Citrus Sinensis ID: 012292

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460------
Protein Sequence
MGIENKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSIGDQIDLVISQKPKDPEVEDPEVSRAEVKILEVKVSRLHTVLESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRNMDLAKELASLKLVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVSKKASQKEEILKGATEDNSISLCTNNVSLEDQREQHSVPIYNLDWTSRVTNDFSFSTKSENFNAIKNIDANHTREGGSAKSHGKERNALQREDTSRFSSVVFGLSNHNSIHQTIADVVQKPTPSRLGSAPTIDIDEDVTLIVPDSAQVQPIVNIKKNPPSPVSLSKPGIFLLVQFQFSLSFRGID
Secondary Structure (PSIPRED)
ccccccccccccEEccccccccccccEEEcccccccHHHHHHHHHHHcccccccccccccccccccccccccHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHcccccccccccccccccccccccccccHHHHccHHHHHHHccccccccHHHHHHHcccccccccccccccccccccHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEEcccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccEEEEEHHccccccHccEEcccccccccHHHHHHHHHHcccccccccccccccccHHHcccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHccccccHHHHHHHHHHHHHHcHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHccccEcccccEccccccccHHHcccccccccccccccccccccccccccccccEEEEEEEEcEccccEEEEccccccccccccccccccccccccccccccccHHHHHccccHHHHHccccEEcccccEEEcccHHccccccccccccccccccccccEEEEEEEEEEEEEcccc
Coil and Loop (DISEMBL)
mgienkfgktICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYcssskkctcpvckqrcsssnsigdQIDLVisqkpkdpevedpevsrAEVKILEVKVSRLHTVLESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRNMDLAKELASLKLvsdlnldeDEVLKFAllgngannkdTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVSKKASQKEEIlkgatednsislctnnvsledqreqhsvpiynldwtsrvtndfsfstksenfnaiknidanhtreggsakshgkernalqredtsrFSSVVFGLSNHNSIHQTIADvvqkptpsrlgsaptididedvtlivpdsaqvqpivnikknppspvslskpgiFLLVQFQFslsfrgid
Flexible Loop (DISEMBL)
mgienkfgktICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRcsssnsigdqidlvisqkpkdpevedpevsraevkilevkvsrlhtvlesqgkeikeinEELCLCKERIKEEAALKNEALRQKVSVEqllhsksqeldKVTLECLKLKQRNMDLAKELASLKLVSDLNLDEDEVLKFallgngannkdtiDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQEletavelkdnevlralkvskkasqkeeilkgatednsisLCTNNvsledqreQHSVpiynldwtsrVTNDFSFSTKSEnfnaiknidanhtreggsakshgkernalqredTSRFSSVVFGLSNHNSIHQTIADVVQKPTPSRLGSAPTIDIDEDVTLIVPDSAQVQPIVNIKKNPPSPVSLSKPGIFLLVQFQFSLSFRGID
Low Complexity Region (SEG)
MGIENKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSIGDQIDLVISQKPKDPEVEDPEVSRAEVKILEVKVSRLHTVLESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRNMDLAKELASLKLVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVSKKASQKEEILKGATEDNSISLCTNNVSLEDQREQHSVPIYNLDWTSRVTNDFSFSTKSENFNAIKNIDANHTREGGSAKSHGKERNALQREDTSRFSSVVFGLSNHNSIHQTIADVVQKPTPSRLGSAPTIDIDEDVTLIVPDSAQVQPIVNIKKNPPSPVSLSKPGIfllvqfqfslsfRGID
Disordered region (IsUnstruct)
*****KFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS*******QIDLV*******************VKILEVKVSRLHTVLESQGKEIKEINEELCLCKERIKEEAAL*********************LDKVTLECLKLKQRNMDLAKELASLKLVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELMAKCNLLGRE****************************************************************C*************SVPIYNLDWTSRVTNDFSFS*******************************************VVFGLSNHNSIHQTIADVV************TIDIDEDVTLIVPDSAQVQPIVNI***********KPGIFLLVQFQFSLSF****
Disordered Region (DISOPRED)
**********ICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSIGDQIDLVISQKPKDPEVEDPEVSRAEVKILEVKVSR**********************************************************************LAKELA***********************************************************************************************************************************************************************************************************************************************************************LSKPGIFLLVQFQFSLSFRGI*
Disordered Region (DISEMBL)
MGIENKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSIGDQIDLVISQK************RAEVKILEVKVSRLHTVLESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRNMDLAKELASLKLVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVSKKASQKEEILKGATEDNSISLCTNNVSLEDQREQHSVPIYNLDWTSRVTNDFSFSTKSENFNAIKNIDANHT*********************SRFSSVVFGLSNHNSIHQTIADVVQKPTPSRLGSAPTIDIDEDVTLIVPDSAQVQPIVNIKKNPPSPVSLSKPGIFLLVQFQFSLSFRGID
Disordered Region (DISPRO)
*****KFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSI***********PKDPEVEDPEVSRAEVKILEVKVSRLHTVLESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRNMDLAKELASLKLVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVSKKASQK***LKG*T*DNSISLCTNNVSLEDQREQHSVPIYNLDWTSRVTNDFSFSTKSENFNAIKNIDANHTREGGSAKSHGKERNALQR**********F*********QTIADVVQKPTPSRLGSAPTIDIDEDVTLIVPDSAQVQPIVNIKKNPPSPVSLSKPGIFLLVQFQFSLSFRGID
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGIENKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSIGDQIDLVISQKPKDPEVEDPEVSRAEVKILEVKVSRLHTVLESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQExxxxxxxxxxxxxxxxxxxxxLASLKLVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELMAKxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxVLRALKVSKKASQKEEILKGATEDNSISLCTNNVSLEDQREQHSVPIYNLDWTSRVTNDFSFSTKSENFNAIKNIDANHTREGGSAKSHGKERNALQREDTSRFSSVVFGLSNHNSIHQTIADVVQKPTPSRLGSAPTIDIDEDVTLIVPDSAQVQPIVNIKKNPPSPVSLSKPGIFLLVQFQFSLSFRGID
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	466	2.2.26 [Sep-21-2011]
Q9Y7K6	741	Uncharacterized RING fing	yes	no	0.098	0.062	0.392	4e-06
Q7X843	349	RING-H2 finger protein AT	no	no	0.210	0.280	0.238	4e-05
Q5SWK7	663	RING finger protein 145 O	yes	no	0.148	0.104	0.293	0.0001
Q99942	180	E3 ubiquitin-protein liga	yes	no	0.175	0.455	0.307	0.0002
Q5M807	180	E3 ubiquitin-protein liga	no	no	0.175	0.455	0.307	0.0003
O35445	180	E3 ubiquitin-protein liga	no	no	0.175	0.455	0.307	0.0003
Q9H9V4	155	RING finger protein 122 O	no	no	0.139	0.419	0.315	0.0003
Q8BP31	155	RING finger protein 122 O	no	no	0.135	0.406	0.346	0.0003
Q8W571	323	RING-H2 finger protein AT	no	no	0.274	0.396	0.239	0.0005
Q0IJ20	695	RING finger protein 145 O	no	no	0.169	0.113	0.325	0.0007

>sp|Q9Y7K6|YGI4_SCHPO Uncharacterized RING finger protein C2A9.04c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPBC2A9.04c PE=4 SV=1

 Score = 53.1 bits (126), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 5/51 (9%)

Query: 11  ICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQ 61
            C ICY+D+    E       CGH+F + CLQ+W E       CTCP+C++
Sbjct: 106 TCPICYDDMNENDEKQATKMPCGHIFGKNCLQKWLE-----NHCTCPLCRK 151

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

>sp|Q7X843|ATL48_ARATH RING-H2 finger protein ATL48 OS=Arabidopsis thaliana GN=ATL48 PE=2 SV=2

 Score = 50.1 bits (118), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 25/105 (23%), Positives = 53/105 (50%), Gaps = 7/105 (6%)

Query: 12  CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSIGD 71
           C++C  +     + L+++ +C H FH  C+  W          TCP+C++  S+SN   +
Sbjct: 207 CAVCLNEFSD-TDKLRLLPVCSHAFHLHCIDTWLL-----SNSTCPLCRRSLSTSNVCYN 260

Query: 72  QIDLVISQKPKDPEVEDPEVSRAEVKILEVKVSRLHTVLESQGKE 116
             + +++      +V+D + S A+ ++  V++ R  +  ESQ + 
Sbjct: 261 HSETLVAPLSGHQQVDDGKASLAK-RVFSVRLGRFKSTNESQSQR 304

Arabidopsis thaliana (taxid: 3702)

>sp|Q5SWK7|RN145_MOUSE RING finger protein 145 OS=Mus musculus GN=Rnf145 PE=2 SV=1

 Score = 48.5 bits (114), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/92 (29%), Positives = 45/92 (48%), Gaps = 23/92 (25%)

Query: 11  ICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSI- 69
           IC+ICY+D+K       VI+ C H FH  CL++W        + TCP+C     +S+ + 
Sbjct: 536 ICAICYQDMKS-----AVITPCSHFFHAGCLKKWL-----YVQDTCPLCHCHLKNSSQLP 585

Query: 70  ------------GDQIDLVISQKPKDPEVEDP 89
                       G + ++V+ + P+ P+ E P
Sbjct: 586 GLGTEAAPQPPAGAEQNIVLQEGPEPPDHESP 617

Mus musculus (taxid: 10090)

>sp|Q99942|RNF5_HUMAN E3 ubiquitin-protein ligase RNF5 OS=Homo sapiens GN=RNF5 PE=1 SV=1

 Score = 47.8 bits (112), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 28/91 (30%), Positives = 45/91 (49%), Gaps = 9/91 (9%)

Query: 12  CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSIGD 71
           C+IC E  +       V+S+CGH++   CL QW E  +  ++  CPVCK   S    +  
Sbjct: 27  CNICLETAR-----EAVVSVCGHLYCWPCLHQWLE--TRPERQECPVCKAGISREKVV-- 77

Query: 72  QIDLVISQKPKDPEVEDPEVSRAEVKILEVK 102
            +    SQKP+DP ++ P   + +    E +
Sbjct: 78  PLYGRGSQKPQDPRLKTPPRPQGQRPAPESR 108

Has E2-dependent E3 ubiquitin-protein ligase activity. May function together with E2 ubiquitin-conjugating enzymes UBE2D1/UBCH5A and UBE2D2/UBC4. Mediates ubiquitination of PXN/paxillin and Salmonella type III secreted protein sopA. May be involved in regulation of cell motility and localization of PXN/paxillin. Mediates the 'Lys-63'-linked polyubiquitination of JKAMP thereby regulating JKAMP function by decreasing its association with components of the proteasome and ERAD; the ubiquitination appears to involve E2 ubiquitin-conjugating enzyme UBE2N. Mediates the 'Lys-48'-linked polyubiquitination of TMEM173 at 'Lys-150' leading to its proteasomal degradation; the ubiquitination occurrs in mitochondria after viral transfection and regulates antiviral responses.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q5M807|RNF5_RAT E3 ubiquitin-protein ligase RNF5 OS=Rattus norvegicus GN=Rnf5 PE=2 SV=1

 Score = 47.0 bits (110), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 28/91 (30%), Positives = 44/91 (48%), Gaps = 9/91 (9%)

Query: 12  CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSIGD 71
           C+IC E  +       V+S+CGH++   CL QW E  +   +  CPVCK   S    +  
Sbjct: 27  CNICLETAR-----EAVVSVCGHLYCWPCLHQWLE--TRPDRQECPVCKAGISREKVV-- 77

Query: 72  QIDLVISQKPKDPEVEDPEVSRAEVKILEVK 102
            +    SQKP+DP ++ P   + +    E +
Sbjct: 78  PLYGRGSQKPQDPRLKTPPRPQGQRPAPESR 108

Has E2-dependent E3 ubiquitin-protein ligase activity. May function together with E2 ubiquitin-conjugating enzymes UBE2D1/UBCH5A and UBE2D2/UBC4. Mediates ubiquitination of PXN/paxillin. May be involved in regulation of cell motility and localization of PXN/paxillin. Mediates the 'Lys-63'-linked polyubiquitination of JKAMP thereby regulating JKAMP function by decreasing its association with components of the proteasome and ERAD; the ubiquitination appears to involve E2 ubiquitin-conjugating enzyme UBE2N. Mediates the 'Lys-48'-linked polyubiquitination of TMEM173 at 'Lys-150' leading to its proteasomal degradation; the ubiquitination occurrs in mitochondria after viral transfection and regulates antiviral responses.

Rattus norvegicus (taxid: 10116)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|O35445|RNF5_MOUSE E3 ubiquitin-protein ligase RNF5 OS=Mus musculus GN=Rnf5 PE=1 SV=1

 Score = 47.0 bits (110), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 28/91 (30%), Positives = 44/91 (48%), Gaps = 9/91 (9%)

Query: 12  CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSIGD 71
           C+IC E  +       V+S+CGH++   CL QW E  +   +  CPVCK   S    +  
Sbjct: 27  CNICLETAR-----EAVVSVCGHLYCWPCLHQWLE--TRPDRQECPVCKAGISREKVV-- 77

Query: 72  QIDLVISQKPKDPEVEDPEVSRAEVKILEVK 102
            +    SQKP+DP ++ P   + +    E +
Sbjct: 78  PLYGRGSQKPQDPRLKTPPRPQGQRPAPESR 108

Has E2-dependent E3 ubiquitin-protein ligase activity. May function together with E2 ubiquitin-conjugating enzymes UBE2D1/UBCH5A and UBE2D2/UBC4. Mediates ubiquitination of PXN/paxillin. May be involved in regulation of cell motility and localization of PXN/paxillin. Mediates the 'Lys-63'-linked polyubiquitination of JKAMP thereby regulating JKAMP function by decreasing its association with components of the proteasome and ERAD; the ubiquitination appears to involve E2 ubiquitin-conjugating enzyme UBE2N. Mediates the 'Lys-48'-linked polyubiquitination of TMEM173 at 'Lys-150 'leading to its proteasomal degradation; the ubiquitination occurrs in mitochondria after viral transfection and regulates antiviral responses.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9H9V4|RN122_HUMAN RING finger protein 122 OS=Homo sapiens GN=RNF122 PE=2 SV=2

 Score = 47.0 bits (110), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 8/73 (10%)

Query: 7   FGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS 66
           +G+T C++C ED K   ++L V+  C H FH  CL +W E      +C CP+C +  +S 
Sbjct: 89  YGQT-CAVCLEDFKG-KDELGVLP-CQHAFHRKCLVKWLEV-----RCVCPMCNKPIASP 140

Query: 67  NSIGDQIDLVISQ 79
           +     I +++ +
Sbjct: 141 SEATQNIGILLDE 153

May induce necrosis and apoptosis. May play a role in cell viability.

Homo sapiens (taxid: 9606)

>sp|Q8BP31|RN122_MOUSE RING finger protein 122 OS=Mus musculus GN=Rnf122 PE=2 SV=1

 Score = 47.0 bits (110), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 26/75 (34%), Positives = 42/75 (56%), Gaps = 12/75 (16%)

Query: 7   FGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS-- 64
           +G+T C++C ED K   ++L V+  C H FH  CL +W E      +C CP+C +  +  
Sbjct: 89  YGQT-CAVCLEDFKG-KDELGVLP-CQHAFHRKCLVKWLEV-----RCVCPMCNKPIAGP 140

Query: 65  --SSNSIGDQIDLVI 77
             +S SIG  +D ++
Sbjct: 141 TETSQSIGILLDELV 155

May induce necrosis and apoptosis. May play a role in cell viability.

Mus musculus (taxid: 10090)

>sp|Q8W571|ATL32_ARATH RING-H2 finger protein ATL32 OS=Arabidopsis thaliana GN=ATL32 PE=2 SV=3

 Score = 46.2 bits (108), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 33/138 (23%), Positives = 66/138 (47%), Gaps = 10/138 (7%)

Query: 12  CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS-SNSIG 70
           C+IC  +L+   E ++++ IC H+FH  C+  W          TCPVC+   ++ SN  G
Sbjct: 124 CAICLNELEDH-ETVRLLPICNHLFHIDCIDTWLY-----SHATCPVCRSNLTAKSNKPG 177

Query: 71  DQIDLVISQKPKDP---EVEDPEVSRAEVKILEVKVSRLHTVLESQGKEIKEINEELCLC 127
           D+ D V     +D    ++E  EV+++  + L  ++S       S G  +   ++     
Sbjct: 178 DEDDGVPLAAMRDHVVVDIETVEVAKSHHRRLSSEISGKFPRSNSTGHSMDRFSDGTERF 237

Query: 128 KERIKEEAALKNEALRQK 145
             R+ ++  ++  A++ +
Sbjct: 238 TLRLPDDVKMRLMAVKGR 255

Arabidopsis thaliana (taxid: 3702)

>sp|Q0IJ20|RN145_XENTR RING finger protein 145 OS=Xenopus tropicalis GN=rnf145 PE=2 SV=1

 Score = 45.8 bits (107), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 28/86 (32%), Positives = 40/86 (46%), Gaps = 7/86 (8%)

Query: 11  ICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSIG 70
           ICSICY+D+        VI+ C H FH  CL++W     +   C C +      ++   G
Sbjct: 536 ICSICYQDMNS-----AVITPCSHFFHPGCLKKWLYVQETCPLCHCQLKSLSQQATGESG 590

Query: 71  DQIDLVISQKPKDPEVEDPEVSRAEV 96
              + V  Q   +P +    VSRAEV
Sbjct: 591 SSTNPVSEQSATNPPLGP--VSRAEV 614

Xenopus tropicalis (taxid: 8364)

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	466
297745325	564	unnamed protein product [Vitis vinifera]	0.937	0.774	0.539	1e-114
255541706	525	protein binding protein, putative [Ricin	0.877	0.779	0.535	1e-113
359489808	597	PREDICTED: uncharacterized protein LOC10	0.946	0.738	0.505	1e-112
356560327	586	PREDICTED: uncharacterized protein LOC10	0.935	0.744	0.489	1e-102
224130394	488	predicted protein [Populus trichocarpa]	0.607	0.579	0.659	2e-99
449495329	561	PREDICTED: uncharacterized protein LOC10	0.946	0.786	0.461	2e-99
357504405	668	Methylenetetrahydrofolate reductase, par	0.931	0.649	0.472	2e-94
147862101	537	hypothetical protein VITISV_015061 [Viti	0.864	0.750	0.503	5e-94
28200786	508	potyviral helper component protease-inte	0.935	0.858	0.444	2e-85
15234116	506	TRAF-interacting protein [Arabidopsis th	0.618	0.569	0.560	3e-79

>gi|297745325|emb|CBI40405.3| unnamed protein product [Vitis vinifera]

 Score =  419 bits (1076), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 246/456 (53%), Positives = 301/456 (66%), Gaps = 19/456 (4%)

Query: 7   FGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS 66
           F KTIC+ICYEDLKPIVEDLQ IS+CGHVFHELCLQQWFEYC++ KK +CPVCKQ CS +
Sbjct: 7   FAKTICTICYEDLKPIVEDLQSISVCGHVFHELCLQQWFEYCANKKKNSCPVCKQTCSLN 66

Query: 67  N-------SIGDQIDLVISQKPKDPEVEDPEVSRAEVKILEVKVSRLHTVLESQGKEIKE 119
                   SIGD  D  +SQKP + E EDP   R EVK LEVKV+ L +VLE   K++KE
Sbjct: 67  GVNRLYFQSIGDASDPTLSQKPLNIE-EDPGALRREVKRLEVKVAGLTSVLERNQKDLKE 125

Query: 120 INEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRNMDLAKE 179
           +NEELCLCKE+ KEEAALKNE L+QK  ++QLL SKSQ+LDK  LEC +L++RNM LAKE
Sbjct: 126 LNEELCLCKEQFKEEAALKNEILKQKAFIQQLLFSKSQDLDKSNLECSRLQERNMALAKE 185

Query: 180 LASLKLVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELMAKCNLLGRE 239
           LA+LKLVSDL+LDE+ VLK A  GN ANNKDTID+L++SLVIRNK+Y ELMAKCNLLGR 
Sbjct: 186 LAALKLVSDLSLDEEGVLKLASFGNEANNKDTIDILKRSLVIRNKSYKELMAKCNLLGRG 245

Query: 240 KARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVSKKASQKEEILKGATEDN 299
           +AR   KLEKAK KI KLKTRVQELETA+E+KDNEVLRAL  SKK   +E  L  + + N
Sbjct: 246 EARSVRKLEKAKGKIQKLKTRVQELETAIEVKDNEVLRALIASKKRIDEEANLN-SIKCN 304

Query: 300 SISLCTNNVSLEDQREQHSVPIYNLDWTSRVTNDFSFSTKSENFNAIKNIDANHTREGGS 359
             S   N+ S ED ++Q +VPI   D    + N    S  + N N+IK+    H      
Sbjct: 305 FSSSPINDFSPEDCKDQPAVPISKSDQIGNLNNGPLSSKTAGNSNSIKDTTM-HELPDPY 363

Query: 360 AKSHGKERNALQRED------TSRFSSVVFGLSNHNSIHQTIADVVQKPTPSRLGSAPTI 413
            K    +  A+Q          S  S         NSI  + +   +  T   +  AP  
Sbjct: 364 LKPKSTKAVAVQNSSILVPGAASAISRKPLAQGPGNSIGLSGS---RTSTEKDMYDAPVA 420

Query: 414 DIDEDVTLIVPDSAQVQPIVNIKKNPPSPVSLSKPG 449
             D+ V L+V D  Q+QP+  I+K  P P+  +KPG
Sbjct: 421 AEDKHVKLLVDDIEQLQPLPQIRKEAPFPIRFAKPG 456

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255541706|ref|XP_002511917.1| protein binding protein, putative [Ricinus communis] gi|223549097|gb|EEF50586.1| protein binding protein, putative [Ricinus communis]

 Score =  416 bits (1068), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 242/452 (53%), Positives = 305/452 (67%), Gaps = 43/452 (9%)

Query: 5   NKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS 64
           N F KTICSICY+DLKPIVEDLQ ISICGHVFHELCLQQWFEYCS+SKKC+CPVCKQ C+
Sbjct: 6   NSFAKTICSICYDDLKPIVEDLQAISICGHVFHELCLQQWFEYCSNSKKCSCPVCKQSCT 65

Query: 65  SSN-------SIGDQIDLVISQKPKDPEVEDPEVSRAEVKILEVKVSRLHTVLESQGKEI 117
            SN       S+GDQ + V+SQK  + + EDPE+ R EVK LEVKV+ L + LE Q KEI
Sbjct: 66  GSNVARLYFQSLGDQNESVLSQKVIECK-EDPELLRGEVKRLEVKVTGLTSNLERQDKEI 124

Query: 118 KEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRNMDLA 177
            ++NEEL L K ++K+E ALKN+ + QK +++QLL  KS+ELD V LECLKL+ RNM LA
Sbjct: 125 NQLNEELDLSKGQLKKEVALKNDVMGQKSAIQQLLLLKSEELDNVKLECLKLQDRNMALA 184

Query: 178 KELASLKLVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELMAKCNLLG 237
           KELA+LKLVSDLNL+EDE+LKFA  GN A+N DTIDVLRKSLV+RNK+Y ELM+KCN LG
Sbjct: 185 KELAALKLVSDLNLEEDEILKFASFGNEASNTDTIDVLRKSLVVRNKSYKELMSKCNQLG 244

Query: 238 REKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVSKKASQKEEILKGATE 297
           R +AR+ +KLEKAKEKI+KLKTR+QELE  VE+KDNE L+ALK SKK   KE  L GA  
Sbjct: 245 RGEARYCKKLEKAKEKISKLKTRIQELEMTVEVKDNEALKALKASKKVHCKEVTLNGAN- 303

Query: 298 DNSISLCTNNVSLEDQREQHSVPIYNLDWTSRVTNDFSFSTKSENFNAIKNIDANHTREG 357
           DNS +L ++  + E+++E+H       D T       +F++   N N I  I A+  +E 
Sbjct: 304 DNSSALLSSLFASENKKEKHFKSASISDQTG------NFNSDQGNLNIISGILADSIKEC 357

Query: 358 GSAKSHGKERNALQREDTSRFSSVVFGLSNHNSIHQTIADVVQKPTPSRLGSAPTIDIDE 417
            S  +  KE           ++    G    N                 + +A T    E
Sbjct: 358 ASIMALNKEIGG------KLYTRPCTGTDKGN-----------------MSAAST----E 390

Query: 418 DVTLIVPDSAQVQPIVNIKKNPPSPVSLSKPG 449
           D  ++V D   V+P++NI+K  PS VS+SKPG
Sbjct: 391 DEVMLVNDVRYVRPMLNIRKESPS-VSVSKPG 421

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359489808|ref|XP_002275425.2| PREDICTED: uncharacterized protein LOC100265462 [Vitis vinifera]

 Score =  413 bits (1061), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 245/485 (50%), Positives = 311/485 (64%), Gaps = 44/485 (9%)

Query: 7   FGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS 66
           F KTIC+ICYEDLKPIVEDLQ IS+CGHVFHELCLQQWFEYC++ KK +CPVCKQ CS +
Sbjct: 7   FAKTICTICYEDLKPIVEDLQSISVCGHVFHELCLQQWFEYCANKKKNSCPVCKQTCSLN 66

Query: 67  N-------SIGDQIDLVISQKPKDPEVEDPEVSRAEVKILEVKVSRLHTVLESQGKEIKE 119
                   SIGD  D  +SQKP + E EDP   R EVK LEVKV+ L +VLE   K++KE
Sbjct: 67  GVNRLYFQSIGDASDPTLSQKPLNIE-EDPGALRREVKRLEVKVAGLTSVLERNQKDLKE 125

Query: 120 INEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRNMDLAKE 179
           +NEELCLCKE+ KEEAALKNE L+QK  ++QLL SKSQ+LDK  LEC +L++RNM LAKE
Sbjct: 126 LNEELCLCKEQFKEEAALKNEILKQKAFIQQLLFSKSQDLDKSNLECSRLQERNMALAKE 185

Query: 180 LASLKLVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELMAKCNLLGRE 239
           LA+LKLVSDL+LDE+ VLK A  GN ANNKDTID+L++SLVIRNK+Y ELMAKCNLLGR 
Sbjct: 186 LAALKLVSDLSLDEEGVLKLASFGNEANNKDTIDILKRSLVIRNKSYKELMAKCNLLGRG 245

Query: 240 KARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVSKKASQKEEILKGATEDN 299
           +AR   KLEKAK KI KLKTRVQELETA+E+KDNEVLRAL  SKK   +E  L  + + N
Sbjct: 246 EARSVRKLEKAKGKIQKLKTRVQELETAIEVKDNEVLRALIASKKRIDEEANLN-SIKCN 304

Query: 300 SISLCTNNVSLEDQREQHSVPIYNLDWTSRVTNDFSFSTKSENFNAIKNIDANHTREGGS 359
             S   N+ S ED ++Q +VPI   D    + N    S  + N N+IK+   ++++   +
Sbjct: 305 FSSSPINDFSPEDCKDQPAVPISKSDQIGNLNNGPLSSKTAGNSNSIKDTSVDYSKSNVN 364

Query: 360 AKSHGKERNA--LQREDTSRFSSVVFGLSN-------------HNS---IHQTIADVVQK 401
             +  ++ +   L   D    S+ +  L +              NS   +    + + +K
Sbjct: 365 VVALDQDIDPCLLIDRDVLEISAAMHELPDPYLKPKSTKAVAVQNSSILVPGAASAISRK 424

Query: 402 PTPSRLGS-----------------APTIDIDEDVTLIVPDSAQVQPIVNIKKNPPSPVS 444
           P     G+                 AP    D+ V L+V D  Q+QP+  I+K  P P+ 
Sbjct: 425 PLAQGPGNSIGLSGSRTSTEKDMYDAPVAAEDKHVKLLVDDIEQLQPLPQIRKEAPFPIR 484

Query: 445 LSKPG 449
            +KPG
Sbjct: 485 FAKPG 489

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356560327|ref|XP_003548444.1| PREDICTED: uncharacterized protein LOC100812811 [Glycine max]

 Score =  379 bits (973), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 237/484 (48%), Positives = 302/484 (62%), Gaps = 48/484 (9%)

Query: 7   FGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS 66
           F   ICSICYE L PI EDLQ +SICGHVFHELCLQQWFEY S  KK TCP+CKQ C +S
Sbjct: 8   FAGIICSICYEPLNPINEDLQSVSICGHVFHELCLQQWFEYSSKGKKHTCPICKQGCRAS 67

Query: 67  N-------SIGDQIDLVISQKPKDPEVEDPEVSRAEVKILEVKVSRLHTVLESQGKEIKE 119
           +       S+GD  + V   K  + E ED  V R EVK LEVKVS L++ +E Q KE++ 
Sbjct: 68  DACRLYFQSVGDANNSVKPSKCFELE-EDAGVLRREVKRLEVKVSGLNSQVEGQTKELEG 126

Query: 120 INEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRNMDLAKE 179
           +NEELC CKE+ K E ALKNEAL QK S++  L  KS+EL+K TLEC +LK+RNM LAKE
Sbjct: 127 LNEELCTCKEQAKIETALKNEALNQKASIQFQLQMKSEELEKSTLECFRLKERNMALAKE 186

Query: 180 LASLKLVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELMAKCNLLGRE 239
           LA+LKLVSDL++DE+EVLK A LGNGAN+KDTID L++SLV+RN++Y ELMAKCN+LGR 
Sbjct: 187 LAALKLVSDLDIDEEEVLKLATLGNGANSKDTIDTLKRSLVMRNRSYKELMAKCNILGRG 246

Query: 240 KARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVSKKASQKEEILKGATEDN 299
           +AR+S+KLEKAKEKI KLK RVQELET  E K+N+ LR+LK+SK     + + +    D+
Sbjct: 247 EARYSKKLEKAKEKITKLKERVQELETLAESKENKYLRSLKLSKITKSSKNLEENIKSDS 306

Query: 300 SISLCTNNVSLEDQREQHSVPIYNLDWTSRVTNDFSF-STKSENFNAIKNIDANHTREGG 358
            + L     S ++Q +Q S+P   +D T+   N  SF S K EN N  KN   N +    
Sbjct: 307 EV-LTACKFSSKEQSKQISIPKSGIDLTAN-NNSKSFQSFKIENSNVTKNKTVNISNGSR 364

Query: 359 SAKSHGKERNALQREDT-SRFSSVVFGLSNHNSIHQTIADVV-QKPTPSR---------- 406
           S  S   +R  +  +D  S  ++ + G S HN   Q   D+   KP+  +          
Sbjct: 365 STFSLDIKREYISIDDNDSEGTNALQGCSKHNYKDQDWDDIAFSKPSLVKLEPVSGIKAE 424

Query: 407 --------LGSAPTIDI------------DEDVTLIVPDSAQV-QPIVNIKKNPPSPVSL 445
                   L  +P +DI            DEDVTL     A + QP+VNI+K  P  +S 
Sbjct: 425 TSLQGKCTLAESPRVDIDIDMANISASAMDEDVTL----QANIKQPMVNIRKESPLTLSN 480

Query: 446 SKPG 449
           S PG
Sbjct: 481 SAPG 484

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224130394|ref|XP_002320826.1| predicted protein [Populus trichocarpa] gi|222861599|gb|EEE99141.1| predicted protein [Populus trichocarpa]

 Score =  369 bits (947), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 192/291 (65%), Positives = 230/291 (79%), Gaps = 8/291 (2%)

Query: 5   NKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS 64
           N F KTICSICYEDLKPIVEDLQ ISICGHVFHELCLQQWFEYCS+ KK +CPVCKQ CS
Sbjct: 7   NSFAKTICSICYEDLKPIVEDLQSISICGHVFHELCLQQWFEYCSNEKKRSCPVCKQNCS 66

Query: 65  SSN-------SIGDQIDLVISQKPKDPEVEDPEVSRAEVKILEVKVSRLHTVLESQGKEI 117
           + N       S+GDQ +    +K  + E EDP++ R EVK LE K+S L+T+LESQ KE+
Sbjct: 67  AQNAGRLYFQSVGDQTEPFGDRKAGECE-EDPKLLRGEVKRLEGKLSGLNTILESQVKEM 125

Query: 118 KEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRNMDLA 177
           K +NEEL LCK+ +K+E  L+  A+ QK S++ LL SKS+ELD + LE ++L+ RNM LA
Sbjct: 126 KHLNEELYLCKDELKKEVKLRTHAMEQKASIQHLLRSKSEELDALKLERIRLQDRNMALA 185

Query: 178 KELASLKLVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELMAKCNLLG 237
           KEL +LKLVSD+NL+EDEVLK A  GN ANNKDT+D+LRKSLVIRNK Y ELMAKCN LG
Sbjct: 186 KELVALKLVSDVNLEEDEVLKLASFGNEANNKDTVDILRKSLVIRNKTYKELMAKCNQLG 245

Query: 238 REKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVSKKASQK 288
           + +AR  ++LEKAKEKINKLKTRV+ELE  VE+KDNE LRALK SKKA+ K
Sbjct: 246 QGEARSCKRLEKAKEKINKLKTRVKELEMVVEVKDNESLRALKASKKANCK 296

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449495329|ref|XP_004159801.1| PREDICTED: uncharacterized protein LOC101225984 [Cucumis sativus]

 Score =  369 bits (946), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 224/485 (46%), Positives = 309/485 (63%), Gaps = 44/485 (9%)

Query: 7   FGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKK-CTCPVCKQRCSS 65
           F KTICSICYEDLKPI+EDLQ ISICGHVFHELCLQQWFEYCS+ KK  +CPVCKQ C  
Sbjct: 7   FAKTICSICYEDLKPIIEDLQSISICGHVFHELCLQQWFEYCSNGKKKYSCPVCKQTCVG 66

Query: 66  SN-------SIGDQIDLVISQKPKDPEVEDPEVSRAEVKILEVKVSRLHTVLESQGKEIK 118
            +       S+GD  D ++++KP D   +DPE+ R+EVK LE++VS L++ LE+QGK+IK
Sbjct: 67  KDVARLYFQSVGDANDSMLAKKPADWIEKDPELLRSEVKRLEMRVSVLNSTLETQGKDIK 126

Query: 119 EINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRNMDLAK 178
           E++EEL LC++ +K+E  L+N+A++QK S+ QLLH KS+EL+  T+EC +L +R+M LAK
Sbjct: 127 ELHEELQLCQDELKKEVGLRNDAMKQKTSMSQLLHLKSEELENTTVECKRLHERSMALAK 186

Query: 179 ELASLKLVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELMAKCNLLGR 238
           ELA+ KL+S+++LDE+EVLK + LG+GA+NKDTID+LRKSLV+RN++Y ELMAKCNLLGR
Sbjct: 187 ELAAFKLISEVDLDEEEVLKLSSLGSGADNKDTIDILRKSLVLRNRSYKELMAKCNLLGR 246

Query: 239 EKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVSKKASQKEEILKGATED 298
            +AR  +KLEKA EKINKLK RVQELE A+E KDNEVLR LK +KK   +  +     + 
Sbjct: 247 GEARSCKKLEKANEKINKLKVRVQELEKAIEEKDNEVLRGLKDAKKLGVQGSV---CCKC 303

Query: 299 NSISLCTNNVSLEDQREQHSVPIYNLDWTSRVTN--DFSFSTKSENFNAIKNIDANHTRE 356
           N +S    + +  D  +  +  I N   +SR     DF   T++ +   + +I  N    
Sbjct: 304 NMVSAKNKSAAATDTLDSTASQI-NEPLSSRKKKIYDFPSDTRTSHLTTV-DIAENTC-- 359

Query: 357 GGSAKSHGKERNALQREDTSRFSSVVFGLSNHNSIHQ--TIADVVQK-----------PT 403
             S      E + ++    S   S +    N  S H   T  ++V+K           P 
Sbjct: 360 -SSMNKKTSECSQVENAKDSTMESQISEEGNRVSYHPQLTSCNLVRKKASERTTNSVNPM 418

Query: 404 PSRLGS---APTIDIDEDVTLIVPDSAQVQPI-VNIKKNPPSPVSLSKPGIFLLVQFQFS 459
           PS   S      +  D  + L+V DSA+ + + +NI++   S +SL+K G          
Sbjct: 419 PSTTVSNIVRTAVPGDACMPLLVEDSAEPEAVLINIRRESSSHISLNKLG---------G 469

Query: 460 LSFRG 464
           +SF G
Sbjct: 470 MSFSG 474

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357504405|ref|XP_003622491.1| Methylenetetrahydrofolate reductase, partial [Medicago truncatula] gi|355497506|gb|AES78709.1| Methylenetetrahydrofolate reductase, partial [Medicago truncatula]

 Score =  352 bits (904), Expect = 2e-94,   Method: Compositional matrix adjust.
 Identities = 214/453 (47%), Positives = 277/453 (61%), Gaps = 19/453 (4%)

Query: 4   ENKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRC 63
           + +F  TICSICYE L P+ EDLQ +SICGHVFHELCLQQWFEYC + KK TCP+CKQ C
Sbjct: 4   DGEFSGTICSICYEPLNPVNEDLQCVSICGHVFHELCLQQWFEYCKTPKKHTCPICKQGC 63

Query: 64  SSSN-------SIGDQIDLVISQKPKDPEVEDPEVSRAEVKILEVKVSRLHTVLESQGKE 116
            + +       SIGD  + V++QK    E ED  V R EVK LE KVS L TVLE Q KE
Sbjct: 64  KAKDACRLYFQSIGDVKEGVVTQKNVGLE-EDSGVLRKEVKRLEGKVSGLSTVLEKQTKE 122

Query: 117 IKEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRNMDL 176
           + E+ +ELC CKE+ K E A K EAL+QK S++  LH KS+EL+K  L+  KL++RNM L
Sbjct: 123 LDELKDELCTCKEQKKIEIASKIEALKQKTSLQFQLHVKSEELEKSNLDRFKLQERNMAL 182

Query: 177 AKELASLKLVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELMAKCNLL 236
           AKELA+LKLVSDL++ EDEVLK A LGNG N+K+T+D L +SLV+RN++Y ELM KCNLL
Sbjct: 183 AKELAALKLVSDLDIGEDEVLKLATLGNGTNSKETVDTLTRSLVLRNRSYKELMTKCNLL 242

Query: 237 GREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVSKKASQKEEILKGAT 296
           GR +AR+S+KLEKA EKI KLK R+QELET +E+K+NE L+ LKV+K    K        
Sbjct: 243 GRGEARYSKKLEKANEKIIKLKARLQELETTMEVKENEYLKHLKVAKNIENK-------I 295

Query: 297 EDNSISLCTNNVSLEDQREQHSVPIYNLDWTSRVTNDFSFSTKSENFNAIKNIDAN-HTR 355
             NS  L  N  S ++Q +Q + P   +D      N    S K EN    KN D N   R
Sbjct: 296 NSNSDVLMANTFSSKEQNKQSTTPKSGMDLNKNDNNKSLQSLKIENSKTAKNKDVNISNR 355

Query: 356 EGGSAKSHGKERNALQREDTSRFSSVVFGLSNHNSIHQ--TIADVVQKPTPSRLGSAPTI 413
              +          +  E+  +      G     S+     +A+  +    + + +    
Sbjct: 356 RKTTLSLDEDIDCIIIDEEEYKEPEAASGTKTKTSLQGICNLAESSRFDIDTEMAAITAG 415

Query: 414 DIDEDVTLIVPDSAQVQPIVNIKKNPPSPVSLS 446
             +EDVTL   ++ Q QP+VNI+K  P   S S
Sbjct: 416 TTNEDVTL-QANAKQAQPMVNIRKESPLTTSSS 447

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147862101|emb|CAN80879.1| hypothetical protein VITISV_015061 [Vitis vinifera]

 Score =  351 bits (900), Expect = 5e-94,   Method: Compositional matrix adjust.
 Identities = 214/425 (50%), Positives = 272/425 (64%), Gaps = 22/425 (5%)

Query: 34  HVFHELCLQQ--WFEYCSSSKKCTCPVCKQRCSSSN-------SIGDQIDLVISQKPKDP 84
           H+    CL +  WFEYC++ KK +CPVCKQ CS +        SIGD  D   SQKP + 
Sbjct: 18  HLRLRPCLPRTLWFEYCANKKKNSCPVCKQTCSLNGVNRLYFQSIGDASDPTXSQKPLNI 77

Query: 85  EVEDPEVSRAEVKILEVKVSRLHTVLESQGKEIKEINEELCLCKERIKEEAALKNEALRQ 144
           E EDP   R EVK LEVKV+ L +VLE   K++KE+NEELCLCKE+ KEEAALKNE L+Q
Sbjct: 78  E-EDPGALRREVKRLEVKVAGLTSVLERNQKDLKELNEELCLCKEQFKEEAALKNEXLKQ 136

Query: 145 KVSVEQLLHSKSQELDKVTLECLKLKQRNMDLAKELASLKLVSDLNLDEDEVLKFALLGN 204
           K  ++QLL SKSQ+LDK  LEC +L++RNM LAKELA+LKLVSDL+LDE+ VLK A  GN
Sbjct: 137 KAFIQQLLFSKSQDLDKSNLECSRLQERNMALAKELAALKLVSDLSLDEEGVLKLASFGN 196

Query: 205 GANNKDTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQEL 264
            ANNKDTID+L++SLVIRNK+Y ELMAKCNLLGR +AR   KLEKAK KI KLKTRVQEL
Sbjct: 197 EANNKDTIDILKRSLVIRNKSYKELMAKCNLLGRGEARSVRKLEKAKGKIQKLKTRVQEL 256

Query: 265 ETAVELKDNEVLRALKVSKKASQKEEILKGATEDNSISLCTNNVSLEDQREQHSVPIYNL 324
           ETA+E+KDNEVLRAL  SKK   +E  L  + + N  S   N+ S ED  +Q +VPI   
Sbjct: 257 ETAIEVKDNEVLRALIASKKRIDEEANLN-SIKCNFSSSPINDFSPEDCMDQPAVPISKS 315

Query: 325 DWTSRVTNDFSFSTKSENFNAIKNIDANHTREGGSAKSHGKERNALQREDTSRFSSVVFG 384
           D    + N    S  + N N+IK+   ++++   S+       +A+ R+  ++      G
Sbjct: 316 DQIGNLNNGPLSSKTAGNSNSIKDTSVDYSKSNNSSILVPGAASAISRKPLAQGPGNSIG 375

Query: 385 LSNHNSIHQTIADVVQKPTPSRLGSAPTIDIDEDVTLIVPDSAQVQPIVNIKKNPPSPVS 444
           LS   +   T  D            AP    D+ V L+V D  Q+QP+  I+K  P P+ 
Sbjct: 376 LSGSRT--STXKDXYD---------APVAAEDKHVKLLVDDIEQLQPLPQIRKEAPFPIR 424

Query: 445 LSKPG 449
            +KPG
Sbjct: 425 FAKPG 429

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|28200786|emb|CAD45374.1| potyviral helper component protease-interacting protein 1 [Solanum tuberosum subsp. andigenum]

 Score =  322 bits (826), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 217/488 (44%), Positives = 284/488 (58%), Gaps = 52/488 (10%)

Query: 5   NKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS 64
           N FGKTICSICYEDL PI+EDLQ ++ICGHVFHELCLQQWFEYC+  KK  CPVCKQ CS
Sbjct: 5   NSFGKTICSICYEDLNPIIEDLQAVTICGHVFHELCLQQWFEYCAKGKKKNCPVCKQACS 64

Query: 65  SSN-------SIGDQIDLVISQKPKDPEVEDPEVSRAEVKILEVKVSRLHTVLESQGKEI 117
             N       SIGD     ++QKP D + ED    + EVK LE KV  L + LE Q K++
Sbjct: 65  EENANRLYFQSIGDPNFTSLTQKPPDYK-EDHRELKNEVKRLERKVVGLTSTLEKQLKDL 123

Query: 118 KEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRNMDLA 177
           K++N EL  CKE +K E  LK EA++Q+ +++QLLH KS+ELD+ TLEC++L+ RNM LA
Sbjct: 124 KDVNAELFTCKEELKMEMTLKIEAVKQEAAIQQLLHLKSKELDQSTLECIRLQDRNMALA 183

Query: 178 KELASLKLVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELMAKCNLLG 237
           KELA+LKLV D NL+E+EVLK A L +  N+K+TIDVL+KSLVIRNKNY ELM KCN L 
Sbjct: 184 KELATLKLVCDFNLEEEEVLKRASLRDDVNSKETIDVLKKSLVIRNKNYEELMTKCNTLD 243

Query: 238 REKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVSKKASQKEEILK---- 293
           R + R+  KL+K KEK NKLK RVQELE A+E KDNE+LR LK SKK  Q  +  K    
Sbjct: 244 RREVRYLRKLQKTKEKKNKLKARVQELEMALEGKDNEILRILKASKKNYQGSKEPKVDRC 303

Query: 294 ------GATEDNSISLCTNNVSLEDQREQHSVPIYNLDWTSRVTNDFSFSTKSENFNAIK 347
                  A  +  + +C    S +D     S P     + S+   D S    +E+  A  
Sbjct: 304 SYENQNKAPAETEVDVCIVTGSCDDL----SRPKRKRKYKSK---DKSIPNMAEDIIAST 356

Query: 348 NIDANHTRE-------GGSAKS-----HGKERNALQREDTSRFSSVVFGLSNHNSIHQTI 395
               NH +E       GG+ ++      G  +N  Q  D  +     F LS   ++    
Sbjct: 357 LHKNNHEKESSKRNKDGGTPETSSYVHEGSYQNLHQPFDHKKAVHDSF-LSRPEAVFGAT 415

Query: 396 ADVVQKPTPSRLGSAPTIDIDEDVTLIVP--------------DSAQVQPIVNIKKNPPS 441
              +   + ++ G + + +  ++    +P              D  Q QP  +I+K   S
Sbjct: 416 GGSLGHGSGNKDGMSASRNCSKNSKENMPPVIILDDDDLPPLDDITQHQPAFHIRKETSS 475

Query: 442 PVSLSKPG 449
           PV L+KPG
Sbjct: 476 PVVLAKPG 483

Source: Solanum tuberosum subsp. andigenum

Species: Solanum tuberosum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15234116|ref|NP_192036.1| TRAF-interacting protein [Arabidopsis thaliana] gi|7267624|emb|CAB80936.1| putative RING zinc finger protein [Arabidopsis thaliana] gi|332656602|gb|AEE82002.1| TRAF-interacting protein [Arabidopsis thaliana]

 Score =  302 bits (773), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 166/296 (56%), Positives = 210/296 (70%), Gaps = 8/296 (2%)

Query: 1   MGIENKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCK 60
           M  EN  G  ICSICYEDLKP+VE+LQ IS CGHVFHELCLQQWFEYC S+ K  CP+CK
Sbjct: 1   MAEENAAGNAICSICYEDLKPVVENLQSISACGHVFHELCLQQWFEYCPSTNKRNCPICK 60

Query: 61  QRCSSSN-------SIGDQIDLVISQKPKDPEVEDPEVSRAEVKILEVKVSRLHTVLESQ 113
           Q+CS  +       S G+Q D + S K    E EDP + R EVK LE KV  L + LE++
Sbjct: 61  QKCSLKDPCRLYFQSSGNQTDSIASDKVVGIE-EDPVLLRGEVKRLEGKVQNLTSALEAK 119

Query: 114 GKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRN 173
            KE  E++++L  C E++KE+   + EAL++  + + LL  KS+E  ++  +C+KL++R 
Sbjct: 120 KKENVEVSDKLHQCNEQLKEDKVKRWEALQEISTTQHLLKLKSEECIQLNSQCVKLQERT 179

Query: 174 MDLAKELASLKLVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELMAKC 233
           + LAKELASLKLVSDL+L+ED+VLK ALLGN A  KDTID L KSLVIRN++Y EL+AKC
Sbjct: 180 VALAKELASLKLVSDLSLEEDDVLKLALLGNNAKTKDTIDTLVKSLVIRNRSYKELLAKC 239

Query: 234 NLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVSKKASQKE 289
           N LGR +AR SEKLEKA EKI KLK R++ELE   E ++N  LR + VSKK S  E
Sbjct: 240 NQLGRGEARSSEKLEKALEKIEKLKKRMRELELITEERENRALRDINVSKKCSYTE 295

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

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	466
TAIR|locus:2125088	506	AT4G01270 [Arabidopsis thalian	0.815	0.750	0.463	2.8e-82
TAIR|locus:504955487	118	AT4G01245 "AT4G01245" [Arabido	0.143	0.567	0.565	2.9e-12
ZFIN|ZDB-GENE-040801-30	453	traip "TRAF-interacting protei	0.572	0.589	0.257	1.8e-10
WB|WBGene00015194	451	B0432.13 [Caenorhabditis elega	0.658	0.680	0.225	1e-08
UNIPROTKB|E7EN91	266	TRAIP "TRAF-interacting protei	0.515	0.902	0.279	2.5e-08
UNIPROTKB|F1PCW0	2240	GOLGA4 "Uncharacterized protei	0.603	0.125	0.246	5.3e-07
TAIR|locus:2162996	983	AT5G41140 "AT5G41140" [Arabido	0.585	0.277	0.275	7.1e-07
ZFIN|ZDB-GENE-091204-454	155	si:ch1073-392o20.1 "si:ch1073-	0.139	0.419	0.337	2e-06
UNIPROTKB|E2R604	467	TRAIP "Uncharacterized protein	0.517	0.516	0.25	2.4e-06
UNIPROTKB|Q9H9V4	155	RNF122 "RING finger protein 12	0.139	0.419	0.315	3.3e-06

TAIR|locus:2125088 AT4G01270 [Arabidopsis thaliana (taxid:3702)]

 Score = 803 (287.7 bits), Expect = 2.8e-82, Sum P(2) = 2.8e-82
 Identities = 184/397 (46%), Positives = 252/397 (63%)

Query:     1 MGIENKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCK 60
             M  EN  G  ICSICYEDLKP+VE+LQ IS CGHVFHELCLQQWFEYC S+ K  CP+CK
Sbjct:     1 MAEENAAGNAICSICYEDLKPVVENLQSISACGHVFHELCLQQWFEYCPSTNKRNCPICK 60

Query:    61 QRCSSSN-------SIGDQIDLVISQKPKDPEVEDPEVSRAEVKILEVKVSRLHTVLESQ 113
             Q+CS  +       S G+Q D + S K    E EDP + R EVK LE KV  L + LE++
Sbjct:    61 QKCSLKDPCRLYFQSSGNQTDSIASDKVVGIE-EDPVLLRGEVKRLEGKVQNLTSALEAK 119

Query:   114 GKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRN 173
              KE  E++++L  C E++KE+   + EAL++  + + LL  KS+E  ++  +C+KL++R 
Sbjct:   120 KKENVEVSDKLHQCNEQLKEDKVKRWEALQEISTTQHLLKLKSEECIQLNSQCVKLQERT 179

Query:   174 MDLAKELASLKLVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELMAKC 233
             + LAKELASLKLVSDL+L+ED+VLK ALLGN A  KDTID L KSLVIRN++Y EL+AKC
Sbjct:   180 VALAKELASLKLVSDLSLEEDDVLKLALLGNNAKTKDTIDTLVKSLVIRNRSYKELLAKC 239

Query:   234 NLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVSKKASQKEEILK 293
             N LGR +AR SEKLEKA EKI KLK R++ELE   E ++N  LR + VSKK S  E + +
Sbjct:   240 NQLGRGEARSSEKLEKALEKIEKLKKRMRELELITEERENRALRDINVSKKCSYTE-VSE 298

Query:   294 GATEDNSISLCTNNVSLEDQREQHSVPIYNLDWTSRVTNDFS-FSTKSENF----NAIKN 348
              A E  S S     +S +++ E+ S P   L+     T   S    + ++F    +++ +
Sbjct:   299 PAIESMS-SF--RMLSSDNKVEKISTPPGKLEEKDGFTIQGSCLRGREDSFVSRTDSVID 355

Query:   349 IDANHTREGGSAKSHGKERNALQREDTSRFSSVVFGL 385
             +D ++  E  ++       N  ++ D S    + F +
Sbjct:   356 VDDDYVPETNTSGIRDWNTNIEEKGDNSMVKDIKFNI 392

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA;ISS

TAIR|locus:504955487 AT4G01245 "AT4G01245" [Arabidopsis thaliana (taxid:3702)]

 Score = 172 (65.6 bits), Expect = 2.9e-12, P = 2.9e-12
 Identities = 39/69 (56%), Positives = 48/69 (69%)

Query:   225 NYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVSKK 284
             +Y EL+AKCN LGR +A+ SEKLEKA EKI KLK R++ELE   E  +N  +R + VSKK
Sbjct:    34 SYKELLAKCNQLGRGEAQSSEKLEKALEKIEKLKKRMRELELITE--ENRAIRDINVSKK 91

Query:   285 ASQKEEILK 293
              S  E  LK
Sbjct:    92 CSYTEVSLK 100

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

ZFIN|ZDB-GENE-040801-30 traip "TRAF-interacting protein" [Danio rerio (taxid:7955)]

 Score = 177 (67.4 bits), Expect = 1.8e-10, P = 1.8e-10
 Identities = 79/307 (25%), Positives = 137/307 (44%)

Query:     9 KTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNS 68
             +  C+IC  D     +D+  I  CGH FH  CL QWF+  S+  K TCP C+++ S+ + 
Sbjct:     4 RAYCTIC-SDFFDNSKDVAAIH-CGHTFHYSCLLQWFQ--SAPNK-TCPQCRKQVSTRHI 58

Query:    69 IGDQI-DLVISQK--PKDPEVEDPEVSRAEVKILEVK---------VSRLHTVLESQGKE 116
             I     D+       P DPE    E+ R +  + E +         V  L   +E Q K+
Sbjct:    59 INKLFFDIAPEDDGAPVDPESLQNELDRMKAVLSEKEKEWREKQKTVDTLKDTIEKQKKD 118

Query:   117 I----KEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQR 172
             +    KEI ++  LC    K+   L+++    + + E+   +K   +   T E L +  +
Sbjct:   119 LDKVRKEIGDKEMLCSVLRKQMNFLESQKNEGQAAKEE---AKRLRVKMKTYESLDVVLQ 175

Query:   173 NMDLAKELASLKLVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELMAK 232
                   E+ ++  ++D+ + +  V + ++     + K   D L+ SL    K+  E+   
Sbjct:   176 GQ--RSEVEAM--ITDMGVGQSAVEQLSIYC--ISLKKEYDNLKGSL----KSSNEM--- 222

Query:   233 CNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVSKKASQKEEIL 292
             C  L RE    + KL+KA  + N+ K  ++ L+  +   D E+  +LK  KK    +  L
Sbjct:   223 CEKLKREMISSNSKLQKATSETNRTKEDMKALQKDLSSADKEIT-SLK--KKVEILQRTL 279

Query:   293 KGATEDN 299
                T  N
Sbjct:   280 STPTRTN 286

GO:0008270 "zinc ion binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

WB|WBGene00015194 B0432.13 [Caenorhabditis elegans (taxid:6239)]

 Score = 161 (61.7 bits), Expect = 1.0e-08, P = 1.0e-08
 Identities = 78/346 (22%), Positives = 154/346 (44%)

Query:    12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSIGD 71
             CSIC+EDLK   + +  I +CGH++H  C+ QW      + K  CP C++    +  +  
Sbjct:    13 CSICFEDLKQN-DKISAI-VCGHIYHHGCISQWI-----ATKRQCPSCRRTVPKNGFVEK 65

Query:    72 ---QIDLVISQKPKDPEVEDPEVS---RAEVKILEVKVSRLHTVLESQGKEIKEINEELC 125
                 +  +  +  K PE++  E        +K+ + K+  L+T  ++    +K + +++ 
Sbjct:    66 LFFDVQRMGGEAEKPPEIDYREEHYKLSTSLKVEQEKLGTLNTENKNLKDTVKSLEKKII 125

Query:   126 LCKERIKEEAALKNEALRQ-KVSVEQLLHSKSQELDKV-----TLECLK-LKQRNMDLAK 178
               K++ ++E       +    +S E+  + K +EL +      T E  K L   + +  K
Sbjct:   126 REKDKYRQEIPKLQATINHLTISSEETAYLK-RELQESKNRLKTCEFYKILTVHSSEADK 184

Query:   179 ELASLKLVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELMAKCNLLGR 238
             +L    L  + NLD ++   F L+ +   NKD  D  R++     K   +L  +   L R
Sbjct:   185 QLGEY-LKKNGNLDTEKF--FQLMKS--TNKDLTDKRREAA----KEIEQLKMEVQSLKR 235

Query:   239 EKARFSEKLEKA-KEKINKLKTRVQELETAVELKDNEVLR-ALKVSKKASQKEEILKGAT 296
               A+    ++K  K+ +  L+ R   ++T +   +N+ LR  L+       K + + G  
Sbjct:   236 A-AQEDAAIKKTLKKTVLDLRERAN-VDTPI---NNKRLRDVLETETPPPAKRKSM-GFD 289

Query:   297 EDNSISLCTNNVSLEDQREQHSVPIYNLDWTSRVTNDFSFSTKSEN 342
             E + +      +S   Q E  + P+ ++  TS+    F+F    ++
Sbjct:   290 ESSQMIDPDGELSFFKQNENRT-PVTSVPSTSKAVLPFNFDDDEDD 334

GO:0008270 "zinc ion binding" evidence=IEA

GO:0040018 "positive regulation of multicellular organism growth" evidence=IMP

UNIPROTKB|E7EN91 TRAIP "TRAF-interacting protein" [Homo sapiens (taxid:9606)]

 Score = 152 (58.6 bits), Expect = 2.5e-08, P = 2.5e-08
 Identities = 79/283 (27%), Positives = 134/283 (47%)

Query:     9 KTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCK----QRCS 64
             + +C+IC  D      D+  I  CGH FH  CL QWFE   S    TCP C+    +   
Sbjct:     4 RALCTIC-SDFFDHSRDVAAIH-CGHTFHLQCLIQWFETAPSR---TCPQCRIQEEENVL 58

Query:    65 SSNSIGDQIDLVISQ-KPKDPEVEDPEVSRAEVK-ILEVKVSRLHTVLESQGK-EI--KE 119
              +  + +++D V +Q   KD E  D +V    ++  LE + + + ++ ++ GK E+    
Sbjct:    59 DAEFLKNELDNVRAQLSQKDKEKRDSQVIIDTLRDTLEERNATVVSLQQALGKAEMLCST 118

Query:   120 INEELCLCKERIKEEAALKNEA--LRQKVS----VEQLLHSKSQELDKVTLECLKLKQRN 173
             + +++   +++  E    + EA  LR K+     +E LL S+  E++++  + + + Q  
Sbjct:   119 LKKQMKYLEQQQDETKQAQEEARRLRSKMKTMEQIELLLQSQRPEVEEMIRD-MGVGQSA 177

Query:   174 MD-LAKELASLKLVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVI-RNKN---YTE 228
             ++ LA    SLK        E E LK A   +G    +  D LRK L   R+K    Y+E
Sbjct:   178 VEQLAVYCVSLK-------KEYENLKEARKASG----EVADKLRKDLFSSRSKLQTVYSE 226

Query:   229 L-MAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVEL 270
             L  AK  L   +K      L+ A ++I  LK ++  L+  + L
Sbjct:   227 LDQAKLELKSAQK-----DLQSADKEIMSLKKKLTMLQETLNL 264

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

UNIPROTKB|F1PCW0 GOLGA4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 154 (59.3 bits), Expect = 5.3e-07, P = 5.3e-07
 Identities = 75/304 (24%), Positives = 140/304 (46%)

Query:   111 ESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVS-VEQLLHSKSQELDKVTLECLKL 169
             E+Q K +K   E L + KE +++E   + +A  +K S + QL    S+ ++ VTL   +L
Sbjct:  1321 ENQIKSMKADIEGLVMEKEALQKEGGNQQQAASEKESCITQLKKELSENINVVTLMKEEL 1380

Query:   170 KQRNMD---LAKELASL--KLVSDLNLDEDEVLKFALLGNGANNKDTI--DVLRKSLVIR 222
             K++  +   L+K+L  L  +L + ++L E E    +L       +  +   V   SL + 
Sbjct:  1381 KEKKSEISSLSKQLTDLNTQLQNSISLTEKEAAISSLSKRYDEQQQELLGQVQDLSLKVE 1440

Query:   223 --NKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRA-- 278
               NK  T  + + + L     +FSE  +KA+ K  + ++ ++EL+  +ELK  E      
Sbjct:  1441 TLNKEKTSALEQVDHLSN---KFSEWKKKAQSKFLQYQSTIKELQMQLELKTKEASEKDE 1497

Query:   279 -LKVSKKA--SQKEEI--LKGATEDNSISLCTNNVSLEDQREQHSVPIYNLD--WTSRVT 331
              +++ K+    Q E +  LKG  ED    L     +LE + +  +  I  L+   T + T
Sbjct:  1498 QIQLLKEDLDQQNERLVCLKGEMEDKKSKLEKKECNLETELKTQTARIAELEEHLTQKTT 1557

Query:   332 NDFSFSTKSENFNAIKNIDANHTREG-GSAKSHGKERNALQREDTSRFSSVVFGLSNHNS 390
                S S    ++N  K+ +    R+     +  G E++   +E   + S +   +S+  S
Sbjct:  1558 EIKSLSEVLNSYNQQKDTEQKEMRQKLQHIQELGDEKDCRVKEAEEKVSRLEKQVSSMKS 1617

Query:   391 IHQT 394
               +T
Sbjct:  1618 ELET 1621

GO:0000042 "protein targeting to Golgi" evidence=IEA

TAIR|locus:2162996 AT5G41140 "AT5G41140" [Arabidopsis thaliana (taxid:3702)]

