Psyllid ID: psy1749

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80-------
Protein Sequence
MEPWFQMGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCKNKLGHSRASVIWHRTQVKV
Secondary Structure (PSIPRED)
ccHHHHHccHHHHHHccccccccccccEEccccccEEcccccccEEcccccccccccccccccccccccHHHHHHHHHHHHcccccc
Secondary Structure Prediction (SSPRO)
ccHHHHcccccccccccccccccccEEEcccccccEEccccccEEEEEEcccccccccHHHccccccccccccccEEEEEEEEEEEc
Coil and Loop (DISEMBL)
mepwfqmggatfdselikccpmcsvpiekdEGCAQMLckrckhvfcWYCLasldddfllrhydkgpcknklghsrasVIWHRTQVKV
Flexible Loop (DISEMBL)
MEPWFQMGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGpcknklghsrasviwhrtqvkv
Low Complexity Region (SEG)
MEPWFQMGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCKNKLGHSRASVIWHRTQVKV
Disordered region (IsUnstruct)
***WFQMGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCKNKLGHSRASVIWH******
Disordered Region (DISOPRED)
********GATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCK**LGHSRASVIWHRTQVK*
Disordered Region (DISEMBL)
MEPWFQMGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCKNKLGHSRASVIWHRTQVKV
Disordered Region (DISPRO)
*E*WFQMGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCKNKLGHSRASVIWHRTQVKV
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MEPWFQMGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCKNKLGHSRASVIWHRTQVKV
Positional Conservation
no confident homologs detected

---

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	87	2.2.26 [Sep-21-2011]
Q6DH94	293	Probable E3 ubiquitin-pro	yes	N/A	0.839	0.249	0.808	2e-29
Q5RFV4	293	Probable E3 ubiquitin-pro	no	N/A	0.839	0.249	0.808	2e-29
P50876	292	Probable E3 ubiquitin-pro	yes	N/A	0.839	0.25	0.808	2e-29
A4IIY1	292	Probable E3 ubiquitin-pro	yes	N/A	0.839	0.25	0.808	3e-29
Q925F3	292	Probable E3 ubiquitin-pro	yes	N/A	0.793	0.236	0.840	5e-29
Q8BKD6	301	E3 ubiquitin-protein liga	no	N/A	0.885	0.255	0.675	6e-27
A5PK27	304	E3 ubiquitin-protein liga	no	N/A	0.885	0.253	0.675	6e-27
Q7Z419	303	E3 ubiquitin-protein liga	no	N/A	0.793	0.227	0.753	8e-27
Q80TT8	1865	Cullin-9 OS=Mus musculus	no	N/A	0.402	0.018	0.628	1e-08
Q8IWT3	2517	Cullin-9 OS=Homo sapiens	no	N/A	0.402	0.013	0.6	3e-08

>sp|Q6DH94|R1442_DANRE Probable E3 ubiquitin-protein ligase RNF144A-B OS=Danio rerio GN=rnf144ab PE=2 SV=1

 Score =  127 bits (318), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 59/73 (80%), Positives = 62/73 (84%)

Query: 13  DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCKNKLG 72
           D   IK CP C V IE+DEGCAQM+CK CKH FCWYCL SLDDDFLL HYDKGPC+NKLG
Sbjct: 179 DEAPIKRCPKCKVYIERDEGCAQMMCKNCKHAFCWYCLESLDDDFLLIHYDKGPCRNKLG 238

Query: 73  HSRASVIWHRTQV 85
           HSRASVIWHRTQV
Sbjct: 239 HSRASVIWHRTQV 251

E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes ube2l3 and ube2l6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.
Danio rerio (taxid: 7955)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp|Q5RFV4|R1441_DANRE Probable E3 ubiquitin-protein ligase RNF144A-A OS=Danio rerio GN=rnf144aa PE=3 SV=1

 Score =  127 bits (318), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 59/73 (80%), Positives = 62/73 (84%)

Query: 13  DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCKNKLG 72
           D   IK CP C V IE+DEGCAQM+CK CKH FCWYCL SLDDDFLL HYDKGPC+NKLG
Sbjct: 179 DDAPIKRCPKCKVYIERDEGCAQMMCKNCKHAFCWYCLESLDDDFLLIHYDKGPCRNKLG 238

Query: 73  HSRASVIWHRTQV 85
           HSRASVIWHRTQV
Sbjct: 239 HSRASVIWHRTQV 251

E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes ube2l3 and ube2l6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.

Danio rerio (taxid: 7955)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|P50876|R144A_HUMAN Probable E3 ubiquitin-protein ligase RNF144A OS=Homo sapiens GN=RNF144A PE=1 SV=2

 Score =  127 bits (318), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 59/73 (80%), Positives = 62/73 (84%)

Query: 13  DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCKNKLG 72
           D   IK CP C V IE+DEGCAQM+CK CKH FCWYCL SLDDDFLL HYDKGPC+NKLG
Sbjct: 178 DDAPIKRCPKCKVYIERDEGCAQMMCKNCKHAFCWYCLESLDDDFLLIHYDKGPCRNKLG 237

Query: 73  HSRASVIWHRTQV 85
           HSRASVIWHRTQV
Sbjct: 238 HSRASVIWHRTQV 250

E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|A4IIY1|R144A_XENTR Probable E3 ubiquitin-protein ligase RNF144A OS=Xenopus tropicalis GN=rnf144a PE=2 SV=1

 Score =  127 bits (318), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 59/73 (80%), Positives = 62/73 (84%)

Query: 13  DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCKNKLG 72
           D   IK CP C V IE+DEGCAQM+CK CKH FCWYCL SLDDDFLL HYDKGPC+NKLG
Sbjct: 178 DDVPIKRCPKCKVYIERDEGCAQMMCKNCKHAFCWYCLESLDDDFLLIHYDKGPCRNKLG 237

Query: 73  HSRASVIWHRTQV 85
           HSRASVIWHRTQV
Sbjct: 238 HSRASVIWHRTQV 250

E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes ube2l3 and ube2l6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.

Xenopus tropicalis (taxid: 8364)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q925F3|R144A_MOUSE Probable E3 ubiquitin-protein ligase RNF144A OS=Mus musculus GN=Rnf144a PE=1 SV=1

 Score =  125 bits (315), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 58/69 (84%), Positives = 61/69 (88%)

Query: 17  IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCKNKLGHSRA 76
           IK CP C V IE+DEGCAQM+CK CKH FCWYCL SLDDDFLL HYDKGPC+NKLGHSRA
Sbjct: 182 IKRCPKCRVYIERDEGCAQMMCKNCKHAFCWYCLESLDDDFLLIHYDKGPCRNKLGHSRA 241

Query: 77  SVIWHRTQV 85
           SVIWHRTQV
Sbjct: 242 SVIWHRTQV 250

E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q8BKD6|R144B_MOUSE E3 ubiquitin-protein ligase RNF144B OS=Mus musculus GN=Rnf144b PE=2 SV=2

 Score =  119 bits (298), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 54/80 (67%), Positives = 66/80 (82%), Gaps = 3/80 (3%)

Query: 9   GATFDSEL---IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKG 65
           GA F ++    IK CP+C + IE++EGCAQM+CK CKH FCWYCL +LD+D  LRHYDKG
Sbjct: 177 GALFGTDADAPIKQCPVCRIYIERNEGCAQMMCKNCKHTFCWYCLQNLDNDIFLRHYDKG 236

Query: 66  PCKNKLGHSRASVIWHRTQV 85
           PC+NKLGHSRASV+W+RTQV
Sbjct: 237 PCRNKLGHSRASVMWNRTQV 256

E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates such as LCMT2, thereby promoting their degradation. Induces apoptosis via a p53/TP53-dependent but caspase-independent mechanism. However, its overexpression also produces a decrease of the ubiquitin-dependent stability of BAX, a pro-apoptotic protein, ultimately leading to protection of cell death; But, it is not an anti-apoptotic protein per se.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|A5PK27|R144B_BOVIN E3 ubiquitin-protein ligase RNF144B OS=Bos taurus GN=RNF144B PE=2 SV=1

 Score =  119 bits (298), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 54/80 (67%), Positives = 65/80 (81%), Gaps = 3/80 (3%)

Query: 9   GATFDSEL---IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKG 65
           G  F +E    IK CP+C V IE++EGCAQM+CK CKH FCWYCL +LD+D  LRHYD+G
Sbjct: 180 GTLFGTETDAPIKQCPVCRVYIERNEGCAQMMCKNCKHTFCWYCLQNLDNDIFLRHYDRG 239

Query: 66  PCKNKLGHSRASVIWHRTQV 85
           PC+NKLGHSRASV+W+RTQV
Sbjct: 240 PCRNKLGHSRASVMWNRTQV 259

E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates such as LCMT2, thereby promoting their degradation. Induces apoptosis via a p53/TP53-dependent but caspase-independent mechanism. However, its overexpression also produces a decrease of the ubiquitin-dependent stability of BAX, a pro-apoptotic protein, ultimately leading to protection of cell death; But, it is not an anti-apoptotic protein per se.

Bos taurus (taxid: 9913)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q7Z419|R144B_HUMAN E3 ubiquitin-protein ligase RNF144B OS=Homo sapiens GN=RNF144B PE=1 SV=1

 Score =  119 bits (297), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 52/69 (75%), Positives = 61/69 (88%)

Query: 17  IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCKNKLGHSRA 76
           IK CP+C V IE++EGCAQM+CK CKH FCWYCL +LD+D  LRHYDKGPC+NKLGHSRA
Sbjct: 190 IKQCPVCRVYIERNEGCAQMMCKNCKHTFCWYCLQNLDNDIFLRHYDKGPCRNKLGHSRA 249

Query: 77  SVIWHRTQV 85
           SV+W+RTQV
Sbjct: 250 SVMWNRTQV 258

E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates such as LCMT2, thereby promoting their degradation. Induces apoptosis via a p53/TP53-dependent but caspase-independent mechanism. However, its overexpression also produces a decrease of the ubiquitin-dependent stability of BAX, a pro-apoptotic protein, ultimately leading to protection of cell death; But, it is not an anti-apoptotic protein per se.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q80TT8|CUL9_MOUSE Cullin-9 OS=Mus musculus GN=Cul9 PE=2 SV=2

 Score = 58.2 bits (139), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 22/35 (62%), Positives = 23/35 (65%)

Query: 18   KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLAS 52
            K CP C  PIEK+EGC  M C RC H FCW CL S
Sbjct: 1573 KRCPSCQAPIEKNEGCLHMTCARCNHGFCWRCLKS 1607

Cytoplasmic anchor protein in p53-associated protein complex. Regulates the subcellular localization of p53 and subsequent function. Seems to be part of an atypical cullin-RING-based E3 ubiquitin-protein ligase complex. In vitro, complexes of CUL9/PARC with either CUL7 or TP53 contain E3 ubiquitin-protein ligase activity.

Mus musculus (taxid: 10090)

>sp|Q8IWT3|CUL9_HUMAN Cullin-9 OS=Homo sapiens GN=CUL9 PE=1 SV=2

 Score = 57.4 bits (137), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 21/35 (60%), Positives = 23/35 (65%)

Query: 18   KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLAS 52
            K CP C  PIEK+EGC  M C +C H FCW CL S
Sbjct: 2234 KRCPSCQAPIEKNEGCLHMTCAKCNHGFCWRCLKS 2268

Cytoplasmic anchor protein in p53-associated protein complex. Regulates the subcellular localization of p53 and subsequent function. Seems to be part of an atypical cullin-RING-based E3 ubiquitin-protein ligase complex. In vitro, complexes of CUL9/PARC with either CUL7 or TP53 contain E3 ubiquitin-protein ligase activity.

Homo sapiens (taxid: 9606)

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	87
195429571	1075	GK19659 [Drosophila willistoni] gi|19415	0.885	0.071	0.909	6e-41
195383714	1168	GJ20127 [Drosophila virilis] gi|19414536	0.885	0.065	0.909	1e-40
195333219	1098	GM20497 [Drosophila sechellia] gi|194125	0.885	0.070	0.909	2e-40
195483647	1104	GE13078 [Drosophila yakuba] gi|194176474	0.885	0.069	0.909	2e-40
28573878	1102	CG33144, isoform A [Drosophila melanogas	0.885	0.069	0.909	2e-40
195582260	1119	GD25960 [Drosophila simulans] gi|1941929	0.885	0.068	0.909	2e-40
194884183	1115	GG22721 [Drosophila erecta] gi|190659362	0.885	0.069	0.909	3e-40
194758010	1116	GF11090 [Drosophila ananassae] gi|190622	0.885	0.068	0.909	3e-40
198460497	1148	GA17318 [Drosophila pseudoobscura pseudo	0.885	0.067	0.909	4e-40
193610524	478	PREDICTED: probable E3 ubiquitin-protein	0.862	0.156	0.986	3e-38

>gi|195429571|ref|XP_002062831.1| GK19659 [Drosophila willistoni] gi|194158916|gb|EDW73817.1| GK19659 [Drosophila willistoni]

 Score =  171 bits (433), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 70/77 (90%), Positives = 74/77 (96%)

Query: 9    GATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCK 68
            G  FD+ELIKCCPMC+VPIEKDEGCAQM+CKRCKHVFCWYCLASLDDDFLLRHYDKGPCK
Sbjct: 945  GIPFDNELIKCCPMCAVPIEKDEGCAQMMCKRCKHVFCWYCLASLDDDFLLRHYDKGPCK 1004

Query: 69   NKLGHSRASVIWHRTQV 85
            NKLGHSRASV+WHR QV
Sbjct: 1005 NKLGHSRASVVWHRAQV 1021

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195383714|ref|XP_002050571.1| GJ20127 [Drosophila virilis] gi|194145368|gb|EDW61764.1| GJ20127 [Drosophila virilis]

 Score =  169 bits (429), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 70/77 (90%), Positives = 74/77 (96%)

Query: 9    GATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCK 68
            G  FD+ELIKCCPMC+VPIEKDEGCAQM+CKRCKHVFCWYCLASLDDDFLLRHYDKGPCK
Sbjct: 1038 GIPFDNELIKCCPMCAVPIEKDEGCAQMMCKRCKHVFCWYCLASLDDDFLLRHYDKGPCK 1097

Query: 69   NKLGHSRASVIWHRTQV 85
            NKLGHSRASV+WHR QV
Sbjct: 1098 NKLGHSRASVVWHRAQV 1114

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195333219|ref|XP_002033289.1| GM20497 [Drosophila sechellia] gi|194125259|gb|EDW47302.1| GM20497 [Drosophila sechellia]

 Score =  169 bits (427), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 70/77 (90%), Positives = 74/77 (96%)

Query: 9    GATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCK 68
            G  FD+ELIKCCPMC+VPIEKDEGCAQM+CKRCKHVFCWYCLASLDDDFLLRHYDKGPCK
Sbjct: 968  GIPFDNELIKCCPMCAVPIEKDEGCAQMMCKRCKHVFCWYCLASLDDDFLLRHYDKGPCK 1027

Query: 69   NKLGHSRASVIWHRTQV 85
            NKLGHSRASV+WHR QV
Sbjct: 1028 NKLGHSRASVVWHRAQV 1044

Source: Drosophila sechellia

Species: Drosophila sechellia

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195483647|ref|XP_002090373.1| GE13078 [Drosophila yakuba] gi|194176474|gb|EDW90085.1| GE13078 [Drosophila yakuba]

 Score =  169 bits (427), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 70/77 (90%), Positives = 74/77 (96%)

Query: 9    GATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCK 68
            G  FD+ELIKCCPMC+VPIEKDEGCAQM+CKRCKHVFCWYCLASLDDDFLLRHYDKGPCK
Sbjct: 974  GIPFDNELIKCCPMCAVPIEKDEGCAQMMCKRCKHVFCWYCLASLDDDFLLRHYDKGPCK 1033

Query: 69   NKLGHSRASVIWHRTQV 85
            NKLGHSRASV+WHR QV
Sbjct: 1034 NKLGHSRASVVWHRAQV 1050

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|28573878|ref|NP_788324.1| CG33144, isoform A [Drosophila melanogaster] gi|320543773|ref|NP_001188904.1| CG33144, isoform B [Drosophila melanogaster] gi|27820080|gb|AAO25066.1| GH08706p [Drosophila melanogaster] gi|28380889|gb|AAF58756.2| CG33144, isoform A [Drosophila melanogaster] gi|220947468|gb|ACL86277.1| CG33144-PA [synthetic construct] gi|318068566|gb|ADV37151.1| CG33144, isoform B [Drosophila melanogaster]

 Score =  169 bits (427), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 70/77 (90%), Positives = 74/77 (96%)

Query: 9    GATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCK 68
            G  FD+ELIKCCPMC+VPIEKDEGCAQM+CKRCKHVFCWYCLASLDDDFLLRHYDKGPCK
Sbjct: 972  GIPFDNELIKCCPMCAVPIEKDEGCAQMMCKRCKHVFCWYCLASLDDDFLLRHYDKGPCK 1031

Query: 69   NKLGHSRASVIWHRTQV 85
            NKLGHSRASV+WHR QV
Sbjct: 1032 NKLGHSRASVVWHRAQV 1048

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195582260|ref|XP_002080946.1| GD25960 [Drosophila simulans] gi|194192955|gb|EDX06531.1| GD25960 [Drosophila simulans]

 Score =  169 bits (427), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 70/77 (90%), Positives = 74/77 (96%)

Query: 9    GATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCK 68
            G  FD+ELIKCCPMC+VPIEKDEGCAQM+CKRCKHVFCWYCLASLDDDFLLRHYDKGPCK
Sbjct: 989  GIPFDNELIKCCPMCAVPIEKDEGCAQMMCKRCKHVFCWYCLASLDDDFLLRHYDKGPCK 1048

Query: 69   NKLGHSRASVIWHRTQV 85
            NKLGHSRASV+WHR QV
Sbjct: 1049 NKLGHSRASVVWHRAQV 1065

Source: Drosophila simulans

Species: Drosophila simulans

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194884183|ref|XP_001976175.1| GG22721 [Drosophila erecta] gi|190659362|gb|EDV56575.1| GG22721 [Drosophila erecta]

 Score =  168 bits (426), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 70/77 (90%), Positives = 74/77 (96%)

Query: 9    GATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCK 68
            G  FD+ELIKCCPMC+VPIEKDEGCAQM+CKRCKHVFCWYCLASLDDDFLLRHYDKGPCK
Sbjct: 985  GIPFDNELIKCCPMCAVPIEKDEGCAQMMCKRCKHVFCWYCLASLDDDFLLRHYDKGPCK 1044

Query: 69   NKLGHSRASVIWHRTQV 85
            NKLGHSRASV+WHR QV
Sbjct: 1045 NKLGHSRASVVWHRAQV 1061

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194758010|ref|XP_001961255.1| GF11090 [Drosophila ananassae] gi|190622553|gb|EDV38077.1| GF11090 [Drosophila ananassae]

 Score =  168 bits (426), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 70/77 (90%), Positives = 74/77 (96%)

Query: 9    GATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCK 68
            G  FD+ELIKCCPMC+VPIEKDEGCAQM+CKRCKHVFCWYCLASLDDDFLLRHYDKGPCK
Sbjct: 986  GIPFDNELIKCCPMCAVPIEKDEGCAQMMCKRCKHVFCWYCLASLDDDFLLRHYDKGPCK 1045

Query: 69   NKLGHSRASVIWHRTQV 85
            NKLGHSRASV+WHR QV
Sbjct: 1046 NKLGHSRASVVWHRAQV 1062

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198460497|ref|XP_001361740.2| GA17318 [Drosophila pseudoobscura pseudoobscura] gi|198137035|gb|EAL26319.2| GA17318 [Drosophila pseudoobscura pseudoobscura]

 Score =  168 bits (426), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 70/77 (90%), Positives = 74/77 (96%)

Query: 9    GATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCK 68
            G  FD+ELIKCCPMC+VPIEKDEGCAQM+CKRCKHVFCWYCLASLDDDFLLRHYDKGPCK
Sbjct: 1018 GIPFDNELIKCCPMCAVPIEKDEGCAQMMCKRCKHVFCWYCLASLDDDFLLRHYDKGPCK 1077

Query: 69   NKLGHSRASVIWHRTQV 85
            NKLGHSRASV+WHR QV
Sbjct: 1078 NKLGHSRASVVWHRAQV 1094

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193610524|ref|XP_001945106.1| PREDICTED: probable E3 ubiquitin-protein ligase RNF144A-A-like [Acyrthosiphon pisum]

 Score =  162 bits (409), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 74/75 (98%), Positives = 75/75 (100%)

Query: 11  TFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCKNK 70
           TFDS+LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCKNK
Sbjct: 353 TFDSDLIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCKNK 412

