Citrus Sinensis ID: 042212

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------
Protein Sequence
MPLEQQRLVFADKSLLADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAGNFEDGWTQADYNIQKESTLHFVLRLS
Secondary Structure (PSIPRED)
ccccccEEEEcccccccccccccccHHHHHHHHcccEEEEEEcccccEEEEEcccccHHHHHHHccccccccccccccccccccccccEEEEEEEcc
Secondary Structure Prediction (SSPRO)
ccccHHHHHHHcccEcHHHccccccEEEEEEccccccEEEEEcccccEEEEEcccccEHHHHHHHHHHHccccccccEcHHHccccccEEEEEEccc
Coil and Loop (DISEMBL)
MPLEQQRLVFADkslladyniqkeSTLHLVARLRGRMQIFVKtstgktitlevessdmidnasrgssspagnfedgwtqadyniqkesTLHFVLRLS
Flexible Loop (DISEMBL)
MPLEQQRLVFADkslladyniqkESTLHLVARLRGRMQifvktstgktitlevessdmidnaSRGSSSPAGNFEDGWTQADYNIQKESTLHFVLRLS
Low Complexity Region (SEG)
MPLEQQRLVFADKSLLADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAGNFEDGWTQADYNIQKESTLHFVLRLS
Disordered region (IsUnstruct)
*******LVFADKSLLADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITL*************************WTQADYNIQKESTLHFV****
Disordered Region (DISOPRED)
MPLEQQRLVFADKSLLADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAGNFEDGWTQADYNIQKESTLHFVLRLS
Disordered Region (DISEMBL)
MPLEQQRLVFADKSLLADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVESSDMI**********AGNFEDGWTQADYNIQKESTLHFVLRLS
Disordered Region (DISPRO)
MPLEQQRLVFADKSLLADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAGNFEDGWTQADYNIQKESTLHFVLRLS
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MPLEQQRLVFADKSLLADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAGNFEDGWTQADYNIQKESTLHFVLRLS
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	0.989	0.314	0.631	7e-30
P69309	305	Polyubiquitin OS=Avena fa	N/A	no	0.989	0.314	0.631	8e-30
Q8H159	457	Polyubiquitin 10 OS=Arabi	yes	no	0.989	0.210	0.631	8e-30
P0CG85	457	Polyubiquitin OS=Nicotian	N/A	no	0.989	0.210	0.631	8e-30
P0CG84	377	Polyubiquitin (Fragment)	N/A	no	0.989	0.254	0.631	8e-30
P0CH32	382	Polyubiquitin 4 OS=Arabid	no	no	0.989	0.251	0.631	9e-30
Q58G87	381	Polyubiquitin 3 OS=Oryza	no	no	0.989	0.251	0.631	9e-30
Q1EC66	306	Polyubiquitin 3 OS=Arabid	no	no	0.989	0.313	0.631	9e-30
P69322	381	Polyubiquitin OS=Pisum sa	N/A	no	0.989	0.251	0.631	9e-30
Q3E7T8	305	Polyubiquitin 14 OS=Arabi	no	no	0.989	0.314	0.631	9e-30

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

 Score =  129 bits (323), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 72/114 (63%), Positives = 75/114 (65%), Gaps = 18/114 (15%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P +QQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct: 77  IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 136

Query: 56  SDMIDNASRGSSSPAG-------------NFEDGWTQADYNIQKESTLHFVLRL 96
           SD IDN         G               EDG T ADYNIQKESTLH VLRL
Sbjct: 137 SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 190

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

 Score =  129 bits (323), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 72/114 (63%), Positives = 75/114 (65%), Gaps = 18/114 (15%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P +QQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct: 36  IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 95

Query: 56  SDMIDNASRGSSSPAG-------------NFEDGWTQADYNIQKESTLHFVLRL 96
           SD IDN         G               EDG T ADYNIQKESTLH VLRL
Sbjct: 96  SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 149

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

 Score =  129 bits (323), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 72/114 (63%), Positives = 75/114 (65%), Gaps = 18/114 (15%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P +QQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct: 36  IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 95

Query: 56  SDMIDNASRGSSSPAG-------------NFEDGWTQADYNIQKESTLHFVLRL 96
           SD IDN         G               EDG T ADYNIQKESTLH VLRL
Sbjct: 96  SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 149

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 =  129 bits (323), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 72/114 (63%), Positives = 75/114 (65%), Gaps = 18/114 (15%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P +QQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct: 36  IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 95

Query: 56  SDMIDNASRGSSSPAG-------------NFEDGWTQADYNIQKESTLHFVLRL 96
           SD IDN         G               EDG T ADYNIQKESTLH VLRL
Sbjct: 96  SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 149

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

 Score =  128 bits (322), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 72/114 (63%), Positives = 75/114 (65%), Gaps = 18/114 (15%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P +QQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct: 32  IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 91

Query: 56  SDMIDNASRGSSSPAG-------------NFEDGWTQADYNIQKESTLHFVLRL 96
           SD IDN         G               EDG T ADYNIQKESTLH VLRL
Sbjct: 92  SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 145

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

 Score =  128 bits (322), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 72/114 (63%), Positives = 75/114 (65%), Gaps = 18/114 (15%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P +QQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct: 36  IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 95

Query: 56  SDMIDNASRGSSSPAG-------------NFEDGWTQADYNIQKESTLHFVLRL 96
           SD IDN         G               EDG T ADYNIQKESTLH VLRL
Sbjct: 96  SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 149

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

 Score =  128 bits (322), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 72/114 (63%), Positives = 75/114 (65%), Gaps = 18/114 (15%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P +QQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct: 36  IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 95

Query: 56  SDMIDNASRGSSSPAG-------------NFEDGWTQADYNIQKESTLHFVLRL 96
           SD IDN         G               EDG T ADYNIQKESTLH VLRL
Sbjct: 96  SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 149

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

 Score =  128 bits (322), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 72/114 (63%), Positives = 75/114 (65%), Gaps = 18/114 (15%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P +QQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct: 36  IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 95

Query: 56  SDMIDNASRGSSSPAG-------------NFEDGWTQADYNIQKESTLHFVLRL 96
           SD IDN         G               EDG T ADYNIQKESTLH VLRL
Sbjct: 96  SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 149

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|P69322|UBIQP_PEA Polyubiquitin OS=Pisum sativum GN=PU1 PE=2 SV=2

 Score =  128 bits (322), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 72/114 (63%), Positives = 75/114 (65%), Gaps = 18/114 (15%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P +QQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct: 36  IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 95

Query: 56  SDMIDNASRGSSSPAG-------------NFEDGWTQADYNIQKESTLHFVLRL 96
           SD IDN         G               EDG T ADYNIQKESTLH VLRL
Sbjct: 96  SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 149

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.

Pisum sativum (taxid: 3888)

>sp|Q3E7T8|UBQ14_ARATH Polyubiquitin 14 OS=Arabidopsis thaliana GN=UBQ14 PE=1 SV=2

 Score =  128 bits (322), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 72/114 (63%), Positives = 75/114 (65%), Gaps = 18/114 (15%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P +QQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct: 36  IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 95

Query: 56  SDMIDNASRGSSSPAG-------------NFEDGWTQADYNIQKESTLHFVLRL 96
           SD IDN         G               EDG T ADYNIQKESTLH VLRL
Sbjct: 96  SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 149

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)

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
297808451	383	predicted protein [Arabidopsis lyrata su	0.989	0.250	0.640	5e-29
260600300	441	ubiquitin [Guzmania wittmackii x Guzmani	0.989	0.217	0.640	1e-28
902584	533	polyubiquitin containing 7 ubiquitin mon	0.989	0.180	0.631	2e-28
162461367	381	polyubiquitin [Zea mays] gi|899608|gb|AA	0.989	0.251	0.631	2e-28
413935668	502	polyubiquitin-like protein [Zea mays]	0.989	0.191	0.631	2e-28
6650740	153	polyubiquitin [Lilium longiflorum]	0.989	0.627	0.651	2e-28
61223100	381	polyubiquitin [Oryza sativa Japonica Gro	0.989	0.251	0.640	2e-28
326517545	457	predicted protein [Hordeum vulgare subsp	0.989	0.210	0.631	3e-28
297805150	537	polyubiquitin [Arabidopsis lyrata subsp.	0.989	0.178	0.631	3e-28
302762631	535	hypothetical protein SELMODRAFT_270468 [	0.989	0.179	0.631	3e-28

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

 Score =  131 bits (330), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 73/114 (64%), Positives = 76/114 (66%), Gaps = 18/114 (15%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +PL+QQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct: 37  IPLDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 96

Query: 56  SDMIDNASRGSSSPAG-------------NFEDGWTQADYNIQKESTLHFVLRL 96
           SD IDN         G               EDG T ADYNIQKESTLH VLRL
Sbjct: 97  SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 150

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|260600300|gb|ACX46987.1| ubiquitin [Guzmania wittmackii x Guzmania lingulata]

 Score =  130 bits (327), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 73/114 (64%), Positives = 75/114 (65%), Gaps = 18/114 (15%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P EQQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct: 188 IPPEQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 247

Query: 56  SDMIDNASRGSSSPAG-------------NFEDGWTQADYNIQKESTLHFVLRL 96
           SD IDN         G               EDG T ADYNIQKESTLH VLRL
Sbjct: 248 SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 301

Source: Guzmania wittmackii x Guzmania lingulata

Species: Guzmania wittmackii x Guzmania lingulata

Genus: Guzmania

Family: Bromeliaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|902584|gb|AAC49013.1| polyubiquitin containing 7 ubiquitin monomers [Zea mays]

 Score =  129 bits (324), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 72/114 (63%), Positives = 75/114 (65%), Gaps = 18/114 (15%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P +QQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct: 340 IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVVRLRGGMQIFVKTLTGKTITLEVES 399

Query: 56  SDMIDNASRGSSSPAG-------------NFEDGWTQADYNIQKESTLHFVLRL 96
           SD IDN         G               EDG T ADYNIQKESTLH VLRL
Sbjct: 400 SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 453

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|162461367|ref|NP_001105376.1| polyubiquitin [Zea mays] gi|899608|gb|AAC49025.1| polyubiquitin [Zea mays]

 Score =  129 bits (324), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 72/114 (63%), Positives = 75/114 (65%), Gaps = 18/114 (15%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P +QQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct: 264 IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVVRLRGGMQIFVKTLTGKTITLEVES 323

Query: 56  SDMIDNASRGSSSPAG-------------NFEDGWTQADYNIQKESTLHFVLRL 96
           SD IDN         G               EDG T ADYNIQKESTLH VLRL
Sbjct: 324 SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 377

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413935668|gb|AFW70219.1| polyubiquitin-like protein [Zea mays]

 Score =  129 bits (324), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 72/114 (63%), Positives = 75/114 (65%), Gaps = 18/114 (15%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P +QQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct: 36  IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 95

Query: 56  SDMIDNASRGSSSPAG-------------NFEDGWTQADYNIQKESTLHFVLRL 96
           SD IDN         G               EDG T ADYNIQKESTLH VLRL
Sbjct: 96  SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 149

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|6650740|gb|AAF21992.1| polyubiquitin [Lilium longiflorum]

 Score =  129 bits (324), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 73/112 (65%), Positives = 77/112 (68%), Gaps = 16/112 (14%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P +QQRL+FA K L     LADYNI KESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct: 36  IPPDQQRLIFAGKQLEDGRTLADYNIHKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 95

Query: 56  SDMIDNAS-----RGSSSP------AGNFEDGWTQADYNIQKESTLHFVLRL 96
           SD IDN       +    P      AG  EDG T ADYNIQKESTLH VLRL
Sbjct: 96  SDTIDNVKAKIHDKEGIPPTTRLIFAGTAEDGRTLADYNIQKESTLHLVLRL 147

Source: Lilium longiflorum

Species: Lilium longiflorum

Genus: Lilium

Family: Liliaceae

Order: Liliales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|61223100|gb|AAX40652.1| polyubiquitin [Oryza sativa Japonica Group]

 Score =  129 bits (324), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 73/114 (64%), Positives = 75/114 (65%), Gaps = 18/114 (15%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P +QQRLVFA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct: 264 IPPDQQRLVFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 323

Query: 56  SDMIDNASRGSSSPAG-------------NFEDGWTQADYNIQKESTLHFVLRL 96
           SD IDN         G               EDG T ADYNIQKESTLH VLRL
Sbjct: 324 SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 377

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326517545|dbj|BAK03691.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  129 bits (324), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 72/114 (63%), Positives = 75/114 (65%), Gaps = 18/114 (15%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P +QQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct: 112 IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 171

Query: 56  SDMIDNASRGSSSPAG-------------NFEDGWTQADYNIQKESTLHFVLRL 96
           SD IDN         G               EDG T ADYNIQKESTLH VLRL
Sbjct: 172 SDTIDNVKAKVQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 225

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

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 =  129 bits (324), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 72/114 (63%), Positives = 75/114 (65%), Gaps = 18/114 (15%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P +QQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct: 419 IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 478

Query: 56  SDMIDNASRGSSSPAG-------------NFEDGWTQADYNIQKESTLHFVLRL 96
           SD IDN         G               EDG T ADYNIQKESTLH VLRL
Sbjct: 479 SDTIDNVKAKIQDKEGIVPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 532

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302762631|ref|XP_002964737.1| hypothetical protein SELMODRAFT_270468 [Selaginella moellendorffii] gi|300166970|gb|EFJ33575.1| hypothetical protein SELMODRAFT_270468 [Selaginella moellendorffii]

 Score =  129 bits (323), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 72/114 (63%), Positives = 75/114 (65%), Gaps = 18/114 (15%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P +QQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct: 36  IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 95

Query: 56  SDMIDNASRGSSSPAG-------------NFEDGWTQADYNIQKESTLHFVLRL 96
           SD IDN         G               EDG T ADYNIQKESTLH VLRL
Sbjct: 96  SDTIDNVKTKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 149

Source: Selaginella moellendorffii

Species: Selaginella moellendorffii

Genus: Selaginella

Family: Selaginellaceae

Order: Selaginellales

Class: Isoetopsida

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:2827139	230	UBQ12 "AT1G55060" [Arabidopsis	0.989	0.417	0.657	1.5e-26
TAIR|locus:2180434	382	UBQ4 "AT5G20620" [Arabidopsis	0.989	0.251	0.649	4e-26
TAIR|locus:2143548	306	UBQ3 "AT5G03240" [Arabidopsis	0.989	0.313	0.649	4e-26
TAIR|locus:2140200	305	UBQ14 "AT4G02890" [Arabidopsis	0.989	0.314	0.649	4e-26
TAIR|locus:2138386	229	UBQ11 "AT4G05050" [Arabidopsis	0.989	0.419	0.649	4e-26
TAIR|locus:2115663	457	UBQ10 "AT4G05320" [Arabidopsis	0.989	0.210	0.649	6.9e-26
TAIR|locus:2206310	319	UBQ13 "AT1G65350" [Arabidopsis	0.979	0.297	0.640	2e-24
POMBASE|SPBC337.08c	382	ubi4 "ubiquitin" [Schizosaccha	0.989	0.251	0.631	1.8e-25
SGD|S000003962	381	UBI4 "Ubiquitin" [Saccharomyce	0.989	0.251	0.631	1.8e-25
ASPGD|ASPL0000049163	305	ubi4 [Emericella nidulans (tax	0.989	0.314	0.631	1.8e-25

TAIR|locus:2827139 UBQ12 "AT1G55060" [Arabidopsis thaliana (taxid:3702)]

 Score = 299 (110.3 bits), Expect = 1.5e-26, P = 1.5e-26
 Identities = 75/114 (65%), Positives = 79/114 (69%)

Query:     1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
             +P +QQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct:   112 IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 171

Query:    56 SDMIDNAS-----RGSSSP-------AGN-FEDGWTQADYNIQKESTLHFVLRL 96
             SD IDN       +   SP       AG   EDG T ADYNIQKESTLH VLRL
Sbjct:   172 SDTIDNVKAKIQDKEGISPDQQRLIFAGKQHEDGRTLADYNIQKESTLHLVLRL 225

GO:0005622 "intracellular" evidence=TAS

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

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

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

 Score = 295 (108.9 bits), Expect = 4.0e-26, P = 4.0e-26
 Identities = 74/114 (64%), Positives = 78/114 (68%)

Query:     1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
             +P +QQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct:   264 IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 323

Query:    56 SDMIDNAS-----RGSSSP-------AGN-FEDGWTQADYNIQKESTLHFVLRL 96
             SD IDN       +    P       AG   EDG T ADYNIQKESTLH VLRL
Sbjct:   324 SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 377

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 = 295 (108.9 bits), Expect = 4.0e-26, P = 4.0e-26
 Identities = 74/114 (64%), Positives = 78/114 (68%)

Query:     1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
             +P +QQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct:   188 IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 247

Query:    56 SDMIDNAS-----RGSSSP-------AGN-FEDGWTQADYNIQKESTLHFVLRL 96
             SD IDN       +    P       AG   EDG T ADYNIQKESTLH VLRL
Sbjct:   248 SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 301

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 = 295 (108.9 bits), Expect = 4.0e-26, P = 4.0e-26
 Identities = 74/114 (64%), Positives = 78/114 (68%)

Query:     1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
             +P +QQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct:   188 IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 247

Query:    56 SDMIDNAS-----RGSSSP-------AGN-FEDGWTQADYNIQKESTLHFVLRL 96
             SD IDN       +    P       AG   EDG T ADYNIQKESTLH VLRL
Sbjct:   248 SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 301

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

GO:0005773 "vacuole" evidence=IDA

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

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

 Score = 295 (108.9 bits), Expect = 4.0e-26, P = 4.0e-26
 Identities = 74/114 (64%), Positives = 78/114 (68%)

Query:     1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
             +P +QQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct:   112 IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 171

Query:    56 SDMIDNAS-----RGSSSP-------AGN-FEDGWTQADYNIQKESTLHFVLRL 96
             SD IDN       +    P       AG   EDG T ADYNIQKESTLH VLRL
Sbjct:   172 SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 225

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 = 295 (108.9 bits), Expect = 6.9e-26, P = 6.9e-26
 Identities = 74/114 (64%), Positives = 78/114 (68%)

Query:     1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
             +P +QQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct:   340 IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 399

Query:    56 SDMIDNAS-----RGSSSP-------AGN-FEDGWTQADYNIQKESTLHFVLRL 96
             SD IDN       +    P       AG   EDG T ADYNIQKESTLH VLRL
Sbjct:   400 SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL 453

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

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

GO:0007568 "aging" evidence=IEP

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

 Score = 279 (103.3 bits), Expect = 2.0e-24, P = 2.0e-24
 Identities = 73/114 (64%), Positives = 77/114 (67%)

