Psyllid ID: psy12853

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------
Protein Sequence
MTSLVSLDDFLLRHYDKGPCKNKLGHSRASVIWHRTQVSGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDVSRS
Secondary Structure (PSIPRED)
cccccccHHHHHHHcccccccccccccHHHHHHHHHccccHHHccccccccccccccEEEcccccEEEcccccccEEEccccccccccccccccccccccccccccccccccccEEcccccccEEcccccccccccc
Secondary Structure Prediction (SSPRO)
cccEEEHHHHHHHHccccccHcccccccEEEEEEEEEEEEcccccHHHccccccccEEEcccccccEEccccccEEHHHHcccccccccccccccccccccccEEEEEccccccEEEcccccEEEEHEHHccccccc
Coil and Loop (DISEMBL)
mtslvslddfllrhydkgpcknklghsrasviwhrtqvsgatfdselikccpmcsvpiekdEGCAQMLckrckhvfcwyclasrdyggatfdselikccpmcsvpiekdEGCAQMLckrckhvfcWYCLasldvsrs
Flexible Loop (DISEMBL)
mtslvsldDFLLRHYDkgpcknklghsrasviWHRTQVSGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDVSRS
Low Complexity Region (SEG)
MTSLVSLDDFLLRHYDKGPCKNKLGHSRASVIWHRTQVSGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDVSRS
Disordered region (IsUnstruct)
*****SLDDFLLRHYDKGPCKNKLGHSRASVIWHRTQVSGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASL*****
Disordered Region (DISOPRED)
**SLVSLDDFLLRHYDKGPCKNKLGHSRASVIWHRTQVSGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCL*SLD****
Disordered Region (DISEMBL)
MTSLVSLDDFLLRHYDKGPCKNKLGHSRASVIWHRTQVSGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDVSRS
Disordered Region (DISPRO)
*TSLVSLDDFLLRHYDKGPCKNKLGHSRASVIWHRTQVSGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASL*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MTSLVSLDDFLLRHYDKGPCKNKLGHSRASVIWHRTQVSGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDVSRS
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	137	2.2.26 [Sep-21-2011]
A4IIY1	292	Probable E3 ubiquitin-pro	yes	N/A	0.240	0.113	0.909	5e-12
P50876	292	Probable E3 ubiquitin-pro	yes	N/A	0.094	0.044	0.909	5e-12
Q925F3	292	Probable E3 ubiquitin-pro	yes	N/A	0.240	0.113	0.909	5e-12
Q5RFV4	293	Probable E3 ubiquitin-pro	yes	N/A	0.240	0.112	0.909	6e-12
Q6DH94	293	Probable E3 ubiquitin-pro	no	N/A	0.240	0.112	0.909	6e-12
A5PK27	304	E3 ubiquitin-protein liga	no	N/A	0.335	0.151	0.612	2e-10
Q7Z419	303	E3 ubiquitin-protein liga	no	N/A	0.299	0.135	0.658	3e-10
Q8BKD6	301	E3 ubiquitin-protein liga	no	N/A	0.335	0.152	0.591	3e-10
Q54CX4	903	Uncharacterized protein D	no	N/A	0.729	0.110	0.285	7e-09
Q80TT8	1865	Cullin-9 OS=Mus musculus	no	N/A	0.255	0.018	0.628	2e-08

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

 Score = 69.7 bits (169), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 30/33 (90%), Positives = 31/33 (93%)

Query: 8   DDFLLRHYDKGPCKNKLGHSRASVIWHRTQVSG 40
           DDFLL HYDKGPC+NKLGHSRASVIWHRTQV G
Sbjct: 220 DDFLLIHYDKGPCRNKLGHSRASVIWHRTQVVG 252

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: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

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

 Score = 69.7 bits (169), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 30/33 (90%), Positives = 31/33 (93%)

Query: 8   DDFLLRHYDKGPCKNKLGHSRASVIWHRTQVSG 40
           DDFLL HYDKGPC+NKLGHSRASVIWHRTQV G
Sbjct: 220 DDFLLIHYDKGPCRNKLGHSRASVIWHRTQVVG 252

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

 Score = 69.7 bits (169), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 30/33 (90%), Positives = 31/33 (93%)

Query: 8   DDFLLRHYDKGPCKNKLGHSRASVIWHRTQVSG 40
           DDFLL HYDKGPC+NKLGHSRASVIWHRTQV G
Sbjct: 220 DDFLLIHYDKGPCRNKLGHSRASVIWHRTQVVG 252

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

 Score = 69.7 bits (169), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 30/33 (90%), Positives = 31/33 (93%)

Query: 8   DDFLLRHYDKGPCKNKLGHSRASVIWHRTQVSG 40
           DDFLL HYDKGPC+NKLGHSRASVIWHRTQV G
Sbjct: 221 DDFLLIHYDKGPCRNKLGHSRASVIWHRTQVVG 253

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

 Score = 69.3 bits (168), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 30/33 (90%), Positives = 31/33 (93%)

Query: 8   DDFLLRHYDKGPCKNKLGHSRASVIWHRTQVSG 40
           DDFLL HYDKGPC+NKLGHSRASVIWHRTQV G
Sbjct: 221 DDFLLIHYDKGPCRNKLGHSRASVIWHRTQVVG 253

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

 Score = 64.3 bits (155), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 30/49 (61%), Positives = 36/49 (73%), Gaps = 3/49 (6%)

Query: 88  GATFDSEL---IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLD 133
           G  F +E    IK CP+C V IE++EGCAQM+CK CKH FCWYCL +LD
Sbjct: 180 GTLFGTETDAPIKQCPVCRVYIERNEGCAQMMCKNCKHTFCWYCLQNLD 228

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 = 63.9 bits (154), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 27/41 (65%), Positives = 32/41 (78%)

Query: 8   DDFLLRHYDKGPCKNKLGHSRASVIWHRTQVSGATFDSELI 48
           +D  LRHYDKGPC+NKLGHSRASV+W+RTQV G      +I
Sbjct: 228 NDIFLRHYDKGPCRNKLGHSRASVMWNRTQVVGILVGLGII 268

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

 Score = 63.5 bits (153), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 29/49 (59%), Positives = 37/49 (75%), Gaps = 3/49 (6%)

Query: 88  GATFDSEL---IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLD 133
           GA F ++    IK CP+C + IE++EGCAQM+CK CKH FCWYCL +LD
Sbjct: 177 GALFGTDADAPIKQCPVCRIYIERNEGCAQMMCKNCKHTFCWYCLQNLD 225

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|Q54CX4|Y5521_DICDI Uncharacterized protein DDB_G0292642 OS=Dictyostelium discoideum GN=DDB_G0292642 PE=4 SV=2

 Score = 59.3 bits (142), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 40/140 (28%), Positives = 55/140 (39%), Gaps = 40/140 (28%)

Query: 21  KNKLGHSRASVIWHRTQVSGATFDSELIKCCPM--CSVPIEKDEGCAQML-CKRCKHVFC 77
           KN L + + S+I        A+  +E IK CP   C  P+        +L C +C + FC
Sbjct: 682 KNWLKYQKFSMI--------ASLKTEPIKWCPTPDCDTPVRGGSERNPILNCPKCSNDFC 733

Query: 78  WYCLASRDYGGATFDSE----------------------------LIKCCPMCSVPIEKD 109
           W C     + GA   +E                             +K CP C   IEK 
Sbjct: 734 WIC-GEYSHEGAKCGTEAMELQGRKNKSIESAATAYIDFLESNKHFVKPCPTCKSHIEKH 792

Query: 110 EGCAQMLCKRCKHVFCWYCL 129
           +GC  M C  C+H FCW C+
Sbjct: 793 DGCNHMTCINCQHQFCWLCM 812

Dictyostelium discoideum (taxid: 44689)

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

 Score = 57.8 bits (138), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 22/35 (62%), Positives = 23/35 (65%)

Query: 49   KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLAS 83
            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)

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	137
195429571	1075	GK19659 [Drosophila willistoni] gi|19415	0.554	0.070	0.622	7e-22
194758010	1116	GF11090 [Drosophila ananassae] gi|190622	0.554	0.068	0.622	3e-21
195383714	1168	GJ20127 [Drosophila virilis] gi|19414536	0.554	0.065	0.622	3e-21
198460497	1148	GA17318 [Drosophila pseudoobscura pseudo	0.554	0.066	0.622	3e-21
28573878	1102	CG33144, isoform A [Drosophila melanogas	0.554	0.068	0.611	6e-21
195582260	1119	GD25960 [Drosophila simulans] gi|1941929	0.554	0.067	0.611	6e-21
195483647	1104	GE13078 [Drosophila yakuba] gi|194176474	0.554	0.068	0.611	6e-21
195333219	1098	GM20497 [Drosophila sechellia] gi|194125	0.554	0.069	0.611	6e-21
194884183	1115	GG22721 [Drosophila erecta] gi|190659362	0.554	0.068	0.611	8e-21
312374426	1322	hypothetical protein AND_15928 [Anophele	0.481	0.049	0.576	8e-20

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

 Score =  108 bits (270), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 56/90 (62%), Positives = 62/90 (68%), Gaps = 14/90 (15%)

Query: 51  CPMCSVPIEKDEGCAQMLCKRCKHV------FCWYCLAS-RDYGGATFDSELIKCCPMCS 103
           CP C     KDE CA  LCK+  H       F    +A  +D  G  FD+ELIKCCPMC+
Sbjct: 908 CPSC-----KDEFCA--LCKKAYHPNISCEEFGRRLIADGQDDIGIPFDNELIKCCPMCA 960

Query: 104 VPIEKDEGCAQMLCKRCKHVFCWYCLASLD 133
           VPIEKDEGCAQM+CKRCKHVFCWYCLASLD
Sbjct: 961 VPIEKDEGCAQMMCKRCKHVFCWYCLASLD 990

Source: Drosophila willistoni

Species: Drosophila willistoni

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 =  106 bits (265), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 56/90 (62%), Positives = 62/90 (68%), Gaps = 14/90 (15%)

Query: 51   CPMCSVPIEKDEGCAQMLCKRCKHV------FCWYCLAS-RDYGGATFDSELIKCCPMCS 103
            CP C     KDE CA  LCK+  H       F    +A  +D  G  FD+ELIKCCPMC+
Sbjct: 949  CPSC-----KDEFCA--LCKKAYHPNISCDEFGRRLIADGQDDIGIPFDNELIKCCPMCA 1001

Query: 104  VPIEKDEGCAQMLCKRCKHVFCWYCLASLD 133
            VPIEKDEGCAQM+CKRCKHVFCWYCLASLD
Sbjct: 1002 VPIEKDEGCAQMMCKRCKHVFCWYCLASLD 1031

Source: Drosophila ananassae

Species: Drosophila ananassae

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 =  106 bits (265), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 56/90 (62%), Positives = 62/90 (68%), Gaps = 14/90 (15%)

Query: 51   CPMCSVPIEKDEGCAQMLCKRCKHV------FCWYCLAS-RDYGGATFDSELIKCCPMCS 103
            CP C     KDE CA  LCK+  H       F    +A  +D  G  FD+ELIKCCPMC+
Sbjct: 1001 CPSC-----KDEFCA--LCKKAFHPNISCEEFGRRLIADGQDDIGIPFDNELIKCCPMCA 1053

Query: 104  VPIEKDEGCAQMLCKRCKHVFCWYCLASLD 133
            VPIEKDEGCAQM+CKRCKHVFCWYCLASLD
Sbjct: 1054 VPIEKDEGCAQMMCKRCKHVFCWYCLASLD 1083

Source: Drosophila virilis

Species: Drosophila virilis

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 =  106 bits (264), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 56/90 (62%), Positives = 62/90 (68%), Gaps = 14/90 (15%)

Query: 51   CPMCSVPIEKDEGCAQMLCKRCKHV------FCWYCLAS-RDYGGATFDSELIKCCPMCS 103
            CP C     KDE CA  LCK+  H       F    +A  +D  G  FD+ELIKCCPMC+
Sbjct: 981  CPSC-----KDEFCA--LCKKAYHPNIGCEEFGRRLIADGQDDIGIPFDNELIKCCPMCA 1033

Query: 104  VPIEKDEGCAQMLCKRCKHVFCWYCLASLD 133
            VPIEKDEGCAQM+CKRCKHVFCWYCLASLD
Sbjct: 1034 VPIEKDEGCAQMMCKRCKHVFCWYCLASLD 1063

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

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 =  105 bits (262), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 55/90 (61%), Positives = 61/90 (67%), Gaps = 14/90 (15%)

Query: 51   CPMCSVPIEKDEGCAQMLCKRCKHV------FCWYCLAS-RDYGGATFDSELIKCCPMCS 103
            CP C     KDE C   LCK+  H       F    +A  +D  G  FD+ELIKCCPMC+
Sbjct: 935  CPSC-----KDEFCG--LCKKAYHPNISCDEFGRRLIADGQDDIGIPFDNELIKCCPMCA 987

Query: 104  VPIEKDEGCAQMLCKRCKHVFCWYCLASLD 133
            VPIEKDEGCAQM+CKRCKHVFCWYCLASLD
Sbjct: 988  VPIEKDEGCAQMMCKRCKHVFCWYCLASLD 1017

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 =  105 bits (262), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 55/90 (61%), Positives = 61/90 (67%), Gaps = 14/90 (15%)

Query: 51   CPMCSVPIEKDEGCAQMLCKRCKHV------FCWYCLAS-RDYGGATFDSELIKCCPMCS 103
            CP C     KDE C   LCK+  H       F    +A  +D  G  FD+ELIKCCPMC+
Sbjct: 952  CPSC-----KDEFCG--LCKKAYHPNISCEEFGRRLIADGQDDIGIPFDNELIKCCPMCA 1004

Query: 104  VPIEKDEGCAQMLCKRCKHVFCWYCLASLD 133
            VPIEKDEGCAQM+CKRCKHVFCWYCLASLD
Sbjct: 1005 VPIEKDEGCAQMMCKRCKHVFCWYCLASLD 1034

Source: Drosophila simulans

Species: Drosophila simulans

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 =  105 bits (262), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 55/90 (61%), Positives = 61/90 (67%), Gaps = 14/90 (15%)

Query: 51   CPMCSVPIEKDEGCAQMLCKRCKHV------FCWYCLAS-RDYGGATFDSELIKCCPMCS 103
            CP C     KDE C   LCK+  H       F    +A  +D  G  FD+ELIKCCPMC+
Sbjct: 937  CPSC-----KDEFCG--LCKKAYHPNISCEEFGRRLIADGQDDIGIPFDNELIKCCPMCA 989

Query: 104  VPIEKDEGCAQMLCKRCKHVFCWYCLASLD 133
            VPIEKDEGCAQM+CKRCKHVFCWYCLASLD
Sbjct: 990  VPIEKDEGCAQMMCKRCKHVFCWYCLASLD 1019

Source: Drosophila yakuba

Species: Drosophila yakuba

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 =  105 bits (262), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 55/90 (61%), Positives = 61/90 (67%), Gaps = 14/90 (15%)

Query: 51   CPMCSVPIEKDEGCAQMLCKRCKHV------FCWYCLAS-RDYGGATFDSELIKCCPMCS 103
            CP C     KDE C   LCK+  H       F    +A  +D  G  FD+ELIKCCPMC+
Sbjct: 931  CPSC-----KDEFCG--LCKKAYHPNISCEEFGRRLIADGQDDIGIPFDNELIKCCPMCA 983

Query: 104  VPIEKDEGCAQMLCKRCKHVFCWYCLASLD 133
            VPIEKDEGCAQM+CKRCKHVFCWYCLASLD
Sbjct: 984  VPIEKDEGCAQMMCKRCKHVFCWYCLASLD 1013

Source: Drosophila sechellia

Species: Drosophila sechellia

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 =  105 bits (261), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 55/90 (61%), Positives = 61/90 (67%), Gaps = 14/90 (15%)

Query: 51   CPMCSVPIEKDEGCAQMLCKRCKHV------FCWYCLAS-RDYGGATFDSELIKCCPMCS 103
            CP C     KDE C   LCK+  H       F    +A  +D  G  FD+ELIKCCPMC+
Sbjct: 948  CPSC-----KDEFCG--LCKKAYHPNISCDEFGRRLIADGQDDIGIPFDNELIKCCPMCA 1000

Query: 104  VPIEKDEGCAQMLCKRCKHVFCWYCLASLD 133
            VPIEKDEGCAQM+CKRCKHVFCWYCLASLD
Sbjct: 1001 VPIEKDEGCAQMMCKRCKHVFCWYCLASLD 1030

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312374426|gb|EFR21983.1| hypothetical protein AND_15928 [Anopheles darlingi]

 Score =  101 bits (252), Expect = 8e-20,   Method: Composition-based stats.
 Identities = 49/85 (57%), Positives = 55/85 (64%), Gaps = 19/85 (22%)

Query: 69   CKRCKHVFC------WYCLAS-------------RDYGGATFDSELIKCCPMCSVPIEKD 109
            C  C+  FC      W+ L S              D  G  FD++LIKCCPMC+VPIEKD
Sbjct: 1179 CHTCREDFCSGCKKPWHPLMSCEENSRRLAVDGQADALGIPFDNDLIKCCPMCTVPIEKD 1238

Query: 110  EGCAQMLCKRCKHVFCWYCLASLDV 134
            EGCAQM+CKRCKHVFCWYCLASLDV
Sbjct: 1239 EGCAQMMCKRCKHVFCWYCLASLDV 1263

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

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	137
FB|FBgn0053144	1102	CG33144 [Drosophila melanogast	0.554	0.068	0.611	4e-22
UNIPROTKB|H7C3G0	264	RNF144A "Probable E3 ubiquitin	0.306	0.159	0.714	2.9e-17
UNIPROTKB|F1S9L4	280	RNF144A "Uncharacterized prote	0.306	0.15	0.714	3.1e-17
UNIPROTKB|F1PYL1	292	RNF144A "Uncharacterized prote	0.306	0.143	0.714	5.5e-17
UNIPROTKB|P50876	292	RNF144A "Probable E3 ubiquitin	0.306	0.143	0.714	5.5e-17
UNIPROTKB|F1MME3	293	RNF144A "Uncharacterized prote	0.306	0.143	0.714	5.8e-17
UNIPROTKB|E1BYS1	292	RNF144A "Uncharacterized prote	0.306	0.143	0.714	7e-17
ZFIN|ZDB-GENE-040718-486	293	rnf144ab "ring finger protein	0.306	0.143	0.714	2.4e-16
ZFIN|ZDB-GENE-040426-1292	292	zgc:63907 "zgc:63907" [Danio r	0.306	0.143	0.674	2.8e-16
MGI|MGI:1344401	292	Rnf144a "ring finger protein 1	0.277	0.130	0.763	3.5e-16

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

 Score = 270 (100.1 bits), Expect = 4.0e-22, P = 4.0e-22
 Identities = 55/90 (61%), Positives = 62/90 (68%)

Query:    51 CPMCSVPIEKDEGCAQMLCKRCKH--VFC----WYCLAS-RDYGGATFDSELIKCCPMCS 103
             CP C     KDE C   LCK+  H  + C       +A  +D  G  FD+ELIKCCPMC+
Sbjct:   935 CPSC-----KDEFCG--LCKKAYHPNISCDEFGRRLIADGQDDIGIPFDNELIKCCPMCA 987

Query:   104 VPIEKDEGCAQMLCKRCKHVFCWYCLASLD 133
             VPIEKDEGCAQM+CKRCKHVFCWYCLASLD
Sbjct:   988 VPIEKDEGCAQMMCKRCKHVFCWYCLASLD 1017

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|H7C3G0 RNF144A "Probable E3 ubiquitin-protein ligase RNF144A" [Homo sapiens (taxid:9606)]

 Score = 181 (68.8 bits), Expect = 2.9e-17, Sum P(2) = 2.9e-17
 Identities = 30/42 (71%), Positives = 32/42 (76%)

Query:    92 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLD 133
             D   IK CP C V IE+DEGCAQM+CK CKH FCWYCL SLD
Sbjct:   174 DDAPIKRCPKCKVYIERDEGCAQMMCKNCKHAFCWYCLESLD 215

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 181 (68.8 bits), Expect = 3.1e-17, Sum P(2) = 3.1e-17
 Identities = 30/42 (71%), Positives = 32/42 (76%)

Query:    92 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLD 133
             D   IK CP C V IE+DEGCAQM+CK CKH FCWYCL SLD
Sbjct:   188 DDAPIKRCPKCKVYIERDEGCAQMMCKNCKHAFCWYCLESLD 229

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 181 (68.8 bits), Expect = 5.5e-17, Sum P(2) = 5.5e-17
 Identities = 30/42 (71%), Positives = 32/42 (76%)

Query:    92 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLD 133
             D   IK CP C V IE+DEGCAQM+CK CKH FCWYCL SLD
Sbjct:   178 DDAPIKRCPKCKVYIERDEGCAQMMCKNCKHAFCWYCLESLD 219

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 = 181 (68.8 bits), Expect = 5.5e-17, Sum P(2) = 5.5e-17
 Identities = 30/42 (71%), Positives = 32/42 (76%)

Query:    92 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLD 133
             D   IK CP C V IE+DEGCAQM+CK CKH FCWYCL SLD
Sbjct:   178 DDAPIKRCPKCKVYIERDEGCAQMMCKNCKHAFCWYCLESLD 219

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

 Score = 181 (68.8 bits), Expect = 5.8e-17, Sum P(2) = 5.8e-17
 Identities = 30/42 (71%), Positives = 32/42 (76%)

Query:    92 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLD 133
             D   IK CP C V IE+DEGCAQM+CK CKH FCWYCL SLD
Sbjct:   179 DDAPIKRCPKCKVYIERDEGCAQMMCKNCKHAFCWYCLESLD 220

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 181 (68.8 bits), Expect = 7.0e-17, Sum P(2) = 7.0e-17
 Identities = 30/42 (71%), Positives = 32/42 (76%)

Query:    92 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLD 133
             D   IK CP C V IE+DEGCAQM+CK CKH FCWYCL SLD
Sbjct:   178 DDAPIKRCPKCKVYIERDEGCAQMMCKNCKHAFCWYCLESLD 219

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005794 "Golgi apparatus" evidence=IEA

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

 Score = 181 (68.8 bits), Expect = 2.4e-16, Sum P(2) = 2.4e-16
 Identities = 30/42 (71%), Positives = 32/42 (76%)

Query:    92 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLD 133
             D   IK CP C V IE+DEGCAQM+CK CKH FCWYCL SLD
Sbjct:   179 DEAPIKRCPKCKVYIERDEGCAQMMCKNCKHAFCWYCLESLD 220

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-040426-1292 zgc:63907 "zgc:63907" [Danio rerio (taxid:7955)]

 Score = 173 (66.0 bits), Expect = 2.8e-16, Sum P(2) = 2.8e-16
 Identities = 29/43 (67%), Positives = 35/43 (81%)

Query:    92 DSEL-IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLD 133
             D+E  IK CP+C V IE+++GCAQMLCK CKH FCWYCL +LD
Sbjct:   165 DTEAAIKQCPVCGVYIERNQGCAQMLCKSCKHTFCWYCLQNLD 207

GO:0008270 "zinc ion binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

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

 Score = 178 (67.7 bits), Expect = 3.5e-16, Sum P(2) = 3.5e-16
 Identities = 29/38 (76%), Positives = 31/38 (81%)

Query:    96 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLD 133
             IK CP C V IE+DEGCAQM+CK CKH FCWYCL SLD
Sbjct:   182 IKRCPKCRVYIERDEGCAQMMCKNCKHAFCWYCLESLD 219

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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	137
KOG1814|consensus	445		99.89
KOG1812|consensus	384		99.87
KOG0006|consensus	446		99.85
KOG1815|consensus	444		99.8
smart00647	64	IBR In Between Ring fingers. the domains occurs be	99.29
PF01485	64	IBR: IBR domain; InterPro: IPR002867 Zinc finger (	99.24
PF01485	64	IBR: IBR domain; InterPro: IPR002867 Zinc finger (	98.67
smart00647	64	IBR In Between Ring fingers. the domains occurs be	98.59
KOG0006|consensus	446		97.48
KOG1814|consensus	445		97.19
KOG1812|consensus	384		97.18
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	96.39
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	96.04
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	96.01
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	95.89
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	95.81
smart00661	52	RPOL9 RNA polymerase subunit 9.	95.5
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	95.49
KOG1815|consensus	444		95.42
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	95.04
PF12773	50	DZR: Double zinc ribbon	94.86
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	94.86
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	94.85
PF12773	50	DZR: Double zinc ribbon	94.67
smart00661	52	RPOL9 RNA polymerase subunit 9.	94.66
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	94.31
PRK14559	645	putative protein serine/threonine phosphatase; Pro	93.97
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	93.64
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	93.38
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	93.29
PRK00432	50	30S ribosomal protein S27ae; Validated	93.15
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	92.96
PRK04023	1121	DNA polymerase II large subunit; Validated	92.96
PF07191	70	zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807	92.93
TIGR00622	112	ssl1 transcription factor ssl1. This family is bas	92.84
PRK14714	1337	DNA polymerase II large subunit; Provisional	92.8
PHA00626	59	hypothetical protein	92.66
PF13248	26	zf-ribbon_3: zinc-ribbon domain	92.64
PRK00432	50	30S ribosomal protein S27ae; Validated	92.23
PF07191	70	zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807	91.65
KOG0317|consensus	293		91.36
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	91.36
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	91.25
PHA02926	242	zinc finger-like protein; Provisional	90.75
PF07754	24	DUF1610: Domain of unknown function (DUF1610); Int	90.54
COG1198	730	PriA Primosomal protein N' (replication factor Y)	90.44
COG1594	113	RPB9 DNA-directed RNA polymerase, subunit M/Transc	90.44
PF08274	30	PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01	90.31
PF09538	108	FYDLN_acid: Protein of unknown function (FYDLN_aci	90.12
TIGR01053	31	LSD1 zinc finger domain, LSD1 subclass. This model	90.01
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	90.0
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	89.77
PF14569	80	zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.	89.52
KOG2932|consensus	389		89.47
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	89.12
PRK00420	112	hypothetical protein; Validated	89.11
PRK14559	645	putative protein serine/threonine phosphatase; Pro	89.04
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	88.96
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	88.84
COG1998	51	RPS31 Ribosomal protein S27AE [Translation, riboso	88.72
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	88.13
PF06677	41	Auto_anti-p27: Sjogren's syndrome/scleroderma auto	87.82
PF14369	35	zf-RING_3: zinc-finger	87.71
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	87.45
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	87.27
KOG2906|consensus	105		87.1
KOG0823|consensus	230		87.02
PF06943	25	zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zin	86.98
PF09538	108	FYDLN_acid: Protein of unknown function (FYDLN_aci	86.96
PRK05654	292	acetyl-CoA carboxylase subunit beta; Validated	86.52
PLN02189	1040	cellulose synthase	86.46
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	86.36
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	86.12
PF14353	128	CpXC: CpXC protein	85.9
KOG0317|consensus	293		85.48
TIGR03655	53	anti_R_Lar restriction alleviation protein, Lar fa	85.31
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	85.16
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	85.12
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	85.1
PF08792	33	A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: I	85.09
TIGR00686	109	phnA alkylphosphonate utilization operon protein P	84.89
PRK00241	256	nudC NADH pyrophosphatase; Reviewed	84.83
PRK08665	752	ribonucleotide-diphosphate reductase subunit alpha	84.8
KOG0320|consensus	187		84.76
KOG2906|consensus	105		84.71
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	84.4
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	84.37
PF14634	44	zf-RING_5: zinc-RING finger domain	84.33
KOG0823|consensus	230		84.31
PHA02929	238	N1R/p28-like protein; Provisional	84.28
COG2816	279	NPY1 NTP pyrophosphohydrolases containing a Zn-fin	84.26
PF14952	44	zf-tcix: Putative treble-clef, zinc-finger, Zn-bin	84.23
TIGR00515	285	accD acetyl-CoA carboxylase, carboxyl transferase,	84.19
CHL00174	296	accD acetyl-CoA carboxylase beta subunit; Reviewed	84.04
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	83.82
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	83.66
PF10122	51	Mu-like_Com: Mu-like prophage protein Com; InterPr	83.61
PF14354	61	Lar_restr_allev: Restriction alleviation protein L	83.47
KOG0978|consensus	698		83.4
PRK14892	99	putative transcription elongation factor Elf1; Pro	83.29
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	82.81
PRK10220	111	hypothetical protein; Provisional	82.76
PLN02638	1079	cellulose synthase A (UDP-forming), catalytic subu	82.69
PRK12495	226	hypothetical protein; Provisional	82.64
PF03119	28	DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc f	81.3
PF15135	278	UPF0515: Uncharacterised protein UPF0515	81.23
PRK00420	112	hypothetical protein; Validated	81.22
PLN02436	1094	cellulose synthase A	81.21
PRK09710	64	lar restriction alleviation and modification prote	80.98
PRK11827	60	hypothetical protein; Provisional	80.78
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	80.35
COG0777	294	AccD Acetyl-CoA carboxylase beta subunit [Lipid me	80.19

>KOG1814|consensus

Probab=99.89  E-value=1e-24  Score=170.31  Aligned_cols=132  Identities=27%  Similarity=0.556  Sum_probs=111.5

Q ss_pred             ccccchHHHHhhcCCCcccccccccchhhhHHHHhhccccccCCCCcccCCC--CCCceeecCCCCeeeccccccccccc
Q psy12853          2 TSLVSLDDFLLRHYDKGPCKNKLGHSRASVIWHRTQVSGATFDSELIKCCPM--CSVPIEKDEGCAQMLCKRCKHVFCWY   79 (137)
Q Consensus         2 ~~l~~~~~f~~~~~~~~~c~~~l~~~~~~~~~~r~~~~~a~~~~~~~~~CP~--C~~~i~~~~~~~~~~C~~C~~~fC~~   79 (137)
                      ++|.+|+.-..+...++..++.+..+ +.++|.+..+++++....+.+|||+  |..+...+++...+.|.+|+..||+.
T Consensus       228 ~~l~Cp~~~C~~~a~~g~vKelvg~E-L~arYe~l~lqk~l~~msdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtl  306 (445)
T KOG1814|consen  228 SCLKCPDPKCGSVAPPGQVKELVGDE-LFARYEKLMLQKTLELMSDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTL  306 (445)
T ss_pred             eeecCCCCCCcccCCchHHHHHHHHH-HHHHHHHHHHHHHHHhhcccccCChhhccCccccCchhhhhhhccCccHHHHH
Confidence            45666776666666777666666554 4579999999988888899999994  99999777899999999999999999


Q ss_pred             ccccccCCC---------------------------------------------CcccccccCCCCCCCcceeecCCCCe
Q psy12853         80 CLASRDYGG---------------------------------------------ATFDSELIKCCPMCSVPIEKDEGCAQ  114 (137)
Q Consensus        80 C~~~~h~~~---------------------------------------------~~~~~~~~~~CP~C~~~iek~~gC~h  114 (137)
                      |+..||+..                                             +.|...+.++||+|++.|||++|||+
T Consensus       307 Ck~t~HG~s~Ck~~~~~~~~l~~~~~~~d~a~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnK  386 (445)
T KOG1814|consen  307 CKLTWHGVSPCKVKAEKLIELYLEYLEADEARKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNK  386 (445)
T ss_pred             HHHhhcCCCcccCchHHHHHHHHHHhhcCHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCccc
Confidence            999999983                                             02334578999999999999999999


Q ss_pred             EEeccCcceeeccccccccc
Q psy12853        115 MLCKRCKHVFCWYCLASLDV  134 (137)
Q Consensus       115 m~C~~C~~~fC~~C~~~~~~  134 (137)
                      |+|.+||+.|||.|+..+.+
T Consensus       387 M~C~~c~~~fc~~c~~~l~~  406 (445)
T KOG1814|consen  387 MHCTKCGTYFCWICAELLYP  406 (445)
T ss_pred             eeeccccccceeehhhhcCC
Confidence            99999999999999998874

>KOG1812|consensus

Probab=99.87  E-value=1.7e-23  Score=166.21  Aligned_cols=131  Identities=24%  Similarity=0.547  Sum_probs=106.1

Q ss_pred             ccccchHHHHhhcCCCcccccccccchhhhHHHHhhccccccCCCCcccCC--CCCCceeecC-----CCCeeecccccc
Q psy12853          2 TSLVSLDDFLLRHYDKGPCKNKLGHSRASVIWHRTQVSGATFDSELIKCCP--MCSVPIEKDE-----GCAQMLCKRCKH   74 (137)
Q Consensus         2 ~~l~~~~~f~~~~~~~~~c~~~l~~~~~~~~~~r~~~~~a~~~~~~~~~CP--~C~~~i~~~~-----~~~~~~C~~C~~   74 (137)
                      +.+.+|+.-....++.+.|...|+. .+.+.|.++..+..+...+.. |||  +|...+....     ......|+.|+.
T Consensus       189 ~~~~C~~~~C~~~l~~~~c~~llt~-kl~e~~e~~~~e~~i~~~~~~-ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~  266 (384)
T KOG1812|consen  189 TVIRCPHDGCESRLTLESCRKLLTP-KLREMWEQRLKEEVIPSLDRV-YCPYPRCSSLMSKTELSSEVKSKRRPCVKCHE  266 (384)
T ss_pred             CCccCCCCCCCccCCHHHHhhhcCH-HHHHHHHHHHHHHhhhhhhcc-cCCCCCchHhhhhhhhccchhhcccccccCCC
Confidence            4556677777788888889999988 566799988776665555555 998  8988877543     345677999999