 Score = 149 (57.5 bits), Expect = 7.1e-07, P = 7.1e-07
 Identities = 84/305 (27%), Positives = 144/305 (47%)

Query:    87 EDPEVSRAEVKILEVKVSRLHTVLESQGKEIKEINEELCLCKERIKEE--AALKNEALRQ 144
             ++  V+R E    E K++ L    + + KE+K ++ +L   K R KE+  A L +E  R+
Sbjct:   681 DELRVNRVEY---EAKLNELSGKTDLKTKEMKRMSADLEYQK-RQKEDVNADLTHEITRR 736

Query:   145 KVSVEQLLHSKSQELDKVTLEC-LKLK---QRNMDLAKELASLKLVSDLN--LDEDEVLK 198
             K  +E +L    +E  K ++E    L    QR +D  KE     L S L   +   + LK
Sbjct:   737 KDEIE-ILRLDLEETRKSSMETEASLSEELQRIID-EKEAVITALKSQLETAIAPCDNLK 794

Query:   199 FALLGNGANNKDTIDVLRKSLV-IRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKL 257
              +L    +NN+  I+ LRK +V +R++   +     NL  RE +  ++ + K +++ N+ 
Sbjct:   795 HSL----SNNESEIENLRKQVVQVRSELEKKEEEMANLENREAS--ADNITKTEQRSNE- 847

Query:   258 KTRVQELETAVELKDNEVLRALKVSKKAS-QKEEILKGATEDNSISLCTNNVSLEDQREQ 316
               R+++LE  ++LK+N    AL+ S K   +KE+ LK   E+    L  N VS   Q   
Sbjct:   848 -DRIKQLEGQIKLKEN----ALEASSKIFIEKEKDLKNRIEELQTKL--NEVSQNSQETD 900

Query:   317 HSVPIYNLDWTSRVTNDFSFSTKSENFNAIKNIDANHTREGGSAKSHGKERNALQREDTS 376
              ++         + T     S KS+N   + N  A+   + G  ++  KE      E + 
Sbjct:   901 ETLQGPEAI-AMQYTEVLPLS-KSDNLQDLVNEVASLREQNGLMETELKEMQERYSEISL 958

Query:   377 RFSSV 381
             RF+ V
Sbjct:   959 RFAEV 963

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

ZFIN|ZDB-GENE-091204-454 si:ch1073-392o20.1 "si:ch1073-392o20.1" [Danio rerio (taxid:7955)]

 Score = 118 (46.6 bits), Expect = 2.0e-06, P = 2.0e-06
 Identities = 26/77 (33%), Positives = 43/77 (55%)

Query:     5 NKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS 64
             N  G+T C++C ED K + ++L V+  C H FH  C+ +W E      +C CP+C +  S
Sbjct:    87 NLHGQT-CAVCLEDFK-VKDELGVLP-CQHAFHRRCVVKWLEV-----RCVCPMCNKPLS 138

Query:    65 SSN----SIGDQIDLVI 77
              S+    S+G  +D ++
Sbjct:   139 GSSEQHQSLGTLLDELV 155

GO:0008270 "zinc ion binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|E2R604 TRAIP "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 140 (54.3 bits), Expect = 2.4e-06, P = 2.4e-06
 Identities = 67/268 (25%), Positives = 119/268 (44%)

Query:     9 KTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNS 68
             + +C+IC  D      D+  I  CGH FH  CL QWFE   S    TCP C+ +      
Sbjct:     4 RALCTIC-SDFFDHSRDVAAIH-CGHTFHLQCLIQWFETAPSR---TCPQCRIQ------ 52

Query:    69 IGDQIDLVISQKPKDPEVEDPEVSRAEVKILEVKVSRLHTVLESQGKEIKEINEELCLCK 128
             +G +   +I++   D   E+  V  AE     +KV  ++ +L +  KE K+    +   +
Sbjct:    53 VGRRT--IINKLFFDLAQEEENVLDAEF----LKVPGIYVILLNSEKEKKDSQAIIDTLR 106

Query:   129 ERIKEEAALKNEALRQKVSVEQLLHS--KSQE--LDKVTLECLKLKQRNMDLAKELASLK 184
             + ++E  A   E+L+  +   ++L S  K Q   L++   E  ++ ++   L  ++ +++
Sbjct:   107 DTLEERNATV-ESLQSALDKAEMLCSTLKKQMKYLEQQQDETKQVHEQMRQLRSKMKTME 165

Query:   185 LVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFS 244
              +  L   +   ++  +   G   +  ++ L    V   K Y  L       G    R  
Sbjct:   166 RIELLLQSQRPEVEEMIRDMGVG-QSAVEQLAVYCVSLKKEYENLKEARKASGELADRLK 224

Query:   245 EKLEKAKEKINKLKTRVQELE-TAVELK 271
             + L  +K   NKL+T   EL+ T +ELK
Sbjct:   225 KDLFSSK---NKLQTVYSELDQTKLELK 249

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|Q9H9V4 RNF122 "RING finger protein 122" [Homo sapiens (taxid:9606)]

 Score = 116 (45.9 bits), Expect = 3.3e-06, P = 3.3e-06
 Identities = 23/73 (31%), Positives = 40/73 (54%)

Query:     7 FGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS 66
             +G+T C++C ED K   ++L V+  C H FH  CL +W E      +C CP+C +  +S 
Sbjct:    89 YGQT-CAVCLEDFKG-KDELGVLP-CQHAFHRKCLVKWLEV-----RCVCPMCNKPIASP 140

Query:    67 NSIGDQIDLVISQ 79
             +     I +++ +
Sbjct:   141 SEATQNIGILLDE 153

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0005794 "Golgi apparatus" 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 Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	6.3.2	0.691

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	466
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	5e-11
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	2e-09
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	7e-08
smart00184	40	smart00184, RING, Ring finger	5e-07
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	5e-06
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	7e-06
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	1e-05
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	1e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	4e-05
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	6e-05
pfam11793	70	pfam11793, FANCL_C, FANCL C-terminal domain	1e-04
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	2e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	5e-04
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	6e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.001
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.001
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	0.001
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.004

>gnl|CDD|238093 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)

 Score = 57.1 bits (138), Expect = 5e-11
 Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 8/52 (15%)

Query: 12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRC 63
          C IC E+ +  V    V+  CGHVF   C+ +W +    S K TCP+C+   
Sbjct: 2  CPICLEEFREPV----VLLPCGHVFCRSCIDKWLK----SGKNTCPLCRTPI 45

Length = 45

>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain

 Score = 53.2 bits (128), Expect = 2e-09
 Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 7/51 (13%)

Query: 12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQR 62
          C IC ++ +P   +  V+  CGHVFH+ CL +W    +     TCP+C+  
Sbjct: 3  CPICLDEFEP--GEEVVVLPCGHVFHKECLDKWLRSSN-----TCPLCRAP 46

Length = 46

>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger)

 Score = 48.3 bits (115), Expect = 7e-08
 Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 9/51 (17%)

Query: 11 ICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQ 61
           C IC + L+  V    V++ CGHVF   C+ ++ +     KK  CP+C+ 
Sbjct: 4  ECPICLDLLRDPV----VLTPCGHVFCRECILRYLK-----KKSKCPICRT 45

Length = 45

>gnl|CDD|214546 smart00184, RING, Ring finger

 Score = 46.0 bits (109), Expect = 5e-07
 Identities = 18/48 (37%), Positives = 23/48 (47%), Gaps = 8/48 (16%)

Query: 12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVC 59
          C IC E+         VI  CGH F   C+++W E    S   TCP+C
Sbjct: 1  CPICLEEYLKDP----VILPCGHTFCRSCIRKWLE----SGNNTCPIC 40

E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s). Length = 40

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 48.9 bits (117), Expect = 5e-06
 Identities = 52/225 (23%), Positives = 98/225 (43%), Gaps = 21/225 (9%)

Query: 90  EVSRAEVKILEVKVSRLHTVLESQGKEIKEINEELCLCKERIKE-----------EAALK 138
           E  ++E++ L  ++  L   L    +EI+E+  E+ L +ER++E              LK
Sbjct: 270 EELKSELEELREELEELQEELLELKEEIEELEGEISLLRERLEELENELEELEERLEELK 329

Query: 139 N--EALRQKVSV-EQLLHSKSQELDKVTLECLKLKQRNMDLAKELASLKLVSDLNLDEDE 195
              EAL++++   E LL    Q L ++     +L+++   L +EL  L       L E E
Sbjct: 330 EKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALREELAELE 389

Query: 196 VLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELM-------AKCNLLGREKARFSEKLE 248
                +       K  I+ L + L   ++   +L        A+   L  E    +E+LE
Sbjct: 390 AELAEIRNELEELKREIESLEERLERLSERLEDLKEELKELEAELEELQTELEELNEELE 449

Query: 249 KAKEKINKLKTRVQELETAVELKDNEVLRALKVSKKASQKEEILK 293
           + +E++ +L+ R++ELE  +     E+ R  K       + + L+
Sbjct: 450 ELEEQLEELRDRLKELERELAELQEELQRLEKELSSLEARLDRLE 494

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 48.2 bits (115), Expect = 7e-06
 Identities = 41/201 (20%), Positives = 94/201 (46%), Gaps = 7/201 (3%)

Query: 90  EVSRAEVKILEVKVSRLHTVLESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVE 149
               A+++ LE ++  L   L S    ++E+  +L   + +++E          +   ++
Sbjct: 677 AELEAQLEKLEEELKSLKNELRSLEDLLEELRRQLEELERQLEELKRELAALEEELEQLQ 736

Query: 150 QLLHSKSQELDKVTLECLKLKQRNMDLAKELASL-KLVSDLNLDEDEVLKFALLGNGANN 208
             L    +EL+++  E  +L++R  +L +EL SL + ++ L  + +E     L       
Sbjct: 737 SRLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEE-----LEEKRQAL 791

Query: 209 KDTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAV 268
           ++ ++ L + L    +    L  +   L + + R  +++E+ +E+I +L+ ++ ELE  +
Sbjct: 792 QEELEELEEELEEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEEL 851

Query: 269 ELKDNEVLRALKVSKKASQKE 289
           E  + E L  LK   +  + E
Sbjct: 852 EELEKE-LEELKEELEELEAE 871

Length = 1163

>gnl|CDD|215715 pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING finger)

 Score = 42.1 bits (99), Expect = 1e-05
 Identities = 19/48 (39%), Positives = 23/48 (47%), Gaps = 8/48 (16%)

Query: 12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVC 59
          C IC E+ K  V  L     CGH+F   C+  W E    S   TCP+C
Sbjct: 1  CPICLEEPKDPVTILP----CGHLFCSKCILSWLE----SGNVTCPLC 40

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. Length = 40

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 47.4 bits (113), Expect = 1e-05
 Identities = 36/208 (17%), Positives = 83/208 (39%), Gaps = 8/208 (3%)

Query: 110 LESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKL 169
           LE + + ++E+   L   +    E   ++ E LR+   + + L  K + L+++  E  +L
Sbjct: 244 LEEEKERLEELKARLLEIESLELEALKIREEELRELERLLEELEEKIERLEELEREIEEL 303

Query: 170 KQRNMDLAKELASLK-LVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIR-NKNYT 227
           ++    L   L  L+ L+  L   E+ + K           + ++   + L    N+   
Sbjct: 304 EEELEGLRALLEELEELLEKLKSLEERLEK------LEEKLEKLESELEELAEEKNELAK 357

Query: 228 ELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVSKKASQ 287
            L  +   L        ++LEKA E++ +L+  +QEL+  +      +    +  ++  +
Sbjct: 358 LLEERLKELEERLEELEKELEKALERLKQLEEAIQELKEELAELSAALEEIQEELEELEK 417

Query: 288 KEEILKGATEDNSISLCTNNVSLEDQRE 315
           + E L+   E+    +      +     
Sbjct: 418 ELEELERELEELEEEIKKLEEQINQLES 445

Length = 908

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 46.2 bits (110), Expect = 3e-05
 Identities = 48/207 (23%), Positives = 96/207 (46%), Gaps = 11/207 (5%)

Query: 93  RAEVKILEVKVSRLHTVLESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQLL 152
           R +++ LE ++  L   L +  +E++++   L   +E ++E      E   +   +E+ L
Sbjct: 708 RRQLEELERQLEELKRELAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEEL 767

Query: 153 HSKSQELDKVTLECLKLKQRNMDLAKELASLKLVSDLNLDEDEVLKFALLGNGANNKDTI 212
            S  + L K+  E  +L+++   L +EL  L+   +      + L+  L     + +   
Sbjct: 768 ESLEEALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALEREL----ESLEQRR 823

Query: 213 DVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKD 272
           + L + +    +   EL  K + L  E     ++LE+ KE++ +L+   +ELE  ++  +
Sbjct: 824 ERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELEDELKELE 883

Query: 273 NEV------LRALKVSKKASQKEEILK 293
            E       LR L+ S+ A  KEEI K
Sbjct: 884 EEKEELEEELRELE-SELAELKEEIEK 909

Length = 1163

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 45.9 bits (109), Expect = 4e-05
 Identities = 43/231 (18%), Positives = 96/231 (41%), Gaps = 8/231 (3%)

Query: 92  SRAEVKILEVKVSRLHTVLESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQL 151
            R E++ LE ++SRL   LE   +E++E  +E+   K  ++E      E   + + +++ 
Sbjct: 237 LRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQEELLELKEE 296

Query: 152 LHSKSQELDKVTLECLKLKQRNMDLAKELASLKLVSDLNLDEDEVLKF-ALLGNGANNKD 210
           +     E+  +     +L+    +L + L  LK    +   ++E+ +   LL        
Sbjct: 297 IEELEGEISLLRERLEELENELEELEERLEELK--EKIEALKEELEERETLLEELEQLLA 354

Query: 211 TIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSE---KLEKAKEKINKLKTRVQELETA 267
            ++  ++ L    K    L     L    +   +E   +L + + ++ +LK  ++ LE  
Sbjct: 355 ELEEAKEEL--EEKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEER 412

Query: 268 VELKDNEVLRALKVSKKASQKEEILKGATEDNSISLCTNNVSLEDQREQHS 318
           +E     +    +  K+   + E L+   E+ +  L      LE+ R++  
Sbjct: 413 LERLSERLEDLKEELKELEAELEELQTELEELNEELEELEEQLEELRDRLK 463

Length = 1163

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 45.4 bits (108), Expect = 6e-05
 Identities = 42/229 (18%), Positives = 93/229 (40%), Gaps = 16/229 (6%)

Query: 71  DQIDLVISQKPKDPEVEDPEVS--RAEVKILEVKVSRLHTVLESQGKEIKEINEELCLCK 128
           ++++  + Q  K+ E    ++S  R ++  LE +V +L   +    KE+ E+  E+   +
Sbjct: 708 EELEEELEQLRKELEELSRQISALRKDLARLEAEVEQLEERIAQLSKELTELEAEIEELE 767

Query: 129 ERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRNMDLAKELASLKLVSD 188
           ER++E      EA  +   +E  +    +EL  +     +L+     L +E A+L+   +
Sbjct: 768 ERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELTLLNEEAANLRERLE 827

Query: 189 LNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLE 248
                      +L    A  +  ++ L + +   +++   L A+   L         +LE
Sbjct: 828 -----------SLERRIAATERRLEDLEEQIEELSEDIESLAAEIEELEELIEELESELE 876

Query: 249 KAKEKINKLKTRVQELETAVELKDNEVLRALKVSKKASQKEEILKGATE 297
               +   L+  +  L + +E    E+    ++  K S+    L+   E
Sbjct: 877 ALLNERASLEEALALLRSELEELSEEL---RELESKRSELRRELEELRE 922

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|204746 pfam11793, FANCL_C, FANCL C-terminal domain

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 20/70 (28%), Positives = 28/70 (40%), Gaps = 17/70 (24%)

Query: 12 CSICY-----EDLKPIV--EDLQVISICGHVFHELCLQQWFEYCSSSKKC------TCPV 58
          C ICY         P +  ++ +    CG  FH  CL +W      S++       TCP 
Sbjct: 5  CGICYAYRLDGGEIPDISCDNPK----CGLPFHIACLYEWLRTLRDSRQSFNVSFGTCPY 60

Query: 59 CKQRCSSSNS 68
          CK + S   S
Sbjct: 61 CKAKISVKFS 70

This domain is found at the C-terminus of the Fancl protein in humans which is the putative E3 ubiquitin ligase subunit of the FA complex (Fanconi anaemia). Eight subunits of the Fanconi anaemia gene products form a multisubunit nuclear complex which is required for mono-ubiquitination of a downstream FA protein, FANCD2. Length = 70

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

 Score = 39.8 bits (93), Expect = 2e-04
 Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 2/34 (5%)

Query: 28 VISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQ 61
          V   C H FH  C+ +W    + + K  CP+C+Q
Sbjct: 48 VWGKCKHNFHMHCILKWLA--TETSKGLCPMCRQ 79

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

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 42.4 bits (100), Expect = 5e-04
 Identities = 42/211 (19%), Positives = 91/211 (43%), Gaps = 13/211 (6%)

Query: 93  RAEVKILEVKVSRLHTVLESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQLL 152
           + E++ LE ++  L        KE+ E    L   KE ++E      E  ++   +E+ L
Sbjct: 558 KEELRQLEDRLQEL--------KELLEELRLLRTRKEELEELRERLKELKKKLKELEERL 609

Query: 153 HSKSQELDKVTLECLKLKQRNMDLAKELASLKLVSDLNLDEDEVLKFALLGNGANNKDTI 212
               + L  + L   + +    +  +EL S     +L  + +E+L+ AL       ++  
Sbjct: 610 SQLEELLQSLELSEAENELE--EAEEELESELEKLNLQAELEELLQAALEELEEKVEELE 667

Query: 213 DVLRKSLVI--RNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVEL 270
             +R+ L      +   E + +   L  E  +  E+LE+  +K+ +++  ++ELE+    
Sbjct: 668 AEIRRELQRIENEEQLEEKLEELEQLEEELEQLREELEELLKKLGEIEQLIEELESRKAE 727

Query: 271 KDNEVLRALKVSKKASQKEEILKGATEDNSI 301
            + E+ + L+  +KA +  E L+       +
Sbjct: 728 LE-ELKKELEKLEKALELLEELREKLGKAGL 757

Length = 908

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

 Score = 38.2 bits (89), Expect = 6e-04
 Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 13/57 (22%)

Query: 12 CSIC---YEDLKPIVEDLQ-----VISICGHVFHELCLQQWFEYCSSSKKCTCPVCK 60
          C+IC   ++   P  +        V   CGH FH  C+ +W +      + TCP+C+
Sbjct: 22 CAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLK-----TRNTCPLCR 73

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

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 41.2 bits (97), Expect = 0.001
 Identities = 46/214 (21%), Positives = 93/214 (43%), Gaps = 14/214 (6%)

Query: 85  EVEDPEVSRAEVKILEVKVSRLHTVLESQGKEIKEINEELCLCKERIKEEAALKNEALRQ 144
           E+E+ E    E++    ++      LE    ++KE  EEL   ++ ++EE     E L +
Sbjct: 745 ELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQEELEELEEELEE 804

Query: 145 KVSVEQLLHSKSQELDKVTLECLKLKQRNMDLAKELASLKLVSDLNLDEDEVLKFALLGN 204
               E+ L +  +EL+ +     +L+Q   +L +E+  L+   D   +E E L+  L   
Sbjct: 805 ---AERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKEL--- 858

Query: 205 GANNKDTIDVLRKSLVIRNKNYT-------ELMAKCNLLGREKARFSEKLEKAKEKINKL 257
               K+ ++ L                   EL  +   L  E A   E++EK +E++ +L
Sbjct: 859 -EELKEELEELEAEKEELEDELKELEEEKEELEEELRELESELAELKEEIEKLRERLEEL 917

Query: 258 KTRVQELETAVELKDNEVLRALKVSKKASQKEEI 291
           + +++ LE  +   + E+    + + +   + EI
Sbjct: 918 EAKLERLEVELPELEEELEEEYEDTLETELEREI 951

Length = 1163

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 41.2 bits (97), Expect = 0.001
 Identities = 43/208 (20%), Positives = 93/208 (44%), Gaps = 13/208 (6%)

Query: 94  AEVKILEVKVSRLHTVLESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQLLH 153
           AE++ LE K+  L   +    +EI+E+ +EL      I   + L+ +    +  +  L  
Sbjct: 260 AELQELEEKLEELRLEVSELEEEIEELQKELYALANEI---SRLEQQKQILRERLANL-- 314

Query: 154 SKSQELDKVTLECLKLKQRNMDLAKELASLKLVSDLNLDEDEVLKFALLGNGANNKDTID 213
              ++L+++  +  +L+ +  +LA+ELA L+      L+E +    +L       +  ++
Sbjct: 315 --ERQLEELEAQLEELESKLDELAEELAELE----EKLEELKEELESLEAELEELEAELE 368

Query: 214 VLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQEL--ETAVELK 271
            L   L    +    L +K   L  + A  + ++E+ + ++ +L+ R + L  E    LK
Sbjct: 369 ELESRLEELEEQLETLRSKVAQLELQIASLNNEIERLEARLERLEDRRERLQQEIEELLK 428

Query: 272 DNEVLRALKVSKKASQKEEILKGATEDN 299
             E     ++  +  + EE L+   E+ 
Sbjct: 429 KLEEAELKELQAELEELEEELEELQEEL 456

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

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

 Score = 41.1 bits (96), Expect = 0.001
 Identities = 25/115 (21%), Positives = 40/115 (34%), Gaps = 27/115 (23%)

Query: 8   GKTICSICYEDL-----KPIVEDLQVIS---ICGHVFHELCLQQWFEYCSSSKKCTCPVC 59
               C+IC +++     +P+   L +      CGH+ H  CL+ W E     ++ TCP+C
Sbjct: 286 SDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLE-----RQQTCPIC 340

Query: 60  KQRCSSSNSIGDQIDLVISQKPKDPEVEDPEVSRAEVKILEVKVSRLHTVLESQG 114
           +        I DQ           P    P V   ++           T     G
Sbjct: 341 R-----RPVIFDQ---------SSPTPASPNVRNTQIATQVPNPDNTPTTTAVPG 381

Length = 491

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 39.7 bits (93), Expect = 0.004
 Identities = 45/201 (22%), Positives = 95/201 (47%), Gaps = 15/201 (7%)

Query: 90  EVSRAEVKILEVKVSRLHTVLESQGKEIKEINEE-------LCLCKERIKEEAAL----K 138
           E +  E++ +E  + RL  +++ + ++++ +  E         L KE+ + E       K
Sbjct: 173 EKALEELEEVEENIERLDLIIDEKRQQLERLRREREKAERYQALLKEKREYEGYELLKEK 232

Query: 139 NEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRNMDLAKELASL-KLVSDLNLDEDEVL 197
               RQK ++E+ L S  +EL+K+T E  +L++R  ++ + L  L K + DL  +E   +
Sbjct: 233 EALERQKEAIERQLASLEEELEKLTEEISELEKRLEEIEQLLEELNKKIKDLGEEEQLRV 292

Query: 198 KFALL---GNGANNKDTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKI 254
           K  +       A+ + +I    + L    +   +L A+ + L  E      ++E+ +++ 
Sbjct: 293 KEKIGELEAEIASLERSIAEKERELEDAEERLAKLEAEIDKLLAEIEELEREIEEERKRR 352

Query: 255 NKLKTRVQELETAVELKDNEV 275
           +KL     EL+  +E    E+
Sbjct: 353 DKLTEEYAELKEELEDLRAEL 373

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	466
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	99.87
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	99.5
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.15
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.13
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.04
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	98.98
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.94
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.9
PHA02929	238	N1R/p28-like protein; Provisional	98.9
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.89
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.87
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.87
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.87
PHA02926	242	zinc finger-like protein; Provisional	98.81
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.78
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.77
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	98.77
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	98.75
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.69
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.69
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.68
PF14634	44	zf-RING_5: zinc-RING finger domain	98.67
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	98.62
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	98.61
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.51
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	98.51
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.51
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.46
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.45
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.45
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.4
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	98.28
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.25
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.2
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.94
KOG4739	233	consensus Uncharacterized protein involved in syna	97.88
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.88
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	97.8
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	97.77
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	97.72
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	97.71
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	97.62
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.51
COG5219	1525	Uncharacterized conserved protein, contains RING Z	97.48
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.47
KOG2660	331	consensus Locus-specific chromosome binding protei	97.43
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.41
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.4
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.31
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	97.27
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	97.27
COG5152	259	Uncharacterized conserved protein, contains RING a	97.24
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.19
PRK02224	880	chromosome segregation protein; Provisional	97.17
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.03
KOG0297	391	consensus TNF receptor-associated factor [Signal t	96.89
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	96.88
TIGR02169	1164	SMC_prok_A chromosome segregation protein SMC, pri	96.86
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	96.83
PF09726	697	Macoilin: Transmembrane protein; InterPro: IPR0191	96.73
PRK11637	428	AmiB activator; Provisional	96.69
TIGR02169	1164	SMC_prok_A chromosome segregation protein SMC, pri	96.68
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	96.66
PF04641	260	Rtf2: Rtf2 RING-finger	96.66
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	96.65
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	96.6
TIGR02168	1179	SMC_prok_B chromosome segregation protein SMC, com	96.55
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	96.48
KOG1941	518	consensus Acetylcholine receptor-associated protei	96.45
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	96.42
PF15619	194	Lebercilin: Ciliary protein causing Leber congenit	96.42
TIGR02168	1179	SMC_prok_B chromosome segregation protein SMC, com	96.42
KOG4445	368	consensus Uncharacterized conserved protein, conta	96.18
PRK11637	428	AmiB activator; Provisional	96.13
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	96.13
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	96.11
COG5222	427	Uncharacterized conserved protein, contains RING Z	96.03
PRK04778	569	septation ring formation regulator EzrA; Provision	96.01
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	96.0
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	95.98
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	95.93
KOG0996	1293	consensus Structural maintenance of chromosome pro	95.93
KOG0995	581	consensus Centromere-associated protein HEC1 [Cell	95.87
PHA03096	284	p28-like protein; Provisional	95.87
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	95.81
COG1196	1163	Smc Chromosome segregation ATPases [Cell division	95.72
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	95.7
KOG3039	303	consensus Uncharacterized conserved protein [Funct	95.52
KOG3002	299	consensus Zn finger protein [General function pred	95.49
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	95.44
KOG0996	1293	consensus Structural maintenance of chromosome pro	95.39
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	95.23
COG1196	1163	Smc Chromosome segregation ATPases [Cell division	95.21
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	95.12
KOG0964	1200	consensus Structural maintenance of chromosome pro	95.1
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	95.05
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	94.95
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	94.94
PHA02825	162	LAP/PHD finger-like protein; Provisional	94.87
KOG1001	674	consensus Helicase-like transcription factor HLTF/	94.81
COG5175	480	MOT2 Transcriptional repressor [Transcription]	94.78
PRK01156	895	chromosome segregation protein; Provisional	94.72
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	94.69
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	94.67
PF09726	697	Macoilin: Transmembrane protein; InterPro: IPR0191	94.59
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	94.55
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	94.44
PF05701	522	WEMBL: Weak chloroplast movement under blue light;	94.41
KOG0977	546	consensus Nuclear envelope protein lamin, intermed	94.35
PF00261	237	Tropomyosin: Tropomyosin; InterPro: IPR000533 Trop	94.33
KOG0161	1930	consensus Myosin class II heavy chain [Cytoskeleto	94.32
PF15290	305	Syntaphilin: Golgi-localised syntaxin-1-binding cl	94.28
PRK09039	343	hypothetical protein; Validated	94.27
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	94.26
PF15254	861	CCDC14: Coiled-coil domain-containing protein 14	94.2
PF05667	594	DUF812: Protein of unknown function (DUF812); Inte	94.16
PHA02862	156	5L protein; Provisional	94.15
KOG4643	1195	consensus Uncharacterized coiled-coil protein [Fun	94.09
PF12128	1201	DUF3584: Protein of unknown function (DUF3584); In	94.08
PRK02224	880	chromosome segregation protein; Provisional	94.07
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	94.01
KOG0980	980	consensus Actin-binding protein SLA2/Huntingtin-in	93.86
PF07888	546	CALCOCO1: Calcium binding and coiled-coil domain (	93.84
PF05667	594	DUF812: Protein of unknown function (DUF812); Inte	93.82
COG5236	493	Uncharacterized conserved protein, contains RING Z	93.76
KOG0971	1243	consensus Microtubule-associated protein dynactin	93.74
COG4372	499	Uncharacterized protein conserved in bacteria with	93.71
PF10174	775	Cast: RIM-binding protein of the cytomatrix active	93.69
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	93.67
PHA02562	562	46 endonuclease subunit; Provisional	93.64
KOG4367	699	consensus Predicted Zn-finger protein [Function un	93.63
KOG0161	1930	consensus Myosin class II heavy chain [Cytoskeleto	93.61
PF06160	560	EzrA: Septation ring formation regulator, EzrA ; I	93.59
PRK09039	343	hypothetical protein; Validated	93.51
KOG0612	1317	consensus Rho-associated, coiled-coil containing p	93.46
KOG0963	629	consensus Transcription factor/CCAAT displacement	93.44
PF00261	237	Tropomyosin: Tropomyosin; InterPro: IPR000533 Trop	93.43
KOG1029	1118	consensus Endocytic adaptor protein intersectin [S	93.42
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	93.41
KOG1899	861	consensus LAR transmembrane tyrosine phosphatase-i	93.36
PF10481	307	CENP-F_N: Cenp-F N-terminal domain; InterPro: IPR0	93.28
KOG4643	1195	consensus Uncharacterized coiled-coil protein [Fun	93.2
PF10168	717	Nup88: Nuclear pore component; InterPro: IPR019321	93.14
PF14662	193	CCDC155: Coiled-coil region of CCDC155	92.96
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	92.92
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	92.83
COG4026	290	Uncharacterized protein containing TOPRIM domain,	92.77
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	92.73
PRK04863	1486	mukB cell division protein MukB; Provisional	92.71
PF13166	712	AAA_13: AAA domain	92.68
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	92.61
KOG0298	1394	consensus DEAD box-containing helicase-like transc	92.58
KOG0933	1174	consensus Structural maintenance of chromosome pro	92.58
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	92.46
KOG0994	1758	consensus Extracellular matrix glycoprotein Lamini	92.42
KOG0977	546	consensus Nuclear envelope protein lamin, intermed	92.07
PF12128	1201	DUF3584: Protein of unknown function (DUF3584); In	92.03
COG0419	908	SbcC ATPase involved in DNA repair [DNA replicatio	91.97
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	91.97
COG4477	570	EzrA Negative regulator of septation ring formatio	91.93
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	91.83
KOG1029	1118	consensus Endocytic adaptor protein intersectin [S	91.77
PF00038	312	Filament: Intermediate filament protein; InterPro:	91.74
KOG1940	276	consensus Zn-finger protein [General function pred	91.69
PF05911	769	DUF869: Plant protein of unknown function (DUF869)	91.69
KOG4674	1822	consensus Uncharacterized conserved coiled-coil pr	91.55
KOG0933	1174	consensus Structural maintenance of chromosome pro	91.45
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	91.24
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	90.89
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	90.86
PF10174	775	Cast: RIM-binding protein of the cytomatrix active	90.86
PF09730	717	BicD: Microtubule-associated protein Bicaudal-D; I	90.41
PF10186	302	Atg14: UV radiation resistance protein and autopha	90.33
PF04849	306	HAP1_N: HAP1 N-terminal conserved region; InterPro	90.17
KOG3053	293	consensus Uncharacterized conserved protein [Funct	89.87
PLN03188	1320	kinesin-12 family protein; Provisional	89.83
KOG4674	1822	consensus Uncharacterized conserved coiled-coil pr	89.77
PF15397	258	DUF4618: Domain of unknown function (DUF4618)	89.66
KOG0980	980	consensus Actin-binding protein SLA2/Huntingtin-in	89.59
PF10473	140	CENP-F_leu_zip: Leucine-rich repeats of kinetochor	89.41
KOG0825	1134	consensus PHD Zn-finger protein [General function	89.35
PF10186	302	Atg14: UV radiation resistance protein and autopha	88.98
PF09789	319	DUF2353: Uncharacterized coiled-coil protein (DUF2	88.68
KOG0979	1072	consensus Structural maintenance of chromosome pro	88.67
KOG0964	1200	consensus Structural maintenance of chromosome pro	88.63
COG2433	652	Uncharacterized conserved protein [Function unknow	88.49
PF05483	786	SCP-1: Synaptonemal complex protein 1 (SCP-1); Int	88.4
KOG0999	772	consensus Microtubule-associated protein Bicaudal-	88.35
KOG1842	505	consensus FYVE finger-containing protein [General	88.28
PF10168	717	Nup88: Nuclear pore component; InterPro: IPR019321	88.27
KOG0962	1294	consensus DNA repair protein RAD50, ABC-type ATPas	88.19
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	88.17
COG4694	758	Uncharacterized protein conserved in bacteria [Fun	88.16
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	87.95
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	87.93
COG4942	420	Membrane-bound metallopeptidase [Cell division and	87.92
KOG0971	1243	consensus Microtubule-associated protein dynactin	87.91
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	87.87
PF00038	312	Filament: Intermediate filament protein; InterPro:	87.84
PRK01156	895	chromosome segregation protein; Provisional	87.6
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	87.53
PF15070	617	GOLGA2L5: Putative golgin subfamily A member 2-lik	87.33
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	87.27
PF00769	246	ERM: Ezrin/radixin/moesin family; InterPro: IPR011	87.13
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	86.9
COG1340	294	Uncharacterized archaeal coiled-coil protein [Func	86.84
KOG0999	772	consensus Microtubule-associated protein Bicaudal-	86.66
COG5109	396	Uncharacterized conserved protein, contains RING Z	86.32
PLN03229	762	acetyl-coenzyme A carboxylase carboxyl transferase	86.24
PF09730	717	BicD: Microtubule-associated protein Bicaudal-D; I	86.12
PF05701	522	WEMBL: Weak chloroplast movement under blue light;	85.85
TIGR02680	1353	conserved hypothetical protein TIGR02680. Members	85.75
PF11559	151	ADIP: Afadin- and alpha -actinin-Binding; InterPro	85.44
PF10498	359	IFT57: Intra-flagellar transport protein 57 ; Inte	85.02
PRK04778	569	septation ring formation regulator EzrA; Provision	84.9
KOG4360	596	consensus Uncharacterized coiled coil protein [Fun	84.56
PF04849	306	HAP1_N: HAP1 N-terminal conserved region; InterPro	84.48
KOG3113	293	consensus Uncharacterized conserved protein [Funct	84.42
PF07926	132	TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro:	84.23
KOG4673	961	consensus Transcription factor TMF, TATA element m	84.17
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	84.02
PF10481	307	CENP-F_N: Cenp-F N-terminal domain; InterPro: IPR0	83.99
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	83.95
PF05622	713	HOOK: HOOK protein; InterPro: IPR008636 This famil	83.76
PF14182	79	YgaB: YgaB-like protein	83.74
KOG3899	381	consensus Uncharacterized conserved protein [Funct	83.68
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	82.94
COG4942	420	Membrane-bound metallopeptidase [Cell division and	81.91
KOG2129	552	consensus Uncharacterized conserved protein H4 [Fu	81.57
PF06160	560	EzrA: Septation ring formation regulator, EzrA ; I	81.3
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	80.93
KOG0976	1265	consensus Rho/Rac1-interacting serine/threonine ki	80.85
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	80.79
KOG1103	561	consensus Predicted coiled-coil protein [Function	80.69
KOG2991	330	consensus Splicing regulator [RNA processing and m	80.48
KOG0612	1317	consensus Rho-associated, coiled-coil containing p	80.47
KOG3039	303	consensus Uncharacterized conserved protein [Funct	80.45
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	80.18
PF15619	194	Lebercilin: Ciliary protein causing Leber congenit	80.09

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

Probab=99.87  E-value=1.5e-21  Score=195.59  Aligned_cols=297  Identities=20%  Similarity=0.160  Sum_probs=239.6

Q ss_pred             CcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCCCCcchhhhhccCCCCCCC-CC
Q 012292            9 KTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSIGDQIDLVISQKPKDPE-VE   87 (466)
Q Consensus         9 eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~~l~~l~~~l~~~~~~~~e-~~   87 (466)
                      -..|.|| ..+.|..+++..+-.|||+||..|+.+|++++|.  +..||.|+-.+......        ++..++.- .+
T Consensus         4 ~A~C~Ic-~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps--~R~cpic~ik~~~r~~~--------N~~~~d~vvEe   72 (465)
T KOG0827|consen    4 MAECHIC-IDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPS--NRGCPICQIKLQERHVA--------NPSTVDHVVEE   72 (465)
T ss_pred             cceeeEe-ccCCccccccccccchhhHHHHHHHHHHHccCCc--cCCCCceeecccceeee--------chhhhhhhhcc
Confidence            3589999 5555667788777779999999999999998774  37999999666555411        12222211 14


Q ss_pred             ChhhHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Q 012292           88 DPEVSRAEVKILEVKVSRLHTVLESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECL  167 (466)
Q Consensus        88 ~~e~l~~El~rLe~kl~~L~~~Le~~~~~lk~L~eel~~~KeQlkeE~~~l~EkLk~~esLeqLL~~q~eEVeklkeE~~  167 (466)
                      ++-....++.++.+++..........+.....+.+.+..+-++..+....+++++.++..+...|..+.+++.+...++.
T Consensus        73 ~~Vld~~~~K~~~gkvk~~~s~~~~~K~dn~e~~d~l~~t~e~~~a~vv~~~~al~ki~~~~~~Lk~~~~~l~q~~~et~  152 (465)
T KOG0827|consen   73 SVVLDWDVGKKCGGKVKYSVSPGWPYKSDNLELQDLLGHTAEDTIAIVVGKIGALKKIVVYSGDLKEDFQDLKQFDPETL  152 (465)
T ss_pred             chhhhHHHHHhhccchhhhcCcCCccccccHHHHHHHhhhHHHHHHHHHHHHHHhhhHHHhHHHHHHHHHHHHhhCHHHH
Confidence            55556667777777888777777777777777888888888888888899999999999999999999999999999999


Q ss_pred             HHHHhhhHHHHHHHhccccccCChhHHHHHHHHhhcCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHH
Q 012292          168 KLKQRNMDLAKELASLKLVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKL  247 (466)
Q Consensus       168 rLq~rn~alakeL~sLKlvsd~~~eEeE~LK~~~lg~~~~~~e~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kL  247 (466)
                      +++++-.+++..++.++.++.+..+     ++...++..-..+.++.|.++|.+...+|+++-.+|+++.+...+...+|
T Consensus       153 ~lqE~~~~L~~~~~~~~~~~lls~~-----~~~~~~e~~~t~~~~~slv~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL  227 (465)
T KOG0827|consen  153 ELQENPSDLLISHEYIFGAALLSIK-----CFFQTAEHWMTSQPTSSLVGSLSICFESLKQNYDKISAIVCGHIYHHGKL  227 (465)
T ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHhhcCchHHHHhhhHhhHHHHHHHHHHHHHHhhcccchhhHH
Confidence            9999999999999999965554443     23333444456678899999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHhccccchhHHhhhcCCCCCccccccccCChhhhhhccCCCcccccCC
Q 012292          248 EKAKEKINKLKTRVQELETAVELKDNEVLRALKVSKKASQKEEILKGATEDNSISLCTNNVSLEDQREQHSVPIYNLDWT  327 (466)
Q Consensus       248 ek~~~ei~~Lk~~v~eLqk~le~~~ne~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  327 (466)
                      +++-..+++|+..+.+|.+.-.+..+ +++++.++++...+ +..+ .       .+....+++++++.+++|+..++.+
T Consensus       228 ~k~L~~~~kl~~~~rel~~~~~e~k~-A~~Dvq~~~ke~~~-lk~p-l-------tMl~~~~~~~~v~~~t~~~~~lE~~  297 (465)
T KOG0827|consen  228 SKWLATKRKLPSCRRELPKNGFEEKL-AFFDVQRMGKEAEK-LKPP-L-------TMLEIDYREEHVKLSTSLKVELEKL  297 (465)
T ss_pred             HHHHHHHHHhHHHHhhhhhhhHHHHH-HHHHHHhhhcchhh-cCCc-h-------HHHHHhccCccccccccCceeeccc
Confidence            99999999999999999999999888 89999999987765 3333 2       2467889999999999999999988


Q ss_pred             CCCC
Q 012292          328 SRVT  331 (466)
Q Consensus       328 ~~~~  331 (466)
                      +-+|
T Consensus       298 ~~~~  301 (465)
T KOG0827|consen  298 GTLN  301 (465)
T ss_pred             Ccce
Confidence            7655

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

Probab=99.50  E-value=5.3e-13  Score=136.99  Aligned_cols=56  Identities=27%  Similarity=0.666  Sum_probs=45.7

Q ss_pred             CCCCCCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccC
Q 012292            2 GIENKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS   65 (466)
Q Consensus         2 ~~~~~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~   65 (466)
                      ++..-.+-++|||||+.+++. -.....+.|.|+||..|+..|+.       .+||+||....+
T Consensus       168 ~~~~~tELPTCpVCLERMD~s-~~gi~t~~c~Hsfh~~cl~~w~~-------~scpvcR~~q~p  223 (493)
T KOG0804|consen  168 PPTGLTELPTCPVCLERMDSS-TTGILTILCNHSFHCSCLMKWWD-------SSCPVCRYCQSP  223 (493)
T ss_pred             CCCCcccCCCcchhHhhcCcc-ccceeeeecccccchHHHhhccc-------CcChhhhhhcCc
Confidence            345556778999999999953 34455788999999999999966       899999998773

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

Probab=99.15  E-value=1.9e-11  Score=88.06  Aligned_cols=41  Identities=37%  Similarity=0.899  Sum_probs=29.9

Q ss_pred             ccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCc
Q 012292           12 CSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVC   59 (466)
Q Consensus        12 CpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~C   59 (466)
                      ||||+++|. |+      +++|||+||..||.+|+.... +....||.|
T Consensus         1 CpiC~~~~~~Pv------~l~CGH~FC~~Cl~~~~~~~~-~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKDPV------SLPCGHSFCRSCLERLWKEPS-GSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SSEE------E-SSSSEEEHHHHHHHHCCSS-SST---SSS
T ss_pred             CCccchhhCCcc------ccCCcCHHHHHHHHHHHHccC-CcCCCCcCC
Confidence            899999999 65      899999999999999987432 223789998

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

Probab=99.13  E-value=1.9e-11  Score=88.53  Aligned_cols=43  Identities=40%  Similarity=1.100  Sum_probs=35.4

Q ss_pred             ccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcC
Q 012292           11 ICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCK   60 (466)
Q Consensus        11 tCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR   60 (466)
                      .|+||++.|.+  ......++|||.||..||..|+.     .+.+||+||
T Consensus         2 ~C~IC~~~~~~--~~~~~~l~C~H~fh~~Ci~~~~~-----~~~~CP~CR   44 (44)
T PF13639_consen    2 ECPICLEEFED--GEKVVKLPCGHVFHRSCIKEWLK-----RNNSCPVCR   44 (44)
T ss_dssp             CETTTTCBHHT--TSCEEEETTSEEEEHHHHHHHHH-----HSSB-TTTH
T ss_pred             CCcCCChhhcC--CCeEEEccCCCeeCHHHHHHHHH-----hCCcCCccC
Confidence            69999999974  23445788999999999999999     457999997

...

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.04  E-value=1.5e-10  Score=108.82  Aligned_cols=55  Identities=31%  Similarity=0.840  Sum_probs=44.3

Q ss_pred             CCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcC-----------CCCCCCCcCcCccccCCC
Q 012292            7 FGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCS-----------SSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         7 ~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~-----------~~~s~~CP~CR~~~~~~~   67 (466)
                      .+++.|+||++.+. |+      +++|||+||+.||..|+....           ......||+||..++...
T Consensus        16 ~~~~~CpICld~~~dPV------vT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~   82 (193)
T PLN03208         16 GGDFDCNICLDQVRDPV------VTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEAT   82 (193)
T ss_pred             CCccCCccCCCcCCCcE------EcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhc
Confidence            45789999999998 53      789999999999999986321           123578999999998765

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

Probab=98.98  E-value=2.8e-10  Score=111.80  Aligned_cols=52  Identities=31%  Similarity=0.822  Sum_probs=44.0

Q ss_pred             CCCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            5 NKFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         5 ~~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      -......|.+||+... |+      .+||||.||+.||..|..     ....||+||..+.+..
T Consensus       235 i~~a~~kC~LCLe~~~~pS------aTpCGHiFCWsCI~~w~~-----ek~eCPlCR~~~~psk  287 (293)
T KOG0317|consen  235 IPEATRKCSLCLENRSNPS------ATPCGHIFCWSCILEWCS-----EKAECPLCREKFQPSK  287 (293)
T ss_pred             CCCCCCceEEEecCCCCCC------cCcCcchHHHHHHHHHHc-----cccCCCcccccCCCcc
Confidence            3445678999999996 65      789999999999999988     4566999999998764

>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=98.94  E-value=5.6e-10  Score=78.89  Aligned_cols=38  Identities=45%  Similarity=1.270  Sum_probs=31.7

Q ss_pred             ccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCc
Q 012292           12 CSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVC   59 (466)
Q Consensus        12 CpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~C   59 (466)
                      |+||++.+. |+     ..++|||+||..|+.+|++     ....||.|
T Consensus         1 C~iC~~~~~~~~-----~~~~CGH~fC~~C~~~~~~-----~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRDPV-----VVTPCGHSFCKECIEKYLE-----KNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SSEE-----EECTTSEEEEHHHHHHHHH-----CTSB-TTT
T ss_pred             CCCCCCcccCcC-----EECCCCCchhHHHHHHHHH-----CcCCCcCC
Confidence            899999997 52     4799999999999999999     46899998

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

Probab=98.90  E-value=7.6e-10  Score=101.87  Aligned_cols=54  Identities=30%  Similarity=0.784  Sum_probs=44.8

Q ss_pred             CCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            6 KFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         6 ~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ......|||||+.+.   +.+++.+.|||+||..||...+.     ....||+||+.++.+.
T Consensus       128 ~~~~~~CPiCl~~~s---ek~~vsTkCGHvFC~~Cik~alk-----~~~~CP~C~kkIt~k~  181 (187)
T KOG0320|consen  128 KEGTYKCPICLDSVS---EKVPVSTKCGHVFCSQCIKDALK-----NTNKCPTCRKKITHKQ  181 (187)
T ss_pred             cccccCCCceecchh---hccccccccchhHHHHHHHHHHH-----hCCCCCCcccccchhh
Confidence            345578999999995   34445789999999999999988     6799999999887654

>PHA02929 N1R/p28-like protein; Provisional

Probab=98.90  E-value=1.1e-09  Score=106.96  Aligned_cols=54  Identities=33%  Similarity=0.724  Sum_probs=41.8

Q ss_pred             CCCccccccccccc-ccc-c-CcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccC
Q 012292            7 FGKTICSICYEDLK-PIV-E-DLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS   65 (466)
Q Consensus         7 ~~eltCpICLe~f~-P~~-~-~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~   65 (466)
                      ..+..|+||++.+. +.. . ....+++|||+||..||.+|+.     ...+||+||.++..
T Consensus       172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~-----~~~tCPlCR~~~~~  228 (238)
T PHA02929        172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK-----EKNTCPVCRTPFIS  228 (238)
T ss_pred             CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh-----cCCCCCCCCCEeeE
Confidence            34689999999876 210 0 1234678999999999999998     57899999998763

>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=98.89  E-value=1.2e-09  Score=81.31  Aligned_cols=46  Identities=35%  Similarity=0.936  Sum_probs=38.7

Q ss_pred             CcccccccccccccccCcceeecCCCc-ccHHHHHHHHHhcCCCCCCCCcCcCcccc
Q 012292            9 KTICSICYEDLKPIVEDLQVISICGHV-FHELCLQQWFEYCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus         9 eltCpICLe~f~P~~~~~~~llpCGHs-FC~~CL~~wle~~~~~~s~~CP~CR~~~~   64 (466)
                      +..|+||++....+     .+.||||. ||..|+.+|+.     ....||+||.++.
T Consensus         2 ~~~C~iC~~~~~~~-----~~~pCgH~~~C~~C~~~~~~-----~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPRDV-----VLLPCGHLCFCEECAERLLK-----RKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBSSE-----EEETTCEEEEEHHHHHHHHH-----TTSBBTTTTBB-S
T ss_pred             cCCCccCCccCCce-----EEeCCCChHHHHHHhHHhcc-----cCCCCCcCChhhc
Confidence            56899999998743     47899999 99999999998     6799999999875

...

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

Probab=98.87  E-value=1e-09  Score=105.03  Aligned_cols=54  Identities=37%  Similarity=0.813  Sum_probs=45.7

Q ss_pred             CCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            6 KFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         6 ~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      .-....|.||||.-. |+      ++.|||.||+.||.+|+...+  ++..||+|+..++...
T Consensus        44 ~~~~FdCNICLd~akdPV------vTlCGHLFCWpClyqWl~~~~--~~~~cPVCK~~Vs~~~   98 (230)
T KOG0823|consen   44 DGGFFDCNICLDLAKDPV------VTLCGHLFCWPCLYQWLQTRP--NSKECPVCKAEVSIDT   98 (230)
T ss_pred             CCCceeeeeeccccCCCE------EeecccceehHHHHHHHhhcC--CCeeCCccccccccce
Confidence            345678999999998 64      789999999999999999643  5788999999998665

>smart00504 Ubox Modified RING finger domain

Probab=98.87  E-value=1.5e-09  Score=83.95  Aligned_cols=48  Identities=25%  Similarity=0.538  Sum_probs=41.4

Q ss_pred             Cccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            9 KTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         9 eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ++.||||.+.+. |+      +++|||+||..||..|+.     ....||.|+.+++..+
T Consensus         1 ~~~Cpi~~~~~~~Pv------~~~~G~v~~~~~i~~~~~-----~~~~cP~~~~~~~~~~   49 (63)
T smart00504        1 EFLCPISLEVMKDPV------ILPSGQTYERRAIEKWLL-----SHGTDPVTGQPLTHED   49 (63)
T ss_pred             CcCCcCCCCcCCCCE------ECCCCCEEeHHHHHHHHH-----HCCCCCCCcCCCChhh
Confidence            468999999998 54      789999999999999998     3578999999886554

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

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.87  E-value=1.9e-07  Score=93.87  Aligned_cols=54  Identities=24%  Similarity=0.567  Sum_probs=39.9

Q ss_pred             CCccccccccc--ccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            8 GKTICSICYED--LKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         8 ~eltCpICLe~--f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ++..||||...  +.|.  ....+.+|||.||.+|+..+|..    +...||.|+.++....
T Consensus         2 d~~~CP~Ck~~~y~np~--~kl~i~~CGH~~C~sCv~~l~~~----~~~~CP~C~~~lrk~~   57 (309)
T TIGR00570         2 DDQGCPRCKTTKYRNPS--LKLMVNVCGHTLCESCVDLLFVR----GSGSCPECDTPLRKNN   57 (309)
T ss_pred             CCCCCCcCCCCCccCcc--cccccCCCCCcccHHHHHHHhcC----CCCCCCCCCCccchhh
Confidence            35689999995  3342  22233489999999999997652    4568999999888665

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).

>PHA02926 zinc finger-like protein; Provisional

Probab=98.81  E-value=2.8e-09  Score=101.51  Aligned_cols=59  Identities=24%  Similarity=0.652  Sum_probs=42.8

Q ss_pred             CCCccccccccccc-c--ccc-CcceeecCCCcccHHHHHHHHHhc-CCCCCCCCcCcCccccC
Q 012292            7 FGKTICSICYEDLK-P--IVE-DLQVISICGHVFHELCLQQWFEYC-SSSKKCTCPVCKQRCSS   65 (466)
Q Consensus         7 ~~eltCpICLe~f~-P--~~~-~~~~llpCGHsFC~~CL~~wle~~-~~~~s~~CP~CR~~~~~   65 (466)
                      ..+..|+||++... +  ..+ .-..+.+|+|+||..||..|.... ..+....||.||..+..
T Consensus       168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~  231 (242)
T PHA02926        168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRN  231 (242)
T ss_pred             cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeee
Confidence            34689999999864 1  111 123467899999999999998843 22346789999998763

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.78  E-value=2.9e-09  Score=110.85  Aligned_cols=50  Identities=26%  Similarity=0.717  Sum_probs=42.5

Q ss_pred             CCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            6 KFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         6 ~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      ....+.|+||++.|. |+      +++|||+||..||..|+.     ....||+||..+...
T Consensus        23 Le~~l~C~IC~d~~~~Pv------itpCgH~FCs~CI~~~l~-----~~~~CP~Cr~~~~~~   73 (397)
T TIGR00599        23 LDTSLRCHICKDFFDVPV------LTSCSHTFCSLCIRRCLS-----NQPKCPLCRAEDQES   73 (397)
T ss_pred             cccccCCCcCchhhhCcc------CCCCCCchhHHHHHHHHh-----CCCCCCCCCCccccc
Confidence            445689999999998 64      789999999999999998     446899999988643

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

>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=98.77  E-value=5.3e-09  Score=74.32  Aligned_cols=41  Identities=39%  Similarity=1.021  Sum_probs=34.7

Q ss_pred             cccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCc
Q 012292           12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVC   59 (466)
Q Consensus        12 CpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~C   59 (466)
                      |+||++.+...    ..+++|||.||..|+..|+..   .....||.|
T Consensus         1 C~iC~~~~~~~----~~~~~C~H~fC~~C~~~~~~~---~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDP----VILLPCGHSFCRDCLRKWLEN---SGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSE----EEETTTSEEEEHHHHHHHHHH---TSSSBTTTT
T ss_pred             CCcCCccccCC----CEEecCCCcchHHHHHHHHHh---cCCccCCcC
Confidence            89999999832    147999999999999999985   367889998

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 ....