Query:     1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
             +P +QQRL+FA K L     LADYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct:    36 IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 95

Query:    56 SDMIDNAS-----RGSSSP-------AGN-FEDGWTQADYNIQKESTLHFVLRL 96
             SD IDN       +    P       AG   EDG T AD NIQKESTLH VLRL
Sbjct:    96 SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLAD-NIQKESTLHLVLRL 148

GO:0005622 "intracellular" evidence=TAS

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

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

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

 Score = 289 (106.8 bits), Expect = 1.8e-25, P = 1.8e-25
 Identities = 72/114 (63%), Positives = 78/114 (68%)

Query:     1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
             +P +QQRL+FA K L     L+DYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct:   264 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 323

Query:    56 SDMIDNAS-----RGSSSP-------AGN-FEDGWTQADYNIQKESTLHFVLRL 96
             SD IDN       +    P       AG   EDG T +DYNIQKESTLH VLRL
Sbjct:   324 SDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL 377

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 = 289 (106.8 bits), Expect = 1.8e-25, P = 1.8e-25
 Identities = 72/114 (63%), Positives = 78/114 (68%)

Query:     1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
             +P +QQRL+FA K L     L+DYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct:   264 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 323

Query:    56 SDMIDNAS-----RGSSSP-------AGN-FEDGWTQADYNIQKESTLHFVLRL 96
             SD IDN       +    P       AG   EDG T +DYNIQKESTLH VLRL
Sbjct:   324 SDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL 377

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

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

 Score = 289 (106.8 bits), Expect = 1.8e-25, P = 1.8e-25
 Identities = 72/114 (63%), Positives = 78/114 (68%)

Query:     1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
             +P +QQRL+FA K L     L+DYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVES
Sbjct:   188 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVES 247

Query:    56 SDMIDNAS-----RGSSSP-------AGN-FEDGWTQADYNIQKESTLHFVLRL 96
             SD IDN       +    P       AG   EDG T +DYNIQKESTLH VLRL
Sbjct:   248 SDTIDNVKTKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL 301

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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	97
cd01803	76	cd01803, Ubiquitin, Ubiquitin	2e-20
cd01803	76	cd01803, Ubiquitin, Ubiquitin	4e-12
pfam00240	69	pfam00240, ubiquitin, Ubiquitin family	1e-07
smart00213	72	smart00213, UBQ, Ubiquitin homologues	3e-07
smart00213	72	smart00213, UBQ, Ubiquitin homologues	8e-07
cd01769	69	cd01769, UBL, Ubiquitin-like domain of UBL	2e-05
cd01806	76	cd01806, Nedd8, Nebb8-like ubiquitin protein	2e-05
cd01769	69	cd01769, UBL, Ubiquitin-like domain of UBL	3e-05
cd01806	76	cd01806, Nedd8, Nebb8-like ubiquitin protein	5e-05
pfam00240	69	pfam00240, ubiquitin, Ubiquitin family	7e-05
cd01809	72	cd01809, Scythe_N, Ubiquitin-like domain of Scythe	8e-04
PTZ00044	76	PTZ00044, PTZ00044, ubiquitin; Provisional	0.002
PTZ00044	76	PTZ00044, PTZ00044, ubiquitin; Provisional	0.003

>gnl|CDD|176398 cd01803, Ubiquitin, Ubiquitin

 Score = 77.2 bits (190), Expect = 2e-20
 Identities = 41/73 (56%), Positives = 43/73 (58%), Gaps = 13/73 (17%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAGN-------------FEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

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

>gnl|CDD|176398 cd01803, Ubiquitin, Ubiquitin

 Score = 56.0 bits (135), Expect = 4e-12
 Identities = 27/40 (67%), Positives = 31/40 (77%), Gaps = 5/40 (12%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG 35
          +P +QQRL+FA K L     L+DYNIQKESTLHLV RLRG
Sbjct: 36 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG 75

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 = 44.1 bits (105), Expect = 1e-07
 Identities = 20/39 (51%), Positives = 28/39 (71%), Gaps = 5/39 (12%)

Query: 1  MPLEQQRLVFA-----DKSLLADYNIQKESTLHLVARLR 34
          +P++QQRL+F+     D + L++Y IQ  STLHLV RLR
Sbjct: 31 IPVDQQRLIFSGKVLEDDTTLSEYGIQDGSTLHLVLRLR 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|214563 smart00213, UBQ, Ubiquitin homologues

 Score = 43.4 bits (103), Expect = 3e-07
 Identities = 28/72 (38%), Positives = 36/72 (50%), Gaps = 13/72 (18%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDN----ASRGSSSPAGNF---------EDGWTQADYN 83
          +++ VKT  GKTITLEV+ SD +       +  +  P             ED  T ADY 
Sbjct: 1  IELTVKTLDGKTITLEVKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVLEDDRTLADYG 60

Query: 84 IQKESTLHFVLR 95
          IQ  ST+H VLR
Sbjct: 61 IQDGSTIHLVLR 72

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

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

 Score = 42.2 bits (100), Expect = 8e-07
 Identities = 20/37 (54%), Positives = 24/37 (64%), Gaps = 5/37 (13%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVAR 32
          +P EQQRL++  K L     LADY IQ  ST+HLV R
Sbjct: 36 IPPEQQRLIYKGKVLEDDRTLADYGIQDGSTIHLVLR 72

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

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

 Score = 38.8 bits (91), Expect = 2e-05
 Identities = 25/69 (36%), Positives = 29/69 (42%), Gaps = 13/69 (18%)

Query: 40 FVKTSTGKTITLEVESSDMIDNA----SRGSSSPAG---------NFEDGWTQADYNIQK 86
           VKT TGKT  LEV   D +       +     P             +D  T +DY IQ 
Sbjct: 1  TVKTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYAGKILKDDKTLSDYGIQD 60

Query: 87 ESTLHFVLR 95
           STLH VLR
Sbjct: 61 GSTLHLVLR 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|176401 cd01806, Nedd8, Nebb8-like ubiquitin protein

 Score = 39.0 bits (91), Expect = 2e-05
 Identities = 23/73 (31%), Positives = 31/73 (42%), Gaps = 13/73 (17%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          M I VKT TGK I +++E +D ++          G                D  T ADY 
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDDKTAADYK 60

Query: 84 IQKESTLHFVLRL 96
          ++  S LH VL L
Sbjct: 61 LEGGSVLHLVLAL 73

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 = 38.4 bits (90), Expect = 3e-05
 Identities = 21/37 (56%), Positives = 25/37 (67%), Gaps = 5/37 (13%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVAR 32
          +P EQQRL++A K L     L+DY IQ  STLHLV R
Sbjct: 33 VPPEQQRLIYAGKILKDDKTLSDYGIQDGSTLHLVLR 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|176401 cd01806, Nedd8, Nebb8-like ubiquitin protein

 Score = 37.8 bits (88), Expect = 5e-05
 Identities = 17/40 (42%), Positives = 25/40 (62%), Gaps = 5/40 (12%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG 35
          +P +QQRL+++ K +      ADY ++  S LHLV  LRG
Sbjct: 36 IPPQQQRLIYSGKQMNDDKTAADYKLEGGSVLHLVLALRG 75

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|215813 pfam00240, ubiquitin, Ubiquitin family

 Score = 37.2 bits (87), Expect = 7e-05
 Identities = 27/69 (39%), Positives = 33/69 (47%), Gaps = 13/69 (18%)

Query: 42 KTSTGKTITLEVESSDMIDN-----ASRGSSSP-------AGNF-EDGWTQADYNIQKES 88
          KT  GKTITLEV+ SD +         +            +G   ED  T ++Y IQ  S
Sbjct: 1  KTLDGKTITLEVDPSDTVSELKEKIEDKEGIPVDQQRLIFSGKVLEDDTTLSEYGIQDGS 60

Query: 89 TLHFVLRLS 97
          TLH VLRL 
Sbjct: 61 TLHLVLRLR 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|176404 cd01809, Scythe_N, Ubiquitin-like domain of Scythe protein

 Score = 34.5 bits (80), Expect = 8e-04
 Identities = 14/36 (38%), Positives = 23/36 (63%), Gaps = 5/36 (13%)

Query: 2  PLEQQRLVFA-----DKSLLADYNIQKESTLHLVAR 32
          P+EQQRL+++     D   L++Y ++   T+HLV R
Sbjct: 37 PVEQQRLIYSGRVLKDDETLSEYKVEDGHTIHLVKR 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 = 33.6 bits (77), Expect = 0.002
 Identities = 19/73 (26%), Positives = 27/73 (36%), Gaps = 13/73 (17%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQI +KT TGK  +   E  + +           G                D    +DY 
Sbjct: 1  MQILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYSGKQMSDDLKLSDYK 60

Query: 84 IQKESTLHFVLRL 96
          +   ST+H VL+L
Sbjct: 61 VVPGSTIHMVLQL 73

Length = 76

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

 Score = 33.3 bits (76), Expect = 0.003
 Identities = 14/37 (37%), Positives = 24/37 (64%), Gaps = 5/37 (13%)

Query: 4  EQQRLVFADKSL-----LADYNIQKESTLHLVARLRG 35
          +Q RL+++ K +     L+DY +   ST+H+V +LRG
Sbjct: 39 KQIRLIYSGKQMSDDLKLSDYKVVPGSTIHMVLQLRG 75

Length = 76

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	97
cd01802	103	AN1_N ubiquitin-like domain of AN1. AN1 (also know	99.87
cd01807	74	GDX_N ubiquitin-like domain of GDX. GDX contains a	99.79
cd01793	74	Fubi Fubi ubiquitin-like protein. Fubi is a ubiqui	99.77
PTZ00044	76	ubiquitin; Provisional	99.76
cd01797	78	NIRF_N amino-terminal ubiquitin-like domain of Np9	99.74
cd01810	74	ISG15_repeat2 ISG15 ubiquitin-like protein, second	99.73
cd01803	76	Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40	99.72
cd01806	76	Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also kn	99.71
cd01798	70	parkin_N amino-terminal ubiquitin-like of parkin p	99.71
KOG0003	128	consensus Ubiquitin/60s ribosomal protein L40 fusi	99.69
cd01804	78	midnolin_N Ubiquitin-like domain of midnolin. midn	99.68
cd01791	73	Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also know	99.67
cd01809	72	Scythe_N Ubiquitin-like domain of Scythe protein.	99.67
cd01792	80	ISG15_repeat1 ISG15 ubiquitin-like protein, first	99.67
cd01805	77	RAD23_N Ubiquitin-like domain of RAD23. RAD23 belo	99.65
cd01794	70	DC_UbP_C dendritic cell derived ubiquitin-like pro	99.65
cd01808	71	hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC	99.65
KOG0004	156	consensus Ubiquitin/40S ribosomal protein S27a fus	99.62
PF00240	69	ubiquitin: Ubiquitin family; InterPro: IPR000626 U	99.61
cd01790	79	Herp_N Homocysteine-responsive endoplasmic reticul	99.55
cd01800	76	SF3a120_C Ubiquitin-like domain of Mammalian splic	99.52
cd01796	71	DDI1_N DNA damage inducible protein 1 ubiquitin-li	99.52
cd01763	87	Sumo Small ubiquitin-related modifier (SUMO). Smal	99.49
KOG0005	70	consensus Ubiquitin-like protein [Cell cycle contr	99.47
cd01812	71	BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-ter	99.45
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	99.42
smart00213	64	UBQ Ubiquitin homologues. Ubiquitin-mediated prote	99.32
cd01813	74	UBP_N UBP ubiquitin processing protease. The UBP (	99.29
KOG0010	493	consensus Ubiquitin-like protein [Posttranslationa	99.22
KOG0011	340	consensus Nucleotide excision repair factor NEF2,	99.22
cd01815	75	BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC	99.17
cd01799	75	Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HO	99.16
cd01793	74	Fubi Fubi ubiquitin-like protein. Fubi is a ubiqui	99.13
cd01814	113	NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and AT	99.09
cd01769	69	UBL Ubiquitin-like domain of UBL. UBLs function by	99.09
KOG0004	156	consensus Ubiquitin/40S ribosomal protein S27a fus	99.07
PF11976	72	Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; Inter	99.04
cd01797	78	NIRF_N amino-terminal ubiquitin-like domain of Np9	99.03
cd01807	74	GDX_N ubiquitin-like domain of GDX. GDX contains a	99.02
cd01815	75	BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC	99.0
KOG0001	75	consensus Ubiquitin and ubiquitin-like proteins [P	98.95
cd01802	103	AN1_N ubiquitin-like domain of AN1. AN1 (also know	98.92
cd01810	74	ISG15_repeat2 ISG15 ubiquitin-like protein, second	98.92
cd01798	70	parkin_N amino-terminal ubiquitin-like of parkin p	98.89
PTZ00044	76	ubiquitin; Provisional	98.88
PF13881	111	Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB	98.87
cd01794	70	DC_UbP_C dendritic cell derived ubiquitin-like pro	98.83
cd01806	76	Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also kn	98.82
PF00240	69	ubiquitin: Ubiquitin family; InterPro: IPR000626 U	98.81
cd01808	71	hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC	98.81
cd01800	76	SF3a120_C Ubiquitin-like domain of Mammalian splic	98.79
cd01795	107	USP48_C USP ubiquitin-specific protease. The USP (	98.77
cd01791	73	Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also know	98.77
cd01803	76	Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40	98.74
cd01804	78	midnolin_N Ubiquitin-like domain of midnolin. midn	98.71
KOG0003	128	consensus Ubiquitin/60s ribosomal protein L40 fusi	98.66
PLN02560	308	enoyl-CoA reductase	98.64
cd01809	72	Scythe_N Ubiquitin-like domain of Scythe protein.	98.63
cd01805	77	RAD23_N Ubiquitin-like domain of RAD23. RAD23 belo	98.62
cd01796	71	DDI1_N DNA damage inducible protein 1 ubiquitin-li	98.61
PF11543	80	UN_NPL4: Nuclear pore localisation protein NPL4; I	98.58
cd01788	119	ElonginB Ubiquitin-like domain of Elongin B. Elong	98.58
KOG0005	70	consensus Ubiquitin-like protein [Cell cycle contr	98.56
cd01789	84	Alp11_N Ubiquitin-like domain of Alp11 tubulin-fol	98.53
cd01792	80	ISG15_repeat1 ISG15 ubiquitin-like protein, first	98.51
cd01763	87	Sumo Small ubiquitin-related modifier (SUMO). Smal	98.5
cd01814	113	NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and AT	98.43
cd01790	79	Herp_N Homocysteine-responsive endoplasmic reticul	98.41
cd01812	71	BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-ter	98.39
KOG0010	493	consensus Ubiquitin-like protein [Posttranslationa	98.37
cd01801	77	Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-	98.35
cd01795	107	USP48_C USP ubiquitin-specific protease. The USP (	98.33
KOG4248	1143	consensus Ubiquitin-like protein, regulator of apo	98.29
cd01799	75	Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HO	98.28
PF14560	87	Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2K	98.24
cd01813	74	UBP_N UBP ubiquitin processing protease. The UBP (	98.05
KOG3493	73	consensus Ubiquitin-like protein [Posttranslationa	97.98
cd01811	80	OASL_repeat1 2'-5' oligoadenylate synthetase-like	97.85
cd00196	69	UBQ Ubiquitin-like proteins. Ubiquitin homologs; I	97.82
cd01769	69	UBL Ubiquitin-like domain of UBL. UBLs function by	97.77
smart00213	64	UBQ Ubiquitin homologues. Ubiquitin-mediated prote	97.73
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	97.72
KOG0001	75	consensus Ubiquitin and ubiquitin-like proteins [P	97.69
PF08817	79	YukD: WXG100 protein secretion system (Wss), prote	97.6
cd01789	84	Alp11_N Ubiquitin-like domain of Alp11 tubulin-fol	97.57
PF00789	82	UBX: UBX domain; InterPro: IPR001012 The UBX domai	97.51
PF11976	72	Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; Inter	97.45
cd01770	79	p47_UBX p47-like ubiquitin domain. p47_UBX p47 is	97.33
KOG4248	1143	consensus Ubiquitin-like protein, regulator of apo	97.3
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	97.29
cd01767	77	UBX UBX (ubiquitin regulatory X) domain. The UBX (	97.28
smart00166	80	UBX Domain present in ubiquitin-regulatory protein	97.24
cd01772	79	SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-subst	97.21
KOG4495	110	consensus RNA polymerase II transcription elongati	96.95
PF13019	162	Telomere_Sde2: Telomere stability and silencing	96.79
cd01774	85	Faf1_like2_UBX Faf1 ike-2 UBX domain. Faf1_like2 i	96.6
cd01801	77	Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-	96.53
KOG1639	297	consensus Steroid reductase required for elongatio	96.52
KOG1769	99	consensus Ubiquitin-like proteins [Posttranslation	96.17
cd01811	80	OASL_repeat1 2'-5' oligoadenylate synthetase-like	96.12
KOG0011	340	consensus Nucleotide excision repair factor NEF2,	96.1
PF14560	87	Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2K	96.08
PF13881	111	Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB	95.96
COG5417	81	Uncharacterized small protein [Function unknown]	95.85
PF11470	65	TUG-UBL1: GLUT4 regulating protein TUG; InterPro:	95.66
cd01771	80	Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated fac	95.45
PF08337	539	Plexin_cytopl: Plexin cytoplasmic RasGAP domain; I	95.32
PF10302	97	DUF2407: DUF2407 ubiquitin-like domain; InterPro:	95.21
PF15044	76	CLU_N: Mitochondrial function, CLU-N-term	95.02
cd01773	82	Faf1_like1_UBX Faf1 ike-1 UBX domain. Faf1_like1 i	94.84
PF10790	76	DUF2604: Protein of Unknown function (DUF2604); In	94.61
PF09379	80	FERM_N: FERM N-terminal domain ; InterPro: IPR0189	94.16
cd01788	119	ElonginB Ubiquitin-like domain of Elongin B. Elong	93.76
PF14453	57	ThiS-like: ThiS-like ubiquitin	93.15
PLN02560	308	enoyl-CoA reductase	92.01
KOG1872	473	consensus Ubiquitin-specific protease [Posttransla	91.99
cd00196	69	UBQ Ubiquitin-like proteins. Ubiquitin homologs; I	91.74
cd06409	86	PB1_MUG70 The MUG70 protein is a product of the me	91.41
KOG0013	231	consensus Uncharacterized conserved protein [Funct	90.82
PF10209	122	DUF2340: Uncharacterized conserved protein (DUF234	90.63
KOG4583	391	consensus Membrane-associated ER protein involved	90.36
smart00295	207	B41 Band 4.1 homologues. Also known as ezrin/radix	90.32
KOG2086	380	consensus Protein tyrosine phosphatase SHP1/Cofact	89.66
KOG3206	234	consensus Alpha-tubulin folding cofactor B [Posttr	89.44
PRK06437	67	hypothetical protein; Provisional	88.98
COG5227	103	SMT3 Ubiquitin-like protein (sentrin) [Posttransla	88.26
TIGR02958	452	sec_mycoba_snm4 secretion protein snm4. Members of	86.63
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	85.72
PRK08364	70	sulfur carrier protein ThiS; Provisional	85.4
PRK06488	65	sulfur carrier protein ThiS; Validated	84.89
PF11620	88	GABP-alpha: GA-binding protein alpha chain; InterP	83.04
PF02824	60	TGS: TGS domain; InterPro: IPR004095 The TGS domai	81.67
PF11069	98	DUF2870: Protein of unknown function (DUF2870); In	80.98
KOG1872	473	consensus Ubiquitin-specific protease [Posttransla	80.93
PRK07440	70	hypothetical protein; Provisional	80.52

>cd01802 AN1_N ubiquitin-like domain of AN1

Probab=99.87  E-value=4.4e-22  Score=122.94  Aligned_cols=80  Identities=24%  Similarity=0.354  Sum_probs=77.0

Q ss_pred             cccccCCCcceeeeeecCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCccccccc
Q 042212           18 DYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNI   84 (97)
Q Consensus        18 ~y~i~~~s~i~l~~~~~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I   84 (97)
                      .+++.+-+++|+.+++++.|+|+||++.|++++++|++++||++||++|+             |+|+.|+|+.+|++|+|
T Consensus         9 ~~~~~~~~~~~~~~~~~~~M~I~Vk~l~G~~~~leV~~~~TV~~lK~kI~~~~gip~~~QrLi~~Gk~L~D~~tL~dy~I   88 (103)
T cd01802           9 FFNEDNMGPFHYKLPFYDTMELFIETLTGTCFELRVSPFETVISVKAKIQRLEGIPVAQQHLIWNNMELEDEYCLNDYNI   88 (103)
T ss_pred             ccccCCcceeEEeeccCCCEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEECCEECCCCCcHHHcCC
Confidence            46788999999999999999999999999999999999999999999998             99999999999999999


Q ss_pred             CCCCEEEEEEeeC
Q 042212           85 QKESTLHFVLRLS   97 (97)
Q Consensus        85 ~~~sti~l~~rl~   97 (97)
                      ++++++++++++|
T Consensus        89 ~~~stL~l~~~l~  101 (103)
T cd01802          89 SEGCTLKLVLAMR  101 (103)
T ss_pred             CCCCEEEEEEecC
Confidence            9999999999975

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.