Q ss_pred             cccccccccccCCCC------------------cccccccCCCCCCCcceeecCCCCeEEeccCcceeecccccccccC
Q psy12853         75 VFCWYCLASRDYGGA------------------TFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDVS  135 (137)
Q Consensus        75 ~fC~~C~~~~h~~~~------------------~~~~~~~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~~~~  135 (137)
                      .||.+|+.+||.+..                  .+.++.|++||+|+..||+++|||||+|+ ||++|||.|+.+|..+
T Consensus       267 ~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~~~~~la~~wr~CpkC~~~ie~~~GCnhm~Cr-C~~~fcy~C~~~~~~~  344 (384)
T KOG1812|consen  267 LFCVKCKVPWHANLSCEEYKKLNPEEYVDDITLKYLAKRWRQCPKCKFMIELSEGCNHMTCR-CGHQFCYMCGGDWKTH  344 (384)
T ss_pred             ceeecCCCcCCCCCCHHHHHHhCCcccccHHHHHHHHHhcCcCcccceeeeecCCcceEEee-ccccchhhcCcchhhC
Confidence            999999999999841                  11136799999999999999999999999 9999999999988654

>KOG0006|consensus

Probab=99.85  E-value=3.5e-22  Score=152.22  Aligned_cols=127  Identities=24%  Similarity=0.552  Sum_probs=100.9

Q ss_pred             chHHHHhhcCCCccccccc----------ccchhhhHHHHhhccccccCCCCcccCC--CCCCceeecCCCCeeeccc-c
Q psy12853          6 SLDDFLLRHYDKGPCKNKL----------GHSRASVIWHRTQVSGATFDSELIKCCP--MCSVPIEKDEGCAQMLCKR-C   72 (137)
Q Consensus         6 ~~~~f~~~~~~~~~c~~~l----------~~~~~~~~~~r~~~~~a~~~~~~~~~CP--~C~~~i~~~~~~~~~~C~~-C   72 (137)
                      ..++|-.++-.+++|.+.|          .++.+ .+|+|+..++.++... .+.||  +|++.+...+++..++|+. |
T Consensus       265 ~~p~~gyslpc~agc~~s~i~e~HHF~ilg~e~Y-~rYQr~atEe~vlq~g-GVlCP~pgCG~gll~EPD~rkvtC~~gC  342 (446)
T KOG0006|consen  265 HDPQLGYSLPCVAGCPNSLIKELHHFRILGEEQY-NRYQRYATEECVLQMG-GVLCPRPGCGAGLLPEPDQRKVTCEGGC  342 (446)
T ss_pred             cCccccccccccCCCchHHHHhhhhheecchhHH-HHHHHhhhhhheeecC-CEecCCCCCCcccccCCCCCcccCCCCc
Confidence            3444555555566666444          33334 4788887777666555 78998  8999999999999999995 9


Q ss_pred             cccccccccccccCCCC------------------------ccc-------ccccCCCCCCCcceeecCCCCeEEecc--
Q psy12853         73 KHVFCWYCLASRDYGGA------------------------TFD-------SELIKCCPMCSVPIEKDEGCAQMLCKR--  119 (137)
Q Consensus        73 ~~~fC~~C~~~~h~~~~------------------------~~~-------~~~~~~CP~C~~~iek~~gC~hm~C~~--  119 (137)
                      ++.||..|...||.+..                        .|+       ...+|+||+|++++||+|||.||.|++  
T Consensus       343 gf~FCR~C~e~yh~geC~~~~~as~t~tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~  422 (446)
T KOG0006|consen  343 GFAFCRECKEAYHEGECSAVFEASGTTTCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQ  422 (446)
T ss_pred             hhHhHHHHHhhhccccceeeeccccccceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecCCCC
Confidence            99999999999999941                        122       336899999999999999999999995  


Q ss_pred             Ccceeeccccccccc
Q psy12853        120 CKHVFCWYCLASLDV  134 (137)
Q Consensus       120 C~~~fC~~C~~~~~~  134 (137)
                      ||.+|||.|+..|..
T Consensus       423 Cg~eWCw~C~tEW~r  437 (446)
T KOG0006|consen  423 CGLEWCWNCGTEWNR  437 (446)
T ss_pred             CCceeEeccCChhhh
Confidence            999999999999975

>KOG1815|consensus

Probab=99.80  E-value=3.5e-20  Score=149.92  Aligned_cols=122  Identities=31%  Similarity=0.647  Sum_probs=100.2

Q ss_pred             cCCCcccccccccchhhhHHHHhhccccccCCCCcccCC--CCCCceee-cCCCCeeecccccccccccccccccCCCC-
Q psy12853         14 HYDKGPCKNKLGHSRASVIWHRTQVSGATFDSELIKCCP--MCSVPIEK-DEGCAQMLCKRCKHVFCWYCLASRDYGGA-   89 (137)
Q Consensus        14 ~~~~~~c~~~l~~~~~~~~~~r~~~~~a~~~~~~~~~CP--~C~~~i~~-~~~~~~~~C~~C~~~fC~~C~~~~h~~~~-   89 (137)
                      ..+...+..........++|.++.+.+++......+|||  +|+.++.. ......+.| .|++.|||.|+.+||.+.. 
T Consensus       124 ~v~~~~i~~~~s~~~~~~ky~~~i~~syve~~~~lkwCP~~~C~~av~~~~~~~~~v~C-~~g~~FC~~C~~~~H~p~~C  202 (444)
T KOG1815|consen  124 LVGEDTVEKLVSDKEDKEKYQRYILRSYVEDNVPLKWCPAPGCGLAVKFGSLESVEVDC-GCGHEFCFACGEESHSPVSC  202 (444)
T ss_pred             cCCCceeeeecCCHHHHHHHHHHHHHHHHhcCCccccCCCCCCCceeeccCCCccceeC-CCCchhHhhccccccCCCcc
Confidence            333344444444434567999999998888888899998  89999886 566788999 5788999999999999951 


Q ss_pred             -----------------cccccccCCCCCCCcceeecCCCCeEEecc--CcceeecccccccccCC
Q psy12853         90 -----------------TFDSELIKCCPMCSVPIEKDEGCAQMLCKR--CKHVFCWYCLASLDVSR  136 (137)
Q Consensus        90 -----------------~~~~~~~~~CP~C~~~iek~~gC~hm~C~~--C~~~fC~~C~~~~~~~~  136 (137)
                                       .|+..++++||+|..+|||++|||||+|..  |+++|||+|.++|.++.
T Consensus       203 ~~~~~wl~k~~~~se~~~wi~~ntk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h~  268 (444)
T KOG1815|consen  203 PGAKKWLKKCRDDSETINWILANTKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDHG  268 (444)
T ss_pred             cchHHHHHhhhhhhhhhhhhhccCccCCCcccchhccCCccccccccCCcCCeeceeeeccccccc
Confidence                             245678999999999999999999999997  99999999999998874

>smart00647 IBR In Between Ring fingers

Probab=99.29  E-value=2.7e-12  Score=77.29  Aligned_cols=57  Identities=26%  Similarity=0.588  Sum_probs=49.2

Q ss_pred             HHHHhhccccccCCCCcccCC--CCCCceeecC--CCCeeecccccccccccccccccCCC
Q psy12853         32 IWHRTQVSGATFDSELIKCCP--MCSVPIEKDE--GCAQMLCKRCKHVFCWYCLASRDYGG   88 (137)
Q Consensus        32 ~~~r~~~~~a~~~~~~~~~CP--~C~~~i~~~~--~~~~~~C~~C~~~fC~~C~~~~h~~~   88 (137)
                      +|++++++.++..+++.+|||  +|..++...+  +...+.|+.|+..||+.|+.+||.+.
T Consensus         2 ~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~   62 (64)
T smart00647        2 KYERLLLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSPV   62 (64)
T ss_pred             hHHHHHHHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCCC
Confidence            566776766666678899999  9999998864  78899999999999999999999874

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=99.24  E-value=2.3e-12  Score=77.53  Aligned_cols=57  Identities=28%  Similarity=0.616  Sum_probs=38.7

Q ss_pred             HHHHhhccccccCCCCcccCC--CCCCceeecCCCCe--eecccccccccccccccccCCC
Q psy12853         32 IWHRTQVSGATFDSELIKCCP--MCSVPIEKDEGCAQ--MLCKRCKHVFCWYCLASRDYGG   88 (137)
Q Consensus        32 ~~~r~~~~~a~~~~~~~~~CP--~C~~~i~~~~~~~~--~~C~~C~~~fC~~C~~~~h~~~   88 (137)
                      +|+++.++.++..+++.+|||  +|+.++..+++...  ++|+.|++.||+.|+.+||.+.
T Consensus         2 ky~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~   62 (64)
T PF01485_consen    2 KYQKFLLKRYLESDPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEGV   62 (64)
T ss_dssp             CHHHCCCHS---S---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTTS
T ss_pred             hHHHHHHHHHHHCCCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCCC
Confidence            567777777777888889998  59999999887666  9999999999999999999974

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.

>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=98.67  E-value=1.1e-08  Score=61.32  Aligned_cols=43  Identities=35%  Similarity=0.823  Sum_probs=32.1

Q ss_pred             cccCCCCC--CCcceeecCCCCe--EEeccCcceeecccccccccCC
Q psy12853         94 ELIKCCPM--CSVPIEKDEGCAQ--MLCKRCKHVFCWYCLASLDVSR  136 (137)
Q Consensus        94 ~~~~~CP~--C~~~iek~~gC~h--m~C~~C~~~fC~~C~~~~~~~~  136 (137)
                      .+.+.||+  |...+++.++.++  |+|..|++.|||.|+.+|+...
T Consensus        16 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~   62 (64)
T PF01485_consen   16 PNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEGV   62 (64)
T ss_dssp             --CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTTS
T ss_pred             CCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCCC
Confidence            45679988  9999999999999  9999999999999999997653

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.

>smart00647 IBR In Between Ring fingers

Probab=98.59  E-value=7e-08  Score=57.78  Aligned_cols=42  Identities=33%  Similarity=0.838  Sum_probs=37.5

Q ss_pred             cccCCCC--CCCcceeecC--CCCeEEeccCcceeecccccccccC
Q psy12853         94 ELIKCCP--MCSVPIEKDE--GCAQMLCKRCKHVFCWYCLASLDVS  135 (137)
Q Consensus        94 ~~~~~CP--~C~~~iek~~--gC~hm~C~~C~~~fC~~C~~~~~~~  135 (137)
                      .+++.||  +|...|+..+  +..+|+|..||+.|||.|+.+|+..
T Consensus        16 ~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~   61 (64)
T smart00647       16 PDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSP   61 (64)
T ss_pred             CCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCC
Confidence            4678899  9999999974  8999999779999999999999764

the domains occurs between pairs og RING fingers

>KOG0006|consensus

Probab=97.48  E-value=6.5e-05  Score=58.36  Aligned_cols=60  Identities=27%  Similarity=0.689  Sum_probs=47.9

Q ss_pred             ccchhhhHHHHhhccccccCCCCcccCCCCCCceeecCCCCeeeccc--ccccccccccccccCC
Q psy12853         25 GHSRASVIWHRTQVSGATFDSELIKCCPMCSVPIEKDEGCAQMLCKR--CKHVFCWYCLASRDYG   87 (137)
Q Consensus        25 ~~~~~~~~~~r~~~~~a~~~~~~~~~CP~C~~~i~~~~~~~~~~C~~--C~~~fC~~C~~~~h~~   87 (137)
                      ++.+++++|....-.   ......+.||+|..+.++++|+..|.|+.  |+...||.|+.+|...
T Consensus       377 e~~a~~arwd~as~~---TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~eWCw~C~tEW~r~  438 (446)
T KOG0006|consen  377 ERAAEQARWDAASKE---TIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLEWCWNCGTEWNRV  438 (446)
T ss_pred             hhhhhhhhhhhhhhh---hhhhccCCCCCccCccccCCceEEeecCCCCCCceeEeccCChhhhh
Confidence            334456677665322   25667899999999999999999999985  9999999999999764

>KOG1814|consensus

Probab=97.19  E-value=0.00018  Score=57.44  Aligned_cols=43  Identities=40%  Similarity=0.891  Sum_probs=38.5

Q ss_pred             CCCCcccCCCCCCceeecCCCCeeecccccccccccccccccC
Q psy12853         44 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDY   86 (137)
Q Consensus        44 ~~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~   86 (137)
                      ...+.+.||.|..+|++.+|++.|.|..|++.|||.|.....+
T Consensus       364 l~~N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l~~  406 (445)
T KOG1814|consen  364 LESNSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELLYP  406 (445)
T ss_pred             HHhcCCCCCcccceeecCCCccceeeccccccceeehhhhcCC
Confidence            3467899999999999999999999999999999999986553

>KOG1812|consensus

Probab=97.18  E-value=0.00018  Score=57.71  Aligned_cols=42  Identities=36%  Similarity=0.886  Sum_probs=38.7

Q ss_pred             CCcccCCCCCCceeecCCCCeeecccccccccccccccccCCC
Q psy12853         46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGG   88 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~   88 (137)
                      ...+.||.|...|+...|++.|+|. |++.||+.|+.+|..+.
T Consensus       304 ~~wr~CpkC~~~ie~~~GCnhm~Cr-C~~~fcy~C~~~~~~~~  345 (384)
T KOG1812|consen  304 KRWRQCPKCKFMIELSEGCNHMTCR-CGHQFCYMCGGDWKTHN  345 (384)
T ss_pred             HhcCcCcccceeeeecCCcceEEee-ccccchhhcCcchhhCC
Confidence            6689999999999999999999997 99999999999987764

>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=96.39  E-value=0.0036  Score=32.40  Aligned_cols=29  Identities=24%  Similarity=0.527  Sum_probs=19.7

Q ss_pred             CcccCCCCCCceeecCCCCeeeccccccc
Q psy12853         47 LIKCCPMCSVPIEKDEGCAQMLCKRCKHV   75 (137)
Q Consensus        47 ~~~~CP~C~~~i~~~~~~~~~~C~~C~~~   75 (137)
                      +.+|||.|+.+.....+....+|+.|+..
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            46799999999999888889999998864

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

>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional

Probab=96.04  E-value=0.0087  Score=35.34  Aligned_cols=47  Identities=28%  Similarity=0.639  Sum_probs=33.1

Q ss_pred             cccCCCCCCceeecCCCCeeeccccccc---ccccccccccCCCCcccccccCCCCCCCc
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHV---FCWYCLASRDYGGATFDSELIKCCPMCSV  104 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~---fC~~C~~~~h~~~~~~~~~~~~~CP~C~~  104 (137)
                      ...|-.|+..|...+....+.||.||..   -|..|++.          .+.-.||+|+.
T Consensus         7 ~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~----------~~~Y~CP~CGF   56 (59)
T PRK14890          7 PPKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQ----------SNPYTCPKCGF   56 (59)
T ss_pred             CccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHhc----------CCceECCCCCC
Confidence            4467789988876666788999999876   45666543          23447888875

>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=96.01  E-value=0.0031  Score=31.20  Aligned_cols=24  Identities=29%  Similarity=0.830  Sum_probs=15.8

Q ss_pred             CCCCCCCcceeecCCCCeEEeccCccee
Q psy12853         97 KCCPMCSVPIEKDEGCAQMLCKRCKHVF  124 (137)
Q Consensus        97 ~~CP~C~~~iek~~gC~hm~C~~C~~~f  124 (137)
                      |.||.|+..|..+    -..|..||+.|
T Consensus         1 K~CP~C~~~V~~~----~~~Cp~CG~~F   24 (26)
T PF10571_consen    1 KTCPECGAEVPES----AKFCPHCGYDF   24 (26)
T ss_pred             CcCCCCcCCchhh----cCcCCCCCCCC
Confidence            5788888888442    24455577776

Several members are annotated as putative helicases.

>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=95.89  E-value=0.003  Score=36.33  Aligned_cols=45  Identities=29%  Similarity=0.727  Sum_probs=24.4

Q ss_pred             CCCCCCceeecC----CCCeeecccccccccccccccccCCCCcccccccCCCCCCC
Q psy12853         51 CPMCSVPIEKDE----GCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCS  103 (137)
Q Consensus        51 CP~C~~~i~~~~----~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~  103 (137)
                      |-+|..++....    +.....|++|+..||..|-.=.|        +....||.|.
T Consensus         2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiH--------E~LH~CPGC~   50 (51)
T PF07975_consen    2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIH--------ETLHNCPGCE   50 (51)
T ss_dssp             ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTT--------TTS-SSSTT-
T ss_pred             CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhh--------ccccCCcCCC
Confidence            445666554432    24679999999999999976444        4577899985

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.

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=95.81  E-value=0.0085  Score=32.09  Aligned_cols=29  Identities=34%  Similarity=0.874  Sum_probs=22.8

Q ss_pred             cccCCCCCCceeecC-----CCCeeecccccccc
Q psy12853         48 IKCCPMCSVPIEKDE-----GCAQMLCKRCKHVF   76 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~-----~~~~~~C~~C~~~f   76 (137)
                      ...||+|+..+..++     +...+.|++|++.|
T Consensus         2 ~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f   35 (37)
T PF13719_consen    2 IITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF   35 (37)
T ss_pred             EEECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence            357999999988754     36689999998876

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=95.50  E-value=0.013  Score=33.36  Aligned_cols=27  Identities=30%  Similarity=0.769  Sum_probs=20.2

Q ss_pred             ccCCCCCCceeecCC--CCeeeccccccc
Q psy12853         49 KCCPMCSVPIEKDEG--CAQMLCKRCKHV   75 (137)
Q Consensus        49 ~~CP~C~~~i~~~~~--~~~~~C~~C~~~   75 (137)
                      ++||.|+..+....+  .+...|+.|++.
T Consensus         1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~   29 (52)
T smart00661        1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYE   29 (52)
T ss_pred             CCCCCCCCccccccCCCCCEEECCcCCCe
Confidence            489999998876543  247889988865

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=95.49  E-value=0.012  Score=31.27  Aligned_cols=28  Identities=36%  Similarity=0.857  Sum_probs=22.2

Q ss_pred             ccCCCCCCceeecC-----CCCeeecccccccc
Q psy12853         49 KCCPMCSVPIEKDE-----GCAQMLCKRCKHVF   76 (137)
Q Consensus        49 ~~CP~C~~~i~~~~-----~~~~~~C~~C~~~f   76 (137)
                      ..||+|+..+..++     ....++|++|++.|
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            57999999888754     35689999998875

>KOG1815|consensus

Probab=95.42  E-value=0.01  Score=48.62  Aligned_cols=44  Identities=57%  Similarity=1.111  Sum_probs=38.3

Q ss_pred             CCCCcccCCCCCCceeecCCCCeeeccc--ccccccccccccccCC
Q psy12853         44 DSELIKCCPMCSVPIEKDEGCAQMLCKR--CKHVFCWYCLASRDYG   87 (137)
Q Consensus        44 ~~~~~~~CP~C~~~i~~~~~~~~~~C~~--C~~~fC~~C~~~~h~~   87 (137)
                      ...+.+.||.|..+++++.|.+.+.|..  |++.|||.|...|...
T Consensus       222 i~~ntk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h  267 (444)
T KOG1815|consen  222 ILANTKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDH  267 (444)
T ss_pred             hhccCccCCCcccchhccCCccccccccCCcCCeeceeeecccccc
Confidence            3677888999999999999999999976  9999999997776555

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

Probab=95.04  E-value=0.019  Score=30.19  Aligned_cols=27  Identities=30%  Similarity=0.936  Sum_probs=15.6

Q ss_pred             ccCCCCCCceeec----CCCCeeeccccccc
Q psy12853         49 KCCPMCSVPIEKD----EGCAQMLCKRCKHV   75 (137)
Q Consensus        49 ~~CP~C~~~i~~~----~~~~~~~C~~C~~~   75 (137)
                      +|||.|+.+++..    ++-.+..|+.|+..
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            5899999998763    24567889998864

>PF12773 DZR: Double zinc ribbon

Probab=94.86  E-value=0.031  Score=31.57  Aligned_cols=14  Identities=36%  Similarity=0.949  Sum_probs=7.7

Q ss_pred             CCcccCCCCCCcee
Q psy12853         46 ELIKCCPMCSVPIE   59 (137)
Q Consensus        46 ~~~~~CP~C~~~i~   59 (137)
                      ++.++||.|+..+.
T Consensus        10 ~~~~fC~~CG~~l~   23 (50)
T PF12773_consen   10 DDAKFCPHCGTPLP   23 (50)
T ss_pred             ccccCChhhcCChh
Confidence            34555666655554

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

Probab=94.86  E-value=0.03  Score=31.26  Aligned_cols=29  Identities=24%  Similarity=0.407  Sum_probs=20.3

Q ss_pred             ccCCCCCCceeecCCCCeeeccccccccc
Q psy12853         49 KCCPMCSVPIEKDEGCAQMLCKRCKHVFC   77 (137)
Q Consensus        49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~fC   77 (137)
                      ..||+|+..+..++....+.||.||..+=
T Consensus         4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~   32 (46)
T PRK00398          4 YKCARCGREVELDEYGTGVRCPYCGYRIL   32 (46)
T ss_pred             EECCCCCCEEEECCCCCceECCCCCCeEE
Confidence            46888888887766544777887776543

>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]

Probab=94.85  E-value=0.022  Score=33.61  Aligned_cols=50  Identities=22%  Similarity=0.472  Sum_probs=33.8

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCc
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSV  104 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~  104 (137)
                      ...|-.|+..|........+.||+||...=+.|..-       -...+.-+||+|+.
T Consensus         9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc~~C-------Rk~g~~Y~Cp~CGF   58 (61)
T COG2888           9 PPVCTSCGREIAPGETAVKFPCPNCGEVEIYRCAKC-------RKLGNPYRCPKCGF   58 (61)
T ss_pred             CceeccCCCEeccCCceeEeeCCCCCceeeehhhhH-------HHcCCceECCCcCc
Confidence            456778999887777788899999995554444321       01234557999875

>PF12773 DZR: Double zinc ribbon

Probab=94.67  E-value=0.019  Score=32.50  Aligned_cols=42  Identities=26%  Similarity=0.566  Sum_probs=25.4

Q ss_pred             CCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853         51 CPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD  109 (137)
Q Consensus        51 CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~  109 (137)
                      ||.|+..+..            +..||..|+....     ......+.||+|+..+...
T Consensus         1 Cp~Cg~~~~~------------~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~~~~~~   42 (50)
T PF12773_consen    1 CPHCGTPNPD------------DAKFCPHCGTPLP-----PPDQSKKICPNCGAENPPN   42 (50)
T ss_pred             CCCcCCcCCc------------cccCChhhcCChh-----hccCCCCCCcCCcCCCcCC
Confidence            6777777543            2556666665322     1133466788888887654

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=94.66  E-value=0.038  Score=31.34  Aligned_cols=27  Identities=26%  Similarity=0.682  Sum_probs=21.0

Q ss_pred             CCCCCCcceeecCC--CCeEEeccCccee
Q psy12853         98 CCPMCSVPIEKDEG--CAQMLCKRCKHVF  124 (137)
Q Consensus        98 ~CP~C~~~iek~~g--C~hm~C~~C~~~f  124 (137)
                      -||.|+.++...++  -++..|+.||+.+
T Consensus         2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~   30 (52)
T smart00661        2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEE   30 (52)
T ss_pred             CCCCCCCccccccCCCCCEEECCcCCCeE
Confidence            58999988877543  4688999999875

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=94.31  E-value=0.058  Score=28.68  Aligned_cols=28  Identities=25%  Similarity=0.717  Sum_probs=19.4

Q ss_pred             ccCCCCCCceeecC-----CCCeeecccccccc
Q psy12853         49 KCCPMCSVPIEKDE-----GCAQMLCKRCKHVF   76 (137)
Q Consensus        49 ~~CP~C~~~i~~~~-----~~~~~~C~~C~~~f   76 (137)
                      ..||+|+..+..++     ....+.|++|+..|
T Consensus         3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~   35 (38)
T TIGR02098         3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW   35 (38)
T ss_pred             EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence            46888888777653     23468888887654

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.

>PRK14559 putative protein serine/threonine phosphatase; Provisional

Probab=93.97  E-value=0.031  Score=47.83  Aligned_cols=10  Identities=40%  Similarity=1.089  Sum_probs=6.1

Q ss_pred             CCCCCCCcce
Q psy12853         97 KCCPMCSVPI  106 (137)
Q Consensus        97 ~~CP~C~~~i  106 (137)
                      +.||+|+..+
T Consensus        28 ~~Cp~CG~~~   37 (645)
T PRK14559         28 KPCPQCGTEV   37 (645)
T ss_pred             CcCCCCCCCC
Confidence            3566666665

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

Probab=93.64  E-value=0.045  Score=28.92  Aligned_cols=27  Identities=22%  Similarity=0.589  Sum_probs=17.5

Q ss_pred             ccCCCCCCceeecC-CCCeeeccccccc
Q psy12853         49 KCCPMCSVPIEKDE-GCAQMLCKRCKHV   75 (137)
Q Consensus        49 ~~CP~C~~~i~~~~-~~~~~~C~~C~~~   75 (137)
                      ++||.|+..+.... ....+.|..|++.
T Consensus         2 ~FCp~C~nlL~p~~~~~~~~~C~~C~Y~   29 (35)
T PF02150_consen    2 RFCPECGNLLYPKEDKEKRVACRTCGYE   29 (35)
T ss_dssp             -BETTTTSBEEEEEETTTTEEESSSS-E
T ss_pred             eeCCCCCccceEcCCCccCcCCCCCCCc
Confidence            68999999987753 2332377777764

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 ....

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

Probab=93.38  E-value=0.089  Score=29.30  Aligned_cols=28  Identities=25%  Similarity=0.446  Sum_probs=16.8

Q ss_pred             CCCCCCcceeecCCCCeEEeccCcceee
Q psy12853         98 CCPMCSVPIEKDEGCAQMLCKRCKHVFC  125 (137)
Q Consensus        98 ~CP~C~~~iek~~gC~hm~C~~C~~~fC  125 (137)
                      +||+|+..++....=..++|..||..+=
T Consensus         5 ~C~~CG~~~~~~~~~~~~~Cp~CG~~~~   32 (46)
T PRK00398          5 KCARCGREVELDEYGTGVRCPYCGYRIL   32 (46)
T ss_pred             ECCCCCCEEEECCCCCceECCCCCCeEE
Confidence            5677776666554433566666666543

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

Probab=93.29  E-value=0.045  Score=31.06  Aligned_cols=47  Identities=23%  Similarity=0.644  Sum_probs=21.0

Q ss_pred             CCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcce
Q psy12853         51 CPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPI  106 (137)
Q Consensus        51 CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~i  106 (137)
                      ||.|...+ -..+.....| .|++.+|.-|...   -.    ....-+||.|+.+.
T Consensus         1 cp~C~e~~-d~~d~~~~PC-~Cgf~IC~~C~~~---i~----~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEEL-DETDKDFYPC-ECGFQICRFCYHD---IL----ENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B---CCCTT--SS-TTS----HHHHHH---HT----TSS-SB-TTT--B-
T ss_pred             CCCccccc-ccCCCccccC-cCCCcHHHHHHHH---HH----hccCCCCCCCCCCC
Confidence            57777777 2245677889 7999999999532   11    12355899999865

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=93.15  E-value=0.06  Score=30.80  Aligned_cols=30  Identities=23%  Similarity=0.441  Sum_probs=20.9

Q ss_pred             CCcccCCCCCCceeecCCCCeeecccccccc
Q psy12853         46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVF   76 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~f   76 (137)
                      ...++||.|+..+.. .....+.|.+|+..+
T Consensus        18 ~~~~fCP~Cg~~~m~-~~~~r~~C~~Cgyt~   47 (50)
T PRK00432         18 RKNKFCPRCGSGFMA-EHLDRWHCGKCGYTE   47 (50)
T ss_pred             EccCcCcCCCcchhe-ccCCcEECCCcCCEE
Confidence            457799999984222 233678899998764

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

Probab=92.96  E-value=0.045  Score=29.17  Aligned_cols=32  Identities=34%  Similarity=0.807  Sum_probs=22.6

Q ss_pred             ecccccccccccccccccCCCCcccccccCCCCCCCcce
Q psy12853         68 LCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPI  106 (137)
Q Consensus        68 ~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~i  106 (137)
                      .-+.|++.||..|...|-..       ...+||.|+..+
T Consensus        14 ~~~~C~H~~c~~C~~~~~~~-------~~~~Cp~C~~~~   45 (45)
T cd00162          14 VLLPCGHVFCRSCIDKWLKS-------GKNTCPLCRTPI   45 (45)
T ss_pred             EecCCCChhcHHHHHHHHHh-------CcCCCCCCCCcC
Confidence            33458999999998765432       345799988653

>PRK04023 DNA polymerase II large subunit; Validated

Probab=92.96  E-value=0.094  Score=46.75  Aligned_cols=48  Identities=19%  Similarity=0.301  Sum_probs=32.4

Q ss_pred             CCCCcccCCCCCCceeecCCCCeeecccccc-----cccccccccccCCCCcccccccCCCCCCCccee
Q psy12853         44 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKH-----VFCWYCLASRDYGGATFDSELIKCCPMCSVPIE  107 (137)
Q Consensus        44 ~~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~-----~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~ie  107 (137)
                      .....++||.|+...      ..+.||.||.     .||-.|+..-.          ...||+|+..+.
T Consensus       622 VEVg~RfCpsCG~~t------~~frCP~CG~~Te~i~fCP~CG~~~~----------~y~CPKCG~El~  674 (1121)
T PRK04023        622 VEIGRRKCPSCGKET------FYRRCPFCGTHTEPVYRCPRCGIEVE----------EDECEKCGREPT  674 (1121)
T ss_pred             ecccCccCCCCCCcC------CcccCCCCCCCCCcceeCccccCcCC----------CCcCCCCCCCCC
Confidence            345578999999874      4578888885     47888864311          235888877654

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

Probab=92.93  E-value=0.12  Score=31.64  Aligned_cols=21  Identities=29%  Similarity=0.874  Sum_probs=7.9

Q ss_pred             CCCCCcceeecCCCCeEEeccCc
Q psy12853         99 CPMCSVPIEKDEGCAQMLCKRCK  121 (137)
Q Consensus        99 CP~C~~~iek~~gC~hm~C~~C~  121 (137)
                      ||.|+..++..+  .+..|..|+
T Consensus         4 CP~C~~~L~~~~--~~~~C~~C~   24 (70)
T PF07191_consen    4 CPKCQQELEWQG--GHYHCEACQ   24 (70)
T ss_dssp             -SSS-SBEEEET--TEEEETTT-
T ss_pred             CCCCCCccEEeC--CEEECcccc
Confidence            444444444444  244444443

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

>TIGR00622 ssl1 transcription factor ssl1

Probab=92.84  E-value=0.13  Score=34.36  Aligned_cols=48  Identities=31%  Similarity=0.761  Sum_probs=36.7

Q ss_pred             cccCCCCCCceeec--------CCCCeeecccccccccccccccccCCCCcccccccCCCCCCC
Q psy12853         48 IKCCPMCSVPIEKD--------EGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCS  103 (137)
Q Consensus        48 ~~~CP~C~~~i~~~--------~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~  103 (137)
                      .+.|-+|...+...        ......+|++|+..||..|..-+|+.        ...||.|.
T Consensus        55 ~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~--------Lh~CPGC~  110 (112)
T TIGR00622        55 SRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHES--------LHCCPGCI  110 (112)
T ss_pred             CCcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhh--------ccCCcCCC
Confidence            45699999987642        12456889999999999998766654        66799986

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

>PRK14714 DNA polymerase II large subunit; Provisional

Probab=92.80  E-value=0.1  Score=47.50  Aligned_cols=49  Identities=24%  Similarity=0.462  Sum_probs=29.9

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccc-----cccccccccCCCCcccccccCCCCCCCccee
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVF-----CWYCLASRDYGGATFDSELIKCCPMCSVPIE  107 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~f-----C~~C~~~~h~~~~~~~~~~~~~CP~C~~~ie  107 (137)
                      .+.||+|+.....      ..||.||...     |-.|+.+...+.     .....||.|+..+.
T Consensus       667 ~rkCPkCG~~t~~------~fCP~CGs~te~vy~CPsCGaev~~de-----s~a~~CP~CGtplv  720 (1337)
T PRK14714        667 RRRCPSCGTETYE------NRCPDCGTHTEPVYVCPDCGAEVPPDE-----SGRVECPRCDVELT  720 (1337)
T ss_pred             EEECCCCCCcccc------ccCcccCCcCCCceeCccCCCccCCCc-----cccccCCCCCCccc
Confidence            5788888886432      2788887664     777766433221     11446777776553

>PHA00626 hypothetical protein

Probab=92.66  E-value=0.11  Score=30.35  Aligned_cols=27  Identities=26%  Similarity=0.602  Sum_probs=18.3

Q ss_pred             CCCCCCc-ceeecCCCC----eEEeccCccee
Q psy12853         98 CCPMCSV-PIEKDEGCA----QMLCKRCKHVF  124 (137)
Q Consensus        98 ~CP~C~~-~iek~~gC~----hm~C~~C~~~f  124 (137)
                      .||+|+. .|-|.+-|+    ...|..||+.|
T Consensus         2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~f   33 (59)
T PHA00626          2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYND   33 (59)
T ss_pred             CCCCCCCceeeeeceecccCcceEcCCCCCee
Confidence            5888888 466765543    37777777766