Query: 71  LGHSRASVIWHRTQV 85
           LGHSRASVIWHRTQV
Sbjct: 413 LGHSRASVIWHRTQV 427

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	87
FB|FBgn0053144	1102	CG33144 [Drosophila melanogast	0.885	0.069	0.909	2.9e-38
UNIPROTKB|E1BYS1	292	RNF144A "Uncharacterized prote	0.839	0.25	0.808	1.6e-31
UNIPROTKB|F1MME3	293	RNF144A "Uncharacterized prote	0.839	0.249	0.808	1.6e-31
UNIPROTKB|F1PYL1	292	RNF144A "Uncharacterized prote	0.839	0.25	0.808	1.6e-31
UNIPROTKB|P50876	292	RNF144A "Probable E3 ubiquitin	0.839	0.25	0.808	1.6e-31
UNIPROTKB|F1S9L4	280	RNF144A "Uncharacterized prote	0.839	0.260	0.808	1.6e-31
ZFIN|ZDB-GENE-041001-88	293	rnf144aa "ring finger protein	0.839	0.249	0.808	1.6e-31
ZFIN|ZDB-GENE-040718-486	293	rnf144ab "ring finger protein	0.839	0.249	0.808	1.6e-31
MGI|MGI:1344401	292	Rnf144a "ring finger protein 1	0.793	0.236	0.840	3.3e-31
RGD|1561737	292	Rnf144a "ring finger protein 1	0.793	0.236	0.840	3.3e-31

FB|FBgn0053144 CG33144 [Drosophila melanogaster (taxid:7227)]

 Score = 421 (153.3 bits), Expect = 2.9e-38, P = 2.9e-38
 Identities = 70/77 (90%), Positives = 74/77 (96%)

Query:     9 GATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCK 68
             G  FD+ELIKCCPMC+VPIEKDEGCAQM+CKRCKHVFCWYCLASLDDDFLLRHYDKGPCK
Sbjct:   972 GIPFDNELIKCCPMCAVPIEKDEGCAQMMCKRCKHVFCWYCLASLDDDFLLRHYDKGPCK 1031

Query:    69 NKLGHSRASVIWHRTQV 85
             NKLGHSRASV+WHR QV
Sbjct:  1032 NKLGHSRASVVWHRAQV 1048

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|E1BYS1 RNF144A "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 346 (126.9 bits), Expect = 1.6e-31, P = 1.6e-31
 Identities = 59/73 (80%), Positives = 62/73 (84%)

Query:    13 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCKNKLG 72
             D   IK CP C V IE+DEGCAQM+CK CKH FCWYCL SLDDDFLL HYDKGPC+NKLG
Sbjct:   178 DDAPIKRCPKCKVYIERDEGCAQMMCKNCKHAFCWYCLESLDDDFLLIHYDKGPCRNKLG 237

Query:    73 HSRASVIWHRTQV 85
             HSRASVIWHRTQV
Sbjct:   238 HSRASVIWHRTQV 250

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005794 "Golgi apparatus" evidence=IEA

UNIPROTKB|F1MME3 RNF144A "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 346 (126.9 bits), Expect = 1.6e-31, P = 1.6e-31
 Identities = 59/73 (80%), Positives = 62/73 (84%)

Query:    13 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCKNKLG 72
             D   IK CP C V IE+DEGCAQM+CK CKH FCWYCL SLDDDFLL HYDKGPC+NKLG
Sbjct:   179 DDAPIKRCPKCKVYIERDEGCAQMMCKNCKHAFCWYCLESLDDDFLLIHYDKGPCRNKLG 238

Query:    73 HSRASVIWHRTQV 85
             HSRASVIWHRTQV
Sbjct:   239 HSRASVIWHRTQV 251

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F1PYL1 RNF144A "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 346 (126.9 bits), Expect = 1.6e-31, P = 1.6e-31
 Identities = 59/73 (80%), Positives = 62/73 (84%)

Query:    13 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCKNKLG 72
             D   IK CP C V IE+DEGCAQM+CK CKH FCWYCL SLDDDFLL HYDKGPC+NKLG
Sbjct:   178 DDAPIKRCPKCKVYIERDEGCAQMMCKNCKHAFCWYCLESLDDDFLLIHYDKGPCRNKLG 237

Query:    73 HSRASVIWHRTQV 85
             HSRASVIWHRTQV
Sbjct:   238 HSRASVIWHRTQV 250

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|P50876 RNF144A "Probable E3 ubiquitin-protein ligase RNF144A" [Homo sapiens (taxid:9606)]

 Score = 346 (126.9 bits), Expect = 1.6e-31, P = 1.6e-31
 Identities = 59/73 (80%), Positives = 62/73 (84%)

Query:    13 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCKNKLG 72
             D   IK CP C V IE+DEGCAQM+CK CKH FCWYCL SLDDDFLL HYDKGPC+NKLG
Sbjct:   178 DDAPIKRCPKCKVYIERDEGCAQMMCKNCKHAFCWYCLESLDDDFLLIHYDKGPCRNKLG 237

Query:    73 HSRASVIWHRTQV 85
             HSRASVIWHRTQV
Sbjct:   238 HSRASVIWHRTQV 250

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0016874 "ligase activity" evidence=IEA

GO:0016567 "protein ubiquitination" evidence=IEA

GO:0005794 "Golgi apparatus" evidence=IDA

UNIPROTKB|F1S9L4 RNF144A "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 346 (126.9 bits), Expect = 1.6e-31, P = 1.6e-31
 Identities = 59/73 (80%), Positives = 62/73 (84%)

Query:    13 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCKNKLG 72
             D   IK CP C V IE+DEGCAQM+CK CKH FCWYCL SLDDDFLL HYDKGPC+NKLG
Sbjct:   188 DDAPIKRCPKCKVYIERDEGCAQMMCKNCKHAFCWYCLESLDDDFLLIHYDKGPCRNKLG 247

Query:    73 HSRASVIWHRTQV 85
             HSRASVIWHRTQV
Sbjct:   248 HSRASVIWHRTQV 260

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

ZFIN|ZDB-GENE-041001-88 rnf144aa "ring finger protein 144aa" [Danio rerio (taxid:7955)]

 Score = 346 (126.9 bits), Expect = 1.6e-31, P = 1.6e-31
 Identities = 59/73 (80%), Positives = 62/73 (84%)

Query:    13 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCKNKLG 72
             D   IK CP C V IE+DEGCAQM+CK CKH FCWYCL SLDDDFLL HYDKGPC+NKLG
Sbjct:   179 DDAPIKRCPKCKVYIERDEGCAQMMCKNCKHAFCWYCLESLDDDFLLIHYDKGPCRNKLG 238

Query:    73 HSRASVIWHRTQV 85
             HSRASVIWHRTQV
Sbjct:   239 HSRASVIWHRTQV 251

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016874 "ligase activity" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0016020 "membrane" evidence=IEA

ZFIN|ZDB-GENE-040718-486 rnf144ab "ring finger protein 144ab" [Danio rerio (taxid:7955)]

 Score = 346 (126.9 bits), Expect = 1.6e-31, P = 1.6e-31
 Identities = 59/73 (80%), Positives = 62/73 (84%)

Query:    13 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCKNKLG 72
             D   IK CP C V IE+DEGCAQM+CK CKH FCWYCL SLDDDFLL HYDKGPC+NKLG
Sbjct:   179 DEAPIKRCPKCKVYIERDEGCAQMMCKNCKHAFCWYCLESLDDDFLLIHYDKGPCRNKLG 238

Query:    73 HSRASVIWHRTQV 85
             HSRASVIWHRTQV
Sbjct:   239 HSRASVIWHRTQV 251

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016874 "ligase activity" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0016020 "membrane" evidence=IEA

MGI|MGI:1344401 Rnf144a "ring finger protein 144A" [Mus musculus (taxid:10090)]

 Score = 343 (125.8 bits), Expect = 3.3e-31, P = 3.3e-31
 Identities = 58/69 (84%), Positives = 61/69 (88%)

Query:    17 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCKNKLGHSRA 76
             IK CP C V IE+DEGCAQM+CK CKH FCWYCL SLDDDFLL HYDKGPC+NKLGHSRA
Sbjct:   182 IKRCPKCRVYIERDEGCAQMMCKNCKHAFCWYCLESLDDDFLLIHYDKGPCRNKLGHSRA 241

Query:    77 SVIWHRTQV 85
             SVIWHRTQV
Sbjct:   242 SVIWHRTQV 250

GO:0005794 "Golgi apparatus" evidence=ISO

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0016874 "ligase activity" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

RGD|1561737 Rnf144a "ring finger protein 144A" [Rattus norvegicus (taxid:10116)]

 Score = 343 (125.8 bits), Expect = 3.3e-31, P = 3.3e-31
 Identities = 58/69 (84%), Positives = 61/69 (88%)

Query:    17 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDKGPCKNKLGHSRA 76
             IK CP C V IE+DEGCAQM+CK CKH FCWYCL SLDDDFLL HYDKGPC+NKLGHSRA
Sbjct:   182 IKRCPKCRVYIERDEGCAQMMCKNCKHAFCWYCLESLDDDFLLIHYDKGPCRNKLGHSRA 241

Query:    77 SVIWHRTQV 85
             SVIWHRTQV
Sbjct:   242 SVIWHRTQV 250

GO:0005794 "Golgi apparatus" evidence=IEA;ISO

GO:0008270 "zinc ion binding" evidence=IEA

---

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)
P50876	R144A_HUMAN	6, ., 3, ., 2, ., -	0.8082	0.8390	0.25	yes	N/A
Q6DH94	R1442_DANRE	6, ., 3, ., 2, ., -	0.8082	0.8390	0.2491	yes	N/A
Q925F3	R144A_MOUSE	6, ., 3, ., 2, ., -	0.8405	0.7931	0.2363	yes	N/A
A4IIY1	R144A_XENTR	6, ., 3, ., 2, ., -	0.8082	0.8390	0.25	yes	N/A
Q9SKC2	ARI11_ARATH	6, ., 3, ., 2, ., -	0.5384	0.4367	0.0701	yes	N/A
Q9P3U4	YKX2_SCHPO	No assigned EC number	0.5714	0.4022	0.0694	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

No hit with e-value below 0.005

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	87
KOG1814|consensus	445		99.62
KOG1812|consensus	384		99.24
KOG0006|consensus	446		99.19
KOG1815|consensus	444		98.99
smart00647	64	IBR In Between Ring fingers. the domains occurs be	98.57
PF01485	64	IBR: IBR domain; InterPro: IPR002867 Zinc finger (	98.57
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	95.4
smart00661	52	RPOL9 RNA polymerase subunit 9.	95.31
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	95.27
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	93.22
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	93.1
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	93.01
PF13248	26	zf-ribbon_3: zinc-ribbon domain	92.52
PHA00626	59	hypothetical protein	92.45
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	92.28
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	91.78
KOG1815|consensus	444		91.72
PRK14559	645	putative protein serine/threonine phosphatase; Pro	91.5
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	91.42
PF01363	69	FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc f	91.39
PF09538	108	FYDLN_acid: Protein of unknown function (FYDLN_aci	91.05
PRK00432	50	30S ribosomal protein S27ae; Validated	90.65
CHL00174	296	accD acetyl-CoA carboxylase beta subunit; Reviewed	90.53
KOG1814|consensus	445		90.24
PF12773	50	DZR: Double zinc ribbon	89.67
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	89.59
PF08274	30	PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01	88.82
TIGR00515	285	accD acetyl-CoA carboxylase, carboxyl transferase,	88.64
PRK05654	292	acetyl-CoA carboxylase subunit beta; Validated	88.62
PRK08665	752	ribonucleotide-diphosphate reductase subunit alpha	88.46
PF07191	70	zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807	87.65
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	86.93
PRK14892	99	putative transcription elongation factor Elf1; Pro	86.34
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	86.28
smart00064	68	FYVE Protein present in Fab1, YOTB, Vac1, and EEA1	86.21
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	85.94
TIGR00686	109	phnA alkylphosphonate utilization operon protein P	85.32
PF03119	28	DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc f	85.09
KOG0317|consensus	293		84.88
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	84.77
PF08792	33	A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: I	84.71
COG0266	273	Nei Formamidopyrimidine-DNA glycosylase [DNA repli	84.07
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	83.85
PF06827	30	zf-FPG_IleRS: Zinc finger found in FPG and IleRS;	83.5
PRK14811	269	formamidopyrimidine-DNA glycosylase; Provisional	83.41
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	83.35
PRK01103	274	formamidopyrimidine/5-formyluracil/ 5-hydroxymethy	83.27
COG0777	294	AccD Acetyl-CoA carboxylase beta subunit [Lipid me	82.96
PRK14810	272	formamidopyrimidine-DNA glycosylase; Provisional	82.88
PRK10445	263	endonuclease VIII; Provisional	82.79
PF10122	51	Mu-like_Com: Mu-like prophage protein Com; InterPr	82.52
PRK13945	282	formamidopyrimidine-DNA glycosylase; Provisional	82.43
KOG2906|consensus	105		82.41
PF06677	41	Auto_anti-p27: Sjogren's syndrome/scleroderma auto	82.3
TIGR00577	272	fpg formamidopyrimidine-DNA glycosylase (fpg). All	82.14
PF14354	61	Lar_restr_allev: Restriction alleviation protein L	81.9
TIGR03655	53	anti_R_Lar restriction alleviation protein, Lar fa	81.71
COG1594	113	RPB9 DNA-directed RNA polymerase, subunit M/Transc	81.4
PRK10220	111	hypothetical protein; Provisional	80.98
PRK00420	112	hypothetical protein; Validated	80.8
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	80.67
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	80.3
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	80.19

>KOG1814|consensus

Probab=99.62  E-value=1.1e-16  Score=126.59  Aligned_cols=62  Identities=32%  Similarity=0.788  Sum_probs=56.4

Q ss_pred             cccCCceeCCCCCCceEeCCCcCeeeccccceeeeecccccccCCccCCCCCC--CCCCCCCCC
Q psy1749          12 FDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHYDK--GPCKNKLGH   73 (87)
Q Consensus        12 ~~~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~~~~~~Hf~~--~~C~~~~~~   73 (87)
                      |...+.|+||+|+++|||++|||+|+|..|++.|||+|+.....++||.||++  +.|+++.+.
T Consensus       363 wl~~N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l~~~nPYkHF~e~~s~c~~~~~~  426 (445)
T KOG1814|consen  363 WLESNSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELLYPENPYKHFSEPGSECYGQFFG  426 (445)
T ss_pred             HHHhcCCCCCcccceeecCCCccceeeccccccceeehhhhcCCCChhhhhcCCcCccccchhh
Confidence            55667799999999999999999999999999999999999999999999998  667888554

>KOG1812|consensus

Probab=99.24  E-value=1.7e-12  Score=101.72  Aligned_cols=42  Identities=36%  Similarity=0.928  Sum_probs=39.8

Q ss_pred             cCCceeCCCCCCceEeCCCcCeeeccccceeeeecccccccCC
Q psy1749          14 SELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDD   56 (87)
Q Consensus        14 ~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~~   56 (87)
                      .+.|+.||+|+..||+++|||||+|+ ||++|||.|+.+|..+
T Consensus       303 a~~wr~CpkC~~~ie~~~GCnhm~Cr-C~~~fcy~C~~~~~~~  344 (384)
T KOG1812|consen  303 AKRWRQCPKCKFMIELSEGCNHMTCR-CGHQFCYMCGGDWKTH  344 (384)
T ss_pred             HHhcCcCcccceeeeecCCcceEEee-ccccchhhcCcchhhC
Confidence            38899999999999999999999999 9999999999999775

>KOG0006|consensus

Probab=99.19  E-value=8.6e-12  Score=97.49  Aligned_cols=52  Identities=31%  Similarity=0.757  Sum_probs=48.1

Q ss_pred             cccCCceeCCCCCCceEeCCCcCeeeccc--cceeeeecccccccCCccCCCCC
Q psy1749          12 FDSELIKCCPMCSVPIEKDEGCAQMLCKR--CKHVFCWYCLASLDDDFLLRHYD   63 (87)
Q Consensus        12 ~~~~~~k~CP~C~~~Iek~~GCnhm~C~~--C~~~FC~~C~~~~~~~~~~~Hf~   63 (87)
                      -|+..+|+||+|++++|+++||.||.|++  ||.+|||.|+-+|.......||-
T Consensus       392 TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r~CmgdHWF  445 (446)
T KOG0006|consen  392 TIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNRVCMGDHWF  445 (446)
T ss_pred             hhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhhhhcccccc
Confidence            57788999999999999999999999996  99999999999999987788874

>KOG1815|consensus

Probab=98.99  E-value=9.3e-11  Score=92.78  Aligned_cols=54  Identities=52%  Similarity=1.099  Sum_probs=47.2

Q ss_pred             ccccccCcc-----cccCCceeCCCCCCceEeCCCcCeeeccc--cceeeeecccccccCC
Q psy1749           3 PWFQMGGAT-----FDSELIKCCPMCSVPIEKDEGCAQMLCKR--CKHVFCWYCLASLDDD   56 (87)
Q Consensus         3 ~w~~~~~~~-----~~~~~~k~CP~C~~~Iek~~GCnhm~C~~--C~~~FC~~C~~~~~~~   56 (87)
                      .|.+..++.     |+..+++.||+|..+|||++|||||+|..  |+.+|||+|++.|..+
T Consensus       207 ~wl~k~~~~se~~~wi~~ntk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h  267 (444)
T KOG1815|consen  207 KWLKKCRDDSETINWILANTKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDH  267 (444)
T ss_pred             HHHHhhhhhhhhhhhhhccCccCCCcccchhccCCccccccccCCcCCeeceeeecccccc
Confidence            455544444     78899999999999999999999999997  9999999999999985

>smart00647 IBR In Between Ring fingers

Probab=98.57  E-value=6.1e-08  Score=56.87  Aligned_cols=41  Identities=34%  Similarity=0.868  Sum_probs=36.5

Q ss_pred             CCceeCC--CCCCceEeCC--CcCeeeccccceeeeecccccccC
Q psy1749          15 ELIKCCP--MCSVPIEKDE--GCAQMLCKRCKHVFCWYCLASLDD   55 (87)
Q Consensus        15 ~~~k~CP--~C~~~Iek~~--GCnhm~C~~C~~~FC~~C~~~~~~   55 (87)
                      .+++.||  +|...|+..+  +..+++|..|+..|||.|+.+|-.
T Consensus        16 ~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~   60 (64)
T smart00647       16 PDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHS   60 (64)
T ss_pred             CCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCC
Confidence            4788999  9999999975  899999977999999999988743

the domains occurs between pairs og RING fingers

>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.57  E-value=2.4e-08  Score=58.49  Aligned_cols=42  Identities=36%  Similarity=0.895  Sum_probs=30.3

Q ss_pred             cCCceeCCC--CCCceEeCCCcCe--eeccccceeeeecccccccC
Q psy1749          14 SELIKCCPM--CSVPIEKDEGCAQ--MLCKRCKHVFCWYCLASLDD   55 (87)
Q Consensus        14 ~~~~k~CP~--C~~~Iek~~GCnh--m~C~~C~~~FC~~C~~~~~~   55 (87)
                      +.+.+.||+  |...|++.++.++  |+|..|+..|||.|+.+|-.
T Consensus        15 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~   60 (64)
T PF01485_consen   15 DPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHE   60 (64)
T ss_dssp             ---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCT
T ss_pred             CCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCC
Confidence            345689988  9999999999999  99999999999999998843

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 a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.

>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=95.40  E-value=0.0063  Score=31.23  Aligned_cols=24  Identities=29%  Similarity=0.833  Sum_probs=16.1

Q ss_pred             eeCCCCCCceEeCCCcCeeeccccceee
Q psy1749          18 KCCPMCSVPIEKDEGCAQMLCKRCKHVF   45 (87)
Q Consensus        18 k~CP~C~~~Iek~~GCnhm~C~~C~~~F   45 (87)
                      |.||.|+..|..+.    ..|..||+.|
T Consensus         1 K~CP~C~~~V~~~~----~~Cp~CG~~F   24 (26)
T PF10571_consen    1 KTCPECGAEVPESA----KFCPHCGYDF   24 (26)
T ss_pred             CcCCCCcCCchhhc----CcCCCCCCCC
Confidence            57999999886432    3444577665

Several members are annotated as putative helicases.