>cd01807 GDX_N ubiquitin-like domain of GDX

Probab=99.79  E-value=3.2e-19  Score=103.92  Aligned_cols=61  Identities=23%  Similarity=0.329  Sum_probs=58.8

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      |+|+||+.+|++++++|++++||+++|++|+             |+|++|+|+++|++|||++++++++++|.+
T Consensus         1 m~i~vk~~~G~~~~l~v~~~~tV~~lK~~i~~~~gi~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~l~l~~~~~   74 (74)
T cd01807           1 MFLTVKLLQGRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLLFKGKALADDKRLSDYSIGPNAKLNLVVRPP   74 (74)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEECCCCCCHHHCCCCCCCEEEEEEcCC
Confidence            7999999999999999999999999999998             999999999999999999999999999864

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

>cd01793 Fubi Fubi ubiquitin-like protein

Probab=99.77  E-value=8.9e-19  Score=102.04  Aligned_cols=59  Identities=27%  Similarity=0.342  Sum_probs=56.2

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      |+|+||+.  ++++++|++++||+++|++|+             |+|++|+|+.+|++|||++++|+|+++|++
T Consensus         1 mqi~vk~~--~~~~l~v~~~~tV~~lK~~i~~~~gip~~~q~Li~~Gk~L~D~~tL~~~~i~~~~tl~l~~~l~   72 (74)
T cd01793           1 MQLFVRAQ--NTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVLLLAGVPLEDDATLGQCGVEELCTLEVAGRLL   72 (74)
T ss_pred             CEEEEECC--CEEEEEECCcCcHHHHHHHHHhhhCCCHHHEEEEECCeECCCCCCHHHcCCCCCCEEEEEEecC
Confidence            79999984  789999999999999999998             999999999999999999999999999985

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.

>PTZ00044 ubiquitin; Provisional

Probab=99.76  E-value=1.8e-18  Score=100.85  Aligned_cols=61  Identities=30%  Similarity=0.482  Sum_probs=59.1

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      |+|+||+++|+++++++++++||+++|++|+             |+|++|+|+.+|++|++++++++|+.++++
T Consensus         1 m~i~vk~~~G~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~   74 (76)
T PTZ00044          1 MQILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYSGKQMSDDLKLSDYKVVPGSTIHMVLQLR   74 (76)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEEccCCCcHHHcCCCCCCEEEEEEEcc
Confidence            7999999999999999999999999999998             999999999999999999999999999875

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

Probab=99.74  E-value=4.6e-18  Score=100.21  Aligned_cols=60  Identities=25%  Similarity=0.375  Sum_probs=57.2

Q ss_pred             eeeEEECCCCCE-EEEe-ecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEee
Q 042212           37 MQIFVKTSTGKT-ITLE-VESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        37 m~i~vk~~~g~~-~~l~-v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      |+|+||+.+|++ ++++ +++++||+++|++|+             |+|++|+|+.+|++|||+++++|++++|+
T Consensus         1 M~I~vk~~~G~~~~~l~~v~~~~TV~~lK~~i~~~~gi~~~~QrLi~~Gk~L~D~~tL~~y~i~~~~~i~l~~~~   75 (78)
T cd01797           1 MWIQVRTMDGKETRTVDSLSRLTKVEELREKIQELFNVEPECQRLFYRGKQMEDGHTLFDYNVGLNDIIQLLVRQ   75 (78)
T ss_pred             CEEEEEcCCCCEEEEeeccCCcCcHHHHHHHHHHHhCCCHHHeEEEeCCEECCCCCCHHHcCCCCCCEEEEEEec
Confidence            899999999997 6895 899999999999999             99999999999999999999999999986

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.

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

Probab=99.73  E-value=6.8e-18  Score=98.31  Aligned_cols=59  Identities=22%  Similarity=0.377  Sum_probs=56.9

Q ss_pred             eEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           39 IFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        39 i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      |+||++.|+++++++++++||+++|++|+             |+|++|+|+++|++|||++++++++++|++
T Consensus         1 i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~q~L~~~G~~L~D~~tL~~~~i~~~~tl~l~~~l~   72 (74)
T cd01810           1 ILVRNDKGRSSIYEVQLTQTVATLKQQVSQRERVQADQFWLSFEGRPMEDEHPLGEYGLKPGCTVFMNLRLR   72 (74)
T ss_pred             CEEECCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEECCEECCCCCCHHHcCCCCCCEEEEEEEcc
Confidence            68999999999999999999999999998             999999999999999999999999999874

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.

>cd01803 Ubiquitin Ubiquitin

Probab=99.72  E-value=1.5e-17  Score=96.60  Aligned_cols=61  Identities=66%  Similarity=0.832  Sum_probs=59.0

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      |+|+||+.+|+++.+++++++||+++|++|+             |+|+.|+|+.+|++||+++++++++++|++
T Consensus         1 m~i~v~~~~g~~~~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~i~l~~~~~   74 (76)
T cd01803           1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   74 (76)
T ss_pred             CEEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCHHHeEEEECCEECCCCCcHHHcCCCCCCEEEEEEEcc
Confidence            7899999999999999999999999999998             999999999999999999999999999975

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

>cd01806 Nedd8 Nebb8-like ubiquitin protein

Probab=99.71  E-value=2.8e-17  Score=95.42  Aligned_cols=61  Identities=36%  Similarity=0.524  Sum_probs=58.9

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      |+|+|++.+|+++.+++++++||+++|++|+             |+|+.|+|+.+|++|++++|+++|+++++|
T Consensus         1 m~i~v~~~~g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~~~g~~L~d~~tl~~~~i~~g~~i~l~~~~~   74 (76)
T cd01806           1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDDKTAADYKLEGGSVLHLVLALR   74 (76)
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEEECCeEccCCCCHHHcCCCCCCEEEEEEEcc
Confidence            7899999999999999999999999999998             999999999999999999999999999875

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.

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

Probab=99.71  E-value=2.3e-17  Score=95.03  Aligned_cols=57  Identities=25%  Similarity=0.379  Sum_probs=55.0

Q ss_pred             eEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           39 IFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        39 i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      |+||+..|+++++++++++||+++|++|+             |+|++|+|+.+|++|||++++++|++.|
T Consensus         1 i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~q~Li~~G~~L~d~~~l~~~~i~~~stl~l~~~   70 (70)
T cd01798           1 VYVRTNTGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVIFAGKELRNTTTIQECDLGQQSILHAVRR   70 (70)
T ss_pred             CEEEcCCCCEEEEEECCCChHHHHHHHHHHHHCCCHHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEeC
Confidence            68999999999999999999999999998             9999999999999999999999999875

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.

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

Probab=99.69  E-value=4.8e-18  Score=104.36  Aligned_cols=61  Identities=69%  Similarity=0.850  Sum_probs=58.9

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      |++|++++.|++.+++++|++||.++|++|+             |+|++|+|+.|+++||++..+|+|+++|||
T Consensus         1 ~~~~~~~~~GKT~~le~EpS~ti~~vKA~i~~~~Gi~~~~~~L~~~~k~LED~~Tla~Y~i~~~~Tl~~~~rL~   74 (128)
T KOG0003|consen    1 MQIFVKTLTGKTITLEVEPSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (128)
T ss_pred             CcEEEEEeeCceEEEEecccchHHHHHHHhccccCCCHHHHHHHhcccccccCCcccccCccchhhhhhhHHHh
Confidence            6899999999999999999999999999999             999999999999999999999999999875

>cd01804 midnolin_N Ubiquitin-like domain of midnolin

Probab=99.68  E-value=9.2e-17  Score=94.56  Aligned_cols=61  Identities=18%  Similarity=0.335  Sum_probs=57.8

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      .|+|+||+..|++++++++++.||++||++|+             |+|+.|+|+ +|++|||++|++|+++..++
T Consensus         1 ~m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~~~~~~~qrL~~~Gk~L~d~-~L~~~gi~~~~~i~l~~~~~   74 (78)
T cd01804           1 PMNLNIHSTTGTRFDLSVPPDETVEGLKKRISQRLKVPKERLALLHRETRLSSG-KLQDLGLGDGSKLTLVPTVE   74 (78)
T ss_pred             CeEEEEEECCCCEEEEEECCcCHHHHHHHHHHHHhCCChHHEEEEECCcCCCCC-cHHHcCCCCCCEEEEEeecc
Confidence            48999999999999999999999999999997             999999999 99999999999999998763

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=99.67  E-value=1.1e-16  Score=93.20  Aligned_cols=57  Identities=18%  Similarity=0.311  Sum_probs=55.2

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEE
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~   93 (97)
                      |.|+|++..|+++.++++|++||++||++|+             |+|+.|+|+.+|++|||++|++|||.
T Consensus         2 ~~i~vkt~~Gk~~~~~v~~~~TV~~LK~~I~~~~~~~~~~qrLi~~Gk~L~D~~tL~~ygi~~~stv~l~   71 (73)
T cd01791           2 IEVVCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFKDHISLGDYEIHDGMNLELY   71 (73)
T ss_pred             EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEeCCcCCCCCCCHHHcCCCCCCEEEEE
Confidence            7899999999999999999999999999998             99999999999999999999999986

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.

>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein

Probab=99.67  E-value=1.4e-16  Score=91.59  Aligned_cols=59  Identities=25%  Similarity=0.322  Sum_probs=56.8

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      |+|+||+.+|+++++++++++||+++|++|+             |+|+.|+|+.+|++||+++|+++|++.|
T Consensus         1 i~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~l~l~~~   72 (72)
T cd01809           1 IEIKVKTLDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYSGRVLKDDETLSEYKVEDGHTIHLVKR   72 (72)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCEECCCcCcHHHCCCCCCCEEEEEeC
Confidence            7899999999999999999999999999998             9999999999999999999999999875

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.

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

Probab=99.67  E-value=1.7e-16  Score=93.69  Aligned_cols=60  Identities=15%  Similarity=0.201  Sum_probs=57.6

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc---------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS---------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~---------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      +|+|+||+..|+++.+++++++||++||++|+               |+|+.|+|+.+|++||+++|++++++++
T Consensus         2 ~~~i~Vk~~~G~~~~~~v~~~~TV~~lK~~I~~~~~i~~~~qrL~~~~~G~~L~D~~tL~~~gi~~gs~l~l~~~   76 (80)
T cd01792           2 GWDLKVKMLGGNEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLAHLDSREVLQDGVPLVSQGLGPGSTVLLVVQ   76 (80)
T ss_pred             ceEEEEEeCCCCEEEEEcCCCCcHHHHHHHHHHHhCCCHHHEEEEeccCCCCCCCCCCHHHcCCCCCCEEEEEEE
Confidence            38999999999999999999999999999998               7899999999999999999999999987

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.

>cd01805 RAD23_N Ubiquitin-like domain of RAD23

Probab=99.65  E-value=2.7e-16  Score=91.75  Aligned_cols=60  Identities=20%  Similarity=0.289  Sum_probs=57.1

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc---------------CCCeeCCCCCcccccccCCCCEEEEEEee
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS---------------SPAGNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~---------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      |+|+|++.+|+++.+++++++||+++|++|+               |+|++|+|+.+|++|||++|++++++++-
T Consensus         1 m~i~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~i~~~~~~   75 (77)
T cd01805           1 MKITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKILKDDTTLEEYKIDEKDFVVVMVSK   75 (77)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEEECCEEccCCCCHHHcCCCCCCEEEEEEec
Confidence            7999999999999999999999999999986               89999999999999999999999998863

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).

>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein

Probab=99.65  E-value=2.4e-16  Score=91.12  Aligned_cols=56  Identities=23%  Similarity=0.318  Sum_probs=53.5

Q ss_pred             eEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEE
Q 042212           39 IFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        39 i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      +.||..+|+++++++++++||+++|++|+             |+|++|+|+.+|++|+|+++++||+++
T Consensus         1 ~~vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~Li~~G~~L~D~~~l~~~~i~~~~tv~~~~   69 (70)
T cd01794           1 LKVRLSTGKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWFFSGKLLTDKTRLQETKIQKDYVVQVIV   69 (70)
T ss_pred             CeEEcCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEECCeECCCCCCHHHcCCCCCCEEEEEe
Confidence            36899999999999999999999999998             999999999999999999999999986

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.

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

Probab=99.65  E-value=2.9e-16  Score=90.71  Aligned_cols=58  Identities=22%  Similarity=0.307  Sum_probs=54.3

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      +.|+||+..|+ ..+++++++||++||++|+             |+|++|+|+.+|++||+++|+++|+++|
T Consensus         1 ~~i~vk~~~g~-~~l~v~~~~TV~~lK~~I~~~~~i~~~~~~Li~~Gk~L~d~~tL~~~~i~~~stl~l~~~   71 (71)
T cd01808           1 IKVTVKTPKDK-EEIEIAEDASVKDFKEAVSKKFKANQEQLVLIFAGKILKDTDTLTQHNIKDGLTVHLVIK   71 (71)
T ss_pred             CEEEEEcCCCC-EEEEECCCChHHHHHHHHHHHhCCCHHHEEEEECCeEcCCCCcHHHcCCCCCCEEEEEEC
Confidence            46899999997 4899999999999999997             9999999999999999999999999986

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.

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

Probab=99.62  E-value=2.9e-16  Score=101.98  Aligned_cols=61  Identities=66%  Similarity=0.840  Sum_probs=59.4

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      |+|||+++.|+++.+++++++||..+|++|+             |+|++|+|+++|+||+|+..+|+|+++++|
T Consensus         1 m~ifVk~l~~kti~~eve~~~ti~~~Kakiq~~egIp~dqqrlifag~qLedgrtlSDY~Iqkestl~l~l~l~   74 (156)
T KOG0004|consen    1 MQIFVKTLTGKTITLEVEANDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   74 (156)
T ss_pred             CccchhhccccceeeeecccccHHHHHHhhhcccCCCchhhhhhhhhcccccCCccccccccccceEEEEEEec
Confidence            7899999999999999999999999999999             999999999999999999999999999985

>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=99.61  E-value=5.8e-16  Score=88.57  Aligned_cols=56  Identities=34%  Similarity=0.529  Sum_probs=53.6

Q ss_pred             ECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           42 KTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        42 k~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      |+++|++++++|++++||.+||++|+             |+|+.|+|+.+|++|||++|++|++++|.|
T Consensus         1 k~~~g~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~~G~~L~d~~tL~~~~i~~~~~I~l~~k~~   69 (69)
T PF00240_consen    1 KTLSGKTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLIYNGKELDDDKTLSDYGIKDGSTIHLVIKPR   69 (69)
T ss_dssp             EETTSEEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEETTEEESTTSBTGGGTTSTTEEEEEEESSE
T ss_pred             CCCCCcEEEEEECCCCCHHHhhhhcccccccccccceeeeeeecccCcCcHHHcCCCCCCEEEEEEecC
Confidence            57899999999999999999999999             999999999999999999999999999875

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 ....

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

Probab=99.55  E-value=6.5e-15  Score=86.88  Aligned_cols=59  Identities=14%  Similarity=0.079  Sum_probs=53.6

Q ss_pred             CeeeEEECCCCCE--EEEeecCCCcHHHhhcccc---------------CCCeeCCCCCcccccc--cCCCCEEEEEE
Q 042212           36 RMQIFVKTSTGKT--ITLEVESSDMIDNASRGSS---------------SPAGNFEDGWTQADYN--IQKESTLHFVL   94 (97)
Q Consensus        36 ~m~i~vk~~~g~~--~~l~v~~~~tV~~lK~~I~---------------~~gk~L~d~~tL~~y~--I~~~sti~l~~   94 (97)
                      ++.+.||+++|++  +++++++++||+++|++|+               |+||.|+|+.||++|+  +.++.|+||+.
T Consensus         1 ~i~l~IK~~~~~~~~~~ve~~~~~TV~~lK~~i~~~~~~~~~~~~QrLIy~GKiLkD~~tL~~~~~~~~~~~tiHLV~   78 (79)
T cd01790           1 PVTLLIKSPNQKYEDQTVSCFLNWTVGELKTHLSRVYPSKPLEQDQRLIYSGKLLPDHLKLRDVLRKQDEYHMVHLVC   78 (79)
T ss_pred             CeEEEEECCCCCeEEEEEecCCcChHHHHHHHHHHhcCCCCChhHeEEEEcCeeccchhhHHHHhhcccCCceEEEEe
Confidence            3789999999998  5556689999999999998               9999999999999996  99999999985

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.