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=92.64  E-value=0.071  Score=26.15  Aligned_cols=11  Identities=36%  Similarity=0.996  Sum_probs=7.3

Q ss_pred             CCCCCCCccee
Q psy12853         97 KCCPMCSVPIE  107 (137)
Q Consensus        97 ~~CP~C~~~ie  107 (137)
                      +.||+|+..|+
T Consensus         3 ~~Cp~Cg~~~~   13 (26)
T PF13248_consen    3 MFCPNCGAEID   13 (26)
T ss_pred             CCCcccCCcCC
Confidence            56777777653

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=92.23  E-value=0.15  Score=29.17  Aligned_cols=28  Identities=21%  Similarity=0.465  Sum_probs=20.8

Q ss_pred             ccCCCCCCCc-ceeecCCCCeEEeccCccee
Q psy12853         95 LIKCCPMCSV-PIEKDEGCAQMLCKRCKHVF  124 (137)
Q Consensus        95 ~~~~CP~C~~-~iek~~gC~hm~C~~C~~~f  124 (137)
                      ..+-||+|+. ......  +.+.|..||+.+
T Consensus        19 ~~~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~   47 (50)
T PRK00432         19 KNKFCPRCGSGFMAEHL--DRWHCGKCGYTE   47 (50)
T ss_pred             ccCcCcCCCcchheccC--CcEECCCcCCEE
Confidence            4568999988 444434  689999999875

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

Probab=91.65  E-value=0.17  Score=31.03  Aligned_cols=57  Identities=26%  Similarity=0.718  Sum_probs=28.9

Q ss_pred             cCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCCCCeEEeccCc--ceeecc
Q psy12853         50 CCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCK--HVFCWY  127 (137)
Q Consensus        50 ~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~gC~hm~C~~C~--~~fC~~  127 (137)
                      .||.|...+...+  ....|..|...|                 ...-.||.|+.++|+-..        ||  -.||=.
T Consensus         3 ~CP~C~~~L~~~~--~~~~C~~C~~~~-----------------~~~a~CPdC~~~Le~LkA--------CGAvdYFC~~   55 (70)
T PF07191_consen    3 TCPKCQQELEWQG--GHYHCEACQKDY-----------------KKEAFCPDCGQPLEVLKA--------CGAVDYFCNH   55 (70)
T ss_dssp             B-SSS-SBEEEET--TEEEETTT--EE-----------------EEEEE-TTT-SB-EEEEE--------TTEEEEE-TT
T ss_pred             cCCCCCCccEEeC--CEEECccccccc-----------------eecccCCCcccHHHHHHH--------hcccceeecc
Confidence            6999999987755  455665554432                 123369999999987543        44  345555


Q ss_pred             cccccc
Q psy12853        128 CLASLD  133 (137)
Q Consensus       128 C~~~~~  133 (137)
                      |.+-.+
T Consensus        56 c~gLiS   61 (70)
T PF07191_consen   56 CHGLIS   61 (70)
T ss_dssp             TT-EE-
T ss_pred             CCceee
Confidence            554433

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

>KOG0317|consensus

Probab=91.36  E-value=0.056  Score=41.65  Aligned_cols=33  Identities=30%  Similarity=0.882  Sum_probs=26.6

Q ss_pred             cccccccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853         69 CKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD  109 (137)
Q Consensus        69 C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~  109 (137)
                      |.-||+.|||.|-.+|-....        .||-|+.....+
T Consensus       254 aTpCGHiFCWsCI~~w~~ek~--------eCPlCR~~~~ps  286 (293)
T KOG0317|consen  254 ATPCGHIFCWSCILEWCSEKA--------ECPLCREKFQPS  286 (293)
T ss_pred             cCcCcchHHHHHHHHHHcccc--------CCCcccccCCCc
Confidence            345999999999999987754        399999887654

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=91.36  E-value=0.12  Score=24.64  Aligned_cols=11  Identities=45%  Similarity=1.090  Sum_probs=7.3

Q ss_pred             CCCCCCcceee
Q psy12853         98 CCPMCSVPIEK  108 (137)
Q Consensus        98 ~CP~C~~~iek  108 (137)
                      .||+|+..|+.
T Consensus         1 ~Cp~CG~~~~~   11 (23)
T PF13240_consen    1 YCPNCGAEIED   11 (23)
T ss_pred             CCcccCCCCCC
Confidence            37777777754

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

Probab=91.25  E-value=0.038  Score=31.23  Aligned_cols=30  Identities=40%  Similarity=0.815  Sum_probs=23.6

Q ss_pred             ccccc-ccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853         71 RCKHV-FCWYCLASRDYGGATFDSELIKCCPMCSVPIEK  108 (137)
Q Consensus        71 ~C~~~-fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek  108 (137)
                      .|++. ||..|...|..        ..++||-|+..|++
T Consensus        19 pCgH~~~C~~C~~~~~~--------~~~~CP~Cr~~i~~   49 (50)
T PF13920_consen   19 PCGHLCFCEECAERLLK--------RKKKCPICRQPIES   49 (50)
T ss_dssp             TTCEEEEEHHHHHHHHH--------TTSBBTTTTBB-SE
T ss_pred             CCCChHHHHHHhHHhcc--------cCCCCCcCChhhcC
Confidence            58999 99999876544        45789999999975

...

>PHA02926 zinc finger-like protein; Provisional

Probab=90.75  E-value=0.082  Score=39.50  Aligned_cols=59  Identities=20%  Similarity=0.481  Sum_probs=37.9

Q ss_pred             cccCCCCCCceeecC--CC-CeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853         48 IKCCPMCSVPIEKDE--GC-AQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK  108 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~--~~-~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek  108 (137)
                      -.-|+=|-..+....  +. ..-.=+.|++.||+.|-..|.....  .....+.||-|++....
T Consensus       170 E~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~--~~~~~rsCPiCR~~f~~  231 (242)
T PHA02926        170 EKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRR--ETGASDNCPICRTRFRN  231 (242)
T ss_pred             CCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhcc--ccCcCCcCCCCcceeee
Confidence            456777776553221  11 1111236999999999999987532  23446789999988753

>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species

Probab=90.54  E-value=0.26  Score=23.81  Aligned_cols=21  Identities=29%  Similarity=0.684  Sum_probs=12.1

Q ss_pred             CCCCceeecCCCCeeeccccc
Q psy12853         53 MCSVPIEKDEGCAQMLCKRCK   73 (137)
Q Consensus        53 ~C~~~i~~~~~~~~~~C~~C~   73 (137)
                      .|+..|..-.....+.||+||
T Consensus         3 sC~~~i~~r~~~v~f~CPnCG   23 (24)
T PF07754_consen    3 SCGRPIAPREQAVPFPCPNCG   23 (24)
T ss_pred             cCCCcccCcccCceEeCCCCC
Confidence            455555543445666777765

It is likely to bind zinc via its four well-conserved cysteine residues.

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

Probab=90.44  E-value=0.34  Score=42.22  Aligned_cols=47  Identities=26%  Similarity=0.665  Sum_probs=34.5

Q ss_pred             CCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCCCCeEEeccCcce-----eecccccc
Q psy12853         64 CAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHV-----FCWYCLAS  131 (137)
Q Consensus        64 ~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~gC~hm~C~~C~~~-----fC~~C~~~  131 (137)
                      ...+.|..||+.+.                     ||+|.....-...=+.|.|..||++     .|-.||..
T Consensus       433 s~~l~C~~Cg~v~~---------------------Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~  484 (730)
T COG1198         433 APLLLCRDCGYIAE---------------------CPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE  484 (730)
T ss_pred             cceeecccCCCccc---------------------CCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence            44667777766553                     8888888776655588888888887     68888876

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

Probab=90.44  E-value=0.3  Score=32.69  Aligned_cols=30  Identities=17%  Similarity=0.595  Sum_probs=23.2

Q ss_pred             cccCCCCCCceeec--CCCCeeeccccccccc
Q psy12853         48 IKCCPMCSVPIEKD--EGCAQMLCKRCKHVFC   77 (137)
Q Consensus        48 ~~~CP~C~~~i~~~--~~~~~~~C~~C~~~fC   77 (137)
                      .++||.|+..+...  ++...+.|++|++..=
T Consensus         2 m~FCp~Cgsll~p~~~~~~~~l~C~kCgye~~   33 (113)
T COG1594           2 MRFCPKCGSLLYPKKDDEGGKLVCRKCGYEEE   33 (113)
T ss_pred             ccccCCccCeeEEeEcCCCcEEECCCCCcchh
Confidence            57999999998874  3456888988877653

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

Probab=90.31  E-value=0.25  Score=25.18  Aligned_cols=26  Identities=27%  Similarity=0.871  Sum_probs=13.7

Q ss_pred             CCCCCCcceeecCCCCeEEeccCccee
Q psy12853         98 CCPMCSVPIEKDEGCAQMLCKRCKHVF  124 (137)
Q Consensus        98 ~CP~C~~~iek~~gC~hm~C~~C~~~f  124 (137)
                      +||.|+....-.+|. .|.|..|+++|
T Consensus         4 ~Cp~C~se~~y~D~~-~~vCp~C~~ew   29 (30)
T PF08274_consen    4 KCPLCGSEYTYEDGE-LLVCPECGHEW   29 (30)
T ss_dssp             --TTT-----EE-SS-SEEETTTTEEE
T ss_pred             CCCCCCCcceeccCC-EEeCCcccccC
Confidence            689998888776664 46788888876

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.

>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=90.12  E-value=0.19  Score=33.47  Aligned_cols=31  Identities=19%  Similarity=0.506  Sum_probs=21.9

Q ss_pred             CcccCCCCCCceeecCCCCeeecccccccccc
Q psy12853         47 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCW   78 (137)
Q Consensus        47 ~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~   78 (137)
                      .-+-||.|+.-|.--.. ..++||+||+.|=.
T Consensus         8 tKR~Cp~CG~kFYDLnk-~PivCP~CG~~~~~   38 (108)
T PF09538_consen    8 TKRTCPSCGAKFYDLNK-DPIVCPKCGTEFPP   38 (108)
T ss_pred             CcccCCCCcchhccCCC-CCccCCCCCCccCc
Confidence            35678999988754333 67889988877643

The function of members of this family is unknown.

>TIGR01053 LSD1 zinc finger domain, LSD1 subclass

Probab=90.01  E-value=0.43  Score=24.50  Aligned_cols=27  Identities=22%  Similarity=0.555  Sum_probs=23.4

Q ss_pred             ccCCCCCCceeecCCCCeeeccccccc
Q psy12853         49 KCCPMCSVPIEKDEGCAQMLCKRCKHV   75 (137)
Q Consensus        49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~   75 (137)
                      ..|.+|+..+.+..|+..+.|..|+..
T Consensus         2 ~~C~~C~t~L~yP~gA~~vrCs~C~~v   28 (31)
T TIGR01053         2 VVCGGCRTLLMYPRGASSVRCALCQTV   28 (31)
T ss_pred             cCcCCCCcEeecCCCCCeEECCCCCeE
Confidence            368999999999999999999988753

This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC

>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=90.00  E-value=0.5  Score=24.15  Aligned_cols=28  Identities=25%  Similarity=0.582  Sum_probs=15.7

Q ss_pred             cCCCCCCCcceeecCCCCeEEeccCcce
Q psy12853         96 IKCCPMCSVPIEKDEGCAQMLCKRCKHV  123 (137)
Q Consensus        96 ~~~CP~C~~~iek~~gC~hm~C~~C~~~  123 (137)
                      .+-||.|+.+.+...+=.-|.|..||.+
T Consensus         3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~~   30 (32)
T PF09297_consen    3 HRFCGRCGAPTKPAPGGWARRCPSCGHE   30 (32)
T ss_dssp             TSB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred             CcccCcCCccccCCCCcCEeECCCCcCE
Confidence            4568888888887766455788877765

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

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=89.77  E-value=0.094  Score=38.33  Aligned_cols=58  Identities=22%  Similarity=0.608  Sum_probs=37.6

Q ss_pred             CCCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCc-------c-cccccCCCCCCCcceee
Q psy12853         45 SELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGAT-------F-DSELIKCCPMCSVPIEK  108 (137)
Q Consensus        45 ~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~-------~-~~~~~~~CP~C~~~iek  108 (137)
                      ......||-|...+.    ...+  ..|++.||+.|...|......       + ...+..+||.|+..|..
T Consensus        15 ~~~~~~CpICld~~~----dPVv--T~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~   80 (193)
T PLN03208         15 SGGDFDCNICLDQVR----DPVV--TLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE   80 (193)
T ss_pred             CCCccCCccCCCcCC----CcEE--cCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence            334567888876542    1222  369999999999988543211       1 12345689999998854

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

Probab=89.52  E-value=0.14  Score=31.98  Aligned_cols=61  Identities=20%  Similarity=0.502  Sum_probs=24.9

Q ss_pred             CcccCCCCCCceeec-CCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCCCCe
Q psy12853         47 LIKCCPMCSVPIEKD-EGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQ  114 (137)
Q Consensus        47 ~~~~CP~C~~~i~~~-~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~gC~h  114 (137)
                      +...|--|+--+-.. +|...+.|..|++-.|..|..       -..++..+-||.|++...+..|+..
T Consensus         8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyE-------YErkeg~q~CpqCkt~ykr~kgsp~   69 (80)
T PF14569_consen    8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYE-------YERKEGNQVCPQCKTRYKRHKGSPR   69 (80)
T ss_dssp             SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHH-------HHHHTS-SB-TTT--B----TT---
T ss_pred             CCcccccccCccccCCCCCEEEEEcccCCccchhHHH-------HHhhcCcccccccCCCcccccCCCC
Confidence            345666788777654 477889999999999999964       1124567899999999988777644

>KOG2932|consensus

Probab=89.47  E-value=0.093  Score=41.01  Aligned_cols=56  Identities=30%  Similarity=0.639  Sum_probs=42.5

Q ss_pred             CCCCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCCCCe
Q psy12853         44 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQ  114 (137)
Q Consensus        44 ~~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~gC~h  114 (137)
                      ..+.+.+|-.|+.+|..-+  +.+   -|++.||+.|...          ...|.||.|.-.|+|.+.|.-
T Consensus        86 l~p~VHfCd~Cd~PI~IYG--RmI---PCkHvFCl~CAr~----------~~dK~Cp~C~d~VqrIeq~~~  141 (389)
T KOG2932|consen   86 LGPRVHFCDRCDFPIAIYG--RMI---PCKHVFCLECARS----------DSDKICPLCDDRVQRIEQIMM  141 (389)
T ss_pred             cCcceEeecccCCcceeee--ccc---ccchhhhhhhhhc----------CccccCcCcccHHHHHHHhcc
Confidence            4566888899999986643  233   3689999999753          347889999999999887643

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=89.12  E-value=0.21  Score=39.07  Aligned_cols=54  Identities=24%  Similarity=0.579  Sum_probs=36.2

Q ss_pred             ccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecC
Q psy12853         49 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDE  110 (137)
Q Consensus        49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~  110 (137)
                      .-||.|..-....+.-..+.= .||+.||-.|....-       ..+..+||.|+..+.+..
T Consensus         4 ~~CP~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l~-------~~~~~~CP~C~~~lrk~~   57 (309)
T TIGR00570         4 QGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLLF-------VRGSGSCPECDTPLRKNN   57 (309)
T ss_pred             CCCCcCCCCCccCcccccccC-CCCCcccHHHHHHHh-------cCCCCCCCCCCCccchhh
Confidence            369999886555444332322 689999999986421       122348999999987753

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

>PRK00420 hypothetical protein; Validated

Probab=89.11  E-value=0.47  Score=31.75  Aligned_cols=40  Identities=23%  Similarity=0.414  Sum_probs=25.8

Q ss_pred             HHHHhhccccccCCCCcccCCCCCCceeecCCCCeeeccccccc
Q psy12853         32 IWHRTQVSGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHV   75 (137)
Q Consensus        32 ~~~r~~~~~a~~~~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~   75 (137)
                      +--++++..+.+.   ...||.|+.++... ....+.||.|+..
T Consensus        10 ~~a~~Ll~Ga~ml---~~~CP~Cg~pLf~l-k~g~~~Cp~Cg~~   49 (112)
T PRK00420         10 KAAELLLKGAKML---SKHCPVCGLPLFEL-KDGEVVCPVHGKV   49 (112)
T ss_pred             HHHHHHHhHHHHc---cCCCCCCCCcceec-CCCceECCCCCCe
Confidence            3334445555442   36899999998874 3446778877764

>PRK14559 putative protein serine/threonine phosphatase; Provisional

Probab=89.04  E-value=0.34  Score=41.67  Aligned_cols=11  Identities=27%  Similarity=0.709  Sum_probs=5.2

Q ss_pred             cCCCCCCCcce
Q psy12853         96 IKCCPMCSVPI  106 (137)
Q Consensus        96 ~~~CP~C~~~i  106 (137)
                      .+-||+|+..+
T Consensus        41 ~~fC~~CG~~~   51 (645)
T PRK14559         41 EAHCPNCGAET   51 (645)
T ss_pred             cccccccCCcc
Confidence            44455554443

>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=88.96  E-value=0.53  Score=25.74  Aligned_cols=26  Identities=27%  Similarity=0.611  Sum_probs=16.6

Q ss_pred             cCCCCCCce-eecCCCCeeeccccccc
Q psy12853         50 CCPMCSVPI-EKDEGCAQMLCKRCKHV   75 (137)
Q Consensus        50 ~CP~C~~~i-~~~~~~~~~~C~~C~~~   75 (137)
                      .||.|+... ..+.....+.|+.||..
T Consensus         2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~V   28 (43)
T PF08271_consen    2 KCPNCGSKEIVFDPERGELVCPNCGLV   28 (43)
T ss_dssp             SBTTTSSSEEEEETTTTEEEETTT-BB
T ss_pred             CCcCCcCCceEEcCCCCeEECCCCCCE
Confidence            588888864 44455666777777654

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.

>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=88.84  E-value=0.18  Score=26.85  Aligned_cols=31  Identities=26%  Similarity=0.752  Sum_probs=19.8

Q ss_pred             CCCCCcceeecCCCCeEEeccCcceeeccccccccc
Q psy12853         99 CPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDV  134 (137)
Q Consensus        99 CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~~~  134 (137)
                      ||-|...+..     -+.-..||+.||+.|...+..
T Consensus         1 C~iC~~~~~~-----~~~~~~CGH~fC~~C~~~~~~   31 (39)
T PF13923_consen    1 CPICLDELRD-----PVVVTPCGHSFCKECIEKYLE   31 (39)
T ss_dssp             ETTTTSB-SS-----EEEECTTSEEEEHHHHHHHHH
T ss_pred             CCCCCCcccC-----cCEECCCCCchhHHHHHHHHH
Confidence            4555444432     335557999999999877643

>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]

Probab=88.72  E-value=0.31  Score=27.75  Aligned_cols=30  Identities=17%  Similarity=0.441  Sum_probs=21.0

Q ss_pred             CCcccCCCCCCceeecCCCCeeeccccccc
Q psy12853         46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHV   75 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~   75 (137)
                      ...+.||+|+.......-..+..|.+|+..
T Consensus        17 rk~~~CPrCG~gvfmA~H~dR~~CGkCgyT   46 (51)
T COG1998          17 RKNRFCPRCGPGVFMADHKDRWACGKCGYT   46 (51)
T ss_pred             EccccCCCCCCcchhhhcCceeEeccccce
Confidence            346799999975554444458888888764

>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=88.13  E-value=0.54  Score=28.15  Aligned_cols=30  Identities=20%  Similarity=0.488  Sum_probs=22.8

Q ss_pred             ccCCCCCCCcceeecCCCCeEEeccCccee
Q psy12853         95 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF  124 (137)
Q Consensus        95 ~~~~CP~C~~~iek~~gC~hm~C~~C~~~f  124 (137)
                      +.+.||.|+...++...=..++|..||..+
T Consensus        27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~   56 (69)
T PF07282_consen   27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFEM   56 (69)
T ss_pred             CccCccCcccccccccccceEEcCCCCCEE
Confidence            578899999999885555568888777653

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

>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=87.82  E-value=0.57  Score=25.61  Aligned_cols=24  Identities=29%  Similarity=0.919  Sum_probs=17.6

Q ss_pred             ccCCCCCCceeecCCCCeeeccccc
Q psy12853         49 KCCPMCSVPIEKDEGCAQMLCKRCK   73 (137)
Q Consensus        49 ~~CP~C~~~i~~~~~~~~~~C~~C~   73 (137)
                      ..||.|+.++..+. ...+.|+.|+
T Consensus        18 ~~Cp~C~~PL~~~k-~g~~~Cv~C~   41 (41)
T PF06677_consen   18 EHCPDCGTPLMRDK-DGKIYCVSCG   41 (41)
T ss_pred             CccCCCCCeeEEec-CCCEECCCCC
Confidence            48999999988743 3457787764

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

>PF14369 zf-RING_3: zinc-finger

Probab=87.71  E-value=0.54  Score=24.76  Aligned_cols=29  Identities=21%  Similarity=0.446  Sum_probs=17.3

Q ss_pred             cccCCCCCCceeecC-CCCeeecccccccc
Q psy12853         48 IKCCPMCSVPIEKDE-GCAQMLCKRCKHVF   76 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~-~~~~~~C~~C~~~f   76 (137)
                      ..||=.|+..+.... +...+.||.|+..|
T Consensus         2 ~ywCh~C~~~V~~~~~~~~~~~CP~C~~gF   31 (35)
T PF14369_consen    2 RYWCHQCNRFVRIAPSPDSDVACPRCHGGF   31 (35)
T ss_pred             CEeCccCCCEeEeCcCCCCCcCCcCCCCcE
Confidence            347777777776643 23334577776554

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

Probab=87.45  E-value=0.64  Score=31.92  Aligned_cols=35  Identities=26%  Similarity=0.632  Sum_probs=23.7

Q ss_pred             HhhccccccCCCCcccCCCCCCceeecCCCCeeecccccc
Q psy12853         35 RTQVSGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKH   74 (137)
Q Consensus        35 r~~~~~a~~~~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~   74 (137)
                      ++++..|.+.   ...||.|+.++...  ...+.||.|++
T Consensus        18 ~lLl~GAkML---~~hCp~Cg~PLF~K--dG~v~CPvC~~   52 (131)
T COG1645          18 ELLLQGAKML---AKHCPKCGTPLFRK--DGEVFCPVCGY   52 (131)
T ss_pred             HHHHhhhHHH---HhhCcccCCcceee--CCeEECCCCCc
Confidence            4445555443   45899999998773  34577887775

>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=87.27  E-value=0.5  Score=28.31  Aligned_cols=33  Identities=18%  Similarity=0.455  Sum_probs=26.2

Q ss_pred             CCCCcccCCCCCCceeecCCCCeeecccccccc
Q psy12853         44 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVF   76 (137)
Q Consensus        44 ~~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~f   76 (137)
                      .....+.||.|+...........+.|+.||..+
T Consensus        24 ~~~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~   56 (69)
T PF07282_consen   24 EAYTSQTCPRCGHRNKKRRSGRVFTCPNCGFEM   56 (69)
T ss_pred             CCCCccCccCcccccccccccceEEcCCCCCEE
Confidence            344688999999998886677889999887653

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

>KOG2906|consensus

Probab=87.10  E-value=0.55  Score=30.60  Aligned_cols=27  Identities=33%  Similarity=0.920  Sum_probs=21.4

Q ss_pred             CCCCCCccee--ecCCCCeEEeccCccee
Q psy12853         98 CCPMCSVPIE--KDEGCAQMLCKRCKHVF  124 (137)
Q Consensus        98 ~CP~C~~~ie--k~~gC~hm~C~~C~~~f  124 (137)
                      -||.|+.++.  ..+.||...|+.|.+.|
T Consensus         3 FCP~Cgn~Live~g~~~~rf~C~tCpY~~   31 (105)
T KOG2906|consen    3 FCPTCGNMLIVESGESCNRFSCRTCPYVF   31 (105)
T ss_pred             ccCCCCCEEEEecCCeEeeEEcCCCCcee
Confidence            4899987654  44559999999999876

>KOG0823|consensus

Probab=87.02  E-value=0.27  Score=36.76  Aligned_cols=48  Identities=25%  Similarity=0.603  Sum_probs=33.7

Q ss_pred             CCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853         53 MCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK  108 (137)
Q Consensus        53 ~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek  108 (137)
                      +|+.-+.. ..++.+++  ||+-|||-|...|-..     ..+.+-||-|+..|..
T Consensus        49 dCNICLd~-akdPVvTl--CGHLFCWpClyqWl~~-----~~~~~~cPVCK~~Vs~   96 (230)
T KOG0823|consen   49 DCNICLDL-AKDPVVTL--CGHLFCWPCLYQWLQT-----RPNSKECPVCKAEVSI   96 (230)
T ss_pred             eeeeeccc-cCCCEEee--cccceehHHHHHHHhh-----cCCCeeCCcccccccc
Confidence            56665544 23566666  9999999999887443     2456778999887754

>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=86.98  E-value=0.84  Score=22.25  Aligned_cols=24  Identities=21%  Similarity=0.577  Sum_probs=20.3

Q ss_pred             CCCCCCceeecCCCCeeecccccc
Q psy12853         51 CPMCSVPIEKDEGCAQMLCKRCKH   74 (137)
Q Consensus        51 CP~C~~~i~~~~~~~~~~C~~C~~   74 (137)
                      |-+|...+.+..|+..+.|..|++
T Consensus         1 C~~Cr~~L~yp~GA~sVrCa~C~~   24 (25)
T PF06943_consen    1 CGGCRTLLMYPRGAPSVRCACCHT   24 (25)
T ss_pred             CCCCCceEEcCCCCCCeECCccCc
Confidence            457889999989999999988865

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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].

>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=86.96  E-value=0.41  Score=31.83  Aligned_cols=27  Identities=22%  Similarity=0.722  Sum_probs=12.7

Q ss_pred             CCCCCCCcceeecCCCCeEEeccCccee
Q psy12853         97 KCCPMCSVPIEKDEGCAQMLCKRCKHVF  124 (137)
Q Consensus        97 ~~CP~C~~~iek~~gC~hm~C~~C~~~f  124 (137)
                      +.||.|+...---.. +-++|..||+.|
T Consensus        10 R~Cp~CG~kFYDLnk-~PivCP~CG~~~   36 (108)
T PF09538_consen   10 RTCPSCGAKFYDLNK-DPIVCPKCGTEF   36 (108)
T ss_pred             ccCCCCcchhccCCC-CCccCCCCCCcc
Confidence            445555554433222 445555555544

The function of members of this family is unknown.

>PRK05654 acetyl-CoA carboxylase subunit beta; Validated

Probab=86.52  E-value=0.13  Score=39.94  Aligned_cols=30  Identities=27%  Similarity=0.664  Sum_probs=23.6

Q ss_pred             ccCCCCCCCcceeecC-CCCeEEeccCccee
Q psy12853         95 LIKCCPMCSVPIEKDE-GCAQMLCKRCKHVF  124 (137)
Q Consensus        95 ~~~~CP~C~~~iek~~-gC~hm~C~~C~~~f  124 (137)
                      .|.+||+|+..+.+.+ .=|.+.|..||++|
T Consensus        26 ~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~   56 (292)
T PRK05654         26 LWTKCPSCGQVLYRKELEANLNVCPKCGHHM   56 (292)
T ss_pred             CeeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence            4889999998887643 44678898899887

>PLN02189 cellulose synthase

Probab=86.46  E-value=0.64  Score=41.82  Aligned_cols=63  Identities=21%  Similarity=0.496  Sum_probs=48.7

Q ss_pred             CCcccCCCCCCceeec-CCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCCCCeE
Q psy12853         46 ELIKCCPMCSVPIEKD-EGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQM  115 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~-~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~gC~hm  115 (137)
                      -+..-|.-|+.-+-.+ +|...+.|..|+.-.|.-|.. +.      .+++.+.||.|++...+-.|++.+
T Consensus        32 ~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cye-ye------r~eg~q~CpqCkt~Y~r~kgs~~v   95 (1040)
T PLN02189         32 LDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYE-YE------RREGTQNCPQCKTRYKRLKGSPRV   95 (1040)
T ss_pred             ccCccccccccccCcCCCCCEEEeeccCCCccccchhh-hh------hhcCCccCcccCCchhhccCCCCc
Confidence            3456788899887664 467889999999999999972 22      235678999999999877777654

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

Probab=86.36  E-value=0.65  Score=31.90  Aligned_cols=25  Identities=32%  Similarity=0.960  Sum_probs=19.3

Q ss_pred             cCCCCCCCcceeecCCCCeEEeccCcc
Q psy12853         96 IKCCPMCSVPIEKDEGCAQMLCKRCKH  122 (137)
Q Consensus        96 ~~~CP~C~~~iek~~gC~hm~C~~C~~  122 (137)
                      .+.||.|++++.+..|  -+.|..||+
T Consensus        28 ~~hCp~Cg~PLF~KdG--~v~CPvC~~   52 (131)
T COG1645          28 AKHCPKCGTPLFRKDG--EVFCPVCGY   52 (131)
T ss_pred             HhhCcccCCcceeeCC--eEECCCCCc
Confidence            5689999999999666  566666664

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

Probab=86.12  E-value=0.78  Score=29.17  Aligned_cols=50  Identities=30%  Similarity=0.750  Sum_probs=34.3

Q ss_pred             cCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853         50 CCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK  108 (137)
Q Consensus        50 ~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek  108 (137)
                      -||+|..+   .++.+.+.. .|++.|=..|...|....     .....||-|+...+.
T Consensus        34 ~Cp~Ck~P---gd~Cplv~g-~C~H~FH~hCI~kWl~~~-----~~~~~CPmCR~~w~~   83 (85)
T PF12861_consen   34 CCPDCKFP---GDDCPLVWG-KCSHNFHMHCILKWLSTQ-----SSKGQCPMCRQPWKF   83 (85)
T ss_pred             CCCCccCC---CCCCceeec-cCccHHHHHHHHHHHccc-----cCCCCCCCcCCeeee
Confidence            35666554   123444444 699999999999888764     224689999988764

>PF14353 CpXC: CpXC protein

Probab=85.90  E-value=0.72  Score=31.15  Aligned_cols=39  Identities=21%  Similarity=0.353  Sum_probs=25.3

Q ss_pred             cCCCCCCceeec-------------------CCCCeeecccccccccccccccccCCC
Q psy12853         50 CCPMCSVPIEKD-------------------EGCAQMLCKRCKHVFCWYCLASRDYGG   88 (137)
Q Consensus        50 ~CP~C~~~i~~~-------------------~~~~~~~C~~C~~~fC~~C~~~~h~~~   88 (137)
                      .||.|+..+...                   +.-..++||.||+.+=..=...+|.+.
T Consensus         3 tCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~D~~   60 (128)
T PF14353_consen    3 TCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYHDPE   60 (128)
T ss_pred             CCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEEcCC
Confidence            588888876642                   123467888888777655555666664

>KOG0317|consensus

Probab=85.48  E-value=0.15  Score=39.33  Aligned_cols=36  Identities=25%  Similarity=0.708  Sum_probs=26.5

Q ss_pred             cccCCCCCCCcceeecCCCCeEEeccCcceeecccccccccC
Q psy12853         94 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDVS  135 (137)
Q Consensus        94 ~~~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~~~~  135 (137)
                      +.+.+|--|....      .|-+|+-||+-|||.|...|-..
T Consensus       237 ~a~~kC~LCLe~~------~~pSaTpCGHiFCWsCI~~w~~e  272 (293)
T KOG0317|consen  237 EATRKCSLCLENR------SNPSATPCGHIFCWSCILEWCSE  272 (293)
T ss_pred             CCCCceEEEecCC------CCCCcCcCcchHHHHHHHHHHcc
Confidence            3456777776655      35778899999999998777543

>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family

Probab=85.31  E-value=0.99  Score=25.83  Aligned_cols=30  Identities=20%  Similarity=0.343  Sum_probs=19.0

Q ss_pred             cCCCCCCCcceee------cCCCCeE-EeccCcceee
Q psy12853         96 IKCCPMCSVPIEK------DEGCAQM-LCKRCKHVFC  125 (137)
Q Consensus        96 ~~~CP~C~~~iek------~~gC~hm-~C~~C~~~fC  125 (137)
                      .++||.|+..-+.      +.+..++ .|..||+..-
T Consensus         1 LkPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~   37 (53)
T TIGR03655         1 LKPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGP   37 (53)
T ss_pred             CCCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCcc
Confidence            4799999876662      2234444 5777777654

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.