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=95.31  E-value=0.016  Score=32.73  Aligned_cols=28  Identities=29%  Similarity=0.695  Sum_probs=22.2

Q ss_pred             eeCCCCCCceEeCCC--cCeeeccccceee
Q psy1749          18 KCCPMCSVPIEKDEG--CAQMLCKRCKHVF   45 (87)
Q Consensus        18 k~CP~C~~~Iek~~G--Cnhm~C~~C~~~F   45 (87)
                      +.||.|+.++...++  -++..|+.||+++
T Consensus         1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~   30 (52)
T smart00661        1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEE   30 (52)
T ss_pred             CCCCCCCCccccccCCCCCEEECCcCCCeE
Confidence            469999999988754  4689999898764

>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional

Probab=95.27  E-value=0.025  Score=31.85  Aligned_cols=30  Identities=23%  Similarity=0.433  Sum_probs=25.3

Q ss_pred             eeCCCCCCceEeCCCcCeeeccccceeeee
Q psy1749          18 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCW   47 (87)
Q Consensus        18 k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~   47 (87)
                      -+||+|+..++.++.=..++|+.||..+-+
T Consensus         4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~   33 (46)
T PRK00398          4 YKCARCGREVELDEYGTGVRCPYCGYRILF   33 (46)
T ss_pred             EECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence            579999999998877668999999987765

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=93.22  E-value=0.13  Score=27.88  Aligned_cols=28  Identities=32%  Similarity=0.858  Sum_probs=22.5

Q ss_pred             eeCCCCCCceEeCC-----CcCeeeccccceee
Q psy1749          18 KCCPMCSVPIEKDE-----GCAQMLCKRCKHVF   45 (87)
Q Consensus        18 k~CP~C~~~Iek~~-----GCnhm~C~~C~~~F   45 (87)
                      ..||+|++..+..+     +=..+.|.+|++.|
T Consensus         3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f   35 (37)
T PF13719_consen    3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF   35 (37)
T ss_pred             EECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence            57999999988764     34479999999887

>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains

Probab=93.10  E-value=0.15  Score=26.68  Aligned_cols=29  Identities=24%  Similarity=0.527  Sum_probs=19.1

Q ss_pred             CceeCCCCCCceEeCCCcCeeecccccee
Q psy1749          16 LIKCCPMCSVPIEKDEGCAQMLCKRCKHV   44 (87)
Q Consensus        16 ~~k~CP~C~~~Iek~~GCnhm~C~~C~~~   44 (87)
                      +.+.||+|+.+.+...+=-.+.|..|+.+
T Consensus         2 ~~rfC~~CG~~t~~~~~g~~r~C~~Cg~~   30 (32)
T PF09297_consen    2 NHRFCGRCGAPTKPAPGGWARRCPSCGHE   30 (32)
T ss_dssp             TTSB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred             CCcccCcCCccccCCCCcCEeECCCCcCE
Confidence            35789999999999988666889988875

; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.

>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C

Probab=93.01  E-value=0.11  Score=28.07  Aligned_cols=27  Identities=30%  Similarity=0.936  Sum_probs=16.6

Q ss_pred             eeCCCCCCceEeC----CCcCeeecccccee
Q psy1749          18 KCCPMCSVPIEKD----EGCAQMLCKRCKHV   44 (87)
Q Consensus        18 k~CP~C~~~Iek~----~GCnhm~C~~C~~~   44 (87)
                      |.||.|+.+++..    ++-..+.|..||..
T Consensus         1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~I   31 (34)
T PF14803_consen    1 KFCPQCGGPLERRIPEGDDRERLVCPACGFI   31 (34)
T ss_dssp             -B-TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred             CccccccChhhhhcCCCCCccceECCCCCCE
Confidence            5799999999985    56788999988864

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=92.52  E-value=0.049  Score=27.48  Aligned_cols=12  Identities=33%  Similarity=0.897  Sum_probs=9.2

Q ss_pred             eeCCCCCCceEe
Q psy1749          18 KCCPMCSVPIEK   29 (87)
Q Consensus        18 k~CP~C~~~Iek   29 (87)
                      +.||+|+..|+.
T Consensus         3 ~~Cp~Cg~~~~~   14 (26)
T PF13248_consen    3 MFCPNCGAEIDP   14 (26)
T ss_pred             CCCcccCCcCCc
Confidence            678999987653

>PHA00626 hypothetical protein

Probab=92.45  E-value=0.12  Score=31.37  Aligned_cols=28  Identities=25%  Similarity=0.559  Sum_probs=21.4

Q ss_pred             eCCCCCC-ceEeCCCcCe----eeccccceeee
Q psy1749          19 CCPMCSV-PIEKDEGCAQ----MLCKRCKHVFC   46 (87)
Q Consensus        19 ~CP~C~~-~Iek~~GCnh----m~C~~C~~~FC   46 (87)
                      .||+|++ -|.|.+-|+.    ..|..||+.|=
T Consensus         2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft   34 (59)
T PHA00626          2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDS   34 (59)
T ss_pred             CCCCCCCceeeeeceecccCcceEcCCCCCeec
Confidence            5999999 4888876554    67887887763

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=92.28  E-value=0.23  Score=26.48  Aligned_cols=28  Identities=25%  Similarity=0.717  Sum_probs=20.8

Q ss_pred             eeCCCCCCceEeCCC-----cCeeeccccceee
Q psy1749          18 KCCPMCSVPIEKDEG-----CAQMLCKRCKHVF   45 (87)
Q Consensus        18 k~CP~C~~~Iek~~G-----Cnhm~C~~C~~~F   45 (87)
                      ..||+|++.++..+.     =..+.|.+|+..|
T Consensus         3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~   35 (38)
T TIGR02098         3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW   35 (38)
T ss_pred             EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence            479999998777631     1378899898876

This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=91.78  E-value=0.071  Score=26.42  Aligned_cols=11  Identities=45%  Similarity=1.090  Sum_probs=8.1

Q ss_pred             eCCCCCCceEe
Q psy1749          19 CCPMCSVPIEK   29 (87)
Q Consensus        19 ~CP~C~~~Iek   29 (87)
                      .||+|+..|+.
T Consensus         1 ~Cp~CG~~~~~   11 (23)
T PF13240_consen    1 YCPNCGAEIED   11 (23)
T ss_pred             CCcccCCCCCC
Confidence            47888888763

>KOG1815|consensus

Probab=91.72  E-value=0.12  Score=41.14  Aligned_cols=45  Identities=22%  Similarity=0.550  Sum_probs=35.7

Q ss_pred             ceeCC--CCCCceEe-CCCcCeeeccccceeeeecccccccCCccCCCC
Q psy1749          17 IKCCP--MCSVPIEK-DEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHY   62 (87)
Q Consensus        17 ~k~CP--~C~~~Iek-~~GCnhm~C~~C~~~FC~~C~~~~~~~~~~~Hf   62 (87)
                      .|-||  .|+..|.. ...+..+.|. |++.|||.|+.++-....+.++
T Consensus       158 lkwCP~~~C~~av~~~~~~~~~v~C~-~g~~FC~~C~~~~H~p~~C~~~  205 (444)
T KOG1815|consen  158 LKWCPAPGCGLAVKFGSLESVEVDCG-CGHEFCFACGEESHSPVSCPGA  205 (444)
T ss_pred             cccCCCCCCCceeeccCCCccceeCC-CCchhHhhccccccCCCcccch
Confidence            55666  69999998 7889999999 9999999999888765443333

>PRK14559 putative protein serine/threonine phosphatase; Provisional

Probab=91.50  E-value=0.095  Score=44.20  Aligned_cols=36  Identities=19%  Similarity=0.500  Sum_probs=28.7

Q ss_pred             cCCceeCCCCCCceEeCCCcCeeecccccee------eeecccccccC
Q psy1749          14 SELIKCCPMCSVPIEKDEGCAQMLCKRCKHV------FCWYCLASLDD   55 (87)
Q Consensus        14 ~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~------FC~~C~~~~~~   55 (87)
                      ..+.|.||+|+..+.      +..|..||+.      ||-.||.....
T Consensus        12 ~~~akFC~~CG~~l~------~~~Cp~CG~~~~~~~~fC~~CG~~~~~   53 (645)
T PRK14559         12 PNNNRFCQKCGTSLT------HKPCPQCGTEVPVDEAHCPNCGAETGT   53 (645)
T ss_pred             CCCCccccccCCCCC------CCcCCCCCCCCCcccccccccCCcccc
Confidence            456789999999884      3578889877      99999987665

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=91.42  E-value=0.28  Score=26.54  Aligned_cols=28  Identities=36%  Similarity=0.857  Sum_probs=21.9

Q ss_pred             eeCCCCCCceEeCC-----CcCeeeccccceee
Q psy1749          18 KCCPMCSVPIEKDE-----GCAQMLCKRCKHVF   45 (87)
Q Consensus        18 k~CP~C~~~Iek~~-----GCnhm~C~~C~~~F   45 (87)
                      ..||+|++..+..+     .=..+.|..|++.|
T Consensus         3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f   35 (36)
T PF13717_consen    3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF   35 (36)
T ss_pred             EECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence            47999999988864     23468899999876

>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=91.39  E-value=0.24  Score=29.39  Aligned_cols=44  Identities=18%  Similarity=0.433  Sum_probs=24.5

Q ss_pred             ccccccCcccccCCceeCCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749           3 PWFQMGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD   55 (87)
Q Consensus         3 ~w~~~~~~~~~~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~   55 (87)
                      +|..+..       ...|+.|++.+..  .-..-.|+.||..||-.|......
T Consensus         2 ~W~~d~~-------~~~C~~C~~~F~~--~~rrhhCr~CG~~vC~~Cs~~~~~   45 (69)
T PF01363_consen    2 HWVPDSE-------ASNCMICGKKFSL--FRRRHHCRNCGRVVCSSCSSQRIP   45 (69)
T ss_dssp             -SSSGGG--------SB-TTT--B-BS--SS-EEE-TTT--EEECCCS-EEEE
T ss_pred             CcCCCCC-------CCcCcCcCCcCCC--ceeeEccCCCCCEECCchhCCEEc
Confidence            4666555       4899999999843  355678999999999999865543

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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....

>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues

Probab=91.05  E-value=0.12  Score=34.55  Aligned_cols=28  Identities=21%  Similarity=0.660  Sum_probs=21.1

Q ss_pred             eeCCCCCCceEeCCCcCeeeccccceeee
Q psy1749          18 KCCPMCSVPIEKDEGCAQMLCKRCKHVFC   46 (87)
Q Consensus        18 k~CP~C~~~Iek~~GCnhm~C~~C~~~FC   46 (87)
                      +.||+|++.+.=-.- +.++|++||+.|=
T Consensus        10 R~Cp~CG~kFYDLnk-~PivCP~CG~~~~   37 (108)
T PF09538_consen   10 RTCPSCGAKFYDLNK-DPIVCPKCGTEFP   37 (108)
T ss_pred             ccCCCCcchhccCCC-CCccCCCCCCccC
Confidence            559999987764444 7899998887763

The function of members of this family is unknown.

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=90.65  E-value=0.22  Score=28.95  Aligned_cols=30  Identities=20%  Similarity=0.440  Sum_probs=21.6

Q ss_pred             cCCceeCCCCCC-ceEeCCCcCeeeccccceee
Q psy1749          14 SELIKCCPMCSV-PIEKDEGCAQMLCKRCKHVF   45 (87)
Q Consensus        14 ~~~~k~CP~C~~-~Iek~~GCnhm~C~~C~~~F   45 (87)
                      ....+.||+|+. .+....  +.+.|..||..+
T Consensus        17 ~~~~~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~   47 (50)
T PRK00432         17 KRKNKFCPRCGSGFMAEHL--DRWHCGKCGYTE   47 (50)
T ss_pred             EEccCcCcCCCcchheccC--CcEECCCcCCEE
Confidence            345678999998 444434  688999998764

>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed

Probab=90.53  E-value=0.073  Score=41.18  Aligned_cols=32  Identities=19%  Similarity=0.211  Sum_probs=26.9

Q ss_pred             CCceeCCCCCCceEeCCC-cCeeeccccceeee
Q psy1749          15 ELIKCCPMCSVPIEKDEG-CAQMLCKRCKHVFC   46 (87)
Q Consensus        15 ~~~k~CP~C~~~Iek~~G-Cnhm~C~~C~~~FC   46 (87)
                      ..|.+||+|+..|.+.+= =|...|++|+++|=
T Consensus        36 ~lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h~r   68 (296)
T CHL00174         36 HLWVQCENCYGLNYKKFLKSKMNICEQCGYHLK   68 (296)
T ss_pred             CCeeECCCccchhhHHHHHHcCCCCCCCCCCcC
Confidence            469999999999988754 67789999999874

>KOG1814|consensus

Probab=90.24  E-value=0.068  Score=43.33  Aligned_cols=41  Identities=29%  Similarity=0.845  Sum_probs=37.2

Q ss_pred             CCceeCCC--CCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749          15 ELIKCCPM--CSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD   55 (87)
Q Consensus        15 ~~~k~CP~--C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~   55 (87)
                      .+++.||+  |..++-.+.|++-..|..|...||..|...|-+
T Consensus       271 sdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~HG  313 (445)
T KOG1814|consen  271 SDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWHG  313 (445)
T ss_pred             cccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhcC
Confidence            46789998  999997789999999999999999999988765

>PF12773 DZR: Double zinc ribbon

Probab=89.67  E-value=0.16  Score=28.53  Aligned_cols=15  Identities=33%  Similarity=0.895  Sum_probs=10.5

Q ss_pred             cCCceeCCCCCCceE
Q psy1749          14 SELIKCCPMCSVPIE   28 (87)
Q Consensus        14 ~~~~k~CP~C~~~Ie   28 (87)
                      ..+.+.||+|++.+.
T Consensus         9 ~~~~~fC~~CG~~l~   23 (50)
T PF12773_consen    9 PDDAKFCPHCGTPLP   23 (50)
T ss_pred             CccccCChhhcCChh
Confidence            345677777777777

>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins

Probab=89.59  E-value=0.32  Score=28.93  Aligned_cols=30  Identities=20%  Similarity=0.440  Sum_probs=22.9

Q ss_pred             CCceeCCCCCCceEeCCCcCeeecccccee
Q psy1749          15 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHV   44 (87)
Q Consensus        15 ~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~   44 (87)
                      ..++.||.|+...++...=...+|..||..
T Consensus        26 ~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~   55 (69)
T PF07282_consen   26 YTSQTCPRCGHRNKKRRSGRVFTCPNCGFE   55 (69)
T ss_pred             CCccCccCcccccccccccceEEcCCCCCE
Confidence            368999999999999444445778877765

More information about these proteins can be found at Protein of the Month: Transposase [].

>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues

Probab=88.82  E-value=0.4  Score=25.31  Aligned_cols=27  Identities=26%  Similarity=0.837  Sum_probs=14.4

Q ss_pred             eeCCCCCCceEeCCCcCeeeccccceee
Q psy1749          18 KCCPMCSVPIEKDEGCAQMLCKRCKHVF   45 (87)
Q Consensus        18 k~CP~C~~~Iek~~GCnhm~C~~C~~~F   45 (87)
                      -.||.|+......+|.. |.|..|+++|
T Consensus         3 p~Cp~C~se~~y~D~~~-~vCp~C~~ew   29 (30)
T PF08274_consen    3 PKCPLCGSEYTYEDGEL-LVCPECGHEW   29 (30)
T ss_dssp             ---TTT-----EE-SSS-EEETTTTEEE
T ss_pred             CCCCCCCCcceeccCCE-EeCCcccccC
Confidence            36999999999887765 5788898876

The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.

>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit

Probab=88.64  E-value=0.1  Score=40.00  Aligned_cols=32  Identities=22%  Similarity=0.532  Sum_probs=26.3

Q ss_pred             CCceeCCCCCCceEeCC-CcCeeeccccceeee
Q psy1749          15 ELIKCCPMCSVPIEKDE-GCAQMLCKRCKHVFC   46 (87)
Q Consensus        15 ~~~k~CP~C~~~Iek~~-GCnhm~C~~C~~~FC   46 (87)
                      ..|.+||+|+..|.+.+ .=|...|++|+++|=
T Consensus        24 ~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~r   56 (285)
T TIGR00515        24 GVWTKCPKCGQVLYTKELERNLEVCPKCDHHMR   56 (285)
T ss_pred             CCeeECCCCcchhhHHHHHhhCCCCCCCCCcCc
Confidence            35999999999998874 356789999999863

The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.

>PRK05654 acetyl-CoA carboxylase subunit beta; Validated

Probab=88.62  E-value=0.11  Score=39.94  Aligned_cols=32  Identities=25%  Similarity=0.616  Sum_probs=26.5

Q ss_pred             cCCceeCCCCCCceEeCC-CcCeeeccccceee
Q psy1749          14 SELIKCCPMCSVPIEKDE-GCAQMLCKRCKHVF   45 (87)
Q Consensus        14 ~~~~k~CP~C~~~Iek~~-GCnhm~C~~C~~~F   45 (87)
                      ...|.+||+|+..|.+.+ .-|...|+.|+++|
T Consensus        24 ~~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~   56 (292)
T PRK05654         24 EGLWTKCPSCGQVLYRKELEANLNVCPKCGHHM   56 (292)
T ss_pred             CCCeeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence            345999999999998864 35678999999998

>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated

Probab=88.46  E-value=0.27  Score=42.10  Aligned_cols=27  Identities=37%  Similarity=1.053  Sum_probs=24.1

Q ss_pred             eeCCCCCCceEeCCCcCeeeccccceeee
Q psy1749          18 KCCPMCSVPIEKDEGCAQMLCKRCKHVFC   46 (87)
Q Consensus        18 k~CP~C~~~Iek~~GCnhm~C~~C~~~FC   46 (87)
                      ..||.|+..+...+||.  +|..||..-|
T Consensus       725 ~~Cp~Cg~~l~~~~GC~--~C~~CG~skC  751 (752)
T PRK08665        725 GACPECGSILEHEEGCV--VCHSCGYSKC  751 (752)
T ss_pred             CCCCCCCcccEECCCCC--cCCCCCCCCC
Confidence            36999999999999998  8999998766

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

Probab=87.65  E-value=0.58  Score=29.28  Aligned_cols=35  Identities=29%  Similarity=0.706  Sum_probs=23.3

Q ss_pred             eCCCCCCceEeCCCcCeeecccccee-----eeecccccccC
Q psy1749          19 CCPMCSVPIEKDEGCAQMLCKRCKHV-----FCWYCLASLDD   55 (87)
Q Consensus        19 ~CP~C~~~Iek~~GCnhm~C~~C~~~-----FC~~C~~~~~~   55 (87)
                      .||.|+..++..+  .+..|..|+.+     +|-.|++++..
T Consensus         3 ~CP~C~~~L~~~~--~~~~C~~C~~~~~~~a~CPdC~~~Le~   42 (70)
T PF07191_consen    3 TCPKCQQELEWQG--GHYHCEACQKDYKKEAFCPDCGQPLEV   42 (70)
T ss_dssp             B-SSS-SBEEEET--TEEEETTT--EEEEEEE-TTT-SB-EE
T ss_pred             cCCCCCCccEEeC--CEEECccccccceecccCCCcccHHHH
Confidence            5999999999988  78888888765     57788887765

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

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=86.93  E-value=0.41  Score=30.68  Aligned_cols=26  Identities=23%  Similarity=0.593  Sum_probs=20.3

Q ss_pred             eeCCCCCCceEeCCCcCeeeccccceee
Q psy1749          18 KCCPMCSVPIEKDEGCAQMLCKRCKHVF   45 (87)
Q Consensus        18 k~CP~C~~~Iek~~GCnhm~C~~C~~~F   45 (87)
                      +.||.|+.++...+  +.+.|..|+..+
T Consensus         1 ~fC~~Cg~~l~~~~--~~~~C~~C~~~~   26 (104)
T TIGR01384         1 KFCPKCGSLMTPKN--GVYVCPSCGYEK   26 (104)
T ss_pred             CCCcccCcccccCC--CeEECcCCCCcc
Confidence            36999999997765  478898888764

There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.

>PRK14892 putative transcription elongation factor Elf1; Provisional

Probab=86.34  E-value=0.46  Score=31.35  Aligned_cols=48  Identities=17%  Similarity=0.315  Sum_probs=32.8

Q ss_pred             CCceeCCCCCCc---eEeCCCcCeeeccccceeeeecccccccCCccCCCC
Q psy1749          15 ELIKCCPMCSVP---IEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRHY   62 (87)
Q Consensus        15 ~~~k~CP~C~~~---Iek~~GCnhm~C~~C~~~FC~~C~~~~~~~~~~~Hf   62 (87)
                      ...-.||+|+..   |.+..|=.|+.|..||..+=..-......-+.|+-|
T Consensus        19 pt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~~V~~l~epIDVY~~w   69 (99)
T PRK14892         19 PKIFECPRCGKVSISVKIKKNIAIITCGNCGLYTEFEVPSVYDEVDVYNKF   69 (99)
T ss_pred             CcEeECCCCCCeEeeeecCCCcceEECCCCCCccCEECCccccchhhHHHH
Confidence            355679999943   233457889999999998876655555554566555

>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=86.28  E-value=0.88  Score=25.05  Aligned_cols=25  Identities=24%  Similarity=0.590  Sum_probs=15.4

Q ss_pred             eCCCCCCce-EeCCCcCeeeccccce
Q psy1749          19 CCPMCSVPI-EKDEGCAQMLCKRCKH   43 (87)
Q Consensus        19 ~CP~C~~~I-ek~~GCnhm~C~~C~~   43 (87)
                      .||.|+..- .-+..=..+.|..||.
T Consensus         2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~   27 (43)
T PF08271_consen    2 KCPNCGSKEIVFDPERGELVCPNCGL   27 (43)
T ss_dssp             SBTTTSSSEEEEETTTTEEEETTT-B
T ss_pred             CCcCCcCCceEEcCCCCeEECCCCCC
Confidence            588888863 4445555567775554

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 a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.