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

Probab=99.52  E-value=1.6e-14  Score=84.51  Aligned_cols=54  Identities=17%  Similarity=0.212  Sum_probs=51.4

Q ss_pred             CCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           44 STGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        44 ~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      ++|+++++++++++||+++|++|+             |+|+.|+|+++|++|+|+++++|+++++++
T Consensus         5 l~g~~~~l~v~~~~TV~~lK~~i~~~~gip~~~q~L~~~G~~L~d~~tL~~~~i~~g~~l~v~~~~~   71 (76)
T cd01800           5 LNGQMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQYEGIFIKDSNSLAYYNLANGTIIHLQLKER   71 (76)
T ss_pred             cCCeEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCEEcCCCCcHHHcCCCCCCEEEEEEecC
Confidence            578999999999999999999998             999999999999999999999999999874

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.

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

Probab=99.52  E-value=1.8e-14  Score=83.32  Aligned_cols=55  Identities=18%  Similarity=0.189  Sum_probs=51.2

Q ss_pred             eEEECC-CCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCC-CcccccccCCCCEEEEE
Q 042212           39 IFVKTS-TGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDG-WTQADYNIQKESTLHFV   93 (97)
Q Consensus        39 i~vk~~-~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~-~tL~~y~I~~~sti~l~   93 (97)
                      |+||+. .|+++.+++++++||+++|++|+             |+|++|+|+ .+|++|||++|+++++.
T Consensus         1 l~v~~~~~g~~~~l~v~~~~TV~~lK~~I~~~~gip~~~q~Li~~Gk~L~D~~~~L~~~gi~~~~~l~l~   70 (71)
T cd01796           1 ITVYTARSETTFSLDVDPDLELENFKALCEAESGIPASQQQLIYNGRELVDNKRLLALYGVKDGDLVVLR   70 (71)
T ss_pred             CEEEECCCCCEEEEEECCcCCHHHHHHHHHHHhCCCHHHeEEEECCeEccCCcccHHHcCCCCCCEEEEe
Confidence            578898 89999999999999999999998             999999987 68999999999999974

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.

>cd01763 Sumo Small ubiquitin-related modifier (SUMO)

Probab=99.49  E-value=8.5e-14  Score=83.43  Aligned_cols=64  Identities=13%  Similarity=0.234  Sum_probs=60.7

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      +..|+|+|++.+|+.+.++|++++|++.||++++             |+|+.|+++.|+++|+++++++|+++++++
T Consensus         9 ~~~i~I~v~~~~g~~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f~G~~L~~~~T~~~l~m~d~d~I~v~l~l~   85 (87)
T cd01763           9 SEHINLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLFDGQRIRDNQTPDDLGMEDGDEIEVMLEQT   85 (87)
T ss_pred             CCeEEEEEECCCCCEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEECCeECCCCCCHHHcCCCCCCEEEEEEecc
Confidence            3559999999999999999999999999999998             999999999999999999999999999875

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.

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

Probab=99.47  E-value=3.6e-14  Score=78.85  Aligned_cols=57  Identities=35%  Similarity=0.491  Sum_probs=54.9

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEE
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~   93 (97)
                      |.|.|++++|+.+.++++|+++|+.+|++++             |+|+++.|+.|-++|++..||++|++
T Consensus         1 m~iKvktLt~KeIeidIep~DkverIKErvEEkeGIPp~qqrli~~gkqm~DD~tA~~Y~~~~GSVlHlv   70 (70)
T KOG0005|consen    1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYAGKQMNDDKTAAHYNLLGGSVLHLV   70 (70)
T ss_pred             CeeeEeeeccceEEEeeCcchHHHHHHHHhhhhcCCCchhhhhhhccccccccccHHHhhhccceeEeeC
Confidence            6789999999999999999999999999999             99999999999999999999999984

>cd01812 BAG1_N Ubiquitin-like domain of BAG1

Probab=99.45  E-value=1.3e-13  Score=79.09  Aligned_cols=57  Identities=14%  Similarity=0.169  Sum_probs=53.4

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEE
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      |+|+||+. |+++++++++++||++||++|+             |+|+.|+|+.+|++||+++|++++++.
T Consensus         1 i~i~vk~~-g~~~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~l~d~~~L~~~~i~~g~~l~v~~   70 (71)
T cd01812           1 IRVRVKHG-GESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIFKGKERDDAETLDMSGVKDGSKVMLLE   70 (71)
T ss_pred             CEEEEEEC-CEEEEEEECCCCcHHHHHHHHHHhhCCChHHeEEeeCCcccCccCcHHHcCCCCCCEEEEec
Confidence            57899997 9999999999999999999998             999999999999999999999999874

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).

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=99.42  E-value=2.6e-13  Score=99.86  Aligned_cols=59  Identities=14%  Similarity=0.254  Sum_probs=56.7

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc----------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS----------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~----------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      |+|+||+++|+++.++|++++||.+||++|+                |+||+|+|+.+|++|||+++++|+++++
T Consensus         1 MkItVKtl~g~~~~IeV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLIy~GkiL~Dd~tL~dy~I~e~~~Ivvmv~   75 (378)
T TIGR00601         1 MTLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVREYKIKEKDFVVVMVS   75 (378)
T ss_pred             CEEEEEeCCCCEEEEEeCCcChHHHHHHHHHHhhCCCCCChhHeEEEECCEECCCCCcHHHcCCCCCCEEEEEec
Confidence            8999999999999999999999999999996                9999999999999999999999999875

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).

>smart00213 UBQ Ubiquitin homologues

Probab=99.32  E-value=2e-12  Score=72.21  Aligned_cols=51  Identities=41%  Similarity=0.474  Sum_probs=48.0

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCC
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKES   88 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~s   88 (97)
                      |+|+||+.+ +++.+++++++||++||++|+             |+|+.|+|+.+|++||+++|+
T Consensus         1 ~~i~vk~~~-~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~~g~~L~d~~tL~~~~i~~~~   64 (64)
T smart00213        1 IELTVKTLD-GTITLEVKPSDTVSELKEKIAELTGIPVEQQRLIYKGKVLEDDRTLADYNIQDGS   64 (64)
T ss_pred             CEEEEEECC-ceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCEECCCCCCHHHcCCcCCC
Confidence            789999998 799999999999999999998             999999999999999999885

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

>cd01813 UBP_N UBP ubiquitin processing protease

Probab=99.29  E-value=6.4e-12  Score=73.25  Aligned_cols=56  Identities=13%  Similarity=0.175  Sum_probs=50.9

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------C---CCeeCCCCCcccccccCCCCEEEEE
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------S---PAGNFEDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~---~gk~L~d~~tL~~y~I~~~sti~l~   93 (97)
                      |.|.||. .|+++.++|++++||++||++|+             |   +|+.++|+.+|++|+|++|+.++++
T Consensus         1 ~~i~vk~-~g~~~~v~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~~~~~Gk~l~D~~~L~~~~i~~g~~i~lm   72 (74)
T cd01813           1 VPVIVKW-GGQEYSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLGLKVKGKPAEDDVKISALKLKPNTKIMMM   72 (74)
T ss_pred             CEEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEeecccCCcCCCCcCHHHcCCCCCCEEEEE
Confidence            4566766 68999999999999999999999             5   8999999999999999999999986

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.

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

Probab=99.22  E-value=9.9e-12  Score=93.04  Aligned_cols=60  Identities=22%  Similarity=0.259  Sum_probs=56.6

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEee
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      .++|.||+.++ ...+.|..+.||.++|+.|.             |+||+|+|+.||..|||++|.||||+++.
T Consensus        15 ~irV~Vkt~~d-k~~~~V~~~ssV~qlKE~I~~~f~a~~dqlvLIfaGrILKD~dTL~~~gI~Dg~TvHLVik~   87 (493)
T KOG0010|consen   15 LIRVTVKTPKD-KYEVNVASDSSVLQLKELIAQRFGAPPDQLVLIYAGRILKDDDTLKQYGIQDGHTVHLVIKS   87 (493)
T ss_pred             eeEEEEecCCc-ceeEecccchHHHHHHHHHHHhcCCChhHeeeeecCccccChhhHHHcCCCCCcEEEEEecc
Confidence            48899999987 88999999999999999999             99999999999999999999999999874

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

Probab=99.22  E-value=1.5e-11  Score=88.28  Aligned_cols=59  Identities=22%  Similarity=0.339  Sum_probs=56.6

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc---------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS---------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~---------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      |+|+||++.|++|++++.|++||.++|++|+               |+||.|.|+.|+.+|++++++.+.+++.
T Consensus         1 m~lt~KtL~q~~F~iev~Pe~tV~evK~kIet~~g~dyP~~~QkLIy~GkiL~D~~tv~Eykv~E~~fiVvMls   74 (340)
T KOG0011|consen    1 MKLTVKTLKQQTFTIEVKPEDTVVEVKKKIETEKGPDYPAEQQKLIYSGKILKDETTVGEYKVKEKKFIVVMLS   74 (340)
T ss_pred             CeeEeeeccCceeEeecCcchhHHHHHHHHHhccCCCCchhhheeeecceeccCCcchhhhccccCceEEEEEe
Confidence            7899999999999999999999999999999               9999999999999999999999988874

>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP

Probab=99.17  E-value=1.7e-11  Score=71.61  Aligned_cols=43  Identities=21%  Similarity=0.230  Sum_probs=38.9

Q ss_pred             eec-CCCcHHHhhcccc----------------CCCeeCCCCCcccccccCCCCEEEEEE
Q 042212           52 EVE-SSDMIDNASRGSS----------------SPAGNFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        52 ~v~-~~~tV~~lK~~I~----------------~~gk~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      +|+ .++||.+||++|+                |+||+|+|++||++|||++|++||++.
T Consensus        15 ~~~~~~~TV~~LK~kI~~~~~egi~~~dqQrLIy~GKiL~D~~TL~dygI~~gstlhLv~   74 (75)
T cd01815          15 DVSPGGYQVSTLKQLIAAQLPDSLPDPELIDLIHCGRKLKDDQTLDFYGIQSGSTIHILR   74 (75)
T ss_pred             CcCCccCcHHHHHHHHHHhhccCCCChHHeEEEeCCcCCCCCCcHHHcCCCCCCEEEEEe
Confidence            344 5789999999997                999999999999999999999999985

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=99.16  E-value=7.3e-11  Score=69.00  Aligned_cols=53  Identities=15%  Similarity=0.058  Sum_probs=47.4

Q ss_pred             ECCCCCEEEEeecCCCcHHHhhcccc------------CCCeeCC-CCCcccccccC-CCCEEEEEE
Q 042212           42 KTSTGKTITLEVESSDMIDNASRGSS------------SPAGNFE-DGWTQADYNIQ-KESTLHFVL   94 (97)
Q Consensus        42 k~~~g~~~~l~v~~~~tV~~lK~~I~------------~~gk~L~-d~~tL~~y~I~-~~sti~l~~   94 (97)
                      +...|.++++++++++||+++|++|+            |+|+.|. |+++|++||++ +|+++++.+
T Consensus         8 ~~~~~~t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL~~G~~L~dD~~tL~~ygi~~~g~~~~l~~   74 (75)
T cd01799           8 AQSHTVTIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRWVIGQRLARDQETLYSHGIRTNGDSAFLYI   74 (75)
T ss_pred             cccCCCeEEEEECCCCcHHHHHHHHHHHHCcCHHHEEEEcCCeeCCCcCCHHHcCCCCCCCEEEEEe
Confidence            44578899999999999999999999            9999995 77999999998 889999864

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.

>cd01793 Fubi Fubi ubiquitin-like protein

Probab=99.13  E-value=3.2e-11  Score=70.00  Aligned_cols=36  Identities=31%  Similarity=0.481  Sum_probs=33.6

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|++|     |++|||++++++|+++++.++
T Consensus        34 ip~~~q~Li~~Gk~L~D~~tL~~~~i~~~~tl~l~~~l~GG   74 (74)
T cd01793          34 IDVEDQVLLLAGVPLEDDATLGQCGVEELCTLEVAGRLLGG   74 (74)
T ss_pred             CCHHHEEEEECCeECCCCCCHHHcCCCCCCEEEEEEecCCC
Confidence            799999999999999     999999999999999997653

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.

>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4

Probab=99.09  E-value=6.8e-11  Score=73.60  Aligned_cols=61  Identities=15%  Similarity=0.133  Sum_probs=53.6

Q ss_pred             CeeeEEECCCCC-EEEEeecCCCcHHHhhcccc--------------------CCCeeCCCCCcccccc------cCCCC
Q 042212           36 RMQIFVKTSTGK-TITLEVESSDMIDNASRGSS--------------------SPAGNFEDGWTQADYN------IQKES   88 (97)
Q Consensus        36 ~m~i~vk~~~g~-~~~l~v~~~~tV~~lK~~I~--------------------~~gk~L~d~~tL~~y~------I~~~s   88 (97)
                      .+.|.+|..+|. .=+..+++++||+++|++|+                    |+||+|+|+.||++|+      +....
T Consensus         4 ~~e~kfrl~dg~digp~~~~~sdTV~~lKekI~~~~p~~ke~~P~~~~~qKLIysGKiLeD~~TL~d~~~p~g~~~~~~~   83 (113)
T cd01814           4 QIEIKFRLYDGSDIGPKRYPAATTVDFLKERVVSQWPKDKEVGPKTVNEVKLISAGKILENSKTVGECRSPVGDIAGGVI   83 (113)
T ss_pred             cEEEEEEccCCCccCccccChhhHHHHHHHHHHHhcccccccCCCCHHHeEEEeCCeecCCCCcHHHhCCcccccCCCce
Confidence            466788888885 44678889999999999997                    9999999999999999      88889


Q ss_pred             EEEEEEee
Q 042212           89 TLHFVLRL   96 (97)
Q Consensus        89 ti~l~~rl   96 (97)
                      |+|+++|.
T Consensus        84 TmHvvlr~   91 (113)
T cd01814          84 TMHVVVQP   91 (113)
T ss_pred             EEEEEecC
Confidence            99999985

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

>cd01769 UBL Ubiquitin-like domain of UBL

Probab=99.09  E-value=2.3e-10  Score=64.48  Aligned_cols=54  Identities=43%  Similarity=0.519  Sum_probs=50.4

Q ss_pred             EECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEE
Q 042212           41 VKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        41 vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      |+..+|+.+.+.++++.||.++|++|+             |+|+.|+|+.+|++|++.++++|++..
T Consensus         2 v~~~~~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l~~~g~~l~d~~~l~~~~v~~~~~i~v~~   68 (69)
T cd01769           2 VKTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYAGKILKDDKTLSDYGIQDGSTLHLVL   68 (69)
T ss_pred             eEccCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCcCCCCcCCHHHCCCCCCCEEEEEE
Confidence            667789999999999999999999998             999999999999999999999999864

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.

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

Probab=99.07  E-value=3.9e-11  Score=78.14  Aligned_cols=36  Identities=75%  Similarity=1.104  Sum_probs=34.5

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||++||||||+|++|     |+||+|+..|++||+++++++
T Consensus        36 Ip~dqqrlifag~qLedgrtlSDY~Iqkestl~l~l~l~Gg   76 (156)
T KOG0004|consen   36 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   76 (156)
T ss_pred             CCchhhhhhhhhcccccCCccccccccccceEEEEEEecCC
Confidence            899999999999999     999999999999999998765

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

Probab=99.04  E-value=1.8e-10  Score=66.17  Aligned_cols=58  Identities=17%  Similarity=0.307  Sum_probs=52.2

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc--------------CCCeeCCCCCcccccccCCCCEEEEEE
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS--------------SPAGNFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~--------------~~gk~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      |+|+|+..+|+.+.+.|.+++++..|++..+              |.|+.|+++.|+++||+++|++|++.+
T Consensus         1 I~i~v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~fdG~~L~~~~T~~~~~ied~d~Idv~I   72 (72)
T PF11976_consen    1 ITIKVRSQDGKEIKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLIFDGKRLDPNDTPEDLGIEDGDTIDVII   72 (72)
T ss_dssp             EEEEEEETTSEEEEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEEETTEEE-TTSCHHHHT-STTEEEEEE-
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCccceEEEEECCEEcCCCCCHHHCCCCCCCEEEEEC
Confidence            6899999999999999999999999998876              999999999999999999999999864

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 ....

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

Probab=99.03  E-value=1.3e-10  Score=68.35  Aligned_cols=35  Identities=31%  Similarity=0.498  Sum_probs=32.8

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++|+|+|+|++|     |++|||++|++|+|++++.+
T Consensus        38 i~~~~QrLi~~Gk~L~D~~tL~~y~i~~~~~i~l~~~~~~   77 (78)
T cd01797          38 VEPECQRLFYRGKQMEDGHTLFDYNVGLNDIIQLLVRQDP   77 (78)
T ss_pred             CCHHHeEEEeCCEECCCCCCHHHcCCCCCCEEEEEEecCC
Confidence            799999999999999     99999999999999998753

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.

>cd01807 GDX_N ubiquitin-like domain of GDX

Probab=99.02  E-value=1.3e-10  Score=67.41  Aligned_cols=33  Identities=52%  Similarity=0.798  Sum_probs=31.5

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARL   33 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~   33 (97)
                      ||+++|+|+|+|++|     |++|||++++++||+++.
T Consensus        36 i~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~l~l~~~~   73 (74)
T cd01807          36 VPEEQQRLLFKGKALADDKRLSDYSIGPNAKLNLVVRP   73 (74)
T ss_pred             CCHHHeEEEECCEECCCCCCHHHCCCCCCCEEEEEEcC
Confidence            699999999999999     999999999999999884

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

>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP

Probab=99.00  E-value=1.7e-10  Score=67.39  Aligned_cols=30  Identities=33%  Similarity=0.469  Sum_probs=28.5

Q ss_pred             CCCceEEEecCccc-----cccccccCCCcceeee
Q 042212            2 PLEQQRLVFADKSL-----LADYNIQKESTLHLVA   31 (97)
Q Consensus         2 p~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~   31 (97)
                      |+++|||+|+|++|     |++|||++|++|||+.
T Consensus        40 ~~dqQrLIy~GKiL~D~~TL~dygI~~gstlhLv~   74 (75)
T cd01815          40 DPELIDLIHCGRKLKDDQTLDFYGIQSGSTIHILR   74 (75)
T ss_pred             ChHHeEEEeCCcCCCCCCcHHHcCCCCCCEEEEEe
Confidence            48999999999999     9999999999999985

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.