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

Probab=98.77  E-value=6.3e-09  Score=83.82  Aligned_cols=46  Identities=43%  Similarity=0.993  Sum_probs=35.1

Q ss_pred             ccccccccccc-c-------cccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcC
Q 012292           10 TICSICYEDLK-P-------IVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCK   60 (466)
Q Consensus        10 ltCpICLe~f~-P-------~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR   60 (466)
                      -.|+||++.|. +       ..+......+|||.||..||.+|+.     ...+||+||
T Consensus        20 d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~-----~~~~CP~CR   73 (73)
T PF12678_consen   20 DNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLK-----QNNTCPLCR   73 (73)
T ss_dssp             SBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHT-----TSSB-TTSS
T ss_pred             CcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHh-----cCCcCCCCC
Confidence            35999999994 2       1123345678999999999999999     567999998

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

>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=98.75  E-value=6.9e-09  Score=73.64  Aligned_cols=44  Identities=41%  Similarity=1.116  Sum_probs=36.0

Q ss_pred             cccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccc
Q 012292           11 ICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRC   63 (466)
Q Consensus        11 tCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~   63 (466)
                      .|+||++.+. +.     .+.+|||.||..|+..|+..    +...||.||..+
T Consensus         1 ~C~iC~~~~~~~~-----~~~~C~H~~c~~C~~~~~~~----~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFREPV-----VLLPCGHVFCRSCIDKWLKS----GKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhhCce-----EecCCCChhcHHHHHHHHHh----CcCCCCCCCCcC
Confidence            5999999984 33     45669999999999999983    467899999753

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

Probab=98.69  E-value=4.1e-09  Score=105.23  Aligned_cols=48  Identities=33%  Similarity=0.863  Sum_probs=43.2

Q ss_pred             Cccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            9 KTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         9 eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      -+.|.||.++|. |.      ++||||+||..||..++.     ....||.|+.+++...
T Consensus        23 lLRC~IC~eyf~ip~------itpCsHtfCSlCIR~~L~-----~~p~CP~C~~~~~Es~   71 (442)
T KOG0287|consen   23 LLRCGICFEYFNIPM------ITPCSHTFCSLCIRKFLS-----YKPQCPTCCVTVTESD   71 (442)
T ss_pred             HHHHhHHHHHhcCce------eccccchHHHHHHHHHhc-----cCCCCCceecccchhh
Confidence            468999999998 64      899999999999999999     5788999999998775

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

Probab=98.69  E-value=1.3e-08  Score=73.67  Aligned_cols=43  Identities=35%  Similarity=0.779  Sum_probs=24.2

Q ss_pred             cccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCc
Q 012292           12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCP   57 (466)
Q Consensus        12 CpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP   57 (466)
                      ||||.+ |.. .++.+++++|||+||..||.+|+.... .+...||
T Consensus         1 CpIc~e-~~~-~~n~P~~L~CGH~~c~~cl~~l~~~~~-~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FST-EENPPMVLPCGHVFCKDCLQKLSKKSD-RNRFKCP   43 (43)
T ss_dssp             -TTT-----T-TSS-EEE-SSS-EEEHHHHHHHHHH-S--S-B--T
T ss_pred             CCcccc-ccC-CCCCCEEEeCccHHHHHHHHHHHhcCC-CCeeeCc
Confidence            999999 753 246667899999999999999988421 2567887

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

Probab=98.68  E-value=9.1e-09  Score=108.10  Aligned_cols=53  Identities=30%  Similarity=0.896  Sum_probs=45.0

Q ss_pred             Cccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            9 KTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         9 eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      +..|||||+... |.      .+.|||.||..||.++|.+..-.+-..||.||..++.++
T Consensus       186 ~~~CPICL~~~~~p~------~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kd  239 (513)
T KOG2164|consen  186 DMQCPICLEPPSVPV------RTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKD  239 (513)
T ss_pred             CCcCCcccCCCCccc------ccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccc
Confidence            789999999987 54      677999999999999988653445678999999999865

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.67  E-value=1.3e-08  Score=73.84  Aligned_cols=44  Identities=36%  Similarity=0.938  Sum_probs=36.4

Q ss_pred             ccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCc
Q 012292           11 ICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQ   61 (466)
Q Consensus        11 tCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~   61 (466)
                      .|+||++.|.  .+..+.+++|||+||..|+..+..     ....||+||+
T Consensus         1 ~C~~C~~~~~--~~~~~~l~~CgH~~C~~C~~~~~~-----~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYS--EERRPRLTSCGHIFCEKCLKKLKG-----KSVKCPICRK   44 (44)
T ss_pred             CCcCcCcccc--CCCCeEEcccCCHHHHHHHHhhcC-----CCCCCcCCCC
Confidence            4999999994  234467899999999999999862     5789999985

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

Probab=98.62  E-value=1.9e-08  Score=101.68  Aligned_cols=53  Identities=30%  Similarity=0.810  Sum_probs=43.4

Q ss_pred             CCCccccccccccc-ccc-------cCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCcccc
Q 012292            7 FGKTICSICYEDLK-PIV-------EDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus         7 ~~eltCpICLe~f~-P~~-------~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~   64 (466)
                      .++-+|.||+|.+. |..       +..++-+||||.||..|+..|++     +..+||.||.++.
T Consensus       285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~E-----RqQTCPICr~p~i  345 (491)
T COG5243         285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLE-----RQQTCPICRRPVI  345 (491)
T ss_pred             CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHH-----hccCCCcccCccc
Confidence            45779999999965 321       13467899999999999999999     7899999999954

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

Probab=98.61  E-value=2.3e-08  Score=101.92  Aligned_cols=52  Identities=35%  Similarity=0.818  Sum_probs=43.0

Q ss_pred             cccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292           10 TICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus        10 ltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      .+|.||+|.|.+  +++..++||+|.||..||..|+..    ....||+|+..+....
T Consensus       230 ~~CaIClEdY~~--GdklRiLPC~H~FH~~CIDpWL~~----~r~~CPvCK~di~~~~  281 (348)
T KOG4628|consen  230 DTCAICLEDYEK--GDKLRILPCSHKFHVNCIDPWLTQ----TRTFCPVCKRDIRTDS  281 (348)
T ss_pred             ceEEEeeccccc--CCeeeEecCCCchhhccchhhHhh----cCccCCCCCCcCCCCC
Confidence            499999999984  356668999999999999999993    3456999999776554

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

Probab=98.51  E-value=3.5e-08  Score=96.89  Aligned_cols=47  Identities=32%  Similarity=0.771  Sum_probs=41.1

Q ss_pred             Cccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            9 KTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         9 eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      .+.|-||-+.|. |.      .++|||+||+.||.+++.     ....||+||..+...
T Consensus        25 ~lrC~IC~~~i~ip~------~TtCgHtFCslCIR~hL~-----~qp~CP~Cr~~~~es   72 (391)
T COG5432          25 MLRCRICDCRISIPC------ETTCGHTFCSLCIRRHLG-----TQPFCPVCREDPCES   72 (391)
T ss_pred             HHHhhhhhheeecce------ecccccchhHHHHHHHhc-----CCCCCccccccHHhh
Confidence            368999999998 64      899999999999999998     678899999987644

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

Probab=98.51  E-value=5.8e-08  Score=95.96  Aligned_cols=52  Identities=27%  Similarity=0.685  Sum_probs=44.1

Q ss_pred             CCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccC
Q 012292            8 GKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS   65 (466)
Q Consensus         8 ~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~   65 (466)
                      ....|.||+..|.-  .+....+||.|.||..|+..|+-    +.+..||+||.++++
T Consensus       322 ~GveCaICms~fiK--~d~~~vlPC~H~FH~~Cv~kW~~----~y~~~CPvCrt~iPP  373 (374)
T COG5540         322 KGVECAICMSNFIK--NDRLRVLPCDHRFHVGCVDKWLL----GYSNKCPVCRTAIPP  373 (374)
T ss_pred             CCceEEEEhhhhcc--cceEEEeccCceechhHHHHHHh----hhcccCCccCCCCCC
Confidence            45789999999973  34567899999999999999988    367899999999875

>smart00184 RING Ring finger

Probab=98.51  E-value=1e-07  Score=65.24  Aligned_cols=39  Identities=46%  Similarity=1.182  Sum_probs=32.5

Q ss_pred             cccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCc
Q 012292           12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVC   59 (466)
Q Consensus        12 CpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~C   59 (466)
                      |+||++.....     ..++|||.||..|+..|+.    .....||.|
T Consensus         1 C~iC~~~~~~~-----~~~~C~H~~c~~C~~~~~~----~~~~~CP~C   39 (39)
T smart00184        1 CPICLEELKDP-----VVLPCGHTFCRSCIRKWLK----SGNNTCPIC   39 (39)
T ss_pred             CCcCccCCCCc-----EEecCCChHHHHHHHHHHH----hCcCCCCCC
Confidence            89999996532     4789999999999999988    256789987

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

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

Probab=98.46  E-value=4.5e-08  Score=95.35  Aligned_cols=46  Identities=35%  Similarity=0.779  Sum_probs=39.5

Q ss_pred             CCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCc
Q 012292            6 KFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQ   61 (466)
Q Consensus         6 ~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~   61 (466)
                      ..+.++||||++.|...     .+++|||+||..|+..++.     ....||.||.
T Consensus        10 ~~~~~~C~iC~~~~~~p-----~~l~C~H~~c~~C~~~~~~-----~~~~Cp~cr~   55 (386)
T KOG2177|consen   10 LQEELTCPICLEYFREP-----VLLPCGHNFCRACLTRSWE-----GPLSCPVCRP   55 (386)
T ss_pred             ccccccChhhHHHhhcC-----ccccccchHhHHHHHHhcC-----CCcCCcccCC
Confidence            45789999999999832     4889999999999999877     4589999994

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

Probab=98.45  E-value=9.2e-08  Score=93.26  Aligned_cols=51  Identities=29%  Similarity=0.742  Sum_probs=41.2

Q ss_pred             CCCccccccccccc-ccccCcceeecCCCcccHHHHHH-HHHhcCCCCCCCCcCcCccccCCC
Q 012292            7 FGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQ-WFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         7 ~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~-wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ..+.-|+||++... |+      .++|||+||+.||.. |-..    ....||+||+.+.+..
T Consensus       213 ~~d~kC~lC~e~~~~ps------~t~CgHlFC~~Cl~~~~t~~----k~~~CplCRak~~pk~  265 (271)
T COG5574         213 LADYKCFLCLEEPEVPS------CTPCGHLFCLSCLLISWTKK----KYEFCPLCRAKVYPKK  265 (271)
T ss_pred             ccccceeeeecccCCcc------cccccchhhHHHHHHHHHhh----ccccCchhhhhccchh
Confidence            45678999999987 64      789999999999999 7551    3455999999887654

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

Probab=98.45  E-value=9.8e-08  Score=76.80  Aligned_cols=50  Identities=28%  Similarity=0.557  Sum_probs=39.0

Q ss_pred             CCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            8 GKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         8 ~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      +.+.||||.+.|. |+      +++|||+|+..||..|+..    +...||+|+.+++...
T Consensus         3 ~~f~CpIt~~lM~dPV------i~~~G~tyer~~I~~~l~~----~~~~~P~t~~~l~~~~   53 (73)
T PF04564_consen    3 DEFLCPITGELMRDPV------ILPSGHTYERSAIERWLEQ----NGGTDPFTRQPLSESD   53 (73)
T ss_dssp             GGGB-TTTSSB-SSEE------EETTSEEEEHHHHHHHHCT----TSSB-TTT-SB-SGGG
T ss_pred             cccCCcCcCcHhhCce------eCCcCCEEcHHHHHHHHHc----CCCCCCCCCCcCCccc
Confidence            4679999999999 65      8999999999999999993    4799999999888654

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

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

Probab=98.40  E-value=2.5e-07  Score=76.14  Aligned_cols=55  Identities=31%  Similarity=0.704  Sum_probs=41.0

Q ss_pred             CCccccccccccc---cc-----ccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCcccc
Q 012292            8 GKTICSICYEDLK---PI-----VEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus         8 ~eltCpICLe~f~---P~-----~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~   64 (466)
                      .+-.|+||.-.|+   |.     .+-....-.|+|.||..||.+|+....  ....||.||+++.
T Consensus        20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~--~~~~CPmCR~~w~   82 (85)
T PF12861_consen   20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQS--SKGQCPMCRQPWK   82 (85)
T ss_pred             CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHcccc--CCCCCCCcCCeee
Confidence            3668999998887   21     112334567999999999999999532  3579999999875

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

Probab=98.28  E-value=2.4e-07  Score=101.63  Aligned_cols=51  Identities=35%  Similarity=0.771  Sum_probs=43.8

Q ss_pred             CCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            8 GKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         8 ~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      +-++||+|...+.+.     .++.|||+||+.|+...+++    +...||.|...|+..+
T Consensus       642 ~~LkCs~Cn~R~Kd~-----vI~kC~H~FC~~Cvq~r~et----RqRKCP~Cn~aFganD  692 (698)
T KOG0978|consen  642 ELLKCSVCNTRWKDA-----VITKCGHVFCEECVQTRYET----RQRKCPKCNAAFGAND  692 (698)
T ss_pred             hceeCCCccCchhhH-----HHHhcchHHHHHHHHHHHHH----hcCCCCCCCCCCCccc
Confidence            358999999888754     47889999999999998885    6799999999998765

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

Probab=98.25  E-value=2e-07  Score=72.50  Aligned_cols=47  Identities=32%  Similarity=0.815  Sum_probs=25.1

Q ss_pred             Cccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            9 KTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         9 eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      -+.|++|.+.++ |+     .+..|.|+||..|+...+.       ..||+|+.+....+
T Consensus         7 lLrCs~C~~~l~~pv-----~l~~CeH~fCs~Ci~~~~~-------~~CPvC~~Paw~qD   54 (65)
T PF14835_consen    7 LLRCSICFDILKEPV-----CLGGCEHIFCSSCIRDCIG-------SECPVCHTPAWIQD   54 (65)
T ss_dssp             TTS-SSS-S--SS-B--------SSS--B-TTTGGGGTT-------TB-SSS--B-S-SS
T ss_pred             hcCCcHHHHHhcCCc-----eeccCccHHHHHHhHHhcC-------CCCCCcCChHHHHH
Confidence            468999999999 75     5789999999999987544       46999999987665

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

Probab=98.20  E-value=6.2e-07  Score=97.96  Aligned_cols=52  Identities=37%  Similarity=0.867  Sum_probs=42.9

Q ss_pred             CCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCcccc
Q 012292            8 GKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus         8 ~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~   64 (466)
                      .+..|+||.|.+.......+..++|||.||..|+..|++     ...+||.||..+.
T Consensus       290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~e-----r~qtCP~CR~~~~  341 (543)
T KOG0802|consen  290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFE-----RQQTCPTCRTVLY  341 (543)
T ss_pred             cCCeeeeechhhccccccccceeecccchHHHHHHHHHH-----HhCcCCcchhhhh
Confidence            467999999999831224456899999999999999999     6899999999443

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

Probab=97.94  E-value=1.2e-06  Score=88.66  Aligned_cols=55  Identities=25%  Similarity=0.429  Sum_probs=44.5

Q ss_pred             CCCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            5 NKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         5 ~~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      +.+.++.|||||+++.-+    ..+..|+|-||..||...+..    +...||.||+.+....
T Consensus        39 ~~~~~v~c~icl~llk~t----mttkeClhrfc~~ci~~a~r~----gn~ecptcRk~l~Skr   93 (381)
T KOG0311|consen   39 MFDIQVICPICLSLLKKT----MTTKECLHRFCFDCIWKALRS----GNNECPTCRKKLVSKR   93 (381)
T ss_pred             HhhhhhccHHHHHHHHhh----cccHHHHHHHHHHHHHHHHHh----cCCCCchHHhhccccc
Confidence            346678999999999833    235679999999999877763    6789999999988765

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

Probab=97.88  E-value=0.00021  Score=69.39  Aligned_cols=50  Identities=28%  Similarity=0.598  Sum_probs=38.4

Q ss_pred             CCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            8 GKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         8 ~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ++..|..|.-.-.   .+..+++.|+|+||..|....       ....||.|+.++....
T Consensus         2 ~~VhCn~C~~~~~---~~~f~LTaC~HvfC~~C~k~~-------~~~~C~lCkk~ir~i~   51 (233)
T KOG4739|consen    2 DFVHCNKCFRFPS---QDPFFLTACRHVFCEPCLKAS-------SPDVCPLCKKSIRIIQ   51 (233)
T ss_pred             ceEEeccccccCC---CCceeeeechhhhhhhhcccC-------Cccccccccceeeeee
Confidence            4578998876643   577789999999999997653       2248999999976554

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

Probab=97.88  E-value=6e-06  Score=82.02  Aligned_cols=50  Identities=32%  Similarity=0.651  Sum_probs=41.5

Q ss_pred             CCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            7 FGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         7 ~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      .-...|+||+.... |+      .++|+|.||+.||......    +..+||+||.+++..
T Consensus         5 ~~~~eC~IC~nt~n~Pv------~l~C~HkFCyiCiKGsy~n----dk~~CavCR~pids~   55 (324)
T KOG0824|consen    5 TKKKECLICYNTGNCPV------NLYCFHKFCYICIKGSYKN----DKKTCAVCRFPIDST   55 (324)
T ss_pred             ccCCcceeeeccCCcCc------cccccchhhhhhhcchhhc----CCCCCceecCCCCcc
Confidence            34568999999987 75      7899999999999985441    567899999999866

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

Probab=97.80  E-value=6.5e-06  Score=80.51  Aligned_cols=61  Identities=30%  Similarity=0.775  Sum_probs=46.9

Q ss_pred             CCCCCCccccccccccc-ccccC----cceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            4 ENKFGKTICSICYEDLK-PIVED----LQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         4 ~~~~~eltCpICLe~f~-P~~~~----~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      +-..++..|.||-..++ .+++.    ....+.|+|+||.-||..|--   -++..+||.|+..+....
T Consensus       219 tkhl~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWci---vGKkqtCPYCKekVdl~r  284 (328)
T KOG1734|consen  219 TKHLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCI---VGKKQTCPYCKEKVDLKR  284 (328)
T ss_pred             CCCCCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhhee---ecCCCCCchHHHHhhHhh
Confidence            34556789999999987 22111    234689999999999999944   457899999999998765

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

Probab=97.77  E-value=9.3e-06  Score=85.07  Aligned_cols=53  Identities=30%  Similarity=0.728  Sum_probs=40.1

Q ss_pred             Cccccccccccc---cccc--Cc-------ceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccC
Q 012292            9 KTICSICYEDLK---PIVE--DL-------QVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS   65 (466)
Q Consensus         9 eltCpICLe~f~---P~~~--~~-------~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~   65 (466)
                      ..-|+||+..++   ..+.  ..       -.++||.|.||..||.+|.+.    .+..||+||.++++
T Consensus       571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~----ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDT----YKLICPVCRCPLPP  635 (636)
T ss_pred             cccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhh----hcccCCccCCCCCC
Confidence            457999999886   1111  01       245799999999999999993    46799999998864

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

Probab=97.72  E-value=1.1e-05  Score=64.56  Aligned_cols=57  Identities=35%  Similarity=0.651  Sum_probs=26.4

Q ss_pred             CcccccccccccccccCccee---ecCCCcccHHHHHHHHHhcCCCC------CCCCcCcCccccC
Q 012292            9 KTICSICYEDLKPIVEDLQVI---SICGHVFHELCLQQWFEYCSSSK------KCTCPVCKQRCSS   65 (466)
Q Consensus         9 eltCpICLe~f~P~~~~~~~l---lpCGHsFC~~CL~~wle~~~~~~------s~~CP~CR~~~~~   65 (466)
                      +..|+||+..+.+..+....+   ..|++.||..||..|+...+.++      ...||.|+.+++-
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~   67 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW   67 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence            568999999865111111112   36999999999999998543322      2359999998753

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

Probab=97.71  E-value=8.5e-05  Score=76.57  Aligned_cols=56  Identities=27%  Similarity=0.726  Sum_probs=44.9

Q ss_pred             CCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            8 GKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         8 ~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      ...+||||++.+.-+.++....+.|||.|-..||++|+.   ......||.|....+.+
T Consensus         3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~---k~~~~~cp~c~~katkr   58 (463)
T KOG1645|consen    3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG---KKTKMQCPLCSGKATKR   58 (463)
T ss_pred             ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHh---hhhhhhCcccCChhHHH
Confidence            356999999999933577777899999999999999995   23467899997655544

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

Probab=97.62  E-value=4.5e-05  Score=61.62  Aligned_cols=51  Identities=29%  Similarity=0.689  Sum_probs=37.7

Q ss_pred             ccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292           11 ICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus        11 tCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      +||-|.--++|..+.+..---|.|.||..||.+|+.     ....||.||+++...
T Consensus        33 ~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~-----Tk~~CPld~q~w~~~   83 (88)
T COG5194          33 TCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLD-----TKGVCPLDRQTWVLA   83 (88)
T ss_pred             cCcccccCCCCCCcceEEEEecchHHHHHHHHHHHh-----hCCCCCCCCceeEEe
Confidence            455555544443444455667999999999999999     468899999987643

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

Probab=97.51  E-value=4.7e-05  Score=79.73  Aligned_cols=50  Identities=26%  Similarity=0.713  Sum_probs=42.6

Q ss_pred             CCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            6 KFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         6 ~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      ...++.|.||+..+- |+      .+||||+||..||.+.+.     ....||.||..+...
T Consensus        81 ~~sef~c~vc~~~l~~pv------~tpcghs~c~~Cl~r~ld-----~~~~cp~Cr~~l~e~  131 (398)
T KOG4159|consen   81 IRSEFECCVCSRALYPPV------VTPCGHSFCLECLDRSLD-----QETECPLCRDELVEL  131 (398)
T ss_pred             ccchhhhhhhHhhcCCCc------cccccccccHHHHHHHhc-----cCCCCcccccccccc
Confidence            356789999999998 54      679999999999999766     678999999988754

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

Probab=97.48  E-value=3.5e-05  Score=85.90  Aligned_cols=55  Identities=33%  Similarity=0.821  Sum_probs=41.3

Q ss_pred             CCCcccccccccccccccCcc--eeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCcccc
Q 012292            7 FGKTICSICYEDLKPIVEDLQ--VISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus         7 ~~eltCpICLe~f~P~~~~~~--~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~   64 (466)
                      .+.-.|+||+..+.-+.+.+|  .+..|.|-||..|+-.|+..   +++.+||.||..++
T Consensus      1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~S---s~~s~CPlCRseit 1523 (1525)
T COG5219        1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFAS---SARSNCPLCRSEIT 1523 (1525)
T ss_pred             CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHh---cCCCCCCccccccc
Confidence            345689999998872222221  24569999999999999994   46789999998775

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

Probab=97.47  E-value=8.2e-05  Score=73.23  Aligned_cols=50  Identities=30%  Similarity=0.703  Sum_probs=40.1

Q ss_pred             CCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCcccc
Q 012292            7 FGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus         7 ~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~   64 (466)
                      ..+.+||+|-+.-. |-     .+.+|||.||+.|+..-..+   +.+.+||.|..++.
T Consensus       237 t~~~~C~~Cg~~PtiP~-----~~~~C~HiyCY~Ci~ts~~~---~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  237 TSDTECPVCGEPPTIPH-----VIGKCGHIYCYYCIATSRLW---DASFTCPLCGENVE  287 (298)
T ss_pred             cCCceeeccCCCCCCCe-----eeccccceeehhhhhhhhcc---hhhcccCccCCCCc
Confidence            45789999999876 53     56779999999999986553   25689999988876

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

Probab=97.43  E-value=3.8e-05  Score=77.41  Aligned_cols=53  Identities=23%  Similarity=0.510  Sum_probs=43.6

Q ss_pred             CCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            6 KFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         6 ~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      .....+|.+|-.+|.++    -.++-|-|+||.+||..+++     ....||.|...+....
T Consensus        12 ~n~~itC~LC~GYliDA----TTI~eCLHTFCkSCivk~l~-----~~~~CP~C~i~ih~t~   64 (331)
T KOG2660|consen   12 LNPHITCRLCGGYLIDA----TTITECLHTFCKSCIVKYLE-----ESKYCPTCDIVIHKTH   64 (331)
T ss_pred             cccceehhhccceeecc----hhHHHHHHHHHHHHHHHHHH-----HhccCCccceeccCcc
Confidence            44568999999999832    14677999999999999999     4789999998887664

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

Probab=97.41  E-value=7.1e-05  Score=76.95  Aligned_cols=60  Identities=27%  Similarity=0.550  Sum_probs=41.2

Q ss_pred             CCCccccccccccccc--ccCccee-ecCCCcccHHHHHHHHHhcC--CCCCCCCcCcCccccCC
Q 012292            7 FGKTICSICYEDLKPI--VEDLQVI-SICGHVFHELCLQQWFEYCS--SSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         7 ~~eltCpICLe~f~P~--~~~~~~l-lpCGHsFC~~CL~~wle~~~--~~~s~~CP~CR~~~~~~   66 (466)
                      ..+-+|.||++.....  ......+ ++|.|.||..||..|-....  ..-+..||.||......
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v  223 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFV  223 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccc
Confidence            3467999999998721  1111222 56999999999999975321  12268999999876543

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

Probab=97.40  E-value=9e-05  Score=56.90  Aligned_cols=47  Identities=26%  Similarity=0.554  Sum_probs=31.0

Q ss_pred             CCCCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcC
Q 012292            4 ENKFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPV   58 (466)
Q Consensus         4 ~~~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~   58 (466)
                      +.....+.|||.+..|. |+     ....|||+|....|.+|+.   ..+...||+
T Consensus         6 ~~~~~~~~CPiT~~~~~~PV-----~s~~C~H~fek~aI~~~i~---~~~~~~CPv   53 (57)
T PF11789_consen    6 EGGTISLKCPITLQPFEDPV-----KSKKCGHTFEKEAILQYIQ---RNGSKRCPV   53 (57)
T ss_dssp             -SSB--SB-TTTSSB-SSEE-----EESSS--EEEHHHHHHHCT---TTS-EE-SC
T ss_pred             eccEeccCCCCcCChhhCCc-----CcCCCCCeecHHHHHHHHH---hcCCCCCCC
Confidence            34455789999999998 75     4568999999999999984   236789998

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

Probab=97.31  E-value=8.2e-05  Score=55.95  Aligned_cols=47  Identities=28%  Similarity=0.657  Sum_probs=36.3

Q ss_pred             CcccccccccccccccCcceeecCCCc-ccHHHHHHHHHhcCCCCCCCCcCcCcccc
Q 012292            9 KTICSICYEDLKPIVEDLQVISICGHV-FHELCLQQWFEYCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus         9 eltCpICLe~f~P~~~~~~~llpCGHs-FC~~CL~~wle~~~~~~s~~CP~CR~~~~   64 (466)
                      ...|.||++--.++     .+..|||. .|+.|-.+.+.    +....||.||.++.
T Consensus         7 ~dECTICye~pvds-----VlYtCGHMCmCy~Cg~rl~~----~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    7 SDECTICYEHPVDS-----VLYTCGHMCMCYACGLRLKK----ALHGCCPICRAPIK   54 (62)
T ss_pred             ccceeeeccCcchH-----HHHHcchHHhHHHHHHHHHH----ccCCcCcchhhHHH
Confidence            47899999987533     36789995 59999777655    26789999999864

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

Probab=97.27  E-value=6.8e-05  Score=60.12  Aligned_cols=53  Identities=30%  Similarity=0.758  Sum_probs=38.6

Q ss_pred             ccccccccccc---cc----ccCcc-eeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCcccc
Q 012292           10 TICSICYEDLK---PI----VEDLQ-VISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus        10 ltCpICLe~f~---P~----~~~~~-~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~   64 (466)
                      .+|.||.-.|+   |.    .++.+ ..--|.|.||..||..|+....  ....||.||+.+.
T Consensus        21 e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~t--sq~~CPmcRq~~~   81 (84)
T KOG1493|consen   21 ETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPT--SQGQCPMCRQTWQ   81 (84)
T ss_pred             CccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCcc--ccccCCcchheeE
Confidence            38999988886   21    12222 2345999999999999998532  4578999999765

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

Probab=97.27  E-value=0.00026  Score=52.65  Aligned_cols=44  Identities=32%  Similarity=0.798  Sum_probs=32.7

Q ss_pred             ccccccccccccccCcceeecCC-----CcccHHHHHHHHHhcCCCCCCCCcCcC
Q 012292           11 ICSICYEDLKPIVEDLQVISICG-----HVFHELCLQQWFEYCSSSKKCTCPVCK   60 (466)
Q Consensus        11 tCpICLe~f~P~~~~~~~llpCG-----HsFC~~CL~~wle~~~~~~s~~CP~CR   60 (466)
                      .|-||++...+   ..+.+.||.     |.||..||.+|+...   +...||+|+
T Consensus         1 ~CrIC~~~~~~---~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~---~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDEGDE---GDPLVSPCRCKGSLKYVHQECLERWINES---GNKTCEICK   49 (49)
T ss_pred             CccCCCCCCCC---CCeeEeccccCCchhHHHHHHHHHHHHHc---CCCcCCCCC
Confidence            48999983322   223467985     899999999999842   456999995

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

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

Probab=97.24  E-value=0.0001  Score=69.33  Aligned_cols=46  Identities=33%  Similarity=0.816  Sum_probs=37.8

Q ss_pred             Cccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccC
Q 012292            9 KTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS   65 (466)
Q Consensus         9 eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~   65 (466)
                      .+.|.||-..|. |+      .+.|||.||..|..+-++     ....|-+|.+....
T Consensus       196 PF~C~iCKkdy~spv------vt~CGH~FC~~Cai~~y~-----kg~~C~~Cgk~t~G  242 (259)
T COG5152         196 PFLCGICKKDYESPV------VTECGHSFCSLCAIRKYQ-----KGDECGVCGKATYG  242 (259)
T ss_pred             ceeehhchhhccchh------hhhcchhHHHHHHHHHhc-----cCCcceecchhhcc
Confidence            358999999998 75      789999999999887655     67899999775543

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

Probab=97.19  E-value=0.00047  Score=73.08  Aligned_cols=58  Identities=28%  Similarity=0.653  Sum_probs=45.9

Q ss_pred             CCCCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            4 ENKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         4 ~~~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      +...+...|.+|-+.-.+.     ....|.|.||..|+..++.....+.+.+||+|...++..
T Consensus       531 ~enk~~~~C~lc~d~aed~-----i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiD  588 (791)
T KOG1002|consen  531 DENKGEVECGLCHDPAEDY-----IESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSID  588 (791)
T ss_pred             ccccCceeecccCChhhhh-----HhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccccc
Confidence            4456678999999987622     257899999999999998865556679999998877643

>PRK02224 chromosome segregation protein; Provisional

Probab=97.17  E-value=0.11  Score=60.21  Aligned_cols=15  Identities=33%  Similarity=0.645  Sum_probs=11.9

Q ss_pred             CCCCcCcCccccCCC
Q 012292           53 KCTCPVCKQRCSSSN   67 (466)
Q Consensus        53 s~~CP~CR~~~~~~~   67 (466)
                      ...||+|..++....
T Consensus       451 ~~~Cp~C~r~~~~~~  465 (880)
T PRK02224        451 AGKCPECGQPVEGSP  465 (880)
T ss_pred             cccCCCCCCcCCCcc
Confidence            468999999887654

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

Probab=97.03  E-value=0.00018  Score=79.19  Aligned_cols=56  Identities=20%  Similarity=0.352  Sum_probs=42.3

Q ss_pred             CCCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            5 NKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         5 ~~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      +.+..-.||+|+..+..-  -...-.+|+|.||..||..|-.     ...+||+||..|....
T Consensus       119 ~~~~~~~CP~Ci~s~~Dq--L~~~~k~c~H~FC~~Ci~sWsR-----~aqTCPiDR~EF~~v~  174 (1134)
T KOG0825|consen  119 QTHVENQCPNCLKSCNDQ--LEESEKHTAHYFCEECVGSWSR-----CAQTCPVDRGEFGEVK  174 (1134)
T ss_pred             hhhhhhhhhHHHHHHHHH--hhccccccccccHHHHhhhhhh-----hcccCchhhhhhheee
Confidence            346667899999887610  1112368999999999999977     5789999999887654

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

Probab=96.89  E-value=0.00045  Score=72.70  Aligned_cols=52  Identities=31%  Similarity=0.735  Sum_probs=43.4

Q ss_pred             CCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            6 KFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         6 ~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ....+.|++|...+. |+     ..+.|||.||..|+..|+.     ....||.|+.......
T Consensus        18 ~~~~l~C~~C~~vl~~p~-----~~~~cgh~fC~~C~~~~~~-----~~~~cp~~~~~~~~~~   70 (391)
T KOG0297|consen   18 LDENLLCPICMSVLRDPV-----QTTTCGHRFCAGCLLESLS-----NHQKCPVCRQELTQAE   70 (391)
T ss_pred             CcccccCccccccccCCC-----CCCCCCCcccccccchhhc-----cCcCCcccccccchhh
Confidence            456799999999998 53     1258999999999999988     4789999998887665

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

Probab=96.88  E-value=0.00042  Score=71.32  Aligned_cols=50  Identities=32%  Similarity=0.805  Sum_probs=40.8

Q ss_pred             cccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292           10 TICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus        10 ltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ..|-||-+-=.++     .+-||||..|..||..|-..   +...+||+||..+....
T Consensus       370 eLCKICaendKdv-----kIEPCGHLlCt~CLa~WQ~s---d~gq~CPFCRcEIKGte  419 (563)
T KOG1785|consen  370 ELCKICAENDKDV-----KIEPCGHLLCTSCLAAWQDS---DEGQTCPFCRCEIKGTE  419 (563)
T ss_pred             HHHHHhhccCCCc-----ccccccchHHHHHHHhhccc---CCCCCCCceeeEecccc
Confidence            4799999876554     57899999999999999652   24789999999987665

>TIGR02169 SMC_prok_A chromosome segregation protein SMC, primarily archaeal type

Probab=96.86  E-value=0.26  Score=58.19  Aligned_cols=46  Identities=11%  Similarity=0.152  Sum_probs=18.4

Q ss_pred             HHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 012292          225 NYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVEL  270 (466)
Q Consensus       225 ~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~  270 (466)
                      .+..+...++.+.++.......+.++..++..++..+..++..+..
T Consensus       442 ~~~~~~~~l~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~l~~~l~~  487 (1164)
T TIGR02169       442 EKEDKALEIKKQEWKLEQLAADLSKYEQELYDLKEEYDRVEKELSK  487 (1164)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333333333333333444444444444444444444433

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.

>TIGR00606 rad50 rad50

Probab=96.83  E-value=0.24  Score=60.05  Aligned_cols=32  Identities=16%  Similarity=0.384  Sum_probs=20.2

Q ss_pred             ccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292           36 FHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus        36 FC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ....++..+++.........||+|...|....
T Consensus       660 ~~~~~~~k~ie~a~~~~~~~C~LC~R~f~~ee  691 (1311)
T TIGR00606       660 GATAVYSQFITQLTDENQSCCPVCQRVFQTEA  691 (1311)
T ss_pred             HHHHHHHHHHHHHhhccCCcCCCCCCCCCChh
Confidence            34455666655321124679999999998664

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

>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes

Probab=96.73  E-value=0.2  Score=56.63  Aligned_cols=19  Identities=26%  Similarity=0.562  Sum_probs=8.0

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q 012292          245 EKLEKAKEKINKLKTRVQE  263 (466)
Q Consensus       245 ~kLek~~~ei~~Lk~~v~e  263 (466)
                      ..+.+-+.||.+||.++.+
T Consensus       636 ~~~~~~d~ei~~lk~ki~~  654 (697)
T PF09726_consen  636 GQLRKKDKEIEELKAKIAQ  654 (697)
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            3344444444444444443

; GO: 0016021 integral to membrane

>PRK11637 AmiB activator; Provisional

Probab=96.69  E-value=1.1  Score=47.79  Aligned_cols=73  Identities=11%  Similarity=0.156  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Q 012292           92 SRAEVKILEVKVSRLHTVLESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTL  164 (466)
Q Consensus        92 l~~El~rLe~kl~~L~~~Le~~~~~lk~L~eel~~~KeQlkeE~~~l~EkLk~~esLeqLL~~q~eEVeklke  164 (466)
                      ++.+++.++..+..+...+......+..+..++..+..++......+......+..++..+.....++..+..
T Consensus        45 ~~~~l~~l~~qi~~~~~~i~~~~~~~~~~~~~l~~l~~qi~~~~~~i~~~~~~i~~~~~ei~~l~~eI~~~q~  117 (428)
T PRK11637         45 NRDQLKSIQQDIAAKEKSVRQQQQQRASLLAQLKKQEEAISQASRKLRETQNTLNQLNKQIDELNASIAKLEQ  117 (428)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444444444444444444333333333333333333333334444444444333333

>TIGR02169 SMC_prok_A chromosome segregation protein SMC, primarily archaeal type

Probab=96.68  E-value=0.48  Score=56.03  Aligned_cols=11  Identities=27%  Similarity=0.407  Sum_probs=5.0

Q ss_pred             ccCCCcccccc
Q 012292          421 LIVPDSAQVQP  431 (466)
Q Consensus       421 ~~~~~~~~~~~  431 (466)
                      ++|+|...+.-
T Consensus       624 ~v~~~l~~a~~  634 (1164)
T TIGR02169       624 LVVEDIEAARR  634 (1164)
T ss_pred             EEEcCHHHHHH
Confidence            44555444333

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.

>KOG0250 consensus DNA repair protein RAD18 (SMC family protein) [Replication, recombination and repair]

Probab=96.66  E-value=0.38  Score=55.82  Aligned_cols=75  Identities=27%  Similarity=0.318  Sum_probs=38.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhhhHHHHHHHhcc
Q 012292          110 LESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRNMDLAKELASLK  184 (466)
Q Consensus       110 Le~~~~~lk~L~eel~~~KeQlkeE~~~l~EkLk~~esLeqLL~~q~eEVeklkeE~~rLq~rn~alakeL~sLK  184 (466)
                      +..+...++..++....+.+.++.......+....+.+++..+.....+++...+++..++..--++..+...++
T Consensus       283 l~~~~~~i~~~qek~~~l~~ki~~~~~k~~~~r~k~teiea~i~~~~~e~~~~d~Ei~~~r~~~~~~~re~~~~~  357 (1074)
T KOG0250|consen  283 LNNQEEEIKKKQEKVDTLQEKIEEKQGKIEEARQKLTEIEAKIGELKDEVDAQDEEIEEARKDLDDLRREVNDLK  357 (1074)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHH
Confidence            333344444444444444444444444444444444456666666666666666666665555444444444444

>PF04641 Rtf2: Rtf2 RING-finger

Probab=96.66  E-value=0.0016  Score=64.87  Aligned_cols=55  Identities=25%  Similarity=0.553  Sum_probs=43.9

Q ss_pred             CCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            6 KFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         6 ~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ....+.|||+...|.+ ..+...+.||||+|++.+|...-      ....||+|-.+|...+
T Consensus       110 ~~~~~~CPvt~~~~~~-~~~fv~l~~cG~V~s~~alke~k------~~~~Cp~c~~~f~~~D  164 (260)
T PF04641_consen  110 SEGRFICPVTGKEFNG-KHKFVYLRPCGCVFSEKALKELK------KSKKCPVCGKPFTEED  164 (260)
T ss_pred             CCceeECCCCCcccCC-ceeEEEEcCCCCEeeHHHHHhhc------ccccccccCCccccCC
Confidence            5667899999999964 23445678999999999999872      2467999999999665

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

Probab=96.65  E-value=0.00059  Score=67.94  Aligned_cols=46  Identities=35%  Similarity=0.756  Sum_probs=38.1

Q ss_pred             ccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292           10 TICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus        10 ltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      .-|.||-..|. |+      .+.|||+||..|-..-++     .+..|++|.+.....
T Consensus       242 f~c~icr~~f~~pV------vt~c~h~fc~~ca~~~~q-----k~~~c~vC~~~t~g~  288 (313)
T KOG1813|consen  242 FKCFICRKYFYRPV------VTKCGHYFCEVCALKPYQ-----KGEKCYVCSQQTHGS  288 (313)
T ss_pred             ccccccccccccch------hhcCCceeehhhhccccc-----cCCcceecccccccc
Confidence            35999999998 76      789999999999887766     678999997766533

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

Probab=96.60  E-value=0.0012  Score=66.60  Aligned_cols=52  Identities=23%  Similarity=0.590  Sum_probs=42.8

Q ss_pred             Cccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCcccc
Q 012292            9 KTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus         9 eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~   64 (466)
                      .+.|-||-+.|. ....+.+..+.|||+||..|+...+..    ....||+||.+..
T Consensus         3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~----~~i~cpfcR~~~~   55 (296)
T KOG4185|consen    3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGN----SRILCPFCRETTE   55 (296)
T ss_pred             CCceeecCccccccCcccCCcccccCceehHhHHHHHhcC----ceeeccCCCCccc
Confidence            468999999998 334577888999999999999987662    5678999999853

>TIGR02168 SMC_prok_B chromosome segregation protein SMC, common bacterial type

Probab=96.55  E-value=0.6  Score=55.02  Aligned_cols=33  Identities=30%  Similarity=0.466  Sum_probs=13.9

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Q 012292           92 SRAEVKILEVKVSRLHTVLESQGKEIKEINEEL  124 (466)
Q Consensus        92 l~~El~rLe~kl~~L~~~Le~~~~~lk~L~eel  124 (466)
                      +..++..+...+..+...+......+..+..++
T Consensus       675 l~~e~~~l~~~~~~l~~~l~~~~~~~~~~~~~l  707 (1179)
T TIGR02168       675 RRREIEELEEKIEELEEKIAELEKALAELRKEL  707 (1179)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444444443333333333333

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.

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

Probab=96.48  E-value=0.0015  Score=55.51  Aligned_cols=30  Identities=27%  Similarity=0.896  Sum_probs=25.8

Q ss_pred             eecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccc
Q 012292           29 ISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRC   63 (466)
Q Consensus        29 llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~   63 (466)
                      =-.|.|.||..||.+|+.     ....||+|.+.-
T Consensus        78 WG~CNHaFH~hCisrWlk-----tr~vCPLdn~eW  107 (114)
T KOG2930|consen   78 WGVCNHAFHFHCISRWLK-----TRNVCPLDNKEW  107 (114)
T ss_pred             eeecchHHHHHHHHHHHh-----hcCcCCCcCcce
Confidence            356999999999999999     578899997654

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

Probab=96.45  E-value=0.0011  Score=68.19  Aligned_cols=51  Identities=33%  Similarity=0.686  Sum_probs=39.9

Q ss_pred             CCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCcc
Q 012292            8 GKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQR   62 (466)
Q Consensus         8 ~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~   62 (466)
                      .++.|..|-+.+---.+.+. .+||.|.||..|+..+++.   ....+||.||+-
T Consensus       364 ~~L~Cg~CGe~~Glk~e~Lq-ALpCsHIfH~rCl~e~L~~---n~~rsCP~Crkl  414 (518)
T KOG1941|consen  364 TELYCGLCGESIGLKNERLQ-ALPCSHIFHLRCLQEILEN---NGTRSCPNCRKL  414 (518)
T ss_pred             HhhhhhhhhhhhcCCccccc-ccchhHHHHHHHHHHHHHh---CCCCCCccHHHH
Confidence            46889999999872123454 5799999999999999973   356899999943

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

Probab=96.42  E-value=0.0022  Score=65.65  Aligned_cols=49  Identities=22%  Similarity=0.531  Sum_probs=38.9

Q ss_pred             CCCcccccccccccccccCcceeecCCCcc-cHHHHHHHHHhcCCCCCCCCcCcCccccC
Q 012292            7 FGKTICSICYEDLKPIVEDLQVISICGHVF-HELCLQQWFEYCSSSKKCTCPVCKQRCSS   65 (466)
Q Consensus         7 ~~eltCpICLe~f~P~~~~~~~llpCGHsF-C~~CL~~wle~~~~~~s~~CP~CR~~~~~   65 (466)
                      ...-.|-||+..-+.+     .++||-|.. |..|-....-     ....||+||+++..
T Consensus       288 ~~gkeCVIClse~rdt-----~vLPCRHLCLCs~Ca~~Lr~-----q~n~CPICRqpi~~  337 (349)
T KOG4265|consen  288 ESGKECVICLSESRDT-----VVLPCRHLCLCSGCAKSLRY-----QTNNCPICRQPIEE  337 (349)
T ss_pred             cCCCeeEEEecCCcce-----EEecchhhehhHhHHHHHHH-----hhcCCCccccchHh
Confidence            3367899999998855     589999954 9999886542     45889999999864

>PF15619 Lebercilin: Ciliary protein causing Leber congenital amaurosis disease

Probab=96.42  E-value=0.94  Score=43.37  Aligned_cols=37  Identities=27%  Similarity=0.423  Sum_probs=27.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHH
Q 012292          238 REKARFSEKLEKAKEKINKLKTRVQELETAVELKDNE  274 (466)
Q Consensus       238 ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~~~ne  274 (466)
                      ++...-.++...+..++..|..++..|...|.+++++
T Consensus       157 rql~~e~kK~~~~~~~~~~l~~ei~~L~~klkEKer~  193 (194)
T PF15619_consen  157 RQLASEKKKHKEAQEEVKSLQEEIQRLNQKLKEKERE  193 (194)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            3444444777778888888888888888888887765

>TIGR02168 SMC_prok_B chromosome segregation protein SMC, common bacterial type

Probab=96.42  E-value=0.85  Score=53.75  Aligned_cols=27  Identities=26%  Similarity=0.353  Sum_probs=11.1

Q ss_pred             hHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 012292           91 VSRAEVKILEVKVSRLHTVLESQGKEI  117 (466)
Q Consensus        91 ~l~~El~rLe~kl~~L~~~Le~~~~~l  117 (466)
                      .+..++..+...+..+...+......+
T Consensus       681 ~l~~~~~~l~~~l~~~~~~~~~~~~~l  707 (1179)
T TIGR02168       681 ELEEKIEELEEKIAELEKALAELRKEL  707 (1179)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444443333333333

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.

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

Probab=96.18  E-value=0.0019  Score=64.50  Aligned_cols=62  Identities=26%  Similarity=0.635  Sum_probs=45.7

Q ss_pred             CCCCCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcC------------------CCCCCCCcCcCcccc
Q 012292            3 IENKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCS------------------SSKKCTCPVCKQRCS   64 (466)
Q Consensus         3 ~~~~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~------------------~~~s~~CP~CR~~~~   64 (466)
                      .++.+....|.|||.-|..  ...+..++|-|.||..|+-+++..+-                  ......||+||.++.
T Consensus       109 T~nn~p~gqCvICLygfa~--~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~  186 (368)
T KOG4445|consen  109 TENNHPNGQCVICLYGFAS--SPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIK  186 (368)
T ss_pred             ccCCCCCCceEEEEEeecC--CCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcc
Confidence            3567778899999999962  23345689999999999999875221                  112356999999887


Q ss_pred             CC
Q 012292           65 SS   66 (466)
Q Consensus        65 ~~   66 (466)
                      ..
T Consensus       187 ~e  188 (368)
T KOG4445|consen  187 IE  188 (368)
T ss_pred             cc
Confidence            54

>PRK11637 AmiB activator; Provisional

Probab=96.13  E-value=2  Score=45.81  Aligned_cols=79  Identities=11%  Similarity=0.075  Sum_probs=42.5

Q ss_pred             ChhhHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Q 012292           88 DPEVSRAEVKILEVKVSRLHTVLESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLEC  166 (466)
Q Consensus        88 ~~e~l~~El~rLe~kl~~L~~~Le~~~~~lk~L~eel~~~KeQlkeE~~~l~EkLk~~esLeqLL~~q~eEVeklkeE~  166 (466)
                      ....+..++......+..+...+.....++..+..++.....++......+...-.+++.++..+...+.++.......
T Consensus        48 ~l~~l~~qi~~~~~~i~~~~~~~~~~~~~l~~l~~qi~~~~~~i~~~~~~i~~~~~ei~~l~~eI~~~q~~l~~~~~~l  126 (428)
T PRK11637         48 QLKSIQQDIAAKEKSVRQQQQQRASLLAQLKKQEEAISQASRKLRETQNTLNQLNKQIDELNASIAKLEQQQAAQERLL  126 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344555566666666655566655555666666666555555444444444444445555555555555555444433

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

Probab=96.13  E-value=0.0033  Score=63.99  Aligned_cols=50  Identities=24%  Similarity=0.466  Sum_probs=40.6

Q ss_pred             CCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccC
Q 012292            6 KFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS   65 (466)
Q Consensus         6 ~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~   65 (466)
                      ..++-.||||+---..+     ++.||+|--|+.||.+++.     +...|=.|+..+..
T Consensus       419 ~sEd~lCpICyA~pi~A-----vf~PC~H~SC~~CI~qHlm-----N~k~CFfCktTv~~  468 (489)
T KOG4692|consen  419 DSEDNLCPICYAGPINA-----VFAPCSHRSCYGCITQHLM-----NCKRCFFCKTTVID  468 (489)
T ss_pred             CcccccCcceecccchh-----hccCCCCchHHHHHHHHHh-----cCCeeeEecceeee
Confidence            35678999998665422     4789999999999999998     78899999887763

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

Probab=96.11  E-value=0.43  Score=49.63  Aligned_cols=139  Identities=15%  Similarity=0.029  Sum_probs=92.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhhhHHHHHHHhccccccCChhHHHHHHHHhhcCCCCCh
Q 012292          130 RIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRNMDLAKELASLKLVSDLNLDEDEVLKFALLGNGANNK  209 (466)
Q Consensus       130 QlkeE~~~l~EkLk~~esLeqLL~~q~eEVeklkeE~~rLq~rn~alakeL~sLKlvsd~~~eEeE~LK~~~lg~~~~~~  209 (466)
                      ++.+....+...++.+..+..+...+.-++..+.....-...---.++.++.+||       ++++.++...-|    ..
T Consensus       153 ~lqE~~~~L~~~~~~~~~~~lls~~~~~~~~e~~~t~~~~~slv~sl~I~~~slK-------~~y~k~~~~~~g----~~  221 (465)
T KOG0827|consen  153 ELQENPSDLLISHEYIFGAALLSIKCFFQTAEHWMTSQPTSSLVGSLSICFESLK-------QNYDKISAIVCG----HI  221 (465)
T ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCchHHHHhhhHhhHHHHH-------HHHHHHHHHhhc----cc
Confidence            4566677777777777777666666666666654333333333334689999999       999999887755    44


Q ss_pred             hHHHHHHHHHHHHHH---HHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--hhHHHHHHHHhcc
Q 012292          210 DTIDVLRKSLVIRNK---NYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVEL--KDNEVLRALKVSK  283 (466)
Q Consensus       210 e~~d~Lkk~l~~~~k---~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~--~~ne~l~~l~~~~  283 (466)
                      ...+.|.+.|....+   .|.+|..    .+-++.-+..+++.+++++.+|+..+..|+..+..  ...+..-++..++
T Consensus       222 ~~~~kL~k~L~~~~kl~~~~rel~~----~~~e~k~A~~Dvq~~~ke~~~lk~pltMl~~~~~~~~v~~~t~~~~~lE~  296 (465)
T KOG0827|consen  222 YHHGKLSKWLATKRKLPSCRRELPK----NGFEEKLAFFDVQRMGKEAEKLKPPLTMLEIDYREEHVKLSTSLKVELEK  296 (465)
T ss_pred             chhhHHHHHHHHHHHhHHHHhhhhh----hhHHHHHHHHHHHhhhcchhhcCCchHHHHHhccCccccccccCceeecc
Confidence            566778888777433   4444443    33333345699999999999999998888888776  3334344444444

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

Probab=96.03  E-value=0.0039  Score=62.19  Aligned_cols=43  Identities=28%  Similarity=0.722  Sum_probs=35.0

Q ss_pred             ccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCc
Q 012292           10 TICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQ   61 (466)
Q Consensus        10 ltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~   61 (466)
                      +-||.|-.++. |.     .+.-|||.||..||...+-.    ..+.||.|..
T Consensus       275 LkCplc~~Llrnp~-----kT~cC~~~fc~eci~~al~d----sDf~CpnC~r  318 (427)
T COG5222         275 LKCPLCHCLLRNPM-----KTPCCGHTFCDECIGTALLD----SDFKCPNCSR  318 (427)
T ss_pred             ccCcchhhhhhCcc-----cCccccchHHHHHHhhhhhh----ccccCCCccc
Confidence            89999999998 54     35579999999999976541    5689999954

>PRK04778 septation ring formation regulator EzrA; Provisional

Probab=96.01  E-value=1.9  Score=47.74  Aligned_cols=63  Identities=14%  Similarity=0.205  Sum_probs=47.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHh
Q 012292          110 LESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQR  172 (466)
Q Consensus       110 Le~~~~~lk~L~eel~~~KeQlkeE~~~l~EkLk~~esLeqLL~~q~eEVeklkeE~~rLq~r  172 (466)
                      ++.....++.+.+++..+-..++.+........+....+...+....+....+..+..++...
T Consensus       277 l~~~~~~~~~i~~~Id~Lyd~lekE~~A~~~vek~~~~l~~~l~~~~e~~~~l~~Ei~~l~~s  339 (569)
T PRK04778        277 LDEAEEKNEEIQERIDQLYDILEREVKARKYVEKNSDTLPDFLEHAKEQNKELKEEIDRVKQS  339 (569)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            355566777777777777777778877777777777778888888888888888888887666

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

Probab=96.00  E-value=0.0032  Score=65.41  Aligned_cols=51  Identities=27%  Similarity=0.503  Sum_probs=38.7

Q ss_pred             cccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCC---CCCCcCcCcc
Q 012292           10 TICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSK---KCTCPVCKQR   62 (466)
Q Consensus        10 ltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~---s~~CP~CR~~   62 (466)
                      ..|.||++...  +.+....+||+|+||..|+..++.....++   ...||.|.-+
T Consensus       185 f~C~ICf~e~~--G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~  238 (445)
T KOG1814|consen  185 FDCCICFEEQM--GQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCG  238 (445)
T ss_pred             ccceeeehhhc--CcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCc
Confidence            57999999986  335667899999999999999988655444   3567766443

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=95.98  E-value=0.003  Score=47.90  Aligned_cols=32  Identities=22%  Similarity=0.576  Sum_probs=26.4

Q ss_pred             eeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292           28 VISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus        28 ~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      .++||||..|..|...+       +...||+|..++...
T Consensus        21 ~~~pCgH~I~~~~f~~~-------rYngCPfC~~~~~~~   52 (55)
T PF14447_consen   21 TVLPCGHLICDNCFPGE-------RYNGCPFCGTPFEFD   52 (55)
T ss_pred             ccccccceeeccccChh-------hccCCCCCCCcccCC
Confidence            47899999999997654       568899999988643

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

Probab=95.93  E-value=0.063  Score=53.70  Aligned_cols=51  Identities=29%  Similarity=0.584  Sum_probs=38.2

Q ss_pred             cccccccccc--ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292           11 ICSICYEDLK--PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus        11 tCpICLe~f~--P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      -||+|--..-  |.  -..++-+|||..|.+|....+.+    +...||.|-.......
T Consensus         2 ~Cp~CKt~~Y~np~--lk~~in~C~H~lCEsCvd~iF~~----g~~~CpeC~~iLRk~n   54 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPD--LKLMINECGHRLCESCVDRIFSL----GPAQCPECMVILRKNN   54 (300)
T ss_pred             CCcccccceecCcc--ceeeeccccchHHHHHHHHHHhc----CCCCCCcccchhhhcc
Confidence            4999975443  42  33455699999999999999885    6789999977665443

>KOG0996 consensus Structural maintenance of chromosome protein 4 (chromosome condensation complex Condensin, subunit C) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]

Probab=95.93  E-value=1.1  Score=52.47  Aligned_cols=77  Identities=23%  Similarity=0.342  Sum_probs=39.1

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHHHHhhhhHHH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--h
Q 012292          208 NKDTIDVLRKSLVIRNKNYTELMAKCNLLGREK--------------ARFSEKLEKAKEKINKLKTRVQELETAVEL--K  271 (466)
Q Consensus       208 ~~e~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree--------------~~~~~kLek~~~ei~~Lk~~v~eLqk~le~--~  271 (466)
                      ....++.|+..|......+++....+..+..+.              ..+.+..+.......++.+++.++...++.  .
T Consensus       519 ~~~~~e~lk~~L~~~~~~~~e~~~~l~~~k~~l~~~k~e~~~~~k~l~~~~~e~~~~~~~~~~~rqrveE~ks~~~~~~s  598 (1293)
T KOG0996|consen  519 GLKKVEELKGKLLASSESLKEKKTELDDLKEELPSLKQELKEKEKELPKLRKEERNLKSQLNKLRQRVEEAKSSLSSSRS  598 (1293)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            445566666666665555555444333333333              333333333333334555555555554444  5


Q ss_pred             hHHHHHHHHhccc
Q 012292          272 DNEVLRALKVSKK  284 (466)
Q Consensus       272 ~ne~l~~l~~~~~  284 (466)
                      .|++|-.|.+-|.
T Consensus       599 ~~kVl~al~r~ke  611 (1293)
T KOG0996|consen  599 RNKVLDALMRLKE  611 (1293)
T ss_pred             hhHHHHHHHHHHH
Confidence            5666666666554

>KOG0995 consensus Centromere-associated protein HEC1 [Cell cycle control, cell division, chromosome partitioning]

Probab=95.87  E-value=1.7  Score=47.50  Aligned_cols=53  Identities=21%  Similarity=0.350  Sum_probs=33.6

Q ss_pred             HHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh---hhHHHHHHHHhc
Q 012292          230 MAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVEL---KDNEVLRALKVS  282 (466)
Q Consensus       230 ~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~---~~ne~l~~l~~~  282 (466)
                      ...-++|.|+..+...+++...+++.+++-+++.--+.++.   .-|.++++|...
T Consensus       338 n~Er~~l~r~l~~i~~~~d~l~k~vw~~~l~~~~~f~~le~~~~~~~~l~~~i~l~  393 (581)
T KOG0995|consen  338 NLERNKLKRELNKIQSELDRLSKEVWELKLEIEDFFKELEKKFIDLNSLIRRIKLG  393 (581)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445566677777777777777777776666655555555   455666666655

>PHA03096 p28-like protein; Provisional

Probab=95.87  E-value=0.0045  Score=62.40  Aligned_cols=51  Identities=29%  Similarity=0.550  Sum_probs=35.0

Q ss_pred             ccccccccccc--ccccCcce-eecCCCcccHHHHHHHHHhcCCCCCCCCcCcCcc
Q 012292           10 TICSICYEDLK--PIVEDLQV-ISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQR   62 (466)
Q Consensus        10 ltCpICLe~f~--P~~~~~~~-llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~   62 (466)
                      -.|.||++...  +..++-.. +..|.|.||..|+..|.....  ....||.||..
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~--~~e~~~~c~~~  232 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESL--YKETEPENRRL  232 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhh--hcccCccccch
Confidence            47999999876  32333333 456999999999999977432  34556666553

>KOG0250 consensus DNA repair protein RAD18 (SMC family protein) [Replication, recombination and repair]

Probab=95.81  E-value=3.1  Score=48.60  Aligned_cols=10  Identities=20%  Similarity=0.072  Sum_probs=6.5

Q ss_pred             cCCCcccccC
Q 012292          317 HSVPIYNLDW  326 (466)
Q Consensus       317 ~~~~~~~~~~  326 (466)
                      +.+|+|.+-.
T Consensus       492 ~~~P~GPlG~  501 (1074)
T KOG0250|consen  492 QTPPKGPLGK  501 (1074)
T ss_pred             CCCCCCCccc
Confidence            5777776643

>COG1196 Smc Chromosome segregation ATPases [Cell division and chromosome partitioning]

Probab=95.72  E-value=2.5  Score=50.83  Aligned_cols=54  Identities=24%  Similarity=0.359  Sum_probs=21.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 012292          216 RKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVE  269 (466)
Q Consensus       216 kk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le  269 (466)
                      ..++........++..++..|..+......+++.+..++..++..+..+...+.
T Consensus       827 ~~ei~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~l~~~l~  880 (1163)
T COG1196         827 EQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELEDELK  880 (1163)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333444444444444444433334444444444444444443333333

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

Probab=95.70  E-value=0.0079  Score=44.52  Aligned_cols=47  Identities=23%  Similarity=0.628  Sum_probs=22.8

Q ss_pred             cccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccc
Q 012292           12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRC   63 (466)
Q Consensus        12 CpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~   63 (466)
                      ||+|.+.++.. +....--+||+-+|.-|....++    .....||-||.+.
T Consensus         1 cp~C~e~~d~~-d~~~~PC~Cgf~IC~~C~~~i~~----~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDET-DKDFYPCECGFQICRFCYHDILE----NEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CC-CTT--SSTTS----HHHHHHHTT----SS-SB-TTT--B-
T ss_pred             CCCcccccccC-CCccccCcCCCcHHHHHHHHHHh----ccCCCCCCCCCCC
Confidence            89999999732 22222347999999999887765    2478999999874

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.52  E-value=0.01  Score=57.82  Aligned_cols=54  Identities=20%  Similarity=0.411  Sum_probs=44.7

Q ss_pred             CCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            8 GKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         8 ~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      .-..||||-+.+..+ .....+-||||+||..|.+..+.     .-..||+|-.++...+
T Consensus       220 ~ryiCpvtrd~LtNt-~~ca~Lr~sg~Vv~~ecvEklir-----~D~v~pv~d~plkdrd  273 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNT-TPCAVLRPSGHVVTKECVEKLIR-----KDMVDPVTDKPLKDRD  273 (303)
T ss_pred             cceecccchhhhcCc-cceEEeccCCcEeeHHHHHHhcc-----ccccccCCCCcCcccc
Confidence            356899999999832 23456789999999999999987     6788999999998776

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

Probab=95.49  E-value=0.0074  Score=61.28  Aligned_cols=46  Identities=26%  Similarity=0.685  Sum_probs=36.6

Q ss_pred             CCCCcccccccccccccccCcceeecC--CCcccHHHHHHHHHhcCCCCCCCCcCcCccccC
Q 012292            6 KFGKTICSICYEDLKPIVEDLQVISIC--GHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS   65 (466)
Q Consensus         6 ~~~eltCpICLe~f~P~~~~~~~llpC--GHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~   65 (466)
                      ..+-+.||||.+.+.|+      +..|  ||.-|..|-..        ....||.||-+++.
T Consensus        45 ~~~lleCPvC~~~l~~P------i~QC~nGHlaCssC~~~--------~~~~CP~Cr~~~g~   92 (299)
T KOG3002|consen   45 DLDLLDCPVCFNPLSPP------IFQCDNGHLACSSCRTK--------VSNKCPTCRLPIGN   92 (299)
T ss_pred             chhhccCchhhccCccc------ceecCCCcEehhhhhhh--------hcccCCcccccccc
Confidence            45678999999999943      3556  79999999653        35789999999983

>TIGR00606 rad50 rad50

Probab=95.44  E-value=2.4  Score=51.59  Aligned_cols=12  Identities=17%  Similarity=0.769  Sum_probs=9.4

Q ss_pred             Cccccccccccc
Q 012292            9 KTICSICYEDLK   20 (466)
Q Consensus         9 eltCpICLe~f~   20 (466)
                      ...||.|-..|.
T Consensus       677 ~~~C~LC~R~f~  688 (1311)
T TIGR00606       677 QSCCPVCQRVFQ  688 (1311)
T ss_pred             CCcCCCCCCCCC
Confidence            457888888887

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

>KOG0996 consensus Structural maintenance of chromosome protein 4 (chromosome condensation complex Condensin, subunit C) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]

Probab=95.39  E-value=2.2  Score=50.21  Aligned_cols=53  Identities=21%  Similarity=0.223  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHH
Q 012292          222 RNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNE  274 (466)
Q Consensus       222 ~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~~~ne  274 (466)
                      +.+..+....+.+.|.....++...+++..-.+..++..+..|+..+..++.+
T Consensus       512 L~~~~~~~~~~~e~lk~~L~~~~~~~~e~~~~l~~~k~~l~~~k~e~~~~~k~  564 (1293)
T KOG0996|consen  512 LLSRHETGLKKVEELKGKLLASSESLKEKKTELDDLKEELPSLKQELKEKEKE  564 (1293)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHh
Confidence            33333334444444444444444444444444444555555444444444443

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

Probab=95.23  E-value=0.032  Score=51.24  Aligned_cols=77  Identities=17%  Similarity=0.419  Sum_probs=45.6

Q ss_pred             CCccccccccccccc------ccCcc-eeecCCCcc-cHHHHHHHHHhcCC--------------------------CCC
Q 012292            8 GKTICSICYEDLKPI------VEDLQ-VISICGHVF-HELCLQQWFEYCSS--------------------------SKK   53 (466)
Q Consensus         8 ~eltCpICLe~f~P~------~~~~~-~llpCGHsF-C~~CL~~wle~~~~--------------------------~~s   53 (466)
                      ++.+||||+|.--.+      +.+.. .-.-|+-+| |..||.++-.....                          ...
T Consensus         1 ed~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (162)
T PF07800_consen    1 EDVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQPE   80 (162)
T ss_pred             CCccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCccccccccccccc
Confidence            478999999986421      01110 112266666 67899998652111                          124


Q ss_pred             CCCcCcCccccCCCCCcchhhhhccCCCCCCC
Q 012292           54 CTCPVCKQRCSSSNSIGDQIDLVISQKPKDPE   85 (466)
Q Consensus        54 ~~CP~CR~~~~~~~~l~~l~~~l~~~~~~~~e   85 (466)
                      ..||+||..+..+. +..-...+++.+...+.
T Consensus        81 L~CPLCRG~V~GWt-vve~AR~~LN~K~RsC~  111 (162)
T PF07800_consen   81 LACPLCRGEVKGWT-VVEPARRFLNAKKRSCS  111 (162)
T ss_pred             ccCccccCceeceE-EchHHHHHhccCCccCc
Confidence            68999999999885 22334555555555444

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

>COG1196 Smc Chromosome segregation ATPases [Cell division and chromosome partitioning]

Probab=95.21  E-value=5.1  Score=48.21  Aligned_cols=63  Identities=24%  Similarity=0.352  Sum_probs=36.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 012292          210 DTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKD  272 (466)
Q Consensus       210 e~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~~~  272 (466)
                      +.++.|...+......++++....+.+..+...+...+..+..+...+...+.++...+....
T Consensus       842 ~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~l~~~l~~~~~~~~~l~~~l~~~~~~~~~~~  904 (1163)
T COG1196         842 EKLDELEEELEELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEELRELESELAELK  904 (1163)
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444555555555555555566666666666666666666666666666666666533

>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association []

Probab=95.12  E-value=4.7  Score=41.51  Aligned_cols=81  Identities=20%  Similarity=0.255  Sum_probs=65.1

Q ss_pred             CCChhHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh---hhHHHHHHHHhc
Q 012292          206 ANNKDTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVEL---KDNEVLRALKVS  282 (466)
Q Consensus       206 ~~~~e~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~---~~ne~l~~l~~~  282 (466)
                      ....+....++.+|.......+.+.+.+..|..+......+++....++.++...+.++++.++.   -+..-+.+|+..
T Consensus       205 ~~D~~eL~~lr~eL~~~~~~i~~~k~~l~el~~el~~l~~~i~~~~~~k~~l~~eI~e~~~~~~~~r~~t~~Ev~~Lk~~  284 (325)
T PF08317_consen  205 SCDQEELEALRQELAEQKEEIEAKKKELAELQEELEELEEKIEELEEQKQELLAEIAEAEKIREECRGWTRSEVKRLKAK  284 (325)
T ss_pred             hcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHH
Confidence            35677888899999888888888888888888888888888999999999999999999988876   344556666665


Q ss_pred             cccc
Q 012292          283 KKAS  286 (466)
Q Consensus       283 ~~~~  286 (466)
                      -...
T Consensus       285 ~~~L  288 (325)
T PF08317_consen  285 VDAL  288 (325)
T ss_pred             HHHH
Confidence            5443

>KOG0964 consensus Structural maintenance of chromosome protein 3 (sister chromatid cohesion complex Cohesin, subunit SMC3) [Cell cycle control, cell division, chromosome partitioning]

Probab=95.10  E-value=4.8  Score=46.67  Aligned_cols=63  Identities=16%  Similarity=0.211  Sum_probs=39.4

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 012292          208 NKDTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVEL  270 (466)
Q Consensus       208 ~~e~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~  270 (466)
                      ..+....|..++...+..+++...+++.|..........+++++.++..++.+..+++..-..
T Consensus       409 ~ke~e~~lq~e~~~~e~~l~~~~e~i~~l~~si~e~~~r~~~~~~~~~~~k~~~del~~~Rk~  471 (1200)
T KOG0964|consen  409 TKEQENILQKEIEDLESELKEKLEEIKELESSINETKGRMEEFDAENTELKRELDELQDKRKE  471 (1200)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445556666666666666666666666666666655566666666666666666666554443

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

Probab=95.05  E-value=1.1  Score=44.02  Aligned_cols=54  Identities=24%  Similarity=0.500  Sum_probs=38.4

Q ss_pred             CCCCCccccccccccc--ccccCcceeec-CCCcccHHHHHHHHHhcCCCCCCCCc--CcCcccc
Q 012292            5 NKFGKTICSICYEDLK--PIVEDLQVISI-CGHVFHELCLQQWFEYCSSSKKCTCP--VCKQRCS   64 (466)
Q Consensus         5 ~~~~eltCpICLe~f~--P~~~~~~~llp-CGHsFC~~CL~~wle~~~~~~s~~CP--~CR~~~~   64 (466)
                      ....+-.||||...--  |.  .+..+-| |=|-.|.+|..+.+..    +...||  -|.+-+.
T Consensus         6 ~~~~d~~CPvCksDrYLnPd--ik~linPECyHrmCESCvdRIFs~----GpAqCP~~gC~kILR   64 (314)
T COG5220           6 EEMEDRRCPVCKSDRYLNPD--IKILINPECYHRMCESCVDRIFSR----GPAQCPYKGCGKILR   64 (314)
T ss_pred             hhhhcccCCccccccccCCC--eEEEECHHHHHHHHHHHHHHHhcC----CCCCCCCccHHHHHH
Confidence            3345668999986544  42  3344455 9999999999999884    567899  7765444

>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]

Probab=94.95  E-value=4.2  Score=40.17  Aligned_cols=26  Identities=8%  Similarity=0.125  Sum_probs=11.9

Q ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHHH
Q 012292          145 KVSVEQLLHSKSQELDKVTLECLKLK  170 (466)
Q Consensus       145 ~esLeqLL~~q~eEVeklkeE~~rLq  170 (466)
                      ++.++........++..+.+...+.+
T Consensus        54 ~e~le~qv~~~e~ei~~~r~r~~~~e   79 (239)
T COG1579          54 LEDLENQVSQLESEIQEIRERIKRAE   79 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444455555544444443

>PF13851 GAS: Growth-arrest specific micro-tubule binding

Probab=94.94  E-value=3.7  Score=39.44  Aligned_cols=85  Identities=19%  Similarity=0.197  Sum_probs=54.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHhcc
Q 012292          212 IDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEK--------AKEKINKLKTRVQELETAVELKDNEVLRALKVSK  283 (466)
Q Consensus       212 ~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek--------~~~ei~~Lk~~v~eLqk~le~~~ne~l~~l~~~~  283 (466)
                      ...+.+.+..+.-.++-|..++.++.++-..+..+++.        +...+--|+.++..|...|+.++-.+-.-|..+.
T Consensus        95 l~~~ek~l~~Lk~e~evL~qr~~kle~ErdeL~~kf~~~i~evqQk~~~kn~lLEkKl~~l~~~lE~keaqL~evl~~~n  174 (201)
T PF13851_consen   95 LKELEKELKDLKWEHEVLEQRFEKLEQERDELYRKFESAIQEVQQKTGLKNLLLEKKLQALSEQLEKKEAQLNEVLAAAN  174 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            34445555555555666666666665555554444444        4444557899999999999999999877777766


Q ss_pred             -ccchhHHhhhcCC
Q 012292          284 -KASQKEEILKGAT  296 (466)
Q Consensus       284 -~~~~~~~~~~~~~  296 (466)
                       .+.....+..++.
T Consensus       175 ldp~~~~~v~~~l~  188 (201)
T PF13851_consen  175 LDPAALSQVSKKLE  188 (201)
T ss_pred             CCHHHHHHHHHHHH
Confidence             4544455555544

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=94.87  E-value=0.03  Score=51.42  Aligned_cols=54  Identities=22%  Similarity=0.672  Sum_probs=39.8

Q ss_pred             CCCCCCcccccccccccccccCcceeecCC--C---cccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            4 ENKFGKTICSICYEDLKPIVEDLQVISICG--H---VFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         4 ~~~~~eltCpICLe~f~P~~~~~~~llpCG--H---sFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      +.+..+..|-||.+...+.      ..||.  .   ..|.+|+++|+..   ++...||+|+.++...
T Consensus         3 ~~s~~~~~CRIC~~~~~~~------~~PC~CkGs~k~VH~sCL~rWi~~---s~~~~CeiC~~~Y~i~   61 (162)
T PHA02825          3 DVSLMDKCCWICKDEYDVV------TNYCNCKNENKIVHKECLEEWINT---SKNKSCKICNGPYNIK   61 (162)
T ss_pred             CcCCCCCeeEecCCCCCCc------cCCcccCCCchHHHHHHHHHHHhc---CCCCcccccCCeEEEE
Confidence            3456678999999886531      23555  4   4499999999984   3678999999988644

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

Probab=94.81  E-value=0.012  Score=65.98  Aligned_cols=49  Identities=29%  Similarity=0.752  Sum_probs=37.9

Q ss_pred             cccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292           10 TICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus        10 ltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ..|+||++ .++.     .+++|||.||..|+...++..   ....||.||..+....
T Consensus       455 ~~c~ic~~-~~~~-----~it~c~h~~c~~c~~~~i~~~---~~~~~~~cr~~l~~~~  503 (674)
T KOG1001|consen  455 HWCHICCD-LDSF-----FITRCGHDFCVECLKKSIQQS---ENAPCPLCRNVLKEKK  503 (674)
T ss_pred             cccccccc-cccc-----eeecccchHHHHHHHhccccc---cCCCCcHHHHHHHHHH
Confidence            78999999 4422     588999999999998877632   2348999998876554

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=94.78  E-value=0.02  Score=58.17  Aligned_cols=55  Identities=18%  Similarity=0.522  Sum_probs=40.7

Q ss_pred             CCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            8 GKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         8 ~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ++-.||.|++.++- .+.-++-.|||--.|.-|....-+.    -+..||-||...+..+
T Consensus        13 eed~cplcie~mdi-tdknf~pc~cgy~ic~fc~~~irq~----lngrcpacrr~y~den   67 (480)
T COG5175          13 EEDYCPLCIEPMDI-TDKNFFPCPCGYQICQFCYNNIRQN----LNGRCPACRRKYDDEN   67 (480)
T ss_pred             ccccCccccccccc-ccCCcccCCcccHHHHHHHHHHHhh----ccCCChHhhhhccccc
Confidence            34459999999982 2334455789999999997766552    4678999999887664

>PRK01156 chromosome segregation protein; Provisional

Probab=94.72  E-value=8.1  Score=45.02  Aligned_cols=12  Identities=33%  Similarity=0.921  Sum_probs=7.3

Q ss_pred             CCCCcCcCcccc
Q 012292           53 KCTCPVCKQRCS   64 (466)
Q Consensus        53 s~~CP~CR~~~~   64 (466)
                      .+.||+|..+.+
T Consensus       452 ~~~Cp~c~~~~~  463 (895)
T PRK01156        452 QSVCPVCGTTLG  463 (895)
T ss_pred             CCCCCCCCCcCC
Confidence            356777766555

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

Probab=94.69  E-value=0.012  Score=49.88  Aligned_cols=32  Identities=38%  Similarity=0.749  Sum_probs=26.2

Q ss_pred             CCcccccccccccccccCcceeecCCCcccHHHHH
Q 012292            8 GKTICSICYEDLKPIVEDLQVISICGHVFHELCLQ   42 (466)
Q Consensus         8 ~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~   42 (466)
                      +.-.|++|-..+..   ......||||+||+.|+.
T Consensus        77 ~~~~C~vC~k~l~~---~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   77 ESTKCSVCGKPLGN---SVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCCCccCcCCcCCC---ceEEEeCCCeEEeccccc
Confidence            45679999999962   345778999999999975

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

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

Probab=94.67  E-value=0.012  Score=43.96  Aligned_cols=48  Identities=21%  Similarity=0.562  Sum_probs=25.0

Q ss_pred             Cccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCcc
Q 012292            9 KTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQR   62 (466)
Q Consensus         9 eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~   62 (466)
                      .+.|||....+. |+     ....|.|.-|.. +..|+..........||+|.++
T Consensus         2 sL~CPls~~~i~~P~-----Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    2 SLRCPLSFQRIRIPV-----RGKNCKHLQCFD-LESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             ESB-TTTSSB-SSEE-----EETT--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred             eeeCCCCCCEEEeCc-----cCCcCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence            368999999998 76     567899987754 4556664333456899999864

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.