>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1

Probab=86.21  E-value=0.42  Score=28.26  Aligned_cols=45  Identities=18%  Similarity=0.522  Sum_probs=32.5

Q ss_pred             cccccccCcccccCCceeCCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749           2 EPWFQMGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD   55 (87)
Q Consensus         2 ~~w~~~~~~~~~~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~   55 (87)
                      ..|..++-.       +.|+.|+...-...  ..-.|+.||..||-.|......
T Consensus         2 ~~W~~~~~~-------~~C~~C~~~F~~~~--rk~hCr~CG~i~C~~C~~~~~~   46 (68)
T smart00064        2 PHWIPDEEV-------SNCMGCGKEFNLTK--RRHHCRNCGRIFCSKCSSKKAP   46 (68)
T ss_pred             CCCcCCCCC-------CcCcccCccccCcc--cccccccCCCCcChHHcCCeee
Confidence            467777553       78999998666432  3456888999999999865554

The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=85.94  E-value=0.94  Score=26.84  Aligned_cols=34  Identities=24%  Similarity=0.469  Sum_probs=24.3

Q ss_pred             eeCCCCCCceEeCCCc--Ceeeccccceeeeecccc
Q psy1749          18 KCCPMCSVPIEKDEGC--AQMLCKRCKHVFCWYCLA   51 (87)
Q Consensus        18 k~CP~C~~~Iek~~GC--nhm~C~~C~~~FC~~C~~   51 (87)
                      -.||.|+..|+..+.-  .-+.|..||+.+=-+-..
T Consensus         3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGaeleVv~~~   38 (54)
T TIGR01206         3 FECPDCGAEIELENPELGELVICDECGAELEVVSLD   38 (54)
T ss_pred             cCCCCCCCEEecCCCccCCEEeCCCCCCEEEEEeCC
Confidence            4799999999997643  247788888877544433

This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.

>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA

Probab=85.32  E-value=0.65  Score=31.36  Aligned_cols=29  Identities=21%  Similarity=0.576  Sum_probs=23.4

Q ss_pred             eeCCCCCCceEeCCCcCeeeccccceeeee
Q psy1749          18 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCW   47 (87)
Q Consensus        18 k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~   47 (87)
                      -.||+|..-..-.+|=+ +.|+.|+++|=-
T Consensus         3 p~CP~C~seytY~dg~~-~iCpeC~~EW~~   31 (109)
T TIGR00686         3 PPCPKCNSEYTYHDGTQ-LICPSCLYEWNE   31 (109)
T ss_pred             CcCCcCCCcceEecCCe-eECccccccccc
Confidence            47999999998888865 789988887643

The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).

>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=85.09  E-value=0.91  Score=23.34  Aligned_cols=21  Identities=29%  Similarity=0.892  Sum_probs=13.2

Q ss_pred             eCCCCCCceEeCCCcCeeecc
Q psy1749          19 CCPMCSVPIEKDEGCAQMLCK   39 (87)
Q Consensus        19 ~CP~C~~~Iek~~GCnhm~C~   39 (87)
                      .||.|++.+.+.++=..+.|.
T Consensus         1 ~CP~C~s~l~~~~~ev~~~C~   21 (28)
T PF03119_consen    1 TCPVCGSKLVREEGEVDIRCP   21 (28)
T ss_dssp             B-TTT--BEEE-CCTTCEEE-
T ss_pred             CcCCCCCEeEcCCCCEeEECC
Confidence            499999999999886677765

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 zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.

>KOG0317|consensus

Probab=84.88  E-value=0.12  Score=40.04  Aligned_cols=38  Identities=24%  Similarity=0.621  Sum_probs=28.3

Q ss_pred             cccCCceeCCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749          12 FDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD   55 (87)
Q Consensus        12 ~~~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~   55 (87)
                      .+..++..|--|....+      +-+|+.||+.|||.|...|-.
T Consensus       234 ~i~~a~~kC~LCLe~~~------~pSaTpCGHiFCWsCI~~w~~  271 (293)
T KOG0317|consen  234 SIPEATRKCSLCLENRS------NPSATPCGHIFCWSCILEWCS  271 (293)
T ss_pred             cCCCCCCceEEEecCCC------CCCcCcCcchHHHHHHHHHHc
Confidence            34455666766665543      567788999999999999986

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=84.77  E-value=1.1  Score=25.29  Aligned_cols=28  Identities=18%  Similarity=0.436  Sum_probs=20.7

Q ss_pred             eCCCCCCceEeCCCcCeeeccccceeeee
Q psy1749          19 CCPMCSVPIEKDEGCAQMLCKRCKHVFCW   47 (87)
Q Consensus        19 ~CP~C~~~Iek~~GCnhm~C~~C~~~FC~   47 (87)
                      .|..|+..++...+ .-+.|++||+..=|
T Consensus         4 ~C~~Cg~~~~~~~~-~~irC~~CG~rIly   31 (44)
T smart00659        4 ICGECGRENEIKSK-DVVRCRECGYRILY   31 (44)
T ss_pred             ECCCCCCEeecCCC-CceECCCCCceEEE
Confidence            58888888887743 66888888876543

present in RNA polymerase I, II and III

>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors []

Probab=84.71  E-value=1.5  Score=23.38  Aligned_cols=30  Identities=20%  Similarity=0.325  Sum_probs=22.2

Q ss_pred             CceeCCCCCCceEeCCCcCeeeccccceee
Q psy1749          16 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF   45 (87)
Q Consensus        16 ~~k~CP~C~~~Iek~~GCnhm~C~~C~~~F   45 (87)
                      +.+.|+.|+.......-=..+.|..|+..|
T Consensus         2 ~~~~C~~C~~~~i~~~~~~~~~C~~Cg~~~   31 (33)
T PF08792_consen    2 NLKKCSKCGGNGIVNKEDDYEVCIFCGSSF   31 (33)
T ss_pred             CceEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence            347899999888776666677787777654

>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]

Probab=84.07  E-value=0.73  Score=35.35  Aligned_cols=27  Identities=33%  Similarity=0.691  Sum_probs=23.5

Q ss_pred             CceeCCCCCCceEeC--CCcCeeeccccc
Q psy1749          16 LIKCCPMCSVPIEKD--EGCAQMLCKRCK   42 (87)
Q Consensus        16 ~~k~CP~C~~~Iek~--~GCnhm~C~~C~   42 (87)
                      .-++|+.|+++|+|.  +|-+.-.|+.|+
T Consensus       244 ~GepC~~CGt~I~k~~~~gR~t~~CP~CQ  272 (273)
T COG0266         244 AGEPCRRCGTPIEKIKLGGRSTFYCPVCQ  272 (273)
T ss_pred             CCCCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence            457899999999997  889888898886

>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2

Probab=83.85  E-value=0.72  Score=24.82  Aligned_cols=28  Identities=21%  Similarity=0.539  Sum_probs=17.6

Q ss_pred             eeCCCCCCceEeCCCc-Ceeeccccceee
Q psy1749          18 KCCPMCSVPIEKDEGC-AQMLCKRCKHVF   45 (87)
Q Consensus        18 k~CP~C~~~Iek~~GC-nhm~C~~C~~~F   45 (87)
                      +.||.|+.+..-..+= ....|+.|++++
T Consensus         2 ~FCp~C~nlL~p~~~~~~~~~C~~C~Y~~   30 (35)
T PF02150_consen    2 RFCPECGNLLYPKEDKEKRVACRTCGYEE   30 (35)
T ss_dssp             -BETTTTSBEEEEEETTTTEEESSSS-EE
T ss_pred             eeCCCCCccceEcCCCccCcCCCCCCCcc
Confidence            5799999887665332 223788887764

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....

>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=83.50  E-value=0.85  Score=23.25  Aligned_cols=25  Identities=40%  Similarity=0.824  Sum_probs=15.2

Q ss_pred             eeCCCCCCceEeC--CCcCeeeccccc
Q psy1749          18 KCCPMCSVPIEKD--EGCAQMLCKRCK   42 (87)
Q Consensus        18 k~CP~C~~~Iek~--~GCnhm~C~~C~   42 (87)
                      +.||+|...|+..  .+-+...|..|.
T Consensus         2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq   28 (30)
T PF06827_consen    2 EKCPRCWNYIEDIGINGRSTYLCPRCQ   28 (30)
T ss_dssp             SB-TTT--BBEEEEETTEEEEE-TTTC
T ss_pred             CcCccCCCcceEeEecCCCCeECcCCc
Confidence            5799999999775  456666677664

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 a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....

>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional

Probab=83.41  E-value=0.8  Score=34.43  Aligned_cols=27  Identities=37%  Similarity=0.826  Sum_probs=21.9

Q ss_pred             ceeCCCCCCceEeC--CCcCeeeccccce
Q psy1749          17 IKCCPMCSVPIEKD--EGCAQMLCKRCKH   43 (87)
Q Consensus        17 ~k~CP~C~~~Iek~--~GCnhm~C~~C~~   43 (87)
                      -++||.|+..|++.  +|-.-..|+.|+.
T Consensus       235 g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ~  263 (269)
T PRK14811        235 GQPCPRCGTPIEKIVVGGRGTHFCPQCQP  263 (269)
T ss_pred             cCCCCcCCCeeEEEEECCCCcEECCCCcC
Confidence            47899999999986  7777777877764

>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=83.35  E-value=0.45  Score=25.43  Aligned_cols=21  Identities=24%  Similarity=0.686  Sum_probs=16.2

Q ss_pred             eeeccccceeeeecccccccC
Q psy1749          35 QMLCKRCKHVFCWYCLASLDD   55 (87)
Q Consensus        35 hm~C~~C~~~FC~~C~~~~~~   55 (87)
                      .++...||+.||+.|...+..
T Consensus        11 ~~~~~~CGH~fC~~C~~~~~~   31 (39)
T PF13923_consen   11 PVVVTPCGHSFCKECIEKYLE   31 (39)
T ss_dssp             EEEECTTSEEEEHHHHHHHHH
T ss_pred             cCEECCCCCchhHHHHHHHHH
Confidence            445556999999999887755

>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated

Probab=83.27  E-value=0.9  Score=34.06  Aligned_cols=27  Identities=37%  Similarity=0.821  Sum_probs=22.0

Q ss_pred             ceeCCCCCCceEeC--CCcCeeeccccce
Q psy1749          17 IKCCPMCSVPIEKD--EGCAQMLCKRCKH   43 (87)
Q Consensus        17 ~k~CP~C~~~Iek~--~GCnhm~C~~C~~   43 (87)
                      -++||.|++.|++.  +|-.-..|+.|+.
T Consensus       245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ~  273 (274)
T PRK01103        245 GEPCRRCGTPIEKIKQGGRSTFFCPRCQK  273 (274)
T ss_pred             CCCCCCCCCeeEEEEECCCCcEECcCCCC
Confidence            46899999999986  6777778887764

>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]

Probab=82.96  E-value=0.51  Score=36.63  Aligned_cols=34  Identities=24%  Similarity=0.535  Sum_probs=28.2

Q ss_pred             cCCceeCCCCCCceEeCC-CcCeeeccccceeeee
Q psy1749          14 SELIKCCPMCSVPIEKDE-GCAQMLCKRCKHVFCW   47 (87)
Q Consensus        14 ~~~~k~CP~C~~~Iek~~-GCnhm~C~~C~~~FC~   47 (87)
                      ...|..||+|+..+.+.+ +=|...|++|+++|=-
T Consensus        25 e~lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ri   59 (294)
T COG0777          25 EGLWTKCPSCGEMLYRKELESNLKVCPKCGHHMRI   59 (294)
T ss_pred             CCceeECCCccceeeHHHHHhhhhcccccCccccc
Confidence            467899999999998875 6778999999988743

>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional

Probab=82.88  E-value=0.94  Score=34.06  Aligned_cols=26  Identities=27%  Similarity=0.678  Sum_probs=21.6

Q ss_pred             ceeCCCCCCceEeC--CCcCeeeccccc
Q psy1749          17 IKCCPMCSVPIEKD--EGCAQMLCKRCK   42 (87)
Q Consensus        17 ~k~CP~C~~~Iek~--~GCnhm~C~~C~   42 (87)
                      .++||.|+..|++.  +|-.-..|+.|+
T Consensus       244 g~pCprCG~~I~~~~~~gR~t~~CP~CQ  271 (272)
T PRK14810        244 GEPCLNCKTPIRRVVVAGRSSHYCPHCQ  271 (272)
T ss_pred             CCcCCCCCCeeEEEEECCCccEECcCCc
Confidence            57899999999986  777777788775

>PRK10445 endonuclease VIII; Provisional

Probab=82.79  E-value=0.96  Score=33.85  Aligned_cols=26  Identities=27%  Similarity=0.532  Sum_probs=22.0

Q ss_pred             ceeCCCCCCceEeC--CCcCeeeccccc
Q psy1749          17 IKCCPMCSVPIEKD--EGCAQMLCKRCK   42 (87)
Q Consensus        17 ~k~CP~C~~~Iek~--~GCnhm~C~~C~   42 (87)
                      -+.||.|+..|++.  +|-.-..|+.|+
T Consensus       235 g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ  262 (263)
T PRK10445        235 GEACERCGGIIEKTTLSSRPFYWCPGCQ  262 (263)
T ss_pred             CCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence            47899999999986  788778888775

>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ]

Probab=82.52  E-value=0.55  Score=27.79  Aligned_cols=29  Identities=24%  Similarity=0.522  Sum_probs=22.3

Q ss_pred             ceeCCCCCCceEeCCCcC--eeeccccceee
Q psy1749          17 IKCCPMCSVPIEKDEGCA--QMLCKRCKHVF   45 (87)
Q Consensus        17 ~k~CP~C~~~Iek~~GCn--hm~C~~C~~~F   45 (87)
                      -.+|++|+.++-+.++-.  .|.|++|++..
T Consensus         4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN   34 (51)
T PF10122_consen    4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTIN   34 (51)
T ss_pred             ceeccchhHHHhhhcCccEEEEECCCCCccc
Confidence            368999999999975554  48899887643

>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional

Probab=82.43  E-value=0.99  Score=34.06  Aligned_cols=26  Identities=35%  Similarity=0.750  Sum_probs=22.1

Q ss_pred             ceeCCCCCCceEeC--CCcCeeeccccc
Q psy1749          17 IKCCPMCSVPIEKD--EGCAQMLCKRCK   42 (87)
Q Consensus        17 ~k~CP~C~~~Iek~--~GCnhm~C~~C~   42 (87)
                      -++||.|+..|++.  +|-+-..|+.|+
T Consensus       254 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ  281 (282)
T PRK13945        254 GKPCRKCGTPIERIKLAGRSTHWCPNCQ  281 (282)
T ss_pred             cCCCCcCCCeeEEEEECCCccEECCCCc
Confidence            47899999999986  788888888776

>KOG2906|consensus

Probab=82.41  E-value=1.3  Score=29.71  Aligned_cols=30  Identities=30%  Similarity=0.791  Sum_probs=23.3

Q ss_pred             eeCCCCCCceEeCCC--cCeeeccccceeeee
Q psy1749          18 KCCPMCSVPIEKDEG--CAQMLCKRCKHVFCW   47 (87)
Q Consensus        18 k~CP~C~~~Iek~~G--Cnhm~C~~C~~~FC~   47 (87)
                      ..||.|+.++...+|  |+...|..|.+.|=-
T Consensus         2 ~FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I   33 (105)
T KOG2906|consen    2 LFCPTCGNMLIVESGESCNRFSCRTCPYVFPI   33 (105)
T ss_pred             cccCCCCCEEEEecCCeEeeEEcCCCCceeeE
Confidence            369999987666544  899999999887754

>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)

Probab=82.30  E-value=1.5  Score=24.60  Aligned_cols=24  Identities=29%  Similarity=0.958  Sum_probs=17.9

Q ss_pred             ceeCCCCCCceEe-CCCcCeeeccccc
Q psy1749          17 IKCCPMCSVPIEK-DEGCAQMLCKRCK   42 (87)
Q Consensus        17 ~k~CP~C~~~Iek-~~GCnhm~C~~C~   42 (87)
                      ...||.|++++-+ .+|  .+.|+.|+
T Consensus        17 ~~~Cp~C~~PL~~~k~g--~~~Cv~C~   41 (41)
T PF06677_consen   17 DEHCPDCGTPLMRDKDG--KIYCVSCG   41 (41)
T ss_pred             cCccCCCCCeeEEecCC--CEECCCCC
Confidence            4679999999998 454  46777663

It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].

>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg)

Probab=82.14  E-value=1.1  Score=33.73  Aligned_cols=26  Identities=35%  Similarity=0.759  Sum_probs=21.3

Q ss_pred             ceeCCCCCCceEeC--CCcCeeeccccc
Q psy1749          17 IKCCPMCSVPIEKD--EGCAQMLCKRCK   42 (87)
Q Consensus        17 ~k~CP~C~~~Iek~--~GCnhm~C~~C~   42 (87)
                      -++||.|+..|++.  +|-+-..|+.|+
T Consensus       245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ  272 (272)
T TIGR00577       245 GEPCRRCGTPIEKIKVGGRGTHFCPQCQ  272 (272)
T ss_pred             CCCCCCCCCeeEEEEECCCCCEECCCCC
Confidence            46899999999986  777777787774

All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PF14354 Lar_restr_allev: Restriction alleviation protein Lar

Probab=81.90  E-value=1.3  Score=25.71  Aligned_cols=28  Identities=25%  Similarity=0.506  Sum_probs=17.7

Q ss_pred             CceeCCCCCCceEeCC---Cc-----Ceeeccccce
Q psy1749          16 LIKCCPMCSVPIEKDE---GC-----AQMLCKRCKH   43 (87)
Q Consensus        16 ~~k~CP~C~~~Iek~~---GC-----nhm~C~~C~~   43 (87)
                      ..|+||.|+.......   +=     ..+.|..||.
T Consensus         2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga   37 (61)
T PF14354_consen    2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA   37 (61)
T ss_pred             CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence            4589999986555432   21     3466776665

>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family

Probab=81.71  E-value=1.3  Score=25.51  Aligned_cols=28  Identities=21%  Similarity=0.376  Sum_probs=16.8

Q ss_pred             eeCCCCCCceEe-C-----CCcCee-eccccceee
Q psy1749          18 KCCPMCSVPIEK-D-----EGCAQM-LCKRCKHVF   45 (87)
Q Consensus        18 k~CP~C~~~Iek-~-----~GCnhm-~C~~C~~~F   45 (87)
                      |+||.|+..-+. .     .+..++ .|..|+++.
T Consensus         2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~   36 (53)
T TIGR03655         2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASG   36 (53)
T ss_pred             CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCc
Confidence            789999987772 1     233333 366555553

Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.

>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]

Probab=81.40  E-value=1.5  Score=29.30  Aligned_cols=29  Identities=17%  Similarity=0.650  Sum_probs=21.8

Q ss_pred             ceeCCCCCCceEeC--CCcCeeeccccceee
Q psy1749          17 IKCCPMCSVPIEKD--EGCAQMLCKRCKHVF   45 (87)
Q Consensus        17 ~k~CP~C~~~Iek~--~GCnhm~C~~C~~~F   45 (87)
                      .+.||+|+.++.-.  ++=+-+.|..||+++
T Consensus         2 m~FCp~Cgsll~p~~~~~~~~l~C~kCgye~   32 (113)
T COG1594           2 MRFCPKCGSLLYPKKDDEGGKLVCRKCGYEE   32 (113)
T ss_pred             ccccCCccCeeEEeEcCCCcEEECCCCCcch
Confidence            47899999998773  233388899888765

>PRK10220 hypothetical protein; Provisional

Probab=80.98  E-value=1.3  Score=30.05  Aligned_cols=28  Identities=21%  Similarity=0.688  Sum_probs=22.7

Q ss_pred             eeCCCCCCceEeCCCcCeeeccccceeee
Q psy1749          18 KCCPMCSVPIEKDEGCAQMLCKRCKHVFC   46 (87)
Q Consensus        18 k~CP~C~~~Iek~~GCnhm~C~~C~~~FC   46 (87)
                      -.||+|..-..-.+|=. +.|+.|+++|=
T Consensus         4 P~CP~C~seytY~d~~~-~vCpeC~hEW~   31 (111)
T PRK10220          4 PHCPKCNSEYTYEDNGM-YICPECAHEWN   31 (111)
T ss_pred             CcCCCCCCcceEcCCCe-EECCcccCcCC
Confidence            57999999988888754 78888888764

>PRK00420 hypothetical protein; Validated

Probab=80.80  E-value=1.5  Score=29.59  Aligned_cols=26  Identities=31%  Similarity=0.874  Sum_probs=18.1

Q ss_pred             CceeCCCCCCceEe-CCCcCeeeccccce
Q psy1749          16 LIKCCPMCSVPIEK-DEGCAQMLCKRCKH   43 (87)
Q Consensus        16 ~~k~CP~C~~~Iek-~~GCnhm~C~~C~~   43 (87)
                      ....||.|+.++.+ .+|  ...|+.||.
T Consensus        22 l~~~CP~Cg~pLf~lk~g--~~~Cp~Cg~   48 (112)
T PRK00420         22 LSKHCPVCGLPLFELKDG--EVVCPVHGK   48 (112)
T ss_pred             ccCCCCCCCCcceecCCC--ceECCCCCC
Confidence            34889999999997 444  455555544

>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair

Probab=80.67  E-value=0.39  Score=28.24  Aligned_cols=31  Identities=29%  Similarity=0.771  Sum_probs=16.7

Q ss_pred             CCCCCCceEeCC----CcCeeeccccceeeeeccc
Q psy1749          20 CPMCSVPIEKDE----GCAQMLCKRCKHVFCWYCL   50 (87)
Q Consensus        20 CP~C~~~Iek~~----GCnhm~C~~C~~~FC~~C~   50 (87)
                      |..|..++....    +-....|.+|+..||..|-
T Consensus         2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD   36 (51)
T PF07975_consen    2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCD   36 (51)
T ss_dssp             ETTTTEE-TTS-------EEE--TTTT--B-HHHH
T ss_pred             CccCCCCCCCcccccccCCeEECCCCCCccccCcC
Confidence            666777666542    3466889999999999985

It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.

