3a1 g.44.1.3 (A:8-87) Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: Protein c14orf4 (KIAA1865)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.09  E-value=0.36  Score=22.56  Aligned_cols=35  Identities=26%  Similarity=0.635  Sum_probs=25.7

Q ss_pred             CCcccccCcCCCCCCeEecCC----CCcccHHHHHHHHHhC
Q 035446            4 DGCCPDCKLPGDDCPLIWGAC----NHAFHLHCILKWVNSQ   40 (59)
Q Consensus         4 ~~~C~IC~~~~~~~~~~~~~C----~H~fh~~Ci~~w~~~~   40 (59)
                      ...|.+|.+..++.-.+  .|    +|.||..|-...++.+
T Consensus         8 ~l~CtlC~erLEdtHFV--QCPsv~~HkFCFpCsr~sik~q   46 (80)
T d2cs3a1           8 PLCCTICHERLEDTHFV--QCPSVPSHKFCFPCSRESIKAQ   46 (80)
T ss_dssp             SCCCSSSCSCCSSTTSE--ECSSCSSCEECHHHHHHHHHHH
T ss_pred             ceeeeeehhhhcCCceE--eCCCCcCCceeccccHHHHHhc
Confidence            35799998766654443  33    6999999999998764

>d2dloa1 g.39.1.3 (A:8-42) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.29  E-value=0.14  Score=20.75  Aligned_cols=26  Identities=35%  Similarity=0.547  Sum_probs=18.4

Q ss_pred             CcccccCcCCCCCCeEecCCCCcccHHH
Q 035446            5 GCCPDCKLPGDDCPLIWGACNHAFHLHC   32 (59)
Q Consensus         5 ~~C~IC~~~~~~~~~~~~~C~H~fh~~C   32 (59)
                      +.|.+|..+..+..+.  .-|-.||..|
T Consensus         9 EkC~~C~~~I~driLr--A~Gk~yHP~C   34 (35)
T d2dloa1           9 EKCATCSQPILDRILR--AMGKAYHPGC   34 (35)
T ss_dssp             CBCTTTCCBCCSCCEE--ETTEEECTTT
T ss_pred             HHHHHhchHHHHHHHH--HhCCCCCCCC
Confidence            5699997776665544  5677888766