Citrus Sinensis ID: 040204

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------
Protein Sequence
IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHGSTLHSVRRFRGGMQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVFGWGSLWMPLLRFDL
Secondary Structure (PSIPRED)
ccccccccccccEEEEcccccccccEEEEEEEccccEEEEEEEccccEEEEccccHHHHHHHccccccccccccEEEEEEcHHccccEEEEcccccc
Secondary Structure Prediction (SSPRO)
HHHHHcccHHHEEEEEccEEcccccEHHHHccccccEEEEEEEccccEEEcccccEHHHHHHHHHHHHcccHHHEEEEEEccccccccccEHHHccc
Coil and Loop (DISEMBL)
IEDKEEILRDQQRFIFAGkrledgrtlvdynihgstlhsvrRFRGGMQIFVESSDTIDNVKAKIqdkkgtppdqqRQIFWFVFGwgslwmpllrfdl
Flexible Loop (DISEMBL)
IEDKEEILRDQQRFifagkrledgrtLVDYNIHgstlhsvrrfRGGMQIFVESSDTIDNVKAKIqdkkgtppdqqRQIFWFVFGWGSLWMPLLRFDL
Low Complexity Region (SEG)
IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHGSTLHSVRRFRGGMQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVFGWGSLWMPLLRFDL
Disordered region (IsUnstruct)
***********QRFIFAGKRLEDGRTLVDYNIHGSTLHSVRRFRGGMQIFVESSDTI******************RQIFWFVFGWGSLWMPLLRF**
Disordered Region (DISOPRED)
IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHGSTLHSVRRFRGGMQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVFGWGSLWMPLLRFD*
Disordered Region (DISEMBL)
IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHGSTLHSVRRFRGGMQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVFGWGSLWMPLLRFDL
Disordered Region (DISPRO)
IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHGSTLHSVRRFRGGMQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVFGWGSLWMPLL**DL
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHGSTLHSVRRFRGGMQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVFGWGSLWMPLLRFDL
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	97	2.2.26 [Sep-21-2011]
P69315	305	Polyubiquitin (Fragment)	N/A	no	0.824	0.262	0.688	5e-26
Q8H159	457	Polyubiquitin 10 OS=Arabi	yes	no	0.824	0.175	0.688	5e-26
P0CG85	457	Polyubiquitin OS=Nicotian	N/A	no	0.824	0.175	0.688	5e-26
P69309	305	Polyubiquitin OS=Avena fa	N/A	no	0.824	0.262	0.688	5e-26
P0CG84	377	Polyubiquitin (Fragment)	N/A	no	0.824	0.212	0.688	5e-26
P0CG83	171	Polyubiquitin (Fragment)	N/A	no	0.824	0.467	0.688	5e-26
Q58G87	381	Polyubiquitin 3 OS=Oryza	no	no	0.824	0.209	0.688	5e-26
P0CH32	382	Polyubiquitin 4 OS=Arabid	no	no	0.824	0.209	0.688	5e-26
Q1EC66	306	Polyubiquitin 3 OS=Arabid	no	no	0.824	0.261	0.688	5e-26
P0CH05	458	Polyubiquitin OS=Petrosel	N/A	no	0.824	0.174	0.688	5e-26

>sp|P69315|UBIQP_LINUS Polyubiquitin (Fragment) OS=Linum usitatissimum PE=3 SV=2

 Score =  116 bits (290), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 64/93 (68%), Positives = 67/93 (72%), Gaps = 13/93 (13%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct: 71  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 130

Query: 52  ----ESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
               ESSDTIDNVKAKIQDK+G PPDQQR IF 
Sbjct: 131 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA 163

Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.
Linum usitatissimum (taxid: 4006)

>sp|Q8H159|UBQ10_ARATH Polyubiquitin 10 OS=Arabidopsis thaliana GN=UBQ10 PE=1 SV=2

 Score =  116 bits (290), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 64/93 (68%), Positives = 67/93 (72%), Gaps = 13/93 (13%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 52  ----ESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
               ESSDTIDNVKAKIQDK+G PPDQQR IF 
Sbjct: 90  TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA 122

Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, and DNA-damage responses. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.

Arabidopsis thaliana (taxid: 3702)

>sp|P0CG85|UBI1P_NICSY Polyubiquitin OS=Nicotiana sylvestris GN=UBI11 PE=2 SV=1

 Score =  116 bits (290), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 64/93 (68%), Positives = 67/93 (72%), Gaps = 13/93 (13%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 52  ----ESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
               ESSDTIDNVKAKIQDK+G PPDQQR IF 
Sbjct: 90  TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA 122

Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-48-linked is involved in protein degradation via the proteasome. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.

Nicotiana sylvestris (taxid: 4096)

>sp|P69309|UBIQP_AVEFA Polyubiquitin OS=Avena fatua PE=2 SV=2

 Score =  116 bits (290), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 64/93 (68%), Positives = 67/93 (72%), Gaps = 13/93 (13%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 52  ----ESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
               ESSDTIDNVKAKIQDK+G PPDQQR IF 
Sbjct: 90  TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA 122

Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-48-linked is involved in protein degradation via the proteasome. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.

Avena fatua (taxid: 4499)

>sp|P0CG84|UBI4P_NICSY Polyubiquitin (Fragment) OS=Nicotiana sylvestris GN=UBI4 PE=2 SV=1

 Score =  116 bits (290), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 64/93 (68%), Positives = 67/93 (72%), Gaps = 13/93 (13%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct: 26  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 85

Query: 52  ----ESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
               ESSDTIDNVKAKIQDK+G PPDQQR IF 
Sbjct: 86  TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA 118

Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.

Nicotiana sylvestris (taxid: 4096)

>sp|P0CG83|UBIQP_HORVU Polyubiquitin (Fragment) OS=Hordeum vulgare PE=2 SV=1

 Score =  116 bits (290), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 64/93 (68%), Positives = 67/93 (72%), Gaps = 13/93 (13%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct: 48  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 107

Query: 52  ----ESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
               ESSDTIDNVKAKIQDK+G PPDQQR IF 
Sbjct: 108 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA 140

Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.

Hordeum vulgare (taxid: 4513)

>sp|Q58G87|UBQ3_ORYSJ Polyubiquitin 3 OS=Oryza sativa subsp. japonica GN=UBQ3 PE=2 SV=2

 Score =  116 bits (290), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 64/93 (68%), Positives = 67/93 (72%), Gaps = 13/93 (13%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 52  ----ESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
               ESSDTIDNVKAKIQDK+G PPDQQR IF 
Sbjct: 90  TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA 122

Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, and DNA-damage responses. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|P0CH32|UBQ4_ARATH Polyubiquitin 4 OS=Arabidopsis thaliana GN=UBQ4 PE=1 SV=1

 Score =  116 bits (290), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 64/93 (68%), Positives = 67/93 (72%), Gaps = 13/93 (13%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 52  ----ESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
               ESSDTIDNVKAKIQDK+G PPDQQR IF 
Sbjct: 90  TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA 122

Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, and DNA-damage responses. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.

Arabidopsis thaliana (taxid: 3702)

>sp|Q1EC66|UBQ3_ARATH Polyubiquitin 3 OS=Arabidopsis thaliana GN=UBQ3 PE=1 SV=1

 Score =  116 bits (290), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 64/93 (68%), Positives = 67/93 (72%), Gaps = 13/93 (13%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 52  ----ESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
               ESSDTIDNVKAKIQDK+G PPDQQR IF 
Sbjct: 90  TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA 122

Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, and DNA-damage responses. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.

Arabidopsis thaliana (taxid: 3702)

>sp|P0CH05|UBI2P_PETCR Polyubiquitin OS=Petroselinum crispum GN=PCUBI4-2 PE=3 SV=1

 Score =  116 bits (290), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 64/93 (68%), Positives = 67/93 (72%), Gaps = 13/93 (13%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 52  ----ESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
               ESSDTIDNVKAKIQDK+G PPDQQR IF 
Sbjct: 90  TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA 122

Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-48-linked is involved in protein degradation via the proteasome. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.

Petroselinum crispum (taxid: 4043)

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	97
6118549	381	ubiquitin precursor [Hevea brasiliensis]	0.958	0.244	0.616	2e-25
443922596	681	polyubiquitin [Rhizoctonia solani AG-1 I	0.814	0.116	0.695	2e-25
37542506	154	polyubiquitin, partial [Prunus avium]	0.824	0.519	0.698	5e-25
61889379	153	polyubiquitin [Capsicum chinense]	0.824	0.522	0.698	8e-25
297805150	537	polyubiquitin [Arabidopsis lyrata subsp.	0.824	0.148	0.688	9e-25
324539232	148	Polyubiquitin-C, partial [Ascaris suum]	0.958	0.628	0.622	1e-24
3789942	381	polyubiquitin [Saccharum hybrid cultivar	0.824	0.209	0.688	1e-24
567767	1054	p125 protein, partial [Bovine viral diar	0.814	0.074	0.673	1e-24
357498827	245	Ubiquitin-like protein [Medicago truncat	0.824	0.326	0.688	1e-24
297808451	383	predicted protein [Arabidopsis lyrata su	0.824	0.208	0.688	1e-24

>gi|6118549|gb|AAF04147.1| ubiquitin precursor [Hevea brasiliensis]

 Score =  119 bits (299), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 69/112 (61%), Positives = 76/112 (67%), Gaps = 19/112 (16%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
           I+DKE I  DQQRFIFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct: 106 IQDKEGIPPDQQRFIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 165

Query: 52  ----ESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVFGWGSLWM--PLLRFDL 97
               ESSDTIDNVKAKIQDK+G PPDQQR     +F   SL M  PL  +++
Sbjct: 166 TLEVESSDTIDNVKAKIQDKEGIPPDQQR----LIFAGSSLRMVAPLADYNI 213

Source: Hevea brasiliensis

Species: Hevea brasiliensis

Genus: Hevea

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|443922596|gb|ELU42015.1| polyubiquitin [Rhizoctonia solani AG-1 IA]

 Score =  119 bits (298), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 64/92 (69%), Positives = 67/92 (72%), Gaps = 13/92 (14%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct: 482 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 541

Query: 52  ----ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
               ESSDTIDNVKAKIQDK+G PPDQQR IF
Sbjct: 542 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF 573

Source: Rhizoctonia solani AG-1 IA

Species: Rhizoctonia solani

Genus: Rhizoctonia

Family: Ceratobasidiaceae

Order: Cantharellales

Class: Agaricomycetes

Phylum: Basidiomycota

Superkingdom: Eukaryota

>gi|37542506|gb|AAL25813.1| polyubiquitin, partial [Prunus avium]

 Score =  118 bits (295), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 65/93 (69%), Positives = 68/93 (73%), Gaps = 13/93 (13%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct: 31  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 90

Query: 52  ----ESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
               ESSDTIDNVKAKIQDK+GTPPDQQR IF 
Sbjct: 91  TLEVESSDTIDNVKAKIQDKEGTPPDQQRLIFA 123

Source: Prunus avium

Species: Prunus avium

Genus: Prunus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|61889379|emb|CAI51312.2| polyubiquitin [Capsicum chinense]

 Score =  117 bits (293), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 65/93 (69%), Positives = 68/93 (73%), Gaps = 13/93 (13%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V RFRGGMQIFV        
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRFRGGMQIFVKTLTGKTI 89

Query: 52  ----ESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
               ESSDTIDNVKAKIQDK+G PPDQQR IF 
Sbjct: 90  TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA 122

Source: Capsicum chinense

Species: Capsicum chinense

Genus: Capsicum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297805150|ref|XP_002870459.1| polyubiquitin [Arabidopsis lyrata subsp. lyrata] gi|297316295|gb|EFH46718.1| polyubiquitin [Arabidopsis lyrata subsp. lyrata]

 Score =  117 bits (293), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 64/93 (68%), Positives = 67/93 (72%), Gaps = 13/93 (13%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIF--------- 50
           IEDKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIF         
Sbjct: 185 IEDKEGIPTDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 244

Query: 51  ---VESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
              VESSDTIDN+KAKIQDK+G PPDQQR IF 
Sbjct: 245 TLEVESSDTIDNLKAKIQDKEGIPPDQQRLIFA 277

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|324539232|gb|ADY49558.1| Polyubiquitin-C, partial [Ascaris suum]

 Score =  117 bits (293), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 66/106 (62%), Positives = 74/106 (69%), Gaps = 13/106 (12%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
           I+DKE I  DQQR IFAGK+LEDGRTL+DYNI   STLH V R RGGMQIFV        
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLLDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 52  ----ESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVFGWGSLWMPLL 93
               ESSDTI+NVKAKIQDK+G PPDQQR IF  +F   +   P+L
Sbjct: 90  TLEVESSDTIENVKAKIQDKEGIPPDQQRLIFAGLFPRITSVFPVL 135

Source: Ascaris suum

Species: Ascaris suum

Genus: Ascaris

Family: Ascarididae

Order: Ascaridida

Class: Chromadorea

Phylum: Nematoda

Superkingdom: Eukaryota

>gi|3789942|gb|AAC67552.1| polyubiquitin [Saccharum hybrid cultivar H32-8560]

 Score =  117 bits (292), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 64/93 (68%), Positives = 67/93 (72%), Gaps = 13/93 (13%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 52  ----ESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
               ESSDTIDNVKAKIQDK+G PPDQQR IF 
Sbjct: 90  TLEVESSDTIDNVKAKIQDKEGIPPDQQRXIFA 122

Source: Saccharum hybrid cultivar H32-8560

Species: Saccharum hybrid cultivar

Genus: Saccharum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|567767|gb|AAA53067.1| p125 protein, partial [Bovine viral diarrhea virus 1]

 Score =  117 bits (292), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 62/92 (67%), Positives = 66/92 (71%), Gaps = 13/92 (14%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIF--------- 50
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIF         
Sbjct: 376 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 435

Query: 51  ---VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
              VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 436 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF 467

Source: Bovine viral diarrhea virus 1

Species: Bovine viral diarrhea virus 1

Genus: Pestivirus

Family: Flaviviridae

Superkingdom: Viruses

>gi|357498827|ref|XP_003619702.1| Ubiquitin-like protein [Medicago truncatula] gi|355494717|gb|AES75920.1| Ubiquitin-like protein [Medicago truncatula]

 Score =  116 bits (291), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 64/93 (68%), Positives = 67/93 (72%), Gaps = 13/93 (13%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct: 81  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 140

Query: 52  ----ESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
               ESSDTIDNVKAKIQDK+G PPDQQR IF 
Sbjct: 141 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA 173

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297808451|ref|XP_002872109.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297317946|gb|EFH48368.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  116 bits (291), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 64/93 (68%), Positives = 67/93 (72%), Gaps = 13/93 (13%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct: 259 IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 318

Query: 52  ----ESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
               ESSDTIDNVKAKIQDK+G PPDQQR IF 
Sbjct: 319 TLEVESSDTIDNVKAKIQDKEGVPPDQQRLIFA 351

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

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	97
TAIR|locus:2180434	382	UBQ4 "AT5G20620" [Arabidopsis	0.814	0.206	0.695	4.2e-24
TAIR|locus:2143548	306	UBQ3 "AT5G03240" [Arabidopsis	0.814	0.258	0.695	4.2e-24
TAIR|locus:2140200	305	UBQ14 "AT4G02890" [Arabidopsis	0.814	0.259	0.695	4.2e-24
TAIR|locus:2206310	319	UBQ13 "AT1G65350" [Arabidopsis	0.814	0.247	0.695	4.2e-24
TAIR|locus:2138386	229	UBQ11 "AT4G05050" [Arabidopsis	0.814	0.344	0.695	4.2e-24
TAIR|locus:2115663	457	UBQ10 "AT4G05320" [Arabidopsis	0.814	0.172	0.695	1e-23
POMBASE|SPBC337.08c	382	ubi4 "ubiquitin" [Schizosaccha	0.814	0.206	0.684	1.4e-23
SGD|S000003962	381	UBI4 "Ubiquitin" [Saccharomyce	0.814	0.207	0.684	1.4e-23
UNIPROTKB|G4MY63	305	MGG_01282 "Polyubiquitin" [Mag	0.814	0.259	0.684	1.4e-23
ASPGD|ASPL0000049163	305	ubi4 [Emericella nidulans (tax	0.814	0.259	0.684	1.4e-23

TAIR|locus:2180434 UBQ4 "AT5G20620" [Arabidopsis thaliana (taxid:3702)]

 Score = 276 (102.2 bits), Expect = 4.2e-24, P = 4.2e-24
 Identities = 64/92 (69%), Positives = 67/92 (72%)

Query:     1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
             I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct:   258 IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 317

Query:    52 ----ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
                 ESSDTIDNVKAKIQDK+G PPDQQR IF
Sbjct:   318 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF 349

GO:0006464 "cellular protein modification process" evidence=ISS

GO:0042787 "protein ubiquitination involved in ubiquitin-dependent protein catabolic process" evidence=ISS

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

TAIR|locus:2143548 UBQ3 "AT5G03240" [Arabidopsis thaliana (taxid:3702)]

 Score = 276 (102.2 bits), Expect = 4.2e-24, P = 4.2e-24
 Identities = 64/92 (69%), Positives = 67/92 (72%)

Query:     1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
             I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct:   182 IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 241

Query:    52 ----ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
                 ESSDTIDNVKAKIQDK+G PPDQQR IF
Sbjct:   242 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF 273

GO:0005622 "intracellular" evidence=TAS

GO:0006464 "cellular protein modification process" evidence=ISS

GO:0010224 "response to UV-B" evidence=IEP

GO:0005773 "vacuole" evidence=IDA

GO:0006623 "protein targeting to vacuole" evidence=RCA

GO:0016192 "vesicle-mediated transport" evidence=RCA

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

TAIR|locus:2140200 UBQ14 "AT4G02890" [Arabidopsis thaliana (taxid:3702)]

 Score = 276 (102.2 bits), Expect = 4.2e-24, P = 4.2e-24
 Identities = 64/92 (69%), Positives = 67/92 (72%)

Query:     1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
             I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct:   182 IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 241

Query:    52 ----ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
                 ESSDTIDNVKAKIQDK+G PPDQQR IF
Sbjct:   242 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF 273

GO:0006464 "cellular protein modification process" evidence=ISS

GO:0005773 "vacuole" evidence=IDA

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

TAIR|locus:2206310 UBQ13 "AT1G65350" [Arabidopsis thaliana (taxid:3702)]

 Score = 276 (102.2 bits), Expect = 4.2e-24, P = 4.2e-24
 Identities = 64/92 (69%), Positives = 67/92 (72%)

Query:     1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
             I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct:    30 IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query:    52 ----ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
                 ESSDTIDNVKAKIQDK+G PPDQQR IF
Sbjct:    90 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF 121

GO:0005622 "intracellular" evidence=TAS

GO:0006464 "cellular protein modification process" evidence=ISS

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

TAIR|locus:2138386 UBQ11 "AT4G05050" [Arabidopsis thaliana (taxid:3702)]

 Score = 276 (102.2 bits), Expect = 4.2e-24, P = 4.2e-24
 Identities = 64/92 (69%), Positives = 67/92 (72%)

Query:     1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
             I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct:   106 IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 165

Query:    52 ----ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
                 ESSDTIDNVKAKIQDK+G PPDQQR IF
Sbjct:   166 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF 197

GO:0005622 "intracellular" evidence=TAS

GO:0006464 "cellular protein modification process" evidence=ISS

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

TAIR|locus:2115663 UBQ10 "AT4G05320" [Arabidopsis thaliana (taxid:3702)]

 Score = 276 (102.2 bits), Expect = 1.0e-23, P = 1.0e-23
 Identities = 64/92 (69%), Positives = 67/92 (72%)

Query:     1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
             I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct:   334 IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 393

Query:    52 ----ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
                 ESSDTIDNVKAKIQDK+G PPDQQR IF
Sbjct:   394 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF 425

GO:0006464 "cellular protein modification process" evidence=ISS;TAS

GO:0009751 "response to salicylic acid stimulus" evidence=IEP

GO:0007568 "aging" evidence=IEP

POMBASE|SPBC337.08c ubi4 "ubiquitin" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 271 (100.5 bits), Expect = 1.4e-23, P = 1.4e-23
 Identities = 63/92 (68%), Positives = 67/92 (72%)

Query:     1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
             I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct:   258 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 317

Query:    52 ----ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
                 ESSDTIDNVK+KIQDK+G PPDQQR IF
Sbjct:   318 TLEVESSDTIDNVKSKIQDKEGIPPDQQRLIF 349

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0007126 "meiosis" evidence=IMP

GO:0016567 "protein ubiquitination" evidence=NAS

GO:0016579 "protein deubiquitination" evidence=NAS

GO:0031386 "protein tag" evidence=NAS

SGD|S000003962 UBI4 "Ubiquitin" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 271 (100.5 bits), Expect = 1.4e-23, P = 1.4e-23
 Identities = 63/92 (68%), Positives = 67/92 (72%)

Query:     1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
             I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct:   258 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 317

Query:    52 ----ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
                 ESSDTIDNVK+KIQDK+G PPDQQR IF
Sbjct:   318 TLEVESSDTIDNVKSKIQDKEGIPPDQQRLIF 349

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA;IC

GO:0006281 "DNA repair" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0016567 "protein ubiquitination" evidence=IMP

GO:0031386 "protein tag" evidence=ISS

GO:0006950 "response to stress" evidence=TAS

GO:0006513 "protein monoubiquitination" evidence=TAS

GO:0000209 "protein polyubiquitination" evidence=TAS

GO:0030437 "ascospore formation" evidence=TAS

GO:0016579 "protein deubiquitination" evidence=TAS

GO:0043008 "ATP-dependent protein binding" evidence=TAS

UNIPROTKB|G4MY63 MGG_01282 "Polyubiquitin" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 271 (100.5 bits), Expect = 1.4e-23, P = 1.4e-23
 Identities = 63/92 (68%), Positives = 67/92 (72%)

Query:     1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
             I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct:   182 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 241

Query:    52 ----ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
                 ESSDTIDNVK+KIQDK+G PPDQQR IF
Sbjct:   242 TLEVESSDTIDNVKSKIQDKEGIPPDQQRLIF 273

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0043581 "mycelium development" evidence=IEP

ASPGD|ASPL0000049163 ubi4 [Emericella nidulans (taxid:162425)]

 Score = 271 (100.5 bits), Expect = 1.4e-23, P = 1.4e-23
 Identities = 63/92 (68%), Positives = 67/92 (72%)

Query:     1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
             I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct:   106 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 165

Query:    52 ----ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
                 ESSDTIDNVK+KIQDK+G PPDQQR IF
Sbjct:   166 TLEVESSDTIDNVKSKIQDKEGIPPDQQRLIF 197

GO:0031386 "protein tag" evidence=ISA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

---

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

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: scaffold_703472.1 annotation not avaliable (537 aa) (Arabidopsis lyrata)

Predicted Functional Partners:

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

---

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	97
cd01803	76	cd01803, Ubiquitin, Ubiquitin	8e-18
pfam00240	69	pfam00240, ubiquitin, Ubiquitin family	9e-13
cd01803	76	cd01803, Ubiquitin, Ubiquitin	1e-12
smart00213	72	smart00213, UBQ, Ubiquitin homologues	2e-10
cd01806	76	cd01806, Nedd8, Nebb8-like ubiquitin protein	5e-10
cd01769	69	cd01769, UBL, Ubiquitin-like domain of UBL	1e-08
pfam00240	69	pfam00240, ubiquitin, Ubiquitin family	5e-07
cd01809	72	cd01809, Scythe_N, Ubiquitin-like domain of Scythe	8e-07
PTZ00044	76	PTZ00044, PTZ00044, ubiquitin; Provisional	1e-06
cd01769	69	cd01769, UBL, Ubiquitin-like domain of UBL	2e-06
smart00213	72	smart00213, UBQ, Ubiquitin homologues	4e-06
cd01806	76	cd01806, Nedd8, Nebb8-like ubiquitin protein	3e-05
cd01805	77	cd01805, RAD23_N, Ubiquitin-like domain of RAD23	5e-04
cd01808	71	cd01808, hPLIC_N, Ubiquitin-like domain of hPLIC-1	0.002
cd01805	77	cd01805, RAD23_N, Ubiquitin-like domain of RAD23	0.003

>gnl|CDD|176398 cd01803, Ubiquitin, Ubiquitin

 Score = 70.7 bits (173), Expect = 8e-18
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76

Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains). Length = 76

>gnl|CDD|215813 pfam00240, ubiquitin, Ubiquitin family

 Score = 57.2 bits (139), Expect = 9e-13
 Identities = 29/45 (64%), Positives = 31/45 (68%), Gaps = 1/45 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFR 44
          IEDKE I  DQQR IF+GK LED  TL +Y I  GSTLH V R R
Sbjct: 25 IEDKEGIPVDQQRLIFSGKVLEDDTTLSEYGIQDGSTLHLVLRLR 69

This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites. Length = 69

>gnl|CDD|176398 cd01803, Ubiquitin, Ubiquitin

 Score = 57.2 bits (138), Expect = 1e-12
 Identities = 28/45 (62%), Positives = 30/45 (66%), Gaps = 12/45 (26%)

Query: 47 MQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          MQIFV            E SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF 45

Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains). Length = 76

>gnl|CDD|214563 smart00213, UBQ, Ubiquitin homologues

 Score = 51.9 bits (125), Expect = 2e-10
 Identities = 23/43 (53%), Positives = 27/43 (62%), Gaps = 1/43 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR 42
          I +   I  +QQR I+ GK LED RTL DY I  GST+H V R
Sbjct: 30 IAELTGIPPEQQRLIYKGKVLEDDRTLADYGIQDGSTIHLVLR 72

Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression. Length = 72

>gnl|CDD|176401 cd01806, Nedd8, Nebb8-like ubiquitin protein

 Score = 50.9 bits (122), Expect = 5e-10
 Identities = 22/47 (46%), Positives = 30/47 (63%), Gaps = 1/47 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-HGSTLHSVRRFRGG 46
          +E+KE I   QQR I++GK++ D +T  DY +  GS LH V   RGG
Sbjct: 30 VEEKEGIPPQQQRLIYSGKQMNDDKTAADYKLEGGSVLHLVLALRGG 76

Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Length = 76

>gnl|CDD|176364 cd01769, UBL, Ubiquitin-like domain of UBL

 Score = 46.9 bits (112), Expect = 1e-08
 Identities = 24/43 (55%), Positives = 29/43 (67%), Gaps = 1/43 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR 42
          I  KE +  +QQR I+AGK L+D +TL DY I  GSTLH V R
Sbjct: 27 IAAKEGVPPEQQRLIYAGKILKDDKTLSDYGIQDGSTLHLVLR 69

UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways. Length = 69

>gnl|CDD|215813 pfam00240, ubiquitin, Ubiquitin family

 Score = 43.0 bits (102), Expect = 5e-07
 Identities = 17/33 (51%), Positives = 24/33 (72%)

Query: 47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          + + V+ SDT+  +K KI+DK+G P DQQR IF
Sbjct: 8  ITLEVDPSDTVSELKEKIEDKEGIPVDQQRLIF 40

This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites. Length = 69

>gnl|CDD|176404 cd01809, Scythe_N, Ubiquitin-like domain of Scythe protein

 Score = 42.2 bits (100), Expect = 8e-07
 Identities = 17/43 (39%), Positives = 28/43 (65%), Gaps = 1/43 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-HGSTLHSVRR 42
          I ++  I  +QQR I++G+ L+D  TL +Y +  G T+H V+R
Sbjct: 30 IAEEVGIPVEQQRLIYSGRVLKDDETLSEYKVEDGHTIHLVKR 72

Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules. Length = 72

>gnl|CDD|185411 PTZ00044, PTZ00044, ubiquitin; Provisional

 Score = 41.7 bits (98), Expect = 1e-06
 Identities = 20/47 (42%), Positives = 30/47 (63%), Gaps = 1/47 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
          +++KE I   Q R I++GK++ D   L DY +  GST+H V + RGG
Sbjct: 30 LQEKEGIDVKQIRLIYSGKQMSDDLKLSDYKVVPGSTIHMVLQLRGG 76

Length = 76

>gnl|CDD|176364 cd01769, UBL, Ubiquitin-like domain of UBL

 Score = 41.1 bits (97), Expect = 2e-06
 Identities = 15/30 (50%), Positives = 20/30 (66%)

Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
          V   DT+  +KAKI  K+G PP+QQR I+ 
Sbjct: 14 VSPDDTVAELKAKIAAKEGVPPEQQRLIYA 43

UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways. Length = 69

>gnl|CDD|214563 smart00213, UBQ, Ubiquitin homologues

 Score = 40.7 bits (96), Expect = 4e-06
 Identities = 14/33 (42%), Positives = 22/33 (66%)

Query: 47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          + + V+ SDT+  +K KI +  G PP+QQR I+
Sbjct: 13 ITLEVKPSDTVSELKEKIAELTGIPPEQQRLIY 45

Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression. Length = 72

>gnl|CDD|176401 cd01806, Nedd8, Nebb8-like ubiquitin protein

 Score = 38.2 bits (89), Expect = 3e-05
 Identities = 12/33 (36%), Positives = 25/33 (75%)

Query: 47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          ++I +E +D ++ +K ++++K+G PP QQR I+
Sbjct: 13 IEIDIEPTDKVERIKERVEEKEGIPPQQQRLIY 45

Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Length = 76

>gnl|CDD|176400 cd01805, RAD23_N, Ubiquitin-like domain of RAD23

 Score = 35.0 bits (81), Expect = 5e-04
 Identities = 11/23 (47%), Positives = 17/23 (73%)

Query: 10 DQQRFIFAGKRLEDGRTLVDYNI 32
          +QQ+ I++GK L+D  TL +Y I
Sbjct: 41 EQQKLIYSGKILKDDTTLEEYKI 63

RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL). Length = 77

>gnl|CDD|176403 cd01808, hPLIC_N, Ubiquitin-like domain of hPLIC-1 and hPLIC2

 Score = 33.6 bits (77), Expect = 0.002
 Identities = 18/44 (40%), Positives = 24/44 (54%), Gaps = 7/44 (15%)

Query: 4  KEEILR------DQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSV 40
          KE + +      +Q   IFAGK L+D  TL  +NI  G T+H V
Sbjct: 26 KEAVSKKFKANQEQLVLIFAGKILKDTDTLTQHNIKDGLTVHLV 69

hPLIC-1 and hPLIC-2 (human homologs of the yeast ubiquitin-like Dsk2 protein) are type2 UBL's (ubiquitin-like) proteins that are thought to serve as adaptors that link the ubiquitination machinery to the proteasome. The hPLIC's have an N-terminal UBL domain that binds the S5a subunit of the proteasome and a C-terminal UBA (ubiquitin-associated) domain that binds a ubiquitylated protein. Length = 71

>gnl|CDD|176400 cd01805, RAD23_N, Ubiquitin-like domain of RAD23

 Score = 33.1 bits (76), Expect = 0.003
 Identities = 14/34 (41%), Positives = 23/34 (67%), Gaps = 2/34 (5%)

Query: 48 QIFVESSDTIDNVKAKIQDKKG--TPPDQQRQIF 79
           I V+  DT+  +K KI+++KG   PP+QQ+ I+
Sbjct: 14 PIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIY 47

RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL). Length = 77

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	97
cd01793	74	Fubi Fubi ubiquitin-like protein. Fubi is a ubiqui	99.48
KOG0004	156	consensus Ubiquitin/40S ribosomal protein S27a fus	99.42
KOG0005	70	consensus Ubiquitin-like protein [Cell cycle contr	99.39
cd01793	74	Fubi Fubi ubiquitin-like protein. Fubi is a ubiqui	99.38
cd01807	74	GDX_N ubiquitin-like domain of GDX. GDX contains a	99.37
cd01802	103	AN1_N ubiquitin-like domain of AN1. AN1 (also know	99.36
cd01810	74	ISG15_repeat2 ISG15 ubiquitin-like protein, second	99.35
KOG0003	128	consensus Ubiquitin/60s ribosomal protein L40 fusi	99.34
cd01802	103	AN1_N ubiquitin-like domain of AN1. AN1 (also know	99.34
cd01797	78	NIRF_N amino-terminal ubiquitin-like domain of Np9	99.33
cd01794	70	DC_UbP_C dendritic cell derived ubiquitin-like pro	99.31
cd01807	74	GDX_N ubiquitin-like domain of GDX. GDX contains a	99.3
PTZ00044	76	ubiquitin; Provisional	99.3
cd01794	70	DC_UbP_C dendritic cell derived ubiquitin-like pro	99.3
cd01798	70	parkin_N amino-terminal ubiquitin-like of parkin p	99.28
cd01815	75	BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC	99.26
cd01806	76	Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also kn	99.25
cd01800	76	SF3a120_C Ubiquitin-like domain of Mammalian splic	99.24
PTZ00044	76	ubiquitin; Provisional	99.23
cd01791	73	Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also know	99.23
cd01803	76	Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40	99.22
cd01810	74	ISG15_repeat2 ISG15 ubiquitin-like protein, second	99.21
KOG0003	128	consensus Ubiquitin/60s ribosomal protein L40 fusi	99.2
cd01798	70	parkin_N amino-terminal ubiquitin-like of parkin p	99.19
cd01797	78	NIRF_N amino-terminal ubiquitin-like domain of Np9	99.18
KOG0005	70	consensus Ubiquitin-like protein [Cell cycle contr	99.17
PF00240	69	ubiquitin: Ubiquitin family; InterPro: IPR000626 U	99.17
cd01808	71	hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC	99.16
cd01796	71	DDI1_N DNA damage inducible protein 1 ubiquitin-li	99.14
cd01804	78	midnolin_N Ubiquitin-like domain of midnolin. midn	99.14
cd01791	73	Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also know	99.13
cd01790	79	Herp_N Homocysteine-responsive endoplasmic reticul	99.11
cd01803	76	Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40	99.09
cd01805	77	RAD23_N Ubiquitin-like domain of RAD23. RAD23 belo	99.09
cd01809	72	Scythe_N Ubiquitin-like domain of Scythe protein.	99.09
cd01805	77	RAD23_N Ubiquitin-like domain of RAD23. RAD23 belo	99.08
cd01806	76	Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also kn	99.08
cd01796	71	DDI1_N DNA damage inducible protein 1 ubiquitin-li	99.08
cd01808	71	hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC	99.06
cd01763	87	Sumo Small ubiquitin-related modifier (SUMO). Smal	99.05
cd01804	78	midnolin_N Ubiquitin-like domain of midnolin. midn	99.05
cd01809	72	Scythe_N Ubiquitin-like domain of Scythe protein.	99.03
PF00240	69	ubiquitin: Ubiquitin family; InterPro: IPR000626 U	99.02
cd01813	74	UBP_N UBP ubiquitin processing protease. The UBP (	99.01
KOG0004	156	consensus Ubiquitin/40S ribosomal protein S27a fus	98.99
cd01792	80	ISG15_repeat1 ISG15 ubiquitin-like protein, first	98.99
cd01812	71	BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-ter	98.98
cd01814	113	NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and AT	98.97
cd01800	76	SF3a120_C Ubiquitin-like domain of Mammalian splic	98.97
cd01814	113	NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and AT	98.96
cd01792	80	ISG15_repeat1 ISG15 ubiquitin-like protein, first	98.96
cd01799	75	Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HO	98.93
smart00213	64	UBQ Ubiquitin homologues. Ubiquitin-mediated prote	98.92
cd01812	71	BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-ter	98.92
cd01815	75	BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC	98.88
cd01799	75	Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HO	98.77
cd01790	79	Herp_N Homocysteine-responsive endoplasmic reticul	98.75
cd01813	74	UBP_N UBP ubiquitin processing protease. The UBP (	98.75
cd01763	87	Sumo Small ubiquitin-related modifier (SUMO). Smal	98.72
cd01795	107	USP48_C USP ubiquitin-specific protease. The USP (	98.71
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	98.66
cd01795	107	USP48_C USP ubiquitin-specific protease. The USP (	98.59
smart00213	64	UBQ Ubiquitin homologues. Ubiquitin-mediated prote	98.57
KOG0010	493	consensus Ubiquitin-like protein [Posttranslationa	98.54
cd01769	69	UBL Ubiquitin-like domain of UBL. UBLs function by	98.45
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	98.44
KOG0001	75	consensus Ubiquitin and ubiquitin-like proteins [P	98.42
cd01769	69	UBL Ubiquitin-like domain of UBL. UBLs function by	98.32
KOG0010	493	consensus Ubiquitin-like protein [Posttranslationa	98.28
PF11976	72	Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; Inter	98.27
KOG0011	340	consensus Nucleotide excision repair factor NEF2,	98.2
cd01789	84	Alp11_N Ubiquitin-like domain of Alp11 tubulin-fol	97.99
PF11976	72	Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; Inter	97.96
cd01789	84	Alp11_N Ubiquitin-like domain of Alp11 tubulin-fol	97.84
KOG0011	340	consensus Nucleotide excision repair factor NEF2,	97.8
PF13881	111	Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB	97.7
PF14560	87	Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2K	97.69
KOG4248	1143	consensus Ubiquitin-like protein, regulator of apo	97.65
PF11543	80	UN_NPL4: Nuclear pore localisation protein NPL4; I	97.54
cd01788	119	ElonginB Ubiquitin-like domain of Elongin B. Elong	97.53
KOG0001	75	consensus Ubiquitin and ubiquitin-like proteins [P	97.49
PLN02560	308	enoyl-CoA reductase	97.32
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	97.27
PF13881	111	Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB	97.25
cd01811	80	OASL_repeat1 2'-5' oligoadenylate synthetase-like	97.23
PF14560	87	Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2K	97.18
cd01801	77	Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-	97.12
cd00196	69	UBQ Ubiquitin-like proteins. Ubiquitin homologs; I	97.1
cd01788	119	ElonginB Ubiquitin-like domain of Elongin B. Elong	97.1
PF10302	97	DUF2407: DUF2407 ubiquitin-like domain; InterPro:	96.96
KOG4248	1143	consensus Ubiquitin-like protein, regulator of apo	96.88
cd01811	80	OASL_repeat1 2'-5' oligoadenylate synthetase-like	96.85
cd00196	69	UBQ Ubiquitin-like proteins. Ubiquitin homologs; I	96.58
PLN02560	308	enoyl-CoA reductase	96.4
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	96.22
KOG1769	99	consensus Ubiquitin-like proteins [Posttranslation	95.81
KOG1872	473	consensus Ubiquitin-specific protease [Posttransla	95.79
cd01801	77	Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-	94.97
KOG4495	110	consensus RNA polymerase II transcription elongati	94.95
KOG1872	473	consensus Ubiquitin-specific protease [Posttransla	93.8
PF11543	80	UN_NPL4: Nuclear pore localisation protein NPL4; I	92.01
KOG3493	73	consensus Ubiquitin-like protein [Posttranslationa	91.28
PF08817	79	YukD: WXG100 protein secretion system (Wss), prote	91.28
KOG4250	732	consensus TANK binding protein kinase TBK1 [Signal	89.8
cd06406	80	PB1_P67 A PB1 domain is present in p67 proteins wh	89.75
smart00455	70	RBD Raf-like Ras-binding domain.	89.61
KOG0013	231	consensus Uncharacterized conserved protein [Funct	89.37
PF11470	65	TUG-UBL1: GLUT4 regulating protein TUG; InterPro:	89.31
PF11470	65	TUG-UBL1: GLUT4 regulating protein TUG; InterPro:	86.77
PF00564	84	PB1: PB1 domain; InterPro: IPR000270 The Phox and	86.17
cd01760	72	RBD Ubiquitin-like domain of RBD-like S/T kinases.	85.36
KOG0013	231	consensus Uncharacterized conserved protein [Funct	84.94
KOG4583	391	consensus Membrane-associated ER protein involved	84.51
smart00166	80	UBX Domain present in ubiquitin-regulatory protein	84.12
COG5227	103	SMT3 Ubiquitin-like protein (sentrin) [Posttransla	83.99
PF11620	88	GABP-alpha: GA-binding protein alpha chain; InterP	83.79
PF13019	162	Telomere_Sde2: Telomere stability and silencing	82.92
COG0299	200	PurN Folate-dependent phosphoribosylglycinamide fo	81.86
PF10302	97	DUF2407: DUF2407 ubiquitin-like domain; InterPro:	80.14

>cd01793 Fubi Fubi ubiquitin-like protein

Probab=99.48  E-value=1.4e-14  Score=84.94  Aligned_cols=46  Identities=33%  Similarity=0.415  Sum_probs=43.3

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++++|+|+++|+|+|+|++|+|+++|++|+|+ ++++|+++++.||
T Consensus        28 i~~~~gip~~~q~Li~~Gk~L~D~~tL~~~~i~~~~tl~l~~~l~GG   74 (74)
T cd01793          28 VAGLEGIDVEDQVLLLAGVPLEDDATLGQCGVEELCTLEVAGRLLGG   74 (74)
T ss_pred             HHhhhCCCHHHEEEEECCeECCCCCCHHHcCCCCCCEEEEEEecCCC
Confidence            467899999999999999999999999999999 9999999998875

Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.

>KOG0004 consensus Ubiquitin/40S ribosomal protein S27a fusion [Translation, ribosomal structure and biogenesis]

Probab=99.42  E-value=4.2e-14  Score=92.85  Aligned_cols=46  Identities=74%  Similarity=1.063  Sum_probs=44.3

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++++|||+++|||+|+|++|+|+++|+||+|+ .+|++++++..||
T Consensus        30 iq~~egIp~dqqrlifag~qLedgrtlSDY~Iqkestl~l~l~l~Gg   76 (156)
T KOG0004|consen   30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   76 (156)
T ss_pred             hhcccCCCchhhhhhhhhcccccCCccccccccccceEEEEEEecCC
Confidence            678999999999999999999999999999999 9999999998887

>KOG0005 consensus Ubiquitin-like protein [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.39  E-value=2e-13  Score=76.71  Aligned_cols=43  Identities=30%  Similarity=0.563  Sum_probs=37.9

Q ss_pred             eeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           41 RRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        41 i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      ++...|  +.|.++|+|+|+.+|++|++++||||.+|||||+|+|
T Consensus         5 vktLt~KeIeidIep~DkverIKErvEEkeGIPp~qqrli~~gkq   49 (70)
T KOG0005|consen    5 VKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYAGKQ   49 (70)
T ss_pred             EeeeccceEEEeeCcchHHHHHHHHhhhhcCCCchhhhhhhcccc
Confidence            344444  5677799999999999999999999999999999999

>cd01793 Fubi Fubi ubiquitin-like protein

Probab=99.38  E-value=8.8e-13  Score=77.29  Aligned_cols=46  Identities=17%  Similarity=0.191  Sum_probs=40.4

Q ss_pred             eeeeeeecceeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           38 HSVRRFRGGMQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        38 ~l~i~~~~g~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .+.++......+.|++++||+++|++|++++|+|+++|+|+|+|++
T Consensus         2 qi~vk~~~~~~l~v~~~~tV~~lK~~i~~~~gip~~~q~Li~~Gk~   47 (74)
T cd01793           2 QLFVRAQNTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVLLLAGVP   47 (74)
T ss_pred             EEEEECCCEEEEEECCcCcHHHHHHHHHhhhCCCHHHEEEEECCeE
Confidence            3455554557788999999999999999999999999999999998

Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.

>cd01807 GDX_N ubiquitin-like domain of GDX

Probab=99.37  E-value=1.7e-13  Score=80.28  Aligned_cols=43  Identities=35%  Similarity=0.594  Sum_probs=40.2

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      |++++|+|+++|+|+|+|++|+|+++|++|||+ +++++++.++
T Consensus        30 i~~~~gi~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~l~l~~~~   73 (74)
T cd01807          30 VSEHLNVPEEQQRLLFKGKALADDKRLSDYSIGPNAKLNLVVRP   73 (74)
T ss_pred             HHHHHCCCHHHeEEEECCEECCCCCCHHHCCCCCCCEEEEEEcC
Confidence            467889999999999999999999999999999 9999999875

GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.

>cd01802 AN1_N ubiquitin-like domain of AN1

Probab=99.36  E-value=1.9e-12  Score=80.62  Aligned_cols=62  Identities=29%  Similarity=0.299  Sum_probs=52.3

Q ss_pred             CCCCCCccceec-ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           22 EDGRTLVDYNIH-GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        22 ~d~~tL~~y~I~-~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +|+..-.+|-.. .+++.+.++..+|  ..+.|++++||.+||++|++++|+|+++|+|+|+|+.
T Consensus        12 ~~~~~~~~~~~~~~~~M~I~Vk~l~G~~~~leV~~~~TV~~lK~kI~~~~gip~~~QrLi~~Gk~   76 (103)
T cd01802          12 EDNMGPFHYKLPFYDTMELFIETLTGTCFELRVSPFETVISVKAKIQRLEGIPVAQQHLIWNNME   76 (103)
T ss_pred             cCCcceeEEeeccCCCEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEECCEE
Confidence            345555566666 7788888888777  5577899999999999999999999999999999998

AN1 (also known as ANUBL1 and RSD-7) is ubiquitin-like protein with a testis-specific expression in rats that has an N-terminal ubiquitin-like domain and a C-terminal zinc-binding domain. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal ubiquitin-like domain of An1 does not undergo proteolytic processing. The function of AN1 is unknown.

>cd01810 ISG15_repeat2 ISG15 ubiquitin-like protein, second repeat of 2

Probab=99.35  E-value=3.6e-13  Score=78.97  Aligned_cols=46  Identities=33%  Similarity=0.626  Sum_probs=42.6

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++.+|+|+++|+|+|+|++|+|+++|++|||+ ++++++..+..+|
T Consensus        28 I~~~~gi~~~~q~L~~~G~~L~D~~tL~~~~i~~~~tl~l~~~l~gg   74 (74)
T cd01810          28 VSQRERVQADQFWLSFEGRPMEDEHPLGEYGLKPGCTVFMNLRLRGG   74 (74)
T ss_pred             HHHHhCCCHHHeEEEECCEECCCCCCHHHcCCCCCCEEEEEEEccCC
Confidence            456789999999999999999999999999999 9999999988765

ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains and becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.

>KOG0003 consensus Ubiquitin/60s ribosomal protein L40 fusion [Translation, ribosomal structure and biogenesis]

Probab=99.34  E-value=3.5e-14  Score=88.31  Aligned_cols=59  Identities=63%  Similarity=0.869  Sum_probs=51.5

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecceeeeeeccchhHHHHH
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGMQIFVESSDTIDNVKA   62 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~~i~v~~~~TV~~lK~   62 (97)
                      |+.++|||+++|+|+|+|++|+|+.|+++|||+ .+|+|++.+..||+   ++|++.--..|+
T Consensus        30 i~~~~Gi~~~~~~L~~~~k~LED~~Tla~Y~i~~~~Tl~~~~rL~GG~---i~~~~aalAmK~   89 (128)
T KOG0003|consen   30 IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI---IEPSLAALAMKY   89 (128)
T ss_pred             hccccCCCHHHHHHHhcccccccCCcccccCccchhhhhhhHHHhcCC---CChhHHHHHHHh
Confidence            578899999999999999999999999999999 99999999999993   466655555554

>cd01802 AN1_N ubiquitin-like domain of AN1

Probab=99.34  E-value=4.5e-13  Score=83.48  Aligned_cols=46  Identities=46%  Similarity=0.603  Sum_probs=42.9

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|+|. ++++++.++..+|
T Consensus        57 I~~~~gip~~~QrLi~~Gk~L~D~~tL~dy~I~~~stL~l~~~l~GG  103 (103)
T cd01802          57 IQRLEGIPVAQQHLIWNNMELEDEYCLNDYNISEGCTLKLVLAMRGG  103 (103)
T ss_pred             HHHHhCCChHHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEecCCC
Confidence            467899999999999999999999999999999 9999999998775

AN1 (also known as ANUBL1 and RSD-7) is ubiquitin-like protein with a testis-specific expression in rats that has an N-terminal ubiquitin-like domain and a C-terminal zinc-binding domain. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal ubiquitin-like domain of An1 does not undergo proteolytic processing. The function of AN1 is unknown.

>cd01797 NIRF_N amino-terminal ubiquitin-like domain of Np95 and NIRF

Probab=99.33  E-value=4.4e-13  Score=79.65  Aligned_cols=44  Identities=32%  Similarity=0.576  Sum_probs=40.9

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFR   44 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~   44 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|||+ +++|+++++..
T Consensus        32 i~~~~gi~~~~QrLi~~Gk~L~D~~tL~~y~i~~~~~i~l~~~~~   76 (78)
T cd01797          32 IQELFNVEPECQRLFYRGKQMEDGHTLFDYNVGLNDIIQLLVRQD   76 (78)
T ss_pred             HHHHhCCCHHHeEEEeCCEECCCCCCHHHcCCCCCCEEEEEEecC
Confidence            467789999999999999999999999999999 99999998864

NIRF_N This CD represents the amino-terminal ubiquitin-like domain of a family of nuclear proteins that includes Np95 and NIRF (Np95/ICBP90-like RING finger) protein. Both Np95 and NIRF have a domain architecture consisting of a ubiquitin-like domain, a PHD finger, a YDG/SRA domain, Rb-binding motifs and a RING finger domain. Both Np95 and NIRF are ubiquitin ligases that ubiquitinate PCNP (PEST-containing nuclear proteins). While Np95 is capable of binding histones, NIRF is involved in cell cycle regulation.

>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein

Probab=99.31  E-value=6.1e-13  Score=77.52  Aligned_cols=41  Identities=24%  Similarity=0.364  Sum_probs=38.6

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVR   41 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i   41 (97)
                      |++.+|+|+++|+|+|+|++|+|+.+|++|+|+ +++||+++
T Consensus        28 I~~~~gi~~~~q~Li~~G~~L~D~~~l~~~~i~~~~tv~~~~   69 (70)
T cd01794          28 LQAAEGVDPCCQRWFFSGKLLTDKTRLQETKIQKDYVVQVIV   69 (70)
T ss_pred             HHHHhCCCHHHeEEEECCeECCCCCCHHHcCCCCCCEEEEEe
Confidence            467789999999999999999999999999999 99999986

DC_UbP (dendritic cell derived ubiquitin-like protein) is a ubiquitin-like protein from human dendritic cells that is expressed in the mitochondrion. The ubiquitin-like domain of this protein is found at the C-terminus and lacks the canonical gly-gly motif of ubiquitin required for ubiquitinization. DC_UbP is expressed in tumor cells but not in normal human adult tissue suggesting a role for DC_UbP in tumorogenesis.

>cd01807 GDX_N ubiquitin-like domain of GDX

Probab=99.30  E-value=4.3e-12  Score=74.31  Aligned_cols=46  Identities=17%  Similarity=0.280  Sum_probs=40.5

Q ss_pred             eeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           38 HSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        38 ~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .+.++..+|  ..+.|++++||+++|++|++++|+|+++|+|+|+|++
T Consensus         2 ~i~vk~~~G~~~~l~v~~~~tV~~lK~~i~~~~gi~~~~q~L~~~G~~   49 (74)
T cd01807           2 FLTVKLLQGRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLLFKGKA   49 (74)
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEE
Confidence            456666666  4577899999999999999999999999999999999

GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.

>PTZ00044 ubiquitin; Provisional

Probab=99.30  E-value=9.6e-13  Score=77.16  Aligned_cols=46  Identities=43%  Similarity=0.762  Sum_probs=42.7

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++.+|+|+++|+|+|+|+.|+|+.+|++|+++ ++++++.++..+|
T Consensus        30 i~~~~gi~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~gg   76 (76)
T PTZ00044         30 LQEKEGIDVKQIRLIYSGKQMSDDLKLSDYKVVPGSTIHMVLQLRGG   76 (76)
T ss_pred             HHHHHCCCHHHeEEEECCEEccCCCcHHHcCCCCCCEEEEEEEccCC
Confidence            467789999999999999999999999999999 9999999998765

>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein

Probab=99.30  E-value=3.4e-12  Score=74.34  Aligned_cols=43  Identities=30%  Similarity=0.424  Sum_probs=38.5

Q ss_pred             eeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           41 RRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        41 i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      ++..+|  +.+.+++++||+++|++|++++|+|+++|+|+|+|+.
T Consensus         3 vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~Li~~G~~   47 (70)
T cd01794           3 VRLSTGKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWFFSGKL   47 (70)
T ss_pred             EEcCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEECCeE
Confidence            455555  5578899999999999999999999999999999999

DC_UbP (dendritic cell derived ubiquitin-like protein) is a ubiquitin-like protein from human dendritic cells that is expressed in the mitochondrion. The ubiquitin-like domain of this protein is found at the C-terminus and lacks the canonical gly-gly motif of ubiquitin required for ubiquitinization. DC_UbP is expressed in tumor cells but not in normal human adult tissue suggesting a role for DC_UbP in tumorogenesis.

>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein

Probab=99.28  E-value=1.1e-12  Score=75.95  Aligned_cols=42  Identities=38%  Similarity=0.641  Sum_probs=39.0

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR   42 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~   42 (97)
                      |++++|+|+++|+|+|+|++|+|+.+|++|+|+ ++++|++.|
T Consensus        28 i~~~~gi~~~~q~Li~~G~~L~d~~~l~~~~i~~~stl~l~~~   70 (70)
T cd01798          28 VAKRQGVPPDQLRVIFAGKELRNTTTIQECDLGQQSILHAVRR   70 (70)
T ss_pred             HHHHHCCCHHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEeC
Confidence            467899999999999999999999999999999 999999864

parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.

>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP

Probab=99.26  E-value=1.5e-12  Score=76.81  Aligned_cols=40  Identities=33%  Similarity=0.582  Sum_probs=35.7

Q ss_pred             ccc--cCCC-CcceEEEECCEEeCCCCCCccceec-ccceeeee
Q 040204            2 EDK--EEIL-RDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVR   41 (97)
Q Consensus         2 ~~~--~gip-~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i   41 (97)
                      +++  +|+| +++|||+|+|+.|+|++||++|||+ ++++|++.
T Consensus        31 ~~~~~egi~~~dqQrLIy~GKiL~D~~TL~dygI~~gstlhLv~   74 (75)
T cd01815          31 AAQLPDSLPDPELIDLIHCGRKLKDDQTLDFYGIQSGSTIHILR   74 (75)
T ss_pred             HHhhccCCCChHHeEEEeCCcCCCCCCcHHHcCCCCCCEEEEEe
Confidence            445  5675 8999999999999999999999999 99999875

BMSC_UbP (bone marrow stromal cell-derived ubiquitin-like protein) has an N-terminal ubiquitin-like (UBQ) domain and a C-terminal ubiquitin-associated (UBA) domain, a domain architecture similar to those of the UBIN, Chap1, and ubiquilin proteins. This CD represents the N-terminal ubiquitin-like domain.

>cd01806 Nedd8 Nebb8-like ubiquitin protein

Probab=99.25  E-value=4.4e-12  Score=73.97  Aligned_cols=46  Identities=48%  Similarity=0.848  Sum_probs=42.5

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++.+|+|++.|+|+|+|+.|+|+.+|++|+|. +++++++.+..+|
T Consensus        30 i~~~~g~~~~~qrL~~~g~~L~d~~tl~~~~i~~g~~i~l~~~~~gg   76 (76)
T cd01806          30 VEEKEGIPPQQQRLIYSGKQMNDDKTAADYKLEGGSVLHLVLALRGG   76 (76)
T ss_pred             HhHhhCCChhhEEEEECCeEccCCCCHHHcCCCCCCEEEEEEEccCC
Confidence            456789999999999999999999999999999 9999999987765

Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.

>cd01800 SF3a120_C Ubiquitin-like domain of Mammalian splicing factor SF3a_120

Probab=99.24  E-value=2.9e-12  Score=75.50  Aligned_cols=46  Identities=26%  Similarity=0.533  Sum_probs=42.7

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++.+|+|+++|+|+|+|+.|+|+++|++|+|. +++++++.+..+|
T Consensus        27 i~~~~gip~~~q~L~~~G~~L~d~~tL~~~~i~~g~~l~v~~~~~gg   73 (76)
T cd01800          27 IHEETGMPAGKQKLQYEGIFIKDSNSLAYYNLANGTIIHLQLKERGG   73 (76)
T ss_pred             HHHHHCCCHHHEEEEECCEEcCCCCcHHHcCCCCCCEEEEEEecCCC
Confidence            456789999999999999999999999999999 9999999998776

SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus.

>PTZ00044 ubiquitin; Provisional

Probab=99.23  E-value=1.9e-11  Score=71.60  Aligned_cols=46  Identities=24%  Similarity=0.263  Sum_probs=41.1

Q ss_pred             eeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           38 HSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        38 ~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .+.++..+|  ..+.+++++||+++|++|++.+|+|+++|+|+|+|+.
T Consensus         2 ~i~vk~~~G~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~   49 (76)
T PTZ00044          2 QILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYSGKQ   49 (76)
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEE
Confidence            466777666  4578899999999999999999999999999999999

>cd01791 Ubl5 UBL5 ubiquitin-like modifier

Probab=99.23  E-value=1.8e-11  Score=71.92  Aligned_cols=47  Identities=26%  Similarity=0.436  Sum_probs=40.5

Q ss_pred             eeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           37 LHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        37 i~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +.+.++...|  +.+.+++++||++||++|+++.|+|+++|||+|+|+.
T Consensus         2 ~~i~vkt~~Gk~~~~~v~~~~TV~~LK~~I~~~~~~~~~~qrLi~~Gk~   50 (73)
T cd01791           2 IEVVCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVLKKWYTI   50 (73)
T ss_pred             EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEeCCcC
Confidence            4556666555  5567899999999999999999999999999999988

UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.

>cd01803 Ubiquitin Ubiquitin

Probab=99.22  E-value=5.4e-12  Score=73.59  Aligned_cols=46  Identities=74%  Similarity=1.063  Sum_probs=42.7

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++.+|+|++.|+|+|+|+.|+|+.+|++|+++ ++++++.++..||
T Consensus        30 i~~~~g~~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~i~l~~~~~gg   76 (76)
T cd01803          30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   76 (76)
T ss_pred             HHHHhCCCHHHeEEEECCEECCCCCcHHHcCCCCCCEEEEEEEccCC
Confidence            456789999999999999999999999999999 9999999998775

Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)

>cd01810 ISG15_repeat2 ISG15 ubiquitin-like protein, second repeat of 2

Probab=99.21  E-value=2.3e-11  Score=71.24  Aligned_cols=44  Identities=18%  Similarity=0.115  Sum_probs=38.7

Q ss_pred             eeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           40 VRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        40 ~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +++...|  ..+.+++++||+++|++|++.+|+|+++|+|+|+|+.
T Consensus         2 ~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~q~L~~~G~~   47 (74)
T cd01810           2 LVRNDKGRSSIYEVQLTQTVATLKQQVSQRERVQADQFWLSFEGRP   47 (74)
T ss_pred             EEECCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEECCEE
Confidence            3455555  4588899999999999999999999999999999999

ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains and becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.

>KOG0003 consensus Ubiquitin/60s ribosomal protein L40 fusion [Translation, ribosomal structure and biogenesis]

Probab=99.20  E-value=4e-12  Score=79.16  Aligned_cols=50  Identities=56%  Similarity=0.680  Sum_probs=42.6

Q ss_pred             eeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           39 SVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        39 l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      +.++..|. +.++++|++||.++|++|++++|+|+++|+|+|+|++  |.|+|
T Consensus         4 ~~~~~~GKT~~le~EpS~ti~~vKA~i~~~~Gi~~~~~~L~~~~k~LED~~Tl   56 (128)
T KOG0003|consen    4 FVKTLTGKTITLEVEPSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL   56 (128)
T ss_pred             EEEEeeCceEEEEecccchHHHHHHHhccccCCCHHHHHHHhcccccccCCcc
Confidence            34455554 5578899999999999999999999999999999999  66765

>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein

Probab=99.19  E-value=3.4e-11  Score=69.72  Aligned_cols=44  Identities=30%  Similarity=0.428  Sum_probs=38.5

Q ss_pred             eeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           40 VRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        40 ~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .++..+|  +.+.+++++||+++|++|++++|+|+++|+|+|+|+.
T Consensus         2 ~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~q~Li~~G~~   47 (70)
T cd01798           2 YVRTNTGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVIFAGKE   47 (70)
T ss_pred             EEEcCCCCEEEEEECCCChHHHHHHHHHHHHCCCHHHeEEEECCeE
Confidence            3455555  5577899999999999999999999999999999999

parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.

>cd01797 NIRF_N amino-terminal ubiquitin-like domain of Np95 and NIRF

Probab=99.18  E-value=3.3e-11  Score=71.54  Aligned_cols=46  Identities=17%  Similarity=0.198  Sum_probs=39.6

Q ss_pred             eeeeeeecce---ee-eeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           38 HSVRRFRGGM---QI-FVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        38 ~l~i~~~~g~---~i-~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .+.++...|.   .+ .+++++||+++|++|++++|+|+++|+|+|+|++
T Consensus         2 ~I~vk~~~G~~~~~l~~v~~~~TV~~lK~~i~~~~gi~~~~QrLi~~Gk~   51 (78)
T cd01797           2 WIQVRTMDGKETRTVDSLSRLTKVEELREKIQELFNVEPECQRLFYRGKQ   51 (78)
T ss_pred             EEEEEcCCCCEEEEeeccCCcCcHHHHHHHHHHHhCCCHHHeEEEeCCEE
Confidence            4566766663   35 3689999999999999999999999999999999

NIRF_N This CD represents the amino-terminal ubiquitin-like domain of a family of nuclear proteins that includes Np95 and NIRF (Np95/ICBP90-like RING finger) protein. Both Np95 and NIRF have a domain architecture consisting of a ubiquitin-like domain, a PHD finger, a YDG/SRA domain, Rb-binding motifs and a RING finger domain. Both Np95 and NIRF are ubiquitin ligases that ubiquitinate PCNP (PEST-containing nuclear proteins). While Np95 is capable of binding histones, NIRF is involved in cell cycle regulation.

>KOG0005 consensus Ubiquitin-like protein [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.17  E-value=3.2e-12  Score=71.90  Aligned_cols=40  Identities=50%  Similarity=0.813  Sum_probs=37.7

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSV   40 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~   40 (97)
                      |++++||||.+|||+|+|+++.|+.|-++|+.. ||.+|++
T Consensus        30 vEEkeGIPp~qqrli~~gkqm~DD~tA~~Y~~~~GSVlHlv   70 (70)
T KOG0005|consen   30 VEEKEGIPPQQQRLIYAGKQMNDDKTAAHYNLLGGSVLHLV   70 (70)
T ss_pred             hhhhcCCCchhhhhhhccccccccccHHHhhhccceeEeeC
Confidence            578999999999999999999999999999999 9999874

>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade

Probab=99.17  E-value=1.6e-11  Score=70.56  Aligned_cols=43  Identities=47%  Similarity=0.750  Sum_probs=39.5

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      |++..|+|++.|+|+|+|+.|+|+.+|++|+|. +++|+++++.
T Consensus        25 i~~~~~~~~~~~~L~~~G~~L~d~~tL~~~~i~~~~~I~l~~k~   68 (69)
T PF00240_consen   25 IAEETGIPPEQQRLIYNGKELDDDKTLSDYGIKDGSTIHLVIKP   68 (69)
T ss_dssp             HHHHHTSTGGGEEEEETTEEESTTSBTGGGTTSTTEEEEEEESS
T ss_pred             cccccccccccceeeeeeecccCcCcHHHcCCCCCCEEEEEEec
Confidence            356789999999999999999999999999999 9999998864

There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....

>cd01808 hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC2

Probab=99.16  E-value=1.2e-11  Score=71.86  Aligned_cols=42  Identities=40%  Similarity=0.517  Sum_probs=38.5

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR   42 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~   42 (97)
                      |++.+|+|+++|+|+|+|+.|+|+.+|++|||+ ++++|++.+
T Consensus        29 I~~~~~i~~~~~~Li~~Gk~L~d~~tL~~~~i~~~stl~l~~~   71 (71)
T cd01808          29 VSKKFKANQEQLVLIFAGKILKDTDTLTQHNIKDGLTVHLVIK   71 (71)
T ss_pred             HHHHhCCCHHHEEEEECCeEcCCCCcHHHcCCCCCCEEEEEEC
Confidence            456789999999999999999999999999999 999999864

hPLIC-1 and hPLIC-2 (human homologs of the yeast ubiquitin-like Dsk2 protein) are type2 UBL's (ubiquitin-like) proteins that are thought to serve as adaptors that link the ubiquitination machinery to the proteasome. The hPLIC's have an N-terminal UBL domain that binds the S5a subunit of the proteasome and a C-terminal UBA (ubiquitin-associated) domain that binds a ubiquitylated protein.

>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain

Probab=99.14  E-value=6.9e-11  Score=68.84  Aligned_cols=37  Identities=24%  Similarity=0.286  Sum_probs=35.2

Q ss_pred             eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        47 ~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      ..+.+++++||+++|++|++.+|+|+++|+|+|+|+.
T Consensus        12 ~~l~v~~~~TV~~lK~~I~~~~gip~~~q~Li~~Gk~   48 (71)
T cd01796          12 FSLDVDPDLELENFKALCEAESGIPASQQQLIYNGRE   48 (71)
T ss_pred             EEEEECCcCCHHHHHHHHHHHhCCCHHHeEEEECCeE
Confidence            5678899999999999999999999999999999998

DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.

>cd01804 midnolin_N Ubiquitin-like domain of midnolin

Probab=99.14  E-value=1.5e-11  Score=72.89  Aligned_cols=46  Identities=24%  Similarity=0.460  Sum_probs=41.9

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecce
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGM   47 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~   47 (97)
                      |+++.|+|+++|+|+|+|+.|+|+ +|++|||. +++++++.+..+|+
T Consensus        31 I~~~~~~~~~~qrL~~~Gk~L~d~-~L~~~gi~~~~~i~l~~~~~~~~   77 (78)
T cd01804          31 ISQRLKVPKERLALLHRETRLSSG-KLQDLGLGDGSKLTLVPTVEAGL   77 (78)
T ss_pred             HHHHhCCChHHEEEEECCcCCCCC-cHHHcCCCCCCEEEEEeeccccC
Confidence            456779999999999999999999 99999999 99999999987773

midnolin_N Midnolin (midbrain nucleolar protein) is expressed in the nucleolus and is thought to regulate genes involved in neurogenesis. Midnolin contains an amino-terminal ubiquitin-like domain.

>cd01791 Ubl5 UBL5 ubiquitin-like modifier

Probab=99.13  E-value=1.3e-11  Score=72.43  Aligned_cols=41  Identities=22%  Similarity=0.184  Sum_probs=37.5

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVR   41 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i   41 (97)
                      |+++.|+|+++|||+|+|+.|+|+.+|++|||. ++++||..
T Consensus        31 I~~~~~~~~~~qrLi~~Gk~L~D~~tL~~ygi~~~stv~l~~   72 (73)
T cd01791          31 IAAQTGTRPEKIVLKKWYTIFKDHISLGDYEIHDGMNLELYY   72 (73)
T ss_pred             HHHHhCCChHHEEEEeCCcCCCCCCCHHHcCCCCCCEEEEEe
Confidence            356679999999999999999999999999999 99999863

UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.

>cd01790 Herp_N Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein

Probab=99.11  E-value=1.4e-10  Score=69.16  Aligned_cols=47  Identities=11%  Similarity=0.017  Sum_probs=37.9

Q ss_pred             eeeeeeeecc----eeeeeeccchhHHHHHhhhhhcC--CCCCceEEEECeEe
Q 040204           37 LHSVRRFRGG----MQIFVESSDTIDNVKAKIQDKKG--TPPDQQRQIFWFVF   83 (97)
Q Consensus        37 i~l~i~~~~g----~~i~v~~~~TV~~lK~~I~~~~g--ip~~~q~Lif~G~~   83 (97)
                      +.+.++.+++    +.+.+++++||.++|++|++..+  .|+++|+|||+||.
T Consensus         2 i~l~IK~~~~~~~~~~ve~~~~~TV~~lK~~i~~~~~~~~~~~~QrLIy~GKi   54 (79)
T cd01790           2 VTLLIKSPNQKYEDQTVSCFLNWTVGELKTHLSRVYPSKPLEQDQRLIYSGKL   54 (79)
T ss_pred             eEEEEECCCCCeEEEEEecCCcChHHHHHHHHHHhcCCCCChhHeEEEEcCee
Confidence            4566777666    33445899999999999998763  56899999999998

Herp (Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein) , is an integral membrane protein that is induced by the endoplasmic reticulum (ER) stress response pathway and is involved in improving the balance of folding capacity and protein loads in the ER. Herp has an N-terminal ubiquitin-like domain that is involved in Herp degradation, but is not necessary for its enhancement of amyloid beta-protein generation.

>cd01803 Ubiquitin Ubiquitin

Probab=99.09  E-value=2.1e-10  Score=66.77  Aligned_cols=46  Identities=54%  Similarity=0.655  Sum_probs=40.7

Q ss_pred             eeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           38 HSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        38 ~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .+.++..+|  +.+.+++++||+++|++|++++|+|+++|+|+|+|+.
T Consensus         2 ~i~v~~~~g~~~~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~~~g~~   49 (76)
T cd01803           2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQ   49 (76)
T ss_pred             EEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCHHHeEEEECCEE
Confidence            466676665  5578899999999999999999999999999999998

Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)

>cd01805 RAD23_N Ubiquitin-like domain of RAD23

Probab=99.09  E-value=2.7e-10  Score=66.73  Aligned_cols=46  Identities=30%  Similarity=0.455  Sum_probs=40.4

Q ss_pred             eeeeeeecc--eeeeeeccchhHHHHHhhhhhcCC--CCCceEEEECeEe
Q 040204           38 HSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGT--PPDQQRQIFWFVF   83 (97)
Q Consensus        38 ~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gi--p~~~q~Lif~G~~   83 (97)
                      .+.++..+|  +.+.+++++||.++|++|++.+|+  |+++|+|+|+|+.
T Consensus         2 ~i~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~~~G~~   51 (77)
T cd01805           2 KITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKI   51 (77)
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEEECCEE
Confidence            456666666  457789999999999999999999  9999999999998

RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL).

>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein

Probab=99.09  E-value=3.8e-11  Score=69.28  Aligned_cols=42  Identities=40%  Similarity=0.748  Sum_probs=38.2

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR   42 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~   42 (97)
                      |++.+|+|++.|+|+|+|+.|+|+.+|++|||+ +++++++.+
T Consensus        30 i~~~~gi~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~l~l~~~   72 (72)
T cd01809          30 IAEEVGIPVEQQRLIYSGRVLKDDETLSEYKVEDGHTIHLVKR   72 (72)
T ss_pred             HHHHHCcCHHHeEEEECCEECCCcCcHHHCCCCCCCEEEEEeC
Confidence            356789999999999999999999999999999 999998764

Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules.

>cd01805 RAD23_N Ubiquitin-like domain of RAD23

Probab=99.08  E-value=6e-11  Score=69.55  Aligned_cols=43  Identities=30%  Similarity=0.468  Sum_probs=39.1

Q ss_pred             CccccCC--CCcceEEEECCEEeCCCCCCccceec-ccceeeeeee
Q 040204            1 IEDKEEI--LRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         1 i~~~~gi--p~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      |++.+|+  |+++|+|+|+|+.|+|+.+|++|||+ +++++++++.
T Consensus        30 i~~~~~i~~~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~i~~~~~~   75 (77)
T cd01805          30 IEEEKGCDYPPEQQKLIYSGKILKDDTTLEEYKIDEKDFVVVMVSK   75 (77)
T ss_pred             HHHhhCCCCChhHeEEEECCEEccCCCCHHHcCCCCCCEEEEEEec
Confidence            3567898  99999999999999999999999999 9999988764

RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL).

>cd01806 Nedd8 Nebb8-like ubiquitin protein

Probab=99.08  E-value=3.3e-10  Score=65.97  Aligned_cols=46  Identities=28%  Similarity=0.489  Sum_probs=40.3

Q ss_pred             eeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           38 HSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        38 ~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .+.++..+|  +.+.+++++||++||++|+++.|+|++.|+|+|+|+.
T Consensus         2 ~i~v~~~~g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~~~g~~   49 (76)
T cd01806           2 LIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQ   49 (76)
T ss_pred             EEEEEeCCCCEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEEECCeE
Confidence            456666666  4567899999999999999999999999999999998

Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.

>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain

Probab=99.08  E-value=3.8e-11  Score=69.95  Aligned_cols=40  Identities=30%  Similarity=0.467  Sum_probs=36.0

Q ss_pred             CccccCCCCcceEEEECCEEeCCC-CCCccceec-ccceeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDG-RTLVDYNIH-GSTLHSV   40 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~-~tL~~y~I~-~sti~l~   40 (97)
                      |++.+|+|+++|+|+|+|++|+|+ .+|++|+|+ ++++++.
T Consensus        29 I~~~~gip~~~q~Li~~Gk~L~D~~~~L~~~gi~~~~~l~l~   70 (71)
T cd01796          29 CEAESGIPASQQQLIYNGRELVDNKRLLALYGVKDGDLVVLR   70 (71)
T ss_pred             HHHHhCCCHHHeEEEECCeEccCCcccHHHcCCCCCCEEEEe
Confidence            467899999999999999999987 689999999 9999863

DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.

>cd01808 hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC2

Probab=99.06  E-value=3.3e-10  Score=65.75  Aligned_cols=45  Identities=13%  Similarity=0.098  Sum_probs=38.5

Q ss_pred             eeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           39 SVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        39 l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +.++...| ..+.+++++||+++|++|++++|+|+++|+|+|+|+.
T Consensus         3 i~vk~~~g~~~l~v~~~~TV~~lK~~I~~~~~i~~~~~~Li~~Gk~   48 (71)
T cd01808           3 VTVKTPKDKEEIEIAEDASVKDFKEAVSKKFKANQEQLVLIFAGKI   48 (71)
T ss_pred             EEEEcCCCCEEEEECCCChHHHHHHHHHHHhCCCHHHEEEEECCeE
Confidence            34444444 5688899999999999999999999999999999998

hPLIC-1 and hPLIC-2 (human homologs of the yeast ubiquitin-like Dsk2 protein) are type2 UBL's (ubiquitin-like) proteins that are thought to serve as adaptors that link the ubiquitination machinery to the proteasome. The hPLIC's have an N-terminal UBL domain that binds the S5a subunit of the proteasome and a C-terminal UBA (ubiquitin-associated) domain that binds a ubiquitylated protein.

>cd01763 Sumo Small ubiquitin-related modifier (SUMO)

Probab=99.05  E-value=1.2e-10  Score=70.35  Aligned_cols=45  Identities=24%  Similarity=0.519  Sum_probs=42.3

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      +++.|+|+++|+|+|+|++|+++.|+++|++. +++|+++.+..+|
T Consensus        42 ~~~~gi~~~~~rf~f~G~~L~~~~T~~~l~m~d~d~I~v~l~l~GG   87 (87)
T cd01763          42 CQRQGLSMNSVRFLFDGQRIRDNQTPDDLGMEDGDEIEVMLEQTGG   87 (87)
T ss_pred             HHHhCCCccceEEEECCeECCCCCCHHHcCCCCCCEEEEEEecccC
Confidence            56789999999999999999999999999999 9999999988776

Small ubiquitin-related modifier (SUMO) proteins are conjugated to numerous intracellular targets and serve to modulate protein interaction, localization, activity or stability. SUMO (also known as "Smt3" and "sentrin" in other organisms) is linked to several different pathways, including nucleocytoplasmic transport. Attachment of SUMO to targets proteins is stimulated by PIAS (Protein inhibitor of activated STATs) proteins which serve as E3-like ligases.

>cd01804 midnolin_N Ubiquitin-like domain of midnolin

Probab=99.05  E-value=3.8e-10  Score=66.85  Aligned_cols=47  Identities=13%  Similarity=0.225  Sum_probs=40.5

Q ss_pred             eeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           37 LHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        37 i~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +.+.++...|  ..+.+++++||++||++|+++.|+|+++|+|+|+|+.
T Consensus         2 m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~~~~~~~qrL~~~Gk~   50 (78)
T cd01804           2 MNLNIHSTTGTRFDLSVPPDETVEGLKKRISQRLKVPKERLALLHRETR   50 (78)
T ss_pred             eEEEEEECCCCEEEEEECCcCHHHHHHHHHHHHhCCChHHEEEEECCcC
Confidence            3455666555  5688899999999999999999999999999999988

midnolin_N Midnolin (midbrain nucleolar protein) is expressed in the nucleolus and is thought to regulate genes involved in neurogenesis. Midnolin contains an amino-terminal ubiquitin-like domain.

>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein

Probab=99.03  E-value=6.1e-10  Score=64.19  Aligned_cols=46  Identities=26%  Similarity=0.252  Sum_probs=39.9

Q ss_pred             eeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           38 HSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        38 ~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .+.++...|  ..+.+++++||+++|++|++..|+|++.|+|+|+|+.
T Consensus         2 ~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~   49 (72)
T cd01809           2 EIKVKTLDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYSGRV   49 (72)
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCEE
Confidence            455666555  5577899999999999999999999999999999998

Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules.

>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade

Probab=99.02  E-value=7.9e-10  Score=63.40  Aligned_cols=42  Identities=33%  Similarity=0.492  Sum_probs=37.9

Q ss_pred             eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        47 ~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      +.+.|++++||.+||++|++..|+|++.|+|+|+|+.  |..+|
T Consensus         8 ~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~~G~~L~d~~tL   51 (69)
T PF00240_consen    8 FTLEVDPDDTVADLKQKIAEETGIPPEQQRLIYNGKELDDDKTL   51 (69)
T ss_dssp             EEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEETTEEESTTSBT
T ss_pred             EEEEECCCCCHHHhhhhcccccccccccceeeeeeecccCcCcH
Confidence            5678899999999999999999999999999999999  44554

There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....