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

Probab=98.95  E-value=3e-09  Score=59.70  Aligned_cols=59  Identities=56%  Similarity=0.675  Sum_probs=55.1

Q ss_pred             eEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           39 IFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        39 i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      +++++..|++..+.+.+..+|..+|.+|+             ++|+.|+|+.++++|+|..++++++..+++
T Consensus         2 ~~~~~~~gk~~~~~~~~~~~i~~~k~~i~~~~~~~~~~q~~~~~~~~l~d~~~l~~~~i~~~~~~~l~~~~~   73 (75)
T KOG0001|consen    2 IFVKTLDGKTITLEVSPSDTIEVVKAKIRDKEGIPVDQQRLIFGGKPLEDGRTLADYNIQEGSTLHLVLSLR   73 (75)
T ss_pred             EEEEecCCCEEEEEecCCCHHHHHHHHHHhhcCCCCeeEEEEECCEECcCCCcHHHhCCCCCCEEEEEEecC
Confidence            57788899999999999999999999999             889999999999999999999999998864

>cd01802 AN1_N ubiquitin-like domain of AN1

Probab=98.92  E-value=6.8e-10  Score=68.52  Aligned_cols=35  Identities=46%  Similarity=0.807  Sum_probs=33.1

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++|+|+|+|+.|     |++|||.++++|||.+++++
T Consensus        63 ip~~~QrLi~~Gk~L~D~~tL~dy~I~~~stL~l~~~l~G  102 (103)
T cd01802          63 IPVAQQHLIWNNMELEDEYCLNDYNISEGCTLKLVLAMRG  102 (103)
T ss_pred             CChHHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEecCC
Confidence            799999999999999     99999999999999998765

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=98.92  E-value=7.4e-10  Score=64.22  Aligned_cols=35  Identities=29%  Similarity=0.566  Sum_probs=32.7

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++|+|+|+|++|     |++|||+++++++|.+++.+
T Consensus        34 i~~~~q~L~~~G~~L~D~~tL~~~~i~~~~tl~l~~~l~g   73 (74)
T cd01810          34 VQADQFWLSFEGRPMEDEHPLGEYGLKPGCTVFMNLRLRG   73 (74)
T ss_pred             CCHHHeEEEECCEECCCCCCHHHcCCCCCCEEEEEEEccC
Confidence            699999999999999     99999999999999998754

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.

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

Probab=98.89  E-value=7.6e-10  Score=63.45  Aligned_cols=32  Identities=38%  Similarity=0.699  Sum_probs=30.1

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVAR   32 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~   32 (97)
                      +|+++|+|+|+|++|     |++|||++||++||+.|
T Consensus        34 i~~~~q~Li~~G~~L~d~~~l~~~~i~~~stl~l~~~   70 (70)
T cd01798          34 VPPDQLRVIFAGKELRNTTTIQECDLGQQSILHAVRR   70 (70)
T ss_pred             CCHHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEeC
Confidence            689999999999999     99999999999999864

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.

>PTZ00044 ubiquitin; Provisional

Probab=98.88  E-value=1.1e-09  Score=63.53  Aligned_cols=35  Identities=40%  Similarity=0.798  Sum_probs=32.9

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++|+|+|+|++|     |++|||++|+++|+.+++.+
T Consensus        36 i~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~g   75 (76)
T PTZ00044         36 IDVKQIRLIYSGKQMSDDLKLSDYKVVPGSTIHMVLQLRG   75 (76)
T ss_pred             CCHHHeEEEECCEEccCCCcHHHcCCCCCCEEEEEEEccC
Confidence            799999999999999     99999999999999998765

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

Probab=98.87  E-value=7.8e-09  Score=64.60  Aligned_cols=60  Identities=17%  Similarity=0.256  Sum_probs=47.6

Q ss_pred             eeeEEECCCCC-EEEEeecCCCcHHHhhcccc--------------------CCCeeCCCCCcccccccCCCC------E
Q 042212           37 MQIFVKTSTGK-TITLEVESSDMIDNASRGSS--------------------SPAGNFEDGWTQADYNIQKES------T   89 (97)
Q Consensus        37 m~i~vk~~~g~-~~~l~v~~~~tV~~lK~~I~--------------------~~gk~L~d~~tL~~y~I~~~s------t   89 (97)
                      +.+.++..+|+ +.++.+++++||.+||+.|.                    |.||.|+|+.||+++++..|.      +
T Consensus         3 i~lkf~l~~G~d~~~~~~~~~~TV~~lKe~i~~~WP~d~~~~p~s~~~lRLI~~GriL~d~~tL~~~~~~~~~~~~~~~v   82 (111)
T PF13881_consen    3 IELKFRLADGKDIGPFRFDPSTTVADLKERIWAEWPEDWEERPKSPSDLRLIYAGRILEDNKTLSDCRLPSGETPGGPTV   82 (111)
T ss_dssp             EEEEEEETTS-EEEEEEE-TTSBHHHHHHHHHHSSSTTSSSTT-SGGGEEEEETTEEE-SSSBTGGGT--TTSETT--EE
T ss_pred             EEEEEEEeCCCcccccccCccChHHHHHHHHHHHCccccccCCCChhhEEEEeCCeecCCcCcHHHhCCCCCCCCCCCEE
Confidence            45666777998 88999999999999999998                    999999999999999998766      6


Q ss_pred             EEEEEee
Q 042212           90 LHFVLRL   96 (97)
Q Consensus        90 i~l~~rl   96 (97)
                      +|+++|.
T Consensus        83 mHlvvrp   89 (111)
T PF13881_consen   83 MHLVVRP   89 (111)
T ss_dssp             EEEEE-S
T ss_pred             EEEEecC
Confidence            8998874

>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein

Probab=98.83  E-value=1.6e-09  Score=62.44  Aligned_cols=31  Identities=29%  Similarity=0.403  Sum_probs=29.6

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVA   31 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~   31 (97)
                      ||+++|+|+|+|+.|     |++|||.++++|||.+
T Consensus        34 i~~~~q~Li~~G~~L~D~~~l~~~~i~~~~tv~~~~   69 (70)
T cd01794          34 VDPCCQRWFFSGKLLTDKTRLQETKIQKDYVVQVIV   69 (70)
T ss_pred             CCHHHeEEEECCeECCCCCCHHHcCCCCCCEEEEEe
Confidence            699999999999999     9999999999999986

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.

>cd01806 Nedd8 Nebb8-like ubiquitin protein

Probab=98.82  E-value=3e-09  Score=61.36  Aligned_cols=35  Identities=49%  Similarity=0.851  Sum_probs=32.8

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      +|+++|+|+|+|+.|     |++|||++|++||++++.++
T Consensus        36 ~~~~~qrL~~~g~~L~d~~tl~~~~i~~g~~i~l~~~~~g   75 (76)
T cd01806          36 IPPQQQRLIYSGKQMNDDKTAADYKLEGGSVLHLVLALRG   75 (76)
T ss_pred             CChhhEEEEECCeEccCCCCHHHcCCCCCCEEEEEEEccC
Confidence            699999999999998     99999999999999998765

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.

>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=98.81  E-value=3.3e-09  Score=60.30  Aligned_cols=33  Identities=52%  Similarity=0.854  Sum_probs=31.3

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARL   33 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~   33 (97)
                      +|+++|+|+|+|+.|     |++|||.+|++|+|+++.
T Consensus        31 ~~~~~~~L~~~G~~L~d~~tL~~~~i~~~~~I~l~~k~   68 (69)
T PF00240_consen   31 IPPEQQRLIYNGKELDDDKTLSDYGIKDGSTIHLVIKP   68 (69)
T ss_dssp             STGGGEEEEETTEEESTTSBTGGGTTSTTEEEEEEESS
T ss_pred             cccccceeeeeeecccCcCcHHHcCCCCCCEEEEEEec
Confidence            699999999999999     999999999999999874

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=98.81  E-value=2.2e-09  Score=61.69  Aligned_cols=32  Identities=44%  Similarity=0.535  Sum_probs=30.0

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVAR   32 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~   32 (97)
                      ||+++|+|+|+|++|     |++|||++||++||+++
T Consensus        35 i~~~~~~Li~~Gk~L~d~~tL~~~~i~~~stl~l~~~   71 (71)
T cd01808          35 ANQEQLVLIFAGKILKDTDTLTQHNIKDGLTVHLVIK   71 (71)
T ss_pred             CCHHHEEEEECCeEcCCCCcHHHcCCCCCCEEEEEEC
Confidence            688999999999999     99999999999999875

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.

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

Probab=98.79  E-value=3.1e-09  Score=61.94  Aligned_cols=35  Identities=34%  Similarity=0.595  Sum_probs=32.8

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++|+|+|+|+.|     |++|||++|++|||+++.++
T Consensus        33 ip~~~q~L~~~G~~L~d~~tL~~~~i~~g~~l~v~~~~~g   72 (76)
T cd01800          33 MPAGKQKLQYEGIFIKDSNSLAYYNLANGTIIHLQLKERG   72 (76)
T ss_pred             CCHHHEEEEECCEEcCCCCcHHHcCCCCCCEEEEEEecCC
Confidence            799999999999998     99999999999999998755

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.

>cd01795 USP48_C USP ubiquitin-specific protease

Probab=98.77  E-value=7.8e-09  Score=63.13  Aligned_cols=49  Identities=12%  Similarity=0.020  Sum_probs=43.6

Q ss_pred             EEEEeecCCCcHHHhhcccc-------------CCCeeCC-CCCcccccccCCCCEEEEEEee
Q 042212           48 TITLEVESSDMIDNASRGSS-------------SPAGNFE-DGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        48 ~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~-d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      ..+++|++++||.+||.+|.             |+|+.|. |.+||++|||.++|++.|.+..
T Consensus        16 ~~~L~V~~~~TVg~LK~lImQ~f~V~P~dQkL~~dG~~L~DDsrTLssyGv~sgSvl~Llide   78 (107)
T cd01795          16 EKALLVSANQTLKELKIQIMHAFSVAPFDQNLSIDGKILSDDCATLGTLGVIPESVILLKADE   78 (107)
T ss_pred             CceEEeCccccHHHHHHHHHHHhcCCcccceeeecCceeccCCccHHhcCCCCCCEEEEEecC
Confidence            45788999999999999998             8899995 5789999999999999998753

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,

>cd01791 Ubl5 UBL5 ubiquitin-like modifier

Probab=98.77  E-value=3.7e-09  Score=61.43  Aligned_cols=31  Identities=26%  Similarity=0.188  Sum_probs=29.2

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVA   31 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~   31 (97)
                      +|+++|||+|+|+.|     |++|||.+||+|||..
T Consensus        37 ~~~~~qrLi~~Gk~L~D~~tL~~ygi~~~stv~l~~   72 (73)
T cd01791          37 TRPEKIVLKKWYTIFKDHISLGDYEIHDGMNLELYY   72 (73)
T ss_pred             CChHHEEEEeCCcCCCCCCCHHHcCCCCCCEEEEEe
Confidence            699999999999999     9999999999999974

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=98.74  E-value=6.3e-09  Score=59.99  Aligned_cols=35  Identities=77%  Similarity=1.145  Sum_probs=32.7

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      +|+++|+|+|+|+.|     |++|||++|+++|+.+++.+
T Consensus        36 ~~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~i~l~~~~~g   75 (76)
T cd01803          36 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG   75 (76)
T ss_pred             CCHHHeEEEECCEECCCCCcHHHcCCCCCCEEEEEEEccC
Confidence            689999999999999     99999999999999998765

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

>cd01804 midnolin_N Ubiquitin-like domain of midnolin

Probab=98.71  E-value=9.4e-09  Score=60.28  Aligned_cols=36  Identities=28%  Similarity=0.439  Sum_probs=33.2

Q ss_pred             CCCCceEEEecCccc----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      +|+++|+|+|+|+.|    |++|||.+|++|+|+..+.++
T Consensus        37 ~~~~~qrL~~~Gk~L~d~~L~~~gi~~~~~i~l~~~~~~~   76 (78)
T cd01804          37 VPKERLALLHRETRLSSGKLQDLGLGDGSKLTLVPTVEAG   76 (78)
T ss_pred             CChHHEEEEECCcCCCCCcHHHcCCCCCCEEEEEeecccc
Confidence            589999999999999    999999999999999987654

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.

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

Probab=98.66  E-value=7.5e-10  Score=68.33  Aligned_cols=36  Identities=78%  Similarity=1.116  Sum_probs=34.2

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|++|     +++|||+..||+|++.++.++
T Consensus        36 i~~~~~~L~~~~k~LED~~Tla~Y~i~~~~Tl~~~~rL~GG   76 (128)
T KOG0003|consen   36 IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
T ss_pred             CCHHHHHHHhcccccccCCcccccCccchhhhhhhHHHhcC
Confidence            799999999999999     999999999999999998765

>PLN02560 enoyl-CoA reductase

Probab=98.64  E-value=4.8e-08  Score=70.51  Aligned_cols=56  Identities=25%  Similarity=0.437  Sum_probs=49.0

Q ss_pred             eeeEEECCCCCEE---EEeecCCCcHHHhhcccc--------------C---CC----eeCCCCCcccccccCCCCEEEE
Q 042212           37 MQIFVKTSTGKTI---TLEVESSDMIDNASRGSS--------------S---PA----GNFEDGWTQADYNIQKESTLHF   92 (97)
Q Consensus        37 m~i~vk~~~g~~~---~l~v~~~~tV~~lK~~I~--------------~---~g----k~L~d~~tL~~y~I~~~sti~l   92 (97)
                      |+|.|+..+|+.+   +++++++.||++||++|+              +   .|    +.|+|+.+|++||+++|+++++
T Consensus         1 M~I~Vk~~~Gk~i~~~~lev~~~aTV~dLK~~Isk~~~~~~~~RqRL~~~~~~gk~~g~~L~d~ktL~d~gv~~gstLy~   80 (308)
T PLN02560          1 MKVTVVSRSGREIIKGGLEVPDSATVADLKKAIHKRKKKYYPSRQRLTLPLPPGKTRPTVLDDSKSLKDYGLGDGGTVVF   80 (308)
T ss_pred             CEEEEEcCCCCeecceeEEcCCCCcHHHHHHHHHHHcCCCChhheEEEEecCCCCcCccccCCCCCHHhcCCCCCceEEE
Confidence            6789998889887   799999999999999997              3   23    3789999999999999999876

>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein

Probab=98.63  E-value=1.6e-08  Score=57.66  Aligned_cols=32  Identities=44%  Similarity=0.920  Sum_probs=29.8

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVAR   32 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~   32 (97)
                      ||++.|+|+|+|+.|     |++|||++|+++|++.+
T Consensus        36 i~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~l~l~~~   72 (72)
T cd01809          36 IPVEQQRLIYSGRVLKDDETLSEYKVEDGHTIHLVKR   72 (72)
T ss_pred             cCHHHeEEEECCEECCCcCcHHHCCCCCCCEEEEEeC
Confidence            689999999999998     99999999999999864

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=98.62  E-value=2.4e-08  Score=57.90  Aligned_cols=33  Identities=30%  Similarity=0.574  Sum_probs=30.6

Q ss_pred             CCCceEEEecCccc-----cccccccCCCcceeeeeec
Q 042212            2 PLEQQRLVFADKSL-----LADYNIQKESTLHLVARLR   34 (97)
Q Consensus         2 p~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~   34 (97)
                      |+++|+|+|+|+.|     |++|||++|+++++.++.+
T Consensus        39 ~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~i~~~~~~~   76 (77)
T cd01805          39 PPEQQKLIYSGKILKDDTTLEEYKIDEKDFVVVMVSKP   76 (77)
T ss_pred             ChhHeEEEECCEEccCCCCHHHcCCCCCCEEEEEEecC
Confidence            89999999999999     9999999999999988743

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).

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

Probab=98.61  E-value=1.6e-08  Score=58.24  Aligned_cols=30  Identities=30%  Similarity=0.565  Sum_probs=28.1

Q ss_pred             CCCCceEEEecCccc------cccccccCCCcceee
Q 042212            1 MPLEQQRLVFADKSL------LADYNIQKESTLHLV   30 (97)
Q Consensus         1 ip~~~q~L~~~~~~L------l~~y~i~~~s~i~l~   30 (97)
                      ||+++|+|+|+|++|      |++|||++|++++|.
T Consensus        35 ip~~~q~Li~~Gk~L~D~~~~L~~~gi~~~~~l~l~   70 (71)
T cd01796          35 IPASQQQLIYNGRELVDNKRLLALYGVKDGDLVVLR   70 (71)
T ss_pred             CCHHHeEEEECCeEccCCcccHHHcCCCCCCEEEEe
Confidence            699999999999999      899999999999974

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.

>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=98.58  E-value=8e-08  Score=56.77  Aligned_cols=59  Identities=17%  Similarity=0.240  Sum_probs=37.7

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc----------------CCCeeC--CCCCcccccccCCCCEEEEE
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS----------------SPAGNF--EDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~----------------~~gk~L--~d~~tL~~y~I~~~sti~l~   93 (97)
                      .+.|.|.||+.+| +..+++++++|+.+|+++|+                -....+  .++.+|+++|++.|+.++|.
T Consensus         2 ~~~milRvrS~dG-~~Rie~~~~~t~~~L~~kI~~~l~~~~~~~~L~~~~~~~~~l~s~~~~tl~~lglkHGdmlyL~   78 (80)
T PF11543_consen    2 ASSMILRVRSKDG-MKRIEVSPSSTLSDLKEKISEQLSIPDSSQSLSKDRNNKEELKSSDSKTLSSLGLKHGDMLYLK   78 (80)
T ss_dssp             ----EEEEE-SSE-EEEEEE-TTSBHHHHHHHHHHHS---TTT---BSSGGGGGCSSS-TT-CCCCT---TT-EEE--
T ss_pred             CccEEEEEECCCC-CEEEEcCCcccHHHHHHHHHHHcCCCCcceEEEecCCCCcccccCCcCCHHHcCCCCccEEEEe
Confidence            3568999999987 56789999999999999999                112344  56899999999999999874

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=98.58  E-value=9.9e-08  Score=59.52  Aligned_cols=58  Identities=22%  Similarity=0.276  Sum_probs=46.6

Q ss_pred             eeEEECCCCC-EEEEeecCCCcHHHhhcccc------------CC-CeeCCCCCccccccc-------CCCCEEEEEEe
Q 042212           38 QIFVKTSTGK-TITLEVESSDMIDNASRGSS------------SP-AGNFEDGWTQADYNI-------QKESTLHFVLR   95 (97)
Q Consensus        38 ~i~vk~~~g~-~~~l~v~~~~tV~~lK~~I~------------~~-gk~L~d~~tL~~y~I-------~~~sti~l~~r   95 (97)
                      -+|++....+ ++.++++++.||.+||++|+            |. +..|+|++||+|||+       ++.+++-|.+|
T Consensus         2 dvFlmIrR~KTTiF~dakes~tVlelK~~iegI~k~pp~dQrL~kd~qvLeD~kTL~d~g~t~~~akaq~pA~vgLa~r   80 (119)
T cd01788           2 DVFLMIRRHKTTIFTDAKESTTVYELKRIVEGILKRPPEDQRLYKDDQLLDDGKTLGDCGFTSQTARPQAPATVGLAFR   80 (119)
T ss_pred             ceEEEEEecceEEEeecCCcccHHHHHHHHHHHhcCChhHheeecCceeecccccHHHcCccccccccCCCCeEEEEEe
Confidence            3444443334 56669999999999999999            54 467899999999999       77999999887

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.