>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=80.30  E-value=0.41  Score=25.46  Aligned_cols=31  Identities=35%  Similarity=0.860  Sum_probs=20.2

Q ss_pred             CCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749          20 CPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD   55 (87)
Q Consensus        20 CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~   55 (87)
                      ||-|...++...     +=..||+.||..|...+-.
T Consensus         1 C~iC~~~~~~~~-----~~~~C~H~fC~~C~~~~~~   31 (41)
T PF00097_consen    1 CPICLEPFEDPV-----ILLPCGHSFCRDCLRKWLE   31 (41)
T ss_dssp             ETTTSSBCSSEE-----EETTTSEEEEHHHHHHHHH
T ss_pred             CCcCCccccCCC-----EEecCCCcchHHHHHHHHH
Confidence            445555444333     3345999999999987765

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 ....

>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]

Probab=80.19  E-value=1.7  Score=30.22  Aligned_cols=24  Identities=42%  Similarity=1.013  Sum_probs=17.8

Q ss_pred             ceeCCCCCCceEeCCCcCeeeccccceeeeeccc
Q psy1749          17 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCL   50 (87)
Q Consensus        17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~   50 (87)
                      -+.||.|+++..+.+|          .-||-+|+
T Consensus        28 ~~hCp~Cg~PLF~KdG----------~v~CPvC~   51 (131)
T COG1645          28 AKHCPKCGTPLFRKDG----------EVFCPVCG   51 (131)
T ss_pred             HhhCcccCCcceeeCC----------eEECCCCC
Confidence            4679999999998654          45555666

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	87
1wd2_A	60	Solution Structure Of The C-Terminal Ring From A Ri		4e-04

>pdb|1WD2|A Chain A, Solution Structure Of The C-Terminal Ring From A Ring-Ibr- Ring (Triad) Motif Length = 60

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 19/37 (51%), Positives = 22/37 (59%), Gaps = 2/37 (5%)
Query: 20 CPMCSVPIEKDEGCAQMLCK--RCKHVFCWYCLASLD 54
          CP C V IEKD GC  M+C+   CK  FCW CL   +
Sbjct: 9  CPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWE 45

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	87
1wd2_A	60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	6e-09

>1wd2_A Ariadne-1 protein homolog; ring, IBR, triad, zinc finger, ligase; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 60

 Score = 46.6 bits (111), Expect = 6e-09
 Identities = 20/41 (48%), Positives = 23/41 (56%), Gaps = 2/41 (4%)

Query: 17 IKCCPMCSVPIEKDEGCAQMLCK--RCKHVFCWYCLASLDD 55
           K CP C V IEKD GC  M+C+   CK  FCW CL   + 
Sbjct: 6  TKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEP 46

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	87
1wd2_A	60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	99.75
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	98.19
2jmo_A	80	Parkin; IBR, E3 ligase, zinc binding domain, RBR;	97.88
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	94.16
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	92.94
2jr6_A	68	UPF0434 protein NMA0874; solution, structural geno	92.5
1x4u_A	84	Zinc finger, FYVE domain containing 27 isoform B;	91.84
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	91.57
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	90.47
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	90.17
2yw8_A	82	RUN and FYVE domain-containing protein 1; structur	89.13
2js4_A	70	UPF0434 protein BB2007; NESG, northeast structural	88.85
2hf1_A	68	Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A	88.73
2jrp_A	81	Putative cytoplasmic protein; two-zinc binding pro	88.69
2pk7_A	69	Uncharacterized protein; NESG, PLR1, putative tetr	88.33
1joc_A	125	EEA1, early endosomal autoantigen 1; FYVE domain,	87.77
1z2q_A	84	LM5-1; membrane protein, FYVE domain, zinc-finger;	87.3
2jne_A	101	Hypothetical protein YFGJ; zinc fingers, two zinc,	87.26
2jny_A	67	Uncharacterized BCR; structure, CGR1, NESG, struct	86.14
3t7l_A	90	Zinc finger FYVE domain-containing protein 16; str	85.15
1wfh_A	64	Zinc finger (AN1-like) family protein; ZF-AN1 doma	84.84
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	84.27
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	84.25
2kpi_A	56	Uncharacterized protein SCO3027; zinc finger, PSI-	83.47
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	83.33
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	83.18
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	82.81
2xzf_A	271	Formamidopyrimidine-DNA glycosylase; hydrolase-DNA	82.79
1wii_A	85	Hypothetical UPF0222 protein MGC4549; domain of un	82.73
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	82.42
3u6p_A	273	Formamidopyrimidine-DNA glycosylase; DNA glycosyla	82.42
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	82.4
1k82_A	268	Formamidopyrimidine-DNA glycosylase; protein-DNA c	82.31
1ee8_A	266	MUTM (FPG) protein; beta sandwich, zinc finger, he	82.31
1k3x_A	262	Endonuclease VIII; hydrolase/DNA, hydrolase-DNA co	82.25
1wfl_A	74	Zinc finger protein 216; ZF-AN1 domain, zinc bindi	82.2
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	82.12
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	81.89
2apo_B	60	Ribosome biogenesis protein NOP10; protein-protein	81.77
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	81.44
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	80.8
1wg2_A	64	Zinc finger (AN1-like) family protein; riken struc	80.69
1twf_L	70	ABC10-alpha, DNA-directed RNA polymerases I, II, a	80.51
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	80.09

>1wd2_A Ariadne-1 protein homolog; ring, IBR, triad, zinc finger, ligase; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=99.75  E-value=2.1e-19  Score=107.98  Aligned_cols=45  Identities=44%  Similarity=1.080  Sum_probs=42.3

Q ss_pred             cccCCceeCCCCCCceEeCCCcCeeeccc--cceeeeecccccccCC
Q psy1749          12 FDSELIKCCPMCSVPIEKDEGCAQMLCKR--CKHVFCWYCLASLDDD   56 (87)
Q Consensus        12 ~~~~~~k~CP~C~~~Iek~~GCnhm~C~~--C~~~FC~~C~~~~~~~   56 (87)
                      |+.+++|+||+|+++|||++|||||+|+.  |+.+|||+|+++|+.+
T Consensus         1 wi~~~~k~CP~C~~~Iek~~GCnhmtC~~~~C~~~FCw~C~~~~~~~   47 (60)
T 1wd2_A            1 WIAANTKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPH   47 (60)
T ss_dssp             CCCCCCCCCTTTCCCCSSCCSCCSSSCCSSGGGSCCSSSSCSCSGGG
T ss_pred             CccccceECcCCCCeeEeCCCCCcEEECCCCcCCEEeeCcCCCcccC
Confidence            56788999999999999999999999998  9999999999999864

>2ct7_A Ring finger protein 31; IBR, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.4

Probab=98.19  E-value=2.7e-06  Score=53.05  Aligned_cols=42  Identities=19%  Similarity=0.532  Sum_probs=36.9

Q ss_pred             cCCceeCCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749          14 SELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD   55 (87)
Q Consensus        14 ~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~   55 (87)
                      ..+.+-||.|...|....+-..++|..|+..||+.|+.+|+.
T Consensus        22 ~~~~~wCP~C~~~~~~~~~~~~v~C~~C~~~FC~~C~~~w~~   63 (86)
T 2ct7_A           22 DPKFLWCAQCSFGFIYEREQLEATCPQCHQTFCVRCKRQWEE   63 (86)
T ss_dssp             CCCEECCSSSCCCEECCCSCSCEECTTTCCEECSSSCSBCCT
T ss_pred             CCCEeECcCCCchheecCCCCceEeCCCCCccccccCCchhh
Confidence            455667999999999888878899989999999999999955

>2jmo_A Parkin; IBR, E3 ligase, zinc binding domain, RBR; NMR {Homo sapiens}

Probab=97.88  E-value=5.4e-06  Score=51.20  Aligned_cols=41  Identities=20%  Similarity=0.522  Sum_probs=36.4

Q ss_pred             CCceeCCC--CCCceEeCCCcCeeecc-----ccceeeeecccccccC
Q psy1749          15 ELIKCCPM--CSVPIEKDEGCAQMLCK-----RCKHVFCWYCLASLDD   55 (87)
Q Consensus        15 ~~~k~CP~--C~~~Iek~~GCnhm~C~-----~C~~~FC~~C~~~~~~   55 (87)
                      ...+-||.  |+..|...++...++|.     .|+..||+.|+.+|-.
T Consensus        23 ~~~~~CP~p~C~~~v~~~~~~~~v~C~~~~~~~C~~~FC~~C~~~wH~   70 (80)
T 2jmo_A           23 MGGVLCPRPGCGAGLLPEPDQRKVTCEGGNGLGCGFAFCRECKEAYHE   70 (80)
T ss_dssp             CSSCCCCSSSCCCCCCCCSCTTSBCTTSSSTTCCSCCEETTTTEECCS
T ss_pred             CCcEECCCCCCCcccEECCCCCcCCCCCCCCCCCCCeeccccCccccC
Confidence            34788998  99999999999999997     7999999999988854

>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1

Probab=94.16  E-value=0.042  Score=30.41  Aligned_cols=31  Identities=26%  Similarity=0.654  Sum_probs=24.0

Q ss_pred             CCceeCCCCCC-ceEeCCCcCeeeccccceee
Q psy1749          15 ELIKCCPMCSV-PIEKDEGCAQMLCKRCKHVF   45 (87)
Q Consensus        15 ~~~k~CP~C~~-~Iek~~GCnhm~C~~C~~~F   45 (87)
                      .....||.|+. .|+.+..-..+.|..||..+
T Consensus         3 ~~~~~CP~C~~~~l~~d~~~gelvC~~CG~v~   34 (50)
T 1pft_A            3 NKQKVCPACESAELIYDPERGEIVCAKCGYVI   34 (50)
T ss_dssp             SSCCSCTTTSCCCEEEETTTTEEEESSSCCBC
T ss_pred             CccEeCcCCCCcceEEcCCCCeEECcccCCcc
Confidence            34568999998 88887777789998776644

>3j20_Y 30S ribosomal protein S27AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=92.94  E-value=0.093  Score=29.66  Aligned_cols=32  Identities=19%  Similarity=0.378  Sum_probs=23.4

Q ss_pred             ccCCceeCCCCCCceEeCCCcCeeecccccee
Q psy1749          13 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHV   44 (87)
Q Consensus        13 ~~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~   44 (87)
                      +....+.||+|+..+.-...=+...|..||..
T Consensus        15 v~~~~k~CP~CG~~~fm~~~~~R~~C~kCG~t   46 (50)
T 3j20_Y           15 VIRKNKFCPRCGPGVFMADHGDRWACGKCGYT   46 (50)
T ss_dssp             EECSSEECSSSCSSCEEEECSSEEECSSSCCE
T ss_pred             EEEecccCCCCCCceEEecCCCeEECCCCCCE
Confidence            45677899999986555444477889888864

>2jr6_A UPF0434 protein NMA0874; solution, structural genomics, PSI, structure initiative, northeast structural genomics consort NESG; NMR {Neisseria meningitidis}

Probab=92.50  E-value=0.095  Score=31.44  Aligned_cols=30  Identities=17%  Similarity=0.364  Sum_probs=25.7

Q ss_pred             CceeCCCCCCceEeCCCcCeeeccccceee
Q psy1749          16 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF   45 (87)
Q Consensus        16 ~~k~CP~C~~~Iek~~GCnhm~C~~C~~~F   45 (87)
                      .+-.||.|+..++.....+.++|..|+..|
T Consensus         7 ~iL~CP~ck~~L~~~~~~~~LiC~~cg~~Y   36 (68)
T 2jr6_A            7 DILVCPVTKGRLEYHQDKQELWSRQAKLAY   36 (68)
T ss_dssp             CCCBCSSSCCBCEEETTTTEEEETTTTEEE
T ss_pred             hheECCCCCCcCeEeCCCCEEEcCCCCcEe
Confidence            456799999999999888999998887766

>1x4u_A Zinc finger, FYVE domain containing 27 isoform B; phosphoinositide binding, zinc binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=91.84  E-value=0.15  Score=31.10  Aligned_cols=43  Identities=19%  Similarity=0.422  Sum_probs=31.2

Q ss_pred             cccccccCcccccCCceeCCCCCCceEeCCCcCeeeccccceeeeecccccc
Q psy1749           2 EPWFQMGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASL   53 (87)
Q Consensus         2 ~~w~~~~~~~~~~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~   53 (87)
                      ..|..|..       ...|..|+......  --.-.|+.||..||..|....
T Consensus         6 ~~W~pd~~-------~~~C~~C~~~F~~~--~RrHHCR~CG~vfC~~Cs~~~   48 (84)
T 1x4u_A            6 SGRYPTNN-------FGNCTGCSATFSVL--KKRRSCSNCGNSFCSRCCSFK   48 (84)
T ss_dssp             CCSCSCCC-------CSSCSSSCCCCCSS--SCCEECSSSCCEECTTTSCEE
T ss_pred             CccccCCC-------CCcCcCcCCccccc--hhhhhhcCCCcEEChhhcCCc
Confidence            45666555       37899999987432  334579999999999998543

>1vq8_Z 50S ribosomal protein L37AE; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1vq4_Z* 1vq6_Z* 1vq5_Z* 1vq7_Z* 1vq9_Z* 1vqk_Z* 1vql_Z* 1vqm_Z* 1vqn_Z* 1vqo_Z* 1vqp_Z* 1yhq_Z* 1yi2_Z* 1yij_Z* 1yit_Z* 1yj9_Z* 1yjn_Z* 1yjw_Z* 2qa4_Z* 1s72_Z* ...

Probab=91.57  E-value=0.1  Score=32.51  Aligned_cols=32  Identities=22%  Similarity=0.477  Sum_probs=27.1

Q ss_pred             CCceeCCCCCCceEeCCCcCeeeccccceeee
Q psy1749          15 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFC   46 (87)
Q Consensus        15 ~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC   46 (87)
                      ...-.||.|+....+..+-..+.|..|+..|-
T Consensus        25 ~~~y~Cp~CG~~~v~r~atGiW~C~~Cg~~~a   56 (83)
T 1vq8_Z           25 NEDHACPNCGEDRVDRQGTGIWQCSYCDYKFT   56 (83)
T ss_dssp             HSCEECSSSCCEEEEEEETTEEEETTTCCEEE
T ss_pred             cccCcCCCCCCcceeccCCCeEECCCCCCEec
Confidence            34568999999999998888999998888764

>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=90.47  E-value=0.078  Score=32.67  Aligned_cols=33  Identities=21%  Similarity=0.647  Sum_probs=26.8

Q ss_pred             eeCCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749          18 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD   55 (87)
Q Consensus        18 k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~   55 (87)
                      -.||-|...+.     +.+++..||+.||+.|...|-.
T Consensus        23 ~~C~IC~~~~~-----~p~~~~~CgH~FC~~Ci~~~~~   55 (100)
T 3lrq_A           23 FRCFICMEKLR-----DARLCPHCSKLCCFSCIRRWLT   55 (100)
T ss_dssp             TBCTTTCSBCS-----SEEECTTTCCEEEHHHHHHHHH
T ss_pred             CCCccCCcccc-----CccccCCCCChhhHHHHHHHHH
Confidence            45999998876     3567677999999999988865

>2k4x_A 30S ribosomal protein S27AE; metal-binding, ribonucleoprotein, zinc, zinc-finger, structural genomics, PSI-2; NMR {Thermoplasma acidophilum} SCOP: g.41.8.8

Probab=90.17  E-value=0.16  Score=29.25  Aligned_cols=33  Identities=21%  Similarity=0.372  Sum_probs=24.0

Q ss_pred             ccCCceeCCCCCCceEeCCCcCeeeccccceee
Q psy1749          13 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVF   45 (87)
Q Consensus        13 ~~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~F   45 (87)
                      +....+.||+|+..+.-+..-+...|..|+..+
T Consensus        14 i~~~~~fCPkCG~~~~ma~~~dr~~C~kCgyt~   46 (55)
T 2k4x_A           14 LVRKHRFCPRCGPGVFLAEHADRYSCGRCGYTE   46 (55)
T ss_dssp             CCCSSCCCTTTTTTCCCEECSSEEECTTTCCCE
T ss_pred             EEEccccCcCCCCceeEeccCCEEECCCCCCEE
Confidence            344578899999866544455688999888764

>2yw8_A RUN and FYVE domain-containing protein 1; structure genomics, structural genomics, NPPSFA; 3.00A {Homo sapiens} PDB: 2yqm_A

Probab=89.13  E-value=0.31  Score=29.51  Aligned_cols=35  Identities=23%  Similarity=0.645  Sum_probs=26.6

Q ss_pred             ceeCCCCCCceEeCCCcCeeeccccceeeeecccccc
Q psy1749          17 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASL   53 (87)
Q Consensus        17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~   53 (87)
                      ...|..|+.....  .--.-.|+.||..||..|....
T Consensus        19 ~~~C~~C~~~Fs~--~~RrHHCR~CG~v~C~~Cs~~~   53 (82)
T 2yw8_A           19 ATHCRQCEKEFSI--SRRKHHCRNCGHIFCNTCSSNE   53 (82)
T ss_dssp             CCBCTTTCCBCBT--TBCCEECTTTCCEECSGGGCEE
T ss_pred             CCcccCcCCcccC--ccccccCCCCCCEEChHHhCCe
Confidence            4689999998653  2334578899999999998654

>2js4_A UPF0434 protein BB2007; NESG, northeast structural genomics consortium, beta, PSI-2, protein structure initiative; NMR {Bordetella bronchiseptica RB50}

Probab=88.85  E-value=0.39  Score=28.84  Aligned_cols=31  Identities=26%  Similarity=0.544  Sum_probs=25.0

Q ss_pred             CceeCCCCCCceEeCCCcCeeeccccceeee
Q psy1749          16 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFC   46 (87)
Q Consensus        16 ~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC   46 (87)
                      .+-.||.|+..++....=+.++|..|+..|=
T Consensus         7 ~iL~CP~ck~~L~~~~~~~~LiC~~cg~~YP   37 (70)
T 2js4_A            7 DILVCPVCKGRLEFQRAQAELVCNADRLAFP   37 (70)
T ss_dssp             CCCBCTTTCCBEEEETTTTEEEETTTTEEEE
T ss_pred             hheECCCCCCcCEEeCCCCEEEcCCCCceec
Confidence            3567999999999987767788987877663

>2hf1_A Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A biosynthes structural genomics, PSI-2, protein structure initiative; 1.90A {Chromobacterium violaceum} SCOP: b.171.1.1

Probab=88.73  E-value=0.35  Score=28.87  Aligned_cols=29  Identities=31%  Similarity=0.761  Sum_probs=23.8

Q ss_pred             ceeCCCCCCceEeCCCcCeeeccccceee
Q psy1749          17 IKCCPMCSVPIEKDEGCAQMLCKRCKHVF   45 (87)
Q Consensus        17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~~F   45 (87)
                      +-.||.|+..++....=+.++|..|+..|
T Consensus         8 iL~CP~ck~~L~~~~~~~~LiC~~cg~~Y   36 (68)
T 2hf1_A            8 ILVCPLCKGPLVFDKSKDELICKGDRLAF   36 (68)
T ss_dssp             ECBCTTTCCBCEEETTTTEEEETTTTEEE
T ss_pred             heECCCCCCcCeEeCCCCEEEcCCCCcEe
Confidence            45799999999988776778898787766

>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2}

Probab=88.69  E-value=0.35  Score=30.08  Aligned_cols=36  Identities=25%  Similarity=0.687  Sum_probs=29.2

Q ss_pred             eeCCCCCCceEeCCCcCeeecccccee-----eeecccccccC
Q psy1749          18 KCCPMCSVPIEKDEGCAQMLCKRCKHV-----FCWYCLASLDD   55 (87)
Q Consensus        18 k~CP~C~~~Iek~~GCnhm~C~~C~~~-----FC~~C~~~~~~   55 (87)
                      ..||.|+..|+.+++  +..|..|+..     ||-.|++++..
T Consensus         3 ~~CP~C~~~l~~~~~--~~~C~~C~~~~~~~afCPeCgq~Le~   43 (81)
T 2jrp_A            3 ITCPVCHHALERNGD--TAHCETCAKDFSLQALCPDCRQPLQV   43 (81)
T ss_dssp             CCCSSSCSCCEECSS--EEECTTTCCEEEEEEECSSSCSCCCE
T ss_pred             CCCCCCCCccccCCC--ceECccccccCCCcccCcchhhHHHH
Confidence            579999999999887  5568888543     78899988875

>2pk7_A Uncharacterized protein; NESG, PLR1, putative tetraacyldisaccharide-1-P 4-kinase, Q4K structural genomics, PSI-2; 2.20A {Pseudomonas fluorescens} SCOP: b.171.1.1

Probab=88.33  E-value=0.46  Score=28.46  Aligned_cols=29  Identities=21%  Similarity=0.604  Sum_probs=23.8