>cd01813 UBP_N UBP ubiquitin processing protease

Probab=99.01  E-value=5.6e-10  Score=65.63  Aligned_cols=45  Identities=20%  Similarity=0.211  Sum_probs=38.5

Q ss_pred             eeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEE---CeEe
Q 040204           39 SVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIF---WFVF   83 (97)
Q Consensus        39 l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif---~G~~   83 (97)
                      +.++..+. +.+.|++++||+++|++|++.+|+|+++|+|+|   +|+.
T Consensus         3 i~vk~~g~~~~v~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~~~~~Gk~   51 (74)
T cd01813           3 VIVKWGGQEYSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLGLKVKGKP   51 (74)
T ss_pred             EEEEECCEEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEeecccCCc
Confidence            44555444 568889999999999999999999999999997   8887

The UBP (ubiquitin processing protease) domain (also referred to as USP which stands for "ubiquitin-specific protease") is present at in a large family of cysteine proteases that specifically cleave ubiquitin conjugates. This family includes Rpn11, UBP6 (USP14), USP7 (HAUSP). This domain is closely related to the amino-terminal ubiquitin-like domain of BAG1 (Bcl2-associated anthanogene1) protein and is found only in eukaryotes.

>KOG0004 consensus Ubiquitin/40S ribosomal protein S27a fusion [Translation, ribosomal structure and biogenesis]

Probab=98.99  E-value=1.4e-10  Score=76.26  Aligned_cols=39  Identities=62%  Similarity=0.699  Sum_probs=35.9

Q ss_pred             eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEeCC
Q 040204           47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVFGW   85 (97)
Q Consensus        47 ~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~~~   85 (97)
                      +...|++++||..+|++||+++|||+++|||||+|++++
T Consensus        13 i~~eve~~~ti~~~Kakiq~~egIp~dqqrlifag~qLe   51 (156)
T KOG0004|consen   13 ITLEVEANDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE   51 (156)
T ss_pred             eeeeecccccHHHHHHhhhcccCCCchhhhhhhhhcccc
Confidence            556779999999999999999999999999999999944

>cd01792 ISG15_repeat1 ISG15 ubiquitin-like protein, first repeat of 2

Probab=98.99  E-value=5.7e-10  Score=66.28  Aligned_cols=47  Identities=26%  Similarity=0.278  Sum_probs=40.6

Q ss_pred             eeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEE--EECeEe
Q 040204           37 LHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQ--IFWFVF   83 (97)
Q Consensus        37 i~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~L--if~G~~   83 (97)
                      +.+.++..+|  +.+.+++++||++||++|+++.|+|+++|+|  +|+|+.
T Consensus         3 ~~i~Vk~~~G~~~~~~v~~~~TV~~lK~~I~~~~~i~~~~qrL~~~~~G~~   53 (80)
T cd01792           3 WDLKVKMLGGNEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLAHLDSREV   53 (80)
T ss_pred             eEEEEEeCCCCEEEEEcCCCCcHHHHHHHHHHHhCCCHHHEEEEeccCCCC
Confidence            5567777766  4456789999999999999999999999999  999987

ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains that becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.

>cd01812 BAG1_N Ubiquitin-like domain of BAG1

Probab=98.98  E-value=8.5e-10  Score=63.54  Aligned_cols=46  Identities=20%  Similarity=0.234  Sum_probs=39.5

Q ss_pred             eeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           38 HSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        38 ~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .+.++..+. ..+.+++++||+++|++|++.+|+|++.|+|+|+|+.
T Consensus         2 ~i~vk~~g~~~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~   48 (71)
T cd01812           2 RVRVKHGGESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIFKGKE   48 (71)
T ss_pred             EEEEEECCEEEEEEECCCCcHHHHHHHHHHhhCCChHHeEEeeCCcc
Confidence            455555543 5577899999999999999999999999999999998

BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).

>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4

Probab=98.97  E-value=2.6e-10  Score=71.72  Aligned_cols=43  Identities=30%  Similarity=0.251  Sum_probs=38.1

Q ss_pred             cccCCC--CcceEEEECCEEeCCCCCCccce------ec-ccceeeeeeeec
Q 040204            3 DKEEIL--RDQQRFIFAGKRLEDGRTLVDYN------IH-GSTLHSVRRFRG   45 (97)
Q Consensus         3 ~~~gip--~~~Q~L~~~g~~L~d~~tL~~y~------I~-~sti~l~i~~~~   45 (97)
                      .++|+|  +++|+|+|+||.|+|++||++|+      +. .+|+|++++...
T Consensus        42 ~ke~~P~~~~~qKLIysGKiLeD~~TL~d~~~p~g~~~~~~~TmHvvlr~~~   93 (113)
T cd01814          42 DKEVGPKTVNEVKLISAGKILENSKTVGECRSPVGDIAGGVITMHVVVQPPL   93 (113)
T ss_pred             ccccCCCCHHHeEEEeCCeecCCCCcHHHhCCcccccCCCceEEEEEecCCC
Confidence            457888  99999999999999999999999      66 789999998654

NTGP5 and ATGP4 are plant-specific isoprenylated GTP-binding proteins with a single fold that resembles ubiquitin. The function of these proteins is unknown.

>cd01800 SF3a120_C Ubiquitin-like domain of Mammalian splicing factor SF3a_120

Probab=98.97  E-value=7.6e-10  Score=65.12  Aligned_cols=37  Identities=24%  Similarity=0.476  Sum_probs=34.9

Q ss_pred             eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        47 ~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +.+.+++++||+++|++|++.+|+|+++|+|+|+|+.
T Consensus        10 ~~l~v~~~~TV~~lK~~i~~~~gip~~~q~L~~~G~~   46 (76)
T cd01800          10 LNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQYEGIF   46 (76)
T ss_pred             EEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCEE
Confidence            4578899999999999999999999999999999997

SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus.

>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4

Probab=98.96  E-value=7.4e-10  Score=69.67  Aligned_cols=53  Identities=17%  Similarity=0.155  Sum_probs=42.4

Q ss_pred             ceeeeeeeeccee---eeeeccchhHHHHHhhh-----hhcCCC--CCceEEEECeEe--CCCcc
Q 040204           36 TLHSVRRFRGGMQ---IFVESSDTIDNVKAKIQ-----DKKGTP--PDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        36 ti~l~i~~~~g~~---i~v~~~~TV~~lK~~I~-----~~~gip--~~~q~Lif~G~~--~~~~~   88 (97)
                      .+.+..|...|..   ..+.+++||++||++|+     +++|+|  +++|+|||+||+  |..+|
T Consensus         4 ~~e~kfrl~dg~digp~~~~~sdTV~~lKekI~~~~p~~ke~~P~~~~~qKLIysGKiLeD~~TL   68 (113)
T cd01814           4 QIEIKFRLYDGSDIGPKRYPAATTVDFLKERVVSQWPKDKEVGPKTVNEVKLISAGKILENSKTV   68 (113)
T ss_pred             cEEEEEEccCCCccCccccChhhHHHHHHHHHHHhcccccccCCCCHHHeEEEeCCeecCCCCcH
Confidence            4667778888844   35589999999999999     666777  999999999999  43443

NTGP5 and ATGP4 are plant-specific isoprenylated GTP-binding proteins with a single fold that resembles ubiquitin. The function of these proteins is unknown.

>cd01792 ISG15_repeat1 ISG15 ubiquitin-like protein, first repeat of 2

Probab=98.96  E-value=1.6e-10  Score=68.65  Aligned_cols=43  Identities=33%  Similarity=0.327  Sum_probs=39.2

Q ss_pred             CccccCCCCcceEE--EECCEEeCCCCCCccceec-ccceeeeeee
Q 040204            1 IEDKEEILRDQQRF--IFAGKRLEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         1 i~~~~gip~~~Q~L--~~~g~~L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      |++++|+|+++|+|  +|+|+.|.|+.+|++|||. +++++++++.
T Consensus        32 I~~~~~i~~~~qrL~~~~~G~~L~D~~tL~~~gi~~gs~l~l~~~~   77 (80)
T cd01792          32 IAQKIGVPAFQQRLAHLDSREVLQDGVPLVSQGLGPGSTVLLVVQN   77 (80)
T ss_pred             HHHHhCCCHHHEEEEeccCCCCCCCCCCHHHcCCCCCCEEEEEEEc
Confidence            45678999999999  8899999999999999999 9999999873

ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains that becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.

>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1

Probab=98.93  E-value=9e-10  Score=64.95  Aligned_cols=36  Identities=25%  Similarity=0.204  Sum_probs=33.9

Q ss_pred             eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        47 ~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      ..+.|++++||++||++|++++|+||++|+| |+|+.
T Consensus        15 ~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL-~~G~~   50 (75)
T cd01799          15 IWLTVRPDMTVAQLKDKVFLDYGFPPAVQRW-VIGQR   50 (75)
T ss_pred             EEEEECCCCcHHHHHHHHHHHHCcCHHHEEE-EcCCe
Confidence            5678899999999999999999999999999 99987

HOIL1_N HOIL-1 (heme-oxidized IRP2 ubiquitin ligase-1) is an E3 ubiquitin-protein ligase that recognizes heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. Hoil-1 has an amino-terminal ubiquitin-like domain as well as an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain.

>smart00213 UBQ Ubiquitin homologues

Probab=98.92  E-value=3e-09  Score=59.57  Aligned_cols=46  Identities=28%  Similarity=0.352  Sum_probs=40.0

Q ss_pred             eeeeeeec-ceeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           38 HSVRRFRG-GMQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        38 ~l~i~~~~-g~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .+.++..+ ...+.|++++||++||++|++..|+|++.|+|+|+|+.
T Consensus         2 ~i~vk~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~~g~~   48 (64)
T smart00213        2 ELTVKTLDGTITLEVKPSDTVSELKEKIAELTGIPVEQQRLIYKGKV   48 (64)
T ss_pred             EEEEEECCceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCEE
Confidence            45566555 35678899999999999999999999999999999998

Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression

>cd01812 BAG1_N Ubiquitin-like domain of BAG1

Probab=98.92  E-value=3.1e-10  Score=65.39  Aligned_cols=41  Identities=24%  Similarity=0.376  Sum_probs=37.5

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVR   41 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i   41 (97)
                      |++.+|+|++.|+|+|+|+.|.|+.+|++|+|. +++++++.
T Consensus        29 i~~~~gi~~~~q~L~~~g~~l~d~~~L~~~~i~~g~~l~v~~   70 (71)
T cd01812          29 LAPVTGVEPRDQKLIFKGKERDDAETLDMSGVKDGSKVMLLE   70 (71)
T ss_pred             HHHhhCCChHHeEEeeCCcccCccCcHHHcCCCCCCEEEEec
Confidence            456789999999999999999999999999999 99998763

BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).

>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP

Probab=98.88  E-value=1.3e-09  Score=64.22  Aligned_cols=37  Identities=16%  Similarity=0.121  Sum_probs=31.0

Q ss_pred             eccchhHHHHHhhhhh--cCCC-CCceEEEECeEe--CCCcc
Q 040204           52 ESSDTIDNVKAKIQDK--KGTP-PDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        52 ~~~~TV~~lK~~I~~~--~gip-~~~q~Lif~G~~--~~~~~   88 (97)
                      ..++||.+||++|+++  +|++ +++|+|||+||+  |..+|
T Consensus        18 ~~~~TV~~LK~kI~~~~~egi~~~dqQrLIy~GKiL~D~~TL   59 (75)
T cd01815          18 PGGYQVSTLKQLIAAQLPDSLPDPELIDLIHCGRKLKDDQTL   59 (75)
T ss_pred             CccCcHHHHHHHHHHhhccCCCChHHeEEEeCCcCCCCCCcH
Confidence            5589999999999999  5675 999999999999  44443

BMSC_UbP (bone marrow stromal cell-derived ubiquitin-like protein) has an N-terminal ubiquitin-like (UBQ) domain and a C-terminal ubiquitin-associated (UBA) domain, a domain architecture similar to those of the UBIN, Chap1, and ubiquilin proteins. This CD represents the N-terminal ubiquitin-like domain.

>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1

Probab=98.77  E-value=2.2e-09  Score=63.31  Aligned_cols=40  Identities=25%  Similarity=0.250  Sum_probs=35.0

Q ss_pred             CccccCCCCcceEEEECCEEeC-CCCCCccceec--ccceeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLE-DGRTLVDYNIH--GSTLHSVR   41 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~-d~~tL~~y~I~--~sti~l~i   41 (97)
                      |++++|||+++|+| |+|+.|. |+++|++||+.  |+++++.+
T Consensus        32 I~~~~gip~~~QrL-~~G~~L~dD~~tL~~ygi~~~g~~~~l~~   74 (75)
T cd01799          32 VFLDYGFPPAVQRW-VIGQRLARDQETLYSHGIRTNGDSAFLYI   74 (75)
T ss_pred             HHHHHCcCHHHEEE-EcCCeeCCCcCCHHHcCCCCCCCEEEEEe
Confidence            45779999999999 9999985 77999999998  79998864

HOIL1_N HOIL-1 (heme-oxidized IRP2 ubiquitin ligase-1) is an E3 ubiquitin-protein ligase that recognizes heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. Hoil-1 has an amino-terminal ubiquitin-like domain as well as an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain.

>cd01790 Herp_N Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein

Probab=98.75  E-value=2.6e-09  Score=63.65  Aligned_cols=35  Identities=34%  Similarity=0.370  Sum_probs=32.3

Q ss_pred             CCCcceEEEECCEEeCCCCCCccce--ec-ccceeeee
Q 040204            7 ILRDQQRFIFAGKRLEDGRTLVDYN--IH-GSTLHSVR   41 (97)
Q Consensus         7 ip~~~Q~L~~~g~~L~d~~tL~~y~--I~-~sti~l~i   41 (97)
                      .|+++|||+|+||.|+|+.||++|.  +. +.+|||+.
T Consensus        41 ~~~~~QrLIy~GKiLkD~~tL~~~~~~~~~~~tiHLV~   78 (79)
T cd01790          41 PLEQDQRLIYSGKLLPDHLKLRDVLRKQDEYHMVHLVC   78 (79)
T ss_pred             CChhHeEEEEcCeeccchhhHHHHhhcccCCceEEEEe
Confidence            5579999999999999999999996  88 99999986

Herp (Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein) , is an integral membrane protein that is induced by the endoplasmic reticulum (ER) stress response pathway and is involved in improving the balance of folding capacity and protein loads in the ER. Herp has an N-terminal ubiquitin-like domain that is involved in Herp degradation, but is not necessary for its enhancement of amyloid beta-protein generation.

>cd01813 UBP_N UBP ubiquitin processing protease

Probab=98.75  E-value=2.4e-09  Score=62.93  Aligned_cols=40  Identities=18%  Similarity=0.341  Sum_probs=36.6

Q ss_pred             CccccCCCCcceEEEE---CCEEeCCCCCCccceec-ccceeee
Q 040204            1 IEDKEEILRDQQRFIF---AGKRLEDGRTLVDYNIH-GSTLHSV   40 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~---~g~~L~d~~tL~~y~I~-~sti~l~   40 (97)
                      |++.+|+|+++|+|+|   .|+.+.|+.+|++|+|. +++++|+
T Consensus        29 i~~~tgvp~~~QKLi~~~~~Gk~l~D~~~L~~~~i~~g~~i~lm   72 (74)
T cd01813          29 IKTLTGVLPERQKLLGLKVKGKPAEDDVKISALKLKPNTKIMMM   72 (74)
T ss_pred             HHHHHCCCHHHEEEEeecccCCcCCCCcCHHHcCCCCCCEEEEE
Confidence            4567899999999996   89999999999999999 9999876

The UBP (ubiquitin processing protease) domain (also referred to as USP which stands for "ubiquitin-specific protease") is present at in a large family of cysteine proteases that specifically cleave ubiquitin conjugates. This family includes Rpn11, UBP6 (USP14), USP7 (HAUSP). This domain is closely related to the amino-terminal ubiquitin-like domain of BAG1 (Bcl2-associated anthanogene1) protein and is found only in eukaryotes.

>cd01763 Sumo Small ubiquitin-related modifier (SUMO)

Probab=98.72  E-value=4.9e-08  Score=58.84  Aligned_cols=50  Identities=10%  Similarity=0.098  Sum_probs=44.0

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      ...|.+.++...|  ..+.|++++|+..||++++++.|+|+++|+|+|+|+.
T Consensus         9 ~~~i~I~v~~~~g~~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f~G~~   60 (87)
T cd01763           9 SEHINLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLFDGQR   60 (87)
T ss_pred             CCeEEEEEECCCCCEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEECCeE
Confidence            4567777777766  4577899999999999999999999999999999999

Small ubiquitin-related modifier (SUMO) proteins are conjugated to numerous intracellular targets and serve to modulate protein interaction, localization, activity or stability. SUMO (also known as "Smt3" and "sentrin" in other organisms) is linked to several different pathways, including nucleocytoplasmic transport. Attachment of SUMO to targets proteins is stimulated by PIAS (Protein inhibitor of activated STATs) proteins which serve as E3-like ligases.

>cd01795 USP48_C USP ubiquitin-specific protease

Probab=98.71  E-value=6.4e-09  Score=64.18  Aligned_cols=42  Identities=21%  Similarity=0.124  Sum_probs=37.8

Q ss_pred             CccccCCCCcceEEEECCEEeC-CCCCCccceec-ccceeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLE-DGRTLVDYNIH-GSTLHSVRR   42 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~-d~~tL~~y~I~-~sti~l~i~   42 (97)
                      |.++.++||.+|+|+|+|+.|+ |.+||++|||. +|++.+.++
T Consensus        34 ImQ~f~V~P~dQkL~~dG~~L~DDsrTLssyGv~sgSvl~Llid   77 (107)
T cd01795          34 IMHAFSVAPFDQNLSIDGKILSDDCATLGTLGVIPESVILLKAD   77 (107)
T ss_pred             HHHHhcCCcccceeeecCceeccCCccHHhcCCCCCCEEEEEec
Confidence            4678899999999999999995 56999999999 999999885

The USP (ubiquitin-specific protease) family is one of at least seven deubiquitylating enzyme (DUB) families capable of deconjugating ubiquitin and ubiquitin-like adducts. While the USP's have a conserved catalytic core domain, they differ in their domain architectures. This subfamily, which includes USP31, and USP48, has a carboxy-terminal ubiquitin-like domain in addition to a DUSP (domain of ubiquitin-specific proteases) domain,

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=98.66  E-value=4.1e-08  Score=73.23  Aligned_cols=46  Identities=24%  Similarity=0.306  Sum_probs=40.3

Q ss_pred             eeeeeeecc--eeeeeeccchhHHHHHhhhhhcC---CCCCceEEEECeEe
Q 040204           38 HSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKG---TPPDQQRQIFWFVF   83 (97)
Q Consensus        38 ~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~g---ip~~~q~Lif~G~~   83 (97)
                      .+.++...|  +.|.|++++||.+||++|++..|   +|+++|+|||+||.
T Consensus         2 kItVKtl~g~~~~IeV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLIy~Gki   52 (378)
T TIGR00601         2 TLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKI   52 (378)
T ss_pred             EEEEEeCCCCEEEEEeCCcChHHHHHHHHHHhhCCCCCChhHeEEEECCEE
Confidence            456666655  56788999999999999999998   99999999999998

All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>cd01795 USP48_C USP ubiquitin-specific protease

Probab=98.59  E-value=6.5e-08  Score=59.75  Aligned_cols=39  Identities=18%  Similarity=0.188  Sum_probs=36.2

Q ss_pred             cceeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           45 GGMQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        45 ~g~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +...+.|++++||.+||.+|.++.++||++|+|+|.|+.
T Consensus        15 ~~~~L~V~~~~TVg~LK~lImQ~f~V~P~dQkL~~dG~~   53 (107)
T cd01795          15 GEKALLVSANQTLKELKIQIMHAFSVAPFDQNLSIDGKI   53 (107)
T ss_pred             CCceEEeCccccHHHHHHHHHHHhcCCcccceeeecCce
Confidence            346788999999999999999999999999999999995

The USP (ubiquitin-specific protease) family is one of at least seven deubiquitylating enzyme (DUB) families capable of deconjugating ubiquitin and ubiquitin-like adducts. While the USP's have a conserved catalytic core domain, they differ in their domain architectures. This subfamily, which includes USP31, and USP48, has a carboxy-terminal ubiquitin-like domain in addition to a DUSP (domain of ubiquitin-specific proteases) domain,

>smart00213 UBQ Ubiquitin homologues

Probab=98.57  E-value=1.8e-08  Score=56.34  Aligned_cols=35  Identities=57%  Similarity=0.844  Sum_probs=31.5

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-cc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GS   35 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~s   35 (97)
                      |++.+|+|++.|+|+|+|+.|+|+.+|++|++. ++
T Consensus        29 i~~~~~~~~~~~~L~~~g~~L~d~~tL~~~~i~~~~   64 (64)
T smart00213       29 IAELTGIPVEQQRLIYKGKVLEDDRTLADYNIQDGS   64 (64)
T ss_pred             HHHHHCCCHHHEEEEECCEECCCCCCHHHcCCcCCC
Confidence            356789999999999999999999999999998 64

Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression

>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]

Probab=98.54  E-value=2.3e-08  Score=75.98  Aligned_cols=46  Identities=35%  Similarity=0.481  Sum_probs=41.2

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |....++|+++++|+|+||.|+|+.||..|||+ |.||||+++....
T Consensus        44 I~~~f~a~~dqlvLIfaGrILKD~dTL~~~gI~Dg~TvHLVik~~~~   90 (493)
T KOG0010|consen   44 IAQRFGAPPDQLVLIYAGRILKDDDTLKQYGIQDGHTVHLVIKSQPR   90 (493)
T ss_pred             HHHhcCCChhHeeeeecCccccChhhHHHcCCCCCcEEEEEeccCCC
Confidence            345678999999999999999999999999999 9999999986643

>cd01769 UBL Ubiquitin-like domain of UBL

Probab=98.45  E-value=6.8e-08  Score=54.62  Aligned_cols=40  Identities=55%  Similarity=0.800  Sum_probs=36.3

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeee
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVR   41 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i   41 (97)
                      ++..|+|++.|+|+|+|+.|+|+.+|++|++. ++++++..
T Consensus        28 ~~~~~~~~~~~~l~~~g~~l~d~~~l~~~~v~~~~~i~v~~   68 (69)
T cd01769          28 AAKEGVPPEQQRLIYAGKILKDDKTLSDYGIQDGSTLHLVL   68 (69)
T ss_pred             HHHHCcChHHEEEEECCcCCCCcCCHHHCCCCCCCEEEEEE
Confidence            45679999999999999999999999999999 99998764

UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=98.44  E-value=8e-08  Score=71.68  Aligned_cols=43  Identities=26%  Similarity=0.380  Sum_probs=37.9

Q ss_pred             ccccC---CCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeee
Q 040204            2 EDKEE---ILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFR   44 (97)
Q Consensus         2 ~~~~g---ip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~   44 (97)
                      ++..|   +|+++|+|+|+||.|+|+++|++|+|+ +++|+++++..
T Consensus        31 ~~~~g~~~ip~~~QkLIy~GkiL~Dd~tL~dy~I~e~~~Ivvmv~k~   77 (378)
T TIGR00601        31 EAEQGKDAYPVAQQKLIYSGKILSDDKTVREYKIKEKDFVVVMVSKP   77 (378)
T ss_pred             HHhhCCCCCChhHeEEEECCEECCCCCcHHHcCCCCCCEEEEEeccC
Confidence            34556   999999999999999999999999999 99998887643

All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG0001 consensus Ubiquitin and ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones; General function prediction only]

Probab=98.42  E-value=2.4e-07  Score=52.11  Aligned_cols=43  Identities=70%  Similarity=0.981  Sum_probs=39.0

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeee
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFR   44 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~   44 (97)
                      +..+|+|+++|++.++|+.|+|+.++++|+|. ++++++..+..
T Consensus        30 ~~~~~~~~~~q~~~~~~~~l~d~~~l~~~~i~~~~~~~l~~~~~   73 (75)
T KOG0001|consen   30 RDKEGIPVDQQRLIFGGKPLEDGRTLADYNIQEGSTLHLVLSLR   73 (75)
T ss_pred             HhhcCCCCeeEEEEECCEECcCCCcHHHhCCCCCCEEEEEEecC
Confidence            45679999999999999999999999999999 99999887654

>cd01769 UBL Ubiquitin-like domain of UBL

Probab=98.32  E-value=1.1e-06  Score=49.57  Aligned_cols=37  Identities=41%  Similarity=0.619  Sum_probs=34.2

Q ss_pred             eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        47 ~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      ..+.+.++.||.++|.+|++..|+|++.|+|+|+|+.
T Consensus        10 ~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l~~~g~~   46 (69)
T cd01769          10 FELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYAGKI   46 (69)
T ss_pred             EEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCcC
Confidence            4566788999999999999999999999999999988

UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.

>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]

Probab=98.28  E-value=8.1e-07  Score=67.70  Aligned_cols=53  Identities=21%  Similarity=0.244  Sum_probs=44.9

Q ss_pred             ceeeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           36 TLHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        36 ti~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      .+.|.++..+. ..+.|..+.||.++|++|....++|+++++|||+||.  |.-+|
T Consensus        15 ~irV~Vkt~~dk~~~~V~~~ssV~qlKE~I~~~f~a~~dqlvLIfaGrILKD~dTL   70 (493)
T KOG0010|consen   15 LIRVTVKTPKDKYEVNVASDSSVLQLKELIAQRFGAPPDQLVLIYAGRILKDDDTL   70 (493)
T ss_pred             eeEEEEecCCcceeEecccchHHHHHHHHHHHhcCCChhHeeeeecCccccChhhH
Confidence            46777777666 5678899999999999999999999999999999998  44443

>PF11976 Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; InterPro: IPR022617 This entry includes small ubiquitin-related modifier (SUMO) proteins

Probab=98.27  E-value=5.7e-07  Score=51.88  Aligned_cols=40  Identities=35%  Similarity=0.529  Sum_probs=34.0

Q ss_pred             ccccCCCC-cceEEEECCEEeCCCCCCccceec-ccceeeee
Q 040204            2 EDKEEILR-DQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVR   41 (97)
Q Consensus         2 ~~~~gip~-~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i   41 (97)
                      +++.|+|+ +..+|+|.|++|.++.|+++|++. +++|++++
T Consensus        31 ~~~~~i~~~~~~~l~fdG~~L~~~~T~~~~~ied~d~Idv~I   72 (72)
T PF11976_consen   31 CEKKGIPPEESIRLIFDGKRLDPNDTPEDLGIEDGDTIDVII   72 (72)
T ss_dssp             HHHHTTTT-TTEEEEETTEEE-TTSCHHHHT-STTEEEEEE-
T ss_pred             HHhhCCCccceEEEEECCEEcCCCCCHHHCCCCCCCEEEEEC
Confidence            35679999 999999999999999999999999 99999864

SUMOs are small proteins that are covalently attached to lysines as post-translational modifications and are used to control multiple cellular process including signal transduction, nuclear transport and DNA replication and repair []. Unlike ubiquitin, they are not involved in protein degradation. This entry also contains the C-terminal Rad60 DNA repair protein SUMO-like domain.; PDB: 3RD2_A 2JXX_A 3RCZ_A 3GOE_A 3A4S_D 3A4R_B 2IO1_D 1U4A_A 2K1F_A 1WZ0_A ....

>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]

Probab=98.20  E-value=1.9e-06  Score=62.97  Aligned_cols=46  Identities=30%  Similarity=0.357  Sum_probs=40.2

Q ss_pred             eeeeeeecc--eeeeeeccchhHHHHHhhhhhcC--CCCCceEEEECeEe
Q 040204           38 HSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKG--TPPDQQRQIFWFVF   83 (97)
Q Consensus        38 ~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~g--ip~~~q~Lif~G~~   83 (97)
                      .+.++...+  ++|.++|++||.++|.+|+...|  +|+++|.|||+||.
T Consensus         2 ~lt~KtL~q~~F~iev~Pe~tV~evK~kIet~~g~dyP~~~QkLIy~Gki   51 (340)
T KOG0011|consen    2 KLTVKTLKQQTFTIEVKPEDTVVEVKKKIETEKGPDYPAEQQKLIYSGKI   51 (340)
T ss_pred             eeEeeeccCceeEeecCcchhHHHHHHHHHhccCCCCchhhheeeeccee
Confidence            345555555  77889999999999999999998  99999999999998

>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B

Probab=97.99  E-value=3.5e-06  Score=50.48  Aligned_cols=41  Identities=24%  Similarity=0.400  Sum_probs=33.9

Q ss_pred             ccccCCCCcceEEE-ECCE-----Ee-CCCCCCccceec-ccceeeeee
Q 040204            2 EDKEEILRDQQRFI-FAGK-----RL-EDGRTLVDYNIH-GSTLHSVRR   42 (97)
Q Consensus         2 ~~~~gip~~~Q~L~-~~g~-----~L-~d~~tL~~y~I~-~sti~l~i~   42 (97)
                      +...|+|++.|+|. |.|+     .| +|+++|++|++. |.+||++-.
T Consensus        33 ~~~~G~~~~~mrL~l~~~~~~~~~~l~~d~~~L~~y~~~dg~~IhVvD~   81 (84)
T cd01789          33 ELVVGTPASSMRLQLFDGDDKLVSKLDDDDALLGSYPVDDGCRIHVIDV   81 (84)
T ss_pred             HHHHCCCccceEEEEEcCCCCeEeecCCCccEeeeccCCCCCEEEEEeC
Confidence            34579999999995 7776     45 788999999999 999998753

Alp11, also known as tubulin-folding cofactor B, is one of at least three proteins required for the proper folding of tubulins prior to their incorporation into microtubules. These cofactors are necessary for the biogenesis of microtubules and for cell viability. Alp11 has three domains including an N-terminal ubiquitin-like domain (represented by this CD) which executes the essential function, a central coiled-coil domain necessary for maintenance of cellular alpha-tubulin levels, and a C-terminal CLIP-170 domain is required for efficient binding to alpha-tubulin.

>PF11976 Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; InterPro: IPR022617 This entry includes small ubiquitin-related modifier (SUMO) proteins

Probab=97.96  E-value=3.9e-05  Score=44.07  Aligned_cols=46  Identities=28%  Similarity=0.359  Sum_probs=40.1

Q ss_pred             eeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCC-CceEEEECeEe
Q 040204           38 HSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPP-DQQRQIFWFVF   83 (97)
Q Consensus        38 ~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~-~~q~Lif~G~~   83 (97)
                      .+.++..+|  ..+.|++++++..+++..+++.|+|+ ++.+|+|.|+.
T Consensus         2 ~i~v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~fdG~~   50 (72)
T PF11976_consen    2 TIKVRSQDGKEIKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLIFDGKR   50 (72)
T ss_dssp             EEEEEETTSEEEEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEEETTEE
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCccceEEEEECCEE
Confidence            455666666  55777999999999999999999999 99999999998

SUMOs are small proteins that are covalently attached to lysines as post-translational modifications and are used to control multiple cellular process including signal transduction, nuclear transport and DNA replication and repair []. Unlike ubiquitin, they are not involved in protein degradation. This entry also contains the C-terminal Rad60 DNA repair protein SUMO-like domain.; PDB: 3RD2_A 2JXX_A 3RCZ_A 3GOE_A 3A4S_D 3A4R_B 2IO1_D 1U4A_A 2K1F_A 1WZ0_A ....

>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B

Probab=97.84  E-value=4.7e-05  Score=45.55  Aligned_cols=35  Identities=26%  Similarity=0.147  Sum_probs=31.4

Q ss_pred             eeeeeccchhHHHHHhhhhhcCCCCCceEEE-ECeE
Q 040204           48 QIFVESSDTIDNVKAKIQDKKGTPPDQQRQI-FWFV   82 (97)
Q Consensus        48 ~i~v~~~~TV~~lK~~I~~~~gip~~~q~Li-f~G~   82 (97)
                      +..+.++.||.+||++++...|+||+.|+|. |.|+
T Consensus        16 ekr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~~~~   51 (84)
T cd01789          16 EKKYSRGLTIAELKKKLELVVGTPASSMRLQLFDGD   51 (84)
T ss_pred             eEecCCCCcHHHHHHHHHHHHCCCccceEEEEEcCC
Confidence            4456899999999999999999999999995 7887

Alp11, also known as tubulin-folding cofactor B, is one of at least three proteins required for the proper folding of tubulins prior to their incorporation into microtubules. These cofactors are necessary for the biogenesis of microtubules and for cell viability. Alp11 has three domains including an N-terminal ubiquitin-like domain (represented by this CD) which executes the essential function, a central coiled-coil domain necessary for maintenance of cellular alpha-tubulin levels, and a C-terminal CLIP-170 domain is required for efficient binding to alpha-tubulin.

>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]

Probab=97.80  E-value=1.1e-05  Score=58.93  Aligned_cols=42  Identities=21%  Similarity=0.362  Sum_probs=36.4

Q ss_pred             cccC--CCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeee
Q 040204            3 DKEE--ILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFR   44 (97)
Q Consensus         3 ~~~g--ip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~   44 (97)
                      ...|  .|+++|+|+|+||.|.|+.++.+|++. ++.+.++++..
T Consensus        32 t~~g~dyP~~~QkLIy~GkiL~D~~tv~Eykv~E~~fiVvMlsK~   76 (340)
T KOG0011|consen   32 TEKGPDYPAEQQKLIYSGKILKDETTVGEYKVKEKKFIVVMLSKD   76 (340)
T ss_pred             hccCCCCchhhheeeecceeccCCcchhhhccccCceEEEEEecC
Confidence            3445  899999999999999999999999999 88877777654

>PF13881 Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB: 1SE9_A 1WGH_A 2GOW_A

Probab=97.70  E-value=4.8e-05  Score=47.96  Aligned_cols=37  Identities=38%  Similarity=0.587  Sum_probs=28.2

Q ss_pred             CCcceEEEECCEEeCCCCCCccceec-cc------ceeeeeeee
Q 040204            8 LRDQQRFIFAGKRLEDGRTLVDYNIH-GS------TLHSVRRFR   44 (97)
Q Consensus         8 p~~~Q~L~~~g~~L~d~~tL~~y~I~-~s------ti~l~i~~~   44 (97)
                      .++..||+|.|+.|+|+.||+++.+. +.      ++||+++..
T Consensus        47 s~~~lRLI~~GriL~d~~tL~~~~~~~~~~~~~~~vmHlvvrp~   90 (111)
T PF13881_consen   47 SPSDLRLIYAGRILEDNKTLSDCRLPSGETPGGPTVMHLVVRPN   90 (111)
T ss_dssp             SGGGEEEEETTEEE-SSSBTGGGT--TTSETT--EEEEEEE-SS
T ss_pred             ChhhEEEEeCCeecCCcCcHHHhCCCCCCCCCCCEEEEEEecCC
Confidence            46789999999999999999999988 54      678877654

>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A

Probab=97.69  E-value=0.00015  Score=43.40  Aligned_cols=34  Identities=24%  Similarity=0.348  Sum_probs=30.1

Q ss_pred             eeeeeeccchhHHHHHhhhhhcCCCCCceEEEEC
Q 040204           47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFW   80 (97)
Q Consensus        47 ~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~   80 (97)
                      .+..+.++.||.+||++++...|+|++.|+|.+.
T Consensus        16 ~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~   49 (87)
T PF14560_consen   16 VEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLK   49 (87)
T ss_dssp             EEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE
T ss_pred             EEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEE
Confidence            3466799999999999999999999999999997

>KOG4248 consensus Ubiquitin-like protein, regulator of apoptosis [Posttranslational modification, protein turnover, chaperones]

Probab=97.65  E-value=2.2e-05  Score=64.35  Aligned_cols=46  Identities=30%  Similarity=0.584  Sum_probs=41.5

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceecccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHGSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~~sti~l~i~~~~g   46 (97)
                      |.++.+|+.+.|||+|+|+.|.|++++.+|+|.|-+|||+-|.+.+
T Consensus        32 ~r~~~ni~s~~qr~i~~grvl~~~k~vq~~~vdgk~~hlverppp~   77 (1143)
T KOG4248|consen   32 IRASVNIPSEKQRLIYQGRVLQDDKKVQEYNVDGKVIHLVERPPPQ   77 (1143)
T ss_pred             HHHhcccccccceeeecceeeccchhhhhccCCCeEEEeeccCCCC
Confidence            4567899999999999999999999999999999999999886644

>PF11543 UN_NPL4: Nuclear pore localisation protein NPL4; InterPro: IPR024682 Npl4, along with Ufd1, forms the heterodimer adaptor complex UN, which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway

Probab=97.54  E-value=0.00014  Score=43.30  Aligned_cols=44  Identities=27%  Similarity=0.345  Sum_probs=29.3

Q ss_pred             cceeeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEE
Q 040204           35 STLHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQI   78 (97)
Q Consensus        35 sti~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Li   78 (97)
                      ..+-+.++.+.| ..|.+++++|+.+||++|++..++|++.|.|.
T Consensus         3 ~~milRvrS~dG~~Rie~~~~~t~~~L~~kI~~~l~~~~~~~~L~   47 (80)
T PF11543_consen    3 SSMILRVRSKDGMKRIEVSPSSTLSDLKEKISEQLSIPDSSQSLS   47 (80)
T ss_dssp             ---EEEEE-SSEEEEEEE-TTSBHHHHHHHHHHHS---TTT---B
T ss_pred             ccEEEEEECCCCCEEEEcCCcccHHHHHHHHHHHcCCCCcceEEE
Confidence            346677888888 55999999999999999999999999988774

Npl4 has a N-terminal ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert []. This entry represents the ubiquitin-like domain.; PDB: 2PJH_A 1WF9_A.

>cd01788 ElonginB Ubiquitin-like domain of Elongin B

Probab=97.53  E-value=0.00015  Score=45.85  Aligned_cols=50  Identities=18%  Similarity=0.080  Sum_probs=36.9

Q ss_pred             eeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe---CCCcc
Q 040204           38 HSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF---GWGSL   88 (97)
Q Consensus        38 ~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~---~~~~~   88 (97)
                      +++++.... +-+..++++||.+||.+|+.-...||++|+|+ .+-+   |.++|
T Consensus         4 FlmIrR~KTTiF~dakes~tVlelK~~iegI~k~pp~dQrL~-kd~qvLeD~kTL   57 (119)
T cd01788           4 FLMIRRHKTTIFTDAKESTTVYELKRIVEGILKRPPEDQRLY-KDDQLLDDGKTL   57 (119)
T ss_pred             EEEEEecceEEEeecCCcccHHHHHHHHHHHhcCChhHheee-cCceeecccccH
Confidence            444543332 33455999999999999999999999999999 4444   44555

Elongin B is part of an E3 ubiquitin ligase complex called VEC that activates ubiquitylation by the E2 ubiquitin-conjugating enzyme Ubc5. VEC is composed of von Hippel-Lindau tumor suppressor protein (pVHL), elongin C, cullin 2, NEDD8, and Rbx1. ElonginB binds elonginC to form the elonginBC complex which is a positive regulator of RNA polymerase II elongation factor Elongin A. The BC complex then binds VHL (von Hippel-Lindau) tumour suppressor protein to form a VCB ternary complex. Elongin B has a ubiquitin-llike domain.

>KOG0001 consensus Ubiquitin and ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones; General function prediction only]

Probab=97.49  E-value=0.00031  Score=39.04  Aligned_cols=37  Identities=54%  Similarity=0.608  Sum_probs=34.6

Q ss_pred             eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        47 ~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      ..+.+.+.++|..+|.+|...+|+|+++|++.|+|+.
T Consensus        12 ~~~~~~~~~~i~~~k~~i~~~~~~~~~~q~~~~~~~~   48 (75)
T KOG0001|consen   12 ITLEVSPSDTIEVVKAKIRDKEGIPVDQQRLIFGGKP   48 (75)
T ss_pred             EEEEecCCCHHHHHHHHHHhhcCCCCeeEEEEECCEE
Confidence            4577899999999999999999999999999999988

>PLN02560 enoyl-CoA reductase

Probab=97.32  E-value=0.00038  Score=50.92  Aligned_cols=33  Identities=27%  Similarity=0.347  Sum_probs=29.9

Q ss_pred             eeeeeccchhHHHHHhhhhhcCC-CCCceEEEEC
Q 040204           48 QIFVESSDTIDNVKAKIQDKKGT-PPDQQRQIFW   80 (97)
Q Consensus        48 ~i~v~~~~TV~~lK~~I~~~~gi-p~~~q~Lif~   80 (97)
                      ++.++++.||++||.+|+++.++ ++++|||++.
T Consensus        17 ~lev~~~aTV~dLK~~Isk~~~~~~~~RqRL~~~   50 (308)
T PLN02560         17 GLEVPDSATVADLKKAIHKRKKKYYPSRQRLTLP   50 (308)
T ss_pred             eEEcCCCCcHHHHHHHHHHHcCCCChhheEEEEe
Confidence            46789999999999999999986 8999999994

>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]

Probab=97.27  E-value=0.00033  Score=51.59  Aligned_cols=40  Identities=30%  Similarity=0.404  Sum_probs=37.4

Q ss_pred             ecceeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           44 RGGMQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        44 ~~g~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      ..++.|.|+.+.+|..||+.++.+.|+|+++.++||+||+
T Consensus        13 ~h~l~v~v~~~t~I~~lke~Vak~~gvp~D~L~viFaGKe   52 (446)
T KOG0006|consen   13 SHGLPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKE   52 (446)
T ss_pred             cCceeEEEecCCCHHHHHHHHHHhhCCChhheEEEEeccc
Confidence            3457899999999999999999999999999999999998

>PF13881 Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB: 1SE9_A 1WGH_A 2GOW_A

Probab=97.25  E-value=0.0012  Score=41.67  Aligned_cols=54  Identities=19%  Similarity=0.198  Sum_probs=38.1

Q ss_pred             ceeeeeeeecce---eeeeeccchhHHHHHhhhhhc-----C--CCCCceEEEECeEe--CCCccc
Q 040204           36 TLHSVRRFRGGM---QIFVESSDTIDNVKAKIQDKK-----G--TPPDQQRQIFWFVF--GWGSLW   89 (97)
Q Consensus        36 ti~l~i~~~~g~---~i~v~~~~TV~~lK~~I~~~~-----g--ip~~~q~Lif~G~~--~~~~~~   89 (97)
                      .|.|..+..+|.   ....++++||.+||+.|-...     .  ..++..||||.||.  |..+|=
T Consensus         2 ~i~lkf~l~~G~d~~~~~~~~~~TV~~lKe~i~~~WP~d~~~~p~s~~~lRLI~~GriL~d~~tL~   67 (111)
T PF13881_consen    2 KIELKFRLADGKDIGPFRFDPSTTVADLKERIWAEWPEDWEERPKSPSDLRLIYAGRILEDNKTLS   67 (111)
T ss_dssp             SEEEEEEETTS-EEEEEEE-TTSBHHHHHHHHHHSSSTTSSSTT-SGGGEEEEETTEEE-SSSBTG
T ss_pred             eEEEEEEEeCCCcccccccCccChHHHHHHHHHHHCccccccCCCChhhEEEEeCCeecCCcCcHH
Confidence            456667776774   244588999999999997542     2  34889999999999  446653

>cd01811 OASL_repeat1 2'-5' oligoadenylate synthetase-like protein, repeat 1 of 2

Probab=97.23  E-value=0.0002  Score=42.11  Aligned_cols=41  Identities=27%  Similarity=0.498  Sum_probs=32.2

Q ss_pred             cccCCCCcceEEEE---CCEE--eCCCCCCccceec-ccceeeeeeee
Q 040204            3 DKEEILRDQQRFIF---AGKR--LEDGRTLVDYNIH-GSTLHSVRRFR   44 (97)
Q Consensus         3 ~~~gip~~~Q~L~~---~g~~--L~d~~tL~~y~I~-~sti~l~i~~~   44 (97)
                      ...|++ ..|||.|   +|++  |.+..+|++|||. +..|.++.+.+
T Consensus        32 ~~~~~~-g~qrLsfQepgg~rqlL~s~~sLA~yGiFs~~~i~lleT~p   78 (80)
T cd01811          32 RSRNCS-GLQRLSFQEPGGERQLLSSRKSLADYGIFSKTNICLLETFP   78 (80)
T ss_pred             HhhCcc-cceEEEeecCCcccccccccccHhhhcceeccEEEEEecCC
Confidence            345666 5999999   4544  7999999999999 98888876643

OASL_repeat1 (2'-5' oligoadenylate synthetase-like protein) belongs to a family of interferon-induced 2'-5' oligoadenylate synthetases which are important for the antiviral activity of interferons. While each member of this famliy has a conserved N-terminal OAS catalytic domain, only OASL has two tandem ubiquitin-like repeats located at the C-terminus and this CD represents one of those repeats.

>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A

Probab=97.18  E-value=9.7e-05  Score=44.21  Aligned_cols=40  Identities=30%  Similarity=0.459  Sum_probs=30.0

Q ss_pred             ccccCCCCcceEEEEC----CEE---e-CCCCCCccceec-ccceeeee
Q 040204            2 EDKEEILRDQQRFIFA----GKR---L-EDGRTLVDYNIH-GSTLHSVR   41 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~----g~~---L-~d~~tL~~y~I~-~sti~l~i   41 (97)
                      +...|+|++.|+|.+.    +..   + .|.++|.+||+. |.+||+.=
T Consensus        34 ~~~~Gi~~~~m~L~l~~~~~~~~~~~~~dd~~~L~~y~~~dg~~i~V~D   82 (87)
T PF14560_consen   34 EKLTGIPPSDMRLQLKSDKDDSKIEELDDDDATLGSYGIKDGMRIHVVD   82 (87)
T ss_dssp             HHHHTS-TTTEEEEEE-TSSSSEEEESSGSSSBCCHHT-STTEEEEEEE
T ss_pred             HHHhCCCcccEEEEEEecCCCccccccCCCccEeecCCCCCCCEEEEEe
Confidence            4568999999999984    222   3 578999999999 99998764

>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13

Probab=97.12  E-value=0.00032  Score=41.08  Aligned_cols=34  Identities=35%  Similarity=0.489  Sum_probs=29.8

Q ss_pred             CCCCcceEEE--ECCEEeCCCCCCccceec-ccceee
Q 040204            6 EILRDQQRFI--FAGKRLEDGRTLVDYNIH-GSTLHS   39 (97)
Q Consensus         6 gip~~~Q~L~--~~g~~L~d~~tL~~y~I~-~sti~l   39 (97)
                      .++++.|+|.  +.|+.|.|+.+|.+||+. ++++++
T Consensus        38 ~~~~~Rqrl~~~~~g~~L~d~~tL~~~gv~~g~~lyv   74 (77)
T cd01801          38 QLTVNRQSLRLEPKGKSLKDDDTLVDLGVGAGATLYV   74 (77)
T ss_pred             CCCcceeEEEeCCCCcccCCcccHhhcCCCCCCEEEE
Confidence            4688999996  689999999999999999 998765

Tsc13_N N-terminal domain of Tsc13. Tsc13 is an enoyl reductase involved in elongation of long chain fatty acids that localizes to the endoplasmic reticulum and is highly enriched in a novel structure marking nuclear-vacuolar junctions.

>cd00196 UBQ Ubiquitin-like proteins

Probab=97.10  E-value=0.0011  Score=34.78  Aligned_cols=42  Identities=33%  Similarity=0.442  Sum_probs=35.5

Q ss_pred             eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEeCCCcc
Q 040204           47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVFGWGSL   88 (97)
Q Consensus        47 ~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~~~~~~   88 (97)
                      ..+.+.++.|++++|.+|.++.|++++.|.|++.|.......
T Consensus        10 ~~~~~~~~~tv~~l~~~i~~~~~~~~~~~~l~~~~~~~~~~~   51 (69)
T cd00196          10 VELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGKILPDSL   51 (69)
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHCcChHHeEEEECCeECCCCC
Confidence            445567899999999999999999999999999998844333

Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate.

>cd01788 ElonginB Ubiquitin-like domain of Elongin B

Probab=97.10  E-value=0.00034  Score=44.30  Aligned_cols=59  Identities=19%  Similarity=0.228  Sum_probs=42.7

Q ss_pred             CCCCcceEEEECCEEeCCCCCCcccee-------c-ccceeeeeeeecc-e-eeeeeccchhHHHHHhh
Q 040204            6 EILRDQQRFIFAGKRLEDGRTLVDYNI-------H-GSTLHSVRRFRGG-M-QIFVESSDTIDNVKAKI   64 (97)
Q Consensus         6 gip~~~Q~L~~~g~~L~d~~tL~~y~I-------~-~sti~l~i~~~~g-~-~i~v~~~~TV~~lK~~I   64 (97)
                      ..||++|+|+-.+..|+|++||++||+       + .+++=+..+...| + .+.+.|..+=-+|=.-+
T Consensus        36 k~pp~dQrL~kd~qvLeD~kTL~d~g~t~~~akaq~pA~vgLa~r~~d~~fE~l~I~p~S~pp~lPdvm  104 (119)
T cd01788          36 KRPPEDQRLYKDDQLLDDGKTLGDCGFTSQTARPQAPATVGLAFRSSDDTFEPLRIEPFSSPPELPDVM  104 (119)
T ss_pred             cCChhHheeecCceeecccccHHHcCccccccccCCCCeEEEEEecCCCCccceeeeeCCCCCCchhhh
Confidence            469999999977778999999999999       6 7788888876544 3 36665554444443333

Elongin B is part of an E3 ubiquitin ligase complex called VEC that activates ubiquitylation by the E2 ubiquitin-conjugating enzyme Ubc5. VEC is composed of von Hippel-Lindau tumor suppressor protein (pVHL), elongin C, cullin 2, NEDD8, and Rbx1. ElonginB binds elonginC to form the elonginBC complex which is a positive regulator of RNA polymerase II elongation factor Elongin A. The BC complex then binds VHL (von Hippel-Lindau) tumour suppressor protein to form a VCB ternary complex. Elongin B has a ubiquitin-llike domain.

>PF10302 DUF2407: DUF2407 ubiquitin-like domain; InterPro: IPR019413 This entry represents a family of proteins of unknown function found in fungi

Probab=96.96  E-value=0.0019  Score=39.82  Aligned_cols=45  Identities=16%  Similarity=0.212  Sum_probs=34.7

Q ss_pred             eeeeeecc---eeeeee--ccchhHHHHHhhhhhc--CCCCCceEEEECeEe
Q 040204           39 SVRRFRGG---MQIFVE--SSDTIDNVKAKIQDKK--GTPPDQQRQIFWFVF   83 (97)
Q Consensus        39 l~i~~~~g---~~i~v~--~~~TV~~lK~~I~~~~--gip~~~q~Lif~G~~   83 (97)
                      ++++...+   ..+.+.  .+.||..||.+|++.-  ...-..+||||+||.
T Consensus         3 l~IRFs~sipDl~L~I~~~~~~Tv~~LK~lIR~~~p~~~s~~rLRlI~~Gr~   54 (97)
T PF10302_consen    3 LTIRFSDSIPDLPLDIPSPNTTTVAWLKQLIRERLPPEPSRRRLRLIYAGRL   54 (97)
T ss_pred             EEEEECCCCCCceeecCCCCcccHHHHHHHHHhhcCCCCccccEEeeecCcc
Confidence            45555544   345554  7899999999999886  367789999999999

They contain a characteristic GFDRL sequence motif.

>KOG4248 consensus Ubiquitin-like protein, regulator of apoptosis [Posttranslational modification, protein turnover, chaperones]

Probab=96.88  E-value=0.0014  Score=54.30  Aligned_cols=37  Identities=22%  Similarity=0.300  Sum_probs=34.3

Q ss_pred             eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        47 ~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      -++.|...+||.++|..|.++.+|+.+.|||||+||.
T Consensus        15 ~t~~ig~q~ti~~~~d~~r~~~ni~s~~qr~i~~grv   51 (1143)
T KOG4248|consen   15 RTFIIGAQMTIKEFKDHIRASVNIPSEKQRLIYQGRV   51 (1143)
T ss_pred             eEEEechHHHHHHHHHHHHHhcccccccceeeeccee
Confidence            3466788999999999999999999999999999998

>cd01811 OASL_repeat1 2'-5' oligoadenylate synthetase-like protein, repeat 1 of 2

Probab=96.85  E-value=0.0034  Score=36.95  Aligned_cols=44  Identities=20%  Similarity=0.190  Sum_probs=36.3

Q ss_pred             eeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECe
Q 040204           37 LHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWF   81 (97)
Q Consensus        37 i~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G   81 (97)
                      |++.+...+.  ..+.|+|..+|..+|++|+...|++- +|||.|+-
T Consensus         1 iqVtV~q~g~~dl~l~vnPy~pI~k~K~kI~~~~~~~g-~qrLsfQe   46 (80)
T cd01811           1 IQVTVEQTGYSDWILRVNPYSPIRKIKEKIRRSRNCSG-LQRLSFQE   46 (80)
T ss_pred             CEEEeeecCCCceEEEeCCcchHHHHHHHHHHhhCccc-ceEEEeec
Confidence            3455666665  45778999999999999999999988 99999963

OASL_repeat1 (2'-5' oligoadenylate synthetase-like protein) belongs to a family of interferon-induced 2'-5' oligoadenylate synthetases which are important for the antiviral activity of interferons. While each member of this famliy has a conserved N-terminal OAS catalytic domain, only OASL has two tandem ubiquitin-like repeats located at the C-terminus and this CD represents one of those repeats.

>cd00196 UBQ Ubiquitin-like proteins

Probab=96.58  E-value=0.0013  Score=34.52  Aligned_cols=40  Identities=38%  Similarity=0.516  Sum_probs=34.4

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeee
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVR   41 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i   41 (97)
                      .++.|++++.+.|+++|..+.+...+.+|++. ++++++..
T Consensus        28 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~   68 (69)
T cd00196          28 AKKLGLPPEQQRLLVNGKILPDSLTLEDYGLQDGDELVLVP   68 (69)
T ss_pred             HHHHCcChHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEe
Confidence            34567899999999999999999888899999 99888764

Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate.

>PLN02560 enoyl-CoA reductase

Probab=96.40  E-value=0.0017  Score=47.54  Aligned_cols=42  Identities=29%  Similarity=0.518  Sum_probs=32.3

Q ss_pred             ccccCC-CCcceEEEEC---CE----EeCCCCCCccceec-ccceeeeeeeec
Q 040204            2 EDKEEI-LRDQQRFIFA---GK----RLEDGRTLVDYNIH-GSTLHSVRRFRG   45 (97)
Q Consensus         2 ~~~~gi-p~~~Q~L~~~---g~----~L~d~~tL~~y~I~-~sti~l~i~~~~   45 (97)
                      +++.++ ++++|||.+.   |+    .|+|+++|++||+. +++++  ++..|
T Consensus        34 sk~~~~~~~~RqRL~~~~~~gk~~g~~L~d~ktL~d~gv~~gstLy--~kDLG   84 (308)
T PLN02560         34 HKRKKKYYPSRQRLTLPLPPGKTRPTVLDDSKSLKDYGLGDGGTVV--FKDLG   84 (308)
T ss_pred             HHHcCCCChhheEEEEecCCCCcCccccCCCCCHHhcCCCCCceEE--EEeCC
Confidence            456676 8999999983   43    78999999999999 88754  44444

>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]

Probab=96.22  E-value=0.0018  Score=47.84  Aligned_cols=42  Identities=31%  Similarity=0.470  Sum_probs=36.9

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeee-eee
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSV-RRF   43 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~-i~~   43 (97)
                      +...|+|+++.+++|+||.|+|+.++..+.+. .+.+|++ .|+
T Consensus        34 ak~~gvp~D~L~viFaGKeLs~~ttv~~cDL~qqs~~hi~~lRP   77 (446)
T KOG0006|consen   34 AKRQGVPADQLRVIFAGKELSNDTTVQNCDLSQQSATHIMLLRP   77 (446)
T ss_pred             HHhhCCChhheEEEEeccccccCceeecccccccchhhhhccCc
Confidence            56789999999999999999999999999988 8888877 444

>KOG1769 consensus Ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones]

Probab=95.81  E-value=0.011  Score=36.56  Aligned_cols=45  Identities=24%  Similarity=0.599  Sum_probs=41.0

Q ss_pred             cccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecce
Q 040204            3 DKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGM   47 (97)
Q Consensus         3 ~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~   47 (97)
                      +..|++.+..|++|+|+++.+.+|-++.+.. ++.|.++....+|.
T Consensus        52 ~r~Gl~~~s~RFlFdG~rI~~~~TP~~L~mEd~D~Iev~~~q~gG~   97 (99)
T KOG1769|consen   52 ERQGLSMNSLRFLFDGQRIRETHTPADLEMEDGDEIEVVQEQTGGF   97 (99)
T ss_pred             HHcCCccceEEEEECCcCcCCCCChhhhCCcCCcEEEEEeecccCC
Confidence            4679999999999999999999999999999 99999998877764

>KOG1872 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]

Probab=95.79  E-value=0.015  Score=44.59  Aligned_cols=45  Identities=18%  Similarity=0.327  Sum_probs=37.5

Q ss_pred             eeeeeecc-eeee-eeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           39 SVRRFRGG-MQIF-VESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        39 l~i~~~~g-~~i~-v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +.++..+. ..+. ++.++|+..+|+++...+|+||+.|++++.|..
T Consensus         6 v~VKW~gk~y~v~~l~~d~t~~vlKaqlf~LTgV~PeRQKv~vKGg~   52 (473)
T KOG1872|consen    6 VIVKWGGKKYPVETLSTDETPSVLKAQLFALTGVPPERQKVMVKGGL   52 (473)
T ss_pred             EeeeecCccccceeccCCCchHHHHHHHHHhcCCCccceeEEEeccc
Confidence            44554444 3344 688999999999999999999999999999998

>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13

Probab=94.97  E-value=0.029  Score=32.68  Aligned_cols=32  Identities=16%  Similarity=-0.031  Sum_probs=26.6

Q ss_pred             eccchhHHHHHhhhhhcC-CCCCceEEE--ECeEe
Q 040204           52 ESSDTIDNVKAKIQDKKG-TPPDQQRQI--FWFVF   83 (97)
Q Consensus        52 ~~~~TV~~lK~~I~~~~g-ip~~~q~Li--f~G~~   83 (97)
                      .++.||.+||..|.+..+ +++++|||.  +.|+.
T Consensus        20 ~~~aTV~dlk~~i~~~~~~~~~~Rqrl~~~~~g~~   54 (77)
T cd01801          20 SGDATIADLKKLIAKSSPQLTVNRQSLRLEPKGKS   54 (77)
T ss_pred             CCCccHHHHHHHHHHHcCCCCcceeEEEeCCCCcc
Confidence            578899999999998865 689999996  66654

Tsc13_N N-terminal domain of Tsc13. Tsc13 is an enoyl reductase involved in elongation of long chain fatty acids that localizes to the endoplasmic reticulum and is highly enriched in a novel structure marking nuclear-vacuolar junctions.

>KOG4495 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin B [Transcription]

Probab=94.95  E-value=0.044  Score=33.83  Aligned_cols=36  Identities=19%  Similarity=0.129  Sum_probs=29.8

Q ss_pred             eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeE
Q 040204           47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFV   82 (97)
Q Consensus        47 ~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~   82 (97)
                      +-+.-+++.||.++|.+++.-..=|++.|+|.--.-
T Consensus        14 if~da~es~tV~elK~~l~gi~~~Pvn~qrL~kmd~   49 (110)
T KOG4495|consen   14 IFTDAKESSTVFELKRKLEGILKRPVNEQRLYKMDT   49 (110)
T ss_pred             EEeecCccccHHHHHHHHHHHHhCCCcchheeecCH
Confidence            334448999999999999999999999999987333

>KOG1872 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]

Probab=93.80  E-value=0.091  Score=40.49  Aligned_cols=44  Identities=16%  Similarity=0.196  Sum_probs=38.8

Q ss_pred             cccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            3 DKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         3 ~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      ..+|+||+.|++...|..+.|+-......|+ |.+++|+-+...+
T Consensus        35 ~LTgV~PeRQKv~vKGg~a~dd~~~~al~iKpn~~lmMmGt~e~~   79 (473)
T KOG1872|consen   35 ALTGVPPERQKVMVKGGLAKDDVDWGALQIKPNETLMMMGTAEAG   79 (473)
T ss_pred             HhcCCCccceeEEEecccccccccccccccCCCCEEEeecccccc
Confidence            4589999999999999999999899999999 9999988765543

>PF11543 UN_NPL4: Nuclear pore localisation protein NPL4; InterPro: IPR024682 Npl4, along with Ufd1, forms the heterodimer adaptor complex UN, which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway

Probab=92.01  E-value=0.022  Score=33.74  Aligned_cols=39  Identities=21%  Similarity=0.256  Sum_probs=18.3

Q ss_pred             ccccCCCCcceEEEE---CCEEe--CCCCCCccceec-ccceeee
Q 040204            2 EDKEEILRDQQRFIF---AGKRL--EDGRTLVDYNIH-GSTLHSV   40 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~---~g~~L--~d~~tL~~y~I~-~sti~l~   40 (97)
                      ++..++|.+.|.|+.   +...+  +++++|+++||+ |+-+++.
T Consensus        34 ~~~l~~~~~~~~L~~~~~~~~~l~s~~~~tl~~lglkHGdmlyL~   78 (80)
T PF11543_consen   34 SEQLSIPDSSQSLSKDRNNKEELKSSDSKTLSSLGLKHGDMLYLK   78 (80)
T ss_dssp             HHHS---TTT---BSSGGGGGCSSS-TT-CCCCT---TT-EEE--
T ss_pred             HHHcCCCCcceEEEecCCCCcccccCCcCCHHHcCCCCccEEEEe
Confidence            456788988998875   22345  578999999999 9998764

Npl4 has a N-terminal ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert []. This entry represents the ubiquitin-like domain.; PDB: 2PJH_A 1WF9_A.

>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]

Probab=91.28  E-value=0.074  Score=30.55  Aligned_cols=31  Identities=26%  Similarity=0.446  Sum_probs=25.4

Q ss_pred             eeeeeeccchhHHHHHhhhhhcCCCCCceEE
Q 040204           47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQ   77 (97)
Q Consensus        47 ~~i~v~~~~TV~~lK~~I~~~~gip~~~q~L   77 (97)
                      ..|...++|||+++|..|..++|..++.-+|
T Consensus        14 VRvKCn~dDtiGD~KKliaaQtGT~~~kivl   44 (73)
T KOG3493|consen   14 VRVKCNTDDTIGDLKKLIAAQTGTRPEKIVL   44 (73)
T ss_pred             EEEEeCCcccccCHHHHHHHhhCCChhHhHH
Confidence            3455589999999999999999988876544

>PF08817 YukD: WXG100 protein secretion system (Wss), protein YukD; InterPro: IPR014921 YukD is a bacterial protein that adopts a ubiquitin-like fold []

Probab=91.28  E-value=0.13  Score=30.10  Aligned_cols=28  Identities=25%  Similarity=0.369  Sum_probs=20.7

Q ss_pred             eEEE-ECCEEeCCCCCCccceec-ccceee
Q 040204           12 QRFI-FAGKRLEDGRTLVDYNIH-GSTLHS   39 (97)
Q Consensus        12 Q~L~-~~g~~L~d~~tL~~y~I~-~sti~l   39 (97)
                      -+|. -+|.+|+++++|++++|. |+.+.+
T Consensus        49 ~~L~~~~g~~L~~~~tL~~~gV~dGd~L~L   78 (79)
T PF08817_consen   49 WVLARAGGRPLDPDQTLADAGVRDGDVLVL   78 (79)
T ss_dssp             EEEG-GGTEEEETTSBCGGGT--TT-EEEE
T ss_pred             EEEEecCCcccCCcCcHhHcCCCCCCEEEe
Confidence            3444 489999999999999999 998875

Ubiquitin covalently binds to protein and flags them for protein degradation, however conjugation assays have indicated that YukD lacks the capacity for covalent bond formation with other proteins []. ; PDB: 2BPS_B.

>KOG4250 consensus TANK binding protein kinase TBK1 [Signal transduction mechanisms]

Probab=89.80  E-value=0.44  Score=38.65  Aligned_cols=50  Identities=16%  Similarity=0.294  Sum_probs=38.8

Q ss_pred             ccceeeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      ...+|++...... ..+.+.++.|...+++.|...+|+|...|.|.|.|.-
T Consensus       313 ~~vvhiFs~~~~~~~~~~~~~~ntl~~~~~~I~~~Tgipe~~qeLL~e~~~  363 (732)
T KOG4250|consen  313 LKVVHIFSMVQATSHEYYVHADNTLHSLIERISKQTGIPEGKQELLFEGGL  363 (732)
T ss_pred             hheeEEEeeccceEEEEecChhhhHHHHHHHHHHhhCCCCccceeeeecCc
Confidence            3445544432222 4567799999999999999999999999999999875

>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis

Probab=89.75  E-value=1.5  Score=26.14  Aligned_cols=38  Identities=16%  Similarity=0.087  Sum_probs=34.0

Q ss_pred             ceeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           46 GMQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        46 g~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      -+-|.|.+.-+...|.++|.++-++|++...|.|....
T Consensus        12 tIaIrvp~~~~y~~L~~ki~~kLkl~~e~i~LsYkde~   49 (80)
T cd06406          12 TVAIQVARGLSYATLLQKISSKLELPAEHITLSYKSEA   49 (80)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCchhcEEEeccCC
Confidence            45567788999999999999999999999999998876

PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain

>smart00455 RBD Raf-like Ras-binding domain

Probab=89.61  E-value=0.8  Score=26.34  Aligned_cols=37  Identities=19%  Similarity=0.109  Sum_probs=32.5

Q ss_pred             eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        47 ~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      ..+.++|..|+.++=+++.++.|+.++...+...|..
T Consensus        12 ~~V~vrpg~tl~e~L~~~~~kr~l~~~~~~v~~~g~~   48 (70)
T smart00455       12 TVVKVRPGKTVRDALAKALKKRGLNPECCVVRLRGEK   48 (70)
T ss_pred             EEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEcCCC
Confidence            4577799999999999999999999999998886643

>KOG0013 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.37  E-value=0.25  Score=34.56  Aligned_cols=40  Identities=25%  Similarity=0.267  Sum_probs=34.0

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeee
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVR   41 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i   41 (97)
                      ..++|+.+..|+.+|+|+.+-|...|.+++|+ ++...+-+
T Consensus       177 ~Aaeg~D~~sQrif~Sg~~l~dkt~LeEc~iekg~rYvlqv  217 (231)
T KOG0013|consen  177 RAAEGVDPLSQRIFFSGGVLVDKTDLEECKIEKGQRYVLQV  217 (231)
T ss_pred             HHhhccchhhheeeccCCceeccccceeeeecCCCEEEEEE
Confidence            35688888999999999999999999999999 87655433

>PF11470 TUG-UBL1: GLUT4 regulating protein TUG; InterPro: IPR021569 TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly

Probab=89.31  E-value=1  Score=25.68  Aligned_cols=37  Identities=16%  Similarity=0.095  Sum_probs=29.2

Q ss_pred             eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        47 ~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      ..|.+.|+.++.++-+...++.|+.+++..|.|+++.
T Consensus         9 ~~vkvtp~~~l~~VL~eac~k~~l~~~~~~L~h~~k~   45 (65)
T PF11470_consen    9 FKVKVTPNTTLNQVLEEACKKFGLDPSSYDLKHNNKP   45 (65)
T ss_dssp             EEE---TTSBHHHHHHHHHHHTT--GGG-EEEETTEE
T ss_pred             EEEEECCCCCHHHHHHHHHHHcCCCccceEEEECCEE
Confidence            5677899999999999999999999999999999998

TUG releases the GLUT4 containing vesicles to the cellular exocytic machinery in response to insulin stimulation which allows translocation to the plasma membrane []. TUG has an N-terminal ubiquitin-like domain (UBL1) which in similar proteins appears to participate in protein-protein interactions []. The region does have a area of negative electrostatic potential and increased backbone motility which leads to suggestions of a potential protein-protein interaction site []. ; PDB: 2AL3_A.

>PF11470 TUG-UBL1: GLUT4 regulating protein TUG; InterPro: IPR021569 TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly

Probab=86.77  E-value=0.52  Score=26.89  Aligned_cols=37  Identities=14%  Similarity=0.023  Sum_probs=25.5

Q ss_pred             cccCCCCcceEEEECCEEeCCCCCCccceec-ccceee
Q 040204            3 DKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHS   39 (97)
Q Consensus         3 ~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l   39 (97)
                      ++.|+.+++=.|.|+++.|+-..+..-.|+. |+++.|
T Consensus        28 ~k~~l~~~~~~L~h~~k~ldlslp~R~snL~n~akLeL   65 (65)
T PF11470_consen   28 KKFGLDPSSYDLKHNNKPLDLSLPFRLSNLPNNAKLEL   65 (65)
T ss_dssp             HHTT--GGG-EEEETTEEESSS-BHHHH---SS-EEEE
T ss_pred             HHcCCCccceEEEECCEEeccccceeecCCCCCCEEeC
Confidence            4678988999999999999999999999999 998764

TUG releases the GLUT4 containing vesicles to the cellular exocytic machinery in response to insulin stimulation which allows translocation to the plasma membrane []. TUG has an N-terminal ubiquitin-like domain (UBL1) which in similar proteins appears to participate in protein-protein interactions []. The region does have a area of negative electrostatic potential and increased backbone motility which leads to suggestions of a potential protein-protein interaction site []. ; PDB: 2AL3_A.

>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins

Probab=86.17  E-value=4  Score=23.39  Aligned_cols=48  Identities=21%  Similarity=0.280  Sum_probs=37.6

Q ss_pred             ceeeeeeeeccee--eeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           36 TLHSVRRFRGGMQ--IFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        36 ti~l~i~~~~g~~--i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      |+.+.+...+...  +.+.++.|..+|+.+|+++.+.+.....|-|.+..
T Consensus         1 t~~vK~~~~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~Y~D~d   50 (84)
T PF00564_consen    1 TVRVKVRYGGDIRRIISLPSDVSFDDLRSKIREKFGLLDEDFQLKYKDED   50 (84)
T ss_dssp             SEEEEEEETTEEEEEEEECSTSHHHHHHHHHHHHHTTSTSSEEEEEEETT
T ss_pred             CEEEEEEECCeeEEEEEcCCCCCHHHHHHHHHHHhCCCCccEEEEeeCCC
Confidence            3445555555532  56677889999999999999999999999998866

The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....

>cd01760 RBD Ubiquitin-like domain of RBD-like S/T kinases

Probab=85.36  E-value=2.1  Score=24.85  Aligned_cols=41  Identities=20%  Similarity=0.213  Sum_probs=34.7

Q ss_pred             eecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           43 FRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        43 ~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .++|  ..+.|+|.+||.++=+++.++.|+.++...|...|..
T Consensus         6 LPng~~t~V~vrpg~ti~d~L~~~c~kr~l~~~~~~v~~~~~~   48 (72)
T cd01760           6 LPNGQRTVVPVRPGMSVRDVLAKACKKRGLNPECCDVFLLGLD   48 (72)
T ss_pred             CcCCCeEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEecCC
Confidence            4444  4578899999999999999999999999988888654

The ras-binding domain (RBD) of the serine/threonine kinase raf is structurally quite similar to the beta-grasp fold of ubiquitin. A raf-like RBD is also present in RGS12 and other members of a family of GTPase activating proteins and TIAM1, a guanine nucleotide exchange protein.

>KOG0013 consensus Uncharacterized conserved protein [Function unknown]

Probab=84.94  E-value=0.75  Score=32.25  Aligned_cols=62  Identities=18%  Similarity=0.141  Sum_probs=44.2

Q ss_pred             CCCCCCccceec---ccceeeeeeee---cceeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           22 EDGRTLVDYNIH---GSTLHSVRRFR---GGMQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        22 ~d~~tL~~y~I~---~sti~l~i~~~---~g~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .|..+++.++.+   +.+..+..+..   ..+.+.+...+||.++|...+.++|+.+-.|+++|.|+.
T Consensus       128 ~d~~s~ei~~ppp~~~~e~~lk~rlTtT~~d~~lta~~~Dtv~eik~~L~Aaeg~D~~sQrif~Sg~~  195 (231)
T KOG0013|consen  128 KDSESLEIPEPPPSNHTEPILKLRLTTTREDFWLTAPHYDTVGEIKRALRAAEGVDPLSQRIFFSGGV  195 (231)
T ss_pred             ccccccccCCCCCCCCCCcchHHHhhhhhhheeecccCcCcHHHHHHHHHHhhccchhhheeeccCCc
Confidence            355566666554   22333333322   224455688999999999999999999999999999988

>KOG4583 consensus Membrane-associated ER protein involved in stress response (contains ubiquitin-like domain) [Posttranslational modification, protein turnover, chaperones]

Probab=84.51  E-value=0.41  Score=35.78  Aligned_cols=51  Identities=12%  Similarity=0.050  Sum_probs=36.3

Q ss_pred             ceeeeeeeecc----eeeeeeccchhHHHHHhhhhhc--CCCCCceEEEECeEeCCC
Q 040204           36 TLHSVRRFRGG----MQIFVESSDTIDNVKAKIQDKK--GTPPDQQRQIFWFVFGWG   86 (97)
Q Consensus        36 ti~l~i~~~~g----~~i~v~~~~TV~~lK~~I~~~~--gip~~~q~Lif~G~~~~~   86 (97)
                      .+.+.++.++.    ..|..+..-||++||.......  .--..+|||||.||.+..
T Consensus         9 ~v~lliks~Nq~y~dl~i~~dl~wtv~~Lk~hls~VyPskpl~~dqrliYsgkllld   65 (391)
T KOG4583|consen    9 PVTLLIKSPNQSYKDLSISLDLKWTVGDLKVHLSQVYPSKPLELDQRLIYSGKLLLD   65 (391)
T ss_pred             ceEEEecCCCccccceeeehhhhhhHHHHhhhHhhcCCCCCchhhHHHHhhcccccc
Confidence            44555555443    3455577889999999988764  344678999999999543

>smart00166 UBX Domain present in ubiquitin-regulatory proteins

Probab=84.12  E-value=4.2  Score=23.50  Aligned_cols=44  Identities=18%  Similarity=0.095  Sum_probs=31.9

Q ss_pred             cceeeeeeeecceee--eeeccchhHHHHHhhhhhcCCCCCceEEE
Q 040204           35 STLHSVRRFRGGMQI--FVESSDTIDNVKAKIQDKKGTPPDQQRQI   78 (97)
Q Consensus        35 sti~l~i~~~~g~~i--~v~~~~TV~~lK~~I~~~~gip~~~q~Li   78 (97)
                      ....+.+|.++|..+  ...+++||.+|.+-+....+.......|+
T Consensus         3 ~~~~I~iRlPdG~ri~~~F~~~~tl~~v~~~v~~~~~~~~~~f~L~   48 (80)
T smart00166        3 DQCRLQIRLPDGSRLVRRFPSSDTLRTVYEFVSAALTDGNDPFTLN   48 (80)
T ss_pred             CeEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHcccCCCCCEEEE
Confidence            345678888888544  44889999999999966566555555554

Present in FAF1 and Shp1p.

>COG5227 SMT3 Ubiquitin-like protein (sentrin) [Posttranslational modification, protein turnover, chaperones]

Probab=83.99  E-value=0.39  Score=29.38  Aligned_cols=43  Identities=26%  Similarity=0.456  Sum_probs=34.6

Q ss_pred             ccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            4 KEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         4 ~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      ..|-..+..|+.|+|+.+.-++|-++++.. +..|..+....||
T Consensus        57 rqGK~m~slRfL~dG~rI~~dqTP~dldmEdnd~iEav~eQvGG  100 (103)
T COG5227          57 RQGKNMSSLRFLFDGKRIDLDQTPGDLDMEDNDEIEAVTEQVGG  100 (103)
T ss_pred             HhCcCcceeEEEEcceecCCCCChhhcCCccchHHHHHHHHhcC
Confidence            456667889999999999999999999998 8877766554444

>PF11620 GABP-alpha: GA-binding protein alpha chain; InterPro: IPR024668 GA-binding protein alpha is a transcription factor capable of interacting with purine rich repeats (GA repeats)

Probab=83.79  E-value=3.4  Score=24.95  Aligned_cols=55  Identities=18%  Similarity=0.277  Sum_probs=29.8

Q ss_pred             cccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeee--cc-eeee---e-eccchh
Q 040204            3 DKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFR--GG-MQIF---V-ESSDTI   57 (97)
Q Consensus         3 ~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~--~g-~~i~---v-~~~~TV   57 (97)
                      .+.|++-+.-.++..+..|+++++|.+-+++ ...+.+.+...  .| ..|.   | +|.++|
T Consensus        24 ~Rl~~~L~~~~f~LQD~~L~~~k~L~dQcVqgeGlVQlnvQi~s~~~~~riNIvdVlKP~e~~   86 (88)
T PF11620_consen   24 RRLGISLSDYEFWLQDIQLEPHKSLVDQCVQGEGLVQLNVQIKSNQGEPRINIVDVLKPAEDV   86 (88)
T ss_dssp             HHH-S--SS-EEEETTEE--TTSBTTTSS----SEEEEEEEEE--TT--EEEEEEEEETTS--
T ss_pred             HhhCCCcCCCeEEeccceecCCccHHHhhccccCEEEEEEEEEecCCCcceEEEEeeccchhc
Confidence            4556777777788888889999999999999 77777665432  22 2222   2 777665

This N-terminal domain found in the transcription factor GABP alpha consists of a five-stranded beta-sheet crossed by a distorted helix and has been termed OST domain. The surface of the GABP alpha OST domain contains two clusters of negatively-charged residues suggesting there are positively-charged partner proteins. The OST domain binds to the CH1 and CH3 domains of the co-activator histone acetyltransferase CBP/p300 [].; PDB: 2JUO_A.