>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes

Probab=94.59  E-value=4.3  Score=46.16  Aligned_cols=26  Identities=27%  Similarity=0.405  Sum_probs=11.8

Q ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHH
Q 012292           98 ILEVKVSRLHTVLESQGKEIKEINEE  123 (466)
Q Consensus        98 rLe~kl~~L~~~Le~~~~~lk~L~ee  123 (466)
                      +|+..+..|...|...+...++|+.+
T Consensus       422 rLE~dvkkLraeLq~~Rq~E~ELRsq  447 (697)
T PF09726_consen  422 RLEADVKKLRAELQSSRQSEQELRSQ  447 (697)
T ss_pred             HHHHHHHHHHHHHHhhhhhHHHHHHH
Confidence            44444444444444444444444444

; GO: 0016021 integral to membrane

>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association []

Probab=94.55  E-value=6.5  Score=40.46  Aligned_cols=79  Identities=25%  Similarity=0.369  Sum_probs=42.4

Q ss_pred             cCChhHHHHHHHHhhcCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHH-----------HHHHH
Q 012292          188 DLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAK-----------EKINK  256 (466)
Q Consensus       188 d~~~eEeE~LK~~~lg~~~~~~e~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~-----------~ei~~  256 (466)
                      ..++.+-+.++...    +.....+...++.+..++...+.+...++.+..+.......++.++           .|+.+
T Consensus       205 ~~D~~eL~~lr~eL----~~~~~~i~~~k~~l~el~~el~~l~~~i~~~~~~k~~l~~eI~e~~~~~~~~r~~t~~Ev~~  280 (325)
T PF08317_consen  205 SCDQEELEALRQEL----AEQKEEIEAKKKELAELQEELEELEEKIEELEEQKQELLAEIAEAEKIREECRGWTRSEVKR  280 (325)
T ss_pred             hcCHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHH
Confidence            34444544444333    2344556666666666666666666666655555555554444433           34556


Q ss_pred             HHHHHHHHHHHHhh
Q 012292          257 LKTRVQELETAVEL  270 (466)
Q Consensus       257 Lk~~v~eLqk~le~  270 (466)
                      |+.++..||.....
T Consensus       281 Lk~~~~~Le~~~gw  294 (325)
T PF08317_consen  281 LKAKVDALEKLTGW  294 (325)
T ss_pred             HHHHHHHHHHHHCc
Confidence            66666666655444

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

Probab=94.44  E-value=0.018  Score=64.72  Aligned_cols=43  Identities=40%  Similarity=0.919  Sum_probs=35.3

Q ss_pred             CCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCc
Q 012292            6 KFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQ   61 (466)
Q Consensus         6 ~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~   61 (466)
                      .+....|..|-..++ |.     +..-|||+||..|+.   +     +...||.|+.
T Consensus       837 i~q~skCs~C~~~LdlP~-----VhF~CgHsyHqhC~e---~-----~~~~CP~C~~  880 (933)
T KOG2114|consen  837 IFQVSKCSACEGTLDLPF-----VHFLCGHSYHQHCLE---D-----KEDKCPKCLP  880 (933)
T ss_pred             eeeeeeecccCCccccce-----eeeecccHHHHHhhc---c-----CcccCCccch
Confidence            345578999999999 76     456799999999998   2     5688999976

>PF05701 WEMBL: Weak chloroplast movement under blue light; InterPro: IPR008545 This family consists of several plant proteins of unknown function

Probab=94.41  E-value=9.6  Score=41.88  Aligned_cols=32  Identities=31%  Similarity=0.409  Sum_probs=14.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 012292          239 EKARFSEKLEKAKEKINKLKTRVQELETAVEL  270 (466)
Q Consensus       239 ee~~~~~kLek~~~ei~~Lk~~v~eLqk~le~  270 (466)
                      +...++.++.+++.++..++..+..++..|..
T Consensus       387 ea~~~~~E~~~~k~E~e~~ka~i~t~E~rL~a  418 (522)
T PF05701_consen  387 EAEEAKEEVEKAKEEAEQTKAAIKTAEERLEA  418 (522)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333344444444444444444444444444

Several sequences in this family are described as being myosin heavy chain-like.

>KOG0977 consensus Nuclear envelope protein lamin, intermediate filament superfamily [Cell cycle control, cell division, chromosome partitioning; Nuclear structure]

Probab=94.35  E-value=4.1  Score=44.76  Aligned_cols=25  Identities=12%  Similarity=0.078  Sum_probs=18.8

Q ss_pred             CChhHHHHHHHHHHHHHHHHHHHHH
Q 012292          207 NNKDTIDVLRKSLVIRNKNYTELMA  231 (466)
Q Consensus       207 ~~~e~~d~Lkk~l~~~~k~yeeL~~  231 (466)
                      +....-..|..+|......|+..+.
T Consensus       239 ~r~~F~~eL~~Ai~eiRaqye~~~~  263 (546)
T KOG0977|consen  239 NREYFKNELALAIREIRAQYEAISR  263 (546)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555677788888888888888774

>PF00261 Tropomyosin: Tropomyosin; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells

Probab=94.33  E-value=5  Score=39.34  Aligned_cols=67  Identities=15%  Similarity=0.253  Sum_probs=45.5

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHH
Q 012292          208 NKDTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNE  274 (466)
Q Consensus       208 ~~e~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~~~ne  274 (466)
                      ..+.++.+-..+..+...+..+...+..|.-.+..+..+.......|..|..++.+.+...+..++.
T Consensus       132 aEeR~e~~E~ki~eLE~el~~~~~~lk~lE~~~~~~~~re~~~e~~i~~L~~~lkeaE~Rae~aE~~  198 (237)
T PF00261_consen  132 AEERAEAAESKIKELEEELKSVGNNLKSLEASEEKASEREDEYEEKIRDLEEKLKEAENRAEFAERR  198 (237)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhhhchhHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445556666666666666666666666666666666667777777778888888887777776665

In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].; PDB: 2EFR_A 2Z5H_C 2Z5I_D 2D3E_B 2EFS_D 3U59_B 1C1G_C 1IHQ_A 3AZD_B 1MV4_B ....

>KOG0161 consensus Myosin class II heavy chain [Cytoskeleton]

Probab=94.32  E-value=8.7  Score=48.19  Aligned_cols=55  Identities=27%  Similarity=0.343  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012292          214 VLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAV  268 (466)
Q Consensus       214 ~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~l  268 (466)
                      .+...+......|+++....+++.++...+..+++.+...+..+...+++|++.+
T Consensus      1467 ~~~tel~kl~~~lee~~e~~e~l~renk~l~~ei~dl~~~~~e~~k~v~elek~~ 1521 (1930)
T KOG0161|consen 1467 QLSTELQKLKNALEELLEQLEELRRENKNLSQEIEDLEEQKDEGGKRVHELEKEK 1521 (1930)
T ss_pred             HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333444444555555555555555555555555555555544444444444333

>PF15290 Syntaphilin: Golgi-localised syntaxin-1-binding clamp

Probab=94.28  E-value=1.5  Score=43.87  Aligned_cols=82  Identities=18%  Similarity=0.249  Sum_probs=55.4

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhhhH
Q 012292           96 VKILEVKVSRLHTVLESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRNMD  175 (466)
Q Consensus        96 l~rLe~kl~~L~~~Le~~~~~lk~L~eel~~~KeQlkeE~~~l~EkLk~~esLeqLL~~q~eEVeklkeE~~rLq~rn~a  175 (466)
                      +..|+.++..-...|.....+|.+|+.++.++++.|-+|.+++-++.-.+.+.+..+..+++-|+.|   +..|-+++-|
T Consensus        70 iRHLkakLkes~~~l~dRetEI~eLksQL~RMrEDWIEEECHRVEAQLALKEARkEIkQLkQvieTm---rssL~ekDkG  146 (305)
T PF15290_consen   70 IRHLKAKLKESENRLHDRETEIDELKSQLARMREDWIEEECHRVEAQLALKEARKEIKQLKQVIETM---RSSLAEKDKG  146 (305)
T ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---Hhhhchhhhh
Confidence            4567778888888888888999999999999999999988887666654444444444444444444   2233344444


Q ss_pred             HHHHH
Q 012292          176 LAKEL  180 (466)
Q Consensus       176 lakeL  180 (466)
                      +.+|+
T Consensus       147 iQKYF  151 (305)
T PF15290_consen  147 IQKYF  151 (305)
T ss_pred             HHHHH
Confidence            44443

>PRK09039 hypothetical protein; Validated

Probab=94.27  E-value=7.5  Score=40.44  Aligned_cols=50  Identities=16%  Similarity=0.228  Sum_probs=20.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012292          213 DVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQ  262 (466)
Q Consensus       213 d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~  262 (466)
                      ..|..+|...+..|.+...++..|+.+...++..|..++..|..++++..
T Consensus       119 ~~l~~~L~~~k~~~se~~~~V~~L~~qI~aLr~Qla~le~~L~~ae~~~~  168 (343)
T PRK09039        119 GELAQELDSEKQVSARALAQVELLNQQIAALRRQLAALEAALDASEKRDR  168 (343)
T ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444444444444444444444334444444333333333

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

Probab=94.26  E-value=0.016  Score=63.22  Aligned_cols=44  Identities=27%  Similarity=0.591  Sum_probs=33.1

Q ss_pred             CcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCc
Q 012292            9 KTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQ   61 (466)
Q Consensus         9 eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~   61 (466)
                      .+.|+||+..|.- ....+..+.|||+.|..|++....       .+|| |..
T Consensus        11 ~l~c~ic~n~f~~-~~~~Pvsl~cghtic~~c~~~lyn-------~scp-~~~   54 (861)
T KOG3161|consen   11 LLLCDICLNLFVV-QRLEPVSLQCGHTICGHCVQLLYN-------ASCP-TKR   54 (861)
T ss_pred             HhhchHHHHHHHH-HhcCcccccccchHHHHHHHhHhh-------ccCC-CCc
Confidence            4679999888861 234445789999999999998644       7899 543

>PF15254 CCDC14: Coiled-coil domain-containing protein 14

Probab=94.20  E-value=5.8  Score=44.91  Aligned_cols=116  Identities=19%  Similarity=0.200  Sum_probs=64.7

Q ss_pred             HHHHHHHhhHHHHHHHHHHHHHHHHhhhHHHHHHHhccccccCChhHHHHHHH-------HhhcCCCCChhHHHHHHHHH
Q 012292          147 SVEQLLHSKSQELDKVTLECLKLKQRNMDLAKELASLKLVSDLNLDEDEVLKF-------ALLGNGANNKDTIDVLRKSL  219 (466)
Q Consensus       147 sLeqLL~~q~eEVeklkeE~~rLq~rn~alakeL~sLKlvsd~~~eEeE~LK~-------~~lg~~~~~~e~~d~Lkk~l  219 (466)
                      .|+.+-..++..+.+......-|+.+|..+.+.++.++       +|...+..       ..+.+..........++.++
T Consensus       431 sLqSlN~~Lq~ql~es~k~~e~lq~kneellk~~e~q~-------~Enk~~~~~~~ekd~~l~~~kq~~d~e~~rik~ev  503 (861)
T PF15254_consen  431 SLQSLNMSLQNQLQESLKSQELLQSKNEELLKVIENQK-------EENKRLRKMFQEKDQELLENKQQFDIETTRIKIEV  503 (861)
T ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHhHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence            34444444444455555556666677777777776666       33333311       11111123444455555555


Q ss_pred             HHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 012292          220 VIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVE  269 (466)
Q Consensus       220 ~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le  269 (466)
                      ....-..+.++-+.+--++|-.-+.-.|...+.||++|++...-||.-..
T Consensus       504 ~eal~~~k~~q~kLe~sekEN~iL~itlrQrDaEi~RL~eLtR~LQ~Sma  553 (861)
T PF15254_consen  504 EEALVNVKSLQFKLEASEKENQILGITLRQRDAEIERLRELTRTLQNSMA  553 (861)
T ss_pred             HHHHHHHHHHhhhHHHHHhhhhHhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44444455555555555566666667788888888888877777766543

>PF05667 DUF812: Protein of unknown function (DUF812); InterPro: IPR008530 This family consists of several eukaryotic proteins of unknown function

Probab=94.16  E-value=5.5  Score=44.46  Aligned_cols=64  Identities=19%  Similarity=0.366  Sum_probs=38.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHH
Q 012292          211 TIDVLRKSLVIRNKNYTELMAKCNLLGREKAR---------FSEKLEKAKEKINKLKTRVQELETAVELKDNE  274 (466)
Q Consensus       211 ~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~---------~~~kLek~~~ei~~Lk~~v~eLqk~le~~~ne  274 (466)
                      .+..+..++......|.+|....+.+.+...|         ..+-+.|-+.+|.++-.....||++++.....
T Consensus       455 ~~k~~~~e~~~Kee~~~qL~~e~e~~~k~~~Rs~Yt~RIlEIv~NI~KQk~eI~KIl~DTr~lQkeiN~l~gk  527 (594)
T PF05667_consen  455 EIKEIEEEIRQKEELYKQLVKELEKLPKDVNRSAYTRRILEIVKNIRKQKEEIEKILSDTRELQKEINSLTGK  527 (594)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444555666666666666544333         23556667777777777777777777766554

>PHA02862 5L protein; Provisional

Probab=94.15  E-value=0.04  Score=49.79  Aligned_cols=49  Identities=37%  Similarity=0.809  Sum_probs=37.1

Q ss_pred             cccccccccccccccCcceeecCC-----CcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292           10 TICSICYEDLKPIVEDLQVISICG-----HVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus        10 ltCpICLe~f~P~~~~~~~llpCG-----HsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ..|=||.+.-.+.      .-||.     ...|..||.+|+.+   .+...||+|+.++....
T Consensus         3 diCWIC~~~~~e~------~~PC~C~GS~K~VHq~CL~~WIn~---S~k~~CeLCkteY~Ik~   56 (156)
T PHA02862          3 DICWICNDVCDER------NNFCGCNEEYKVVHIKCMQLWINY---SKKKECNLCKTKYNIKK   56 (156)
T ss_pred             CEEEEecCcCCCC------cccccccCcchhHHHHHHHHHHhc---CCCcCccCCCCeEEEEE
Confidence            5799999986532      24654     46799999999974   46789999999876543

>KOG4643 consensus Uncharacterized coiled-coil protein [Function unknown]

Probab=94.09  E-value=7.9  Score=45.06  Aligned_cols=58  Identities=16%  Similarity=0.190  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012292          211 TIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAV  268 (466)
Q Consensus       211 ~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~l  268 (466)
                      .++.+...+..+.+..++|-.+|+.|+.+..++.+.+.+....-+.|..+.+.|+.+.
T Consensus       395 s~Ee~~SK~leleke~KnLs~k~e~Leeri~ql~qq~~eled~~K~L~~E~ekl~~e~  452 (1195)
T KOG4643|consen  395 SYEELISKHLELEKEHKNLSKKHEILEERINQLLQQLAELEDLEKKLQFELEKLLEET  452 (1195)
T ss_pred             hHHHHHHHHHHHHHHhHhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555555666666667777777777666666555544444444444444444333

>PF12128 DUF3584: Protein of unknown function (DUF3584); InterPro: IPR021979 This family consist of uncharacterised bacterial proteins

Probab=94.08  E-value=17  Score=43.98  Aligned_cols=99  Identities=17%  Similarity=0.271  Sum_probs=72.3

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHhccccchh
Q 012292          209 KDTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVSKKASQK  288 (466)
Q Consensus       209 ~e~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~~~ne~l~~l~~~~~~~~~  288 (466)
                      ...++............+..+....+.+.+....+...|..+..++.+++.++.+|+..|.-....++.-|+.. .+.-.
T Consensus       475 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~~~~~l~~~L~p~~gSL~~fL~~~-~p~We  553 (1201)
T PF12128_consen  475 DKRLEQAQEQQNQAQQAVEELQAEEQELRKERDQAEEELRQARRELEELRAQIAELQRQLDPQKGSLLEFLRKN-KPGWE  553 (1201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCcHHHHHHhC-CCcHH
Confidence            34455555555566666777777777777777777789999999999999999999999999999999999766 44444


Q ss_pred             HHhhhcCCCCCccccccccCChh
Q 012292          289 EEILKGATEDNSISLCTNNVSLE  311 (466)
Q Consensus       289 ~~~~~~~~~~~~~~~~~~~~~~~  311 (466)
                      .-|-+-|+   ..-|...||+|.
T Consensus       554 ~tIGKVid---~eLL~r~dL~P~  573 (1201)
T PF12128_consen  554 QTIGKVID---EELLYRTDLEPQ  573 (1201)
T ss_pred             HHhHhhCC---HHHhcCCCCCCe
Confidence            44555554   335666677653

>PRK02224 chromosome segregation protein; Provisional

Probab=94.07  E-value=15  Score=42.68  Aligned_cols=12  Identities=17%  Similarity=0.476  Sum_probs=7.4

Q ss_pred             Cccccccccccc
Q 012292            9 KTICSICYEDLK   20 (466)
Q Consensus         9 eltCpICLe~f~   20 (466)
                      ...||+|--.|.
T Consensus       451 ~~~Cp~C~r~~~  462 (880)
T PRK02224        451 AGKCPECGQPVE  462 (880)
T ss_pred             cccCCCCCCcCC
Confidence            346777776654

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

Probab=94.01  E-value=0.041  Score=57.19  Aligned_cols=55  Identities=25%  Similarity=0.446  Sum_probs=41.4

Q ss_pred             CCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCcccc
Q 012292            6 KFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus         6 ~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~   64 (466)
                      .|.-.+|||=-+.-.  .+++|+.+.|||+.|..-|.+....  +..++.||.|-....
T Consensus       331 fHSvF~CPVlKeqts--deNPPm~L~CGHVISkdAlnrLS~n--g~~sfKCPYCP~e~~  385 (394)
T KOG2817|consen  331 FHSVFICPVLKEQTS--DENPPMMLICGHVISKDALNRLSKN--GSQSFKCPYCPVEQL  385 (394)
T ss_pred             ccceeecccchhhcc--CCCCCeeeeccceecHHHHHHHhhC--CCeeeeCCCCCcccC
Confidence            456689999777765  3467789999999999999998662  223589999965443

>KOG0980 consensus Actin-binding protein SLA2/Huntingtin-interacting protein Hip1 [Cytoskeleton]

Probab=93.86  E-value=16  Score=42.20  Aligned_cols=50  Identities=16%  Similarity=0.167  Sum_probs=32.6

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHH
Q 012292          208 NKDTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKL  257 (466)
Q Consensus       208 ~~e~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~L  257 (466)
                      -.++++.+.++.-..+-.++++..+.+.+++|...+.-+++++...+..+
T Consensus       471 L~d~le~~~~~~~~~~~K~e~~~~~le~l~~El~~l~~e~~~lq~~~~~~  520 (980)
T KOG0980|consen  471 LNDQLEELQRAAGRAETKTESQAKALESLRQELALLLIELEELQRTLSNL  520 (980)
T ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhH
Confidence            45566666666666666777777777777777777666666666554433

>PF07888 CALCOCO1: Calcium binding and coiled-coil domain (CALCOCO1) like; InterPro: IPR012852 Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein expressed by Mus musculus (CoCoA, Q8CGU1 from SWISSPROT)

Probab=93.84  E-value=13  Score=41.07  Aligned_cols=61  Identities=15%  Similarity=0.219  Sum_probs=36.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHhh
Q 012292          210 DTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFS-------EKLEKAKEKINKLKTRVQELETAVEL  270 (466)
Q Consensus       210 e~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~-------~kLek~~~ei~~Lk~~v~eLqk~le~  270 (466)
                      .-.+.|+..|.........-..+...|+++...+.       .+|..+.-+...|+.++.++...|.+
T Consensus       283 ~e~e~LkeqLr~~qe~lqaSqq~~~~L~~EL~~~~~~RDrt~aeLh~aRLe~aql~~qLad~~l~lke  350 (546)
T PF07888_consen  283 QENEALKEQLRSAQEQLQASQQEAELLRKELSDAVNVRDRTMAELHQARLEAAQLKLQLADASLELKE  350 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHH
Confidence            33455666655555555555555666666633322       56677777777777777777666655

This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1 (Q61026 from SWISSPROT), and thus enhances transcriptional activation by a number of nuclear receptors. CoCoA has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region [].

>PF05667 DUF812: Protein of unknown function (DUF812); InterPro: IPR008530 This family consists of several eukaryotic proteins of unknown function

Probab=93.82  E-value=14  Score=41.40  Aligned_cols=21  Identities=24%  Similarity=0.468  Sum_probs=7.7

Q ss_pred             HhHHHHHHHHHHHHHHHHHHH
Q 012292          104 SRLHTVLESQGKEIKEINEEL  124 (466)
Q Consensus       104 ~~L~~~Le~~~~~lk~L~eel  124 (466)
                      ..+...++.....+..+..++
T Consensus       331 ~~l~~~l~~l~~~i~~~~~~~  351 (594)
T PF05667_consen  331 EELQEQLDELESQIEELEAEI  351 (594)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333333333

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

Probab=93.76  E-value=0.051  Score=55.45  Aligned_cols=50  Identities=22%  Similarity=0.482  Sum_probs=38.0

Q ss_pred             CCCCcccccccccccccccCcceeecCCCcccHHHHHHHHH-hcCCCCCCCCcCcCcccc
Q 012292            6 KFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFE-YCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus         6 ~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle-~~~~~~s~~CP~CR~~~~   64 (466)
                      ..+...|-||-+-+.-+     +.+||+|-.|..|-.+.-. |    ....||+||....
T Consensus        58 DEen~~C~ICA~~~TYs-----~~~PC~H~~CH~Ca~RlRALY----~~K~C~~CrTE~e  108 (493)
T COG5236          58 DEENMNCQICAGSTTYS-----ARYPCGHQICHACAVRLRALY----MQKGCPLCRTETE  108 (493)
T ss_pred             ccccceeEEecCCceEE-----EeccCCchHHHHHHHHHHHHH----hccCCCccccccc
Confidence            44567899999998733     4799999999999765322 1    4688999998643

>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]

Probab=93.74  E-value=16  Score=42.31  Aligned_cols=64  Identities=13%  Similarity=0.220  Sum_probs=32.2

Q ss_pred             hHHHHHHHHHHHHHH-HHHHHHHHHhhhh-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhH
Q 012292          210 DTIDVLRKSLVIRNK-NYTELMAKCNLLG-------REKARFSEKLEKAKEKINKLKTRVQELETAVELKDN  273 (466)
Q Consensus       210 e~~d~Lkk~l~~~~k-~yeeL~~k~e~L~-------ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~~~n  273 (466)
                      ++.+.+...|+..++ ...+|+..++++.       ++...+.+-+=..+..|.+-++.+..|+..+....+
T Consensus       475 Ealee~~EQL~Esn~ele~DLreEld~~~g~~kel~~r~~aaqet~yDrdqTI~KfRelva~Lqdqlqe~~d  546 (1243)
T KOG0971|consen  475 EALEEMNEQLQESNRELELDLREELDMAKGARKELQKRVEAAQETVYDRDQTIKKFRELVAHLQDQLQELTD  546 (1243)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            445555555555555 2334555554442       222222233333455566666666666666665444

>COG4372 Uncharacterized protein conserved in bacteria with the myosin-like domain [Function unknown]

Probab=93.71  E-value=11  Score=39.74  Aligned_cols=37  Identities=8%  Similarity=0.044  Sum_probs=27.4

Q ss_pred             CCChhHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHH
Q 012292          206 ANNKDTIDVLRKSLVIRNKNYTELMAKCNLLGREKAR  242 (466)
Q Consensus       206 ~~~~e~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~  242 (466)
                      ++-.+++..+.+++..+.....++..+++++......
T Consensus       206 a~r~~a~q~r~~ela~r~aa~Qq~~q~i~qrd~~i~q  242 (499)
T COG4372         206 ATRANAAQARTEELARRAAAAQQTAQAIQQRDAQISQ  242 (499)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3467788899999998888877777777776654443

>PF10174 Cast: RIM-binding protein of the cytomatrix active zone; InterPro: IPR019323 This entry represents a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion []

Probab=93.69  E-value=16  Score=42.07  Aligned_cols=63  Identities=16%  Similarity=0.309  Sum_probs=39.8

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHH
Q 012292          208 NKDTIDVLRKSLVIRNKNYTELMAKCNLLGREKA-RFSEKLEKAKEKINKLKTRVQELETAVELKDNE  274 (466)
Q Consensus       208 ~~e~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~-~~~~kLek~~~ei~~Lk~~v~eLqk~le~~~ne  274 (466)
                      ...+...|-+.+....+..+.|..    +..... .....++....++..++.++..||+.|..++-.
T Consensus       431 ~~~~~~~lEea~~eker~~e~l~e----~r~~~e~e~~Eele~~~~e~~~lk~~~~~LQ~eLsEk~~~  494 (775)
T PF10174_consen  431 EDEALETLEEALREKERLQERLEE----QRERAEKERQEELETYQKELKELKAKLESLQKELSEKELQ  494 (775)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHH
Confidence            334445555555554444444432    322222 223788889999999999999999999987744

Located at the C terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). These proteins also contain four coiled-coil domains [].

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

Probab=93.67  E-value=0.059  Score=48.08  Aligned_cols=54  Identities=28%  Similarity=0.618  Sum_probs=40.9

Q ss_pred             CCcccccccccccccccCcceeec---CCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            8 GKTICSICYEDLKPIVEDLQVISI---CGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         8 ~eltCpICLe~f~P~~~~~~~llp---CGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      .-..|.||.|...+.    +++.|   ||-..|..|....|+++.  -.+.||+|+..|....
T Consensus        79 ~lYeCnIC~etS~ee----~FLKPneCCgY~iCn~Cya~LWK~~~--~ypvCPvCkTSFKss~  135 (140)
T PF05290_consen   79 KLYECNICKETSAEE----RFLKPNECCGYSICNACYANLWKFCN--LYPVCPVCKTSFKSSS  135 (140)
T ss_pred             CceeccCcccccchh----hcCCcccccchHHHHHHHHHHHHHcc--cCCCCCcccccccccc
Confidence            345899999987521    23333   999999999999888654  6789999999987553

>PHA02562 46 endonuclease subunit; Provisional

Probab=93.64  E-value=13  Score=40.59  Aligned_cols=22  Identities=9%  Similarity=0.371  Sum_probs=10.9

Q ss_pred             hhHHHHHHHHHHHHHhHHHHHH
Q 012292           90 EVSRAEVKILEVKVSRLHTVLE  111 (466)
Q Consensus        90 e~l~~El~rLe~kl~~L~~~Le  111 (466)
                      ..+..++..+...+..+...+.
T Consensus       177 ~e~~~~i~~l~~~i~~l~~~i~  198 (562)
T PHA02562        177 RELNQQIQTLDMKIDHIQQQIK  198 (562)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3455555555555544444443

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

Probab=93.63  E-value=0.036  Score=57.96  Aligned_cols=34  Identities=24%  Similarity=0.516  Sum_probs=29.7

Q ss_pred             CCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHH
Q 012292            7 FGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFE   46 (466)
Q Consensus         7 ~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle   46 (466)
                      .+++.||||-..|. |+      ++||||+.|..|-...+-
T Consensus         2 eeelkc~vc~~f~~epi------il~c~h~lc~~ca~~~~~   36 (699)
T KOG4367|consen    2 EEELKCPVCGSFYREPI------ILPCSHNLCQACARNILV   36 (699)
T ss_pred             cccccCceehhhccCce------EeecccHHHHHHHHhhcc
Confidence            46899999999999 65      899999999999887654

>KOG0161 consensus Myosin class II heavy chain [Cytoskeleton]

Probab=93.61  E-value=15  Score=46.17  Aligned_cols=47  Identities=23%  Similarity=0.241  Sum_probs=23.1

Q ss_pred             HHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 012292          225 NYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELK  271 (466)
Q Consensus       225 ~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~~  271 (466)
                      ..++|..++..|..+...-+....+++.....|...+++|+..|+..
T Consensus      1098 ~i~eL~~~i~el~e~le~er~~r~K~ek~r~dL~~ele~l~~~Lee~ 1144 (1930)
T KOG0161|consen 1098 QIKELEARIKELEEELEAERASRAKAERQRRDLSEELEELKEELEEQ 1144 (1930)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33334444444444443334444455555555555566666665554

>PF06160 EzrA: Septation ring formation regulator, EzrA ; InterPro: IPR010379 During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site

Probab=93.59  E-value=14  Score=40.89  Aligned_cols=62  Identities=15%  Similarity=0.160  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHh
Q 012292          111 ESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQR  172 (466)
Q Consensus       111 e~~~~~lk~L~eel~~~KeQlkeE~~~l~EkLk~~esLeqLL~~q~eEVeklkeE~~rLq~r  172 (466)
                      +.....+..+.+++..+-..++.|........+....+...+.........+..+..++...
T Consensus       274 ~~~~~~~~~i~~~Id~lYd~le~E~~Ak~~V~~~~~~l~~~l~~~~~~~~~l~~e~~~v~~s  335 (560)
T PF06160_consen  274 DEVEEENEEIEERIDQLYDILEKEVEAKKYVEKNLKELYEYLEHAKEQNKELKEELERVSQS  335 (560)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            33445555566666666666666666666666666666666666666666666666665444

EzrA modulates the frequency and position of FtsZ ring formation [].; GO: 0000921 septin ring assembly, 0005940 septin ring, 0016021 integral to membrane

>PRK09039 hypothetical protein; Validated

Probab=93.51  E-value=9.8  Score=39.56  Aligned_cols=35  Identities=14%  Similarity=0.347  Sum_probs=14.4

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 012292          236 LGREKARFSEKLEKAKEKINKLKTRVQELETAVEL  270 (466)
Q Consensus       236 L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~  270 (466)
                      |++........|..++.+....+.++..|+..|+.
T Consensus       149 Lr~Qla~le~~L~~ae~~~~~~~~~i~~L~~~L~~  183 (343)
T PRK09039        149 LRRQLAALEAALDASEKRDRESQAKIADLGRRLNV  183 (343)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333334444444444444444444444444

>KOG0612 consensus Rho-associated, coiled-coil containing protein kinase [Signal transduction mechanisms]

Probab=93.46  E-value=19  Score=43.02  Aligned_cols=6  Identities=33%  Similarity=0.479  Sum_probs=2.3

Q ss_pred             cccccc
Q 012292           14 ICYEDL   19 (466)
Q Consensus        14 ICLe~f   19 (466)
                      ||-+.+
T Consensus       371 ~~~dd~  376 (1317)
T KOG0612|consen  371 VDEDDL  376 (1317)
T ss_pred             cccccc
Confidence            333333

>KOG0963 consensus Transcription factor/CCAAT displacement protein CDP1 [Transcription]

Probab=93.44  E-value=13  Score=41.14  Aligned_cols=34  Identities=29%  Similarity=0.451  Sum_probs=22.6

Q ss_pred             hHHHHHHHHhhcCC--CCCh-hHHHHHHHHHHHHHHH
Q 012292          192 DEDEVLKFALLGNG--ANNK-DTIDVLRKSLVIRNKN  225 (466)
Q Consensus       192 eEeE~LK~~~lg~~--~~~~-e~~d~Lkk~l~~~~k~  225 (466)
                      .|-.+||..-||..  ++.. +++.+|-..|...|+.
T Consensus       351 ~ELsiLk~ief~~se~a~~~~~~~~~leslLl~knr~  387 (629)
T KOG0963|consen  351 KELSILKAIEFGDSEEANDEDETAKTLESLLLEKNRK  387 (629)
T ss_pred             HHHHHHHHhhcCCcccccccccccchHHHHHHHHHhh
Confidence            66667777777732  3344 6777888877777764

>PF00261 Tropomyosin: Tropomyosin; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells

Probab=93.43  E-value=8.4  Score=37.77  Aligned_cols=58  Identities=7%  Similarity=0.244  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 012292          214 VLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELK  271 (466)
Q Consensus       214 ~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~~  271 (466)
                      .+...+..+...+.+...+.+...+....+...+..+..++...+.++..++..|+..
T Consensus       173 ~~e~~i~~L~~~lkeaE~Rae~aE~~v~~Le~~id~le~eL~~~k~~~~~~~~eld~~  230 (237)
T PF00261_consen  173 EYEEKIRDLEEKLKEAENRAEFAERRVKKLEKEIDRLEDELEKEKEKYKKVQEELDQT  230 (237)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333444444444444444444444444444445555555555555555555555443

In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].; PDB: 2EFR_A 2Z5H_C 2Z5I_D 2D3E_B 2EFS_D 3U59_B 1C1G_C 1IHQ_A 3AZD_B 1MV4_B ....

>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]

Probab=93.42  E-value=11  Score=42.90  Aligned_cols=51  Identities=16%  Similarity=0.219  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012292          218 SLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAV  268 (466)
Q Consensus       218 ~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~l  268 (466)
                      ++...++..+-.+..+.+|..+...++.+|.++--|...|..+++..|...
T Consensus       473 ~ie~~~~q~e~~isei~qlqarikE~q~kl~~l~~Ekq~l~~qlkq~q~a~  523 (1118)
T KOG1029|consen  473 EIEEVTKQRELMISEIDQLQARIKELQEKLQKLAPEKQELNHQLKQKQSAH  523 (1118)
T ss_pred             HHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhhhhc
Confidence            333444444444455555555555556666666666666655555444433

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

Probab=93.41  E-value=0.052  Score=55.13  Aligned_cols=47  Identities=26%  Similarity=0.639  Sum_probs=36.5

Q ss_pred             CCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCcccc
Q 012292            8 GKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus         8 ~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~   64 (466)
                      +...||||+.... |.     .+..-|-+||+.|+-.++.     ....||+=..+..
T Consensus       299 ~~~~CpvClk~r~Npt-----vl~vSGyVfCY~Ci~~Yv~-----~~~~CPVT~~p~~  346 (357)
T KOG0826|consen  299 DREVCPVCLKKRQNPT-----VLEVSGYVFCYPCIFSYVV-----NYGHCPVTGYPAS  346 (357)
T ss_pred             ccccChhHHhccCCCc-----eEEecceEEeHHHHHHHHH-----hcCCCCccCCcch
Confidence            3468999999987 54     3455699999999999988     5788997655443

>KOG1899 consensus LAR transmembrane tyrosine phosphatase-interacting protein liprin [General function prediction only]

Probab=93.36  E-value=16  Score=40.69  Aligned_cols=75  Identities=17%  Similarity=0.258  Sum_probs=44.8

Q ss_pred             hhhHHHHHHHHHH-------HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHH
Q 012292           89 PEVSRAEVKILEV-------KVSRLHTVLESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDK  161 (466)
Q Consensus        89 ~e~l~~El~rLe~-------kl~~L~~~Le~~~~~lk~L~eel~~~KeQlkeE~~~l~EkLk~~esLeqLL~~q~eEVek  161 (466)
                      ...++..+.||+.       .+.-|.++++.|..+|.+|+--+..-+.++-....+++..+-...+|+..---+-.||..
T Consensus       106 ~~~yQerLaRLe~dkesL~LQvsvLteqVeaQgEKIrDLE~cie~kr~kLnatEEmLQqellsrtsLETqKlDLmaevSe  185 (861)
T KOG1899|consen  106 YPEYQERLARLEMDKESLQLQVSVLTEQVEAQGEKIRDLETCIEEKRNKLNATEEMLQQELLSRTSLETQKLDLMAEVSE  185 (861)
T ss_pred             chHHHHHHHHHhcchhhheehHHHHHHHHHHhhhhHHHHHHHHHHHHhhhchHHHHHHHHHHhhhhHHHHHhHHHHHHHH
Confidence            3446666666665       555577888888888888877666555555555556655555444444433333444444


Q ss_pred             HH
Q 012292          162 VT  163 (466)
Q Consensus       162 lk  163 (466)
                      ++
T Consensus       186 LK  187 (861)
T KOG1899|consen  186 LK  187 (861)
T ss_pred             hH
Confidence            43

>PF10481 CENP-F_N: Cenp-F N-terminal domain; InterPro: IPR018463 Mitosin or centromere-associated protein-F (Cenp-F) is found bound across the centromere as one of the proteins of the outer layer of the kinetochore []

Probab=93.28  E-value=3.3  Score=41.42  Aligned_cols=46  Identities=24%  Similarity=0.262  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhhhHHHHHHHhcc
Q 012292          139 NEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRNMDLAKELASLK  184 (466)
Q Consensus       139 ~EkLk~~esLeqLL~~q~eEVeklkeE~~rLq~rn~alakeL~sLK  184 (466)
                      ..+.=++++++..|+.++..++.-+.+..-|..+|..+...+..|.
T Consensus        35 qQrQfQleSlEAaLqKQKqK~e~ek~e~s~LkREnq~l~e~c~~le   80 (307)
T PF10481_consen   35 QQRQFQLESLEAALQKQKQKVEEEKNEYSALKRENQSLMESCENLE   80 (307)
T ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhHHHHHHHHH
Confidence            3444566788888998888888888888888888776666666665

Most of the kinetochore/centromere functions appear to depend upon binding of the C-terminal part of the molecule, whereas the N-terminal part, here, may be a cytoplasmic player in controlling the function of microtubules and dynein [].

>KOG4643 consensus Uncharacterized coiled-coil protein [Function unknown]

Probab=93.20  E-value=17  Score=42.43  Aligned_cols=88  Identities=16%  Similarity=0.078  Sum_probs=49.0

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHhh------hhHHHHHH
Q 012292          208 NKDTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTR---VQELETAVEL------KDNEVLRA  278 (466)
Q Consensus       208 ~~e~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~---v~eLqk~le~------~~ne~l~~  278 (466)
                      -++.++.|+..+...-..|+.+..+|+.|.....-+.++-.-+-.+|..|+..   ...|+...+.      ....++-.
T Consensus       507 l~a~~~elkeQ~kt~~~qye~~~~k~eeLe~~l~~lE~ENa~LlkqI~~Lk~t~qn~~~LEq~~n~lE~~~~elkk~ida  586 (1195)
T KOG4643|consen  507 LHALKNELKEQYKTCDIQYELLSNKLEELEELLGNLEEENAHLLKQIQSLKTTSQNGALLEQNNNDLELIHNELKKYIDA  586 (1195)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhHHHHHHHHhhhHHHHHHHHHHHHHHH
Confidence            44556666666666666777777777777766666555555566666666651   1122222222      23334444


Q ss_pred             HHhccccchhHHhhhcCC
Q 012292          279 LKVSKKASQKEEILKGAT  296 (466)
Q Consensus       279 l~~~~~~~~~~~~~~~~~  296 (466)
                      |. +-++....+.+.+.+
T Consensus       587 L~-alrrhke~LE~e~mn  603 (1195)
T KOG4643|consen  587 LN-ALRRHKEKLEEEIMN  603 (1195)
T ss_pred             HH-HHHHHHHHHHHHHhh
Confidence            44 445555555555544

>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs

Probab=93.14  E-value=4.6  Score=46.06  Aligned_cols=101  Identities=22%  Similarity=0.353  Sum_probs=58.6

Q ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhhhHHHHHHHhccccccCChhHHHHHHHHhhcCCCCChhHHHHHHHHHHH
Q 012292          142 LRQKVSVEQLLHSKSQELDKVTLECLKLKQRNMDLAKELASLKLVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVI  221 (466)
Q Consensus       142 Lk~~esLeqLL~~q~eEVeklkeE~~rLq~rn~alakeL~sLKlvsd~~~eEeE~LK~~~lg~~~~~~e~~d~Lkk~l~~  221 (466)
                      .+....++.+...|..++..+.++...++.+...++..++..+       +..+.|                  .+.+  
T Consensus       564 ~~rv~~Lk~~~e~Ql~~L~~l~e~~~~l~~~ae~LaeR~e~a~-------d~Qe~L------------------~~R~--  616 (717)
T PF10168_consen  564 QRRVKLLKQQKEQQLKELQELQEERKSLRESAEKLAERYEEAK-------DKQEKL------------------MKRV--  616 (717)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHH------------------HHHH--
Confidence            3334455566667777777777777777777666655555555       333333                  1111  


Q ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 012292          222 RNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVEL  270 (466)
Q Consensus       222 ~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~  270 (466)
                       ...+..+....-.|...|..+.++|+....++..|+..++++++.++.
T Consensus       617 -~~vl~~l~~~~P~LS~AEr~~~~EL~~~~~~l~~l~~si~~lk~k~~~  664 (717)
T PF10168_consen  617 -DRVLQLLNSQLPVLSEAEREFKKELERMKDQLQDLKASIEQLKKKLDY  664 (717)
T ss_pred             -HHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             112222333333455666677777777777777777777777666665

It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].

>PF14662 CCDC155: Coiled-coil region of CCDC155

Probab=92.96  E-value=8.4  Score=36.75  Aligned_cols=60  Identities=17%  Similarity=0.225  Sum_probs=46.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 012292          211 TIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVEL  270 (466)
Q Consensus       211 ~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~  270 (466)
                      -.+-|+-.+..+...+..|++.+.+++++.-.+..+++.+..+..+|......+++....
T Consensus        68 EledLk~~~~~lEE~~~~L~aq~rqlEkE~q~L~~~i~~Lqeen~kl~~e~~~lk~~~~e  127 (193)
T PF14662_consen   68 ELEDLKTLAKSLEEENRSLLAQARQLEKEQQSLVAEIETLQEENGKLLAERDGLKKRSKE  127 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhhHHHHHHH
Confidence            344555666677778888898888898888888888888888888887777777777666

>smart00787 Spc7 Spc7 kinetochore protein

Probab=92.92  E-value=13  Score=38.33  Aligned_cols=79  Identities=20%  Similarity=0.179  Sum_probs=61.2

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh---hhHHHHHHHHhccc
Q 012292          208 NKDTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVEL---KDNEVLRALKVSKK  284 (466)
Q Consensus       208 ~~e~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~---~~ne~l~~l~~~~~  284 (466)
                      ..+..+.++.++............+++.++.+......+++....++.++...+.++++.++.   -+..-+++|+..-.
T Consensus       202 d~~eL~~lk~~l~~~~~ei~~~~~~l~e~~~~l~~l~~~I~~~~~~k~e~~~~I~~ae~~~~~~r~~t~~Ei~~Lk~~~~  281 (312)
T smart00787      202 DPTELDRAKEKLKKLLQEIMIKVKKLEELEEELQELESKIEDLTNKKSELNTEIAEAEKKLEQCRGFTFKEIEKLKEQLK  281 (312)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHH
Confidence            556677777777777777788888888888888888899999999999999999999998877   33444566665544


Q ss_pred             cc
Q 012292          285 AS  286 (466)
Q Consensus       285 ~~  286 (466)
                      +.
T Consensus       282 ~L  283 (312)
T smart00787      282 LL  283 (312)
T ss_pred             HH
Confidence            43

This domain is found in cell division proteins which are required for kinetochore-spindle association.

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

Probab=92.83  E-value=0.066  Score=60.27  Aligned_cols=52  Identities=31%  Similarity=0.683  Sum_probs=32.0

Q ss_pred             CCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCC--CCCCCCcCcC
Q 012292            8 GKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSS--SKKCTCPVCK   60 (466)
Q Consensus         8 ~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~--~~s~~CP~CR   60 (466)
                      ....|-||++.+... ...-....|=|+||+.||..|......  +..+.||.|+
T Consensus       190 ~~yeCmIC~e~I~~t-~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cq  243 (950)
T KOG1952|consen  190 RKYECMICTERIKRT-APVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQ  243 (950)
T ss_pred             CceEEEEeeeecccc-CCceecchhhhhhhHHHHHHHHHHhhhccCccccCCccc
Confidence            346788888887731 111223446688888888888664222  2467788887

>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]

Probab=92.77  E-value=1.2  Score=43.18  Aligned_cols=69  Identities=32%  Similarity=0.416  Sum_probs=61.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHh
Q 012292          213 DVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKV  281 (466)
Q Consensus       213 d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~~~ne~l~~l~~  281 (466)
                      +.|.+.+-.+...|+++..+++.|..+..++..++.+.-.+..+|+++..+|+-.++..+.+.+++|.+
T Consensus       152 eeL~~eleele~e~ee~~erlk~le~E~s~LeE~~~~l~~ev~~L~~r~~ELe~~~El~e~~~i~dl~~  220 (290)
T COG4026         152 EELLKELEELEAEYEEVQERLKRLEVENSRLEEMLKKLPGEVYDLKKRWDELEPGVELPEEELISDLVK  220 (290)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhHHHHHHHHHHHhcccccchHHHHHHHHHH
Confidence            345555666677899999999999999999999999999999999999999999999999999999987

>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]

Probab=92.73  E-value=11  Score=37.25  Aligned_cols=29  Identities=14%  Similarity=0.236  Sum_probs=15.6

Q ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHh
Q 012292          144 QKVSVEQLLHSKSQELDKVTLECLKLKQR  172 (466)
Q Consensus       144 ~~esLeqLL~~q~eEVeklkeE~~rLq~r  172 (466)
                      .++.++..+.....++.+...++..++.+
T Consensus        46 ~~~~~~~e~e~le~qv~~~e~ei~~~r~r   74 (239)
T COG1579          46 ALEALEIELEDLENQVSQLESEIQEIRER   74 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33345555555555566655555555444

>PRK04863 mukB cell division protein MukB; Provisional

Probab=92.71  E-value=28  Score=43.15  Aligned_cols=21  Identities=19%  Similarity=0.357  Sum_probs=14.8

Q ss_pred             cccCCCccccccccccccCCC
Q 012292          420 TLIVPDSAQVQPIVNIKKNPP  440 (466)
Q Consensus       420 ~~~~~~~~~~~~~~~~~~~~~  440 (466)
                      ++.|+|..++.-.++..-.-|
T Consensus       712 ~iVv~d~~~A~~ai~~L~~~p  732 (1486)
T PRK04863        712 AIVVPDLSDAAEQLAGLEDCP  732 (1486)
T ss_pred             eEEeCCHHHHHHHHHhccCCc
Confidence            566777777777777766644

>PF13166 AAA_13: AAA domain

Probab=92.68  E-value=6.5  Score=44.40  Aligned_cols=49  Identities=35%  Similarity=0.492  Sum_probs=30.6

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh------hhhHHHHHHH
Q 012292          231 AKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVE------LKDNEVLRAL  279 (466)
Q Consensus       231 ~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le------~~~ne~l~~l  279 (466)
                      ..+..+.+.......++..+..++..++.++.+|+..+.      ..=|+.|.++
T Consensus       417 ~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~i~~l~~~~~~~~~~~~~iN~~L~~~  471 (712)
T PF13166_consen  417 KEIKELEKEINSLEKKLKKAKEEIKKIEKEIKELEAQLKNTEPAADRINEELKRL  471 (712)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHh
Confidence            333344444555556666677777777777777776666      3566777777

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

Probab=92.61  E-value=22  Score=40.34  Aligned_cols=50  Identities=12%  Similarity=0.135  Sum_probs=20.9

Q ss_pred             HHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 012292          220 VIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVE  269 (466)
Q Consensus       220 ~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le  269 (466)
                      +...+..+.|+.+.+........+...+.....++..++.+...|+..++
T Consensus       562 ~e~~~~~~~Lq~~~ek~~~~le~i~~~~~e~~~ele~~~~k~~rleEE~e  611 (698)
T KOG0978|consen  562 QEAKQSLEDLQIELEKSEAKLEQIQEQYAELELELEIEKFKRKRLEEELE  611 (698)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333444444444444444444444444444444444444444444433

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

Probab=92.58  E-value=0.038  Score=64.63  Aligned_cols=47  Identities=30%  Similarity=0.658  Sum_probs=38.5

Q ss_pred             CcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCcccc
Q 012292            9 KTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus         9 eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~   64 (466)
                      -..|+||++.+..-    ..+..|||.||..|...|+.     .+..||.|...+.
T Consensus      1153 ~~~c~ic~dil~~~----~~I~~cgh~~c~~c~~~~l~-----~~s~~~~~ksi~~ 1199 (1394)
T KOG0298|consen 1153 HFVCEICLDILRNQ----GGIAGCGHEPCCRCDELWLY-----ASSRCPICKSIKG 1199 (1394)
T ss_pred             ccchHHHHHHHHhc----CCeeeechhHhhhHHHHHHH-----HhccCcchhhhhh
Confidence            45899999999721    14678999999999999999     6789999985544

>KOG0933 consensus Structural maintenance of chromosome protein 2 (chromosome condensation complex Condensin, subunit E) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]

Probab=92.58  E-value=26  Score=41.10  Aligned_cols=14  Identities=29%  Similarity=0.311  Sum_probs=7.8

Q ss_pred             CCCCcccccCCCce
Q 012292          438 NPPSPVSLSKPGIF  451 (466)
Q Consensus       438 ~~~~~~~~~~~~~~  451 (466)
                      .+-|-|+-.|-|-|
T Consensus      1135 ~sQFIVVSLKeGMF 1148 (1174)
T KOG0933|consen 1135 HSQFIVVSLKEGMF 1148 (1174)
T ss_pred             CCeEEEEEchhhcc
Confidence            34455555566665

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

Probab=92.46  E-value=0.067  Score=49.93  Aligned_cols=37  Identities=30%  Similarity=0.786  Sum_probs=27.4

Q ss_pred             ecCCCcccHHHHHHHHHhcCCC-CC-----CCCcCcCccccCC
Q 012292           30 SICGHVFHELCLQQWFEYCSSS-KK-----CTCPVCKQRCSSS   66 (466)
Q Consensus        30 lpCGHsFC~~CL~~wle~~~~~-~s-----~~CP~CR~~~~~~   66 (466)
                      ..||..||.-||..|+..--.. ++     ..||.|-.++..+
T Consensus       188 ~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialK  230 (234)
T KOG3268|consen  188 IQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALK  230 (234)
T ss_pred             cccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceee
Confidence            5799999999999999831111 11     3699999888754

>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]

Probab=92.42  E-value=11  Score=44.51  Aligned_cols=24  Identities=13%  Similarity=0.104  Sum_probs=11.7

Q ss_pred             CChhHHHHHHHHHHHHHHHHHHHH
Q 012292          207 NNKDTIDVLRKSLVIRNKNYTELM  230 (466)
Q Consensus       207 ~~~e~~d~Lkk~l~~~~k~yeeL~  230 (466)
                      ...+.+..|..+|..+-.++.++.
T Consensus      1508 ~tpeqi~~L~~~I~e~v~sL~nVd 1531 (1758)
T KOG0994|consen 1508 LTPEQIQQLTGEIQERVASLPNVD 1531 (1758)
T ss_pred             CCHHHHHHHHHHHHHHHHhcccHH
Confidence            344555555555555544443333

>KOG0977 consensus Nuclear envelope protein lamin, intermediate filament superfamily [Cell cycle control, cell division, chromosome partitioning; Nuclear structure]

Probab=92.07  E-value=22  Score=39.19  Aligned_cols=63  Identities=22%  Similarity=0.263  Sum_probs=28.0

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 012292          208 NKDTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVEL  270 (466)
Q Consensus       208 ~~e~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~  270 (466)
                      ....+..+++.+..+......|......|..+..++++.|+....=-..+.-+++.|...|+-
T Consensus       153 leAe~~~~krr~~~le~e~~~Lk~en~rl~~~l~~~r~~ld~Etllr~d~~n~~q~Lleel~f  215 (546)
T KOG0977|consen  153 LEAEINTLKRRIKALEDELKRLKAENSRLREELARARKQLDDETLLRVDLQNRVQTLLEELAF  215 (546)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence            344444555544444445555555445555555544444443332223333334444444433

>PF12128 DUF3584: Protein of unknown function (DUF3584); InterPro: IPR021979 This family consist of uncharacterised bacterial proteins

Probab=92.03  E-value=21  Score=43.19  Aligned_cols=37  Identities=22%  Similarity=0.282  Sum_probs=16.0

Q ss_pred             ChhhHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Q 012292           88 DPEVSRAEVKILEVKVSRLHTVLESQGKEIKEINEEL  124 (466)
Q Consensus        88 ~~e~l~~El~rLe~kl~~L~~~Le~~~~~lk~L~eel  124 (466)
                      +.+.++.++..+...+.......+...+.++....++
T Consensus       601 ~ee~L~~~l~~~~~~l~~~~~~~~~~e~~l~~~~~~~  637 (1201)
T PF12128_consen  601 SEEELRERLEQAEDQLQSAEERQEELEKQLKQINKKI  637 (1201)
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445555555555544444433333333333333333

>COG0419 SbcC ATPase involved in DNA repair [DNA replication, recombination, and repair]

Probab=91.97  E-value=31  Score=40.54  Aligned_cols=30  Identities=17%  Similarity=0.236  Sum_probs=22.1

Q ss_pred             cccccccccccCC--CCCCCCCCCCccCCccc
Q 012292          390 SIHQTIADVVQKP--TPSRLGSAPTIDIDEDV  419 (466)
Q Consensus       390 ~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~  419 (466)
                      ++--.++|+|+..  ++.=+-+=|++.-|++-
T Consensus       827 alrLALs~~~~~~~~l~~l~LDEpf~~LD~e~  858 (908)
T COG0419         827 ALRLALSDLLQGRARLELLFLDEPFGTLDEER  858 (908)
T ss_pred             HHHHHHHHHHhcccCCCeeEeeCCCCCCCHHH
Confidence            4556788999988  67667777777777763

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

Probab=91.97  E-value=0.085  Score=59.78  Aligned_cols=36  Identities=28%  Similarity=0.479  Sum_probs=28.7

Q ss_pred             CCcccccccccccccccCcceeecCCCcccHHHHHHHHH
Q 012292            8 GKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFE   46 (466)
Q Consensus         8 ~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle   46 (466)
                      ..-+|.+|.-.+-   ..+...-||||.||..||.+...
T Consensus       816 p~d~C~~C~~~ll---~~pF~vf~CgH~FH~~Cl~~~v~  851 (911)
T KOG2034|consen  816 PQDSCDHCGRPLL---IKPFYVFPCGHCFHRDCLIRHVL  851 (911)
T ss_pred             CccchHHhcchhh---cCcceeeeccchHHHHHHHHHHH
Confidence            3458999998885   23457789999999999998765

>COG4477 EzrA Negative regulator of septation ring formation [Cell division and chromosome partitioning]

Probab=91.93  E-value=22  Score=38.89  Aligned_cols=141  Identities=18%  Similarity=0.241  Sum_probs=69.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhhh----------HHHHHHHh
Q 012292          113 QGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRNM----------DLAKELAS  182 (466)
Q Consensus       113 ~~~~lk~L~eel~~~KeQlkeE~~~l~EkLk~~esLeqLL~~q~eEVeklkeE~~rLq~rn~----------alakeL~s  182 (466)
                      ...++..+++++..+-..+..+....+...+.+..+..-+....+..+.+..++..++....          +..+.|.+
T Consensus       279 aeeel~~I~e~ie~lYd~lE~EveA~~~V~~~~~~l~~~l~k~ke~n~~L~~Eie~V~~sY~l~e~e~~~vr~~e~eL~e  358 (570)
T COG4477         279 AEEELGLIQEKIESLYDLLEREVEAKNVVEENLPILPDYLEKAKENNEHLKEEIERVKESYRLAETELGSVRKFEKELKE  358 (570)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHHHhccChhHHHHHHHHHHHHHH
Confidence            33445555555555555555555555555555555555555555555555555555544422          11222222


Q ss_pred             ccccccCChhHHHHHHHHhhcCCC----CChhHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHH
Q 012292          183 LKLVSDLNLDEDEVLKFALLGNGA----NNKDTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLK  258 (466)
Q Consensus       183 LKlvsd~~~eEeE~LK~~~lg~~~----~~~e~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk  258 (466)
                      +.      ..-.++++  .++-..    .-++....+.+.+...++...++.....+|++++..++..|...+.++..++
T Consensus       359 l~------~~~~~i~~--~~~~~~~~yS~lq~~l~~~~~~l~~i~~~q~~~~e~L~~LrkdEl~Are~l~~~~~~l~eik  430 (570)
T COG4477         359 LE------SVLDEILE--NIEAQEVAYSELQDNLEEIEKALTDIEDEQEKVQEHLTSLRKDELEARENLERLKSKLHEIK  430 (570)
T ss_pred             HH------HHHHHHHH--HhhcccccHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            22      00111111  111001    1344555555555555556666666666677777777666666666666555


Q ss_pred             HHH
Q 012292          259 TRV  261 (466)
Q Consensus       259 ~~v  261 (466)
                      ..+
T Consensus       431 R~m  433 (570)
T COG4477         431 RYM  433 (570)
T ss_pred             HHH
Confidence            443

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

Probab=91.83  E-value=0.21  Score=48.41  Aligned_cols=60  Identities=23%  Similarity=0.453  Sum_probs=42.8

Q ss_pred             CCCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCC---CCCCCCcCcCccccCCC
Q 012292            5 NKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSS---SKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         5 ~~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~---~~s~~CP~CR~~~~~~~   67 (466)
                      ++.-..-|..|--.+..  .+. ..+.|-|.||+.|+..|...-+.   .....||.|...+-+..
T Consensus        46 DsDY~pNC~LC~t~La~--gdt-~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~  108 (299)
T KOG3970|consen   46 DSDYNPNCRLCNTPLAS--GDT-TRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPI  108 (299)
T ss_pred             hcCCCCCCceeCCcccc--Ccc-eeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCc
Confidence            34456789999988862  222 25789999999999999764332   24578999988876553

>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]

Probab=91.77  E-value=28  Score=39.76  Aligned_cols=59  Identities=14%  Similarity=0.118  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 012292          212 IDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVEL  270 (466)
Q Consensus       212 ~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~  270 (466)
                      ...|.+......--...|+.+...|.+|.....++..-.+.++++||+.+-..+-+.+.
T Consensus       530 ~s~L~aa~~~ke~irq~ikdqldelskE~esk~~eidi~n~qlkelk~~~~~q~lake~  588 (1118)
T KOG1029|consen  530 KSELEAARRKKELIRQAIKDQLDELSKETESKLNEIDIFNNQLKELKEDVNSQQLAKEE  588 (1118)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHH
Confidence            55666655555556667777777788888777777777777788888777766666555

>PF00038 Filament: Intermediate filament protein; InterPro: IPR016044 Intermediate filaments (IF) [, , ] are proteins which are primordial components of the cytoskeleton and the nuclear envelope

Probab=91.74  E-value=16  Score=36.86  Aligned_cols=40  Identities=33%  Similarity=0.506  Sum_probs=24.9

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 012292          231 AKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVEL  270 (466)
Q Consensus       231 ~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~  270 (466)
                      .+++.+..........+..++.++..++..++.|+..++.
T Consensus       195 ~k~~~l~~~~~~~~~~~~~~~~E~~~~r~~~~~l~~el~~  234 (312)
T PF00038_consen  195 SKLEELRQQSEKSSEELESAKEELKELRRQIQSLQAELES  234 (312)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccccccchhHhHHHHHHhhhhHhhhhhhc
Confidence            3444555555555566666777777777777766666665

They generally form filamentous structures 8 to 14 nm wide. IF proteins are members of a very large multigene family of proteins which has been subdivided in five major subgroups: Type I: Acidic cytokeratins. Type II: Basic cytokeratins. Type III: Vimentin, desmin, glial fibrillary acidic protein (GFAP), peripherin, and plasticin. Type IV: Neurofilaments L, H and M, alpha-internexin and nestin. Type V: Nuclear lamins A, B1, B2 and C. All IF proteins are structurally similar in that they consist of: a central rod domain comprising some 300 to 350 residues which is arranged in coiled-coiled alpha-helices, with at least two short characteristic interruptions; a N-terminal non-helical domain (head) of variable length; and a C-terminal domain (tail) which is also non-helical, and which shows extreme length variation between different IF proteins. While IF proteins are evolutionary and structurally related, they have limited sequence homologies except in several regions of the rod domain. This entry represents the central rod domain found in IF proteins.; PDB: 3TNU_B 3KLT_D 1GK4_F 3TRT_A 3G1E_A 3UF1_C 1GK6_B 1GK7_A 3TYY_B 3V4W_A ....