Q ss_pred             ceeCCCCCCceEeCCCcCeeeccccceee
Q psy1749          17 IKCCPMCSVPIEKDEGCAQMLCKRCKHVF   45 (87)
Q Consensus        17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~~F   45 (87)
                      +-.||.|+..++....=+.++|..|+..|
T Consensus         8 iL~CP~ck~~L~~~~~~~~LiC~~cg~~Y   36 (69)
T 2pk7_A            8 ILACPICKGPLKLSADKTELISKGAGLAY   36 (69)
T ss_dssp             TCCCTTTCCCCEECTTSSEEEETTTTEEE
T ss_pred             heeCCCCCCcCeEeCCCCEEEcCCCCcEe
Confidence            45799999999988776778898787766

>1joc_A EEA1, early endosomal autoantigen 1; FYVE domain, inositol 3-phosphate binding, membrane protein; HET: ITP; 2.20A {Homo sapiens} SCOP: g.50.1.1 h.1.21.1 PDB: 1hyi_A* 1hyj_A

Probab=87.77  E-value=0.45  Score=31.08  Aligned_cols=35  Identities=23%  Similarity=0.642  Sum_probs=26.8

Q ss_pred             ceeCCCCCCceEeCCCcCeeeccccceeeeecccccc
Q psy1749          17 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASL   53 (87)
Q Consensus        17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~   53 (87)
                      ...|+.|+.....  .--.-.|+.||..||..|....
T Consensus        69 ~~~C~~C~~~Fs~--~~RrHHCR~CG~vfC~~Cs~~~  103 (125)
T 1joc_A           69 VQNCMACGKGFSV--TVRRHHCRQCGNIFCAECSAKN  103 (125)
T ss_dssp             CCBCTTTCCBCCS--SSCCEECTTTCCEECGGGSCEE
T ss_pred             CCCCcCcCCcccc--ccccccCCCCCeEEChHHhCCc
Confidence            4789999997653  2344579999999999998654

>1z2q_A LM5-1; membrane protein, FYVE domain, zinc-finger; NMR {Leishmania major}

Probab=87.30  E-value=0.42  Score=29.01  Aligned_cols=35  Identities=20%  Similarity=0.517  Sum_probs=27.1

Q ss_pred             ceeCCCCCCceEeCCCcCeeeccccceeeeecccccc
Q psy1749          17 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASL   53 (87)
Q Consensus        17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~   53 (87)
                      ...|..|+......  --.-.|+.||..||..|....
T Consensus        21 ~~~C~~C~~~Fs~~--~RrHHCR~CG~v~C~~Cs~~~   55 (84)
T 1z2q_A           21 APACNGCGCVFTTT--VRRHHCRNCGYVLCGDCSRHR   55 (84)
T ss_dssp             CCBCTTTCCBCCTT--SCCEECTTTCCEECTGGGCCE
T ss_pred             CCCCcCcCCccccc--hhcccccCCCcEEChHHhCCe
Confidence            47899999986543  234579999999999998554

>2jne_A Hypothetical protein YFGJ; zinc fingers, two zinc, structural genomics, PSI-2, protein structure initiative; NMR {Escherichia coli} SCOP: g.41.18.1

Probab=87.26  E-value=0.46  Score=30.77  Aligned_cols=36  Identities=28%  Similarity=0.764  Sum_probs=29.8

Q ss_pred             eeCCCCCCceEeCCCcCeeecccccee-----eeecccccccC
Q psy1749          18 KCCPMCSVPIEKDEGCAQMLCKRCKHV-----FCWYCLASLDD   55 (87)
Q Consensus        18 k~CP~C~~~Iek~~GCnhm~C~~C~~~-----FC~~C~~~~~~   55 (87)
                      ..||.|+..++..+|  +..|..|+..     +|-.|++++..
T Consensus        33 ~~CP~Cq~eL~~~g~--~~hC~~C~~~f~~~a~CPdC~q~Lev   73 (101)
T 2jne_A           33 LHCPQCQHVLDQDNG--HARCRSCGEFIEMKALCPDCHQPLQV   73 (101)
T ss_dssp             CBCSSSCSBEEEETT--EEEETTTCCEEEEEEECTTTCSBCEE
T ss_pred             ccCccCCCcceecCC--EEECccccchhhccccCcchhhHHHH
Confidence            689999999999887  6679888765     57788888775

>2jny_A Uncharacterized BCR; structure, CGR1, NESG, structural genomics, PSI-2, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: b.171.1.1

Probab=86.14  E-value=0.62  Score=27.77  Aligned_cols=30  Identities=17%  Similarity=0.282  Sum_probs=24.2

Q ss_pred             CceeCCCCCCceEeCCCcCeeeccccceee
Q psy1749          16 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF   45 (87)
Q Consensus        16 ~~k~CP~C~~~Iek~~GCnhm~C~~C~~~F   45 (87)
                      .+-.||.|+.+++....=+.+.|..|+..|
T Consensus         9 eiL~CP~ck~~L~~~~~~g~LvC~~c~~~Y   38 (67)
T 2jny_A            9 EVLACPKDKGPLRYLESEQLLVNERLNLAY   38 (67)
T ss_dssp             CCCBCTTTCCBCEEETTTTEEEETTTTEEE
T ss_pred             HHhCCCCCCCcCeEeCCCCEEEcCCCCccc
Confidence            456799999999988776778888777666

>3t7l_A Zinc finger FYVE domain-containing protein 16; structural genomics consortium, SGC, lipid BIND protein, transport protein; 1.09A {Homo sapiens}

Probab=85.15  E-value=0.77  Score=28.27  Aligned_cols=36  Identities=25%  Similarity=0.522  Sum_probs=27.1

Q ss_pred             ceeCCCCCCceEeCCCcCeeeccccceeeeeccccccc
Q psy1749          17 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLD   54 (87)
Q Consensus        17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~   54 (87)
                      ...|..|+......  --.-.|+.||..||..|.....
T Consensus        20 ~~~C~~C~~~F~~~--~RrhhCr~CG~v~C~~Cs~~~~   55 (90)
T 3t7l_A           20 APNCMNCQVKFTFT--KRRHHCRACGKVFCGVCCNRKC   55 (90)
T ss_dssp             CCBCTTTCCBCCSS--SCCEECTTTCCEECGGGSCEEE
T ss_pred             CCcCcCCCCcccch--hhCccccCCCCEECCcccCCee
Confidence            46799999877532  2345699999999999986554

>1wfh_A Zinc finger (AN1-like) family protein; ZF-AN1 domain, zinc binding, structural genomics, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} SCOP: g.80.1.1

Probab=84.84  E-value=0.57  Score=27.96  Aligned_cols=35  Identities=17%  Similarity=0.499  Sum_probs=26.9

Q ss_pred             ccCCceeCCCCCCceEeCCCcCeeeccccceeeeeccccc
Q psy1749          13 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLAS   52 (87)
Q Consensus        13 ~~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~   52 (87)
                      .+....+|..|+..+...    -..|+ |+..||-.=.-+
T Consensus        11 ~k~~~~rC~~C~kkvgl~----~f~Cr-Cg~~FC~~HRy~   45 (64)
T 1wfh_A           11 PPQRPNRCTVCRKRVGLT----GFMCR-CGTTFCGSHRYP   45 (64)
T ss_dssp             CCSSCCCCTTTCCCCCTT----CEECS-SSCEECTTTCST
T ss_pred             CCCcCCcChhhCCccCcc----CEEee-cCCEeccccCCc
Confidence            355678999999988776    48896 999999765433

>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=84.27  E-value=0.86  Score=29.19  Aligned_cols=30  Identities=17%  Similarity=0.410  Sum_probs=24.3

Q ss_pred             CceeCCCCCCceEeCC----CcCeeeccccceee
Q psy1749          16 LIKCCPMCSVPIEKDE----GCAQMLCKRCKHVF   45 (87)
Q Consensus        16 ~~k~CP~C~~~Iek~~----GCnhm~C~~C~~~F   45 (87)
                      ..+.||.|+.++....    +.+.+.|+.|++.+
T Consensus         3 ~m~FCp~Cgn~L~~~~~~~~~~~~~~C~~C~y~~   36 (113)
T 3h0g_I            3 NFQYCIECNNMLYPREDKVDRVLRLACRNCDYSE   36 (113)
T ss_dssp             CCCCCSSSCCCCEECCCTTTCCCCEECSSSCCEE
T ss_pred             cceeCcCCCCEeeEcccCCCCeeEEECCCCCCeE
Confidence            3578999999986653    57789999999877

>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae}

Probab=84.25  E-value=0.48  Score=31.58  Aligned_cols=33  Identities=18%  Similarity=0.363  Sum_probs=24.7

Q ss_pred             ccCCceeCCCCCCceEeCC----CcCeeeccccceee
Q psy1749          13 DSELIKCCPMCSVPIEKDE----GCAQMLCKRCKHVF   45 (87)
Q Consensus        13 ~~~~~k~CP~C~~~Iek~~----GCnhm~C~~C~~~F   45 (87)
                      .....+.||.|+.++.-.+    +...+.|+.|++++
T Consensus        20 ~~~~~~FCPeCgNmL~pked~~~~~l~~~CrtCgY~~   56 (133)
T 3qt1_I           20 HMTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVE   56 (133)
T ss_dssp             --CCCCBCTTTCCBCBCCBCTTTCCBCCBCSSSCCBC
T ss_pred             cccCCeeCCCCCCEeeECccCCCceeEEECCCCCCcE
Confidence            3456899999999875442    57789999999865

>2kpi_A Uncharacterized protein SCO3027; zinc finger, PSI-2, NESG, all beta, structural genomics, protein structure initiative; NMR {Streptomyces coelicolor}

Probab=83.47  E-value=0.99  Score=25.83  Aligned_cols=28  Identities=32%  Similarity=0.972  Sum_probs=22.0

Q ss_pred             CceeCCCCCCceEeCCCcCeeecc--ccceee
Q psy1749          16 LIKCCPMCSVPIEKDEGCAQMLCK--RCKHVF   45 (87)
Q Consensus        16 ~~k~CP~C~~~Iek~~GCnhm~C~--~C~~~F   45 (87)
                      .+-.||.|+..++...  +.+.|.  .|+..|
T Consensus         9 ~iL~CP~c~~~L~~~~--~~L~C~~~~c~~~Y   38 (56)
T 2kpi_A            9 EILACPACHAPLEERD--AELICTGQDCGLAY   38 (56)
T ss_dssp             TSCCCSSSCSCEEEET--TEEEECSSSCCCEE
T ss_pred             hheeCCCCCCcceecC--CEEEcCCcCCCcEE
Confidence            4458999999998887  778887  776655

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

Probab=83.33  E-value=0.28  Score=27.24  Aligned_cols=34  Identities=26%  Similarity=0.735  Sum_probs=25.6

Q ss_pred             CceeCCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749          16 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD   55 (87)
Q Consensus        16 ~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~   55 (87)
                      ....||-|...+..     .++-. ||+.||..|...|-.
T Consensus        19 ~~~~C~IC~~~~~~-----p~~~~-CgH~fC~~Ci~~~~~   52 (63)
T 2ysj_A           19 EEVICPICLDILQK-----PVTID-CGHNFCLKCITQIGE   52 (63)
T ss_dssp             CCCBCTTTCSBCSS-----CEECT-TSSEECHHHHHHHHH
T ss_pred             cCCCCCcCCchhCC-----eEEeC-CCCcchHHHHHHHHH
Confidence            34579999887763     34434 999999999988865

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

Probab=83.18  E-value=0.36  Score=27.33  Aligned_cols=34  Identities=24%  Similarity=0.700  Sum_probs=25.9

Q ss_pred             CceeCCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749          16 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD   55 (87)
Q Consensus        16 ~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~   55 (87)
                      ....||-|...+.     +.++-. ||+.||..|...|-.
T Consensus        19 ~~~~C~IC~~~~~-----~~~~~~-CgH~fC~~Ci~~~~~   52 (73)
T 2ysl_A           19 EEVICPICLDILQ-----KPVTID-CGHNFCLKCITQIGE   52 (73)
T ss_dssp             CCCBCTTTCSBCS-----SEEECT-TCCEEEHHHHHHHCS
T ss_pred             cCCEeccCCcccC-----CeEEcC-CCChhhHHHHHHHHH
Confidence            3457999998766     234444 999999999988875

>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=82.81  E-value=0.54  Score=26.39  Aligned_cols=39  Identities=21%  Similarity=0.402  Sum_probs=27.2

Q ss_pred             cCCceeCCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749          14 SELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD   55 (87)
Q Consensus        14 ~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~   55 (87)
                      ......||-|...++...  . .....|++.||..|...|-.
T Consensus        11 ~~~~~~C~IC~~~~~~~~--~-~~~~~C~H~fc~~Ci~~~~~   49 (69)
T 2kiz_A           11 EDTEEKCTICLSILEEGE--D-VRRLPCMHLFHQVCVDQWLI   49 (69)
T ss_dssp             TTCCCSBTTTTBCCCSSS--C-EEECTTSCEEEHHHHHHHHH
T ss_pred             CCCCCCCeeCCccccCCC--c-EEEeCCCCHHHHHHHHHHHH
Confidence            345567999988775332  2 23334999999999988865

>2xzf_A Formamidopyrimidine-DNA glycosylase; hydrolase-DNA complex; HET: VET; 1.80A {Lactococcus lactis subsp} PDB: 1pm5_A* 1xc8_A* 1pji_A* 2xzu_A* 3c58_A* 1tdz_A* 1nnj_A 1kfv_A 1pjj_A*

Probab=82.79  E-value=0.54  Score=34.24  Aligned_cols=27  Identities=26%  Similarity=0.610  Sum_probs=22.3

Q ss_pred             ceeCCCCCCceEeC--CCcCeeeccccce
Q psy1749          17 IKCCPMCSVPIEKD--EGCAQMLCKRCKH   43 (87)
Q Consensus        17 ~k~CP~C~~~Iek~--~GCnhm~C~~C~~   43 (87)
                      .++||.|+.+|++.  +|-+-..|+.|+.
T Consensus       242 G~pC~~CG~~I~~~~~~gR~t~~CP~CQ~  270 (271)
T 2xzf_A          242 GEKCSRCGAEIQKIKVAGRGTHFCPVCQQ  270 (271)
T ss_dssp             TSBCTTTCCBCEEEEETTEEEEECTTTSC
T ss_pred             CCCCCCCCCEeeEEEECCCceEECCCCCC
Confidence            37899999999997  6777778887864

>1wii_A Hypothetical UPF0222 protein MGC4549; domain of unknown function, zinc finger, metal-binding protein, structural genomics; NMR {Mus musculus} SCOP: g.41.3.4

Probab=82.73  E-value=0.81  Score=28.49  Aligned_cols=35  Identities=17%  Similarity=0.420  Sum_probs=25.7

Q ss_pred             CceeCCCCCCc------eEeCCCcCeeeccccceeeeeccc
Q psy1749          16 LIKCCPMCSVP------IEKDEGCAQMLCKRCKHVFCWYCL   50 (87)
Q Consensus        16 ~~k~CP~C~~~------Iek~~GCnhm~C~~C~~~FC~~C~   50 (87)
                      ..-.||.|+..      |.+..|-.++.|..|+..|=..-.
T Consensus        22 t~F~CPfCnh~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~   62 (85)
T 1wii_A           22 TQFTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPIT   62 (85)
T ss_dssp             SCCCCTTTCCSSCEEEEEETTTTEEEEEESSSCCEEEEECC
T ss_pred             CeEcCCCCCCCCeEEEEEEccCCEEEEEcccCCCeEEeccC
Confidence            34569999876      444678888999989888855433

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

Probab=82.42  E-value=0.49  Score=26.52  Aligned_cols=42  Identities=24%  Similarity=0.509  Sum_probs=28.8

Q ss_pred             cCCceeCCCCCCceEeC-CCcCeeeccccceeeeecccccccC
Q psy1749          14 SELIKCCPMCSVPIEKD-EGCAQMLCKRCKHVFCWYCLASLDD   55 (87)
Q Consensus        14 ~~~~k~CP~C~~~Iek~-~GCnhm~C~~C~~~FC~~C~~~~~~   55 (87)
                      ......||-|...+... .+=..+.-..||+.||..|...|-.
T Consensus         7 ~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~   49 (71)
T 3ng2_A            7 PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLK   49 (71)
T ss_dssp             CTTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHH
T ss_pred             CCCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHH
Confidence            34557799999887653 1112333445999999999988865

>3u6p_A Formamidopyrimidine-DNA glycosylase; DNA glycosylase, DNA repair, sequence context; HET: DNA 08Q; 1.60A {Geobacillus stearothermophilus} PDB: 3u6d_A* 3u6c_A* 3u6l_A* 3u6m_A* 3u6o_A* 3u6e_A* 3u6q_A* 3u6s_A* 3gp1_A* 3sbj_A* 2f5q_A* 2f5s_A* 3gq4_A* 3gpy_A* 2f5n_A 2f5o_A 2f5p_A 3sau_A* 3sar_A* 3sav_A* ...

Probab=82.42  E-value=0.56  Score=34.26  Aligned_cols=26  Identities=38%  Similarity=0.832  Sum_probs=21.6

Q ss_pred             ceeCCCCCCceEeC--CCcCeeeccccc
Q psy1749          17 IKCCPMCSVPIEKD--EGCAQMLCKRCK   42 (87)
Q Consensus        17 ~k~CP~C~~~Iek~--~GCnhm~C~~C~   42 (87)
                      .++||.|+++|++.  +|-+-..|+.|+
T Consensus       245 g~pC~~CG~~I~~~~~~gR~t~~CP~CQ  272 (273)
T 3u6p_A          245 GNPCKRCGTPIEKTVVAGRGTHYCPRCQ  272 (273)
T ss_dssp             TSBCTTTCCBCEEEEETTEEEEECTTTC
T ss_pred             cCCCCCCCCeEEEEEECCCCeEECCCCC
Confidence            37999999999985  677777888776

>1twf_I B12.6, DNA-directed RNA polymerase II 14.2 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.3.1 g.41.3.1 PDB: 1i3q_I 1i6h_I 1k83_I* 1nik_I 1nt9_I 1pqv_I 1r5u_I 1r9s_I* 1r9t_I* 1sfo_I* 1twa_I* 1twc_I* 1i50_I* 1twg_I* 1twh_I* 1wcm_I 1y1v_I 1y1w_I 1y1y_I 1y77_I* ...