>PF13019 Telomere_Sde2: Telomere stability and silencing

Probab=82.92  E-value=3.1  Score=27.94  Aligned_cols=34  Identities=15%  Similarity=0.290  Sum_probs=27.3

Q ss_pred             eeeeeeccchhHHHHHhhhhhcCCCCCce-EEEEC
Q 040204           47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQ-RQIFW   80 (97)
Q Consensus        47 ~~i~v~~~~TV~~lK~~I~~~~gip~~~q-~Lif~   80 (97)
                      ..+.+.++.||.+|+..|.+..++|+..| .|.+.
T Consensus        17 l~~~lp~~ttv~dL~~~l~~~~~~~~~~~~~L~~~   51 (162)
T PF13019_consen   17 LSLSLPSTTTVSDLKDRLSERLPIPSSSQLYLTTN   51 (162)
T ss_pred             EEeeCCCCCcHHHHHHHHHhhcCCCccceeEEEEe
Confidence            34556888999999999999999998874 45554

>COG0299 PurN Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism]

Probab=81.86  E-value=1.5  Score=30.35  Aligned_cols=42  Identities=19%  Similarity=0.289  Sum_probs=31.9

Q ss_pred             ccceec--ccceeeeeeeeccee------eeeeccchhHHHHHhhhhhcC
Q 040204           28 VDYNIH--GSTLHSVRRFRGGMQ------IFVESSDTIDNVKAKIQDKKG   69 (97)
Q Consensus        28 ~~y~I~--~sti~l~i~~~~g~~------i~v~~~~TV~~lK~~I~~~~g   69 (97)
                      -++|.+  |+|+|++-.-.++-+      +.|.+.||.+++.++|++.|-
T Consensus       125 ~~aG~k~sG~TVH~V~e~vD~GpII~Q~~Vpv~~~Dt~etl~~RV~~~Eh  174 (200)
T COG0299         125 LEAGVKVSGCTVHFVTEGVDTGPIIAQAAVPVLPGDTAETLEARVLEQEH  174 (200)
T ss_pred             HHcCCCccCcEEEEEccCCCCCCeEEEEeeeecCCCCHHHHHHHHHHHHH
Confidence            356776  999999886544422      445889999999999998874

>PF10302 DUF2407: DUF2407 ubiquitin-like domain; InterPro: IPR019413 This entry represents a family of proteins of unknown function found in fungi

Probab=80.14  E-value=0.97  Score=27.73  Aligned_cols=23  Identities=35%  Similarity=0.527  Sum_probs=18.2

Q ss_pred             CCcceEEEECCEEeCCCCCCccc
Q 040204            8 LRDQQRFIFAGKRLEDGRTLVDY   30 (97)
Q Consensus         8 p~~~Q~L~~~g~~L~d~~tL~~y   30 (97)
                      .-..+||+|+|+.|.|+..++.-
T Consensus        42 s~~rLRlI~~Gr~L~d~t~l~~~   64 (97)
T PF10302_consen   42 SRRRLRLIYAGRLLNDHTDLSSE   64 (97)
T ss_pred             ccccEEeeecCcccCccchhhhh
Confidence            34569999999999998776643

They contain a characteristic GFDRL sequence motif.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	97
3b08_A	152	Crystal Structure Of The Mouse Hoil1-L-Nzf In Compl		8e-26
2zvn_A	154	Nemo Cozi Domain Incomplex With Diubiquitin In P212		8e-26
3u30_A	172	Crystal Structure Of A Linear-Specific Ubiquitin Fa		8e-26
2w9n_A	152	Crystal Structure Of Linear Di-Ubiquitin Length = 1		9e-26
2y5b_B	152	Structure Of Usp21 In Complex With Linear Diubiquit		7e-25
3q3f_A	189	Engineering Domain-Swapped Binding Interfaces By Mu		2e-12
3q3f_A	189	Engineering Domain-Swapped Binding Interfaces By Mu		1e-07
2jwz_A	76	Mutations In The Hydrophobic Core Of Ubiquitin Diff		2e-12
2jwz_A	76	Mutations In The Hydrophobic Core Of Ubiquitin Diff		2e-08
1yx5_B	98	Solution Structure Of S5a Uim-1UBIQUITIN COMPLEX Le		3e-12
1yx5_B	98	Solution Structure Of S5a Uim-1UBIQUITIN COMPLEX Le		7e-08
2fcs_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		4e-12
2fcs_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		7e-07
3u5e_m	128	The Structure Of The Eukaryotic Ribosome At 3.0 A R		5e-12
3u5e_m	128	The Structure Of The Eukaryotic Ribosome At 3.0 A R		1e-08
2zcb_A	76	Crystal Structure Of Ubiquitin P37aP38A Length = 76		5e-12
2zcb_A	76	Crystal Structure Of Ubiquitin P37aP38A Length = 76		5e-06
4a18_K	129	T.Thermophila 60s Ribosomal Subunit In Complex With		7e-12
4a18_K	129	T.Thermophila 60s Ribosomal Subunit In Complex With		3e-08
1yj1_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		7e-12
1yj1_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		6e-07
2gbj_A	84	Crystal Structure Of The 9-10 8 Glycine Insertion M		1e-11
2gbj_A	84	Crystal Structure Of The 9-10 8 Glycine Insertion M		7e-08
3olm_D	79	Structure And Function Of A Ubiquitin Binding Site		1e-11
3olm_D	79	Structure And Function Of A Ubiquitin Binding Site		1e-08
1aar_A	76	Structure Of A Diubiquitin Conjugate And A Model Fo		1e-11
1aar_A	76	Structure Of A Diubiquitin Conjugate And A Model Fo		7e-08
4ap4_C	80	Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Le		1e-11
4ap4_C	80	Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Le		2e-08
1yiw_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		1e-11
1yiw_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		7e-08
2gbk_A	83	Crystal Structure Of The 9-10 Moad Insertion Mutant		1e-11
2gbk_A	83	Crystal Structure Of The 9-10 Moad Insertion Mutant		1e-09
1s1q_B	76	Tsg101(Uev) Domain In Complex With Ubiquitin Length		1e-11
1s1q_B	76	Tsg101(Uev) Domain In Complex With Ubiquitin Length		8e-08
2znv_C	77	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		1e-11
2znv_C	77	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		8e-08
3l0w_B	169	Structure Of Split Monoubiquitinated Pcna With Ubiq		1e-11
3l0w_B	169	Structure Of Split Monoubiquitinated Pcna With Ubiq		2e-08
2ld9_A	77	Backbone Structure Of Ubiquitin Determined Using Ba		1e-11
2ld9_A	77	Backbone Structure Of Ubiquitin Determined Using Ba		2e-08
3nob_A	78	Structure Of K11-Linked Di-Ubiquitin Length = 78		1e-11
3nob_A	78	Structure Of K11-Linked Di-Ubiquitin Length = 78		7e-08
3jvz_X	81	E2~ubiquitin-Hect Length = 81		1e-11
3jvz_X	81	E2~ubiquitin-Hect Length = 81		3e-08
1otr_B	76	Solution Structure Of A Cue-Ubiquitin Complex Lengt		1e-11
1otr_B	76	Solution Structure Of A Cue-Ubiquitin Complex Lengt		2e-08
3u5g_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		1e-11
3u5g_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		1e-08
3zf7_s	128	High-resolution Cryo-electron Microscopy Structure		1e-11
3zf7_s	128	High-resolution Cryo-electron Microscopy Structure		2e-08
1sif_A	88	Crystal Structure Of A Multiple Hydrophobic Core Mu		2e-11
1sif_A	88	Crystal Structure Of A Multiple Hydrophobic Core Mu		4e-07
2khw_B	79	Solution Structure Of The Human Polymerase Iota Ubm		2e-11
2khw_B	79	Solution Structure Of The Human Polymerase Iota Ubm		7e-08
2znv_B	76	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		2e-11
2znv_B	76	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		7e-08
3dvg_X	80	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		2e-11
3dvg_X	80	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		8e-08
4ii3_B	96	Crystal Structure Of S. Pombe Ubiquitin Activating		2e-11
4ii3_B	96	Crystal Structure Of S. Pombe Ubiquitin Activating		1e-08
4hcn_B	98	Crystal Structure Of Burkholderia Pseudomallei Effe		2e-11
4hcn_B	98	Crystal Structure Of Burkholderia Pseudomallei Effe		2e-08
3vdz_A	111	Tailoring Encodable Lanthanide-Binding Tags As Mri		2e-11
3vdz_A	111	Tailoring Encodable Lanthanide-Binding Tags As Mri		9e-08
3dvg_Y	79	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		2e-11
3dvg_Y	79	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		7e-08
1ud7_A	76	Solution Structure Of The Designed Hydrophobic Core		3e-11
1ud7_A	76	Solution Structure Of The Designed Hydrophobic Core		4e-07
2ojr_A	111	Structure Of Ubiquitin Solved By Sad Using The Lant		3e-11
2ojr_A	111	Structure Of Ubiquitin Solved By Sad Using The Lant		1e-07
1zgu_B	76	Solution Structure Of The Human Mms2-Ubiquitin Comp		3e-11
1zgu_B	76	Solution Structure Of The Human Mms2-Ubiquitin Comp		7e-08
4hjk_A	77	U7ub7 Disulfide Variant Length = 77		3e-11
4hjk_A	77	U7ub7 Disulfide Variant Length = 77		3e-07
2o6v_D	76	Crystal Structure And Solution Nmr Studies Of Lys48		4e-11
2o6v_D	76	Crystal Structure And Solution Nmr Studies Of Lys48		7e-08
1c3t_A	76	Rotamer Strain As A Determinant Of Protein Structur		5e-11
1c3t_A	76	Rotamer Strain As A Determinant Of Protein Structur		3e-07
2k6d_B	76	Cin85 Sh3-C Domain In Complex With Ubiquitin Length		5e-11
2k6d_B	76	Cin85 Sh3-C Domain In Complex With Ubiquitin Length		7e-08
1xd3_B	75	Crystal Structure Of Uchl3-Ubvme Complex Length = 7		6e-11
1xd3_B	75	Crystal Structure Of Uchl3-Ubvme Complex Length = 7		7e-08
1cmx_B	76	Structural Basis For The Specificity Of Ubiquitin C		6e-11
1cmx_B	76	Structural Basis For The Specificity Of Ubiquitin C		7e-08
3rul_A	79	New Strategy To Analyze Structures Of Glycopeptide-		6e-11
3rul_A	79	New Strategy To Analyze Structures Of Glycopeptide-		8e-08
2xk5_B	76	Crystal Structure Of K6-Linked Diubiquitin Length =		6e-11
2xk5_B	76	Crystal Structure Of K6-Linked Diubiquitin Length =		4e-07
2o6v_B	76	Crystal Structure And Solution Nmr Studies Of Lys48		7e-11
2o6v_B	76	Crystal Structure And Solution Nmr Studies Of Lys48		7e-08
3h7s_B	76	Crystal Structures Of K63-Linked Di- And Tri-Ubiqui		9e-11
3h7s_A	76	Crystal Structures Of K63-Linked Di- And Tri-Ubiqui		7e-08
3k9o_B	96	The Crystal Structure Of E2-25k And Ubb+1 Complex L		9e-11
3k9o_B	96	The Crystal Structure Of E2-25k And Ubb+1 Complex L		3e-08
4ii2_B	83	Crystal Structure Of Ubiquitin Activating Enzyme 1		1e-10
4ii2_B	83	Crystal Structure Of Ubiquitin Activating Enzyme 1		3e-08
2kdi_A	114	Solution Structure Of A UbiquitinUIM FUSION PROTEIN		2e-10
2kdi_A	114	Solution Structure Of A UbiquitinUIM FUSION PROTEIN		7e-08
4gsw_A	80	Crystal Structure Of Ubiquitin From Entamoeba Histo		2e-10
4gsw_A	80	Crystal Structure Of Ubiquitin From Entamoeba Histo		5e-06
1ogw_A	76	Synthetic Ubiquitin With Fluoro-Leu At 50 And 67 Le		2e-10
1ogw_A	76	Synthetic Ubiquitin With Fluoro-Leu At 50 And 67 Le		9e-08
3v6c_B	91	Crystal Structure Of Usp2 In Complex With Mutated U		2e-10
3v6c_B	91	Crystal Structure Of Usp2 In Complex With Mutated U		4e-09
2k25_A	103	Automated Nmr Structure Of The Ubb By Fapsy Length		2e-10
2k25_A	103	Automated Nmr Structure Of The Ubb By Fapsy Length		7e-09
3v6e_B	91	Crystal Structure Of Usp2 And A Mutant Form Of Ubiq		2e-10
3v6e_B	91	Crystal Structure Of Usp2 And A Mutant Form Of Ubiq		4e-09
3ai5_A	307	Crystal Structure Of Yeast Enhanced Green Fluoresce		5e-10
3ai5_A	307	Crystal Structure Of Yeast Enhanced Green Fluoresce		3e-08
2gbr_A	81	Crystal Structure Of The 35-36 Moad Insertion Mutan		6e-10
2gbr_A	81	Crystal Structure Of The 35-36 Moad Insertion Mutan		6e-06
4hk2_A	78	U7ub25.2540 Length = 78		7e-10
4hk2_A	78	U7ub25.2540 Length = 78		8e-07
3ldz_F	73	Crystal Structure Of Human Stam1 Vhs Domain In Comp		1e-09
3ldz_F	73	Crystal Structure Of Human Stam1 Vhs Domain In Comp		7e-08
2gbm_A	84	Crystal Structure Of The 35-36 8 Glycine Insertion		1e-09
2gbm_A	84	Crystal Structure Of The 35-36 8 Glycine Insertion		8e-05
3ons_A	72	Crystal Structure Of Human Ubiquitin In A New Cryst		1e-09
3ons_A	72	Crystal Structure Of Human Ubiquitin In A New Cryst		8e-08
3u5c_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		4e-09
3u5c_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		1e-08
1zw7_A	82	Elimination Of The C-Cap In Ubiquitin Structure, Dy		4e-09
1zw7_A	82	Elimination Of The C-Cap In Ubiquitin Structure, Dy		2e-06
3n3k_B	85	The Catalytic Domain Of Usp8 In Complex With A Usp8		6e-09
3n3k_B	85	The Catalytic Domain Of Usp8 In Complex With A Usp8		7e-08
2jvc_A	82	Nmr Solution Structure Of Ubiquitin Like Protein Le		2e-08
2jvc_A	82	Nmr Solution Structure Of Ubiquitin Like Protein Le		1e-05
1gjz_A	53	Solution Structure Of A Dimeric N-Terminal Fragment		3e-08
3mtn_B	85	Usp21 In Complex With A Ubiquitin-based, Usp21-spec		5e-08
3mtn_B	85	Usp21 In Complex With A Ubiquitin-based, Usp21-spec		1e-07
4i6l_B	76	Crystal Structure Of Otub1 In Complex With Ubiquiti		7e-08
1bt0_A	76	Structure Of Ubiquitin-Like Protein, Rub1 Length =		6e-07
1bt0_A	76	Structure Of Ubiquitin-Like Protein, Rub1 Length =		5e-04
3dbh_I	88	Structural Dissection Of A Gating Mechanism Prevent		2e-06
3dbl_I	88	Structural Dissection Of A Gating Mechanism Prevent		5e-06
4hcp_B	78	Crystal Structure Of Burkholderia Pseudomallei Effe		5e-06
1ndd_B	76	Structure Of Nedd8 Length = 76		6e-06
3gzn_I	82	Structure Of Nedd8-Activating Enzyme In Complex Wit		6e-06
2bkr_B	77	Nedd8 Nedp1 Complex Length = 77		6e-06
2nvu_I	81	Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C1		6e-06
2nvu_I	81	Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C1		8e-04
4f8c_B	88	Structure Of The Cif:nedd8 Complex - Yersinia Pseud		7e-06
3dqv_A	81	Structural Insights Into Nedd8 Activation Of Cullin		2e-05

>pdb|3B08|A Chain A, Crystal Structure Of The Mouse Hoil1-L-Nzf In Complex With Linear Di- Ubiquitin Length = 152

Iteration: 1
 Score =  111 bits (278), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 62/93 (66%), Positives = 66/93 (70%), Gaps = 13/93 (13%)
Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIF--------- 50
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIF         
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89
Query: 51  ---VESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
              VE SDTI+NVKAKIQDK+G PPDQQR IF 
Sbjct: 90  TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA 122

>pdb|2ZVN|A Chain A, Nemo Cozi Domain Incomplex With Diubiquitin In P212121 Space Group Length = 154

Iteration: 1
 Score =  111 bits (278), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 62/93 (66%), Positives = 66/93 (70%), Gaps = 13/93 (13%)
Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIF--------- 50
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIF         
Sbjct: 32  IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 91
Query: 51  ---VESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
              VE SDTI+NVKAKIQDK+G PPDQQR IF 
Sbjct: 92  TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA 124

>pdb|3U30|A Chain A, Crystal Structure Of A Linear-Specific Ubiquitin Fab Bound To Linear Ubiquitin Length = 172

Iteration: 1
 Score =  111 bits (278), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 62/93 (66%), Positives = 66/93 (70%), Gaps = 13/93 (13%)
Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIF--------- 50
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIF         
Sbjct: 50  IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 109
Query: 51  ---VESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
              VE SDTI+NVKAKIQDK+G PPDQQR IF 
Sbjct: 110 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA 142

>pdb|2W9N|A Chain A, Crystal Structure Of Linear Di-Ubiquitin Length = 152

Iteration: 1
 Score =  111 bits (278), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 62/93 (66%), Positives = 66/93 (70%), Gaps = 13/93 (13%)
Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIF--------- 50
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIF         
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89
Query: 51  ---VESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
              VE SDTI+NVKAKIQDK+G PPDQQR IF 
Sbjct: 90  TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA 122

>pdb|2Y5B|B Chain B, Structure Of Usp21 In Complex With Linear Diubiquitin-Aldehyde Length = 152

Iteration: 1
 Score =  108 bits (270), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 61/93 (65%), Positives = 65/93 (69%), Gaps = 13/93 (13%)
Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIF--------- 50
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RG MQIF         
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGHMQIFVKTLTGKTI 89
Query: 51  ---VESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
              VE SDTI+NVKAKIQDK+G PPDQQR IF 
Sbjct: 90  TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA 122

>pdb|3Q3F|A Chain A, Engineering Domain-Swapped Binding Interfaces By Mutually Exclusive Folding: Insertion Of Ubiquitin Into Position 103 Of Barnase Length = 189

Iteration: 1
 Score = 67.4 bits (163), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 36/53 (67%), Positives = 39/53 (73%), Gaps = 1/53 (1%)
Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFVE 52
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG Q F +
Sbjct: 135 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGGQTFTK 187

>pdb|3Q3F|A Chain A, Engineering Domain-Swapped Binding Interfaces By Mutually Exclusive Folding: Insertion Of Ubiquitin Into Position 103 Of Barnase Length = 189

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 26/29 (89%)
Query: 51  VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
           VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 122 VEPSDTIENVKAKIQDKEGIPPDQQRLIF 150

>pdb|2JWZ|A Chain A, Mutations In The Hydrophobic Core Of Ubiquitin Differentially Affect Its Recognition By Receptor Proteins Length = 76

Iteration: 1
 Score = 67.4 bits (163), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 35/47 (74%), Positives = 37/47 (78%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLHSV R RGG
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHSVLRLRGG 76

>pdb|2JWZ|A Chain A, Mutations In The Hydrophobic Core Of Ubiquitin Differentially Affect Its Recognition By Receptor Proteins Length = 76

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/29 (86%), Positives = 27/29 (93%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VESSDTIDNVK+KIQDK+G PPDQQR IF
Sbjct: 17 VESSDTIDNVKSKIQDKEGIPPDQQRLIF 45

>pdb|1YX5|B Chain B, Solution Structure Of S5a Uim-1UBIQUITIN COMPLEX Length = 98

Iteration: 1
 Score = 66.6 bits (161), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 37/66 (56%), Positives = 45/66 (68%), Gaps = 4/66 (6%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFVESSDTIDN 59
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG      +S ++D 
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGRD---PNSSSVDK 86
Query: 60 VKAKIQ 65
          + A ++
Sbjct: 87 LAAALE 92

>pdb|1YX5|B Chain B, Solution Structure Of S5a Uim-1UBIQUITIN COMPLEX Length = 98

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 24/30 (80%), Positives = 26/30 (86%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
          VE SDTI+NVKAKIQDK+G PPDQQR IF 
Sbjct: 17 VEPSDTIENVKAKIQDKEGIPPDQQRLIFA 46

>pdb|2FCS|A Chain A, X-Ray Crystal Structure Of A Chemically Synthesized [l-Gln35]ubiquitin With A Cubic Space Group Length = 76

Iteration: 1
 Score = 66.6 bits (161), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 37/47 (78%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE+I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 30 IQDKEQIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76

>pdb|2FCS|A Chain A, X-Ray Crystal Structure Of A Chemically Synthesized [l-Gln35]ubiquitin With A Cubic Space Group Length = 76

Iteration: 1
 Score = 48.9 bits (115), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 23/29 (79%), Positives = 25/29 (86%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+  PPDQQR IF
Sbjct: 17 VEPSDTIENVKAKIQDKEQIPPDQQRLIF 45

>pdb|3U5E|MM Chain m, The Structure Of The Eukaryotic Ribosome At 3.0 A Resolution. This Entry Contains Proteins Of The 60s Subunit, Ribosome A Length = 128

Iteration: 1
 Score = 66.2 bits (160), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 34/48 (70%), Positives = 37/48 (77%), Gaps = 1/48 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGM 47
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG+
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGI 77

>pdb|3U5E|MM Chain m, The Structure Of The Eukaryotic Ribosome At 3.0 A Resolution. This Entry Contains Proteins Of The 60s Subunit, Ribosome A Length = 128

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/29 (86%), Positives = 27/29 (93%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VESSDTIDNVK+KIQDK+G PPDQQR IF
Sbjct: 17 VESSDTIDNVKSKIQDKEGIPPDQQRLIF 45

>pdb|2ZCB|A Chain A, Crystal Structure Of Ubiquitin P37aP38A Length = 76

Iteration: 1
 Score = 65.9 bits (159), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 30 IQDKEGIAADQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76

>pdb|2ZCB|A Chain A, Crystal Structure Of Ubiquitin P37aP38A Length = 76

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 22/29 (75%), Positives = 24/29 (82%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G   DQQR IF
Sbjct: 17 VEPSDTIENVKAKIQDKEGIAADQQRLIF 45

>pdb|4A18|K Chain K, T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 26s Rrna And Proteins Of Molecule 1 Length = 129

Iteration: 1
 Score = 65.5 bits (158), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76

>pdb|4A18|K Chain K, T.Thermophila 60s Ribosomal Subunit In Complex With Initiation Factor 6. This File Contains 26s Rrna And Proteins Of Molecule 1 Length = 129

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 24/30 (80%), Positives = 27/30 (90%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
          VE+SDTI+NVKAKIQDK+G PPDQQR IF 
Sbjct: 17 VEASDTIENVKAKIQDKEGIPPDQQRLIFA 46

>pdb|1YJ1|A Chain A, X-Ray Crystal Structure Of A Chemically Synthesized [d-Gln35]ubiquitin Length = 76

Iteration: 1
 Score = 65.5 bits (158), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 30 IQDKEXIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76

>pdb|1YJ1|A Chain A, X-Ray Crystal Structure Of A Chemically Synthesized [d-Gln35]ubiquitin Length = 76

Iteration: 1
 Score = 49.3 bits (116), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 23/29 (79%), Positives = 25/29 (86%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+  PPDQQR IF
Sbjct: 17 VEPSDTIENVKAKIQDKEXIPPDQQRLIF 45

>pdb|2GBJ|A Chain A, Crystal Structure Of The 9-10 8 Glycine Insertion Mutant Of Ubiquitin. Length = 84

Iteration: 1
 Score = 65.1 bits (157), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 38 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 84

>pdb|2GBJ|A Chain A, Crystal Structure Of The 9-10 8 Glycine Insertion Mutant Of Ubiquitin. Length = 84

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 26/29 (89%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 25 VEPSDTIENVKAKIQDKEGIPPDQQRLIF 53

>pdb|3OLM|D Chain D, Structure And Function Of A Ubiquitin Binding Site Within The Catalytic Domain Of A Hect Ubiquitin Ligase Length = 79

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 33 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 79

>pdb|3OLM|D Chain D, Structure And Function Of A Ubiquitin Binding Site Within The Catalytic Domain Of A Hect Ubiquitin Ligase Length = 79

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/30 (83%), Positives = 27/30 (90%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
          VESSDTIDNVK+KIQDK+G PPDQQR IF 
Sbjct: 20 VESSDTIDNVKSKIQDKEGIPPDQQRLIFA 49

>pdb|1AAR|A Chain A, Structure Of A Diubiquitin Conjugate And A Model For Interaction With Ubiquitin Conjugating Enzyme (E2) Length = 76

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76

>pdb|1AAR|A Chain A, Structure Of A Diubiquitin Conjugate And A Model For Interaction With Ubiquitin Conjugating Enzyme (E2) Length = 76

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 26/29 (89%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 17 VEPSDTIENVKAKIQDKEGIPPDQQRLIF 45

>pdb|4AP4|C Chain C, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Length = 80

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 34 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 80

>pdb|4AP4|C Chain C, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Length = 80

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/46 (63%), Positives = 31/46 (67%), Gaps = 12/46 (26%)
Query: 46 GMQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          GMQIFV            E SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 4  GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF 49

>pdb|1YIW|A Chain A, X-Ray Crystal Structure Of A Chemically Synthesized Ubiquitin Length = 76

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76

>pdb|1YIW|A Chain A, X-Ray Crystal Structure Of A Chemically Synthesized Ubiquitin Length = 76

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 26/29 (89%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 17 VEPSDTIENVKAKIQDKEGIPPDQQRLIF 45

>pdb|2GBK|A Chain A, Crystal Structure Of The 9-10 Moad Insertion Mutant Of Ubiquitin Length = 83

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 37 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 83

>pdb|2GBK|A Chain A, Crystal Structure Of The 9-10 Moad Insertion Mutant Of Ubiquitin Length = 83

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 31/46 (67%), Positives = 33/46 (71%), Gaps = 2/46 (4%)
Query: 36 TLHSVRRFRGGMQIF--VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          TL  VR   GG  I   VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 7  TLTQVRELVGGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF 52

>pdb|1S1Q|B Chain B, Tsg101(Uev) Domain In Complex With Ubiquitin Length = 76

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76

>pdb|1S1Q|B Chain B, Tsg101(Uev) Domain In Complex With Ubiquitin Length = 76

Iteration: 1
 Score = 52.0 bits (123), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 26/29 (89%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 17 VEPSDTIENVKAKIQDKEGIPPDQQRLIF 45

>pdb|2ZNV|C Chain C, Crystal Structure Of Human Amsh-Lp Dub Domain In Complex With Lys63-Linked Ubiquitin Dimer Length = 77

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76

>pdb|2ZNV|C Chain C, Crystal Structure Of Human Amsh-Lp Dub Domain In Complex With Lys63-Linked Ubiquitin Dimer Length = 77

Iteration: 1
 Score = 52.0 bits (123), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 26/29 (89%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 17 VEPSDTIENVKAKIQDKEGIPPDQQRLIF 45

>pdb|3L0W|B Chain B, Structure Of Split Monoubiquitinated Pcna With Ubiquitin In Position Two Length = 169

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76

>pdb|3L0W|B Chain B, Structure Of Split Monoubiquitinated Pcna With Ubiquitin In Position Two Length = 169

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/29 (86%), Positives = 27/29 (93%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VESSDTIDNVK+KIQDK+G PPDQQR IF
Sbjct: 17 VESSDTIDNVKSKIQDKEGIPPDQQRLIF 45

>pdb|2LD9|A Chain A, Backbone Structure Of Ubiquitin Determined Using Backbone Amide Noes And Backbone N-H And N-C Rdcs Length = 77

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 31 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 77

>pdb|2LD9|A Chain A, Backbone Structure Of Ubiquitin Determined Using Backbone Amide Noes And Backbone N-H And N-C Rdcs Length = 77

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/46 (63%), Positives = 31/46 (67%), Gaps = 12/46 (26%)
Query: 46 GMQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          GMQIFV            E SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 1  GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF 46

>pdb|3NOB|A Chain A, Structure Of K11-Linked Di-Ubiquitin Length = 78

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 32 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 78

>pdb|3NOB|A Chain A, Structure Of K11-Linked Di-Ubiquitin Length = 78

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 26/29 (89%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 19 VEPSDTIENVKAKIQDKEGIPPDQQRLIF 47

>pdb|3JVZ|X Chain X, E2~ubiquitin-Hect Length = 81

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 35 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 81

>pdb|3JVZ|X Chain X, E2~ubiquitin-Hect Length = 81

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 29/48 (60%), Positives = 31/48 (64%), Gaps = 12/48 (25%)
Query: 45 GGMQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
          G MQIFV            E SDTI+NVKAKIQDK+G PPDQQR IF 
Sbjct: 4  GSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA 51

>pdb|1OTR|B Chain B, Solution Structure Of A Cue-Ubiquitin Complex Length = 76

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76

>pdb|1OTR|B Chain B, Solution Structure Of A Cue-Ubiquitin Complex Length = 76

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/29 (86%), Positives = 27/29 (93%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VESSDTIDNVK+KIQDK+G PPDQQR IF
Sbjct: 17 VESSDTIDNVKSKIQDKEGIPPDQQRLIF 45

>pdb|3U5G|FF Chain f, The Structure Of The Eukaryotic Ribosome At 3.0 A Resolution. This Entry Contains Proteins Of The 40s Subunit, Ribosome B Length = 152

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76

>pdb|3U5G|FF Chain f, The Structure Of The Eukaryotic Ribosome At 3.0 A Resolution. This Entry Contains Proteins Of The 40s Subunit, Ribosome B Length = 152

Iteration: 1
 Score = 55.1 bits (131), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/29 (86%), Positives = 27/29 (93%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VESSDTIDNVK+KIQDK+G PPDQQR IF
Sbjct: 17 VESSDTIDNVKSKIQDKEGIPPDQQRLIF 45

>pdb|3ZF7|SS Chain s, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 128

Iteration: 1
 Score = 64.3 bits (155), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 33/48 (68%), Positives = 37/48 (77%), Gaps = 1/48 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGM 47
          I+DKE I  DQQR IFAGK+LE+GRTL DYNI   STLH V R RGG+
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEEGRTLADYNIQKESTLHLVLRLRGGV 77

>pdb|3ZF7|SS Chain s, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 128

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 27/29 (93%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE+SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 17 VEASDTIENVKAKIQDKEGIPPDQQRLIF 45

>pdb|1SIF|A Chain A, Crystal Structure Of A Multiple Hydrophobic Core Mutant Of Ubiquitin Length = 88

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 39 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 85

>pdb|1SIF|A Chain A, Crystal Structure Of A Multiple Hydrophobic Core Mutant Of Ubiquitin Length = 88

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 22/31 (70%), Positives = 27/31 (87%)
Query: 49 IFVESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          + +E SDTI+N+KAKIQDK+G PPDQQR IF
Sbjct: 24 VEMEPSDTIENLKAKIQDKEGIPPDQQRLIF 54

>pdb|2KHW|B Chain B, Solution Structure Of The Human Polymerase Iota Ubm2- Ubiquitin Complex Length = 79

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 33 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 79

>pdb|2KHW|B Chain B, Solution Structure Of The Human Polymerase Iota Ubm2- Ubiquitin Complex Length = 79

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 26/29 (89%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 20 VEPSDTIENVKAKIQDKEGIPPDQQRLIF 48

>pdb|2ZNV|B Chain B, Crystal Structure Of Human Amsh-Lp Dub Domain In Complex With Lys63-Linked Ubiquitin Dimer Length = 76

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRGG 76

>pdb|2ZNV|B Chain B, Crystal Structure Of Human Amsh-Lp Dub Domain In Complex With Lys63-Linked Ubiquitin Dimer Length = 76

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 26/29 (89%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 17 VEPSDTIENVKAKIQDKEGIPPDQQRLIF 45

>pdb|3DVG|X Chain X, Crystal Structure Of K63-Specific Fab Apu.3a8 Bound To K63-Linked Di- Ubiquitin Length = 80

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 33 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 79

>pdb|3DVG|X Chain X, Crystal Structure Of K63-Specific Fab Apu.3a8 Bound To K63-Linked Di- Ubiquitin Length = 80

Iteration: 1
 Score = 52.0 bits (123), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 24/30 (80%), Positives = 26/30 (86%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
          VE SDTI+NVKAKIQDK+G PPDQQR IF 
Sbjct: 20 VEPSDTIENVKAKIQDKEGIPPDQQRLIFA 49

>pdb|4II3|B Chain B, Crystal Structure Of S. Pombe Ubiquitin Activating Enzyme 1 (uba1) In Complex With Ubiquitin And Atp/mg Length = 96

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 50 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 96

>pdb|4II3|B Chain B, Crystal Structure Of S. Pombe Ubiquitin Activating Enzyme 1 (uba1) In Complex With Ubiquitin And Atp/mg Length = 96

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/30 (83%), Positives = 27/30 (90%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
          VESSDTIDNVK+KIQDK+G PPDQQR IF 
Sbjct: 37 VESSDTIDNVKSKIQDKEGIPPDQQRLIFA 66

>pdb|4HCN|B Chain B, Crystal Structure Of Burkholderia Pseudomallei Effector Protein Chbp In Complex With Ubiquitin Length = 98

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 52 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 98

>pdb|4HCN|B Chain B, Crystal Structure Of Burkholderia Pseudomallei Effector Protein Chbp In Complex With Ubiquitin Length = 98

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/29 (86%), Positives = 27/29 (93%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VESSDTIDNVK+KIQDK+G PPDQQR IF
Sbjct: 39 VESSDTIDNVKSKIQDKEGIPPDQQRLIF 67

>pdb|3VDZ|A Chain A, Tailoring Encodable Lanthanide-Binding Tags As Mri Contrast Agents: Xq-Dse3-Ubiquitin At 2.4 Angstroms Length = 111

Iteration: 1
 Score = 63.9 bits (154), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 65  IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 111

>pdb|3VDZ|A Chain A, Tailoring Encodable Lanthanide-Binding Tags As Mri Contrast Agents: Xq-Dse3-Ubiquitin At 2.4 Angstroms Length = 111

Iteration: 1
 Score = 52.0 bits (123), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 24/34 (70%), Positives = 28/34 (82%)
Query: 47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
          + + VE SDTI+NVKAKIQDK+G PPDQQR IF 
Sbjct: 48 ITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA 81

>pdb|3DVG|Y Chain Y, Crystal Structure Of K63-Specific Fab Apu.3a8 Bound To K63-Linked Di- Ubiquitin Length = 79

Iteration: 1
 Score = 63.9 bits (154), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 33 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRGG 79

>pdb|3DVG|Y Chain Y, Crystal Structure Of K63-Specific Fab Apu.3a8 Bound To K63-Linked Di- Ubiquitin Length = 79

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 26/29 (89%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 20 VEPSDTIENVKAKIQDKEGIPPDQQRLIF 48

>pdb|1UD7|A Chain A, Solution Structure Of The Designed Hydrophobic Core Mutant Of Ubiquitin, 1d7 Length = 76

Iteration: 1
 Score = 63.5 bits (153), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 33/47 (70%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   ST+H V R RGG
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTIHLVLRLRGG 76

>pdb|1UD7|A Chain A, Solution Structure Of The Designed Hydrophobic Core Mutant Of Ubiquitin, 1d7 Length = 76

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 23/33 (69%), Positives = 27/33 (81%)
Query: 47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          + I VE SDT++N KAKIQDK+G PPDQQR IF
Sbjct: 13 VTIEVEPSDTVENFKAKIQDKEGIPPDQQRLIF 45

>pdb|2OJR|A Chain A, Structure Of Ubiquitin Solved By Sad Using The Lanthanide- Binding Tag Length = 111

Iteration: 1
 Score = 63.5 bits (153), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 65  IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 111

>pdb|2OJR|A Chain A, Structure Of Ubiquitin Solved By Sad Using The Lanthanide- Binding Tag Length = 111

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/33 (72%), Positives = 28/33 (84%)
Query: 47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          + + VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 48 ITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF 80

>pdb|1ZGU|B Chain B, Solution Structure Of The Human Mms2-Ubiquitin Complex Length = 76

Iteration: 1
 Score = 63.5 bits (153), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 33/47 (70%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAG++LEDGRTL DYNI   STLH V R RGG
Sbjct: 30 IQDKEGIPPDQQRLIFAGRQLEDGRTLSDYNIQKESTLHLVLRLRGG 76

>pdb|1ZGU|B Chain B, Solution Structure Of The Human Mms2-Ubiquitin Complex Length = 76

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 26/29 (89%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 17 VEPSDTIENVKAKIQDKEGIPPDQQRLIF 45

>pdb|4HJK|A Chain A, U7ub7 Disulfide Variant Length = 77

Iteration: 1
 Score = 63.5 bits (153), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 33/47 (70%), Positives = 35/47 (74%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DK     DQQR IFAGK+LEDGRTL DYNI   STLH VRR RGG
Sbjct: 31 IQDKIGYPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHCVRRLRGG 77

>pdb|4HJK|A Chain A, U7ub7 Disulfide Variant Length = 77

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 25/29 (86%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK G PPDQQR IF
Sbjct: 18 VEPSDTIENVKAKIQDKIGYPPDQQRLIF 46

>pdb|2O6V|D Chain D, Crystal Structure And Solution Nmr Studies Of Lys48-Linked Tetraubiquitin At Neutral Ph Length = 76

Iteration: 1
 Score = 62.8 bits (151), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 33/47 (70%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
          I+DKE I  DQQR IFAG++LEDGRTL DYNI   STLH V R RGG
Sbjct: 30 IQDKEGIPPDQQRLIFAGRQLEDGRTLSDYNIQRESTLHLVLRLRGG 76

>pdb|2O6V|D Chain D, Crystal Structure And Solution Nmr Studies Of Lys48-Linked Tetraubiquitin At Neutral Ph Length = 76

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 26/29 (89%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 17 VEPSDTIENVKAKIQDKEGIPPDQQRLIF 45

>pdb|1C3T|A Chain A, Rotamer Strain As A Determinant Of Protein Structural Specificity Length = 76

Iteration: 1
 Score = 62.8 bits (151), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 32/47 (68%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYN+   ST+H V R RGG
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNLQKESTIHLVLRLRGG 76

>pdb|1C3T|A Chain A, Rotamer Strain As A Determinant Of Protein Structural Specificity Length = 76

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 21/33 (63%), Positives = 28/33 (84%)
Query: 47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          + + +E SDT++N+KAKIQDK+G PPDQQR IF
Sbjct: 13 LTVELEPSDTVENLKAKIQDKEGIPPDQQRLIF 45

>pdb|2K6D|B Chain B, Cin85 Sh3-C Domain In Complex With Ubiquitin Length = 76

Iteration: 1
 Score = 62.8 bits (151), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 33/46 (71%), Positives = 35/46 (76%), Gaps = 1/46 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRG 45
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RG
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG 75

>pdb|2K6D|B Chain B, Cin85 Sh3-C Domain In Complex With Ubiquitin Length = 76

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 26/29 (89%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 17 VEPSDTIENVKAKIQDKEGIPPDQQRLIF 45

>pdb|1XD3|B Chain B, Crystal Structure Of Uchl3-Ubvme Complex Length = 75

Iteration: 1
 Score = 62.4 bits (150), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 33/46 (71%), Positives = 35/46 (76%), Gaps = 1/46 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRG 45
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RG
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG 75

>pdb|1XD3|B Chain B, Crystal Structure Of Uchl3-Ubvme Complex Length = 75

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 26/29 (89%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 17 VEPSDTIENVKAKIQDKEGIPPDQQRLIF 45

>pdb|1CMX|B Chain B, Structural Basis For The Specificity Of Ubiquitin C- Terminal Hydrolases Length = 76

Iteration: 1
 Score = 62.4 bits (150), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 33/46 (71%), Positives = 35/46 (76%), Gaps = 1/46 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRG 45
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RG
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG 75

>pdb|1CMX|B Chain B, Structural Basis For The Specificity Of Ubiquitin C- Terminal Hydrolases Length = 76

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 26/29 (89%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 17 VEPSDTIENVKAKIQDKEGIPPDQQRLIF 45

>pdb|3RUL|A Chain A, New Strategy To Analyze Structures Of Glycopeptide-Target Complexes Length = 79

Iteration: 1
 Score = 62.4 bits (150), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 33/46 (71%), Positives = 35/46 (76%), Gaps = 1/46 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRG 45
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RG
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG 75

>pdb|3RUL|A Chain A, New Strategy To Analyze Structures Of Glycopeptide-Target Complexes Length = 79

Iteration: 1
 Score = 52.0 bits (123), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 26/29 (89%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 17 VEPSDTIENVKAKIQDKEGIPPDQQRLIF 45

>pdb|2XK5|B Chain B, Crystal Structure Of K6-Linked Diubiquitin Length = 76

Iteration: 1
 Score = 62.4 bits (150), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 33/47 (70%), Positives = 35/47 (74%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I   QQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 30 IQDKEGIPPQQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76

>pdb|2XK5|B Chain B, Crystal Structure Of K6-Linked Diubiquitin Length = 76

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 23/29 (79%), Positives = 25/29 (86%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G PP QQR IF
Sbjct: 17 VEPSDTIENVKAKIQDKEGIPPQQQRLIF 45

>pdb|2O6V|B Chain B, Crystal Structure And Solution Nmr Studies Of Lys48-Linked Tetraubiquitin At Neutral Ph Length = 76

Iteration: 1
 Score = 62.0 bits (149), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 33/47 (70%), Positives = 35/47 (74%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
          I+DKE I  DQQR IFAG +LEDGRTL DYNI   STLH V R RGG
Sbjct: 30 IQDKEGIPPDQQRLIFAGXQLEDGRTLSDYNIQRESTLHLVLRLRGG 76

>pdb|2O6V|B Chain B, Crystal Structure And Solution Nmr Studies Of Lys48-Linked Tetraubiquitin At Neutral Ph Length = 76

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 26/29 (89%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 17 VEPSDTIENVKAKIQDKEGIPPDQQRLIF 45

>pdb|3H7S|A Chain A, Crystal Structures Of K63-Linked Di- And Tri-Ubiquitin Reveal A Highly Extended Chain Architecture Length = 76

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 26/29 (89%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 17 VEPSDTIENVKAKIQDKEGIPPDQQRLIF 45

>pdb|3K9O|B Chain B, The Crystal Structure Of E2-25k And Ubb+1 Complex Length = 96

Iteration: 1
 Score = 62.0 bits (149), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 33/46 (71%), Positives = 35/46 (76%), Gaps = 1/46 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRG 45
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RG
Sbjct: 31 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG 76

>pdb|3K9O|B Chain B, The Crystal Structure Of E2-25k And Ubb+1 Complex Length = 96

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 29/47 (61%), Positives = 31/47 (65%), Gaps = 12/47 (25%)
Query: 46 GMQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
          GMQIFV            E SDTI+NVKAKIQDK+G PPDQQR IF 
Sbjct: 1  GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA 47

>pdb|4II2|B Chain B, Crystal Structure Of Ubiquitin Activating Enzyme 1 (uba1) In Complex With The Ub E2 Ubc4, Ubiquitin, And Atp/mg Length = 83

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 32/47 (68%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
          I+D+E I  DQQR IFAG++LEDGRTL DYNI   STLH V R RGG
Sbjct: 37 IQDREGIPPDQQRLIFAGRQLEDGRTLADYNIQRESTLHLVLRLRGG 83

>pdb|4II2|B Chain B, Crystal Structure Of Ubiquitin Activating Enzyme 1 (uba1) In Complex With The Ub E2 Ubc4, Ubiquitin, And Atp/mg Length = 83

Iteration: 1
 Score = 53.1 bits (126), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 23/29 (79%), Positives = 27/29 (93%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VESSDTIDNV+A+IQD++G PPDQQR IF
Sbjct: 24 VESSDTIDNVRARIQDREGIPPDQQRLIF 52

>pdb|2KDI|A Chain A, Solution Structure Of A UbiquitinUIM FUSION PROTEIN Length = 114

Iteration: 1
 Score = 61.2 bits (147), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 33/47 (70%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
          I+DKE I  DQQR I+AGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 39 IQDKEGIPPDQQRLIWAGKQLEDGRTLSDYNIQRESTLHLVLRLRGG 85

>pdb|2KDI|A Chain A, Solution Structure Of A UbiquitinUIM FUSION PROTEIN Length = 114

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 24/28 (85%), Positives = 26/28 (92%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQI 78
          VESSDTIDNVK+KIQDK+G PPDQQR I
Sbjct: 26 VESSDTIDNVKSKIQDKEGIPPDQQRLI 53

>pdb|4GSW|A Chain A, Crystal Structure Of Ubiquitin From Entamoeba Histolytica To 2.15 Angstrom Length = 80

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/47 (65%), Positives = 36/47 (76%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I++KE I  DQQR IFAGK+LE+G+TL DYNI   STLH V R RGG
Sbjct: 33 IQEKEGIPPDQQRLIFAGKQLEEGKTLSDYNIQKESTLHLVLRLRGG 79

>pdb|4GSW|A Chain A, Crystal Structure Of Ubiquitin From Entamoeba Histolytica To 2.15 Angstrom Length = 80

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 20/29 (68%), Positives = 25/29 (86%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE +D+ID +KAKIQ+K+G PPDQQR IF
Sbjct: 20 VEPNDSIDAIKAKIQEKEGIPPDQQRLIF 48

>pdb|1OGW|A Chain A, Synthetic Ubiquitin With Fluoro-Leu At 50 And 67 Length = 76

Iteration: 1
 Score = 60.5 bits (145), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/47 (68%), Positives = 34/47 (72%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+ EDGRTL DYNI   ST H V R RGG
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQXEDGRTLSDYNIQKESTXHLVLRLRGG 76

>pdb|1OGW|A Chain A, Synthetic Ubiquitin With Fluoro-Leu At 50 And 67 Length = 76

Iteration: 1
 Score = 52.0 bits (123), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 26/29 (89%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 17 VEPSDTIENVKAKIQDKEGIPPDQQRLIF 45

>pdb|3V6C|B Chain B, Crystal Structure Of Usp2 In Complex With Mutated Ubiquitin Length = 91

Iteration: 1
 Score = 60.5 bits (145), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/45 (71%), Positives = 34/45 (75%), Gaps = 1/45 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFR 44
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R R
Sbjct: 47 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 91

>pdb|3V6C|B Chain B, Crystal Structure Of Usp2 In Complex With Mutated Ubiquitin Length = 91

Iteration: 1
 Score = 56.2 bits (134), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 30/49 (61%), Positives = 32/49 (65%), Gaps = 12/49 (24%)
Query: 44 RGGMQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
          RG MQIFV            E SDTI+NVKAKIQDK+G PPDQQR IF 
Sbjct: 15 RGSMQIFVNTLTGTHITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA 63

>pdb|2K25|A Chain A, Automated Nmr Structure Of The Ubb By Fapsy Length = 103

Iteration: 1
 Score = 60.5 bits (145), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/46 (69%), Positives = 35/46 (76%), Gaps = 1/46 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRG 45
          I+DKE I  DQQR IFAGK+LEDGRTL +YNI   STLH V R RG
Sbjct: 38 IQDKEGIPPDQQRLIFAGKQLEDGRTLSEYNIQKESTLHLVLRLRG 83

>pdb|2K25|A Chain A, Automated Nmr Structure Of The Ubb By Fapsy Length = 103

Iteration: 1
 Score = 55.5 bits (132), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 30/49 (61%), Positives = 32/49 (65%), Gaps = 12/49 (24%)
Query: 44 RGGMQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
          RG MQIFV            E SDTI+NVKAKIQDK+G PPDQQR IF 
Sbjct: 6  RGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA 54

>pdb|3V6E|B Chain B, Crystal Structure Of Usp2 And A Mutant Form Of Ubiquitin Length = 91

Iteration: 1
 Score = 60.5 bits (145), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/45 (71%), Positives = 34/45 (75%), Gaps = 1/45 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFR 44
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R R
Sbjct: 47 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 91

>pdb|3V6E|B Chain B, Crystal Structure Of Usp2 And A Mutant Form Of Ubiquitin Length = 91

Iteration: 1
 Score = 56.2 bits (134), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 30/49 (61%), Positives = 32/49 (65%), Gaps = 12/49 (24%)
Query: 44 RGGMQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
          RG MQIFV            E SDTI+NVKAKIQDK+G PPDQQR IF 
Sbjct: 15 RGSMQIFVNTLSGKHITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA 63

>pdb|3AI5|A Chain A, Crystal Structure Of Yeast Enhanced Green Fluorescent Protein- Ubiquitin Fusion Protein Length = 307

Iteration: 1
 Score = 59.7 bits (143), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 32/45 (71%), Positives = 34/45 (75%), Gaps = 1/45 (2%)
Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFR 44
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R R
Sbjct: 263 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 307

>pdb|3AI5|A Chain A, Crystal Structure Of Yeast Enhanced Green Fluorescent Protein- Ubiquitin Fusion Protein Length = 307

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 29/47 (61%), Positives = 31/47 (65%), Gaps = 12/47 (25%)
Query: 45  GGMQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
           G MQIFV            E SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 232 GSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF 278

>pdb|2GBR|A Chain A, Crystal Structure Of The 35-36 Moad Insertion Mutant Of Ubiquitin Length = 81

Iteration: 1
 Score = 58.9 bits (141), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 34/52 (65%), Positives = 36/52 (69%), Gaps = 6/52 (11%)
Query: 1  IEDKE-----EILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DKE      I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 30 IQDKEGRWALAIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 81

>pdb|2GBR|A Chain A, Crystal Structure Of The 35-36 Moad Insertion Mutant Of Ubiquitin Length = 81

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 24/34 (70%), Positives = 26/34 (76%), Gaps = 5/34 (14%)
Query: 51 VESSDTIDNVKAKIQDKKG-----TPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G      PPDQQR IF
Sbjct: 17 VEPSDTIENVKAKIQDKEGRWALAIPPDQQRLIF 50

>pdb|4HK2|A Chain A, U7ub25.2540 Length = 78

Iteration: 1
 Score = 58.9 bits (141), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 33/47 (70%), Positives = 34/47 (72%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+DK  I  DQQ  IFAGKRLEDGRTL DYNI   STL  VRR RGG
Sbjct: 32 IQDKLGIPPDQQWLIFAGKRLEDGRTLSDYNIQKESTLRGVRRLRGG 78

>pdb|4HK2|A Chain A, U7ub25.2540 Length = 78

Iteration: 1
 Score = 48.9 bits (115), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 28/52 (53%), Positives = 30/52 (57%), Gaps = 16/52 (30%)
Query: 45 GGMQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVFG 84
          G MQIFV            E SDTI+NVKAKIQDK G PPDQQ    W +F 
Sbjct: 1  GSMQIFVKFRTGKTYTLEVEPSDTIENVKAKIQDKLGIPPDQQ----WLIFA 48

>pdb|3LDZ|F Chain F, Crystal Structure Of Human Stam1 Vhs Domain In Complex With Ubiquitin Length = 73

Iteration: 1
 Score = 58.5 bits (140), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 31/44 (70%), Positives = 33/44 (75%), Gaps = 1/44 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRF 43
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R 
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL 73

>pdb|3LDZ|F Chain F, Crystal Structure Of Human Stam1 Vhs Domain In Complex With Ubiquitin Length = 73

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 26/29 (89%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 17 VEPSDTIENVKAKIQDKEGIPPDQQRLIF 45

>pdb|2GBM|A Chain A, Crystal Structure Of The 35-36 8 Glycine Insertion Mutant Of Ubiquitin Length = 84

Iteration: 1
 Score = 58.5 bits (140), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 29/38 (76%), Positives = 30/38 (78%), Gaps = 1/38 (2%)
Query: 10 DQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 47 DQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 84

>pdb|2GBM|A Chain A, Crystal Structure Of The 35-36 8 Glycine Insertion Mutant Of Ubiquitin Length = 84

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 24/37 (64%), Positives = 26/37 (70%), Gaps = 8/37 (21%)
Query: 51 VESSDTIDNVKAKIQDKKGT--------PPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G         PPDQQR IF
Sbjct: 17 VEPSDTIENVKAKIQDKEGGGGGGGGGIPPDQQRLIF 53

>pdb|3ONS|A Chain A, Crystal Structure Of Human Ubiquitin In A New Crystal Form Length = 72

Iteration: 1
 Score = 57.8 bits (138), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 31/43 (72%), Positives = 33/43 (76%), Gaps = 1/43 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRR 42
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72

>pdb|3ONS|A Chain A, Crystal Structure Of Human Ubiquitin In A New Crystal Form Length = 72

Iteration: 1
 Score = 52.0 bits (123), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 26/29 (89%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 17 VEPSDTIENVKAKIQDKEGIPPDQQRLIF 45

>pdb|3U5C|FF Chain f, The Structure Of The Eukaryotic Ribosome At 3.0 A Resolution. This Entry Contains Proteins Of The 40s Subunit, Ribosome A Length = 152

Iteration: 1
 Score = 56.6 bits (135), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 30/41 (73%), Positives = 32/41 (78%), Gaps = 1/41 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSV 40
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV 70

>pdb|3U5C|FF Chain f, The Structure Of The Eukaryotic Ribosome At 3.0 A Resolution. This Entry Contains Proteins Of The 40s Subunit, Ribosome A Length = 152

Iteration: 1
 Score = 55.1 bits (131), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/29 (86%), Positives = 27/29 (93%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VESSDTIDNVK+KIQDK+G PPDQQR IF
Sbjct: 17 VESSDTIDNVKSKIQDKEGIPPDQQRLIF 45

>pdb|1ZW7|A Chain A, Elimination Of The C-Cap In Ubiquitin Structure, Dynamics And Thermodynamic Consequences Length = 82

Iteration: 1
 Score = 56.2 bits (134), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 30/47 (63%), Positives = 32/47 (68%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGG 46
          I+    I  DQQ  IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 30 IQAAPGIPPDQQELIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76

>pdb|1ZW7|A Chain A, Elimination Of The C-Cap In Ubiquitin Structure, Dynamics And Thermodynamic Consequences Length = 82

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/41 (58%), Positives = 28/41 (68%), Gaps = 1/41 (2%)
Query: 40 VRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          V+   G  + + VESSDTIDNVK+KIQ   G PPDQQ  IF
Sbjct: 5  VKTLTGATITLEVESSDTIDNVKSKIQAAPGIPPDQQELIF 45

>pdb|3N3K|B Chain B, The Catalytic Domain Of Usp8 In Complex With A Usp8 Specific Inhibitor Length = 85

Iteration: 1
 Score = 55.8 bits (133), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 26/36 (72%), Positives = 29/36 (80%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHGST 36
          I+DKE I  DQQR IFAGK+LEDGRTL DYNIH  +
Sbjct: 33 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIHNHS 68

>pdb|3N3K|B Chain B, The Catalytic Domain Of Usp8 In Complex With A Usp8 Specific Inhibitor Length = 85

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 24/30 (80%), Positives = 26/30 (86%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
          VE SDTI+NVKAKIQDK+G PPDQQR IF 
Sbjct: 20 VEPSDTIENVKAKIQDKEGIPPDQQRLIFA 49

>pdb|2JVC|A Chain A, Nmr Solution Structure Of Ubiquitin Like Protein Length = 82

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 28/48 (58%), Positives = 32/48 (66%), Gaps = 1/48 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGM 47
          I DKE I  DQQR IF GK+LED   + DYN+   STLH V R RGG+
Sbjct: 35 IYDKEGIPPDQQRLIFGGKQLEDSNAMSDYNVQKESTLHLVLRLRGGV 82

>pdb|2JVC|A Chain A, Nmr Solution Structure Of Ubiquitin Like Protein Length = 82

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/47 (51%), Positives = 29/47 (61%), Gaps = 12/47 (25%)
Query: 45 GGMQIFVES------------SDTIDNVKAKIQDKKGTPPDQQRQIF 79
          G MQIFV++            +DT+  VKAKI DK+G PPDQQR IF
Sbjct: 4  GSMQIFVKTLTGKTITIDVDHADTVGAVKAKIYDKEGIPPDQQRLIF 50

>pdb|1GJZ|A Chain A, Solution Structure Of A Dimeric N-Terminal Fragment Of Human Ubiquitin Length = 53

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 29/47 (61%), Positives = 31/47 (65%), Gaps = 12/47 (25%)
Query: 45 GGMQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          G MQIFV            E SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 1  GSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF 47

>pdb|3MTN|B Chain B, Usp21 In Complex With A Ubiquitin-based, Usp21-specific Inhibitor Length = 85

Iteration: 1
 Score = 52.8 bits (125), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 25/33 (75%), Positives = 27/33 (81%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH 33
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI 
Sbjct: 33 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 65

>pdb|3MTN|B Chain B, Usp21 In Complex With A Ubiquitin-based, Usp21-specific Inhibitor Length = 85

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/29 (82%), Positives = 26/29 (89%)
Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          VE SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 20 VEPSDTIENVKAKIQDKEGIPPDQQRLIF 48

>pdb|4I6L|B Chain B, Crystal Structure Of Otub1 In Complex With Ubiquitin Variant Length = 76

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 27/47 (57%), Positives = 31/47 (65%), Gaps = 12/47 (25%)
Query: 45 GGMQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          G MQIFV            E SDTI+NVKAKIQDK+G PPDQQ+ +F
Sbjct: 1  GSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQKLLF 47

>pdb|1BT0|A Chain A, Structure Of Ubiquitin-Like Protein, Rub1 Length = 76

Iteration: 1
 Score = 49.3 bits (116), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 26/47 (55%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
          +E+KE I   QQR I+AGK+L D +T  DYNI  GS LH V   RGG
Sbjct: 30 VEEKEGIPPVQQRLIYAGKQLADDKTAKDYNIEGGSVLHLVLALRGG 76

>pdb|1BT0|A Chain A, Structure Of Ubiquitin-Like Protein, Rub1 Length = 76

Iteration: 1
 Score = 39.7 bits (91), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 15/33 (45%), Positives = 26/33 (78%)
Query: 47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          ++I +E +DTID +K ++++K+G PP QQR I+
Sbjct: 13 IEIDIEPTDTIDRIKERVEEKEGIPPVQQRLIY 45

>pdb|3DBH|I Chain I, Structural Dissection Of A Gating Mechanism Preventing Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1- Uba3arg190ala-Nedd8ala72arg) Length = 88

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/47 (51%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-HGSTLHSVRRFRGG 46
          +E+KE I   QQR I++GK++ D +T  DY I  GS LH V R RGG
Sbjct: 42 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLRLRGG 88

>pdb|3DBL|I Chain I, Structural Dissection Of A Gating Mechanism Preventing Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1- Uba3arg190wt-Nedd8ala72gln) Length = 88

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-HGSTLHSVRRFRGG 46
          +E+KE I   QQR I++GK++ D +T  DY I  GS LH V + RGG
Sbjct: 42 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLQLRGG 88

>pdb|4HCP|B Chain B, Crystal Structure Of Burkholderia Pseudomallei Effector Protein Chbp In Complex With Nedd8 Length = 78

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-HGSTLHSVRRFRGG 46
          +E+KE I   QQR I++GK++ D +T  DY I  GS LH V   RGG
Sbjct: 32 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG 78

>pdb|1NDD|B Chain B, Structure Of Nedd8 Length = 76

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-HGSTLHSVRRFRGG 46
          +E+KE I   QQR I++GK++ D +T  DY I  GS LH V   RGG
Sbjct: 30 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG 76

>pdb|3GZN|I Chain I, Structure Of Nedd8-Activating Enzyme In Complex With Nedd8 And Mln4924 Length = 82

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-HGSTLHSVRRFRGG 46
          +E+KE I   QQR I++GK++ D +T  DY I  GS LH V   RGG
Sbjct: 36 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG 82

>pdb|2BKR|B Chain B, Nedd8 Nedp1 Complex Length = 77

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-HGSTLHSVRRFRGG 46
          +E+KE I   QQR I++GK++ D +T  DY I  GS LH V   RGG
Sbjct: 31 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG 77

>pdb|2NVU|I Chain I, Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C111a), A Trapped Ubiquitin-Like Protein Activation Complex Length = 81

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-HGSTLHSVRRFRGG 46
          +E+KE I   QQR I++GK++ D +T  DY I  GS LH V   RGG
Sbjct: 35 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG 81

>pdb|2NVU|I Chain I, Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C111a), A Trapped Ubiquitin-Like Protein Activation Complex Length = 81

Iteration: 1
 Score = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 17/47 (36%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 34 GSTLHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          GS L  V+   G  ++I +E +D ++ +K ++++K+G PP QQR I+
Sbjct: 4  GSMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIY 50

>pdb|4F8C|B Chain B, Structure Of The Cif:nedd8 Complex - Yersinia Pseudotuberculosis Cycle Inhibiting Factor In Complex With Human Nedd8 Length = 88

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-HGSTLHSVRRFRGG 46
          +E+KE I   QQR I++GK++ D +T  DY I  GS LH V   RGG
Sbjct: 30 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG 76

>pdb|3DQV|A Chain A, Structural Insights Into Nedd8 Activation Of Cullin-Ring Ligases: Conformational Control Of Conjugation Length = 81

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
          +E+KE I   QQR I++GK+  D +T  DY I  GS LH V   RGG
Sbjct: 35 VEEKEGIPPQQQRLIYSGKQXNDEKTAADYKIXGGSVLHLVLALRGG 81

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	97
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	2e-21
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	4e-17
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	5e-21
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	8e-14
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	9e-21
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	1e-15
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	1e-10
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	4e-20
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	2e-15
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	2e-09
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	1e-19
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	9e-13
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	1e-19
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	1e-18
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	3e-07
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	2e-19
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	3e-09
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	3e-19
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	5e-17
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	1e-10
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	8e-19
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	1e-14
3u5c_F	225	RP14, S2, YS8, 40S ribosomal protein S5; translati	1e-18
3u5c_F	225	RP14, S2, YS8, 40S ribosomal protein S5; translati	3e-14
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	2e-18
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	8e-13
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	3e-18
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	2e-12
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	5e-18
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	2e-12
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	6e-18
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	2e-09
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	7e-18
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	9e-12
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	8e-18
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	2e-12
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	8e-18
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	5e-12
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	9e-18
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	2e-12
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	2e-04
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	1e-17
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	1e-10
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	1e-17
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	2e-12
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	2e-17
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	8e-13
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	3e-17
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	4e-10
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	6e-17
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	1e-11
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	8e-17
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	5e-13
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	1e-16
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	9e-15
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	1e-16
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	1e-14
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	1e-16
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	6e-12
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	1e-16
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	6e-14
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	2e-16
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	4e-11
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	2e-16
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	9e-12
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	3e-16
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	3e-12
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	3e-16
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	4e-14
1we6_A	111	Splicing factor, putative; structural genomics, ub	5e-16
1we6_A	111	Splicing factor, putative; structural genomics, ub	2e-06
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	6e-16
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	2e-14
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	2e-15
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	4e-07
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	3e-15
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	3e-09
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	4e-15
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	1e-12
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	5e-15
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	7e-13
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	5e-14
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	1e-13
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	7e-14
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	1e-11
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	1e-13
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	2e-13
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	1e-13
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	9e-12
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	5e-13
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	1e-10
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	2e-12
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	1e-10
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	3e-12
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	7e-11
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	4e-10
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	6e-08
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	1e-08
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	5e-08
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	2e-08
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	1e-07
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	7e-06
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	2e-05
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	1e-04
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	2e-04
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	2e-04
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	3e-04
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	9e-04

>3m63_B Ubiquitin domain-containing protein DSK2; armadillo-like repeats, UBL conjugation pathway, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} Length = 101

 Score = 80.1 bits (198), Expect = 2e-21
 Identities = 17/75 (22%), Positives = 24/75 (32%), Gaps = 18/75 (24%)

Query: 19 KRLEDGRTLVDYNI-HGSTLHSVRRFRGGMQIF-------------VESSDTIDNVKAKI 64
          K       + DY+I     L+    F+G M +              V    T+   K  I
Sbjct: 2  KHHHHHHPMSDYDIPTTENLY----FQGAMSLNIHIKSGQDKWEVNVAPESTVLQFKEAI 57

Query: 65 QDKKGTPPDQQRQIF 79
              G P   QR I+
Sbjct: 58 NKANGIPVANQRLIY 72

>3m63_B Ubiquitin domain-containing protein DSK2; armadillo-like repeats, UBL conjugation pathway, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} Length = 101

 Score = 68.9 bits (169), Expect = 4e-17
 Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 1/43 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR 42
          I     I    QR I++GK L+D +T+  Y+I  G ++H V+ 
Sbjct: 57 INKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS 99

>4dwf_A HLA-B-associated transcript 3; ubiquitin-like domain, BAT3 protein, PF00240, structural GEN joint center for structural genomics, JCSG; 1.80A {Homo sapiens} PDB: 1wx9_A Length = 90

 Score = 78.5 bits (194), Expect = 5e-21
 Identities = 16/54 (29%), Positives = 27/54 (50%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHGSTLHSVRRFRGGMQIFVESS 54
          I     I  ++QR I+ G+ L+D + L +YN+ G  +H V R      +   +S
Sbjct: 35 IAASVSIPSEKQRLIYQGRVLQDDKKLQEYNVGGKVIHLVERAPPQTHLPSGAS 88

>4dwf_A HLA-B-associated transcript 3; ubiquitin-like domain, BAT3 protein, PF00240, structural GEN joint center for structural genomics, JCSG; 1.80A {Homo sapiens} PDB: 1wx9_A Length = 90

 Score = 60.4 bits (147), Expect = 8e-14
 Identities = 7/47 (14%), Positives = 15/47 (31%), Gaps = 12/47 (25%)

Query: 45 GGMQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
            +++ V             +   +   K  I      P ++QR I+
Sbjct: 4  DSLEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIY 50

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens} Length = 172

 Score = 80.1 bits (197), Expect = 9e-21
 Identities = 62/92 (67%), Positives = 66/92 (71%), Gaps = 13/92 (14%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct: 50  IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 109

Query: 52  ----ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
               E SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 110 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF 141

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens} Length = 172

 Score = 66.6 bits (162), Expect = 1e-15
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 126 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 172

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens} Length = 172

 Score = 53.9 bits (129), Expect = 1e-10
 Identities = 29/59 (49%), Positives = 32/59 (54%), Gaps = 12/59 (20%)

Query: 33 HGSTLHSVRRFRGGMQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          H      +      MQIFV            E SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 7  HHHHSSGLVPRGSHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF 65

>3b08_A Polyubiquitin-C, ubiquitin; protein complex, signaling protein-metal binding protein COM; HET: TRE; 1.70A {Homo sapiens} PDB: 2w9n_A* 3b0a_A* 3axc_A 2zvn_A 2zvo_A 2y5b_B Length = 152

 Score = 78.1 bits (192), Expect = 4e-20
 Identities = 62/92 (67%), Positives = 66/92 (71%), Gaps = 13/92 (14%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHG-STLHSVRRFRGGMQIFV-------- 51
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGGMQIFV        
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 52  ----ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
               E SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 90  TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF 121

>3b08_A Polyubiquitin-C, ubiquitin; protein complex, signaling protein-metal binding protein COM; HET: TRE; 1.70A {Homo sapiens} PDB: 2w9n_A* 3b0a_A* 3axc_A 2zvn_A 2zvo_A 2y5b_B Length = 152

 Score = 66.2 bits (161), Expect = 2e-15
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 106 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 152

>3b08_A Polyubiquitin-C, ubiquitin; protein complex, signaling protein-metal binding protein COM; HET: TRE; 1.70A {Homo sapiens} PDB: 2w9n_A* 3b0a_A* 3axc_A 2zvn_A 2zvo_A 2y5b_B Length = 152

 Score = 50.4 bits (120), Expect = 2e-09
 Identities = 28/45 (62%), Positives = 30/45 (66%), Gaps = 12/45 (26%)

Query: 47 MQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          MQIFV            E SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF 45

>4fbj_B NEDD8; effector-HOST target complex, glutamine deamidase, deamidati bacterial effector, cell cycle-protein binding complex; 1.60A {Homo sapiens} PDB: 4f8c_B Length = 88

 Score = 75.1 bits (185), Expect = 1e-19
 Identities = 23/56 (41%), Positives = 32/56 (57%), Gaps = 1/56 (1%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGMQIFVESSD 55
          +E+KE I   QQR I++GK++ D +T  DY I  GS LH V   RGG  +  +   
Sbjct: 30 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGGGGLRQKHHH 85

>4fbj_B NEDD8; effector-HOST target complex, glutamine deamidase, deamidati bacterial effector, cell cycle-protein binding complex; 1.60A {Homo sapiens} PDB: 4f8c_B Length = 88

 Score = 57.3 bits (139), Expect = 9e-13
 Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 12/45 (26%)

Query: 47 MQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          M I V            E +D ++ +K ++++K+G PP QQR I+
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIY 45

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens} Length = 189

 Score = 77.7 bits (191), Expect = 1e-19
 Identities = 31/87 (35%), Positives = 42/87 (48%), Gaps = 8/87 (9%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLV--DYNIHGSTLHSVRRFRGG------MQIFVE 52
           +  K      +    +        R L   D+ I+ +T H   +          + + VE
Sbjct: 64  LPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYGGQIFVKTLTGKTITLEVE 123

Query: 53  SSDTIDNVKAKIQDKKGTPPDQQRQIF 79
            SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 124 PSDTIENVKAKIQDKEGIPPDQQRLIF 150

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens} Length = 189

 Score = 75.0 bits (184), Expect = 1e-18
 Identities = 36/52 (69%), Positives = 38/52 (73%), Gaps = 1/52 (1%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-HGSTLHSVRRFRGGMQIFV 51
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG Q F 
Sbjct: 135 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGGQTFT 186

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens} Length = 189

 Score = 45.0 bits (106), Expect = 3e-07
 Identities = 5/27 (18%), Positives = 9/27 (33%)

Query: 53 SSDTIDNVKAKIQDKKGTPPDQQRQIF 79
            D   N + K+  K G    +    +
Sbjct: 53 GGDIFSNREGKLPGKSGRTWREADINY 79

>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure, northeast structural genomics consortium, protein structure initiative, NESG; NMR {Homo sapiens} Length = 88

 Score = 74.7 bits (184), Expect = 2e-19
 Identities = 16/54 (29%), Positives = 23/54 (42%), Gaps = 1/54 (1%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-HGSTLHSVRRFRGGMQIFVES 53
          +   E +  D     F GK LED   L +Y +   ST+    R RGG++     
Sbjct: 34 VSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRGGLEHHHHH 87

>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure, northeast structural genomics consortium, protein structure initiative, NESG; NMR {Homo sapiens} Length = 88

 Score = 48.2 bits (115), Expect = 3e-09
 Identities = 7/45 (15%), Positives = 15/45 (33%), Gaps = 12/45 (26%)

Query: 47 MQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          + I V              + T+ ++K ++   +G   D     F
Sbjct: 5  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTF 49

>3rt3_B Ubiquitin-like protein ISG15; ubiquitin-like domain, isgylation, antiviral protein-viral P complex; 2.01A {Homo sapiens} PDB: 3sdl_C 3r66_C 3pse_B 1z2m_A Length = 159

 Score = 75.8 bits (186), Expect = 3e-19
 Identities = 20/95 (21%), Positives = 33/95 (34%), Gaps = 16/95 (16%)

Query: 1   IEDKEEILRDQQRFIF--AGKRLEDGRTLVDYNI-HGSTLHSVRRFRG-GMQIFV----- 51
           I  K  +   QQR     +G  L+D   L    +  GST+  V       + I V     
Sbjct: 32  ITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDKSDEPLSILVRNNKG 91

Query: 52  -------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
                    + T+ ++K ++   +G   D     F
Sbjct: 92  RSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTF 126

>3rt3_B Ubiquitin-like protein ISG15; ubiquitin-like domain, isgylation, antiviral protein-viral P complex; 2.01A {Homo sapiens} PDB: 3sdl_C 3r66_C 3pse_B 1z2m_A Length = 159

 Score = 70.4 bits (172), Expect = 5e-17
 Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGMQ 48
           +   E +  D     F GK LED   L +Y +   ST+    R RGG +
Sbjct: 111 VSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRGGGR 159

>3rt3_B Ubiquitin-like protein ISG15; ubiquitin-like domain, isgylation, antiviral protein-viral P complex; 2.01A {Homo sapiens} PDB: 3sdl_C 3r66_C 3pse_B 1z2m_A Length = 159

 Score = 53.4 bits (128), Expect = 1e-10
 Identities = 12/46 (26%), Positives = 17/46 (36%), Gaps = 12/46 (26%)

Query: 46 GMQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          G  + V             SS ++  +KA+I  K G    QQR   
Sbjct: 2  GWDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAV 47

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens} Length = 88

 Score = 72.7 bits (179), Expect = 8e-19
 Identities = 15/42 (35%), Positives = 24/42 (57%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHGSTLHSVRR 42
          I     I  ++QR I+ G+ L+D + L +YN+ G  +H V R
Sbjct: 47 IAASVSIPSEKQRLIYQGRVLQDDKKLQEYNVGGKVIHLVER 88

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens} Length = 88

 Score = 62.3 bits (152), Expect = 1e-14
 Identities = 7/59 (11%), Positives = 17/59 (28%), Gaps = 12/59 (20%)

Query: 33 HGSTLHSVRRFRGGMQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
             +  +       +++ V             +   +   K  I      P ++QR I+
Sbjct: 4  PNDSTSTAVEEPDSLEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIY 62

>3u5c_F RP14, S2, YS8, 40S ribosomal protein S5; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_F 3o30_D 3o2z_D 3u5g_F 3jyv_G* 2noq_F 1s1h_G 3iz6_F Length = 225

 Score = 74.1 bits (182), Expect = 1e-18
 Identities = 4/49 (8%), Positives = 12/49 (24%), Gaps = 1/49 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-HGSTLHSVRRFRGGMQ 48
           E+ ++   + + F        + +     +         V    G   
Sbjct: 30 PEEVQQAQTEIKLFNKWSFEEVEVKDASLVDYVQVRQPIFVAHTAGRYA 78

>3u5c_F RP14, S2, YS8, 40S ribosomal protein S5; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_F 3o30_D 3o2z_D 3u5g_F 3jyv_G* 2noq_F 1s1h_G 3iz6_F Length = 225

 Score = 62.9 bits (153), Expect = 3e-14
 Identities = 2/45 (4%), Positives = 8/45 (17%), Gaps = 12/45 (26%)

Query: 47 MQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          M                E    +       ++ +    + +    
Sbjct: 1  MSDTEAPVEVQEDFEVVEEFTPVVLATPIPEEVQQAQTEIKLFNK 45

>1ndd_A NEDD8, protein (ubiquitin-like protein NEDD8); proteolysis, signaling protei; 1.60A {Homo sapiens} SCOP: d.15.1.1 PDB: 1r4m_I 1r4n_I* 1xt9_B 2ko3_A 3gzn_I* 2bkr_B 2nvu_I* 3dqv_A 1bt0_A Length = 76

 Score = 71.5 bits (176), Expect = 2e-18
 Identities = 23/47 (48%), Positives = 30/47 (63%), Gaps = 1/47 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
          +E+KE I   QQR I++GK++ D +T  DY I  GS LH V   RGG
Sbjct: 30 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG 76

>1ndd_A NEDD8, protein (ubiquitin-like protein NEDD8); proteolysis, signaling protei; 1.60A {Homo sapiens} SCOP: d.15.1.1 PDB: 1r4m_I 1r4n_I* 1xt9_B 2ko3_A 3gzn_I* 2bkr_B 2nvu_I* 3dqv_A 1bt0_A Length = 76

 Score = 57.2 bits (139), Expect = 8e-13
 Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 12/45 (26%)

Query: 47 MQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          M I V            E +D ++ +K ++++K+G PP QQR I+
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIY 45

>1wx7_A Ubiquilin 3; ubiquitin-like domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 106

 Score = 72.0 bits (177), Expect = 3e-18
 Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 1/57 (1%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGMQIFVESSDT 56
           I  + +   DQ   IFAGK L+D  +L    +  G T+H V + +         +  
Sbjct: 46  ISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHRAMGNECPASG 102

>1wx7_A Ubiquilin 3; ubiquitin-like domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 106

 Score = 57.0 bits (138), Expect = 2e-12
 Identities = 10/44 (22%), Positives = 17/44 (38%), Gaps = 11/44 (25%)

Query: 47 MQIFV-----------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          +++ V             + TI  +K +I  +    PDQ   IF
Sbjct: 18 IKVTVKTPKDKEDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIF 61

>3a9j_A Ubiquitin; protein complex, cytoplasm, isopeptide bond, metal-binding, zinc; 1.18A {Mus musculus} PDB: 3a1q_B 2znv_B 3a9k_A 3h7p_A 3jsv_A 3dvg_Y 3dvn_Y 3nob_A 2o6v_D* 3jw0_X 3jvz_X 3nhe_B* 1aar_A 1d3z_A 1f9j_A 1fxt_B 1g6j_A 1nbf_C 1cmx_B 1q5w_B ... Length = 76

 Score = 70.4 bits (173), Expect = 5e-18
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRGG 76

>3a9j_A Ubiquitin; protein complex, cytoplasm, isopeptide bond, metal-binding, zinc; 1.18A {Mus musculus} PDB: 3a1q_B 2znv_B 3a9k_A 3h7p_A 3jsv_A 3dvg_Y 3dvn_Y 3nob_A 2o6v_D* 3jw0_X 3jvz_X 3nhe_B* 1aar_A 1d3z_A 1f9j_A 1fxt_B 1g6j_A 1nbf_C 1cmx_B 1q5w_B ... Length = 76

 Score = 56.2 bits (136), Expect = 2e-12
 Identities = 28/45 (62%), Positives = 30/45 (66%), Gaps = 12/45 (26%)

Query: 47 MQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          MQIFV            E SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF 45

>1we7_A SF3A1 protein; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: d.15.1.1 PDB: 1zkh_A Length = 115

 Score = 71.4 bits (175), Expect = 6e-18
 Identities = 11/47 (23%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
           I +   +   +Q+  + G  ++D  +L  YN+  G+ +H   + R G
Sbjct: 65  IHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMASGAVIHLALKERSG 111

>1we7_A SF3A1 protein; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: d.15.1.1 PDB: 1zkh_A Length = 115

 Score = 49.4 bits (118), Expect = 2e-09
 Identities = 7/33 (21%), Positives = 16/33 (48%)

Query: 47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          +   +  +D +  +K KI +  G P  +Q+  +
Sbjct: 48 LVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQY 80

>1yx5_B Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo sapiens} SCOP: d.15.1.1 PDB: 1yx6_B Length = 98

 Score = 71.0 bits (174), Expect = 7e-18
 Identities = 36/58 (62%), Positives = 39/58 (67%), Gaps = 1/58 (1%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGMQIFVESSDTI 57
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG      S D +
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGRDPNSSSVDKL 87