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

Probab=91.69  E-value=0.097  Score=52.50  Aligned_cols=46  Identities=30%  Similarity=0.637  Sum_probs=35.7

Q ss_pred             cccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCc
Q 012292           10 TICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQ   61 (466)
Q Consensus        10 ltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~   61 (466)
                      ..||||.+.+.+. ...+..++|||.-|..|+....-     ..-+||.|..
T Consensus       159 ~ncPic~e~l~~s-~~~~~~~~CgH~~h~~cf~e~~~-----~~y~CP~C~~  204 (276)
T KOG1940|consen  159 FNCPICKEYLFLS-FEDAGVLKCGHYMHSRCFEEMIC-----EGYTCPICSK  204 (276)
T ss_pred             CCCchhHHHhccc-cccCCccCcccchHHHHHHHHhc-----cCCCCCcccc
Confidence            4599999998842 33345689999999999887655     3399999987

>PF05911 DUF869: Plant protein of unknown function (DUF869); InterPro: IPR008587 This family consists of a number of sequences found in plants

Probab=91.69  E-value=29  Score=40.00  Aligned_cols=58  Identities=22%  Similarity=0.274  Sum_probs=37.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 012292          213 DVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVEL  270 (466)
Q Consensus       213 d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~  270 (466)
                      ..|.+.|..+.++..+|....-+...+...+..+|+...+++..||=++.-|++.|+-
T Consensus       109 ~~l~~~l~~~~~~i~~l~~~~~~~e~~~~~l~~~l~~~eken~~Lkye~~~~~kelei  166 (769)
T PF05911_consen  109 SALSKALQEKEKLIAELSEEKSQAEAEIEDLMARLESTEKENSSLKYELHVLSKELEI  166 (769)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455555566666666665555555556666677777777777777777777777665

The function of this family is unknown.

>KOG4674 consensus Uncharacterized conserved coiled-coil protein [Function unknown]

Probab=91.55  E-value=46  Score=41.71  Aligned_cols=20  Identities=25%  Similarity=0.481  Sum_probs=8.7

Q ss_pred             HHHHHHHHHHHHHHHHHhhh
Q 012292          252 EKINKLKTRVQELETAVELK  271 (466)
Q Consensus       252 ~ei~~Lk~~v~eLqk~le~~  271 (466)
                      +.|..|...++.|.+.++..
T Consensus       805 ~~i~eL~~el~~lk~klq~~  824 (1822)
T KOG4674|consen  805 SRIKELERELQKLKKKLQEK  824 (1822)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444443

>KOG0933 consensus Structural maintenance of chromosome protein 2 (chromosome condensation complex Condensin, subunit E) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]

Probab=91.45  E-value=35  Score=40.14  Aligned_cols=13  Identities=23%  Similarity=0.511  Sum_probs=4.8

Q ss_pred             HHHHHHHHHHHHH
Q 012292          248 EKAKEKINKLKTR  260 (466)
Q Consensus       248 ek~~~ei~~Lk~~  260 (466)
                      +++..++++++..
T Consensus       909 kkle~e~~~~~~e  921 (1174)
T KOG0933|consen  909 KKLEHEVTKLESE  921 (1174)
T ss_pred             HHHHhHHHHhhhh
Confidence            3333333333333

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

Probab=91.24  E-value=0.16  Score=37.33  Aligned_cols=42  Identities=31%  Similarity=0.749  Sum_probs=26.9

Q ss_pred             cccccccccccccCcceeecCCC-----cccHHHHHHHHHhcCCCCCCCCcCc
Q 012292           12 CSICYEDLKPIVEDLQVISICGH-----VFHELCLQQWFEYCSSSKKCTCPVC   59 (466)
Q Consensus        12 CpICLe~f~P~~~~~~~llpCGH-----sFC~~CL~~wle~~~~~~s~~CP~C   59 (466)
                      |-||++.-.+.   .+.+.||+-     ..|..||.+|+...   +...|++|
T Consensus         1 CrIC~~~~~~~---~~li~pC~C~Gs~~~vH~~CL~~W~~~~---~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEED---EPLISPCRCKGSMKYVHRSCLERWIRES---GNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSS---S-EE-SSS-SSCCGSEECCHHHHHHHHH---T-SB-TTT
T ss_pred             CeEeCCcCCCC---CceecccccCCCcchhHHHHHHHHHHhc---CCCcCCCC
Confidence            67899887632   134678763     56999999999952   56779988

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

Probab=90.89  E-value=0.11  Score=46.72  Aligned_cols=36  Identities=22%  Similarity=0.623  Sum_probs=27.4

Q ss_pred             CcccccccccccccccCcceeecCC------CcccHHHHHHHHH
Q 012292            9 KTICSICYEDLKPIVEDLQVISICG------HVFHELCLQQWFE   46 (466)
Q Consensus         9 eltCpICLe~f~P~~~~~~~llpCG------HsFC~~CL~~wle   46 (466)
                      ...|.||++.+.. ...+ ..++||      |.||..|+.+|-.
T Consensus        26 ~~EC~IC~~~I~~-~~Gv-V~vt~~g~lnLEkmfc~~C~~rw~~   67 (134)
T PF05883_consen   26 TVECQICFDRIDN-NDGV-VYVTDGGTLNLEKMFCADCDKRWRR   67 (134)
T ss_pred             Ceeehhhhhhhhc-CCCE-EEEecCCeehHHHHHHHHHHHHHHh
Confidence            5789999999974 2233 345676      8899999999943

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

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

Probab=90.86  E-value=0.08  Score=53.37  Aligned_cols=30  Identities=30%  Similarity=0.653  Sum_probs=22.8

Q ss_pred             eeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCcccc
Q 012292           28 VISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus        28 ~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~   64 (466)
                      .++||.|+||+.|-..-       ....||.|-.++-
T Consensus       105 RmIPCkHvFCl~CAr~~-------~dK~Cp~C~d~Vq  134 (389)
T KOG2932|consen  105 RMIPCKHVFCLECARSD-------SDKICPLCDDRVQ  134 (389)
T ss_pred             cccccchhhhhhhhhcC-------ccccCcCcccHHH
Confidence            47899999999996542       2478999966553

>PF10174 Cast: RIM-binding protein of the cytomatrix active zone; InterPro: IPR019323 This entry represents a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion []

Probab=90.86  E-value=36  Score=39.30  Aligned_cols=27  Identities=22%  Similarity=0.166  Sum_probs=14.0

Q ss_pred             hHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 012292           91 VSRAEVKILEVKVSRLHTVLESQGKEI  117 (466)
Q Consensus        91 ~l~~El~rLe~kl~~L~~~Le~~~~~l  117 (466)
                      .++.+.++|+..++.....+......+
T Consensus         7 ~~q~E~e~L~~ele~~~~~l~~~~~~i   33 (775)
T PF10174_consen    7 RLQRENERLRRELERKQSKLGSSMNSI   33 (775)
T ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHhH
Confidence            345555555555555555554444443

Located at the C terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). These proteins also contain four coiled-coil domains [].

>PF09730 BicD: Microtubule-associated protein Bicaudal-D; InterPro: IPR018477 BicD proteins consist of three coiled-coiled domains and are involved in dynein-mediated minus end-directed transport from the Golgi apparatus to the endoplasmic reticulum (ER) []

Probab=90.41  E-value=38  Score=38.76  Aligned_cols=26  Identities=23%  Similarity=0.313  Sum_probs=17.2

Q ss_pred             HHHHHHHHHhhhhHHHHHHHHHHHHH
Q 012292          225 NYTELMAKCNLLGREKARFSEKLEKA  250 (466)
Q Consensus       225 ~yeeL~~k~e~L~ree~~~~~kLek~  250 (466)
                      .|+.++..+..|..+..-++..++.+
T Consensus       122 efE~~Khei~rl~Ee~~~l~~qlee~  147 (717)
T PF09730_consen  122 EFEGLKHEIKRLEEEIELLNSQLEEA  147 (717)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67777777777777666665555544

Glycogen synthase kinase-3beta (GSK-3beta) is required for the binding of BICD to dynein but not to dynactin, acting to maintain the anchoring of microtubules to the centromere []. It appears that amino-acid residues 437-617 of BicD and the kinase activity of GSK-3 are necessary for the formation of a complex between BicD and GSK-3beta in intact cells [].; GO: 0006810 transport, 0005794 Golgi apparatus

>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking

Probab=90.33  E-value=20  Score=35.51  Aligned_cols=37  Identities=19%  Similarity=0.451  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHh
Q 012292          245 EKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKV  281 (466)
Q Consensus       245 ~kLek~~~ei~~Lk~~v~eLqk~le~~~ne~l~~l~~  281 (466)
                      +.+++...++...+.++..++..+..+...+++.|..
T Consensus       119 ~~~~~~~~~~~~~~~~l~~l~~~l~~~r~~l~~~l~~  155 (302)
T PF10186_consen  119 EQLEELQNELEERKQRLSQLQSQLARRRRQLIQELSE  155 (302)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4556666777788888888888888888887777654

In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy

>PF04849 HAP1_N: HAP1 N-terminal conserved region; InterPro: IPR006933 This family is defined by an N-terminal conserved region found in several huntingtin-associated protein 1 (HAP1) homologues

Probab=90.17  E-value=24  Score=36.15  Aligned_cols=68  Identities=18%  Similarity=0.233  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHH
Q 012292          212 IDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALK  280 (466)
Q Consensus       212 ~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~~~ne~l~~l~  280 (466)
                      |..|...++.+.+.++++...-+.|..-...++..=..+..|+..|++++.+...-|.+..-+ |+.++
T Consensus       236 It~LlsqivdlQ~r~k~~~~EnEeL~q~L~~ske~Q~~L~aEL~elqdkY~E~~~mL~EaQEE-lk~lR  303 (306)
T PF04849_consen  236 ITSLLSQIVDLQQRCKQLAAENEELQQHLQASKESQRQLQAELQELQDKYAECMAMLHEAQEE-LKTLR  303 (306)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHhh
Confidence            334444444444445555544444444444443333345566777777777766666665554 34433

HAP1 binds to huntingtin in a polyglutamine repeat-length-dependent manner. However, its possible role in the pathogenesis of Huntingtons disease is unclear. This family also includes a similar N-terminal conserved region from hypothetical protein products of ALS2CR3 genes found in the human juvenile amyotrophic lateral sclerosis critical region 2q33-2q34 [].

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.87  E-value=0.18  Score=49.69  Aligned_cols=60  Identities=20%  Similarity=0.491  Sum_probs=40.6

Q ss_pred             CCCCCCcccccccccccccccCcceeecCC-----CcccHHHHHHHHHhcCC---CCCCCCcCcCcccc
Q 012292            4 ENKFGKTICSICYEDLKPIVEDLQVISICG-----HVFHELCLQQWFEYCSS---SKKCTCPVCKQRCS   64 (466)
Q Consensus         4 ~~~~~eltCpICLe~f~P~~~~~~~llpCG-----HsFC~~CL~~wle~~~~---~~s~~CP~CR~~~~   64 (466)
                      ++...+-.|=||+..=.+. ....-.-||.     |..|++||.+|+.....   .....||+|+....
T Consensus        15 ~~~e~eR~CWiCF~TdeDn-~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYi   82 (293)
T KOG3053|consen   15 DNQELERCCWICFATDEDN-RLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYI   82 (293)
T ss_pred             CccccceeEEEEeccCccc-chhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhe
Confidence            4456677899999875421 1111234553     78899999999986444   34568999988654

>PLN03188 kinesin-12 family protein; Provisional

Probab=89.83  E-value=37  Score=40.89  Aligned_cols=29  Identities=28%  Similarity=0.399  Sum_probs=17.5

Q ss_pred             HHHHHHHHHHHHHHHHhhh------HHHHHHHhcc
Q 012292          156 SQELDKVTLECLKLKQRNM------DLAKELASLK  184 (466)
Q Consensus       156 ~eEVeklkeE~~rLq~rn~------alakeL~sLK  184 (466)
                      .+-|+.++...++.-.+..      +++.++..|+
T Consensus      1134 ~egi~dvkkaaakag~kg~~~~f~~alaae~s~l~ 1168 (1320)
T PLN03188       1134 QEGIDDVKKAAARAGVRGAESKFINALAAEISALK 1168 (1320)
T ss_pred             HHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHH
Confidence            3446666666666655553      3466666666

>KOG4674 consensus Uncharacterized conserved coiled-coil protein [Function unknown]

Probab=89.77  E-value=64  Score=40.49  Aligned_cols=56  Identities=21%  Similarity=0.285  Sum_probs=37.5

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012292          209 KDTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQEL  264 (466)
Q Consensus       209 ~e~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eL  264 (466)
                      ...+..|+..|......|..+....+.|......+.++++....++.++++.....
T Consensus       216 s~~~~~L~~~L~~~~~~~~~~q~~~~~l~q~~~eLs~~ie~~~~~ls~~k~t~~s~  271 (1822)
T KOG4674|consen  216 SIEVEQLEEKLSDLKESLAELQEKNKSLKQQNEELSKKIESLNLELSKLKDTAESS  271 (1822)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Confidence            34566777777777777777777777777776666676666666666665544433

>PF15397 DUF4618: Domain of unknown function (DUF4618)

Probab=89.66  E-value=24  Score=35.35  Aligned_cols=45  Identities=18%  Similarity=0.443  Sum_probs=36.6

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHH
Q 012292          235 LLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRAL  279 (466)
Q Consensus       235 ~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~~~ne~l~~l  279 (466)
                      .+.++....+...+..+.+|..|+..|+.|+....+..+-+.-++
T Consensus       190 ~m~kei~~~re~i~el~e~I~~L~~eV~~L~~~~~~~Re~iF~dv  234 (258)
T PF15397_consen  190 VMQKEIVQFREEIDELEEEIPQLRAEVEQLQAQAQDPREVIFADV  234 (258)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchHHHhhHHH
Confidence            346677777888889999999999999999999887666666665

>KOG0980 consensus Actin-binding protein SLA2/Huntingtin-interacting protein Hip1 [Cytoskeleton]

Probab=89.59  E-value=46  Score=38.57  Aligned_cols=44  Identities=23%  Similarity=0.326  Sum_probs=20.1

Q ss_pred             HHHHHHHHHhhhhHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHH
Q 012292          225 NYTELMAKCNLLGREKARFS-------EKLEKAKEKINKLKTRVQELETAV  268 (466)
Q Consensus       225 ~yeeL~~k~e~L~ree~~~~-------~kLek~~~ei~~Lk~~v~eLqk~l  268 (466)
                      ...+|..+++.+.++..+..       +.|+..+.|...+-.+++.|+..+
T Consensus       467 ~~~~L~d~le~~~~~~~~~~~K~e~~~~~le~l~~El~~l~~e~~~lq~~~  517 (980)
T KOG0980|consen  467 ENTNLNDQLEELQRAAGRAETKTESQAKALESLRQELALLLIELEELQRTL  517 (980)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            33444444444444444432       444444444444444555555443

>PF10473 CENP-F_leu_zip: Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; InterPro: IPR019513 Cenp-F, a centromeric kinetochore, microtubule-binding protein consisting of two 1,600-amino acid-long coils, is essential for the full functioning of the mitotic checkpoint pathway [, ]

Probab=89.41  E-value=16  Score=33.16  Aligned_cols=68  Identities=26%  Similarity=0.391  Sum_probs=41.2

Q ss_pred             CChhHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHH
Q 012292          207 NNKDTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNE  274 (466)
Q Consensus       207 ~~~e~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~~~ne  274 (466)
                      ++...+.+|...+-..+.....|.....-+.++.....+.+++....|..|......+...|+.++.+
T Consensus        49 n~k~eie~L~~el~~lt~el~~L~~EL~~l~sEk~~L~k~lq~~q~kv~eLE~~~~~~~~~l~~~E~e  116 (140)
T PF10473_consen   49 NSKAEIETLEEELEELTSELNQLELELDTLRSEKENLDKELQKKQEKVSELESLNSSLENLLQEKEQE  116 (140)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            34455555555555555555555555555555555555666666666666666666666666665555

There are several leucine-rich repeats along the sequence of LEK1 that are considered to be zippers, though they do not appear to be binding DNA directly in this instance []. ; GO: 0008134 transcription factor binding, 0042803 protein homodimerization activity, 0045502 dynein binding

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

Probab=89.35  E-value=0.2  Score=56.01  Aligned_cols=59  Identities=17%  Similarity=0.175  Sum_probs=41.5

Q ss_pred             CCcccccccccccccccCcceeec---CCCcccHHHHHHHHHhcC-CCCCCCCcCcCccccCCC
Q 012292            8 GKTICSICYEDLKPIVEDLQVISI---CGHVFHELCLQQWFEYCS-SSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         8 ~eltCpICLe~f~P~~~~~~~llp---CGHsFC~~CL~~wle~~~-~~~s~~CP~CR~~~~~~~   67 (466)
                      +.-+|.||.-.+.+. .+...+.|   |+|.||..||..|.+.-- ....-.||+|...|..+.
T Consensus        95 ~s~Ss~~C~~E~S~~-~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWs  157 (1134)
T KOG0825|consen   95 ESDTSPVCEKEHSPD-VDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWS  157 (1134)
T ss_pred             cccccchhheecCCc-ccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhhhhh
Confidence            456788888877731 13333556   999999999999987321 124567999998887775

>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking

Probab=88.98  E-value=25  Score=34.77  Aligned_cols=10  Identities=10%  Similarity=0.541  Sum_probs=6.2

Q ss_pred             CcccHHHHHH
Q 012292           34 HVFHELCLQQ   43 (466)
Q Consensus        34 HsFC~~CL~~   43 (466)
                      +.||..|+..
T Consensus        11 ~~~C~~C~~~   20 (302)
T PF10186_consen   11 RFYCANCVNN   20 (302)
T ss_pred             CeECHHHHHH
Confidence            4567777654

In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy

>PF09789 DUF2353: Uncharacterized coiled-coil protein (DUF2353); InterPro: IPR019179 Members of this family have been annotated as being coiled-coil domain-containing protein 149, however they currently have no known function

Probab=88.68  E-value=32  Score=35.52  Aligned_cols=24  Identities=25%  Similarity=0.344  Sum_probs=12.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhh
Q 012292          247 LEKAKEKINKLKTRVQELETAVEL  270 (466)
Q Consensus       247 Lek~~~ei~~Lk~~v~eLqk~le~  270 (466)
                      +..+-.|+.-|++++..+|.+.+-
T Consensus       191 IDaLi~ENRyL~erl~q~qeE~~l  214 (319)
T PF09789_consen  191 IDALIMENRYLKERLKQLQEEKEL  214 (319)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333444445555555555555544

>KOG0979 consensus Structural maintenance of chromosome protein SMC5/Spr18, SMC superfamily [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=88.67  E-value=57  Score=38.41  Aligned_cols=13  Identities=23%  Similarity=0.478  Sum_probs=6.6

Q ss_pred             CCCcccccccccc
Q 012292            7 FGKTICSICYEDL   19 (466)
Q Consensus         7 ~~eltCpICLe~f   19 (466)
                      .....|.||+..=
T Consensus        55 KSSiVcAIcLglg   67 (1072)
T KOG0979|consen   55 KSSIVCAICLGLG   67 (1072)
T ss_pred             chHHHHHHHHHcC
Confidence            3345555555543

>KOG0964 consensus Structural maintenance of chromosome protein 3 (sister chromatid cohesion complex Cohesin, subunit SMC3) [Cell cycle control, cell division, chromosome partitioning]

Probab=88.63  E-value=57  Score=38.36  Aligned_cols=177  Identities=19%  Similarity=0.217  Sum_probs=91.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhhhHHHHHHHhccccccCChhHH-HHH-HHHhhcCCCCChhHHH
Q 012292          136 ALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRNMDLAKELASLKLVSDLNLDED-EVL-KFALLGNGANNKDTID  213 (466)
Q Consensus       136 ~~l~EkLk~~esLeqLL~~q~eEVeklkeE~~rLq~rn~alakeL~sLKlvsd~~~eEe-E~L-K~~~lg~~~~~~e~~d  213 (466)
                      ...+.++..+..+...+....+|++...-....+.++..-+...+..|.       ... +.+ |.++....++..+.-.
T Consensus       321 q~r~~~l~~l~~~~~ki~e~~~EL~~I~Pky~~l~~ee~~~~~rl~~l~-------~~~~~l~~Kqgr~sqFssk~eRDk  393 (1200)
T KOG0964|consen  321 QQRNLALHVLQKVKDKIEEKKDELSKIEPKYNSLVDEEKRLKKRLAKLE-------QKQRDLLAKQGRYSQFSSKEERDK  393 (1200)
T ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHhHHHHHHHHHHHHH-------HHHHHHHHhhccccccCcHHHHHH
Confidence            3334444544455555555555555544444444444443344444444       222 222 4444444445555555


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHH---HHHHhcc-ccchhH
Q 012292          214 VLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVL---RALKVSK-KASQKE  289 (466)
Q Consensus       214 ~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~~~ne~l---~~l~~~~-~~~~~~  289 (466)
                      -++.++...+....+.....+.|..+...+.+.|++..++|.+|...+.+..-.++....+..   +.+-..- +....-
T Consensus       394 wir~ei~~l~~~i~~~ke~e~~lq~e~~~~e~~l~~~~e~i~~l~~si~e~~~r~~~~~~~~~~~k~~~del~~~Rk~lW  473 (1200)
T KOG0964|consen  394 WIRSEIEKLKRGINDTKEQENILQKEIEDLESELKEKLEEIKELESSINETKGRMEEFDAENTELKRELDELQDKRKELW  473 (1200)
T ss_pred             HHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            667777777777667777777777777777777777777777776666655555554211111   1110000 111222


Q ss_pred             HhhhcCCCCCccccccccCChhhhhhccCCCc
Q 012292          290 EILKGATEDNSISLCTNNVSLEDQREQHSVPI  321 (466)
Q Consensus       290 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  321 (466)
                      +.+..+.  ....-.-.|++..++.=..+++.
T Consensus       474 REE~~l~--~~i~~~~~dl~~~~~~L~~~~~r  503 (1200)
T KOG0964|consen  474 REEKKLR--SLIANLEEDLSRAEKNLRATMNR  503 (1200)
T ss_pred             HHHHHHH--HHHHHHHHHHHHHHHHHHHhccc
Confidence            3333333  22333444777777777777663

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=88.49  E-value=11  Score=41.91  Aligned_cols=90  Identities=23%  Similarity=0.364  Sum_probs=49.3

Q ss_pred             hhHHHHHHHHHHHHHHHHhhhHHHHHHHhccccccCChhHHHHHHHHhhcCCCCChhHHHHHHHHHHHHHHHHHHHHHHH
Q 012292          154 SKSQELDKVTLECLKLKQRNMDLAKELASLKLVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELMAKC  233 (466)
Q Consensus       154 ~q~eEVeklkeE~~rLq~rn~alakeL~sLKlvsd~~~eEeE~LK~~~lg~~~~~~e~~d~Lkk~l~~~~k~yeeL~~k~  233 (466)
                      ....++..+.....+++++|-.|..++..|+       .+.++|+...           +.+++.+-    .-.....++
T Consensus       419 ~~~~~i~~~~~~ve~l~~e~~~L~~~~ee~k-------~eie~L~~~l-----------~~~~r~~~----~~~~~~rei  476 (652)
T COG2433         419 VYEKRIKKLEETVERLEEENSELKRELEELK-------REIEKLESEL-----------ERFRREVR----DKVRKDREI  476 (652)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHH-----------HHHHHHHH----HHHhhhHHH
Confidence            3344455555566666666666666666777       5655553211           11222111    111122445


Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012292          234 NLLGREKARFSEKLEKAKEKINKLKTRVQELE  265 (466)
Q Consensus       234 e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLq  265 (466)
                      +.+.++..++.++|++.+..++.|+.++.+|.
T Consensus       477 ~~~~~~I~~L~~~L~e~~~~ve~L~~~l~~l~  508 (652)
T COG2433         477 RARDRRIERLEKELEEKKKRVEELERKLAELR  508 (652)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            55566666666677777777777777776666

>PF05483 SCP-1: Synaptonemal complex protein 1 (SCP-1); InterPro: IPR008827 Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex

Probab=88.40  E-value=49  Score=37.36  Aligned_cols=74  Identities=22%  Similarity=0.284  Sum_probs=59.3

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHhcc
Q 012292          210 DTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVSK  283 (466)
Q Consensus       210 e~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~~~ne~l~~l~~~~  283 (466)
                      ..+..|++.+-...+..++|...-..|.+....-.+++..+...|.+|+..++.+++..++....+.++|-..+
T Consensus       594 nk~~~LrKqvEnk~K~ieeLqqeNk~LKKk~~aE~kq~~~~eikVn~L~~E~e~~kk~~eE~~~~~~keie~K~  667 (786)
T PF05483_consen  594 NKCNNLRKQVENKNKNIEELQQENKALKKKITAESKQSNVYEIKVNKLQEELENLKKKHEEETDKYQKEIESKS  667 (786)
T ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Confidence            45667888887778888888887777888777777888888888999999999999988887777777776433

Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase [].; GO: 0007130 synaptonemal complex assembly, 0000795 synaptonemal complex

>KOG0999 consensus Microtubule-associated protein Bicaudal-D [Intracellular trafficking, secretion, and vesicular transport]

Probab=88.35  E-value=45  Score=36.80  Aligned_cols=26  Identities=27%  Similarity=0.376  Sum_probs=17.0

Q ss_pred             HHHHHHHHHhhhhHHHHHHHHHHHHH
Q 012292          225 NYTELMAKCNLLGREKARFSEKLEKA  250 (466)
Q Consensus       225 ~yeeL~~k~e~L~ree~~~~~kLek~  250 (466)
                      .|+.|+..++.|..+..-++..++.+
T Consensus       195 EyEglkheikRleEe~elln~q~ee~  220 (772)
T KOG0999|consen  195 EYEGLKHEIKRLEEETELLNSQLEEA  220 (772)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67777777777776666666555443

>KOG1842 consensus FYVE finger-containing protein [General function prediction only]

Probab=88.28  E-value=2.6  Score=44.73  Aligned_cols=38  Identities=16%  Similarity=0.359  Sum_probs=27.3

Q ss_pred             CCCCCcccccccccccccccCcceeecCCCcccHHHHHH
Q 012292            5 NKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQ   43 (466)
Q Consensus         5 ~~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~   43 (466)
                      +......||+|-..|.-.. +.+..-=||-+.|..|-.-
T Consensus       176 DDs~V~~CP~Ca~~F~l~r-RrHHCRLCG~VmC~~C~k~  213 (505)
T KOG1842|consen  176 DDSSVQFCPECANSFGLTR-RRHHCRLCGRVMCRDCSKF  213 (505)
T ss_pred             CCCcccccccccchhhhHH-HhhhhhhcchHHHHHHHHh
Confidence            4556789999999997222 2233445999999999764

>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs

Probab=88.27  E-value=54  Score=37.64  Aligned_cols=7  Identities=29%  Similarity=0.377  Sum_probs=5.0

Q ss_pred             CCccccc
Q 012292            8 GKTICSI   14 (466)
Q Consensus         8 ~eltCpI   14 (466)
                      ...+|||
T Consensus       363 ~~~~cpI  369 (717)
T PF10168_consen  363 LSYSCPI  369 (717)
T ss_pred             CCCCcce
Confidence            4568888

It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].

>KOG0962 consensus DNA repair protein RAD50, ABC-type ATPase/SMC superfamily [Replication, recombination and repair]

Probab=88.19  E-value=70  Score=38.84  Aligned_cols=63  Identities=21%  Similarity=0.257  Sum_probs=35.1

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 012292          208 NKDTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVEL  270 (466)
Q Consensus       208 ~~e~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~  270 (466)
                      ..-+++.+..+.......+..+...++.+.++.......+..+..-...++.....+...|..
T Consensus       817 ~i~t~~E~~~Ek~~~~~~~~~~rke~E~~~k~~~~~~~~i~~l~~~~~e~k~~~~~~~~~l~~  879 (1294)
T KOG0962|consen  817 GIRTVDELRKEKSKKQESLDKLRKEIECLQKEVIEQEREISRLINLRNELKEEKQKIERSLAR  879 (1294)
T ss_pred             chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444666666666666666666766666666666655544444444444444444444433333

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

Probab=88.17  E-value=0.21  Score=51.43  Aligned_cols=31  Identities=39%  Similarity=0.664  Sum_probs=22.4

Q ss_pred             ceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccC
Q 012292           27 QVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS   65 (466)
Q Consensus        27 ~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~   65 (466)
                      ...+||||+.|  |..-..      ....||+||..+..
T Consensus       318 ~~fvpcGh~cc--ct~cs~------~l~~CPvCR~rI~~  348 (355)
T KOG1571|consen  318 AVFVPCGHVCC--CTLCSK------HLPQCPVCRQRIRL  348 (355)
T ss_pred             eeeecCCcEEE--chHHHh------hCCCCchhHHHHHH
Confidence            45789999977  655332      35679999987753

>COG4694 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=88.16  E-value=31  Score=38.16  Aligned_cols=88  Identities=18%  Similarity=0.259  Sum_probs=57.7

Q ss_pred             HHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHhcc---ccchhHHhhhcCCCCCcc
Q 012292          225 NYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVSK---KASQKEEILKGATEDNSI  301 (466)
Q Consensus       225 ~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~~~ne~l~~l~~~~---~~~~~~~~~~~~~~~~~~  301 (466)
                      .|..+.++|+.|+++..-..++++++..|+.+|++-+-...=...+....+++-..++.   -++.++.--..+.  |+.
T Consensus       446 ~Y~g~ekk~n~LE~e~kn~~~ev~kls~ei~~ie~~l~~~~~~vke~nq~l~~g~gra~~~L~~~~kek~y~i~r--~~g  523 (758)
T COG4694         446 KYCGLEKKINNLEKEIKNNQEEVKKLSNEIKEIEKFLVSIKPIVKEINQTLLKGYGRANFSLACTEKEKFYRIQR--EDG  523 (758)
T ss_pred             HHHHHHHHHhHHHHHHHhhHHHHHHHHHHHHHHHHHHhhchhhHHHHHHHHHhhcchheeeeeeccchhhheeec--ccC
Confidence            68899999999999998888888888888777776653332222222223333333333   4455555555666  678


Q ss_pred             ccccccCChhhhh
Q 012292          302 SLCTNNVSLEDQR  314 (466)
Q Consensus       302 ~~~~~~~~~~~~~  314 (466)
                      .+.-+.||--|+.
T Consensus       524 ~~~gn~LSEGekt  536 (758)
T COG4694         524 QLVGNTLSEGEKT  536 (758)
T ss_pred             ccccccccccchh
Confidence            8888888877764

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

Probab=87.95  E-value=0.29  Score=51.57  Aligned_cols=51  Identities=29%  Similarity=0.578  Sum_probs=34.0

Q ss_pred             CCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCC-CCCCCCcC
Q 012292            7 FGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSS-SKKCTCPV   58 (466)
Q Consensus         7 ~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~-~~s~~CP~   58 (466)
                      ....+|.||+..+.. .++...+..|+|-||..|+.++++.... +....||.
T Consensus       144 ~~~~~C~iC~~e~~~-~~~~f~~~~C~H~fC~~C~k~~iev~~~~~~~~~C~~  195 (384)
T KOG1812|consen  144 LPKEECGICFVEDPE-AEDMFSVLKCGHRFCKDCVKQHIEVKLLSGTVIRCPH  195 (384)
T ss_pred             cccccCccCcccccc-HhhhHHHhcccchhhhHHhHHHhhhhhccCCCccCCC
Confidence            346799999944431 2233336789999999999999884321 33456653

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

Probab=87.93  E-value=0.23  Score=36.61  Aligned_cols=33  Identities=21%  Similarity=0.594  Sum_probs=22.9

Q ss_pred             eecCC-CcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292           29 ISICG-HVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus        29 llpCG-HsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      +..|. |..|..|+...+.     .+..||+|..+++..
T Consensus        15 Li~C~dHYLCl~CLt~ml~-----~s~~C~iC~~~LPtk   48 (50)
T PF03854_consen   15 LIKCSDHYLCLNCLTLMLS-----RSDRCPICGKPLPTK   48 (50)
T ss_dssp             EEE-SS-EEEHHHHHHT-S-----SSSEETTTTEE----
T ss_pred             eeeecchhHHHHHHHHHhc-----cccCCCcccCcCccc
Confidence            56787 8889999998877     789999999987643

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.

>COG4942 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]

Probab=87.92  E-value=42  Score=35.94  Aligned_cols=60  Identities=17%  Similarity=0.194  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012292           92 SRAEVKILEVKVSRLHTVLESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQL  151 (466)
Q Consensus        92 l~~El~rLe~kl~~L~~~Le~~~~~lk~L~eel~~~KeQlkeE~~~l~EkLk~~esLeqL  151 (466)
                      .+.++..++..+....+........+++++.++..+..++.+....+...-+.++.+...
T Consensus        43 ~q~ei~~~~~~i~~~~~~~~kL~~~lk~~e~~i~~~~~ql~~s~~~l~~~~~~I~~~~~~  102 (420)
T COG4942          43 IQKEIAALEKKIREQQDQRAKLEKQLKSLETEIASLEAQLIETADDLKKLRKQIADLNAR  102 (420)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHH
Confidence            455566666666665556666666666666666666655555555554444444444333

>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]

Probab=87.91  E-value=61  Score=37.84  Aligned_cols=34  Identities=32%  Similarity=0.461  Sum_probs=18.2

Q ss_pred             HHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012292          229 LMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQ  262 (466)
Q Consensus       229 L~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~  262 (466)
                      +...++.|.+-..++..++..++..|..|+++|.
T Consensus       408 k~sE~~eL~r~kE~Lsr~~d~aEs~iadlkEQVD  441 (1243)
T KOG0971|consen  408 KNSELEELRRQKERLSRELDQAESTIADLKEQVD  441 (1243)
T ss_pred             HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344445555555555555555666665555553

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

Probab=87.87  E-value=0.37  Score=57.14  Aligned_cols=55  Identities=24%  Similarity=0.603  Sum_probs=36.7

Q ss_pred             CCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCC-----CCCCCcCcCcccc
Q 012292            8 GKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSS-----KKCTCPVCKQRCS   64 (466)
Q Consensus         8 ~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~-----~s~~CP~CR~~~~   64 (466)
                      .+-.|-||+-.--.  .-+.--+.|||.||..|..+.++.+=.+     +-..||.|..++.
T Consensus      3485 ~DDmCmICFTE~L~--AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3485 ADDMCMICFTEALS--AAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred             cCceEEEEehhhhC--CCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence            45679999865431  0111357899999999999877732222     2357999987665

>PF00038 Filament: Intermediate filament protein; InterPro: IPR016044 Intermediate filaments (IF) [, , ] are proteins which are primordial components of the cytoskeleton and the nuclear envelope

Probab=87.84  E-value=33  Score=34.63  Aligned_cols=38  Identities=21%  Similarity=0.218  Sum_probs=16.1

Q ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Q 012292           92 SRAEVKILEVKVSRLHTVLESQGKEIKEINEELCLCKE  129 (466)
Q Consensus        92 l~~El~rLe~kl~~L~~~Le~~~~~lk~L~eel~~~Ke  129 (466)
                      +..++..++..++.+...-.....++..+..++..++.
T Consensus        52 ye~el~~lr~~id~~~~eka~l~~e~~~l~~e~~~~r~   89 (312)
T PF00038_consen   52 YEEELRELRRQIDDLSKEKARLELEIDNLKEELEDLRR   89 (312)
T ss_dssp             HHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHHHHhHHhhhhHHHHhhHHhhhhhhHHHHHHHHHH
Confidence            44455555554444433333333333334444443333

They generally form filamentous structures 8 to 14 nm wide. IF proteins are members of a very large multigene family of proteins which has been subdivided in five major subgroups: Type I: Acidic cytokeratins. Type II: Basic cytokeratins. Type III: Vimentin, desmin, glial fibrillary acidic protein (GFAP), peripherin, and plasticin. Type IV: Neurofilaments L, H and M, alpha-internexin and nestin. Type V: Nuclear lamins A, B1, B2 and C. All IF proteins are structurally similar in that they consist of: a central rod domain comprising some 300 to 350 residues which is arranged in coiled-coiled alpha-helices, with at least two short characteristic interruptions; a N-terminal non-helical domain (head) of variable length; and a C-terminal domain (tail) which is also non-helical, and which shows extreme length variation between different IF proteins. While IF proteins are evolutionary and structurally related, they have limited sequence homologies except in several regions of the rod domain. This entry represents the central rod domain found in IF proteins.; PDB: 3TNU_B 3KLT_D 1GK4_F 3TRT_A 3G1E_A 3UF1_C 1GK6_B 1GK7_A 3TYY_B 3V4W_A ....

>PRK01156 chromosome segregation protein; Provisional

Probab=87.60  E-value=63  Score=37.70  Aligned_cols=10  Identities=30%  Similarity=1.032  Sum_probs=4.9

Q ss_pred             cccccccccc
Q 012292           10 TICSICYEDL   19 (466)
Q Consensus        10 ltCpICLe~f   19 (466)
                      ..||+|....
T Consensus       453 ~~Cp~c~~~~  462 (895)
T PRK01156        453 SVCPVCGTTL  462 (895)
T ss_pred             CCCCCCCCcC
Confidence            3455555444

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

Probab=87.53  E-value=0.14  Score=57.09  Aligned_cols=53  Identities=30%  Similarity=0.656  Sum_probs=41.9

Q ss_pred             CCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            6 KFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         6 ~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      ..-.+.||||+..+. |+      .+.|-|.||..|+...+.+.+  +...||+|+......
T Consensus        18 ~~k~lEc~ic~~~~~~p~------~~kc~~~~l~~~~n~~f~~~~--~~~~~~lc~~~~eK~   71 (684)
T KOG4362|consen   18 MQKILECPICLEHVKEPS------LLKCDHIFLKFCLNKLFESKK--GPKQCALCKSDIEKR   71 (684)
T ss_pred             HhhhccCCceeEEeeccc------hhhhhHHHHhhhhhceeeccC--ccccchhhhhhhhhh
Confidence            345789999999998 64      689999999999987666433  378899999766644

>PF15070 GOLGA2L5: Putative golgin subfamily A member 2-like protein 5

Probab=87.33  E-value=56  Score=36.81  Aligned_cols=10  Identities=20%  Similarity=0.195  Sum_probs=3.5

Q ss_pred             HHHHHHHHHH
Q 012292          159 LDKVTLECLK  168 (466)
Q Consensus       159 VeklkeE~~r  168 (466)
                      +..+.+...+
T Consensus       124 L~ELE~~le~  133 (617)
T PF15070_consen  124 LAELEEELER  133 (617)
T ss_pred             HHHHHHHHHH
Confidence            3333333333

>PF12325 TMF_TATA_bd: TATA element modulatory factor 1 TATA binding; InterPro: IPR022091 This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes []

Probab=87.27  E-value=20  Score=31.68  Aligned_cols=34  Identities=24%  Similarity=0.368  Sum_probs=17.9

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 012292          236 LGREKARFSEKLEKAKEKINKLKTRVQELETAVE  269 (466)
Q Consensus       236 L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le  269 (466)
                      |......+..-|-+-.+++++|+..|.+++.-+.
T Consensus        80 l~~ry~t~LellGEK~E~veEL~~Dv~DlK~myr  113 (120)
T PF12325_consen   80 LQQRYQTLLELLGEKSEEVEELRADVQDLKEMYR  113 (120)
T ss_pred             HHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHH
Confidence            3333344444455555566666666666655443

The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs []. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family [].

>PF00769 ERM: Ezrin/radixin/moesin family; InterPro: IPR011259 The ERM family consists of three closely-related proteins, ezrin, radixin and moesin []

Probab=87.13  E-value=22  Score=35.29  Aligned_cols=62  Identities=19%  Similarity=0.259  Sum_probs=38.5

Q ss_pred             HHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHhccccc
Q 012292          225 NYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVSKKAS  286 (466)
Q Consensus       225 ~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~~~ne~l~~l~~~~~~~  286 (466)
                      ....|..++..+.....++....+....+...|+.++...+..++....+++.-+..+..++
T Consensus        76 Ek~~Le~e~~e~~~~i~~l~ee~~~ke~Ea~~lq~el~~ar~~~~~ak~~L~~~~~~~~~p~  137 (246)
T PF00769_consen   76 EKEQLEQELREAEAEIARLEEESERKEEEAEELQEELEEAREDEEEAKEELLEVMSAPPPPP  137 (246)
T ss_dssp             -----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HTTS--G
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccc
Confidence            34445555556666666766777778888888888888888888888888777666665444

Ezrin was first identified as a constituent of microvilli [], radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions [], and moesin as a heparin binding protein []. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain; an extended alpha-helical domain; and a charged C-terminal domain []. Ezrin, radixin and merlin also contain a polyproline region between the helical and C-terminal domains. The N-terminal domain is highly conserved, and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily. ERM proteins crosslink actin filaments with plasma membranes. They co-localise with CD44 at actin filament-plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains [].; GO: 0008092 cytoskeletal protein binding, 0005737 cytoplasm, 0019898 extrinsic to membrane; PDB: 2I1J_A 2I1K_A 1E5W_A 1EF1_C.

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

Probab=86.90  E-value=0.45  Score=49.59  Aligned_cols=33  Identities=27%  Similarity=0.777  Sum_probs=24.2

Q ss_pred             CcccHHHHHHHHHhcCC--------CCCCCCcCcCccccCC
Q 012292           34 HVFHELCLQQWFEYCSS--------SKKCTCPVCKQRCSSS   66 (466)
Q Consensus        34 HsFC~~CL~~wle~~~~--------~~s~~CP~CR~~~~~~   66 (466)
                      -..|..|+-+|+..+..        .++..||+||++|...
T Consensus       313 PmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCil  353 (358)
T PF10272_consen  313 PMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCIL  353 (358)
T ss_pred             chHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceee
Confidence            34577999999984331        3567899999998643

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

>COG1340 Uncharacterized archaeal coiled-coil protein [Function unknown]

Probab=86.84  E-value=39  Score=34.46  Aligned_cols=31  Identities=16%  Similarity=0.356  Sum_probs=15.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhH
Q 012292          243 FSEKLEKAKEKINKLKTRVQELETAVELKDN  273 (466)
Q Consensus       243 ~~~kLek~~~ei~~Lk~~v~eLqk~le~~~n  273 (466)
                      +-.++.++...+..++..+..+++.+...+.
T Consensus       212 ~he~~ve~~~~~~e~~ee~~~~~~elre~~k  242 (294)
T COG1340         212 LHEEFVELSKKIDELHEEFRNLQNELRELEK  242 (294)
T ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence            3344444445555555555555555555443

>KOG0999 consensus Microtubule-associated protein Bicaudal-D [Intracellular trafficking, secretion, and vesicular transport]

Probab=86.66  E-value=56  Score=36.09  Aligned_cols=46  Identities=22%  Similarity=0.330  Sum_probs=30.7

Q ss_pred             HHHHHHHHHhhhhHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHhh
Q 012292          225 NYTELMAKCNLLGREKARFS---EKLEKAKEKINKLKTRVQELETAVEL  270 (466)
Q Consensus       225 ~yeeL~~k~e~L~ree~~~~---~kLek~~~ei~~Lk~~v~eLqk~le~  270 (466)
                      .|.+|...-=.|.+.+..++   =+++-++-+|.+|.+.+.-|...+++
T Consensus       171 eYSELEEENIsLQKqVs~LR~sQVEyEglkheikRleEe~elln~q~ee  219 (772)
T KOG0999|consen  171 EYSELEEENISLQKQVSNLRQSQVEYEGLKHEIKRLEEETELLNSQLEE  219 (772)
T ss_pred             HHHHHHHhcchHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            55555544444455555444   56788888888888888877777666

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

Probab=86.32  E-value=0.5  Score=47.97  Aligned_cols=54  Identities=24%  Similarity=0.387  Sum_probs=40.6

Q ss_pred             CCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccc
Q 012292            6 KFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRC   63 (466)
Q Consensus         6 ~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~   63 (466)
                      .+.-.+|||--+.-.  .+++|+++.|||+.-..-+.+..+  ++..+..||.|-...
T Consensus       333 fHs~FiCPVlKe~~t--~ENpP~ml~CgHVIskeal~~LS~--nG~~~FKCPYCP~~~  386 (396)
T COG5109         333 FHSLFICPVLKELCT--DENPPVMLECGHVISKEALSVLSQ--NGVLSFKCPYCPEMS  386 (396)
T ss_pred             ccceeeccccHhhhc--ccCCCeeeeccceeeHHHHHHHhh--cCcEEeeCCCCCcch
Confidence            456678999777764  346678999999999999888755  333578999995543

>PLN03229 acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha; Provisional

Probab=86.24  E-value=69  Score=36.71  Aligned_cols=48  Identities=27%  Similarity=0.376  Sum_probs=30.4

Q ss_pred             ChhHHHHHHHHHHHHHH---HHHHHHHHHhhhhHHHHHHH--------HHHHHHHHHHH
Q 012292          208 NKDTIDVLRKSLVIRNK---NYTELMAKCNLLGREKARFS--------EKLEKAKEKIN  255 (466)
Q Consensus       208 ~~e~~d~Lkk~l~~~~k---~yeeL~~k~e~L~ree~~~~--------~kLek~~~ei~  255 (466)
                      ..+.++.|..++...-.   .--+|+.|+|.|..|.+.+-        ++++.++.+|.
T Consensus       647 ~k~KIe~L~~eIkkkIe~av~ss~LK~k~E~Lk~Evaka~~~pd~~~k~kieal~~qik  705 (762)
T PLN03229        647 LQEKIESLNEEINKKIERVIRSSDLKSKIELLKLEVAKASKTPDVTEKEKIEALEQQIK  705 (762)
T ss_pred             hHHHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHH
Confidence            35677777776544333   23457788888888876654        55666666654

>PF09730 BicD: Microtubule-associated protein Bicaudal-D; InterPro: IPR018477 BicD proteins consist of three coiled-coiled domains and are involved in dynein-mediated minus end-directed transport from the Golgi apparatus to the endoplasmic reticulum (ER) []

Probab=86.12  E-value=70  Score=36.68  Aligned_cols=6  Identities=33%  Similarity=0.717  Sum_probs=2.1

Q ss_pred             HhhhHH
Q 012292          171 QRNMDL  176 (466)
Q Consensus       171 ~rn~al  176 (466)
                      ++|.++
T Consensus       104 eENisl  109 (717)
T PF09730_consen  104 EENISL  109 (717)
T ss_pred             HHHHHH
Confidence            333333

Glycogen synthase kinase-3beta (GSK-3beta) is required for the binding of BICD to dynein but not to dynactin, acting to maintain the anchoring of microtubules to the centromere []. It appears that amino-acid residues 437-617 of BicD and the kinase activity of GSK-3 are necessary for the formation of a complex between BicD and GSK-3beta in intact cells [].; GO: 0006810 transport, 0005794 Golgi apparatus

>PF05701 WEMBL: Weak chloroplast movement under blue light; InterPro: IPR008545 This family consists of several plant proteins of unknown function

Probab=85.85  E-value=60  Score=35.71  Aligned_cols=53  Identities=26%  Similarity=0.344  Sum_probs=31.4

Q ss_pred             HHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHH
Q 012292          228 ELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALK  280 (466)
Q Consensus       228 eL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~~~ne~l~~l~  280 (466)
                      ++...+.++..+-..++...+.+..++.+++..+...+..+...+..+.-.++
T Consensus       369 ~l~~~Lqql~~Eae~Ak~ea~~~~~E~~~~k~E~e~~ka~i~t~E~rL~aa~k  421 (522)
T PF05701_consen  369 ELPKALQQLSSEAEEAKKEAEEAKEEVEKAKEEAEQTKAAIKTAEERLEAALK  421 (522)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455555556666666666666666666666666666666665555444433

Several sequences in this family are described as being myosin heavy chain-like.

>TIGR02680 conserved hypothetical protein TIGR02680

Probab=85.75  E-value=1e+02  Score=38.14  Aligned_cols=122  Identities=17%  Similarity=0.174  Sum_probs=58.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhhhHHHHHHHhccccccCChhHHHHHHHHhhcCCCCChhHH
Q 012292          133 EEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRNMDLAKELASLKLVSDLNLDEDEVLKFALLGNGANNKDTI  212 (466)
Q Consensus       133 eE~~~l~EkLk~~esLeqLL~~q~eEVeklkeE~~rLq~rn~alakeL~sLKlvsd~~~eEeE~LK~~~lg~~~~~~e~~  212 (466)
                      .....+......++.+...+.....+++....+...+..+-..+...+..+.       ++.+.|+         .+++.
T Consensus       266 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~le~~~~~l~-------~~~~~l~---------~~~a~  329 (1353)
T TIGR02680       266 RRATRLRSAQTQYDQLSRDLGRARDELETAREEERELDARTEALEREADALR-------TRLEALQ---------GSPAY  329 (1353)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHhc---------CCHHH
Confidence            3334444445555555566666666666666666665555444444444444       4444442         11222


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 012292          213 DVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELK  271 (466)
Q Consensus       213 d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~~  271 (466)
                      .. .+++.......+++....+...+........+++...++..+..++.++.+.++..
T Consensus       330 ~~-~~eL~el~~ql~~~~~~a~~~~~~~~~a~~~~e~~~~~~~~~~~r~~~~~~~l~~~  387 (1353)
T TIGR02680       330 QD-AEELERARADAEALQAAAADARQAIREAESRLEEERRRLDEEAGRLDDAERELRAA  387 (1353)
T ss_pred             HH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            11 12222223333333333333333333344556666666666666666666665543

Members of this protein family belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Proteins in this family average over 1400 amino acids in length.

>PF11559 ADIP: Afadin- and alpha -actinin-Binding; InterPro: IPR021622 This family is found in mammals where it is localised at cell-cell adherens junctions [], and in Sch

Probab=85.44  E-value=28  Score=31.48  Aligned_cols=28  Identities=32%  Similarity=0.571  Sum_probs=16.7

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012292          235 LLGREKARFSEKLEKAKEKINKLKTRVQ  262 (466)
Q Consensus       235 ~L~ree~~~~~kLek~~~ei~~Lk~~v~  262 (466)
                      .+..-......++.+-+.||.+|++++.
T Consensus       123 ~~~~~~tq~~~e~rkke~E~~kLk~rL~  150 (151)
T PF11559_consen  123 QLQQRKTQYEHELRKKEREIEKLKERLN  150 (151)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3333344555666667777777777653

pombe and other fungi where it anchors spindle-pole bodies to spindle microtubules []. It is a coiled-coil structure, and in pombe, it is required for anchoring the minus end of spindle microtubules to the centrosome equivalent, the spindle-pole body. The name ADIP derives from the family being composed of Afadin- and alpha -Actinin-Binding Proteins Localised at Cell-Cell Adherens Junctions.

>PF10498 IFT57: Intra-flagellar transport protein 57 ; InterPro: IPR019530 Eukaryotic cilia and flagella are specialised organelles found at the periphery of cells of diverse organisms

Probab=85.02  E-value=54  Score=34.43  Aligned_cols=53  Identities=13%  Similarity=0.272  Sum_probs=29.2

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHhhhhHH------HHHHHHHHHHHHHHHHHHHHHH
Q 012292          209 KDTIDVLRKSLVIRNKNYTELMAKCNLLGRE------KARFSEKLEKAKEKINKLKTRV  261 (466)
Q Consensus       209 ~e~~d~Lkk~l~~~~k~yeeL~~k~e~L~re------e~~~~~kLek~~~ei~~Lk~~v  261 (466)
                      .+.+..+.+.|......+++++..++.-+..      ..+.++.+.+++.||..+.-++
T Consensus       293 s~~V~~~t~~L~~IseeLe~vK~emeerg~~mtD~sPlv~IKqAl~kLk~EI~qMdvrI  351 (359)
T PF10498_consen  293 SEGVSERTRELAEISEELEQVKQEMEERGSSMTDGSPLVKIKQALTKLKQEIKQMDVRI  351 (359)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHhhhhh
Confidence            3456667777777777777777755544322      2333344444444444444333

Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bi-directional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated []. This protein is known as Huntington-interacting protein-1 in humans.

>PRK04778 septation ring formation regulator EzrA; Provisional

Probab=84.90  E-value=69  Score=35.57  Aligned_cols=50  Identities=22%  Similarity=0.312  Sum_probs=31.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 012292          210 DTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKT  259 (466)
Q Consensus       210 e~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~  259 (466)
                      +..+.+...+...++...++..+++.|.+++..++++|++....+..++.
T Consensus       383 e~leel~e~leeie~eq~ei~e~l~~Lrk~E~eAr~kL~~~~~~L~~ikr  432 (569)
T PRK04778        383 EELEEILKQLEEIEKEQEKLSEMLQGLRKDELEAREKLERYRNKLHEIKR  432 (569)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455555666666666666677777777777766666666666665553

>KOG4360 consensus Uncharacterized coiled coil protein [Function unknown]

Probab=84.56  E-value=67  Score=35.14  Aligned_cols=45  Identities=20%  Similarity=0.276  Sum_probs=25.8

Q ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhhhHHHHHHHhcc
Q 012292          140 EALRQKVSVEQLLHSKSQELDKVTLECLKLKQRNMDLAKELASLK  184 (466)
Q Consensus       140 EkLk~~esLeqLL~~q~eEVeklkeE~~rLq~rn~alakeL~sLK  184 (466)
                      ..++++..+........+++.....+..+.++.+..+...+..++
T Consensus       202 ~~~KelrdtN~q~~s~~eel~~kt~el~~q~Ee~skLlsql~d~q  246 (596)
T KOG4360|consen  202 DCVKELRDTNTQARSGQEELQSKTKELSRQQEENSKLLSQLVDLQ  246 (596)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence            344444455555555566666666666666666665555555554

>PF04849 HAP1_N: HAP1 N-terminal conserved region; InterPro: IPR006933 This family is defined by an N-terminal conserved region found in several huntingtin-associated protein 1 (HAP1) homologues

Probab=84.48  E-value=52  Score=33.78  Aligned_cols=105  Identities=13%  Similarity=0.174  Sum_probs=58.9

Q ss_pred             HHHHHHHHHHHHhhhHHHHHHHhccccccCChhHHHHHHHHhhcCCCCChhHHHHHHHHHHHHHHHHHHHHHHHhhhhHH
Q 012292          160 DKVTLECLKLKQRNMDLAKELASLKLVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRNKNYTELMAKCNLLGRE  239 (466)
Q Consensus       160 eklkeE~~rLq~rn~alakeL~sLKlvsd~~~eEeE~LK~~~lg~~~~~~e~~d~Lkk~l~~~~k~yeeL~~k~e~L~re  239 (466)
                      +.+.+.+..|.++|..+..+...|+--...-.+.+..|=..-...-..++..+..|...|+.....+......|.+|-.+
T Consensus       163 e~Lq~Klk~LEeEN~~LR~Ea~~L~~et~~~EekEqqLv~dcv~QL~~An~qia~LseELa~k~Ee~~rQQEEIt~Llsq  242 (306)
T PF04849_consen  163 EALQEKLKSLEEENEQLRSEASQLKTETDTYEEKEQQLVLDCVKQLSEANQQIASLSEELARKTEENRRQQEEITSLLSQ  242 (306)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44445555555666655555555552111111223333111111113466667777777777777777777777777777


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 012292          240 KARFSEKLEKAKEKINKLKTRVQEL  264 (466)
Q Consensus       240 e~~~~~kLek~~~ei~~Lk~~v~eL  264 (466)
                      .+.+.+++.....|.++|...+...
T Consensus       243 ivdlQ~r~k~~~~EnEeL~q~L~~s  267 (306)
T PF04849_consen  243 IVDLQQRCKQLAAENEELQQHLQAS  267 (306)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHH
Confidence            7777777777777766666555443

HAP1 binds to huntingtin in a polyglutamine repeat-length-dependent manner. However, its possible role in the pathogenesis of Huntingtons disease is unclear. This family also includes a similar N-terminal conserved region from hypothetical protein products of ALS2CR3 genes found in the human juvenile amyotrophic lateral sclerosis critical region 2q33-2q34 [].