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

Probab=98.56  E-value=1e-08  Score=57.15  Aligned_cols=30  Identities=50%  Similarity=0.806  Sum_probs=28.5

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLV   30 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~   30 (97)
                      ||+.+|||+|+|+|+     -++|++..||++|++
T Consensus        36 IPp~qqrli~~gkqm~DD~tA~~Y~~~~GSVlHlv   70 (70)
T KOG0005|consen   36 IPPQQQRLIYAGKQMNDDKTAAHYNLLGGSVLHLV   70 (70)
T ss_pred             CCchhhhhhhccccccccccHHHhhhccceeEeeC
Confidence            899999999999999     889999999999985

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

Probab=98.53  E-value=2.1e-07  Score=55.37  Aligned_cols=56  Identities=9%  Similarity=0.168  Sum_probs=43.8

Q ss_pred             eeEEECC-CCCEEEEeecCCCcHHHhhcccc--------------CCCe-----eC-CCCCcccccccCCCCEEEEE
Q 042212           38 QIFVKTS-TGKTITLEVESSDMIDNASRGSS--------------SPAG-----NF-EDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        38 ~i~vk~~-~g~~~~l~v~~~~tV~~lK~~I~--------------~~gk-----~L-~d~~tL~~y~I~~~sti~l~   93 (97)
                      .++|... +....+..+++++||.+||++++              |.|+     .| +|+.+|++||+++|++||++
T Consensus         3 ~v~i~~~~~~~~~ekr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~~~~~~~~~~l~~d~~~L~~y~~~dg~~IhVv   79 (84)
T cd01789           3 TVNITSSADSFSFEKKYSRGLTIAELKKKLELVVGTPASSMRLQLFDGDDKLVSKLDDDDALLGSYPVDDGCRIHVI   79 (84)
T ss_pred             EEEEEeCCCceeeeEecCCCCcHHHHHHHHHHHHCCCccceEEEEEcCCCCeEeecCCCccEeeeccCCCCCEEEEE
Confidence            3445443 23445556999999999999998              6666     45 77889999999999999986

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.

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

Probab=98.51  E-value=5e-08  Score=57.34  Aligned_cols=33  Identities=33%  Similarity=0.353  Sum_probs=30.7

Q ss_pred             CCCCceEE--EecCccc-----cccccccCCCcceeeeee
Q 042212            1 MPLEQQRL--VFADKSL-----LADYNIQKESTLHLVARL   33 (97)
Q Consensus         1 ip~~~q~L--~~~~~~L-----l~~y~i~~~s~i~l~~~~   33 (97)
                      ||+++|+|  +|+|+.|     |++|||.+|++|+|+++.
T Consensus        38 i~~~~qrL~~~~~G~~L~D~~tL~~~gi~~gs~l~l~~~~   77 (80)
T cd01792          38 VPAFQQRLAHLDSREVLQDGVPLVSQGLGPGSTVLLVVQN   77 (80)
T ss_pred             CCHHHEEEEeccCCCCCCCCCCHHHcCCCCCCEEEEEEEc
Confidence            68999999  8999999     999999999999999873

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.

>cd01763 Sumo Small ubiquitin-related modifier (SUMO)

Probab=98.50  E-value=1.1e-07  Score=56.84  Aligned_cols=35  Identities=11%  Similarity=0.405  Sum_probs=32.8

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++|+|+|+|++|     +++|||++|++|+++++..+
T Consensus        47 i~~~~~rf~f~G~~L~~~~T~~~l~m~d~d~I~v~l~l~G   86 (87)
T cd01763          47 LSMNSVRFLFDGQRIRDNQTPDDLGMEDGDEIEVMLEQTG   86 (87)
T ss_pred             CCccceEEEECCeECCCCCCHHHcCCCCCCEEEEEEeccc
Confidence            689999999999999     99999999999999998765

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.

>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4

Probab=98.43  E-value=1e-07  Score=59.41  Aligned_cols=33  Identities=21%  Similarity=0.269  Sum_probs=30.7

Q ss_pred             CCceEEEecCccc-----ccccc------ccCCCcceeeeeecC
Q 042212            3 LEQQRLVFADKSL-----LADYN------IQKESTLHLVARLRG   35 (97)
Q Consensus         3 ~~~q~L~~~~~~L-----l~~y~------i~~~s~i~l~~~~~~   35 (97)
                      +++|+|||+|+.|     |++|+      +...+|+|++++.+.
T Consensus        50 ~~~qKLIysGKiLeD~~TL~d~~~p~g~~~~~~~TmHvvlr~~~   93 (113)
T cd01814          50 VNEVKLISAGKILENSKTVGECRSPVGDIAGGVITMHVVVQPPL   93 (113)
T ss_pred             HHHeEEEeCCeecCCCCcHHHhCCcccccCCCceEEEEEecCCC
Confidence            8999999999999     99999      888999999999754

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

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

Probab=98.41  E-value=1.1e-07  Score=56.02  Aligned_cols=30  Identities=33%  Similarity=0.443  Sum_probs=27.8

Q ss_pred             CCCceEEEecCccc-----ccccc--ccCCCcceeee
Q 042212            2 PLEQQRLVFADKSL-----LADYN--IQKESTLHLVA   31 (97)
Q Consensus         2 p~~~q~L~~~~~~L-----l~~y~--i~~~s~i~l~~   31 (97)
                      |+++|||||+||.|     |++|+  +.+|.++||+.
T Consensus        42 ~~~~QrLIy~GKiLkD~~tL~~~~~~~~~~~tiHLV~   78 (79)
T cd01790          42 LEQDQRLIYSGKLLPDHLKLRDVLRKQDEYHMVHLVC   78 (79)
T ss_pred             ChhHeEEEEcCeeccchhhHHHHhhcccCCceEEEEe
Confidence            47999999999999     99996  99999999985

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.

>cd01812 BAG1_N Ubiquitin-like domain of BAG1

Probab=98.39  E-value=1.6e-07  Score=53.43  Aligned_cols=31  Identities=23%  Similarity=0.352  Sum_probs=28.9

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVA   31 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~   31 (97)
                      ||+++|+|+|+|+.|     |++|||.+|++|+++.
T Consensus        35 i~~~~q~L~~~g~~l~d~~~L~~~~i~~g~~l~v~~   70 (71)
T cd01812          35 VEPRDQKLIFKGKERDDAETLDMSGVKDGSKVMLLE   70 (71)
T ss_pred             CChHHeEEeeCCcccCccCcHHHcCCCCCCEEEEec
Confidence            689999999999999     9999999999999864

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).

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

Probab=98.37  E-value=2e-07  Score=70.31  Aligned_cols=34  Identities=38%  Similarity=0.627  Sum_probs=32.0

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeec
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLR   34 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~   34 (97)
                      +|+++|+|||+||.|     |..|||++|.|||||++..
T Consensus        50 a~~dqlvLIfaGrILKD~dTL~~~gI~Dg~TvHLVik~~   88 (493)
T KOG0010|consen   50 APPDQLVLIYAGRILKDDDTLKQYGIQDGHTVHLVIKSQ   88 (493)
T ss_pred             CChhHeeeeecCccccChhhHHHcCCCCCcEEEEEeccC
Confidence            589999999999999     9999999999999999864

>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13

Probab=98.35  E-value=6.7e-07  Score=52.17  Aligned_cols=39  Identities=15%  Similarity=0.156  Sum_probs=35.7

Q ss_pred             cCCCcHHHhhcccc----------------CCCeeCCCCCcccccccCCCCEEEE
Q 042212           54 ESSDMIDNASRGSS----------------SPAGNFEDGWTQADYNIQKESTLHF   92 (97)
Q Consensus        54 ~~~~tV~~lK~~I~----------------~~gk~L~d~~tL~~y~I~~~sti~l   92 (97)
                      +++.||.+||..|+                +.|+.|.|+.+|++||+.+|+++++
T Consensus        20 ~~~aTV~dlk~~i~~~~~~~~~~Rqrl~~~~~g~~L~d~~tL~~~gv~~g~~lyv   74 (77)
T cd01801          20 SGDATIADLKKLIAKSSPQLTVNRQSLRLEPKGKSLKDDDTLVDLGVGAGATLYV   74 (77)
T ss_pred             CCCccHHHHHHHHHHHcCCCCcceeEEEeCCCCcccCCcccHhhcCCCCCCEEEE
Confidence            48889999999987                7899999999999999999999876

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.

>cd01795 USP48_C USP ubiquitin-specific protease

Probab=98.33  E-value=3.6e-07  Score=55.88  Aligned_cols=34  Identities=26%  Similarity=0.215  Sum_probs=31.7

Q ss_pred             CCCCceEEEecCccc------cccccccCCCcceeeeeec
Q 042212            1 MPLEQQRLVFADKSL------LADYNIQKESTLHLVARLR   34 (97)
Q Consensus         1 ip~~~q~L~~~~~~L------l~~y~i~~~s~i~l~~~~~   34 (97)
                      +|+++|+|+|+|+.|      |++|||..+|+|+|.++.+
T Consensus        40 V~P~dQkL~~dG~~L~DDsrTLssyGv~sgSvl~LlideP   79 (107)
T cd01795          40 VAPFDQNLSIDGKILSDDCATLGTLGVIPESVILLKADEP   79 (107)
T ss_pred             CCcccceeeecCceeccCCccHHhcCCCCCCEEEEEecCC
Confidence            689999999999998      9999999999999999754

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,

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

Probab=98.29  E-value=5.2e-07  Score=72.86  Aligned_cols=57  Identities=21%  Similarity=0.289  Sum_probs=54.1

Q ss_pred             eeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           38 QIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        38 ~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      .+.||+++.++.++.+...+||+++|..|.             |.|++|.|++++.+|+| +|-+|||+=|
T Consensus         4 ~v~vktld~r~~t~~ig~q~ti~~~~d~~r~~~ni~s~~qr~i~~grvl~~~k~vq~~~v-dgk~~hlver   73 (1143)
T KOG4248|consen    4 NVLVKTLDSRTRTFIIGAQMTIKEFKDHIRASVNIPSEKQRLIYQGRVLQDDKKVQEYNV-DGKVIHLVER   73 (1143)
T ss_pred             ceeeeecccceeEEEechHHHHHHHHHHHHHhcccccccceeeecceeeccchhhhhccC-CCeEEEeecc
Confidence            378999999999999999999999999998             99999999999999999 9999999865

>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1

Probab=98.28  E-value=4.1e-07  Score=53.05  Aligned_cols=30  Identities=23%  Similarity=0.286  Sum_probs=27.6

Q ss_pred             CCCCceEEEecCccc------ccccccc-CCCcceeee
Q 042212            1 MPLEQQRLVFADKSL------LADYNIQ-KESTLHLVA   31 (97)
Q Consensus         1 ip~~~q~L~~~~~~L------l~~y~i~-~~s~i~l~~   31 (97)
                      ||+++|+| |+|+.|      |++||++ +|+++||.+
T Consensus        38 ip~~~QrL-~~G~~L~dD~~tL~~ygi~~~g~~~~l~~   74 (75)
T cd01799          38 FPPAVQRW-VIGQRLARDQETLYSHGIRTNGDSAFLYI   74 (75)
T ss_pred             cCHHHEEE-EcCCeeCCCcCCHHHcCCCCCCCEEEEEe
Confidence            79999999 999888      9999999 889999875

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.

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

Probab=98.24  E-value=1.7e-06  Score=51.53  Aligned_cols=56  Identities=16%  Similarity=0.329  Sum_probs=42.6

Q ss_pred             eeEEECCCC--CEEEEeecCCCcHHHhhcccc--------------C---CC---eeC-CCCCcccccccCCCCEEEEE
Q 042212           38 QIFVKTSTG--KTITLEVESSDMIDNASRGSS--------------S---PA---GNF-EDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        38 ~i~vk~~~g--~~~~l~v~~~~tV~~lK~~I~--------------~---~g---k~L-~d~~tL~~y~I~~~sti~l~   93 (97)
                      .++|.....  ...+..+++++||.+||.+|+              +   ++   ..+ +|+++|++||+++|.+||+.
T Consensus         3 ~l~It~~~~~~~~~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~~~~~~~~~~~~~dd~~~L~~y~~~dg~~i~V~   81 (87)
T PF14560_consen    3 KLFITSSNSKQRSVEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLKSDKDDSKIEELDDDDATLGSYGIKDGMRIHVV   81 (87)
T ss_dssp             EEEEEESSSSSSEEEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE-TSSSSEEEESSGSSSBCCHHT-STTEEEEEE
T ss_pred             EEEEEeCCCCCeeEEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEEecCCCccccccCCCccEeecCCCCCCCEEEEE
Confidence            455544433  588889999999999999999              2   22   223 67899999999999999985

>cd01813 UBP_N UBP ubiquitin processing protease

Probab=98.05  E-value=2.3e-06  Score=49.68  Aligned_cols=30  Identities=13%  Similarity=0.298  Sum_probs=27.7

Q ss_pred             CCCCceEEEe---cCccc-----cccccccCCCcceee
Q 042212            1 MPLEQQRLVF---ADKSL-----LADYNIQKESTLHLV   30 (97)
Q Consensus         1 ip~~~q~L~~---~~~~L-----l~~y~i~~~s~i~l~   30 (97)
                      ||+++|+|+|   .|+.|     |++|||.+|+.++|+
T Consensus        35 vp~~~QKLi~~~~~Gk~l~D~~~L~~~~i~~g~~i~lm   72 (74)
T cd01813          35 VLPERQKLLGLKVKGKPAEDDVKISALKLKPNTKIMMM   72 (74)
T ss_pred             CCHHHEEEEeecccCCcCCCCcCHHHcCCCCCCEEEEE
Confidence            7999999996   89888     999999999999986

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.

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

Probab=97.98  E-value=3.3e-06  Score=47.75  Aligned_cols=56  Identities=20%  Similarity=0.329  Sum_probs=47.5

Q ss_pred             eeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEE
Q 042212           38 QIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        38 ~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~   93 (97)
                      ++.++..-|+.+.+.+.+++||.++|..|+             --+..+.|.-+|++|.|.+|..+.+.
T Consensus         3 ev~~nDrLGKKVRvKCn~dDtiGD~KKliaaQtGT~~~kivl~k~~~i~kd~I~L~dyeihdg~~lely   71 (73)
T KOG3493|consen    3 EVVLNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFKDHITLSDYEIHDGMNLELY   71 (73)
T ss_pred             eehhhhhcCceEEEEeCCcccccCHHHHHHHhhCCChhHhHHHhhhhhhhcccceeeEEeccCccEEEe
Confidence            456677789999999999999999999998             23455789999999999999888764

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

Probab=97.85  E-value=3.4e-05  Score=44.87  Aligned_cols=57  Identities=16%  Similarity=0.187  Sum_probs=46.5

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc----CCC-------------eeCCCCCcccccccCCCCEEEEE
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS----SPA-------------GNFEDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~----~~g-------------k~L~d~~tL~~y~I~~~sti~l~   93 (97)
                      +++.|+-..+...++.|+|..+|..+|++|.    |.|             ..|.+..+|++|||=.+..|-++
T Consensus         1 iqVtV~q~g~~dl~l~vnPy~pI~k~K~kI~~~~~~~g~qrLsfQepgg~rqlL~s~~sLA~yGiFs~~~i~ll   74 (80)
T cd01811           1 IQVTVEQTGYSDWILRVNPYSPIRKIKEKIRRSRNCSGLQRLSFQEPGGERQLLSSRKSLADYGIFSKTNICLL   74 (80)
T ss_pred             CEEEeeecCCCceEEEeCCcchHHHHHHHHHHhhCcccceEEEeecCCcccccccccccHhhhcceeccEEEEE
Confidence            4678888777889999999999999999999    222             34688999999999877666554

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=97.82  E-value=6.2e-05  Score=39.66  Aligned_cols=52  Identities=25%  Similarity=0.311  Sum_probs=46.0

Q ss_pred             CCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEE
Q 042212           43 TSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        43 ~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      ..+|+...+.+.+..|+.++|++++             ++|..+.+...+.+|++.+++++++..
T Consensus         4 ~~~~~~~~~~~~~~~tv~~l~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~   68 (69)
T cd00196           4 LNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGKILPDSLTLEDYGLQDGDELVLVP   68 (69)
T ss_pred             ecCCCEEEEEcCCCCcHHHHHHHHHHHHCcChHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEe
Confidence            3478889999999999999999987             888899888888899999999999864

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.

>cd01769 UBL Ubiquitin-like domain of UBL

Probab=97.77  E-value=2e-05  Score=43.98  Aligned_cols=31  Identities=65%  Similarity=0.924  Sum_probs=28.5

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVA   31 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~   31 (97)
                      +|++.|+|+|+|+.|     |.+||+.++++|++..
T Consensus        33 ~~~~~~~l~~~g~~l~d~~~l~~~~v~~~~~i~v~~   68 (69)
T cd01769          33 VPPEQQRLIYAGKILKDDKTLSDYGIQDGSTLHLVL   68 (69)
T ss_pred             cChHHEEEEECCcCCCCcCCHHHCCCCCCCEEEEEE
Confidence            588999999999999     9999999999999864

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.