>1yx5_B Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo sapiens} SCOP: d.15.1.1 PDB: 1yx6_B Length = 98

 Score = 55.2 bits (133), Expect = 9e-12
 Identities = 28/45 (62%), Positives = 30/45 (66%), Gaps = 12/45 (26%)

Query: 47 MQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          MQIFV            E SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF 45

>1ttn_A DC-UBP, dendritic cell-derived ubiquitin-like protein; ubiquitin-like domain, solution structure, signaling protein; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 106

 Score = 70.9 bits (174), Expect = 8e-18
 Identities = 10/54 (18%), Positives = 19/54 (35%), Gaps = 1/54 (1%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGMQIFVES 53
           +   E +    QR+ F+G+ L D     +  I     +  +          VE+
Sbjct: 53  LHAAEGVEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQPVQNPTPVEN 106

>1ttn_A DC-UBP, dendritic cell-derived ubiquitin-like protein; ubiquitin-like domain, solution structure, signaling protein; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 106

 Score = 57.1 bits (138), Expect = 2e-12
 Identities = 11/45 (24%), Positives = 19/45 (42%), Gaps = 12/45 (26%)

Query: 47 MQIF------------VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
           Q+             V S+DT+ ++K ++   +G  P  QR  F
Sbjct: 24 CQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFF 68

>1wh3_A 59 kDa 2'-5'-oligoadenylate synthetase like protein; P59 OASL, ubiquitin family, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 87

 Score = 70.1 bits (172), Expect = 8e-18
 Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
          IED++ + + QQ+  F G+ L+D   L  Y I    TL   ++   G
Sbjct: 37 IEDQQGLPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKGSG 83

>1wh3_A 59 kDa 2'-5'-oligoadenylate synthetase like protein; P59 OASL, ubiquitin family, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 87

 Score = 55.5 bits (134), Expect = 5e-12
 Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 12/47 (25%)

Query: 45 GGMQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
           G+Q+FV              +  I  +K +I+D++G P  QQ+  F
Sbjct: 6  SGIQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEF 52

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B Length = 169

 Score = 72.3 bits (177), Expect = 9e-18
 Identities = 36/91 (39%), Positives = 47/91 (51%), Gaps = 16/91 (17%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-HGSTLHSVRRFR--------------- 44
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R R               
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGGGETIKFVADGDI 89

Query: 45  GGMQIFVESSDTIDNVKAKIQDKKGTPPDQQ 75
           G   + ++    +++ +  I+ +   P D  
Sbjct: 90  GSGSVIIKPFVDMEHPETSIKLEMDQPVDLT 120

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B Length = 169

 Score = 58.4 bits (141), Expect = 2e-12
 Identities = 29/45 (64%), Positives = 31/45 (68%), Gaps = 12/45 (26%)

Query: 47 MQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          MQIFV            ESSDTIDNVK+KIQDK+G PPDQQR IF
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIF 45

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B Length = 169

 Score = 36.9 bits (85), Expect = 2e-04
 Identities = 10/45 (22%), Positives = 16/45 (35%), Gaps = 8/45 (17%)

Query: 15  IFAGKRLED---GRTL---VDYNI-HGSTLHSVRRFRGG-MQIFV 51
            F  K L D   G +L   V   +   +        + G +Q F+
Sbjct: 120 TFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKSGFLQFFL 164

>1wx8_A Riken cDNA 4931431F19; ubiquitin-like domain, ubiquilin 1-like, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 Length = 96

 Score = 70.1 bits (172), Expect = 1e-17
 Identities = 17/47 (36%), Positives = 19/47 (40%), Gaps = 1/47 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
          I        D+   IF GK L D   L    I  GST+H V R   G
Sbjct: 46 ISKYLHCNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVRSHSG 92

>1wx8_A Riken cDNA 4931431F19; ubiquitin-like domain, ubiquilin 1-like, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 Length = 96

 Score = 52.4 bits (126), Expect = 1e-10
 Identities = 6/44 (13%), Positives = 13/44 (29%), Gaps = 11/44 (25%)

Query: 47 MQIFV-----------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          +++ V             +  +   K +I        D+   IF
Sbjct: 18 IRVSVKTPQDCHEFFLAENSNVRRFKKQISKYLHCNADRLVLIF 61

>1wy8_A NP95-like ring finger protein, isoform A; ubiquitin-like domain, NP95/ICBP90-like ring finger (NIRF), ubiquitin ligase, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 89

 Score = 69.7 bits (171), Expect = 1e-17
 Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
          +    ++  + QR  + GK+LE+G TL DY++     +  + R   G
Sbjct: 39 VWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVRPDSG 85

>1wy8_A NP95-like ring finger protein, isoform A; ubiquitin-like domain, NP95/ICBP90-like ring finger (NIRF), ubiquitin ligase, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 89

 Score = 56.6 bits (137), Expect = 2e-12
 Identities = 9/48 (18%), Positives = 16/48 (33%), Gaps = 14/48 (29%)

Query: 46 GMQIFV--------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          GM I V                  TI+ ++ ++       P+ QR  +
Sbjct: 7  GMWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFY 54

>3k9o_B Ubiquitin, UBB+1; E2-25K, complex structure, ATP-binding, isopeptide BO ligase, nucleotide-binding, UBL conjugation pathway; 1.80A {Homo sapiens} PDB: 2k25_A 2kx0_A Length = 96

 Score = 69.8 bits (171), Expect = 2e-17
 Identities = 33/50 (66%), Positives = 36/50 (72%), Gaps = 1/50 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGMQI 49
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RG   +
Sbjct: 31 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGYADL 80

>3k9o_B Ubiquitin, UBB+1; E2-25K, complex structure, ATP-binding, isopeptide BO ligase, nucleotide-binding, UBL conjugation pathway; 1.80A {Homo sapiens} PDB: 2k25_A 2kx0_A Length = 96

 Score = 57.9 bits (140), Expect = 8e-13
 Identities = 29/46 (63%), Positives = 31/46 (67%), Gaps = 12/46 (26%)

Query: 46 GMQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          GMQIFV            E SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 1  GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF 46

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 125

 Score = 69.9 bits (171), Expect = 3e-17
 Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 1/47 (2%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
           I  + +   DQ   IFAGK L+D  TL+ + IH G T+H V +    
Sbjct: 61  ISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIKRDPN 107

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 125

 Score = 51.8 bits (124), Expect = 4e-10
 Identities = 7/44 (15%), Positives = 15/44 (34%), Gaps = 11/44 (25%)

Query: 47 MQIFV-----------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          +++ V             + ++   K  I  +  +  DQ   IF
Sbjct: 33 IKVTVKTPKEKEEFAVPENSSVQQFKEAISKRFKSQTDQLVLIF 76

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens} Length = 101

 Score = 68.6 bits (168), Expect = 6e-17
 Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 1/43 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR 42
          I  + +   DQ   IFAGK L+D  TL  + IH G T+H V +
Sbjct: 54 ISKRFKSHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIK 96

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens} Length = 101

 Score = 55.1 bits (133), Expect = 1e-11
 Identities = 8/44 (18%), Positives = 16/44 (36%), Gaps = 11/44 (25%)

Query: 47 MQIFV-----------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          M++ V             + ++   K +I  +  +  DQ   IF
Sbjct: 26 MKVTVKTPKEKEEFAVPENSSVQQFKEEISKRFKSHTDQLVLIF 69

>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling proteins; 1.15A {Saccharomyces cerevisiae} SCOP: d.15.1.1 PDB: 2bwe_S Length = 77

 Score = 67.6 bits (166), Expect = 8e-17
 Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 1/43 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR 42
          I     I    QR I++GK L+D +T+  Y+I  G ++H V+ 
Sbjct: 33 INKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS 75

>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling proteins; 1.15A {Saccharomyces cerevisiae} SCOP: d.15.1.1 PDB: 2bwe_S Length = 77

 Score = 57.6 bits (140), Expect = 5e-13
 Identities = 10/46 (21%), Positives = 13/46 (28%), Gaps = 13/46 (28%)

Query: 47 MQIF-------------VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          M +              V    T+   K  I    G P   QR I+
Sbjct: 3  MSLNIHIKSGQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIY 48

>2l7r_A Ubiquitin-like protein FUBI; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; NMR {Homo sapiens} Length = 93

 Score = 67.9 bits (166), Expect = 1e-16
 Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 1/47 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
          +   E I  + Q  + AG  LED  TL    +   +TL    R  GG
Sbjct: 47 VASLEGIAPEDQVVLLAGAPLEDEATLGQCGVEALTTLEVAGRMLGG 93

>2l7r_A Ubiquitin-like protein FUBI; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; NMR {Homo sapiens} Length = 93

 Score = 62.9 bits (153), Expect = 9e-15
 Identities = 14/57 (24%), Positives = 22/57 (38%), Gaps = 10/57 (17%)

Query: 33 HGSTLHSVRRFRGGMQIFV----------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          H     S    RG MQ+FV             +T+  +KA +   +G  P+ Q  + 
Sbjct: 6  HHHHHSSGLVPRGSMQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLL 62

>1sif_A Ubiquitin; hydrophobic mutants, folding, stability, structural protein; 2.18A {Homo sapiens} SCOP: d.15.1.1 Length = 88

 Score = 67.4 bits (165), Expect = 1e-16
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 39 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 85

>1sif_A Ubiquitin; hydrophobic mutants, folding, stability, structural protein; 2.18A {Homo sapiens} SCOP: d.15.1.1 Length = 88

 Score = 62.4 bits (152), Expect = 1e-14
 Identities = 26/54 (48%), Positives = 32/54 (59%), Gaps = 12/54 (22%)

Query: 38 HSVRRFRGGMQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          H       G+Q+F+            E SDTI+N+KAKIQDK+G PPDQQR IF
Sbjct: 1  HHHHHHLQGLQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEGIPPDQQRLIF 54

>3mtn_B UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquitin-specific protease activity, hydrolase, ubiquitin B structural genomics consortium, SGC; 2.70A {Homo sapiens} Length = 85

 Score = 67.4 bits (165), Expect = 1e-16
 Identities = 32/47 (68%), Positives = 35/47 (74%), Gaps = 1/47 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STL  + R RGG
Sbjct: 33 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKWSTLFLLLRLRGG 79

>3mtn_B UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquitin-specific protease activity, hydrolase, ubiquitin B structural genomics consortium, SGC; 2.70A {Homo sapiens} Length = 85

 Score = 55.4 bits (134), Expect = 6e-12
 Identities = 28/47 (59%), Positives = 30/47 (63%), Gaps = 12/47 (25%)

Query: 45 GGMQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
            MQIFV            E SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 2  SHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF 48

>3dbh_I NEDD8; cell cycle, activating enzyme, apoptosis, membrane, UBL conjugation pathway, ATP-binding, ligase, nucleotide- binding, polymorphism; 2.85A {Homo sapiens} SCOP: k.45.1.1 PDB: 3dbr_I 3dbl_I Length = 88

 Score = 67.0 bits (164), Expect = 1e-16
 Identities = 24/47 (51%), Positives = 31/47 (65%), Gaps = 1/47 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
          +E+KE I   QQR I++GK++ D +T  DY I  GS LH V R RGG
Sbjct: 42 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLRLRGG 88

>3dbh_I NEDD8; cell cycle, activating enzyme, apoptosis, membrane, UBL conjugation pathway, ATP-binding, ligase, nucleotide- binding, polymorphism; 2.85A {Homo sapiens} SCOP: k.45.1.1 PDB: 3dbr_I 3dbl_I Length = 88

 Score = 60.5 bits (147), Expect = 6e-14
 Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 12/48 (25%)

Query: 44 RGGMQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
           G M I V            E +D ++ +K ++++K+G PP QQR I+
Sbjct: 10 GGSMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIY 57

>3b1l_X E3 ubiquitin-protein ligase parkin; proteasome, ALFA-beta-protein; 1.85A {Mus musculus} PDB: 1mg8_A 2zeq_A 2knb_A 1iyf_A Length = 76

 Score = 66.5 bits (163), Expect = 2e-16
 Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 1/46 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRG 45
          +  ++ +  DQ R IFAGK L +  T+ + ++   S +H V+R R 
Sbjct: 30 VAKQQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRR 75

>3b1l_X E3 ubiquitin-protein ligase parkin; proteasome, ALFA-beta-protein; 1.85A {Mus musculus} PDB: 1mg8_A 2zeq_A 2knb_A 1iyf_A Length = 76

 Score = 53.1 bits (128), Expect = 4e-11
 Identities = 13/45 (28%), Positives = 20/45 (44%), Gaps = 12/45 (26%)

Query: 47 MQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          M +FV            +S  +I  +K  +  ++G P DQ R IF
Sbjct: 1  MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKQQGVPADQLRVIF 45

>1yqb_A Ubiquilin 3; structural genomics consortium, ubiquitin, ubiquitin-like domain, structural genomics, signaling protein SGC; 2.00A {Homo sapiens} SCOP: d.15.1.1 Length = 100

 Score = 67.0 bits (164), Expect = 2e-16
 Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 1/43 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR 42
          I  + +   DQ   IFAGK L+D  +L    +  G T+H V +
Sbjct: 51 ISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIK 93

>1yqb_A Ubiquilin 3; structural genomics consortium, ubiquitin, ubiquitin-like domain, structural genomics, signaling protein SGC; 2.00A {Homo sapiens} SCOP: d.15.1.1 Length = 100

 Score = 55.4 bits (134), Expect = 9e-12
 Identities = 13/63 (20%), Positives = 23/63 (36%), Gaps = 12/63 (19%)

Query: 29 DYNIHGSTLHSVRRFRGG-MQIFV-----------ESSDTIDNVKAKIQDKKGTPPDQQR 76
           ++ H  +   V R     +++ V             + TI  +K +I  +    PDQ  
Sbjct: 4  SHHHHHHSSGLVPRGSPHLIKVTVKTPKDKEDFSVTDTCTIQQLKEEISQRFKAHPDQLV 63

Query: 77 QIF 79
           IF
Sbjct: 64 LIF 66

>3n3k_B Ubiquitin; hydrolase, protease, thiol protease, DUB, zinc ribbon, inhibitor, ubiqu acetylation, cytoplasm, isopeptide bond, nucleus; 2.60A {Homo sapiens} Length = 85

 Score = 66.2 bits (162), Expect = 3e-16
 Identities = 31/47 (65%), Positives = 36/47 (76%), Gaps = 1/47 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNIH  S L+ + + RGG
Sbjct: 33 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIHNHSALYLLLKLRGG 79

>3n3k_B Ubiquitin; hydrolase, protease, thiol protease, DUB, zinc ribbon, inhibitor, ubiqu acetylation, cytoplasm, isopeptide bond, nucleus; 2.60A {Homo sapiens} Length = 85

 Score = 56.2 bits (136), Expect = 3e-12
 Identities = 26/45 (57%), Positives = 29/45 (64%), Gaps = 12/45 (26%)

Query: 47 MQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          M+I V            E SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 4  MRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEGIPPDQQRLIF 48

>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion protein; ubiquitin interacting motif, UIM, protein domain interface; NMR {Saccharomyces cerevisiae} Length = 114

 Score = 66.8 bits (163), Expect = 3e-16
 Identities = 33/48 (68%), Positives = 36/48 (75%), Gaps = 1/48 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGM 47
          I+DKE I  DQQR I+AGK+LEDGRTL DYNI   STLH V R RGG 
Sbjct: 39 IQDKEGIPPDQQRLIWAGKQLEDGRTLSDYNIQRESTLHLVLRLRGGS 86

>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion protein; ubiquitin interacting motif, UIM, protein domain interface; NMR {Saccharomyces cerevisiae} Length = 114

 Score = 61.8 bits (150), Expect = 4e-14
 Identities = 27/51 (52%), Positives = 30/51 (58%), Gaps = 12/51 (23%)

Query: 41 RRFRGGMQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
              G  QIF             ESSDTIDNVK+KIQDK+G PPDQQR I+
Sbjct: 4  HHHHGEFQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIW 54

>1we6_A Splicing factor, putative; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: d.15.1.1 Length = 111

 Score = 66.4 bits (162), Expect = 5e-16
 Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-HGSTLHSVRRFRGGMQ 48
           I  + +I  ++Q+       L+D  +L  YN+  G  L    R R G  
Sbjct: 61  IAGEIQIPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLRERSGPS 109

>1we6_A Splicing factor, putative; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: d.15.1.1 Length = 111

 Score = 41.7 bits (98), Expect = 2e-06
 Identities = 10/34 (29%), Positives = 20/34 (58%), Gaps = 1/34 (2%)

Query: 47 MQIFVES-SDTIDNVKAKIQDKKGTPPDQQRQIF 79
          M+I V+S S+ + ++K KI  +   P ++Q+   
Sbjct: 43 MEITVQSLSENVGSLKEKIAGEIQIPANKQKLSG 76

>2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing, protein binding; 2.60A {Homo sapiens} Length = 111

 Score = 66.4 bits (162), Expect = 6e-16
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 65  IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 111

>2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing, protein binding; 2.60A {Homo sapiens} Length = 111

 Score = 62.2 bits (151), Expect = 2e-14
 Identities = 31/78 (39%), Positives = 36/78 (46%), Gaps = 15/78 (19%)

Query: 14 FIFAGKRLEDGRTLVDYNIHGSTLHSVRRFRGGMQIFV------------ESSDTIDNVK 61
                 +E     +D N   +           MQIFV            E SDTI+NVK
Sbjct: 6  DTNNDGWIEGDELYIDTN---NDGWIEGDELLAMQIFVKTLTGKTITLEVEPSDTIENVK 62

Query: 62 AKIQDKKGTPPDQQRQIF 79
          AKIQDK+G PPDQQR IF
Sbjct: 63 AKIQDKEGIPPDQQRLIF 80

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B* Length = 307

 Score = 68.7 bits (167), Expect = 2e-15
 Identities = 32/45 (71%), Positives = 34/45 (75%), Gaps = 1/45 (2%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFR 44
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R R
Sbjct: 263 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 307

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B* Length = 307

 Score = 45.2 bits (106), Expect = 4e-07
 Identities = 29/73 (39%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 8   LRDQQRFIFAGKRLEDGRTLVDYNIHGSTLHSVRRFRG-GMQIFVESSDTIDNVKAKIQD 66
               +        +     +    I GS    V+   G  + + VE SDTI+NVKAKIQD
Sbjct: 206 SALSKDPNEKRDHMVLLEFVTAAGITGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQD 265

Query: 67  KKGTPPDQQRQIF 79
           K+G PPDQQR IF
Sbjct: 266 KEGIPPDQQRLIF 278

>3phx_B Ubiquitin-like protein ISG15; OTU domain, DE-ubiquitinase, DE-isgylase, hydrolase-protein complex; 1.60A {Homo sapiens} Length = 79

 Score = 63.6 bits (155), Expect = 3e-15
 Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 1/46 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-HGSTLHSVRRFRG 45
          +   E +  D     F GK LED   L +Y +   ST+    R RG
Sbjct: 34 VSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRG 79

>3phx_B Ubiquitin-like protein ISG15; OTU domain, DE-ubiquitinase, DE-isgylase, hydrolase-protein complex; 1.60A {Homo sapiens} Length = 79

 Score = 48.1 bits (115), Expect = 3e-09
 Identities = 7/45 (15%), Positives = 15/45 (33%), Gaps = 12/45 (26%)

Query: 47 MQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          + I V              + T+ ++K ++   +G   D     F
Sbjct: 5  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTF 49

>2dzi_A Ubiquitin-like protein 4A; GDX, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 81

 Score = 63.1 bits (154), Expect = 4e-15
 Identities = 17/43 (39%), Positives = 25/43 (58%), Gaps = 1/43 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR 42
          + +K  +   QQR +F GK L DG+ L DY+I   S L+ V +
Sbjct: 37 VSEKLNVPVRQQRLLFKGKALADGKRLSDYSIGPNSKLNLVVK 79

>2dzi_A Ubiquitin-like protein 4A; GDX, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 81

 Score = 56.9 bits (138), Expect = 1e-12
 Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 12/48 (25%)

Query: 44 RGGMQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
            GMQ+ V               + +  +K  + +K   P  QQR +F
Sbjct: 5  SSGMQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLNVPVRQQRLLF 52

>2faz_A Ubiquitin-like containing PHD and ring finger DOM protein 1; cell cycle, DNA damage, DNA repair, DNA-binding, ligase, Met binding, nuclear protein; 2.00A {Homo sapiens} SCOP: d.15.1.1 Length = 78

 Score = 63.1 bits (154), Expect = 5e-15
 Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR 42
          I++   +    QR  + GK++EDG TL DY +    T+  + R
Sbjct: 34 IQELFHVEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLLVR 76

>2faz_A Ubiquitin-like containing PHD and ring finger DOM protein 1; cell cycle, DNA damage, DNA repair, DNA-binding, ligase, Met binding, nuclear protein; 2.00A {Homo sapiens} SCOP: d.15.1.1 Length = 78

 Score = 57.4 bits (139), Expect = 7e-13
 Identities = 10/49 (20%), Positives = 16/49 (32%), Gaps = 14/49 (28%)

Query: 45 GGMQIFV--------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          G M I V                   ++ ++ KIQ+     P  QR  +
Sbjct: 1  GSMWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFY 49

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9 Length = 189

 Score = 63.2 bits (153), Expect = 5e-14
 Identities = 9/72 (12%), Positives = 16/72 (22%), Gaps = 4/72 (5%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHGSTLHSVRRFRGGMQIFVESSDTIDNV 60
          I        D    +  G    +   + D      T +   +  GG +   + S T    
Sbjct: 30 ISQDMGFEIDMMTLVNNGFIAPNTELVTDD----VTYYLSLKLLGGKKKKKKKSYTTKKK 85

Query: 61 KAKIQDKKGTPP 72
                      
Sbjct: 86 TKHRHVHTKLGA 97

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9 Length = 189

 Score = 62.1 bits (150), Expect = 1e-13
 Identities = 8/45 (17%), Positives = 16/45 (35%), Gaps = 12/45 (26%)

Query: 47 MQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          MQ+ V            E   ++ ++K++I    G   D    + 
Sbjct: 1  MQVQVKTLEGETKIYTLEQGTSVLDLKSQISQDMGFEIDMMTLVN 45

>1uel_A HHR23B, UV excision repair protein RAD23 homolog B; UBL, UIM, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 95

 Score = 60.4 bits (147), Expect = 7e-14
 Identities = 12/50 (24%), Positives = 20/50 (40%), Gaps = 4/50 (8%)

Query: 1  IEDKE---EILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
          IE ++         Q+ I+AGK L D   L +Y I   + +  +      
Sbjct: 30 IESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKPKA 79

>1uel_A HHR23B, UV excision repair protein RAD23 homolog B; UBL, UIM, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 95

 Score = 54.6 bits (132), Expect = 1e-11
 Identities = 11/48 (22%), Positives = 21/48 (43%), Gaps = 15/48 (31%)

Query: 47 MQIF------------VESSDTIDNVKAKIQDKKGT---PPDQQRQIF 79
          MQ+             ++  +T+  +K KI+ +KG    P   Q+ I+
Sbjct: 1  MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIY 48

>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana, uncharacterized putative protein, NESG, structural genomics; NMR {Arabidopsis thaliana} Length = 84

 Score = 59.2 bits (144), Expect = 1e-13
 Identities = 10/40 (25%), Positives = 15/40 (37%), Gaps = 2/40 (5%)

Query: 1  IEDKEEILRDQQRFIFAGK-RLEDGRTLVDYNI-HGSTLH 38
          IE  + I   +Q  I  G   L +  T+    I   S + 
Sbjct: 40 IERSQHIPVSKQTLIVDGIVILREDLTVEQCQIVPTSDIQ 79

>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana, uncharacterized putative protein, NESG, structural genomics; NMR {Arabidopsis thaliana} Length = 84

 Score = 58.8 bits (143), Expect = 2e-13
 Identities = 11/45 (24%), Positives = 17/45 (37%), Gaps = 12/45 (26%)

Query: 47 MQIF------------VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          M+              V+  DT+  VK KI+  +  P  +Q  I 
Sbjct: 11 MKFLVENLNGSSFELEVDYRDTLLVVKQKIERSQHIPVSKQTLIV 55

>3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} Length = 106

 Score = 60.1 bits (146), Expect = 1e-13
 Identities = 8/43 (18%), Positives = 19/43 (44%), Gaps = 1/43 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR 42
          +         Q + I++GK L+D +T+ +  +  G  +  +  
Sbjct: 31 LAQSISCEESQIKLIYSGKVLQDSKTVSECGLKDGDQVVFMVS 73

>3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} Length = 106

 Score = 55.5 bits (134), Expect = 9e-12
 Identities = 8/45 (17%), Positives = 15/45 (33%), Gaps = 12/45 (26%)

Query: 47 MQIF------------VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          + +             +E S+TI   K K+         Q + I+
Sbjct: 2  VSLTFKNFKKEKVPLDLEPSNTILETKTKLAQSISCEESQIKLIY 46

>2wyq_A HHR23A, UV excision repair protein RAD23 homolog A; DNA binding protein, DNA excision repair, proteasomal degrad polyubiquitin; 1.65A {Homo sapiens} PDB: 1p98_A 1p9d_U 1p1a_A Length = 85

 Score = 58.0 bits (141), Expect = 5e-13
 Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 5/51 (9%)

Query: 1  IEDKE---EILRDQQRFIFAGKRLEDGRTLVDYNI-HGSTLHS-VRRFRGG 46
          IE ++         Q+ I+AGK L D   + DY I   + +   V + + G
Sbjct: 35 IEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTKTKAG 85

>2wyq_A HHR23A, UV excision repair protein RAD23 homolog A; DNA binding protein, DNA excision repair, proteasomal degrad polyubiquitin; 1.65A {Homo sapiens} PDB: 1p98_A 1p9d_U 1p1a_A Length = 85

 Score = 51.9 bits (125), Expect = 1e-10
 Identities = 11/48 (22%), Positives = 20/48 (41%), Gaps = 15/48 (31%)

Query: 47 MQIF------------VESSDTIDNVKAKIQDKKGT---PPDQQRQIF 79
          + I             +E  +T+  +K KI+ +KG    P   Q+ I+
Sbjct: 6  VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIY 53

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} Length = 94

 Score = 56.6 bits (137), Expect = 2e-12
 Identities = 8/54 (14%), Positives = 20/54 (37%), Gaps = 11/54 (20%)

Query: 37 LHSVRRFRGGMQIF-----------VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
           H        + +            V+ ++T+ ++K KI   + TP  + +  +
Sbjct: 6  HHHSHAAVRKIHVTVKFPSKQFTVEVDRTETVSSLKDKIHIVENTPIKRMQLYY 59

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} Length = 94

 Score = 52.4 bits (126), Expect = 1e-10
 Identities = 10/44 (22%), Positives = 18/44 (40%), Gaps = 2/44 (4%)

Query: 1  IEDKEEILRDQQRFIFAGKRL-EDGRTLVDYNIH-GSTLHSVRR 42
          I   E     + +  ++G  L +D R L +Y I   S +    +
Sbjct: 44 IHIVENTPIKRMQLYYSGIELADDYRNLNEYGITEFSEIVVFLK 87

>3u5e_m 60S ribosomal protein L40; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3u5i_m 4a18_K 4a19_K 4a1b_K 4a1d_K 4adx_5 3izc_p 3izs_p 3iz5_p 3izr_p Length = 128

 Score = 57.4 bits (138), Expect = 3e-12
 Identities = 36/73 (49%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGMQIFVESSDTIDN 59
           I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG+      +     
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGIIEPSLKALASKY 89

Query: 60  VKAKIQDKKGTPP 72
              K   +K    
Sbjct: 90  NCDKSVCRKCYAR 102

>3u5e_m 60S ribosomal protein L40; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3u5i_m 4a18_K 4a19_K 4a1b_K 4a1d_K 4adx_5 3izc_p 3izs_p 3iz5_p 3izr_p Length = 128

 Score = 53.5 bits (128), Expect = 7e-11
 Identities = 29/45 (64%), Positives = 31/45 (68%), Gaps = 12/45 (26%)

Query: 47 MQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          MQIFV            ESSDTIDNVK+KIQDK+G PPDQQR IF
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIF 45

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana} Length = 85

 Score = 50.8 bits (122), Expect = 4e-10
 Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 1/39 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-HGSTLH 38
          ++    +L   Q+ IF GK L +  TL   ++  G+ L 
Sbjct: 41 LQPITNVLPRGQKLIFKGKVLVETSTLKQSDVGSGAKLM 79

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana} Length = 85

 Score = 45.0 bits (107), Expect = 6e-08
 Identities = 8/31 (25%), Positives = 16/31 (51%)

Query: 49 IFVESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          + V    T+ ++K+++Q      P  Q+ IF
Sbjct: 26 LSVSPDCTVKDLKSQLQPITNVLPRGQKLIF 56

>1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair, proteasome-mediated degradation, protein- protein interaction, replication; NMR {Homo sapiens} SCOP: a.5.2.1 a.5.2.1 a.189.1.1 d.15.1.1 PDB: 1qze_A 1tp4_A Length = 368

 Score = 49.2 bits (116), Expect = 1e-08
 Identities = 11/50 (22%), Positives = 20/50 (40%), Gaps = 15/50 (30%)

Query: 45 GGMQIF------------VESSDTIDNVKAKIQDKKGT---PPDQQRQIF 79
            + I             +E  +T+  +K KI+ +KG    P   Q+ I+
Sbjct: 6  SAVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIY 55

>1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair, proteasome-mediated degradation, protein- protein interaction, replication; NMR {Homo sapiens} SCOP: a.5.2.1 a.5.2.1 a.189.1.1 d.15.1.1 PDB: 1qze_A 1tp4_A Length = 368

 Score = 47.7 bits (112), Expect = 5e-08
 Identities = 12/57 (21%), Positives = 22/57 (38%), Gaps = 2/57 (3%)

Query: 2  EDKEEILRDQQRFIFAGKRLEDGRTLVDYNI--HGSTLHSVRRFRGGMQIFVESSDT 56
          + ++      Q+ I+AGK L D   + DY I      +  V + + G         +
Sbjct: 41 KGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTKTKAGQGTSAPPEAS 97

>1x1m_A Ubiquitin-like protein SB132; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.15.1.1 Length = 107

 Score = 47.1 bits (111), Expect = 2e-08
 Identities = 13/34 (38%), Positives = 22/34 (64%), Gaps = 1/34 (2%)

Query: 10 DQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR 42
          +    I+ G++L+D +TL  Y I  GST+H +R+
Sbjct: 66 ELIDLIYCGRKLKDDQTLDFYGIQPGSTVHVLRK 99

>1v5o_A 1700011N24RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 Length = 102

 Score = 44.6 bits (105), Expect = 1e-07
 Identities = 7/56 (12%), Positives = 25/56 (44%), Gaps = 2/56 (3%)

Query: 1  IEDKEEILRDQQRFIFAGKRL-EDGRTLVDYNIH-GSTLHSVRRFRGGMQIFVESS 54
           E +  +  ++ + ++  + L +D  +L  Y +  G  +  +++   G++    + 
Sbjct: 41 CELESGVPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVLLQKDNVGLRTPGRTP 96

>1v5o_A 1700011N24RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 Length = 102

 Score = 40.0 bits (93), Expect = 7e-06
 Identities = 4/29 (13%), Positives = 13/29 (44%)

Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          V     + N +   + + G P ++ + ++
Sbjct: 28 VNPDFELSNFRVLCELESGVPAEEAQIVY 56

>2dzm_A FAS-associated factor 1; ubiquitin-like domain, HFAF1, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 100

 Score = 39.3 bits (91), Expect = 2e-05
 Identities = 5/33 (15%), Positives = 15/33 (45%)

Query: 48 QIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
           + +E + T+  +K  ++++   P  +     W
Sbjct: 22 DVVLEDTCTVGEIKQILENELQIPVSKMLLKGW 54

>1wia_A Hypothetical ubiquitin-like protein (riken cDNA 2010008E23); 'structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 Length = 95

 Score = 36.9 bits (85), Expect = 1e-04
 Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 2/36 (5%)

Query: 9  RDQQRFIFAGKRL-EDGRTLVDYNI-HGSTLHSVRR 42
            Q + I+ G+ L +  RTL   NI +   +H  R 
Sbjct: 42 ESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRS 77

>1v86_A DNA segment, CHR 7, wayne state university 128, expressed; ubiquitin fold, structural genomics, D7WSU128E protein; HET: DNA; NMR {Mus musculus} SCOP: d.15.1.1 Length = 95

 Score = 36.3 bits (84), Expect = 2e-04
 Identities = 17/59 (28%), Positives = 23/59 (38%), Gaps = 10/59 (16%)

Query: 22 EDGRTLVDYNI-HGSTLHSVRRFRGGMQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
            G+ LVD  I    T H V+         V    T   +K KI    G PP  Q+ ++
Sbjct: 12 GVGKELVDLKIIWNKTKHDVK---------VPLDSTGSELKQKIHSITGLPPAMQKVMY 61

>1t0y_A Tubulin folding cofactor B; ubiquitin-like, cytoskeleton, microtubule, CESG, structural genomics, protein structure initiative, PSI; NMR {Caenorhabditis elegans} SCOP: d.15.1.1 Length = 122

 Score = 36.8 bits (85), Expect = 2e-04
 Identities = 9/49 (18%), Positives = 19/49 (38%), Gaps = 6/49 (12%)

Query: 28 VDYNIHGSTLHSVRRFRGGMQIFVESSDTIDNVKAKIQDKKGTPPDQQR 76
           D  I  +           M+    +  +++++K K++   GT  D  R
Sbjct: 7  YDLEIT-TNATDFP-----MEKKYPAGMSLNDLKKKLELVVGTTVDSMR 49

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A Length = 105

 Score = 36.1 bits (83), Expect = 3e-04
 Identities = 7/29 (24%), Positives = 13/29 (44%)

Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          V    T+ ++K  +    G PP  Q+ + 
Sbjct: 43 VRPDMTVASLKDMVFLDYGFPPVLQQWVI 71

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens} Length = 125

 Score = 35.0 bits (80), Expect = 9e-04
 Identities = 9/36 (25%), Positives = 15/36 (41%), Gaps = 3/36 (8%)

Query: 10 DQQRFIFAGKRLEDGRTLVDYNI---HGSTLHSVRR 42
          +  R I+ G+ L    TL    +     + +H V R
Sbjct: 64 NILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLVAR 99

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	97
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.91
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.91
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.88
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	99.53
1wju_A	100	NEDD8 ultimate buster-1; ubiquitin-like domain, st	99.48
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	99.44
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	99.4
2uyz_B	79	Small ubiquitin-related modifier 1; sumoylation, c	99.4
2lxa_A	87	Ubiquitin-like protein MDY2; ubiquitin-like domain	99.39
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	99.38
4ajy_B	118	Transcription elongation factor B polypeptide 2; E	99.38
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	99.37
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	99.37
1wyw_B	97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	99.35
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	99.35
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	99.35
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	99.34
1wju_A	100	NEDD8 ultimate buster-1; ubiquitin-like domain, st	99.34
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	99.34
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	99.33
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	99.33
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	99.32
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	99.32
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	99.32
4hcn_B	98	Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidas	99.32
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	99.31
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	99.31
2lxa_A	87	Ubiquitin-like protein MDY2; ubiquitin-like domain	99.31
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	99.31
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	99.3
4ajy_B	118	Transcription elongation factor B polypeptide 2; E	99.3
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	99.29
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	99.29
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	99.29
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	99.29
4a20_A	98	Ubiquitin-like protein MDY2; protein binding, GET-	99.29
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	99.29
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	99.29
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	99.28
1se9_A	126	Ubiquitin family; ubiquitin-like, cell-free, wheat	99.28
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	99.28
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	99.28
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	99.28
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	99.27
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	99.27
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	99.27
3vdz_A	111	Ubiquitin-40S ribosomal protein S27A; gadolinium,	99.27
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	99.26
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.26
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	99.26
3v6c_B	91	Ubiquitin; structural genomics, structural genomic	99.25
3v6c_B	91	Ubiquitin; structural genomics, structural genomic	99.25
2uyz_B	79	Small ubiquitin-related modifier 1; sumoylation, c	99.25
4a20_A	98	Ubiquitin-like protein MDY2; protein binding, GET-	99.25
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	99.25
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	98.9
4hcn_B	98	Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidas	99.25
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	99.25
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	99.24
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	99.24
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	99.23
1se9_A	126	Ubiquitin family; ubiquitin-like, cell-free, wheat	99.23
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	99.23
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	99.23
1wyw_B	97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	99.22
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	99.22
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	99.22
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	99.22
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	99.22
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	99.22
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	99.22
1we6_A	111	Splicing factor, putative; structural genomics, ub	99.22
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	99.22
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	99.21
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	99.21
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	99.21
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	99.2
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	99.2
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.19
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	99.19
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	99.19
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	99.19
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	99.19
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	99.19
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	99.19
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	99.18
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	99.18
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	99.18
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	99.17
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	99.17
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	99.17
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	99.17
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	99.17
3u5c_f	152	40S ribosomal protein S31; translation, ribosome,	99.17
4b6w_A	86	Tubulin-specific chaperone; CAP-Gly, ubiquitin-lik	99.16
2kjr_A	95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	99.16
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	99.16
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	99.16
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	99.16
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	99.16
3vdz_A	111	Ubiquitin-40S ribosomal protein S27A; gadolinium,	99.16
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	99.16
2kj6_A	97	Tubulin folding cofactor B; methods development, N	99.16
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	99.15
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	99.15
4b6w_A	86	Tubulin-specific chaperone; CAP-Gly, ubiquitin-lik	99.15
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	99.14
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	99.14
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	99.14
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	99.14
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.14
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	99.13
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	99.12
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	99.12
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	99.12
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	99.12
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	99.11
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	99.11
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	99.1
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	99.1
2daf_A	118	FLJ35834 protein; hypothetical protein FLJ35834, u	99.09
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	99.09
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	99.07
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	99.07
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	99.07
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	99.06
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	99.06
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	99.06
1we6_A	111	Splicing factor, putative; structural genomics, ub	99.05
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	99.05
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	99.05
1wxv_A	92	BAG-family molecular chaperone regulator-1; struct	99.05
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	99.04
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	99.03
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	99.03
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	99.02
1v6e_A	95	Cytoskeleton-associated protein 1; tubulin-specifi	99.02
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	98.58
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	99.01
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	99.0
1wxv_A	92	BAG-family molecular chaperone regulator-1; struct	98.99
2kjr_A	95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	98.97
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	98.95
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	98.94
2kj6_A	97	Tubulin folding cofactor B; methods development, N	98.93
3u5c_f	152	40S ribosomal protein S31; translation, ribosome,	98.92
2dzj_A	88	Synaptic glycoprotein SC2; ubiquitin-like fold, st	98.91
4efo_A	94	Serine/threonine-protein kinase TBK1; ubiquitin li	98.9
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	98.9
2daf_A	118	FLJ35834 protein; hypothetical protein FLJ35834, u	98.89
2io1_B	94	Small ubiquitin-related modifier 3 precursor; SUMO	98.89
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	98.85
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	98.85
1v6e_A	95	Cytoskeleton-associated protein 1; tubulin-specifi	98.84
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	98.83
2dzj_A	88	Synaptic glycoprotein SC2; ubiquitin-like fold, st	98.82
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	98.82
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	98.82
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	98.81
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	98.8
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	98.76
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	98.76
2io0_B	91	Small ubiquitin-related modifier 2 precursor; SUMO	98.76
1wf9_A	107	NPL4 family protein; beta-grAsp fold like domain,	98.75
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	98.75
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	98.73
2d07_B	93	Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Ho	98.72
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	98.72
2eke_C	106	Ubiquitin-like protein SMT3; UBC9, SUMO binding mo	98.64
1wm3_A	72	Ubiquitin-like protein SMT3B; ubiquitin fold, half	98.63
2kzr_A	86	Ubiquitin thioesterase OTU1; structural genomics,	98.61
1wz0_A	104	Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-li	98.52
2io1_B	94	Small ubiquitin-related modifier 3 precursor; SUMO	98.48
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	98.48
3a4r_A	79	Nfatc2-interacting protein; ubiquitin fold, coiled	98.46
2k8h_A	110	Small ubiquitin protein; SUMO, post-translational	98.43
1wf9_A	107	NPL4 family protein; beta-grAsp fold like domain,	98.43
2io0_B	91	Small ubiquitin-related modifier 2 precursor; SUMO	98.35
1wm3_A	72	Ubiquitin-like protein SMT3B; ubiquitin fold, half	98.34
2kzr_A	86	Ubiquitin thioesterase OTU1; structural genomics,	98.3
3a4r_A	79	Nfatc2-interacting protein; ubiquitin fold, coiled	98.23
2d07_B	93	Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Ho	98.17
2k8h_A	110	Small ubiquitin protein; SUMO, post-translational	98.13
1wjn_A	97	Tubulin-folding protein TBCE; ubiquitin-like domai	98.11
1wjn_A	97	Tubulin-folding protein TBCE; ubiquitin-like domai	98.08
3pge_A	200	SUMO-modified proliferating cell nuclear antigen;	98.07
1wz0_A	104	Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-li	98.04
2eke_C	106	Ubiquitin-like protein SMT3; UBC9, SUMO binding mo	98.03
3kyd_D	115	Small ubiquitin-related modifier 1; SUMO, thioeste	97.98
3tix_A	207	Ubiquitin-like protein SMT3, RNA-induced transcri	97.88
3v7o_A	227	Minor nucleoprotein VP30; ssgcid, seattle structur	97.73
3kyd_D	115	Small ubiquitin-related modifier 1; SUMO, thioeste	97.4
4efo_A	94	Serine/threonine-protein kinase TBK1; ubiquitin li	97.33
2pjh_A	80	Protein NPL4, nuclear protein localization protein	97.32
3goe_A	82	DNA repair protein RAD60; SUMO-like domain, sumoyl	97.3
3pge_A	200	SUMO-modified proliferating cell nuclear antigen;	97.14
3ix6_A	360	TS, tsase, thymidylate synthase; niaid, ssgcid, se	97.13
3uf8_A	209	Ubiquitin-like protein SMT3, peptidyl-prolyl CIS-	96.98
4da1_A	389	Protein phosphatase 1K, mitochondrial; metal-ION-a	96.88
3tix_A	207	Ubiquitin-like protein SMT3, RNA-induced transcri	96.68
3uf8_A	209	Ubiquitin-like protein SMT3, peptidyl-prolyl CIS-	96.61
2jxx_A	97	Nfatc2-interacting protein; nuclear factor of acti	96.46
2l76_A	95	Nfatc2-interacting protein; ubiquitin-like domain,	96.25
3goe_A	82	DNA repair protein RAD60; SUMO-like domain, sumoyl	95.86
3v7o_A	227	Minor nucleoprotein VP30; ssgcid, seattle structur	95.34
2pjh_A	80	Protein NPL4, nuclear protein localization protein	94.46
2jxx_A	97	Nfatc2-interacting protein; nuclear factor of acti	94.3
2al3_A	90	TUG long isoform; TUG UBL1 insulin, endocytosis/ex	93.91
3ivf_A	371	Talin-1; FERM domain, cell membrane, cell projecti	92.23
2kvr_A	130	Ubiquitin carboxyl-terminal hydrolase 7; USP7, ubi	92.15
2l76_A	95	Nfatc2-interacting protein; ubiquitin-like domain,	91.83
3ix6_A	360	TS, tsase, thymidylate synthase; niaid, ssgcid, se	91.79
4da1_A	389	Protein phosphatase 1K, mitochondrial; metal-ION-a	90.26
4eut_A	396	Serine/threonine-protein kinase TBK1; ATP binding,	89.38
2juo_A	89	GA-binding protein alpha chain; OST, ubiquitin, tr	88.29
2al3_A	90	TUG long isoform; TUG UBL1 insulin, endocytosis/ex	88.15
2kc2_A	128	Talin-1, F1; FERM, adhesion, cell membrane, cell p	87.94
1oey_A	83	P67-PHOX, neutrophil cytosol factor 2; immune syst	85.52
2bps_A	81	YUKD protein; ubiquitin-like protein, ubiquitin; 2	85.51
2ylm_A	530	Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70	83.59
3qx1_A	84	FAS-associated factor 1; UBX, protein binding, P97	82.75
3qa8_A	676	MGC80376 protein; kinase ubiquitin-like domain, ph	82.6

>3rt3_B Ubiquitin-like protein ISG15; ubiquitin-like domain, isgylation, antiviral protein-viral P complex; 2.01A {Homo sapiens} PDB: 3sdl_C 3r66_C 3pse_B 1z2m_A

Probab=99.91  E-value=8e-25  Score=143.33  Aligned_cols=89  Identities=24%  Similarity=0.168  Sum_probs=78.2

Q ss_pred             CccccCCCCcceEEE-E-CCEEeCCCCCCccceec-ccceeeeee-eecceee------------eeeccchhHHHHHhh
Q 040204            1 IEDKEEILRDQQRFI-F-AGKRLEDGRTLVDYNIH-GSTLHSVRR-FRGGMQI------------FVESSDTIDNVKAKI   64 (97)
Q Consensus         1 i~~~~gip~~~Q~L~-~-~g~~L~d~~tL~~y~I~-~sti~l~i~-~~~g~~i------------~v~~~~TV~~lK~~I   64 (97)
                      |++.+|+|+++|+|+ | +|+.|+|+.+|++|+|. +++++++.+ +++++.|            .|++++||+++|++|
T Consensus        32 I~~~~gip~~~QrL~~~~~g~~L~d~~tL~~y~i~~~~~l~l~~~~~~~~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i  111 (159)
T 3rt3_B           32 ITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDKSDEPLSILVRNNKGRSSTYEVRLTQTVAHLKQQV  111 (159)
T ss_dssp             HHHHHCCCGGGEEEEEETTCCBCCTTSCGGGGTCCTTCEEEEEECCCCCCEEEEEECTTSCEEEEEECTTSBHHHHHHHH
T ss_pred             HHHHhCCCHHHEEEEEcCCCCCCCCCCCHHHcCCCCCCEEEEEccCCCCcEEEEEECCCCCEEEEEeCCCCCHHHHHHHH
Confidence            456789999999999 9 89999999999999999 999999998 3555444            448899999999999


Q ss_pred             hhhcCCCCCceEEEECeEe--CCCccc
Q 040204           65 QDKKGTPPDQQRQIFWFVF--GWGSLW   89 (97)
Q Consensus        65 ~~~~gip~~~q~Lif~G~~--~~~~~~   89 (97)
                      ++++|+|+++|+|+|+|++  |..+|-
T Consensus       112 ~~~~gip~~~q~L~~~G~~L~d~~tL~  138 (159)
T 3rt3_B          112 SGLEGVQDDLFWLTFEGKPLEDQLPLG  138 (159)
T ss_dssp             HHHHTCCGGGEEEEETTEECCTTSBGG
T ss_pred             HHHHCCCHHHEEEEECCeecCCCCCHH
Confidence            9999999999999999999  545553

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}

Probab=99.91  E-value=1.1e-24  Score=144.66  Aligned_cols=88  Identities=72%  Similarity=0.958  Sum_probs=79.5

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecceeeee------------eccchhHHHHHhhhhh
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGMQIFV------------ESSDTIDNVKAKIQDK   67 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~~i~v------------~~~~TV~~lK~~I~~~   67 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|+|. +++++++++..+++.++|            ++++||.+||++|+++
T Consensus        50 I~~~~gip~~~QrL~~~g~~L~d~~tL~~~~i~~~~~l~l~~~~~gg~~i~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~  129 (172)
T 3u30_A           50 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDK  129 (172)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTCBTGGGTCCTTCEEEEEECCCCCEEEEEEESSCCEEEEEECTTCBHHHHHHHHHHH
T ss_pred             HHHHHCcChHHEEEEECCccccccCCHhHcCCcccceeeeeecccccccceeecccCcceeEEecCCCCHHHHHHHHHHH
Confidence            456789999999999999999999999999999 999999998887765554            7899999999999999


Q ss_pred             cCCCCCceEEEECeEe--CCCcc
Q 040204           68 KGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        68 ~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      +|+|+++|+|+|+|++  |..+|
T Consensus       130 ~gip~~~q~L~~~g~~L~D~~tL  152 (172)
T 3u30_A          130 EGIPPDQQRLIFAGKQLEDGRTL  152 (172)
T ss_dssp             HCCCGGGCCEEETTEECCTTSBS
T ss_pred             hCCCceeEEEEECCccCCCCCcH
Confidence            9999999999999999  44555

>3b08_A Polyubiquitin-C, ubiquitin; protein complex, signaling protein-metal binding protein COM; HET: TRE; 1.70A {Homo sapiens} PDB: 2w9n_A* 3b0a_A* 3axc_A 2zvn_A 2zvo_A 2y5b_B

Probab=99.88  E-value=5.4e-23  Score=132.85  Aligned_cols=89  Identities=71%  Similarity=0.935  Sum_probs=78.3

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecceeee------------eeccchhHHHHHhhhhh
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGMQIF------------VESSDTIDNVKAKIQDK   67 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~~i~------------v~~~~TV~~lK~~I~~~   67 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|+|. +++++++.+..+++.|.            +++++||.++|++|+++
T Consensus        30 i~~~~gip~~~q~L~~~g~~L~d~~tL~~~~i~~~~~l~l~~~~~~~~~i~Vk~~~g~~~~~~v~~~~tv~~lK~~i~~~  109 (152)
T 3b08_A           30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDK  109 (152)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCTTCEEEEEEESSSCEEEEEECTTCBHHHHHHHHHHH
T ss_pred             HHHHHCcChHHeEEEECCeECcCcccHHHhccCCCCeeEEEeecccccceeeeecCCCEEEEEeCCCCcHHHHHHHHHHH
Confidence            356789999999999999999999999999999 99999998876655444            47899999999999999


Q ss_pred             cCCCCCceEEEECeEe--CCCccc
Q 040204           68 KGTPPDQQRQIFWFVF--GWGSLW   89 (97)
Q Consensus        68 ~gip~~~q~Lif~G~~--~~~~~~   89 (97)
                      +|+|+++|+|+|+|+.  |..+|-
T Consensus       110 ~gi~~~~qrL~~~g~~L~d~~tL~  133 (152)
T 3b08_A          110 EGIPPDQQRLIFAGKQLEDGRTLS  133 (152)
T ss_dssp             HCCCGGGEEEEETTEECCTTSBTG
T ss_pred             hCcChhhEEEEECCEECCCCCCHH
Confidence            9999999999999998  445554

>3plu_A Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-1, SNU66, peptide binding protein; 1.40A {Saccharomyces cerevisiae} PDB: 3plv_A 1m94_A 1p0r_A

Probab=99.53  E-value=1.6e-14  Score=87.56  Aligned_cols=56  Identities=18%  Similarity=0.085  Sum_probs=48.9

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCccc
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSLW   89 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~~   89 (97)
                      ...+.+.++...|  ..+.++|++||.+||++|++++|+||++|+|+|+|++  |+.+|-
T Consensus        19 ~~mIqI~Vk~~~Gkk~~v~v~p~DTI~~LK~~I~~k~Gip~~qQrLif~Gk~LkD~~TL~   78 (93)
T 3plu_A           19 SHMIEVVVNDRLGKKVRVKCLGEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHISLE   78 (93)
T ss_dssp             -CEEEEEEECTTSCEEEEEEETTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBTG
T ss_pred             CceEEEEEECCCCCEEEEEECCcCHHHHHHHHHHHHhCCCHHHEEEEeCCEEccCcCCHH
Confidence            5678889988777  4577799999999999999999999999999999999  666663

>1wju_A NEDD8 ultimate buster-1; ubiquitin-like domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, protein binding; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.48  E-value=6.4e-14  Score=86.00  Aligned_cols=49  Identities=12%  Similarity=-0.022  Sum_probs=41.6

Q ss_pred             cceeeeeeeec--c--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           35 STLHSVRRFRG--G--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        35 sti~l~i~~~~--g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +|+++..+...  +  +.+.|++++||.+||++|++++|+||++|+|||+||+
T Consensus        16 ati~V~~~~~~~~~~~~~lev~~~~TV~~lK~kI~~k~gip~~qQrLI~~GKi   68 (100)
T 1wju_A           16 ATIEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFGLQENYIKIVINKKQ   68 (100)
T ss_dssp             EEEEEECCTTTCCSSSEEEEEESSSBHHHHHHHHHHHTTCCSTTCEEEETTEE
T ss_pred             EEEEEEecCCCCCCcEEEEEeCCcCHHHHHHHHHHHHHCcCHHHeEEEeCCeE
Confidence            46666554421  2  6788899999999999999999999999999999999

>1uh6_A Ubiquitin-like 5; beta-grAsp fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.44  E-value=2.9e-13  Score=83.03  Aligned_cols=65  Identities=25%  Similarity=0.331  Sum_probs=51.7

Q ss_pred             CCCCccceec--ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           24 GRTLVDYNIH--GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        24 ~~tL~~y~I~--~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      +.++...+-.  ...+.+.++...|  +.+.|++++||.+||++|++++|+|+++|||+|+|++  |..+|
T Consensus        14 ~~~~~~~~~~~~~~mm~I~VKtl~Gk~i~lev~p~dTV~~lK~~Ia~k~Gip~~qQrLi~~Gk~L~D~~TL   84 (100)
T 1uh6_A           14 GASLVPRGSEGAATMIEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSL   84 (100)
T ss_dssp             CCSSCCCCCSSCCCEEEEEEECSSSSCEEEEEETTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCSSCBH
T ss_pred             ccccccccCCCCCCeEEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhCCCHHHEEEEECCEECCCCCCH
Confidence            3444445544  3358888887755  6688899999999999999999999999999999999  44443

>3phx_B Ubiquitin-like protein ISG15; OTU domain, DE-ubiquitinase, DE-isgylase, hydrolase-protein complex; 1.60A {Homo sapiens}

Probab=99.40  E-value=9.4e-14  Score=80.90  Aligned_cols=45  Identities=33%  Similarity=0.445  Sum_probs=41.4

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeec
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRG   45 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~   45 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|+|. +++++++++..|
T Consensus        34 i~~~~gip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~l~l~~rl~G   79 (79)
T 3phx_B           34 VSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRG   79 (79)
T ss_dssp             HHHHHTCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCBC
T ss_pred             HHhhcCCCHHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCC
Confidence            356789999999999999999999999999999 999999998764

>2uyz_B Small ubiquitin-related modifier 1; sumoylation, cell division, nuclear protein, ubiquitin-like modifier, UBL conjugation pathway; 1.4A {Homo sapiens} SCOP: d.15.1.1 PDB: 2vrr_B 2iy0_B 2iy1_B 2g4d_B 2las_A 2io2_B 1z5s_B 3uip_B* 1tgz_B* 2bf8_B

Probab=99.40  E-value=6.5e-14  Score=81.58  Aligned_cols=46  Identities=20%  Similarity=0.444  Sum_probs=42.2

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++++|+|+++|+|+|+|++|+|++|+++|+|. +++|+++++..||
T Consensus        33 i~~~~gi~~~~qrL~~~G~~L~d~~tl~~~~i~~~~~i~l~~~~~GG   79 (79)
T 2uyz_B           33 YCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGG   79 (79)
T ss_dssp             HHHHHTCCGGGEEEEETTEECCTTCCHHHHTCCTTEEEEEEECCCC-
T ss_pred             HHHHHCCCcccEEEEECCEEeCCCCCHHHcCCCCCCEEEEEEeccCC
Confidence            356789999999999999999999999999999 9999999998876

>2lxa_A Ubiquitin-like protein MDY2; ubiquitin-like domain, protein-protein interaction, SGT2 BIN domain, GET pathway, protein binding; NMR {Saccharomyces cerevisiae}

Probab=99.39  E-value=5.3e-13  Score=79.93  Aligned_cols=52  Identities=17%  Similarity=0.114  Sum_probs=43.2

Q ss_pred             eeeeeeeecc--eeeeee--ccchhHHHHHhh-hhhcCCCCCceEEEECeEe--CCCcc
Q 040204           37 LHSVRRFRGG--MQIFVE--SSDTIDNVKAKI-QDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        37 i~l~i~~~~g--~~i~v~--~~~TV~~lK~~I-~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      +.+.++...|  +.+.|+  +++||.++|++| ++++|+|+++|+|+|+|++  |..+|
T Consensus         2 mqI~VKtl~g~~~~i~v~v~~~~TV~~lK~~I~~~~~gip~~~QrLi~~Gk~L~D~~tL   60 (87)
T 2lxa_A            2 VHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFL   60 (87)
T ss_dssp             CEEEEEECSSSCEECCEECCTTCBHHHHHHHHHHTTSCSSSTTEEEEETTEECCTTCBH
T ss_pred             EEEEEEcCCCCEEEEEEcCCCCCcHHHHHHHHHHHhcCCChHHEEEEECCEECcCcCCH
Confidence            4567777666  556655  999999999999 9999999999999999999  44444

>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion protein; ubiquitin interacting motif, UIM, protein domain interface; NMR {Saccharomyces cerevisiae}

Probab=99.38  E-value=2.4e-13  Score=84.96  Aligned_cols=59  Identities=56%  Similarity=0.758  Sum_probs=52.1

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecceeeeeeccchhHH
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGMQIFVESSDTIDN   59 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~~i~v~~~~TV~~   59 (97)
                      |++.+|+|+++|+|+|+|+.|+|+.+|++|+|. +++|+++.+..+|..+++++..++..
T Consensus        39 I~~~~gip~~~qrLi~~Gk~L~D~~tL~~ygI~~gstI~l~~~~~GG~~~~~~~~~~~~g   98 (114)
T 2kdi_A           39 IQDKEGIPPDQQRLIWAGKQLEDGRTLSDYNIQRESTLHLVLRLRGGSMGGAADEEELIR   98 (114)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTCBTTTTTCCSSCEEEEEECCCSSCCCSSCSSSHHHH
T ss_pred             HHHHHCcChHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEEcCCCceeeccccccccC
Confidence            356789999999999999999999999999999 99999999999998888876555543

>4ajy_B Transcription elongation factor B polypeptide 2; E3 ubiquitin ligase, transcription factor, hypoxic signaling transcription; 1.73A {Homo sapiens} PDB: 1lqb_A 1vcb_A 2c9w_B 2izv_B 2jz3_B 2xai_C 3dcg_A 3zrc_A* 3zrf_A 3ztc_A* 3ztd_A* 3zun_A* 1lm8_B 4b95_A* 2fnj_B 4b9k_A* 4awj_A*

Probab=99.38  E-value=9.2e-13  Score=82.87  Aligned_cols=52  Identities=19%  Similarity=0.068  Sum_probs=42.3

Q ss_pred             eeeeeeec-ceeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCccc
Q 040204           38 HSVRRFRG-GMQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSLW   89 (97)
Q Consensus        38 ~l~i~~~~-g~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~~   89 (97)
                      ++.++... .+.+.+++++||.+||++|++++|+|+++|||||+|++  |.++|-
T Consensus         4 Fl~Ikr~ktTI~ldve~sdTV~~lK~kI~~~~giPp~qQrLI~~Gk~LeD~kTL~   58 (118)
T 4ajy_B            4 FLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLG   58 (118)
T ss_dssp             EEEEEEBTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTT
T ss_pred             EEEEecCCEEEEEEcCCCChHHHHHHHHHHHHCCCHHHeEEEeCCeECCCcCCHH
Confidence            34444333 25567899999999999999999999999999999999  666664

>3phx_B Ubiquitin-like protein ISG15; OTU domain, DE-ubiquitinase, DE-isgylase, hydrolase-protein complex; 1.60A {Homo sapiens}

Probab=99.37  E-value=1.2e-12  Score=76.12  Aligned_cols=54  Identities=19%  Similarity=0.093  Sum_probs=46.3

Q ss_pred             cceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           35 STLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        35 sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      +++.+.++..+|  +.+.|++++||+++|++|++++|+|+++|+|+|+|++  |..+|
T Consensus         3 ~~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~G~~L~d~~tL   60 (79)
T 3phx_B            3 EPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPL   60 (79)
T ss_dssp             CCEEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBG
T ss_pred             CCEEEEEEeCCCCEEEEEECCcChHHHHHHHHHhhcCCCHHHEEEEECCEECCCCCcH
Confidence            467788887766  5578899999999999999999999999999999998  44444

>4fbj_B NEDD8; effector-HOST target complex, glutamine deamidase, deamidati bacterial effector, cell cycle-protein binding complex; 1.60A {Homo sapiens} PDB: 4f8c_B

Probab=99.37  E-value=1.6e-13  Score=81.84  Aligned_cols=48  Identities=48%  Similarity=0.767  Sum_probs=41.8

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeeccee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGMQ   48 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~~   48 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|+|. +++++++++..||..
T Consensus        30 I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~l~l~~rl~Gg~~   78 (88)
T 4fbj_B           30 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGGGG   78 (88)
T ss_dssp             HHHHHCCCGGGCEEEETTEECCTTSBTTTTTCCTTCEEEEECBCC----
T ss_pred             HHHHHCcChhHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEECCCCCC
Confidence            356789999999999999999999999999999 999999999999853

>1wyw_B Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Homo sapiens} SCOP: d.15.1.1 PDB: 1y8r_C* 2asq_A 2pe6_B 1a5r_A 2kqs_A 3kyc_D* 3rzw_C

Probab=99.35  E-value=1.6e-13  Score=83.29  Aligned_cols=46  Identities=20%  Similarity=0.444  Sum_probs=42.9

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++++|||+++|+|+|+|++|+|++||++|+|. +++|+++++..||
T Consensus        51 i~~~~gip~~~qrLif~Gk~L~d~~tl~dy~i~~g~~I~l~~~~~GG   97 (97)
T 1wyw_B           51 YCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGG   97 (97)
T ss_dssp             HHHHHTCCGGGEEEEETTEECCTTCCHHHHTCCTTCEEEEEESSSCC
T ss_pred             HHHHHCCChhhEEEEECCeEcCCCCCHHHCCCCCCCEEEEEEecCCC
Confidence            356789999999999999999999999999999 9999999998876

>2fnj_B Transcription elongation factor B polypeptide 2; beta-sandwich, lectin-like, SPRY, protein transport/signaling protein complex; 1.80A {Mus musculus} SCOP: d.15.1.1 PDB: 1lm8_B 1lqb_A 1vcb_A 2c9w_B 2izv_B 2jz3_B 2xai_C 3dcg_A 3zrc_A* 3zrf_A

Probab=99.35  E-value=1.5e-12  Score=81.95  Aligned_cols=42  Identities=19%  Similarity=0.124  Sum_probs=38.2

Q ss_pred             eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        47 ~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      +.+.|++++||.+||++|++++|+|+++|||+|+|++  |..+|
T Consensus        14 i~lev~~sdTV~~lK~kI~~~egIP~~qQrLi~~Gk~LeD~~TL   57 (118)
T 2fnj_B           14 IFTDAKESSTVFELKRIVEGILKRPPEEQRLYKDDQLLDDGKTL   57 (118)
T ss_dssp             EEEEEETTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBH
T ss_pred             EEEEeCCcChHHHHHHHHHHHhCCCHHHeEEEECCeECCCCCCH
Confidence            5678899999999999999999999999999999999  55555

>3plu_A Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-1, SNU66, peptide binding protein; 1.40A {Saccharomyces cerevisiae} PDB: 3plv_A 1m94_A 1p0r_A

Probab=99.35  E-value=2.9e-13  Score=81.98  Aligned_cols=40  Identities=20%  Similarity=0.253  Sum_probs=37.9

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSV   40 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~   40 (97)
                      |++++|+|+++|+|+|+|++|+|+.||++|+|+ +++++|.
T Consensus        51 I~~k~Gip~~qQrLif~Gk~LkD~~TL~dY~I~dgstLhL~   91 (93)
T 3plu_A           51 LSLQIGTQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLELY   91 (93)
T ss_dssp             HHHHHTCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEE
T ss_pred             HHHHhCCCHHHEEEEeCCEEccCcCCHHHcCCCCCCEEEEE
Confidence            467899999999999999999999999999999 9999986

>1ndd_A NEDD8, protein (ubiquitin-like protein NEDD8); proteolysis, signaling protei; 1.60A {Homo sapiens} SCOP: d.15.1.1 PDB: 1r4m_I 1r4n_I* 1xt9_B 2ko3_A 3gzn_I* 2bkr_B 2nvu_I* 3dqv_A 1bt0_A

Probab=99.34  E-value=3.6e-13  Score=77.26  Aligned_cols=46  Identities=50%  Similarity=0.833  Sum_probs=41.2

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++.+|+|++.|+|+|+|+.|+|+.+|++|+|. +++++++++..||
T Consensus        30 i~~~~~i~~~~q~L~~~g~~L~d~~tL~~~~i~~g~~i~l~~~~~GG   76 (76)
T 1ndd_A           30 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG   76 (76)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCC--
T ss_pred             HHHHHCcChHHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCCC
Confidence            356789999999999999999999999999999 9999999998876

>1wju_A NEDD8 ultimate buster-1; ubiquitin-like domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, protein binding; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.34  E-value=1.9e-13  Score=83.88  Aligned_cols=44  Identities=16%  Similarity=0.266  Sum_probs=38.7

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeec
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRG   45 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~   45 (97)
                      |++++|+|+++|+|+|+||+|+|++||++|+|+ +++| ++++..+
T Consensus        49 I~~k~gip~~qQrLI~~GKiL~D~~TL~~y~I~~gsti-~vl~lrg   93 (100)
T 1wju_A           49 IAETFGLQENYIKIVINKKQLQLGKTLEEQGVAHNVKA-MVLELKQ   93 (100)
T ss_dssp             HHHHTTCCSTTCEEEETTEECCTTSBHHHHTCCSSEEE-EEECCCC
T ss_pred             HHHHHCcCHHHeEEEeCCeECCCCCcHHHcCCCCCCEE-EEEEECC
Confidence            567899999999999999999999999999999 9999 4554443

>2fnj_B Transcription elongation factor B polypeptide 2; beta-sandwich, lectin-like, SPRY, protein transport/signaling protein complex; 1.80A {Mus musculus} SCOP: d.15.1.1 PDB: 1lm8_B 1lqb_A 1vcb_A 2c9w_B 2izv_B 2jz3_B 2xai_C 3dcg_A 3zrc_A* 3zrf_A

Probab=99.34  E-value=2.2e-13  Score=85.84  Aligned_cols=58  Identities=19%  Similarity=0.243  Sum_probs=47.2

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec--------ccceeeeeeeecc-ee-eeeeccchhHH
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH--------GSTLHSVRRFRGG-MQ-IFVESSDTIDN   59 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~--------~sti~l~i~~~~g-~~-i~v~~~~TV~~   59 (97)
                      |++++|||+++|||+|+|++|+|++||++|||.        +++++++++ .+| ++ +.+.+..+-.+
T Consensus        31 I~~~egIP~~qQrLi~~Gk~LeD~~TLsdy~I~~~~a~~q~~stL~L~lr-~~g~fe~l~i~~~s~pp~   98 (118)
T 2fnj_B           31 VEGILKRPPEEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFR-ADDTFEALRIEPFSSPPE   98 (118)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTSBHHHHTCCTTTSBTTBCEEEEEEEB-SSSCBCCCCBCCCCCCCC
T ss_pred             HHHHhCCCHHHeEEEECCeECCCCCCHHHcCcccccccCCCCCEEEEEec-CCCceeeeEEecCCCCCC
Confidence            467899999999999999999999999999998        689999999 544 43 56655444333

>3dbh_I NEDD8; cell cycle, activating enzyme, apoptosis, membrane, UBL conjugation pathway, ATP-binding, ligase, nucleotide- binding, polymorphism; 2.85A {Homo sapiens} SCOP: d.15.1.1 PDB: 3dbr_I 3dbl_I

Probab=99.33  E-value=2.4e-13  Score=80.41  Aligned_cols=46  Identities=52%  Similarity=0.871  Sum_probs=42.8

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|+|. +++|+++++..||
T Consensus        42 i~~~~gip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~i~l~~rl~GG   88 (88)
T 3dbh_I           42 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLRLRGG   88 (88)
T ss_dssp             HHHHHCCCGGGCCEEETTEECCTTSBGGGGTCCTTCEEEECCCCCCC
T ss_pred             HHHHHCcCHHHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEeCCCC
Confidence            356789999999999999999999999999999 9999999998876

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens}

Probab=99.33  E-value=3.3e-12  Score=75.71  Aligned_cols=55  Identities=16%  Similarity=0.180  Sum_probs=47.2

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      ...+.+.++..+|  +.+.|++++||.+||++|++.+|+|+++|+|+|+|+.  |..+|
T Consensus        15 ~~~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~D~~tL   73 (88)
T 4eew_A           15 PDSLEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKL   73 (88)
T ss_dssp             CCEEEEEEEETTSCEEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBG
T ss_pred             CCeEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEECCCCCcH
Confidence            5668888888666  4578899999999999999999999999999999999  54554

>4dwf_A HLA-B-associated transcript 3; ubiquitin-like domain, BAT3 protein, PF00240, structural GEN joint center for structural genomics, JCSG; 1.80A {Homo sapiens} PDB: 1wx9_A

Probab=99.32  E-value=3.6e-12  Score=75.82  Aligned_cols=55  Identities=16%  Similarity=0.174  Sum_probs=47.2

Q ss_pred             cceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCccc
Q 040204           35 STLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSLW   89 (97)
Q Consensus        35 sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~~   89 (97)
                      +++.+.++..+|  +.+.|++++||.+||++|++++|+|+++|+|+|+|++  |..+|-
T Consensus         4 ~~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~d~~tL~   62 (90)
T 4dwf_A            4 DSLEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQ   62 (90)
T ss_dssp             CEEEEEEEETTCCEEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGG
T ss_pred             cEEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCeECCCCCCHH
Confidence            467788888766  5578899999999999999999999999999999999  545554

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.32  E-value=4.1e-13  Score=81.21  Aligned_cols=47  Identities=21%  Similarity=0.244  Sum_probs=43.4

Q ss_pred             CccccCCCCcceEEEECCEEeCCC-CCCccceec-ccceeeeeeeecce
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDG-RTLVDYNIH-GSTLHSVRRFRGGM   47 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~-~tL~~y~I~-~sti~l~i~~~~g~   47 (97)
                      |++++|+|+++|+|+|+|+.|+|+ .+|++|+|. +++|+|+++..+|-
T Consensus        44 I~~~~gip~~~QrLi~~Gk~L~D~~~tL~~ygI~~gstl~lv~r~~gg~   92 (94)
T 2kan_A           44 IHIVENTPIKRMQLYYSGIELADDYRNLNEYGITEFSEIVVFLKSINRA   92 (94)
T ss_dssp             HHHHSSSCTTTEEEEETTEEECCTTSBHHHHTCCTTEEEEEEECCCSSC
T ss_pred             HHHHHCcCHHHEEEEECCEECCCCcccHHHCCCCCCCEEEEEEeCCCCC
Confidence            356789999999999999999999 999999999 99999999998873

>3n3k_B Ubiquitin; hydrolase, protease, thiol protease, DUB, zinc ribbon, inhibitor, ubiqu acetylation, cytoplasm, isopeptide bond, nucleus; 2.60A {Homo sapiens} SCOP: d.15.1.1

Probab=99.32  E-value=5.5e-13  Score=78.25  Aligned_cols=46  Identities=67%  Similarity=0.995  Sum_probs=41.5

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++.+|+|+++|+|+|+|+.|+|+.+|++|+|+ +++|+++++..+|
T Consensus        33 i~~~~~ip~~~qrL~~~g~~L~d~~tL~~~~i~~~~~i~l~~rl~GG   79 (85)
T 3n3k_B           33 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIHNHSALYLLLKLRGG   79 (85)
T ss_dssp             HHHHHCCCGGGEEEEETBEECCTTCBTTTTTCCTTCEEEEEECCC--
T ss_pred             HHHHHCCCHHHEEEEECCeECCCCCCHHHCCCCCCCEEEEEEeccCC
Confidence            356789999999999999999999999999999 9999999998876

>4hcn_B Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidase, NEDD8, protein binding; 2.60A {Saccharomyces cerevisiae}

Probab=99.32  E-value=5.1e-13  Score=81.11  Aligned_cols=46  Identities=74%  Similarity=1.063  Sum_probs=42.9

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|+|. +++|+++++..||
T Consensus        52 I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~i~l~~rl~GG   98 (98)
T 4hcn_B           52 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   98 (98)
T ss_dssp             HHHHHCCCGGGCEEEETTEECCTTCBSGGGTCCTTEEEEEECBCSCC
T ss_pred             HHHHhCCChhHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCCC
Confidence            356789999999999999999999999999999 9999999998876

>3a9j_A Ubiquitin; protein complex, cytoplasm, isopeptide bond, metal-binding, zinc; 1.18A {Mus musculus} PDB: 3a1q_B 2znv_B 3a9k_A 3h7p_A 3jsv_A 3dvg_Y 3dvn_Y 3nob_A 2o6v_D* 3jw0_X 3jvz_X 3nhe_B* 1aar_A 1d3z_A 1f9j_A 1fxt_B 1g6j_A 1nbf_C 1cmx_B 1q5w_B ...