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]

Probab=84.42  E-value=1.3  Score=43.84  Aligned_cols=53  Identities=23%  Similarity=0.463  Sum_probs=39.0

Q ss_pred             CCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            7 FGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         7 ~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      .....|||---.|... ..-..+-+|||+|-..-+.+.       ....|++|...+...+
T Consensus       109 ~a~fiCPvtgleMng~-~~F~~l~~CGcV~SerAlKei-------kas~C~~C~a~y~~~d  161 (293)
T KOG3113|consen  109 RARFICPVTGLEMNGK-YRFCALRCCGCVFSERALKEI-------KASVCHVCGAAYQEDD  161 (293)
T ss_pred             cceeecccccceecce-EEEEEEeccceeccHHHHHHh-------hhccccccCCcccccC
Confidence            3457899876666521 122356789999999998887       4589999999887665

>PF07926 TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro: IPR012929 This domain is found in a number of proteins, including TPR protein (P12270 from SWISSPROT) and yeast myosin-like proteins 1 (MLP1, Q02455 from SWISSPROT) and 2 (MLP2, P40457 from SWISSPROT)

Probab=84.23  E-value=30  Score=30.80  Aligned_cols=25  Identities=16%  Similarity=0.360  Sum_probs=10.3

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHH
Q 012292          237 GREKARFSEKLEKAKEKINKLKTRV  261 (466)
Q Consensus       237 ~ree~~~~~kLek~~~ei~~Lk~~v  261 (466)
                      .++...+..++..+..++.-|...+
T Consensus       104 e~e~~~~~~r~~dL~~QN~lLh~Ql  128 (132)
T PF07926_consen  104 EKELSELEQRIEDLNEQNKLLHDQL  128 (132)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333344444444444444443

These proteins share a number of features; for example, they all have coiled-coil regions and all three are associated with nuclear pores [, , ]. TPR is thought to be a component of nuclear pore complex- attached intranuclear filaments [], and is implicated in nuclear protein import []. Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerisation of kinase domains or by targeting these kinases to the nuclear pore complex []. MLP1 and MLP2 are involved in the process of telomere length regulation, where they are thought to interact with proteins such as Tel1p and modulate their activity []. ; GO: 0006606 protein import into nucleus, 0005643 nuclear pore

>KOG4673 consensus Transcription factor TMF, TATA element modulatory factor [Transcription]

Probab=84.17  E-value=81  Score=35.77  Aligned_cols=11  Identities=9%  Similarity=0.377  Sum_probs=5.9

Q ss_pred             HHHHHHHHHhh
Q 012292          260 RVQELETAVEL  270 (466)
Q Consensus       260 ~v~eLqk~le~  270 (466)
                      +++.||.+|..
T Consensus       645 QIE~lQ~tl~~  655 (961)
T KOG4673|consen  645 QIEALQETLSK  655 (961)
T ss_pred             HHHHHHHHHhh
Confidence            45556655554

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

Probab=84.02  E-value=0.23  Score=49.82  Aligned_cols=39  Identities=31%  Similarity=0.703  Sum_probs=26.1

Q ss_pred             ccccccc-ccccCcceeecCCCcc-cHHHHHHHHHhcCCCCCCCCcCcCcccc
Q 012292           14 ICYEDLK-PIVEDLQVISICGHVF-HELCLQQWFEYCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus        14 ICLe~f~-P~~~~~~~llpCGHsF-C~~CL~~wle~~~~~~s~~CP~CR~~~~   64 (466)
                      .|--=|+ |.  +. ++++|||.. |..|-.+.         ..||+||+.+.
T Consensus       302 LC~ICmDaP~--DC-vfLeCGHmVtCt~CGkrm---------~eCPICRqyi~  342 (350)
T KOG4275|consen  302 LCAICMDAPR--DC-VFLECGHMVTCTKCGKRM---------NECPICRQYIV  342 (350)
T ss_pred             HHHHHhcCCc--ce-EEeecCcEEeehhhcccc---------ccCchHHHHHH
Confidence            3444455 42  33 468999955 99996543         47999998654

>PF10481 CENP-F_N: Cenp-F N-terminal domain; InterPro: IPR018463 Mitosin or centromere-associated protein-F (Cenp-F) is found bound across the centromere as one of the proteins of the outer layer of the kinetochore []

Probab=83.99  E-value=51  Score=33.27  Aligned_cols=61  Identities=13%  Similarity=0.187  Sum_probs=31.3

Q ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHH
Q 012292          102 KVSRLHTVLESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKV  162 (466)
Q Consensus       102 kl~~L~~~Le~~~~~lk~L~eel~~~KeQlkeE~~~l~EkLk~~esLeqLL~~q~eEVekl  162 (466)
                      .++.+...|+.++...+.-..++..+++...-.......-.+....+.+.+..+...|..+
T Consensus        40 QleSlEAaLqKQKqK~e~ek~e~s~LkREnq~l~e~c~~lek~rqKlshdlq~Ke~qv~~l  100 (307)
T PF10481_consen   40 QLESLEAALQKQKQKVEEEKNEYSALKRENQSLMESCENLEKTRQKLSHDLQVKESQVNFL  100 (307)
T ss_pred             hHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhHHHHHHHHHHHHHHhhHHHhhhHHHHHHH
Confidence            5666777777777666666666666654322222222222233334445555554444444

Most of the kinetochore/centromere functions appear to depend upon binding of the C-terminal part of the molecule, whereas the N-terminal part, here, may be a cytoplasmic player in controlling the function of microtubules and dynein [].

>PF12718 Tropomyosin_1: Tropomyosin like; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells

Probab=83.95  E-value=33  Score=31.14  Aligned_cols=17  Identities=29%  Similarity=0.477  Sum_probs=6.1

Q ss_pred             HHHHHHHHHHHHHHHHH
Q 012292          246 KLEKAKEKINKLKTRVQ  262 (466)
Q Consensus       246 kLek~~~ei~~Lk~~v~  262 (466)
                      +|..++.....+..+|+
T Consensus       102 kl~e~d~~ae~~eRkv~  118 (143)
T PF12718_consen  102 KLREADVKAEHFERKVK  118 (143)
T ss_pred             HHHHHHHHhHHHHHHHH
Confidence            33333333333333333

In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].

>PF05622 HOOK: HOOK protein; InterPro: IPR008636 This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms

Probab=83.76  E-value=0.34  Score=55.10  Aligned_cols=15  Identities=7%  Similarity=0.208  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHHH
Q 012292          211 TIDVLRKSLVIRNKN  225 (466)
Q Consensus       211 ~~d~Lkk~l~~~~k~  225 (466)
                      .++.+++.+..++..
T Consensus       364 qle~~k~qi~eLe~~  378 (713)
T PF05622_consen  364 QLEEYKKQIQELEQK  378 (713)
T ss_dssp             ---------------
T ss_pred             HHHHHHHHHHHHHHH
Confidence            334444444433333

The different members of the Homo sapiens gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three Homo sapiens HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerisation and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes [], whereas both HOOK1 and HOOK2 are localised to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head [].; GO: 0008017 microtubule binding, 0000226 microtubule cytoskeleton organization, 0005737 cytoplasm; PDB: 1WIX_A.

>PF14182 YgaB: YgaB-like protein

Probab=83.74  E-value=8.2  Score=31.57  Aligned_cols=54  Identities=22%  Similarity=0.498  Sum_probs=46.7

Q ss_pred             HHHhhhhHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHhccc
Q 012292          231 AKCNLLGREKARFS--EKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVSKK  284 (466)
Q Consensus       231 ~k~e~L~ree~~~~--~kLek~~~ei~~Lk~~v~eLqk~le~~~ne~l~~l~~~~~  284 (466)
                      .+|.+..++.....  .+|.....||...+..++++++..+.-.+++++.-..+++
T Consensus        24 ERCqeIE~eL~~l~~ea~l~~i~~EI~~mkk~Lk~Iq~~Fe~QTeeVI~sy~~~~~   79 (79)
T PF14182_consen   24 ERCQEIEKELKELEREAELHSIQEEISQMKKELKEIQRVFEKQTEEVIRSYQSEEK   79 (79)
T ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            56777777777766  7889999999999999999999999999999998777654

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=83.68  E-value=0.69  Score=46.49  Aligned_cols=36  Identities=22%  Similarity=0.563  Sum_probs=26.9

Q ss_pred             CCCcccHHHHHHHHHhcCC--------CCCCCCcCcCccccCCC
Q 012292           32 CGHVFHELCLQQWFEYCSS--------SKKCTCPVCKQRCSSSN   67 (466)
Q Consensus        32 CGHsFC~~CL~~wle~~~~--------~~s~~CP~CR~~~~~~~   67 (466)
                      |....|.+||-+|+.....        .++.+||.||+.+...+
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~d  368 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRD  368 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEee
Confidence            5566788999999873322        26789999999987554

>smart00787 Spc7 Spc7 kinetochore protein

Probab=82.94  E-value=61  Score=33.38  Aligned_cols=10  Identities=40%  Similarity=0.601  Sum_probs=3.7

Q ss_pred             HHHHHHHHHH
Q 012292          256 KLKTRVQELE  265 (466)
Q Consensus       256 ~Lk~~v~eLq  265 (466)
                      +|+.++..||
T Consensus       275 ~Lk~~~~~Le  284 (312)
T smart00787      275 KLKEQLKLLQ  284 (312)
T ss_pred             HHHHHHHHHH
Confidence            3333333333

This domain is found in cell division proteins which are required for kinetochore-spindle association.

>COG4942 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]

Probab=81.91  E-value=78  Score=33.93  Aligned_cols=31  Identities=10%  Similarity=0.213  Sum_probs=13.1

Q ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Q 012292           98 ILEVKVSRLHTVLESQGKEIKEINEELCLCK  128 (466)
Q Consensus        98 rLe~kl~~L~~~Le~~~~~lk~L~eel~~~K  128 (466)
                      .....+..+...+....++...|+.++..++
T Consensus        42 q~q~ei~~~~~~i~~~~~~~~kL~~~lk~~e   72 (420)
T COG4942          42 QIQKEIAALEKKIREQQDQRAKLEKQLKSLE   72 (420)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333444444444444444444444444333

>KOG2129 consensus Uncharacterized conserved protein H4 [Function unknown]

Probab=81.57  E-value=79  Score=33.77  Aligned_cols=39  Identities=13%  Similarity=0.118  Sum_probs=18.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhh--hhHHHHHHHHhccc
Q 012292          246 KLEKAKEKINKLKTRVQELETAVEL--KDNEVLRALKVSKK  284 (466)
Q Consensus       246 kLek~~~ei~~Lk~~v~eLqk~le~--~~ne~l~~l~~~~~  284 (466)
                      |+.+...|-...++....||..|..  -.+|+|.|...++-
T Consensus       279 k~~qy~~Ee~~~reen~rlQrkL~~e~erRealcr~lsEse  319 (552)
T KOG2129|consen  279 KLMQYRAEEVDHREENERLQRKLINELERREALCRMLSESE  319 (552)
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence            3344444444444444445544443  33456666655553

>PF06160 EzrA: Septation ring formation regulator, EzrA ; InterPro: IPR010379 During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site

Probab=81.30  E-value=95  Score=34.50  Aligned_cols=115  Identities=20%  Similarity=0.249  Sum_probs=60.6

Q ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHhhhHHHHHHHhccccccCChhHHHHHHHHhhcCCCCChhHHHHHHHHHHHHH
Q 012292          144 QKVSVEQLLHSKSQELDKVTLECLKLKQRNMDLAKELASLKLVSDLNLDEDEVLKFALLGNGANNKDTIDVLRKSLVIRN  223 (466)
Q Consensus       144 ~~esLeqLL~~q~eEVeklkeE~~rLq~rn~alakeL~sLKlvsd~~~eEeE~LK~~~lg~~~~~~e~~d~Lkk~l~~~~  223 (466)
                      .+..++.++....+++..+..+...|......-..+...|+       +.+..++...+.+...=..+++.|-+.|....
T Consensus       102 ~i~~~~~~l~~~e~~i~~i~~~l~~L~~~e~~nr~~i~~l~-------~~y~~lrk~ll~~~~~~G~a~~~Le~~L~~ie  174 (560)
T PF06160_consen  102 AIKEIEEQLDEIEEDIKEILDELDELLESEEKNREEIEELK-------EKYRELRKELLAHSFSYGPAIEELEKQLENIE  174 (560)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhhhhhchhHHHHHHHHHHHH
Confidence            33344555555555555555555555554444456666677       66666655555544455566777777666666


Q ss_pred             H---HHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 012292          224 K---NYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVEL  270 (466)
Q Consensus       224 k---~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~  270 (466)
                      .   .+++|+.     ..+-..+..-|.+++..+..|+..+..+=..+..
T Consensus       175 ~~F~~f~~lt~-----~GD~~~A~eil~~l~~~~~~l~~~~e~IP~l~~~  219 (560)
T PF06160_consen  175 EEFSEFEELTE-----NGDYLEAREILEKLKEETDELEEIMEDIPKLYKE  219 (560)
T ss_pred             HHHHHHHHHHH-----CCCHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence            5   4555554     3333333344444444444444444443333333

EzrA modulates the frequency and position of FtsZ ring formation [].; GO: 0000921 septin ring assembly, 0005940 septin ring, 0016021 integral to membrane

>PF04156 IncA: IncA protein; InterPro: IPR007285 Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion

Probab=80.93  E-value=49  Score=30.91  Aligned_cols=7  Identities=29%  Similarity=0.264  Sum_probs=2.7

Q ss_pred             HHHHHHH
Q 012292          225 NYTELMA  231 (466)
Q Consensus       225 ~yeeL~~  231 (466)
                      .|+++.+
T Consensus       138 ~~~~~~~  144 (191)
T PF04156_consen  138 SIKELEK  144 (191)
T ss_pred             HHHHHHH
Confidence            3333333

The inclusion is nonfusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA (Inclusion membrane protein A), is functionally associated with the homotypic fusion of inclusions [].

>KOG0976 consensus Rho/Rac1-interacting serine/threonine kinase Citron [Signal transduction mechanisms]

Probab=80.85  E-value=1.2e+02  Score=35.24  Aligned_cols=14  Identities=7%  Similarity=0.166  Sum_probs=5.3

Q ss_pred             HHHHHHHHHHHHHH
Q 012292          115 KEIKEINEELCLCK  128 (466)
Q Consensus       115 ~~lk~L~eel~~~K  128 (466)
                      .+.+.+++.+....
T Consensus       120 ~ekq~lQ~ti~~~q  133 (1265)
T KOG0976|consen  120 MEKQKLQDTIQGAQ  133 (1265)
T ss_pred             HHHHHHHHHHHHHH
Confidence            33333444333333

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

Probab=80.79  E-value=0.86  Score=48.10  Aligned_cols=38  Identities=21%  Similarity=0.385  Sum_probs=28.1

Q ss_pred             CcccccccccccccccCcceeecCCCcccHHHHHHHHH
Q 012292            9 KTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFE   46 (466)
Q Consensus         9 eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle   46 (466)
                      +..||.|.-.+.-.....+++..|||-||+.|...|..
T Consensus       306 wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~  343 (384)
T KOG1812|consen  306 WRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKT  343 (384)
T ss_pred             cCcCcccceeeeecCCcceEEeeccccchhhcCcchhh
Confidence            56788888777622234445556999999999999976

>KOG1103 consensus Predicted coiled-coil protein [Function unknown]

Probab=80.69  E-value=77  Score=33.08  Aligned_cols=53  Identities=26%  Similarity=0.315  Sum_probs=32.7

Q ss_pred             HHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh-hhHHHHH
Q 012292          225 NYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVEL-KDNEVLR  277 (466)
Q Consensus       225 ~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~-~~ne~l~  277 (466)
                      ..+++....++|..+..+..+.-..++.|...|++-|+.|+..+.- +.|+.|.
T Consensus       246 ~i~EfdiEre~LRAel~ree~r~K~lKeEmeSLkeiVkdlEA~hQh~~pNeqLk  299 (561)
T KOG1103|consen  246 LIEEFDIEREFLRAELEREEKRQKMLKEEMESLKEIVKDLEADHQHLRPNEQLK  299 (561)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCcccccc
Confidence            4445555445555444444444445677788888888888877766 6666443

>KOG2991 consensus Splicing regulator [RNA processing and modification]

Probab=80.48  E-value=66  Score=32.20  Aligned_cols=23  Identities=22%  Similarity=0.294  Sum_probs=11.3

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHH
Q 012292          208 NKDTIDVLRKSLVIRNKNYTELM  230 (466)
Q Consensus       208 ~~e~~d~Lkk~l~~~~k~yeeL~  230 (466)
                      +...+-.|..+|+--++.-++|+
T Consensus       234 s~Gria~Le~eLAmQKs~seElk  256 (330)
T KOG2991|consen  234 SEGRIAELEIELAMQKSQSEELK  256 (330)
T ss_pred             hcccHHHHHHHHHHHHhhHHHHH
Confidence            44445555555555444444444

>KOG0612 consensus Rho-associated, coiled-coil containing protein kinase [Signal transduction mechanisms]

Probab=80.47  E-value=1.4e+02  Score=36.03  Aligned_cols=14  Identities=21%  Similarity=0.453  Sum_probs=6.3

Q ss_pred             HHHHHHHHHHHHhh
Q 012292          257 LKTRVQELETAVEL  270 (466)
Q Consensus       257 Lk~~v~eLqk~le~  270 (466)
                      +..+++.++..++.
T Consensus       672 ~e~~lk~~q~~~eq  685 (1317)
T KOG0612|consen  672 LERKLKMLQNELEQ  685 (1317)
T ss_pred             HHHHHHHHHHHHHH
Confidence            33344444444444

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=80.45  E-value=1.3  Score=43.63  Aligned_cols=38  Identities=16%  Similarity=0.311  Sum_probs=31.7

Q ss_pred             CCCCCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHH
Q 012292            3 IENKFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFE   46 (466)
Q Consensus         3 ~~~~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle   46 (466)
                      .++....--|+.||..+. |+      +.|=||.||..||..++-
T Consensus        37 rDsiK~FdcCsLtLqPc~dPv------it~~GylfdrEaILe~il   75 (303)
T KOG3039|consen   37 RDSIKPFDCCSLTLQPCRDPV------ITPDGYLFDREAILEYIL   75 (303)
T ss_pred             ccccCCcceeeeecccccCCc------cCCCCeeeeHHHHHHHHH
Confidence            455666778999999998 65      789999999999998755

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

Probab=80.18  E-value=1.4  Score=31.85  Aligned_cols=41  Identities=27%  Similarity=0.630  Sum_probs=20.7

Q ss_pred             cccccccccccccCccee--ecCCCcccHHHHHHHHHhcCCCCCCCCcCc
Q 012292           12 CSICYEDLKPIVEDLQVI--SICGHVFHELCLQQWFEYCSSSKKCTCPVC   59 (466)
Q Consensus        12 CpICLe~f~P~~~~~~~l--lpCGHsFC~~CL~~wle~~~~~~s~~CP~C   59 (466)
                      |.+|-+...-.    ..-  ..|+=.+|..|+..++...   ....||.|
T Consensus         1 C~~C~~iv~~G----~~C~~~~C~~r~H~~C~~~y~r~~---~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQG----QRCSNRDCNVRLHDDCFKKYFRHR---SNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSS----EE-SS--S--EE-HHHHHHHTTT----SS-B-TTT
T ss_pred             CcccchhHeee----ccCCCCccCchHHHHHHHHHHhcC---CCCCCcCC
Confidence            67888887611    011  2488899999999998832   22379988

; PDB: 3NW0_A 2CT0_A.

>PF15619 Lebercilin: Ciliary protein causing Leber congenital amaurosis disease

Probab=80.09  E-value=57  Score=31.22  Aligned_cols=72  Identities=15%  Similarity=0.190  Sum_probs=30.2

Q ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhhh
Q 012292          103 VSRLHTVLESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQLLHSKSQELDKVTLECLKLKQRNM  174 (466)
Q Consensus       103 l~~L~~~Le~~~~~lk~L~eel~~~KeQlkeE~~~l~EkLk~~esLeqLL~~q~eEVeklkeE~~rLq~rn~  174 (466)
                      +..|...+......++.+..+...++..-......+...-..-..+.+++..-.+|+..+.....+.+....
T Consensus        14 i~~L~n~l~elq~~l~~l~~ENk~Lk~lq~Rq~kAL~k~e~~e~~Lpqll~~h~eEvr~Lr~~LR~~q~~~r   85 (194)
T PF15619_consen   14 IKELQNELAELQRKLQELRKENKTLKQLQKRQEKALQKYEDTEAELPQLLQRHNEEVRVLRERLRKSQEQER   85 (194)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444555555544442211122222111122224445555555555555554444444433

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	466
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	3e-13
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	7e-13
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	2e-12
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	4e-11
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-11
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-05
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	1e-10
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	7e-10
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	7e-10
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	1e-09
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	2e-09
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	2e-09
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	3e-09
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	3e-08
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	4e-08
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	7e-08
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	1e-07
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	5e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-06
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	2e-07
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	3e-07
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	4e-07
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	5e-07
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	6e-07
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	6e-07
2ect_A	78	Ring finger protein 126; metal binding protein, st	7e-07
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	1e-06
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	1e-06
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	2e-06
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	2e-06
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	3e-06
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	3e-06
3nw0_A	238	Non-structural maintenance of chromosomes element	4e-06
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	5e-06
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	6e-06
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	6e-06
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	7e-06
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	7e-06
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	9e-06
1z6u_A	150	NP95-like ring finger protein isoform B; structura	9e-06
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	1e-05
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	2e-05
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	2e-05
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	3e-05
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	3e-05
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	4e-05
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	4e-05
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	7e-05
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	8e-05
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	9e-05
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	1e-04
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	3e-04
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	3e-04
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	4e-04
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	5e-04

>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus} Length = 71

 Score = 63.7 bits (155), Expect = 3e-13
 Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 7/62 (11%)

Query: 8  GKTICSICYEDLKPIVEDLQVISI--CGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS 65
          G   C IC +    IV++ ++I    CGHVF   CL+   +        TCP C+++ + 
Sbjct: 9  GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLK-----NANTCPTCRKKINH 63

Query: 66 SN 67
            
Sbjct: 64 KR 65

>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding; HET: SUC; 1.50A {Homo sapiens} Length = 64

 Score = 62.5 bits (152), Expect = 7e-13
 Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 7/62 (11%)

Query: 8  GKTICSICYEDLKPIVEDLQVISI--CGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS 65
              C IC +    IV++ ++I    CGHVF   CL+   +        TCP C+++ + 
Sbjct: 2  AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLK-----NANTCPTCRKKINH 56

Query: 66 SN 67
            
Sbjct: 57 KR 58

>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 69

 Score = 61.1 bits (148), Expect = 2e-12
 Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 7/60 (11%)

Query: 8  GKTICSICYEDLKPIVEDLQVISI--CGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS 65
          G   C IC +    IV++ ++I    CGHVF   CL+   +        TCP C+++ + 
Sbjct: 14 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLK-----NANTCPTCRKKINH 68

>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 Length = 55

 Score = 57.3 bits (139), Expect = 4e-11
 Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 6/53 (11%)

Query: 8  GKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCK 60
          G + C IC ED+        V+  CGH+ H  C ++  +     +   CP+C 
Sbjct: 4  GSSGCPICLEDIHTSRVVAHVLP-CGHLLHRTCYEEMLK-----EGYRCPLCS 50

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 64.1 bits (155), Expect = 6e-11
 Identities = 48/299 (16%), Positives = 99/299 (33%), Gaps = 72/299 (24%)

Query: 82  KDPEVEDPE------VSRAEVK-ILEVK-----VSRLHTVLESQGKEIKE--INEELCL- 126
            + + +D +      +S+ E+  I+  K       RL   L S+ +E+ +  + E L + 
Sbjct: 31  DNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRIN 90

Query: 127 ---CKERIKEEAALKNEALRQKVSVEQL--LHSKSQELDKVTLECLKLKQRNMDLAKELA 181
                  IK E   +  ++  ++ +EQ   L++ +Q   K  +  L+   +   L + L 
Sbjct: 91  YKFLMSPIKTEQ--RQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLK---LRQALL 145

Query: 182 SLK-----------------LVSDLNLDEDEVLKFAL------LGNGANNKDTIDVLRKS 218
            L+                 +  D+ L      K         L N  + +  +++L+K 
Sbjct: 146 ELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKL 205

Query: 219 LVIRNKNYTEL-------MAKCNLLGREKARF--SEKLEKA---------KEKINKLKTR 260
           L   + N+T           + + +  E  R   S+  E            +  N     
Sbjct: 206 LYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLS 265

Query: 261 VQELETAVELKDNEVLRALKVSK-KASQKEEILKGATEDNSISLCTN--NVSLEDQREQ 316
            + L T    +  +V   L  +       +      T D   SL     +   +D   +
Sbjct: 266 CKILLTT---RFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPRE 321

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 46.0 bits (108), Expect = 3e-05
 Identities = 47/365 (12%), Positives = 111/365 (30%), Gaps = 89/365 (24%)

Query: 73  IDLVISQKPKDPEVEDPEVSRAEVKILEVKVSRLHTVLESQGKEIKEIN-EELCLCKERI 131
            D + +       ++   ++    ++  + +  L    +   +E+   N   L +  E I
Sbjct: 278 TDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESI 337

Query: 132 KEEAA-LKNEALRQKVSVEQLLHSKSQELDKVTLECLK---LKQRNMDLAKELASLKLVS 187
           ++  A   N         + +   K   + + +L  L+    ++    L+          
Sbjct: 338 RDGLATWDN--------WKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLS------VFPP 383

Query: 188 DLNLDEDEVLKFALLGNGANNKDTIDVL----RKSLVIRNKN---------YTELMAKCN 234
             ++    +L  +L+       D + V+    + SLV +            Y EL  K  
Sbjct: 384 SAHIPT-ILL--SLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLE 440

Query: 235 LLGREKARFSEK--LEKAKEKINKLKTRVQE---------LETAVELKDNEVLRALKVSK 283
                     +   + K  +  + +   + +         L+     +   + R + +  
Sbjct: 441 NEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDF 500

Query: 284 K-ASQKEEILKGATEDNSISLCTNNVSLEDQR--EQH---SVPIYNLDWTSRVTNDFSFS 337
           +   QK  I   +T  N+     N  +L+  +  + +   + P Y      R+ N     
Sbjct: 501 RFLEQK--IRHDSTAWNASGSILN--TLQQLKFYKPYICDNDPKY-----ERLVNAI--- 548

Query: 338 TKSENFNAIKNIDANHTREGGSAKSHGKERNALQREDTSRFSSVVFGLSN-HNSIHQTIA 396
               +F  +  I+ N            K  + L+             L     +I +   
Sbjct: 549 ---LDF--LPKIEENLIC--------SKYTDLLR-----------IALMAEDEAIFEEAH 584

Query: 397 DVVQK 401
             VQ+
Sbjct: 585 KQVQR 589

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

 Score = 56.6 bits (137), Expect = 1e-10
 Identities = 16/54 (29%), Positives = 23/54 (42%), Gaps = 9/54 (16%)

Query: 12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS 65
          C IC ED      +  +   C H F  +C+ +W       +  TCP+CK    S
Sbjct: 8  CPICLEDP----SNYSMALPCLHAFCYVCITRWIR-----QNPTCPLCKVPVES 52

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 72

 Score = 54.4 bits (131), Expect = 7e-10
 Identities = 15/59 (25%), Positives = 22/59 (37%), Gaps = 9/59 (15%)

Query: 11 ICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSI 69
          +CSIC   L     D   I+ C H F + C+ + F          CP C      +  +
Sbjct: 17 LCSICKGYLI----DATTITECLHTFCKSCIVRHFY-----YSNRCPKCNIVVHQTQPL 66

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

 Score = 53.9 bits (130), Expect = 7e-10
 Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 11/57 (19%)

Query: 12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNS 68
          C IC +    ++  L     C H F + C+ +W +     +   CP+C+ + + +N 
Sbjct: 18 CCICMDGRADLI--LP----CAHSFCQKCIDKWSD-----RHRNCPICRLQMTGANE 63

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

 Score = 54.8 bits (131), Expect = 1e-09
 Identities = 16/62 (25%), Positives = 21/62 (33%), Gaps = 13/62 (20%)

Query: 12 CSICYEDLKPIV-------------EDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPV 58
          C IC E L                   +  ++ C H FH LCL   +   +      CP 
Sbjct: 28 CIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPS 87

Query: 59 CK 60
          CK
Sbjct: 88 CK 89

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

 Score = 58.2 bits (140), Expect = 2e-09
 Identities = 18/58 (31%), Positives = 24/58 (41%), Gaps = 9/58 (15%)

Query: 12  CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSI 69
           C IC E+ K +      I  CGH+    CL  W E    S+   CP C+     +  I
Sbjct: 335 CKICAENDKDVK-----IEPCGHLMCTSCLTSWQE----SEGQGCPFCRCEIKGTEPI 383

>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} Length = 100

 Score = 53.7 bits (129), Expect = 2e-09
 Identities = 12/56 (21%), Positives = 23/56 (41%), Gaps = 8/56 (14%)

Query: 12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN 67
          C IC E L+    D ++   C  +    C+++W     + ++  CP C+       
Sbjct: 25 CFICMEKLR----DARLCPHCSKLCCFSCIRRWL----TEQRAQCPHCRAPLQLRE 72

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

 Score = 52.2 bits (125), Expect = 3e-09
 Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 7/50 (14%)

Query: 12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQ 61
          C+IC+     ++   Q    CG   H  C+ ++F+   S+ +  CP C  
Sbjct: 18 CNICHS----LLIQGQSCETCGIRMHLPCVAKYFQ---SNAEPRCPHCND 60

>2d8t_A Dactylidin, ring finger protein 146; RNF146, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 71

 Score = 49.4 bits (118), Expect = 3e-08
 Identities = 14/57 (24%), Positives = 20/57 (35%), Gaps = 12/57 (21%)

Query: 12 CSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN 67
          C+IC +    P      V   C HVF  LC++             C +C+Q      
Sbjct: 18 CAICLQTCVHP------VSLPCKHVFCYLCVKGASW-----LGKRCALCRQEIPEDF 63

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 81

 Score = 49.5 bits (118), Expect = 4e-08
 Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 12/51 (23%)

Query: 12 CSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQ 61
          C IC +  + P      V++ C H F E C  + F          C +C Q
Sbjct: 18 CFICRQAFQNP------VVTKCRHYFCESCALEHFR-----ATPRCYICDQ 57

>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens} Length = 74

 Score = 48.6 bits (116), Expect = 7e-08
 Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 7/58 (12%)

Query: 12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSI 69
          C IC + +     D  VI  CG+ + + C++        S + TCP C Q   S +++
Sbjct: 18 CLICKDIMT----DAVVIPCCGNSYCDECIRTALL---ESDEHTCPTCHQNDVSPDAL 68

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus} Length = 133

 Score = 49.8 bits (118), Expect = 1e-07
 Identities = 17/84 (20%), Positives = 32/84 (38%), Gaps = 2/84 (2%)

Query: 12 CSICYEDLKPIVEDLQ--VISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSI 69
          C IC +    IV++ +  V + CGHVF   CL+   +  ++   C   +  +R       
Sbjct: 10 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYIG 69

Query: 70 GDQIDLVISQKPKDPEVEDPEVSR 93
             +   I        V++  +  
Sbjct: 70 SGTVSCPICMDGYSEIVQNGRLIV 93

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus} Length = 133

 Score = 42.1 bits (98), Expect = 5e-05
 Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 7/58 (12%)

Query: 12  CSICYEDLKPIV--EDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN 67
           C IC +    IV    L V + CGHVF   CL+   +        TCP C+++ +   
Sbjct: 75  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLK-----NANTCPTCRKKINHKR 127

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 52.9 bits (127), Expect = 2e-07
 Identities = 48/284 (16%), Positives = 106/284 (37%), Gaps = 5/284 (1%)

Query: 90   EVSRAEVKILEVKVSRLHTVLESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVE 149
            + + AE+K LE K ++L        ++++   E     +E     AA K E       +E
Sbjct: 874  QKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILHEME 933

Query: 150  QLLHSKSQELDKVTLECLKLKQRNMDLAKELASLKLVSDLNLDEDEVLKFALLGNGANNK 209
              +  + +   ++  E  K++Q+ +DL ++L   +        + ++ K    G     +
Sbjct: 934  ARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEA----ARQKLQLEKVTADGKIKKME 989

Query: 210  DTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVE 269
            D I ++        K    L  + + L    A   EK +   +  NK ++ + ELE  ++
Sbjct: 990  DDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLK 1049

Query: 270  LKDNEVLRALKVSKKASQKEEILKGATEDNSISLCTNNVSLEDQREQHSVPIYNLDWTSR 329
             ++       K+ +K   +   L     +    +      L  + E+    +  L+  + 
Sbjct: 1050 KEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALARLEDETS 1109

Query: 330  VTNDFSFSTKSENFNAIKNIDANHTREGGSAKSHGKERNALQRE 373
              N+       E  + I ++  +   E  +     K++  L  E
Sbjct: 1110 QKNNAL-KKIRELESHISDLQEDLESEKAARNKAEKQKRDLSEE 1152

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 49.4 bits (118), Expect = 2e-06
 Identities = 33/205 (16%), Positives = 64/205 (31%), Gaps = 4/205 (1%)

Query: 94   AEVKILEVKVSRLHTVLESQGKEIKEINEELCLCKERIKEEAALKNEALRQKVSVEQLLH 153
             ++K +E  +  +        KE K + E +      + EE        + K   E ++ 
Sbjct: 983  GKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMIS 1042

Query: 154  SKSQELDKVTLECLKLKQRNMDLAKELASLKLVSDLNLDEDEVLKFALLGNGANNKDTID 213
                 L K      +L++    L  E + L       + E +     L    A  ++ + 
Sbjct: 1043 ELEVRLKKEEKSRQELEKIKRKLEGESSDL----HEQIAELQAQIAELKAQLAKKEEELQ 1098

Query: 214  VLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDN 273
                 L          + K   L    +   E LE  K   NK + + ++L   +E    
Sbjct: 1099 AALARLEDETSQKNNALKKIRELESHISDLQEDLESEKAARNKAEKQKRDLSEELEALKT 1158

Query: 274  EVLRALKVSKKASQKEEILKGATED 298
            E+   L  +    +         +D
Sbjct: 1159 ELEDTLDTTATQQELRGSDYKDDDD 1183

>1wim_A KIAA0161 protein; ring finger domain, UBCM4-interacting protein 4, UIP4, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 94

 Score = 47.9 bits (114), Expect = 2e-07
 Identities = 15/73 (20%), Positives = 31/73 (42%), Gaps = 8/73 (10%)

Query: 12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYC---SSSKKCTCPVCKQRCSSSNS 68
          C +C  +     E +  I+ C  +F  LCL+Q+ E           +CP     C     
Sbjct: 8  CKLCLGEYPV--EQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAA--CPKQGH 63

Query: 69 IGD-QIDLVISQK 80
          + + +I+ +++ +
Sbjct: 64 LQENEIECMVAAE 76

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

 Score = 47.1 bits (112), Expect = 3e-07
 Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 7/50 (14%)

Query: 12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQ 61
          C++C ED KP  ++L +   C H FH  CL +W E      +  CP+C  
Sbjct: 18 CAVCLEDFKPR-DELGICP-CKHAFHRKCLIKWLE-----VRKVCPLCNM 60

>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 Length = 108

 Score = 47.5 bits (113), Expect = 4e-07
 Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 9/59 (15%)

Query: 11 ICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSI 69
          +C +C         D   I  C H F + C+ ++ E         CP+C  +   +  +
Sbjct: 17 MCVLCGGYFI----DATTIIECLHSFCKTCIVRYLE-----TSKYCPICDVQVHKTRPL 66

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

 Score = 46.4 bits (110), Expect = 5e-07
 Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 6/50 (12%)

Query: 12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQ 61
          C  C  + K   + + V   C H FH  C+  W +  +      CP+C+Q
Sbjct: 29 CLRCQAENKQ-EDCVVVWGECNHSFHNCCMSLWVKQNN-----RCPLCQQ 72

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

 Score = 45.3 bits (108), Expect = 6e-07
 Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 8/53 (15%)

Query: 12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS 64
          C++C  +L+   E+ + +  CGH FH  C+  W    S     TCP+C  R +
Sbjct: 8  CAVCLAELEDG-EEARFLPRCGHGFHAECVDMWLGSHS-----TCPLC--RLT 52

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

 Score = 50.6 bits (120), Expect = 6e-07
 Identities = 18/64 (28%), Positives = 27/64 (42%), Gaps = 9/64 (14%)

Query: 12  CSICYEDLKPIVEDLQVI---SICGHVFHELCLQQWFEYCSSSKK------CTCPVCKQR 62
           C+IC+       E   V    + C    H +CL++WF+     K         CP CK +
Sbjct: 311 CNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAK 370

Query: 63  CSSS 66
            S+S
Sbjct: 371 LSTS 374

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

 Score = 45.9 bits (109), Expect = 7e-07
 Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 7/50 (14%)

Query: 12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQ 61
          C +C ED     E ++ +  C H+FH+ C+  W E     +  +CPVC++
Sbjct: 18 CPVCKEDYALG-ESVRQLP-CNHLFHDSCIVPWLE-----QHDSCPVCRK 60

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

 Score = 45.8 bits (109), Expect = 1e-06
 Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 7/54 (12%)

Query: 8  GKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQ 61
           +  C IC  +     +    +  C H FH+ C+  W +     K  TCPVC+ 
Sbjct: 39 QEMCCPICCSEYV-KGDVATELP-CHHYFHKPCVSIWLQ-----KSGTCPVCRC 85

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens} Length = 99

 Score = 45.5 bits (108), Expect = 1e-06
 Identities = 13/57 (22%), Positives = 22/57 (38%), Gaps = 9/57 (15%)

Query: 11 ICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN 67
           C IC+E          +I  C H +  LC++++        K  CP C    +  +
Sbjct: 24 RCGICFEYFN----IAMIIPQCSHNYCSLCIRKFLS-----YKTQCPTCCVTVTEPD 71

>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 66

 Score = 44.0 bits (104), Expect = 2e-06
 Identities = 16/66 (24%), Positives = 24/66 (36%), Gaps = 14/66 (21%)

Query: 3  IENKFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQ 61
          +E+K+    C  C+  L  P        + CGH F E C+        SS    C  C++
Sbjct: 12 VEDKY---KCEKCHLVLCSP------KQTECGHRFCESCMAALL----SSSSPKCTACQE 58

Query: 62 RCSSSN 67
                
Sbjct: 59 SIVKDK 64

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

 Score = 44.2 bits (105), Expect = 2e-06
 Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 7/57 (12%)

Query: 10 TICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS 66
          T+C +C  D +   + L+V+  C H FH  C+ +W +        TCP+C+     S
Sbjct: 24 TLCVVCMCDFESR-QLLRVLP-CNHEFHAKCVDKWLKANR-----TCPICRADSGPS 73

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 73

 Score = 43.9 bits (104), Expect = 3e-06
 Identities = 19/58 (32%), Positives = 25/58 (43%), Gaps = 9/58 (15%)

Query: 11 ICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN 67
          IC IC + L+ P      V   CGH F   C+ Q  E  +S     CP+CK     + 
Sbjct: 22 ICPICLDILQKP------VTIDCGHNFCLKCITQIGE--TSCGFFKCPLCKTSVRKNA 71

>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus} Length = 85

 Score = 44.3 bits (105), Expect = 3e-06
 Identities = 19/59 (32%), Positives = 25/59 (42%), Gaps = 8/59 (13%)

Query: 11 ICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSK-KCTCPVCKQRCSSSN 67
           C IC E LK P      V + C H F   C+   +E   ++  K  CPVC+      N
Sbjct: 21 TCPICLELLKEP------VSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGN 73

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

 Score = 47.0 bits (111), Expect = 4e-06
 Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 7/56 (12%)

Query: 8   GKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRC 63
              IC+IC+     ++   Q    CG   H  C+ ++F    S+ +  CP C    
Sbjct: 179 AVKICNICHS----LLIQGQSCETCGIRMHLPCVAKYF---QSNAEPRCPHCNDYW 227

>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 Length = 165

 Score = 45.7 bits (108), Expect = 5e-06
 Identities = 23/115 (20%), Positives = 43/115 (37%), Gaps = 10/115 (8%)

Query: 11  ICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSIG 70
           +C IC + LK    +      C H F   C+         S    CP C+++  S  S+ 
Sbjct: 56  MCPICLDMLK----NTMTTKECLHRFCADCIITALR----SGNKECPTCRKKLVSKRSLR 107

Query: 71  D--QIDLVISQKPKDPEVEDPEVSRAEVKILEVKVSRLHTVLESQGKEIKEINEE 123
                D +IS+     +  +    R   +I +    +  +    +G +I+ +N  
Sbjct: 108 PDPNFDALISKIYPSRDEYEAHQERVLARINKHNNQQALSHSIEEGLKIQAMNRL 162

>2ecv_A Tripartite motif-containing protein 5; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 85

 Score = 43.4 bits (103), Expect = 6e-06
 Identities = 17/59 (28%), Positives = 23/59 (38%), Gaps = 8/59 (13%)

Query: 11 ICSICYEDLK-PIVEDLQVISICGHVFHELCLQQ-WFEYCSSSKKCTCPVCKQRCSSSN 67
           C IC E L  P      +   CGH F + CL     +      + +CPVC+      N
Sbjct: 21 TCPICLELLTQP------LSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPEN 73

>3l11_A E3 ubiquitin-protein ligase RNF168; E3 ligase, ring domain, DNA damage, chromatin regulator, chromosomal protein, DNA repair, metal-binding; 2.12A {Homo sapiens} Length = 115

 Score = 44.1 bits (104), Expect = 6e-06
 Identities = 19/67 (28%), Positives = 27/67 (40%), Gaps = 11/67 (16%)

Query: 12 CSICYEDL-KPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSIG 70
          C IC E L +P      V   C H   + C Q   E  S      CP C++R SS     
Sbjct: 18 CGICMEILVEP------VTLPCNHTLCKPCFQSTVEKASLC----CPFCRRRVSSWTRYH 67

Query: 71 DQIDLVI 77
           + + ++
Sbjct: 68 TRRNSLV 74

>3fl2_A E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA damage, DNA repair, ring finger domain, metal binding, DNA replication; 1.75A {Homo sapiens} Length = 124

 Score = 44.6 bits (105), Expect = 7e-06
 Identities = 13/58 (22%), Positives = 24/58 (41%), Gaps = 11/58 (18%)

Query: 12  CSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNS 68
           C  C E +  P      + ++C H   + CL + F     ++  +CP C+     S +
Sbjct: 55  CICCQELVFRP------ITTVCQHNVCKDCLDRSFR----AQVFSCPACRYDLGRSYA 102

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

 Score = 42.7 bits (101), Expect = 7e-06
 Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 7/50 (14%)

Query: 12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQ 61
          C+IC   L+   ED++ +  C H+FH++C+ QW           CP+C+ 
Sbjct: 17 CTICLSILEEG-EDVRRLP-CMHLFHQVCVDQWLI-----TNKKCPICRV 59

>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing, mRNA splicing; NMR {Homo sapiens} Length = 92

 Score = 43.2 bits (102), Expect = 9e-06
 Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 7/54 (12%)

Query: 12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS 65
          C IC +    I+ D  VI  CG+ + + C++        S + TCP C Q   S
Sbjct: 16 CLICKD----IMTDAVVIPCCGNSYCDECIRTALL---ESDEHTCPTCHQNDVS 62

>1z6u_A NP95-like ring finger protein isoform B; structural genomics consortium, ligase, ubiquitin-protein ligase, cell cycle regulation, SGC; 2.10A {Homo sapiens} Length = 150

 Score = 44.6 bits (105), Expect = 9e-06
 Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 11/58 (18%)

Query: 12  CSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNS 68
           C  C E +  P      V + C H   + CLQ+ F+    ++  +CP C+     +  
Sbjct: 81  CVCCQELVYQP------VTTECFHNVCKDCLQRSFK----AQVFSCPACRHDLGQNYI 128

>2egp_A Tripartite motif-containing protein 34; ZF-C3HC4 domain, tripartite motif protein 34, interferon- responsive finger protein 1; NMR {Homo sapiens} Length = 79

 Score = 42.3 bits (100), Expect = 1e-05
 Identities = 16/59 (27%), Positives = 22/59 (37%), Gaps = 9/59 (15%)

Query: 12 CSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKK--CTCPVCKQRCSSSN 67
          C IC E L  P      +   CGH     C+    +   +S     +CPVC    S  +
Sbjct: 15 CPICLELLTEP------LSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEH 67

>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 Length = 112

 Score = 42.8 bits (101), Expect = 2e-05
 Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 9/57 (15%)

Query: 12 CSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN 67
          C IC E +K P      V + C H+F + C+ +            CP+CK   +  +
Sbjct: 24 CPICLELIKEP------VSTKCDHIFCKFCMLKLLN--QKKGPSQCPLCKNDITKRS 72

>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 Length = 116

 Score = 42.6 bits (100), Expect = 2e-05
 Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 11/58 (18%)

Query: 11 ICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN 67
           C IC   L  P      V + C H+F  +C+ +  +         CP C+  C  ++
Sbjct: 25 SCQICEHILADP------VETSCKHLFCRICILRCLK----VMGSYCPSCRYPCFPTD 72

>4epo_C E3 ubiquitin-protein ligase RNF8; coiled-coil, E3 ubiquitin ligase, protein binding complex; 4.80A {Homo sapiens} Length = 149

 Score = 43.1 bits (101), Expect = 3e-05
 Identities = 15/57 (26%), Positives = 22/57 (38%), Gaps = 10/57 (17%)

Query: 12  CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNS 68
           C IC E     V        C H F   C+ +W +     +K  CP+C++   S   
Sbjct: 67  CIICSEYFIEAV-----TLNCAHSFCSYCINEWMK-----RKIECPICRKDIKSKTY 113

>2ct2_A Tripartite motif protein 32; zinc-finger protein HT2A, TAT- interacting protein, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 88

 Score = 41.6 bits (98), Expect = 3e-05
 Identities = 14/53 (26%), Positives = 20/53 (37%), Gaps = 3/53 (5%)

Query: 12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS 64
          C IC E         +++  CGH     CL++     SS     CP C +   
Sbjct: 18 CPICMESFTEEQLRPKLLH-CGHTICRQCLEKLLA--SSINGVRCPFCSKITR 67

>2ecj_A Tripartite motif-containing protein 39; TRIM39, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 58

 Score = 40.4 bits (95), Expect = 4e-05
 Identities = 20/50 (40%), Positives = 26/50 (52%), Gaps = 9/50 (18%)

Query: 11 ICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVC 59
           CS+C E LK P      VI  CGH F + C+ +W+E     +   CPVC
Sbjct: 17 SCSVCLEYLKEP------VIIECGHNFCKACITRWWE--DLERDFPCPVC 58

>3hcs_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.20A {Homo sapiens} Length = 170

 Score = 43.2 bits (101), Expect = 4e-05
 Identities = 14/58 (24%), Positives = 22/58 (37%), Gaps = 9/58 (15%)

Query: 9  KTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS 66
          K  C IC   L+  V+     + CGH F + C+ +            CPV  +    +
Sbjct: 18 KYECPICLMALREAVQ-----TPCGHRFCKACIIKS----IRDAGHKCPVDNEILLEN 66

>3hct_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 3hcu_A 2eci_A 2jmd_A Length = 118

 Score = 41.3 bits (97), Expect = 7e-05
 Identities = 13/58 (22%), Positives = 20/58 (34%), Gaps = 11/58 (18%)

Query: 11 ICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN 67
           C IC   L+        V + CGH F + C+ +            CPV  +    + 
Sbjct: 20 ECPICLMALREA------VQTPCGHRFCKACIIKSI----RDAGHKCPVDNEILLENQ 67

>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 Length = 117

 Score = 41.0 bits (96), Expect = 8e-05
 Identities = 13/56 (23%), Positives = 18/56 (32%), Gaps = 11/56 (19%)

Query: 12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN 67
          CS C   L+  V     +  C H+F   C+              CPVC       +
Sbjct: 25 CSRCTNILREPV----CLGGCEHIFCSNCVSDCIGTG-------CPVCYTPAWIQD 69

>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 39.9 bits (93), Expect = 9e-05
 Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 11/57 (19%)

Query: 11 ICSICYEDLKPIVEDLQVISICG-----HVFHELCLQQWFEYCSSSKKCTCPVCKQR 62
          IC IC+ +     ++  +I+ C      H  H+ CLQQW     SS    C +CK  
Sbjct: 17 ICRICHCEGD---DESPLITPCHCTGSLHFVHQACLQQWI---KSSDTRCCELCKYE 67

>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 63

 Score = 38.9 bits (91), Expect = 1e-04
 Identities = 18/50 (36%), Positives = 23/50 (46%), Gaps = 9/50 (18%)

Query: 11 ICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVC 59
          IC IC + L+ P      V   CGH F   C+ Q  E  +S     CP+C
Sbjct: 22 ICPICLDILQKP------VTIDCGHNFCLKCITQIGE--TSCGFFKCPLC 63

>1e4u_A Transcriptional repressor NOT4; gene regulation, transcriptional control; NMR {Homo sapiens} SCOP: g.44.1.1 PDB: 1ur6_B Length = 78

 Score = 38.5 bits (89), Expect = 3e-04
 Identities = 10/63 (15%), Positives = 22/63 (34%), Gaps = 5/63 (7%)

Query: 12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSIGD 71
          C +C E L+    +    + CG+     C  +     +      CP C++      ++  
Sbjct: 14 CPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGL----CPACRKPYPEDPAVYK 68

Query: 72 QID 74
           + 
Sbjct: 69 PLS 71

>3knv_A TNF receptor-associated factor 2; cross-brace, alternative splicing, apoptosis, cytoplasm, metal-binding, UBL conjugation, zinc, zinc-finger; 1.90A {Homo sapiens} Length = 141

 Score = 40.1 bits (93), Expect = 3e-04
 Identities = 13/55 (23%), Positives = 18/55 (32%), Gaps = 9/55 (16%)

Query: 11 ICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS 65
          +CS C   L+   +     + CGH +   CL        SS    C  C      
Sbjct: 33 LCSACRNVLRRPFQ-----AQCGHRYCSFCLASIL----SSGPQNCAACVHEGIY 78

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 56

 Score = 37.3 bits (87), Expect = 4e-04
 Identities = 13/62 (20%), Positives = 20/62 (32%), Gaps = 15/62 (24%)

Query: 4  ENKFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQR 62
          E +F    C  C  + K P       +  C H     CL+        +    CP+C+  
Sbjct: 1  EEEFQFLRCQQCQAEAKCP------KLLPCLHTLCSGCLE--------ASGMQCPICQAP 46

Query: 63 CS 64
            
Sbjct: 47 WP 48

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

 Score = 38.7 bits (89), Expect = 5e-04
 Identities = 12/63 (19%), Positives = 23/63 (36%), Gaps = 18/63 (28%)

Query: 12 CSICYEDLKPIVEDLQV-------------ISICGHVFHELCLQQWFEYCSSSKKCTCPV 58
          C+IC   +  +  + Q                +C H FH  C+ +W +      +  CP+
Sbjct: 40 CAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLK-----TRQVCPL 94

Query: 59 CKQ 61
            +
Sbjct: 95 DNR 97

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	466
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.27
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.27
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.26
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.25
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.25
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.24
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.24
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.23
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.23
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.23
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.23
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.23
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.22
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.22
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.22
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.21
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.21
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.21
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.2
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.2
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.2
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.19
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.19
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.19
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.17
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.17
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.16
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.15
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.15
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.15
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.13
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.13
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.11
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.11
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.11
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.1
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.09
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.09
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.09
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.07
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.05
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.05
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.05
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.04
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.03
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.01
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.01
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.0
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.98
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	98.95
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.93
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.91
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.85
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.81
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.81
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.8
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	98.79
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.78
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.77
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	98.76
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	98.71
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.71
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.64
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.57
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.5
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.44
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	98.4
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.16
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.12
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.01
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	96.99
3nw0_A	238	Non-structural maintenance of chromosomes element	96.87
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	96.17
1c1g_A	284	Tropomyosin; contractIle protein; 7.00A {Sus scrof	96.11
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	96.03
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	95.93
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	95.87
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	95.69
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	95.54
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	95.34
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	95.09
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	93.67
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	93.55
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	93.41
1ic2_A	81	Tropomyosin alpha chain, skeletal muscle; alpha-he	92.87
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	92.26
3u1c_A	101	Tropomyosin alpha-1 chain; anti-parallel coiled co	92.05
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	90.69
3u59_A	101	Tropomyosin beta chain; muscle contraction, actin,	90.6
3i2d_A	371	E3 SUMO-protein ligase SIZ1; signal transduction,	88.36
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	87.47
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	87.47
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	87.16
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	87.13
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	87.02
4fo9_A	360	E3 SUMO-protein ligase PIAS2; E3 ligase, pinit dom	86.21
3trt_A	77	Vimentin; cytoskeleton, intermediate filament, alp	86.04
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	83.68
1we9_A	64	PHD finger family protein; structural genomics, PH	83.55
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	82.67
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	82.23
2yt5_A	66	Metal-response element-binding transcription facto	81.99
1deb_A	54	APC protein, adenomatous polyposis coli protein; c	81.62

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

Probab=99.27  E-value=2.7e-12  Score=102.42  Aligned_cols=55  Identities=22%  Similarity=0.424  Sum_probs=46.1

Q ss_pred             CCCCCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            3 IENKFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         3 ~~~~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      .....+++.||||++.|. |+      +++|||+||..||..|+..    +...||+||.++....
T Consensus         2 ~~~~~~~~~C~IC~~~~~~Pv------~~~CgH~fc~~Ci~~~~~~----~~~~CP~C~~~~~~~~   57 (78)
T 1t1h_A            2 SPEFPEYFRCPISLELMKDPV------IVSTGQTYERSSIQKWLDA----GHKTCPKSQETLLHAG   57 (78)
T ss_dssp             CCCCSSSSSCTTTSCCCSSEE------EETTTEEEEHHHHHHHHTT----TCCBCTTTCCBCSSCC
T ss_pred             CcCCcccCCCCCccccccCCE------EcCCCCeecHHHHHHHHHH----CcCCCCCCcCCCChhh
Confidence            345567899999999998 54      7899999999999999982    4789999999987553

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

Probab=99.27  E-value=3e-12  Score=100.85  Aligned_cols=54  Identities=26%  Similarity=0.512  Sum_probs=44.8

Q ss_pred             CCCCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            4 ENKFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         4 ~~~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ....+.+.|+||++.|. |+     .+++|||+||..||..|+.     ....||+||..+...+
T Consensus        10 ~~~~~~~~C~IC~~~~~~p~-----~~~~CgH~fC~~Ci~~~~~-----~~~~CP~Cr~~~~~~~   64 (72)
T 2djb_A           10 SELTPYILCSICKGYLIDAT-----TITECLHTFCKSCIVRHFY-----YSNRCPKCNIVVHQTQ   64 (72)
T ss_dssp             CCCCGGGSCTTTSSCCSSCE-----ECSSSCCEECHHHHHHHHH-----HCSSCTTTCCCCCSSC
T ss_pred             hhcCCCCCCCCCChHHHCcC-----EECCCCCHHHHHHHHHHHH-----cCCcCCCcCcccCccc
Confidence            34456789999999997 53     2349999999999999998     4689999999998765

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

Probab=99.26  E-value=1.5e-12  Score=115.57  Aligned_cols=47  Identities=30%  Similarity=0.851  Sum_probs=41.3

Q ss_pred             Cccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            9 KTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         9 eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      +++|+||++.|. |+      ++||||+||..||..|+.     ....||+||.++...
T Consensus        53 ~~~C~iC~~~~~~~~------~~~CgH~fc~~Ci~~~~~-----~~~~CP~Cr~~~~~~  100 (138)
T 4ayc_A           53 ELQCIICSEYFIEAV------TLNCAHSFCSYCINEWMK-----RKIECPICRKDIKSK  100 (138)
T ss_dssp             HSBCTTTCSBCSSEE------EETTSCEEEHHHHHHHTT-----TCSBCTTTCCBCCCE
T ss_pred             cCCCcccCcccCCce------ECCCCCCccHHHHHHHHH-----cCCcCCCCCCcCCCC
Confidence            578999999998 53      789999999999999988     568899999998654

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

Probab=99.25  E-value=3.1e-12  Score=101.45  Aligned_cols=55  Identities=22%  Similarity=0.570  Sum_probs=44.9

Q ss_pred             CCCCCCccccccccccc-ccccCcceeec-CCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            4 ENKFGKTICSICYEDLK-PIVEDLQVISI-CGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         4 ~~~~~eltCpICLe~f~-P~~~~~~~llp-CGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ....+++.|+||++.|. |+      .++ |||+||..||..|+...   +...||+||.++...+
T Consensus        10 ~~~~~~~~C~IC~~~~~~p~------~~~~CgH~fC~~Ci~~~~~~~---~~~~CP~Cr~~~~~~~   66 (74)
T 2yur_A           10 DPIPDELLCLICKDIMTDAV------VIPCCGNSYCDECIRTALLES---DEHTCPTCHQNDVSPD   66 (74)
T ss_dssp             CCSCGGGSCSSSCCCCTTCE------ECSSSCCEECTTHHHHHHHHS---SSSCCSSSCCSSCCTT
T ss_pred             ccCCCCCCCcCCChHHhCCe------EcCCCCCHHHHHHHHHHHHhc---CCCcCCCCCCcCCCcc
Confidence            44556789999999998 54      688 99999999999999841   2478999999876554

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

Probab=99.25  E-value=3.4e-12  Score=98.81  Aligned_cols=56  Identities=30%  Similarity=0.711  Sum_probs=44.7

Q ss_pred             CCCCCccccccccccc-cc-ccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccC
Q 012292            5 NKFGKTICSICYEDLK-PI-VEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS   65 (466)
Q Consensus         5 ~~~~eltCpICLe~f~-P~-~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~   65 (466)
                      ...+...|+||++.|. +. ....+.+++|||+||..||..|+.     ....||+||..+..
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~-----~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           11 RPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLK-----NANTCPTCRKKINH   68 (69)
T ss_dssp             CTTCCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHH-----HCSSCTTTCCCCCC
T ss_pred             CCCCCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHH-----cCCCCCCCCCccCc
Confidence            4456789999999998 31 123335789999999999999998     46799999998864

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

Probab=99.24  E-value=4.4e-12  Score=104.31  Aligned_cols=52  Identities=21%  Similarity=0.572  Sum_probs=43.2

Q ss_pred             CCCCCCccccccccccc-ccccCcceeec-CCCcccHHHHHHHHHhcCCCCCCCCcCcCcccc
Q 012292            4 ENKFGKTICSICYEDLK-PIVEDLQVISI-CGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus         4 ~~~~~eltCpICLe~f~-P~~~~~~~llp-CGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~   64 (466)
                      +...+++.||||++.|. |+      +++ |||+||..||..|+...   +...||+||..+.
T Consensus         8 ~~~~~~~~C~IC~~~~~~p~------~~~~CgH~fC~~Ci~~~~~~~---~~~~CP~Cr~~~~   61 (92)
T 3ztg_A            8 DPIPDELLCLICKDIMTDAV------VIPCCGNSYCDECIRTALLES---DEHTCPTCHQNDV   61 (92)
T ss_dssp             CCCCTTTEETTTTEECSSCE------ECTTTCCEECHHHHHHHHHHC---TTCCCTTTCCSSC
T ss_pred             ccCCcCCCCCCCChhhcCce------ECCCCCCHHHHHHHHHHHHhc---CCCcCcCCCCcCC
Confidence            34456799999999998 54      788 99999999999999731   3479999999974

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

Probab=99.24  E-value=3.4e-12  Score=99.64  Aligned_cols=58  Identities=29%  Similarity=0.689  Sum_probs=46.4

Q ss_pred             CCCCCccccccccccc-cc-ccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            5 NKFGKTICSICYEDLK-PI-VEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         5 ~~~~eltCpICLe~f~-P~-~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ...++..|+||++.|. |. .......++|||+||..||..|+.     ....||+||..+...+
T Consensus         6 ~~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~-----~~~~CP~Cr~~~~~~~   65 (71)
T 3ng2_A            6 RPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLK-----NANTCPTCRKKINHKR   65 (71)
T ss_dssp             CCTTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHH-----HCSBCTTTCCBCCCCS
T ss_pred             CCCCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHH-----cCCCCCCCCCccChhh
Confidence            3456789999999997 41 123345789999999999999998     4579999999998654

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

Probab=99.23  E-value=4.6e-12  Score=101.95  Aligned_cols=49  Identities=27%  Similarity=0.614  Sum_probs=42.4

Q ss_pred             CCCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCcccc
Q 012292            5 NKFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus         5 ~~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~   64 (466)
                      .....+.|+||++.|. |+      +++|||+||..||..|+.     ....||+||.++.
T Consensus        11 ~~~~~~~C~IC~~~~~~p~------~~~CgH~fC~~Ci~~~~~-----~~~~CP~Cr~~~~   60 (81)
T 2csy_A           11 EEEIPFRCFICRQAFQNPV------VTKCRHYFCESCALEHFR-----ATPRCYICDQPTG   60 (81)
T ss_dssp             CCCCCSBCSSSCSBCCSEE------ECTTSCEEEHHHHHHHHH-----HCSBCSSSCCBCC
T ss_pred             cCCCCCCCcCCCchhcCee------EccCCCHhHHHHHHHHHH-----CCCcCCCcCcccc
Confidence            3445789999999998 53      789999999999999998     4679999999986