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

Probab=85.16  E-value=0.29  Score=26.76  Aligned_cols=28  Identities=32%  Similarity=0.620  Sum_probs=16.8

Q ss_pred             cccccccccccccccCCCCcccccccCCCCCC
Q psy12853         71 RCKHVFCWYCLASRDYGGATFDSELIKCCPMC  102 (137)
Q Consensus        71 ~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C  102 (137)
                      .||+.||..|...+-....    .....||.|
T Consensus        15 ~CGH~FC~~Cl~~~~~~~~----~~~~~CP~C   42 (42)
T PF15227_consen   15 PCGHSFCRSCLERLWKEPS----GSGFSCPEC   42 (42)
T ss_dssp             SSSSEEEHHHHHHHHCCSS----SST---SSS
T ss_pred             CCcCHHHHHHHHHHHHccC----CcCCCCcCC
Confidence            6999999999886544422    111578876

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=85.12  E-value=0.5  Score=25.16  Aligned_cols=13  Identities=23%  Similarity=0.848  Sum_probs=7.9

Q ss_pred             cCCCCCCCcceee
Q psy12853         96 IKCCPMCSVPIEK  108 (137)
Q Consensus        96 ~~~CP~C~~~iek  108 (137)
                      ...||.|+..++|
T Consensus        26 ~~~CP~Cg~~~~r   38 (41)
T smart00834       26 LATCPECGGDVRR   38 (41)
T ss_pred             CCCCCCCCCccee
Confidence            4457777665554

CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=85.10  E-value=0.69  Score=30.09  Aligned_cols=27  Identities=22%  Similarity=0.534  Sum_probs=20.1

Q ss_pred             ccCCCCCCceeecCCCCeeeccccccccc
Q psy12853         49 KCCPMCSVPIEKDEGCAQMLCKRCKHVFC   77 (137)
Q Consensus        49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~fC   77 (137)
                      .+||+|+..+....  ..+.|+.|++.+=
T Consensus         1 ~fC~~Cg~~l~~~~--~~~~C~~C~~~~~   27 (104)
T TIGR01384         1 KFCPKCGSLMTPKN--GVYVCPSCGYEKE   27 (104)
T ss_pred             CCCcccCcccccCC--CeEECcCCCCccc
Confidence            37999999986543  4688988887654

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.

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

Probab=85.09  E-value=1.2  Score=23.17  Aligned_cols=29  Identities=21%  Similarity=0.370  Sum_probs=20.4

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccc
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVF   76 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~f   76 (137)
                      .+.|+.|+...+.........|+.|+..|
T Consensus         3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~~~   31 (33)
T PF08792_consen    3 LKKCSKCGGNGIVNKEDDYEVCIFCGSSF   31 (33)
T ss_pred             ceEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence            45688898887775556667777777653

>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA

Probab=84.89  E-value=0.78  Score=30.40  Aligned_cols=28  Identities=25%  Similarity=0.682  Sum_probs=21.4

Q ss_pred             ccCCCCCCceeecCCCCeeeccccccccc
Q psy12853         49 KCCPMCSVPIEKDEGCAQMLCKRCKHVFC   77 (137)
Q Consensus        49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~fC   77 (137)
                      -.||.|+.-+.+.++. .+.||.|++.+=
T Consensus         3 p~CP~C~seytY~dg~-~~iCpeC~~EW~   30 (109)
T TIGR00686         3 PPCPKCNSEYTYHDGT-QLICPSCLYEWN   30 (109)
T ss_pred             CcCCcCCCcceEecCC-eeECcccccccc
Confidence            4699999999887765 588888776553

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).

>PRK00241 nudC NADH pyrophosphatase; Reviewed

Probab=84.83  E-value=0.72  Score=35.12  Aligned_cols=31  Identities=23%  Similarity=0.558  Sum_probs=24.9

Q ss_pred             CCCcccCCCCCCceeecCCCCeeeccccccc
Q psy12853         45 SELIKCCPMCSVPIEKDEGCAQMLCKRCKHV   75 (137)
Q Consensus        45 ~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~   75 (137)
                      ....+|||.|+..+....+.....|+.|+..
T Consensus        96 ~~~~~fC~~CG~~~~~~~~~~~~~C~~c~~~  126 (256)
T PRK00241         96 YRSHRFCGYCGHPMHPSKTEWAMLCPHCRER  126 (256)
T ss_pred             hhcCccccccCCCCeecCCceeEECCCCCCE
Confidence            3558899999999887777777889988743

>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated

Probab=84.80  E-value=0.58  Score=40.97  Aligned_cols=27  Identities=37%  Similarity=1.053  Sum_probs=24.1

Q ss_pred             CCCCCCCcceeecCCCCeEEeccCcceee
Q psy12853         97 KCCPMCSVPIEKDEGCAQMLCKRCKHVFC  125 (137)
Q Consensus        97 ~~CP~C~~~iek~~gC~hm~C~~C~~~fC  125 (137)
                      ..||.|+..+...+||.  +|..||+.=|
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

>KOG0320|consensus

Probab=84.76  E-value=0.26  Score=35.57  Aligned_cols=49  Identities=27%  Similarity=0.693  Sum_probs=30.7

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK  108 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek  108 (137)
                      ..-||.|-..+.....    .=.+||+.||..|.+..        ..++.+||-|+..|.+
T Consensus       131 ~~~CPiCl~~~sek~~----vsTkCGHvFC~~Cik~a--------lk~~~~CP~C~kkIt~  179 (187)
T KOG0320|consen  131 TYKCPICLDSVSEKVP----VSTKCGHVFCSQCIKDA--------LKNTNKCPTCRKKITH  179 (187)
T ss_pred             ccCCCceecchhhccc----cccccchhHHHHHHHHH--------HHhCCCCCCcccccch
Confidence            3556665554433221    12379999999997531        2356789999976643

>KOG2906|consensus

Probab=84.71  E-value=0.84  Score=29.77  Aligned_cols=31  Identities=29%  Similarity=0.745  Sum_probs=23.4

Q ss_pred             ccCCCCCCceeecCC--CCeeeccccccccccc
Q psy12853         49 KCCPMCSVPIEKDEG--CAQMLCKRCKHVFCWY   79 (137)
Q Consensus        49 ~~CP~C~~~i~~~~~--~~~~~C~~C~~~fC~~   79 (137)
                      .+||.|+..++...+  .+.+.|..|.+.+=..
T Consensus         2 ~FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I~   34 (105)
T KOG2906|consen    2 LFCPTCGNMLIVESGESCNRFSCRTCPYVFPIS   34 (105)
T ss_pred             cccCCCCCEEEEecCCeEeeEEcCCCCceeeEe
Confidence            589999999887654  4677888777766554

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

Probab=84.40  E-value=0.52  Score=28.40  Aligned_cols=37  Identities=22%  Similarity=0.671  Sum_probs=15.1

Q ss_pred             ccCCCCCCCcceeec---CCCCeEEeccCccee----ecccccc
Q psy12853         95 LIKCCPMCSVPIEKD---EGCAQMLCKRCKHVF----CWYCLAS  131 (137)
Q Consensus        95 ~~~~CP~C~~~iek~---~gC~hm~C~~C~~~f----C~~C~~~  131 (137)
                      ..-+|++|.......   +||.|+.|+.|=..+    |-+|..|
T Consensus         6 ~lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~P   49 (65)
T PF14835_consen    6 ELLRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTP   49 (65)
T ss_dssp             HTTS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B
T ss_pred             HhcCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCCh
Confidence            345788888777653   778887777663222    5555443

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=84.37  E-value=1.1  Score=25.94  Aligned_cols=27  Identities=26%  Similarity=0.645  Sum_probs=15.8

Q ss_pred             cCCCCCCceeecC--CCCeeecccccccc
Q psy12853         50 CCPMCSVPIEKDE--GCAQMLCKRCKHVF   76 (137)
Q Consensus        50 ~CP~C~~~i~~~~--~~~~~~C~~C~~~f   76 (137)
                      .||.|+..|...+  ....+.|+.||..+
T Consensus         4 ~CP~CG~~iev~~~~~GeiV~Cp~CGael   32 (54)
T TIGR01206         4 ECPDCGAEIELENPELGELVICDECGAEL   32 (54)
T ss_pred             CCCCCCCEEecCCCccCCEEeCCCCCCEE
Confidence            5777777776543  13455666666543

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.

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=84.33  E-value=0.85  Score=24.90  Aligned_cols=26  Identities=35%  Similarity=0.857  Sum_probs=19.5

Q ss_pred             cccccccccccccccCCCCcccccccCCCCCCCc
Q psy12853         71 RCKHVFCWYCLASRDYGGATFDSELIKCCPMCSV  104 (137)
Q Consensus        71 ~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~  104 (137)
                      .|++.||..|.....        .....||-|+.
T Consensus        19 ~CgH~~C~~C~~~~~--------~~~~~CP~C~k   44 (44)
T PF14634_consen   19 SCGHIFCEKCLKKLK--------GKSVKCPICRK   44 (44)
T ss_pred             ccCCHHHHHHHHhhc--------CCCCCCcCCCC
Confidence            689999999986543        33568998863

>KOG0823|consensus

Probab=84.31  E-value=0.33  Score=36.35  Aligned_cols=20  Identities=40%  Similarity=1.001  Sum_probs=16.3

Q ss_pred             EEeccCcceeecccccccccCC
Q psy12853        115 MLCKRCKHVFCWYCLASLDVSR  136 (137)
Q Consensus       115 m~C~~C~~~fC~~C~~~~~~~~  136 (137)
                      +|+  ||+-|||-|.-.|...+
T Consensus        62 vTl--CGHLFCWpClyqWl~~~   81 (230)
T KOG0823|consen   62 VTL--CGHLFCWPCLYQWLQTR   81 (230)
T ss_pred             Eee--cccceehHHHHHHHhhc
Confidence            555  99999999998887643

>PHA02929 N1R/p28-like protein; Provisional

Probab=84.28  E-value=0.95  Score=34.22  Aligned_cols=53  Identities=26%  Similarity=0.550  Sum_probs=36.5

Q ss_pred             CcccCCCCCCceeecCCC--CeeecccccccccccccccccCCCCcccccccCCCCCCCccee
Q psy12853         47 LIKCCPMCSVPIEKDEGC--AQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIE  107 (137)
Q Consensus        47 ~~~~CP~C~~~i~~~~~~--~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~ie  107 (137)
                      ....||=|...+......  ....=+.|++.||..|..+|...        ...||-|+..+.
T Consensus       173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~--------~~tCPlCR~~~~  227 (238)
T PHA02929        173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE--------KNTCPVCRTPFI  227 (238)
T ss_pred             CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc--------CCCCCCCCCEee
Confidence            356889888876543211  11222379999999999998754        247999998875

>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]

Probab=84.26  E-value=0.62  Score=35.98  Aligned_cols=32  Identities=22%  Similarity=0.405  Sum_probs=26.9

Q ss_pred             CCCCcccCCCCCCceeecCCCCeeeccccccc
Q psy12853         44 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHV   75 (137)
Q Consensus        44 ~~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~   75 (137)
                      -..+.++||+|+.......+....+|++|++.
T Consensus       107 w~~~~RFCg~CG~~~~~~~~g~~~~C~~cg~~  138 (279)
T COG2816         107 WYRSHRFCGRCGTKTYPREGGWARVCPKCGHE  138 (279)
T ss_pred             HHhhCcCCCCCCCcCccccCceeeeCCCCCCc
Confidence            34668999999999998888899999998654

>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding

Probab=84.23  E-value=0.59  Score=25.86  Aligned_cols=22  Identities=32%  Similarity=0.628  Sum_probs=16.2

Q ss_pred             ccccCCCCCCCcceeecCCCCeEEec
Q psy12853         93 SELIKCCPMCSVPIEKDEGCAQMLCK  118 (137)
Q Consensus        93 ~~~~~~CP~C~~~iek~~gC~hm~C~  118 (137)
                      ...+++||+|++.-    |..-+.|.
T Consensus         8 lRGirkCp~CGt~N----G~R~~~CK   29 (44)
T PF14952_consen    8 LRGIRKCPKCGTYN----GTRGLSCK   29 (44)
T ss_pred             HhccccCCcCcCcc----Cccccccc
Confidence            45689999999887    55555555

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

Probab=84.19  E-value=0.19  Score=38.98  Aligned_cols=30  Identities=23%  Similarity=0.600  Sum_probs=22.9

Q ss_pred             ccCCCCCCCcceeecC-CCCeEEeccCccee
Q psy12853         95 LIKCCPMCSVPIEKDE-GCAQMLCKRCKHVF  124 (137)
Q Consensus        95 ~~~~CP~C~~~iek~~-gC~hm~C~~C~~~f  124 (137)
                      .|.+||+|+..+.+.+ .=|...|..||++|
T Consensus        25 ~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~   55 (285)
T TIGR00515        25 VWTKCPKCGQVLYTKELERNLEVCPKCDHHM   55 (285)
T ss_pred             CeeECCCCcchhhHHHHHhhCCCCCCCCCcC
Confidence            4888999988887743 45667888888875

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.

>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed

Probab=84.04  E-value=0.18  Score=39.25  Aligned_cols=30  Identities=20%  Similarity=0.288  Sum_probs=20.0

Q ss_pred             ccCCCCCCCcceeecC-CCCeEEeccCccee
Q psy12853         95 LIKCCPMCSVPIEKDE-GCAQMLCKRCKHVF  124 (137)
Q Consensus        95 ~~~~CP~C~~~iek~~-gC~hm~C~~C~~~f  124 (137)
                      .|.+||+|+..+.+.. .=|...|..||++|
T Consensus        37 lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h~   67 (296)
T CHL00174         37 LWVQCENCYGLNYKKFLKSKMNICEQCGYHL   67 (296)
T ss_pred             CeeECCCccchhhHHHHHHcCCCCCCCCCCc
Confidence            3677777777776643 35566777777765

>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=83.82  E-value=0.3  Score=26.05  Aligned_cols=31  Identities=35%  Similarity=0.811  Sum_probs=19.2

Q ss_pred             CCCCCcceeecCCCCeEEeccCcceeeccccccccc
Q psy12853         99 CPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDV  134 (137)
Q Consensus        99 CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~~~  134 (137)
                      ||-|....+...     +=..||+.||..|...+-.
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            455555544332     3346889999988876643

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 ....

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=83.66  E-value=0.91  Score=29.51  Aligned_cols=25  Identities=20%  Similarity=0.574  Sum_probs=16.4

Q ss_pred             CCCCCCcceeecCCCCeEEeccCccee
Q psy12853         98 CCPMCSVPIEKDEGCAQMLCKRCKHVF  124 (137)
Q Consensus        98 ~CP~C~~~iek~~gC~hm~C~~C~~~f  124 (137)
                      -||+|+.++...+  +.+.|..||+.+
T Consensus         2 fC~~Cg~~l~~~~--~~~~C~~C~~~~   26 (104)
T TIGR01384         2 FCPKCGSLMTPKN--GVYVCPSCGYEK   26 (104)
T ss_pred             CCcccCcccccCC--CeEECcCCCCcc
Confidence            4777777775544  367777777654

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.

>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=83.61  E-value=0.53  Score=26.94  Aligned_cols=25  Identities=28%  Similarity=0.669  Sum_probs=11.0

Q ss_pred             CCCCCCcceeecCCCC--eEEeccCcc
Q psy12853         98 CCPMCSVPIEKDEGCA--QMLCKRCKH  122 (137)
Q Consensus        98 ~CP~C~~~iek~~gC~--hm~C~~C~~  122 (137)
                      +|++|+.++-+.++=.  .|.|.+||+
T Consensus         6 RC~~CnklLa~~g~~~~leIKCpRC~t   32 (51)
T PF10122_consen    6 RCGHCNKLLAKAGEVIELEIKCPRCKT   32 (51)
T ss_pred             eccchhHHHhhhcCccEEEEECCCCCc
Confidence            4555555554433222  244544443

>PF14354 Lar_restr_allev: Restriction alleviation protein Lar

Probab=83.47  E-value=1.1  Score=26.10  Aligned_cols=28  Identities=29%  Similarity=0.544  Sum_probs=18.3

Q ss_pred             ccCCCCCCCcceeec---CCC-----CeEEeccCcc
Q psy12853         95 LIKCCPMCSVPIEKD---EGC-----AQMLCKRCKH  122 (137)
Q Consensus        95 ~~~~CP~C~~~iek~---~gC-----~hm~C~~C~~  122 (137)
                      ..++||.|+......   .+=     .+|.|..||.
T Consensus         2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga   37 (61)
T PF14354_consen    2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA   37 (61)
T ss_pred             CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence            478999998554432   121     4588887776

>KOG0978|consensus

Probab=83.40  E-value=0.26  Score=42.49  Aligned_cols=49  Identities=22%  Similarity=0.610  Sum_probs=32.8

Q ss_pred             CCCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcce
Q psy12853         45 SELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPI  106 (137)
Q Consensus        45 ~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~i  106 (137)
                      ......||-|+.-.  .+ .-.   ++|++.||..|-..       ......++||+|+...
T Consensus       640 yK~~LkCs~Cn~R~--Kd-~vI---~kC~H~FC~~Cvq~-------r~etRqRKCP~Cn~aF  688 (698)
T KOG0978|consen  640 YKELLKCSVCNTRW--KD-AVI---TKCGHVFCEECVQT-------RYETRQRKCPKCNAAF  688 (698)
T ss_pred             HHhceeCCCccCch--hh-HHH---HhcchHHHHHHHHH-------HHHHhcCCCCCCCCCC
Confidence            35578899888321  11 101   27999999999753       2334578999999876

>PRK14892 putative transcription elongation factor Elf1; Provisional

Probab=83.29  E-value=1.1  Score=29.29  Aligned_cols=14  Identities=21%  Similarity=0.404  Sum_probs=8.3

Q ss_pred             CCCeEEeccCccee
Q psy12853        111 GCAQMLCKRCKHVF  124 (137)
Q Consensus       111 gC~hm~C~~C~~~f  124 (137)
                      |=-|+.|..||+.+
T Consensus        39 ~~~h~~C~~CG~y~   52 (99)
T PRK14892         39 NIAIITCGNCGLYT   52 (99)
T ss_pred             CcceEECCCCCCcc
Confidence            34466666666654

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=82.81  E-value=1.3  Score=24.47  Aligned_cols=8  Identities=25%  Similarity=0.605  Sum_probs=3.1

Q ss_pred             CCCCCCce
Q psy12853         51 CPMCSVPI   58 (137)
Q Consensus        51 CP~C~~~i   58 (137)
                      |.+|+..+
T Consensus         5 C~~Cg~~~   12 (44)
T smart00659        5 CGECGREN   12 (44)
T ss_pred             CCCCCCEe
Confidence            33444433

present in RNA polymerase I, II and III

>PRK10220 hypothetical protein; Provisional

Probab=82.76  E-value=1.2  Score=29.61  Aligned_cols=27  Identities=22%  Similarity=0.732  Sum_probs=20.2

Q ss_pred             ccCCCCCCceeecCCCCeeecccccccc
Q psy12853         49 KCCPMCSVPIEKDEGCAQMLCKRCKHVF   76 (137)
Q Consensus        49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~f   76 (137)
                      --||.|+.-+.+.++. .+.||.|++++
T Consensus         4 P~CP~C~seytY~d~~-~~vCpeC~hEW   30 (111)
T PRK10220          4 PHCPKCNSEYTYEDNG-MYICPECAHEW   30 (111)
T ss_pred             CcCCCCCCcceEcCCC-eEECCcccCcC
Confidence            4699999999887764 47788766554

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

Probab=82.69  E-value=1  Score=40.71  Aligned_cols=63  Identities=19%  Similarity=0.533  Sum_probs=48.2

Q ss_pred             CCcccCCCCCCceeec-CCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCCCCeE
Q psy12853         46 ELIKCCPMCSVPIEKD-EGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQM  115 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~-~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~gC~hm  115 (137)
                      .+..-|--|+--+-.+ +|...+.|..|+.-.|.-|.. +..      +++.+-||.|++...+-.|+..+
T Consensus        15 ~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYE-YEr------~eG~q~CPqCktrYkr~kgsprv   78 (1079)
T PLN02638         15 GGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYE-YER------KDGNQSCPQCKTKYKRHKGSPAI   78 (1079)
T ss_pred             cCCceeeecccccCcCCCCCEEEEeccCCCccccchhh-hhh------hcCCccCCccCCchhhhcCCCCc
Confidence            3455677788877665 578889999999999999972 222      35688999999999887777653

>PRK12495 hypothetical protein; Provisional

Probab=82.64  E-value=0.52  Score=35.12  Aligned_cols=27  Identities=30%  Similarity=0.716  Sum_probs=17.9

Q ss_pred             CCCcccCCCCCCceeecCCCCeeeccccc
Q psy12853         45 SELIKCCPMCSVPIEKDEGCAQMLCKRCK   73 (137)
Q Consensus        45 ~~~~~~CP~C~~~i~~~~~~~~~~C~~C~   73 (137)
                      .....+|+.|+.+|....|  .+.|+.|+
T Consensus        39 tmsa~hC~~CG~PIpa~pG--~~~Cp~CQ   65 (226)
T PRK12495         39 TMTNAHCDECGDPIFRHDG--QEFCPTCQ   65 (226)
T ss_pred             ccchhhcccccCcccCCCC--eeECCCCC
Confidence            3457899999999985433  34455444

>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=81.30  E-value=1.6  Score=21.73  Aligned_cols=21  Identities=29%  Similarity=0.892  Sum_probs=12.9

Q ss_pred             cCCCCCCceeecCCCCeeecc
Q psy12853         50 CCPMCSVPIEKDEGCAQMLCK   70 (137)
Q Consensus        50 ~CP~C~~~i~~~~~~~~~~C~   70 (137)
                      .||.|+..+.+.++.....|+
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            489999999988777677775

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.

>PF15135 UPF0515: Uncharacterised protein UPF0515

Probab=81.23  E-value=1.7  Score=33.07  Aligned_cols=62  Identities=26%  Similarity=0.582  Sum_probs=41.4

Q ss_pred             CCeeecccccccccccccccccCCCCcccccccCCCCCCCccee-----ecCCCCeEEeccCccee-----------ecc
Q psy12853         64 CAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIE-----KDEGCAQMLCKRCKHVF-----------CWY  127 (137)
Q Consensus        64 ~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~ie-----k~~gC~hm~C~~C~~~f-----------C~~  127 (137)
                      ...+.|..|.......+..          ...+-+|-+|+..++     |.-|=-...|.+|++.|           ||.
T Consensus       110 drqFaC~~Cd~~WwRrvp~----------rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G~~qm~v~sPCy~  179 (278)
T PF15135_consen  110 DRQFACSSCDHMWWRRVPQ----------RKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRGFAQMGVPSPCYG  179 (278)
T ss_pred             ceeeeccccchHHHhccCc----------ccccccccccccccCCCccccccceeeeecccccccchhhhhcCCCCCccC
Confidence            4677888887776654432          244567777777654     44566667787888777           888


Q ss_pred             cccccccC
Q psy12853        128 CLASLDVS  135 (137)
Q Consensus       128 C~~~~~~~  135 (137)
                      |+.+..++
T Consensus       180 C~~~v~P~  187 (278)
T PF15135_consen  180 CGNPVYPS  187 (278)
T ss_pred             CCCccCcc
Confidence            88776553

>PRK00420 hypothetical protein; Validated

Probab=81.22  E-value=1.6  Score=29.19  Aligned_cols=25  Identities=28%  Similarity=0.856  Sum_probs=18.1

Q ss_pred             cCCCCCCCcceee-cCCCCeEEeccCcc
Q psy12853         96 IKCCPMCSVPIEK-DEGCAQMLCKRCKH  122 (137)
Q Consensus        96 ~~~CP~C~~~iek-~~gC~hm~C~~C~~  122 (137)
                      ...||.|+.++.+ ..|  ...|..||.
T Consensus        23 ~~~CP~Cg~pLf~lk~g--~~~Cp~Cg~   48 (112)
T PRK00420         23 SKHCPVCGLPLFELKDG--EVVCPVHGK   48 (112)
T ss_pred             cCCCCCCCCcceecCCC--ceECCCCCC
Confidence            4689999999987 555  566666655

>PLN02436 cellulose synthase A

Probab=81.21  E-value=1.5  Score=39.71  Aligned_cols=63  Identities=22%  Similarity=0.542  Sum_probs=47.9

Q ss_pred             CCcccCCCCCCceeec-CCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCCCCeE
Q psy12853         46 ELIKCCPMCSVPIEKD-EGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQM  115 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~-~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~gC~hm  115 (137)
                      -+..-|--|+--+-.+ +|...+.|..|+...|.-|.. +.      .+++.+.||.|++...+-.|++.+
T Consensus        34 ~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cye-ye------r~eg~~~Cpqckt~Y~r~kgs~~~   97 (1094)
T PLN02436         34 LSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYE-YE------RREGNQACPQCKTRYKRIKGSPRV   97 (1094)
T ss_pred             cCCccccccccccCcCCCCCEEEeeccCCCccccchhh-hh------hhcCCccCcccCCchhhccCCCCc
Confidence            3455777888877654 577889999999999999972 22      235678999999999877676653

>PRK09710 lar restriction alleviation and modification protein; Reviewed

Probab=80.98  E-value=1.8  Score=26.01  Aligned_cols=31  Identities=26%  Similarity=0.625  Sum_probs=21.4

Q ss_pred             cccCCCCCCCcceee---cCCCCeEEeccCccee
Q psy12853         94 ELIKCCPMCSVPIEK---DEGCAQMLCKRCKHVF  124 (137)
Q Consensus        94 ~~~~~CP~C~~~iek---~~gC~hm~C~~C~~~f  124 (137)
                      .++|+||.|+..+.+   .+|=-...|..|+..-
T Consensus         4 d~lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA~~   37 (64)
T PRK09710          4 DNVKPCPFCGCPSVTVKAISGYYRAKCNGCESRT   37 (64)
T ss_pred             ccccCCCCCCCceeEEEecCceEEEEcCCCCcCc
Confidence            358999999877665   3443347777787753

>PRK11827 hypothetical protein; Provisional

Probab=80.78  E-value=2  Score=25.51  Aligned_cols=28  Identities=21%  Similarity=0.521  Sum_probs=19.9

Q ss_pred             cccCCCCCCceeecCCCCeeeccccccc
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHV   75 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~   75 (137)
                      ..-||.|...+..+.+.+...|..|+..
T Consensus         8 ILaCP~ckg~L~~~~~~~~Lic~~~~la   35 (60)
T PRK11827          8 IIACPVCNGKLWYNQEKQELICKLDNLA   35 (60)
T ss_pred             heECCCCCCcCeEcCCCCeEECCccCee
Confidence            4468989888888766667777665543

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=80.35  E-value=0.81  Score=33.51  Aligned_cols=35  Identities=26%  Similarity=0.680  Sum_probs=24.7

Q ss_pred             ccccCCCCCCCcceeecCCCCeEEeccCcceeecccccccc
Q psy12853         93 SELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLD  133 (137)
Q Consensus        93 ~~~~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~~  133 (137)
                      ..+.-.||-|...++..     +. +.||+.|||.|...|.
T Consensus        15 ~~~~~~CpICld~~~dP-----Vv-T~CGH~FC~~CI~~wl   49 (193)
T PLN03208         15 SGGDFDCNICLDQVRDP-----VV-TLCGHLFCWPCIHKWT   49 (193)
T ss_pred             CCCccCCccCCCcCCCc-----EE-cCCCchhHHHHHHHHH
Confidence            34556899998766321     22 4699999999998773

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

Probab=80.19  E-value=0.54  Score=36.26  Aligned_cols=31  Identities=26%  Similarity=0.627  Sum_probs=24.9

Q ss_pred             cccCCCCCCCcceeecC-CCCeEEeccCccee
Q psy12853         94 ELIKCCPMCSVPIEKDE-GCAQMLCKRCKHVF  124 (137)
Q Consensus        94 ~~~~~CP~C~~~iek~~-gC~hm~C~~C~~~f  124 (137)
                      ..|.+||+|+..+-+.+ +=|...|.+|+++|
T Consensus        26 ~lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~   57 (294)
T COG0777          26 GLWTKCPSCGEMLYRKELESNLKVCPKCGHHM   57 (294)
T ss_pred             CceeECCCccceeeHHHHHhhhhcccccCccc
Confidence            45888999999888754 67788888898876

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	137
1wd2_A	60	Solution Structure Of The C-Terminal Ring From A Ri		2e-04
1wd2_A	60	Solution Structure Of The C-Terminal Ring From A Ri		3e-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 = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 48 IKCCPMCSVPIEKDEGCAQMLCK--RCKHVFCWYCLASRDYGGATF 91
           K CP C V IEKD GC  M+C+   CK  FCW CL   +  G+ +
Sbjct: 6  TKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPHGSAW 51

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/44 (47%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 96  IKCCPMCSVPIEKDEGCAQMLCK--RCKHVFCWYCLASLDVSRS 137
            K CP C V IEKD GC  M+C+   CK  FCW CL   +   S
Sbjct: 6   TKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPHGS 49

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	137
1wd2_A	60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	8e-08
1wd2_A	60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	8e-08

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

 Score = 45.5 bits (108), Expect = 8e-08
 Identities = 21/46 (45%), Positives = 26/46 (56%), Gaps = 2/46 (4%)

Query: 48 IKCCPMCSVPIEKDEGCAQMLCK--RCKHVFCWYCLASRDYGGATF 91
           K CP C V IEKD GC  M+C+   CK  FCW CL   +  G+ +
Sbjct: 6  TKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPHGSAW 51

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

 Score = 45.1 bits (107), Expect = 8e-08
 Identities = 20/38 (52%), Positives = 22/38 (57%), Gaps = 2/38 (5%)

Query: 96  IKCCPMCSVPIEKDEGCAQMLCK--RCKHVFCWYCLAS 131
            K CP C V IEKD GC  M+C+   CK  FCW CL  
Sbjct: 6   TKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGP 43

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	137
1wd2_A	60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	99.76
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	99.35
2jmo_A	80	Parkin; IBR, E3 ligase, zinc binding domain, RBR;	99.2
1wd2_A	60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	98.62
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	98.0
2jmo_A	80	Parkin; IBR, E3 ligase, zinc binding domain, RBR;	97.9
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	96.76
2jrp_A	81	Putative cytoplasmic protein; two-zinc binding pro	96.69
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	95.77
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	94.92
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	94.85
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	94.79
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	94.4
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	94.34
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	94.32
2jrp_A	81	Putative cytoplasmic protein; two-zinc binding pro	94.15
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	94.02
2jne_A	101	Hypothetical protein YFGJ; zinc fingers, two zinc,	93.94
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	93.93
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	93.87
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	93.65
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	93.37
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	93.28
1z60_A	59	TFIIH basal transcription factor complex P44 subun	93.22
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	93.0
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	92.89
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	92.68
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	92.62
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	92.43
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	92.33
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	92.22
2jr6_A	68	UPF0434 protein NMA0874; solution, structural geno	92.1
2ect_A	78	Ring finger protein 126; metal binding protein, st	92.07
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	91.87
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	91.87
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	91.81
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	91.78
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	91.51
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	91.34
2jne_A	101	Hypothetical protein YFGJ; zinc fingers, two zinc,	91.24
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	91.24
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	91.22
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	91.14
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	91.01
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	90.5
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	90.47
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	90.03
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	89.95
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	89.58
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	89.4
1gh9_A	71	8.3 kDa protein (gene MTH1184); beta+alpha complex	89.34
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	88.95
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	88.95
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	88.93
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	88.92
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	88.85
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	88.79
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	88.72
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	88.57
2pk7_A	69	Uncharacterized protein; NESG, PLR1, putative tetr	88.39
2jr6_A	68	UPF0434 protein NMA0874; solution, structural geno	88.31
2hf1_A	68	Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A	88.28
2js4_A	70	UPF0434 protein BB2007; NESG, northeast structural	88.22
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	88.19
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	88.03
2js4_A	70	UPF0434 protein BB2007; NESG, northeast structural	88.0
2pk7_A	69	Uncharacterized protein; NESG, PLR1, putative tetr	87.93
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	87.92
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	87.92
2hf1_A	68	Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A	87.55
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	87.06
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	86.26
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	86.09
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	86.05
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	86.0
2jny_A	67	Uncharacterized BCR; structure, CGR1, NESG, struct	85.94
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	85.89
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	85.79
2jny_A	67	Uncharacterized BCR; structure, CGR1, NESG, struct	84.49
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	84.44
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	84.18
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	83.65
2kpi_A	56	Uncharacterized protein SCO3027; zinc finger, PSI-	83.38
1wfl_A	74	Zinc finger protein 216; ZF-AN1 domain, zinc bindi	83.34
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	82.82
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	82.42
1wfh_A	64	Zinc finger (AN1-like) family protein; ZF-AN1 doma	82.23
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	81.98
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	81.71
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	81.66
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	81.14
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	80.91
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	80.76
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	80.37
1wg2_A	64	Zinc finger (AN1-like) family protein; riken struc	80.29

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

Probab=99.76  E-value=1.2e-19  Score=108.02  Aligned_cols=45  Identities=44%  Similarity=1.068  Sum_probs=41.8

Q ss_pred             ccccccCCCCCCCcceeecCCCCeEEecc--CcceeecccccccccC
Q psy12853         91 FDSELIKCCPMCSVPIEKDEGCAQMLCKR--CKHVFCWYCLASLDVS  135 (137)
Q Consensus        91 ~~~~~~~~CP~C~~~iek~~gC~hm~C~~--C~~~fC~~C~~~~~~~  135 (137)
                      |+.+++|+||+|+++|||++|||||+|+.  |+++|||+|+++|..+
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            45678999999999999999999999998  9999999999999865

>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=99.35  E-value=1.8e-13  Score=86.76  Aligned_cols=59  Identities=19%  Similarity=0.486  Sum_probs=52.9