Probab=99.31  E-value=8e-13  Score=75.78  Aligned_cols=46  Identities=74%  Similarity=1.063  Sum_probs=42.6

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++.+|+|++.|+|+|+|+.|+|+.+|++|+|. +++++++++..||
T Consensus        30 i~~~~~i~~~~q~L~~~g~~L~d~~tL~~~~i~~g~~i~l~~~~~GG   76 (76)
T 3a9j_A           30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRGG   76 (76)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTCBTGGGTCCTTCEEEEEECCCCC
T ss_pred             HHHHHCcCHHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEEeCCCC
Confidence            356789999999999999999999999999999 9999999998876

>3n3k_B Ubiquitin; hydrolase, protease, thiol protease, DUB, zinc ribbon, inhibitor, ubiqu acetylation, cytoplasm, isopeptide bond, nucleus; 2.60A {Homo sapiens} SCOP: d.15.1.1

Probab=99.31  E-value=4e-12  Score=74.50  Aligned_cols=50  Identities=56%  Similarity=0.667  Sum_probs=43.1

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      ++++.+.++..+|  +.+.|++++||.+||++|++++++|+++|+|+|+|+.
T Consensus         1 gs~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~~ip~~~qrL~~~g~~   52 (85)
T 3n3k_B            1 GSHMRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQ   52 (85)
T ss_dssp             ---CEEEEECGGGCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETBEE
T ss_pred             CCeEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCeE
Confidence            4678888887766  5677899999999999999999999999999999998

>2lxa_A Ubiquitin-like protein MDY2; ubiquitin-like domain, protein-protein interaction, SGT2 BIN domain, GET pathway, protein binding; NMR {Saccharomyces cerevisiae}

Probab=99.31  E-value=6.4e-13  Score=79.58  Aligned_cols=42  Identities=19%  Similarity=0.293  Sum_probs=39.2

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCcccee-c-ccceeeeeee
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-H-GSTLHSVRRF   43 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I-~-~sti~l~i~~   43 (97)
                      ++++|+|+++|||+|+|+.|+|+.+|++|+| + +++++++.++
T Consensus        35 ~~~~gip~~~QrLi~~Gk~L~D~~tL~~y~I~~~~stl~v~~~~   78 (87)
T 2lxa_A           35 SEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKP   78 (87)
T ss_dssp             HTTSCSSSTTEEEEETTEECCTTCBHHHHCCCGGGCEEEEEECC
T ss_pred             HHhcCCChHHEEEEECCEECcCcCCHHHcCCCCCCCEEEEEcCC
Confidence            6778999999999999999999999999999 7 9999998865

>2faz_A Ubiquitin-like containing PHD and ring finger DOM protein 1; cell cycle, DNA damage, DNA repair, DNA-binding, ligase, Met binding, nuclear protein; 2.00A {Homo sapiens} SCOP: d.15.1.1

Probab=99.31  E-value=8.2e-13  Score=76.58  Aligned_cols=43  Identities=33%  Similarity=0.590  Sum_probs=39.8

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      |++++|+|+++|+|+|+|+.|+|+++|++|+|. +++++++.+.
T Consensus        34 i~~~~gip~~~qrL~~~g~~L~d~~tL~~~~i~~g~~i~l~~r~   77 (78)
T 2faz_A           34 IQELFHVEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLLVRQ   77 (78)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTCBTTTTTCCTTCEEEEEECC
T ss_pred             HHHHHCcChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEeC
Confidence            356789999999999999999999999999999 9999999875

>2l7r_A Ubiquitin-like protein FUBI; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=99.30  E-value=3.6e-13  Score=81.19  Aligned_cols=46  Identities=33%  Similarity=0.442  Sum_probs=42.9

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|+|. +++|+++++..||
T Consensus        47 I~~~~gip~~~qrLi~~Gk~L~D~~tL~~y~I~~gstI~lv~rl~GG   93 (93)
T 2l7r_A           47 VASLEGIAPEDQVVLLAGAPLEDEATLGQCGVEALTTLEVAGRMLGG   93 (93)
T ss_dssp             HHHHHTCCGGGCEEEETTEECCTTSBHHHHTCCSSCEEEEECCCCCC
T ss_pred             HHHHhCcChhHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCCC
Confidence            356789999999999999999999999999999 9999999998876

>4ajy_B Transcription elongation factor B polypeptide 2; E3 ubiquitin ligase, transcription factor, hypoxic signaling transcription; 1.73A {Homo sapiens} PDB: 1lqb_A 1vcb_A 2c9w_B 2izv_B 2jz3_B 2xai_C 3dcg_A 3zrc_A* 3zrf_A 3ztc_A* 3ztd_A* 3zun_A* 1lm8_B 4b95_A* 2fnj_B 4b9k_A* 4awj_A*

Probab=99.30  E-value=9.5e-13  Score=82.81  Aligned_cols=53  Identities=23%  Similarity=0.293  Sum_probs=44.3

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec--------ccceeeeeeeeccee-eeeec
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH--------GSTLHSVRRFRGGMQ-IFVES   53 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~--------~sti~l~i~~~~g~~-i~v~~   53 (97)
                      |++++|||+++|||+|+|+.|+|++||++|||.        +++|+++.+..+.++ +.|.|
T Consensus        31 I~~~~giPp~qQrLI~~Gk~LeD~kTL~dy~I~~~ta~~q~~atl~Lvlr~~~~fE~l~i~p   92 (118)
T 4ajy_B           31 VEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALCIEP   92 (118)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTSBTTTTTCCGGGSBTTBCEEEEEEECCSSCCCCCCBCC
T ss_pred             HHHHHCCCHHHeEEEeCCeECCCcCCHHHcCCCcCcccCCCCCEEEEEEecCCCccceEEec
Confidence            467899999999999999999999999999995        469999999755443 55533

>3k9o_B Ubiquitin, UBB+1; E2-25K, complex structure, ATP-binding, isopeptide BO ligase, nucleotide-binding, UBL conjugation pathway; 1.80A {Homo sapiens} PDB: 2k25_A 2kx0_A

Probab=99.29  E-value=1e-12  Score=78.99  Aligned_cols=50  Identities=66%  Similarity=0.907  Sum_probs=42.6

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecceeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGMQIF   50 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~~i~   50 (97)
                      |++.+|+|++.|+|+|+|+.|+|+.+|++|+|. +++|+++++..+|....
T Consensus        31 i~~~~gip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~i~l~~r~~gG~~~~   81 (96)
T 3k9o_B           31 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGYADLR   81 (96)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCCC-----
T ss_pred             HHhhhCCChhHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEEcCCCCccc
Confidence            356789999999999999999999999999999 99999999999986543

>1sif_A Ubiquitin; hydrophobic mutants, folding, stability, structural protein; 2.18A {Homo sapiens} SCOP: d.15.1.1

Probab=99.29  E-value=8.1e-13  Score=78.77  Aligned_cols=46  Identities=74%  Similarity=1.063  Sum_probs=38.8

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++++|+|++.|+|+|+|+.|+|+.+|++|+|. +++|+++++..||
T Consensus        39 I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~r~~GG   85 (88)
T 1sif_A           39 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   85 (88)
T ss_dssp             HHHHHCCCGGGCEEEETTEECCTTSBSGGGTCCTTCEEEEEC-----
T ss_pred             HHHHHCcChhhEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCCC
Confidence            356789999999999999999999999999999 9999999999887

>1yx5_B Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo sapiens} SCOP: d.15.1.1 PDB: 1yx6_B

Probab=99.29  E-value=1.3e-12  Score=79.11  Aligned_cols=52  Identities=65%  Similarity=0.894  Sum_probs=43.4

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecceeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGMQIFVE   52 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~~i~v~   52 (97)
                      |++.+|+|+++|+|+|+|+.|+|+.+|++|+|. +++|+++.+..+|.+++.+
T Consensus        30 I~~~~gi~~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~gG~~i~~~   82 (98)
T 1yx5_B           30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGRDPNSS   82 (98)
T ss_dssp             HHHHTCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCCCC------
T ss_pred             HHHHHCcChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEeCCCCCcCccc
Confidence            356789999999999999999999999999999 9999999999998777653

>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana, uncharacterized putative protein, NESG, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.29  E-value=6.5e-12  Score=74.45  Aligned_cols=50  Identities=24%  Similarity=0.223  Sum_probs=44.0

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      -+-+.+.++..+|  +.+.|++++||++||++|++++|+|+++|+|+|+|++
T Consensus         8 ~~~~~i~vk~l~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~   59 (84)
T 2kk8_A            8 HSHMKFLVENLNGSSFELEVDYRDTLLVVKQKIERSQHIPVSKQTLIVDGIV   59 (84)
T ss_dssp             CCCEEEEEEETTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEE
T ss_pred             cCceEEEEEecCCcEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCEE
Confidence            3556777777766  5678899999999999999999999999999999998

>4a20_A Ubiquitin-like protein MDY2; protein binding, GET-pathway, tail-anchored proteins; 1.78A {Saccharomyces cerevisiae} PDB: 2lxc_A 4goc_A

Probab=99.29  E-value=7e-12  Score=76.54  Aligned_cols=55  Identities=16%  Similarity=0.114  Sum_probs=45.6

Q ss_pred             ccceeeeeeeecc--eee--eeeccchhHHHHHhh-hhhcCCCCCceEEEECeEe--CCCcc
Q 040204           34 GSTLHSVRRFRGG--MQI--FVESSDTIDNVKAKI-QDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i--~v~~~~TV~~lK~~I-~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      .+++.+.++..+|  +.+  .|++++||.+||++| ++.+|+|+++|+|+|+|++  |..+|
T Consensus        17 ~~~m~I~VKtl~g~~~~i~v~v~~~~TV~~lK~~I~~~~~gip~~~QrLi~~Gk~L~D~~tL   78 (98)
T 4a20_A           17 NAAVHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFL   78 (98)
T ss_dssp             -CCEEEEEEECSSSCEEEEEEECTTCBHHHHHHHHHHTTSCSCGGGEEEEETTEEECTTCBG
T ss_pred             CCCEEEEEEcCCCCEEEEEEecCCCChHHHHHHHHHHHhcCCChhhEEEEECCEECcCcCCH
Confidence            5788899988777  345  446999999999999 8899999999999999998  54554

>3mtn_B UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquitin-specific protease activity, hydrolase, ubiquitin B structural genomics consortium, SGC; 2.70A {Homo sapiens} SCOP: d.15.1.1

Probab=99.29  E-value=5.9e-12  Score=73.69  Aligned_cols=50  Identities=54%  Similarity=0.678  Sum_probs=44.1

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      ++++.+.++..+|  +.+.+++++||.+||++|++++++|+++|+|+|+|+.
T Consensus         1 gs~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~~i~~~~qrL~~~g~~   52 (85)
T 3mtn_B            1 GSHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQ   52 (85)
T ss_dssp             --CEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEE
T ss_pred             CCeEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHCcChHHEEEEECCEE
Confidence            4778888988776  5677899999999999999999999999999999998

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.29  E-value=7.7e-12  Score=75.55  Aligned_cols=50  Identities=18%  Similarity=0.276  Sum_probs=45.1

Q ss_pred             ccceeeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .+.+.+.++..++ +.+.|++++||.+||++|++++|+|+++|+|+|+|++
T Consensus        13 ~~~~~I~Vk~~~~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~   63 (94)
T 2kan_A           13 VRKIHVTVKFPSKQFTVEVDRTETVSSLKDKIHIVENTPIKRMQLYYSGIE   63 (94)
T ss_dssp             SCCEEEEEECSSCEEEEEECTTCBHHHHHHHHHHHSSSCTTTEEEEETTEE
T ss_pred             CCCEEEEEEcCCcEEEEEECCCCcHHHHHHHHHHHHCcCHHHEEEEECCEE
Confidence            4678888887775 5688899999999999999999999999999999998

>1wy8_A NP95-like ring finger protein, isoform A; ubiquitin-like domain, NP95/ICBP90-like ring finger (NIRF), ubiquitin ligase, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.28  E-value=8.3e-13  Score=78.42  Aligned_cols=47  Identities=28%  Similarity=0.473  Sum_probs=43.4

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecce
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGM   47 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~   47 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|+|. +++|+++++..+|.
T Consensus        39 i~~~~gip~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~~~gG~   86 (89)
T 1wy8_A           39 VWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVRPDSGP   86 (89)
T ss_dssp             HHHHSCCCTTTEEEEETTEECCSSSBHHHHTCCTTCEEEEEECCCCSS
T ss_pred             HHHHHCcChhhEEEEECCeECCCCCCHHHCCCCCCCEEEEEEeCCCCC
Confidence            356789999999999999999999999999999 99999999988873

>1se9_A Ubiquitin family; ubiquitin-like, cell-free, wheat GERM, structural genomics, protein structure initiative, CESG; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=99.28  E-value=2.7e-12  Score=81.63  Aligned_cols=45  Identities=29%  Similarity=0.414  Sum_probs=40.9

Q ss_pred             ccccCCCC--cceEEEECCEEeCCCCCCccceec-c------cceeeeeeeecc
Q 040204            2 EDKEEILR--DQQRFIFAGKRLEDGRTLVDYNIH-G------STLHSVRRFRGG   46 (97)
Q Consensus         2 ~~~~gip~--~~Q~L~~~g~~L~d~~tL~~y~I~-~------sti~l~i~~~~g   46 (97)
                      ++++|+|+  ++|||+|+|+.|+|++||++|+|+ +      +++||+.+..++
T Consensus        53 ~dkegiP~~~~qQrLIy~GK~LeD~~TLsdy~I~~~~~~~~v~tmhlVlrl~g~  106 (126)
T 1se9_A           53 REKENGPKTVKEVKLISAGKVLENSKTVKDYRSPVSNLAGAVTTMHVIIQAPVT  106 (126)
T ss_dssp             TTCSSSCCSGGGEEEEETTEECCTTSBGGGGSCCTTSCTTCCEEEEEEECCCSS
T ss_pred             cccccCCCChhhEEEEECCeECcCCCcHHHcCCCcCCccCCcEEEEEEeccCCc
Confidence            45789996  899999999999999999999999 8      789999998876

>1wh3_A 59 kDa 2'-5'-oligoadenylate synthetase like protein; P59 OASL, ubiquitin family, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.28  E-value=8.2e-13  Score=78.06  Aligned_cols=47  Identities=32%  Similarity=0.417  Sum_probs=43.5

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecce
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGM   47 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~   47 (97)
                      |++.+|+|+++|+|+|+|+.|+|+.+|++|+|. +++|+++.+..+|.
T Consensus        37 i~~~~gi~~~~qrL~~~Gk~L~d~~tL~~~~i~~g~~i~l~~~~~GG~   84 (87)
T 1wh3_A           37 IEDQQGLPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKGSGP   84 (87)
T ss_dssp             HHHHTCCCTTTEEEEETTEECCSSSBHHHHTCCTTEEEEEEECSCCCS
T ss_pred             HHHHhCCChHHEEEEECCEEccCCCCHHHCCCCCCCEEEEEEeccCCC
Confidence            356789999999999999999999999999999 99999999998873

>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana, uncharacterized putative protein, NESG, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.28  E-value=7.4e-13  Score=78.58  Aligned_cols=43  Identities=23%  Similarity=0.224  Sum_probs=39.5

Q ss_pred             CccccCCCCcceEEEECCEE-eCCCCCCccceec-ccceeeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKR-LEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~-L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      |++++|+|+++|+|+|+|+. |+|+++|++|+|. +++|++++++
T Consensus        40 I~~~~gip~~~QrLi~~Gk~lL~D~~tL~~y~I~~gs~i~lv~~p   84 (84)
T 2kk8_A           40 IERSQHIPVSKQTLIVDGIVILREDLTVEQCQIVPTSDIQLEVSS   84 (84)
T ss_dssp             HHHHHTCCGGGEEEEETTEECCCSSSBHHHHTCCTTSCEEEEECC
T ss_pred             HHHHHCcChHHEEEEECCEEecCCcCCHHHcCCCCCCEEEEEEcC
Confidence            45678999999999999999 9999999999999 9999998763

>4fbj_B NEDD8; effector-HOST target complex, glutamine deamidase, deamidati bacterial effector, cell cycle-protein binding complex; 1.60A {Homo sapiens} PDB: 4f8c_B

Probab=99.28  E-value=6.7e-12  Score=74.75  Aligned_cols=51  Identities=25%  Similarity=0.409  Sum_probs=42.7

Q ss_pred             eeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           38 HSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        38 ~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      .+.++..+|  +.+.|++++||++||++|++.+|+|+++|+|+|+|++  |..+|
T Consensus         2 ~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL   56 (88)
T 4fbj_B            2 LIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTA   56 (88)
T ss_dssp             EEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBT
T ss_pred             EEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHCcChhHEEEEECCeECCCCCcH
Confidence            456666555  5677899999999999999999999999999999999  44444

>3mtn_B UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquitin-specific protease activity, hydrolase, ubiquitin B structural genomics consortium, SGC; 2.70A {Homo sapiens} SCOP: d.15.1.1

Probab=99.27  E-value=1.3e-12  Score=76.51  Aligned_cols=46  Identities=70%  Similarity=0.985  Sum_probs=42.8

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|+|. +++++++++..+|
T Consensus        33 i~~~~~i~~~~qrL~~~g~~L~d~~tL~~~~i~~~~~l~l~~r~~GG   79 (85)
T 3mtn_B           33 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKWSTLFLLLRLRGG   79 (85)
T ss_dssp             HHHHHCCCGGGCEEEETTEECCTTSBTGGGTCCTTCEEEEECCCCCC
T ss_pred             HHHHHCcChHHEEEEECCEECCCCCCHHHcCCCCCCEEEEEEECcCC
Confidence            356789999999999999999999999999999 9999999998876

>1wgh_A Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.27  E-value=1.8e-11  Score=76.87  Aligned_cols=60  Identities=15%  Similarity=0.275  Sum_probs=47.9

Q ss_pred             cceecccceeeeeeeecc--eeeeeeccchhHHHHHhhhh------hcCC--CCCceEEEECeEe--CCCcc
Q 040204           29 DYNIHGSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQD------KKGT--PPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        29 ~y~I~~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~------~~gi--p~~~q~Lif~G~~--~~~~~   88 (97)
                      .+.+....+.+.++...|  +.+.|++++||.+||++|++      ++|+  |+++|||||+||+  |..+|
T Consensus         9 ~~~~~~~~m~I~vKtl~G~t~~lev~~s~TV~~lK~kI~~~~p~dwke~~p~p~~qqrLIy~GK~LeD~~TL   80 (116)
T 1wgh_A            9 SSHVPADMINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTL   80 (116)
T ss_dssp             CCCCCSSSEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEEETTEEECSSCBT
T ss_pred             cCCCCCCeEEEEEEeCCCCEEEEEECCcCHHHHHHHHHHHhcccccccCCCCChHHEEEEECCcCCCCCCcH
Confidence            344445578888887666  56888999999999999999      7785  6999999999999  44443

>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure, northeast structural genomics consortium, protein structure initiative, NESG; NMR {Homo sapiens}

Probab=99.27  E-value=4.5e-13  Score=79.85  Aligned_cols=47  Identities=34%  Similarity=0.492  Sum_probs=39.8

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecce
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGM   47 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~   47 (97)
                      |++.+|+|+++|+|+|+|+.|+|+.+|++|+|. +++|+++.+..+|.
T Consensus        34 I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~~I~~g~~i~l~~~~~gg~   81 (88)
T 2hj8_A           34 VSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRGGL   81 (88)
T ss_dssp             HHHHTCSCTTTEEEESSSSCCCTTSBHHHHHCSTTCEEEEEEC-----
T ss_pred             HHHHhCCChhHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEEcCCCc
Confidence            356789999999999999999999999999999 99999999988874

>3vdz_A Ubiquitin-40S ribosomal protein S27A; gadolinium, MRI contrast agent, peptide-based contrast agent lanthanide binding TAG; 2.40A {Synthetic construct} PDB: 2ojr_A

Probab=99.27  E-value=1.7e-12  Score=80.56  Aligned_cols=46  Identities=74%  Similarity=1.063  Sum_probs=42.2

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|+|. +++|+++++..||
T Consensus        65 I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~gI~~gs~I~l~~rl~GG  111 (111)
T 3vdz_A           65 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  111 (111)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTSBTTTTTCCTTCEEEEEECCCC-
T ss_pred             HHHHhCCChHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCCC
Confidence            356789999999999999999999999999999 9999999998876

>3dbh_I NEDD8; cell cycle, activating enzyme, apoptosis, membrane, UBL conjugation pathway, ATP-binding, ligase, nucleotide- binding, polymorphism; 2.85A {Homo sapiens} SCOP: d.15.1.1 PDB: 3dbr_I 3dbl_I

Probab=99.26  E-value=7.7e-12  Score=73.78  Aligned_cols=55  Identities=25%  Similarity=0.448  Sum_probs=47.3

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      ++++.+.++..+|  +.+.|++++||.+||++|++.+|+|+++|+|+|+|+.  |..+|
T Consensus        10 ~~~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~G~~L~d~~tL   68 (88)
T 3dbh_I           10 GGSMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTA   68 (88)
T ss_dssp             CCCEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCCEEETTEECCTTSBG
T ss_pred             CCcEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHCcCHHHEEEEECCeECCCCCcH
Confidence            5678888887666  5678899999999999999999999999999999998  44444

>3rt3_B Ubiquitin-like protein ISG15; ubiquitin-like domain, isgylation, antiviral protein-viral P complex; 2.01A {Homo sapiens} PDB: 3sdl_C 3r66_C 3pse_B 1z2m_A

Probab=99.26  E-value=1.6e-12  Score=84.51  Aligned_cols=47  Identities=34%  Similarity=0.448  Sum_probs=41.7

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecce
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGM   47 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~   47 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|+|+ +++++++++..||.
T Consensus       111 i~~~~gip~~~q~L~~~G~~L~d~~tL~~y~i~~g~~l~l~~rl~GG~  158 (159)
T 3rt3_B          111 VSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRGGG  158 (159)
T ss_dssp             HHHHHTCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCC---
T ss_pred             HHHHHCCCHHHEEEEECCeecCCCCCHHHcCCCCCCEEEEEEecCCCC
Confidence            356789999999999999999999999999999 99999999998873

>1wgd_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; ENDPLASMIC reticulum stress, UBL domain; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.26  E-value=1.2e-12  Score=78.66  Aligned_cols=45  Identities=29%  Similarity=0.375  Sum_probs=41.5

Q ss_pred             cccc--CCCCcceEEEECCEEeCCCCCCccc--eec-ccceeeeeeeecc
Q 040204            2 EDKE--EILRDQQRFIFAGKRLEDGRTLVDY--NIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         2 ~~~~--gip~~~Q~L~~~g~~L~d~~tL~~y--~I~-~sti~l~i~~~~g   46 (97)
                      ++++  |+|+++|+|+|+|+.|+|+.+|++|  +|. +++|||+++..+|
T Consensus        40 ~~~~~~~i~~~~QrLi~~Gk~L~D~~tL~~~~~~i~~~~~i~lv~~~~gg   89 (93)
T 1wgd_A           40 SRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVCNVKSG   89 (93)
T ss_dssp             HHHSTTCCCTTTCEEEETTEECCSSSCHHHHSCSSSCSEEEEEECCCCCC
T ss_pred             HHHhcCCCChHHeEEEECCEECcCcCCHHHHhcCCCCCCEEEEEeCCCCC
Confidence            4455  9999999999999999999999999  999 9999999998876

>3v6c_B Ubiquitin; structural genomics, structural genomics consortium, SGC, UB protease, hydrolase-signaling protein complex; 1.70A {Homo sapiens} PDB: 3v6e_B

Probab=99.25  E-value=1.2e-11  Score=73.87  Aligned_cols=55  Identities=47%  Similarity=0.559  Sum_probs=47.6

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      ...+.+.++..+|  +.+.|++++||.+||++|++.+|+|+++|+|+|+|+.  |..+|
T Consensus        15 ~~~m~i~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL   73 (91)
T 3v6c_B           15 RGSMQIFVNTLTGTHITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL   73 (91)
T ss_dssp             CCSEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTCBT
T ss_pred             CCeEEEEEEeCCCCEEEEEECCCCCHHHHHHHHHhhhCCChhhEEEEECCeECCCcCcH
Confidence            6688888887776  5577899999999999999999999999999999998  44444

>3v6c_B Ubiquitin; structural genomics, structural genomics consortium, SGC, UB protease, hydrolase-signaling protein complex; 1.70A {Homo sapiens} PDB: 3v6e_B

Probab=99.25  E-value=1.8e-12  Score=77.48  Aligned_cols=43  Identities=72%  Similarity=0.999  Sum_probs=39.9

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      |++.+|+|+++|+|+|+|+.|+|+.+|++|||. +++|+++++.
T Consensus        47 I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~rl   90 (91)
T 3v6c_B           47 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL   90 (91)
T ss_dssp             HHHHHCCCGGGCEEEETTEECCTTCBTGGGTCCTTCEEEEECCC
T ss_pred             HHhhhCCChhhEEEEECCeECCCcCcHHHCCCCCCCEEEEEEec
Confidence            356789999999999999999999999999999 9999999875

>2uyz_B Small ubiquitin-related modifier 1; sumoylation, cell division, nuclear protein, ubiquitin-like modifier, UBL conjugation pathway; 1.4A {Homo sapiens} SCOP: d.15.1.1 PDB: 2vrr_B 2iy0_B 2iy1_B 2g4d_B 2las_A 2io2_B 1z5s_B 3uip_B* 1tgz_B* 2bf8_B

Probab=99.25  E-value=1.1e-11  Score=71.96  Aligned_cols=48  Identities=13%  Similarity=0.123  Sum_probs=42.6

Q ss_pred             ceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           36 TLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        36 ti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .+.+.++...|  +.+.|++++||.+||++|++++|+|+++|+|+|+|++
T Consensus         3 ~m~i~vk~~~g~~~~~~v~~~~tv~~lk~~i~~~~gi~~~~qrL~~~G~~   52 (79)
T 2uyz_B            3 YIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQR   52 (79)
T ss_dssp             EEEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEE
T ss_pred             eEEEEEECCCCCEEEEEECCCChHHHHHHHHHHHHCCCcccEEEEECCEE
Confidence            46677776665  5578899999999999999999999999999999998

>4a20_A Ubiquitin-like protein MDY2; protein binding, GET-pathway, tail-anchored proteins; 1.78A {Saccharomyces cerevisiae} PDB: 2lxc_A 4goc_A

Probab=99.25  E-value=3.5e-12  Score=77.89  Aligned_cols=43  Identities=19%  Similarity=0.288  Sum_probs=39.5

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCcccee-c-ccceeeeeeee
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-H-GSTLHSVRRFR   44 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I-~-~sti~l~i~~~   44 (97)
                      ++.+|+|+++|||+|+|+.|+|+.+|++|+| + +++|+++++.+
T Consensus        53 ~~~~gip~~~QrLi~~Gk~L~D~~tL~dy~I~~~g~ti~lmvskp   97 (98)
T 4a20_A           53 SEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKPN   97 (98)
T ss_dssp             HTTSCSCGGGEEEEETTEEECTTCBGGGSCCBTTBCEEEEEECCC
T ss_pred             HHhcCCChhhEEEEECCEECcCcCCHHHcCcCCCCCEEEEEEeCC
Confidence            5678999999999999999999999999999 8 99999998643

>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure, northeast structural genomics consortium, protein structure initiative, NESG; NMR {Homo sapiens}

Probab=99.25  E-value=1e-11  Score=73.93  Aligned_cols=49  Identities=18%  Similarity=0.120  Sum_probs=43.2

Q ss_pred             cceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           35 STLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        35 sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +.+.+.++...|  +.+.|++++||++||++|++.+|+|+++|+|+|+|+.
T Consensus         3 ~~m~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~   53 (88)
T 2hj8_A            3 EPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKP   53 (88)
T ss_dssp             CEEEEEEEETTSCEEEEEEESSSBHHHHHHHHHHHTCSCTTTEEEESSSSC
T ss_pred             ccEEEEEECCCCCEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEECCEE
Confidence            457778887655  5578899999999999999999999999999999998

>3b1l_X E3 ubiquitin-protein ligase parkin; proteasome, ALFA-beta-protein; 1.85A {Mus musculus} PDB: 1mg8_A 2zeq_A 2knb_A 1iyf_A

Probab=98.90  E-value=6.1e-13  Score=76.72  Aligned_cols=45  Identities=33%  Similarity=0.508  Sum_probs=41.8

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeec
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRG   45 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~   45 (97)
                      |++.+|+|++.|+|+|+|+.|+|+.+|++|+|. +++++++++.+|
T Consensus        30 i~~~~gi~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~rlrg   75 (76)
T 3b1l_X           30 VAKQQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRR   75 (76)
Confidence            467789999999999999999999999999999 999999998765

>4hcn_B Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidase, NEDD8, protein binding; 2.60A {Saccharomyces cerevisiae}

Probab=99.25  E-value=1.1e-11  Score=75.06  Aligned_cols=55  Identities=51%  Similarity=0.623  Sum_probs=46.5

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      +..+.+.++..+|  +.+.|++++||.+||++|++++|+|+++|+|+|+|+.  |..+|
T Consensus        20 ~~~m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL   78 (98)
T 4hcn_B           20 GRPMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTL   78 (98)
T ss_dssp             --CCEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTCBS
T ss_pred             CCeEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEECCEECCCCCcH
Confidence            6788999987776  5677899999999999999999999999999999998  44444

>1we7_A SF3A1 protein; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: d.15.1.1 PDB: 1zkh_A

Probab=99.25  E-value=1.9e-12  Score=80.70  Aligned_cols=47  Identities=23%  Similarity=0.461  Sum_probs=43.6

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecce
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGM   47 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~   47 (97)
                      |++.+|+|+++|+|+|+|+.|+|+.+|++|+|. +++|+++++..+|.
T Consensus        65 I~~~~gip~~~QrL~~~Gk~L~D~~tL~~y~i~~g~~i~lv~rl~GGk  112 (115)
T 1we7_A           65 IHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMASGAVIHLALKERSGP  112 (115)
T ss_dssp             HHHHSSCCTTTEEEEETTEEECTTSBHHHHTCCSSCEEEEEECCCSCC
T ss_pred             HHHHHCCChHHEEEEECCEECCCCCCHHHCCCCCCCEEEEEEEcCCCC
Confidence            356789999999999999999999999999999 99999999998873

>1uh6_A Ubiquitin-like 5; beta-grAsp fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.24  E-value=1.2e-12  Score=80.28  Aligned_cols=41  Identities=22%  Similarity=0.178  Sum_probs=38.2

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVR   41 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i   41 (97)
                      |++++|+|+++|+|+|+|++|+|+.+|++|+|. +++|+|..
T Consensus        58 Ia~k~Gip~~qQrLi~~Gk~L~D~~TL~dygI~~gstlhL~~   99 (100)
T 1uh6_A           58 IAAQTGTRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLELYY   99 (100)
T ss_dssp             HHHHHCCCGGGCEEEETTEECCSSCBHHHHTCCTTEEEEEEC
T ss_pred             HHHHhCCCHHHEEEEECCEECCCCCCHHHcCCCCCCEEEEEe
Confidence            467899999999999999999999999999999 99999863

>3m63_B Ubiquitin domain-containing protein DSK2; armadillo-like repeats, UBL conjugation pathway, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=99.24  E-value=7.1e-12  Score=76.66  Aligned_cols=64  Identities=22%  Similarity=0.288  Sum_probs=41.8

Q ss_pred             CCCCccceec-cc--------ceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           24 GRTLVDYNIH-GS--------TLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        24 ~~tL~~y~I~-~s--------ti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      ..++++|.|. -.        .+.+.++. +|  +.+.|++++||++||++|++++|+|+++|+|+|+|++  |..+|
T Consensus         7 ~~~~~~~~~~~t~~l~l~~~m~i~I~Vk~-~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL   83 (101)
T 3m63_B            7 HHPMSDYDIPTTENLYFQGAMSLNIHIKS-GQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTV   83 (101)
T ss_dssp             ----------------------CCEEEEC-SSCCCCBCCCTTSBHHHHHHHHHHHHSCCSTTCCEEETTEECCTTSBT
T ss_pred             cCCccccCCCcceeecccCCcEEEEEEEE-CCEEEEEEeCCCCCHHHHHHHHHHHHCcChHHEEEEECCEECCCcCcH
Confidence            4567778775 22        34455554 44  5577899999999999999999999999999999998  43444

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B

Probab=99.23  E-value=3.4e-12  Score=84.58  Aligned_cols=47  Identities=72%  Similarity=1.016  Sum_probs=42.4

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecce
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGM   47 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~   47 (97)
                      |++++|+|+++|+|+|+|+.|+|+++|++|+|+ ++++|++++..+|.
T Consensus        30 I~~~~gip~~~QrLi~~Gk~L~D~~tL~~y~I~~gstI~Lvlrl~GG~   77 (169)
T 3l0w_B           30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGG   77 (169)
T ss_dssp             HHHHHCCCTTTEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCCC--
T ss_pred             HHHHHCcCHHHEEEEECCccccCcCcHHHcCCCCCCEEEEEEEecccc
Confidence            356789999999999999999999999999999 99999999988773

>1se9_A Ubiquitin family; ubiquitin-like, cell-free, wheat GERM, structural genomics, protein structure initiative, CESG; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=99.23  E-value=1.7e-11  Score=77.90  Aligned_cols=55  Identities=15%  Similarity=0.186  Sum_probs=46.1

Q ss_pred             ccceeeeeeeecc--e-eeeeeccchhHHHHHhh-----hhhcCCCC--CceEEEECeEe--CCCcc
Q 040204           34 GSTLHSVRRFRGG--M-QIFVESSDTIDNVKAKI-----QDKKGTPP--DQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~~~~g--~-~i~v~~~~TV~~lK~~I-----~~~~gip~--~~q~Lif~G~~--~~~~~   88 (97)
                      ...+.+.++...|  + .+.+++++||.+||++|     ++++|+|+  ++|||||+||+  |..+|
T Consensus        14 ~~~~~i~~kt~~G~~i~~l~v~psdTV~~lK~kI~~~~p~dkegiP~~~~qQrLIy~GK~LeD~~TL   80 (126)
T 1se9_A           14 HNQLEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSKTV   80 (126)
T ss_dssp             CCCEEEEEEETTSCEEEEEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEEETTEECCTTSBG
T ss_pred             cccEEEEEEECCCCEEEeeecCccCHHHHHHHHHHhhcccccccCCCChhhEEEEECCeECcCCCcH
Confidence            4678888888877  3 46789999999999999     77889996  89999999999  54555

>2faz_A Ubiquitin-like containing PHD and ring finger DOM protein 1; cell cycle, DNA damage, DNA repair, DNA-binding, ligase, Met binding, nuclear protein; 2.00A {Homo sapiens} SCOP: d.15.1.1

Probab=99.23  E-value=2.4e-11  Score=70.32  Aligned_cols=53  Identities=17%  Similarity=0.169  Sum_probs=44.2

Q ss_pred             ceeeeeeeecc--e-eee-eeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           36 TLHSVRRFRGG--M-QIF-VESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        36 ti~l~i~~~~g--~-~i~-v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      .+.+.++..+|  + .+. |++++||++||++|++++|+|+++|+|+|+|++  |..+|
T Consensus         2 ~m~i~Vk~~~g~~~~~l~~v~~~~tv~~lK~~i~~~~gip~~~qrL~~~g~~L~d~~tL   60 (78)
T 2faz_A            2 SMWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTL   60 (78)
T ss_dssp             CEEEEEEETTSSCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBT
T ss_pred             cEEEEEEECCCCEEEEEeccCCCCCHHHHHHHHHHHHCcChhhEEEEECCEECCCCCCH
Confidence            45677777655  2 577 899999999999999999999999999999998  44444

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens}

Probab=99.23  E-value=1e-11  Score=78.92  Aligned_cols=63  Identities=17%  Similarity=0.274  Sum_probs=48.3

Q ss_pred             CCccceecccceeeeeeeecc--eeeeeeccchhHHHHHhhhh------hcCCC--CCceEEEECeEe--CCCcc
Q 040204           26 TLVDYNIHGSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQD------KKGTP--PDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        26 tL~~y~I~~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~------~~gip--~~~q~Lif~G~~--~~~~~   88 (97)
                      .|....+....+.+.++...|  +.+.|++++||.+||++|++      ++|+|  +++|||||+||+  |..+|
T Consensus         7 ~~~~~~~~~~~m~I~vktl~G~~~~lev~~s~TV~~lK~~I~~~~p~dwke~ip~~~~~qrLIy~GK~LeD~~TL   81 (125)
T 2gow_A            7 HLESSNVPADMINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTL   81 (125)
T ss_dssp             ---CCSCCTTCEEEEEECTTSCEEEEEECTTSBHHHHHHHHHSSCCCSCCCCTTCCGGGEEEESSSSEEESSCBT
T ss_pred             cccccCCCCCeEEEEEEeCCCCEEEEEeCCccHHHHHHHHHHHHCCcccccCCCCChHHEEEEECCcCCCCCCcH
Confidence            344444445567788877666  56888999999999999998      88984  999999999999  55554

>1wyw_B Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Homo sapiens} SCOP: d.15.1.1 PDB: 1y8r_C* 2asq_A 2pe6_B 1a5r_A 2kqs_A 3kyc_D* 3rzw_C

Probab=99.22  E-value=1.8e-11  Score=74.17  Aligned_cols=50  Identities=14%  Similarity=0.163  Sum_probs=45.1

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +..+.+.++...|  +.+.|++++||.+||++|++++|+|+++|+|+|+|++
T Consensus        19 ~~~m~I~Vk~~~g~~~~l~v~~~~tv~~lK~~i~~~~gip~~~qrLif~Gk~   70 (97)
T 1wyw_B           19 GEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQR   70 (97)
T ss_dssp             CCEEEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEE
T ss_pred             CCcEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCChhhEEEEECCeE
Confidence            5578888887766  5678899999999999999999999999999999998

>4dwf_A HLA-B-associated transcript 3; ubiquitin-like domain, BAT3 protein, PF00240, structural GEN joint center for structural genomics, JCSG; 1.80A {Homo sapiens} PDB: 1wx9_A

Probab=99.22  E-value=3.7e-12  Score=75.80  Aligned_cols=46  Identities=33%  Similarity=0.590  Sum_probs=41.3

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceecccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHGSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~~sti~l~i~~~~g   46 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|+|.+++||++.+..++
T Consensus        35 i~~~~gip~~~qrLi~~Gk~L~d~~tL~~~~i~g~~i~l~~~~~~~   80 (90)
T 4dwf_A           35 IAASVSIPSEKQRLIYQGRVLQDDKKLQEYNVGGKVIHLVERAPPQ   80 (90)
T ss_dssp             HHHHHTCCGGGEEEEETTEECCTTSBGGGGTCTTEEEEEEECCCC-
T ss_pred             HHHHhCCCHHHEEEEECCeECCCCCCHHHcCCCCcEEEEEecCCCC
Confidence            3567899999999999999999999999999989999999987654

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens}

Probab=99.22  E-value=1.8e-12  Score=87.48  Aligned_cols=51  Identities=71%  Similarity=0.996  Sum_probs=47.4

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecceeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGMQIFV   51 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~~i~v   51 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|+|+ +++|+|+++..+|..++|
T Consensus       135 I~~~~gIp~~~QrLi~~Gk~L~D~~tL~dygI~~gstI~LvlrlrGG~~~fv  186 (189)
T 3q3f_A          135 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGGQTFT  186 (189)
T ss_dssp             HHHHHCCCGGGCCEEETTEECCTTCBGGGGTCCTTCEEEECCCCCCCCCCCC
T ss_pred             HHhccCCCHHHEEEEECCEECCCCCCHHHCCCCCCCEEEEEEEcCCCCcceE
Confidence            356789999999999999999999999999999 999999999999987766

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A

Probab=99.22  E-value=2.3e-11  Score=75.18  Aligned_cols=55  Identities=16%  Similarity=0.082  Sum_probs=45.1

Q ss_pred             ccceeeeeeeec----ceeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           34 GSTLHSVRRFRG----GMQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~~~~----g~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      .-.+.+.++...    .+.+.|+|++||++||++|++++|+||++|||+|+|++  |.++|
T Consensus        22 ~i~l~v~v~d~~s~~~~i~l~V~ps~TV~~LK~~I~~k~Gipp~~QRli~ggkll~D~~TL   82 (105)
T 4dbg_A           22 DIRLWVSVEDAQMHTVTIWLTVRPDMTVASLKDMVFLDYGFPPVLQQWVIGQRLARDQETL   82 (105)
T ss_dssp             CEEEEEEEEESSSCCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEEECTTCBT
T ss_pred             cEEEEEEEEccCCCCceEEEEECCcChHHHHHHHHHHHhCCCHHHEEEeccCeEccCcCcH
Confidence            345666666543    25678899999999999999999999999999999998  55655

>1wh3_A 59 kDa 2'-5'-oligoadenylate synthetase like protein; P59 OASL, ubiquitin family, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.22  E-value=3.2e-11  Score=71.12  Aligned_cols=55  Identities=24%  Similarity=0.339  Sum_probs=46.5

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      .+++.+.++...|  +.+.|++++||.+||++|++.+|+|+++|+|+|+|+.  |..+|
T Consensus         5 ~~~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~qrL~~~Gk~L~d~~tL   63 (87)
T 1wh3_A            5 SSGIQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGL   63 (87)
T ss_dssp             SSSEEEEEEETTTEEEEEEECSSSBHHHHHHHHHHHTCCCTTTEEEEETTEECCSSSBH
T ss_pred             CCCEEEEEEcCCCCEEEEEeCCCChHHHHHHHHHHHhCCChHHEEEEECCEEccCCCCH
Confidence            4577888887655  5678899999999999999999999999999999998  44444

>2dzi_A Ubiquitin-like protein 4A; GDX, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.22  E-value=4e-12  Score=73.88  Aligned_cols=43  Identities=40%  Similarity=0.616  Sum_probs=39.6

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      |++.+|+|++.|+|+|+|+.|+|+.+|++|+|. +++|++++++
T Consensus        37 i~~~~~i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~~   80 (81)
T 2dzi_A           37 VSEKLNVPVRQQRLLFKGKALADGKRLSDYSIGPNSKLNLVVKP   80 (81)
T ss_dssp             HHHHTCCCTTTCEEEETTEECCTTSBGGGGTCCSSBCCEEECCC
T ss_pred             HHHHHCcCHHHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            356789999999999999999999999999999 9999998875

>2dzi_A Ubiquitin-like protein 4A; GDX, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.22  E-value=3.6e-11  Score=69.75  Aligned_cols=55  Identities=20%  Similarity=0.207  Sum_probs=46.4

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      ..++.+.++..+|  +.+.+++++||++||++|++.+|+|+++|+|+|+|+.  |..+|
T Consensus         5 ~~~m~i~vk~~~g~~~~~~v~~~~tV~~LK~~i~~~~~i~~~~qrL~~~gk~L~d~~tL   63 (81)
T 2dzi_A            5 SSGMQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLNVPVRQQRLLFKGKALADGKRL   63 (81)
T ss_dssp             SSSEEEEEEETTSCEEEEEECSSCBHHHHHHHHHHHTCCCTTTCEEEETTEECCTTSBG
T ss_pred             CCcEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHEEEEECCeECCCCCcH
Confidence            4567888887665  5678899999999999999999999999999999998  44444

>1we6_A Splicing factor, putative; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=99.22  E-value=1.7e-12  Score=80.40  Aligned_cols=46  Identities=28%  Similarity=0.366  Sum_probs=43.2

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++.+|+|+++|+|+|+|+.|+|+.+|++|+|. +++|+++++..+|
T Consensus        61 I~~~~gip~~~QrL~~~Gk~L~D~~tL~~y~I~~g~~l~l~~r~~GG  107 (111)
T 1we6_A           61 IAGEIQIPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLRERSG  107 (111)
T ss_dssp             HHHHTTCCTTTSEEECSSSBCCTTSBTTTTTCSSSCEEEEECSSCCS
T ss_pred             HHHHHCCCHHHeEEEECCEECCCCCcHHHCCCCCCCEEEEEEEcCCC
Confidence            456789999999999999999999999999999 9999999999887

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens}

Probab=99.22  E-value=1.7e-11  Score=74.91  Aligned_cols=55  Identities=15%  Similarity=0.152  Sum_probs=43.3

Q ss_pred             ccceeeeeeeecce----eeeeeccchhHHHHHhhhhh-cCCC-CCceEEEECeEe--CCCcc
Q 040204           34 GSTLHSVRRFRGGM----QIFVESSDTIDNVKAKIQDK-KGTP-PDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~~~~g~----~i~v~~~~TV~~lK~~I~~~-~gip-~~~q~Lif~G~~--~~~~~   88 (97)
                      .+.+.+.++..++.    .+.|++++||.+||++|+++ +|+| +++|||||+||+  |..+|
T Consensus        21 ~~~m~I~VK~~~g~~~~i~l~v~~~~TV~~LK~~I~~~~~g~pp~~~QrLIy~Gk~L~D~~tL   83 (99)
T 2kdb_A           21 GHPVTLIIKAPNQKYSDQTISCFLNWTVGKLKTHLSNVYPSKPLTKDQRLVYSGRLLPDHLQL   83 (99)
T ss_dssp             --CEEEEEECTTSSSCCEEEEECTTSBHHHHHHHHHHHSTTCCCTTTCCEEETTEEECTTSBT
T ss_pred             CCeEEEEEEcCCCCEEEEEEEcCCCCHHHHHHHHHHHHhcCCCChhhEEEEECCEECCCCCCH
Confidence            45688888876653    56779999999999999986 6766 599999999999  54554

>1wgd_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; ENDPLASMIC reticulum stress, UBL domain; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.21  E-value=2.6e-11  Score=72.72  Aligned_cols=49  Identities=14%  Similarity=0.139  Sum_probs=41.8

Q ss_pred             cceeeeeeeecce--eee--eeccchhHHHHHhhhhhc--CCCCCceEEEECeEe
Q 040204           35 STLHSVRRFRGGM--QIF--VESSDTIDNVKAKIQDKK--GTPPDQQRQIFWFVF   83 (97)
Q Consensus        35 sti~l~i~~~~g~--~i~--v~~~~TV~~lK~~I~~~~--gip~~~q~Lif~G~~   83 (97)
                      +.+.+.++..++.  .+.  +++++||.+||++|++.+  |+|+++|+|+|+|+.
T Consensus         6 ~~m~i~Vk~~~~~~~~~~v~v~~~~TV~~lK~~I~~~~~~~i~~~~QrLi~~Gk~   60 (93)
T 1wgd_A            6 SGVTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKL   60 (93)
T ss_dssp             CCCEEEEECSSSSCCCEEEECCTTSCHHHHHHHHHHHSTTCCCTTTCEEEETTEE
T ss_pred             cEEEEEEEeCCCCeEEEEEecCCCCcHHHHHHHHHHHhcCCCChHHeEEEECCEE
Confidence            4677888876663  444  459999999999999998  999999999999998

>3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=99.21  E-value=1.6e-11  Score=75.59  Aligned_cols=52  Identities=15%  Similarity=0.077  Sum_probs=42.8

Q ss_pred             eeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           37 LHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        37 i~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      +.+.++..+|  +.+.|++++||.+||++|++++|+|+++|+|+|+|++  |..+|
T Consensus         2 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL   57 (106)
T 3m62_B            2 VSLTFKNFKKEKVPLDLEPSNTILETKTKLAQSISCEESQIKLIYSGKVLQDSKTV   57 (106)
T ss_dssp             -CEEEECTTCCEEEECCCTTSBHHHHHHHHHHTTTSCGGGCEEEETTEECCTTSBT
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCChhhEEEEECCEECCCcCCH
Confidence            4566776555  5577899999999999999999999999999999998  44444

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens}

Probab=99.21  E-value=5e-12  Score=74.93  Aligned_cols=42  Identities=36%  Similarity=0.691  Sum_probs=38.3

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceecccceeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHGSTLHSVRR   42 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~~sti~l~i~   42 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|+|.++++|++.|
T Consensus        47 i~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i~g~~i~lv~R   88 (88)
T 4eew_A           47 IAASVSIPSEKQRLIYQGRVLQDDKKLQEYNVGGKVIHLVER   88 (88)
T ss_dssp             HHHHHTCCGGGEEEEETTEECCTTSBGGGGTCTTEEEEEEEC
T ss_pred             HHHHhCCCHHHEEEEECCEECCCCCcHHHcCCCCcEEEEEEC
Confidence            356789999999999999999999999999998999999864

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.20  E-value=4e-11  Score=71.04  Aligned_cols=49  Identities=24%  Similarity=0.337  Sum_probs=42.0

Q ss_pred             cceeeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           35 STLHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        35 sti~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +++.++.+..+. +.+.+++++||.+||++|++.+|+|+++|+|+|+|+.
T Consensus        11 ~~~~~~~~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~   60 (85)
T 2kd0_A           11 STIKLTVKFGGKSIPLSVSPDCTVKDLKSQLQPITNVLPRGQKLIFKGKV   60 (85)
T ss_dssp             CCEEEEEEETTEEEEEEECTTSBHHHHHHHHHHHHCCCTTTCEEEETTEE
T ss_pred             CcEEEEEEECCEEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCeE
Confidence            456566655544 5688899999999999999999999999999999998

>3u5e_m 60S ribosomal protein L40; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3u5i_m 4b6a_m 4a18_K 4a19_K 4a1b_K 4a1d_K 4adx_5 3izc_p 3izs_p 3iz5_p 3izr_p

Probab=99.20  E-value=1.6e-12  Score=82.49  Aligned_cols=47  Identities=72%  Similarity=1.059  Sum_probs=0.5

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecce
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGM   47 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~   47 (97)
                      |++.+|+|+++|+|+|+|+.|+|+.+|++|+|. +++|+++++..||.
T Consensus        30 I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~~I~~gsti~l~~rl~GG~   77 (128)
T 3u5e_m           30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGI   77 (128)
T ss_dssp             -----------------------------------------------C
T ss_pred             HHHHhCcChHHEEEEECCEECCCCCchhhhccCCCCEEEEEEEcCCCC
Confidence            567899999999999999999999999999999 99999999999984

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}

Probab=99.19  E-value=3.3e-12  Score=84.24  Aligned_cols=46  Identities=74%  Similarity=1.063  Sum_probs=38.9

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++++|+|+++|+|+|+|+.|+|+++|++|+|+ +++++++++..||
T Consensus       126 I~~~~gip~~~q~L~~~g~~L~D~~tL~~y~i~~g~tl~l~~rlrgG  172 (172)
T 3u30_A          126 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  172 (172)
T ss_dssp             HHHHHCCCGGGCCEEETTEECCTTSBSGGGTCCTTCEEEECC-----
T ss_pred             HHHHhCCCceeEEEEECCccCCCCCcHHHhCCCCCCEEEEEEecCCC
Confidence            356789999999999999999999999999999 9999999998876

>2wyq_A HHR23A, UV excision repair protein RAD23 homolog A; DNA binding protein, DNA excision repair, proteasomal degrad polyubiquitin; 1.65A {Homo sapiens} PDB: 1p98_A 1p9d_U 1p1a_A

Probab=99.19  E-value=4.6e-11  Score=70.05  Aligned_cols=54  Identities=17%  Similarity=0.161  Sum_probs=44.8

Q ss_pred             ceeeeeeeecc--eeeeeeccchhHHHHHhhhhh---cCCCCCceEEEECeEe--CCCccc
Q 040204           36 TLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDK---KGTPPDQQRQIFWFVF--GWGSLW   89 (97)
Q Consensus        36 ti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~---~gip~~~q~Lif~G~~--~~~~~~   89 (97)
                      .+.+.++..+|  +.+.|++++||++||++|++.   +|+|+++|+|+|+|+.  |..+|-
T Consensus         5 ~m~i~vk~~~g~~~~~~v~~~~TV~~lK~~i~~~~~~~gip~~~qrLi~~Gk~L~D~~tL~   65 (85)
T 2wyq_A            5 AVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIR   65 (85)
T ss_dssp             CEEEEEEETTSCEEEEEECTTSBHHHHHHHHHHHHCTTTCCGGGEEEEETTEECCTTSBGG
T ss_pred             eEEEEEEECCCCEEEEEECCCCCHHHHHHHHHhhccccCCCHHHeEEEECCEECcCCCCHH
Confidence            46677777655  567889999999999999997   8999999999999998  445543

>3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=99.19  E-value=5.9e-12  Score=77.56  Aligned_cols=45  Identities=18%  Similarity=0.350  Sum_probs=40.2

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeec
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRG   45 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~   45 (97)
                      |++.+|+|+++|+|+|+|+.|+|+.+|++|||+ +++|+++++...
T Consensus        31 I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~~i~~g~~i~lv~~~~~   76 (106)
T 3m62_B           31 LAQSISCEESQIKLIYSGKVLQDSKTVSECGLKDGDQVVFMVSQKK   76 (106)
T ss_dssp             HHHTTTSCGGGCEEEETTEECCTTSBTTTTTCCTTCEEEEECCC--
T ss_pred             HHHHHCCChhhEEEEECCEECCCcCCHHHcCCCCCCEEEEEEcCCC
Confidence            456789999999999999999999999999999 999999997554

>2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing, protein binding; 2.60A {Homo sapiens}

Probab=99.19  E-value=7.6e-12  Score=77.53  Aligned_cols=46  Identities=74%  Similarity=1.063  Sum_probs=42.1

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|+|. +++|+++++..||
T Consensus        65 I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~gI~~gs~I~l~~rl~GG  111 (111)
T 2ojr_A           65 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  111 (111)
T ss_dssp             HHHHHCCCTTTEEEEETTEECCSSCBTTTTTCCTTCEEEEEECCCC-
T ss_pred             HHHHHCcCcccEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCCC
Confidence            356789999999999999999999999999999 9999999998876

>1yqb_A Ubiquilin 3; structural genomics consortium, ubiquitin, ubiquitin-like domain, structural genomics, signaling protein SGC; 2.00A {Homo sapiens} SCOP: d.15.1.1

Probab=99.19  E-value=4.1e-12  Score=77.56  Aligned_cols=46  Identities=33%  Similarity=0.425  Sum_probs=42.2

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++.+|+|+++|+|+|+|+.|+|+.+|++|+|. +++|+++.+..++
T Consensus        51 I~~~~gip~~~QrLi~~Gk~L~D~~tL~~ygI~~gstI~l~~r~~~~   97 (100)
T 1yqb_A           51 ISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHR   97 (100)
T ss_dssp             HHHHHTCCGGGEEEEETTEECCTTSBHHHHTCCTTCEEEEEECCCCS
T ss_pred             HHHHHCcChhhEEEEECCEECCCcCcHHHCCCCCCCEEEEEEcCCCC
Confidence            356789999999999999999999999999999 9999999987765

>2wyq_A HHR23A, UV excision repair protein RAD23 homolog A; DNA binding protein, DNA excision repair, proteasomal degrad polyubiquitin; 1.65A {Homo sapiens} PDB: 1p98_A 1p9d_U 1p1a_A

Probab=99.19  E-value=9.1e-12  Score=73.12  Aligned_cols=40  Identities=25%  Similarity=0.350  Sum_probs=36.7

Q ss_pred             cCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeee
Q 040204            5 EEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFR   44 (97)
Q Consensus         5 ~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~   44 (97)
                      +|+|+++|+|+|+|+.|+|+.+|++|+|. +++|+++.+..
T Consensus        42 ~gip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~i~l~~~~~   82 (85)
T 2wyq_A           42 DAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTKT   82 (85)
T ss_dssp             TTCCGGGEEEEETTEECCTTSBGGGGCCCTTSEEEEEEC--
T ss_pred             cCCCHHHeEEEECCEECcCCCCHHHcCCCCCCEEEEEEcCC
Confidence            89999999999999999999999999999 99999988654

>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling proteins; 1.15A {Saccharomyces cerevisiae} SCOP: d.15.1.1 PDB: 2bwe_S

Probab=99.19  E-value=8.3e-12  Score=71.87  Aligned_cols=42  Identities=36%  Similarity=0.638  Sum_probs=38.5

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR   42 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~   42 (97)
                      |++.+|+|++.|+|+|+|+.|+|+.+|++|||. +++++++.+
T Consensus        33 i~~~~~i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~   75 (77)
T 2bwf_A           33 INKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS   75 (77)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEEC
T ss_pred             HHHHhCCCHHHEEEEECCeEcCCCCCHHHcCCCCCCEEEEEEc
Confidence            356789999999999999999999999999999 999998765

>1yqb_A Ubiquilin 3; structural genomics consortium, ubiquitin, ubiquitin-like domain, structural genomics, signaling protein SGC; 2.00A {Homo sapiens} SCOP: d.15.1.1

Probab=99.18  E-value=4.6e-11  Score=72.87  Aligned_cols=55  Identities=22%  Similarity=0.154  Sum_probs=47.0

Q ss_pred             ccceeeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           34 GSTLHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      ..++.+.++..+| +.+.|++++||.+||++|++.+|+|+++|+|+|+|+.  |..+|
T Consensus        20 ~~~m~I~Vk~~~g~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL   77 (100)
T 1yqb_A           20 PHLIKVTVKTPKDKEDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSL   77 (100)
T ss_dssp             TTEEEEEEECSSCEEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBH
T ss_pred             CCeEEEEEEcCCCcEEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEECCCcCcH
Confidence            5578888887665 6688899999999999999999999999999999998  44444

>1wx8_A Riken cDNA 4931431F19; ubiquitin-like domain, ubiquilin 1-like, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.18  E-value=2.4e-12  Score=77.57  Aligned_cols=46  Identities=37%  Similarity=0.435  Sum_probs=42.5

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++.+|+|+++|+|+|+|+.|+|+.+|++|+|. +++|+++.+..+|
T Consensus        46 I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~~g   92 (96)
T 1wx8_A           46 ISKYLHCNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVRSHSG   92 (96)
T ss_dssp             HHHHTCSCTTTBCCEETTEECCTTSCHHHHTCCTTEEEECCBCCSSC
T ss_pred             HHHHhCCCHHHEEEEECCEECCCcCCHHHCCCCCCCEEEEEEeCCCC
Confidence            356789999999999999999999999999999 9999999988776

>1uel_A HHR23B, UV excision repair protein RAD23 homolog B; UBL, UIM, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.18  E-value=1.1e-11  Score=74.77  Aligned_cols=42  Identities=24%  Similarity=0.347  Sum_probs=38.8

Q ss_pred             cCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            5 EEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         5 ~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      +|+|+++|+|+|+|+.|+|+.+|++|+|. +++|+++.+...+
T Consensus        37 ~gip~~~qrLi~~Gk~L~D~~tL~~ygI~~g~~i~l~~~~~~~   79 (95)
T 1uel_A           37 DAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKPKA   79 (95)
T ss_dssp             TTCCTTTEEEEETTEECCTTSBGGGGTCCSSSEEEEEESSCCC
T ss_pred             CCCChhhEEEEECCEECCCcCcHHHCCCCCCCEEEEEEeCCCC
Confidence            79999999999999999999999999999 9999999876543

>1wgg_A Ubiquitin carboxyl-terminal hydrolase 14; ubiquitin specific protease 14, USP14, ubiquitin-like fold, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.17  E-value=3.7e-11  Score=72.82  Aligned_cols=50  Identities=12%  Similarity=0.094  Sum_probs=43.4

Q ss_pred             ccceeeeeeeecc-e-eeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG-M-QIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g-~-~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      ..++.+.++..+. + .+.|++++||.+||++|++.+|+|+++|+|+|+|++
T Consensus         5 ~~~m~i~Vk~~g~~~~~l~v~~~~TV~~lK~~I~~~tgip~~~QkLi~~Gk~   56 (96)
T 1wgg_A            5 SSGYSVTVKWGKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGT   56 (96)
T ss_dssp             CCEEEEEEEETTEEEEEEEEESSSCHHHHHHHHHHHTCCCTTTSCCEETTEE
T ss_pred             CcEEEEEEEECCEEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCcC
Confidence            4567778875444 5 488899999999999999999999999999999999

>1ndd_A NEDD8, protein (ubiquitin-like protein NEDD8); proteolysis, signaling protei; 1.60A {Homo sapiens} SCOP: d.15.1.1 PDB: 1r4m_I 1r4n_I* 1xt9_B 2ko3_A 3gzn_I* 2bkr_B 2nvu_I* 3dqv_A 1bt0_A

Probab=99.17  E-value=5.4e-11  Score=67.98  Aligned_cols=46  Identities=28%  Similarity=0.489  Sum_probs=40.4

Q ss_pred             eeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           38 HSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        38 ~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .+.++..+|  +.+.+++++||.+||++|++.+|+|+++|+|+|+|+.
T Consensus         2 ~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~~i~~~~q~L~~~g~~   49 (76)
T 1ndd_A            2 LIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQ   49 (76)
T ss_dssp             EEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEE
T ss_pred             EEEEECCCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCEE
Confidence            456666555  5677899999999999999999999999999999998

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.17  E-value=1.2e-11  Score=78.45  Aligned_cols=47  Identities=38%  Similarity=0.464  Sum_probs=39.6

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecce
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGM   47 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~   47 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|+|. +++|+|+.+..+|.
T Consensus        61 I~~~~gip~~~QrLi~~Gk~L~D~~tL~dygI~~gstI~lv~~~~gg~  108 (125)
T 1j8c_A           61 ISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIKRDPNS  108 (125)
T ss_dssp             HHHHHCSCSSSEEEEETTEEESTTSCGGGTTCSSSEEEEEEEC-----
T ss_pred             HHHHHCcCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEEeccCCCC
Confidence            356789999999999999999999999999999 99999999988773

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=99.17  E-value=5.9e-11  Score=72.45  Aligned_cols=59  Identities=15%  Similarity=0.122  Sum_probs=46.8

Q ss_pred             ceec-ccceeeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           30 YNIH-GSTLHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        30 y~I~-~sti~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      +.+. .+++.+.++..+. +.+.|++++||++||++|++.+|+|+++|+|+|+|+.  |..+|
T Consensus        18 ~~~~~~~~m~I~Vk~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL   80 (101)
T 2klc_A           18 YFQGHPKIMKVTVKTPKEKEEFAVPENSSVQQFKEEISKRFKSHTDQLVLIFAGKILKDQDTL   80 (101)
T ss_dssp             -----CCCEEEEEECSSCEEEEEECSCCCHHHHHHHHHHHHTCCGGGEEEEETTEEECTTCCT
T ss_pred             ccCCCCCeEEEEEEeCCcEEEEEECCCCCHHHHHHHHHHHHCcChhhEEEEECCEECCCcCcH
Confidence            4445 6778888887643 5688899999999999999999999999999999998  44444

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=99.17  E-value=1.4e-11  Score=75.29  Aligned_cols=45  Identities=40%  Similarity=0.495  Sum_probs=40.8

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeec
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRG   45 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~   45 (97)
                      |++.+|+|++.|+|+|+|+.|+|+.+|++|+|. +++|+++.+..+
T Consensus        54 I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~gI~~g~~I~l~~~~~~   99 (101)
T 2klc_A           54 ISKRFKSHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQN   99 (101)
T ss_dssp             HHHHHTCCGGGEEEEETTEEECTTCCTGGGTCCTTCEEEEEECCSS
T ss_pred             HHHHHCcChhhEEEEECCEECCCcCcHHHcCCCCCCEEEEEEcCCC
Confidence            356789999999999999999999999999999 999999987654

>3u5c_f 40S ribosomal protein S31; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3u5g_f

Probab=99.17  E-value=2.6e-12  Score=84.06  Aligned_cols=46  Identities=74%  Similarity=1.063  Sum_probs=0.0

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++.+|+|+++|+|+|+|+.|+|+.+|++|+|. +++|+++++..+|
T Consensus        30 I~~~~gip~~~QrLi~~Gk~L~D~~tL~dygI~~gstL~Lvlrl~GG   76 (152)
T 3u5c_f           30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   76 (152)
T ss_dssp             -----------------------------------------------
T ss_pred             HHHHhCCCHHHEEEEECCEEccccCcHHHcCCCCCCEEEEEeeccCC
Confidence            567899999999999999999999999999999 9999999999887

>4b6w_A Tubulin-specific chaperone; CAP-Gly, ubiquitin-like; HET: MSE; 2.35A {Trypanosoma brucei brucei strain 927}

Probab=99.16  E-value=5.2e-12  Score=75.38  Aligned_cols=44  Identities=11%  Similarity=0.100  Sum_probs=39.0

Q ss_pred             CccccCCCCcceEEEE-------CCEEeCCCCCCccceec-ccceeeeeeee
Q 040204            1 IEDKEEILRDQQRFIF-------AGKRLEDGRTLVDYNIH-GSTLHSVRRFR   44 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~-------~g~~L~d~~tL~~y~I~-~sti~l~i~~~   44 (97)
                      |+.++|||+++|||+|       .|+.|+|+++|++|||+ |++|||+-+.+
T Consensus        34 i~~~~Gip~~~QrLi~~~~~~~~~g~~l~d~~tL~~Y~i~~g~~ihlvd~~P   85 (86)
T 4b6w_A           34 VFTHFATPPEYMQLQLIDDRGITIEKNMANDKQLGYYQCRDEFVIHVVDLQP   85 (86)
T ss_dssp             HHTTSCCCGGGEEEEEECTTSCEEESSCCTTSBGGGGTCCTTCEEEEEECCC
T ss_pred             HHHHHCCCHHHEEEEEecCCCCceeeEcCCCCCHHHCCCCCCCEEEEEeCCC
Confidence            4678999999999996       58889999999999999 99999986543

>2kjr_A CG11242; UBL, ubiquitin, ubiquitin-like, structural genomics, PSI-2, protein structure initiative; NMR {Drosophila melanogaster}

Probab=99.16  E-value=6.7e-11  Score=71.74  Aligned_cols=48  Identities=8%  Similarity=0.064  Sum_probs=41.3

Q ss_pred             ccceeeeeeeecc----eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECe
Q 040204           34 GSTLHSVRRFRGG----MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWF   81 (97)
Q Consensus        34 ~sti~l~i~~~~g----~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G   81 (97)
                      .+.|.+.++...+    .++.+++++||++||++|++++|+||++|||+|+|
T Consensus        13 ~~~v~l~It~s~~~~~~~~~~v~~~~TV~~LK~kI~~~~GiP~~~QrL~~~~   64 (95)
T 2kjr_A           13 SDFIKVNVSNSHNDAVAFEVKLAKDLTVAQLKTKLEILTGGCAGTMKVQVFK   64 (95)
T ss_dssp             CCEEEEEEEESSCSCEEEEEEEETTCBHHHHHHHHHHHHCSCTTTEEEEEEE
T ss_pred             CCeEEEEEEECCCCceEEEEEeCccCHHHHHHHHHHHHHCcCHHHeEEEEec
Confidence            5677777776544    56788999999999999999999999999999984

>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling proteins; 1.15A {Saccharomyces cerevisiae} SCOP: d.15.1.1 PDB: 2bwe_S

Probab=99.16  E-value=8.3e-11  Score=67.58  Aligned_cols=51  Identities=22%  Similarity=0.234  Sum_probs=42.4

Q ss_pred             eeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           37 LHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        37 i~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      +.+.++. +|  +.+.+++++||.+||++|++.+|+|+++|+|+|+|+.  |..+|
T Consensus         5 m~i~vk~-~g~~~~~~v~~~~tV~~LK~~i~~~~~i~~~~qrL~~~gk~L~d~~tL   59 (77)
T 2bwf_A            5 LNIHIKS-GQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTV   59 (77)
T ss_dssp             EEEEEEE-TTEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBT
T ss_pred             EEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHhCCCHHHEEEEECCeEcCCCCCH
Confidence            4566666 44  5578899999999999999999999999999999998  44444

>1ttn_A DC-UBP, dendritic cell-derived ubiquitin-like protein; ubiquitin-like domain, solution structure, signaling protein; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.16  E-value=6.5e-11  Score=72.74  Aligned_cols=50  Identities=26%  Similarity=0.371  Sum_probs=44.9

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +..+.+.++..+|  +.+.|++++||.+||++|++++|+|+++|+|+|+|++
T Consensus        21 ~~~m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~   72 (106)
T 1ttn_A           21 GYECQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRP   72 (106)
T ss_dssp             CCSEEEEEEETTTEEEEEEECTTSHHHHHHHHHHHTTCCCSTTCEEEETTEE
T ss_pred             CCeEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHHCcCcccEEEEECCEE
Confidence            5578888887666  5578899999999999999999999999999999998

>1uel_A HHR23B, UV excision repair protein RAD23 homolog B; UBL, UIM, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.16  E-value=7.7e-11  Score=71.01  Aligned_cols=51  Identities=18%  Similarity=0.218  Sum_probs=42.3

Q ss_pred             eeeeeeecc--eeeeeeccchhHHHHHhhhhh---cCCCCCceEEEECeEe--CCCcc
Q 040204           38 HSVRRFRGG--MQIFVESSDTIDNVKAKIQDK---KGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        38 ~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~---~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      .+.++..+|  +.+.|++++||.+||++|++.   +|+|+++|+|+|+|+.  |..+|
T Consensus         2 ~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~~~~gip~~~qrLi~~Gk~L~D~~tL   59 (95)
T 1uel_A            2 QVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTAL   59 (95)
T ss_dssp             EEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEETTEECCTTSBG
T ss_pred             EEEEEeCCCCEEEEEECCCCHHHHHHHHHHhhcccCCCChhhEEEEECCEECCCcCcH
Confidence            456666545  567889999999999999999   8999999999999998  44444

>1wy8_A NP95-like ring finger protein, isoform A; ubiquitin-like domain, NP95/ICBP90-like ring finger (NIRF), ubiquitin ligase, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.16  E-value=1e-10  Score=69.25  Aligned_cols=55  Identities=20%  Similarity=0.151  Sum_probs=45.9

Q ss_pred             ccceeeeeeeecc---eee-eeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           34 GSTLHSVRRFRGG---MQI-FVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~~~~g---~~i-~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      ...+.+.++...|   +.+ .|++++||.+||++|++.+|+|+++|+|+|+|+.  |..+|
T Consensus         5 ~~~m~i~Vk~~~g~~~~~l~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~gk~L~d~~tL   65 (89)
T 1wy8_A            5 SSGMWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTL   65 (89)
T ss_dssp             SSCEEEEEEETTCSCEEEEEEECTTCBHHHHHHHHHHHSCCCTTTEEEEETTEECCSSSBH
T ss_pred             CCcEEEEEEECCCCceEEEEecCCCCCHHHHHHHHHHHHCcChhhEEEEECCeECCCCCCH
Confidence            3567888887654   567 4899999999999999999999999999999998  43444

>3vdz_A Ubiquitin-40S ribosomal protein S27A; gadolinium, MRI contrast agent, peptide-based contrast agent lanthanide binding TAG; 2.40A {Synthetic construct} PDB: 2ojr_A

Probab=99.16  E-value=7.3e-11  Score=73.14  Aligned_cols=50  Identities=50%  Similarity=0.582  Sum_probs=44.7

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      ...+.+.++..+|  +.+.|++++||.+||++|++++|+|+++|+|+|+|+.
T Consensus        33 ~~~m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~   84 (111)
T 3vdz_A           33 LLAMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQ   84 (111)
T ss_dssp             GGCEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEE
T ss_pred             CccEEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHhCCChHHEEEEECCEE
Confidence            4578888887766  5678899999999999999999999999999999998

>1sif_A Ubiquitin; hydrophobic mutants, folding, stability, structural protein; 2.18A {Homo sapiens} SCOP: d.15.1.1

Probab=99.16  E-value=6.2e-11  Score=70.50  Aligned_cols=52  Identities=48%  Similarity=0.579  Sum_probs=43.1

Q ss_pred             eeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           37 LHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        37 i~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      +.+.++..+|  +.+.|++++||++||++|++.+|+|+++|+|+|+|+.  |..+|
T Consensus        10 ~~i~v~~~~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL   65 (88)
T 1sif_A           10 LQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL   65 (88)
T ss_dssp             CEEEEEETTSCEEEEECCTTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBS
T ss_pred             eEEEEEeCCCCEEEEEECCCChHHHHHHHHHHHHCcChhhEEEEECCEECCCCCcH
Confidence            4556666665  5577899999999999999999999999999999998  44444

>2kj6_A Tubulin folding cofactor B; methods development, NESG, solution PSI-2, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.16  E-value=4.8e-11  Score=72.69  Aligned_cols=49  Identities=14%  Similarity=0.093  Sum_probs=42.1

Q ss_pred             ccceeeeeeeecc----eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeE
Q 040204           34 GSTLHSVRRFRGG----MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFV   82 (97)
Q Consensus        34 ~sti~l~i~~~~g----~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~   82 (97)
                      .+.|.+.++....    .++.+++++||++||++|++++|+||++|||+|.|+
T Consensus        12 ~~~v~l~It~s~~~~~~~e~~v~~~~TV~~LK~kIe~~~Gip~~~QrLi~~g~   64 (97)
T 2kj6_A           12 DDSVHLHITHANLKSFSADARFSPQMSVEAVKEKLWKKCGTSVNSMALELYDD   64 (97)
T ss_dssp             CCCEEEEEEETTSSCCCEEEEECTTCCHHHHHHHHHHHHCCCTTSEEEEEECS
T ss_pred             CceEEEEEEECCCCceEEEEEeCCCChHHHHHHHHHHHHCcCHHHeEEEEecC
Confidence            5677777776433    567889999999999999999999999999999985

>3k9o_B Ubiquitin, UBB+1; E2-25K, complex structure, ATP-binding, isopeptide BO ligase, nucleotide-binding, UBL conjugation pathway; 1.80A {Homo sapiens} PDB: 2k25_A 2kx0_A

Probab=99.15  E-value=7.2e-11  Score=70.81  Aligned_cols=52  Identities=50%  Similarity=0.601  Sum_probs=43.6

Q ss_pred             eeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           37 LHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        37 i~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      +.+.++..+|  +.+.|++++||.+||++|++.+|+|+++|+|+|+|+.  |..+|
T Consensus         2 m~i~vk~~~g~~~~~~v~~~~TV~~LK~~i~~~~gip~~~qrL~~~G~~L~d~~tL   57 (96)
T 3k9o_B            2 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL   57 (96)
T ss_dssp             CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBT
T ss_pred             cEEEEEeCCCCEEEEEECCCCCHHHHHHHHHhhhCCChhHEEEEECCEECCCCCcH
Confidence            4567776665  5577899999999999999999999999999999998  44444

>3m63_B Ubiquitin domain-containing protein DSK2; armadillo-like repeats, UBL conjugation pathway, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=99.15  E-value=7.4e-12  Score=76.59  Aligned_cols=43  Identities=35%  Similarity=0.603  Sum_probs=39.3

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|||+ +++|+++.+.
T Consensus        57 I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~gI~~g~tI~lv~~~  100 (101)
T 3m63_B           57 INKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKSQ  100 (101)
T ss_dssp             HHHHHSCCSTTCCEEETTEECCTTSBTTTTTCCTTEEEEECCCC
T ss_pred             HHHHHCcChHHEEEEECCEECCCcCcHHHCCCCCCCEEEEEeCC
Confidence            356789999999999999999999999999999 9999998753

>4b6w_A Tubulin-specific chaperone; CAP-Gly, ubiquitin-like; HET: MSE; 2.35A {Trypanosoma brucei brucei strain 927}

Probab=99.15  E-value=6e-11  Score=70.71  Aligned_cols=53  Identities=13%  Similarity=0.041  Sum_probs=40.6

Q ss_pred             ceeeeeeee--cc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEE-------CeEe--CCCcc
Q 040204           36 TLHSVRRFR--GG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIF-------WFVF--GWGSL   88 (97)
Q Consensus        36 ti~l~i~~~--~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif-------~G~~--~~~~~   88 (97)
                      +|.+.++-.  +.  .++.+++++||++||++|++++|+||++|+|+|       .|++  |..+|
T Consensus         2 ~V~v~iths~~~~~~~E~r~~~s~TI~~lK~ki~~~~Gip~~~QrLi~~~~~~~~~g~~l~d~~tL   67 (86)
T 4b6w_A            2 VVKVSLTHSASRMRVPEKRYGLAQTIESIKENVFTHFATPPEYMQLQLIDDRGITIEKNMANDKQL   67 (86)
T ss_dssp             EEEEEEEETTCSCCEEEEEEETTSBHHHHHHHHHTTSCCCGGGEEEEEECTTSCEEESSCCTTSBG
T ss_pred             EEEEEEEEcCCCCeEEEEEcCccCcHHHHHHHHHHHHCCCHHHEEEEEecCCCCceeeEcCCCCCH
Confidence            445555432  22  467789999999999999999999999999997       5776  44554

>1wx7_A Ubiquilin 3; ubiquitin-like domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.14  E-value=1e-11  Score=76.23  Aligned_cols=46  Identities=33%  Similarity=0.425  Sum_probs=42.5

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++.+|+|+++|+|+|+|+.|+|+++|++|+|. +++|+|+.+..++
T Consensus        46 I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~~~   92 (106)
T 1wx7_A           46 ISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHR   92 (106)
T ss_dssp             HHHHHTCCTTTEEEEETTEECCTTSCHHHHTCCTTEEEEEEECCCCC
T ss_pred             HHHHHCcChhhEEEEECCEECCCcCcHHHcCCCCCCEEEEEEcCCCC
Confidence            356789999999999999999999999999999 9999999988776

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A

Probab=99.14  E-value=1.9e-11  Score=75.57  Aligned_cols=42  Identities=12%  Similarity=0.048  Sum_probs=38.6

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCcccee-c-ccceeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-H-GSTLHSVRR   42 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I-~-~sti~l~i~   42 (97)
                      |++++|||+++||++|+|+.++|++||++||| + |+++||++-
T Consensus        56 I~~k~Gipp~~QRli~ggkll~D~~TL~~ygI~~~G~t~hL~l~   99 (105)
T 4dbg_A           56 VFLDYGFPPVLQQWVIGQRLARDQETLHSHGVRQNGDSAYLYLL   99 (105)
T ss_dssp             HHHHHCCCGGGEEEEETTEEECTTCBTGGGTCCSTTCEEEEEEC
T ss_pred             HHHHhCCCHHHEEEeccCeEccCcCcHHHcCCCCCCCEEEEEEE
Confidence            45789999999999999999999999999999 6 999999874

>1v5t_A 8430435I17RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 PDB: 2kx3_A

Probab=99.14  E-value=7.6e-11  Score=70.48  Aligned_cols=50  Identities=18%  Similarity=0.262  Sum_probs=42.8

Q ss_pred             ccceeeeeeeecc-eee-eeeccchhHHHHHhhhhhcCCCCCceEEE---ECeEe
Q 040204           34 GSTLHSVRRFRGG-MQI-FVESSDTIDNVKAKIQDKKGTPPDQQRQI---FWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g-~~i-~v~~~~TV~~lK~~I~~~~gip~~~q~Li---f~G~~   83 (97)
                      .+++.+.++..+. +.+ .|++++||.+||++|++++|+|+++|+|+   |+|++
T Consensus         5 ~~~m~i~Vk~~g~~~~i~~v~~~~TV~~lK~~I~~~~gip~~~QkLi~~k~~Gk~   59 (90)
T 1v5t_A            5 SSGLPIIVKWGGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKP   59 (90)
T ss_dssp             CCSCCEEEEETTEEEEECSCCSSSBHHHHHHHHHHHTCCCTTTCEEESCEETTEE
T ss_pred             CceEEEEEEECCEEEEEEEeCCCCCHHHHHHHHHHHHCcCHHHeEEEeeccCCcC
Confidence            3457777775433 557 88999999999999999999999999999   99998

>2l7r_A Ubiquitin-like protein FUBI; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=99.14  E-value=6.6e-11  Score=71.15  Aligned_cols=55  Identities=16%  Similarity=0.187  Sum_probs=43.8

Q ss_pred             ccceeeeeeeecceeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           34 GSTLHSVRRFRGGMQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~~~~g~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      ...+.+.++....+.+.|++++||.+||++|++++|+|+++|+|+|+|++  |..+|
T Consensus        17 ~~~m~I~Vk~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL   73 (93)
T 2l7r_A           17 RGSMQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAGAPLEDEATL   73 (93)
T ss_dssp             ---CEEEEESSSEEEEECCSSCBHHHHHHHHHHHHTCCGGGCEEEETTEECCTTSBH
T ss_pred             CCcEEEEEECCCEEEEEeCCCCcHHHHHHHHHHHhCcChhHEEEEECCEECCCCCcH
Confidence            45677777772236688899999999999999999999999999999998  44444

>3b08_A Polyubiquitin-C, ubiquitin; protein complex, signaling protein-metal binding protein COM; HET: TRE; 1.70A {Homo sapiens} PDB: 2w9n_A* 3b0a_A* 3axc_A 2zvn_A 2zvo_A 2y5b_B

Probab=99.14  E-value=1.8e-11  Score=78.44  Aligned_cols=46  Identities=74%  Similarity=1.063  Sum_probs=42.1

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++++|+|++.|+|+|+|+.|+|+.+|++|+|. +++++++.+..||
T Consensus       106 i~~~~gi~~~~qrL~~~g~~L~d~~tL~~~~i~~~~~i~l~~r~~GG  152 (152)
T 3b08_A          106 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  152 (152)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCCC-
T ss_pred             HHHHhCcChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEecCCC
Confidence            356789999999999999999999999999999 9999999998876

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.13  E-value=1.5e-11  Score=72.91  Aligned_cols=42  Identities=26%  Similarity=0.426  Sum_probs=38.4

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR   42 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~   42 (97)
                      |++.+|+|+++|+|+|+|+.|+|+.+|++|+|. +++|+++.+
T Consensus        41 I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~l~l~~s   83 (85)
T 2kd0_A           41 LQPITNVLPRGQKLIFKGKVLVETSTLKQSDVGSGAKLMLMAS   83 (85)
T ss_dssp             HHHHHCCCTTTCEEEETTEECCTTCBTTTTTCCTTEEEEEECC
T ss_pred             HHHHHCcChHHEEEEECCeECCCcCCHHHCCCCCCCEEEEEEe
Confidence            356789999999999999999999999999999 999998764

>1ttn_A DC-UBP, dendritic cell-derived ubiquitin-like protein; ubiquitin-like domain, solution structure, signaling protein; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.12  E-value=1.2e-11  Score=76.12  Aligned_cols=46  Identities=17%  Similarity=0.286  Sum_probs=41.6

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++++|+|+++|+|+|+|+.|+|+++|++|+|. +++|+++.+....
T Consensus        53 I~~~~gip~~~qrLi~~Gk~L~D~~tL~~ygI~~g~ti~lv~~~~~~   99 (106)
T 1ttn_A           53 LHAAEGVEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQPVQ   99 (106)
T ss_dssp             HHHTTCCCSTTCEEEETTEECCTTSHHHHCCCSSSCEEEEECCCSSC
T ss_pred             HHHHHCcCcccEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCCC
Confidence            356789999999999999999999999999999 9999999876543

>1wx7_A Ubiquilin 3; ubiquitin-like domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.12  E-value=1.4e-10  Score=71.14  Aligned_cols=50  Identities=20%  Similarity=0.159  Sum_probs=43.9

Q ss_pred             ccceeeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      ...+.+.++..++ +.+.|++++||.+||++|++.+|+|+++|+|+|+|+.
T Consensus        15 ~~~m~I~Vk~~~g~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~   65 (106)
T 1wx7_A           15 PHLIKVTVKTPKDKEDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKI   65 (106)
T ss_dssp             SSEEEEEEECSSCEEEEEEETTCCHHHHHHHHHHHHTCCTTTEEEEETTEE
T ss_pred             CceEEEEEEeCCCcEEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEE
Confidence            3467788876655 6688899999999999999999999999999999998

>1v5o_A 1700011N24RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.12  E-value=8.2e-12  Score=76.31  Aligned_cols=46  Identities=15%  Similarity=0.307  Sum_probs=41.9

Q ss_pred             CccccCCCCcceEEEECCEEeCCC-CCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDG-RTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~-~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++++|+|+++|+|+|+|+.|+|+ ++|++|+|+ +++|+|+.+..+|
T Consensus        41 I~~~~gip~~~qrL~~~gk~L~D~~~tL~~ygI~~g~~l~l~~~~~gg   88 (102)
T 1v5o_A           41 CELESGVPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVLLQKDNVG   88 (102)
T ss_dssp             HHHHTCCCGGGBCEEETTEEECCSSSBHHHHTCCTTEEEEECBCCCCC
T ss_pred             HHHHHCcChHHeEEEECCEECCCCcccHHHCCCCCCCEEEEEECCCCC
Confidence            456789999999999999999988 799999999 9999999988776

>3a9j_A Ubiquitin; protein complex, cytoplasm, isopeptide bond, metal-binding, zinc; 1.18A {Mus musculus} PDB: 3a1q_B 2znv_B 3a9k_A 3h7p_A 3jsv_A 3dvg_Y 3dvn_Y 3nob_A 2o6v_D* 3jw0_X 3jvz_X 3nhe_B* 1aar_A 1d3z_A 1f9j_A 1fxt_B 1g6j_A 1nbf_C 1cmx_B 1q5w_B ...