>smart00213 UBQ Ubiquitin homologues

Probab=97.73  E-value=1.4e-05  Score=44.06  Aligned_cols=25  Identities=64%  Similarity=0.999  Sum_probs=23.1

Q ss_pred             CCCCceEEEecCccc-----cccccccCCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKES   25 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s   25 (97)
                      +|+++|+|+|+|+.|     |++|||.+|+
T Consensus        35 ~~~~~~~L~~~g~~L~d~~tL~~~~i~~~~   64 (64)
T smart00213       35 IPVEQQRLIYKGKVLEDDRTLADYNIQDGS   64 (64)
T ss_pred             CCHHHEEEEECCEECCCCCCHHHcCCcCCC
Confidence            688999999999999     9999999986

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

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=97.72  E-value=2e-05  Score=58.47  Aligned_cols=34  Identities=24%  Similarity=0.539  Sum_probs=31.2

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeec
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLR   34 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~   34 (97)
                      +|+++|+|+|+|+.|     |++|||.++++|+++++.+
T Consensus        39 ip~~~QkLIy~GkiL~Dd~tL~dy~I~e~~~Ivvmv~k~   77 (378)
T TIGR00601        39 YPVAQQKLIYSGKILSDDKTVREYKIKEKDFVVVMVSKP   77 (378)
T ss_pred             CChhHeEEEECCEECCCCCcHHHcCCCCCCEEEEEeccC
Confidence            588999999999999     9999999999999998753

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=97.69  E-value=4.6e-05  Score=42.25  Aligned_cols=34  Identities=68%  Similarity=1.040  Sum_probs=31.4

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeec
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLR   34 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~   34 (97)
                      ||.++|++.|.|+.|     +.+|+|.+++++++..+++
T Consensus        35 ~~~~~q~~~~~~~~l~d~~~l~~~~i~~~~~~~l~~~~~   73 (75)
T KOG0001|consen   35 IPVDQQRLIFGGKPLEDGRTLADYNIQEGSTLHLVLSLR   73 (75)
T ss_pred             CCCeeEEEEECCEECcCCCcHHHhCCCCCCEEEEEEecC
Confidence            688999999999998     9999999999999998764

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

Probab=97.60  E-value=0.00013  Score=42.60  Aligned_cols=56  Identities=13%  Similarity=0.188  Sum_probs=41.5

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc--------------------CCCeeCCCCCcccccccCCCCEEEE
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS--------------------SPAGNFEDGWTQADYNIQKESTLHF   92 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~--------------------~~gk~L~d~~tL~~y~I~~~sti~l   92 (97)
                      +.|.|...+|+.+.+.+..+.+|+++...+.                    -+|..|+++.||+++||.+|+.+.+
T Consensus         3 ~rVtv~~~~~~~~Dl~lP~~vpv~~li~~l~~~~~~~~~~~~~~~~~~L~~~~g~~L~~~~tL~~~gV~dGd~L~L   78 (79)
T PF08817_consen    3 CRVTVDAGNGRQVDLALPADVPVAELIPELVELLGLPGDDPPGHGQWVLARAGGRPLDPDQTLADAGVRDGDVLVL   78 (79)
T ss_dssp             EEEEEE-TT--EEEEEEETTSBTTHHHHHHHHHS---S---TT-E-EEEG-GGTEEEETTSBCGGGT--TT-EEEE
T ss_pred             EEEEEEcCCCcEEEEEcCCCCcHHHHHHHHHHHhCCccCCCCCcceEEEEecCCcccCCcCcHhHcCCCCCCEEEe
Confidence            3566666557888999999999998887766                    5678899999999999999999886

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.

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

Probab=97.57  E-value=7.9e-05  Score=44.17  Aligned_cols=31  Identities=26%  Similarity=0.567  Sum_probs=26.9

Q ss_pred             CCCCceEEE-ecCc-----cc------cccccccCCCcceeee
Q 042212            1 MPLEQQRLV-FADK-----SL------LADYNIQKESTLHLVA   31 (97)
Q Consensus         1 ip~~~q~L~-~~~~-----~L------l~~y~i~~~s~i~l~~   31 (97)
                      +|+..|+|. |.++     .|      |++||+++|++||++=
T Consensus        38 ~~~~~mrL~l~~~~~~~~~~l~~d~~~L~~y~~~dg~~IhVvD   80 (84)
T cd01789          38 TPASSMRLQLFDGDDKLVSKLDDDDALLGSYPVDDGCRIHVID   80 (84)
T ss_pred             CCccceEEEEEcCCCCeEeecCCCccEeeeccCCCCCEEEEEe
Confidence            689999995 8887     46      9999999999999864

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.

>PF00789 UBX: UBX domain; InterPro: IPR001012 The UBX domain is found in ubiquitin-regulatory proteins, which are members of the ubiquitination pathway, as well as a number of other proteins including FAF-1 (FAS-associated factor 1), the human Rep-8 reproduction protein and several hypothetical proteins from yeast

Probab=97.51  E-value=0.00049  Score=40.15  Aligned_cols=59  Identities=17%  Similarity=0.174  Sum_probs=50.6

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc----------------CCCeeCCCC--CcccccccCCCCEEEEE
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS----------------SPAGNFEDG--WTQADYNIQKESTLHFV   93 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~----------------~~gk~L~d~--~tL~~y~I~~~sti~l~   93 (97)
                      +...|.||.++|+.+.-...+++|+.+|.+-|.                |-.+.+.++  .||++.|+.+++++++.
T Consensus         5 ~~~~I~vRlpdG~~l~~~F~~~~tl~~l~~~v~~~~~~~~~~~f~L~~~~Pr~~l~~~~~~tl~e~~l~p~~~l~v~   81 (82)
T PF00789_consen    5 DVVRIQVRLPDGSRLQRRFPKSDTLQDLYDFVESQLFSPEESDFELITAFPRRELTDEDSKTLEEAGLLPSATLIVE   81 (82)
T ss_dssp             SEEEEEEEETTSTEEEEEEETTSBHHHHHHHHHHHHHCTTTSSEEEEESSSTEECCSTTTSBTCCCTTSSCEEEEEE
T ss_pred             CEEEEEEECCCCCEEEEEECCcchHHHHHHHHHHhcCCCCCccEEEEeCCCCcCCCccccccHHHhcCCCCeEEEEE
Confidence            457889999999999999999999999998887                566777544  69999999999998874

The function of the UBX domain is not known although the fragment of avian FAF-1 containing the UBX domain causes apoptosis of transfected cells.; GO: 0005515 protein binding; PDB: 3QX1_A 1H8C_A 3QCA_B 3QQ8_B 3QC8_B 3R3M_A 3QWZ_B 1S3S_H 1JRU_A 1I42_A ....

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

Probab=97.45  E-value=7.9e-05  Score=42.41  Aligned_cols=31  Identities=32%  Similarity=0.579  Sum_probs=27.0

Q ss_pred             CCC-CceEEEecCccc-----cccccccCCCcceeee
Q 042212            1 MPL-EQQRLVFADKSL-----LADYNIQKESTLHLVA   31 (97)
Q Consensus         1 ip~-~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~   31 (97)
                      +|. ++.+|+|.|+.|     +++|||.+|++|++++
T Consensus        36 i~~~~~~~l~fdG~~L~~~~T~~~~~ied~d~Idv~I   72 (72)
T PF11976_consen   36 IPPEESIRLIFDGKRLDPNDTPEDLGIEDGDTIDVII   72 (72)
T ss_dssp             TTT-TTEEEEETTEEE-TTSCHHHHT-STTEEEEEE-
T ss_pred             CCccceEEEEECCEEcCCCCCHHHCCCCCCCEEEEEC
Confidence            577 899999999999     9999999999999864

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 ....

>cd01770 p47_UBX p47-like ubiquitin domain

Probab=97.33  E-value=0.00071  Score=39.72  Aligned_cols=55  Identities=16%  Similarity=0.233  Sum_probs=46.0

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc----------------CCCeeCCC-CCcccccccCCCCEE
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS----------------SPAGNFED-GWTQADYNIQKESTL   90 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~----------------~~gk~L~d-~~tL~~y~I~~~sti   90 (97)
                      ..+|.||.++|+.+...+..++||++|.+-|.                |-.+.|.| +.||.+.|+.+.+.+
T Consensus         4 ~t~iqiRlpdG~r~~~rF~~~~tv~~l~~~v~~~~~~~~~~~f~L~t~fP~k~l~~~~~Tl~eagL~~s~v~   75 (79)
T cd01770           4 TTSIQIRLADGKRLVQKFNSSHRVSDVRDFIVNARPEFAARPFTLMTAFPVKELSDESLTLKEANLLNAVIV   75 (79)
T ss_pred             eeEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHhCCCCCCCCEEEecCCCCcccCCCCCcHHHCCCcCcEEE
Confidence            46789999999999999999999999998876                66677744 789999999875543

p47_UBX p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events. p47 has carboxy-terminal SEP and UBX domains. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.

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

Probab=97.30  E-value=0.00013  Score=59.45  Aligned_cols=34  Identities=35%  Similarity=0.718  Sum_probs=31.8

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||.++|||||+||.|     +.+||| +|.+|||+.|.+.
T Consensus        38 i~s~~qr~i~~grvl~~~k~vq~~~v-dgk~~hlverppp   76 (1143)
T KOG4248|consen   38 IPSEKQRLIYQGRVLQDDKKVQEYNV-DGKVIHLVERPPP   76 (1143)
T ss_pred             cccccceeeecceeeccchhhhhccC-CCeEEEeeccCCC
Confidence            789999999999999     999999 9999999999653

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

Probab=97.29  E-value=0.0002  Score=52.21  Aligned_cols=57  Identities=16%  Similarity=0.261  Sum_probs=47.4

Q ss_pred             eeeEEECC---CCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEE
Q 042212           37 MQIFVKTS---TGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        37 m~i~vk~~---~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~   93 (97)
                      |.++|+..   ....++++|+.+.+|.+||+.++             |+||+|.|+.++..+.+..-+.+|++
T Consensus         1 m~~lvqf~~~~~~h~l~v~v~~~t~I~~lke~Vak~~gvp~D~L~viFaGKeLs~~ttv~~cDL~qqs~~hi~   73 (446)
T KOG0006|consen    1 MIVLVQFNKTGSSHGLPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELSNDTTVQNCDLSQQSATHIM   73 (446)
T ss_pred             CeEEEEeCCccccCceeEEEecCCCHHHHHHHHHHhhCCChhheEEEEeccccccCceeecccccccchhhhh
Confidence            44555543   23568889999999999999988             99999999999999999888888877

>cd01767 UBX UBX (ubiquitin regulatory X) domain

Probab=97.28  E-value=0.0014  Score=37.96  Aligned_cols=56  Identities=11%  Similarity=0.136  Sum_probs=46.0

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc--------------CCCeeCC---CCCcccccccCCCCEEEE
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS--------------SPAGNFE---DGWTQADYNIQKESTLHF   92 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~--------------~~gk~L~---d~~tL~~y~I~~~sti~l   92 (97)
                      ...|.||.++|+.+.-...+++|+.+|.+-|.              |-.+.+.   ++.||.+.|+.+ +++.+
T Consensus         2 ~t~i~iRlpdG~~~~~~F~~~~tl~~l~~fv~~~~~~~~~f~L~t~~Pr~~~~~~~~~~TL~e~gL~~-s~~~~   74 (77)
T cd01767           2 TTKIQIRLPDGKRLEQRFNSTHKLSDVRDFVESNGPPAEPFTLMTSFPRRVLTDLDYELTLQEAGLVN-EVVFQ   74 (77)
T ss_pred             cEEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHcCCCCCCEEEEeCCCCccCCCCCccCcHHHcCCcc-ceEEE
Confidence            35788999999999999999999999998886              6667775   478999999995 44433

The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation.

>smart00166 UBX Domain present in ubiquitin-regulatory proteins

Probab=97.24  E-value=0.0012  Score=38.46  Aligned_cols=58  Identities=19%  Similarity=0.232  Sum_probs=49.4

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc---------------CCCeeCCC---CCcccccccCCCCEEEE
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS---------------SPAGNFED---GWTQADYNIQKESTLHF   92 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~---------------~~gk~L~d---~~tL~~y~I~~~sti~l   92 (97)
                      +...|.||.++|+.+.-...+++|+.++.+-+.               |-.+.+.+   +.||.+.|+.+.+++.+
T Consensus         3 ~~~~I~iRlPdG~ri~~~F~~~~tl~~v~~~v~~~~~~~~~~f~L~t~~Prk~l~~~d~~~tL~e~gL~p~~~l~v   78 (80)
T smart00166        3 DQCRLQIRLPDGSRLVRRFPSSDTLRTVYEFVSAALTDGNDPFTLNSPFPRRTFTKDDYSKTLLELALLPSSTLVL   78 (80)
T ss_pred             CeEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHcccCCCCCEEEEeCCCCcCCccccccCCHHHCCCCCceEEEE
Confidence            356889999999999999999999999999883               66777854   47999999998888766

Present in FAF1 and Shp1p.

>cd01772 SAKS1_UBX SAKS1-like UBX domain

Probab=97.21  E-value=0.0014  Score=38.38  Aligned_cols=57  Identities=11%  Similarity=0.147  Sum_probs=49.3

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc--------------CCCeeCCC---CCcccccccCCCCEEEE
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS--------------SPAGNFED---GWTQADYNIQKESTLHF   92 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~--------------~~gk~L~d---~~tL~~y~I~~~sti~l   92 (97)
                      ...|.||.++|+.+.-....++|++++.+-|+              |--|.+.+   +.||.+.|+.+.+++.+
T Consensus         4 ~~~i~iRlp~G~~~~~~F~~~~tl~~v~~fV~~~~~~~~~f~L~t~fPrk~~~~~d~~~TL~elgL~Psa~L~v   77 (79)
T cd01772           4 ETRIQIRLLDGTTLKQTFKAREQLAAVRLFVELNTGNGGPFTLMTPFPRKVFTEDDMEKPLQELGLVPSAVLIV   77 (79)
T ss_pred             EEEEEEECCCCCEEEEEeCCCChHHHHHHHHHHcCCCCCCEEEEeCCCCeECCcccccCCHHHCCCCCceEEEE
Confidence            35788999999999999999999999999997              66677854   58999999999998876

SAKS1 (SAPK-substrate-1), also known as Y33K, is a widely expressed protein containing N-terminal UBA (ubiquitin-associated) and C-terminal UBX (ubiqiutin-like) domains that was identified as a substrate of stress-activated protein kinases (SAPKs). SAKS1 is related evolutionarily to two other UBA/UBX-containing proteins, p47 and Faf1. The UBA and UBX domains of SAKS1 bind ubiquitin tetramers and valosin-containing protein (VCP), respectively suggesting a role for SAKS1 as an adaptor that directs VCP to polyubiquitinated proteins facilitating its destruction by the proteasome. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.

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

Probab=96.95  E-value=0.00065  Score=41.38  Aligned_cols=46  Identities=22%  Similarity=0.195  Sum_probs=35.9

Q ss_pred             CEEEEeecCCCcHHHhhcccc------------CC---CeeCCCCCcccccc-------cCCCCEEEE
Q 042212           47 KTITLEVESSDMIDNASRGSS------------SP---AGNFEDGWTQADYN-------IQKESTLHF   92 (97)
Q Consensus        47 ~~~~l~v~~~~tV~~lK~~I~------------~~---gk~L~d~~tL~~y~-------I~~~sti~l   92 (97)
                      .++.++++++.||-++|.+++            |.   .+.|+|..||+|+|       .+..+++-|
T Consensus        12 ttif~da~es~tV~elK~~l~gi~~~Pvn~qrL~kmd~eqlL~D~ktL~d~gfts~~ak~q~pA~vgL   79 (110)
T KOG4495|consen   12 TTIFTDAKESSTVFELKRKLEGILKRPVNEQRLYKMDTEQLLDDGKTLGDCGFTSQTAKPQAPATVGL   79 (110)
T ss_pred             eeEEeecCccccHHHHHHHHHHHHhCCCcchheeecCHHHHhhccchhhhccccccccccCCCceeee
Confidence            466779999999999999998            22   26689999999995       455555554

>PF13019 Telomere_Sde2: Telomere stability and silencing

Probab=96.79  E-value=0.0043  Score=41.16  Aligned_cols=61  Identities=20%  Similarity=0.334  Sum_probs=44.6

Q ss_pred             eeeEEECCCC----CEEEEeecCCCcHHHhhcccc---------------CCCeeC--CCCCcccccccCCC----CEEE
Q 042212           37 MQIFVKTSTG----KTITLEVESSDMIDNASRGSS---------------SPAGNF--EDGWTQADYNIQKE----STLH   91 (97)
Q Consensus        37 m~i~vk~~~g----~~~~l~v~~~~tV~~lK~~I~---------------~~gk~L--~d~~tL~~y~I~~~----sti~   91 (97)
                      |+|+|++++|    .++.+.+.++.||.+|+..|.               ..++.|  .++..++.+.-.+.    -+++
T Consensus         1 i~Vlvss~~g~~lp~tl~~~lp~~ttv~dL~~~l~~~~~~~~~~~~~L~~~~n~~l~~~~~~~~s~l~~~~~~~~~~~l~   80 (162)
T PF13019_consen    1 INVLVSSFDGLTLPPTLSLSLPSTTTVSDLKDRLSERLPIPSSSQLYLTTNSNGQLSPSSDIPLSSLLSSSQDSDFITLR   80 (162)
T ss_pred             CeEEEecCCCCCCCCeEEeeCCCCCcHHHHHHHHHhhcCCCccceeEEEEeCCCeeCCCccccHHhhccCcCCCCceEEE
Confidence            6899999999    589999999999999999998               234444  45555666654443    3567


Q ss_pred             EEEeeC
Q 042212           92 FVLRLS   97 (97)
Q Consensus        92 l~~rl~   97 (97)
                      +.+|++
T Consensus        81 l~~rl~   86 (162)
T PF13019_consen   81 LSLRLR   86 (162)
T ss_pred             EEEecc
Confidence            766653

>cd01774 Faf1_like2_UBX Faf1 ike-2 UBX domain

Probab=96.60  E-value=0.01  Score=35.26  Aligned_cols=59  Identities=10%  Similarity=0.028  Sum_probs=49.0

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc--------------CCCeeCC--------CCCcccccccCCCCEEEE
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS--------------SPAGNFE--------DGWTQADYNIQKESTLHF   92 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~--------------~~gk~L~--------d~~tL~~y~I~~~sti~l   92 (97)
                      +..+|.+|.++|+.+.-....++|+++|..-|.              |--+.++        .+.||.+.|+.+..++.+
T Consensus         3 ~~~~I~iRlp~G~Rl~rrF~~~~tl~~l~~fv~~~~~~~~~f~L~t~FPrr~~~~~~~~~~~~~~TL~eaGL~~s~~L~V   82 (85)
T cd01774           3 DTVKIVFKLPNGTRVERRFLFTQSLRVIHDFLFSLKETPEKFQIVTNFPRRVLPCLPSEGDPPPPTLLEAGLSNSEVLFV   82 (85)
T ss_pred             ceEEEEEECCCCCEEEEEeCCCCcHHHHHHHHHhCCCCCCcEEEecCCCCccccccccccCcCCCCHHHcCCCCccEEEE
Confidence            457899999999999999999999999998877              4446775        367999999998888765


Q ss_pred             E
Q 042212           93 V   93 (97)
Q Consensus        93 ~   93 (97)
                      .
T Consensus        83 ~   83 (85)
T cd01774          83 Q   83 (85)
T ss_pred             e
Confidence            3

Faf1_like2 is a protein of unknown function with a domain architecture that includes the UAS (ubiquitin-associated) and UBX (ubiquitin-like) domains. This protein is related to other UBA/UBX-containing proteins like Faf1, p47, and SAKS1 and may serve as an adaptor molecule that shuttles proteins to the proteasome for degradation. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.

>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13

Probab=96.53  E-value=0.0021  Score=37.28  Aligned_cols=29  Identities=31%  Similarity=0.394  Sum_probs=24.6

Q ss_pred             CCCCceEEE--ecCccc-----cccccccCCCccee
Q 042212            1 MPLEQQRLV--FADKSL-----LADYNIQKESTLHL   29 (97)
Q Consensus         1 ip~~~q~L~--~~~~~L-----l~~y~i~~~s~i~l   29 (97)
                      +|+++|||.  +.|+.|     |++||+.+|+++|+
T Consensus        39 ~~~~Rqrl~~~~~g~~L~d~~tL~~~gv~~g~~lyv   74 (77)
T cd01801          39 LTVNRQSLRLEPKGKSLKDDDTLVDLGVGAGATLYV   74 (77)
T ss_pred             CCcceeEEEeCCCCcccCCcccHhhcCCCCCCEEEE
Confidence            367899996  778888     99999999999875

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.