Q ss_pred             hhHHHHhhccccccCCCCcccCCCCCCceeecCCCCeeecccccccccccccccc---cCCC
Q psy12853         30 SVIWHRTQVSGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASR---DYGG   88 (137)
Q Consensus        30 ~~~~~r~~~~~a~~~~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~---h~~~   88 (137)
                      .++|++++++.++..+++++|||+|+.+++.+++...++|+.|++.||+.|+.+|   |.+.
T Consensus         7 ~e~y~~~l~e~~v~~~~~~~wCP~C~~~~~~~~~~~~v~C~~C~~~FC~~C~~~w~~~H~~~   68 (86)
T 2ct7_A            7 GALFHKKLTEGVLMRDPKFLWCAQCSFGFIYEREQLEATCPQCHQTFCVRCKRQWEEQHRGR   68 (86)
T ss_dssp             CCSSSSCCCCSCCCSCCCEECCSSSCCCEECCCSCSCEECTTTCCEECSSSCSBCCTTTTTS
T ss_pred             HHHHHHHHHHHHHhcCCCEeECcCCCchheecCCCCceEeCCCCCccccccCCchhhcCCCC
Confidence            3577788888888889999999999999988877888999999999999999999   9996

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

Probab=99.20  E-value=2e-12  Score=80.88  Aligned_cols=56  Identities=14%  Similarity=0.356  Sum_probs=49.3

Q ss_pred             hhHHHHhhccccccCCCCcccCC--CCCCceeecCCCCeeecc-----cccccccccccccccC
Q psy12853         30 SVIWHRTQVSGATFDSELIKCCP--MCSVPIEKDEGCAQMLCK-----RCKHVFCWYCLASRDY   86 (137)
Q Consensus        30 ~~~~~r~~~~~a~~~~~~~~~CP--~C~~~i~~~~~~~~~~C~-----~C~~~fC~~C~~~~h~   86 (137)
                      .++|+++.+++++..+. .+|||  +|+.++..+++...++|+     .|++.||+.|+.+||.
T Consensus         8 ~~rY~~~~~e~~v~~~~-~~~CP~p~C~~~v~~~~~~~~v~C~~~~~~~C~~~FC~~C~~~wH~   70 (80)
T 2jmo_A            8 YNRYQQYGAEECVLQMG-GVLCPRPGCGAGLLPEPDQRKVTCEGGNGLGCGFAFCRECKEAYHE   70 (80)
T ss_dssp             CCSCCCSSSCCSSCCCS-SCCCCSSSCCCCCCCCSCTTSBCTTSSSTTCCSCCEETTTTEECCS
T ss_pred             HHHHHHHHHHHHhhhCC-cEECCCCCCCcccEECCCCCcCCCCCCCCCCCCCeeccccCccccC
Confidence            35778888888777775 99999  699999988788889998     9999999999999999

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

Probab=98.62  E-value=1.4e-08  Score=59.82  Aligned_cols=43  Identities=47%  Similarity=1.093  Sum_probs=38.6

Q ss_pred             CCCcccCCCCCCceeecCCCCeeeccc--ccccccccccccccCC
Q psy12853         45 SELIKCCPMCSVPIEKDEGCAQMLCKR--CKHVFCWYCLASRDYG   87 (137)
Q Consensus        45 ~~~~~~CP~C~~~i~~~~~~~~~~C~~--C~~~fC~~C~~~~h~~   87 (137)
                      ..+.+.||+|..+|++++|.+.|+|..  |+..|||.|+.+|...
T Consensus         3 ~~~~k~CP~C~~~Iek~~GCnhmtC~~~~C~~~FCw~C~~~~~~~   47 (60)
T 1wd2_A            3 AANTKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPH   47 (60)
T ss_dssp             CCCCCCCTTTCCCCSSCCSCCSSSCCSSGGGSCCSSSSCSCSGGG
T ss_pred             cccceECcCCCCeeEeCCCCCcEEECCCCcCCEEeeCcCCCcccC
Confidence            356789999999999999999999987  9999999999988654

>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=98.00  E-value=5.9e-06  Score=51.82  Aligned_cols=38  Identities=21%  Similarity=0.540  Sum_probs=33.8

Q ss_pred             ccCCCCCCCcceeecCCCCeEEeccCcceeeccccccc
Q psy12853         95 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASL  132 (137)
Q Consensus        95 ~~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~  132 (137)
                      +.+-||+|..++...++-..++|..||+.||+.|+.+|
T Consensus        24 ~~~wCP~C~~~~~~~~~~~~v~C~~C~~~FC~~C~~~w   61 (86)
T 2ct7_A           24 KFLWCAQCSFGFIYEREQLEATCPQCHQTFCVRCKRQW   61 (86)
T ss_dssp             CEECCSSSCCCEECCCSCSCEECTTTCCEECSSSCSBC
T ss_pred             CEeECcCCCchheecCCCCceEeCCCCCccccccCCch
Confidence            45569999999888777778999889999999999999

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

Probab=97.90  E-value=6.1e-06  Score=51.11  Aligned_cols=40  Identities=20%  Similarity=0.513  Sum_probs=36.2

Q ss_pred             ccCCCCC--CCcceeecCCCCeEEec-----cCcceeeccccccccc
Q psy12853         95 LIKCCPM--CSVPIEKDEGCAQMLCK-----RCKHVFCWYCLASLDV  134 (137)
Q Consensus        95 ~~~~CP~--C~~~iek~~gC~hm~C~-----~C~~~fC~~C~~~~~~  134 (137)
                      ..+-||.  |+..|...++...++|.     .||+.||+.|+++|+.
T Consensus        24 ~~~~CP~p~C~~~v~~~~~~~~v~C~~~~~~~C~~~FC~~C~~~wH~   70 (80)
T 2jmo_A           24 GGVLCPRPGCGAGLLPEPDQRKVTCEGGNGLGCGFAFCRECKEAYHE   70 (80)
T ss_dssp             SSCCCCSSSCCCCCCCCSCTTSBCTTSSSTTCCSCCEETTTTEECCS
T ss_pred             CcEECCCCCCCcccEECCCCCcCCCCCCCCCCCCCeeccccCccccC
Confidence            4788997  99999988889999997     7999999999999976

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

Probab=96.76  E-value=0.00034  Score=46.08  Aligned_cols=87  Identities=24%  Similarity=0.478  Sum_probs=52.9

Q ss_pred             CcccCCCCCCceeec-CCCCeeecccccccccccccccccCCCC----------------cccccccCCCCCCCcceeec
Q psy12853         47 LIKCCPMCSVPIEKD-EGCAQMLCKRCKHVFCWYCLASRDYGGA----------------TFDSELIKCCPMCSVPIEKD  109 (137)
Q Consensus        47 ~~~~CP~C~~~i~~~-~~~~~~~C~~C~~~fC~~C~~~~h~~~~----------------~~~~~~~~~CP~C~~~iek~  109 (137)
                      +...||-|...+... .+...+.-..||+.||..|...|-....                .+.+.....||-|...++..
T Consensus         6 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~l~~l~i~~~~~~C~iC~~~~~~~   85 (133)
T 4ap4_A            6 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYIGSGTVSCPICMDGYSEI   85 (133)
T ss_dssp             CSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTCSBCTTTCCBCTTTCEEECBCSSSSCBCTTTCCBHHHH
T ss_pred             CCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhCCCCCCCCCcCccccccccccCCCCCCCCCCCCccccc
Confidence            355788888776542 1122223337999999999988854321                12233455677777666543


Q ss_pred             --CCCCeEEeccCcceeeccccccccc
Q psy12853        110 --EGCAQMLCKRCKHVFCWYCLASLDV  134 (137)
Q Consensus       110 --~gC~hm~C~~C~~~fC~~C~~~~~~  134 (137)
                        .+-..+.. .||+.||+.|...|..
T Consensus        86 ~~~~~~~~~~-~CgH~fc~~Ci~~~~~  111 (133)
T 4ap4_A           86 VQNGRLIVST-ECGHVFCSQCLRDSLK  111 (133)
T ss_dssp             HHTTCCEEEE-TTSBEEEHHHHHHHHH
T ss_pred             cccCcceEeC-CCCChhhHHHHHHHHH
Confidence              12222444 4999999998877743

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

Probab=96.69  E-value=0.0019  Score=39.84  Aligned_cols=60  Identities=25%  Similarity=0.640  Sum_probs=40.3

Q ss_pred             ccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCCCCeEEeccCc--ceeec
Q psy12853         49 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCK--HVFCW  126 (137)
Q Consensus        49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~gC~hm~C~~C~--~~fC~  126 (137)
                      ..||.|...+..+++  ...|..|+..|=                ... .||.|+.++|+        |..||  -.||-
T Consensus         3 ~~CP~C~~~l~~~~~--~~~C~~C~~~~~----------------~~a-fCPeCgq~Le~--------lkACGA~~yFC~   55 (81)
T 2jrp_A            3 ITCPVCHHALERNGD--TAHCETCAKDFS----------------LQA-LCPDCRQPLQV--------LKACGAVDYFCQ   55 (81)
T ss_dssp             CCCSSSCSCCEECSS--EEECTTTCCEEE----------------EEE-ECSSSCSCCCE--------EEETTEEEECCT
T ss_pred             CCCCCCCCccccCCC--ceECccccccCC----------------Ccc-cCcchhhHHHH--------HHhcCCcCeeec
Confidence            579999999987543  445655544321                112 79999999988        55676  46788


Q ss_pred             ccccccccC
Q psy12853        127 YCLASLDVS  135 (137)
Q Consensus       127 ~C~~~~~~~  135 (137)
                      .|++-.+.+
T Consensus        56 ~C~~LiSkk   64 (81)
T 2jrp_A           56 NGHGLISKK   64 (81)
T ss_dssp             TTTCCCCTT
T ss_pred             cCCCEeecc
Confidence            887765543

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

Probab=95.77  E-value=0.0064  Score=34.02  Aligned_cols=31  Identities=19%  Similarity=0.399  Sum_probs=23.6

Q ss_pred             CCcccCCCCCCceeecCCCCeeecccccccc
Q psy12853         46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVF   76 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~f   76 (137)
                      ...++||.|+..+..........|++|+..+
T Consensus        17 ~~~k~CP~CG~~~fm~~~~~R~~C~kCG~t~   47 (50)
T 3j20_Y           17 RKNKFCPRCGPGVFMADHGDRWACGKCGYTE   47 (50)
T ss_dssp             CSSEECSSSCSSCEEEECSSEEECSSSCCEE
T ss_pred             EecccCCCCCCceEEecCCCeEECCCCCCEE
Confidence            4589999999865554556788999998754

>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=94.92  E-value=0.0058  Score=38.68  Aligned_cols=49  Identities=22%  Similarity=0.657  Sum_probs=36.8

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK  108 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek  108 (137)
                      ...||-|...+.     ..+.+..||+.||..|...|-...       ...||.|+..+..
T Consensus        22 ~~~C~IC~~~~~-----~p~~~~~CgH~FC~~Ci~~~~~~~-------~~~CP~Cr~~~~~   70 (100)
T 3lrq_A           22 VFRCFICMEKLR-----DARLCPHCSKLCCFSCIRRWLTEQ-------RAQCPHCRAPLQL   70 (100)
T ss_dssp             HTBCTTTCSBCS-----SEEECTTTCCEEEHHHHHHHHHHT-------CSBCTTTCCBCCG
T ss_pred             CCCCccCCcccc-----CccccCCCCChhhHHHHHHHHHHC-------cCCCCCCCCcCCH
Confidence            446888887764     356777899999999998764332       1579999998854

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

Probab=94.85  E-value=0.023  Score=32.81  Aligned_cols=51  Identities=27%  Similarity=0.462  Sum_probs=36.0

Q ss_pred             CCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853         46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD  109 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~  109 (137)
                      .....||-|...+...     +. ..|++.||..|...|-.       .....||.|+..+...
T Consensus        13 ~~~~~C~IC~~~~~~p-----~~-~~CgH~fC~~Ci~~~~~-------~~~~~CP~Cr~~~~~~   63 (66)
T 2ecy_A           13 EDKYKCEKCHLVLCSP-----KQ-TECGHRFCESCMAALLS-------SSSPKCTACQESIVKD   63 (66)
T ss_dssp             CCCEECTTTCCEESSC-----CC-CSSSCCCCHHHHHHHHT-------TSSCCCTTTCCCCCTT
T ss_pred             CcCCCCCCCChHhcCe-----eE-CCCCCHHHHHHHHHHHH-------hCcCCCCCCCcCCChh
Confidence            4456799888776421     11 26999999999987753       2245799999988654

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

Probab=94.79  E-value=0.032  Score=30.80  Aligned_cols=29  Identities=28%  Similarity=0.713  Sum_probs=23.9

Q ss_pred             cccCCCCCC-ceeecCCCCeeecccccccc
Q psy12853         48 IKCCPMCSV-PIEKDEGCAQMLCKRCKHVF   76 (137)
Q Consensus        48 ~~~CP~C~~-~i~~~~~~~~~~C~~C~~~f   76 (137)
                      ...||.|+. .+..+.....+.|+.||..+
T Consensus         5 ~~~CP~C~~~~l~~d~~~gelvC~~CG~v~   34 (50)
T 1pft_A            5 QKVCPACESAELIYDPERGEIVCAKCGYVI   34 (50)
T ss_dssp             CCSCTTTSCCCEEEETTTTEEEESSSCCBC
T ss_pred             cEeCcCCCCcceEEcCCCCeEECcccCCcc
Confidence            557999998 88888777889999888765

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=94.40  E-value=0.0037  Score=39.96  Aligned_cols=51  Identities=35%  Similarity=0.789  Sum_probs=36.6

Q ss_pred             ccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCC
Q psy12853         49 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEG  111 (137)
Q Consensus        49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~g  111 (137)
                      .+|+.|+.+|..-+  +.+   -|++.||+.|...|.       ....+.||.|+.+|++.+-
T Consensus         2 hfC~~C~~Pi~iyg--RmI---PCkHvFCydCa~~~~-------~~~~k~Cp~C~~~V~rVe~   52 (101)
T 3vk6_A            2 HFCDKCGLPIKVYG--RMI---PCKHVFCYDCAILHE-------KKGDKMCPGCSDPVQRIEQ   52 (101)
T ss_dssp             CBCTTTCSBCSEEE--EEE---TTCCEEEHHHHHHHH-------HTTCCBCTTTCCBCSEEEE
T ss_pred             eecCccCCCeEEEe--eec---cccccHHHHHHHHHH-------hccCCCCcCcCCeeeeeEE
Confidence            47899999986532  222   378999999976532       2345689999999988654

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

Probab=94.34  E-value=0.063  Score=29.54  Aligned_cols=49  Identities=24%  Similarity=0.524  Sum_probs=33.8

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcce
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPI  106 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~i  106 (137)
                      ...||-|...+..  +...+.-+.|++.||..|...|-..        ...||.|+..+
T Consensus         5 ~~~C~IC~~~~~~--~~~~~~~~~C~H~f~~~Ci~~w~~~--------~~~CP~Cr~~~   53 (55)
T 1iym_A            5 GVECAVCLAELED--GEEARFLPRCGHGFHAECVDMWLGS--------HSTCPLCRLTV   53 (55)
T ss_dssp             SCCCTTTCCCCCT--TSCCEECSSSCCEECTTHHHHTTTT--------CCSCSSSCCCS
T ss_pred             CCcCccCCccccC--CCceEECCCCCCcccHHHHHHHHHc--------CCcCcCCCCEe
Confidence            3457777666543  2234445569999999999888543        34799998876

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

Probab=94.32  E-value=0.053  Score=31.67  Aligned_cols=53  Identities=26%  Similarity=0.609  Sum_probs=37.3

Q ss_pred             CCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853         46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD  109 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~  109 (137)
                      .....||-|...+..     .+.- .|++.||..|...|-..     ......||.|+..+.+.
T Consensus        18 ~~~~~C~IC~~~~~~-----~~~~-~CgH~fC~~Ci~~~~~~-----~~~~~~CP~Cr~~~~~~   70 (73)
T 2ysl_A           18 QEEVICPICLDILQK-----PVTI-DCGHNFCLKCITQIGET-----SCGFFKCPLCKTSVRKN   70 (73)
T ss_dssp             CCCCBCTTTCSBCSS-----EEEC-TTCCEEEHHHHHHHCSS-----SCSCCCCSSSCCCCCCC
T ss_pred             ccCCEeccCCcccCC-----eEEc-CCCChhhHHHHHHHHHc-----CCCCCCCCCCCCcCCcc
Confidence            445678988876541     2222 69999999999877542     12356899999998764

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

Probab=94.15  E-value=0.052  Score=33.31  Aligned_cols=35  Identities=26%  Similarity=0.734  Sum_probs=29.0

Q ss_pred             CCCCCCCcceeecCCCCeEEeccCcce-----eecccccccc
Q psy12853         97 KCCPMCSVPIEKDEGCAQMLCKRCKHV-----FCWYCLASLD  133 (137)
Q Consensus        97 ~~CP~C~~~iek~~gC~hm~C~~C~~~-----fC~~C~~~~~  133 (137)
                      ..||.|+..+++.++  +..|..|+..     ||-.|++++.
T Consensus         3 ~~CP~C~~~l~~~~~--~~~C~~C~~~~~~~afCPeCgq~Le   42 (81)
T 2jrp_A            3 ITCPVCHHALERNGD--TAHCETCAKDFSLQALCPDCRQPLQ   42 (81)
T ss_dssp             CCCSSSCSCCEECSS--EEECTTTCCEEEEEEECSSSCSCCC
T ss_pred             CCCCCCCCccccCCC--ceECccccccCCCcccCcchhhHHH
Confidence            579999999999877  7779989765     6888888875

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

Probab=94.02  E-value=0.0067  Score=39.65  Aligned_cols=57  Identities=25%  Similarity=0.545  Sum_probs=37.0

Q ss_pred             CCCcccCCCCCCceeecC-CCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853         45 SELIKCCPMCSVPIEKDE-GCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD  109 (137)
Q Consensus        45 ~~~~~~CP~C~~~i~~~~-~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~  109 (137)
                      +++...||-|...+.... .........|++.||..|...|...        .+.||.|+..+++.
T Consensus        69 ~~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~--------~~~CP~Cr~~~~~~  126 (133)
T 4ap4_A           69 GSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN--------ANTCPTCRKKINHK  126 (133)
T ss_dssp             SSSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHH--------CSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHc--------CCCCCCCCCcCChh
Confidence            344555666665554321 1122233379999999999887643        46899999999765

>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=93.94  E-value=0.053  Score=34.35  Aligned_cols=24  Identities=29%  Similarity=0.901  Sum_probs=11.1

Q ss_pred             CCCCCCCcceeecCCCCeEEeccCcc
Q psy12853         97 KCCPMCSVPIEKDEGCAQMLCKRCKH  122 (137)
Q Consensus        97 ~~CP~C~~~iek~~gC~hm~C~~C~~  122 (137)
                      ..||.|+..++..+|  +..|..|+.
T Consensus        33 ~~CP~Cq~eL~~~g~--~~hC~~C~~   56 (101)
T 2jne_A           33 LHCPQCQHVLDQDNG--HARCRSCGE   56 (101)
T ss_dssp             CBCSSSCSBEEEETT--EEEETTTCC
T ss_pred             ccCccCCCcceecCC--EEECccccc
Confidence            345555554444444  444444443

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

Probab=93.93  E-value=0.02  Score=34.78  Aligned_cols=57  Identities=23%  Similarity=0.463  Sum_probs=37.9

Q ss_pred             CCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853         46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD  109 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~  109 (137)
                      .....||-|...+.... ...+.- .|++.||..|...|-...     .....||.|+..+...
T Consensus        13 ~~~~~C~IC~~~~~~~~-~~~~~~-~CgH~fC~~Ci~~~~~~~-----~~~~~CP~Cr~~~~~~   69 (88)
T 2ct2_A           13 REVLECPICMESFTEEQ-LRPKLL-HCGHTICRQCLEKLLASS-----INGVRCPFCSKITRIT   69 (88)
T ss_dssp             CSCCBCTTTCCBCCTTS-SCEEEC-SSSCEEEHHHHHHHHHHC-----SSCBCCTTTCCCBCCS
T ss_pred             cCCCCCccCCccccccC-CCeEEC-CCCChhhHHHHHHHHHcC-----CCCcCCCCCCCcccch
Confidence            34567898887764322 113333 599999999998764321     1356899999988654

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

Probab=93.87  E-value=0.059  Score=32.62  Aligned_cols=55  Identities=29%  Similarity=0.642  Sum_probs=37.0

Q ss_pred             CCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853         46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD  109 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~  109 (137)
                      .+...||-|-.++... +.....| .||+.||..|...+-..       ....||.|+..+...
T Consensus         9 ~~~~~CpICle~~~~~-d~~~~p~-~CGH~fC~~Cl~~~~~~-------~~~~CP~CR~~~~~~   63 (78)
T 1e4u_A            9 EDPVECPLCMEPLEID-DINFFPC-TCGYQICRFCWHRIRTD-------ENGLCPACRKPYPED   63 (78)
T ss_dssp             CCCCBCTTTCCBCCTT-TTTCCSS-TTSCCCCHHHHHHHTTS-------SCSBCTTTCCBCSSC
T ss_pred             ccCCcCCccCccCccc-ccccccc-CCCCCcCHHHHHHHHhc-------CCCCCCCCCCccCCC
Confidence            3456799888866432 2233445 69999999998654221       246899999988653

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

Probab=93.65  E-value=0.016  Score=33.84  Aligned_cols=56  Identities=25%  Similarity=0.574  Sum_probs=39.1

Q ss_pred             CCcccCCCCCCceeec-CCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853         46 ELIKCCPMCSVPIEKD-EGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD  109 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~-~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~  109 (137)
                      .....||-|...+... .+...+.-..|++.||..|...|-..        ...||.|+..+...
T Consensus         8 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~--------~~~CP~Cr~~~~~~   64 (71)
T 3ng2_A            8 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN--------ANTCPTCRKKINHK   64 (71)
T ss_dssp             TTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHH--------CSBCTTTCCBCCCC
T ss_pred             CCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHc--------CCCCCCCCCccChh
Confidence            3456788888876543 22333344579999999999877432        25899999998754

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

Probab=93.37  E-value=0.029  Score=32.96  Aligned_cols=51  Identities=22%  Similarity=0.566  Sum_probs=36.2

Q ss_pred             CCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853         46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD  109 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~  109 (137)
                      .....||-|...+..     .+.-..|++.||..|...|-..        ...||.|+..+...
T Consensus        13 ~~~~~C~IC~~~~~~-----p~~~~~CgH~fC~~Ci~~~~~~--------~~~CP~Cr~~~~~~   63 (72)
T 2djb_A           13 TPYILCSICKGYLID-----ATTITECLHTFCKSCIVRHFYY--------SNRCPKCNIVVHQT   63 (72)
T ss_dssp             CGGGSCTTTSSCCSS-----CEECSSSCCEECHHHHHHHHHH--------CSSCTTTCCCCCSS
T ss_pred             CCCCCCCCCChHHHC-----cCEECCCCCHHHHHHHHHHHHc--------CCcCCCcCcccCcc
Confidence            345678888766532     2333469999999998776432        35899999998764

>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=93.28  E-value=0.059  Score=30.62  Aligned_cols=31  Identities=23%  Similarity=0.449  Sum_probs=23.1

Q ss_pred             CCcccCCCCCCceeecCCCCeeecccccccc
Q psy12853         46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVF   76 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~f   76 (137)
                      ...++||.|+..+........+.|++|+...
T Consensus        16 ~~~~fCPkCG~~~~ma~~~dr~~C~kCgyt~   46 (55)
T 2k4x_A           16 RKHRFCPRCGPGVFLAEHADRYSCGRCGYTE   46 (55)
T ss_dssp             CSSCCCTTTTTTCCCEECSSEEECTTTCCCE
T ss_pred             EccccCcCCCCceeEeccCCEEECCCCCCEE
Confidence            4578999999866544445688999988764

>1z60_A TFIIH basal transcription factor complex P44 subunit; basic transcription factor, zinc binding protein, ring finger; NMR {Homo sapiens} SCOP: g.49.1.2

Probab=93.22  E-value=0.044  Score=31.62  Aligned_cols=44  Identities=25%  Similarity=0.668  Sum_probs=32.6

Q ss_pred             ccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCC
Q psy12853         49 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCS  103 (137)
Q Consensus        49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~  103 (137)
                      +.|-.|...+.   +.....|++|+..||..|-.=.|        +....||.|.
T Consensus        16 ~~C~~C~~~~~---~~~~y~C~~C~~~FC~dCD~fiH--------e~Lh~CPgC~   59 (59)
T 1z60_A           16 RFCYGCQGELK---DQHVYVCAVCQNVFCVDCDVFVH--------DSLHSCPGCI   59 (59)
T ss_dssp             CEETTTTEECT---TSEEECCTTTTCCBCHHHHHTTT--------TTSCSSSTTC
T ss_pred             CcccccCcccC---CCccEECCccCcCcccchhHHHH--------hhccCCcCCC
Confidence            45888888773   12247899999999999976444        4467899884

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

Probab=93.00  E-value=0.12  Score=28.40  Aligned_cols=29  Identities=28%  Similarity=0.713  Sum_probs=22.4

Q ss_pred             cCCCCCCCc-ceeecCCCCeEEeccCccee
Q psy12853         96 IKCCPMCSV-PIEKDEGCAQMLCKRCKHVF  124 (137)
Q Consensus        96 ~~~CP~C~~-~iek~~gC~hm~C~~C~~~f  124 (137)
                      ...||.|+. .+.....=..+.|..||..|
T Consensus         5 ~~~CP~C~~~~l~~d~~~gelvC~~CG~v~   34 (50)
T 1pft_A            5 QKVCPACESAELIYDPERGEIVCAKCGYVI   34 (50)
T ss_dssp             CCSCTTTSCCCEEEETTTTEEEESSSCCBC
T ss_pred             cEeCcCCCCcceEEcCCCCeEECcccCCcc
Confidence            567999988 77666666679999888754

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

Probab=92.89  E-value=0.086  Score=30.77  Aligned_cols=48  Identities=27%  Similarity=0.692  Sum_probs=33.7

Q ss_pred             CcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853         47 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK  108 (137)
Q Consensus        47 ~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek  108 (137)
                      ....||-|...+..     .+.- .|++.||..|...|-..        ...||.|+..|..
T Consensus        14 ~~~~C~IC~~~~~~-----~~~~-~CgH~fC~~Ci~~~~~~--------~~~CP~Cr~~~~~   61 (71)
T 2d8t_A           14 TVPECAICLQTCVH-----PVSL-PCKHVFCYLCVKGASWL--------GKRCALCRQEIPE   61 (71)
T ss_dssp             SCCBCSSSSSBCSS-----EEEE-TTTEEEEHHHHHHCTTC--------SSBCSSSCCBCCH
T ss_pred             CCCCCccCCcccCC-----CEEc-cCCCHHHHHHHHHHHHC--------CCcCcCcCchhCH
Confidence            34578888766521     2333 49999999999877543        2589999998864

>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=92.68  E-value=0.045  Score=30.10  Aligned_cols=49  Identities=24%  Similarity=0.465  Sum_probs=32.6

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcce
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPI  106 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~i  106 (137)
                      ...||-|...+..  +...+.-..|++.||..|...|-..        ...||.|+..+
T Consensus         5 ~~~C~IC~~~~~~--~~~~~~~~~CgH~fc~~Ci~~~~~~--------~~~CP~Cr~~~   53 (55)
T 2ecm_A            5 SSGCPICLEDIHT--SRVVAHVLPCGHLLHRTCYEEMLKE--------GYRCPLCSGPS   53 (55)
T ss_dssp             CCSCTTTCCCCCT--TTSCEEECTTSCEEETTHHHHHHHH--------TCCCTTSCCSS
T ss_pred             CCcCcccChhhcC--CCcCeEecCCCCcccHHHHHHHHHc--------CCcCCCCCCcC
Confidence            3467777666532  2223444468999999999876432        26899998876

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

Probab=92.62  E-value=0.029  Score=33.24  Aligned_cols=54  Identities=20%  Similarity=0.463  Sum_probs=37.3

Q ss_pred             CcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCC
Q psy12853         47 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEG  111 (137)
Q Consensus        47 ~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~g  111 (137)
                      ....||-|...+....   .+....|++.||..|...|-..        ...||.|+..+...+|
T Consensus        22 ~~~~C~IC~~~~~~~~---~~~~l~C~H~fh~~Ci~~w~~~--------~~~CP~Cr~~~~~~~g   75 (75)
T 1x4j_A           22 EQTLCVVCMCDFESRQ---LLRVLPCNHEFHAKCVDKWLKA--------NRTCPICRADSGPSSG   75 (75)
T ss_dssp             SCCEETTTTEECCBTC---EEEEETTTEEEETTHHHHHHHH--------CSSCTTTCCCCCCCCC
T ss_pred             CCCCCeECCcccCCCC---eEEEECCCCHhHHHHHHHHHHc--------CCcCcCcCCcCCCCCC
Confidence            3456887776654322   3333358999999999887532        2479999999987665

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=92.43  E-value=0.22  Score=27.68  Aligned_cols=45  Identities=24%  Similarity=0.554  Sum_probs=30.8

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD  109 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~  109 (137)
                      ...||-|...+...   ..   ..|++.||..|...           ....||.|+..+...
T Consensus         6 ~~~C~IC~~~~~~p---~~---l~CgH~fC~~Ci~~-----------~~~~CP~Cr~~~~~~   50 (56)
T 1bor_A            6 FLRCQQCQAEAKCP---KL---LPCLHTLCSGCLEA-----------SGMQCPICQAPWPLG   50 (56)
T ss_dssp             CSSCSSSCSSCBCC---SC---STTSCCSBTTTCSS-----------SSSSCSSCCSSSSCC
T ss_pred             CCCceEeCCccCCe---EE---cCCCCcccHHHHcc-----------CCCCCCcCCcEeecC
Confidence            44678777665421   11   25899999999754           245799999988653

>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=92.33  E-value=0.084  Score=29.95  Aligned_cols=30  Identities=23%  Similarity=0.460  Sum_probs=22.9

Q ss_pred             ccCCCCCCCcceeecCCCCeEEeccCccee
Q psy12853         95 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF  124 (137)
Q Consensus        95 ~~~~CP~C~~~iek~~gC~hm~C~~C~~~f  124 (137)
                      ..+.||+|+..+.-...-+.+.|..||+.+
T Consensus        17 ~~~fCPkCG~~~~ma~~~dr~~C~kCgyt~   46 (55)
T 2k4x_A           17 KHRFCPRCGPGVFLAEHADRYSCGRCGYTE   46 (55)
T ss_dssp             SSCCCTTTTTTCCCEECSSEEECTTTCCCE
T ss_pred             ccccCcCCCCceeEeccCCEEECCCCCCEE
Confidence            467899999866544445799999999875

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

Probab=92.22  E-value=0.037  Score=31.77  Aligned_cols=52  Identities=25%  Similarity=0.583  Sum_probs=33.1

Q ss_pred             ccCCCCCC-ceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853         49 KCCPMCSV-PIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD  109 (137)
Q Consensus        49 ~~CP~C~~-~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~  109 (137)
                      ..||-|.. .+.. +....+. ..||+.||..|...|-..       ....||.|+..+.+.
T Consensus         4 ~~C~IC~~~~~~~-~~~~~~~-~~CgH~fC~~Ci~~~~~~-------~~~~CP~Cr~~~~~~   56 (65)
T 1g25_A            4 QGCPRCKTTKYRN-PSLKLMV-NVCGHTLCESCVDLLFVR-------GAGNCPECGTPLRKS   56 (65)
T ss_dssp             TCCSTTTTHHHHC-SSCCEEE-CTTCCCEEHHHHHHHHHT-------TSSSCTTTCCCCSSC
T ss_pred             CcCCcCCCCccCC-CccCeec-CCCCCHhHHHHHHHHHHc-------CCCcCCCCCCccccc
Confidence            35777776 4332 2221122 269999999998776221       235799999998764

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

Probab=92.10  E-value=0.14  Score=30.37  Aligned_cols=30  Identities=17%  Similarity=0.364  Sum_probs=25.6

Q ss_pred             ccCCCCCCCcceeecCCCCeEEeccCccee
Q psy12853         95 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF  124 (137)
Q Consensus        95 ~~~~CP~C~~~iek~~gC~hm~C~~C~~~f  124 (137)
                      .+..||.|+..++-......+.|..||..|
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            466899999999988888899998888766

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

Probab=92.07  E-value=0.073  Score=31.58  Aligned_cols=52  Identities=21%  Similarity=0.426  Sum_probs=34.9

Q ss_pred             CCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853         46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK  108 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek  108 (137)
                      .....||-|...+....  ..+. ..|++.||..|...|-..        ...||.|+..+..
T Consensus        13 ~~~~~C~IC~~~~~~~~--~~~~-~~C~H~fc~~Ci~~~~~~--------~~~CP~Cr~~~~~   64 (78)
T 2ect_A           13 GSGLECPVCKEDYALGE--SVRQ-LPCNHLFHDSCIVPWLEQ--------HDSCPVCRKSLTG   64 (78)
T ss_dssp             SSSCCCTTTTSCCCTTS--CEEE-CTTSCEEETTTTHHHHTT--------TCSCTTTCCCCCC
T ss_pred             CCCCCCeeCCccccCCC--CEEE-eCCCCeecHHHHHHHHHc--------CCcCcCcCCccCC
Confidence            33557888877664322  1111 148999999999887543        2489999988865

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

Probab=91.87  E-value=0.066  Score=33.39  Aligned_cols=48  Identities=23%  Similarity=0.583  Sum_probs=35.0