Probab=99.12  E-value=1.4e-10  Score=66.28  Aligned_cols=51  Identities=51%  Similarity=0.595  Sum_probs=42.5

Q ss_pred             eeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           38 HSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        38 ~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      .+.++..+|  +.+.+++++||.+||++|++..|+|+++|+|+|+|+.  |..+|
T Consensus         2 ~i~vk~~~g~~~~i~v~~~~tv~~lK~~i~~~~~i~~~~q~L~~~g~~L~d~~tL   56 (76)
T 3a9j_A            2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL   56 (76)
T ss_dssp             EEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBT
T ss_pred             EEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCeECCCCCcH
Confidence            456666555  5677899999999999999999999999999999998  43444

>1wx8_A Riken cDNA 4931431F19; ubiquitin-like domain, ubiquilin 1-like, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.11  E-value=1e-10  Score=70.33  Aligned_cols=50  Identities=12%  Similarity=0.123  Sum_probs=43.6

Q ss_pred             ccceeeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      ..++.+.++..+. +.+.|++++||.+||++|++.+|+|+++|+|+|+|+.
T Consensus        15 ~~~m~i~Vk~~g~~~~~~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~   65 (96)
T 1wx8_A           15 SRIIRVSVKTPQDCHEFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKI   65 (96)
T ss_dssp             SCEEEEEEECSSSEEEEEEETTCCHHHHHHHHHHHTCSCTTTBCCEETTEE
T ss_pred             CCcEEEEEEECCeEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEE
Confidence            3567777777633 5678899999999999999999999999999999998

>1wgh_A Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.11  E-value=3.8e-11  Score=75.36  Aligned_cols=42  Identities=29%  Similarity=0.366  Sum_probs=36.4

Q ss_pred             ccCC--CCcceEEEECCEEeCCCCCCccceec-c--cceeeeeeeec
Q 040204            4 KEEI--LRDQQRFIFAGKRLEDGRTLVDYNIH-G--STLHSVRRFRG   45 (97)
Q Consensus         4 ~~gi--p~~~Q~L~~~g~~L~d~~tL~~y~I~-~--sti~l~i~~~~   45 (97)
                      ++|+  |+++|||+|+|+.|+|++||++|+|+ +  +++||+++...
T Consensus        55 ke~~p~p~~qqrLIy~GK~LeD~~TL~~y~I~~~~~~tlhLvlr~~~  101 (116)
T 1wgh_A           55 EEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLVARETL  101 (116)
T ss_dssp             SCCCCCCTTTEEEEETTEEECSSCBTTTTTCCSSCEEEEEEEECSSC
T ss_pred             ccCCCCChHHEEEEECCcCCCCCCcHHHcCCCCCCceEEEEEccCCC
Confidence            5675  69999999999999999999999997 5  67888887653

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B

Probab=99.10  E-value=1.7e-10  Score=76.40  Aligned_cols=51  Identities=53%  Similarity=0.611  Sum_probs=43.3

Q ss_pred             eeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           38 HSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        38 ~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      .+.++..+|  +.+.|++++||.+||++|++++|+|+++|+|+|+|++  |..+|
T Consensus         2 qI~Vk~~~Gk~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL   56 (169)
T 3l0w_B            2 QIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTL   56 (169)
T ss_dssp             EEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHCCCTTTEEEEETTEECCTTSBG
T ss_pred             EEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHHCcCHHHEEEEECCccccCcCcH
Confidence            466676665  5678899999999999999999999999999999999  44444

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9

Probab=99.10  E-value=8.8e-12  Score=84.08  Aligned_cols=51  Identities=12%  Similarity=0.038  Sum_probs=0.0

Q ss_pred             eeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           38 HSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        38 ~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      .+.++..+|  +.+.|++++||.+||++|++.+|||+++|+|+|+|++  |..+|
T Consensus         2 qI~VKtL~GktitLeV~~sdTV~~LK~kI~~keGIP~~qQRLIf~GK~LeD~~TL   56 (189)
T 2xzm_9            2 QVQVKTLEGETKIYTLEQGTSVLDLKSQISQDMGFEIDMMTLVNNGFIAPNTELV   56 (189)
T ss_dssp             -------------------------------------------------------
T ss_pred             EEEEEcCCCCEEEEEECCcChHHHHHHHHHHHhCcChhHEEEEecCeECCCCCcc
Confidence            455665555  5678899999999999999999999999999999998  44443

>2daf_A FLJ35834 protein; hypothetical protein FLJ35834, ubiquitin-like domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.09  E-value=3.7e-11  Score=75.40  Aligned_cols=45  Identities=16%  Similarity=0.136  Sum_probs=40.9

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      ++..++|++.|+|+|+|+.|+|+.||++|||+ +.|+||+++....
T Consensus        47 s~~~~iP~e~qrLIy~GKiLKD~eTL~~~gIk~g~TIhLvi~s~~p   92 (118)
T 2daf_A           47 SHLLGIPHSVLQIRYSGKILKNNETLVQHGVKPQEIVQVEIFSTNP   92 (118)
T ss_dssp             HHHHTCCTTTEEEEETTEEECSSCCHHHHSCCSSCEEEEEEEESCT
T ss_pred             HhhhCCChHHEEEEECCeEcCCcchHHHcCCCCCCEEEEEEecCCC
Confidence            45679999999999999999999999999999 9999999986543

>1yx5_B Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo sapiens} SCOP: d.15.1.1 PDB: 1yx6_B

Probab=99.09  E-value=2.2e-10  Score=69.15  Aligned_cols=46  Identities=54%  Similarity=0.655  Sum_probs=40.5

Q ss_pred             eeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           38 HSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        38 ~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .+.++..+|  +.+.|++++||.+||++|++.+|+|+++|+|+|+|+.
T Consensus         2 ~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~gi~~~~qrL~~~Gk~   49 (98)
T 1yx5_B            2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQ   49 (98)
T ss_dssp             EEEEEETTSCEEEEECCTTCBHHHHHHHHHHHTCCCGGGEEEEETTEE
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEE
Confidence            456666555  5678899999999999999999999999999999998

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.07  E-value=3.2e-10  Score=71.74  Aligned_cols=55  Identities=15%  Similarity=0.118  Sum_probs=45.9

Q ss_pred             ccceeeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           34 GSTLHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      .+++.+.++..+. +.+.|++++||.+||++|++.+|+|+++|+|+|+|+.  |..+|
T Consensus        30 ~~~m~I~Vk~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL   87 (125)
T 1j8c_A           30 PKIIKVTVKTPKEKEEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTL   87 (125)
T ss_dssp             CCCEEEEEECSSCEEEEEECTTCCHHHHHHHHHHHHCSCSSSEEEEETTEEESTTSCG
T ss_pred             CCcEEEEEEeCCeEEEEEECCCCcHHHHHHHHHHHHCcCcceEEEEECCEEcCCCCCH
Confidence            3567787777633 5678899999999999999999999999999999998  44444

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens}

Probab=99.07  E-value=3.9e-11  Score=76.18  Aligned_cols=43  Identities=28%  Similarity=0.365  Sum_probs=37.8

Q ss_pred             ccCCC--CcceEEEECCEEeCCCCCCccceec-cc--ceeeeeeeecc
Q 040204            4 KEEIL--RDQQRFIFAGKRLEDGRTLVDYNIH-GS--TLHSVRRFRGG   46 (97)
Q Consensus         4 ~~gip--~~~Q~L~~~g~~L~d~~tL~~y~I~-~s--ti~l~i~~~~g   46 (97)
                      ++|+|  +++|||+|+|+.|+|+.||++|+|+ ++  ++||+++..++
T Consensus        56 ke~ip~~~~~qrLIy~GK~LeD~~TL~~y~I~~~~~~tlhlv~r~~~~  103 (125)
T 2gow_A           56 EEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLVARETLP  103 (125)
T ss_dssp             CCCTTCCGGGEEEESSSSEEESSCBTGGGCCCTTSEEEEEEEECSCCS
T ss_pred             ccCCCCChHHEEEEECCcCCCCCCcHHHcCCCCCCceEEEEEecCCCC
Confidence            67884  8999999999999999999999998 65  78888887654

>1v86_A DNA segment, CHR 7, wayne state university 128, expressed; ubiquitin fold, structural genomics, D7WSU128E protein; HET: DNA; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.07  E-value=8.9e-11  Score=70.92  Aligned_cols=50  Identities=18%  Similarity=0.197  Sum_probs=43.2

Q ss_pred             ccceeeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      ..++.+.++..+. +.+.+++++||.+||++|++.+|+|+++|+|+|+|++
T Consensus        15 ~~~~~i~Vk~~g~~~~i~v~~~~TV~~LK~~I~~~tgip~~~QrL~~~Gk~   65 (95)
T 1v86_A           15 KELVDLKIIWNKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGLV   65 (95)
T ss_dssp             CCCEEEEEEETTEEEEEEECTTSBHHHHHHHHHHHHCSCSTTCCCBSSSBC
T ss_pred             CceEEEEEEECCEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCee
Confidence            4567777775443 5688899999999999999999999999999999998

>2dzm_A FAS-associated factor 1; ubiquitin-like domain, HFAF1, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.06  E-value=1.7e-10  Score=70.65  Aligned_cols=47  Identities=13%  Similarity=0.114  Sum_probs=38.7

Q ss_pred             eeeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEE--CeEe
Q 040204           37 LHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIF--WFVF   83 (97)
Q Consensus        37 i~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif--~G~~   83 (97)
                      +.+.++..++ +.|.|++++||++||++|++++||||++|+|+|  +|+.
T Consensus        10 ~~~~vk~~Gk~~~v~v~~~~TV~~LK~~I~~~tgIpp~~QkLi~~~~gkL   59 (100)
T 2dzm_A           10 LDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGDV   59 (100)
T ss_dssp             EEEEEECSSCEEEEEEETTSBHHHHHHHHHHHHCCCTTTCCEECCSSSCC
T ss_pred             EEEEEEeCCeEEEEEECCCCcHHHHHHHHHHHHCCChhHeEEEccCCCCC
Confidence            3445555444 668889999999999999999999999999997  6664

>2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing, protein binding; 2.60A {Homo sapiens}

Probab=99.06  E-value=4.1e-10  Score=69.61  Aligned_cols=49  Identities=51%  Similarity=0.624  Sum_probs=44.3

Q ss_pred             cceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           35 STLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        35 sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +++.+.++..+|  +.+.|++++||.+||++|++.+|+|+++|+|+|+|+.
T Consensus        34 ~~m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~   84 (111)
T 2ojr_A           34 LAMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQ   84 (111)
T ss_dssp             SCEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHCCCTTTEEEEETTEE
T ss_pred             CeEEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHHHCcCcccEEEEECCEE
Confidence            578888887665  5678899999999999999999999999999999998

>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion protein; ubiquitin interacting motif, UIM, protein domain interface; NMR {Saccharomyces cerevisiae}

Probab=99.06  E-value=2.8e-10  Score=70.89  Aligned_cols=53  Identities=49%  Similarity=0.587  Sum_probs=43.9

Q ss_pred             ceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           36 TLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        36 ti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      .+.+.++..+|  +.+.|++++||++||++|++.+|+|+++|+|+|+|+.  |..+|
T Consensus         9 ~~~i~vk~l~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL   65 (114)
T 2kdi_A            9 EFQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLEDGRTL   65 (114)
T ss_dssp             CCEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBT
T ss_pred             cEEEEEEeCCCcEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCEECCCCCcH
Confidence            35566666666  5577899999999999999999999999999999998  44444

>1we6_A Splicing factor, putative; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=99.05  E-value=2.1e-10  Score=70.94  Aligned_cols=55  Identities=25%  Similarity=0.206  Sum_probs=46.2

Q ss_pred             ccceeeeeeee---cc--eeeeeec-cchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           34 GSTLHSVRRFR---GG--MQIFVES-SDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~~~---~g--~~i~v~~-~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      ...+.+.++..   +|  +.+.|++ ++||.+||++|++.+|+|+++|+|+|+|++  |..+|
T Consensus        25 ~~~i~i~Vk~~~~~~g~~~~l~v~~l~~TV~~LK~~I~~~~gip~~~QrL~~~Gk~L~D~~tL   87 (111)
T 1we6_A           25 PGPATIRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSL   87 (111)
T ss_dssp             CSCEEEEECCTTCSSSCCEEEEESCSSSBHHHHHHHHHHHTTCCTTTSEEECSSSBCCTTSBT
T ss_pred             CCcEEEEEEecccCCCcEEEEEecCCCCcHHHHHHHHHHHHCCCHHHeEEEECCEECCCCCcH
Confidence            45688888876   44  5678897 999999999999999999999999999998  44444

>1we7_A SF3A1 protein; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: d.15.1.1 PDB: 1zkh_A

Probab=99.05  E-value=4.6e-10  Score=69.81  Aligned_cols=50  Identities=18%  Similarity=0.337  Sum_probs=42.5

Q ss_pred             ccceeeeeeeec----------c--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRG----------G--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~----------g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      ...|.+.++.++          |  +.+.|++++||.+||++|++.+|+|+++|+|+|+|+.
T Consensus        23 ~~~i~l~V~~p~~~~~~~~~L~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrL~~~Gk~   84 (115)
T 1we7_A           23 KGPVSIKVQVPNMQDKTEWKLNGQGLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIF   84 (115)
T ss_dssp             CSCEEEEEEECCCSSSCSSCCSSEEEEEEECSCSBTHHHHHHHHHHSSCCTTTEEEEETTEE
T ss_pred             CCCEEEEEEcCCCccccccccCCeEEEEEECCCCCHHHHHHHHHHHHCCChHHEEEEECCEE
Confidence            346667666653          2  5678899999999999999999999999999999998

>1x1m_A Ubiquitin-like protein SB132; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.05  E-value=4.9e-11  Score=73.46  Aligned_cols=43  Identities=33%  Similarity=0.547  Sum_probs=39.1

Q ss_pred             cccc--CCCCcc-eEEEECCEEeCCCCCCccceec-ccceeeeeeee
Q 040204            2 EDKE--EILRDQ-QRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFR   44 (97)
Q Consensus         2 ~~~~--gip~~~-Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~   44 (97)
                      ++++  |+|+++ |+|+|+|+.|+|+++|++|+|+ +++|+++.+..
T Consensus        55 ~~~~~~gip~~~~qrLi~~Gk~L~D~~tL~~y~i~~g~~i~lv~~~~  101 (107)
T 1x1m_A           55 AGKLQESVPDPELIDLIYCGRKLKDDQTLDFYGIQPGSTVHVLRKSW  101 (107)
T ss_dssp             HHHCTTTCCCSSSEEEEETTEECCTTCBHHHHTCCTTCEEEEEESSC
T ss_pred             HHHhccCCChhhcEEEEECCeECCCCCcHHHcCCCCCCEEEEEeCCC
Confidence            4556  999999 9999999999999999999999 99999988754

>1wxv_A BAG-family molecular chaperone regulator-1; structural genomics, apoptosis, riken structural genomics/proteomics initiative, RSGI, NPPSFA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.05  E-value=5.2e-10  Score=66.76  Aligned_cols=50  Identities=18%  Similarity=0.212  Sum_probs=42.6

Q ss_pred             ccceeeeeeeecc-eeeeeecc-----chhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG-MQIFVESS-----DTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g-~~i~v~~~-----~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .+++.+.++..+. +.+.++++     +||.+||++|++.+|+|+++|+|+|+|+.
T Consensus         5 ~~~~~v~Vk~~~~~~~i~v~~~~~~~~~TV~~LK~~i~~~~gip~~~qrL~~~Gk~   60 (92)
T 1wxv_A            5 SSGLTVTVTHSNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKS   60 (92)
T ss_dssp             CSSEEEEEECSSSEEEEEECCCSSSSSCBHHHHHHHHHHHTCCCTTTCEEEETTEE
T ss_pred             CCeEEEEEEECCEEEEEEECCCcCcccCcHHHHHHHHHHHHCcCHHHEEEEECCee
Confidence            4567777776543 56778885     99999999999999999999999999998

>1wgg_A Ubiquitin carboxyl-terminal hydrolase 14; ubiquitin specific protease 14, USP14, ubiquitin-like fold, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.04  E-value=3.9e-11  Score=72.74  Aligned_cols=43  Identities=14%  Similarity=0.202  Sum_probs=39.1

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFR   44 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~   44 (97)
                      |++++|||+++|+|+|+|+.|+|+ +|++|+|. +++|+|+.+..
T Consensus        37 I~~~tgip~~~QkLi~~Gk~L~D~-tL~~~~I~~g~~i~l~~~~~   80 (96)
T 1wgg_A           37 LFALTGVQPARQKVMVKGGTLKDD-DWGNIKMKNGMTVLMMGSAD   80 (96)
T ss_dssp             HHHHTCCCTTTSCCEETTEECCSS-CCCSCCCCSSCEEECCCCCC
T ss_pred             HHHHHCcCHHHeEEEECCcCCCCC-CHHHCCCCCCCEEEEEecch
Confidence            467899999999999999999999 99999999 99999987654

>1v2y_A 3300001G02RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.03  E-value=1e-10  Score=72.21  Aligned_cols=50  Identities=16%  Similarity=-0.029  Sum_probs=43.0

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCC---------------CceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPP---------------DQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~---------------~~q~Lif~G~~   83 (97)
                      +..+.+.++..+|  +.|.|++++||++||++|++++++|+               ++|+|+|+|++
T Consensus         5 ~~~M~I~Vk~l~g~~~~v~V~~~~TV~dLK~~I~~~~~i~~~~q~g~~~isw~~~w~q~~Li~~Gk~   71 (105)
T 1v2y_A            5 SSGMTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEK   71 (105)
T ss_dssp             CCSEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHHHHHHHTTCCCCCCHHHHHTTEEEESSSCE
T ss_pred             CCcEEEEEEecCCCEEEEEECCCChHHHHHHHHHHHhCCCcccccCcceeeeeecceeEEEEeCCcC
Confidence            4567788877766  66888999999999999999999987               46799999998

>1v5o_A 1700011N24RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.03  E-value=4.4e-10  Score=68.54  Aligned_cols=49  Identities=10%  Similarity=0.152  Sum_probs=41.6

Q ss_pred             cceeeeeeeec------ceeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           35 STLHSVRRFRG------GMQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        35 sti~l~i~~~~------g~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +.+.+.++...      .+.+.|++++||++||++|++.+|+|+++|+|+|+|++
T Consensus         6 ~~m~I~Vk~~~~~~~~~~~~i~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~gk~   60 (102)
T 1v5o_A            6 SGMLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQL   60 (102)
T ss_dssp             CCEEEEEEECCCCCCCCEEEEEECTTCBHHHHHHHHHHHTCCCGGGBCEEETTEE
T ss_pred             CeEEEEEEECCCCcCceEEEEEcCCCCCHHHHHHHHHHHHCcChHHeEEEECCEE
Confidence            34667676642      24578899999999999999999999999999999998

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens}

Probab=99.02  E-value=3e-10  Score=76.59  Aligned_cols=53  Identities=49%  Similarity=0.538  Sum_probs=45.2

Q ss_pred             ceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           36 TLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        36 ti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      .+.+.++..+|  +.+.|++++||.+||++|++.+|+|+++|+|+|+|++  |..+|
T Consensus       105 eMqI~VKtl~Gkt~~l~V~~s~TV~~LK~kI~~~~gIp~~~QrLi~~Gk~L~D~~tL  161 (189)
T 3q3f_A          105 GGQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL  161 (189)
T ss_dssp             CEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCCEEETTEECCTTCBG
T ss_pred             ceeeeeecCCCCEEEEEeCCCCcHHHHHHHHHhccCCCHHHEEEEECCEECCCCCCH
Confidence            46777777666  5678899999999999999999999999999999998  44444

>1v6e_A Cytoskeleton-associated protein 1; tubulin-specific chaperone B, tubulin folding cofactor B, microtubule, ubiquitin-like fold, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.02  E-value=3e-10  Score=68.45  Aligned_cols=46  Identities=15%  Similarity=0.019  Sum_probs=39.1

Q ss_pred             ceeeeeeeecc---eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECe
Q 040204           36 TLHSVRRFRGG---MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWF   81 (97)
Q Consensus        36 ti~l~i~~~~g---~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G   81 (97)
                      .|.+.++..+.   .++.+++++||++||++|++++|+|+++|+|+|+|
T Consensus         7 ~v~l~I~~~~~~~~~~~~v~~~~TV~~lK~ki~~~~gip~~~qrL~~~~   55 (95)
T 1v6e_A            7 GVMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVGSPASCMELELYG   55 (95)
T ss_dssp             CEEEEEEETTSSSCEEEEECTTSBHHHHHHHHHHHTCSCTTTCBCEEEC
T ss_pred             EEEEEEEECCCCeeEEEEcCccCHHHHHHHHHHHHHCCCHHHeEEEEeC
Confidence            35555655444   66888999999999999999999999999999987

>3b1l_X E3 ubiquitin-protein ligase parkin; proteasome, ALFA-beta-protein; 1.85A {Mus musculus} PDB: 1mg8_A 2zeq_A 2knb_A 1iyf_A

Probab=98.58  E-value=2.9e-11  Score=69.55  Aligned_cols=46  Identities=28%  Similarity=0.357  Sum_probs=39.8

Q ss_pred             eeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           38 HSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        38 ~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .+.++..+|  +.+.+++++||++||++|++.+|+|+++|+|+|+|+.
T Consensus         2 ~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~qrL~~~gk~   49 (76)
T 3b1l_X            2 IVFVRFNSSYGFPVEVDSDTSILQLKEVVAKQQGVPADQLRVIFAGKE   49 (76)
Confidence            345565555  4677899999999999999999999999999999998

>1v5t_A 8430435I17RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 PDB: 2kx3_A

Probab=99.01  E-value=6.3e-11  Score=70.85  Aligned_cols=43  Identities=14%  Similarity=0.288  Sum_probs=39.4

Q ss_pred             CccccCCCCcceEEE---ECCEEeCCCCCCccceec-ccceeeeeee
Q 040204            1 IEDKEEILRDQQRFI---FAGKRLEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         1 i~~~~gip~~~Q~L~---~~g~~L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      |++++|||+++|+|+   |+|++|+|+.+|++|+|. +++|+|+.+.
T Consensus        37 I~~~~gip~~~QkLi~~k~~Gk~L~D~~~L~~~~i~~g~~l~l~~~~   83 (90)
T 1v5t_A           37 LKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMGTR   83 (90)
T ss_dssp             HHHHTCCCTTTCEEESCEETTEECCTTSBHHHHTCCTTEEEEEECCC
T ss_pred             HHHHHCcCHHHeEEEeeccCCcCcCCCCCHHHcCCCCCCEEEEEecC
Confidence            467899999999999   999999999999999999 9999998754

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens}

Probab=99.00  E-value=5.6e-11  Score=72.60  Aligned_cols=36  Identities=25%  Similarity=0.342  Sum_probs=32.9

Q ss_pred             cCCC-CcceEEEECCEEeCCCCCCccc--eec-ccceeee
Q 040204            5 EEIL-RDQQRFIFAGKRLEDGRTLVDY--NIH-GSTLHSV   40 (97)
Q Consensus         5 ~gip-~~~Q~L~~~g~~L~d~~tL~~y--~I~-~sti~l~   40 (97)
                      +|+| +++|||+|+|+.|+|+.+|++|  +|. +++|+|+
T Consensus        60 ~g~pp~~~QrLIy~Gk~L~D~~tL~~y~~~I~~~~tihLv   99 (99)
T 2kdb_A           60 PSKPLTKDQRLVYSGRLLPDHLQLKDILRKQDEYHMVHLV   99 (99)
T ss_dssp             TTCCCTTTCCEEETTEEECTTSBTHHHHTTTCSEEEEEEC
T ss_pred             cCCCChhhEEEEECCEECCCCCCHHHHhcCCCCCCEEEeC
Confidence            5666 5999999999999999999999  999 9999974

>1wxv_A BAG-family molecular chaperone regulator-1; structural genomics, apoptosis, riken structural genomics/proteomics initiative, RSGI, NPPSFA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=98.99  E-value=8.3e-11  Score=70.29  Aligned_cols=44  Identities=23%  Similarity=0.410  Sum_probs=38.7

Q ss_pred             CccccCCCCcceEEEECCEEeCC-CCCCccceec-ccceeeeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLED-GRTLVDYNIH-GSTLHSVRRFR   44 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d-~~tL~~y~I~-~sti~l~i~~~   44 (97)
                      |++.+|+|+++|+|+|+|+.|+| +.+|++|+|. +++|+|+.+..
T Consensus        41 i~~~~gip~~~qrL~~~Gk~L~D~~~~L~~~~i~~g~~i~l~~~~~   86 (92)
T 1wxv_A           41 VEEVIGVPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVMLIGKKN   86 (92)
T ss_dssp             HHHHTCCCTTTCEEEETTEEECCSSSBHHHHTCCSSEEEEEESCCS
T ss_pred             HHHHHCcCHHHEEEEECCeecCCCcccHHHCCCCCCCEEEEEecCC
Confidence            35678999999999999999998 6689999999 99999987643

>2kjr_A CG11242; UBL, ubiquitin, ubiquitin-like, structural genomics, PSI-2, protein structure initiative; NMR {Drosophila melanogaster}

Probab=98.97  E-value=1.1e-10  Score=70.76  Aligned_cols=40  Identities=18%  Similarity=0.130  Sum_probs=35.1

Q ss_pred             CccccCCCCcceEEEEC--CE---Ee-CCCCCCccceec-ccceeee
Q 040204            1 IEDKEEILRDQQRFIFA--GK---RL-EDGRTLVDYNIH-GSTLHSV   40 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~--g~---~L-~d~~tL~~y~I~-~sti~l~   40 (97)
                      |++++|||+++|||+|+  |+   .| +|+++|++|||+ +++|+|+
T Consensus        47 I~~~~GiP~~~QrL~~~~~g~~~~~L~~D~~tL~~Y~i~~gstihlv   93 (95)
T 2kjr_A           47 LEILTGGCAGTMKVQVFKGDTCVSTMDNNDAQLGYYANSDGLRLHVV   93 (95)
T ss_dssp             HHHHHCSCTTTEEEEEEETTEEEEECCCTTSBHHHHCCSSSCEEEEE
T ss_pred             HHHHHCcCHHHeEEEEecCCcccceeCCCCCCHhHCCcCCCCEEEEE
Confidence            46789999999999997  55   45 899999999999 9999975

>3u5e_m 60S ribosomal protein L40; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3u5i_m 4b6a_m 4a18_K 4a19_K 4a1b_K 4a1d_K 4adx_5 3izc_p 3izs_p 3iz5_p 3izr_p

Probab=98.95  E-value=7.2e-11  Score=74.80  Aligned_cols=46  Identities=57%  Similarity=0.673  Sum_probs=0.0

Q ss_pred             eeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           38 HSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        38 ~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .+.++..+|  +.+.|++++||.+||++|++.+|+|+++|+|+|+|++
T Consensus         2 ~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~   49 (128)
T 3u5e_m            2 QIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQ   49 (128)
T ss_dssp             ------------------------------------------------
T ss_pred             EEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHhCcChHHEEEEECCEE
Confidence            345555555  5677899999999999999999999999999999998

>1t0y_A Tubulin folding cofactor B; ubiquitin-like, cytoskeleton, microtubule, CESG, structural genomics, protein structure initiative, PSI; NMR {Caenorhabditis elegans} SCOP: d.15.1.1

Probab=98.94  E-value=1.6e-09  Score=68.14  Aligned_cols=47  Identities=15%  Similarity=0.115  Sum_probs=40.3

Q ss_pred             cceeeeeeeecc---eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECe
Q 040204           35 STLHSVRRFRGG---MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWF   81 (97)
Q Consensus        35 sti~l~i~~~~g---~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G   81 (97)
                      +.|.+.++..++   .++.+++++||++||++|++++|+||++|||+|.|
T Consensus         5 ~~v~l~V~~~~~~~~~e~~v~~~~TV~~lK~ki~~~~Gip~~~qrL~~~g   54 (122)
T 1t0y_A            5 EVYDLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFD   54 (122)
T ss_dssp             CEEEEEEEESSCCSCEEEEEETTSBHHHHHHHHHHHHCCCTTTEEEEEEC
T ss_pred             CEEEEEEEECCCCccEEEEeCCCCcHHHHHHHHHHHhCCCHHHeEEEEec
Confidence            356666666554   66888999999999999999999999999999988

>2kj6_A Tubulin folding cofactor B; methods development, NESG, solution PSI-2, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=98.93  E-value=1e-10  Score=71.18  Aligned_cols=42  Identities=17%  Similarity=0.152  Sum_probs=36.1

Q ss_pred             CccccCCCCcceEEEECC---EE----eCCCCCCccceec-ccceeeeee
Q 040204            1 IEDKEEILRDQQRFIFAG---KR----LEDGRTLVDYNIH-GSTLHSVRR   42 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g---~~----L~d~~tL~~y~I~-~sti~l~i~   42 (97)
                      |++++|||+++|||+|+|   +.    ++|+++|++|+|+ +++|+++-+
T Consensus        46 Ie~~~Gip~~~QrLi~~g~~g~~~~~L~~D~~tL~~Y~I~~g~~Ihlvd~   95 (97)
T 2kj6_A           46 LWKKCGTSVNSMALELYDDSGSKVAVLSDDSRPLGFFSPFDGFRLHIIDL   95 (97)
T ss_dssp             HHHHHCCCTTSEEEEEECSSSCBCCCSSGGGSCHHHHCCCSCCEEEEEEC
T ss_pred             HHHHHCcCHHHeEEEEecCCCcccceecCCcCCHHHCCCCCCCEEEEEeC
Confidence            467899999999999987   33    4899999999999 999998753

>3u5c_f 40S ribosomal protein S31; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3u5g_f

Probab=98.92  E-value=1.1e-10  Score=76.22  Aligned_cols=46  Identities=57%  Similarity=0.673  Sum_probs=0.0

Q ss_pred             eeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           38 HSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        38 ~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .+.++..+|  +.+.|++++||.+||++|++.+|+|+++|+|+|+|++
T Consensus         2 qI~VK~l~G~~~~l~V~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~   49 (152)
T 3u5c_f            2 QIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQ   49 (152)
T ss_dssp             ------------------------------------------------
T ss_pred             EEEEEeCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEE
Confidence            355555555  5577899999999999999999999999999999998

>2dzj_A Synaptic glycoprotein SC2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.91  E-value=1.1e-09  Score=65.37  Aligned_cols=47  Identities=15%  Similarity=-0.089  Sum_probs=39.1

Q ss_pred             eeeeeeeecce----ee-eeeccchhHHHHHhhhh-hcCCCCCceEEEEC--eEe
Q 040204           37 LHSVRRFRGGM----QI-FVESSDTIDNVKAKIQD-KKGTPPDQQRQIFW--FVF   83 (97)
Q Consensus        37 i~l~i~~~~g~----~i-~v~~~~TV~~lK~~I~~-~~gip~~~q~Lif~--G~~   83 (97)
                      +.+.++...|.    .+ .|++++||.+||++|++ ++|+||++|+|+|.  |++
T Consensus        11 M~I~Vk~~~g~~~~~~l~~v~~~~TV~~lK~~I~~~~~~i~~~~QrL~~~~~Gk~   65 (88)
T 2dzj_A           11 YEVEILDAKTREKLCFLDKVEPHATIAEIKNLFTKTHPQWYPARQSLRLDPKGKS   65 (88)
T ss_dssp             EEEEEEESSSCCCCEEEEEECSSCBHHHHHHHHHHHCSSSCTTTCCEESSTTSCC
T ss_pred             EEEEEECCCCCEEeeEEeEcCCCCcHHHHHHHHHHHhcCCChHHeEEEecCCCcC
Confidence            55666666542    36 89999999999999999 48999999999987  888

>4efo_A Serine/threonine-protein kinase TBK1; ubiquitin like domain, transferase; 1.77A {Homo sapiens}

Probab=98.90  E-value=1.7e-09  Score=65.42  Aligned_cols=37  Identities=14%  Similarity=0.088  Sum_probs=35.0

Q ss_pred             eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        47 ~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      ..+.+.+++||..+|++|++++|||+++|+|+|+|++
T Consensus        26 h~v~I~~~etv~~~ke~V~eqTgIp~~~Q~LL~eg~~   62 (94)
T 4efo_A           26 HKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRR   62 (94)
T ss_dssp             EEEEEETTCBHHHHHHHHHHHHCCCGGGEEEEETTEE
T ss_pred             EEEEeccchHHHHHHHHHHHHhCCCHHHHHHHhCCCc
Confidence            4578899999999999999999999999999999988

>1x1m_A Ubiquitin-like protein SB132; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.15.1.1

Probab=98.90  E-value=2.8e-09  Score=65.46  Aligned_cols=50  Identities=16%  Similarity=0.046  Sum_probs=40.8

Q ss_pred             ccceeeeeeeecc-----eeee--------eecc-chhHHHHHhhhhhc--CCCCCc-eEEEECeEe
Q 040204           34 GSTLHSVRRFRGG-----MQIF--------VESS-DTIDNVKAKIQDKK--GTPPDQ-QRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g-----~~i~--------v~~~-~TV~~lK~~I~~~~--gip~~~-q~Lif~G~~   83 (97)
                      .+.+.+.++..++     +.+.        |+++ +||.+||++|++.+  |+|+++ |+|+|+|+.
T Consensus        10 ~~~~~i~Vk~~~~~~~~~~~l~v~~~~~~~v~~~~~TV~~LK~~i~~~~~~gip~~~~qrLi~~Gk~   76 (107)
T 1x1m_A           10 LSDWHLAVKLADQPLAPKSILQLPETELGEYSLGGYSISFLKQLIAGKLQESVPDPELIDLIYCGRK   76 (107)
T ss_dssp             CCSCCEEEEETTCTTSCCEEECCCCCSSCSSCCCCCBHHHHHHHHHHHCTTTCCCSSSEEEEETTEE
T ss_pred             CCceEEEEEeCCCCCccEEEEEecCccccccCcccCCHHHHHHHHHHHhccCCChhhcEEEEECCeE
Confidence            4567777776554     3455        3454 99999999999999  999999 999999998

>2daf_A FLJ35834 protein; hypothetical protein FLJ35834, ubiquitin-like domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.89  E-value=3e-09  Score=66.72  Aligned_cols=55  Identities=13%  Similarity=0.043  Sum_probs=44.2

Q ss_pred             ccceeeeee-eecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           34 GSTLHSVRR-FRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~-~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      ++++.+.+. .+++  +.+.++++.||.+||+.+.+..++|+++|+|+|+||.  |.-+|
T Consensus        13 ~~~itvkv~l~~~~~k~tv~v~~d~TV~dLKe~ls~~~~iP~e~qrLIy~GKiLKD~eTL   72 (118)
T 2daf_A           13 DSLATVKVVLIPVGQEIVIPFKVDTILKYLKDHFSHLLGIPHSVLQIRYSGKILKNNETL   72 (118)
T ss_dssp             SSCEEEEEEETTTCCEEEEEECSSSCSHHHHHHHHHHHTCCTTTEEEEETTEEECSSCCH
T ss_pred             CccEEEEEEEcCCCcEEEEEeCCCCcHHHHHHHHHhhhCCChHHEEEEECCeEcCCcchH
Confidence            555666654 2233  6678899999999999999999999999999999998  54444

>2io1_B Small ubiquitin-related modifier 3 precursor; SUMO, SENP, ULP, complex, protein binding, hydrolase; 2.60A {Homo sapiens} SCOP: d.15.1.1

Probab=98.89  E-value=1.2e-09  Score=65.98  Aligned_cols=46  Identities=20%  Similarity=0.403  Sum_probs=43.3

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecce
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGM   47 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~   47 (97)
                      ++++|+|+++|+|+|+|++|.++.|+++|++. +++|+++.+..+|.
T Consensus        38 ~~~~gi~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~~~GG~   84 (94)
T 2io1_B           38 CERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGGV   84 (94)
T ss_dssp             HHHHTCCGGGEEEEETTEECCTTCCTTTTTCCTTCEEEEEECCEESC
T ss_pred             HHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEeccCCC
Confidence            46789999999999999999999999999999 99999999998884

>1v2y_A 3300001G02RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=98.85  E-value=1.1e-10  Score=72.10  Aligned_cols=37  Identities=22%  Similarity=0.412  Sum_probs=33.0

Q ss_pred             cceEEEECCEEeC-CCCCCccceec-ccceeeeeeeecc
Q 040204           10 DQQRFIFAGKRLE-DGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus        10 ~~Q~L~~~g~~L~-d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      .+|+|+|+|+.|. |+.||++|||. +++||++.++.+.
T Consensus        61 ~q~~Li~~Gk~L~dD~~tL~dygI~~g~~l~lv~~lr~~   99 (105)
T 1v2y_A           61 RTYHLTSAGEKLTEDRKKLRDYGIRNRDEVSFIKKLGQK   99 (105)
T ss_dssp             TTEEEESSSCEECCSSSBHHHHTCCSSEEEEEEECSCSC
T ss_pred             eeEEEEeCCcCccCCcCCHHHcCCCCCCEEEEEehhccC
Confidence            4679999999996 66999999999 9999999988765

>2dzm_A FAS-associated factor 1; ubiquitin-like domain, HFAF1, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.85  E-value=1.6e-10  Score=70.71  Aligned_cols=44  Identities=16%  Similarity=0.166  Sum_probs=38.7

Q ss_pred             CccccCCCCcceEEEE--CCEEeCCCCCCccceec-ccceeeeeeeec
Q 040204            1 IEDKEEILRDQQRFIF--AGKRLEDGRTLVDYNIH-GSTLHSVRRFRG   45 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~--~g~~L~d~~tL~~y~I~-~sti~l~i~~~~   45 (97)
                      |++++|||+++|+|+|  +|+ |+|+.+|++|+|+ +++++|+.....
T Consensus        38 I~~~tgIpp~~QkLi~~~~gk-L~D~~tLs~~~I~~gstL~lvl~~~~   84 (100)
T 2dzm_A           38 LENELQIPVSKMLLKGWKTGD-VEDSTVLKSLHLPKNNSLYVLTPDLP   84 (100)
T ss_dssp             HHHHHCCCTTTCCEECCSSSC-CCTTSBHHHHCCCSEEEEEECCSSSC
T ss_pred             HHHHHCCChhHeEEEccCCCC-CCCcCCHHHcCCCCCCEEEEEecCCC
Confidence            4678999999999997  676 9999999999999 999999886544

>1v6e_A Cytoskeleton-associated protein 1; tubulin-specific chaperone B, tubulin folding cofactor B, microtubule, ubiquitin-like fold, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=98.84  E-value=4.1e-10  Score=67.85  Aligned_cols=42  Identities=17%  Similarity=0.196  Sum_probs=36.1

Q ss_pred             CccccCCCCcceEEEECC---EE----eCCCCCCccceec-ccceeeeee
Q 040204            1 IEDKEEILRDQQRFIFAG---KR----LEDGRTLVDYNIH-GSTLHSVRR   42 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g---~~----L~d~~tL~~y~I~-~sti~l~i~   42 (97)
                      |++++|||+++|+|+|+|   +.    ++|+++|++|||. +++||++-.
T Consensus        38 i~~~~gip~~~qrL~~~~~~g~~~~~l~~D~~tL~~y~i~~g~~l~v~d~   87 (95)
T 1v6e_A           38 LELVVGSPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIHVIDH   87 (95)
T ss_dssp             HHHHTCSCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCEEEEBCC
T ss_pred             HHHHHCCCHHHeEEEEeCCCCccccccCCCcCCHhHCCCCCCCEEEEEEC
Confidence            467899999999999976   54    5899999999999 999998753

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B*

Probab=98.83  E-value=5.4e-09  Score=75.03  Aligned_cols=55  Identities=47%  Similarity=0.573  Sum_probs=46.1

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      ...+.+.++..+|  +.+.|++++||++||++|++++|+|+++|+|+|+|++  |..+|
T Consensus       231 ~~~MqI~VKtl~Gk~~~leV~~s~TV~dLK~kI~~~~GIp~~~QRLi~~Gk~L~D~~TL  289 (307)
T 3ai5_A          231 TGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL  289 (307)
T ss_dssp             CCCEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBT
T ss_pred             CCeEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEeCCeecCCCCCH
Confidence            3467777877655  5677899999999999999999999999999999998  44444

>2dzj_A Synaptic glycoprotein SC2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.82  E-value=4.8e-10  Score=66.95  Aligned_cols=38  Identities=21%  Similarity=0.249  Sum_probs=34.0

Q ss_pred             cc-ccCCCCcceEEEEC--CEEeCCCCCCccceec-ccceee
Q 040204            2 ED-KEEILRDQQRFIFA--GKRLEDGRTLVDYNIH-GSTLHS   39 (97)
Q Consensus         2 ~~-~~gip~~~Q~L~~~--g~~L~d~~tL~~y~I~-~sti~l   39 (97)
                      ++ ++|+|+++|+|+|.  |+.|+|+.+|++|+|. +++|++
T Consensus        44 ~~~~~~i~~~~QrL~~~~~Gk~L~D~~tL~~y~i~~~stl~~   85 (88)
T 2dzj_A           44 TKTHPQWYPARQSLRLDPKGKSLKDEDVLQKLPVGTTATLYF   85 (88)
T ss_dssp             HHHCSSSCTTTCCEESSTTSCCCCTTCBTTTSSCCSEEEEEE
T ss_pred             HHHhcCCChHHeEEEecCCCcCcCCCCCHHHcCCCCCCEEEE
Confidence            44 58999999999986  9999999999999999 998765

>1wia_A Hypothetical ubiquitin-like protein (riken cDNA 2010008E23); 'structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=98.82  E-value=7e-09  Score=62.12  Aligned_cols=47  Identities=17%  Similarity=0.184  Sum_probs=40.8

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      ...+.+.++..+|  +.+.|++++||.+||++|++.+   +++|+|+|+|+.
T Consensus         5 ~~~m~i~Vk~~~g~~~~~~v~~~~TV~~LK~~i~~~~---~~~qrLi~~Gk~   53 (95)
T 1wia_A            5 SSGINVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQ---ESQMKLIYQGRL   53 (95)
T ss_dssp             CCSEEEEEEETTTEEEEEEECSSSBHHHHHHHHSSST---TTTCEEEETTEE
T ss_pred             CCeEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHhhC---cCcEEEEECCEE
Confidence            4567888887655  5678899999999999999988   899999999998

>1wia_A Hypothetical ubiquitin-like protein (riken cDNA 2010008E23); 'structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=98.82  E-value=1.8e-09  Score=64.79  Aligned_cols=38  Identities=34%  Similarity=0.567  Sum_probs=34.7

Q ss_pred             CcceEEEECCEEeCCC-CCCccceec-ccceeeeeeeecc
Q 040204            9 RDQQRFIFAGKRLEDG-RTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         9 ~~~Q~L~~~g~~L~d~-~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      +++|+|+|+|+.|+|+ ++|++|+|. +++||++.+....
T Consensus        42 ~~~qrLi~~Gk~L~D~~~tL~~y~i~~g~~i~l~~~~~~~   81 (95)
T 1wia_A           42 ESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRSPPGA   81 (95)
T ss_dssp             TTTCEEEETTEECCCSSCBTTTTTCCTTEEEEEECCCCCC
T ss_pred             cCcEEEEECCEEccCCcCCHHHcCCCCCCEEEEEECCCCC
Confidence            7899999999999999 999999999 9999999876543

>1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair, proteasome-mediated degradation, protein- protein interaction, replication; NMR {Homo sapiens} SCOP: a.5.2.1 a.5.2.1 a.189.1.1 d.15.1.1 PDB: 1qze_A 1tp4_A

Probab=98.81  E-value=3.5e-09  Score=77.60  Aligned_cols=55  Identities=18%  Similarity=0.192  Sum_probs=45.6

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhh---hcCCCCCceEEEECeEe--CCCcc
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQD---KKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~---~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      ...+.+.++...|  +.|.|++++||.+||.+|++   ++|+|+++|+|+|+||.  |..+|
T Consensus         5 ~~~M~I~VKtl~Gk~~~leV~~~~TV~~LK~~I~~~~~~~gip~~~QrLiy~GK~L~D~~tL   66 (368)
T 1oqy_A            5 SSAVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPI   66 (368)
T ss_dssp             -CCCCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSSEECSSSBT
T ss_pred             CceEEEEEEeCCCCEEEEEeCCCChHHHHHHHHHHHhCcCCCChhheEEEECCeecCCcCCH
Confidence            3567888888765  56778999999999999999   68899999999999998  44444

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B*

Probab=98.80  E-value=1.5e-09  Score=77.94  Aligned_cols=43  Identities=72%  Similarity=0.999  Sum_probs=38.6

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|+|. +++|+|+++.
T Consensus       263 I~~~~GIp~~~QRLi~~Gk~L~D~~TLsdygI~~gstL~LvlRL  306 (307)
T 3ai5_A          263 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  306 (307)
T ss_dssp             HHHHHCCCGGGCEEEETTEECCTTSBTGGGTCCTTCEEEEEC--
T ss_pred             HHHHHCcChHHEEEEeCCeecCCCCCHHHcCCCCCCEEEEEEeC
Confidence            456789999999999999999999999999999 9999999875

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9

Probab=98.76  E-value=8.4e-10  Score=74.40  Aligned_cols=43  Identities=14%  Similarity=0.101  Sum_probs=0.4

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceecccceeeeeeeecce
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHGSTLHSVRRFRGGM   47 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~~sti~l~i~~~~g~   47 (97)
                      |++.+|||+++|+|+|+|++|+|+.+|+    .+++|||++++.+|.
T Consensus        30 I~~keGIP~~qQRLIf~GK~LeD~~TLs----~~STLhLvlRLrGG~   72 (189)
T 2xzm_9           30 ISQDMGFEIDMMTLVNNGFIAPNTELVT----DDVTYYLSLKLLGGK   72 (189)
T ss_dssp             ----------------------------------------------C
T ss_pred             HHHHhCcChhHEEEEecCeECCCCCccc----CCCEEEEEEecCCCc
Confidence            5778999999999999999999999998    679999999998874

>1t0y_A Tubulin folding cofactor B; ubiquitin-like, cytoskeleton, microtubule, CESG, structural genomics, protein structure initiative, PSI; NMR {Caenorhabditis elegans} SCOP: d.15.1.1

Probab=98.76  E-value=2e-09  Score=67.69  Aligned_cols=43  Identities=19%  Similarity=0.266  Sum_probs=36.7

Q ss_pred             CccccCCCCcceEEEECC---E---E-eCCCCCCccceec-ccceeeeeee
Q 040204            1 IEDKEEILRDQQRFIFAG---K---R-LEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g---~---~-L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      |++++|||+++|||+|.|   +   . ++|+++|++|||. +++|||+-..
T Consensus        37 i~~~~Gip~~~qrL~~~g~~~~~~~~l~~D~~tL~~y~i~~g~~ihvvd~~   87 (122)
T 1t0y_A           37 LELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHAVDVT   87 (122)
T ss_dssp             HHHHHCCCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEEEEEECT
T ss_pred             HHHHhCCCHHHeEEEEecCCCccccccCCCcCCHHHCCCCCCCEEEEEeCC
Confidence            456799999999999976   4   3 4899999999999 9999998643

>2io0_B Small ubiquitin-related modifier 2 precursor; SUMO, SENP, ULP, complex, protein binding, hydrolase; 2.30A {Homo sapiens} SCOP: d.15.1.1

Probab=98.76  E-value=6.9e-09  Score=62.36  Aligned_cols=46  Identities=20%  Similarity=0.403  Sum_probs=43.1

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecce
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGM   47 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~   47 (97)
                      +++.|+|+++++|+|+|++|.++.|.++|++. +++|+++....+|.
T Consensus        36 ~~~~gi~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~q~gg~   82 (91)
T 2io0_B           36 CERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGGV   82 (91)
T ss_dssp             HHHTTCCSTTEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCCCCC
T ss_pred             HHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEeccCCc
Confidence            46789999999999999999999999999999 99999999988884

>1wf9_A NPL4 family protein; beta-grAsp fold like domain, hypothetical protein, structural genomics, NPPSFA; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=98.75  E-value=4.4e-09  Score=64.70  Aligned_cols=48  Identities=25%  Similarity=0.151  Sum_probs=42.2

Q ss_pred             cceeeeeeeecc-eeeeee-ccchhHHHHHhhhhhcCCCCCceEEEECeE
Q 040204           35 STLHSVRRFRGG-MQIFVE-SSDTIDNVKAKIQDKKGTPPDQQRQIFWFV   82 (97)
Q Consensus        35 sti~l~i~~~~g-~~i~v~-~~~TV~~lK~~I~~~~gip~~~q~Lif~G~   82 (97)
                      +.+.+.++..+| ..|.|+ +++||.+||++|++++|+|+++|+|+|.|+
T Consensus         6 ~~M~irvrs~~G~~~v~v~~~~~Tv~~LK~kI~~~~gip~~~QrL~~~~~   55 (107)
T 1wf9_A            6 SGTMLRVRSRDGLERVSVDGPHITVSQLKTLIQDQLQIPIHNQTLSTNRN   55 (107)
T ss_dssp             CCEEEEEECSSCEEEEEECCTTSBHHHHHHHHHHHSCCCTTTCCCBSSGG
T ss_pred             CeEEEEEECCCCCEEEEECCCCCcHHHHHHHHHHHhCcCcccCEEEECCc
Confidence            456777877777 458888 999999999999999999999999999988

>1v86_A DNA segment, CHR 7, wayne state university 128, expressed; ubiquitin fold, structural genomics, D7WSU128E protein; HET: DNA; NMR {Mus musculus} SCOP: d.15.1.1

Probab=98.75  E-value=3e-10  Score=68.57  Aligned_cols=42  Identities=17%  Similarity=0.295  Sum_probs=36.9

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      |++.+|+|+++|+|+|.|+.| |+.+|++|+|. +++|+|+.+.
T Consensus        46 I~~~tgip~~~QrL~~~Gk~L-dd~tL~~~~i~~g~~i~lv~~~   88 (95)
T 1v86_A           46 IHSITGLPPAMQKVMYKGLVP-EDKTLREIKVTSGAKIMVVGST   88 (95)
T ss_dssp             HHHHHCSCSTTCCCBSSSBCC-SSSBHHHHCCCTTEEEEECCSS
T ss_pred             HHHHHCcCHHHeEEEECCeeC-CcCcHHHCCCCCCCEEEEEecc
Confidence            456789999999999999999 45599999999 9999998754

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster}

Probab=98.73  E-value=6.6e-09  Score=74.85  Aligned_cols=49  Identities=14%  Similarity=0.282  Sum_probs=42.5

Q ss_pred             cceeeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEE---ECeEe
Q 040204           35 STLHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQI---FWFVF   83 (97)
Q Consensus        35 sti~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Li---f~G~~   83 (97)
                      .++.+.++..|. +.|.|++++||.+||++|++++|+||++|+|+   |+|++
T Consensus         4 ~~i~i~Vk~~g~~~~v~v~~~~Tv~~lK~~I~~~tgVpp~~QkLi~~k~~Gk~   56 (320)
T 3shq_A            4 KEVVVIVKWSGKEYPVDLTDQDTVEVLRHEIFRKTQVRPERQKLLNLKYKGKT   56 (320)
T ss_dssp             CEEEEEEEETTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGCEETTCBSSSSB
T ss_pred             ceEEEEEEECCEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEeecccCCcc
Confidence            456777776444 56888999999999999999999999999999   89988

>2d07_B Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Homo sapiens} SCOP: d.15.1.1 PDB: 2rpq_A 2awt_A 2io3_B 2iyd_B 1u4a_A 2k1f_A

Probab=98.72  E-value=8.2e-09  Score=62.15  Aligned_cols=45  Identities=20%  Similarity=0.401  Sum_probs=39.8

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      +++.|+|+++++|+|.|++|.++.|.++|++. +++|+++.+..||
T Consensus        48 ~~~~gi~~~~~rf~fdG~~l~~~~Tp~dl~medgD~Idv~~~q~GG   93 (93)
T 2d07_B           48 CERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGG   93 (93)
T ss_dssp             HHHHTCCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECC---
T ss_pred             HHHhCCCccceEEEECCEEcCCCCCHHHcCCCCCCEEEEEeeccCC
Confidence            46789999999999999999999999999999 9999999987765

>1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair, proteasome-mediated degradation, protein- protein interaction, replication; NMR {Homo sapiens} SCOP: a.5.2.1 a.5.2.1 a.189.1.1 d.15.1.1 PDB: 1qze_A 1tp4_A

Probab=98.72  E-value=3.8e-09  Score=77.43  Aligned_cols=43  Identities=28%  Similarity=0.479  Sum_probs=37.9

Q ss_pred             ccCCCCcceEEEECCEEeCCCCCCccceec-ccce-eeeeeeecc
Q 040204            4 KEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTL-HSVRRFRGG   46 (97)
Q Consensus         4 ~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti-~l~i~~~~g   46 (97)
                      ++|||+++|+|+|+||.|+|+++|++|+|+ +++| +++.+..++
T Consensus        43 ~~gip~~~QrLiy~GK~L~D~~tL~dygI~~gstIv~lv~k~~~~   87 (368)
T 1oqy_A           43 RDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTKTKAG   87 (368)
T ss_dssp             SSSCCSTEEEEESSSSEECSSSBTTTTCCCTTSCEEEEEECCCSS
T ss_pred             cCCCChhheEEEECCeecCCcCCHHHcCCCCCCEEEEEEecCCCC
Confidence            578999999999999999999999999999 9998 666665544

>2eke_C Ubiquitin-like protein SMT3; UBC9, SUMO binding motif, SBM, ligase/protein binding complex; 1.90A {Saccharomyces cerevisiae} SCOP: d.15.1.1

Probab=98.64  E-value=2e-08  Score=62.01  Aligned_cols=45  Identities=22%  Similarity=0.439  Sum_probs=39.7

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      +++.|+++++++|+|+|++|.++.|.++|++. +++|+++.+..||
T Consensus        61 ~ek~gi~~~~~rF~FdG~rl~~~~Tp~dl~medgD~Idv~~~q~GG  106 (106)
T 2eke_C           61 AKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGG  106 (106)
T ss_dssp             HHHHTCCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECC---
T ss_pred             HHHhCCCcccEEEEECCeEcCCCCCHHHcCCCCCCEEEEEeecccC
Confidence            46789999999999999999999999999999 9999999987765

>1wm3_A Ubiquitin-like protein SMT3B; ubiquitin fold, half-open barrel, two helices, protein transport; 1.20A {Homo sapiens} SCOP: d.15.1.1 PDB: 1wm2_A 3uin_B 3uio_B 2ckh_B

Probab=98.63  E-value=2.1e-08  Score=57.54  Aligned_cols=40  Identities=18%  Similarity=0.351  Sum_probs=36.9

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeee
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVR   41 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i   41 (97)
                      +++.|+|+++++|+|+|++|.++.|.++|++. +++|+++.
T Consensus        32 ~~~~gi~~~~~rf~fdG~~l~~~~Tp~~l~medgD~Idv~~   72 (72)
T 1wm3_A           32 CERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQ   72 (72)
T ss_dssp             HHHHTCCTTTCEEEETTEECCTTCCTTTTTCCTTEEEEEEC
T ss_pred             HHHhCCCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEEC
Confidence            46789999999999999999999999999999 99999863

>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative, hydrolase; NMR {Mus musculus}

Probab=98.61  E-value=3e-08  Score=58.48  Aligned_cols=44  Identities=18%  Similarity=0.360  Sum_probs=37.8

Q ss_pred             eeeeeeecce-eee-eeccchhHHHHHhhhhhcCCCCCceEEEECe
Q 040204           38 HSVRRFRGGM-QIF-VESSDTIDNVKAKIQDKKGTPPDQQRQIFWF   81 (97)
Q Consensus        38 ~l~i~~~~g~-~i~-v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G   81 (97)
                      .+.++..+|. .+. +++++||.+||++|++++|+|+++|+|+|++
T Consensus         2 ~i~vr~~~G~~~v~~l~~~~Tv~~Lk~~I~~~~gi~~~~qrL~~~~   47 (86)
T 2kzr_A            2 RVRCKAKGGTHLLQGLSSRTRLRELQGQIAAITGIAPGSQRILVGY   47 (86)
T ss_dssp             CEEEEETTEEEEECSCCTTCBHHHHHHHHHHHTCCCTTTCCCEESS
T ss_pred             EEEEEcCCCCEEeeecCCCCCHHHHHHHHHHHhCCCccceEEEeCC
Confidence            4667777774 366 7899999999999999999999999999985

>1wz0_A Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-like molecule, structural genomics, sentrin2, NPPFSA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=98.52  E-value=1.5e-08  Score=62.31  Aligned_cols=45  Identities=18%  Similarity=0.355  Sum_probs=42.2

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      +++.|+|+++++|+|.|++|.++.|.++|++. +++|+++....||
T Consensus        55 ~ek~gi~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~q~GG  100 (104)
T 1wz0_A           55 CERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTSG  100 (104)
T ss_dssp             HHHHTCCTTTSCEESSSSBCCTTSCTTTTTCCTTEEEEECCCCCCC
T ss_pred             HHHhCCCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEeccCC
Confidence            46789999999999999999999999999999 9999999988877

>2io1_B Small ubiquitin-related modifier 3 precursor; SUMO, SENP, ULP, complex, protein binding, hydrolase; 2.60A {Homo sapiens} SCOP: d.15.1.1

Probab=98.48  E-value=3.2e-07  Score=55.25  Aligned_cols=50  Identities=12%  Similarity=0.066  Sum_probs=42.9

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +..|.+.++...|  +.+.|++++++..|++.++++.|+|+++++++|.|++
T Consensus         5 ~~~i~ikVk~~~g~~i~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~FdG~~   56 (94)
T 2io1_B            5 NDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQP   56 (94)
T ss_dssp             -CEEEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEE
T ss_pred             CCeEEEEEECCCCCEEEEEECCCCHHHHHHHHHHHHhCCCcccEEEEECCEE
Confidence            3456677776566  5577899999999999999999999999999999999

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster}

Probab=98.48  E-value=1.4e-08  Score=73.13  Aligned_cols=45  Identities=18%  Similarity=0.305  Sum_probs=39.3

Q ss_pred             CccccCCCCcceEEE---ECCEEeCCCCCCccceec-ccceeeeeeeec
Q 040204            1 IEDKEEILRDQQRFI---FAGKRLEDGRTLVDYNIH-GSTLHSVRRFRG   45 (97)
Q Consensus         1 i~~~~gip~~~Q~L~---~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~   45 (97)
                      |++++|||+++|+|+   |+|+.|+|+.+|++|+|+ |++|+|+.+...
T Consensus        34 I~~~tgVpp~~QkLi~~k~~Gk~l~D~~~L~~~~ik~g~~l~L~gs~~~   82 (320)
T 3shq_A           34 IFRKTQVRPERQKLLNLKYKGKTAADNVKISALELKPNFKLMMVGSTEA   82 (320)
T ss_dssp             HHHHHCCCGGGCEETTCBSSSSBCCTTSBTTSSCCC--CEEEEECCCC-
T ss_pred             HHHHHCcCHHHeEEeecccCCcccCccccHHHcCCCCCCEEEEEccchh
Confidence            467899999999999   899999999999999999 999999876544

>3a4r_A Nfatc2-interacting protein; ubiquitin fold, coiled coil, cytoplasm, methylation, nucleus, transcription; 1.00A {Mus musculus} PDB: 3a4s_C 3rd2_A

Probab=98.46  E-value=6.1e-08  Score=56.60  Aligned_cols=39  Identities=18%  Similarity=0.350  Sum_probs=36.4

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeee
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSV   40 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~   40 (97)
                      +++.|+|+++++|+|.|++|.++.|.++|++. +++|+++
T Consensus        39 ~~~~gi~~~~~rf~fdG~~l~~~~Tp~~l~medgD~Idv~   78 (79)
T 3a4r_A           39 EEAMGLSGHKLSFFFDGTKLSGKELPADLGLESGDLIEVW   78 (79)
T ss_dssp             HHHHTCTTCCCEEEETTEECCSCCCHHHHTCCTTCEEEEE
T ss_pred             HHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEe
Confidence            46789999999999999999999999999999 9999875

>2k8h_A Small ubiquitin protein; SUMO, post-translational modifier, signaling protein; NMR {Trypanosoma brucei}

Probab=98.43  E-value=2e-08  Score=62.38  Aligned_cols=47  Identities=21%  Similarity=0.497  Sum_probs=42.6

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeeccee
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGMQ   48 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~~   48 (97)
                      +++.|+|+++++|+|.|++|.++.|.++|++. +++|+++....+|.+
T Consensus        57 ~ek~gi~~~~~rfiFdG~~L~~~~Tp~dl~mEDgD~Idv~~~q~Gg~~  104 (110)
T 2k8h_A           57 CKKQGISRNSVRFLFDGTPIDETKTPEELGMEDDDVIDAMVEQTGGLE  104 (110)
T ss_dssp             HHHHTCCSSSCEEESSSCBCCSSSHHHHHHCSSEEEEEEECCCCCC--
T ss_pred             HHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEcccCccc
Confidence            46789999999999999999999999999999 999999999988853

>1wf9_A NPL4 family protein; beta-grAsp fold like domain, hypothetical protein, structural genomics, NPPSFA; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=98.43  E-value=1.2e-08  Score=62.77  Aligned_cols=42  Identities=17%  Similarity=0.176  Sum_probs=37.0

Q ss_pred             CccccCCCCcceEEEECCE-----------E----eCCCCCCccceec-ccceeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGK-----------R----LEDGRTLVDYNIH-GSTLHSVRR   42 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~-----------~----L~d~~tL~~y~I~-~sti~l~i~   42 (97)
                      |++++|||+++|+|+|+|+           .    ++|+++|++|||. +++|||...
T Consensus        37 I~~~~gip~~~QrL~~~~~~~~~k~~~~~~~l~~~l~d~~tL~~~gi~~G~~L~l~~~   94 (107)
T 1wf9_A           37 IQDQLQIPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLAHGSMVYLAYE   94 (107)
T ss_dssp             HHHHSCCCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTCCCTTCEEECCCS
T ss_pred             HHHHhCcCcccCEEEECCccccccCccccccccccCCCCCCHHHCCCCCCCEEEEEeC
Confidence            4567899999999999888           4    5899999999999 999998765

>2io0_B Small ubiquitin-related modifier 2 precursor; SUMO, SENP, ULP, complex, protein binding, hydrolase; 2.30A {Homo sapiens} SCOP: d.15.1.1

Probab=98.35  E-value=1.1e-06  Score=52.60  Aligned_cols=49  Identities=12%  Similarity=0.064  Sum_probs=42.6

Q ss_pred             cceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           35 STLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        35 sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      ..|.+.++..+|  +.+.|++++++..|++..+++.|+|+++++++|.|++
T Consensus         4 ~~i~ikVk~~~g~~v~~~vk~~t~l~kl~~~y~~~~gi~~~~~rf~FdG~~   54 (91)
T 2io0_B            4 DHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQP   54 (91)
T ss_dssp             CEEEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHTTCCSTTEEEEETTEE
T ss_pred             CeEEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEE
Confidence            456677776665  5577799999999999999999999999999999999

>1wm3_A Ubiquitin-like protein SMT3B; ubiquitin fold, half-open barrel, two helices, protein transport; 1.20A {Homo sapiens} SCOP: d.15.1.1 PDB: 1wm2_A 3uin_B 3uio_B 2ckh_B

Probab=98.34  E-value=1e-06  Score=50.37  Aligned_cols=47  Identities=13%  Similarity=0.065  Sum_probs=40.1

Q ss_pred             eeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           37 LHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        37 i~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      |.+.++...|  ..+.|++++++..|++..+++.|+|+++++++|.|++
T Consensus         2 i~lkV~~~~g~~v~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~~   50 (72)
T 1wm3_A            2 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQP   50 (72)
T ss_dssp             EEEEEECTTSCEEEEEECTTSCTHHHHHHHHHHHTCCTTTCEEEETTEE
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcceEEEEECCEE
Confidence            3455555555  5577799999999999999999999999999999999

>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative, hydrolase; NMR {Mus musculus}

Probab=98.30  E-value=9e-08  Score=56.41  Aligned_cols=42  Identities=26%  Similarity=0.271  Sum_probs=35.7

Q ss_pred             CccccCCCCcceEEEEC--CEEeC---CCCCCccceec-ccceeeeee
Q 040204            1 IEDKEEILRDQQRFIFA--GKRLE---DGRTLVDYNIH-GSTLHSVRR   42 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~--g~~L~---d~~tL~~y~I~-~sti~l~i~   42 (97)
                      |++++|||+++|+|+|+  +++|+   |+.+|++|||. |++|++...
T Consensus        30 I~~~~gi~~~~qrL~~~~p~k~l~l~~~~~tL~~~gl~~g~~l~v~~~   77 (86)
T 2kzr_A           30 IAAITGIAPGSQRILVGYPPECLDLSDRDITLGDLPIQSGDMLIVEED   77 (86)
T ss_dssp             HHHHTCCCTTTCCCEESSCCCCCCCCCSSCBTTTSSCCTTCEEECCCC
T ss_pred             HHHHhCCCccceEEEeCCCCcccccCCCCCCHHHcCCCCCCEEEEEeC
Confidence            45678999999999996  47774   68999999999 999988754

>3a4r_A Nfatc2-interacting protein; ubiquitin fold, coiled coil, cytoplasm, methylation, nucleus, transcription; 1.00A {Mus musculus} PDB: 3a4s_C 3rd2_A

Probab=98.23  E-value=3.1e-06  Score=49.19  Aligned_cols=50  Identities=8%  Similarity=0.044  Sum_probs=43.2

Q ss_pred             ccceeeeeeeecc---eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG---MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g---~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +..|.+.++..+|   +.+.|++++++..|+...+++.|+++++++++|.|++
T Consensus         5 ~~~i~ikV~~~~g~~~i~~~i~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~~   57 (79)
T 3a4r_A            5 SQELRLRVQGKEKHQMLEISLSPDSPLKVLMSHYEEAMGLSGHKLSFFFDGTK   57 (79)
T ss_dssp             CCCEEEEEECSSTTCEEEEEECTTSCHHHHHHHHHHHHTCTTCCCEEEETTEE
T ss_pred             CCEEEEEEEeCCCCEEEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEE
Confidence            4467777776655   4577799999999999999999999999999999999

>2d07_B Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Homo sapiens} SCOP: d.15.1.1 PDB: 2rpq_A 2awt_A 2io3_B 2iyd_B 1u4a_A 2k1f_A

Probab=98.17  E-value=4.2e-06  Score=50.11  Aligned_cols=50  Identities=12%  Similarity=0.066  Sum_probs=43.3

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +..|.+.++...|  +.+.|++++++..|+...+++.|+++++++++|.|++
T Consensus        15 ~~~i~ikV~~~~g~~i~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~~   66 (93)
T 2d07_B           15 NDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQP   66 (93)
T ss_dssp             CCEEEEEEECTTSCEEEEEEETTSCHHHHHHHHHHHHTCCGGGEEEEETTEE
T ss_pred             CCeEEEEEECCCCCEEEEEEccCCHHHHHHHHHHHHhCCCccceEEEECCEE
Confidence            4566777766566  5577799999999999999999999999999999999

>2k8h_A Small ubiquitin protein; SUMO, post-translational modifier, signaling protein; NMR {Trypanosoma brucei}

Probab=98.13  E-value=3.9e-06  Score=51.92  Aligned_cols=50  Identities=14%  Similarity=0.084  Sum_probs=44.4

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +..|.+.++...|  +.+.|++++++..|+...+++.|+|+++++++|.|++
T Consensus        24 ~~~I~IkVk~~~g~~i~fkVk~~t~l~kL~~ay~ek~gi~~~~~rfiFdG~~   75 (110)
T 2k8h_A           24 TALVAVKVVNADGAEMFFRIKSRTALKKLIDTYCKKQGISRNSVRFLFDGTP   75 (110)
T ss_dssp             CCCEEEEEEETTSCCEEEEECTTSSHHHHHHHHHHHHTCCSSSCEEESSSCB
T ss_pred             CCeEEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEE
Confidence            5678888877666  5577899999999999999999999999999999998

>1wjn_A Tubulin-folding protein TBCE; ubiquitin-like domain, progressive motor neuropathy, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=98.11  E-value=6e-06  Score=49.47  Aligned_cols=47  Identities=13%  Similarity=0.042  Sum_probs=38.0

Q ss_pred             cceeeeeeee---cc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECe
Q 040204           35 STLHSVRRFR---GG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWF   81 (97)
Q Consensus        35 sti~l~i~~~---~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G   81 (97)
                      ..+.+.++..   ++  +++.+.++.||.+||.+|+...|+|+..|+|.|.+
T Consensus         8 ~~v~l~I~~~~~~~~~~~e~~l~~~~TV~~LK~~i~~~~gip~~~q~L~~~~   59 (97)
T 1wjn_A            8 QLLTLKIKCSNQPERQILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYES   59 (97)
T ss_dssp             CEEEEEEEESSCSSSCCEEEEEETTSBHHHHHHHHHTTTTCCTTTCEEEEEC
T ss_pred             ccEEEEEEecCCCCCcEEEEECCCCCCHHHHHHHHHHHHCCChhHeEEEEEc
Confidence            4556656542   33  45677999999999999999999999999999984

>1wjn_A Tubulin-folding protein TBCE; ubiquitin-like domain, progressive motor neuropathy, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=98.08  E-value=1.2e-06  Score=52.60  Aligned_cols=43  Identities=14%  Similarity=0.125  Sum_probs=35.2

Q ss_pred             CccccCCCCcceEEEECC-------EEe-CCCCCCccceec-ccceeeeeee
Q 040204            1 IEDKEEILRDQQRFIFAG-------KRL-EDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g-------~~L-~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      |++..|+|+..|+|+|.+       ..| +|.++|++|+|. |++|++..+.
T Consensus        42 i~~~~gip~~~q~L~~~~~~~~~~~~~L~~d~~~L~~y~i~~G~~I~V~d~~   93 (97)
T 1wjn_A           42 LSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCLLVRWSG   93 (97)
T ss_dssp             HHTTTTCCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTCCTTCEEEEECCS
T ss_pred             HHHHHCCChhHeEEEEEcCCCCceeeccCCCcccHhhcCCCCCCEEEEEecC
Confidence            356789999999999962       225 678999999999 9999987743

>3pge_A SUMO-modified proliferating cell nuclear antigen; DNA replication, DNA binding protein; 2.80A {Saccharomyces cerevisiae}

Probab=98.07  E-value=2.4e-06  Score=57.93  Aligned_cols=45  Identities=22%  Similarity=0.439  Sum_probs=41.2

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      +++.|+|+.++|++|.|++|.++.|.+++++. +++|+++....+|
T Consensus        59 ~er~Gi~~~~~RF~FdG~rI~~~~TP~dL~MEdgD~Idv~~~q~gg  104 (200)
T 3pge_A           59 AKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGG  104 (200)
T ss_dssp             HHHHSSCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCSCC
T ss_pred             HHHhCCChhhEEEEECCEEcCCCCCHHHcCCCCCCEEEEEeccCcC
Confidence            46789999999999999999999999999999 9999999876654

>1wz0_A Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-like molecule, structural genomics, sentrin2, NPPFSA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=98.04  E-value=4.7e-06  Score=51.00  Aligned_cols=50  Identities=12%  Similarity=0.066  Sum_probs=43.6

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +..|.+.++...|  +.+.|++++++..|+...+++.|+++++++++|.|++
T Consensus        22 ~~~I~IkVk~~~g~~i~~kVk~~t~l~kL~~~y~ek~gi~~~~~rf~FdG~~   73 (104)
T 1wz0_A           22 NDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQP   73 (104)
T ss_dssp             SCCEEEEEECSSSCEEEEEECTTSCHHHHHHHHHHHHTCCTTTSCEESSSSB
T ss_pred             CCeEEEEEECCCCCEEEEEEcCCChHHHHHHHHHHHhCCCcceEEEEECCEE
Confidence            4567777776666  5577799999999999999999999999999999998

>2eke_C Ubiquitin-like protein SMT3; UBC9, SUMO binding motif, SBM, ligase/protein binding complex; 1.90A {Saccharomyces cerevisiae} SCOP: d.15.1.1

Probab=98.03  E-value=1.1e-05  Score=49.60  Aligned_cols=49  Identities=8%  Similarity=0.134  Sum_probs=42.9

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +..|.+.++. .|  ..+.|++++++..|+...+++.|+++++++++|.|++
T Consensus        29 ~~~I~IkV~~-~g~~i~fkIk~tt~l~kL~~ay~ek~gi~~~~~rF~FdG~r   79 (106)
T 2eke_C           29 ETHINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIR   79 (106)
T ss_dssp             CSEEEEEEEC-SSCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEE
T ss_pred             CCeEEEEEec-CCcEEEEEeCCCCHHHHHHHHHHHHhCCCcccEEEEECCeE
Confidence            4567777777 66  4567799999999999999999999999999999999

>3kyd_D Small ubiquitin-related modifier 1; SUMO, thioester, adenylation, inhibitor, TETR intermediate, ligase, nucleus, phosphoprotein; HET: VMX; 2.61A {Homo sapiens} SCOP: d.15.1.1

Probab=97.98  E-value=6.4e-06  Score=51.37  Aligned_cols=42  Identities=17%  Similarity=0.389  Sum_probs=38.6

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeee
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      +++.|+++++++++|.|++|.++.|.+++++. +++|.++...
T Consensus        71 ~er~Gl~~~~irFlFDG~rI~~~~TP~dL~MEDgD~IdV~~~Q  113 (115)
T 3kyd_D           71 CQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQ  113 (115)
T ss_dssp             HHHHTCCTTSEEEEETTEECCTTCCTTTTTCCTTCEEEEEECC
T ss_pred             HHHhCCChhhEEEEECCeECCCCCCHHHcCCCCCCEEEEEeec
Confidence            45689999999999999999999999999999 9999998754

>3tix_A Ubiquitin-like protein SMT3, RNA-induced transcri silencing complex protein TAS3; PIN, rossmann fold, SPOC, alpha-helical hairpin, heterochrom silencing, RITS, RNAI, argonaute; 2.90A {Saccharomyces cerevisiae}

Probab=97.88  E-value=4.9e-06  Score=56.24  Aligned_cols=46  Identities=17%  Similarity=0.383  Sum_probs=43.0

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecce
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGM   47 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~   47 (97)
                      +++.|+|+.+++++|.|++|.++.|.+++++. +++|+++....||.
T Consensus        87 cERqGL~~~sIRFLFDGqRI~~ddTPeDLdMEDGDtIDV~leQ~GG~  133 (207)
T 3tix_A           87 AKRQGKEMDSLTFLYDGIEIQADQTPEDLDMEDNDIIEAHREQIGGL  133 (207)
T ss_dssp             HHHTTCCGGGSCEEETTEECCSSCCTTTTTCCTTEEEEECCCCCTTG
T ss_pred             HHHhCCCcccEEEEECCeecCCCCCHHHcCCCCCCEEEEEEeccCCC
Confidence            45789999999999999999999999999999 99999999998883

>3v7o_A Minor nucleoprotein VP30; ssgcid, seattle structural genomics center for infectious disease, SMT, transcription; 2.25A {Reston ebolavirus}

Probab=97.73  E-value=4.3e-06  Score=57.21  Aligned_cols=49  Identities=20%  Similarity=0.426  Sum_probs=2.8

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecceeee
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGMQIF   50 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~~i~   50 (97)
                      +++.|+|++++|++|+|+++.++.|.+++++. |++|+++....||..+.
T Consensus        51 cERqGLs~~siRFLFDGqRI~dddTPadL~MEDGDtIDV~leQ~GG~~~~  100 (227)
T 3v7o_A           51 AKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGLTLA  100 (227)
T ss_dssp             ---------------------------------------------CCCHH
T ss_pred             HHHhCCCccceEEEECCEecCCCCCHHHcCCCCCCEEEEEecccCCchHh
Confidence            56789999999999999999999999999999 99999999999986443

>3kyd_D Small ubiquitin-related modifier 1; SUMO, thioester, adenylation, inhibitor, TETR intermediate, ligase, nucleus, phosphoprotein; HET: VMX; 2.61A {Homo sapiens} SCOP: d.15.1.1

Probab=97.40  E-value=0.0004  Score=43.17  Aligned_cols=54  Identities=13%  Similarity=0.134  Sum_probs=43.3