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

Probab=99.23  E-value=7.4e-12  Score=101.66  Aligned_cols=62  Identities=19%  Similarity=0.457  Sum_probs=48.6

Q ss_pred             CCCCCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            3 IENKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         3 ~~~~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      .+...+.+.|+||++.|.. ....+.+++|||+||..||..|+...  .....||+||..+....
T Consensus         9 ~~~~~~~~~C~IC~~~~~~-~~~~~~~~~CgH~fC~~Ci~~~~~~~--~~~~~CP~Cr~~~~~~~   70 (88)
T 2ct2_A            9 LDALREVLECPICMESFTE-EQLRPKLLHCGHTICRQCLEKLLASS--INGVRCPFCSKITRITS   70 (88)
T ss_dssp             CCCCCSCCBCTTTCCBCCT-TSSCEEECSSSCEEEHHHHHHHHHHC--SSCBCCTTTCCCBCCSS
T ss_pred             hhhccCCCCCccCCccccc-cCCCeEECCCCChhhHHHHHHHHHcC--CCCcCCCCCCCcccchh
Confidence            4556678899999999974 12335678999999999999999842  13589999999987653

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

Probab=99.23  E-value=5.9e-12  Score=97.36  Aligned_cols=53  Identities=26%  Similarity=0.510  Sum_probs=44.2

Q ss_pred             CCCCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            4 ENKFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         4 ~~~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      +...+.+.|+||++.+. |+      .++|||+||..||..|+.    .....||.||.++...
T Consensus        10 ~~~~~~~~C~IC~~~~~~p~------~~~CgH~fC~~Ci~~~~~----~~~~~CP~Cr~~~~~~   63 (66)
T 2ecy_A           10 KTVEDKYKCEKCHLVLCSPK------QTECGHRFCESCMAALLS----SSSPKCTACQESIVKD   63 (66)
T ss_dssp             CSCCCCEECTTTCCEESSCC------CCSSSCCCCHHHHHHHHT----TSSCCCTTTCCCCCTT
T ss_pred             hcCCcCCCCCCCChHhcCee------ECCCCCHHHHHHHHHHHH----hCcCCCCCCCcCCChh
Confidence            34456789999999998 54      579999999999999996    2567899999998754

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

Probab=99.23  E-value=5.2e-12  Score=93.73  Aligned_cols=52  Identities=29%  Similarity=0.750  Sum_probs=42.8

Q ss_pred             CCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCcccc
Q 012292            7 FGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus         7 ~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~   64 (466)
                      .....|+||++.|.. ....+..++|||+||..||..|+.     ....||+||..+.
T Consensus         3 ~~~~~C~IC~~~~~~-~~~~~~~~~CgH~fc~~Ci~~~~~-----~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            3 SGSSGCPICLEDIHT-SRVVAHVLPCGHLLHRTCYEEMLK-----EGYRCPLCSGPSS   54 (55)
T ss_dssp             SCCCSCTTTCCCCCT-TTSCEEECTTSCEEETTHHHHHHH-----HTCCCTTSCCSSC
T ss_pred             CCCCcCcccChhhcC-CCcCeEecCCCCcccHHHHHHHHH-----cCCcCCCCCCcCC
Confidence            456789999999963 224456889999999999999999     3489999999875

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

Probab=99.23  E-value=5e-12  Score=100.82  Aligned_cols=56  Identities=29%  Similarity=0.679  Sum_probs=45.5

Q ss_pred             CCCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            5 NKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         5 ~~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      .......|+||++.|...  .....++|||+||..||.+|+.     ....||+||..+....
T Consensus        11 ~~~~~~~C~IC~~~~~~~--~~~~~~~C~H~fc~~Ci~~~~~-----~~~~CP~Cr~~~~~~~   66 (78)
T 2ect_A           11 HVGSGLECPVCKEDYALG--ESVRQLPCNHLFHDSCIVPWLE-----QHDSCPVCRKSLTGQN   66 (78)
T ss_dssp             TSSSSCCCTTTTSCCCTT--SCEEECTTSCEEETTTTHHHHT-----TTCSCTTTCCCCCCSC
T ss_pred             cCCCCCCCeeCCccccCC--CCEEEeCCCCeecHHHHHHHHH-----cCCcCcCcCCccCCcc
Confidence            445678999999999721  2334679999999999999998     5579999999998765

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

Probab=99.22  E-value=8.6e-12  Score=97.09  Aligned_cols=56  Identities=25%  Similarity=0.644  Sum_probs=44.5

Q ss_pred             CCCCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            4 ENKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         4 ~~~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      +.......|+||++.|..  ...+..++|||.||..||..|+.     ....||+||..+...
T Consensus         9 ~~~~~~~~C~IC~~~~~~--~~~~~~~~C~H~fc~~Ci~~~~~-----~~~~CP~Cr~~~~~~   64 (69)
T 2kiz_A            9 TEEDTEEKCTICLSILEE--GEDVRRLPCMHLFHQVCVDQWLI-----TNKKCPICRVDIEAQ   64 (69)
T ss_dssp             CSTTCCCSBTTTTBCCCS--SSCEEECTTSCEEEHHHHHHHHH-----HCSBCTTTCSBSCSC
T ss_pred             CcCCCCCCCeeCCccccC--CCcEEEeCCCCHHHHHHHHHHHH-----cCCCCcCcCccccCc
Confidence            345567899999999962  12345789999999999999998     456799999988754

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

Probab=99.22  E-value=6.4e-12  Score=98.70  Aligned_cols=54  Identities=33%  Similarity=0.646  Sum_probs=44.0

Q ss_pred             CCCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            5 NKFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         5 ~~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      ...+.+.|+||++.|. |+      +++|||+||..||..|+..  .+....||+||..+...
T Consensus        16 ~~~~~~~C~IC~~~~~~~~------~~~CgH~fC~~Ci~~~~~~--~~~~~~CP~Cr~~~~~~   70 (73)
T 2ysl_A           16 KLQEEVICPICLDILQKPV------TIDCGHNFCLKCITQIGET--SCGFFKCPLCKTSVRKN   70 (73)
T ss_dssp             CCCCCCBCTTTCSBCSSEE------ECTTCCEEEHHHHHHHCSS--SCSCCCCSSSCCCCCCC
T ss_pred             hCccCCEeccCCcccCCeE------EcCCCChhhHHHHHHHHHc--CCCCCCCCCCCCcCCcc
Confidence            3456789999999998 43      6799999999999999862  12467999999998754

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

Probab=99.22  E-value=4.4e-12  Score=99.61  Aligned_cols=52  Identities=25%  Similarity=0.451  Sum_probs=43.3

Q ss_pred             CCCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            5 NKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         5 ~~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      ...+...|+||++.+...     ..++|||+||..||..|+.     ....||+||..+...
T Consensus        11 ~~~~~~~C~IC~~~~~~~-----~~~~CgH~fC~~Ci~~~~~-----~~~~CP~Cr~~~~~~   62 (71)
T 2d8t_A           11 PSLTVPECAICLQTCVHP-----VSLPCKHVFCYLCVKGASW-----LGKRCALCRQEIPED   62 (71)
T ss_dssp             SSSSCCBCSSSSSBCSSE-----EEETTTEEEEHHHHHHCTT-----CSSBCSSSCCBCCHH
T ss_pred             cCCCCCCCccCCcccCCC-----EEccCCCHHHHHHHHHHHH-----CCCcCcCcCchhCHh
Confidence            345678999999999832     3689999999999999987     568999999998744

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

Probab=99.21  E-value=9.9e-12  Score=99.88  Aligned_cols=57  Identities=32%  Similarity=0.623  Sum_probs=45.9

Q ss_pred             CCCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcC-CCCCCCCcCcCccccCCC
Q 012292            5 NKFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCS-SSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         5 ~~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~-~~~s~~CP~CR~~~~~~~   67 (466)
                      ...+.+.|+||++.|. |+      +++|||+||..||..|+.... .+....||.||..+....
T Consensus        15 ~~~~~~~C~IC~~~~~~p~------~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~   73 (85)
T 2ecw_A           15 MIKEEVTCPICLELLKEPV------SADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGN   73 (85)
T ss_dssp             CCCTTTSCTTTCSCCSSCE------ECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTTC
T ss_pred             hCccCCCCcCCChhhCcce------eCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHHh
Confidence            3456789999999998 53      789999999999999998532 123689999999988654

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

Probab=99.21  E-value=9.6e-12  Score=95.87  Aligned_cols=54  Identities=26%  Similarity=0.584  Sum_probs=43.2

Q ss_pred             CCcccccccc-ccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            8 GKTICSICYE-DLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         8 ~eltCpICLe-~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ++..||||++ .|. |.  ....+++|||+||..||.+|+..    +...||.||.++...+
T Consensus         2 ~~~~C~IC~~~~~~~~~--~~~~~~~CgH~fC~~Ci~~~~~~----~~~~CP~Cr~~~~~~~   57 (65)
T 1g25_A            2 DDQGCPRCKTTKYRNPS--LKLMVNVCGHTLCESCVDLLFVR----GAGNCPECGTPLRKSN   57 (65)
T ss_dssp             CTTCCSTTTTHHHHCSS--CCEEECTTCCCEEHHHHHHHHHT----TSSSCTTTCCCCSSCC
T ss_pred             CCCcCCcCCCCccCCCc--cCeecCCCCCHhHHHHHHHHHHc----CCCcCCCCCCcccccc
Confidence            4689999999 776 42  22246799999999999999872    4578999999998654

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

Probab=99.21  E-value=3e-12  Score=107.53  Aligned_cols=50  Identities=22%  Similarity=0.638  Sum_probs=42.3

Q ss_pred             CCccccccccccc-ccccCccee-ecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            8 GKTICSICYEDLK-PIVEDLQVI-SICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         8 ~eltCpICLe~f~-P~~~~~~~l-lpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      +++.|+||++.|. |+      . ++|||+||..||..|+..    ....||.||.++....
T Consensus        21 ~~~~C~IC~~~~~~p~------~~~~CgH~FC~~Ci~~~~~~----~~~~CP~Cr~~~~~~~   72 (100)
T 3lrq_A           21 EVFRCFICMEKLRDAR------LCPHCSKLCCFSCIRRWLTE----QRAQCPHCRAPLQLRE   72 (100)
T ss_dssp             HHTBCTTTCSBCSSEE------ECTTTCCEEEHHHHHHHHHH----TCSBCTTTCCBCCGGG
T ss_pred             CCCCCccCCccccCcc------ccCCCCChhhHHHHHHHHHH----CcCCCCCCCCcCCHHH
Confidence            4689999999998 54      5 899999999999999994    2379999999997553

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

Probab=99.20  E-value=6.7e-12  Score=99.49  Aligned_cols=54  Identities=30%  Similarity=0.814  Sum_probs=43.9

Q ss_pred             CCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            6 KFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         6 ~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      ..+...|+||++.|...  .....++|||.||..||..|+.     ....||+||..+...
T Consensus        20 ~~~~~~C~IC~~~~~~~--~~~~~l~C~H~fh~~Ci~~w~~-----~~~~CP~Cr~~~~~~   73 (75)
T 1x4j_A           20 QSEQTLCVVCMCDFESR--QLLRVLPCNHEFHAKCVDKWLK-----ANRTCPICRADSGPS   73 (75)
T ss_dssp             SSSCCEETTTTEECCBT--CEEEEETTTEEEETTHHHHHHH-----HCSSCTTTCCCCCCC
T ss_pred             cCCCCCCeECCcccCCC--CeEEEECCCCHhHHHHHHHHHH-----cCCcCcCcCCcCCCC
Confidence            44678999999999731  2345689999999999999998     457899999988754

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

Probab=99.20  E-value=3.2e-12  Score=101.89  Aligned_cols=58  Identities=29%  Similarity=0.538  Sum_probs=45.8

Q ss_pred             CCCCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcC--CCCCCCCcCcCccccCCC
Q 012292            4 ENKFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCS--SSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         4 ~~~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~--~~~s~~CP~CR~~~~~~~   67 (466)
                      ....+.+.|+||++.|. |+      +++|||+||..||..|+....  .+....||.||..+....
T Consensus         7 ~~~~~~~~C~IC~~~~~~p~------~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~~   67 (79)
T 2egp_A            7 GNVQEEVTCPICLELLTEPL------SLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEH   67 (79)
T ss_dssp             CCCCCCCEETTTTEECSSCC------CCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSSG
T ss_pred             hhcccCCCCcCCCcccCCee------ECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHhh
Confidence            34556889999999998 54      689999999999999987311  123679999999998654

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

Probab=99.20  E-value=6.9e-12  Score=95.65  Aligned_cols=55  Identities=29%  Similarity=0.699  Sum_probs=44.4

Q ss_pred             CCccccccccccc-cc-ccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            8 GKTICSICYEDLK-PI-VEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         8 ~eltCpICLe~f~-P~-~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      +...|+||++.|. |. ....+..++|||+||..|+..|+.     ....||.||.++...+
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~-----~~~~CP~Cr~~~~~~~   58 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLK-----NANTCPTCRKKINHKR   58 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHH-----HCSBCTTTCCBCTTTC
T ss_pred             CCCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHH-----cCCCCCCCCccCCccc
Confidence            4679999999997 31 123345789999999999999998     4679999999988654

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

Probab=99.19  E-value=7e-12  Score=109.01  Aligned_cols=48  Identities=27%  Similarity=0.611  Sum_probs=41.7

Q ss_pred             CCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccC
Q 012292            8 GKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS   65 (466)
Q Consensus         8 ~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~   65 (466)
                      +.++||||++.|. |+      +++|||+||..||..|+..    +...||.||.++..
T Consensus        51 ~~~~C~IC~~~~~~p~------~~~CgH~fC~~Ci~~~~~~----~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           51 ETFQCICCQELVFRPI------TTVCQHNVCKDCLDRSFRA----QVFSCPACRYDLGR   99 (124)
T ss_dssp             HHTBCTTTSSBCSSEE------ECTTSCEEEHHHHHHHHHT----TCCBCTTTCCBCCT
T ss_pred             cCCCCCcCChHHcCcE------EeeCCCcccHHHHHHHHhH----CcCCCCCCCccCCC
Confidence            4578999999998 54      7899999999999999982    45699999999986

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

Probab=99.19  E-value=1.3e-11  Score=97.32  Aligned_cols=56  Identities=34%  Similarity=0.755  Sum_probs=44.1

Q ss_pred             CCCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            5 NKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         5 ~~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ....+..|+||++.|...  .....++|||.||..||..|+.     ....||+||.++....
T Consensus        11 ~~~~~~~C~IC~~~~~~~--~~~~~~~C~H~f~~~Ci~~~~~-----~~~~CP~Cr~~~~~~~   66 (74)
T 2ep4_A           11 ELNLHELCAVCLEDFKPR--DELGICPCKHAFHRKCLIKWLE-----VRKVCPLCNMPVLQLA   66 (74)
T ss_dssp             CCCCSCBCSSSCCBCCSS--SCEEEETTTEEEEHHHHHHHHH-----HCSBCTTTCCBCSSCC
T ss_pred             cCCCCCCCcCCCcccCCC--CcEEEcCCCCEecHHHHHHHHH-----cCCcCCCcCccccccc
Confidence            345578999999999731  2234569999999999999998     3468999999987543

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

Probab=99.19  E-value=1.1e-11  Score=102.37  Aligned_cols=53  Identities=30%  Similarity=0.692  Sum_probs=43.5

Q ss_pred             CCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccC
Q 012292            6 KFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS   65 (466)
Q Consensus         6 ~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~   65 (466)
                      ...+..|+||++.|..  ......++|||.||..||..|+.     ....||+||..+..
T Consensus        37 ~~~~~~C~IC~~~~~~--~~~~~~l~C~H~Fh~~Ci~~wl~-----~~~~CP~Cr~~~~~   89 (91)
T 2l0b_A           37 VGQEMCCPICCSEYVK--GDVATELPCHHYFHKPCVSIWLQ-----KSGTCPVCRCMFPP   89 (91)
T ss_dssp             SSSCSEETTTTEECCT--TCEEEEETTTEEEEHHHHHHHHT-----TTCBCTTTCCBSSC
T ss_pred             cCCCCCCcccChhhcC--CCcEEecCCCChHHHHHHHHHHH-----cCCcCcCcCccCCC
Confidence            3457789999999973  13345689999999999999998     56799999998864

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

Probab=99.17  E-value=1.4e-11  Score=98.96  Aligned_cols=57  Identities=32%  Similarity=0.656  Sum_probs=45.6

Q ss_pred             CCCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcC-CCCCCCCcCcCccccCCC
Q 012292            5 NKFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCS-SSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         5 ~~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~-~~~s~~CP~CR~~~~~~~   67 (466)
                      ...+.+.|+||++.|. |.      .++|||+||..|+..|+.... .++...||.||..+....
T Consensus        15 ~~~~~~~C~IC~~~~~~p~------~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~   73 (85)
T 2ecv_A           15 NVKEEVTCPICLELLTQPL------SLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPEN   73 (85)
T ss_dssp             CCCCCCCCTTTCSCCSSCB------CCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSS
T ss_pred             HccCCCCCCCCCcccCCce------eCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHh
Confidence            3456789999999998 43      679999999999999998411 123689999999998654

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

Probab=99.17  E-value=1.1e-11  Score=92.16  Aligned_cols=51  Identities=27%  Similarity=0.725  Sum_probs=41.1

Q ss_pred             CCCcccccccccccccccCcceeec-CCCcccHHHHHHHHHhcCCCCCCCCcCcCcccc
Q 012292            7 FGKTICSICYEDLKPIVEDLQVISI-CGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus         7 ~~eltCpICLe~f~P~~~~~~~llp-CGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~   64 (466)
                      .+...|+||++.|...  .....++ |||.||..||..|+.     ....||+||.++.
T Consensus         3 ~~~~~C~IC~~~~~~~--~~~~~~~~C~H~f~~~Ci~~w~~-----~~~~CP~Cr~~~~   54 (55)
T 1iym_A            3 DDGVECAVCLAELEDG--EEARFLPRCGHGFHAECVDMWLG-----SHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTT--SCCEECSSSCCEECTTHHHHTTT-----TCCSCSSSCCCSC
T ss_pred             CCCCcCccCCccccCC--CceEECCCCCCcccHHHHHHHHH-----cCCcCcCCCCEeE
Confidence            4567999999999741  2234565 999999999999987     5678999999874

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

Probab=99.16  E-value=1.5e-11  Score=103.64  Aligned_cols=52  Identities=12%  Similarity=0.077  Sum_probs=45.0

Q ss_pred             CCCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            5 NKFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         5 ~~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ..-+++.||||++.|. |+      +++|||+||..||..|+.     ...+||+||.+++...
T Consensus        25 ~~p~~~~CpI~~~~m~dPV------~~~cGhtf~r~~I~~~l~-----~~~~cP~~~~~l~~~~   77 (100)
T 2kre_A           25 DAPDEFRDPLMDTLMTDPV------RLPSGTIMDRSIILRHLL-----NSPTDPFNRQTLTESM   77 (100)
T ss_dssp             SCSTTTBCTTTCSBCSSEE------EETTTEEEEHHHHHHHTT-----SCSBCSSSCCBCCTTS
T ss_pred             cCcHhhCCcCccCcccCCe------ECCCCCEEchHHHHHHHH-----cCCCCCCCCCCCChhh
Confidence            4456799999999998 65      789999999999999988     4689999999988654

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

Probab=99.15  E-value=1.9e-11  Score=99.92  Aligned_cols=52  Identities=13%  Similarity=0.069  Sum_probs=44.5

Q ss_pred             CCCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            5 NKFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         5 ~~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ..-+++.||||++.|. |+      +++|||+||..||..|+.     ...+||+||.++....
T Consensus        10 ~~p~~~~CpI~~~~m~dPV------~~~cGhtf~r~~I~~~l~-----~~~~cP~~~~~l~~~~   62 (85)
T 2kr4_A           10 DAPDEFRDPLMDTLMTDPV------RLPSGTVMDRSIILRHLL-----NSPTDPFNRQMLTESM   62 (85)
T ss_dssp             TCCTTTBCTTTCSBCSSEE------ECTTSCEEEHHHHHHHHH-----HCSBCTTTCCBCCGGG
T ss_pred             cCchheECcccCchhcCCe------ECCCCCEECHHHHHHHHh-----cCCCCCCCcCCCChHh
Confidence            3456899999999998 65      789999999999999998     3579999999887543

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

Probab=99.15  E-value=1.7e-11  Score=104.10  Aligned_cols=49  Identities=20%  Similarity=0.556  Sum_probs=42.4

Q ss_pred             CCCccccccccccc-ccccCcceee-cCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            7 FGKTICSICYEDLK-PIVEDLQVIS-ICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         7 ~~eltCpICLe~f~-P~~~~~~~ll-pCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      .+++.|+||++.|. |+      .+ +|||+||..||..|+.     ....||.||..+...
T Consensus        13 ~~~~~C~IC~~~~~~p~------~~~~CgH~fC~~Ci~~~~~-----~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           13 NPHLMCVLCGGYFIDAT------TIIECLHSFCKTCIVRYLE-----TSKYCPICDVQVHKT   63 (108)
T ss_dssp             GGGTBCTTTSSBCSSEE------EETTTCCEEEHHHHHHHHT-----SCSBCTTTCCBSCSS
T ss_pred             CCcCCCccCChHHhCcC------EeCCCCChhhHHHHHHHHH-----hCCcCcCCCcccccc
Confidence            45789999999998 54      55 9999999999999998     468999999998754

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

Probab=99.15  E-value=1.4e-11  Score=95.44  Aligned_cols=49  Identities=33%  Similarity=0.701  Sum_probs=41.7

Q ss_pred             CCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccC
Q 012292            7 FGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS   65 (466)
Q Consensus         7 ~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~   65 (466)
                      .....|+||++.+. |+     ..++|||+||..|+..|+.     ....||.||.++..
T Consensus         3 ~~~~~C~IC~~~~~~~~-----~~~~C~H~fc~~Ci~~~~~-----~~~~CP~Cr~~~~~   52 (68)
T 1chc_A            3 TVAERCPICLEDPSNYS-----MALPCLHAFCYVCITRWIR-----QNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCCSSCCSCCCSCE-----EETTTTEEESTTHHHHHHH-----HSCSTTTTCCCCCC
T ss_pred             CCCCCCeeCCccccCCc-----EecCCCCeeHHHHHHHHHh-----CcCcCcCCChhhHh
Confidence            34678999999997 32     5789999999999999998     45799999998874

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

Probab=99.13  E-value=1.8e-11  Score=102.21  Aligned_cols=48  Identities=27%  Similarity=0.758  Sum_probs=41.1

Q ss_pred             CCccccccccccc-ccccCcceee-cCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            8 GKTICSICYEDLK-PIVEDLQVIS-ICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         8 ~eltCpICLe~f~-P~~~~~~~ll-pCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      +.+.|+||++.|. |+      .+ +|||+||..||..|+.     ....||+||..+...
T Consensus        21 ~~~~C~IC~~~~~~p~------~~~~CgH~fC~~Ci~~~~~-----~~~~CP~Cr~~~~~~   70 (99)
T 2y43_A           21 DLLRCGICFEYFNIAM------IIPQCSHNYCSLCIRKFLS-----YKTQCPTCCVTVTEP   70 (99)
T ss_dssp             HHTBCTTTCSBCSSEE------ECTTTCCEEEHHHHHHHHT-----TCCBCTTTCCBCCGG
T ss_pred             CCCCcccCChhhCCcC------EECCCCCHhhHHHHHHHHH-----CCCCCCCCCCcCChh
Confidence            3578999999998 53      45 8999999999999998     568999999998754

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

Probab=99.13  E-value=4.1e-11  Score=91.63  Aligned_cols=47  Identities=36%  Similarity=0.715  Sum_probs=38.8

Q ss_pred             CCCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCc
Q 012292            5 NKFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVC   59 (466)
Q Consensus         5 ~~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~C   59 (466)
                      ...+++.|+||++.|. |+      .++|||+||..||.+|+..  .+....||+|
T Consensus        16 ~~~~~~~C~IC~~~~~~p~------~~~CgH~fC~~Ci~~~~~~--~~~~~~CP~C   63 (63)
T 2ysj_A           16 KLQEEVICPICLDILQKPV------TIDCGHNFCLKCITQIGET--SCGFFKCPLC   63 (63)
T ss_dssp             CCCCCCBCTTTCSBCSSCE------ECTTSSEECHHHHHHHHHH--CSSCCCCSCC
T ss_pred             hCccCCCCCcCCchhCCeE------EeCCCCcchHHHHHHHHHc--CCCCCcCcCC
Confidence            3456789999999998 53      6799999999999999984  1246789998

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

Probab=99.11  E-value=4.5e-11  Score=96.29  Aligned_cols=57  Identities=21%  Similarity=0.528  Sum_probs=43.4

Q ss_pred             CCCCCCcccccccccccccccCcceee--cCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            4 ENKFGKTICSICYEDLKPIVEDLQVIS--ICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         4 ~~~~~eltCpICLe~f~P~~~~~~~ll--pCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ....++++||||++.+..  .+. .+.  +|||+||..|+..|+..    ....||.||.++....
T Consensus         6 ~~~~~~~~CpICle~~~~--~d~-~~~p~~CGH~fC~~Cl~~~~~~----~~~~CP~CR~~~~~~~   64 (78)
T 1e4u_A            6 DAKEDPVECPLCMEPLEI--DDI-NFFPCTCGYQICRFCWHRIRTD----ENGLCPACRKPYPEDP   64 (78)
T ss_dssp             CCCCCCCBCTTTCCBCCT--TTT-TCCSSTTSCCCCHHHHHHHTTS----SCSBCTTTCCBCSSCS
T ss_pred             cccccCCcCCccCccCcc--ccc-cccccCCCCCcCHHHHHHHHhc----CCCCCCCCCCccCCCc
Confidence            345678999999998851  011 234  49999999999998752    4689999999998765

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

Probab=99.11  E-value=1.3e-11  Score=96.36  Aligned_cols=53  Identities=25%  Similarity=0.758  Sum_probs=44.7

Q ss_pred             CCCCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            4 ENKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         4 ~~~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ....+...|+||++.+..      .+++|||+||..||..|+.     ....||+||.++....
T Consensus        10 ~~~~~~~~C~IC~~~~~~------~~~~CgH~fc~~Ci~~~~~-----~~~~CP~Cr~~~~~~~   62 (70)
T 2ecn_A           10 KQLTDEEECCICMDGRAD------LILPCAHSFCQKCIDKWSD-----RHRNCPICRLQMTGAN   62 (70)
T ss_dssp             CCCCCCCCCSSSCCSCCS------EEETTTEEECHHHHHHSSC-----CCSSCHHHHHCTTCCC
T ss_pred             hcCCCCCCCeeCCcCccC------cccCCCCcccHHHHHHHHH-----CcCcCCCcCCcccCCC
Confidence            344567899999999864      4789999999999999987     6789999999988654

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

Probab=99.11  E-value=5e-11  Score=101.78  Aligned_cols=60  Identities=27%  Similarity=0.526  Sum_probs=44.5

Q ss_pred             CCcccccccccccccc-------------cCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            8 GKTICSICYEDLKPIV-------------EDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         8 ~eltCpICLe~f~P~~-------------~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      .+..|+||++.|....             .....+++|||.||..||..|+..........||+||..+....
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~~   96 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKT   96 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCS
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCCC
Confidence            4569999999996211             01233789999999999999996433235689999999987553

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

Probab=99.10  E-value=5.3e-11  Score=99.95  Aligned_cols=52  Identities=8%  Similarity=0.072  Sum_probs=44.7

Q ss_pred             CCCCCccccccccccc-ccccCcceeecCC-CcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            5 NKFGKTICSICYEDLK-PIVEDLQVISICG-HVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         5 ~~~~eltCpICLe~f~-P~~~~~~~llpCG-HsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ..-+++.||||++.|. |+      +++|| |+||..||..|+.     ...+||+||.++....
T Consensus        18 ~~p~~~~CpI~~~~m~dPV------~~~cG~htf~r~cI~~~l~-----~~~~cP~~~~~l~~~~   71 (98)
T 1wgm_A           18 DACDEFLDPIMSTLMCDPV------VLPSSRVTVDRSTIARHLL-----SDQTDPFNRSPLTMDQ   71 (98)
T ss_dssp             SCCTTTBCTTTCSBCSSEE------ECTTTCCEEEHHHHHHHTT-----TSCBCTTTCSBCCTTT
T ss_pred             cCcHhcCCcCccccccCCe------ECCCCCeEECHHHHHHHHH-----hCCCCCCCCCCCChhh
Confidence            3456789999999998 65      78999 9999999999998     3579999999987654

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

Probab=99.09  E-value=3.8e-11  Score=108.33  Aligned_cols=49  Identities=27%  Similarity=0.613  Sum_probs=42.3

Q ss_pred             CCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            8 GKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         8 ~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      +.+.|+||++.|. |+      +++|||+||..||..|+..    ....||+||..+...
T Consensus        77 ~~~~C~IC~~~~~~pv------~~~CgH~fC~~Ci~~~~~~----~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           77 QSFMCVCCQELVYQPV------TTECFHNVCKDCLQRSFKA----QVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHTBCTTTSSBCSSEE------ECTTSCEEEHHHHHHHHHT----TCCBCTTTCCBCCTT
T ss_pred             cCCEeecCChhhcCCE------EcCCCCchhHHHHHHHHHh----CCCcCCCCCccCCCC
Confidence            4578999999998 54      6899999999999999982    446899999999866

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

Probab=99.09  E-value=5.3e-11  Score=101.04  Aligned_cols=51  Identities=27%  Similarity=0.735  Sum_probs=42.1

Q ss_pred             Cccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            9 KTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         9 eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      .+.|+||++.|. |+      .++|||+||..||..|+...  .+...||+||.++....
T Consensus        21 ~~~C~IC~~~~~~p~------~~~CgH~fC~~Ci~~~~~~~--~~~~~CP~Cr~~~~~~~   72 (112)
T 1jm7_A           21 ILECPICLELIKEPV------STKCDHIFCKFCMLKLLNQK--KGPSQCPLCKNDITKRS   72 (112)
T ss_dssp             HTSCSSSCCCCSSCC------BCTTSCCCCSHHHHHHHHSS--SSSCCCTTTSCCCCTTT
T ss_pred             CCCCcccChhhcCeE------ECCCCCHHHHHHHHHHHHhC--CCCCCCcCCCCcCCHhh
Confidence            578999999998 54      68999999999999999832  13468999999988654

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

Probab=99.09  E-value=5.9e-11  Score=95.90  Aligned_cols=54  Identities=26%  Similarity=0.664  Sum_probs=41.8

Q ss_pred             CCcccccccccccc----------cccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            8 GKTICSICYEDLKP----------IVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         8 ~eltCpICLe~f~P----------~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      ++..|+||++.|..          ..+....+++|||.||..||.+|+.     ...+||+||.++...
T Consensus        14 ~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~-----~~~~CP~CR~~~~~~   77 (81)
T 2ecl_A           14 ECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVK-----QNNRCPLCQQDWVVQ   77 (81)
T ss_dssp             CCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTT-----TCCBCTTTCCBCCEE
T ss_pred             CCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHH-----hCCCCCCcCCCcchh
Confidence            56789999999963          1222344556999999999999998     567999999988643

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

Probab=99.07  E-value=1e-11  Score=106.43  Aligned_cols=50  Identities=34%  Similarity=0.731  Sum_probs=42.1

Q ss_pred             CCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccC
Q 012292            6 KFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS   65 (466)
Q Consensus         6 ~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~   65 (466)
                      ..+++.|+||++.|. |+      +++|||+||..||..|+..    +...||.||..+..
T Consensus        12 ~~~~~~C~iC~~~~~~p~------~~~CgH~fC~~Ci~~~~~~----~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           12 SLSECQCGICMEILVEPV------TLPCNHTLCKPCFQSTVEK----ASLCCPFCRRRVSS   62 (115)
T ss_dssp             CHHHHBCTTTCSBCSSCE------ECTTSCEECHHHHCCCCCT----TTSBCTTTCCBCHH
T ss_pred             CCCCCCCccCCcccCcee------EcCCCCHHhHHHHHHHHhH----CcCCCCCCCcccCc
Confidence            344688999999998 54      6799999999999999862    46899999998874

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

Probab=99.05  E-value=8.3e-11  Score=88.01  Aligned_cols=47  Identities=43%  Similarity=0.984  Sum_probs=38.3

Q ss_pred             CCCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCc
Q 012292            5 NKFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVC   59 (466)
Q Consensus         5 ~~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~C   59 (466)
                      ...+...|+||++.|. |+      +++|||+||..||..|+..  ......||+|
T Consensus        11 ~~~~~~~C~IC~~~~~~p~------~~~CgH~fC~~Ci~~~~~~--~~~~~~CP~C   58 (58)
T 2ecj_A           11 NLQVEASCSVCLEYLKEPV------IIECGHNFCKACITRWWED--LERDFPCPVC   58 (58)
T ss_dssp             CSCCCCBCSSSCCBCSSCC------CCSSCCCCCHHHHHHHTTS--SCCSCCCSCC
T ss_pred             ccccCCCCccCCcccCccE------eCCCCCccCHHHHHHHHHh--cCCCCCCCCC
Confidence            3456789999999998 53      6899999999999999762  1256899998

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

Probab=99.05  E-value=3.3e-11  Score=90.59  Aligned_cols=49  Identities=24%  Similarity=0.557  Sum_probs=40.9

Q ss_pred             CCCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            5 NKFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         5 ~~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ...+.+.|+||++.|. |.      +++|||+||..|+..|        ...||+||..+....
T Consensus         2 ee~~~~~C~IC~~~~~~p~------~l~CgH~fC~~Ci~~~--------~~~CP~Cr~~~~~~~   51 (56)
T 1bor_A            2 EEFQFLRCQQCQAEAKCPK------LLPCLHTLCSGCLEAS--------GMQCPICQAPWPLGA   51 (56)
T ss_dssp             CSCCCSSCSSSCSSCBCCS------CSTTSCCSBTTTCSSS--------SSSCSSCCSSSSCCS
T ss_pred             CcccCCCceEeCCccCCeE------EcCCCCcccHHHHccC--------CCCCCcCCcEeecCC
Confidence            3467899999999998 54      7899999999998763        478999999987653

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

Probab=99.05  E-value=6.4e-11  Score=107.91  Aligned_cols=50  Identities=26%  Similarity=0.618  Sum_probs=41.4

Q ss_pred             CCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            8 GKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         8 ~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      ..+.|+||++.|. |+     .+++|||+||..||..|+..    +...||+||.++...
T Consensus        53 ~~~~C~IC~~~~~~p~-----~~~~CgH~fC~~Ci~~~~~~----~~~~CP~Cr~~~~~~  103 (165)
T 2ckl_B           53 SELMCPICLDMLKNTM-----TTKECLHRFCADCIITALRS----GNKECPTCRKKLVSK  103 (165)
T ss_dssp             HHHBCTTTSSBCSSEE-----EETTTCCEEEHHHHHHHHHT----TCCBCTTTCCBCCSG
T ss_pred             CCCCCcccChHhhCcC-----EeCCCCChhHHHHHHHHHHh----CcCCCCCCCCcCCCc
Confidence            4569999999998 53     33499999999999999982    368899999998654

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=99.04  E-value=9.5e-11  Score=114.15  Aligned_cols=53  Identities=13%  Similarity=0.201  Sum_probs=44.3

Q ss_pred             CCCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            5 NKFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         5 ~~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ..-..+.||||++.|. |+      +++|||+||..||..|+..    +..+||+||.+++...
T Consensus       204 ~~~~~~~c~i~~~~~~dPv------~~~~gh~f~~~~i~~~~~~----~~~~cP~~~~~~~~~~  257 (281)
T 2c2l_A          204 DIPDYLCGKISFELMREPC------ITPSGITYDRKDIEEHLQR----VGHFNPVTRSPLTQEQ  257 (281)
T ss_dssp             CCCSTTBCTTTCSBCSSEE------ECSSCCEEETTHHHHHHHH----TCSSCTTTCCCCCGGG
T ss_pred             CCCcccCCcCcCCHhcCCe------ECCCCCEECHHHHHHHHHH----CCCCCcCCCCCCchhc
Confidence            4456889999999998 65      7899999999999999984    2345999999997654

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

Probab=99.03  E-value=9.8e-11  Score=101.62  Aligned_cols=57  Identities=30%  Similarity=0.696  Sum_probs=45.8

Q ss_pred             CCCCccccccccccc-cc-ccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            6 KFGKTICSICYEDLK-PI-VEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         6 ~~~eltCpICLe~f~-P~-~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ..+.+.|+||++.|. |+ ..+....++|||+||..||.+|+.     ....||+||..+....
T Consensus         4 ~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~-----~~~~CP~Cr~~~~~~~   62 (133)
T 4ap4_A            4 GSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLK-----NANTCPTCRKKINHKR   62 (133)
T ss_dssp             -CCSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHT-----TCSBCTTTCCBCTTTC
T ss_pred             CCCCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHH-----hCCCCCCCCCcCcccc
Confidence            356789999999997 41 123335789999999999999998     5679999999998665

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

Probab=99.01  E-value=1e-10  Score=100.85  Aligned_cols=53  Identities=25%  Similarity=0.480  Sum_probs=44.0

Q ss_pred             CCCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            5 NKFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         5 ~~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ...+.+.|+||++.|. |+      .++|||+||..||..|+..    ....||+||.++....
T Consensus        14 ~~~~~~~C~IC~~~~~~p~------~~~CgH~fC~~Ci~~~~~~----~~~~CP~Cr~~~~~~~   67 (118)
T 3hct_A           14 PLESKYECPICLMALREAV------QTPCGHRFCKACIIKSIRD----AGHKCPVDNEILLENQ   67 (118)
T ss_dssp             CCCGGGBCTTTCSBCSSEE------ECTTSCEEEHHHHHHHHHH----HCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCCcCChhhcCeE------ECCcCChhhHHHHHHHHhh----CCCCCCCCCCCcCHHh
Confidence            4456789999999998 53      6899999999999999984    2349999999988654

>2yu4_A E3 SUMO-protein ligase NSE2; SP-ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.01  E-value=2.2e-10  Score=95.15  Aligned_cols=57  Identities=28%  Similarity=0.567  Sum_probs=44.2

Q ss_pred             CCCCCccccccccccc-ccccCcceeec-CCCcccHHHHHHHHHhc-CCCCCCCCcC--cCcc-ccCCC
Q 012292            5 NKFGKTICSICYEDLK-PIVEDLQVISI-CGHVFHELCLQQWFEYC-SSSKKCTCPV--CKQR-CSSSN   67 (466)
Q Consensus         5 ~~~~eltCpICLe~f~-P~~~~~~~llp-CGHsFC~~CL~~wle~~-~~~~s~~CP~--CR~~-~~~~~   67 (466)
                      +....+.||||++.|. |+      +++ |||+||..||..||... ..++...||+  |+.. +....
T Consensus         3 ~~~~~~~CPI~~~~~~dPV------~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~~~~   65 (94)
T 2yu4_A            3 SGSSGFTCPITKEEMKKPV------KNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRKSD   65 (94)
T ss_dssp             SCSSCCBCTTTCSBCSSEE------EESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBCGGG
T ss_pred             CCCcEeECcCcCchhcCCE------EcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccCHhh
Confidence            3456789999999998 65      675 99999999999999842 1123579999  9877 55443

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

Probab=99.00  E-value=1.5e-10  Score=99.23  Aligned_cols=50  Identities=26%  Similarity=0.731  Sum_probs=42.6

Q ss_pred             CCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            8 GKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         8 ~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      +.+.||||++.|. |+      .++|||+||..||..|+..    ....||.||.++....
T Consensus        22 ~~~~C~IC~~~~~~p~------~~~CgH~fC~~Ci~~~~~~----~~~~CP~Cr~~~~~~~   72 (116)
T 1rmd_A           22 KSISCQICEHILADPV------ETSCKHLFCRICILRCLKV----MGSYCPSCRYPCFPTD   72 (116)
T ss_dssp             HHTBCTTTCSBCSSEE------ECTTSCEEEHHHHHHHHHH----TCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCCcHhcCcE------EcCCCCcccHHHHHHHHhH----CcCcCCCCCCCCCHhh
Confidence            3578999999998 54      6899999999999999984    3578999999988654

>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=98.98  E-value=8e-11  Score=101.42  Aligned_cols=46  Identities=28%  Similarity=0.595  Sum_probs=39.7

Q ss_pred             CCccccccccccc-ccccCcceee-cCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            8 GKTICSICYEDLK-PIVEDLQVIS-ICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         8 ~eltCpICLe~f~-P~~~~~~~ll-pCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      +.+.||||++.|. |+      ++ +|||+||..||..|+.       ..||+||.++...
T Consensus        21 ~~~~C~IC~~~~~~pv------~~~~CgH~fC~~Ci~~~~~-------~~CP~Cr~~~~~~   68 (117)
T 1jm7_B           21 KLLRCSRCTNILREPV------CLGGCEHIFCSNCVSDCIG-------TGCPVCYTPAWIQ   68 (117)
T ss_dssp             HTTSCSSSCSCCSSCB------CCCSSSCCBCTTTGGGGTT-------TBCSSSCCBCSCS
T ss_pred             hCCCCCCCChHhhCcc------EeCCCCCHHHHHHHHHHhc-------CCCcCCCCcCccc
Confidence            4689999999998 64      56 9999999999999965       7899999998644

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

Probab=98.95  E-value=5.3e-10  Score=95.22  Aligned_cols=53  Identities=23%  Similarity=0.608  Sum_probs=41.9

Q ss_pred             CCccccccccccccc-------------ccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccC
Q 012292            8 GKTICSICYEDLKPI-------------VEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS   65 (466)
Q Consensus         8 ~eltCpICLe~f~P~-------------~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~   65 (466)
                      ++..|+||++.|...             .+.....++|||.||..||..|+.     ...+||+||..+..
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~-----~~~~CP~Cr~~~~~  101 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLK-----TRQVCPLDNREWEF  101 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHT-----TCSBCSSSCSBCCE
T ss_pred             CCCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHH-----cCCcCcCCCCccee
Confidence            456899999999721             112345689999999999999998     57899999998653

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C

Probab=98.93  E-value=4.6e-10  Score=104.07  Aligned_cols=53  Identities=13%  Similarity=0.186  Sum_probs=44.1

Q ss_pred             CCCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            5 NKFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         5 ~~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ..-..+.||||++.|. |+      ++||||+||..||..|+..    +..+||+||.+++...
T Consensus       102 ~ip~~f~CPI~~elm~DPV------~~~~Ghtfer~~I~~~l~~----~~~tcP~t~~~l~~~~  155 (179)
T 2f42_A          102 EIPDYLCGKISFELMREPC------ITPSGITYDRKDIEEHLQR----VGHFDPVTRSPLTQDQ  155 (179)
T ss_dssp             CCCGGGBCTTTCSBCSSEE------ECTTSCEEEHHHHHHHHHH----TCSBCTTTCCBCCGGG
T ss_pred             CCcHhhcccCccccCCCCe------ECCCCCEECHHHHHHHHHh----CCCCCCCCcCCCChhh
Confidence            3456789999999998 65      7899999999999999984    2237999999987654

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

Probab=98.91  E-value=1.5e-10  Score=103.32  Aligned_cols=49  Identities=27%  Similarity=0.611  Sum_probs=41.3

Q ss_pred             CCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCcccc
Q 012292            6 KFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus         6 ~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~   64 (466)
                      ..+.+.|+||++.|. |+      .++|||+||..||..|+..    +...||+||.++.
T Consensus        28 l~~~~~C~IC~~~~~~pv------~~~CgH~FC~~Ci~~~~~~----~~~~CP~Cr~~~~   77 (141)
T 3knv_A           28 LEAKYLCSACRNVLRRPF------QAQCGHRYCSFCLASILSS----GPQNCAACVHEGI   77 (141)
T ss_dssp             CCGGGBCTTTCSBCSSEE------ECTTSCEEEHHHHHHHGGG----SCEECHHHHHTTC
T ss_pred             CCcCcCCCCCChhhcCcE------ECCCCCccCHHHHHHHHhc----CCCCCCCCCCccc
Confidence            346789999999998 54      6899999999999999872    3468999999764

>3htk_C E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-ring, ring, ATP-binding, chromosomal protein, coiled coil, DNA damage; 2.31A {Saccharomyces cerevisiae}

Probab=98.85  E-value=9.1e-10  Score=107.23  Aligned_cols=56  Identities=25%  Similarity=0.491  Sum_probs=45.3

Q ss_pred             CCCCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcC--cCccccCCC
Q 012292            4 ENKFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPV--CKQRCSSSN   67 (466)
Q Consensus         4 ~~~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~--CR~~~~~~~   67 (466)
                      +.....++||||++.|. |+     ..+.|||+||..||..||..   ++...||+  ||..+...+
T Consensus       176 ~~~~~el~CPIcl~~f~DPV-----ts~~CGHsFcR~cI~~~~~~---~~~~~CPvtGCr~~l~~~d  234 (267)
T 3htk_C          176 EGGKIELTCPITCKPYEAPL-----ISRKCNHVFDRDGIQNYLQG---YTTRDCPQAACSQVVSMRD  234 (267)
T ss_dssp             CSSBCCSBCTTTSSBCSSEE-----EESSSCCEEEHHHHHHHSTT---CSCEECSGGGCSCEECGGG
T ss_pred             cCCceeeECcCccCcccCCe-----eeCCCCCcccHHHHHHHHHh---CCCCCCCcccccCcCchhh
Confidence            44567899999999999 75     23599999999999999872   24578999  999887554

>3hcs_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.20A {Homo sapiens}

Probab=98.81  E-value=1.8e-09  Score=98.72  Aligned_cols=53  Identities=25%  Similarity=0.480  Sum_probs=44.3

Q ss_pred             CCCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            5 NKFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         5 ~~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ...+.+.||||++.|. |+      .++|||+||..||..|+..    ....||.||.++....
T Consensus        14 ~~~~~~~C~IC~~~~~~pv------~~~CgH~fC~~Ci~~~~~~----~~~~CP~Cr~~~~~~~   67 (170)
T 3hcs_A           14 PLESKYECPICLMALREAV------QTPCGHRFCKACIIKSIRD----AGHKCPVDNEILLENQ   67 (170)
T ss_dssp             CCCGGGBCTTTCSBCSSEE------ECTTSCEEEHHHHHHHHHH----HCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCCCCChhhcCcE------ECCCCCHHHHHHHHHHHHh----CCCCCCCCccCcchhh
Confidence            4456789999999998 54      6899999999999999983    2359999999988654

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

Probab=98.81  E-value=1.5e-09  Score=94.12  Aligned_cols=56  Identities=30%  Similarity=0.715  Sum_probs=44.8

Q ss_pred             CCCccccccccccc-cc-ccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            7 FGKTICSICYEDLK-PI-VEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         7 ~~eltCpICLe~f~-P~-~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      .+...|+||++.|. +. ..+....++|||+||..||.+|+.     ....||+||..+...+
T Consensus        70 ~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~-----~~~~CP~Cr~~~~~~~  127 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLK-----NANTCPTCRKKINHKR  127 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHH-----HCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHH-----cCCCCCCCCCcCChhc
Confidence            45678999999997 31 123335789999999999999999     4679999999987654

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

Probab=98.80  E-value=8e-10  Score=87.66  Aligned_cols=44  Identities=27%  Similarity=0.662  Sum_probs=37.3

Q ss_pred             CcccccccccccccccCcceeecCCCc-ccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            9 KTICSICYEDLKPIVEDLQVISICGHV-FHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         9 eltCpICLe~f~P~~~~~~~llpCGHs-FC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      +..|+||++.+..+     .++||||+ ||..|+..|         ..||+||.++...
T Consensus        24 ~~~C~iC~~~~~~~-----~~~pCgH~~~C~~C~~~~---------~~CP~Cr~~i~~~   68 (74)
T 4ic3_A           24 EKLCKICMDRNIAI-----VFVPCGHLVTCKQCAEAV---------DKCPMCYTVITFK   68 (74)
T ss_dssp             HTBCTTTSSSBCCE-----EEETTCCBCCCHHHHTTC---------SBCTTTCCBCSEE
T ss_pred             CCCCCCCCCCCCCE-----EEcCCCChhHHHHhhhcC---------ccCCCcCcCccCc
Confidence            57899999999832     37899999 999999887         6799999988743

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

Probab=98.79  E-value=2.5e-09  Score=109.90  Aligned_cols=50  Identities=32%  Similarity=0.763  Sum_probs=42.0

Q ss_pred             CcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            9 KTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         9 eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ...|+||++.+..+     ..+||||+||..|+..|+..    ....||.||.++....
T Consensus       332 ~~~C~ICle~~~~p-----v~lpCGH~FC~~Ci~~wl~~----~~~~CP~CR~~i~~~~  381 (389)
T 2y1n_A          332 FQLCKICAENDKDV-----KIEPCGHLMCTSCLTSWQES----EGQGCPFCRCEIKGTE  381 (389)
T ss_dssp             SSBCTTTSSSBCCE-----EEETTCCEECHHHHHHHHHH----TCSBCTTTCCBCCEEE
T ss_pred             CCCCCccCcCCCCe-----EEeCCCChhhHHHHHHHHhc----CCCCCCCCCCccCCce
Confidence            47999999999732     47899999999999999883    4678999999987553

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

Probab=98.78  E-value=2.4e-09  Score=82.62  Aligned_cols=49  Identities=27%  Similarity=0.442  Sum_probs=40.1

Q ss_pred             CCCcccccccccccccccCcceee--cCCCc-ccHHHHHHHHHhcCCCCCCCCcCcCccccC
Q 012292            7 FGKTICSICYEDLKPIVEDLQVIS--ICGHV-FHELCLQQWFEYCSSSKKCTCPVCKQRCSS   65 (466)
Q Consensus         7 ~~eltCpICLe~f~P~~~~~~~ll--pCGHs-FC~~CL~~wle~~~~~~s~~CP~CR~~~~~   65 (466)
                      .++..|+||++.+..+     .++  ||||. ||..|+..|+.     ....||+||.++..
T Consensus         6 ~~~~~C~IC~~~~~~~-----~~~~~pCgH~~~C~~C~~~~~~-----~~~~CPiCR~~i~~   57 (64)
T 2vje_A            6 NAIEPCVICQGRPKNG-----CIVHGKTGHLMACFTCAKKLKK-----RNKPCPVCRQPIQM   57 (64)
T ss_dssp             GGGSCCTTTSSSCSCE-----EEEETTEEEEEECHHHHHHHHH-----TTCCCTTTCCCCCE
T ss_pred             CCcCCCCcCCCCCCCE-----EEECCCCCChhhHHHHHHHHHH-----cCCcCCCcCcchhc
Confidence            3566899999998732     245  99999 89999999988     56789999998863

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

Probab=98.77  E-value=3e-09  Score=81.86  Aligned_cols=49  Identities=22%  Similarity=0.398  Sum_probs=39.7

Q ss_pred             CCCcccccccccccccccCcceee--cCCCc-ccHHHHHHHHHhcCCCCCCCCcCcCccccC
Q 012292            7 FGKTICSICYEDLKPIVEDLQVIS--ICGHV-FHELCLQQWFEYCSSSKKCTCPVCKQRCSS   65 (466)
Q Consensus         7 ~~eltCpICLe~f~P~~~~~~~ll--pCGHs-FC~~CL~~wle~~~~~~s~~CP~CR~~~~~   65 (466)
                      .....|+||++.+..+     .++  ||||. ||..|+..|+.     ....||+||.++..
T Consensus         5 ~~~~~C~IC~~~~~~~-----~~~~~pCgH~~~C~~C~~~~~~-----~~~~CPiCR~~i~~   56 (63)
T 2vje_B            5 NLLKPCSLCEKRPRDG-----NIIHGRTGHLVTCFHCARRLKK-----AGASCPICKKEIQL   56 (63)
T ss_dssp             GGGSBCTTTSSSBSCE-----EEEETTEEEEEECHHHHHHHHH-----TTCBCTTTCCBCCE
T ss_pred             CcCCCCcccCCcCCCe-----EEEecCCCCHhHHHHHHHHHHH-----hCCcCCCcCchhhc
Confidence            3456899999988632     245  99998 99999999987     45789999998863

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

Probab=98.76  E-value=1e-09  Score=95.05  Aligned_cols=53  Identities=23%  Similarity=0.608  Sum_probs=0.9

Q ss_pred             CCccccccccccccc-------------ccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccC
Q 012292            8 GKTICSICYEDLKPI-------------VEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS   65 (466)
Q Consensus         8 ~eltCpICLe~f~P~-------------~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~   65 (466)
                      .+-.|+||++.|...             .+.....++|||.||..||..|+.     ...+||+||..+..
T Consensus        47 ~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~-----~~~~CP~Cr~~~~~  112 (117)
T 4a0k_B           47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLK-----TRQVCPLDNREWEF  112 (117)
T ss_dssp             CC---------------------------------------------------------------------
T ss_pred             CCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHH-----cCCcCCCCCCeeee
Confidence            346899999999721             111233468999999999999998     56899999998753

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

Probab=98.71  E-value=1.4e-08  Score=82.05  Aligned_cols=58  Identities=28%  Similarity=0.583  Sum_probs=44.6

Q ss_pred             CCCCCCcccccccccccccccCcceeecCC-----CcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            4 ENKFGKTICSICYEDLKPIVEDLQVISICG-----HVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         4 ~~~~~eltCpICLe~f~P~~~~~~~llpCG-----HsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ....++..|.||++.|.+.  . ..++||+     |.||..||.+|+...   +...||+||..+....
T Consensus        10 ~~~~~~~~C~IC~~~~~~~--~-~l~~pC~C~Gs~h~fH~~Cl~~Wl~~~---~~~~CplCr~~~~~~~   72 (80)
T 2d8s_A           10 ITPSSQDICRICHCEGDDE--S-PLITPCHCTGSLHFVHQACLQQWIKSS---DTRCCELCKYEFIMET   72 (80)
T ss_dssp             CCCTTSCCCSSSCCCCCSS--S-CEECSSSCCSSSCCEETTHHHHHHHHH---CCSBCSSSCCBCCCCC
T ss_pred             CCCCCCCCCeEcCccccCC--C-eeEeccccCCcCCeeCHHHHHHHHhhC---CCCCCCCCCCeeecCc
Confidence            3445677999999998631  2 2368996     999999999999842   3469999999987553

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

Probab=98.71  E-value=4.2e-09  Score=83.59  Aligned_cols=44  Identities=27%  Similarity=0.668  Sum_probs=36.1

Q ss_pred             CcccccccccccccccCcceeecCCCc-ccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            9 KTICSICYEDLKPIVEDLQVISICGHV-FHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         9 eltCpICLe~f~P~~~~~~~llpCGHs-FC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      ...|+||++.+..+     .++||||. ||..|+..         ...||+||.++...
T Consensus        25 ~~~C~IC~~~~~~~-----~~~pCgH~~~C~~C~~~---------~~~CP~Cr~~i~~~   69 (75)
T 2ecg_A           25 EKLCKICMDRNIAI-----VFVPCGHLVTCKQCAEA---------VDKCPMCYTVITFK   69 (75)
T ss_dssp             HHSCSSSCSSCCCB-----CCSSSCCCCBCHHHHHH---------CSBCTTTCCBCCCC
T ss_pred             CCCCCcCCCCCCCE-----EEecCCCHHHHHHHhhC---------CCCCccCCceecCc
Confidence            46899999999832     37899999 99999964         27899999998754

>1wim_A KIAA0161 protein; ring finger domain, UBCM4-interacting protein 4, UIP4, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.64  E-value=7.4e-09  Score=85.56  Aligned_cols=53  Identities=26%  Similarity=0.683  Sum_probs=39.4

Q ss_pred             CCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCC-C--CCCCCcC--cCcc
Q 012292            7 FGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSS-S--KKCTCPV--CKQR   62 (466)
Q Consensus         7 ~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~-~--~s~~CP~--CR~~   62 (466)
                      ....+|+||++.+. |.   ...+.+|||.||..|+.+|+..... +  ....||.  |+..
T Consensus         3 ~~~~~C~IC~~~~~~~~---~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            3 SGSSGCKLCLGEYPVEQ---MTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             CSBCCCSSSCCCCBGGG---EEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CCCcCCcccCccccccc---ceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            35789999999997 32   2223479999999999999874311 1  2468999  9988

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

Probab=98.57  E-value=1.3e-08  Score=81.83  Aligned_cols=44  Identities=32%  Similarity=0.746  Sum_probs=36.9

Q ss_pred             CcccccccccccccccCcceeecCCCc-ccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            9 KTICSICYEDLKPIVEDLQVISICGHV-FHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         9 eltCpICLe~f~P~~~~~~~llpCGHs-FC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      +..|+||++.+..+     .++||||. ||..|+..|         ..||+||.++...
T Consensus        18 ~~~C~IC~~~~~~~-----v~~pCgH~~~C~~C~~~~---------~~CP~Cr~~i~~~   62 (79)
T 2yho_A           18 AMLCMVCCEEEINS-----TFCPCGHTVCCESCAAQL---------QSCPVCRSRVEHV   62 (79)
T ss_dssp             HTBCTTTSSSBCCE-----EEETTCBCCBCHHHHTTC---------SBCTTTCCBCCEE
T ss_pred             CCEeEEeCcccCcE-----EEECCCCHHHHHHHHHhc---------CcCCCCCchhhCe
Confidence            46899999998732     47899999 999999876         3799999998754

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.50  E-value=5.9e-08  Score=75.81  Aligned_cols=46  Identities=24%  Similarity=0.530  Sum_probs=37.7

Q ss_pred             CCCcccccccccccccccCcceeecCCCc-ccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            7 FGKTICSICYEDLKPIVEDLQVISICGHV-FHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         7 ~~eltCpICLe~f~P~~~~~~~llpCGHs-FC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      .+...|+||++.+..+     .++||||. ||..|+..         ...||+||.++...
T Consensus        13 ~~~~~C~IC~~~~~~~-----v~~pCgH~~~C~~C~~~---------~~~CP~CR~~i~~~   59 (68)
T 2ea5_A           13 ENSKDCVVCQNGTVNW-----VLLPCRHTCLCDGCVKY---------FQQCPMCRQFVQES   59 (68)
T ss_dssp             CCSSCCSSSSSSCCCC-----EETTTTBCCSCTTHHHH---------CSSCTTTCCCCCCE
T ss_pred             CCCCCCCCcCcCCCCE-----EEECCCChhhhHHHHhc---------CCCCCCCCcchhce
Confidence            3468999999998733     47899999 99999884         26899999988754

>2bay_A PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin ligase, E3 ligase; 1.50A {Saccharomyces cerevisiae} SCOP: g.44.1.2 PDB: 1n87_A

Probab=98.44  E-value=6.4e-08  Score=74.11  Aligned_cols=48  Identities=19%  Similarity=0.369  Sum_probs=40.5

Q ss_pred             Cccccccccccc-ccccCcceee-cCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            9 KTICSICYEDLK-PIVEDLQVIS-ICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         9 eltCpICLe~f~-P~~~~~~~ll-pCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      .+.||||++.|. |+      ++ +|||+|+..||..|+..     ..+||+++.++...+
T Consensus         3 ~~~CpIs~~~m~dPV------~~~~sG~~yer~~I~~~l~~-----~~~cP~t~~~L~~~~   52 (61)
T 2bay_A            3 HMLCAISGKVPRRPV------LSPKSRTIFEKSLLEQYVKD-----TGNDPITNEPLSIEE   52 (61)
T ss_dssp             -CCCTTTCSCCSSEE------EETTTTEEEEHHHHHHHHHH-----HSBCTTTCCBCCGGG
T ss_pred             eEEecCCCCCCCCCE------EeCCCCcEEcHHHHHHHHHh-----CCCCcCCcCCCChhh
Confidence            368999999998 54      66 89999999999999983     456999999987654

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

Probab=98.40  E-value=1.3e-07  Score=75.17  Aligned_cols=51  Identities=25%  Similarity=0.564  Sum_probs=40.1

Q ss_pred             CcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            9 KTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         9 eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      ...|.||++.+.+. .   ....|+|.||..||.+||...   ...+||.||..+...
T Consensus        15 i~~C~IC~~~i~~g-~---~C~~C~h~fH~~Ci~kWl~~~---~~~~CP~Cr~~w~~~   65 (74)
T 2ct0_A           15 VKICNICHSLLIQG-Q---SCETCGIRMHLPCVAKYFQSN---AEPRCPHCNDYWPHE   65 (74)
T ss_dssp             SCBCSSSCCBCSSS-E---ECSSSCCEECHHHHHHHSTTC---SSCCCTTTCSCCCSC
T ss_pred             CCcCcchhhHcccC-C---ccCCCCchhhHHHHHHHHHhc---CCCCCCCCcCcCCCC
Confidence            47899999999852 1   233899999999999999831   238999999887644

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

Probab=98.16  E-value=6.5e-07  Score=90.09  Aligned_cols=58  Identities=26%  Similarity=0.572  Sum_probs=41.5

Q ss_pred             CCCcccccccccccccccCcc---e-eecCCCcccHHHHHHHHHhcCCCC------CCCCcCcCccccC
Q 012292            7 FGKTICSICYEDLKPIVEDLQ---V-ISICGHVFHELCLQQWFEYCSSSK------KCTCPVCKQRCSS   65 (466)
Q Consensus         7 ~~eltCpICLe~f~P~~~~~~---~-llpCGHsFC~~CL~~wle~~~~~~------s~~CP~CR~~~~~   65 (466)
                      .....|+||+..+.+. ...+   + ...|||.||..||..|+...+.++      ...||.||.+++.
T Consensus       306 e~~~ECaICys~~l~~-g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~  373 (381)
T 3k1l_B          306 NEELRCNICFAYRLDG-GEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLST  373 (381)
T ss_dssp             CSCCSCSSSCCSSCTT-CCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEG
T ss_pred             cCCccCcccceeecCC-CCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCc
Confidence            3566899999998741 1111   1 247999999999999998543211      2579999998874