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK  108 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek  108 (137)
                      ...||-|...+..     .+.-+.||+.||..|...|-..        ...||.|+..+..
T Consensus        22 ~~~C~IC~~~~~~-----p~~~~~CgH~fC~~Ci~~~~~~--------~~~CP~Cr~~~~~   69 (99)
T 2y43_A           22 LLRCGICFEYFNI-----AMIIPQCSHNYCSLCIRKFLSY--------KTQCPTCCVTVTE   69 (99)
T ss_dssp             HTBCTTTCSBCSS-----EEECTTTCCEEEHHHHHHHHTT--------CCBCTTTCCBCCG
T ss_pred             CCCcccCChhhCC-----cCEECCCCCHhhHHHHHHHHHC--------CCCCCCCCCcCCh
Confidence            3468888776632     3344579999999999877653        2479999998865

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

Probab=91.87  E-value=0.097  Score=30.95  Aligned_cols=56  Identities=20%  Similarity=0.530  Sum_probs=36.7

Q ss_pred             CCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853         46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK  108 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek  108 (137)
                      .....||-|...+..     .+.- .|++.||..|...|-..... .......||.|+..+..
T Consensus        10 ~~~~~C~IC~~~~~~-----p~~l-~CgH~fC~~Ci~~~~~~~~~-~~~~~~~CP~Cr~~~~~   65 (79)
T 2egp_A           10 QEEVTCPICLELLTE-----PLSL-DCGHSLCRACITVSNKEAVT-SMGGKSSCPVCGISYSF   65 (79)
T ss_dssp             CCCCEETTTTEECSS-----CCCC-SSSCCCCHHHHSCCCCCCSS-SCCCCCCCSSSCCCCCS
T ss_pred             ccCCCCcCCCcccCC-----eeEC-CCCCHHHHHHHHHHHHhccc-CCCCCCcCCCCCCcCCH
Confidence            345578888766532     1122 59999999999877554211 11346789999998865

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

Probab=91.81  E-value=0.083  Score=33.51  Aligned_cols=49  Identities=27%  Similarity=0.561  Sum_probs=35.8

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD  109 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~  109 (137)
                      ...||-|...+.     ..+.-..||+.||..|...|-..        ...||.|+..+...
T Consensus        15 ~~~C~IC~~~~~-----~p~~~~~CgH~fC~~Ci~~~~~~--------~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           15 HLMCVLCGGYFI-----DATTIIECLHSFCKTCIVRYLET--------SKYCPICDVQVHKT   63 (108)
T ss_dssp             GTBCTTTSSBCS-----SEEEETTTCCEEEHHHHHHHHTS--------CSBCTTTCCBSCSS
T ss_pred             cCCCccCChHHh-----CcCEeCCCCChhhHHHHHHHHHh--------CCcCcCCCcccccc
Confidence            457888877663     23444469999999999877543        26799999988754

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

Probab=91.78  E-value=0.15  Score=32.77  Aligned_cols=46  Identities=24%  Similarity=0.634  Sum_probs=32.7

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK  108 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek  108 (137)
                      ...||-|...+..    + +.=..||+.||..|...|-.          ..||.|+..+..
T Consensus        22 ~~~C~IC~~~~~~----p-v~~~~CgH~fC~~Ci~~~~~----------~~CP~Cr~~~~~   67 (117)
T 1jm7_B           22 LLRCSRCTNILRE----P-VCLGGCEHIFCSNCVSDCIG----------TGCPVCYTPAWI   67 (117)
T ss_dssp             TTSCSSSCSCCSS----C-BCCCSSSCCBCTTTGGGGTT----------TBCSSSCCBCSC
T ss_pred             CCCCCCCChHhhC----c-cEeCCCCCHHHHHHHHHHhc----------CCCcCCCCcCcc
Confidence            4578888776632    1 22225899999999987643          579999988854

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

Probab=91.51  E-value=0.098  Score=30.86  Aligned_cols=52  Identities=15%  Similarity=0.340  Sum_probs=35.2

Q ss_pred             CCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853         46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK  108 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek  108 (137)
                      +....||-|...+.     ..+.=+.|++.||..|...|-..      .....||.|+..+.+
T Consensus        13 ~~~~~C~IC~~~~~-----~p~~~~~CgH~fC~~Ci~~~~~~------~~~~~CP~Cr~~~~~   64 (74)
T 2yur_A           13 PDELLCLICKDIMT-----DAVVIPCCGNSYCDECIRTALLE------SDEHTCPTCHQNDVS   64 (74)
T ss_dssp             CGGGSCSSSCCCCT-----TCEECSSSCCEECTTHHHHHHHH------SSSSCCSSSCCSSCC
T ss_pred             CCCCCCcCCChHHh-----CCeEcCCCCCHHHHHHHHHHHHh------cCCCcCCCCCCcCCC
Confidence            44567888876653     23343459999999998876432      124689999987544

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

Probab=91.34  E-value=0.076  Score=32.54  Aligned_cols=50  Identities=16%  Similarity=0.366  Sum_probs=34.0

Q ss_pred             CCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcce
Q psy12853         46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPI  106 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~i  106 (137)
                      +....||-|...+.     ..+.-+.||+.||..|...|-..      .....||.|+..+
T Consensus        11 ~~~~~C~IC~~~~~-----~p~~~~~CgH~fC~~Ci~~~~~~------~~~~~CP~Cr~~~   60 (92)
T 3ztg_A           11 PDELLCLICKDIMT-----DAVVIPCCGNSYCDECIRTALLE------SDEHTCPTCHQND   60 (92)
T ss_dssp             CTTTEETTTTEECS-----SCEECTTTCCEECHHHHHHHHHH------CTTCCCTTTCCSS
T ss_pred             CcCCCCCCCChhhc-----CceECCCCCCHHHHHHHHHHHHh------cCCCcCcCCCCcC
Confidence            34567888887653     22333459999999998766321      1235899999886

>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=91.24  E-value=0.17  Score=32.07  Aligned_cols=45  Identities=27%  Similarity=0.795  Sum_probs=31.4

Q ss_pred             ccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCCC
Q psy12853         49 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGC  112 (137)
Q Consensus        49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~gC  112 (137)
                      ..||.|...+..+++  .+.|..|+..|=                 ..-.||.|+.++|+-..|
T Consensus        33 ~~CP~Cq~eL~~~g~--~~hC~~C~~~f~-----------------~~a~CPdC~q~LevLkAC   77 (101)
T 2jne_A           33 LHCPQCQHVLDQDNG--HARCRSCGEFIE-----------------MKALCPDCHQPLQVLKAC   77 (101)
T ss_dssp             CBCSSSCSBEEEETT--EEEETTTCCEEE-----------------EEEECTTTCSBCEEEEET
T ss_pred             ccCccCCCcceecCC--EEECccccchhh-----------------ccccCcchhhHHHHHHHh
Confidence            799999999987543  455666555332                 233699999999986543

>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=91.24  E-value=0.068  Score=33.58  Aligned_cols=33  Identities=21%  Similarity=0.686  Sum_probs=23.8

Q ss_pred             cCCCCCCCcceeecCCCCeEEeccCcceeecccccccc
Q psy12853         96 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLD  133 (137)
Q Consensus        96 ~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~~  133 (137)
                      ...||-|...+..     -+++..||+.||+.|...|-
T Consensus        22 ~~~C~IC~~~~~~-----p~~~~~CgH~FC~~Ci~~~~   54 (100)
T 3lrq_A           22 VFRCFICMEKLRD-----ARLCPHCSKLCCFSCIRRWL   54 (100)
T ss_dssp             HTBCTTTCSBCSS-----EEECTTTCCEEEHHHHHHHH
T ss_pred             CCCCccCCccccC-----ccccCCCCChhhHHHHHHHH
Confidence            4579999888753     45656788888888876653

>1weo_A Cellulose synthase, catalytic subunit (IRX3); structure genomics, ring-finger, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: g.44.1.1

Probab=91.22  E-value=0.14  Score=31.87  Aligned_cols=60  Identities=23%  Similarity=0.466  Sum_probs=45.7

Q ss_pred             CcccCCCCCCceeec-CCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCCCC
Q psy12853         47 LIKCCPMCSVPIEKD-EGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCA  113 (137)
Q Consensus        47 ~~~~CP~C~~~i~~~-~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~gC~  113 (137)
                      +...|--|+--+-.. ++...+.|..|++-.|.-|..-       ...+..+.||.|++.+.+..|.-
T Consensus        15 ~~qiCqiCGD~VG~~~~Ge~FVAC~eC~FPvCrpCyEY-------ErkeG~q~CpqCktrYkr~kgsp   75 (93)
T 1weo_A           15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEY-------ERREGTQNCPQCKTRYKRLRGSP   75 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHH-------HHHTSCSSCTTTCCCCCCCTTCC
T ss_pred             CCCccccccCccccCCCCCEEEeeeccCChhhHHHHHH-------HHhccCccccccCCccccccCCC
Confidence            456777888877665 4678899999999999999641       12456789999999998766553

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

Probab=91.14  E-value=0.15  Score=28.31  Aligned_cols=30  Identities=20%  Similarity=0.408  Sum_probs=20.4

Q ss_pred             ccCCCCCCCcceeecCCCCeEEeccCccee
Q psy12853         95 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF  124 (137)
Q Consensus        95 ~~~~CP~C~~~iek~~gC~hm~C~~C~~~f  124 (137)
                      ..+-||+|+..+.-...=+...|.+||..+
T Consensus        18 ~~k~CP~CG~~~fm~~~~~R~~C~kCG~t~   47 (50)
T 3j20_Y           18 KNKFCPRCGPGVFMADHGDRWACGKCGYTE   47 (50)
T ss_dssp             SSEECSSSCSSCEEEECSSEEECSSSCCEE
T ss_pred             ecccCCCCCCceEEecCCCeEECCCCCCEE
Confidence            467799998754443333678888888754

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

Probab=91.01  E-value=0.06  Score=30.93  Aligned_cols=55  Identities=25%  Similarity=0.559  Sum_probs=37.5

Q ss_pred             CCcccCCCCCCceeecC-CCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853         46 ELIKCCPMCSVPIEKDE-GCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK  108 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~~-~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek  108 (137)
                      .....||-|...+.... ....+.-..|++.||..|...|-..        ...||.|+..|.+
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~--------~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           13 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN--------ANTCPTCRKKINH   68 (69)
T ss_dssp             TCCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHH--------CSSCTTTCCCCCC
T ss_pred             CCCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHc--------CCCCCCCCCccCc
Confidence            44567888888765432 2223333479999999999877432        3589999988754

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

Probab=90.50  E-value=0.031  Score=31.73  Aligned_cols=53  Identities=26%  Similarity=0.614  Sum_probs=35.1

Q ss_pred             ccCCCCCCceeecC-CCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853         49 KCCPMCSVPIEKDE-GCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD  109 (137)
Q Consensus        49 ~~CP~C~~~i~~~~-~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~  109 (137)
                      ..||-|...+.... +...+.-..|++.||..|...|-..        ...||.|+..+...
T Consensus         4 ~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~--------~~~CP~Cr~~~~~~   57 (64)
T 2xeu_A            4 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN--------ANTCPTCRKKINHK   57 (64)
T ss_dssp             CBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHH--------CSBCTTTCCBCTTT
T ss_pred             CCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHc--------CCCCCCCCccCCcc
Confidence            35777777664421 2223333479999999999876432        34899999988653

>4ic3_A E3 ubiquitin-protein ligase XIAP; ring domain, zinc-finger, E3 ligase; 1.78A {Homo sapiens} PDB: 4ic2_A

Probab=90.47  E-value=0.093  Score=31.12  Aligned_cols=42  Identities=29%  Similarity=0.602  Sum_probs=29.4

Q ss_pred             ccCCCCCCceeecCCCCeeeccccccc-ccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853         49 KCCPMCSVPIEKDEGCAQMLCKRCKHV-FCWYCLASRDYGGATFDSELIKCCPMCSVPIEK  108 (137)
Q Consensus        49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~-fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek  108 (137)
                      ..||-|...+..     .+. ..|++. ||..|...|            ..||-|+..|.+
T Consensus        25 ~~C~iC~~~~~~-----~~~-~pCgH~~~C~~C~~~~------------~~CP~Cr~~i~~   67 (74)
T 4ic3_A           25 KLCKICMDRNIA-----IVF-VPCGHLVTCKQCAEAV------------DKCPMCYTVITF   67 (74)
T ss_dssp             TBCTTTSSSBCC-----EEE-ETTCCBCCCHHHHTTC------------SBCTTTCCBCSE
T ss_pred             CCCCCCCCCCCC-----EEE-cCCCChhHHHHhhhcC------------ccCCCcCcCccC
Confidence            467777654321     111 258999 999997654            789999999875

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

Probab=90.03  E-value=0.054  Score=32.40  Aligned_cols=56  Identities=23%  Similarity=0.598  Sum_probs=36.5

Q ss_pred             CCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853         46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD  109 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~  109 (137)
                      .....||-|...+..     .+.- .|++.||..|...|-....  .......||.|+..+...
T Consensus        17 ~~~~~C~IC~~~~~~-----p~~~-~CgH~fC~~Ci~~~~~~~~--~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecw_A           17 KEEVTCPICLELLKE-----PVSA-DCNHSFCRACITLNYESNR--NTDGKGNCPVCRVPYPFG   72 (85)
T ss_dssp             CTTTSCTTTCSCCSS-----CEEC-TTSCCBCHHHHHHHHHHSB--CTTSCBCCTTTCCCCCTT
T ss_pred             ccCCCCcCCChhhCc-----ceeC-CCCCHHHHHHHHHHHHhcc--CCCCCCCCCCCCCcCCHH
Confidence            335578888776532     2233 5999999999986643311  112357899999988653

>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=89.95  E-value=0.048  Score=33.67  Aligned_cols=31  Identities=23%  Similarity=0.483  Sum_probs=26.0

Q ss_pred             CcccCCCCCCceeecCCCCeeeccccccccc
Q psy12853         47 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFC   77 (137)
Q Consensus        47 ~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC   77 (137)
                      ....||.|+....+..+.....|+.|+..|-
T Consensus        26 ~~y~Cp~CG~~~v~r~atGiW~C~~Cg~~~a   56 (83)
T 1vq8_Z           26 EDHACPNCGEDRVDRQGTGIWQCSYCDYKFT   56 (83)
T ss_dssp             SCEECSSSCCEEEEEEETTEEEETTTCCEEE
T ss_pred             ccCcCCCCCCcceeccCCCeEECCCCCCEec
Confidence            3668999999888877788999999888775

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

Probab=89.58  E-value=0.26  Score=31.94  Aligned_cols=31  Identities=16%  Similarity=0.385  Sum_probs=23.9

Q ss_pred             CcccCCCCCCceeecC----CCCeeeccccccccc
Q psy12853         47 LIKCCPMCSVPIEKDE----GCAQMLCKRCKHVFC   77 (137)
Q Consensus        47 ~~~~CP~C~~~i~~~~----~~~~~~C~~C~~~fC   77 (137)
                      ...+||.|+..+....    +...+.|+.|++.+=
T Consensus         3 ~m~FCp~Cgn~L~~~~~~~~~~~~~~C~~C~y~~~   37 (113)
T 3h0g_I            3 NFQYCIECNNMLYPREDKVDRVLRLACRNCDYSEI   37 (113)
T ss_dssp             CCCCCSSSCCCCEECCCTTTCCCCEECSSSCCEEC
T ss_pred             cceeCcCCCCEeeEcccCCCCeeEEECCCCCCeEE
Confidence            3679999999987753    245799999988663

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

Probab=89.40  E-value=0.082  Score=31.00  Aligned_cols=52  Identities=29%  Similarity=0.686  Sum_probs=35.1

Q ss_pred             CCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853         46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK  108 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek  108 (137)
                      .....||-|...+....  ..+.- .|++.||..|...|-..        ...||.|+..|..
T Consensus        13 ~~~~~C~IC~~~~~~~~--~~~~~-~C~H~f~~~Ci~~~~~~--------~~~CP~Cr~~~~~   64 (74)
T 2ep4_A           13 NLHELCAVCLEDFKPRD--ELGIC-PCKHAFHRKCLIKWLEV--------RKVCPLCNMPVLQ   64 (74)
T ss_dssp             CCSCBCSSSCCBCCSSS--CEEEE-TTTEEEEHHHHHHHHHH--------CSBCTTTCCBCSS
T ss_pred             CCCCCCcCCCcccCCCC--cEEEc-CCCCEecHHHHHHHHHc--------CCcCCCcCccccc
Confidence            33557888887764322  22222 48999999999877532        2379999988764

>1gh9_A 8.3 kDa protein (gene MTH1184); beta+alpha complex structure, structural genomics, PSI, protein structure initiative; NMR {Methanothermobacterthermautotrophicus} SCOP: g.41.6.1

Probab=89.34  E-value=0.19  Score=30.03  Aligned_cols=33  Identities=21%  Similarity=0.348  Sum_probs=25.1

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccccccccc
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLA   82 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~   82 (137)
                      ..-|| |+.....+++....+|| ||..+=..=..
T Consensus         4 vv~C~-C~~~~~~~~~~kT~~C~-CG~~~~~~k~r   36 (71)
T 1gh9_A            4 IFRCD-CGRALYSREGAKTRKCV-CGRTVNVKDRR   36 (71)
T ss_dssp             EEEET-TSCCEEEETTCSEEEET-TTEEEECCSSS
T ss_pred             EEECC-CCCEEEEcCCCcEEECC-CCCeeeeceEE
Confidence            45789 99998888888899998 88776544333

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

Probab=88.95  E-value=0.11  Score=30.94  Aligned_cols=56  Identities=21%  Similarity=0.575  Sum_probs=35.9

Q ss_pred             CCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853         46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD  109 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~  109 (137)
                      .....||-|...+..    . +.- .|++.||..|...|-....  .......||.|+..+...
T Consensus        17 ~~~~~C~IC~~~~~~----p-~~~-~CgH~fC~~Ci~~~~~~~~--~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecv_A           17 KEEVTCPICLELLTQ----P-LSL-DCGHSFCQACLTANHKKSM--LDKGESSCPVCRISYQPE   72 (85)
T ss_dssp             CCCCCCTTTCSCCSS----C-BCC-SSSCCBCTTHHHHHHHHHH--HTTSCCCCTTTCCSSCSS
T ss_pred             cCCCCCCCCCcccCC----c-eeC-CCCCHHHHHHHHHHHHHhh--cCCCCCcCCCCCCccCHH
Confidence            345678888776632    1 111 5999999999876632200  012256899999988753

>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=88.95  E-value=0.18  Score=31.03  Aligned_cols=30  Identities=23%  Similarity=0.530  Sum_probs=25.7

Q ss_pred             cCCCCCCCcceeecCCCCeEEeccCcceee
Q psy12853         96 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFC  125 (137)
Q Consensus        96 ~~~CP~C~~~iek~~gC~hm~C~~C~~~fC  125 (137)
                      ..+||.|+....+..+=..+.|..||+.|-
T Consensus        27 ~y~Cp~CG~~~v~r~atGiW~C~~Cg~~~a   56 (83)
T 1vq8_Z           27 DHACPNCGEDRVDRQGTGIWQCSYCDYKFT   56 (83)
T ss_dssp             CEECSSSCCEEEEEEETTEEEETTTCCEEE
T ss_pred             cCcCCCCCCcceeccCCCeEECCCCCCEec
Confidence            558999999888877777999999999874

>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=88.93  E-value=0.22  Score=32.74  Aligned_cols=30  Identities=17%  Similarity=0.381  Sum_probs=23.5

Q ss_pred             CcccCCCCCCceeec----CCCCeeecccccccc
Q psy12853         47 LIKCCPMCSVPIEKD----EGCAQMLCKRCKHVF   76 (137)
Q Consensus        47 ~~~~CP~C~~~i~~~----~~~~~~~C~~C~~~f   76 (137)
                      ...+||.|+..+...    .+...+.|+.|++..
T Consensus         3 ~~~FCp~CgnlL~~~~~~~~~~~~~~C~~C~y~~   36 (122)
T 1twf_I            3 TFRFCRDCNNMLYPREDKENNRLLFECRTCSYVE   36 (122)
T ss_dssp             CCCBCSSSCCBCEEEEETTTTEEEEECSSSSCEE
T ss_pred             CCCcccccCccCcccccCcCCCCEEECCcCCCee
Confidence            368999999988765    345679999998755

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

Probab=88.92  E-value=0.15  Score=30.46  Aligned_cols=48  Identities=23%  Similarity=0.610  Sum_probs=34.0

Q ss_pred             CCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCccee
Q psy12853         46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIE  107 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~ie  107 (137)
                      .....||-|...+..     .+. ..|++.||..|...|-..        ...||.|+..+.
T Consensus        13 ~~~~~C~IC~~~~~~-----p~~-~~CgH~fC~~Ci~~~~~~--------~~~CP~Cr~~~~   60 (81)
T 2csy_A           13 EIPFRCFICRQAFQN-----PVV-TKCRHYFCESCALEHFRA--------TPRCYICDQPTG   60 (81)
T ss_dssp             CCCSBCSSSCSBCCS-----EEE-CTTSCEEEHHHHHHHHHH--------CSBCSSSCCBCC
T ss_pred             CCCCCCcCCCchhcC-----eeE-ccCCCHhHHHHHHHHHHC--------CCcCCCcCcccc
Confidence            335578888776632     233 369999999998876432        457999999885

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

Probab=88.85  E-value=0.1  Score=34.68  Aligned_cols=46  Identities=28%  Similarity=0.631  Sum_probs=33.0

Q ss_pred             ccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853         49 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK  108 (137)
Q Consensus        49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek  108 (137)
                      ..||-|...+.     ..+.- .||+.||..|...|-..        ...||.|+..|..
T Consensus        54 ~~C~iC~~~~~-----~~~~~-~CgH~fc~~Ci~~~~~~--------~~~CP~Cr~~~~~   99 (138)
T 4ayc_A           54 LQCIICSEYFI-----EAVTL-NCAHSFCSYCINEWMKR--------KIECPICRKDIKS   99 (138)
T ss_dssp             SBCTTTCSBCS-----SEEEE-TTSCEEEHHHHHHHTTT--------CSBCTTTCCBCCC
T ss_pred             CCCcccCcccC-----CceEC-CCCCCccHHHHHHHHHc--------CCcCCCCCCcCCC
Confidence            36998887663     12333 49999999999877543        3469999998853

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

Probab=88.79  E-value=0.22  Score=33.36  Aligned_cols=33  Identities=18%  Similarity=0.363  Sum_probs=24.0

Q ss_pred             CCCCcccCCCCCCceeecC----CCCeeecccccccc
Q psy12853         44 DSELIKCCPMCSVPIEKDE----GCAQMLCKRCKHVF   76 (137)
Q Consensus        44 ~~~~~~~CP~C~~~i~~~~----~~~~~~C~~C~~~f   76 (137)
                      .....++||.|+..+....    +...+.|+.|++..
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            3456899999999987653    24478898888765

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

Probab=88.72  E-value=0.32  Score=28.66  Aligned_cols=50  Identities=10%  Similarity=0.136  Sum_probs=35.1

Q ss_pred             CCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853         46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK  108 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek  108 (137)
                      +....||-|...+..     .+.- .||+.||..|...|-..       +...||.|+..+..
T Consensus         6 ~~~~~C~IC~~~~~~-----Pv~~-~CgH~fc~~Ci~~~~~~-------~~~~CP~C~~~~~~   55 (78)
T 1t1h_A            6 PEYFRCPISLELMKD-----PVIV-STGQTYERSSIQKWLDA-------GHKTCPKSQETLLH   55 (78)
T ss_dssp             SSSSSCTTTSCCCSS-----EEEE-TTTEEEEHHHHHHHHTT-------TCCBCTTTCCBCSS
T ss_pred             cccCCCCCccccccC-----CEEc-CCCCeecHHHHHHHHHH-------CcCCCCCCcCCCCh
Confidence            345678888776632     2333 59999999999876542       24579999998854

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

Probab=88.57  E-value=0.12  Score=35.27  Aligned_cols=48  Identities=29%  Similarity=0.595  Sum_probs=34.7

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCccee
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIE  107 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~ie  107 (137)
                      ...||-|...+.     ..+....|++.||..|...|-..       ....||.|+..+.
T Consensus        54 ~~~C~IC~~~~~-----~p~~~~~CgH~fC~~Ci~~~~~~-------~~~~CP~Cr~~~~  101 (165)
T 2ckl_B           54 ELMCPICLDMLK-----NTMTTKECLHRFCADCIITALRS-------GNKECPTCRKKLV  101 (165)
T ss_dssp             HHBCTTTSSBCS-----SEEEETTTCCEEEHHHHHHHHHT-------TCCBCTTTCCBCC
T ss_pred             CCCCcccChHhh-----CcCEeCCCCChhHHHHHHHHHHh-------CcCCCCCCCCcCC
Confidence            347898877664     24555579999999999876432       2457999998874

>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=88.39  E-value=0.35  Score=28.66  Aligned_cols=29  Identities=21%  Similarity=0.604  Sum_probs=21.2

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccc
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVF   76 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~f   76 (137)
                      ..-||.|...+..+.+.....|+.|+..|
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            45688888888877666777787766554

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

Probab=88.31  E-value=0.3  Score=28.83  Aligned_cols=29  Identities=17%  Similarity=0.422  Sum_probs=21.6

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccc
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVF   76 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~f   76 (137)
                      ..-||.|...+..+.......|+.|+..|
T Consensus         8 iL~CP~ck~~L~~~~~~~~LiC~~cg~~Y   36 (68)
T 2jr6_A            8 ILVCPVTKGRLEYHQDKQELWSRQAKLAY   36 (68)
T ss_dssp             CCBCSSSCCBCEEETTTTEEEETTTTEEE
T ss_pred             heECCCCCCcCeEeCCCCEEEcCCCCcEe
Confidence            55789999988887766777777766554

>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=88.28  E-value=0.32  Score=28.73  Aligned_cols=29  Identities=31%  Similarity=0.761  Sum_probs=21.5

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccc
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVF   76 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~f   76 (137)
                      ..-||.|...+..+.......|+.|+..|
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            45789999888887766777787766554

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

Probab=88.22  E-value=0.35  Score=28.75  Aligned_cols=29  Identities=28%  Similarity=0.662  Sum_probs=22.2

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccc
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVF   76 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~f   76 (137)
                      ..-||.|...+..+.......|+.|+..|
T Consensus         8 iL~CP~ck~~L~~~~~~~~LiC~~cg~~Y   36 (70)
T 2js4_A            8 ILVCPVCKGRLEFQRAQAELVCNADRLAF   36 (70)
T ss_dssp             CCBCTTTCCBEEEETTTTEEEETTTTEEE
T ss_pred             heECCCCCCcCEEeCCCCEEEcCCCCcee
Confidence            55799999998887766778887766554

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

Probab=88.19  E-value=0.19  Score=32.10  Aligned_cols=47  Identities=26%  Similarity=0.611  Sum_probs=33.2

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCccee
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIE  107 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~ie  107 (137)
                      ...||-|...+..    ..+.  .||+.||..|...|-..       ....||.|+..+.
T Consensus        15 ~~~C~iC~~~~~~----p~~~--~CgH~fC~~Ci~~~~~~-------~~~~CP~Cr~~~~   61 (115)
T 3l11_A           15 ECQCGICMEILVE----PVTL--PCNHTLCKPCFQSTVEK-------ASLCCPFCRRRVS   61 (115)
T ss_dssp             HHBCTTTCSBCSS----CEEC--TTSCEECHHHHCCCCCT-------TTSBCTTTCCBCH
T ss_pred             CCCCccCCcccCc----eeEc--CCCCHHhHHHHHHHHhH-------CcCCCCCCCcccC
Confidence            4568888876532    2222  59999999999876542       2367999999875

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=88.03  E-value=0.68  Score=28.73  Aligned_cols=78  Identities=18%  Similarity=0.352  Sum_probs=48.2

Q ss_pred             ccCCCCCCceeecCCCCeeecccccccccccccccccCCCCccc-----------ccccCCCCCCC-cceeecCCCCeEE
Q psy12853         49 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFD-----------SELIKCCPMCS-VPIEKDEGCAQML  116 (137)
Q Consensus        49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~-----------~~~~~~CP~C~-~~iek~~gC~hm~  116 (137)
                      ..|+-|...+.   ......|..|+..||..|...+|.......           ......|+.-. ..+       .+.
T Consensus         4 ~~C~~C~~~~~---~~av~~C~~C~~~~C~~Cl~~~h~~~~~~~~h~l~~~~~~~~~~~~~C~~H~~e~l-------~~f   73 (101)
T 2jun_A            4 VLCQFCDQDPA---QDAVKTCVTCEVSYCDECLKATHPNKKPFTGHRLIEPIPDSHIRGLMCLEHEDEKV-------NMY   73 (101)
T ss_dssp             CBCTTCCSSSC---CBCCEEETTTTEEECHHHHHHHSCSCSSSTTCCBSSCCCSCCSSCCCCSSCSSSCC-------CEE
T ss_pred             CCCcCCCCCCC---CCceEECCcCChHHhHHHCHHHhccCCccCCCeeeccccccCccCCcCcCcCCCcc-------eEE
Confidence            45777764321   235678999999999999998676422110           01122455442 222       578


Q ss_pred             eccCcceeeccccc-ccccCC
Q psy12853        117 CKRCKHVFCWYCLA-SLDVSR  136 (137)
Q Consensus       117 C~~C~~~fC~~C~~-~~~~~~  136 (137)
                      |..|+...|+.|.. .-..+|
T Consensus        74 C~~~~~~iC~~C~~~~~H~~H   94 (101)
T 2jun_A           74 CVTDDQLICALCKLVGRHRDH   94 (101)
T ss_dssp             ETTTTEEECHHHHHHTTTSSS
T ss_pred             CCCCCCccchhcCCCCCcCCC
Confidence            99999999999975 333333

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

Probab=88.00  E-value=0.53  Score=27.94  Aligned_cols=30  Identities=27%  Similarity=0.596  Sum_probs=23.8

Q ss_pred             ccCCCCCCCcceeecCCCCeEEeccCccee
Q psy12853         95 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF  124 (137)
Q Consensus        95 ~~~~CP~C~~~iek~~gC~hm~C~~C~~~f  124 (137)
                      .+..||.|+..++-..+=..+.|..||..|
T Consensus         7 ~iL~CP~ck~~L~~~~~~~~LiC~~cg~~Y   36 (70)
T 2js4_A            7 DILVCPVCKGRLEFQRAQAELVCNADRLAF   36 (70)
T ss_dssp             CCCBCTTTCCBEEEETTTTEEEETTTTEEE
T ss_pred             hheECCCCCCcCEEeCCCCEEEcCCCCcee
Confidence            466899999998887665678898888766

>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=87.93  E-value=0.6  Score=27.60  Aligned_cols=30  Identities=20%  Similarity=0.540  Sum_probs=23.5

Q ss_pred             ccCCCCCCCcceeecCCCCeEEeccCccee
Q psy12853         95 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF  124 (137)
Q Consensus        95 ~~~~CP~C~~~iek~~gC~hm~C~~C~~~f  124 (137)
                      .+..||.|+..++-..+=..+.|..||..|
T Consensus         7 eiL~CP~ck~~L~~~~~~~~LiC~~cg~~Y   36 (69)
T 2pk7_A            7 DILACPICKGPLKLSADKTELISKGAGLAY   36 (69)
T ss_dssp             GTCCCTTTCCCCEECTTSSEEEETTTTEEE
T ss_pred             hheeCCCCCCcCeEeCCCCEEEcCCCCcEe
Confidence            466899999998876655678898888765

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

Probab=87.92  E-value=0.21  Score=30.02  Aligned_cols=52  Identities=19%  Similarity=0.501  Sum_probs=34.0

Q ss_pred             ccCCCCCCceeec---------CCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853         49 KCCPMCSVPIEKD---------EGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK  108 (137)
Q Consensus        49 ~~CP~C~~~i~~~---------~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek  108 (137)
                      ..|+-|...+...         .+...+.=+.|++.|+..|...|-...        ..||-|+..+..
T Consensus        16 ~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~--------~~CP~CR~~~~~   76 (81)
T 2ecl_A           16 DTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQN--------NRCPLCQQDWVV   76 (81)
T ss_dssp             SCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTC--------CBCTTTCCBCCE
T ss_pred             CCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhC--------CCCCCcCCCcch
Confidence            3466666655431         223333444799999999998885442        379999988754

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

Probab=87.92  E-value=0.45  Score=25.85  Aligned_cols=38  Identities=26%  Similarity=0.387  Sum_probs=24.8

Q ss_pred             cCCCCCCCcceeecCCCCeEEeccCcceeecccccccccC
Q psy12853         96 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDVS  135 (137)
Q Consensus        96 ~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~~~~  135 (137)
                      ...||-|...++..+.  .+.-..||+.||..|...|...
T Consensus         5 ~~~C~IC~~~~~~~~~--~~~~~~C~H~f~~~Ci~~w~~~   42 (55)
T 1iym_A            5 GVECAVCLAELEDGEE--ARFLPRCGHGFHAECVDMWLGS   42 (55)
T ss_dssp             SCCCTTTCCCCCTTSC--CEECSSSCCEECTTHHHHTTTT
T ss_pred             CCcCccCCccccCCCc--eEECCCCCCcccHHHHHHHHHc
Confidence            3468888877755432  2333348888888888877543