Q ss_pred             ceec--ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           30 YNIH--GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        30 y~I~--~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      -+.+  +..|.+.+...+|  +.+.|++++++..|+...+++.|+++++++++|.|+.
T Consensus        32 ~~~k~~~~~I~LKV~~qdg~ev~fkIk~tt~L~KLm~aY~er~Gl~~~~irFlFDG~r   89 (115)
T 3kyd_D           32 LGDKKEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQR   89 (115)
T ss_dssp             -------CEEEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHHTCCTTSEEEEETTEE
T ss_pred             ccCCCCCCeEEEEEEcCCCCEEEEEEccCChHHHHHHHHHHHhCCChhhEEEEECCeE
Confidence            3444  5677777777666  4466799999999999999999999999999999998

>4efo_A Serine/threonine-protein kinase TBK1; ubiquitin like domain, transferase; 1.77A {Homo sapiens}

Probab=97.33  E-value=0.00014  Score=43.77  Aligned_cols=33  Identities=27%  Similarity=0.565  Sum_probs=25.7

Q ss_pred             CccccCCCCcceEEEECCEEe--CCCCCCccceec
Q 040204            1 IEDKEEILRDQQRFIFAGKRL--EDGRTLVDYNIH   33 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L--~d~~tL~~y~I~   33 (97)
                      |++++|||+++|+|+|+|+.+  +.++.-..|.-.
T Consensus        43 V~eqTgIp~~~Q~LL~eg~~l~l~p~~~a~~~p~T   77 (94)
T 4efo_A           43 VYKQTKIISSNQELIYEGRRLVLEPGRLAQHFPKT   77 (94)
T ss_dssp             HHHHHCCCGGGEEEEETTEEECCCTTCBGGGSCCC
T ss_pred             HHHHhCCCHHHHHHHhCCCccccCCCCccccCCCC
Confidence            467899999999999999885  555556666544

>2pjh_A Protein NPL4, nuclear protein localization protein 4 homolog; UFD1, NPL4, AAA, protein binding, transport protein; NMR {Mus musculus}

Probab=97.32  E-value=0.00012  Score=42.58  Aligned_cols=46  Identities=11%  Similarity=-0.002  Sum_probs=37.5

Q ss_pred             eeeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeE
Q 040204           37 LHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFV   82 (97)
Q Consensus        37 i~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~   82 (97)
                      +.+.++.++| ..|.+++++||.+|+++|.+..+++++.|.+.++-.
T Consensus         5 m~lRvrs~~G~~Ri~v~~~~t~~~L~~~I~~~~~i~~~~~~l~~~~~   51 (80)
T 2pjh_A            5 IIIRVQSPDGVKRITATKRETAATFLKKVAKEFGFQNNGFSVYINRN   51 (80)
T ss_dssp             CCCEEECSSEEEECCCCSSCCHHHHHHHHHHHTCCCTTTCCCCCSCC
T ss_pred             EEEEEECCCCCEEEEcCCcChHHHHHHHHHHHcCCCCCcceEEecCC
Confidence            4566777777 458889999999999999999999988887765543

>3goe_A DNA repair protein RAD60; SUMO-like domain, sumoylation, SUMO, genome stability, DNA damage, DNA recombination, nucleus; HET: DNA; 0.97A {Schizosaccharomyces pombe} PDB: 3rcz_A*

Probab=97.30  E-value=0.00018  Score=41.93  Aligned_cols=39  Identities=15%  Similarity=0.233  Sum_probs=35.6

Q ss_pred             cccCCCCc-ceEEEECCEEeCCCCCCccceec-ccceeeee
Q 040204            3 DKEEILRD-QQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVR   41 (97)
Q Consensus         3 ~~~gip~~-~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i   41 (97)
                      .+.|||++ ..+|.|.|.+|..+.++++|++. ++.|.+++
T Consensus        41 ~~~~I~~~~~IrllFDGdRLdp~~tp~DlemeD~D~IDvmL   81 (82)
T 3goe_A           41 TEVKISFHERIRLEFEGEWLDPNDQVQSTELEDEDQVSVVL   81 (82)
T ss_dssp             HHHTCCCCTTCEEEETTEECCTTSBGGGSSCCTTCEEEEEC
T ss_pred             HHcCCCcCceEEEEEcCcccCccCChhhhCCcCCceeeeee
Confidence            45799999 89999999999999999999999 99988765

>3pge_A SUMO-modified proliferating cell nuclear antigen; DNA replication, DNA binding protein; 2.80A {Saccharomyces cerevisiae}

Probab=97.14  E-value=0.00084  Score=45.39  Aligned_cols=49  Identities=8%  Similarity=0.134  Sum_probs=41.4

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +..|.+.+.. .|  ..+.|++++++..|+...+++.|+|++++|++|.|+.
T Consensus        27 ~~~I~LkV~~-~g~~v~fkIk~~t~l~kL~~ay~er~Gi~~~~~RF~FdG~r   77 (200)
T 3pge_A           27 ETHINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIR   77 (200)
T ss_dssp             CCCEEEEEEC-SSCEEEEEECTTSCTHHHHHHHHHHHSSCGGGEEEEETTEE
T ss_pred             CCeEEEEEec-CCCEEEEEEecCCHHHHHHHHHHHHhCCChhhEEEEECCEE
Confidence            4456666654 44  4567799999999999999999999999999999998

>3ix6_A TS, tsase, thymidylate synthase; niaid, ssgcid, seattle structural center for infectious DISE brucellosis, orchitis, epididymitis, mastitis; 2.20A {Brucella melitensis}

Probab=97.13  E-value=6.8e-05  Score=54.79  Aligned_cols=48  Identities=23%  Similarity=0.448  Sum_probs=1.5

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecceee
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGMQI   49 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~~i   49 (97)
                      +++.|++++++++.|.|+++.++.|.+++++. |++|+++....||+..
T Consensus        51 ~~r~G~~~~~~rFlFdG~rI~~~~TP~~L~MEDgD~Idv~~~Q~g~~~~   99 (360)
T 3ix6_A           51 AKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGMRT   99 (360)
T ss_dssp             ----------------------------------------------CHH
T ss_pred             HHHhCCCcceEEEEECCeECCCCCChHHcCCCccchhhhhhccCchHHH
Confidence            56789999999999999999999999999999 9999999999998643

>3uf8_A Ubiquitin-like protein SMT3, peptidyl-prolyl CIS- isomerase; ssgcid, seattle structural genomics center for in disease; HET: FK5; 1.50A {Burkholderia pseudomallei} PDB: 4ggq_C* 3vaw_A* 3uqa_A* 4g50_A* 4fn2_A* 3uqb_A* 4giv_A* 1euv_B 3v60_A 3v61_A 3v62_A*

Probab=96.98  E-value=0.00053  Score=46.38  Aligned_cols=48  Identities=21%  Similarity=0.423  Sum_probs=43.3

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecceee
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGMQI   49 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~~i   49 (97)
                      +++.|+|+++++++|.|+++.++.|..+.++. +++|.++....+|..+
T Consensus        51 ~~~~g~~~~~~~f~fdG~~i~~~~Tpk~L~~ed~d~I~~~~eq~Gg~t~   99 (209)
T 3uf8_A           51 AKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGSTV   99 (209)
T ss_dssp             HHHHTCCGGGCEEEETTEECCTTCCTTTTTCCTTEEEEEECSCTTCCCC
T ss_pred             HHhhCCChheEEEEECCEeccCCCChHHhhhcccccchhhccccccccc
Confidence            46789999999999999999999999999999 9999999988877543

>4da1_A Protein phosphatase 1K, mitochondrial; metal-ION-assisted catalysis, dehydrogenase phosphatase, hydrolase; 2.38A {Homo sapiens} PDB: 3qht_A 1l2n_A

Probab=96.88  E-value=0.00016  Score=52.80  Aligned_cols=50  Identities=18%  Similarity=0.427  Sum_probs=0.0

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecceeeee
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGMQIFV   51 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~~i~v   51 (97)
                      +++.|+++.+++++|+|+++.++.|.+++++. +++|.++....+|....+
T Consensus        60 ~~~~g~~~~~~~f~f~G~~i~~~~Tp~~l~med~d~i~~~~~q~gg~n~~~  110 (389)
T 4da1_A           60 AKRQGKEMDSLRFLYDGIRIQADQAPEDLDMEDNDIIEAHREQIGGENLYF  110 (389)
T ss_dssp             ---------------------------------------------------
T ss_pred             HHHhCCCcceEEEEECCEEcCCCCCHHHcCCCCCCEeeeeeccccccccce
Confidence            46789999999999999999999999999999 999999999999876555

>3tix_A Ubiquitin-like protein SMT3, RNA-induced transcri silencing complex protein TAS3; PIN, rossmann fold, SPOC, alpha-helical hairpin, heterochrom silencing, RITS, RNAI, argonaute; 2.90A {Saccharomyces cerevisiae}

Probab=96.68  E-value=0.0026  Score=42.97  Aligned_cols=49  Identities=6%  Similarity=0.096  Sum_probs=41.7

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +..|.+.+.. .|  +.+.|++++++..|+...+++.|+++++++++|.|+.
T Consensus        55 ~e~InLKVk~-dG~eV~FKIKrtTpL~KLmeAYcERqGL~~~sIRFLFDGqR  105 (207)
T 3tix_A           55 ETHINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLTFLYDGIE  105 (207)
T ss_dssp             CCEEEEEEEC-SSCEEEEEEETTSCTHHHHHHHHHHTTCCGGGSCEEETTEE
T ss_pred             CCcEEEEEec-CCCEEEEEEccCChHHHHHHHHHHHhCCCcccEEEEECCee
Confidence            4556666654 44  5567799999999999999999999999999999998

>3uf8_A Ubiquitin-like protein SMT3, peptidyl-prolyl CIS- isomerase; ssgcid, seattle structural genomics center for in disease; HET: FK5; 1.50A {Burkholderia pseudomallei} PDB: 4ggq_C* 3vaw_A* 3uqa_A* 4g50_A* 4fn2_A* 3uqb_A* 4giv_A* 1euv_B 3v60_A 3v61_A 3v62_A*

Probab=96.61  E-value=0.0038  Score=42.10  Aligned_cols=50  Identities=6%  Similarity=0.084  Sum_probs=42.5

Q ss_pred             ccceeeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +..|.+.+...++ ..+.++.+++...|+...+++.|+++++++++|.|+.
T Consensus        19 ~~~i~ikv~~~~~~v~~~i~~~~~l~kl~~~y~~~~g~~~~~~~f~fdG~~   69 (209)
T 3uf8_A           19 ETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIR   69 (209)
T ss_dssp             CSEEEEEEECSSCEEEEEEETTSCTHHHHHHHHHHHTCCGGGCEEEETTEE
T ss_pred             CCcEEEEEEcCCCEEEEEEeeCCHHHHHHHHHHHhhCCChheEEEEECCEe
Confidence            6677777765333 4567799999999999999999999999999999998

>2jxx_A Nfatc2-interacting protein; nuclear factor of activated T-cells, cytoplasmic 2- interacting protein, ubiquitin like homologue; NMR {Homo sapiens}

Probab=96.46  E-value=0.0015  Score=39.39  Aligned_cols=38  Identities=16%  Similarity=0.320  Sum_probs=34.8

Q ss_pred             cccCCCCcceEEEECCEEeCCCCCCccceec-ccceeee
Q 040204            3 DKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSV   40 (97)
Q Consensus         3 ~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~   40 (97)
                      ++.|++++.-+++|.|.+|..+.|.+++++. +++|.++
T Consensus        58 ~~~g~~~~~vrF~FDG~rI~~~~TP~dLdMEDgD~IDv~   96 (97)
T 2jxx_A           58 EAMGLSGRKLSFFFDGTKLSGRELPADLGMESGDLIEVW   96 (97)
T ss_dssp             HHTTCSSSCCEEEETTEECCSCSCHHHHTCCTTEEEEEE
T ss_pred             HHHCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEe
Confidence            4678999999999999999999999999999 9998764

>2l76_A Nfatc2-interacting protein; ubiquitin-like domain, structural genomics, PSI-biology, Pro structure initiative; NMR {Homo sapiens}

Probab=96.25  E-value=0.0025  Score=38.25  Aligned_cols=42  Identities=10%  Similarity=0.081  Sum_probs=38.1

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeee
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      +++.|++++.-++.|.|.++.++.|-++.++. +++|.++...
T Consensus        51 c~r~gv~~~sirFlfDG~rI~~~~TP~~L~meD~DiID~~~~~   93 (95)
T 2l76_A           51 ATHLGVSPSRILLLFGETELSPTATPRTLKLGVADIIDCVVLT   93 (95)
T ss_dssp             HHHHTSCGGGEEEEETTEECCTTSCHHHHTCCSSCEEEEEECC
T ss_pred             HhhcCCChhhEEEEECCcCCCCCCCHhHcCCCCCCEEEEEEec
Confidence            45789999999999999999999999999999 9999987743

>3goe_A DNA repair protein RAD60; SUMO-like domain, sumoylation, SUMO, genome stability, DNA damage, DNA recombination, nucleus; HET: DNA; 0.97A {Schizosaccharomyces pombe} PDB: 3rcz_A*

Probab=95.86  E-value=0.02  Score=33.25  Aligned_cols=40  Identities=8%  Similarity=0.021  Sum_probs=36.3

Q ss_pred             ecceeeeeeccchhHHHHHhhhhhcCCCCC-ceEEEECeEe
Q 040204           44 RGGMQIFVESSDTIDNVKAKIQDKKGTPPD-QQRQIFWFVF   83 (97)
Q Consensus        44 ~~g~~i~v~~~~TV~~lK~~I~~~~gip~~-~q~Lif~G~~   83 (97)
                      ++.+.+.|+++.+|..+-..-..+.|||++ .-+|.|.|..
T Consensus        19 ~~dl~f~I~~~t~v~kLi~ayc~~~~I~~~~~IrllFDGdR   59 (82)
T 3goe_A           19 SEDLRLSIPVDFTVKDLIKRYCTEVKISFHERIRLEFEGEW   59 (82)
T ss_dssp             SCCEEEEEETTSBHHHHHHHHHHHHTCCCCTTCEEEETTEE
T ss_pred             CCCeEEEecCCCCHHHHHHHHHHHcCCCcCceEEEEEcCcc
Confidence            344778889999999999999999999999 9999999987

>3v7o_A Minor nucleoprotein VP30; ssgcid, seattle structural genomics center for infectious disease, SMT, transcription; 2.25A {Reston ebolavirus}

Probab=95.34  E-value=0.0028  Score=43.36  Aligned_cols=49  Identities=8%  Similarity=0.163  Sum_probs=0.0

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +..|.+.+. .+|  ..+.|+++++...|+...+++.|++++++|++|.|+.
T Consensus        19 ~e~InLKV~-qdGseV~FKIKrtTpL~KLM~AYcERqGLs~~siRFLFDGqR   69 (227)
T 3v7o_A           19 ETHINLKVS-DGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIR   69 (227)
T ss_dssp             ----------------------------------------------------
T ss_pred             CCeEEEEEe-CCCCEEEEEEccCChHHHHHHHHHHHhCCCccceEEEECCEe
Confidence            455666663 344  4566799999999999999999999999999999998

>2pjh_A Protein NPL4, nuclear protein localization protein 4 homolog; UFD1, NPL4, AAA, protein binding, transport protein; NMR {Mus musculus}

Probab=94.46  E-value=0.0052  Score=35.47  Aligned_cols=39  Identities=10%  Similarity=0.112  Sum_probs=31.0

Q ss_pred             ccccCCCCcceEEEECCEE-----eCCCCCCccceec-ccceeee
Q 040204            2 EDKEEILRDQQRFIFAGKR-----LEDGRTLVDYNIH-GSTLHSV   40 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~-----L~d~~tL~~y~I~-~sti~l~   40 (97)
                      +++.+++++.|.++++..+     +.++.+|+++||. |+.+++.
T Consensus        34 ~~~~~i~~~~~~l~~~~~p~~~l~~~~~~~l~~lgl~hGd~l~l~   78 (80)
T 2pjh_A           34 AKEFGFQNNGFSVYINRNKTGEITASSSKSLHLLKIKHGDLLFLF   78 (80)
T ss_dssp             HHHTCCCTTTCCCCCSCCGGGGSSSCCCCTTTTTCCCTTCCEEC-
T ss_pred             HHHcCCCCCcceEEecCCCCCcccCCCCCCHHHcCCCCCCEEEEe
Confidence            4567899888888876655     4588899999999 9999874

>2jxx_A Nfatc2-interacting protein; nuclear factor of activated T-cells, cytoplasmic 2- interacting protein, ubiquitin like homologue; NMR {Homo sapiens}

Probab=94.30  E-value=0.18  Score=30.06  Aligned_cols=50  Identities=6%  Similarity=0.052  Sum_probs=42.8

Q ss_pred             ccceeeeeeeecc---eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG---MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g---~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +..|.+.+...+|   ..+.|+++++...|...-.++.|++++..+++|.|..
T Consensus        23 ~~~I~LkV~~~dg~~~v~fkIk~~t~l~kLm~aY~~~~g~~~~~vrF~FDG~r   75 (97)
T 2jxx_A           23 SQQLQLRVQGKEKHQTLEVSLSRDSPLKTLMSHYEEAMGLSGRKLSFFFDGTK   75 (97)
T ss_dssp             CSEEEEEEEESSSSCEEEEEEETTSCHHHHHHHHHHHTTCSSSCCEEEETTEE
T ss_pred             CCeEEEEEEcCCCCEEEEEEECCCChHHHHHHHHHHHHCCCcccEEEEECCEE
Confidence            5567777776655   3567799999999999999999999999999999998

>2al3_A TUG long isoform; TUG UBL1 insulin, endocytosis/exocytosis complex; NMR {Mus musculus} SCOP: d.15.1.2

Probab=93.91  E-value=0.14  Score=30.25  Aligned_cols=47  Identities=13%  Similarity=0.028  Sum_probs=40.7

Q ss_pred             eeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           37 LHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        37 i~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +++.+-..++  ..|.|.|+.++.++-+.-.++.|+.+++..|.|+++.
T Consensus        10 m~v~Vl~~n~rr~~VKvtp~t~L~~VL~eaC~K~gl~~~~~~Lkh~~k~   58 (90)
T 2al3_A           10 SAVSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQDFNPSEYDLKFQRTV   58 (90)
T ss_dssp             CCEEEECTTSCEEEECCCTTSBHHHHHHHHHHHTTCCGGGCEEEETTEE
T ss_pred             cEEEEEcCCCcEEEEEECCCCCHHHHHHHHHHHhCCChhhCeEEeCCEe
Confidence            4566656555  5688899999999999999999999999999999999

>3ivf_A Talin-1; FERM domain, cell membrane, cell projection, cytoskeleton, M phosphoprotein, cell adhesion, structural protein; 1.94A {Mus musculus} PDB: 2kma_A 2kc1_A

Probab=92.23  E-value=0.26  Score=35.31  Aligned_cols=73  Identities=23%  Similarity=0.327  Sum_probs=54.0

Q ss_pred             CCcceEEEE------CCEEeCCCCCCccceec-ccceeee-------eeeecc--eeeeeeccchhHHHHHhhhhhcCCC
Q 040204            8 LRDQQRFIF------AGKRLEDGRTLVDYNIH-GSTLHSV-------RRFRGG--MQIFVESSDTIDNVKAKIQDKKGTP   71 (97)
Q Consensus         8 p~~~Q~L~~------~g~~L~d~~tL~~y~I~-~sti~l~-------i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip   71 (97)
                      +.++=-|+.      .|.=|++++||..|++. ++.+...       +...+|  ..+.++++.|+.++-+.|.++.|+.
T Consensus        43 ~~~~y~l~~~~~~~~~~~Wl~~~~~l~~y~~~~~~~l~~~~~~~~~~V~l~dg~~~~~~vd~~tt~~el~~~v~~~l~L~  122 (371)
T 3ivf_A           43 PPNDFGLFLSDDDPKKGIWLEAGKALDYYMLRNGDTMEYRKKQRPLKIRMLDGTVKTIMVDDSKTVTDMLMTICARIGIT  122 (371)
T ss_dssp             CGGGEEEEECCSSGGGCEECCTTSBGGGGTCCTTCEEEEEECEEEEEEECTTSCEEEEEEETTSBHHHHHHHHHHHTTCS
T ss_pred             CHHHCeEeccCCCCCcCEeccCCCCHHHhCCCCCceeeccCceeEEEEECcCCCEEEEEECCCCCHHHHHHHHHHHcCCC
Confidence            445556666      23448889999999999 8876664       445566  3467799999999999999999875


Q ss_pred             -CCceEEEEC
Q 040204           72 -PDQQRQIFW   80 (97)
Q Consensus        72 -~~~q~Lif~   80 (97)
                       .+-.-|.+.
T Consensus       123 e~~~FgL~~~  132 (371)
T 3ivf_A          123 NHDEYSLVRE  132 (371)
T ss_dssp             CGGGEEEECC
T ss_pred             CccccEEEEE
Confidence             555666664

>2kvr_A Ubiquitin carboxyl-terminal hydrolase 7; USP7, ubiquitin-like domain, UBL, ubiquitin specific protease, HOST-virus interaction, nucleus, protease; NMR {Homo sapiens}

Probab=92.15  E-value=0.12  Score=32.45  Aligned_cols=32  Identities=19%  Similarity=0.199  Sum_probs=28.6

Q ss_pred             eeeeeccchhHHHHHhhhhhcCCCCCceEEEE
Q 040204           48 QIFVESSDTIDNVKAKIQDKKGTPPDQQRQIF   79 (97)
Q Consensus        48 ~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif   79 (97)
                      .+.|..++|+.++|..|.+..|+|+++|||-.
T Consensus        59 ~~rv~k~~~~~~~~~~va~~lg~~~~~~RlW~   90 (130)
T 2kvr_A           59 VFKVLKNSSLAEFVQSLSQTMGFPQDQIRLWP   90 (130)
T ss_dssp             EEECCTTSBHHHHHHHHHHHHCCCGGGCEEEE
T ss_pred             eEEEeccCcHHHHHHHHHHHhCCCcccEEEEE
Confidence            45678899999999999999999999999864

>2l76_A Nfatc2-interacting protein; ubiquitin-like domain, structural genomics, PSI-biology, Pro structure initiative; NMR {Homo sapiens}

Probab=91.83  E-value=0.88  Score=27.07  Aligned_cols=50  Identities=14%  Similarity=0.169  Sum_probs=41.5

Q ss_pred             ccceeeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +..|.+.++..++ ..+.++.++....|...-.++.|++++..++.|.|..
T Consensus        19 ~~~IniKV~~~g~ev~FkIK~tt~l~KL~~aYc~r~gv~~~sirFlfDG~r   69 (95)
T 2l76_A           19 PRLFPLKIRCRADLVRLPLRMSEPLQSVVDHMATHLGVSPSRILLLFGETE   69 (95)
T ss_dssp             CCCEEEEEECSSSEEEEEECSSSCTHHHHHHHHHHHTSCGGGEEEEETTEE
T ss_pred             CCeEEEEEEcCCcEEEEEEecCChHHHHHHHHHhhcCCChhhEEEEECCcC
Confidence            4557777775433 4566789999999999999999999999999999987

>3ix6_A TS, tsase, thymidylate synthase; niaid, ssgcid, seattle structural center for infectious DISE brucellosis, orchitis, epididymitis, mastitis; 2.20A {Brucella melitensis}

Probab=91.79  E-value=0.031  Score=40.80  Aligned_cols=50  Identities=6%  Similarity=0.084  Sum_probs=0.0

Q ss_pred             ccceeeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +..|.+.++..+. ..+.|+++++...|+...+++.|+++++++++|.|+.
T Consensus        19 ~~~I~LKV~~~g~~v~FkIk~~t~l~kLm~aY~~r~G~~~~~~rFlFdG~r   69 (360)
T 3ix6_A           19 ETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIR   69 (360)
T ss_dssp             ---------------------------------------------------
T ss_pred             CCeEEEEEecCCcEEEEEEecCChHHHHHHHHHHHhCCCcceEEEEECCeE
Confidence            4455555554322 4567799999999999999999999999999999998

>4da1_A Protein phosphatase 1K, mitochondrial; metal-ION-assisted catalysis, dehydrogenase phosphatase, hydrolase; 2.38A {Homo sapiens} PDB: 3qht_A 1l2n_A

Probab=90.26  E-value=0.053  Score=39.33  Aligned_cols=50  Identities=6%  Similarity=0.084  Sum_probs=0.0

Q ss_pred             ccceeeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +..|.+.+...+. ..+.|+++++...|+....++.|++++++++.|.|+.
T Consensus        28 ~~~i~lkv~~~~~~~~~~i~~~~~~~~l~~~y~~~~g~~~~~~~f~f~G~~   78 (389)
T 4da1_A           28 ETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIR   78 (389)
T ss_dssp             ---------------------------------------------------
T ss_pred             CCcEEEEEecCCcEEEEEECCCChHHHHHHHHHHHhCCCcceEEEEECCEE
Confidence            3445555544222 4467799999999999999999999999999999998

>4eut_A Serine/threonine-protein kinase TBK1; ATP binding, phosphorylation, transferase-transferas inhibitor complex; HET: BX7; 2.60A {Homo sapiens}

Probab=89.38  E-value=0.35  Score=34.38  Aligned_cols=33  Identities=15%  Similarity=0.149  Sum_probs=30.4

Q ss_pred             eeeeccchhHHHHHhhhhhcCCCCCceEEEECe
Q 040204           49 IFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWF   81 (97)
Q Consensus        49 i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G   81 (97)
                      +.+.+..|+.++++++++.++++++.|.|+|.+
T Consensus       326 ~~~~~~~~~~~~~~~~~~~t~i~~~~q~~l~~~  358 (396)
T 4eut_A          326 IYIHSYNTATIFHELVYKQTKIISSNQELIYEG  358 (396)
T ss_dssp             EEECTTCBHHHHHHHHHHHHCCCSTTEEEESSS
T ss_pred             EEcCchhHHHHHHHHHHHhcCCChhhhHHHhcC
Confidence            445788999999999999999999999999998

>2juo_A GA-binding protein alpha chain; OST, ubiquitin, transcription factor, ensemble, DNA-binding, nucleus, transcription regulation; NMR {Mus musculus}

Probab=88.29  E-value=1  Score=26.31  Aligned_cols=42  Identities=17%  Similarity=0.259  Sum_probs=34.4

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeee
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      +.+.|++-+.-.++..+..|+++++|.+-+++ ...+.+.+..
T Consensus        23 e~Rl~i~L~~y~f~LQd~~L~~~k~LvdQcVqgeGlVQinvqi   65 (89)
T 2juo_A           23 EPRLQCSLDAHEICLQDIQLDPDRSLFDQGVKTDGTVQLSVQV   65 (89)
T ss_dssp             HHHHCSCCSSCEEEETTEECCTTSBTTTSSCCCCSEEEEEEEE
T ss_pred             HHHhcCCcccCeEEeeccccCCCccHHHhhcccccEEEEEEEE
Confidence            44567888888888899999999999999999 7777666644

>2al3_A TUG long isoform; TUG UBL1 insulin, endocytosis/exocytosis complex; NMR {Mus musculus} SCOP: d.15.1.2

Probab=88.15  E-value=0.31  Score=28.80  Aligned_cols=42  Identities=14%  Similarity=0.097  Sum_probs=37.3

Q ss_pred             cccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeee
Q 040204            3 DKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFR   44 (97)
Q Consensus         3 ~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~   44 (97)
                      ++.|+.+++-.|.|++++|+-..++.-.|+. |+++.++....
T Consensus        41 ~K~gl~~~~~~Lkh~~k~lDLSlpfRlsgLpnnAkLELv~~s~   83 (90)
T 2al3_A           41 RRQDFNPSEYDLKFQRTVLDLSLQWRFANLPNNAKLEMVPVSR   83 (90)
T ss_dssp             HHTTCCGGGCEEEETTEEESSSCBHHHHCCCSSCEEEEECSSS
T ss_pred             HHhCCChhhCeEEeCCEeccccceeEecCCCCCCEEEEEEccC
Confidence            5688998999999999999999999999999 99999887543

>2kc2_A Talin-1, F1; FERM, adhesion, cell membrane, cell projection, cytoplasm, cytoskeleton, membrane, phosphoprotein, structural protein; NMR {Mus musculus}

Probab=87.94  E-value=0.66  Score=29.03  Aligned_cols=41  Identities=20%  Similarity=0.249  Sum_probs=31.9

Q ss_pred             eeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCC-ceEEEE
Q 040204           39 SVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPD-QQRQIF   79 (97)
Q Consensus        39 l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~-~q~Lif   79 (97)
                      +.+++.+|  ..+.|+.+.||.+++..|+.+.||+.. ...|+.
T Consensus        14 LkV~llDg~~ktl~VD~S~~V~~lv~~Ic~kigI~n~~ey~L~~   57 (128)
T 2kc2_A           14 LKIRMLDGTVKTIMVDDSKTVTDMLMTICARIGITNHDEYSLVR   57 (128)
T ss_dssp             EEEECTTSCEEEEEEEECSSHHHHHHHHHHHHTCCCCSSEEEEE
T ss_pred             EEEEcCCCCEEEEEeCCCcCHHHHHHHHHHHhCCCCcccccccc
Confidence            56677777  467789999999999999999998743 344443

>1oey_A P67-PHOX, neutrophil cytosol factor 2; immune system, PB1 heterodimer/complex, NADPH oxidase, PB1 D heterodimerization; 2.0A {Homo sapiens} SCOP: d.15.2.2

Probab=85.52  E-value=1.6  Score=25.22  Aligned_cols=38  Identities=5%  Similarity=-0.018  Sum_probs=33.5

Q ss_pred             ceeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           46 GMQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        46 g~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .+-|.|.+.-+..+|.++|.++-++|++.-.|.|....
T Consensus        15 tvairvp~~~~y~~L~~~l~~kL~l~~~~~~LsYk~~~   52 (83)
T 1oey_A           15 TVVMKTQPGLPYSQVRDMVSKKLELRLEHTKLSYRPRD   52 (83)
T ss_dssp             EEEEEECTTCCHHHHHHHHHHHTTCCGGGCCEEECCTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCcceeEEEeeCCC
Confidence            34566788999999999999999999999999999875

>2bps_A YUKD protein; ubiquitin-like protein, ubiquitin; 2.7A {Bacillus subtilis}

Probab=85.51  E-value=0.23  Score=28.72  Aligned_cols=29  Identities=24%  Similarity=0.247  Sum_probs=25.0

Q ss_pred             ceEEEECCEEeCCCCCCccceec-ccceee
Q 040204           11 QQRFIFAGKRLEDGRTLVDYNIH-GSTLHS   39 (97)
Q Consensus        11 ~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l   39 (97)
                      +.+....+..|.+++.|++|+|. |+.+.+
T Consensus        51 ~irv~NK~~~L~~~~~L~d~~ItnGD~Lei   80 (81)
T 2bps_A           51 WIRVVNKDKVFSGECKLSDCGITNGDRLEI   80 (81)
T ss_dssp             EEEEGGGTEEEETTSBTGGGTCCTTCEEEE
T ss_pred             EEEEecCCEEEcCCCEEeeCCcCCCCEEEE
Confidence            56677788899999999999999 998864

>2ylm_A Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70A {Homo sapiens}

Probab=83.59  E-value=0.91  Score=34.45  Aligned_cols=32  Identities=19%  Similarity=0.199  Sum_probs=28.8

Q ss_pred             eeeeeccchhHHHHHhhhhhcCCCCCceEEEE
Q 040204           48 QIFVESSDTIDNVKAKIQDKKGTPPDQQRQIF   79 (97)
Q Consensus        48 ~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif   79 (97)
                      .+.|..++|+.++|++|.+..|+|+++|||=.
T Consensus        39 ~~rv~k~~~~~~l~~~va~~lg~~~~~~RlW~   70 (530)
T 2ylm_A           39 VFKVLKNSSLAEFVQSLSQTMGFPQDQIRLWP   70 (530)
T ss_dssp             EEEEETTSBHHHHHHHHHHHHTSCGGGEEEEE
T ss_pred             eEEEcCcCCHHHHHHHHHHHhCcCcccEEEEE
Confidence            46778999999999999999999999999843

>3qx1_A FAS-associated factor 1; UBX, protein binding, P97 binding; 1.60A {Homo sapiens} PDB: 3qwz_B* 3qc8_B 3qca_A 3qq8_B 3r3m_B 1h8c_A

Probab=82.75  E-value=3.8  Score=23.03  Aligned_cols=45  Identities=18%  Similarity=0.113  Sum_probs=35.0

Q ss_pred             ccceeeeeeeecceee--eeeccchhHHHHHhhhhhcCCCCCceEEEE
Q 040204           34 GSTLHSVRRFRGGMQI--FVESSDTIDNVKAKIQDKKGTPPDQQRQIF   79 (97)
Q Consensus        34 ~sti~l~i~~~~g~~i--~v~~~~TV~~lK~~I~~~~gip~~~q~Lif   79 (97)
                      ..+..+.+|+++|..+  ....++||.+|.+-|.. .+.++....|+-
T Consensus         5 ~~~~~i~iRlpdG~r~~~~F~~~~tl~~v~~fv~~-~~~~~~~f~L~t   51 (84)
T 3qx1_A            5 EPVSKLRIRTPSGEFLERRFLASNKLQIVFDFVAS-KGFPWDEYKLLS   51 (84)
T ss_dssp             CCEEEEEEECTTSCEEEEEEETTSBHHHHHHHHHH-TTCCTTTEEEEC
T ss_pred             CCeEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHH-cCCCCCCeEEEe
Confidence            4566788888888543  34889999999999987 667778888873

>3qa8_A MGC80376 protein; kinase ubiquitin-like domain, phosphorylation, kinase domain ubiquitin-like domain, kinase, substrate binding; 3.60A {Xenopus laevis} PDB: 3qad_A* 3rzf_A*

Probab=82.60  E-value=0.92  Score=35.47  Aligned_cols=36  Identities=19%  Similarity=0.295  Sum_probs=32.2

Q ss_pred             eeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           48 QIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        48 ~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .+.+.+++|+.+++..|++.+|||++.|.+++.+..
T Consensus       325 ~~~i~~~~tl~~l~~~i~~~T~i~~~~q~~~~~~~~  360 (676)
T 3qa8_A          325 TYPVTENENLQNLKSWLQQDTGIPEEEQELLQASGL  360 (676)
T ss_dssp             EEECCTTCCHHHHHHHHHTTSCCCSTTCEEESSSSC
T ss_pred             eeecCCCccHHHHHHHHHHHhCCCHHHHHHHhccCC
Confidence            355688999999999999999999999999998755

---

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	97
d1wx9a1	73	d.15.1.1 (A:8-80) Large proline-rich protein BAT3	4e-13
d1wx9a1	73	d.15.1.1 (A:8-80) Large proline-rich protein BAT3	9e-07
d1zkha1	86	d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-t	7e-13
d1zkha1	86	d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-t	5e-08
d2zeqa1	78	d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin	1e-12
d2zeqa1	78	d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin	6e-08
d1wh3a_	87	d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like	2e-12
d1wh3a_	87	d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like	7e-08
d1ogwa_	76	d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [Tax	3e-12
d1ogwa_	76	d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [Tax	4e-07
d2c9wb1	103	d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens)	4e-12
d2c9wb1	103	d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens)	1e-07
d1bt0a_	73	d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis t	1e-11
d1bt0a_	73	d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis t	8e-07
d1wgda_	93	d.15.1.1 (A:) Homocysteine-responsive endoplasmic	2e-11
d1wgda_	93	d.15.1.1 (A:) Homocysteine-responsive endoplasmic	1e-05
d2bwfa1	73	d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyc	2e-11
d2bwfa1	73	d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyc	2e-07
d1x1ma1	94	d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse	6e-11
d1euvb_	79	d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yea	1e-10
d1z2ma2	76	d.15.1.1 (A:79-154) Interferon-induced 15 kDa prot	7e-10
d1z2ma2	76	d.15.1.1 (A:79-154) Interferon-induced 15 kDa prot	7e-07
d1uela_	95	d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homol	2e-09
d1uela_	95	d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homol	0.002
d2faza1	76	d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING fing	4e-09
d2faza1	76	d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING fing	7e-09
d1v5oa_	102	d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus mu	4e-09
d1v5oa_	102	d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus mu	4e-05
d1wgha_	116	d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mous	5e-09
d1wgha_	116	d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mous	1e-05
d1uh6a_	100	d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mous	1e-08
d1uh6a_	100	d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mous	1e-08
d1wy8a1	76	d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING fing	2e-08
d1wy8a1	76	d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING fing	2e-08
d1se9a_	101	d.15.1.1 (A:) Hypothetical protein At3g01050 {Thal	2e-08
d1se9a_	101	d.15.1.1 (A:) Hypothetical protein At3g01050 {Thal	0.001
d1oqya4	77	d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 h	2e-08
d1oqya4	77	d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 h	1e-05
d1v2ya_	105	d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik	2e-08
d1v2ya_	105	d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik	2e-07
d1wjna_	97	d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse	7e-08
d1wjna_	97	d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse	2e-05
d1ttna1	80	d.15.1.1 (A:21-100) Dendritic cell-derived ubiquit	7e-08
d1ttna1	80	d.15.1.1 (A:21-100) Dendritic cell-derived ubiquit	3e-04
d1we6a_	111	d.15.1.1 (A:) Splicing factor 3 subunit 1, C-termi	7e-08
d1wiaa_	95	d.15.1.1 (A:) Ubiquitin-like protein bab25500 (201	2e-07
d1wiaa_	95	d.15.1.1 (A:) Ubiquitin-like protein bab25500 (201	4e-06
d1wxva1	81	d.15.1.1 (A:7-87) Bag-family molecular chaperone r	4e-07
d1wxva1	81	d.15.1.1 (A:7-87) Bag-family molecular chaperone r	6e-07
d1v5ta_	90	d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus mu	4e-07
d1v5ta_	90	d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus mu	7e-07
d1z2ma1	76	d.15.1.1 (A:3-78) Interferon-induced 15 kDa protei	8e-07
d1z2ma1	76	d.15.1.1 (A:3-78) Interferon-induced 15 kDa protei	6e-05
d1v6ea_	95	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	1e-06
d1v6ea_	95	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	5e-06
d1j8ca_	103	d.15.1.1 (A:) Ubiquitin-like N-terminal domain of	1e-06
d1j8ca_	103	d.15.1.1 (A:) Ubiquitin-like N-terminal domain of	1e-06
d1yqba1	84	d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapien	2e-06
d1yqba1	84	d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapien	3e-04
d1wx8a1	83	d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus muscul	3e-06
d1wx8a1	83	d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus muscul	3e-05
d1t0ya_	90	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	4e-06
d1t0ya_	90	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	7e-06
d2uyzb1	77	d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human	3e-05
d1v86a_	95	d.15.1.1 (A:) hypothetical D7wsu128e protein {Mous	4e-05
d1v86a_	95	d.15.1.1 (A:) hypothetical D7wsu128e protein {Mous	6e-04
d1m94a_	73	d.15.1.1 (A:) Ubiquitin-like modifier protein hub1	7e-05
d1m94a_	73	d.15.1.1 (A:) Ubiquitin-like modifier protein hub1	0.002
d1wjua_	100	d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human	2e-04

>d1wx9a1 d.15.1.1 (A:8-80) Large proline-rich protein BAT3 {Human (Homo sapiens) [TaxId: 9606]} Length = 73

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Large proline-rich protein BAT3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.8 bits (137), Expect = 4e-13
 Identities = 15/42 (35%), Positives = 24/42 (57%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHGSTLHSVRR 42
          I     I  ++QR I+ G+ L+D + L +YN+ G  +H V R
Sbjct: 30 IAASVSIPSEKQRLIYQGRVLQDDKKLQEYNVGGKVIHLVER 71

>d1wx9a1 d.15.1.1 (A:8-80) Large proline-rich protein BAT3 {Human (Homo sapiens) [TaxId: 9606]} Length = 73

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Large proline-rich protein BAT3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.6 bits (95), Expect = 9e-07
 Identities = 7/45 (15%), Positives = 15/45 (33%), Gaps = 12/45 (26%)

Query: 47 MQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          +++ V             +   +   K  I      P ++QR I+
Sbjct: 1  LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIY 45

>d1zkha1 d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Splicing factor 3 subunit 1, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.4 bits (136), Expect = 7e-13
 Identities = 11/46 (23%), Positives = 23/46 (50%), Gaps = 1/46 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRG 45
          I +   +   +Q+  + G  ++D  +L  YN+  G+ +H   + RG
Sbjct: 41 IHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMANGAVIHLALKERG 86

>d1zkha1 d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Splicing factor 3 subunit 1, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.1 bits (104), Expect = 5e-08
 Identities = 7/30 (23%), Positives = 15/30 (50%)

Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
          +  +D +  +K KI +  G P  +Q+  + 
Sbjct: 28 LPLTDQVSVIKVKIHEATGMPAGKQKLQYE 57

>d2zeqa1 d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of parkin
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 56.1 bits (135), Expect = 1e-12
 Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 1/46 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-HGSTLHSVRRFRG 45
          +  ++ +  DQ R IFAGK L +  T+ + ++   S +H V+R R 
Sbjct: 32 VAKRQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRR 77

>d2zeqa1 d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of parkin
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.7 bits (103), Expect = 6e-08
 Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 12/46 (26%)

Query: 46 GMQIFVE------------SSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          GM +FV             S  +I  +K  +  ++G P DQ R IF
Sbjct: 2  GMIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVIF 47

>d1wh3a_ d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like protein, OASL {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 2'-5'-oligoadenylate synthetase-like protein, OASL
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.3 bits (133), Expect = 2e-12
 Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-HGSTLHSVRRFRGG 46
          IED++ + + QQ+  F G+ L+D   L  Y I    TL   ++   G
Sbjct: 37 IEDQQGLPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKGSG 83

>d1wh3a_ d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like protein, OASL {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 2'-5'-oligoadenylate synthetase-like protein, OASL
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.8 bits (103), Expect = 7e-08
 Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 12/46 (26%)

Query: 46 GMQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          G+Q+FV              +  I  +K +I+D++G P  QQ+  F
Sbjct: 7  GIQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEF 52

>d1ogwa_ d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.9 bits (132), Expect = 3e-12
 Identities = 34/47 (72%), Positives = 36/47 (76%), Gaps = 1/47 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-HGSTLHSVRRFRGG 46
          I+DKE I  DQQR IFAGK+LEDGRTL DYNI   STLH V R RGG
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76

>d1ogwa_ d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.4 bits (97), Expect = 4e-07
 Identities = 28/45 (62%), Positives = 30/45 (66%), Gaps = 12/45 (26%)

Query: 47 MQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          MQIFV            E SDTI+NVKAKIQDK+G PPDQQR IF
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF 45

>d2c9wb1 d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Elongin B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.2 bits (133), Expect = 4e-12
 Identities = 11/56 (19%), Positives = 21/56 (37%), Gaps = 8/56 (14%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNI--------HGSTLHSVRRFRGGMQ 48
          +E   +   D+QR     + L+DG+TL +             +T+    R     +
Sbjct: 30 VEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFE 85

>d2c9wb1 d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Elongin B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.7 bits (103), Expect = 1e-07
 Identities = 11/38 (28%), Positives = 17/38 (44%), Gaps = 2/38 (5%)

Query: 44 RGGMQIF--VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          R    IF   + S T+  +K  ++     PPD+QR   
Sbjct: 8  RHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYK 45

>d1bt0a_ d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 73

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Rub1
species: Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 53.0 bits (127), Expect = 1e-11
 Identities = 23/43 (53%), Positives = 28/43 (65%), Gaps = 1/43 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-HGSTLHSVRR 42
          +E+KE I   QQR I+AGK+L D +T  DYNI  GS LH V  
Sbjct: 30 VEEKEGIPPVQQRLIYAGKQLADDKTAKDYNIEGGSVLHLVLA 72

>d1bt0a_ d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 73

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Rub1
species: Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 40.6 bits (95), Expect = 8e-07
 Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 12/46 (26%)

Query: 47 MQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
          M I V            E +DTID +K ++++K+G PP QQR I+ 
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLIYA 46

>d1wgda_ d.15.1.1 (A:) Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.3 bits (128), Expect = 2e-11
 Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 5/51 (9%)

Query: 1  IEDK--EEILRDQQRFIFAGKRLEDGRTLVDYNIH---GSTLHSVRRFRGG 46
          +     E    + QR I++GK L D + L D          LH V   + G
Sbjct: 39 LSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVCNVKSG 89

>d1wgda_ d.15.1.1 (A:) Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.9 bits (88), Expect = 1e-05
 Identities = 6/31 (19%), Positives = 14/31 (45%), Gaps = 2/31 (6%)

Query: 51 VESSDTIDNVKAKIQDKKGT--PPDQQRQIF 79
           +   ++ ++KA +         P+ QR I+
Sbjct: 26 GDRGWSVGHLKAHLSRVYPERPRPEDQRLIY 56

>d2bwfa1 d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 73

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: DSK2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 52.5 bits (126), Expect = 2e-11
 Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 1/43 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR 42
          I     I    QR I++GK L+D +T+  Y+I  G ++H V+ 
Sbjct: 30 INKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS 72

>d2bwfa1 d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 73

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: DSK2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 42.4 bits (100), Expect = 2e-07
 Identities = 9/30 (30%), Positives = 11/30 (36%)

Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
          V    T+   K  I    G P   QR I+ 
Sbjct: 17 VAPESTVLQFKEAINKANGIPVANQRLIYS 46

>d1x1ma1 d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 7
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.8 bits (124), Expect = 6e-11
 Identities = 13/34 (38%), Positives = 22/34 (64%), Gaps = 1/34 (2%)

Query: 10 DQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR 42
          +    I+ G++L+D +TL  Y I  GST+H +R+
Sbjct: 59 ELIDLIYCGRKLKDDQTLDFYGIQPGSTVHVLRK 92

>d1euvb_ d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932]} Length = 79

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-1 (smt3 homologue)
species: Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932]

 Score = 50.6 bits (121), Expect = 1e-10
 Identities = 10/47 (21%), Positives = 21/47 (44%), Gaps = 1/47 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
             ++    D  RF++ G R++  +T  D ++     + + R   GG
Sbjct: 33 FAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGG 79

>d1z2ma2 d.15.1.1 (A:79-154) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.7 bits (116), Expect = 7e-10
 Identities = 13/43 (30%), Positives = 18/43 (41%), Gaps = 1/43 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR 42
          +   E +  D     F GK LED   L +Y +   ST+    R
Sbjct: 33 VSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLR 75

>d1z2ma2 d.15.1.1 (A:79-154) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.0 bits (96), Expect = 7e-07
 Identities = 7/45 (15%), Positives = 15/45 (33%), Gaps = 12/45 (26%)

Query: 47 MQIFV------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          + I V              + T+ ++K ++   +G   D     F
Sbjct: 4  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTF 48

>d1uela_ d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homolog B (Hhr23B) {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of Rad23 homolog B (Hhr23B)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.1 bits (114), Expect = 2e-09
 Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 1/42 (2%)

Query: 2  EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR 42
          + K+      Q+ I+AGK L D   L +Y I   + +  +  
Sbjct: 34 KGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVT 75

>d1uela_ d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homolog B (Hhr23B) {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of Rad23 homolog B (Hhr23B)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.3 bits (73), Expect = 0.002
 Identities = 10/48 (20%), Positives = 20/48 (41%), Gaps = 15/48 (31%)

Query: 47 MQIF------------VESSDTIDNVKAKIQDKK---GTPPDQQRQIF 79
          MQ+             ++  +T+  +K KI+ +K     P   Q+ I+
Sbjct: 1  MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIY 48

>d2faza1 d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING finger domain-containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like PHD and RING finger domain-containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.8 bits (111), Expect = 4e-09
 Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR 42
          I++   +    QR  + GK++EDG TL DY +    T+  + R
Sbjct: 32 IQELFHVEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLLVR 74

>d2faza1 d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING finger domain-containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like PHD and RING finger domain-containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.0 bits (109), Expect = 7e-09
 Identities = 9/47 (19%), Positives = 15/47 (31%), Gaps = 14/47 (29%)

Query: 47 MQIFV--------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          M I V                   ++ ++ KIQ+     P  QR  +
Sbjct: 1  MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFY 47

>d1v5oa_ d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 102

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 1700011n24rik protein
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.3 bits (112), Expect = 4e-09
 Identities = 6/56 (10%), Positives = 24/56 (42%), Gaps = 2/56 (3%)

Query: 1  IEDKEEILRDQQRFIFAGK-RLEDGRTLVDYNIH-GSTLHSVRRFRGGMQIFVESS 54
           E +  +  ++ + ++  +   +D  +L  Y +  G  +  +++   G++    + 
Sbjct: 41 CELESGVPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVLLQKDNVGLRTPGRTP 96

>d1v5oa_ d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 102

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 1700011n24rik protein
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.9 bits (85), Expect = 4e-05
 Identities = 7/51 (13%), Positives = 16/51 (31%), Gaps = 16/51 (31%)

Query: 45 GGMQIFV----------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
           GM I V                     + N +   + + G P ++ + ++
Sbjct: 6  SGMLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVY 56

>d1wgha_ d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 116

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3, Ubl3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.3 bits (112), Expect = 5e-09
 Identities = 10/44 (22%), Positives = 19/44 (43%), Gaps = 3/44 (6%)

Query: 2  EDKEEILRDQQRFIFAGKRLEDGRTLVDYNI---HGSTLHSVRR 42
          E+++    +  R I+ G+ L    TL    +     + +H V R
Sbjct: 55 EEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLVAR 98

>d1wgha_ d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 116

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3, Ubl3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.8 bits (90), Expect = 1e-05
 Identities = 4/37 (10%), Positives = 16/37 (43%), Gaps = 8/37 (21%)

Query: 51 VESSDTIDNVKAKI--------QDKKGTPPDQQRQIF 79
             +D+  ++   +        ++++ + P+  R I+
Sbjct: 33 FSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIY 69

>d1uh6a_ d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 100

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 5, ubl5
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.1 bits (109), Expect = 1e-08
 Identities = 9/39 (23%), Positives = 14/39 (35%), Gaps = 1/39 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLH 38
          I  +     ++          +D  +L DY IH G  L 
Sbjct: 58 IAAQTGTRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLE 96

>d1uh6a_ d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 100

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 5, ubl5
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.1 bits (109), Expect = 1e-08
 Identities = 13/72 (18%), Positives = 25/72 (34%), Gaps = 17/72 (23%)

Query: 29 DYNIH-GSTLHSVRRFRGG----MQIF------------VESSDTIDNVKAKIQDKKGTP 71
           ++ H  S    V R   G    +++               + DTI ++K  I  + GT 
Sbjct: 6  HHHHHHSSGASLVPRGSEGAATMIEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTR 65

Query: 72 PDQQRQIFWFVF 83
           ++     W+  
Sbjct: 66 WNKIVLKKWYTI 77

>d1wy8a1 d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING finger domain-containing protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like PHD and RING finger domain-containing protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.9 bits (106), Expect = 2e-08
 Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 1/43 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR 42
          +    ++  + QR  + GK+LE+G TL DY++     +  + R
Sbjct: 32 VWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVR 74

>d1wy8a1 d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING finger domain-containing protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like PHD and RING finger domain-containing protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.9 bits (106), Expect = 2e-08
 Identities = 8/47 (17%), Positives = 15/47 (31%), Gaps = 14/47 (29%)

Query: 47 MQIFV--------------ESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          M I V                  TI+ ++ ++       P+ QR  +
Sbjct: 1  MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFY 47

>d1se9a_ d.15.1.1 (A:) Hypothetical protein At3g01050 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 101

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Hypothetical protein At3g01050
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 45.3 bits (107), Expect = 2e-08
 Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 7/40 (17%)

Query: 10 DQQRFIFAGKRLEDGRTLVDYNIHG-------STLHSVRR 42
           + + I AGK LE+ +T+ DY           +T+H + +
Sbjct: 54 KEVKLISAGKVLENSKTVKDYRSPVSNLAGAVTTMHVIIQ 93

>d1se9a_ d.15.1.1 (A:) Hypothetical protein At3g01050 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 101

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Hypothetical protein At3g01050
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 33.4 bits (76), Expect = 0.001
 Identities = 5/36 (13%), Positives = 12/36 (33%), Gaps = 7/36 (19%)

Query: 51 VESSDTIDNVKAKIQD-----KKGTP--PDQQRQIF 79
             + T+  +K  +       K+  P    + + I 
Sbjct: 25 FPDATTVSALKETVISEWPREKENGPKTVKEVKLIS 60

>d1oqya4 d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 homolog A (Hhr23a) {Human (Homo sapiens) [TaxId: 9606]} Length = 77

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of Rad23 homolog A (Hhr23a)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.9 bits (106), Expect = 2e-08
 Identities = 10/36 (27%), Positives = 17/36 (47%), Gaps = 1/36 (2%)

Query: 4  KEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLH 38
          ++      Q+ I+AGK L D   + DY I   + + 
Sbjct: 38 RDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVV 73

>d1oqya4 d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 homolog A (Hhr23a) {Human (Homo sapiens) [TaxId: 9606]} Length = 77

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of Rad23 homolog A (Hhr23a)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.5 bits (87), Expect = 1e-05
 Identities = 11/49 (22%), Positives = 20/49 (40%), Gaps = 15/49 (30%)

Query: 46 GMQIF------------VESSDTIDNVKAKIQDKKGT---PPDQQRQIF 79
           + I             +E  +T+  +K KI+ +KG    P   Q+ I+
Sbjct: 2  AVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIY 50

>d1v2ya_ d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik {Mouse (Mus musculus) [TaxId: 10090]} Length = 105

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3300001g02rik
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.4 bits (107), Expect = 2e-08
 Identities = 10/52 (19%), Positives = 21/52 (40%), Gaps = 3/52 (5%)

Query: 39 SVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVFGWGSLW 89
           V +  G  M + V  + T+ ++K  IQ       +++  +      W  +W
Sbjct: 11 RVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGV--QHISWSYVW 60

>d1v2ya_ d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik {Mouse (Mus musculus) [TaxId: 10090]} Length = 105

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3300001g02rik
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.7 bits (100), Expect = 2e-07
 Identities = 9/63 (14%), Positives = 23/63 (36%), Gaps = 17/63 (26%)

Query: 1  IEDKEEILRDQQR---------------FIFAGKRLEDGR-TLVDYNIH-GSTLHSVRRF 43
          I+   ++ ++++                   AG++L + R  L DY I     +  +++ 
Sbjct: 37 IQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLRDYGIRNRDEVSFIKKL 96

Query: 44 RGG 46
             
Sbjct: 97 GQK 99

>d1wjna_ d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Tubulin-folding protein TbcE
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.1 bits (104), Expect = 7e-08
 Identities = 5/30 (16%), Positives = 10/30 (33%)

Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIFW 80
          +  S T+  VK  +      P  +    + 
Sbjct: 29 LPDSMTVQKVKGLLSRLLKVPVSELLLSYE 58

>d1wjna_ d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Tubulin-folding protein TbcE
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.6 bits (87), Expect = 2e-05
 Identities = 5/47 (10%), Positives = 15/47 (31%), Gaps = 9/47 (19%)

Query: 1  IEDKEEILRDQQRFIFAGKRLE--------DGRTLVDYNIH-GSTLH 38
          +    ++   +    +   ++         D + L  Y++  G  L 
Sbjct: 42 LSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCLL 88

>d1ttna1 d.15.1.1 (A:21-100) Dendritic cell-derived ubiquitin-like protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Dendritic cell-derived ubiquitin-like protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.8 bits (103), Expect = 7e-08
 Identities = 8/41 (19%), Positives = 16/41 (39%), Gaps = 1/41 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNI-HGSTLHSV 40
          +   E +    QR+ F+G+ L D     +  I     +  +
Sbjct: 33 LHAAEGVEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVI 73

>d1ttna1 d.15.1.1 (A:21-100) Dendritic cell-derived ubiquitin-like protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Dendritic cell-derived ubiquitin-like protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.5 bits (79), Expect = 3e-04
 Identities = 10/29 (34%), Positives = 17/29 (58%)

Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          V S+DT+ ++K ++   +G  P  QR  F
Sbjct: 20 VRSTDTVFHMKRRLHAAEGVEPGSQRWFF 48

>d1we6a_ d.15.1.1 (A:) Splicing factor 3 subunit 1, C-terminal domain {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 111

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Splicing factor 3 subunit 1, C-terminal domain
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 44.2 bits (104), Expect = 7e-08
 Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 1/47 (2%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
           I  + +I  ++Q+       L+D  +L  YN+  G  L    R R G
Sbjct: 61  IAGEIQIPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLRERSG 107

>d1wiaa_ d.15.1.1 (A:) Ubiquitin-like protein bab25500 (2010008E23Rik) {Mouse (Mus musculus) [TaxId: 10090]} Length = 95

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein bab25500 (2010008E23Rik)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.0 bits (101), Expect = 2e-07
 Identities = 11/44 (25%), Positives = 18/44 (40%), Gaps = 5/44 (11%)

Query: 1  IEDKEEILRDQQRFIFAGK-RLEDGRTLVDYNI-HGSTLHSVRR 42
              +E    Q + I+ G+   +  RTL   NI +   +H  R 
Sbjct: 37 YFPGQE---SQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRS 77

>d1wiaa_ d.15.1.1 (A:) Ubiquitin-like protein bab25500 (2010008E23Rik) {Mouse (Mus musculus) [TaxId: 10090]} Length = 95

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein bab25500 (2010008E23Rik)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.5 bits (92), Expect = 4e-06
 Identities = 7/47 (14%), Positives = 14/47 (29%), Gaps = 15/47 (31%)

Query: 45 GGMQIF------------VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
           G+ +                 DT+  +K+K          Q + I+
Sbjct: 6  SGINVRLKFLNDTEELAVARPEDTVGTLKSKYFPG---QESQMKLIY 49

>d1wxva1 d.15.1.1 (A:7-87) Bag-family molecular chaperone regulator-1 {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Bag-family molecular chaperone regulator-1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.8 bits (98), Expect = 4e-07
 Identities = 6/31 (19%), Positives = 13/31 (41%)

Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIFWF 81
            S   + ++   +++  G P   Q+ IF  
Sbjct: 22 GSSEPVVQDLAQVVEEVIGVPQSFQKLIFKG 52

>d1wxva1 d.15.1.1 (A:7-87) Bag-family molecular chaperone regulator-1 {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Bag-family molecular chaperone regulator-1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.4 bits (97), Expect = 6e-07
 Identities = 11/44 (25%), Positives = 19/44 (43%), Gaps = 2/44 (4%)

Query: 1  IEDKEEILRDQQRFIFAGKRL-EDGRTLVDYNIH-GSTLHSVRR 42
          +E+   + +  Q+ IF GK L E    L    I  G  +  + +
Sbjct: 35 VEEVIGVPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVMLIGK 78

>d1v5ta_ d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 90

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 8430435i17rik protein
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.9 bits (98), Expect = 4e-07
 Identities = 7/50 (14%), Positives = 19/50 (38%), Gaps = 4/50 (8%)

Query: 1  IEDKEEILRDQQRFI---FAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
          ++    +L ++Q+ +     GK  E+   L    +   + +  +     G
Sbjct: 37 LKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMGTRESG 86

>d1v5ta_ d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 90

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 8430435i17rik protein
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.5 bits (97), Expect = 7e-07
 Identities = 8/34 (23%), Positives = 18/34 (52%)

Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVFG 84
          +   DT+ ++K  ++   G  P++Q+ +   V G
Sbjct: 24 LSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKG 57

>d1z2ma1 d.15.1.1 (A:3-78) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.0 bits (96), Expect = 8e-07
 Identities = 13/45 (28%), Positives = 18/45 (40%), Gaps = 3/45 (6%)

Query: 1  IEDKEEILRDQQRFIF--AGKRLEDGRTLVDYNIH-GSTLHSVRR 42
          I  K  +   QQR     +G  L+D   L    +  GST+  V  
Sbjct: 30 ITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVD 74

>d1z2ma1 d.15.1.1 (A:3-78) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.0 bits (83), Expect = 6e-05
 Identities = 10/31 (32%), Positives = 15/31 (48%)

Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIFWF 81
          + SS ++  +KA+I  K G    QQR     
Sbjct: 17 LSSSMSVSELKAQITQKIGVHAFQQRLAVHP 47

>d1v6ea_ d.15.1.1 (A:) Ubiquitin-like domain of tubulin folding cofactor B {Mouse (Mus musculus) [TaxId: 10090]} Length = 95

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of tubulin folding cofactor B
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.1 bits (96), Expect = 1e-06
 Identities = 6/50 (12%), Positives = 12/50 (24%), Gaps = 8/50 (16%)

Query: 1  IEDKEEILRDQQRFIFAGKR-------LEDGRTLVDYNIH-GSTLHSVRR 42
          +E               G          ++   L  Y +  G  +H +  
Sbjct: 38 LELVVGSPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIHVIDH 87

>d1v6ea_ d.15.1.1 (A:) Ubiquitin-like domain of tubulin folding cofactor B {Mouse (Mus musculus) [TaxId: 10090]} Length = 95

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of tubulin folding cofactor B
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.1 bits (91), Expect = 5e-06
 Identities = 10/48 (20%), Positives = 17/48 (35%), Gaps = 13/48 (27%)

Query: 46 GMQIFVESS-------------DTIDNVKAKIQDKKGTPPDQQRQIFW 80
          G+ +F+ SS              TI   K K++   G+P        +
Sbjct: 7  GVMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVGSPASCMELELY 54

>d1j8ca_ d.15.1.1 (A:) Ubiquitin-like N-terminal domain of PLIC-2 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like N-terminal domain of PLIC-2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.1 bits (96), Expect = 1e-06
 Identities = 7/33 (21%), Positives = 12/33 (36%)

Query: 49 IFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWF 81
            V  + ++   K  I  +  +  DQ   IF  
Sbjct: 46 FAVPENSSVQQFKEAISKRFKSQTDQLVLIFAG 78

>d1j8ca_ d.15.1.1 (A:) Ubiquitin-like N-terminal domain of PLIC-2 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like N-terminal domain of PLIC-2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.1 bits (96), Expect = 1e-06
 Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 1/43 (2%)

Query: 1   IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR 42
           I  + +   DQ   IFAGK L+D  TL+ + IH G T+H V +
Sbjct: 61  ISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIK 103

>d1yqba1 d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquilin-3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.0 bits (93), Expect = 2e-06
 Identities = 8/42 (19%), Positives = 13/42 (30%), Gaps = 1/42 (2%)

Query: 49 IFVESSDTIDNVKAKIQDKKGTPPDQQR-QIFWFVFGWGSLW 89
            V  + TI  +K +I  +    PDQ        +       
Sbjct: 21 FSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSL 62

>d1yqba1 d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquilin-3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.2 bits (78), Expect = 3e-04
 Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 1/43 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR 42
          I  + +   DQ   IFAGK L+D  +L    +  G T+H V +
Sbjct: 36 ISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIK 78

>d1wx8a1 d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]} Length = 83

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 4931431F19Rik
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.6 bits (92), Expect = 3e-06
 Identities = 7/42 (16%), Positives = 15/42 (35%)

Query: 40 VRRFRGGMQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWF 81
          V+  +   + F+  +  +   K +I        D+   IF  
Sbjct: 15 VKTPQDCHEFFLAENSNVRRFKKQISKYLHCNADRLVLIFTG 56

>d1wx8a1 d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]} Length = 83

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 4931431F19Rik
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.9 bits (85), Expect = 3e-05
 Identities = 16/43 (37%), Positives = 18/43 (41%), Gaps = 1/43 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR 42
          I        D+   IF GK L D   L    I  GST+H V R
Sbjct: 39 ISKYLHCNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVR 81

>d1t0ya_ d.15.1.1 (A:) Ubiquitin-like domain of tubulin folding cofactor B {Nematode (Caenorhabditis elegans) [TaxId: 6239]} Length = 90

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of tubulin folding cofactor B
species: Nematode (Caenorhabditis elegans) [TaxId: 6239]

 Score = 39.1 bits (91), Expect = 4e-06
 Identities = 10/54 (18%), Positives = 17/54 (31%), Gaps = 9/54 (16%)

Query: 1  IEDKEEILRDQQRFIFAGKR-------LEDGRTLVDYNIH-GSTLHSVRRFRGG 46
          +E       D  R               +  ++L D  +  G  +H+V    GG
Sbjct: 35 LELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHAVDV-TGG 87

>d1t0ya_ d.15.1.1 (A:) Ubiquitin-like domain of tubulin folding cofactor B {Nematode (Caenorhabditis elegans) [TaxId: 6239]} Length = 90

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of tubulin folding cofactor B
species: Nematode (Caenorhabditis elegans) [TaxId: 6239]

 Score = 38.7 bits (90), Expect = 7e-06
 Identities = 7/33 (21%), Positives = 16/33 (48%)

Query: 47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
          M+    +  +++++K K++   GT  D  R   
Sbjct: 18 MEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQL 50

>d2uyzb1 d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human (Homo sapiens) [TaxId: 9606]} Length = 77

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-1 (smt3 homologue)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.0 bits (86), Expect = 3e-05
 Identities = 8/46 (17%), Positives = 19/46 (41%), Gaps = 1/46 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRG 45
             ++ +  +  RF+F G+R+ D  T  +  +     +   +   G
Sbjct: 32 YCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTG 77

>d1v86a_ d.15.1.1 (A:) hypothetical D7wsu128e protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 95

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: hypothetical D7wsu128e protein
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.8 bits (85), Expect = 4e-05
 Identities = 17/54 (31%), Positives = 21/54 (38%), Gaps = 10/54 (18%)

Query: 24 GRTLVDYNI-HGSTLHSVRRFRGGMQIFVESSDTIDNVKAKIQDKKGTPPDQQR 76
          G+ LVD  I    T H V+         V    T   +K KI    G PP  Q+
Sbjct: 14 GKELVDLKIIWNKTKHDVK---------VPLDSTGSELKQKIHSITGLPPAMQK 58

>d1v86a_ d.15.1.1 (A:) hypothetical D7wsu128e protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 95

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: hypothetical D7wsu128e protein
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 33.8 bits (77), Expect = 6e-04
 Identities = 7/47 (14%), Positives = 18/47 (38%), Gaps = 2/47 (4%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG 46
          I     +    Q+ ++    + + +TL +  +  G+ +  V     G
Sbjct: 46 IHSITGLPPAMQKVMY-KGLVPEDKTLREIKVTSGAKIMVVGSTISG 91

>d1m94a_ d.15.1.1 (A:) Ubiquitin-like modifier protein hub1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 73

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like modifier protein hub1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 35.8 bits (82), Expect = 7e-05
 Identities = 8/39 (20%), Positives = 16/39 (41%), Gaps = 1/39 (2%)

Query: 1  IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLH 38
          +  +     ++      G  L+D  +L DY +H  + L 
Sbjct: 31 LSLQIGTQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLE 69

>d1m94a_ d.15.1.1 (A:) Ubiquitin-like modifier protein hub1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 73

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like modifier protein hub1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 31.6 bits (71), Expect = 0.002
 Identities = 5/35 (14%), Positives = 16/35 (45%)

Query: 47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWF 81
          +++   + D++ + K  +  + GT P++       
Sbjct: 14 VRVKCLAEDSVGDFKKVLSLQIGTQPNKIVLQKGG 48

>d1wjua_ d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens) [TaxId: 9606]} Length = 100

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: NEDD8 ultimate buster-1, NUB1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.0 bits (80), Expect = 2e-04
 Identities = 4/29 (13%), Positives = 11/29 (37%)

Query: 51 VESSDTIDNVKAKIQDKKGTPPDQQRQIF 79
               T   +++KI +  G   +  + + 
Sbjct: 36 TRLHITGRELRSKIAETFGLQENYIKIVI 64

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	97
d1wh3a_	87	2'-5'-oligoadenylate synthetase-like protein, OASL	99.51
d2zeqa1	78	Ubiquitin-like domain of parkin {Mouse (Mus muscul	99.51
d1ogwa_	76	Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}	99.48
d2faza1	76	Ubiquitin-like PHD and RING finger domain-containi	99.47
d1z2ma2	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.47
d1wh3a_	87	2'-5'-oligoadenylate synthetase-like protein, OASL	99.46
d2bwfa1	73	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.46
d2zeqa1	78	Ubiquitin-like domain of parkin {Mouse (Mus muscul	99.45
d1bt0a_	73	Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxI	99.45
d1z2ma2	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.45
d1wx9a1	73	Large proline-rich protein BAT3 {Human (Homo sapie	99.44
d1ttna1	80	Dendritic cell-derived ubiquitin-like protein {Hum	99.43
d1wy8a1	76	Ubiquitin-like PHD and RING finger domain-containi	99.43
d1bt0a_	73	Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxI	99.42
d2bwfa1	73	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.41
d1m94a_	73	Ubiquitin-like modifier protein hub1 {Baker's yeas	99.4
d1zkha1	86	Splicing factor 3 subunit 1, C-terminal domain {Hu	99.39
d1we6a_	111	Splicing factor 3 subunit 1, C-terminal domain {Th	99.39
d1ttna1	80	Dendritic cell-derived ubiquitin-like protein {Hum	99.37
d1uh6a_	100	Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculu	99.36
d1yqba1	84	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	99.35
d1ogwa_	76	Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}	99.35
d1yqba1	84	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	99.35
d1oqya4	77	Ubiquitin-like domain of Rad23 homolog A (Hhr23a)	99.34
d1wx9a1	73	Large proline-rich protein BAT3 {Human (Homo sapie	99.33
d1z2ma1	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.33
d1z2ma1	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.32
d2c9wb1	103	Elongin B {Human (Homo sapiens) [TaxId: 9606]}	99.32
d2faza1	76	Ubiquitin-like PHD and RING finger domain-containi	99.32
d1wy8a1	76	Ubiquitin-like PHD and RING finger domain-containi	99.31
d1j8ca_	103	Ubiquitin-like N-terminal domain of PLIC-2 {Human	99.29
d1wx8a1	83	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	99.29
d1m94a_	73	Ubiquitin-like modifier protein hub1 {Baker's yeas	99.28
d1wgha_	116	Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculu	99.28
d1wx8a1	83	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	99.26
d1se9a_	101	Hypothetical protein At3g01050 {Thale cress (Arabi	99.26
d1oqya4	77	Ubiquitin-like domain of Rad23 homolog A (Hhr23a)	99.23
d1j8ca_	103	Ubiquitin-like N-terminal domain of PLIC-2 {Human	99.23
d1uela_	95	Ubiquitin-like domain of Rad23 homolog B (Hhr23B)	99.22
d1se9a_	101	Hypothetical protein At3g01050 {Thale cress (Arabi	99.21
d1uela_	95	Ubiquitin-like domain of Rad23 homolog B (Hhr23B)	99.2
d1wgda_	93	Homocysteine-responsive endoplasmic reticulum-resi	99.19
d1uh6a_	100	Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculu	99.19
d1wgga_	96	Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (M	99.18
d2c9wb1	103	Elongin B {Human (Homo sapiens) [TaxId: 9606]}	99.17
d1wjua_	100	NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens	99.17
d1v86a_	95	hypothetical D7wsu128e protein {Mouse (Mus musculu	99.15
d1v5oa_	102	1700011n24rik protein {Mouse (Mus musculus) [TaxId	99.14
d1we6a_	111	Splicing factor 3 subunit 1, C-terminal domain {Th	99.14
d1x1ma1	94	Ubiquitin-like protein 7 {Mouse (Mus musculus) [Ta	99.12
d1zkha1	86	Splicing factor 3 subunit 1, C-terminal domain {Hu	99.12
d1wgha_	116	Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculu	99.11
d1v5ta_	90	8430435i17rik protein {Mouse (Mus musculus) [TaxId	99.1
d1euvb_	79	SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomy	99.09
d1v5oa_	102	1700011n24rik protein {Mouse (Mus musculus) [TaxId	99.08
d1wxva1	81	Bag-family molecular chaperone regulator-1 {Human	99.08
d1wjua_	100	NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens	99.08
d1wxva1	81	Bag-family molecular chaperone regulator-1 {Human	99.05
d1wgga_	96	Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (M	99.01
d1v5ta_	90	8430435i17rik protein {Mouse (Mus musculus) [TaxId	99.0
d1wiaa_	95	Ubiquitin-like protein bab25500 (2010008E23Rik) {M	98.99
d1wgda_	93	Homocysteine-responsive endoplasmic reticulum-resi	98.93
d1v86a_	95	hypothetical D7wsu128e protein {Mouse (Mus musculu	98.92
d1v2ya_	105	Ubiquitin-like protein 3300001g02rik {Mouse (Mus m	98.91
d1wiaa_	95	Ubiquitin-like protein bab25500 (2010008E23Rik) {M	98.87
d1v2ya_	105	Ubiquitin-like protein 3300001g02rik {Mouse (Mus m	98.78
d1v6ea_	95	Ubiquitin-like domain of tubulin folding cofactor	98.75
d1v6ea_	95	Ubiquitin-like domain of tubulin folding cofactor	98.74
d1wjna_	97	Tubulin-folding protein TbcE {Mouse (Mus musculus)	98.69
d2uyzb1	77	SUMO-1 (smt3 homologue) {Human (Homo sapiens) [Tax	98.57
d1wjna_	97	Tubulin-folding protein TbcE {Mouse (Mus musculus)	98.51
d1t0ya_	90	Ubiquitin-like domain of tubulin folding cofactor	98.49
d1x1ma1	94	Ubiquitin-like protein 7 {Mouse (Mus musculus) [Ta	98.48
d1euvb_	79	SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomy	98.43
d1t0ya_	90	Ubiquitin-like domain of tubulin folding cofactor	98.41
d2uyzb1	77	SUMO-1 (smt3 homologue) {Human (Homo sapiens) [Tax	98.1
d1wf9a1	94	NPL4-like protein 1 {Thale cress (Arabidopsis thal	97.6
d1wm3a_	72	SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}	97.3
d1wm3a_	72	SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}	96.39
d2al3a1	76	Tether containing UBX domain for GLUT4 (Tug) {Mous	95.74
d1wf9a1	94	NPL4-like protein 1 {Thale cress (Arabidopsis thal	94.8
d2al3a1	76	Tether containing UBX domain for GLUT4 (Tug) {Mous	88.46
d1wxma1	73	A-Raf proto-oncogene serine/threonine-protein kina	83.37
d1c1yb_	77	c-Raf1 RBD {Human (Homo sapiens) [TaxId: 9606]}	80.84

>d1wh3a_ d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like protein, OASL {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 2'-5'-oligoadenylate synthetase-like protein, OASL
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1.8e-14  Score=84.69  Aligned_cols=55  Identities=24%  Similarity=0.339  Sum_probs=48.7

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      .+.+.+.++..+|  +.+.|++++||.++|++|++++|||+++|+|+|+|++  |..+|
T Consensus         5 s~~mqI~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~~tL   63 (87)
T d1wh3a_           5 SSGIQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGL   63 (87)
T ss_dssp             SSSEEEEEEETTTEEEEEEECSSSBHHHHHHHHHHHTCCCTTTEEEEETTEECCSSSBH
T ss_pred             CCcEEEEEECCCCCEEEEEECCcCcHHHHHHHHHHHHCcChHHeEEEeeceEcCCCCcH
Confidence            5788899998877  5678899999999999999999999999999999999  44554

>d2zeqa1 d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of parkin
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.51  E-value=2.8e-15  Score=86.73  Aligned_cols=45  Identities=33%  Similarity=0.517  Sum_probs=42.0

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeec
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRG   45 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~   45 (97)
                      |++++|||+++|+|+|+|+.|+|+.+|++|+|. +++||++.++.+
T Consensus        32 i~~~~gip~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lv~R~rg   77 (78)
T d2zeqa1          32 VAKRQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRR   77 (78)
T ss_dssp             HHHHHTCCGGGEEEEETTEEECTTCBGGGSSCCTTCEEEEEESSCC
T ss_pred             HHHHHCcChhHeEEEEeeeEcCCCCCHHHcCCCCCCEEEEEeccCC
Confidence            456799999999999999999999999999999 999999998765

>d1ogwa_ d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=5.2e-15  Score=85.01  Aligned_cols=46  Identities=74%  Similarity=1.063  Sum_probs=43.0

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |+++.|+|+++|+|+|+|+.|+|+.||++|+|. +++|+++++..||
T Consensus        30 I~~~~gi~~~~qrL~~~Gk~L~d~~tL~~y~i~~~s~I~L~~rlrgG   76 (76)
T d1ogwa_          30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   76 (76)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECTTCC
T ss_pred             hhhhcCCChHHEEeEECCeEcCCCCCHHHcCCCCCCEEEEEEecCCC
Confidence            356789999999999999999999999999999 9999999998876

>d2faza1 d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING finger domain-containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like PHD and RING finger domain-containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=8.5e-15  Score=84.34  Aligned_cols=43  Identities=33%  Similarity=0.590  Sum_probs=40.4

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      |++++|||+++|+|+|+|+.|+|+.+|++|||+ +++||+++|.
T Consensus        32 I~~~~gip~~~qrLi~~Gk~L~D~~tL~~y~I~~~sti~lv~r~   75 (76)
T d2faza1          32 IQELFHVEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLLVRQ   75 (76)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTCBTTTTTCCTTCEEEEEECC
T ss_pred             HHHHHCcChHHeEEEEeeEeccCCCcHHHcCCCCCCEEEEEEEc
Confidence            467899999999999999999999999999999 9999999875

>d1z2ma2 d.15.1.1 (A:79-154) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=8.5e-15  Score=84.06  Aligned_cols=43  Identities=30%  Similarity=0.378  Sum_probs=40.1

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|||+ +++|++++|+
T Consensus        33 I~~~~gi~~~~qrL~~~gk~L~d~~tL~~y~I~~~sti~l~lRL   76 (76)
T d1z2ma2          33 VSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRL   76 (76)
T ss_dssp             HHHHHTCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECC
T ss_pred             HHHHhcCChhHeEEEECCeECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            467899999999999999999999999999999 9999998863