Probab=82.40  E-value=0.86  Score=29.57  Aligned_cols=31  Identities=16%  Similarity=0.337  Sum_probs=24.9

Q ss_pred             CceeCCCCCCceEeC----CCcCeeeccccceeee
Q psy1749          16 LIKCCPMCSVPIEKD----EGCAQMLCKRCKHVFC   46 (87)
Q Consensus        16 ~~k~CP~C~~~Iek~----~GCnhm~C~~C~~~FC   46 (87)
                      ..+.||.|+.++.-.    .+-+.+.|+.|++.+=
T Consensus         3 ~~~FCp~CgnlL~~~~~~~~~~~~~~C~~C~y~~~   37 (122)
T 1twf_I            3 TFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEE   37 (122)
T ss_dssp             CCCBCSSSCCBCEEEEETTTTEEEEECSSSSCEEE
T ss_pred             CCCcccccCccCcccccCcCCCCEEECCcCCCeee
Confidence            458899999988754    5678899999998764

>1k82_A Formamidopyrimidine-DNA glycosylase; protein-DNA complex, DNA repair, beta sandwich, zinc finger, helix two-turns helix, hydrolase/DNA complex; HET: PED; 2.10A {Escherichia coli} SCOP: a.156.1.2 b.113.1.1 g.39.1.8

Probab=82.31  E-value=0.57  Score=34.08  Aligned_cols=26  Identities=27%  Similarity=0.724  Sum_probs=21.6

Q ss_pred             ceeCCCCCCceEeC--CCcCeeeccccc
Q psy1749          17 IKCCPMCSVPIEKD--EGCAQMLCKRCK   42 (87)
Q Consensus        17 ~k~CP~C~~~Iek~--~GCnhm~C~~C~   42 (87)
                      .++||.|+.+|++.  +|-+-..|+.|+
T Consensus       240 g~pC~~CG~~I~~~~~~gR~t~~CP~CQ  267 (268)
T 1k82_A          240 GEPCRVCGTPIVATKHAQRATFYCRQCQ  267 (268)
T ss_dssp             TSBCTTTCCBCEEEEETTEEEEECTTTC
T ss_pred             CCCCCCCCCEeeEEEECCCceEECCCCC
Confidence            37899999999997  677777788776

>1ee8_A MUTM (FPG) protein; beta sandwich, zinc finger, helix two-turns helix, riken STR genomics/proteomics initiative, RSGI, structural genomics; 1.90A {Thermus thermophilus} SCOP: a.156.1.2 b.113.1.1 g.39.1.8

Probab=82.31  E-value=0.61  Score=33.97  Aligned_cols=27  Identities=30%  Similarity=0.780  Sum_probs=22.0

Q ss_pred             ceeCCCCCCceEeC--CCcCeeeccccce
Q psy1749          17 IKCCPMCSVPIEKD--EGCAQMLCKRCKH   43 (87)
Q Consensus        17 ~k~CP~C~~~Iek~--~GCnhm~C~~C~~   43 (87)
                      .++||.|+.+|++.  +|-+-..|+.|+.
T Consensus       235 g~pC~~CG~~I~~~~~~gR~t~~CP~CQ~  263 (266)
T 1ee8_A          235 GLPCPACGRPVERRVVAGRGTHFCPTCQG  263 (266)
T ss_dssp             TSBCTTTCCBCEEEESSSCEEEECTTTTT
T ss_pred             CCCCCCCCCEeeEEEECCCceEECCCCCC
Confidence            37899999999996  6777777887764

>1k3x_A Endonuclease VIII; hydrolase/DNA, hydrolase-DNA complex; HET: BRU PED; 1.25A {Escherichia coli} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 PDB: 1k3w_A* 1q39_A 2ea0_A* 2oq4_A* 1q3c_A 2opf_A* 1q3b_A*

Probab=82.25  E-value=0.58  Score=33.91  Aligned_cols=26  Identities=27%  Similarity=0.515  Sum_probs=21.7

Q ss_pred             ceeCCCCCCceEeC--CCcCeeeccccc
Q psy1749          17 IKCCPMCSVPIEKD--EGCAQMLCKRCK   42 (87)
Q Consensus        17 ~k~CP~C~~~Iek~--~GCnhm~C~~C~   42 (87)
                      .++||.|+.+|++.  +|-+-..|+.|+
T Consensus       234 g~pC~~CG~~I~~~~~~gR~t~~CP~CQ  261 (262)
T 1k3x_A          234 GEPCERCGSIIEKTTLSSRPFYWCPGCQ  261 (262)
T ss_dssp             TSBCTTTCCBCEEEEETTEEEEECTTTC
T ss_pred             cCCCCCCCCEeEEEEECCCCeEECCCCC
Confidence            36899999999986  677778888776

>1wfl_A Zinc finger protein 216; ZF-AN1 domain, zinc binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.80.1.1

Probab=82.20  E-value=0.58  Score=28.68  Aligned_cols=31  Identities=23%  Similarity=0.525  Sum_probs=24.6

Q ss_pred             CceeCCCCCCceEeCCCcCeeeccccceeeeecccc
Q psy1749          16 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLA   51 (87)
Q Consensus        16 ~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~   51 (87)
                      ...+|..|+..|++.+    ..|+ |+..||-.=..
T Consensus        24 ~~nRC~~CrKkvgL~g----f~Cr-Cg~~FCs~HRy   54 (74)
T 1wfl_A           24 KKNRCFMCRKKVGLTG----FDCR-CGNLFCGLHRY   54 (74)
T ss_dssp             CTTBCSSSCCBCGGGC----EECT-TSCEECSSSCS
T ss_pred             cCCcChhhCCcccccC----eecC-CCCEechhcCC
Confidence            4458999999988763    8999 99999975443

>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=82.12  E-value=0.57  Score=24.97  Aligned_cols=38  Identities=18%  Similarity=0.397  Sum_probs=26.7

Q ss_pred             CceeCCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749          16 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD   55 (87)
Q Consensus        16 ~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~   55 (87)
                      ....||-|...+...+  ..+.-..|++.||..|...|-.
T Consensus         4 ~~~~C~IC~~~~~~~~--~~~~~~~CgH~fc~~Ci~~~~~   41 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSR--VVAHVLPCGHLLHRTCYEEMLK   41 (55)
T ss_dssp             CCCSCTTTCCCCCTTT--SCEEECTTSCEEETTHHHHHHH
T ss_pred             CCCcCcccChhhcCCC--cCeEecCCCCcccHHHHHHHHH
Confidence            3467999988775322  2344445999999999988865

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

Probab=81.89  E-value=0.36  Score=28.18  Aligned_cols=38  Identities=26%  Similarity=0.594  Sum_probs=26.3

Q ss_pred             CceeCCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749          16 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD   55 (87)
Q Consensus        16 ~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~   55 (87)
                      ....||-|...+...... .+.-. ||+.||..|...|-.
T Consensus        14 ~~~~C~IC~~~~~~~~~~-~~~~~-CgH~fC~~Ci~~~~~   51 (88)
T 2ct2_A           14 EVLECPICMESFTEEQLR-PKLLH-CGHTICRQCLEKLLA   51 (88)
T ss_dssp             SCCBCTTTCCBCCTTSSC-EEECS-SSCEEEHHHHHHHHH
T ss_pred             CCCCCccCCccccccCCC-eEECC-CCChhhHHHHHHHHH
Confidence            345699999887654321 23334 999999999988864

>2apo_B Ribosome biogenesis protein NOP10; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: g.41.16.1 PDB: 2aqc_A

Probab=81.77  E-value=1.1  Score=26.30  Aligned_cols=15  Identities=27%  Similarity=0.530  Sum_probs=11.9

Q ss_pred             cCCceeCCCCCCceE
Q psy1749          14 SELIKCCPMCSVPIE   28 (87)
Q Consensus        14 ~~~~k~CP~C~~~Ie   28 (87)
                      +...+.||+|++..-
T Consensus         3 ks~mr~C~~CgvYTL   17 (60)
T 2apo_B            3 EMRMKKCPKCGLYTL   17 (60)
T ss_dssp             CCCCEECTTTCCEES
T ss_pred             hhhceeCCCCCCEec
Confidence            456799999988765

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

Probab=81.44  E-value=0.43  Score=25.55  Aligned_cols=37  Identities=24%  Similarity=0.408  Sum_probs=26.8

Q ss_pred             ceeCCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749          17 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD   55 (87)
Q Consensus        17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~   55 (87)
                      ...||-|...++..+.  .+.-..|++.||..|...|-.
T Consensus         5 ~~~C~IC~~~~~~~~~--~~~~~~C~H~f~~~Ci~~w~~   41 (55)
T 1iym_A            5 GVECAVCLAELEDGEE--ARFLPRCGHGFHAECVDMWLG   41 (55)
T ss_dssp             SCCCTTTCCCCCTTSC--CEECSSSCCEECTTHHHHTTT
T ss_pred             CCcCccCCccccCCCc--eEECCCCCCcccHHHHHHHHH
Confidence            4579999888765443  223335999999999998875

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

Probab=80.80  E-value=0.34  Score=27.68  Aligned_cols=34  Identities=21%  Similarity=0.459  Sum_probs=24.2

Q ss_pred             ceeCCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749          17 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD   55 (87)
Q Consensus        17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~   55 (87)
                      ...||-|...+..     .++-..||+.||..|...|-.
T Consensus        15 ~~~C~IC~~~~~~-----p~~~~~CgH~fC~~Ci~~~~~   48 (72)
T 2djb_A           15 YILCSICKGYLID-----ATTITECLHTFCKSCIVRHFY   48 (72)
T ss_dssp             GGSCTTTSSCCSS-----CEECSSSCCEECHHHHHHHHH
T ss_pred             CCCCCCCChHHHC-----cCEECCCCCHHHHHHHHHHHH
Confidence            4579999887754     344435888888888877754

>1wg2_A Zinc finger (AN1-like) family protein; riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.80.1.1

Probab=80.69  E-value=0.75  Score=27.44  Aligned_cols=33  Identities=21%  Similarity=0.391  Sum_probs=24.9

Q ss_pred             CCceeCCCCCCceEeCCCcCeeeccccceeeeeccccc
Q psy1749          15 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLAS   52 (87)
Q Consensus        15 ~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~   52 (87)
                      ....+|..|+..+...    -..|+ |+..||-.=.-+
T Consensus        13 ~~~~rC~~C~kkvgl~----~f~Cr-Cg~~FC~~HR~~   45 (64)
T 1wg2_A           13 RPNNRCFSCNKKVGVM----GFKCK-CGSTFCGSHRYP   45 (64)
T ss_dssp             CCSCSCTTTCCCCTTS----CEECT-TSCEECSSSCSS
T ss_pred             CcCCcChhhCCccccc----CeEee-cCCEecccCCCc
Confidence            4557899999987765    48895 999999764433

>1twf_L ABC10-alpha, DNA-directed RNA polymerases I, II, and III 7.7 K polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.9.2 PDB: 1i3q_L 1i6h_L 1k83_L* 1nik_L 1nt9_L 1pqv_L 1r5u_L 1r9s_L* 1r9t_L* 1sfo_L* 1twa_L* 1twc_L* 1i50_L* 1twg_L* 1twh_L* 1wcm_L 1y1v_L 1y1w_L 1y1y_L 1y77_L* ...

Probab=80.51  E-value=0.63  Score=27.97  Aligned_cols=28  Identities=29%  Similarity=0.584  Sum_probs=19.9

Q ss_pred             CceeCCCCCCceEeCCCcCeeecccccee
Q psy1749          16 LIKCCPMCSVPIEKDEGCAQMLCKRCKHV   44 (87)
Q Consensus        16 ~~k~CP~C~~~Iek~~GCnhm~C~~C~~~   44 (87)
                      -.-.|+.|+..++..++ +-+.|+.||+.
T Consensus        27 v~Y~C~~CG~~~e~~~~-d~irCp~CG~R   54 (70)
T 1twf_L           27 LKYICAECSSKLSLSRT-DAVRCKDCGHR   54 (70)
T ss_dssp             CCEECSSSCCEECCCTT-STTCCSSSCCC
T ss_pred             EEEECCCCCCcceeCCC-CCccCCCCCce
Confidence            33469999999887744 55678777764

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

Probab=80.09  E-value=0.62  Score=26.00  Aligned_cols=35  Identities=23%  Similarity=0.675  Sum_probs=23.9

Q ss_pred             CceeCCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749          16 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD   55 (87)
Q Consensus        16 ~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~   55 (87)
                      ....||-|...+..     ...-..||+.||..|...|-.
T Consensus         4 ~~~~C~IC~~~~~~-----~~~~~~C~H~fc~~Ci~~~~~   38 (68)
T 1chc_A            4 VAERCPICLEDPSN-----YSMALPCLHAFCYVCITRWIR   38 (68)
T ss_dssp             CCCCCSSCCSCCCS-----CEEETTTTEEESTTHHHHHHH
T ss_pred             CCCCCeeCCccccC-----CcEecCCCCeeHHHHHHHHHh
Confidence            34679999888652     123334888888888877754

---

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	87
d2ct7a1	73	g.44.1.4 (A:8-80) Ring finger protein 31 {Human (H	6e-08
d1wd2a_	60	g.44.1.1 (A:) Ariadne-1 protein homolog {Human (Ho	2e-07

>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]} Length = 73

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: IBR domain
domain: Ring finger protein 31
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.5 bits (102), Expect = 6e-08
 Identities = 8/40 (20%), Positives = 13/40 (32%)

Query: 17 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDD 56
             C  CS     +    +  C +C   FC  C    ++ 
Sbjct: 18 FLWCAQCSFGFIYEREQLEATCPQCHQTFCVRCKRQWEEQ 57

>d1wd2a_ g.44.1.1 (A:) Ariadne-1 protein homolog {Human (Homo sapiens) [TaxId: 9606]} Length = 60

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Ariadne-1 protein homolog
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.4 bits (97), Expect = 2e-07
 Identities = 20/40 (50%), Positives = 23/40 (57%), Gaps = 2/40 (5%)

Query: 18 KCCPMCSVPIEKDEGCAQMLCK--RCKHVFCWYCLASLDD 55
          K CP C V IEKD GC  M+C+   CK  FCW CL   + 
Sbjct: 7  KECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEP 46

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	87
d1wd2a_	60	Ariadne-1 protein homolog {Human (Homo sapiens) [T	99.75
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	99.31
d1joca1	64	Eea1 {Human (Homo sapiens) [TaxId: 9606]}	93.19
d2f9yb1	263	Acetyl-coenzyme A carboxylase carboxyl transferase	92.35
d2akla2	38	Hypothetical protein PA0128, N-terminal domain {Ps	92.13
d1zbdb_	124	Effector domain of rabphilin-3a {Rat (Rattus norve	91.88
d1k3xa3	40	Endonuclease VIII {Escherichia coli [TaxId: 562]}	91.25
d1wfha_	64	Zinc finger A20 and AN1 domains containing protein	90.96
d2jnea1	71	Hypothetical protein YfgJ {Escherichia coli [TaxId	89.39
d1tdza3	47	DNA repair protein MutM (Fpg) {Lactococcus lactis	89.21
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	88.56
d1r2za3	46	DNA repair protein MutM (Fpg) {Bacillus stearother	88.5
d1k82a3	44	DNA repair protein MutM (Fpg) {Escherichia coli [T	87.89
d1wffa_	85	ANUBL1 (AN1, ubiquitin-like, homolog) {Mouse (Mus	86.96
d1ee8a3	56	DNA repair protein MutM (Fpg) {Thermus thermophilu	85.84
d2jnya1	59	Uncharacterized protein Cgl1405/cg1592 {Corynebact	85.64
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	85.11
d2hf1a1	59	Hypothetical protein CV3345 {Chromobacterium viola	85.1
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	84.85
d1wfpa_	74	Zinc finger A20 and AN1 domains containing protein	84.78
d1wfla_	74	Zinc finger A20 domain containing protein 2 {Mouse	84.51
d2pk7a1	59	Uncharacterized protein PFL1779 {Pseudomonas fluor	83.85
d2k4xa1	55	Ribosomal protein S27ae {Thermoplasma acidophilum	83.19
d1dvpa2	72	Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7	82.37
d1wfka_	88	Zinc finger FYVE domain containing protein 19 {Mou	81.44
d1vfya_	67	vps27p protein {Baker's yeast (Saccharomyces cerev	80.7

>d1wd2a_ g.44.1.1 (A:) Ariadne-1 protein homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Ariadne-1 protein homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=1.1e-19  Score=107.90  Aligned_cols=45  Identities=44%  Similarity=1.080  Sum_probs=41.5

Q ss_pred             cccCCceeCCCCCCceEeCCCcCeeecc--ccceeeeecccccccCC
Q psy1749          12 FDSELIKCCPMCSVPIEKDEGCAQMLCK--RCKHVFCWYCLASLDDD   56 (87)
Q Consensus        12 ~~~~~~k~CP~C~~~Iek~~GCnhm~C~--~C~~~FC~~C~~~~~~~   56 (87)
                      |+.+++|+||+|+++|||++|||||+|+  .|+.+|||+|+++|+.+
T Consensus         1 wi~~ntK~CP~C~~~ieK~~GCnhM~C~~~~C~~~fCw~C~~~~~~~   47 (60)
T d1wd2a_           1 WIAANTKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPH   47 (60)
T ss_dssp             CCCCCCCCCTTTCCCCSSCCSCCSSSCCSSGGGSCCSSSSCSCSGGG
T ss_pred             CchhcCcCCCCCCCeEEECCCCCCeEeCCCCCCCeEECCCCCccccC
Confidence            5678899999999999999999999996  59999999999999873

>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: IBR domain
domain: Ring finger protein 31
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.31  E-value=1.1e-12  Score=79.08  Aligned_cols=45  Identities=18%  Similarity=0.496  Sum_probs=41.5

Q ss_pred             ccccCCceeCCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749          11 TFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD   55 (87)
Q Consensus        11 ~~~~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~   55 (87)
                      +....+++.||+|+.+|++++||++|+|..|+..|||.|+.+|..
T Consensus        12 l~~~~~~k~CP~C~~~~~~~~~~~~~~C~~C~~~fC~~C~~~w~~   56 (73)
T d2ct7a1          12 LMRDPKFLWCAQCSFGFIYEREQLEATCPQCHQTFCVRCKRQWEE   56 (73)
T ss_dssp             CCSCCCEECCSSSCCCEECCCSCSCEECTTTCCEECSSSCSBCCT
T ss_pred             HHHCCCCCCCCCCCCEeEECCCCCEEEcCCCCCeECcccCcchhc
Confidence            355678999999999999999999999988999999999999976

>d1joca1 g.50.1.1 (A:1348-1411) Eea1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Eea1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.19  E-value=0.043  Score=30.71  Aligned_cols=42  Identities=21%  Similarity=0.581  Sum_probs=31.3

Q ss_pred             ccccccCcccccCCceeCCCCCCceEeCCCcCeeeccccceeeeecccccc
Q psy1749           3 PWFQMGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASL   53 (87)
Q Consensus         3 ~w~~~~~~~~~~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~   53 (87)
                      +|..|..+       ..|+.|+.......  ..-.|+.||..||..|....
T Consensus         1 rW~~d~~~-------~~C~~C~~~F~~~~--rrHHCR~CG~v~C~~Cs~~~   42 (64)
T d1joca1           1 KWAEDNEV-------QNCMACGKGFSVTV--RRHHCRQCGNIFCAECSAKN   42 (64)
T ss_dssp             CCCCGGGC-------CBCTTTCCBCCSSS--CCEECTTTCCEECGGGSCEE
T ss_pred             CCCCcccC-------CcCcCcCCcccCCc--cccchhhhCCeecccccCCc
Confidence            47666664       78999998875432  34579999999999998544

>d2f9yb1 c.14.1.4 (B:23-285) Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta, AccD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: ClpP/crotonase
superfamily: ClpP/crotonase
family: Biotin dependent carboxylase carboxyltransferase domain
domain: Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta, AccD
species: Escherichia coli [TaxId: 562]

Probab=92.35  E-value=0.013  Score=40.88  Aligned_cols=29  Identities=21%  Similarity=0.476  Sum_probs=25.2

Q ss_pred             ceeCCCCCCceEeCCCc-Ceeeccccceee
Q psy1749          17 IKCCPMCSVPIEKDEGC-AQMLCKRCKHVF   45 (87)
Q Consensus        17 ~k~CP~C~~~Iek~~GC-nhm~C~~C~~~F   45 (87)
                      |+.||+|+.+|.+.+== |...|.+|+++|
T Consensus         2 W~~C~~C~~~~~~~~l~~~~~vC~~C~~h~   31 (263)
T d2f9yb1           2 WTKCDSCGQVLYRAELERNLEVCPKCDHHM   31 (263)
T ss_dssp             EECCTTTCCCEETTHHHHTTTBCTTTCCBC
T ss_pred             cCcCCCCcceeeHHHHHHhCCCCcCCCCCC
Confidence            88999999999998654 566898999998

>d2akla2 g.41.3.5 (A:3-40) Hypothetical protein PA0128, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: PhnA zinc-binding domain
domain: Hypothetical protein PA0128, N-terminal domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=92.13  E-value=0.045  Score=28.50  Aligned_cols=27  Identities=26%  Similarity=0.839  Sum_probs=21.3

Q ss_pred             eeCCCCCCceEeCCCcCeeeccccceee
Q psy1749          18 KCCPMCSVPIEKDEGCAQMLCKRCKHVF   45 (87)
Q Consensus        18 k~CP~C~~~Iek~~GCnhm~C~~C~~~F   45 (87)
                      -.||+|+....-.+|= .+.|..|+++|
T Consensus         4 P~CP~C~seytYedg~-l~vCPeC~hEW   30 (38)
T d2akla2           4 PPCPQCNSEYTYEDGA-LLVCPECAHEW   30 (38)
T ss_dssp             CCCTTTCCCCCEECSS-SEEETTTTEEE
T ss_pred             CcCCCCCCcceEcCCC-EEECCcccCcC
Confidence            4799999988888773 46788888876

>d1zbdb_ g.50.1.1 (B:) Effector domain of rabphilin-3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Effector domain of rabphilin-3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=91.88  E-value=0.047  Score=33.96  Aligned_cols=38  Identities=21%  Similarity=0.553  Sum_probs=29.6

Q ss_pred             cCCceeCCCCCCceEeCCCcCeeeccccceeeeeccccc
Q psy1749          14 SELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLAS   52 (87)
Q Consensus        14 ~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~   52 (87)
                      ..+.+.|+.|+..+..... ....|..|+..||-.|+..
T Consensus        45 ~~~~~~C~~C~~~f~~~~~-~~~~C~~C~~~~C~~C~~~   82 (124)
T d1zbdb_          45 GDGVNRCILCGEQLGMLGS-ASVVCEDCKKNVCTKCGVE   82 (124)
T ss_dssp             SCSSSBCSSSCCBCSTTSC-CEEECTTTCCEEETTSEEE
T ss_pred             ccCCCcCcccCCcccCCCC-CCCcCccCCcccccCCCCC
Confidence            3456789999998775544 3458999999999999854

>d1k3xa3 g.39.1.8 (A:223-262) Endonuclease VIII {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins
domain: Endonuclease VIII
species: Escherichia coli [TaxId: 562]

Probab=91.25  E-value=0.05  Score=28.26  Aligned_cols=26  Identities=27%  Similarity=0.515  Sum_probs=20.9

Q ss_pred             ceeCCCCCCceEeC--CCcCeeeccccc
Q psy1749          17 IKCCPMCSVPIEKD--EGCAQMLCKRCK   42 (87)
Q Consensus        17 ~k~CP~C~~~Iek~--~GCnhm~C~~C~   42 (87)
                      .++||.|+.+|.+.  +|-.-..|+.|+
T Consensus        12 g~pC~~C~~~I~~~~~~gR~t~~Cp~CQ   39 (40)
T d1k3xa3          12 GEPCERCGSIIEKTTLSSRPFYWCPGCQ   39 (40)
T ss_dssp             TSBCTTTCCBCEEEEETTEEEEECTTTC
T ss_pred             CCccCcCCCEEEEEEECCCCCEEChhhC
Confidence            47899999999997  666667777765