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=98.12  E-value=2.5e-06  Score=64.97  Aligned_cols=52  Identities=25%  Similarity=0.682  Sum_probs=39.2

Q ss_pred             CCCCcccccccccccccccCcceeecCC--C---cccHHHHHHHHHhcCCCCCCCCcCcCccccC
Q 012292            6 KFGKTICSICYEDLKPIVEDLQVISICG--H---VFHELCLQQWFEYCSSSKKCTCPVCKQRCSS   65 (466)
Q Consensus         6 ~~~eltCpICLe~f~P~~~~~~~llpCG--H---sFC~~CL~~wle~~~~~~s~~CP~CR~~~~~   65 (466)
                      ..+...|.||++...+   .  .+.||.  |   .||..||.+|+...   ++..||+|+..+..
T Consensus         3 ~~~~~~CrIC~~~~~~---~--l~~PC~C~gs~~~~H~~Cl~~W~~~~---~~~~C~~C~~~~~~   59 (60)
T 1vyx_A            3 DEDVPVCWICNEELGN---E--RFRACGCTGELENVHRSCLSTWLTIS---RNTACQICGVVYNT   59 (60)
T ss_dssp             TCSCCEETTTTEECSC---C--CCCSCCCSSGGGSCCHHHHHHHHHHH---TCSBCTTTCCBCCC
T ss_pred             CCCCCEeEEeecCCCC---c--eecCcCCCCchhhhHHHHHHHHHHhC---CCCccCCCCCeeec
Confidence            3456789999987542   1  257865  4   89999999999842   46899999998763

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

Probab=98.01  E-value=3.9e-06  Score=69.88  Aligned_cols=49  Identities=22%  Similarity=0.387  Sum_probs=39.3

Q ss_pred             ccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292           11 ICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus        11 tCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      .|++|--++.-    -..++||.|+||+.|+..|...    +...||.|+.++..-.
T Consensus         3 fC~~C~~Pi~i----ygRmIPCkHvFCydCa~~~~~~----~~k~Cp~C~~~V~rVe   51 (101)
T 3vk6_A            3 FCDKCGLPIKV----YGRMIPCKHVFCYDCAILHEKK----GDKMCPGCSDPVQRIE   51 (101)
T ss_dssp             BCTTTCSBCSE----EEEEETTCCEEEHHHHHHHHHT----TCCBCTTTCCBCSEEE
T ss_pred             ecCccCCCeEE----EeeeccccccHHHHHHHHHHhc----cCCCCcCcCCeeeeeE
Confidence            68999888761    1258999999999999999862    5689999999987443

>3t6p_A Baculoviral IAP repeat-containing protein 2; ring, BIR, CARD, UBA, apoptosis, ubiquitin ligase, SMAC/ ubiquitin, caspase, IAP family, SMAC mimetic; 1.90A {Homo sapiens} PDB: 1qbh_A 2l9m_A 3eb5_A 3eb6_A 4auq_B

Probab=96.99  E-value=0.00012  Score=74.41  Aligned_cols=31  Identities=26%  Similarity=0.683  Sum_probs=26.4

Q ss_pred             ceeecCCCc-ccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292           27 QVISICGHV-FHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus        27 ~~llpCGHs-FC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      +.++||||+ ||..|+..|         ..||.||.++...
T Consensus       308 ~v~lpCgH~~fC~~C~~~~---------~~CP~CR~~i~~~  339 (345)
T 3t6p_A          308 VVFIPCGHLVVCQECAPSL---------RKCPICRGIIKGT  339 (345)
T ss_dssp             EEEETTCCEEECTTTGGGC---------SBCTTTCCBCCEE
T ss_pred             eEEcCCCChhHhHHHHhcC---------CcCCCCCCCccCe
Confidence            457899999 999999877         5799999998743

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

Probab=96.87  E-value=0.00059  Score=65.77  Aligned_cols=51  Identities=25%  Similarity=0.560  Sum_probs=39.6

Q ss_pred             CcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            9 KTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         9 eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      ...|.||.+.+.+.   . ....|+|.||..|+..|+..   .+...||.|+...+..
T Consensus       180 i~~C~iC~~iv~~g---~-~C~~C~~~~H~~C~~~~~~~---~~~~~CP~C~~~W~~~  230 (238)
T 3nw0_A          180 VKICNICHSLLIQG---Q-SCETCGIRMHLPCVAKYFQS---NAEPRCPHCNDYWPHE  230 (238)
T ss_dssp             CCBCTTTCSBCSSC---E-ECSSSCCEECHHHHHHHTTT---CSSCBCTTTCCBCCSC
T ss_pred             CCcCcchhhHHhCC---c-ccCccChHHHHHHHHHHHHh---CCCCCCCCCCCCCCCC
Confidence            56899999999842   1 23349999999999999873   2357999999987644

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A

Probab=96.17  E-value=0.022  Score=66.42  Aligned_cols=32  Identities=13%  Similarity=0.138  Sum_probs=11.8

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Q 012292           96 VKILEVKVSRLHTVLESQGKEIKEINEELCLC  127 (466)
Q Consensus        96 l~rLe~kl~~L~~~Le~~~~~lk~L~eel~~~  127 (466)
                      +..++..+..+...+......+..+..+...+
T Consensus       866 L~el~~~L~~le~~l~ele~~l~~Le~e~~~l  897 (1184)
T 1i84_S          866 LQRTKERQQKAEAELKELEQKHTQLCEEKNLL  897 (1184)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333333333333333333333

>1c1g_A Tropomyosin; contractIle protein; 7.00A {Sus scrofa} SCOP: h.1.5.1 PDB: 2tma_A 2w49_A 2w4u_A

Probab=96.11  E-value=0.84  Score=42.07  Aligned_cols=28  Identities=18%  Similarity=0.328  Sum_probs=12.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012292          241 ARFSEKLEKAKEKINKLKTRVQELETAV  268 (466)
Q Consensus       241 ~~~~~kLek~~~ei~~Lk~~v~eLqk~l  268 (466)
                      ......+..+...+..+..++..+...+
T Consensus       177 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~  204 (284)
T 1c1g_A          177 ERAEERAELSEGKCAELEEEIKTVTNNL  204 (284)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333444444444444444444444433

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

Probab=96.03  E-value=0.0028  Score=52.23  Aligned_cols=34  Identities=21%  Similarity=0.560  Sum_probs=25.8

Q ss_pred             CCccccccccc-ccccccCcceeecCCCcccHHHHHHH
Q 012292            8 GKTICSICYED-LKPIVEDLQVISICGHVFHELCLQQW   44 (466)
Q Consensus         8 ~eltCpICLe~-f~P~~~~~~~llpCGHsFC~~CL~~w   44 (466)
                      ++++|+||.+. +.++   +...++|+|+||..|+..|
T Consensus         2 ee~~C~~C~~~~~~~a---v~~C~~C~~~~C~~Cl~~~   36 (101)
T 2jun_A            2 EKVLCQFCDQDPAQDA---VKTCVTCEVSYCDECLKAT   36 (101)
T ss_dssp             CCCBCTTCCSSSCCBC---CEEETTTTEEECHHHHHHH
T ss_pred             CCCCCcCCCCCCCCCc---eEECCcCChHHhHHHCHHH
Confidence            57899999976 4432   1123899999999999984

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A

Probab=95.93  E-value=0.03  Score=65.28  Aligned_cols=36  Identities=17%  Similarity=0.224  Sum_probs=17.8

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012292           95 EVKILEVKVSRLHTVLESQGKEIKEINEELCLCKER  130 (466)
Q Consensus        95 El~rLe~kl~~L~~~Le~~~~~lk~L~eel~~~KeQ  130 (466)
                      ++..++..+..+...+......+..++.++..+.++
T Consensus       858 El~~L~~eL~el~~~L~~le~~l~ele~~l~~Le~e  893 (1184)
T 1i84_S          858 EMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEE  893 (1184)
T ss_dssp             HCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444455555555555555555555555444433

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=95.87  E-value=0.74  Score=58.55  Aligned_cols=62  Identities=19%  Similarity=0.333  Sum_probs=33.6

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 012292          209 KDTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVEL  270 (466)
Q Consensus       209 ~e~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~  270 (466)
                      ++....|...+..++..|++...+.+.|+.+......+|++|..=|..|-.+-..|....+.
T Consensus      2034 ~~~L~~le~~l~~L~~~~~~~~~ek~~L~~e~~~~~~kl~rA~~Li~gL~~Ek~RW~~~~~~ 2095 (3245)
T 3vkg_A         2034 VATITALEKSIATYKEEYATLIRETEQIKTESSKVKNKVDRSIALLDNLNSERGRWEQQSEN 2095 (3245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccHHHHHHH
Confidence            33444445555555555555555555555555555566666655555555555444444444

>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}

Probab=95.69  E-value=1.6  Score=41.88  Aligned_cols=44  Identities=7%  Similarity=0.121  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Q 012292          213 DVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINK  256 (466)
Q Consensus       213 d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~  256 (466)
                      +.+++.+........+++.+++.+..........+.....++..
T Consensus       100 e~~~~~i~~lE~eile~~e~ie~~~~~l~~~~~~l~~~~~~l~~  143 (256)
T 3na7_A          100 DIAKERSNQANREIENLQNEIKRKSEKQEDLKKEMLELEKLALE  143 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445555555555555555555555555544444444444433

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=95.54  E-value=0.2  Score=53.26  Aligned_cols=56  Identities=14%  Similarity=0.153  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 012292          215 LRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVEL  270 (466)
Q Consensus       215 Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~  270 (466)
                      ++++....++.|+++.++++.+++.....+++++++..|++.+++++++|+..+..
T Consensus       528 ~~~~~~~~~~~~~~~~~~~~~le~~~~~~~~~~~~l~~e~~~~~~~~~~l~~~~~~  583 (597)
T 3oja_B          528 RRTEADAKQKETEDLEQENIALEKQLDNKRAKQAELRQETSLKRQKVKQLEAKKNR  583 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC-
T ss_pred             HHHhhhhhhcchhhHHhhhHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            33344444556666666666666666666667777777777777777777666654

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=95.34  E-value=2  Score=54.74  Aligned_cols=72  Identities=15%  Similarity=0.231  Sum_probs=45.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHhcc
Q 012292          211 TIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVSK  283 (466)
Q Consensus       211 ~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~~~ne~l~~l~~~~  283 (466)
                      ....+..++...+..++++++++..++.....++.+++++..|...|+.+++..+..|+.++ .++..|-.+|
T Consensus      2015 ~l~~ae~~l~~~~~~L~~~~~~L~~le~~l~~L~~~~~~~~~ek~~L~~e~~~~~~kl~rA~-~Li~gL~~Ek 2086 (3245)
T 3vkg_A         2015 EVEQLENAANELKLKQDEIVATITALEKSIATYKEEYATLIRETEQIKTESSKVKNKVDRSI-ALLDNLNSER 2086 (3245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHhhhhcc
Confidence            34444455555555666666667777777777777777777777777777777777766433 3444444444

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus}

Probab=95.09  E-value=0.33  Score=56.05  Aligned_cols=56  Identities=21%  Similarity=0.194  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 012292          212 IDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVEL  270 (466)
Q Consensus       212 ~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~  270 (466)
                      ++.|.+++....+.++.+..+++++..   .+..++..+.+++.+|++++.+|+..+..
T Consensus       993 ~~~l~~~~~~~~ke~~~lee~~~~~~~---~L~~kv~~L~~e~~~L~qq~~~l~~~~~~ 1048 (1080)
T 2dfs_A          993 IAKLRKELHQTQTEKKTIEEWADKYKH---ETEQLVSELKEQNTLLKTEKEELNRRIHD 1048 (1080)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444555555555554444442   22355555556666666666666543333

>3o0z_A RHO-associated protein kinase 1; coiled-coil, transferase; HET: MSE; 2.33A {Homo sapiens}

Probab=93.67  E-value=3.9  Score=36.94  Aligned_cols=62  Identities=16%  Similarity=0.137  Sum_probs=47.0

Q ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHhc
Q 012292          221 IRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEVLRALKVS  282 (466)
Q Consensus       221 ~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~~~ne~l~~l~~~  282 (466)
                      -+.....+|..++..|.-+..+++..+.++..+...|.+++-.|++.-.+.+=+++=.|+.-
T Consensus        87 q~se~~~elq~ri~~L~~El~~~k~~~~k~~~e~r~L~Ekl~~lEKe~a~~eid~~~eLKal  148 (168)
T 3o0z_A           87 HDSEMIGDLQARITSLQEEVKHLKHNLEKVEGERKEAQDMLNHSEKEKNNLEIDLNYKLKSL  148 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence            34445566777888888888888888888888888888888888888877776555555543

>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}

Probab=93.55  E-value=5.3  Score=38.13  Aligned_cols=21  Identities=10%  Similarity=0.142  Sum_probs=8.3

Q ss_pred             HHHHHHhhHHHHHHHHHHHHH
Q 012292          148 VEQLLHSKSQELDKVTLECLK  168 (466)
Q Consensus       148 LeqLL~~q~eEVeklkeE~~r  168 (466)
                      ++..+.....++..+...+.+
T Consensus        58 ~~~~~~~~e~~i~~~~~ri~~   78 (256)
T 3na7_A           58 LKLQVSKNEQTLQDTNAKIAS   78 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            333333344444444333333

>1ic2_A Tropomyosin alpha chain, skeletal muscle; alpha-helical coiled coil, alanine, symmetry, axial stagger, BEND, contractIle protein; 2.00A {Gallus gallus} SCOP: h.1.5.1

Probab=92.87  E-value=1  Score=35.75  Aligned_cols=63  Identities=10%  Similarity=0.248  Sum_probs=54.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHH
Q 012292          213 DVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDNEV  275 (466)
Q Consensus       213 d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~~~ne~  275 (466)
                      +.|++.|..++...+....+.+++..........+.++..++..|..+++.|+..|+.....+
T Consensus         2 ~~ikkKm~~lk~e~d~a~~~~~~~e~~l~~~e~~~~~~E~ev~~L~kKiq~lE~eld~~ee~l   64 (81)
T 1ic2_A            2 DAIKKKMQMLKLDKENALDRAEQAEADKKAAEERSKQLEDELVALQKKLKGTEDELDKYSESL   64 (81)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            468889999999999999999999988888889999999999999999999999998855443

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus}

Probab=92.26  E-value=2.4  Score=48.97  Aligned_cols=21  Identities=29%  Similarity=0.408  Sum_probs=0.0

Q ss_pred             HHHHhHHHHHHHHHHHHHHHH
Q 012292          101 VKVSRLHTVLESQGKEIKEIN  121 (466)
Q Consensus       101 ~kl~~L~~~Le~~~~~lk~L~  121 (466)
                      .++..+...++...++...+.
T Consensus       928 ~kl~eLq~rL~~~e~~n~~L~  948 (1080)
T 2dfs_A          928 NKIMQLQRKIDEQNKEYKSLL  948 (1080)
T ss_dssp             ---------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            334444443433333333333

>3u1c_A Tropomyosin alpha-1 chain; anti-parallel coiled coil, contractIle protein; 1.80A {Gallus gallus} PDB: 3u1a_A

Probab=92.05  E-value=1.3  Score=36.61  Aligned_cols=63  Identities=11%  Similarity=0.215  Sum_probs=53.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhH
Q 012292          211 TIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDN  273 (466)
Q Consensus       211 ~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~~~n  273 (466)
                      +.|++++.|..++-..++...+.+++......+.....++..+|..|..+++.|+..|+....
T Consensus         3 ~MdaIKkKm~~lk~e~e~a~drae~~e~~~k~~e~~~~~~E~Ei~sL~kk~~~lE~eld~~ee   65 (101)
T 3u1c_A            3 HMDAIKKKMQMLKLDKENALDRAEQAEADKKAAEERSKQLEDDIVQLEKQLRVTEDSRDQVLE   65 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            578999999999998888888888888888777788888888888888888888888876443

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=90.69  E-value=4.6  Score=42.68  Aligned_cols=15  Identities=13%  Similarity=0.126  Sum_probs=10.0

Q ss_pred             CCcccHHHHHHHHHh
Q 012292           33 GHVFHELCLQQWFEY   47 (466)
Q Consensus        33 GHsFC~~CL~~wle~   47 (466)
                      |-.|...|+..|+..
T Consensus       354 ~N~~~~~~~~~~~~~  368 (597)
T 3oja_B          354 HNDWDCNSLRALFRN  368 (597)
T ss_dssp             SSCEEHHHHHHHTTT
T ss_pred             CCCCCChhHHHHHHH
Confidence            334566788888764

>3u59_A Tropomyosin beta chain; muscle contraction, actin, contractIle protein; 2.50A {Gallus gallus}

Probab=90.60  E-value=2.1  Score=35.30  Aligned_cols=63  Identities=11%  Similarity=0.261  Sum_probs=53.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhH
Q 012292          211 TIDVLRKSLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELKDN  273 (466)
Q Consensus       211 ~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~~~n  273 (466)
                      ..+++++.|..++-..++...+.+++......+.....++..+|..|+.+++.|+..++....
T Consensus         3 ~md~iKkKm~~lk~e~e~a~d~ae~~e~~~k~~e~~~~~~E~ei~sL~kKiq~lE~eld~~~e   65 (101)
T 3u59_A            3 SMEAIKKKMQMLKLDKENAIDRAEQAEADKKQAEDRCKQLEEEQQGLQKKLKGTEDEVEKYSE   65 (101)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            478899999999999999999999998888888888888889999999999888888876443

>3i2d_A E3 SUMO-protein ligase SIZ1; signal transduction, replication, ring E3, PIAS, ubiquitin, UBC9, metal-binding, nucleus; 2.60A {Saccharomyces cerevisiae}

Probab=88.36  E-value=0.2  Score=50.92  Aligned_cols=53  Identities=23%  Similarity=0.357  Sum_probs=39.5

Q ss_pred             Cccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            9 KTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         9 eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      .+.||+-+..+. |+     ....|.|.-|.. +..|+..........||+|...+...+
T Consensus       249 SL~CPlS~~ri~~Pv-----Rg~~C~HlQCFD-l~sfL~~~~~~~~W~CPIC~k~~~~~d  302 (371)
T 3i2d_A          249 SLQCPISYTRMKYPS-----KSINCKHLQCFD-ALWFLHSQLQIPTWQCPVCQIDIALEN  302 (371)
T ss_dssp             ESBCTTTSSBCSSEE-----EETTCCSSCCEE-HHHHHHHHHHSCCCBCTTTCCBCCGGG
T ss_pred             eecCCCccccccccC-----cCCcCCCcceEC-HHHHHHHhhcCCceeCCCCCcccCHHH
Confidence            478999999998 76     567899996654 334554333357899999999888776

>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=87.47  E-value=1.1  Score=36.39  Aligned_cols=56  Identities=23%  Similarity=0.506  Sum_probs=38.7

Q ss_pred             CCCCCccccccccccc-ccccCcc-eeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCcccc
Q 012292            5 NKFGKTICSICYEDLK-PIVEDLQ-VISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus         5 ~~~~eltCpICLe~f~-P~~~~~~-~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~   64 (466)
                      .......|.||-+.+- .+...++ ..-.|+--.|..|+.--..    .++..||.|+.++.
T Consensus        12 ~~~~~qiCqiCGD~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErk----eG~q~CpqCktrYk   69 (93)
T 1weo_A           12 KNLDGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERR----EGTQNCPQCKTRYK   69 (93)
T ss_dssp             SCCSSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHH----TSCSSCTTTCCCCC
T ss_pred             cccCCCccccccCccccCCCCCEEEeeeccCChhhHHHHHHHHh----ccCccccccCCccc
Confidence            3345679999999976 2222222 1245777889999985433    37899999999886

>3hnw_A Uncharacterized protein; coiled-coil, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.20A {Eubacterium eligens}

Probab=87.47  E-value=3.8  Score=35.81  Aligned_cols=42  Identities=17%  Similarity=0.141  Sum_probs=19.7

Q ss_pred             HHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 012292          230 MAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVELK  271 (466)
Q Consensus       230 ~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~~  271 (466)
                      ...+..|..+...+.-+++.+..++++|++++.+|++.+-..
T Consensus        88 ~kE~~~lK~el~~~~~k~e~~~~e~~~l~~~~~~l~~~~~~l  129 (138)
T 3hnw_A           88 DKEIYDLKHELIAAQIKAESSAKEIKELKSEINKYQKNIVKL  129 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333444444444455555555555555555555444443

>2cs3_A Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.3

Probab=87.16  E-value=0.58  Score=37.26  Aligned_cols=53  Identities=25%  Similarity=0.400  Sum_probs=35.2

Q ss_pred             CCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCc
Q 012292            6 KFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVC   59 (466)
Q Consensus         6 ~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~C   59 (466)
                      ....+.|.+|.+.+.++ ..+++-..=+|-||..|-...++....+.-..||.=
T Consensus        12 ~~a~l~CtlC~erLEdt-HFVQCPsv~~HkFCFpCsr~sIk~q~~~~EvyCPSG   64 (93)
T 2cs3_A           12 NSGPLCCTICHERLEDT-HFVQCPSVPSHKFCFPCSRESIKAQGATGEVYCPSG   64 (93)
T ss_dssp             SCCSCCCSSSCSCCSST-TSEECSSCSSCEECHHHHHHHHHHHHSSSCCCCTTS
T ss_pred             CCCeeEeecchhhhccC-ceeeCCCccCCeeeccccHHHHHhcCCCCcEECCCC
Confidence            34568999999999743 222222234699999999998885544445556643

>1wil_A KIAA1045 protein; ring finger domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: g.50.1.3

Probab=87.13  E-value=0.54  Score=37.76  Aligned_cols=56  Identities=21%  Similarity=0.523  Sum_probs=35.5

Q ss_pred             CCCCCCCcccccccccccccccCcceeecCCCcccHHHHHHH--HH---------hcCCCCCCCCcCcCc
Q 012292            3 IENKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQW--FE---------YCSSSKKCTCPVCKQ   61 (466)
Q Consensus         3 ~~~~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~w--le---------~~~~~~s~~CP~CR~   61 (466)
                      .+....+..|+||-..-..   .+.-.-.|+-+||..||.+.  +.         .........||.|..
T Consensus         9 ~e~~~~D~~C~VC~~~t~~---~l~pCRvC~RvfH~~CL~r~gy~~~~~a~e~~l~A~T~~GWSC~~Cen   75 (89)
T 1wil_A            9 REPVVNDEMCDVCEVWTAE---SLFPCRVCTRVFHDGCLRRMGYIQGDSAAEVTEMAHTETGWSCHYCDN   75 (89)
T ss_dssp             CCCCCCSCCCTTTCCCCSS---CCSSCSSSSSCCCHHHHHHHTSCCCCCCCSCSCCCSSSSSCCCTTTCC
T ss_pred             ccCCCCCcccCcccccccc---ceeccccccccccHhhcccccccccHHHHHHHHccCCCCCccccccch
Confidence            3455677899999744321   11113469999999999985  11         112235688999943

>3hnw_A Uncharacterized protein; coiled-coil, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.20A {Eubacterium eligens}

Probab=87.02  E-value=5.6  Score=34.72  Aligned_cols=52  Identities=17%  Similarity=0.252  Sum_probs=23.1

Q ss_pred             HHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 012292          218 SLVIRNKNYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVE  269 (466)
Q Consensus       218 ~l~~~~k~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le  269 (466)
                      .+....+....|+.....+......+.++++++..++..|..++..|+..++
T Consensus        83 ~l~~~~kE~~~lK~el~~~~~k~e~~~~e~~~l~~~~~~l~~~~~~le~~~~  134 (138)
T 3hnw_A           83 DIENKDKEIYDLKHELIAAQIKAESSAKEIKELKSEINKYQKNIVKLETELN  134 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333344333333444444444444555555555555555554444

>4fo9_A E3 SUMO-protein ligase PIAS2; E3 ligase, pinit domain, SP-ring domain, structural GE consortium, SGC; 2.39A {Homo sapiens} PDB: 2asq_B

Probab=86.21  E-value=0.26  Score=49.92  Aligned_cols=53  Identities=17%  Similarity=0.396  Sum_probs=39.4

Q ss_pred             Cccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            9 KTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         9 eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      .+.|||-+..+. |+     ....|.|.-|.. +..|+..........||+|.+.+...+
T Consensus       215 SL~CPlS~~ri~~P~-----Rg~~C~HlqCFD-l~sfL~~~~~~~~W~CPiC~k~~~~~d  268 (360)
T 4fo9_A          215 SLMCPLGKMRLTIPC-----RAVTCTHLQCFD-AALYLQMNEKKPTWICPVCDKKAAYES  268 (360)
T ss_dssp             ESBCTTTCSBCSSEE-----EETTCCCCCCEE-HHHHHHHHHHSCCCBCTTTCSBCCGGG
T ss_pred             eeeCCCccceeccCC-----cCCCCCCCccCC-HHHHHHHHhhCCCeECCCCCcccCHHH
Confidence            478999999998 76     467899996654 334554333346899999999988776

>3trt_A Vimentin; cytoskeleton, intermediate filament, alpha-helix, structural protein; 2.30A {Homo sapiens} PDB: 3klt_A*

Probab=86.04  E-value=3.8  Score=31.76  Aligned_cols=40  Identities=25%  Similarity=0.342  Sum_probs=32.7

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 012292          231 AKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAVEL  270 (466)
Q Consensus       231 ~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~le~  270 (466)
                      .+++.|.....+....+..++.||.+|+..++.|+..|+.
T Consensus        35 ~k~eel~~~~~~~~~~l~~~k~Ei~elrr~iq~L~~el~s   74 (77)
T 3trt_A           35 SKFADLSEAANRNNDALRQAKQESTEYRRQVQSLTMEVDA   74 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4555666666666688999999999999999999998875

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=83.68  E-value=0.62  Score=35.63  Aligned_cols=53  Identities=17%  Similarity=0.307  Sum_probs=36.8

Q ss_pred             CCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCcccc
Q 012292            6 KFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus         6 ~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~   64 (466)
                      ......|.||.+.     ..+...-.|...||..|+...+...+ .+...||.|.....
T Consensus         9 ~~~~~~C~vC~~~-----~~ll~Cd~C~~~~H~~Cl~P~l~~~P-~g~W~C~~C~~~~~   61 (66)
T 2lri_C            9 LAPGARCGVCGDG-----TDVLRCTHCAAAFHWRCHFPAGTSRP-GTGLRCRSCSGDVT   61 (66)
T ss_dssp             CCTTCCCTTTSCC-----TTCEECSSSCCEECHHHHCTTTCCCC-SSSCCCTTTTTCCC
T ss_pred             CCCCCCcCCCCCC-----CeEEECCCCCCceecccCCCccCcCC-CCCEECccccCCCc
Confidence            3445679999753     23344456899999999987666433 35789999976543

>1we9_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=83.55  E-value=0.18  Score=37.98  Aligned_cols=59  Identities=20%  Similarity=0.379  Sum_probs=36.9

Q ss_pred             CCCCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccc
Q 012292            4 ENKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRC   63 (466)
Q Consensus         4 ~~~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~   63 (466)
                      +++.+...|+||...+.+. ...+..-.|..-||..|+.-............||.|+..-
T Consensus         1 ~s~~e~~~C~~C~~~~~~~-~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k~   59 (64)
T 1we9_A            1 GSSGSSGQCGACGESYAAD-EFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKS   59 (64)
T ss_dssp             CCCSSCCCCSSSCCCCCSS-SCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTTT
T ss_pred             CCCCCCCCCCCCCCccCCC-CCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcCcC
Confidence            3566788999999888532 2222234688899999975421111112468899997643

>2v71_A Nuclear distribution protein NUDE-like 1; developmental protein, nuclear protein, neurogenesis, cytosk LIS1 binding, differentiation; 2.24A {Rattus norvegicus}

Probab=82.67  E-value=29  Score=31.82  Aligned_cols=28  Identities=11%  Similarity=0.146  Sum_probs=12.4

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHH
Q 012292           94 AEVKILEVKVSRLHTVLESQGKEIKEIN  121 (466)
Q Consensus        94 ~El~rLe~kl~~L~~~Le~~~~~lk~L~  121 (466)
                      .++..++.....+...+.....++..+.
T Consensus        10 ee~~ywk~~~~~~~q~~~~le~El~EFq   37 (189)
T 2v71_A           10 EETAYWKELSMKYKQSFQEARDELVEFQ   37 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444444444333

>3m62_A Ubiquitin conjugation factor E4; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} PDB: 3m63_A* 2qiz_A 2qj0_A

Probab=82.23  E-value=0.69  Score=52.41  Aligned_cols=51  Identities=12%  Similarity=0.133  Sum_probs=42.3

Q ss_pred             CCCCccccccccccc-ccccCcceeecCC-CcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            6 KFGKTICSICYEDLK-PIVEDLQVISICG-HVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         6 ~~~eltCpICLe~f~-P~~~~~~~llpCG-HsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      .=++..|||-++.|. |+      ++|.| |+|=..+|.+|+.     ...+||+=|.+++...
T Consensus       888 iP~~F~cPIs~~lM~DPV------ilpsG~~TydR~~I~~wl~-----~~~tdP~Tr~~L~~~~  940 (968)
T 3m62_A          888 VPDEFLDPLMYTIMKDPV------ILPASKMNIDRSTIKAHLL-----SDSTDPFNRMPLKLED  940 (968)
T ss_dssp             SCGGGBCTTTCSBCSSEE------ECTTTCCEEEHHHHHHHHT-----TCCBCTTTCCBCCGGG
T ss_pred             CcHHhCCcchhhHHhCCe------EcCCCCEEECHHHHHHHHh-----cCCCCCCCCCCCCccc
Confidence            345788999999998 65      88998 6999999999998     4578999888887543

>2yt5_A Metal-response element-binding transcription factor 2; zinc-regulated factor 1, ZIRF1, metal-response element DNA-binding protein M96; NMR {Mus musculus}

Probab=81.99  E-value=0.14  Score=38.92  Aligned_cols=61  Identities=21%  Similarity=0.531  Sum_probs=40.6

Q ss_pred             CCCCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHh--cCCCCCCCCcCcCcccc
Q 012292            4 ENKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEY--CSSSKKCTCPVCKQRCS   64 (466)
Q Consensus         4 ~~~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~--~~~~~s~~CP~CR~~~~   64 (466)
                      ++...+..|.||..........+...-.|...||..|+..-+..  -+..+...||.|.....
T Consensus         1 g~~~~~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~~~   63 (66)
T 2yt5_A            1 GSSGSSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFATT   63 (66)
T ss_dssp             CCCCCCCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHTTS
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCccc
Confidence            35667889999998754222344555678899999998753321  01236789999976543

>1deb_A APC protein, adenomatous polyposis coli protein; coiled coil, tumor suppressor, structural protein; 2.40A {Homo sapiens} SCOP: h.1.18.1

Probab=81.62  E-value=8.7  Score=27.66  Aligned_cols=44  Identities=20%  Similarity=0.461  Sum_probs=34.9

Q ss_pred             HHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012292          225 NYTELMAKCNLLGREKARFSEKLEKAKEKINKLKTRVQELETAV  268 (466)
Q Consensus       225 ~yeeL~~k~e~L~ree~~~~~kLek~~~ei~~Lk~~v~eLqk~l  268 (466)
                      .|++|..+++.|++|-.-++++|+.-...+.+|+.+-..++..+
T Consensus         4 sYdQL~~QVe~Lk~ENshLrrEL~dNS~~lskLE~ets~mKevl   47 (54)
T 1deb_A            4 SYDQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVL   47 (54)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHhhHHHHHHHHhhhhhHHHHH
Confidence            58888888888888888888888888888888877766665444

---

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	466
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	2e-10
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	3e-10
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	1e-09
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	2e-09
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	6e-09
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	3e-08
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	4e-08
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	1e-07
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	8e-07
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	8e-07
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	2e-06
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	3e-06
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	2e-05
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	1e-04
d2c2la2	80	g.44.1.2 (A:225-304) STIP1 homology and U box-cont	0.002

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]} Length = 60

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]

 Score = 54.5 bits (130), Expect = 2e-10
 Identities = 11/54 (20%), Positives = 17/54 (31%), Gaps = 3/54 (5%)

Query: 11 ICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS 64
          +C IC E+L          +      H  CL  W       +   C +C    +
Sbjct: 8  VCWICNEELGNERFRACGCTGELENVHRSCLSTWLTIS---RNTACQICGVVYN 58

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]} Length = 55

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

 Score = 53.7 bits (129), Expect = 3e-10
 Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 6/51 (11%)

Query: 12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQR 62
          C++C  +L+   E+ + +  CGH FH  C+  W          TCP+C+  
Sbjct: 8  CAVCLAELED-GEEARFLPRCGHGFHAECVDMWLG-----SHSTCPLCRLT 52

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]} Length = 79

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

 Score = 52.3 bits (125), Expect = 1e-09
 Identities = 18/59 (30%), Positives = 25/59 (42%), Gaps = 9/59 (15%)

Query: 11 ICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSI 69
          +C IC E+ K +      I  CGH+    CL  W E    S+   CP C+     +  I
Sbjct: 25 LCKICAENDKDVK-----IEPCGHLMCTSCLTSWQE----SEGQGCPFCRCEIKGTEPI 74

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

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]

 Score = 52.2 bits (125), Expect = 2e-09
 Identities = 13/57 (22%), Positives = 22/57 (38%), Gaps = 9/57 (15%)

Query: 11 ICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN 67
           C IC   L        V + C H+F  +C+ +  +         CP C+  C  ++
Sbjct: 25 SCQICEHILAD-----PVETSCKHLFCRICILRCLK----VMGSYCPSCRYPCFPTD 72

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]} Length = 68

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

 Score = 49.9 bits (119), Expect = 6e-09
 Identities = 19/69 (27%), Positives = 28/69 (40%), Gaps = 16/69 (23%)

Query: 12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS------- 64
          C IC ED      +  +   C H F  +C+ +W       +  TCP+CK           
Sbjct: 8  CPICLEDPS----NYSMALPCLHAFCYVCITRWIR-----QNPTCPLCKVPVESVVHTIE 58

Query: 65 SSNSIGDQI 73
          S +  GDQ+
Sbjct: 59 SDSEFGDQL 67

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 65

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]

 Score = 48.2 bits (114), Expect = 3e-08
 Identities = 13/56 (23%), Positives = 18/56 (32%), Gaps = 4/56 (7%)

Query: 12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN 67
          C  C            ++++CGH   E C+   F          CP C      SN
Sbjct: 6  CPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVR----GAGNCPECGTPLRKSN 57

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]} Length = 56

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]

 Score = 47.6 bits (113), Expect = 4e-08
 Identities = 12/63 (19%), Positives = 18/63 (28%), Gaps = 13/63 (20%)

Query: 4  ENKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRC 63
          E +F    C  C  + K        +  C H     CL+             CP+C+   
Sbjct: 1  EEEFQFLRCQQCQAEAKCPK-----LLPCLHTLCSGCLEAS--------GMQCPICQAPW 47

Query: 64 SSS 66
             
Sbjct: 48 PLG 50

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]} Length = 94

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.0 bits (111), Expect = 1e-07
 Identities = 14/62 (22%), Positives = 23/62 (37%), Gaps = 5/62 (8%)

Query: 8  GKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYC---SSSKKCTCPVCKQRCS 64
          G + C +C  +     E +  I+ C  +F  LCL+Q+ E           +CP       
Sbjct: 4  GSSGCKLCLGEYPV--EQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ 61

Query: 65 SS 66
            
Sbjct: 62 GH 63

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 114

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

 Score = 45.8 bits (107), Expect = 8e-07
 Identities = 16/63 (25%), Positives = 21/63 (33%), Gaps = 13/63 (20%)

Query: 11 ICSICYEDLKPIV-------------EDLQVISICGHVFHELCLQQWFEYCSSSKKCTCP 57
           C IC E L                   +  ++ C H FH LCL   +   +      CP
Sbjct: 27 DCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCP 86

Query: 58 VCK 60
           CK
Sbjct: 87 SCK 89

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 103

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

 Score = 45.1 bits (106), Expect = 8e-07
 Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 7/56 (12%)

Query: 12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN 67
          C IC E +K  V      + C H+F + C+ +            CP+CK   +  +
Sbjct: 24 CPICLELIKEPV-----STKCDHIFCKFCMLKLLN--QKKGPSQCPLCKNDITKRS 72

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]} Length = 52

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]

 Score = 42.8 bits (100), Expect = 2e-06
 Identities = 10/50 (20%), Positives = 19/50 (38%), Gaps = 5/50 (10%)

Query: 12 CSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQ 61
          C +C E L+    +    + CG+     C  +     +      CP C++
Sbjct: 3  CPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENG----LCPACRK 47

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

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

 Score = 43.2 bits (101), Expect = 3e-06
 Identities = 12/63 (19%), Positives = 23/63 (36%), Gaps = 18/63 (28%)

Query: 12 CSICYEDLKPIVEDLQ-------------VISICGHVFHELCLQQWFEYCSSSKKCTCPV 58
          C+IC   +  +  + Q                +C H FH  C+ +W +      +  CP+
Sbjct: 24 CAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLK-----TRQVCPL 78

Query: 59 CKQ 61
            +
Sbjct: 79 DNR 81

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

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]

 Score = 39.7 bits (92), Expect = 2e-05
 Identities = 7/59 (11%), Positives = 20/59 (33%), Gaps = 9/59 (15%)

Query: 11 ICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSI 69
          +C+I  +  +       +      +F +  L+Q+ +          P+  +  S    +
Sbjct: 2  LCAISGKVPR----RPVLSPKSRTIFEKSLLEQYVKDT-----GNDPITNEPLSIEEIV 51

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 97

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]

 Score = 38.6 bits (89), Expect = 1e-04
 Identities = 15/84 (17%), Positives = 26/84 (30%), Gaps = 13/84 (15%)

Query: 11 ICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSIG 70
           CS C   L+        +  C H+F   C+              CPVC       +   
Sbjct: 24 RCSRCTNILREP----VCLGGCEHIFCSNCVSDCI-------GTGCPVCYTPAWIQDLKI 72

Query: 71 DQI--DLVISQKPKDPEVEDPEVS 92
          ++    ++         + D E+S
Sbjct: 73 NRQLDSMIQLCSKLRNLLHDNELS 96

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 80

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.8 bits (79), Expect = 0.002
 Identities = 7/59 (11%), Positives = 18/59 (30%), Gaps = 9/59 (15%)

Query: 11 ICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSNSI 69
             I +E ++        I+  G  +    +++  +          PV +   +    I
Sbjct: 9  CGKISFELMREPC-----ITPSGITYDRKDIEEHLQRV----GHFNPVTRSPLTQEQLI 58

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	466
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.31
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.31
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.3
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.29
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.28
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.25
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.25
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.19
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.18
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.17
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.16
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.13
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.11
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	98.96
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.86
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.82
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.36
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	90.44
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	90.42
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	88.82
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	87.34
d1seta1	110	Seryl-tRNA synthetase (SerRS) {Thermus thermophilu	83.32

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.31  E-value=5.5e-13  Score=101.90  Aligned_cols=56  Identities=23%  Similarity=0.453  Sum_probs=43.3

Q ss_pred             CCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            8 GKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         8 ~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ++.+||||++.+.........+++|||+||..||.+|+..    +...||+||.++...+
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~----~~~~CP~CR~~i~~~~   57 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVR----GAGNCPECGTPLRKSN   57 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHT----TSSSCTTTCCCCSSCC
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCc----CcCCCCCCCcCccccc
Confidence            5789999999865212233456799999999999999973    4567999999987553

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

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

Probab=99.31  E-value=3.4e-13  Score=99.83  Aligned_cols=52  Identities=29%  Similarity=0.805  Sum_probs=41.9

Q ss_pred             CCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCcccc
Q 012292            7 FGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus         7 ~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~   64 (466)
                      .++..|+||++.|.+ .+....+++|||.||..||.+|+.     .+.+||+||.++.
T Consensus         3 ed~~~C~ICl~~~~~-~~~~~~l~~C~H~Fh~~Ci~~Wl~-----~~~~CP~CR~~i~   54 (55)
T d1iyma_           3 DDGVECAVCLAELED-GEEARFLPRCGHGFHAECVDMWLG-----SHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCT-TSCCEECSSSCCEECTTHHHHTTT-----TCCSCSSSCCCSC
T ss_pred             CCCCCCeEECccccC-CCEEEEeCCCCCcccHHHHHHHHH-----hCCcCCCCCCEeE
Confidence            456789999999984 234444557999999999999998     5678999999764

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

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

Probab=99.30  E-value=5.4e-13  Score=107.62  Aligned_cols=50  Identities=26%  Similarity=0.731  Sum_probs=42.7

Q ss_pred             CCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            8 GKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         8 ~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ..++||||++.|. |+      +++|||+||..||..|++.    +...||+||.++...+
T Consensus        22 ~~l~C~IC~~~~~~pv------~~~CgH~FC~~Ci~~~~~~----~~~~CP~Cr~p~~~~~   72 (86)
T d1rmda2          22 KSISCQICEHILADPV------ETSCKHLFCRICILRCLKV----MGSYCPSCRYPCFPTD   72 (86)
T ss_dssp             HHTBCTTTCSBCSSEE------ECTTSCEEEHHHHHHHHHH----TCSBCTTTCCBCCGGG
T ss_pred             cCcCCccCCcchhcce------ecCCCChhhHHHHHHHHhh----CCCcCcccCCCCChhh
Confidence            4478999999998 54      7899999999999999973    4578999999987554

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

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

Probab=99.29  E-value=4.9e-13  Score=97.75  Aligned_cols=51  Identities=20%  Similarity=0.466  Sum_probs=41.0

Q ss_pred             cccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccC
Q 012292           10 TICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS   65 (466)
Q Consensus        10 ltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~   65 (466)
                      +.||||++.|.+ ....+..++|||.||..|+.+|+..    .+..||+||.++..
T Consensus         1 leCpICl~~~~~-~~~~~~~~~CgH~~c~~C~~~w~~~----~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           1 VECPLCMEPLEI-DDINFFPCTCGYQICRFCWHRIRTD----ENGLCPACRKPYPE   51 (52)
T ss_dssp             CEETTTTEECCG-GGTTCCSSSSSCCCCHHHHHHHTTT----SCCBCTTTCCBCSC
T ss_pred             CCCcCCChhhhC-CCceEEecCCCCccchHHHHHHHhh----cCCCCCccCCcCCC
Confidence            469999999974 2344456799999999999999873    45689999999864

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

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

Probab=99.28  E-value=1e-12  Score=109.17  Aligned_cols=51  Identities=27%  Similarity=0.735  Sum_probs=42.2

Q ss_pred             Cccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            9 KTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         9 eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      .+.||||++.|. |+      +++|||+||..||..|+...  ++...||.||.++....
T Consensus        21 ~l~CpIC~~~~~~pv------~~~CgH~fC~~Ci~~~~~~~--~~~~~CP~Cr~~~~~~~   72 (103)
T d1jm7a_          21 ILECPICLELIKEPV------STKCDHIFCKFCMLKLLNQK--KGPSQCPLCKNDITKRS   72 (103)
T ss_dssp             HTSCSSSCCCCSSCC------BCTTSCCCCSHHHHHHHHSS--SSSCCCTTTSCCCCTTT
T ss_pred             CcCCCccCchhCCeE------EcCCCCchhhHHHHHHHHHC--CCCCcCcCCCCcCChhh
Confidence            478999999998 64      78999999999999999832  23468999999987553

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

Probab=99.25  E-value=7.1e-13  Score=102.12  Aligned_cols=45  Identities=33%  Similarity=0.790  Sum_probs=39.0

Q ss_pred             ccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCcccc
Q 012292           10 TICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus        10 ltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~   64 (466)
                      -.||||++.|. ++     ..++|||+||..||.+|+.     .+..||+||.++.
T Consensus         6 d~C~IC~~~~~~~~-----~~~~C~H~Fc~~Ci~~w~~-----~~~~CP~CR~~i~   51 (68)
T d1chca_           6 ERCPICLEDPSNYS-----MALPCLHAFCYVCITRWIR-----QNPTCPLCKVPVE   51 (68)
T ss_dssp             CCCSSCCSCCCSCE-----EETTTTEEESTTHHHHHHH-----HSCSTTTTCCCCC
T ss_pred             CCCccCCcCccCCc-----EEeCCCCcCcHHHHHHHHH-----hCCcCCCCCcchH
Confidence            46999999996 43     4689999999999999999     4678999999875

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

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

Probab=99.25  E-value=2.1e-12  Score=102.44  Aligned_cols=51  Identities=31%  Similarity=0.741  Sum_probs=42.1

Q ss_pred             CCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            8 GKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         8 ~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ....|+||++.+..+     .+++|||+||..||..|+..    +...||+||..+....
T Consensus        22 ~~~~C~IC~~~~~~~-----~~~~CgH~fC~~Ci~~wl~~----~~~~CP~Cr~~i~~~~   72 (79)
T d1fbva4          22 TFQLCKICAENDKDV-----KIEPCGHLMCTSCLTSWQES----EGQGCPFCRCEIKGTE   72 (79)
T ss_dssp             CTTBCTTTSSSBCCE-----ECSSSCCEECHHHHHHHHHT----TCCSCTTTCCCCCCCC
T ss_pred             CCCCCccCCCcCCCe-----EEeCCCCeeeHHHHHHHHHH----CcCcCCCCCcCccCCc
Confidence            345799999999732     47899999999999999982    4578999999997654

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

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

Probab=99.19  E-value=2.3e-12  Score=95.52  Aligned_cols=48  Identities=17%  Similarity=0.355  Sum_probs=40.7

Q ss_pred             ccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292           10 TICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus        10 ltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      +.|+||++.|. |+     .+..|||+||..||.+|+.     .+..||+||.++...+
T Consensus         1 l~C~Ic~~~~~~Pv-----~~~~cGh~fc~~cI~~~l~-----~~~~CP~c~~~l~~~d   49 (56)
T d2baya1           1 MLCAISGKVPRRPV-----LSPKSRTIFEKSLLEQYVK-----DTGNDPITNEPLSIEE   49 (56)
T ss_dssp             CCCTTTCSCCSSEE-----EETTTTEEEEHHHHHHHHH-----HHSBCTTTCCBCCGGG
T ss_pred             CCCccCCchHHhcC-----ccCCCCCcccHHHHHHHHh-----hccCCCccCCcCCHHh
Confidence            57999999998 64     2346999999999999999     4678999999988654

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.18  E-value=4.3e-12  Score=100.59  Aligned_cols=50  Identities=14%  Similarity=0.237  Sum_probs=43.4

Q ss_pred             CCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            8 GKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         8 ~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      +++.||||++.|. |+      +++|||+||..||.+|+..    +...||.||.+++...
T Consensus         6 ~~l~CpIc~~l~~dPv------~~~cGhtfc~~ci~~~l~~----~~~~cP~c~~~l~~~~   56 (80)
T d2c2la2           6 DYLCGKISFELMREPC------ITPSGITYDRKDIEEHLQR----VGHFNPVTRSPLTQEQ   56 (80)
T ss_dssp             STTBCTTTCSBCSSEE------ECSSCCEEETTHHHHHHHH----TCSSCTTTCCCCCGGG
T ss_pred             ccccCcCcCchhhhhc------ccCCcCeecHHHHHHHHhc----CCccCCCccccccccc
Confidence            6789999999998 64      7899999999999999983    4578999999887554

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: E3 ubiquitin ligase PUB14
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.17  E-value=7.7e-12  Score=98.54  Aligned_cols=53  Identities=23%  Similarity=0.454  Sum_probs=45.0

Q ss_pred             CCCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            5 NKFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         5 ~~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ..-+++.||||++.|. |+      +++|||+||..||..|+..    +...||.|+.+++...
T Consensus         4 eiP~~l~CpIc~~~m~dPV------~~~cgh~fc~~ci~~~~~~----~~~~cP~~~~~l~~~~   57 (78)
T d1t1ha_           4 EFPEYFRCPISLELMKDPV------IVSTGQTYERSSIQKWLDA----GHKTCPKSQETLLHAG   57 (78)
T ss_dssp             CCSSSSSCTTTSCCCSSEE------EETTTEEEEHHHHHHHHTT----TCCBCTTTCCBCSSCC
T ss_pred             CCCccCCCcCcCchhhCce------EccCCCcchHHHHHHHHHH----CCCCCCcccccCCccc
Confidence            3447899999999998 64      7899999999999999982    4578999999987654

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

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

Probab=99.16  E-value=2.6e-12  Score=95.28  Aligned_cols=48  Identities=25%  Similarity=0.562  Sum_probs=40.3

Q ss_pred             CCCCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            6 KFGKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         6 ~~~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      .++.+.|+||++.|. |+      ++||||+||..||.+|        ...||+||.+++...
T Consensus         3 e~~~l~C~IC~~~~~~p~------~lpCgH~fC~~Ci~~~--------~~~CP~Cr~~~~~~~   51 (56)
T d1bora_           3 EFQFLRCQQCQAEAKCPK------LLPCLHTLCSGCLEAS--------GMQCPICQAPWPLGA   51 (56)
T ss_dssp             SCCCSSCSSSCSSCBCCS------CSTTSCCSBTTTCSSS--------SSSCSSCCSSSSCCS
T ss_pred             ccCCCCCcccCcccCCCE------EecCCCHHhHHHHHcC--------CCcCcCCCCcccCCC
Confidence            456789999999998 53      7899999999999765        468999999998654

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

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

Probab=99.13  E-value=2.1e-11  Score=102.56  Aligned_cols=59  Identities=27%  Similarity=0.514  Sum_probs=45.0

Q ss_pred             CCcccccccccccc-cc------------cCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCC
Q 012292            8 GKTICSICYEDLKP-IV------------EDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSS   66 (466)
Q Consensus         8 ~eltCpICLe~f~P-~~------------~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~   66 (466)
                      .+..|+||++.|.. ..            .....+++|||.||..||..|+......+..+||+||..+...
T Consensus        24 ~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T d1v87a_          24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             ccccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhccC
Confidence            34579999999862 11            1234678999999999999999965444567899999988655

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.11  E-value=4.8e-12  Score=103.89  Aligned_cols=48  Identities=27%  Similarity=0.630  Sum_probs=39.7

Q ss_pred             CCccccccccccc-ccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            8 GKTICSICYEDLK-PIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         8 ~eltCpICLe~f~-P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      ..++||||++.|. |+     .+++|||+||..||.+|+.       ..||.||.++...+
T Consensus        21 ~~l~C~IC~~~~~~pv-----~~~~CgH~fC~~Ci~~~~~-------~~CP~Cr~~~~~~~   69 (97)
T d1jm7b_          21 KLLRCSRCTNILREPV-----CLGGCEHIFCSNCVSDCIG-------TGCPVCYTPAWIQD   69 (97)
T ss_dssp             HTTSCSSSCSCCSSCB-----CCCSSSCCBCTTTGGGGTT-------TBCSSSCCBCSCSS
T ss_pred             hcCCCccCCchhhcCc-----eeCCCCCchhHHHHHHHHh-------ccccccCCcCchhh
Confidence            3579999999998 64     3468999999999999975       45999999887553

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

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

Probab=98.96  E-value=2.3e-10  Score=92.11  Aligned_cols=52  Identities=21%  Similarity=0.613  Sum_probs=40.8

Q ss_pred             Cccccccccccccccc-------------CcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccC
Q 012292            9 KTICSICYEDLKPIVE-------------DLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS   65 (466)
Q Consensus         9 eltCpICLe~f~P~~~-------------~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~   65 (466)
                      +-.|+||++.+.....             .....++|||.||..||.+|++     .+.+||+||..+..
T Consensus        21 ~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~-----~~~~CP~CR~~~~~   85 (88)
T d3dplr1          21 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLK-----TRQVCPLDNREWEF   85 (88)
T ss_dssp             SCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHT-----TCSBCSSSCSBCCE
T ss_pred             CCcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHH-----HCCcCCCCCCcccc
Confidence            4469999998862111             1346789999999999999999     56889999998763

>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=98.86  E-value=8e-10  Score=82.48  Aligned_cols=57  Identities=19%  Similarity=0.364  Sum_probs=40.3

Q ss_pred             CCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccC
Q 012292            6 KFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS   65 (466)
Q Consensus         6 ~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~   65 (466)
                      ..+...|+||++.+.......-....|+|.||..||.+|+...   ++.+||+||+++..
T Consensus         3 ded~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~---~~~~CP~Cr~~~~~   59 (60)
T d1vyxa_           3 DEDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTIS---RNTACQICGVVYNT   59 (60)
T ss_dssp             TCSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHH---TCSBCTTTCCBCCC
T ss_pred             CCCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhC---CCCCCcccCCeeec
Confidence            3456789999998872111111122346999999999999742   45789999998864

>d1wgma_ g.44.1.2 (A:) Ubiquitin conjugation factor E4A {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Ubiquitin conjugation factor E4A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.82  E-value=1.2e-09  Score=89.77  Aligned_cols=51  Identities=8%  Similarity=0.059  Sum_probs=42.7

Q ss_pred             CCCCccccccccccc-ccccCcceeecCC-CcccHHHHHHHHHhcCCCCCCCCcCcCccccCCC
Q 012292            6 KFGKTICSICYEDLK-PIVEDLQVISICG-HVFHELCLQQWFEYCSSSKKCTCPVCKQRCSSSN   67 (466)
Q Consensus         6 ~~~eltCpICLe~f~-P~~~~~~~llpCG-HsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~~~   67 (466)
                      .-+++.||||+++|. |+      +++|| |+||..||.+|+.     ....||+||.++....
T Consensus        19 ~P~~f~CPI~~~lm~dPV------~~~~~~~ty~r~~I~~~l~-----~~~~~P~~~~~l~~~~   71 (98)
T d1wgma_          19 ACDEFLDPIMSTLMCDPV------VLPSSRVTVDRSTIARHLL-----SDQTDPFNRSPLTMDQ   71 (98)
T ss_dssp             CCTTTBCTTTCSBCSSEE------ECTTTCCEEEHHHHHHHTT-----TSCBCTTTCSBCCTTT
T ss_pred             CcHHhCCcCchhHHHHHH------hcccccchhhHHHHHHHHH-----hcCCcccccccccchh
Confidence            345799999999999 65      77776 5899999999998     5678999999987654

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.36  E-value=9.7e-08  Score=76.86  Aligned_cols=53  Identities=26%  Similarity=0.612  Sum_probs=38.4

Q ss_pred             CCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCC---CCCCCCcCcCc
Q 012292            7 FGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSS---SKKCTCPVCKQ   61 (466)
Q Consensus         7 ~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~---~~s~~CP~CR~   61 (466)
                      .....|+||++.+..  .+.+.+++|||.||..|+..|+...-.   .....||.|+-
T Consensus         3 ~~~~~C~IC~~~~~~--~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           3 SGSSGCKLCLGEYPV--EQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             CSBCCCSSSCCCCBG--GGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCCCcCccCCCcccC--CceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            345689999999852  233456789999999999999984321   22457998754

>d2cs3a1 g.44.1.3 (A:8-87) Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: Protein c14orf4 (KIAA1865)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.44  E-value=0.12  Score=38.21  Aligned_cols=54  Identities=24%  Similarity=0.391  Sum_probs=36.6

Q ss_pred             CCCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCc
Q 012292            5 NKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVC   59 (466)
Q Consensus         5 ~~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~C   59 (466)
                      .....+.|.+|.+.+.++ ..+++-..=+|-||..|-...++....++-..||.=
T Consensus         4 ~~~~~l~CtlC~erLEdt-HFVQCPsv~~HkFCFpCsr~sik~q~~~~evyCPSG   57 (80)
T d2cs3a1           4 ANSGPLCCTICHERLEDT-HFVQCPSVPSHKFCFPCSRESIKAQGATGEVYCPSG   57 (80)
T ss_dssp             CSCCSCCCSSSCSCCSST-TSEECSSCSSCEECHHHHHHHHHHHHSSSCCCCTTS
T ss_pred             CCCCceeeeeehhhhcCC-ceEeCCCCcCCceeccccHHHHHhcCCCCcEECCCC
Confidence            344568999999999743 222222224799999999998886555555666643

>d1wila_ g.50.1.3 (A:) Hypothetical protein KIAA1045 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: variant PHD-like domain
domain: Hypothetical protein KIAA1045
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.42  E-value=0.11  Score=39.59  Aligned_cols=56  Identities=21%  Similarity=0.573  Sum_probs=36.3

Q ss_pred             CCCCCCCcccccccccccccccCcceeecCCCcccHHHHHHH--HH---------hcCCCCCCCCcCcCc
Q 012292            3 IENKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQW--FE---------YCSSSKKCTCPVCKQ   61 (466)
Q Consensus         3 ~~~~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~w--le---------~~~~~~s~~CP~CR~   61 (466)
                      .++...+..|+|| +.|.. +...+ .--|+-+||..|+.+.  +.         ........+|+.|-.
T Consensus         9 re~v~~D~mC~vC-~v~t~-~~l~p-CRvCtRv~H~~CL~r~gyl~~e~a~e~~e~A~T~~GWSC~~C~n   75 (89)
T d1wila_           9 REPVVNDEMCDVC-EVWTA-ESLFP-CRVCTRVFHDGCLRRMGYIQGDSAAEVTEMAHTETGWSCHYCDN   75 (89)
T ss_dssp             CCCCCCSCCCTTT-CCCCS-SCCSS-CSSSSSCCCHHHHHHHTSCCCCCCCSCSCCCSSSSSCCCTTTCC
T ss_pred             ccCCCcCcccccc-Ccccc-cceec-ceeecchhhHHHHHHhcccccHHHHHHHHhhcCCCCcchhhhcc
Confidence            4556778899999 77762 11122 2358999999999986  22         111234578999954

>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=88.82  E-value=0.38  Score=36.76  Aligned_cols=59  Identities=22%  Similarity=0.449  Sum_probs=40.6

Q ss_pred             CCCCCCCccccccccccc-ccccCcc-eeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCccccC
Q 012292            3 IENKFGKTICSICYEDLK-PIVEDLQ-VISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCSS   65 (466)
Q Consensus         3 ~~~~~~eltCpICLe~f~-P~~~~~~-~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~~   65 (466)
                      +-......+|.||-+.+- .+...++ ..-.|+--.|..|.+--..    .++..||.|+.++..
T Consensus        10 p~~~~~~q~CqiCGd~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErk----eG~q~CpqCkt~Ykr   70 (93)
T d1weoa_          10 PLKNLDGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERR----EGTQNCPQCKTRYKR   70 (93)
T ss_dssp             CCSCCSSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHH----TSCSSCTTTCCCCCC
T ss_pred             ChhhcccchhhhcccccccCCCCCEEEEecccCCccchHHHHHHHh----ccCccCcccCChhhh
Confidence            344566789999999987 2222222 1234777789999885433    378999999998864

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At5g26210
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=87.34  E-value=0.044  Score=39.68  Aligned_cols=59  Identities=20%  Similarity=0.386  Sum_probs=37.4

Q ss_pred             CCCCCcccccccccccccccCcceeecCCCcccHHHHHHHHHhcCCCCCCCCcCcCcccc
Q 012292            5 NKFGKTICSICYEDLKPIVEDLQVISICGHVFHELCLQQWFEYCSSSKKCTCPVCKQRCS   64 (466)
Q Consensus         5 ~~~~eltCpICLe~f~P~~~~~~~llpCGHsFC~~CL~~wle~~~~~~s~~CP~CR~~~~   64 (466)
                      +......|+||.....+. ...+.--.|+..||..|+..-...........||.|+....
T Consensus         2 ~~~~~~~C~~C~~~~~~~-~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~~~   60 (64)
T d1we9a_           2 SSGSSGQCGACGESYAAD-EFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKSG   60 (64)
T ss_dssp             CCSSCCCCSSSCCCCCSS-SCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTTTC
T ss_pred             cCCCCCcCcCcCCCCCCC-CCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCcCC
Confidence            445567999999877632 22233457999999999853211111124688999986544

>d1seta1 a.2.7.1 (A:1-110) Seryl-tRNA synthetase (SerRS) {Thermus thermophilus, strain hb27 [TaxId: 274]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: tRNA-binding arm
family: Seryl-tRNA synthetase (SerRS)
domain: Seryl-tRNA synthetase (SerRS)
species: Thermus thermophilus, strain hb27 [TaxId: 274]

Probab=83.32  E-value=2.5  Score=33.03  Aligned_cols=70  Identities=17%  Similarity=0.204  Sum_probs=48.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHH
Q 012292          210 DTIDVLRKSLVIRNKNYTELMAKCNLLGREKARFS-EKLEKAKEKINKLKTRVQELETAVELKDNEVLRAL  279 (466)
Q Consensus       210 e~~d~Lkk~l~~~~k~yeeL~~k~e~L~ree~~~~-~kLek~~~ei~~Lk~~v~eLqk~le~~~ne~l~~l  279 (466)
                      +.+-.|-.........+++|.++-+.+.++...+. ...+....+...|++++..|+..+...+.++...+
T Consensus        28 d~i~~ld~~rr~l~~~~e~l~~~rN~~sk~i~k~~~~~~~~l~~~~k~lk~~i~~le~~~~~~~~~l~~~l   98 (110)
T d1seta1          28 EALLALDREVQELKKRLQEVQTERNQVAKRVPKAPPEEKEALIARGKALGEEAKRLEEALREKEARLEALL   98 (110)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44444555555555677777777777776665444 55566778888999999999999988888765544