>d1wh3a_ d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like protein, OASL {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 2'-5'-oligoadenylate synthetase-like protein, OASL
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.46  E-value=5.6e-15  Score=86.96  Aligned_cols=46  Identities=33%  Similarity=0.444  Sum_probs=42.8

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++++|||+++|+|+|+|+.|+|+++|++|+|. +++|||+.+..++
T Consensus        37 I~~~~gip~~~qrLi~~Gk~L~d~~tL~~y~I~~~stl~l~~r~~~g   83 (87)
T d1wh3a_          37 IEDQQGLPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKGSG   83 (87)
T ss_dssp             HHHHTCCCTTTEEEEETTEECCSSSBHHHHTCCTTEEEEEEECSCCC
T ss_pred             HHHHHCcChHHeEEEeeceEcCCCCcHHHcCCCCCCEEEEEecCCCC
Confidence            467899999999999999999999999999999 9999999987765

>d2bwfa1 d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: DSK2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.46  E-value=6.2e-14  Score=79.91  Aligned_cols=53  Identities=19%  Similarity=0.188  Sum_probs=44.6

Q ss_pred             ceeeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           36 TLHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        36 ti~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      ++.+.++..++ +.+.|++++||.++|++|++.+|+|+++|+|+|+|++  |..+|
T Consensus         1 si~I~Vk~~~~~~~i~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL   56 (73)
T d2bwfa1           1 SLNIHIKSGQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTV   56 (73)
T ss_dssp             EEEEEEEETTEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBT
T ss_pred             CEEEEEEeCCeEEEEEECCCChHHHHHHHHHHHHCcChHHeEEEECCeEccCCCcH
Confidence            35666766555 6788999999999999999999999999999999999  44444

>d2zeqa1 d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of parkin
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.45  E-value=6.9e-14  Score=80.75  Aligned_cols=52  Identities=25%  Similarity=0.332  Sum_probs=44.3

Q ss_pred             eeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           37 LHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        37 i~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      +.+.++..+|  +.+.|++++||+++|++|++++|+|+++|+|+|+|++  |..+|
T Consensus         3 M~I~Vk~~~g~t~~l~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~d~~tL   58 (78)
T d2zeqa1           3 MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVIFAGKELPNHLTV   58 (78)
T ss_dssp             EEEEEESSSSSCEEEEECTTCBHHHHHHHHHHHHTCCGGGEEEEETTEEECTTCBG
T ss_pred             eEEEEEcCCCCEEEEEEcccccHHHHHHHHHHHHCcChhHeEEEEeeeEcCCCCCH
Confidence            4567776665  6688899999999999999999999999999999999  44444

>d1bt0a_ d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Rub1
species: Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.45  E-value=1.3e-14  Score=82.66  Aligned_cols=43  Identities=53%  Similarity=0.770  Sum_probs=39.9

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|+|+ ++++|+++|+
T Consensus        30 i~~~~gi~~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lvlrL   73 (73)
T d1bt0a_          30 VEEKEGIPPVQQRLIYAGKQLADDKTAKDYNIEGGSVLHLVLAL   73 (73)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECC
T ss_pred             HHHHhCCChHHEEEEECCeEcCCCCcHHHcCCCCCCEEEEEeeC
Confidence            356789999999999999999999999999999 9999999873

>d1z2ma2 d.15.1.1 (A:79-154) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.45  E-value=8.4e-14  Score=79.77  Aligned_cols=54  Identities=19%  Similarity=0.093  Sum_probs=46.9

Q ss_pred             cceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           35 STLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        35 sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      ..+.+.++..+|  +.+.|++++||.++|++|++++|+|+++|+|+|+|++  |..+|
T Consensus         2 ~~~qi~Vk~~~G~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~qrL~~~gk~L~d~~tL   59 (76)
T d1z2ma2           2 EPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPL   59 (76)
T ss_dssp             CCEEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBG
T ss_pred             CCEEEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHhcCChhHeEEEECCeECCCCCcH
Confidence            467888888777  5688899999999999999999999999999999999  44444

>d1wx9a1 d.15.1.1 (A:8-80) Large proline-rich protein BAT3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Large proline-rich protein BAT3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.44  E-value=4.6e-14  Score=80.51  Aligned_cols=52  Identities=17%  Similarity=0.188  Sum_probs=44.0

Q ss_pred             eeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           37 LHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        37 i~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      +.+.++..+|  +.+.|++++||+++|++|++++|+|+++|+|+|+|++  |..+|
T Consensus         1 m~I~Vk~~~g~~~~l~V~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~~tL   56 (73)
T d1wx9a1           1 LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKL   56 (73)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHCCCTTTCCCEETTEECCSSSBH
T ss_pred             CEEEEEcCCCCEEEEEECCCChHHHHHHHHHHHhCCChHHEEEEECCeEccCCCCH
Confidence            3566776665  5688899999999999999999999999999999999  44443

>d1ttna1 d.15.1.1 (A:21-100) Dendritic cell-derived ubiquitin-like protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Dendritic cell-derived ubiquitin-like protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.43  E-value=1.3e-13  Score=79.83  Aligned_cols=55  Identities=24%  Similarity=0.309  Sum_probs=47.5

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      |..+.+.++...|  +.+.|++++||+++|++|++++|+|+++|+|+|+|++  |..+|
T Consensus         1 g~e~qi~Vk~~~G~~~~l~V~~~~tV~~lK~~I~~~~~ip~~~qrLi~~Gk~L~d~~tL   59 (80)
T d1ttna1           1 GYECQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKF   59 (80)
T ss_dssp             CCSEEEEEEETTTEEEEEEECTTSHHHHHHHHHHHTTCCCSTTCEEEETTEECCTTSHH
T ss_pred             CCeEEEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCcccEEEEECceEcCCCCcH
Confidence            3567888888877  5678899999999999999999999999999999999  44443

>d1wy8a1 d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING finger domain-containing protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like PHD and RING finger domain-containing protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.43  E-value=1.6e-14  Score=83.21  Aligned_cols=43  Identities=28%  Similarity=0.483  Sum_probs=40.2

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      |++++|||+++|+|+|+|+.|+|+.+|++|||. +++||+++++
T Consensus        32 I~~~~gip~~~qrLi~~Gk~L~d~~tL~~y~I~~~s~i~lv~rp   75 (76)
T d1wy8a1          32 VWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVRP   75 (76)
T ss_dssp             HHHHSCCCTTTEEEEETTEECCSSSBHHHHTCCTTCEEEEEECC
T ss_pred             HHHHHCCCchhcEEEEEeeEecCCCCHHHcCCCCCCEEEEEEcc
Confidence            467899999999999999999999999999999 9999999874

>d1bt0a_ d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Rub1
species: Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.42  E-value=1.4e-13  Score=78.33  Aligned_cols=46  Identities=35%  Similarity=0.498  Sum_probs=41.3

Q ss_pred             eeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           38 HSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        38 ~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .+.++...|  +.+.|++++||+++|++|++++|+|+++|+|+|+|++
T Consensus         2 ~I~Vk~~~G~~~~l~V~~~~tV~~lK~~i~~~~gi~~~~qrLi~~Gk~   49 (73)
T d1bt0a_           2 LIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLIYAGKQ   49 (73)
T ss_dssp             EEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEE
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhCCChHHEEEEECCeE
Confidence            456676666  6688899999999999999999999999999999999

>d2bwfa1 d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: DSK2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.41  E-value=4e-14  Score=80.72  Aligned_cols=42  Identities=36%  Similarity=0.638  Sum_probs=39.0

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR   42 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~   42 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|||. |++|||+.+
T Consensus        30 I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~I~~g~~i~lV~~   72 (73)
T d2bwfa1          30 INKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS   72 (73)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEEC
T ss_pred             HHHHHCcChHHeEEEECCeEccCCCcHHHCCCCCCCEEEEEee
Confidence            356789999999999999999999999999999 999999865

>d1m94a_ d.15.1.1 (A:) Ubiquitin-like modifier protein hub1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like modifier protein hub1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.40  E-value=1.9e-13  Score=77.92  Aligned_cols=52  Identities=19%  Similarity=0.126  Sum_probs=44.7

Q ss_pred             eeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           37 LHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        37 i~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      +.+.++...|  +.+.|++++||+++|++|++++|+|+++|+|+|+|+.  |..+|
T Consensus         2 i~i~vk~~~Gk~~~v~V~~~~tV~~lK~~I~~~~~i~~~~q~Li~~Gk~L~d~~tL   57 (73)
T d1m94a_           2 IEVVVNDRLGKKVRVKCLAEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHISL   57 (73)
T ss_dssp             EEEEEEETTTEEEEEEECTTSBHHHHHHHHHHHHCCTTTSEEEESSSCEECTTSBH
T ss_pred             eEEEEECCCCCEEEEEECCcCcHHHHHHHHHHhhcccccEEEEEEEeEEecccCcH
Confidence            4567777666  6688899999999999999999999999999999999  54554

>d1zkha1 d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Splicing factor 3 subunit 1, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.39  E-value=3.4e-14  Score=83.53  Aligned_cols=45  Identities=24%  Similarity=0.496  Sum_probs=41.7

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeec
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRG   45 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~   45 (97)
                      |++++|+|+++|+|+|+|+.|+|+.||++|||. +++|||+++.+|
T Consensus        41 I~~~~~ip~~~q~Li~~Gk~L~D~~tL~dY~I~~gsti~l~~r~RG   86 (86)
T d1zkha1          41 IHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMANGAVIHLALKERG   86 (86)
T ss_dssp             HHHHTCCCTTTEEEEETTEEECTTSBHHHHTCCTTEEEEEEESCCC
T ss_pred             HHhhhcCChHHEEEEeCCcCcCCCCCHHHcCCCCCCEEEEEEecCC
Confidence            467899999999999999999999999999999 999999998654

>d1we6a_ d.15.1.1 (A:) Splicing factor 3 subunit 1, C-terminal domain {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Splicing factor 3 subunit 1, C-terminal domain
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.39  E-value=2.1e-14  Score=88.13  Aligned_cols=47  Identities=28%  Similarity=0.341  Sum_probs=44.1

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecce
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGGM   47 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g~   47 (97)
                      |++++|+|+++|+|+|+|+.|+|+.||++|||. +++|+|+++.+||.
T Consensus        61 I~~~~gip~~~QrLi~~Gk~L~D~~tL~~ynI~~gsti~L~lr~rGG~  108 (111)
T d1we6a_          61 IAGEIQIPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLRERSGP  108 (111)
T ss_dssp             HHHHTTCCTTTSEEECSSSBCCTTSBTTTTTCSSSCEEEEECSSCCSS
T ss_pred             HHHHHCCCccceEEEEeeEEccccCCHHHcCCCCCCEEEEEeeCCCCC
Confidence            457899999999999999999999999999999 99999999999873

>d1ttna1 d.15.1.1 (A:21-100) Dendritic cell-derived ubiquitin-like protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Dendritic cell-derived ubiquitin-like protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.37  E-value=4.1e-14  Score=81.96  Aligned_cols=44  Identities=18%  Similarity=0.331  Sum_probs=40.7

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFR   44 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~   44 (97)
                      |++++|+|+++|+|+|+|+.|+|+++|++|+|+ +++||++++.+
T Consensus        33 I~~~~~ip~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lvi~~p   77 (80)
T d1ttna1          33 LHAAEGVEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQP   77 (80)
T ss_dssp             HHHTTCCCSTTCEEEETTEECCTTSHHHHCCCSSSCEEEEECCCS
T ss_pred             HHHHhCCCcccEEEEECceEcCCCCcHHHcCCCCCCEEEEEecCC
Confidence            467899999999999999999999999999999 99999998754

>d1uh6a_ d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 5, ubl5
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.36  E-value=5.3e-13  Score=80.41  Aligned_cols=54  Identities=24%  Similarity=0.325  Sum_probs=46.7

Q ss_pred             cceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           35 STLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        35 sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      ..+.+.++...|  +.+.|.|++||++||++|++++|+|+++|+|+|+|++  |..+|
T Consensus        27 ~~i~V~V~~~~Gk~~~v~V~p~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL   84 (100)
T d1uh6a_          27 TMIEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSL   84 (100)
T ss_dssp             CEEEEEEECSSSSCEEEEEETTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCSSCBH
T ss_pred             ceEEEEEECCCCCEEEEEECCcChHHHHHHHHHHHHCCCcceEEEEEEeecccCcCCH
Confidence            357888888766  6788899999999999999999999999999999999  44443

>d1yqba1 d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquilin-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.35  E-value=7.4e-14  Score=81.60  Aligned_cols=45  Identities=33%  Similarity=0.442  Sum_probs=41.5

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeec
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRG   45 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~   45 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|||. |++|+|+++...
T Consensus        36 i~~~~gi~~~~qrL~~~Gk~L~D~~tL~~y~i~~gsti~lv~r~~~   81 (84)
T d1yqba1          36 ISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQH   81 (84)
T ss_dssp             HHHHHTCCGGGEEEEETTEECCTTSBHHHHTCCTTCEEEEEECCCC
T ss_pred             HHHHHCcCchhEEEEEeeeeccccCcHHHcCCCCCCEEEEEECCCC
Confidence            457799999999999999999999999999999 999999988654

>d1ogwa_ d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.35  E-value=7.8e-13  Score=75.66  Aligned_cols=47  Identities=53%  Similarity=0.661  Sum_probs=41.9

Q ss_pred             eeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           37 LHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        37 i~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +.+.++..+|  +.+.|++++||.++|++|+++.|+|+++|+|+|+|++
T Consensus         1 MqI~Vk~l~G~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~qrL~~~Gk~   49 (76)
T d1ogwa_           1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQ   49 (76)
T ss_dssp             CEEEEEETTSCEEEEECCTTSBHHHHHHHHHHHHCCCGGGEEEEETTEE
T ss_pred             CEEEEEcCCCCEEEEEECCCCcHHHHHHhhhhhcCCChHHEEeEECCeE
Confidence            3567776666  6678899999999999999999999999999999999

>d1yqba1 d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquilin-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.35  E-value=8.4e-13  Score=76.98  Aligned_cols=49  Identities=20%  Similarity=0.173  Sum_probs=44.7

Q ss_pred             cceeeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           35 STLHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        35 sti~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .+|.+.++..++ ..+.|++++||++||++|++++|+|+++|+|+|+|++
T Consensus         6 ~~i~I~Vkt~~~~~~~~V~~~~tV~~lK~~i~~~~gi~~~~qrL~~~Gk~   55 (84)
T d1yqba1           6 HLIKVTVKTPKDKEDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKI   55 (84)
T ss_dssp             TEEEEEEECSSCEEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEE
T ss_pred             CEEEEEEEcCCCcEEEEECCCCcHHHHHHHHHHHHCcCchhEEEEEeeee
Confidence            368888887766 6688999999999999999999999999999999999

>d1oqya4 d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 homolog A (Hhr23a) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of Rad23 homolog A (Hhr23a)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.34  E-value=5.8e-13  Score=76.43  Aligned_cols=54  Identities=22%  Similarity=0.238  Sum_probs=45.8

Q ss_pred             cceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcC---CCCCceEEEECeEe--CCCcc
Q 040204           35 STLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKG---TPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        35 sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~g---ip~~~q~Lif~G~~--~~~~~   88 (97)
                      +.+.+.++...|  +.+.|++++||+++|++|+++.|   +|+++|+|+|+|+.  |..+|
T Consensus         1 s~~~i~vk~l~g~~~~l~v~~~~TV~~lK~~i~~~~g~~~i~~~~qrLi~~Gk~L~D~~tL   61 (77)
T d1oqya4           1 SAVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPI   61 (77)
T ss_dssp             CCCCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSSEECSSSBT
T ss_pred             CcEEEEEECCCCCEEEEEECCCCcHHHHHHHHHHhcCCCCCChHHEEeEECCcCccCCCcH
Confidence            457788887776  66788999999999999999987   99999999999999  44443

>d1wx9a1 d.15.1.1 (A:8-80) Large proline-rich protein BAT3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Large proline-rich protein BAT3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.33  E-value=3.3e-14  Score=81.14  Aligned_cols=43  Identities=35%  Similarity=0.658  Sum_probs=39.4

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceecccceeeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIHGSTLHSVRRF   43 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~~sti~l~i~~   43 (97)
                      |++++|+|+++|+|+|+|+.|+|+++|++|+|.++++||+.+.
T Consensus        30 I~~~~gip~~~qrLi~~Gk~L~d~~tL~dy~i~~~ti~lv~r~   72 (73)
T d1wx9a1          30 IAASVSIPSEKQRLIYQGRVLQDDKKLQEYNVGGKVIHLVERA   72 (73)
T ss_dssp             HHHHHCCCTTTCCCEETTEECCSSSBHHHHTCTTEEEBCCCSS
T ss_pred             HHHHhCCChHHEEEEECCeEccCCCCHHHhCCCCCEEEEEecC
Confidence            4678999999999999999999999999999998899998765

>d1z2ma1 d.15.1.1 (A:3-78) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.33  E-value=2e-13  Score=78.41  Aligned_cols=43  Identities=30%  Similarity=0.285  Sum_probs=39.4

Q ss_pred             CccccCCCCcceEEEE--CCEEeCCCCCCccceec-ccceeeeeee
Q 040204            1 IEDKEEILRDQQRFIF--AGKRLEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~--~g~~L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      |++++|+|+++|+|+|  +|+.|+|+.+|++|||. |++|+|+++.
T Consensus        30 I~~~~gip~~~QrLi~~~~Gk~L~D~~tL~~y~i~~g~~i~lv~~~   75 (76)
T d1z2ma1          30 ITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDK   75 (76)
T ss_dssp             HHHHHCCCGGGEEEEEETTCCBCCSSSCSGGGTCCTTCEEEEEECC
T ss_pred             HHHHhccCCccEEEEEcCCCeeccCCCcHHHcCCCCCCEEEEEEEC
Confidence            4567899999999999  69999999999999999 9999999863

>d1z2ma1 d.15.1.1 (A:3-78) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.32  E-value=1.2e-12  Score=75.02  Aligned_cols=51  Identities=27%  Similarity=0.235  Sum_probs=43.3

Q ss_pred             eeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEE--CeEe--CCCcc
Q 040204           38 HSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIF--WFVF--GWGSL   88 (97)
Q Consensus        38 ~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif--~G~~--~~~~~   88 (97)
                      .+.++..+|  +.+.|++++||+++|++|++++|+|+++|+|+|  +|+.  |..+|
T Consensus         2 ~l~Vk~l~G~~~~v~V~~~~tV~~lK~~I~~~~gip~~~QrLi~~~~Gk~L~D~~tL   58 (76)
T d1z2ma1           2 DLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPL   58 (76)
T ss_dssp             EEEEEESSSCEEEEECCSSCCHHHHHHHHHHHHCCCGGGEEEEEETTCCBCCSSSCS
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhccCCccEEEEEcCCCeeccCCCcH
Confidence            356676666  568889999999999999999999999999999  7988  55554

>d2c9wb1 d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Elongin B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.32  E-value=1.5e-12  Score=78.81  Aligned_cols=51  Identities=20%  Similarity=0.096  Sum_probs=41.7

Q ss_pred             eeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           38 HSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        38 ~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      ++.++..+. +.+.|++++||.+||++|++++|+|+++|+|+|+|++  |..+|
T Consensus         3 fv~i~~~k~Ti~l~v~~~~TV~~lK~~I~~~~gip~~~QrLi~~Gk~L~D~~TL   56 (103)
T d2c9wb1           3 FLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTL   56 (103)
T ss_dssp             EEEEEEBTEEEEEEECTTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBH
T ss_pred             EEEEeCCCEEEEEEeCCCCcHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCH
Confidence            344443332 5678899999999999999999999999999999999  55655

>d2faza1 d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING finger domain-containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like PHD and RING finger domain-containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.32  E-value=1.8e-12  Score=74.34  Aligned_cols=51  Identities=18%  Similarity=0.154  Sum_probs=41.6

Q ss_pred             eeeeeeecc---eee-eeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           38 HSVRRFRGG---MQI-FVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        38 ~l~i~~~~g---~~i-~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      .+.++..+|   ..+ .+++++||+++|++|++++|+|+++|+|+|+|+.  |..+|
T Consensus         2 ~I~Vktl~Gk~t~~l~~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL   58 (76)
T d2faza1           2 WIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTL   58 (76)
T ss_dssp             EEEEEETTSSCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBT
T ss_pred             EEEEEeCCCCcEEEEecCCCCCCHHHHHHHHHHHHCcChHHeEEEEeeEeccCCCcH
Confidence            456676665   234 3699999999999999999999999999999999  44444

>d1wy8a1 d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING finger domain-containing protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like PHD and RING finger domain-containing protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.31  E-value=2.4e-12  Score=73.80  Aligned_cols=51  Identities=20%  Similarity=0.135  Sum_probs=42.1

Q ss_pred             eeeeeeecc---eee-eeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           38 HSVRRFRGG---MQI-FVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        38 ~l~i~~~~g---~~i-~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      .+.++..+|   ..+ .|++++||++||++|++++|+|+++|+|+|+|++  |..+|
T Consensus         2 ~I~Vk~l~G~~t~~~~~v~~~~TV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~~tL   58 (76)
T d1wy8a1           2 WIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTL   58 (76)
T ss_dssp             EEEEEETTCSCEEEEEEECTTCBHHHHHHHHHHHSCCCTTTEEEEETTEECCSSSBH
T ss_pred             EEEEEeCCCCceEEEeccCCCChHHHHHHHHHHHHCCCchhcEEEEEeeEecCCCCH
Confidence            456666665   334 4899999999999999999999999999999999  44444

>d1j8ca_ d.15.1.1 (A:) Ubiquitin-like N-terminal domain of PLIC-2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like N-terminal domain of PLIC-2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.29  E-value=6.4e-13  Score=80.18  Aligned_cols=42  Identities=43%  Similarity=0.567  Sum_probs=39.2

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR   42 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~   42 (97)
                      |++.+|+|+++|+|+|+|+.|+|+.+|++|||+ |++|||++|
T Consensus        61 I~~~~gi~~~~qrLi~~Gk~L~D~~tL~~~~I~~g~~I~lvlr  103 (103)
T d1j8ca_          61 ISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIK  103 (103)
T ss_dssp             HHHHHCSCSSSEEEEETTEEESTTSCGGGTTCSSSEEEEEEEC
T ss_pred             HHHHHCcCHHHeeeeeeeecccCCCcHHHcCCCCCCEEEEEEC
Confidence            456789999999999999999999999999999 999999875

>d1wx8a1 d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 4931431F19Rik
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.29  E-value=2.1e-12  Score=75.08  Aligned_cols=50  Identities=12%  Similarity=0.123  Sum_probs=45.1

Q ss_pred             ccceeeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      ..++.+.++..++ ..+.|++++||.+||++|++.+|+|+++|+|+|+|++
T Consensus         8 ~~~i~v~Vk~~~~~~~i~v~~~~tV~~lK~~I~~~~~v~~~~qrL~f~Gk~   58 (83)
T d1wx8a1           8 SRIIRVSVKTPQDCHEFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKI   58 (83)
T ss_dssp             SCEEEEEEECSSSEEEEEEETTCCHHHHHHHHHHHTCSCTTTBCCEETTEE
T ss_pred             CCeEEEEEEcCCCcEEEEECCCChHHHHHHHHHHHhCCChhHEEEEEEhhc
Confidence            4578888887666 6688899999999999999999999999999999999

>d1m94a_ d.15.1.1 (A:) Ubiquitin-like modifier protein hub1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like modifier protein hub1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.28  E-value=1.8e-13  Score=77.96  Aligned_cols=41  Identities=20%  Similarity=0.232  Sum_probs=37.9

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVR   41 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i   41 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|+|+ |++++|..
T Consensus        31 I~~~~~i~~~~q~Li~~Gk~L~d~~tL~~y~I~~gstl~L~~   72 (73)
T d1m94a_          31 LSLQIGTQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLELYY   72 (73)
T ss_dssp             HHHHHCCTTTSEEEESSSCEECTTSBHHHHTCCTTEEEEEEE
T ss_pred             HHHhhcccccEEEEEEEeEEecccCcHHHcCCCCCCEEEEEE
Confidence            457789999999999999999999999999999 99999863

>d1wgha_ d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3, Ubl3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.28  E-value=5e-12  Score=77.90  Aligned_cols=60  Identities=13%  Similarity=0.279  Sum_probs=49.6

Q ss_pred             cceecccceeeeeeeecc--eeeeeeccchhHHHHHhh--------hhhcCCCCCceEEEECeEe--CCCcc
Q 040204           29 DYNIHGSTLHSVRRFRGG--MQIFVESSDTIDNVKAKI--------QDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        29 ~y~I~~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I--------~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      .......+|.+.++..+|  ..+.|++++||.+||++|        +++.|+||++|||||+||.  |..+|
T Consensus         9 s~~~~~~~i~i~v~~l~Gk~~~~~v~p~~TV~~lK~~I~~~~p~~~~e~~~~~~~~qRLiy~Gk~L~D~~tL   80 (116)
T d1wgha_           9 SSHVPADMINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTL   80 (116)
T ss_dssp             CCCCCSSSEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEEETTEEECSSCBT
T ss_pred             cCCCCCCeEEEEEEEcCCCEEEEEECCcchHHHHHHHHHhhcccccccccCCChHHeEEEECCEEecCCCCH
Confidence            333336788899988777  557889999999999999        6888999999999999999  55554

>d1wx8a1 d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 4931431F19Rik
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.26  E-value=2.2e-13  Score=79.34  Aligned_cols=43  Identities=37%  Similarity=0.407  Sum_probs=39.7

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      |++.+|+|+++|+|+|+|+.|+|+.+|++|||. |++|+|+++.
T Consensus        39 I~~~~~v~~~~qrL~f~Gk~L~d~~tL~~~gI~~gs~I~lv~r~   82 (83)
T d1wx8a1          39 ISKYLHCNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVRS   82 (83)
T ss_dssp             HHHHTCSCTTTBCCEETTEECCTTSCHHHHTCCTTEEEECCBCC
T ss_pred             HHHHhCCChhHEEEEEEhhccccCCcHHHcCCCCCCEEEEEEeC
Confidence            356789999999999999999999999999999 9999998864

>d1se9a_ d.15.1.1 (A:) Hypothetical protein At3g01050 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Hypothetical protein At3g01050
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.26  E-value=2.1e-12  Score=77.86  Aligned_cols=43  Identities=30%  Similarity=0.397  Sum_probs=38.8

Q ss_pred             cccCCC--CcceEEEECCEEeCCCCCCccceec-cc------ceeeeeeeec
Q 040204            3 DKEEIL--RDQQRFIFAGKRLEDGRTLVDYNIH-GS------TLHSVRRFRG   45 (97)
Q Consensus         3 ~~~gip--~~~Q~L~~~g~~L~d~~tL~~y~I~-~s------ti~l~i~~~~   45 (97)
                      +++|+|  +++|||+|+|+.|+|++||++|+|. |+      ++||+++.+.
T Consensus        45 ~k~~iP~~~~~qRLIf~Gk~L~D~~tL~dy~i~~g~~~~~~~tmHlVvrpp~   96 (101)
T d1se9a_          45 EKENGPKTVKEVKLISAGKVLENSKTVKDYRSPVSNLAGAVTTMHVIIQAPV   96 (101)
T ss_dssp             TCSSSCCSGGGEEEEETTEECCTTSBGGGGSCCTTSCTTCCEEEEEEECCCS
T ss_pred             cccCCCCCcccEEEEECCeEecCCCCHHHcCCCCCCcCCCceEEEEEeCCCC
Confidence            358998  7899999999999999999999999 86      9999998754

>d1oqya4 d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 homolog A (Hhr23a) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of Rad23 homolog A (Hhr23a)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.23  E-value=1.4e-12  Score=74.79  Aligned_cols=37  Identities=27%  Similarity=0.385  Sum_probs=34.6

Q ss_pred             CCCCcceEEEECCEEeCCCCCCccceec-ccceeeeee
Q 040204            6 EILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR   42 (97)
Q Consensus         6 gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~   42 (97)
                      .+|+++|+|+|+|+.|+|+++|++|||+ +++++++++
T Consensus        40 ~i~~~~qrLi~~Gk~L~D~~tL~~y~I~~~s~i~~~vs   77 (77)
T d1oqya4          40 AFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVT   77 (77)
T ss_dssp             SCCSTEEEEESSSSEECSSSBTTTTCCCTTSCEEEEEE
T ss_pred             CCChHHEEeEECCcCccCCCcHHHcCCCCCCEEEEEEC
Confidence            3999999999999999999999999999 999998863

>d1j8ca_ d.15.1.1 (A:) Ubiquitin-like N-terminal domain of PLIC-2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like N-terminal domain of PLIC-2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.23  E-value=1.1e-11  Score=74.59  Aligned_cols=55  Identities=15%  Similarity=0.118  Sum_probs=47.2

Q ss_pred             ccceeeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           34 GSTLHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      ..+|.+.++..++ ..+.|++++||.+||++|++.+|+|+++|+|+|+|++  |..+|
T Consensus        30 ~~~i~V~Vk~~~~~~~i~V~~~~tV~~LK~~I~~~~gi~~~~qrLi~~Gk~L~D~~tL   87 (103)
T d1j8ca_          30 PKIIKVTVKTPKEKEEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTL   87 (103)
T ss_dssp             CCCEEEEEECSSCEEEEEECTTCCHHHHHHHHHHHHCSCSSSEEEEETTEEESTTSCG
T ss_pred             CCeEEEEEECCCccEEEEECCCChHHHHHHHHHHHHCcCHHHeeeeeeeecccCCCcH
Confidence            4478888877665 6788999999999999999999999999999999999  44444

>d1uela_ d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homolog B (Hhr23B) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of Rad23 homolog B (Hhr23B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.22  E-value=1.2e-11  Score=73.38  Aligned_cols=51  Identities=22%  Similarity=0.275  Sum_probs=42.4

Q ss_pred             eeeeeeecc--eeeeeeccchhHHHHHhhhhhcC---CCCCceEEEECeEe--CCCcc
Q 040204           38 HSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKG---TPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        38 ~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~g---ip~~~q~Lif~G~~--~~~~~   88 (97)
                      .+.++..+|  +.+.|++++||.++|++|+++.|   +|+++|+|+|+|++  |..+|
T Consensus         2 ~I~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~~~~i~~~~qrLi~~Gk~L~d~~tL   59 (95)
T d1uela_           2 QVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTAL   59 (95)
T ss_dssp             EEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEETTEECCTTSBG
T ss_pred             EEEEEeCCCCEEEEEECCCccHHHHHHHHHhhhcccCCCccceEEEECCeEccCCCcH
Confidence            466676666  67888999999999999999875   89999999999999  44443

>d1se9a_ d.15.1.1 (A:) Hypothetical protein At3g01050 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Hypothetical protein At3g01050
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.21  E-value=1.5e-11  Score=74.01  Aligned_cols=55  Identities=13%  Similarity=0.109  Sum_probs=46.6

Q ss_pred             ccceeeeeeeecce---eeeeeccchhHHHHHhhhhh-----cCCC--CCceEEEECeEe--CCCcc
Q 040204           34 GSTLHSVRRFRGGM---QIFVESSDTIDNVKAKIQDK-----KGTP--PDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~~~~g~---~i~v~~~~TV~~lK~~I~~~-----~gip--~~~q~Lif~G~~--~~~~~   88 (97)
                      +.++.+.++..+|.   .+.+++++||.+||++|++.     +|+|  +++|||||+||+  |..+|
T Consensus         5 ~~~i~I~~r~~~G~~i~~~~v~~s~TV~~lK~~I~~~~~~~k~~iP~~~~~qRLIf~Gk~L~D~~tL   71 (101)
T d1se9a_           5 HNQLEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSKTV   71 (101)
T ss_dssp             CCCEEEEEEETTSCEEEEEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEEETTEECCTTSBG
T ss_pred             cceEEEEEEeCCCCeecceecCccCHHHHHHHHHHHhccccccCCCCCcccEEEEECCeEecCCCCH
Confidence            57888999998883   36779999999999999764     7898  889999999999  55655

>d1uela_ d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homolog B (Hhr23B) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of Rad23 homolog B (Hhr23B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.20  E-value=2.9e-12  Score=76.07  Aligned_cols=42  Identities=24%  Similarity=0.347  Sum_probs=37.9

Q ss_pred             cCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            5 EEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         5 ~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      .++|+++|+|+|+|+.|+|+.+|++|||. +++|+++++.+.+
T Consensus        37 ~~i~~~~qrLi~~Gk~L~d~~tL~~y~I~~~s~i~lv~~~~~~   79 (95)
T d1uela_          37 DAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKPKA   79 (95)
T ss_dssp             TTCCTTTEEEEETTEECCTTSBGGGGTCCSSSEEEEEESSCCC
T ss_pred             cCCCccceEEEECCeEccCCCcHHHcCCCCCCEEEEEECCCCC
Confidence            35899999999999999999999999999 9999999875543

>d1wgda_ d.15.1.1 (A:) Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.19  E-value=1.8e-11  Score=72.58  Aligned_cols=50  Identities=14%  Similarity=0.177  Sum_probs=42.2

Q ss_pred             ccceeeeeeeecc----eeeeeeccchhHHHHHhhhhhcC--CCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG----MQIFVESSDTIDNVKAKIQDKKG--TPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g----~~i~v~~~~TV~~lK~~I~~~~g--ip~~~q~Lif~G~~   83 (97)
                      .+.+.+.++..++    +.+.+++++||.+||++|++..+  +|+++|||||+||+
T Consensus         5 s~~i~l~Ik~~~~~~~~~~~~v~~~~TV~~LK~~I~~~~~~~~~~~~qrLIy~Gk~   60 (93)
T d1wgda_           5 SSGVTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKL   60 (93)
T ss_dssp             SCCCEEEEECSSSSCCCEEEECCTTSCHHHHHHHHHHHSTTCCCTTTCEEEETTEE
T ss_pred             CCcEEEEEECCCCCceeEEEEcCCCCcHHHHHHHHHHHcCCCCChHHEEEEECCeE
Confidence            3467777776544    56777999999999999999854  99999999999999

>d1uh6a_ d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 5, ubl5
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.19  E-value=1.4e-12  Score=78.57  Aligned_cols=41  Identities=22%  Similarity=0.178  Sum_probs=38.4

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVR   41 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i   41 (97)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|+|+ |++|+|+.
T Consensus        58 I~~~~gip~~~qrLi~~Gk~L~D~~tL~dygI~~GstI~L~~   99 (100)
T d1uh6a_          58 IAAQTGTRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLELYY   99 (100)
T ss_dssp             HHHHHCCCGGGCEEEETTEECCSSCBHHHHTCCTTEEEEEEC
T ss_pred             HHHHHCCCcceEEEEEEeecccCcCCHHHcCCCCCCEEEEEE
Confidence            467899999999999999999999999999999 99999875

>d1wgga_ d.15.1.1 (A:) Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin carboxyl-terminal hydrolase 14
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.18  E-value=1.5e-11  Score=73.24  Aligned_cols=50  Identities=12%  Similarity=0.070  Sum_probs=44.9

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .+.+.+.++..++  ..+.|++++||.+||++|++.+|+|+++|+|+|+|++
T Consensus         5 s~~~~I~VK~~~~~~~~v~v~~~~tV~~lK~~i~~~~gvp~~~QkLi~~Gk~   56 (96)
T d1wgga_           5 SSGYSVTVKWGKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGT   56 (96)
T ss_dssp             CCEEEEEEEETTEEEEEEEEESSSCHHHHHHHHHHHTCCCTTTSCCEETTEE
T ss_pred             CCceEEEEEeCCCCEEEEEECCCCcHHHHHHHhhhhcCccceeeEEeecCcc
Confidence            4577888888776  3588899999999999999999999999999999998

>d2c9wb1 d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Elongin B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.17  E-value=2.9e-12  Score=77.47  Aligned_cols=47  Identities=23%  Similarity=0.253  Sum_probs=40.4

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec--------ccceeeeeeeecce
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH--------GSTLHSVRRFRGGM   47 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~--------~sti~l~i~~~~g~   47 (97)
                      |++++|||+++|+|+|+|++|+|++||++|||.        .+++++.++..++.
T Consensus        30 I~~~~gip~~~QrLi~~Gk~L~D~~TL~dYgI~~~~~~~~~~~~~~l~~~~~~~~   84 (103)
T d2c9wb1          30 VEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTF   84 (103)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTSBHHHHTCCTTTSBTTBCEEEEEEEEETTEE
T ss_pred             HHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCcccccccCCcEEEEEEecCCCc
Confidence            467899999999999999999999999999994        44777877766664

>d1wjua_ d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: NEDD8 ultimate buster-1, NUB1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.17  E-value=1.7e-11  Score=73.59  Aligned_cols=55  Identities=11%  Similarity=-0.028  Sum_probs=45.3

Q ss_pred             ccceeeeee--eecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           34 GSTLHSVRR--FRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~--~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      -+|+.+.+.  ...+  +.+.|++++||.+||.+|+++.|+|+++|+|+|+|+.  |..+|
T Consensus        15 ~ati~V~~~~~~~~g~~~~lev~~~~TV~~LK~~I~~~~gi~~~~qkLi~~Gk~L~d~~tL   75 (100)
T d1wjua_          15 IATIEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFGLQENYIKIVINKKQLQLGKTL   75 (100)
T ss_dssp             EEEEEEECCTTTCCSSSEEEEEESSSBHHHHHHHHHHHTTCCSTTCEEEETTEECCTTSBH
T ss_pred             eEEEEEEEeeccCCCeEEEEEECCCcHHHHHHHHHHHHHCCCCeeEEEEEcccCcCCCcCH
Confidence            457777763  3333  6789999999999999999999999999999999999  44443

>d1v86a_ d.15.1.1 (A:) hypothetical D7wsu128e protein {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: hypothetical D7wsu128e protein
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.15  E-value=1.2e-11  Score=73.63  Aligned_cols=55  Identities=18%  Similarity=0.170  Sum_probs=46.1

Q ss_pred             ccceeeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe-CCCcc
Q 040204           34 GSTLHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF-GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~-~~~~~   88 (97)
                      ...|.+.+...+. +.|.|++++||.+||++|++.+|+|+++|+|+|+|+. |..+|
T Consensus        15 ~~~i~v~V~~~~k~~~i~v~~~~TV~~LK~~I~~~tgvp~~~q~Li~~g~l~D~~tL   71 (95)
T d1v86a_          15 KELVDLKIIWNKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGLVPEDKTL   71 (95)
T ss_dssp             CCCEEEEEEETTEEEEEEECTTSBHHHHHHHHHHHHCSCSTTCCCBSSSBCCSSSBH
T ss_pred             ccEEEEEEEECCEEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEecccccCCCcH
Confidence            4567887775444 6788999999999999999999999999999999987 54444

>d1v5oa_ d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 1700011n24rik protein
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.14  E-value=2e-11  Score=73.50  Aligned_cols=37  Identities=11%  Similarity=0.276  Sum_probs=35.8

Q ss_pred             eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        47 ~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +.+.|++++||++||++|++++|+|+++|+|+|+|+.
T Consensus        24 ~~l~V~~~~tV~~LK~~Ie~~~gip~~~Q~Li~~Gk~   60 (102)
T d1v5oa_          24 FSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQL   60 (102)
T ss_dssp             EEEEECTTCBHHHHHHHHHHHTCCCGGGBCEEETTEE
T ss_pred             EEEEECCcccHHHHHHHHHHHhCCCcceEEEEeCCeE
Confidence            6788999999999999999999999999999999998

>d1we6a_ d.15.1.1 (A:) Splicing factor 3 subunit 1, C-terminal domain {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Splicing factor 3 subunit 1, C-terminal domain
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.14  E-value=1.6e-11  Score=75.06  Aligned_cols=55  Identities=27%  Similarity=0.298  Sum_probs=43.5

Q ss_pred             ccceeeeeeee-cc--eeeeeec-cchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           34 GSTLHSVRRFR-GG--MQIFVES-SDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~~~-~g--~~i~v~~-~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      ..++.+.+... +|  +.+.|.+ ++||.+||++|++++|+|+++|+|+|+|++  |..+|
T Consensus        27 ~~ti~V~v~~~~~G~~i~l~v~~~sdtV~~lK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL   87 (111)
T d1we6a_          27 PATIRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSL   87 (111)
T ss_dssp             CEEEEECCTTCSSSCCEEEEESCSSSBHHHHHHHHHHHTTCCTTTSEEECSSSBCCTTSBT
T ss_pred             CEEEEEEcccCCCCeEEEEEecCCccHHHHHHHHHHHHHCCCccceEEEEeeEEccccCCH
Confidence            44666665433 34  5677776 999999999999999999999999999998  54554

>d1x1ma1 d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 7
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.12  E-value=1.2e-11  Score=73.54  Aligned_cols=39  Identities=36%  Similarity=0.639  Sum_probs=35.1

Q ss_pred             cCCC-CcceEEEECCEEeCCCCCCccceec-ccceeeeeee
Q 040204            5 EEIL-RDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         5 ~gip-~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      +++| +++|+|+|+|+.|+|+.+|++|||+ |++||++.|.
T Consensus        53 ~~~P~p~~~rLIy~Gk~L~D~~tL~~y~I~~gstihLV~r~   93 (94)
T d1x1ma1          53 ESVPDPELIDLIYCGRKLKDDQTLDFYGIQPGSTVHVLRKS   93 (94)
T ss_dssp             TTCCCSSSEEEEETTEECCTTCBHHHHTCCTTCEEEEEESS
T ss_pred             cCCCChhheEEEECCeEECCCccHHHcCCCCCCEEEEEEeC
Confidence            3554 6899999999999999999999999 9999999874

>d1zkha1 d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Splicing factor 3 subunit 1, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.12  E-value=4e-11  Score=70.11  Aligned_cols=42  Identities=24%  Similarity=0.403  Sum_probs=37.8

Q ss_pred             eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe--CCCcc
Q 040204           47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        47 ~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~--~~~~~   88 (97)
                      +.+.|++++||+++|++|++++|+|+++|+|+|+|+.  |..+|
T Consensus        24 ~~l~v~~~~tV~~lK~~I~~~~~ip~~~q~Li~~Gk~L~D~~tL   67 (86)
T d1zkha1          24 LVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSL   67 (86)
T ss_dssp             EEEEECTTSBHHHHHHHHHHHTCCCTTTEEEEETTEEECTTSBH
T ss_pred             EEEEECCCChHHHHHHHHHhhhcCChHHEEEEeCCcCcCCCCCH
Confidence            5678899999999999999999999999999999999  54543

>d1wgha_ d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3, Ubl3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.11  E-value=3.1e-11  Score=74.27  Aligned_cols=41  Identities=29%  Similarity=0.445  Sum_probs=36.3

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccc--eeeeee
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GST--LHSVRR   42 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~st--i~l~i~   42 (97)
                      +++.|+|+++|||+|+|+.|+|+.+|++|+|. |++  |||+++
T Consensus        55 ~e~~~~~~~~qRLiy~Gk~L~D~~tL~~~~i~~g~~~~lhlv~r   98 (116)
T d1wgha_          55 EEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLVAR   98 (116)
T ss_dssp             SCCCCCCTTTEEEEETTEEECSSCBTTTTTCCSSCEEEEEEEEC
T ss_pred             ccccCCChHHeEEEECCEEecCCCCHHHcCCCCCCEEEEEEEeC
Confidence            46789999999999999999999999999999 987  555555

>d1v5ta_ d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 8430435i17rik protein
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.10  E-value=6.4e-11  Score=69.53  Aligned_cols=55  Identities=18%  Similarity=0.215  Sum_probs=45.2

Q ss_pred             ccceeeeeeeecc-eee-eeeccchhHHHHHhhhhhcCCCCCceEEE---ECeEe--CCCcc
Q 040204           34 GSTLHSVRRFRGG-MQI-FVESSDTIDNVKAKIQDKKGTPPDQQRQI---FWFVF--GWGSL   88 (97)
Q Consensus        34 ~sti~l~i~~~~g-~~i-~v~~~~TV~~lK~~I~~~~gip~~~q~Li---f~G~~--~~~~~   88 (97)
                      .+.+.+.++..++ +.+ .|++++||.+||++|++++|+|+++|+|+   |+|+.  |..+|
T Consensus         5 s~~~~i~Vk~~~~~~~i~~v~~~~tV~~LK~~i~~~t~vp~~~QkLi~~~~~Gk~L~D~~tL   66 (90)
T d1v5ta_           5 SSGLPIIVKWGGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKL   66 (90)
T ss_dssp             CCSCCEEEEETTEEEEECSCCSSSBHHHHHHHHHHHTCCCTTTCEEESCEETTEECCTTSBH
T ss_pred             CCcEEEEEEECCeEEEEEEeCCCCcHHHHHHHHHHHHcCCHHHhhhhhhccCCcCCCCcCcH
Confidence            3567788887655 445 58999999999999999999999999999   68998  54444

>d1euvb_ d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-1 (smt3 homologue)
species: Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932]

Probab=99.09  E-value=3.6e-11  Score=69.05  Aligned_cols=45  Identities=22%  Similarity=0.439  Sum_probs=42.4

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      +++.|+|+++|+|+|+|+.|.++.|+++|+|. +++|+++++..||
T Consensus        34 ~~~~~i~~~~~~l~f~G~~l~~~~T~~~~~i~dgd~I~v~~~q~GG   79 (79)
T d1euvb_          34 AKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGG   79 (79)
T ss_dssp             HHHTTCCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCBCC
T ss_pred             HHHhCCChHhEEEEECCEEeCCCCCHHHCCCCCCCEEEEEEeccCC
Confidence            46789999999999999999999999999999 9999999998876

>d1v5oa_ d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 1700011n24rik protein
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.08  E-value=6.8e-12  Score=75.64  Aligned_cols=46  Identities=15%  Similarity=0.296  Sum_probs=40.3

Q ss_pred             CccccCCCCcceEEEECCEEeC-CCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLE-DGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~-d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |+.++|||+++|+|+|+|+.|. |+++|++|||. +++|+|+.+...+
T Consensus        41 Ie~~~gip~~~Q~Li~~Gk~L~dd~~tL~~~gI~~g~~i~l~~r~~~~   88 (102)
T d1v5oa_          41 CELESGVPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVLLQKDNVG   88 (102)
T ss_dssp             HHHHTCCCGGGBCEEETTEEECCSSSBHHHHTCCTTEEEEECBCCCCC
T ss_pred             HHHHhCCCcceEEEEeCCeEeecccCCHHHcCCCCCCEEEEEECCCCC
Confidence            4668999999999999999995 56899999999 9999998876554

>d1wxva1 d.15.1.1 (A:7-87) Bag-family molecular chaperone regulator-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Bag-family molecular chaperone regulator-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.08  E-value=9.9e-12  Score=71.95  Aligned_cols=44  Identities=23%  Similarity=0.367  Sum_probs=38.9

Q ss_pred             CccccCCCCcceEEEECCEEeC-CCCCCccceec-ccceeeeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLE-DGRTLVDYNIH-GSTLHSVRRFR   44 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~-d~~tL~~y~I~-~sti~l~i~~~   44 (97)
                      |++.+|+|+++|+|+|+|+.|. |+.+|++|||. |++|+|+.+..
T Consensus        35 I~~~tgvp~~~QkL~~~G~~L~~d~~tL~~~gi~~g~~i~lv~~~~   80 (81)
T d1wxva1          35 VEEVIGVPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVMLIGKKN   80 (81)
T ss_dssp             HHHHTCCCTTTCEEEETTEEECCSSSBHHHHTCCSSEEEEEESCCS
T ss_pred             HHHHHCcCHHHEEeeecCeEeCcCCCChHHCCCCCCCEEEEEEecC
Confidence            4567999999999999999995 67899999999 99999987643

>d1wjua_ d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: NEDD8 ultimate buster-1, NUB1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.08  E-value=1.1e-11  Score=74.47  Aligned_cols=44  Identities=14%  Similarity=0.206  Sum_probs=39.5

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFR   44 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~   44 (97)
                      |+++.|+|+++|+|+|+|+.|+|+.||++|+|. +++|+++....
T Consensus        49 I~~~~gi~~~~qkLi~~Gk~L~d~~tL~~~gI~~~s~i~vi~~~~   93 (100)
T d1wjua_          49 IAETFGLQENYIKIVINKKQLQLGKTLEEQGVAHNVKAMVLELKQ   93 (100)
T ss_dssp             HHHHTTCCSTTCEEEETTEECCTTSBHHHHTCCSSEEEEEECCCC
T ss_pred             HHHHHCCCCeeEEEEEcccCcCCCcCHHHcCCCCCCEEEEEEcCC
Confidence            457789999999999999999999999999999 99998876543

>d1wxva1 d.15.1.1 (A:7-87) Bag-family molecular chaperone regulator-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Bag-family molecular chaperone regulator-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.05  E-value=1.9e-10  Score=66.32  Aligned_cols=32  Identities=19%  Similarity=0.260  Sum_probs=30.9

Q ss_pred             eccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           52 ESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        52 ~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      ++++||++||++|++.+|+|+++|+|+|+|+.
T Consensus        23 ~~~~Tv~~LK~~I~~~tgvp~~~QkL~~~G~~   54 (81)
T d1wxva1          23 SSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKS   54 (81)
T ss_dssp             SSSCBHHHHHHHHHHHTCCCTTTCEEEETTEE
T ss_pred             CCccHHHHHHHHHHHHHCcCHHHEEeeecCeE
Confidence            67899999999999999999999999999998

>d1wgga_ d.15.1.1 (A:) Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin carboxyl-terminal hydrolase 14
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.01  E-value=2.9e-11  Score=71.95  Aligned_cols=42  Identities=14%  Similarity=0.209  Sum_probs=37.5

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeee
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      |++.+|||+++|+|+|+|+.|+|+ +|++|+|+ |++|+|+.+.
T Consensus        37 i~~~~gvp~~~QkLi~~Gk~L~d~-tL~~~gi~~g~~i~lv~t~   79 (96)
T d1wgga_          37 LFALTGVQPARQKVMVKGGTLKDD-DWGNIKMKNGMTVLMMGSA   79 (96)
T ss_dssp             HHHHTCCCTTTSCCEETTEECCSS-CCCSCCCCSSCEEECCCCC
T ss_pred             hhhhcCccceeeEEeecCcccCCC-cHHHCCCCCCCEEEEEeeC
Confidence            356789999999999999999986 79999999 9999998653

>d1v5ta_ d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 8430435i17rik protein
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.00  E-value=3.6e-11  Score=70.65  Aligned_cols=45  Identities=13%  Similarity=0.281  Sum_probs=40.3

Q ss_pred             CccccCCCCcceEEE---ECCEEeCCCCCCccceec-ccceeeeeeeec
Q 040204            1 IEDKEEILRDQQRFI---FAGKRLEDGRTLVDYNIH-GSTLHSVRRFRG   45 (97)
Q Consensus         1 i~~~~gip~~~Q~L~---~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~   45 (97)
                      |++++|+|+++|+|+   |.|+.|+|+.+|++|+|. |++|+|+.+...
T Consensus        37 i~~~t~vp~~~QkLi~~~~~Gk~L~D~~tL~~~~i~~g~~i~lv~s~~~   85 (90)
T d1v5ta_          37 LKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMGTRES   85 (90)
T ss_dssp             HHHHTCCCTTTCEEESCEETTEECCTTSBHHHHTCCTTEEEEEECCCSS
T ss_pred             HHHHHcCCHHHhhhhhhccCCcCCCCcCcHHHcCCCCCCEEEEEeeCCC
Confidence            467899999999999   699999999999999999 999999876543

>d1wiaa_ d.15.1.1 (A:) Ubiquitin-like protein bab25500 (2010008E23Rik) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein bab25500 (2010008E23Rik)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.99  E-value=4.9e-10  Score=66.52  Aligned_cols=47  Identities=17%  Similarity=0.172  Sum_probs=41.7

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .++|.+.++..+|  ..+.|++++||.+||++|++   +++++|+|+|+|++
T Consensus         5 ~s~m~i~vK~l~~~~~~v~v~~~~TV~~lK~~i~~---~~~~~qrLi~~Gk~   53 (95)
T d1wiaa_           5 SSGINVRLKFLNDTEELAVARPEDTVGTLKSKYFP---GQESQMKLIYQGRL   53 (95)
T ss_dssp             CCSEEEEEEETTTEEEEEEECSSSBHHHHHHHHSS---STTTTCEEEETTEE
T ss_pred             CCcEEEEEEcCCCCEEEEEECCcCcHHHHHHHHhc---CCcceeEEEECCEE
Confidence            6789999999888  55778999999999999974   68899999999999

>d1wgda_ d.15.1.1 (A:) Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.93  E-value=1.3e-10  Score=68.78  Aligned_cols=41  Identities=32%  Similarity=0.391  Sum_probs=35.5

Q ss_pred             cCCCCcceEEEECCEEeCCCCCCccceec-c--cceeeeeeeec
Q 040204            5 EEILRDQQRFIFAGKRLEDGRTLVDYNIH-G--STLHSVRRFRG   45 (97)
Q Consensus         5 ~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~--sti~l~i~~~~   45 (97)
                      ..+|+++|||+|+|+.|+|+.+|++|... +  .+|||+.+..+
T Consensus        45 ~~~~~~~qrLIy~Gk~L~D~~~L~d~~~~~~~~~viHLV~~~~~   88 (93)
T d1wgda_          45 ERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVCNVKS   88 (93)
T ss_dssp             TCCCTTTCEEEETTEECCSSSCHHHHSCSSSCSEEEEEECCCCC
T ss_pred             CCCChHHEEEEECCeEccCCCCHHHhCcccCCCCEEEEEecCCC
Confidence            35899999999999999999999999876 4  49999987654

>d1v86a_ d.15.1.1 (A:) hypothetical D7wsu128e protein {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: hypothetical D7wsu128e protein
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.92  E-value=1.8e-11  Score=72.72  Aligned_cols=45  Identities=18%  Similarity=0.351  Sum_probs=40.0

Q ss_pred             CccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeecc
Q 040204            1 IEDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      |++.+|+|+++|+|+|+|+ |.|+.+|++|+|. +++|+|+.+..+|
T Consensus        46 I~~~tgvp~~~q~Li~~g~-l~D~~tL~~~~I~~gs~i~lvgs~~~g   91 (95)
T d1v86a_          46 IHSITGLPPAMQKVMYKGL-VPEDKTLREIKVTSGAKIMVVGSTISG   91 (95)
T ss_dssp             HHHHHCSCSTTCCCBSSSB-CCSSSBHHHHCCCTTEEEEECCSSCCC
T ss_pred             HHHHhCCChhHEEEEeccc-ccCCCcHHHCCCCCCCEEEEEecCCCC
Confidence            4677999999999999997 9999999999999 9999998766544

>d1v2ya_ d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3300001g02rik
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.91  E-value=9.1e-11  Score=70.84  Aligned_cols=50  Identities=16%  Similarity=0.013  Sum_probs=45.0

Q ss_pred             ccceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceE---------------EEECeEe
Q 040204           34 GSTLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQR---------------QIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~---------------Lif~G~~   83 (97)
                      .+.+.+.++..+|  +.|.|++++||++||++|++.+++|+++|+               |+|+|+.
T Consensus         5 ss~M~v~Vk~~~G~~~~v~V~~~~TV~~LK~~I~~~~~ip~~~Qr~~~~~~~~~~~~~~~Li~~G~~   71 (105)
T d1v2ya_           5 SSGMTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEK   71 (105)
T ss_dssp             CCSEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHHHHHHHTTCCCCCCHHHHHTTEEEESSSCE
T ss_pred             CCcEEEEEEeCCCCEEEEEECCCChHHHHHHHHHHHHCcCHHHhcccccccccccccceEEEECCEE
Confidence            4578888887777  678889999999999999999999999997               9999998

>d1wiaa_ d.15.1.1 (A:) Ubiquitin-like protein bab25500 (2010008E23Rik) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein bab25500 (2010008E23Rik)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.87  E-value=5e-10  Score=66.46  Aligned_cols=42  Identities=29%  Similarity=0.404  Sum_probs=36.9

Q ss_pred             cCCCCcceEEEECCEEeC-CCCCCccceec-ccceeeeeeeecc
Q 040204            5 EEILRDQQRFIFAGKRLE-DGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         5 ~gip~~~Q~L~~~g~~L~-d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      +.+++++|+|+|+|+.|. |.++|++|+|. +++||++++.+++
T Consensus        38 ~~~~~~~qrLi~~Gk~L~dd~~tL~~y~i~~g~~v~l~~~~~~~   81 (95)
T d1wiaa_          38 FPGQESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRSPPGA   81 (95)
T ss_dssp             SSSTTTTCEEEETTEECCCSSCBTTTTTCCTTEEEEEECCCCCC
T ss_pred             hcCCcceeEEEECCEEcccCCCCHHHcCCCCCCEEEEEEcCCCC
Confidence            467889999999999996 56899999999 9999999876654

>d1v2ya_ d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3300001g02rik
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.78  E-value=4.5e-11  Score=72.24  Aligned_cols=44  Identities=18%  Similarity=0.444  Sum_probs=38.1

Q ss_pred             CccccCCCCcceE---------------EEECCEEeCCC-CCCccceec-ccceeeeeeee
Q 040204            1 IEDKEEILRDQQR---------------FIFAGKRLEDG-RTLVDYNIH-GSTLHSVRRFR   44 (97)
Q Consensus         1 i~~~~gip~~~Q~---------------L~~~g~~L~d~-~tL~~y~I~-~sti~l~i~~~   44 (97)
                      |++.+|||+++|+               |+|+|+.|.|+ .+|.+|+|. +++|||+.+..
T Consensus        37 I~~~~~ip~~~Qr~~~~~~~~~~~~~~~Li~~G~~L~d~~~tL~~~gI~~g~~l~lv~r~~   97 (105)
T d1v2ya_          37 IQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLRDYGIRNRDEVSFIKKLG   97 (105)
T ss_dssp             HHHHHHHHHHHTTCCCCCCHHHHHTTEEEESSSCEECCSSSBHHHHTCCSSEEEEEEECSC
T ss_pred             HHHHHCcCHHHhcccccccccccccceEEEECCEECcccCCCHHHcCCCCCCEEEEEEecC
Confidence            3567889999887               99999999766 589999999 99999998764

>d1v6ea_ d.15.1.1 (A:) Ubiquitin-like domain of tubulin folding cofactor B {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of tubulin folding cofactor B
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.75  E-value=4.3e-10  Score=66.72  Aligned_cols=45  Identities=16%  Similarity=0.166  Sum_probs=39.2

Q ss_pred             ccccCCCCcceEEEECCE-------EeCCCCCCccceec-ccceeeeeeeecc
Q 040204            2 EDKEEILRDQQRFIFAGK-------RLEDGRTLVDYNIH-GSTLHSVRRFRGG   46 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~-------~L~d~~tL~~y~I~-~sti~l~i~~~~g   46 (97)
                      +..+|+|+++|+|+|.|+       .++|+++|++|+|. |++|||+.+.+.+
T Consensus        39 e~~tGip~~~qrL~~~~~~~~~~~~l~~d~~~L~~y~i~dg~~ihlvd~~p~~   91 (95)
T d1v6ea_          39 ELVVGSPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIHVIDHSGSG   91 (95)
T ss_dssp             HHHTCSCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCEEEEBCCSCCS
T ss_pred             HHHhCcCchhEEEEEeCCCCceeecccCCcCCHHHCCCCCCCEEEEEeCCCCC
Confidence            467899999999999776       47899999999999 9999999876654

>d1v6ea_ d.15.1.1 (A:) Ubiquitin-like domain of tubulin folding cofactor B {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of tubulin folding cofactor B
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.74  E-value=5.5e-09  Score=61.77  Aligned_cols=50  Identities=16%  Similarity=0.038  Sum_probs=42.3

Q ss_pred             ccceeeeeeee-cc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFR-GG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~-~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .+.|.++++.. .+  .+..++++.||.+||++|+..+|+|+++|+|+|.|+.
T Consensus         5 ss~v~v~I~s~~~~~~~E~r~~~~~TV~~LK~kle~~tGip~~~qrL~~~~~~   57 (95)
T d1v6ea_           5 SSGVMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVGSPASCMELELYGAD   57 (95)
T ss_dssp             CCCEEEEEEETTSSSCEEEEECTTSBHHHHHHHHHHHTCSCTTTCBCEEECSS
T ss_pred             CCcEEEEEEECCCCcEEEEEeCCCCCHHHHHHHHHHHhCcCchhEEEEEeCCC
Confidence            46677777764 33  4567899999999999999999999999999999984

>d1wjna_ d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Tubulin-folding protein TbcE
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.69  E-value=1.3e-08  Score=60.30  Aligned_cols=50  Identities=14%  Similarity=0.063  Sum_probs=41.3

Q ss_pred             ccceeeeeeeec---c--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           34 GSTLHSVRRFRG---G--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        34 ~sti~l~i~~~~---g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +..+.+.++++.   +  +++.|++++||.+||.+|+...|+|+++|+|+|.|+.
T Consensus         7 ~~~iti~i~~~~~~~~~~~~~kv~~~~TV~~LK~~i~~~~gip~~~qrL~y~~~~   61 (97)
T d1wjna_           7 GQLLTLKIKCSNQPERQILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSK   61 (97)
T ss_dssp             SCEEEEEEEESSCSSSCCEEEEEETTSBHHHHHHHHHTTTTCCTTTCEEEEECTT
T ss_pred             CCeEEEEEEeCCCCCCceEEEEcCCCCCHHHHHHHHHHHHCcChHHeEEEecCCC
Confidence            345666666543   2  5678899999999999999999999999999999974

>d2uyzb1 d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-1 (smt3 homologue)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.57  E-value=1.1e-08  Score=58.05  Aligned_cols=44  Identities=18%  Similarity=0.419  Sum_probs=39.8

Q ss_pred             ccccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeeeeec
Q 040204            2 EDKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRRFRG   45 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~~~~   45 (97)
                      +++.|+|+++++|+|+|++|.++.|+++|++. +++|+++.+..|
T Consensus        33 ~~~~~~~~~~~~f~fdG~~l~~~~T~~~l~~edgD~Idv~~~q~G   77 (77)
T d2uyzb1          33 CQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTG   77 (77)
T ss_dssp             HHHHTCCGGGEEEEETTEECCTTCCHHHHTCCTTEEEEEEECCCC
T ss_pred             HHHhCCChhHEEEEECCEECCCCCCHHHcCCCCCCEEEEEEecCC
Confidence            45679999999999999999999999999999 999999986543

>d1wjna_ d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Tubulin-folding protein TbcE
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.51  E-value=9.5e-09  Score=60.85  Aligned_cols=41  Identities=17%  Similarity=0.215  Sum_probs=34.7

Q ss_pred             CccccCCCCcceEEEECCE-------EeC-CCCCCccceec-ccceeeee
Q 040204            1 IEDKEEILRDQQRFIFAGK-------RLE-DGRTLVDYNIH-GSTLHSVR   41 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~g~-------~L~-d~~tL~~y~I~-~sti~l~i   41 (97)
                      |++.+|||+++|+|+|.|+       +|+ |+++|.+|+|. |++|+|.-
T Consensus        42 i~~~~gip~~~qrL~y~~~~~~~~~~~l~~d~~tL~~YgI~dg~~I~V~~   91 (97)
T d1wjna_          42 LSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCLLVRW   91 (97)
T ss_dssp             HHTTTTCCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTCCTTCEEEEEC
T ss_pred             HHHHHCcChHHeEEEecCCCCCcccceecCCCcCHhhccCCCCCEEEEEe
Confidence            3567899999999999776       353 78999999999 99999764

>d1t0ya_ d.15.1.1 (A:) Ubiquitin-like domain of tubulin folding cofactor B {Nematode (Caenorhabditis elegans) [TaxId: 6239]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of tubulin folding cofactor B
species: Nematode (Caenorhabditis elegans) [TaxId: 6239]

Probab=98.49  E-value=1.3e-08  Score=59.57  Aligned_cols=42  Identities=19%  Similarity=0.209  Sum_probs=35.4

Q ss_pred             ccccCCCCcceEEEECCE-------EeCCCCCCccceec-ccceeeeeee
Q 040204            2 EDKEEILRDQQRFIFAGK-------RLEDGRTLVDYNIH-GSTLHSVRRF   43 (97)
Q Consensus         2 ~~~~gip~~~Q~L~~~g~-------~L~d~~tL~~y~I~-~sti~l~i~~   43 (97)
                      +..+|+|++.|+|+|.|+       ..+|+++|.+|||. |++||++=..
T Consensus        36 e~~~Gip~~~q~L~~~~~~~~~~~~l~dd~~~L~~ygi~dG~~Ihvvd~~   85 (90)
T d1t0ya_          36 ELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHAVDVT   85 (90)
T ss_dssp             HHHHCCCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEEEEEECT
T ss_pred             HHHHCCChhheEEEEeCCCCCcccccccCCCCHHHCCCCCCCEEEEEeCC
Confidence            456899999999999765       35788999999999 9999986543

>d1x1ma1 d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 7
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.48  E-value=1.6e-07  Score=55.26  Aligned_cols=37  Identities=22%  Similarity=0.144  Sum_probs=29.3

Q ss_pred             eccchhHHHHHhhhhhc--CCC-CCceEEEECeEe--CCCcc
Q 040204           52 ESSDTIDNVKAKIQDKK--GTP-PDQQRQIFWFVF--GWGSL   88 (97)
Q Consensus        52 ~~~~TV~~lK~~I~~~~--gip-~~~q~Lif~G~~--~~~~~   88 (97)
                      ..+.||.++|++|.++.  ++| |++|+|||+||+  |..+|
T Consensus        35 ~~~~tV~~lK~~i~~~~~~~~P~p~~~rLIy~Gk~L~D~~tL   76 (94)
T d1x1ma1          35 LGGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTL   76 (94)
T ss_dssp             CCCCBHHHHHHHHHHHCTTTCCCSSSEEEEETTEECCTTCBH
T ss_pred             CCccCHHHHHHHHHHHcccCCCChhheEEEECCeEECCCccH
Confidence            34779999999998774  555 799999999999  44443

>d1euvb_ d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-1 (smt3 homologue)
species: Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932]

Probab=98.43  E-value=3.1e-07  Score=52.03  Aligned_cols=48  Identities=6%  Similarity=0.082  Sum_probs=39.7

Q ss_pred             ceeeeeeeecc-eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           36 TLHSVRRFRGG-MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        36 ti~l~i~~~~g-~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .|.+.++..+. ..+.|++++++..||+.++++.|+|+++|+|+|+|+.
T Consensus         4 ~I~ikv~~~~~~~~f~v~~~~~~~~l~~~~~~~~~i~~~~~~l~f~G~~   52 (79)
T d1euvb_           4 HINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIR   52 (79)
T ss_dssp             EEEEEEESSSCEEEEEEETTSCTHHHHHHHHHHTTCCGGGEEEEETTEE
T ss_pred             EEEEEECCCCeEEEEEECCCCcHHHHHHHHHHHhCCChHhEEEEECCEE
Confidence            34555544333 4567899999999999999999999999999999999

>d1t0ya_ d.15.1.1 (A:) Ubiquitin-like domain of tubulin folding cofactor B {Nematode (Caenorhabditis elegans) [TaxId: 6239]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of tubulin folding cofactor B
species: Nematode (Caenorhabditis elegans) [TaxId: 6239]

Probab=98.41  E-value=2.2e-07  Score=54.06  Aligned_cols=47  Identities=15%  Similarity=0.067  Sum_probs=38.2

Q ss_pred             eeeeeeeec-c--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           37 LHSVRRFRG-G--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        37 i~l~i~~~~-g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +++.++... +  .+..+.++.||.+||++|+...|+|++.|+|+|.|+.
T Consensus         5 ~~l~it~~~t~~~~E~r~~~~~TV~~LK~kle~~~Gip~~~q~L~~~~~~   54 (90)
T d1t0ya_           5 YDLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGD   54 (90)
T ss_dssp             EEEEEEESSCCSCEEEEEETTSBHHHHHHHHHHHHCCCTTTEEEEEECSS
T ss_pred             EEEEEEECCCccEEEEecCCCCCHHHHHHHHHHHHCCChhheEEEEeCCC
Confidence            455555422 2  4566799999999999999999999999999999974

>d2uyzb1 d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-1 (smt3 homologue)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.10  E-value=3.3e-06  Score=47.39  Aligned_cols=48  Identities=13%  Similarity=0.123  Sum_probs=41.4

Q ss_pred             ceeeeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           36 TLHSVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        36 ti~l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      .|.+.++..+|  ..+.|++++++..|++..+++.|+|+++++|+|.|+.
T Consensus         2 ~I~ikv~~~dg~~v~f~v~~~t~l~kl~~~y~~~~~~~~~~~~f~fdG~~   51 (77)
T d2uyzb1           2 YIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQR   51 (77)
T ss_dssp             EEEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEE
T ss_pred             EEEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCChhHEEEEECCEE
Confidence            35566666666  3466799999999999999999999999999999998

>d1wf9a1 d.15.1.1 (A:8-101) NPL4-like protein 1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: NPL4-like protein 1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=97.60  E-value=2.5e-05  Score=45.35  Aligned_cols=41  Identities=27%  Similarity=0.301  Sum_probs=34.3

Q ss_pred             eeeeeecce-eeeee-ccchhHHHHHhhhhhcCCCCCceEEEE
Q 040204           39 SVRRFRGGM-QIFVE-SSDTIDNVKAKIQDKKGTPPDQQRQIF   79 (97)
Q Consensus        39 l~i~~~~g~-~i~v~-~~~TV~~lK~~I~~~~gip~~~q~Lif   79 (97)
                      +.+|+..|. .|.|+ ++.||.+||++|++.-++|.++|.|.-
T Consensus         3 iRiRsrdG~eRv~v~~~~~Tl~~LK~~Ie~~L~VPv~~Q~LSl   45 (94)
T d1wf9a1           3 LRVRSRDGLERVSVDGPHITVSQLKTLIQDQLQIPIHNQTLST   45 (94)
T ss_dssp             EEEECSSCEEEEEECCTTSBHHHHHHHHHHHSCCCTTTCCCBS
T ss_pred             EEEEecCCceEEEecCCCCcHHHHHHHHHHHhCCCcccceeec
Confidence            456777885 48885 467999999999999999999999854

>d1wm3a_ d.15.1.1 (A:) SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.30  E-value=9.5e-05  Score=40.75  Aligned_cols=38  Identities=18%  Similarity=0.383  Sum_probs=34.6

Q ss_pred             cccCCCCcceEEEECCEEeCCCCCCccceec-ccceeee
Q 040204            3 DKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSV   40 (97)
Q Consensus         3 ~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~   40 (97)
                      +..|++++..+++|+|..+..+.|.+++++. +++|.+.
T Consensus        33 ~~~~~~~~~~~f~fdG~~i~~~~Tp~~l~med~D~Idv~   71 (72)
T d1wm3a_          33 ERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVF   71 (72)
T ss_dssp             HHHTCCTTTCEEEETTEECCTTCCTTTTTCCTTEEEEEE
T ss_pred             HHhCCCccceEEEECCEEcCCCCCHHHcCCCCCCEEEEE
Confidence            4568999999999999999999999999999 9998764

>d1wm3a_ d.15.1.1 (A:) SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.39  E-value=0.0044  Score=33.66  Aligned_cols=45  Identities=13%  Similarity=0.039  Sum_probs=37.9

Q ss_pred             eeeeeecc--eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe
Q 040204           39 SVRRFRGG--MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF   83 (97)
Q Consensus        39 l~i~~~~g--~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~   83 (97)
                      +.+...+|  +.+.|+++++...|...-.++.|+++++.+++|.|+.
T Consensus         4 lkv~~~~g~~v~f~vk~~t~l~kl~~~y~~~~~~~~~~~~f~fdG~~   50 (72)
T d1wm3a_           4 LKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQP   50 (72)
T ss_dssp             EEEECTTSCEEEEEECTTSCTHHHHHHHHHHHTCCTTTCEEEETTEE
T ss_pred             EEEECCCCCEEEEEEcCCChHHHHHHHHHHHhCCCccceEEEECCEE
Confidence            34444445  4567799999999999999999999999999999998

>d2al3a1 d.15.1.2 (A:10-85) Tether containing UBX domain for GLUT4 (Tug) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: Tether containing UBX domain for GLUT4 (Tug)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.74  E-value=0.0095  Score=32.95  Aligned_cols=43  Identities=14%  Similarity=0.151  Sum_probs=37.9

Q ss_pred             eeeeeeccchhHHHHHhhhhhcCCCCCceEEEECeEe-CCCccc
Q 040204           47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQIFWFVF-GWGSLW   89 (97)
Q Consensus        47 ~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Lif~G~~-~~~~~~   89 (97)
                      .+|.|.|++|+.++-+...++.|+.+++..|-|+++. |+--.|
T Consensus        13 ~~VKvtP~t~l~~VL~eaC~k~~~~~~~~~Lkh~~k~ldLsl~~   56 (76)
T d2al3a1          13 HTVKVTPSTVLLQVLEDTCRRQDFNPSEYDLKFQRTVLDLSLQW   56 (76)
T ss_dssp             EEECCCTTSBHHHHHHHHHHHTTCCGGGCEEEETTEEESSSCBH
T ss_pred             EEEEeCCCcCHHHHHHHHHHHhCCChhHceeeeCCEEcCcccee
Confidence            5688899999999999999999999999999999999 554333

>d1wf9a1 d.15.1.1 (A:8-101) NPL4-like protein 1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: NPL4-like protein 1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=94.80  E-value=0.0017  Score=37.35  Aligned_cols=42  Identities=19%  Similarity=0.192  Sum_probs=32.3

Q ss_pred             CccccCCCCcceEEEEC--------------CEEeCC-CCCCccceec-ccceeeeee
Q 040204            1 IEDKEEILRDQQRFIFA--------------GKRLED-GRTLVDYNIH-GSTLHSVRR   42 (97)
Q Consensus         1 i~~~~gip~~~Q~L~~~--------------g~~L~d-~~tL~~y~I~-~sti~l~i~   42 (97)
                      |++..+||.++|+|..+              -..|.| ..+|+++||. ||.+++...
T Consensus        30 Ie~~L~VPv~~Q~LSl~~~llL~k~P~~~~~~~~l~d~~~~L~sl~i~hGsivyL~y~   87 (94)
T d1wf9a1          30 IQDQLQIPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLAHGSMVYLAYE   87 (94)
T ss_dssp             HHHHSCCCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTCCCTTCEEECCCS
T ss_pred             HHHHhCCCcccceeecChhhhccCCccccchhhhccCCccCHHHcCccCceEEEEEee
Confidence            46778999999999653              233654 4669999999 999998654

>d2al3a1 d.15.1.2 (A:10-85) Tether containing UBX domain for GLUT4 (Tug) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: Tether containing UBX domain for GLUT4 (Tug)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.46  E-value=0.14  Score=27.99  Aligned_cols=40  Identities=13%  Similarity=0.086  Sum_probs=36.4

Q ss_pred             cccCCCCcceEEEECCEEeCCCCCCccceec-ccceeeeee
Q 040204            3 DKEEILRDQQRFIFAGKRLEDGRTLVDYNIH-GSTLHSVRR   42 (97)
Q Consensus         3 ~~~gip~~~Q~L~~~g~~L~d~~tL~~y~I~-~sti~l~i~   42 (97)
                      ++.|+.+++-.|.|+++.|+-..++...|+. |+.+.|+..
T Consensus        32 ~k~~~~~~~~~Lkh~~k~ldLsl~~R~sgLpnnakLELv~~   72 (76)
T d2al3a1          32 RRQDFNPSEYDLKFQRTVLDLSLQWRFANLPNNAKLEMVPV   72 (76)
T ss_dssp             HHTTCCGGGCEEEETTEEESSSCBHHHHCCCSSCEEEEECS
T ss_pred             HHhCCChhHceeeeCCEEcCccceeeecCCCCCCEEEEEEc
Confidence            5788999999999999999999999999999 999998764

>d1wxma1 d.15.1.5 (A:8-80) A-Raf proto-oncogene serine/threonine-protein kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ras-binding domain, RBD
domain: A-Raf proto-oncogene serine/threonine-protein kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.37  E-value=1.1  Score=23.90  Aligned_cols=32  Identities=13%  Similarity=0.037  Sum_probs=27.7

Q ss_pred             eeeeeeccchhHHHHHhhhhhcCCCCCceEEE
Q 040204           47 MQIFVESSDTIDNVKAKIQDKKGTPPDQQRQI   78 (97)
Q Consensus        47 ~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Li   78 (97)
                      ..+.+.|..|+.++-.++.++-|++++.-.+.
T Consensus        13 T~V~vrpG~tir~~L~k~l~kRgl~~~~~~V~   44 (73)
T d1wxma1          13 TVVTVRDGMSVYDSLDKALKVRGLNQDCCVVY   44 (73)
T ss_dssp             EEEECCSSCBSHHHHHHHHHTTTCCSSSEEEE
T ss_pred             EEEEecCCCCHHHHHHHHHHHcCCCHHHEEEE
Confidence            44788999999999999999999998776663

>d1c1yb_ d.15.1.5 (B:) c-Raf1 RBD {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ras-binding domain, RBD
domain: c-Raf1 RBD
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.84  E-value=1.3  Score=23.84  Aligned_cols=44  Identities=11%  Similarity=0.126  Sum_probs=32.3

Q ss_pred             cceeeeeeeecceeeeeeccchhHHHHHhhhhhcCCCCCceEEE
Q 040204           35 STLHSVRRFRGGMQIFVESSDTIDNVKAKIQDKKGTPPDQQRQI   78 (97)
Q Consensus        35 sti~l~i~~~~g~~i~v~~~~TV~~lK~~I~~~~gip~~~q~Li   78 (97)
                      +|+.++........+.+.|..|+.++-.+..++-|++++.-.+.
T Consensus         2 ~~iRv~LPngq~T~V~vrpG~tird~L~k~l~kRgl~~~~c~V~   45 (77)
T d1c1yb_           2 NTIRVFLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVF   45 (77)
T ss_dssp             CEEEEEETTTEEEEEECCTTCBHHHHHHHHHHTTTCCGGGEEEE
T ss_pred             ceEEEECCCCCeEEEEecCCCCHHHHHHHHHHHcCCCHHHEEEE
Confidence            34444443222245888999999999999999999998766664