>d1wfha_ g.80.1.1 (A:) Zinc finger A20 and AN1 domains containing protein At2g36320 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: AN1-like Zinc finger
superfamily: AN1-like Zinc finger
family: AN1-like Zinc finger
domain: Zinc finger A20 and AN1 domains containing protein At2g36320
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=90.96  E-value=0.13  Score=29.44  Aligned_cols=40  Identities=15%  Similarity=0.372  Sum_probs=30.6

Q ss_pred             ccccCCceeCCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749          11 TFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD   55 (87)
Q Consensus        11 ~~~~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~   55 (87)
                      ........+|..|+..|...+    ++|+ |+..||-.-..+..-
T Consensus         9 ~~~~~k~~RC~~C~KKl~l~~----~~Cr-Cg~~FC~~HR~pe~H   48 (64)
T d1wfha_           9 PSPPQRPNRCTVCRKRVGLTG----FMCR-CGTTFCGSHRYPEVH   48 (64)
T ss_dssp             CCCCSSCCCCTTTCCCCCTTC----EECS-SSCEECTTTCSTTTT
T ss_pred             CCCCCCCCcChhhCCCcccee----eecc-CCCEehhhcCCCcCc
Confidence            344566779999999888753    7999 999999877655544

>d2jnea1 g.41.18.1 (A:1-71) Hypothetical protein YfgJ {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: YfgJ-like
family: YfgJ-like
domain: Hypothetical protein YfgJ
species: Escherichia coli [TaxId: 562]

Probab=89.39  E-value=0.14  Score=29.85  Aligned_cols=36  Identities=28%  Similarity=0.764  Sum_probs=29.1

Q ss_pred             eeCCCCCCceEeCCCcCeeecccccee-----eeecccccccC
Q psy1749          18 KCCPMCSVPIEKDEGCAQMLCKRCKHV-----FCWYCLASLDD   55 (87)
Q Consensus        18 k~CP~C~~~Iek~~GCnhm~C~~C~~~-----FC~~C~~~~~~   55 (87)
                      -.||.|+..++..+|  +..|..|...     ||-.|..++..
T Consensus         3 ~~CP~C~~eL~~~~~--~~~C~~C~~~~~~~a~CPdC~~~Le~   43 (71)
T d2jnea1           3 LHCPQCQHVLDQDNG--HARCRSCGEFIEMKALCPDCHQPLQV   43 (71)
T ss_dssp             CBCSSSCSBEEEETT--EEEETTTCCEEEEEEECTTTCSBCEE
T ss_pred             CcCCCccCcccccCC--CEehhhhhhhheeEEeCCccccHHHH
Confidence            469999999999887  8888888765     57778877765

>d1tdza3 g.39.1.8 (A:225-271) DNA repair protein MutM (Fpg) {Lactococcus lactis [TaxId: 1358]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins
domain: DNA repair protein MutM (Fpg)
species: Lactococcus lactis [TaxId: 1358]

Probab=89.21  E-value=0.092  Score=27.95  Aligned_cols=27  Identities=26%  Similarity=0.610  Sum_probs=21.4

Q ss_pred             ceeCCCCCCceEeC--CCcCeeeccccce
Q psy1749          17 IKCCPMCSVPIEKD--EGCAQMLCKRCKH   43 (87)
Q Consensus        17 ~k~CP~C~~~Iek~--~GCnhm~C~~C~~   43 (87)
                      -++||.|+.+|++.  +|-.-..|+.|..
T Consensus        18 g~~C~~C~~~I~~~~~~gR~t~~Cp~CQk   46 (47)
T d1tdza3          18 GEKCSRCGAEIQKIKVAGRGTHFCPVCQQ   46 (47)
T ss_dssp             TSBCTTTCCBCEEEEETTEEEEECTTTSC
T ss_pred             CCCcCCCCcEEEEEEECCcccEECccccC
Confidence            47899999999997  6777777777753

>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=88.56  E-value=0.07  Score=29.66  Aligned_cols=36  Identities=22%  Similarity=0.656  Sum_probs=27.4

Q ss_pred             CCceeCCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749          15 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD   55 (87)
Q Consensus        15 ~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~   55 (87)
                      +....||=|...++.     ......||+.||..|...|-.
T Consensus         3 ~~~d~C~IC~~~~~~-----~~~~~~C~H~Fc~~Ci~~w~~   38 (68)
T d1chca_           3 TVAERCPICLEDPSN-----YSMALPCLHAFCYVCITRWIR   38 (68)
T ss_dssp             CCCCCCSSCCSCCCS-----CEEETTTTEEESTTHHHHHHH
T ss_pred             CCCCCCccCCcCccC-----CcEEeCCCCcCcHHHHHHHHH
Confidence            344679999887742     345667999999999988865

>d1r2za3 g.39.1.8 (A:229-274) DNA repair protein MutM (Fpg) {Bacillus stearothermophilus [TaxId: 1422]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins
domain: DNA repair protein MutM (Fpg)
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=88.50  E-value=0.11  Score=27.46  Aligned_cols=27  Identities=37%  Similarity=0.781  Sum_probs=20.7

Q ss_pred             CceeCCCCCCceEeC--CCcCeeeccccc
Q psy1749          16 LIKCCPMCSVPIEKD--EGCAQMLCKRCK   42 (87)
Q Consensus        16 ~~k~CP~C~~~Iek~--~GCnhm~C~~C~   42 (87)
                      .-++||+|+.+|.+.  +|-.-..|+.|.
T Consensus        17 ~g~~C~~C~~~I~~~~~~gR~t~~Cp~CQ   45 (46)
T d1r2za3          17 QGNPCKRCGTPIEKTVVAGRGTHYCPRCQ   45 (46)
T ss_dssp             TTSBCTTTCCBCEEEEETTEEEEECTTTC
T ss_pred             CCCccCCCCCeEEEEEECCCcCEEChhhC
Confidence            347899999999996  666666677664

>d1k82a3 g.39.1.8 (A:225-268) DNA repair protein MutM (Fpg) {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins
domain: DNA repair protein MutM (Fpg)
species: Escherichia coli [TaxId: 562]

Probab=87.89  E-value=0.13  Score=27.01  Aligned_cols=26  Identities=27%  Similarity=0.724  Sum_probs=19.8

Q ss_pred             ceeCCCCCCceEeC--CCcCeeeccccc
Q psy1749          17 IKCCPMCSVPIEKD--EGCAQMLCKRCK   42 (87)
Q Consensus        17 ~k~CP~C~~~Iek~--~GCnhm~C~~C~   42 (87)
                      -++||+|+..|++.  +|-.-..|+.|.
T Consensus        16 g~~C~~C~~~I~~~~~~~R~t~~Cp~CQ   43 (44)
T d1k82a3          16 GEPCRVCGTPIVATKHAQRATFYCRQCQ   43 (44)
T ss_dssp             TSBCTTTCCBCEEEEETTEEEEECTTTC
T ss_pred             CCCcCCCCCEEEEEEECCcccEEChhhc
Confidence            46899999999997  566656676664

>d1wffa_ g.80.1.1 (A:) ANUBL1 (AN1, ubiquitin-like, homolog) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: AN1-like Zinc finger
superfamily: AN1-like Zinc finger
family: AN1-like Zinc finger
domain: ANUBL1 (AN1, ubiquitin-like, homolog)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.96  E-value=0.27  Score=29.40  Aligned_cols=41  Identities=17%  Similarity=0.389  Sum_probs=30.5

Q ss_pred             CceeCCCCCCceEeCCCcCeeeccccceeeeecccccccCCccCC
Q psy1749          16 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLR   60 (87)
Q Consensus        16 ~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~~~~~~   60 (87)
                      ...+|..|+..|....   -++|+ |+..||-....+..-...|+
T Consensus        24 ~~~RC~~C~KKl~l~~---~~~Cr-Cg~~FC~~HR~pe~H~CtfD   64 (85)
T d1wffa_          24 IMKHCFLCGKKTGLAT---SFECR-CGNNFCASHRYAEAHGCNYD   64 (85)
T ss_dssp             CCCBCSSSCCBCSSSS---CEECT-TCCEECTTTCSTGGGTCCSC
T ss_pred             cCCcChhcCCeecCCc---CeecC-CCCEehhhcCCCcCcCCCcc
Confidence            3458999999997653   37998 99999998886665444443

>d1ee8a3 g.39.1.8 (A:211-266) DNA repair protein MutM (Fpg) {Thermus thermophilus [TaxId: 274]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins
domain: DNA repair protein MutM (Fpg)
species: Thermus thermophilus [TaxId: 274]

Probab=85.84  E-value=0.2  Score=27.40  Aligned_cols=27  Identities=30%  Similarity=0.780  Sum_probs=20.9

Q ss_pred             ceeCCCCCCceEeC--CCcCeeeccccce
Q psy1749          17 IKCCPMCSVPIEKD--EGCAQMLCKRCKH   43 (87)
Q Consensus        17 ~k~CP~C~~~Iek~--~GCnhm~C~~C~~   43 (87)
                      .+.||.|+.+|.+.  +|-.-..|..|+.
T Consensus        25 g~~C~~C~~~I~~~~~~~R~t~~Cp~CQ~   53 (56)
T d1ee8a3          25 GLPCPACGRPVERRVVAGRGTHFCPTCQG   53 (56)
T ss_dssp             TSBCTTTCCBCEEEESSSCEEEECTTTTT
T ss_pred             CcccccCCceEEEEEECCCcCEECcCccC
Confidence            36899999999996  5666677777754

>d2jnya1 b.171.1.1 (A:1-59) Uncharacterized protein Cgl1405/cg1592 {Corynebacterium glutamicum [TaxId: 1718]}

class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Uncharacterized protein Cgl1405/cg1592
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=85.64  E-value=0.35  Score=26.79  Aligned_cols=30  Identities=17%  Similarity=0.282  Sum_probs=24.3

Q ss_pred             CceeCCCCCCceEeCCCcCeeeccccceee
Q psy1749          16 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF   45 (87)
Q Consensus        16 ~~k~CP~C~~~Iek~~GCnhm~C~~C~~~F   45 (87)
                      .+-.||.|+..++....=+-+.|..|+..|
T Consensus         9 ~iL~CP~ck~~L~~~~~~~~Lvc~~~~~~Y   38 (59)
T d2jnya1           9 EVLACPKDKGPLRYLESEQLLVNERLNLAY   38 (59)
T ss_dssp             CCCBCTTTCCBCEEETTTTEEEETTTTEEE
T ss_pred             HHhcCCCCCCEeEEeCCCCEEEcCccCccc
Confidence            456799999999988777778888787665

>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=85.11  E-value=0.14  Score=29.99  Aligned_cols=32  Identities=22%  Similarity=0.648  Sum_probs=24.7

Q ss_pred             eCCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749          19 CCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD   55 (87)
Q Consensus        19 ~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~   55 (87)
                      .||-|...+..     .++...||+.||..|...|-.
T Consensus        24 ~C~IC~~~~~~-----pv~~~~CgH~fC~~Ci~~~~~   55 (97)
T d1jm7b_          24 RCSRCTNILRE-----PVCLGGCEHIFCSNCVSDCIG   55 (97)
T ss_dssp             SCSSSCSCCSS-----CBCCCSSSCCBCTTTGGGGTT
T ss_pred             CCccCCchhhc-----CceeCCCCCchhHHHHHHHHh
Confidence            69999998853     355545999999999877754

>d2hf1a1 b.171.1.1 (A:2-60) Hypothetical protein CV3345 {Chromobacterium violaceum [TaxId: 536]}

class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Hypothetical protein CV3345
species: Chromobacterium violaceum [TaxId: 536]

Probab=85.10  E-value=0.36  Score=26.76  Aligned_cols=29  Identities=31%  Similarity=0.761  Sum_probs=24.4

Q ss_pred             ceeCCCCCCceEeCCCcCeeeccccceee
Q psy1749          17 IKCCPMCSVPIEKDEGCAQMLCKRCKHVF   45 (87)
Q Consensus        17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~~F   45 (87)
                      +-.||.|+..++....=+.+.|..|+..|
T Consensus         7 iL~CP~ck~~L~~~~~~~~Lvc~~~~l~Y   35 (59)
T d2hf1a1           7 ILVCPLCKGPLVFDKSKDELICKGDRLAF   35 (59)
T ss_dssp             ECBCTTTCCBCEEETTTTEEEETTTTEEE
T ss_pred             hhcCCCCCCeeeEeCCCCEEecCCcCccc
Confidence            45799999999988887889998887665

>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=84.85  E-value=0.079  Score=29.28  Aligned_cols=37  Identities=24%  Similarity=0.531  Sum_probs=27.8

Q ss_pred             eeCCCCCCceEeCCCcCeeeccccceeeeecccccccC
Q psy1749          18 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDD   55 (87)
Q Consensus        18 k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~   55 (87)
                      ..||-|...+.......-+.-. ||+.||..|...|-.
T Consensus         4 ~~CpIC~~~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~   40 (65)
T d1g25a_           4 QGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFV   40 (65)
T ss_dssp             TCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHH
T ss_pred             CCCCcCCceeecCCceEEEeCc-cChHhhHHHHHHHhC
Confidence            4699998877666555555545 999999999988853

>d1wfpa_ g.80.1.1 (A:) Zinc finger A20 and AN1 domains containing protein At1g12440 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: AN1-like Zinc finger
superfamily: AN1-like Zinc finger
family: AN1-like Zinc finger
domain: Zinc finger A20 and AN1 domains containing protein At1g12440
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=84.78  E-value=0.37  Score=28.08  Aligned_cols=43  Identities=14%  Similarity=0.349  Sum_probs=30.9

Q ss_pred             cCCceeCCCCCCceEeCCCcCeeeccccceeeeecccccccCCccCCC
Q psy1749          14 SELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRH   61 (87)
Q Consensus        14 ~~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~~~~~~H   61 (87)
                      +....+|..|+..|...    .+.|+ |+..||-....+..-...|.+
T Consensus        22 k~kk~RC~~C~KKl~l~----~~~Cr-Cg~~FC~~HR~pe~H~C~fDy   64 (74)
T d1wfpa_          22 KSTATRCLSCNKKVGVT----GFKCR-CGSTFCGTHRYPESHECQFDF   64 (74)
T ss_dssp             TCCCCBCSSSCCBCTTT----CEECT-TSCEECTTTCSTTTSCCCSCT
T ss_pred             CCCCCcChhcCCccCCC----ceecC-CCChhhhccCCccCcCCCCcc
Confidence            34567899999877654    37898 999999888766554434433

>d1wfla_ g.80.1.1 (A:) Zinc finger A20 domain containing protein 2 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: AN1-like Zinc finger
superfamily: AN1-like Zinc finger
family: AN1-like Zinc finger
domain: Zinc finger A20 domain containing protein 2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=84.51  E-value=0.41  Score=27.86  Aligned_cols=42  Identities=19%  Similarity=0.349  Sum_probs=30.4

Q ss_pred             CCceeCCCCCCceEeCCCcCeeeccccceeeeecccccccCCccCCC
Q psy1749          15 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDDDFLLRH   61 (87)
Q Consensus        15 ~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~~~~~~~~H   61 (87)
                      ..-.+|..|+..|...    .++|+ |+..||-.-..+..-...|.+
T Consensus        23 ~k~~RC~~C~KKl~l~----~~~Cr-Cg~~FC~~HR~pe~H~CtfDy   64 (74)
T d1wfla_          23 PKKNRCFMCRKKVGLT----GFDCR-CGNLFCGLHRYSDKHNCPYDY   64 (74)
T ss_dssp             SCTTBCSSSCCBCGGG----CEECT-TSCEECSSSCSTTTTTCCCCG
T ss_pred             CCCCcChhhCCcccce----eeEcc-CCCEehhhcCCCcCcCCCCcc
Confidence            3456899999888775    37998 999999887765554444443

>d2pk7a1 b.171.1.1 (A:3-61) Uncharacterized protein PFL1779 {Pseudomonas fluorescens [TaxId: 294]}

class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Uncharacterized protein PFL1779
species: Pseudomonas fluorescens [TaxId: 294]

Probab=83.85  E-value=0.52  Score=26.12  Aligned_cols=29  Identities=21%  Similarity=0.604  Sum_probs=24.5

Q ss_pred             ceeCCCCCCceEeCCCcCeeeccccceee
Q psy1749          17 IKCCPMCSVPIEKDEGCAQMLCKRCKHVF   45 (87)
Q Consensus        17 ~k~CP~C~~~Iek~~GCnhm~C~~C~~~F   45 (87)
                      +-.||.|+..++....=+.+.|..|+-.|
T Consensus         6 iL~CP~ck~~L~~~~~~~~Lvc~~~~laY   34 (59)
T d2pk7a1           6 ILACPICKGPLKLSADKTELISKGAGLAY   34 (59)
T ss_dssp             TCCCTTTCCCCEECTTSSEEEETTTTEEE
T ss_pred             heECCCCCCcceEeCCCCEEecCCcCccc
Confidence            46799999999998888889999887665

>d2k4xa1 g.41.8.8 (A:1-55) Ribosomal protein S27ae {Thermoplasma acidophilum [TaxId: 2303]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein S27a
domain: Ribosomal protein S27ae
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=83.19  E-value=0.23  Score=27.54  Aligned_cols=29  Identities=24%  Similarity=0.520  Sum_probs=23.5

Q ss_pred             CceeCCCCCCceEeCCCcCeeecccccee
Q psy1749          16 LIKCCPMCSVPIEKDEGCAQMLCKRCKHV   44 (87)
Q Consensus        16 ~~k~CP~C~~~Iek~~GCnhm~C~~C~~~   44 (87)
                      .-+.||+|+.-|.....=+...|-.||.-
T Consensus        17 ~~k~CP~CG~GvFmA~H~dR~~CGKCgyT   45 (55)
T d2k4xa1          17 KHRFCPRCGPGVFLAEHADRYSCGRCGYT   45 (55)
T ss_dssp             SSCCCTTTTTTCCCEECSSEEECTTTCCC
T ss_pred             ecCcCcCCCCcEEeeecCCCccccCCccc
Confidence            34779999998888877789999988753

>d1dvpa2 g.50.1.1 (A:149-220) Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Hrs
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=82.37  E-value=0.46  Score=26.83  Aligned_cols=33  Identities=30%  Similarity=0.775  Sum_probs=24.9

Q ss_pred             eeCCCCCCceEeCCCcCeeeccccceeeeeccccc
Q psy1749          18 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLAS   52 (87)
Q Consensus        18 k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~   52 (87)
                      ..|+.|++.+....  -.-.|+.||..||-.|...
T Consensus        14 ~~C~~C~~~F~~~~--rrhhCr~CG~~~C~~C~~~   46 (72)
T d1dvpa2          14 RVCHRCRVEFTFTN--RKHHCRNCGQVFCGQCTAK   46 (72)
T ss_dssp             SBCTTTCCBCCSSS--CCEECTTTCCEECSTTSCE
T ss_pred             CccccCCCcccCcc--ccccccccCCeeChhhhCC
Confidence            35999999775433  2456889999999999743

>d1wfka_ g.50.1.1 (A:) Zinc finger FYVE domain containing protein 19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Zinc finger FYVE domain containing protein 19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=81.44  E-value=0.7  Score=27.07  Aligned_cols=37  Identities=27%  Similarity=0.485  Sum_probs=28.1

Q ss_pred             CCceeCCCCCCceEeCCCcCeeeccccceeeeecccccc
Q psy1749          15 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASL   53 (87)
Q Consensus        15 ~~~k~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~   53 (87)
                      ..-..|..|++.+..  ---.-.|+.||..||..|....
T Consensus         7 ~~~s~C~~C~~~Fs~--~~rrhhCr~CG~vfC~~Cs~~~   43 (88)
T d1wfka_           7 GMESRCYGCAVKFTL--FKKEYGCKNCGRAFCNGCLSFS   43 (88)
T ss_dssp             CCCSBCTTTCCBCCS--SSCEEECSSSCCEEETTTSCEE
T ss_pred             cccCcCcccCchhcc--ccccccccccChhhChHHhCCc
Confidence            345679999998743  3335789999999999998643

>d1vfya_ g.50.1.1 (A:) vps27p protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: vps27p protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=80.70  E-value=0.83  Score=25.25  Aligned_cols=33  Identities=24%  Similarity=0.511  Sum_probs=24.8

Q ss_pred             eCCCCCCceEeCCCcCeeeccccceeeeecccccc
Q psy1749          19 CCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASL   53 (87)
Q Consensus        19 ~CP~C~~~Iek~~GCnhm~C~~C~~~FC~~C~~~~   53 (87)
                      .|+.|+..+...  --.-.|+.||..||-.|....
T Consensus         7 ~C~~C~~~F~~~--~rkhhCr~CG~~fC~~Cs~~~   39 (67)
T d1vfya_           7 ACMICSKKFSLL--NRKHHCRSCGGVFCQEHSSNS   39 (67)
T ss_dssp             BCTTTCCBCBTT--BCCEECTTTCCEECGGGSCEE
T ss_pred             ccccCCCcccCc--ccccccccCCCEecccccCCc
Confidence            499999877543  234578899999999997443