>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=87.55  E-value=0.46  Score=28.02  Aligned_cols=30  Identities=30%  Similarity=0.705  Sum_probs=23.4

Q ss_pred             ccCCCCCCCcceeecCCCCeEEeccCccee
Q psy12853         95 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF  124 (137)
Q Consensus        95 ~~~~CP~C~~~iek~~gC~hm~C~~C~~~f  124 (137)
                      .+..||.|+..++-..+=..+.|..||..|
T Consensus         7 ~iL~CP~ck~~L~~~~~~~~LiC~~cg~~Y   36 (68)
T 2hf1_A            7 EILVCPLCKGPLVFDKSKDELICKGDRLAF   36 (68)
T ss_dssp             EECBCTTTCCBCEEETTTTEEEETTTTEEE
T ss_pred             hheECCCCCCcCeEeCCCCEEEcCCCCcEe
Confidence            456899999988877665678888888765

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

Probab=87.06  E-value=0.14  Score=32.36  Aligned_cols=51  Identities=29%  Similarity=0.711  Sum_probs=34.2

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD  109 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~  109 (137)
                      ...||-|...+..    . +. ..||+.||..|...|-...     .....||.|+..+...
T Consensus        21 ~~~C~IC~~~~~~----p-~~-~~CgH~fC~~Ci~~~~~~~-----~~~~~CP~Cr~~~~~~   71 (112)
T 1jm7_A           21 ILECPICLELIKE----P-VS-TKCDHIFCKFCMLKLLNQK-----KGPSQCPLCKNDITKR   71 (112)
T ss_dssp             HTSCSSSCCCCSS----C-CB-CTTSCCCCSHHHHHHHHSS-----SSSCCCTTTSCCCCTT
T ss_pred             CCCCcccChhhcC----e-EE-CCCCCHHHHHHHHHHHHhC-----CCCCCCcCCCCcCCHh
Confidence            3468888776532    1 11 2599999999988764331     1235899999988653

>1dl6_A Transcription factor II B (TFIIB); zinc ribbon, gene regulation; NMR {Homo sapiens} SCOP: g.41.3.1 PDB: 1rly_A 1ro4_A

Probab=86.26  E-value=0.52  Score=26.82  Aligned_cols=29  Identities=24%  Similarity=0.476  Sum_probs=20.7

Q ss_pred             cccCCCCCC-ceeecCCCCeeecccccccc
Q psy12853         48 IKCCPMCSV-PIEKDEGCAQMLCKRCKHVF   76 (137)
Q Consensus        48 ~~~CP~C~~-~i~~~~~~~~~~C~~C~~~f   76 (137)
                      ...||.|+. .+..+.....+.|..||..+
T Consensus        11 ~~~Cp~C~~~~lv~D~~~ge~vC~~CGlVl   40 (58)
T 1dl6_A           11 RVTCPNHPDAILVEDYRAGDMICPECGLVV   40 (58)
T ss_dssp             CCSBTTBSSSCCEECSSSCCEECTTTCCEE
T ss_pred             cccCcCCCCCceeEeCCCCeEEeCCCCCEE
Confidence            447999987 56666666678888776554

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

Probab=86.09  E-value=0.19  Score=31.99  Aligned_cols=60  Identities=22%  Similarity=0.463  Sum_probs=37.5

Q ss_pred             ccCCCCCCceeecC-----------C-CCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCC
Q psy12853         49 KCCPMCSVPIEKDE-----------G-CAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEG  111 (137)
Q Consensus        49 ~~CP~C~~~i~~~~-----------~-~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~g  111 (137)
                      ..||-|-..+....           . ...+.-..|++.||..|...|-....   ......||-|+..+....|
T Consensus        26 ~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~---~~~~~~CP~CR~~~~~~~g   97 (114)
T 1v87_A           26 EDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGN---KDGSLQCPSCKTIYGEKTG   97 (114)
T ss_dssp             CEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTC---CSSCCBCTTTCCBSSSCSS
T ss_pred             CcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHccc---CCCCCcCCCCCCccCCCCC
Confidence            47888876654321           0 11222447999999999988852111   1234589999998876544

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

Probab=86.05  E-value=0.22  Score=28.14  Aligned_cols=34  Identities=26%  Similarity=0.683  Sum_probs=24.9

Q ss_pred             ccCCCCCCCcceeecCCCCeEEeccCcceeeccccccccc
Q psy12853         95 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDV  134 (137)
Q Consensus        95 ~~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~~~  134 (137)
                      ....||-|...+..     -++- .||+.||+.|...|..
T Consensus        19 ~~~~C~IC~~~~~~-----p~~~-~CgH~fC~~Ci~~~~~   52 (63)
T 2ysj_A           19 EEVICPICLDILQK-----PVTI-DCGHNFCLKCITQIGE   52 (63)
T ss_dssp             CCCBCTTTCSBCSS-----CEEC-TTSSEECHHHHHHHHH
T ss_pred             cCCCCCcCCchhCC-----eEEe-CCCCcchHHHHHHHHH
Confidence            34579999887753     3333 5999999999888753

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

Probab=86.00  E-value=0.77  Score=25.09  Aligned_cols=46  Identities=24%  Similarity=0.558  Sum_probs=30.1

Q ss_pred             CCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCC
Q psy12853         46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMC  102 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C  102 (137)
                      .....||-|...+...     +. ..|++.||..|...|-...     .....||.|
T Consensus        13 ~~~~~C~IC~~~~~~p-----~~-~~CgH~fC~~Ci~~~~~~~-----~~~~~CP~C   58 (58)
T 2ecj_A           13 QVEASCSVCLEYLKEP-----VI-IECGHNFCKACITRWWEDL-----ERDFPCPVC   58 (58)
T ss_dssp             CCCCBCSSSCCBCSSC-----CC-CSSCCCCCHHHHHHHTTSS-----CCSCCCSCC
T ss_pred             ccCCCCccCCcccCcc-----Ee-CCCCCccCHHHHHHHHHhc-----CCCCCCCCC
Confidence            3456788887766431     11 2599999999998874321     234578876

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

Probab=85.94  E-value=0.52  Score=27.72  Aligned_cols=29  Identities=17%  Similarity=0.323  Sum_probs=20.8

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccc
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVF   76 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~f   76 (137)
                      ..-||.|..++..+.......|+.|+..|
T Consensus        10 iL~CP~ck~~L~~~~~~g~LvC~~c~~~Y   38 (67)
T 2jny_A           10 VLACPKDKGPLRYLESEQLLVNERLNLAY   38 (67)
T ss_dssp             CCBCTTTCCBCEEETTTTEEEETTTTEEE
T ss_pred             HhCCCCCCCcCeEeCCCCEEEcCCCCccc
Confidence            45788888888877666677777765544

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

Probab=85.89  E-value=0.24  Score=28.87  Aligned_cols=33  Identities=21%  Similarity=0.522  Sum_probs=18.3

Q ss_pred             ccCCCCCCCcceeecCCCCeEEeccCcceeeccccccc
Q psy12853         95 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASL  132 (137)
Q Consensus        95 ~~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~  132 (137)
                      ....||-|...+...     ++-..||+.||+.|...|
T Consensus        14 ~~~~C~IC~~~~~~p-----~~~~~CgH~fC~~Ci~~~   46 (72)
T 2djb_A           14 PYILCSICKGYLIDA-----TTITECLHTFCKSCIVRH   46 (72)
T ss_dssp             GGGSCTTTSSCCSSC-----EECSSSCCEECHHHHHHH
T ss_pred             CCCCCCCCChHHHCc-----CEECCCCCHHHHHHHHHH
Confidence            456799998877542     222235555555554433

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

Probab=85.79  E-value=0.11  Score=33.69  Aligned_cols=48  Identities=21%  Similarity=0.494  Sum_probs=34.0

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK  108 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek  108 (137)
                      ...||-|...+..     .+.= .||+.||..|...|-.       .....||.|+..+..
T Consensus        52 ~~~C~IC~~~~~~-----p~~~-~CgH~fC~~Ci~~~~~-------~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           52 TFQCICCQELVFR-----PITT-VCQHNVCKDCLDRSFR-------AQVFSCPACRYDLGR   99 (124)
T ss_dssp             HTBCTTTSSBCSS-----EEEC-TTSCEEEHHHHHHHHH-------TTCCBCTTTCCBCCT
T ss_pred             CCCCCcCChHHcC-----cEEe-eCCCcccHHHHHHHHh-------HCcCCCCCCCccCCC
Confidence            3568988876642     2222 6999999999876643       123479999999865

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

Probab=84.49  E-value=1  Score=26.49  Aligned_cols=30  Identities=17%  Similarity=0.282  Sum_probs=23.4

Q ss_pred             ccCCCCCCCcceeecCCCCeEEeccCccee
Q psy12853         95 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF  124 (137)
Q Consensus        95 ~~~~CP~C~~~iek~~gC~hm~C~~C~~~f  124 (137)
                      .+..||.|+..++-...=+.+.|..||..|
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            466899999988877655678888887765

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

Probab=84.44  E-value=0.81  Score=29.52  Aligned_cols=29  Identities=14%  Similarity=0.448  Sum_probs=22.6

Q ss_pred             cCCCCCCCcceeec----CCCCeEEeccCccee
Q psy12853         96 IKCCPMCSVPIEKD----EGCAQMLCKRCKHVF  124 (137)
Q Consensus        96 ~~~CP~C~~~iek~----~gC~hm~C~~C~~~f  124 (137)
                      .+-||.|+.++...    .+.+.+.|+.|++.+
T Consensus         4 m~FCp~Cgn~L~~~~~~~~~~~~~~C~~C~y~~   36 (113)
T 3h0g_I            4 FQYCIECNNMLYPREDKVDRVLRLACRNCDYSE   36 (113)
T ss_dssp             CCCCSSSCCCCEECCCTTTCCCCEECSSSCCEE
T ss_pred             ceeCcCCCCEeeEcccCCCCeeEEECCCCCCeE
Confidence            45799999887653    257789999999876

>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=84.18  E-value=0.73  Score=26.29  Aligned_cols=35  Identities=23%  Similarity=0.498  Sum_probs=19.6

Q ss_pred             ccCCCCCCCcceeecCCCCeEEeccCcceeeccccccc
Q psy12853         95 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASL  132 (137)
Q Consensus        95 ~~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~  132 (137)
                      ....||-|...++....   +.-..||+.||..|...|
T Consensus        13 ~~~~C~IC~~~~~~~~~---~~~~~C~H~fc~~Ci~~~   47 (69)
T 2kiz_A           13 TEEKCTICLSILEEGED---VRRLPCMHLFHQVCVDQW   47 (69)
T ss_dssp             CCCSBTTTTBCCCSSSC---EEECTTSCEEEHHHHHHH
T ss_pred             CCCCCeeCCccccCCCc---EEEeCCCCHHHHHHHHHH
Confidence            45678888776643221   222236666666666554

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

Probab=83.65  E-value=0.29  Score=29.37  Aligned_cols=37  Identities=27%  Similarity=0.613  Sum_probs=21.9

Q ss_pred             ccCCCCCCCcceeecCCCCeEEeccCcceeecccccccc
Q psy12853         95 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLD  133 (137)
Q Consensus        95 ~~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~~  133 (137)
                      ....||-|...+.....- -+.- .||+.||..|...|-
T Consensus        14 ~~~~C~IC~~~~~~~~~~-~~~~-~CgH~fC~~Ci~~~~   50 (88)
T 2ct2_A           14 EVLECPICMESFTEEQLR-PKLL-HCGHTICRQCLEKLL   50 (88)
T ss_dssp             SCCBCTTTCCBCCTTSSC-EEEC-SSSCEEEHHHHHHHH
T ss_pred             CCCCCccCCccccccCCC-eEEC-CCCChhhHHHHHHHH
Confidence            345799998777543211 2222 477777777766653

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

Probab=83.38  E-value=1.3  Score=24.91  Aligned_cols=28  Identities=32%  Similarity=0.972  Sum_probs=22.9

Q ss_pred             ccCCCCCCCcceeecCCCCeEEec--cCccee
Q psy12853         95 LIKCCPMCSVPIEKDEGCAQMLCK--RCKHVF  124 (137)
Q Consensus        95 ~~~~CP~C~~~iek~~gC~hm~C~--~C~~~f  124 (137)
                      ..-.||.|+..++...  ..+.|.  .||..|
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            4668999999988877  688898  788766

>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=83.34  E-value=0.63  Score=27.91  Aligned_cols=27  Identities=26%  Similarity=0.699  Sum_probs=22.7

Q ss_pred             cCCCCCCCcceeecCCCCeEEeccCcceeecc
Q psy12853         96 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWY  127 (137)
Q Consensus        96 ~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~  127 (137)
                      ..+|..|+..|+..+    +.|+ ||..||-.
T Consensus        25 ~nRC~~CrKkvgL~g----f~Cr-Cg~~FCs~   51 (74)
T 1wfl_A           25 KNRCFMCRKKVGLTG----FDCR-CGNLFCGL   51 (74)
T ss_dssp             TTBCSSSCCBCGGGC----EECT-TSCEECSS
T ss_pred             CCcChhhCCcccccC----eecC-CCCEechh
Confidence            458999999988774    8998 99999974

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

Probab=82.82  E-value=0.48  Score=29.01  Aligned_cols=50  Identities=24%  Similarity=0.508  Sum_probs=33.6

Q ss_pred             CcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCccee
Q psy12853         47 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIE  107 (137)
Q Consensus        47 ~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~ie  107 (137)
                      ....||-|...+...  ...+.- .|++.||..|...|-..        ...||.|+..+.
T Consensus        39 ~~~~C~IC~~~~~~~--~~~~~l-~C~H~Fh~~Ci~~wl~~--------~~~CP~Cr~~~~   88 (91)
T 2l0b_A           39 QEMCCPICCSEYVKG--DVATEL-PCHHYFHKPCVSIWLQK--------SGTCPVCRCMFP   88 (91)
T ss_dssp             SCSEETTTTEECCTT--CEEEEE-TTTEEEEHHHHHHHHTT--------TCBCTTTCCBSS
T ss_pred             CCCCCcccChhhcCC--CcEEec-CCCChHHHHHHHHHHHc--------CCcCcCcCccCC
Confidence            345688887665432  222223 48999999999888643        237999998774

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

Probab=82.42  E-value=0.37  Score=30.76  Aligned_cols=49  Identities=24%  Similarity=0.590  Sum_probs=33.3

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD  109 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~  109 (137)
                      ...||-|...+..     .+. ..||+.||..|...|-..       ....||.|+..+...
T Consensus        23 ~~~C~IC~~~~~~-----p~~-~~CgH~fC~~Ci~~~~~~-------~~~~CP~Cr~~~~~~   71 (116)
T 1rmd_A           23 SISCQICEHILAD-----PVE-TSCKHLFCRICILRCLKV-------MGSYCPSCRYPCFPT   71 (116)
T ss_dssp             HTBCTTTCSBCSS-----EEE-CTTSCEEEHHHHHHHHHH-------TCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCcHhcC-----cEE-cCCCCcccHHHHHHHHhH-------CcCcCCCCCCCCCHh
Confidence            3468888776632     233 269999999998766432       134699998887653

>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=82.23  E-value=1.1  Score=26.12  Aligned_cols=29  Identities=21%  Similarity=0.666  Sum_probs=23.1

Q ss_pred             cccCCCCCCCcceeecCCCCeEEeccCcceeecc
Q psy12853         94 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWY  127 (137)
Q Consensus        94 ~~~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~  127 (137)
                      ....+|..|+..+...    -+.|+ ||..||..
T Consensus        13 ~~~~rC~~C~kkvgl~----~f~Cr-Cg~~FC~~   41 (64)
T 1wfh_A           13 QRPNRCTVCRKRVGLT----GFMCR-CGTTFCGS   41 (64)
T ss_dssp             SSCCCCTTTCCCCCTT----CEECS-SSCEECTT
T ss_pred             CcCCcChhhCCccCcc----CEEee-cCCEeccc
Confidence            3457899999988665    48996 99999974

>2yho_A E3 ubiquitin-protein ligase mylip; ligase, E2 ligase-E3 ligase complex, ring zinc-finger, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 2yhn_A

Probab=81.98  E-value=0.55  Score=28.14  Aligned_cols=42  Identities=26%  Similarity=0.673  Sum_probs=28.1

Q ss_pred             ccCCCCCCceeecCCCCeeeccccccc-ccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853         49 KCCPMCSVPIEKDEGCAQMLCKRCKHV-FCWYCLASRDYGGATFDSELIKCCPMCSVPIEK  108 (137)
Q Consensus        49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~-fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek  108 (137)
                      ..|+-|.....     ..+. .-||+. ||..|...            ++.||-|+..|+.
T Consensus        19 ~~C~IC~~~~~-----~~v~-~pCgH~~~C~~C~~~------------~~~CP~Cr~~i~~   61 (79)
T 2yho_A           19 MLCMVCCEEEI-----NSTF-CPCGHTVCCESCAAQ------------LQSCPVCRSRVEH   61 (79)
T ss_dssp             TBCTTTSSSBC-----CEEE-ETTCBCCBCHHHHTT------------CSBCTTTCCBCCE
T ss_pred             CEeEEeCcccC-----cEEE-ECCCCHHHHHHHHHh------------cCcCCCCCchhhC
Confidence            36777754331     1111 158998 99999754            3489999999876

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=81.71  E-value=0.43  Score=28.09  Aligned_cols=44  Identities=27%  Similarity=0.579  Sum_probs=29.6

Q ss_pred             cccCCCCCCceeecCCCCeeeccccccc-ccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHV-FCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD  109 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~-fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~  109 (137)
                      ...||-|...+..     .+. ..|++. ||..|..            ..+.||.|+..|+..
T Consensus        25 ~~~C~IC~~~~~~-----~~~-~pCgH~~~C~~C~~------------~~~~CP~Cr~~i~~~   69 (75)
T 2ecg_A           25 EKLCKICMDRNIA-----IVF-VPCGHLVTCKQCAE------------AVDKCPMCYTVITFK   69 (75)
T ss_dssp             HHSCSSSCSSCCC-----BCC-SSSCCCCBCHHHHH------------HCSBCTTTCCBCCCC
T ss_pred             CCCCCcCCCCCCC-----EEE-ecCCCHHHHHHHhh------------CCCCCccCCceecCc
Confidence            3468877655321     111 258999 9999973            247899999998763

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

Probab=81.66  E-value=0.75  Score=26.13  Aligned_cols=25  Identities=24%  Similarity=0.693  Sum_probs=13.5

Q ss_pred             cCCCCCCCcceee---cCCCCeEEeccC
Q psy12853         96 IKCCPMCSVPIEK---DEGCAQMLCKRC  120 (137)
Q Consensus        96 ~~~CP~C~~~iek---~~gC~hm~C~~C  120 (137)
                      ...||-|...+..   ...|.|+.|..|
T Consensus         5 ~~~C~IC~~~~~~~~~~~~C~H~fc~~C   32 (68)
T 1chc_A            5 AERCPICLEDPSNYSMALPCLHAFCYVC   32 (68)
T ss_dssp             CCCCSSCCSCCCSCEEETTTTEEESTTH
T ss_pred             CCCCeeCCccccCCcEecCCCCeeHHHH
Confidence            4568888777643   123444444444

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

Probab=81.14  E-value=0.52  Score=29.14  Aligned_cols=33  Identities=21%  Similarity=0.622  Sum_probs=20.1

Q ss_pred             cCCCCCCCcceeecCCCCeEEeccCcceeecccccccc
Q psy12853         96 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLD  133 (137)
Q Consensus        96 ~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~~  133 (137)
                      ...||-|...+..     -++-..||+.||..|...|-
T Consensus        22 ~~~C~IC~~~~~~-----p~~~~~CgH~fC~~Ci~~~~   54 (99)
T 2y43_A           22 LLRCGICFEYFNI-----AMIIPQCSHNYCSLCIRKFL   54 (99)
T ss_dssp             HTBCTTTCSBCSS-----EEECTTTCCEEEHHHHHHHH
T ss_pred             CCCcccCChhhCC-----cCEECCCCCHhhHHHHHHHH
Confidence            4579999877753     23333466666666655543

>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=80.91  E-value=0.81  Score=29.95  Aligned_cols=29  Identities=17%  Similarity=0.409  Sum_probs=22.5

Q ss_pred             cCCCCCCCcceeec----CCCCeEEeccCccee
Q psy12853         96 IKCCPMCSVPIEKD----EGCAQMLCKRCKHVF  124 (137)
Q Consensus        96 ~~~CP~C~~~iek~----~gC~hm~C~~C~~~f  124 (137)
                      .+-||.|+.++.-.    .+-+.+.|+.||+.+
T Consensus         4 ~~FCp~CgnlL~~~~~~~~~~~~~~C~~C~y~~   36 (122)
T 1twf_I            4 FRFCRDCNNMLYPREDKENNRLLFECRTCSYVE   36 (122)
T ss_dssp             CCBCSSSCCBCEEEEETTTTEEEEECSSSSCEE
T ss_pred             CCcccccCccCcccccCcCCCCEEECCcCCCee
Confidence            46799999887743    557789999999876

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

Probab=80.76  E-value=0.59  Score=29.39  Aligned_cols=32  Identities=22%  Similarity=0.505  Sum_probs=20.4

Q ss_pred             cCCCCCCCcceeecCCCCeEEeccCcceeeccccccc
Q psy12853         96 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASL  132 (137)
Q Consensus        96 ~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~  132 (137)
                      ...||-|...+..     -++-..||+.||..|...|
T Consensus        15 ~~~C~IC~~~~~~-----p~~~~~CgH~fC~~Ci~~~   46 (108)
T 2ckl_A           15 HLMCVLCGGYFID-----ATTIIECLHSFCKTCIVRY   46 (108)
T ss_dssp             GTBCTTTSSBCSS-----EEEETTTCCEEEHHHHHHH
T ss_pred             cCCCccCChHHhC-----cCEeCCCCChhhHHHHHHH
Confidence            4579999887743     3444347777777666555

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

Probab=80.37  E-value=0.6  Score=31.71  Aligned_cols=31  Identities=32%  Similarity=0.784  Sum_probs=18.3

Q ss_pred             CCCCCCCcceeecCCCCeEEeccCcceeeccccccc
Q psy12853         97 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASL  132 (137)
Q Consensus        97 ~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~  132 (137)
                      ..||-|...+..     -++...||+.||+.|...|
T Consensus        55 ~~C~IC~~~~~~-----p~~~~~CgH~fC~~Ci~~~   85 (165)
T 2ckl_B           55 LMCPICLDMLKN-----TMTTKECLHRFCADCIITA   85 (165)
T ss_dssp             HBCTTTSSBCSS-----EEEETTTCCEEEHHHHHHH
T ss_pred             CCCcccChHhhC-----cCEeCCCCChhHHHHHHHH
Confidence            368888777653     2344346666666665544

>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=80.29  E-value=1  Score=26.25  Aligned_cols=28  Identities=25%  Similarity=0.518  Sum_probs=22.1

Q ss_pred             ccCCCCCCCcceeecCCCCeEEeccCcceeecc
Q psy12853         95 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWY  127 (137)
Q Consensus        95 ~~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~  127 (137)
                      ...+|..|+..+...    -++|+ ||..||-.
T Consensus        14 ~~~rC~~C~kkvgl~----~f~Cr-Cg~~FC~~   41 (64)
T 1wg2_A           14 PNNRCFSCNKKVGVM----GFKCK-CGSTFCGS   41 (64)
T ss_dssp             CSCSCTTTCCCCTTS----CEECT-TSCEECSS
T ss_pred             cCCcChhhCCccccc----CeEee-cCCEeccc
Confidence            356899999887655    48995 99999974

---

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	137
d2ct7a1	73	g.44.1.4 (A:8-80) Ring finger protein 31 {Human (H	8e-07
d2ct7a1	73	g.44.1.4 (A:8-80) Ring finger protein 31 {Human (H	8e-07
d1wd2a_	60	g.44.1.1 (A:) Ariadne-1 protein homolog {Human (Ho	3e-06
d1wd2a_	60	g.44.1.1 (A:) Ariadne-1 protein homolog {Human (Ho	3e-06

>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 = 41.9 bits (98), Expect = 8e-07
 Identities = 8/35 (22%), Positives = 11/35 (31%)

Query: 48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLA 82
             C  CS     +    +  C +C   FC  C  
Sbjct: 18 FLWCAQCSFGFIYEREQLEATCPQCHQTFCVRCKR 52

>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 = 41.9 bits (98), Expect = 8e-07
 Identities = 8/35 (22%), Positives = 11/35 (31%)

Query: 96  IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLA 130
              C  CS     +    +  C +C   FC  C  
Sbjct: 18  FLWCAQCSFGFIYEREQLEATCPQCHQTFCVRCKR 52

>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 = 40.2 bits (94), Expect = 3e-06
 Identities = 20/36 (55%), Positives = 22/36 (61%), Gaps = 2/36 (5%)

Query: 49 KCCPMCSVPIEKDEGCAQMLCK--RCKHVFCWYCLA 82
          K CP C V IEKD GC  M+C+   CK  FCW CL 
Sbjct: 7  KECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLG 42

>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 = 40.2 bits (94), Expect = 3e-06
 Identities = 20/36 (55%), Positives = 22/36 (61%), Gaps = 2/36 (5%)

Query: 97  KCCPMCSVPIEKDEGCAQMLCK--RCKHVFCWYCLA 130
           K CP C V IEKD GC  M+C+   CK  FCW CL 
Sbjct: 7   KECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLG 42

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	137
d1wd2a_	60	Ariadne-1 protein homolog {Human (Homo sapiens) [T	99.76
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	99.47
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	99.35
d1wd2a_	60	Ariadne-1 protein homolog {Human (Homo sapiens) [T	98.62
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	95.37
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	95.27
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	94.92
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	94.89
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	94.23
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	94.02
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	93.53
d2jnea1	71	Hypothetical protein YfgJ {Escherichia coli [TaxId	93.52
d2akla2	38	Hypothetical protein PA0128, N-terminal domain {Ps	92.82
d2akla2	38	Hypothetical protein PA0128, N-terminal domain {Ps	92.55
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	92.2
d2k4xa1	55	Ribosomal protein S27ae {Thermoplasma acidophilum	92.17
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	91.79
d2jnea1	71	Hypothetical protein YfgJ {Escherichia coli [TaxId	91.14
d2k4xa1	55	Ribosomal protein S27ae {Thermoplasma acidophilum	91.06
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	90.75
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	90.53
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	90.16
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	89.43
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	89.27
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	88.86
d1wfha_	64	Zinc finger A20 and AN1 domains containing protein	88.83
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	88.57
d2jnya1	59	Uncharacterized protein Cgl1405/cg1592 {Corynebact	87.33
d2pk7a1	59	Uncharacterized protein PFL1779 {Pseudomonas fluor	86.88
d1zbdb_	124	Effector domain of rabphilin-3a {Rat (Rattus norve	86.57
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	86.45
d2hf1a1	59	Hypothetical protein CV3345 {Chromobacterium viola	85.95
d2jnya1	59	Uncharacterized protein Cgl1405/cg1592 {Corynebact	85.24
d1zbdb_	124	Effector domain of rabphilin-3a {Rat (Rattus norve	84.86
d1k3xa3	40	Endonuclease VIII {Escherichia coli [TaxId: 562]}	84.76
d1wfla_	74	Zinc finger A20 domain containing protein 2 {Mouse	84.61
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	84.51
d1joca1	64	Eea1 {Human (Homo sapiens) [TaxId: 9606]}	83.72
d1wffa_	85	ANUBL1 (AN1, ubiquitin-like, homolog) {Mouse (Mus	83.48
d2pk7a1	59	Uncharacterized protein PFL1779 {Pseudomonas fluor	83.26
d2hf1a1	59	Hypothetical protein CV3345 {Chromobacterium viola	82.91
d1wfka_	88	Zinc finger FYVE domain containing protein 19 {Mou	82.54

>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=99.76  E-value=4.2e-20  Score=108.42  Aligned_cols=45  Identities=44%  Similarity=1.068  Sum_probs=41.3

Q ss_pred             ccccccCCCCCCCcceeecCCCCeEEec--cCcceeecccccccccC
Q psy12853         91 FDSELIKCCPMCSVPIEKDEGCAQMLCK--RCKHVFCWYCLASLDVS  135 (137)
Q Consensus        91 ~~~~~~~~CP~C~~~iek~~gC~hm~C~--~C~~~fC~~C~~~~~~~  135 (137)
                      |+.+++|+||+|+++|||++|||||+|+  +||++|||+|++++.++
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            4567899999999999999999999996  59999999999999875

>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=99.47  E-value=4.6e-15  Score=89.97  Aligned_cols=57  Identities=19%  Similarity=0.500  Sum_probs=51.8

Q ss_pred             HHHHhhccccccCCCCcccCCCCCCceeecCCCCeeecccccccccccccccc---cCCC
Q psy12853         32 IWHRTQVSGATFDSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASR---DYGG   88 (137)
Q Consensus        32 ~~~r~~~~~a~~~~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~---h~~~   88 (137)
                      +|++++++.++..+++++|||+|+.+++.+++.+.++|+.|+..||+.|+.+|   |.+.
T Consensus         2 ~Y~~~l~~~~l~~~~~~k~CP~C~~~~~~~~~~~~~~C~~C~~~fC~~C~~~w~~~H~~~   61 (73)
T d2ct7a1           2 LFHKKLTEGVLMRDPKFLWCAQCSFGFIYEREQLEATCPQCHQTFCVRCKRQWEEQHRGR   61 (73)
T ss_dssp             SSSSCCCCSCCCSCCCEECCSSSCCCEECCCSCSCEECTTTCCEECSSSCSBCCTTTTTS
T ss_pred             hHHHHHHHHHHHHCCCCCCCCCCCCEeEECCCCCEEEcCCCCCeECcccCcchhcCCCCC
Confidence            45677777788899999999999999999999999999999999999999999   8774

>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=99.35  E-value=3.1e-13  Score=81.69  Aligned_cols=44  Identities=18%  Similarity=0.479  Sum_probs=40.7

Q ss_pred             ccccCCCCCCCcceeecCCCCeEEeccCcceeecccccccccCC
Q psy12853         93 SELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDVSR  136 (137)
Q Consensus        93 ~~~~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~~~~~  136 (137)
                      ..+++.||+|+.+|++.+||++|+|..||+.|||.|+++|.+.|
T Consensus        15 ~~~~k~CP~C~~~~~~~~~~~~~~C~~C~~~fC~~C~~~w~~~H   58 (73)
T d2ct7a1          15 DPKFLWCAQCSFGFIYEREQLEATCPQCHQTFCVRCKRQWEEQH   58 (73)
T ss_dssp             CCCEECCSSSCCCEECCCSCSCEECTTTCCEECSSSCSBCCTTT
T ss_pred             CCCCCCCCCCCCEeEECCCCCEEEcCCCCCeECcccCcchhcCC
Confidence            45789999999999999999999998899999999999997665

>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=98.62  E-value=6.6e-09  Score=59.85  Aligned_cols=42  Identities=48%  Similarity=1.130  Sum_probs=37.2

Q ss_pred             CCCcccCCCCCCceeecCCCCeeecc--cccccccccccccccC
Q psy12853         45 SELIKCCPMCSVPIEKDEGCAQMLCK--RCKHVFCWYCLASRDY   86 (137)
Q Consensus        45 ~~~~~~CP~C~~~i~~~~~~~~~~C~--~C~~~fC~~C~~~~h~   86 (137)
                      ..+.+.||+|+.+|++.+|.+.|+|.  .|+..|||.|+.+|..
T Consensus         3 ~~ntK~CP~C~~~ieK~~GCnhM~C~~~~C~~~fCw~C~~~~~~   46 (60)
T d1wd2a_           3 AANTKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEP   46 (60)
T ss_dssp             CCCCCCCTTTCCCCSSCCSCCSSSCCSSGGGSCCSSSSCSCSGG
T ss_pred             hhcCcCCCCCCCeEEECCCCCCeEeCCCCCCCeEECCCCCcccc
Confidence            35689999999999999999999994  6999999999987643

>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=95.37  E-value=0.002  Score=36.43  Aligned_cols=52  Identities=25%  Similarity=0.568  Sum_probs=34.8

Q ss_pred             cCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853         50 CCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD  109 (137)
Q Consensus        50 ~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~  109 (137)
                      -||-|...+...+....+.- .|++.||..|...|-.       .....||.|+..|.++
T Consensus         5 ~CpIC~~~~~~~~~~~~~~~-~C~H~fc~~Ci~~~~~-------~~~~~CP~CR~~i~~~   56 (65)
T d1g25a_           5 GCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLLFV-------RGAGNCPECGTPLRKS   56 (65)
T ss_dssp             CCSTTTTHHHHCSSCCEEEC-TTCCCEEHHHHHHHHH-------TTSSSCTTTCCCCSSC
T ss_pred             CCCcCCceeecCCceEEEeC-ccChHhhHHHHHHHhC-------cCcCCCCCCCcCcccc
Confidence            57777665544333333443 6999999999987732       1234699999998664

>d1z60a1 g.49.1.2 (A:328-386) TFIIH p44 subunit cysteine-rich domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Cysteine-rich domain
superfamily: Cysteine-rich domain
family: TFIIH p44 subunit cysteine-rich domain
domain: TFIIH p44 subunit cysteine-rich domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.27  E-value=0.0045  Score=34.31  Aligned_cols=46  Identities=24%  Similarity=0.587  Sum_probs=34.5

Q ss_pred             CcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCC
Q psy12853         47 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCS  103 (137)
Q Consensus        47 ~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~  103 (137)
                      ..++|-+|...+   .+....+|++|+..||..|-.=.|        +....||.|.
T Consensus        14 ~~~~C~gC~~~l---~~~~~y~C~~C~~~FC~dCD~fiH--------e~lh~CpgCl   59 (59)
T d1z60a1          14 GERFCYGCQGEL---KDQHVYVCAVCQNVFCVDCDVFVH--------DSLHSCPGCI   59 (59)
T ss_dssp             SCCEETTTTEEC---TTSEEECCTTTTCCBCHHHHHTTT--------TTSCSSSTTC
T ss_pred             CCCCccCCCCcC---CCCceEECcCCCCccccccchhhh--------hhhcCCCCCC
Confidence            356888898665   234568899999999999976444        4577899883

>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=94.92  E-value=0.011  Score=35.70  Aligned_cols=45  Identities=24%  Similarity=0.614  Sum_probs=33.1

Q ss_pred             ccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853         49 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK  108 (137)
Q Consensus        49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek  108 (137)
                      ..||-|...+.     ..+....||+.||..|...|-.          ..||.|+..+..
T Consensus        23 l~C~IC~~~~~-----~pv~~~~CgH~fC~~Ci~~~~~----------~~CP~Cr~~~~~   67 (97)
T d1jm7b_          23 LRCSRCTNILR-----EPVCLGGCEHIFCSNCVSDCIG----------TGCPVCYTPAWI   67 (97)
T ss_dssp             TSCSSSCSCCS-----SCBCCCSSSCCBCTTTGGGGTT----------TBCSSSCCBCSC
T ss_pred             CCCccCCchhh-----cCceeCCCCCchhHHHHHHHHh----------ccccccCCcCch
Confidence            46998988773     2344556999999999877642          249999988754

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

Probab=94.89  E-value=0.015  Score=31.60  Aligned_cols=48  Identities=25%  Similarity=0.566  Sum_probs=34.8

Q ss_pred             ccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcce
Q psy12853         49 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPI  106 (137)
Q Consensus        49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~i  106 (137)
                      ..||=|-..+..  +....+.+.|++.|+..|...|-..        ...||-|+..|
T Consensus         6 ~~C~ICl~~~~~--~~~~~~l~~C~H~Fh~~Ci~~Wl~~--------~~~CP~CR~~i   53 (55)
T d1iyma_           6 VECAVCLAELED--GEEARFLPRCGHGFHAECVDMWLGS--------HSTCPLCRLTV   53 (55)
T ss_dssp             CCCTTTCCCCCT--TSCCEECSSSCCEECTTHHHHTTTT--------CCSCSSSCCCS
T ss_pred             CCCeEECccccC--CCEEEEeCCCCCcccHHHHHHHHHh--------CCcCCCCCCEe
Confidence            347777766653  3344566779999999999988543        23699999876

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.23  E-value=0.0055  Score=32.98  Aligned_cols=49  Identities=29%  Similarity=0.771  Sum_probs=31.5

Q ss_pred             CCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853         51 CPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK  108 (137)
Q Consensus        51 CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek  108 (137)
                      ||=|-..+...+ .....+ .|++.||..|...|-...       ..+||.|+.++..
T Consensus         3 CpICl~~~~~~~-~~~~~~-~CgH~~c~~C~~~w~~~~-------~~~CP~CR~~~~~   51 (52)
T d1ur6b_           3 CPLCMEPLEIDD-INFFPC-TCGYQICRFCWHRIRTDE-------NGLCPACRKPYPE   51 (52)
T ss_dssp             ETTTTEECCGGG-TTCCSS-SSSCCCCHHHHHHHTTTS-------CCBCTTTCCBCSC
T ss_pred             CcCCChhhhCCC-ceEEec-CCCCccchHHHHHHHhhc-------CCCCCccCCcCCC
Confidence            555654443222 223344 599999999988775432       2369999998754

>d1weoa_ g.44.1.1 (A:) Cellulose synthase A catalytic subunit 7, IRX3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Cellulose synthase A catalytic subunit 7, IRX3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=94.02  E-value=0.017  Score=34.30  Aligned_cols=64  Identities=22%  Similarity=0.444  Sum_probs=48.8

Q ss_pred             CCCcccCCCCCCceeec-CCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCCCCeE
Q psy12853         45 SELIKCCPMCSVPIEKD-EGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGCAQM  115 (137)
Q Consensus        45 ~~~~~~CP~C~~~i~~~-~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~gC~hm  115 (137)
                      +-+...|--|+--|-.. ++...+.|..|++-.|.-|..       -...+..+.||.|+++..+..|+-.|
T Consensus        13 ~~~~q~CqiCGd~VG~~~~Ge~FVAC~eC~FPvCrpCyE-------YErkeG~q~CpqCkt~Ykr~kgsprv   77 (93)
T d1weoa_          13 NLDGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYE-------YERREGTQNCPQCKTRYKRLRGSPRV   77 (93)
T ss_dssp             CCSSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHH-------HHHHTSCSSCTTTCCCCCCCTTCCCC
T ss_pred             hcccchhhhcccccccCCCCCEEEEecccCCccchHHHH-------HHHhccCccCcccCChhhhhcCCCCC
Confidence            34466777888887665 477889999999999999964       11234578999999999988776543

>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=93.53  E-value=0.013  Score=33.06  Aligned_cols=47  Identities=30%  Similarity=0.793  Sum_probs=33.4

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCccee
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIE  107 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~ie  107 (137)
                      ...||=|-..+.     ..+....|++.||..|...|-..        ...||-|+..|.
T Consensus         5 ~d~C~IC~~~~~-----~~~~~~~C~H~Fc~~Ci~~w~~~--------~~~CP~CR~~i~   51 (68)
T d1chca_           5 AERCPICLEDPS-----NYSMALPCLHAFCYVCITRWIRQ--------NPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCSSCCSCCC-----SCEEETTTTEEESTTHHHHHHHH--------SCSTTTTCCCCC
T ss_pred             CCCCccCCcCcc-----CCcEEeCCCCcCcHHHHHHHHHh--------CCcCCCCCcchH
Confidence            445777766552     23455679999999999877432        357999999875

>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=93.52  E-value=0.04  Score=31.38  Aligned_cols=34  Identities=29%  Similarity=0.848  Sum_probs=19.6

Q ss_pred             CCCCCCcceeecCCCCeEEeccCccee-----ecccccccc
Q psy12853         98 CCPMCSVPIEKDEGCAQMLCKRCKHVF-----CWYCLASLD  133 (137)
Q Consensus        98 ~CP~C~~~iek~~gC~hm~C~~C~~~f-----C~~C~~~~~  133 (137)
                      .||.|...++..+|  +..|..|...|     |-.|+.++.
T Consensus         4 ~CP~C~~eL~~~~~--~~~C~~C~~~~~~~a~CPdC~~~Le   42 (71)
T d2jnea1           4 HCPQCQHVLDQDNG--HARCRSCGEFIEMKALCPDCHQPLQ   42 (71)
T ss_dssp             BCSSSCSBEEEETT--EEEETTTCCEEEEEEECTTTCSBCE
T ss_pred             cCCCccCcccccCC--CEehhhhhhhheeEEeCCccccHHH
Confidence            46666666666555  66666665543     555555543

>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=92.82  E-value=0.026  Score=28.29  Aligned_cols=27  Identities=30%  Similarity=0.853  Sum_probs=19.7

Q ss_pred             cccCCCCCCceeecCCCCeeeccccccc
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHV   75 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~   75 (137)
                      +-.||.|+..+.+.++ ..+.||.|++.
T Consensus         3 lP~CP~C~seytYedg-~l~vCPeC~hE   29 (38)
T d2akla2           3 LPPCPQCNSEYTYEDG-ALLVCPECAHE   29 (38)
T ss_dssp             SCCCTTTCCCCCEECS-SSEEETTTTEE
T ss_pred             CCcCCCCCCcceEcCC-CEEECCcccCc
Confidence            3469999999888665 45678776553

>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=92.55  E-value=0.049  Score=27.24  Aligned_cols=28  Identities=29%  Similarity=0.865  Sum_probs=21.5

Q ss_pred             cCCCCCCCcceeecCCCCeEEeccCccee
Q psy12853         96 IKCCPMCSVPIEKDEGCAQMLCKRCKHVF  124 (137)
Q Consensus        96 ~~~CP~C~~~iek~~gC~hm~C~~C~~~f  124 (137)
                      .-+||+|+....=.+| ..+.|..|+++|
T Consensus         3 lP~CP~C~seytYedg-~l~vCPeC~hEW   30 (38)
T d2akla2           3 LPPCPQCNSEYTYEDG-ALLVCPECAHEW   30 (38)
T ss_dssp             SCCCTTTCCCCCEECS-SSEEETTTTEEE
T ss_pred             CCcCCCCCCcceEcCC-CEEECCcccCcC
Confidence            3479999988876666 467888888886

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.20  E-value=0.022  Score=34.65  Aligned_cols=49  Identities=29%  Similarity=0.715  Sum_probs=33.2

Q ss_pred             ccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853         49 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK  108 (137)
Q Consensus        49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek  108 (137)
                      ..||-|...+..     .++- .||+.||..|...|-..     ..+...||.|+..+..
T Consensus        22 l~CpIC~~~~~~-----pv~~-~CgH~fC~~Ci~~~~~~-----~~~~~~CP~Cr~~~~~   70 (103)
T d1jm7a_          22 LECPICLELIKE-----PVST-KCDHIFCKFCMLKLLNQ-----KKGPSQCPLCKNDITK   70 (103)
T ss_dssp             TSCSSSCCCCSS-----CCBC-TTSCCCCSHHHHHHHHS-----SSSSCCCTTTSCCCCT
T ss_pred             cCCCccCchhCC-----eEEc-CCCCchhhHHHHHHHHH-----CCCCCcCcCCCCcCCh
Confidence            469988876632     2332 59999999998776322     1234579999988754

>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=92.17  E-value=0.044  Score=29.63  Aligned_cols=31  Identities=23%  Similarity=0.449  Sum_probs=23.3

Q ss_pred             CCcccCCCCCCceeecCCCCeeecccccccc
Q psy12853         46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVF   76 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~f   76 (137)
                      +..+.||+|+..+....-.++..|.+|+...
T Consensus        16 r~~k~CP~CG~GvFmA~H~dR~~CGKCgyTe   46 (55)
T d2k4xa1          16 RKHRFCPRCGPGVFLAEHADRYSCGRCGYTE   46 (55)
T ss_dssp             CSSCCCTTTTTTCCCEECSSEEECTTTCCCE
T ss_pred             EecCcCcCCCCcEEeeecCCCccccCCcccE
Confidence            3467999998876665556789999988653

>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=91.79  E-value=0.038  Score=31.01  Aligned_cols=35  Identities=23%  Similarity=0.659  Sum_probs=24.8

Q ss_pred             ccCCCCCCCcceeecCCCCeEEeccCcceeeccccccccc
Q psy12853         95 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDV  134 (137)
Q Consensus        95 ~~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~~~  134 (137)
                      ....||-|...++.     ......||+.||+.|...|-.
T Consensus         4 ~~d~C~IC~~~~~~-----~~~~~~C~H~Fc~~Ci~~w~~   38 (68)
T d1chca_           4 VAERCPICLEDPSN-----YSMALPCLHAFCYVCITRWIR   38 (68)
T ss_dssp             CCCCCSSCCSCCCS-----CEEETTTTEEESTTHHHHHHH
T ss_pred             CCCCCccCCcCccC-----CcEEeCCCCcCcHHHHHHHHH
Confidence            45579999877642     345667888888888877643

>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=91.14  E-value=0.12  Score=29.33  Aligned_cols=45  Identities=27%  Similarity=0.795  Sum_probs=30.4

Q ss_pred             ccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecCCC
Q psy12853         49 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDEGC  112 (137)
Q Consensus        49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~gC  112 (137)
                      ..||.|...+...++  ...|..|...|=                 ..-.||.|+.++|+-.-|
T Consensus         3 ~~CP~C~~eL~~~~~--~~~C~~C~~~~~-----------------~~a~CPdC~~~Le~LkAC   47 (71)
T d2jnea1           3 LHCPQCQHVLDQDNG--HARCRSCGEFIE-----------------MKALCPDCHQPLQVLKAC   47 (71)
T ss_dssp             CBCSSSCSBEEEETT--EEEETTTCCEEE-----------------EEEECTTTCSBCEEEEET
T ss_pred             CcCCCccCcccccCC--CEehhhhhhhhe-----------------eEEeCCccccHHHHHHhc
Confidence            369999999877543  566666555443                 233699999999886543

>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=91.06  E-value=0.061  Score=29.04  Aligned_cols=29  Identities=24%  Similarity=0.500  Sum_probs=24.3

Q ss_pred             cCCCCCCCcceeecCCCCeEEeccCccee
Q psy12853         96 IKCCPMCSVPIEKDEGCAQMLCKRCKHVF  124 (137)
Q Consensus        96 ~~~CP~C~~~iek~~gC~hm~C~~C~~~f  124 (137)
                      .+.||+|+.-|.....=|.+.|.+||+-.
T Consensus        18 ~k~CP~CG~GvFmA~H~dR~~CGKCgyTe   46 (55)
T d2k4xa1          18 HRFCPRCGPGVFLAEHADRYSCGRCGYTE   46 (55)
T ss_dssp             SCCCTTTTTTCCCEECSSEEECTTTCCCE
T ss_pred             cCcCcCCCCcEEeeecCCCccccCCcccE
Confidence            46899999888887777899999998753

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.75  E-value=0.069  Score=28.89  Aligned_cols=46  Identities=26%  Similarity=0.583  Sum_probs=31.0

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecC
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDE  110 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~  110 (137)
                      ...||-|...+..     .+.- .|++.||..|...           ...+||.|+..|....
T Consensus         6 ~l~C~IC~~~~~~-----p~~l-pCgH~fC~~Ci~~-----------~~~~CP~Cr~~~~~~~   51 (56)
T d1bora_           6 FLRCQQCQAEAKC-----PKLL-PCLHTLCSGCLEA-----------SGMQCPICQAPWPLGA   51 (56)
T ss_dssp             CSSCSSSCSSCBC-----CSCS-TTSCCSBTTTCSS-----------SSSSCSSCCSSSSCCS
T ss_pred             CCCCcccCcccCC-----CEEe-cCCCHHhHHHHHc-----------CCCcCcCCCCcccCCC
Confidence            3468878765531     1233 4899999999743           2447999999886543

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

Probab=90.53  E-value=0.046  Score=29.48  Aligned_cols=38  Identities=26%  Similarity=0.432  Sum_probs=28.2

Q ss_pred             CCCCCCCcceeecCCCCeEEeccCcceeecccccccccCC
Q psy12853         97 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLDVSR  136 (137)
Q Consensus        97 ~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~~~~~  136 (137)
                      ..||-|...++..+.  -++...||+.|+..|...|-..+
T Consensus         6 ~~C~ICl~~~~~~~~--~~~l~~C~H~Fh~~Ci~~Wl~~~   43 (55)
T d1iyma_           6 VECAVCLAELEDGEE--ARFLPRCGHGFHAECVDMWLGSH   43 (55)
T ss_dssp             CCCTTTCCCCCTTSC--CEECSSSCCEECTTHHHHTTTTC
T ss_pred             CCCeEECccccCCCE--EEEeCCCCCcccHHHHHHHHHhC
Confidence            469999888876443  24455699999999999987654

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.16  E-value=0.017  Score=34.37  Aligned_cols=48  Identities=25%  Similarity=0.615  Sum_probs=33.5

Q ss_pred             ccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853         49 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD  109 (137)
Q Consensus        49 ~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~  109 (137)
                      .-||=|...+.     ..+.= .||+.||..|...|-.       ...+.||.|+.++...
T Consensus        24 l~C~IC~~~~~-----~pv~~-~CgH~FC~~Ci~~~~~-------~~~~~CP~Cr~p~~~~   71 (86)
T d1rmda2          24 ISCQICEHILA-----DPVET-SCKHLFCRICILRCLK-------VMGSYCPSCRYPCFPT   71 (86)
T ss_dssp             TBCTTTCSBCS-----SEEEC-TTSCEEEHHHHHHHHH-------HTCSBCTTTCCBCCGG
T ss_pred             cCCccCCcchh-----cceec-CCCChhhHHHHHHHHh-------hCCCcCcccCCCCChh
Confidence            45888877653     22333 5999999999987632       2234699999987654

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=89.43  E-value=0.036  Score=32.17  Aligned_cols=50  Identities=26%  Similarity=0.626  Sum_probs=33.8

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeecC
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKDE  110 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~~  110 (137)
                      ...||-|-..+.     ..+. ..||+.||..|...|-.       ...+.||-|+..|....
T Consensus        23 ~~~C~IC~~~~~-----~~~~-~~CgH~fC~~Ci~~wl~-------~~~~~CP~Cr~~i~~~~   72 (79)
T d1fbva4          23 FQLCKICAENDK-----DVKI-EPCGHLMCTSCLTSWQE-------SEGQGCPFCRCEIKGTE   72 (79)
T ss_dssp             TTBCTTTSSSBC-----CEEC-SSSCCEECHHHHHHHHH-------TTCCSCTTTCCCCCCCC
T ss_pred             CCCCccCCCcCC-----CeEE-eCCCCeeeHHHHHHHHH-------HCcCcCCCCCcCccCCc
Confidence            446888865432     1222 35999999999877632       23457999999997643

>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=89.27  E-value=0.069  Score=31.91  Aligned_cols=33  Identities=21%  Similarity=0.630  Sum_probs=22.5

Q ss_pred             cCCCCCCCcceeecCCCCeEEeccCcceeecccccccc
Q psy12853         96 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLD  133 (137)
Q Consensus        96 ~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~~  133 (137)
                      ...||-|...+...     ++...||+.||..|...|-
T Consensus        22 ~l~C~IC~~~~~~p-----v~~~~CgH~fC~~Ci~~~~   54 (97)
T d1jm7b_          22 LLRCSRCTNILREP-----VCLGGCEHIFCSNCVSDCI   54 (97)
T ss_dssp             TTSCSSSCSCCSSC-----BCCCSSSCCBCTTTGGGGT
T ss_pred             cCCCccCCchhhcC-----ceeCCCCCchhHHHHHHHH
Confidence            45799999888542     4444577777777766654

>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=88.86  E-value=0.05  Score=30.24  Aligned_cols=36  Identities=25%  Similarity=0.570  Sum_probs=23.3

Q ss_pred             CCCCCCCcceeecCCCCeEEeccCcceeecccccccc
Q psy12853         97 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASLD  133 (137)
Q Consensus        97 ~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~~~  133 (137)
                      ..||-|...+.....-.-+.- .||+.||..|...|-
T Consensus         4 ~~CpIC~~~~~~~~~~~~~~~-~C~H~fc~~Ci~~~~   39 (65)
T d1g25a_           4 QGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLLF   39 (65)
T ss_dssp             TCCSTTTTHHHHCSSCCEEEC-TTCCCEEHHHHHHHH
T ss_pred             CCCCcCCceeecCCceEEEeC-ccChHhhHHHHHHHh
Confidence            469999876655444444443 377777777777663

>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=88.83  E-value=0.13  Score=28.66  Aligned_cols=32  Identities=19%  Similarity=0.544  Sum_probs=24.5

Q ss_pred             cccCCCCCCCcceeecCCCCeEEeccCcceeeccccc
Q psy12853         94 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLA  130 (137)
Q Consensus        94 ~~~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~  130 (137)
                      ....+|..|+..|...    .++|+ ||..||-.-.-
T Consensus        13 ~k~~RC~~C~KKl~l~----~~~Cr-Cg~~FC~~HR~   44 (64)
T d1wfha_          13 QRPNRCTVCRKRVGLT----GFMCR-CGTTFCGSHRY   44 (64)
T ss_dssp             SSCCCCTTTCCCCCTT----CEECS-SSCEECTTTCS
T ss_pred             CCCCcChhhCCCccce----eeecc-CCCEehhhcCC
Confidence            3456899999888654    38997 99999986543

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

Probab=88.57  E-value=0.064  Score=29.18  Aligned_cols=55  Identities=18%  Similarity=0.292  Sum_probs=34.1

Q ss_pred             CCcccCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCccee
Q psy12853         46 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIE  107 (137)
Q Consensus        46 ~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~ie  107 (137)
                      .+..-|+-|...+.. .......|..|++.|+..|...|-..      .....||-|++.+.
T Consensus         4 ed~~~C~IC~~~~~~-~~~~~c~c~~c~h~~H~~Cl~~W~~~------~~~~~CP~Cr~~~~   58 (60)
T d1vyxa_           4 EDVPVCWICNEELGN-ERFRACGCTGELENVHRSCLSTWLTI------SRNTACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECSC-CCCCSCCCSSGGGSCCHHHHHHHHHH------HTCSBCTTTCCBCC
T ss_pred             CCCCCCccCCccCCC-ceeEecccCCCCCEEcHHHHHHHHhh------CCCCCCcccCCeee
Confidence            334456666543321 22333456788999999999887321      12347999998764

>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=87.33  E-value=0.29  Score=26.71  Aligned_cols=30  Identities=17%  Similarity=0.282  Sum_probs=24.6

Q ss_pred             ccCCCCCCCcceeecCCCCeEEeccCccee
Q psy12853         95 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF  124 (137)
Q Consensus        95 ~~~~CP~C~~~iek~~gC~hm~C~~C~~~f  124 (137)
                      .+..||.|+..++..++=+...|..||..|
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            467899999999887776788898888765

>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=86.88  E-value=0.38  Score=26.25  Aligned_cols=30  Identities=20%  Similarity=0.540  Sum_probs=25.2

Q ss_pred             ccCCCCCCCcceeecCCCCeEEeccCccee
Q psy12853         95 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF  124 (137)
Q Consensus        95 ~~~~CP~C~~~iek~~gC~hm~C~~C~~~f  124 (137)
                      .+..||.|+..++-...=+...|..|+..|
T Consensus         5 ~iL~CP~ck~~L~~~~~~~~Lvc~~~~laY   34 (59)
T d2pk7a1           5 DILACPICKGPLKLSADKTELISKGAGLAY   34 (59)
T ss_dssp             GTCCCTTTCCCCEECTTSSEEEETTTTEEE
T ss_pred             hheECCCCCCcceEeCCCCEEecCCcCccc
Confidence            456899999999988877889999888665

>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=86.57  E-value=0.2  Score=31.33  Aligned_cols=35  Identities=23%  Similarity=0.613  Sum_probs=25.3

Q ss_pred             cCCCCCCCcceeecCCCCeEEeccCcceeecccccc
Q psy12853         96 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLAS  131 (137)
Q Consensus        96 ~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~  131 (137)
                      ...|+.|+..+..... ...+|+.||..||-.|+..
T Consensus        48 ~~~C~~C~~~f~~~~~-~~~~C~~C~~~~C~~C~~~   82 (124)
T d1zbdb_          48 VNRCILCGEQLGMLGS-ASVVCEDCKKNVCTKCGVE   82 (124)
T ss_dssp             SSBCSSSCCBCSTTSC-CEEECTTTCCEEETTSEEE
T ss_pred             CCcCcccCCcccCCCC-CCCcCccCCcccccCCCCC
Confidence            4568888877654332 3568999999999999754

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=86.45  E-value=0.067  Score=28.79  Aligned_cols=47  Identities=13%  Similarity=0.200  Sum_probs=31.6

Q ss_pred             cCCCCCCceeecCCCCeeecccccccccccccccccCCCCcccccccCCCCCCCcceeec
Q psy12853         50 CCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEKD  109 (137)
Q Consensus        50 ~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek~  109 (137)
                      .||=|...+.     ..+.-+.||+.||..|-..|=..        ...||-|+..+...
T Consensus         2 ~C~Ic~~~~~-----~Pv~~~~cGh~fc~~cI~~~l~~--------~~~CP~c~~~l~~~   48 (56)
T d2baya1           2 LCAISGKVPR-----RPVLSPKSRTIFEKSLLEQYVKD--------TGNDPITNEPLSIE   48 (56)
T ss_dssp             CCTTTCSCCS-----SEEEETTTTEEEEHHHHHHHHHH--------HSBCTTTCCBCCGG
T ss_pred             CCccCCchHH-----hcCccCCCCCcccHHHHHHHHhh--------ccCCCccCCcCCHH
Confidence            3555555442     34555679999999998776322        34699999887653

>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=85.95  E-value=0.31  Score=26.57  Aligned_cols=30  Identities=30%  Similarity=0.705  Sum_probs=25.0

Q ss_pred             ccCCCCCCCcceeecCCCCeEEeccCccee
Q psy12853         95 LIKCCPMCSVPIEKDEGCAQMLCKRCKHVF  124 (137)
Q Consensus        95 ~~~~CP~C~~~iek~~gC~hm~C~~C~~~f  124 (137)
                      .+..||.|+..++-..+=+...|..|+..|
T Consensus         6 ~iL~CP~ck~~L~~~~~~~~Lvc~~~~l~Y   35 (59)
T d2hf1a1           6 EILVCPLCKGPLVFDKSKDELICKGDRLAF   35 (59)
T ss_dssp             EECBCTTTCCBCEEETTTTEEEETTTTEEE
T ss_pred             hhhcCCCCCCeeeEeCCCCEEecCCcCccc
Confidence            356799999999988777889999888765

>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=85.24  E-value=0.29  Score=26.72  Aligned_cols=29  Identities=17%  Similarity=0.323  Sum_probs=21.2

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccc
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVF   76 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~f   76 (137)
                      ..-||.|+..++.+.+.....|+.|+..|
T Consensus        10 iL~CP~ck~~L~~~~~~~~Lvc~~~~~~Y   38 (59)
T d2jnya1          10 VLACPKDKGPLRYLESEQLLVNERLNLAY   38 (59)
T ss_dssp             CCBCTTTCCBCEEETTTTEEEETTTTEEE
T ss_pred             HhcCCCCCCEeEEeCCCCEEEcCccCccc
Confidence            45688888888887777777777766544

>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=84.86  E-value=0.1  Score=32.74  Aligned_cols=39  Identities=23%  Similarity=0.597  Sum_probs=30.3

Q ss_pred             CCCCcccCCCCCCceeecCCCCeeeccccccccccccccc
Q psy12853         44 DSELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLAS   83 (137)
Q Consensus        44 ~~~~~~~CP~C~~~i~~~~~~~~~~C~~C~~~fC~~C~~~   83 (137)
                      ...+..-|+.|+..+... ......|..|+..||..|+..
T Consensus        44 ~~~~~~~C~~C~~~f~~~-~~~~~~C~~C~~~~C~~C~~~   82 (124)
T d1zbdb_          44 AGDGVNRCILCGEQLGML-GSASVVCEDCKKNVCTKCGVE   82 (124)
T ss_dssp             CSCSSSBCSSSCCBCSTT-SCCEEECTTTCCEEETTSEEE
T ss_pred             hccCCCcCcccCCcccCC-CCCCCcCccCCcccccCCCCC
Confidence            455667899999887543 235678999999999999864

>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=84.76  E-value=0.28  Score=24.61  Aligned_cols=27  Identities=26%  Similarity=0.447  Sum_probs=18.5

Q ss_pred             ccCCCCCCCcceeec--CCCCeEEeccCc
Q psy12853         95 LIKCCPMCSVPIEKD--EGCAQMLCKRCK  121 (137)
Q Consensus        95 ~~~~CP~C~~~iek~--~gC~hm~C~~C~  121 (137)
                      ..++||.|+.+|.+.  +|=.-..|..|.
T Consensus        11 ~g~pC~~C~~~I~~~~~~gR~t~~Cp~CQ   39 (40)
T d1k3xa3          11 DGEPCERCGSIIEKTTLSSRPFYWCPGCQ   39 (40)
T ss_dssp             TTSBCTTTCCBCEEEEETTEEEEECTTTC
T ss_pred             CCCccCcCCCEEEEEEECCCCCEEChhhC
Confidence            467899999999985  454345555443

>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=84.61  E-value=0.26  Score=28.19  Aligned_cols=30  Identities=23%  Similarity=0.564  Sum_probs=23.6

Q ss_pred             cCCCCCCCcceeecCCCCeEEeccCcceeeccccc
Q psy12853         96 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLA  130 (137)
Q Consensus        96 ~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~  130 (137)
                      -.+|..|+..|...    -++|+ ||..||-.-.-
T Consensus        25 ~~RC~~C~KKl~l~----~~~Cr-Cg~~FC~~HR~   54 (74)
T d1wfla_          25 KNRCFMCRKKVGLT----GFDCR-CGNLFCGLHRY   54 (74)
T ss_dssp             TTBCSSSCCBCGGG----CEECT-TSCEECSSSCS
T ss_pred             CCcChhhCCcccce----eeEcc-CCCEehhhcCC
Confidence            45899999888765    37997 99999986554

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=84.51  E-value=0.072  Score=32.66  Aligned_cols=36  Identities=25%  Similarity=0.566  Sum_probs=25.9

Q ss_pred             ccccccccccccccccCCCCcccccccCCCCCCCcceee
Q psy12853         70 KRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIEK  108 (137)
Q Consensus        70 ~~C~~~fC~~C~~~~h~~~~~~~~~~~~~CP~C~~~iek  108 (137)
                      ..|++.|+..|...|.....   ..+...||-|+..+-.
T Consensus        59 ~~CgH~FH~~Ci~~Wl~~~~---~~~~~~CP~CR~~~~~   94 (114)
T d1v87a_          59 TKCSHAFHLLCLLAMYCNGN---KDGSLQCPSCKTIYGE   94 (114)
T ss_dssp             SSSCCEECHHHHHHHHHHTC---CSSCCBCTTTCCBSSS
T ss_pred             CCCCChhhHHHHHHHHHhcC---cCCCCccccccchhcc
Confidence            47999999999998864321   1223579999987743

>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=83.72  E-value=0.55  Score=25.73  Aligned_cols=36  Identities=22%  Similarity=0.627  Sum_probs=26.8

Q ss_pred             cccCCCCCCCcceeecCCCCeEEeccCcceeecccccc
Q psy12853         94 ELIKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLAS  131 (137)
Q Consensus        94 ~~~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~  131 (137)
                      .....|+.|+.......  ..-.|+.||..||..|...
T Consensus         6 ~~~~~C~~C~~~F~~~~--rrHHCR~CG~v~C~~Cs~~   41 (64)
T d1joca1           6 NEVQNCMACGKGFSVTV--RRHHCRQCGNIFCAECSAK   41 (64)
T ss_dssp             GGCCBCTTTCCBCCSSS--CCEECTTTCCEECGGGSCE
T ss_pred             ccCCcCcCcCCcccCCc--cccchhhhCCeecccccCC
Confidence            34667999988764432  3468999999999999764

>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=83.48  E-value=0.33  Score=28.49  Aligned_cols=32  Identities=22%  Similarity=0.538  Sum_probs=24.7

Q ss_pred             cCCCCCCCcceeecCCCCeEEeccCcceeecccccc
Q psy12853         96 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLAS  131 (137)
Q Consensus        96 ~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~  131 (137)
                      ..+|..|+..|....   -++|+ ||..||-...-+
T Consensus        25 ~~RC~~C~KKl~l~~---~~~Cr-Cg~~FC~~HR~p   56 (85)
T d1wffa_          25 MKHCFLCGKKTGLAT---SFECR-CGNNFCASHRYA   56 (85)
T ss_dssp             CCBCSSSCCBCSSSS---CEECT-TCCEECTTTCST
T ss_pred             CCcChhcCCeecCCc---CeecC-CCCEehhhcCCC
Confidence            458999999886543   37997 999999876544

>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=83.26  E-value=0.44  Score=25.95  Aligned_cols=29  Identities=21%  Similarity=0.604  Sum_probs=21.8

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccc
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVF   76 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~f   76 (137)
                      ..-||.|...+..+.+.+...|..|+..|
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            44689999999888777778887766443

>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=82.91  E-value=0.41  Score=26.05  Aligned_cols=29  Identities=31%  Similarity=0.761  Sum_probs=21.6

Q ss_pred             cccCCCCCCceeecCCCCeeecccccccc
Q psy12853         48 IKCCPMCSVPIEKDEGCAQMLCKRCKHVF   76 (137)
Q Consensus        48 ~~~CP~C~~~i~~~~~~~~~~C~~C~~~f   76 (137)
                      ..-||.|...+..+.+.+...|..|+..|
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            34689999998887777778887766544

>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=82.54  E-value=0.76  Score=26.86  Aligned_cols=34  Identities=29%  Similarity=0.528  Sum_probs=25.7

Q ss_pred             cCCCCCCCcceeecCCCCeEEeccCcceeecccccc
Q psy12853         96 IKCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLAS  131 (137)
Q Consensus        96 ~~~CP~C~~~iek~~gC~hm~C~~C~~~fC~~C~~~  131 (137)
                      ..+|..|+.....  .--.-.|+.||..||..|...
T Consensus         9 ~s~C~~C~~~Fs~--~~rrhhCr~CG~vfC~~Cs~~   42 (88)
T d1wfka_           9 ESRCYGCAVKFTL--FKKEYGCKNCGRAFCNGCLSF   42 (88)
T ss_dssp             CSBCTTTCCBCCS--SSCEEECSSSCCEEETTTSCE
T ss_pred             cCcCcccCchhcc--ccccccccccChhhChHHhCC
Confidence            4568888887733  233688999999999999864