>KOG1639 consensus Steroid reductase required for elongation of the very long chain fatty acids [Lipid transport and metabolism]

Probab=96.52  E-value=0.0031  Score=44.62  Aligned_cols=56  Identities=18%  Similarity=0.239  Sum_probs=43.3

Q ss_pred             eeeEEECCCC-CEEE-EeecCCCcHHHhhcccc------------------CCCeeCCCCCcccccccCCCCEEEE
Q 042212           37 MQIFVKTSTG-KTIT-LEVESSDMIDNASRGSS------------------SPAGNFEDGWTQADYNIQKESTLHF   92 (97)
Q Consensus        37 m~i~vk~~~g-~~~~-l~v~~~~tV~~lK~~I~------------------~~gk~L~d~~tL~~y~I~~~sti~l   92 (97)
                      |.|.+...++ -..+ .+.+...|+.|+++.+.                  -+|+.|.|+.+|++|+..+++++.+
T Consensus         1 m~It~~srs~~~~~~~~~~s~~~ti~d~~~~~~~~~~k~~~~~~r~tlr~e~kgkpl~~~s~l~e~~~~s~~~i~v   76 (297)
T KOG1639|consen    1 MEITIASRSKGLRIKEKDLSGSETIDDLLKAISAKNLKITPYRIRLTLRVEPKGKPLIDNSKLQEYGDGSGATIYV   76 (297)
T ss_pred             CceeeeccCCCceeeeecCCCCCcHHHHHHHHHHhhhccCccchhheeeccCCCccccchhHHHHhccCCCCEEEE
Confidence            4566655443 2333 56778899999997766                  6799999999999999999988765

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

Probab=96.17  E-value=0.023  Score=34.73  Aligned_cols=60  Identities=12%  Similarity=0.252  Sum_probs=51.0

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      -+.+.|+.-+|..+.+.|..+...+.|+.--+             |+|+.+.+.+|-++.+.++++.|.++..
T Consensus        20 hi~LKV~gqd~~~~~Fkikr~t~LkKLM~aYc~r~Gl~~~s~RFlFdG~rI~~~~TP~~L~mEd~D~Iev~~~   92 (99)
T KOG1769|consen   20 HINLKVKGQDGSVVVFKIKRHTPLKKLMKAYCERQGLSMNSLRFLFDGQRIRETHTPADLEMEDGDEIEVVQE   92 (99)
T ss_pred             eEEEEEecCCCCEEEEEeecCChHHHHHHHHHHHcCCccceEEEEECCcCcCCCCChhhhCCcCCcEEEEEee
Confidence            36667777777888999999998888876655             9999999999999999999999988753

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

Probab=96.12  E-value=0.0048  Score=35.95  Aligned_cols=32  Identities=34%  Similarity=0.574  Sum_probs=26.4

Q ss_pred             CceEEEecC----ccc------cccccccCCCcceeeeeecC
Q 042212            4 EQQRLVFAD----KSL------LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         4 ~~q~L~~~~----~~L------l~~y~i~~~s~i~l~~~~~~   35 (97)
                      .+|||.|..    ++|      |++|||..+.+|.|+.+.+.
T Consensus        38 g~qrLsfQepgg~rqlL~s~~sLA~yGiFs~~~i~lleT~p~   79 (80)
T cd01811          38 GLQRLSFQEPGGERQLLSSRKSLADYGIFSKTNICLLETFPP   79 (80)
T ss_pred             cceEEEeecCCcccccccccccHhhhcceeccEEEEEecCCC
Confidence            479999865    665      99999999999999887543

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.

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

Probab=96.10  E-value=0.0033  Score=45.87  Aligned_cols=34  Identities=24%  Similarity=0.537  Sum_probs=31.1

Q ss_pred             CCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            2 PLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         2 p~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      |+++|+|||+|+.|     +.+|+|.+++-|.++++-+.
T Consensus        39 P~~~QkLIy~GkiL~D~~tv~Eykv~E~~fiVvMlsK~k   77 (340)
T KOG0011|consen   39 PAEQQKLIYSGKILKDETTVGEYKVKEKKFIVVMLSKDK   77 (340)
T ss_pred             chhhheeeecceeccCCcchhhhccccCceEEEEEecCc
Confidence            88999999999999     99999999999999887553

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

Probab=96.08  E-value=0.0045  Score=36.59  Aligned_cols=32  Identities=34%  Similarity=0.609  Sum_probs=23.1

Q ss_pred             CCCCceEEEec-C--cc----c------cccccccCCCcceeeee
Q 042212            1 MPLEQQRLVFA-D--KS----L------LADYNIQKESTLHLVAR   32 (97)
Q Consensus         1 ip~~~q~L~~~-~--~~----L------l~~y~i~~~s~i~l~~~   32 (97)
                      ||++.|+|.+. .  ..    +      |.+||+++|.+||+.=.
T Consensus        39 i~~~~m~L~l~~~~~~~~~~~~~dd~~~L~~y~~~dg~~i~V~D~   83 (87)
T PF14560_consen   39 IPPSDMRLQLKSDKDDSKIEELDDDDATLGSYGIKDGMRIHVVDT   83 (87)
T ss_dssp             S-TTTEEEEEE-TSSSSEEEESSGSSSBCCHHT-STTEEEEEEE-
T ss_pred             CCcccEEEEEEecCCCccccccCCCccEeecCCCCCCCEEEEEeC
Confidence            68999999976 1  11    1      99999999999997643

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

Probab=95.96  E-value=0.0095  Score=37.17  Aligned_cols=32  Identities=31%  Similarity=0.544  Sum_probs=24.2

Q ss_pred             CCceEEEecCccc-----cccccccCCC------cceeeeeec
Q 042212            3 LEQQRLVFADKSL-----LADYNIQKES------TLHLVARLR   34 (97)
Q Consensus         3 ~~~q~L~~~~~~L-----l~~y~i~~~s------~i~l~~~~~   34 (97)
                      ++..||||.||.|     |++|++..|.      ++||+++..
T Consensus        48 ~~~lRLI~~GriL~d~~tL~~~~~~~~~~~~~~~vmHlvvrp~   90 (111)
T PF13881_consen   48 PSDLRLIYAGRILEDNKTLSDCRLPSGETPGGPTVMHLVVRPN   90 (111)
T ss_dssp             GGGEEEEETTEEE-SSSBTGGGT--TTSETT--EEEEEEE-SS
T ss_pred             hhhEEEEeCCeecCCcCcHHHhCCCCCCCCCCCEEEEEEecCC
Confidence            4679999999999     9999999876      678888754

>COG5417 Uncharacterized small protein [Function unknown]

Probab=95.85  E-value=0.032  Score=32.54  Aligned_cols=52  Identities=17%  Similarity=0.087  Sum_probs=41.2

Q ss_pred             EECCCCCEEEEeecCCCcHHHhhcccc------------------CCCeeCCCCCcccccccCCCCEEEE
Q 042212           41 VKTSTGKTITLEVESSDMIDNASRGSS------------------SPAGNFEDGWTQADYNIQKESTLHF   92 (97)
Q Consensus        41 vk~~~g~~~~l~v~~~~tV~~lK~~I~------------------~~gk~L~d~~tL~~y~I~~~sti~l   92 (97)
                      ++.-+|.++-+.++...+++.+-.-+.                  -.++.|.++..|.+|+|.+|+.+.+
T Consensus        11 ~t~y~g~~yDLrl~d~~pikklIdivwe~~kis~~~reg~~Ikv~nKa~llsgd~kL~d~~IadGD~Lei   80 (81)
T COG5417          11 FTNYNGGTYDLRLPDYLPIKKLIDIVWESLKISIFDREGTQIKVMNKAQLLSGDDKLIDYQIADGDILEI   80 (81)
T ss_pred             eEecCCceEEEeccccchHHHHHHHHHHHhhccccccCCCEEEEeccceEecCCceEEeccccCCCEEEe
Confidence            345568889999988888876644333                  5688899999999999999998765

>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=95.66  E-value=0.016  Score=32.81  Aligned_cols=50  Identities=6%  Similarity=0.080  Sum_probs=34.7

Q ss_pred             CCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEE
Q 042212           43 TSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHF   92 (97)
Q Consensus        43 ~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l   92 (97)
                      ..+++.+.+.+.|+.++.++-+...             |+++.|+-+.++.-.|+.+|+.+.|
T Consensus         3 ~~~~rr~~vkvtp~~~l~~VL~eac~k~~l~~~~~~L~h~~k~ldlslp~R~snL~n~akLeL   65 (65)
T PF11470_consen    3 CYNFRRFKVKVTPNTTLNQVLEEACKKFGLDPSSYDLKHNNKPLDLSLPFRLSNLPNNAKLEL   65 (65)
T ss_dssp             -TTS-EEEE---TTSBHHHHHHHHHHHTT--GGG-EEEETTEEESSS-BHHHH---SS-EEEE
T ss_pred             ccCCcEEEEEECCCCCHHHHHHHHHHHcCCCccceEEEECCEEeccccceeecCCCCCCEEeC
Confidence            4578999999999999998866655             8899999999999999999999875

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.

>cd01771 Faf1_UBX Faf1 UBX domain

Probab=95.45  E-value=0.087  Score=30.89  Aligned_cols=59  Identities=12%  Similarity=0.122  Sum_probs=48.7

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc--------------CCCeeCC---CCCcccccccCCCCEEEEE
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS--------------SPAGNFE---DGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~--------------~~gk~L~---d~~tL~~y~I~~~sti~l~   93 (97)
                      +..+|.||.++|+.+.-....++++.+|-.-+.              |--+.+.   .+.||.+.|+.+..++.+-
T Consensus         3 ~~~~i~iRlP~G~r~~rrF~~t~~L~~l~~fv~~~~~~~~~f~L~t~fPRk~~~~~d~~~TL~e~gL~p~~~L~Ve   78 (80)
T cd01771           3 PISKLRVRTPSGDFLERRFLGDTPLQVLLNFVASKGYPIDEYKLLSSWPRRDLTQLDPNFTLLELKLYPQETLILE   78 (80)
T ss_pred             CeEEEEEECCCCCEEEEEeCCCCcHHHHHHHHHhcCCCCCCEEEecCCCCCCCcCCCCCCcHHHcCCCCCcEEEEE
Confidence            346889999999999999999999999988876              5556663   3579999999999988764

Faf1 (fas-associated factor1) is a nucleolar protein that was first identified as an interaction partner of the death receptor Fas. Faf1 contains N-terminal UAS (ubiquitin-associated) and C-terminal UBX (ubiquitin-like) domains and is closely related to other UBA/UBX-containing proteins like p47, Rep8 and SAKS1. Faf1 is thought to be involved in 18S rRNA synthesis and/or 40S ribosomal subunit assembly. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.

>PF08337 Plexin_cytopl: Plexin cytoplasmic RasGAP domain; InterPro: IPR013548 This domain is found at C terminus of various plexins (e

Probab=95.32  E-value=0.015  Score=45.20  Aligned_cols=59  Identities=19%  Similarity=0.238  Sum_probs=41.4

Q ss_pred             eeeEEECC--CCCEEEEeecCCCcHHHhhcccc-------------------------CCCe-eCCCC------------
Q 042212           37 MQIFVKTS--TGKTITLEVESSDMIDNASRGSS-------------------------SPAG-NFEDG------------   76 (97)
Q Consensus        37 m~i~vk~~--~g~~~~l~v~~~~tV~~lK~~I~-------------------------~~gk-~L~d~------------   76 (97)
                      +.+.|-..  .+..+.+.|-..|||.++|+||-                         -+|+ .|.|.            
T Consensus       190 ltl~v~~~~~~~~~i~VkVLdCDTItQVKeKiLDavyk~~p~S~rp~~~d~dLEwr~~~~~~~iL~D~D~ts~~~~~wkr  269 (539)
T PF08337_consen  190 LTLNVVPQEEGSEEIPVKVLDCDTITQVKEKILDAVYKNTPYSQRPRADDVDLEWRQGRGGRLILQDEDSTSKVEGGWKR  269 (539)
T ss_dssp             EEEEEECTTTSSTCEEEEEETTSBHHHHHHHHHHHHTTTS-GGGS--GGGEEEEEEETTSEEEEESSSSTTSEEETTEEE
T ss_pred             EEEEEEecCCCCceEEEEEEecCcccHHHHHHHHHHHcCCCCCCCCCccccceeeecCCCCcccccCCCCCcccCCCceE
Confidence            45554332  23568888999999999999998                         2233 45443            


Q ss_pred             -CcccccccCCCCEEEEEEe
Q 042212           77 -WTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        77 -~tL~~y~I~~~sti~l~~r   95 (97)
                       .||++|+|.+|+++.++.+
T Consensus       270 LNTL~HY~V~dga~vaLv~k  289 (539)
T PF08337_consen  270 LNTLAHYKVPDGATVALVPK  289 (539)
T ss_dssp             --BHHHHT--TTEEEEEEES
T ss_pred             eccHhhcCCCCCceEEEeec
Confidence             4899999999999999876

g. P51805 from SWISSPROT). Plexins are receptors for semaphorins, and plexin signalling is important in pathfinding and patterning of both neurons and developing blood vessels [, ]. The cytoplasmic region, which has been called a SEX domain [], and is involved in downstream signalling pathways, by interaction with proteins such as Rac1, RhoD, Rnd1 and other plexins []. ; PDB: 3H6N_A 4E71_A 4E74_A 3IG3_A 2REX_C 2JPH_A 2R2O_A 3HM6_X 3SU8_X 3SUA_E ....

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

Probab=95.21  E-value=0.019  Score=35.00  Aligned_cols=35  Identities=6%  Similarity=0.023  Sum_probs=29.0

Q ss_pred             EEEEeec--CCCcHHHhhcccc---------------CCCeeCCCCCccccc
Q 042212           48 TITLEVE--SSDMIDNASRGSS---------------SPAGNFEDGWTQADY   82 (97)
Q Consensus        48 ~~~l~v~--~~~tV~~lK~~I~---------------~~gk~L~d~~tL~~y   82 (97)
                      .+.+++.  .+.||..||..|.               |+|+.|.|...|+.-
T Consensus        13 Dl~L~I~~~~~~Tv~~LK~lIR~~~p~~~s~~rLRlI~~Gr~L~d~t~l~~~   64 (97)
T PF10302_consen   13 DLPLDIPSPNTTTVAWLKQLIRERLPPEPSRRRLRLIYAGRLLNDHTDLSSE   64 (97)
T ss_pred             CceeecCCCCcccHHHHHHHHHhhcCCCCccccEEeeecCcccCccchhhhh
Confidence            3667776  8899999999998               999999998777653

They contain a characteristic GFDRL sequence motif.

>PF15044 CLU_N: Mitochondrial function, CLU-N-term

Probab=95.02  E-value=0.017  Score=33.59  Aligned_cols=43  Identities=14%  Similarity=0.220  Sum_probs=37.1

Q ss_pred             ecCCCcHHHhhcccc--------------CCCeeCCCCCcccccc-cCCCCEEEEEEe
Q 042212           53 VESSDMIDNASRGSS--------------SPAGNFEDGWTQADYN-IQKESTLHFVLR   95 (97)
Q Consensus        53 v~~~~tV~~lK~~I~--------------~~gk~L~d~~tL~~y~-I~~~sti~l~~r   95 (97)
                      |+++++|.++++-+.              ++|+.|+|...|++.. +++|+++.++..
T Consensus         1 v~~~d~v~dvrq~L~~~~~t~~~Tn~~L~~~g~~L~~~~el~~i~~~~~~~~L~lve~   58 (76)
T PF15044_consen    1 VSPTDTVQDVRQVLAESPETCYLTNFSLEHNGQRLDDFVELSEIEGIKDGCVLELVEE   58 (76)
T ss_pred             CChhhHHHHHHHHHHhCccccceeEEEEEECCCccCCchhhhhhhCCCCCcEEEEEec
Confidence            578899999999888              8999999988888874 888999998754

>cd01773 Faf1_like1_UBX Faf1 ike-1 UBX domain

Probab=94.84  E-value=0.18  Score=29.88  Aligned_cols=60  Identities=10%  Similarity=0.143  Sum_probs=48.5

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc--------------CCCeeC---CCCCcccccccCCCCEEEEEE
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS--------------SPAGNF---EDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~--------------~~gk~L---~d~~tL~~y~I~~~sti~l~~   94 (97)
                      +.-+|.||.++|+...-....++++++|-.-++              |--|.+   +.+.||.+.|+.+.+++.+--
T Consensus         4 ~~t~i~vRlP~G~r~~rrF~~~~~L~~v~~fv~~~g~~~~~f~L~t~FPRr~~~~~d~~~TL~e~GL~P~~~LfVq~   80 (82)
T cd01773           4 PKARLMLRYPDGKREQIALPEQAKLLALVRHVQSKGYPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQE   80 (82)
T ss_pred             CeeEEEEECCCCCEEEEEeCCCCcHHHHHHHHHhcCCCCCCEEEecCCCCcccCCcccCCCHHHcCCCCCcEEEEec
Confidence            446899999999999999999999999977776              334555   335799999999999988753

Faf1_like1 is a protein of unknown function with a domain architecture that includes the UAS (ubiquitin-associated) and UBX (ubiquitin-like) domains. This protein is related to other UBA/UBX-containing proteins like Faf1, p47, and SAKS1 and may serve as an adaptor molecule that shuttles proteins to the proteasome for degradation. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.

>PF10790 DUF2604: Protein of Unknown function (DUF2604); InterPro: IPR019726 This entry represents bacterial proteins with undetermined function

Probab=94.61  E-value=0.067  Score=30.39  Aligned_cols=51  Identities=10%  Similarity=0.226  Sum_probs=37.5

Q ss_pred             CCCEEEEeecCCCcHHHhhccc-c----------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           45 TGKTITLEVESSDMIDNASRGS-S----------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        45 ~g~~~~l~v~~~~tV~~lK~~I-~----------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      +|+...++..++...--+.++- +                -+|..|+-++.++|||+.++-++.+.++
T Consensus         4 NGqPv~VEANvnaPLh~v~akALe~sgNvgQP~ENWElkDe~G~vlD~~kKveD~GftngvkLFLsLK   71 (76)
T PF10790_consen    4 NGQPVQVEANVNAPLHPVRAKALEQSGNVGQPPENWELKDESGQVLDVNKKVEDFGFTNGVKLFLSLK   71 (76)
T ss_pred             CCCceeeecCCCCcchHHHHHHHhhccccCCCcccceeeccCCcEeeccchhhhccccccceEEEEee
Confidence            5777777777666433332221 1                6788888899999999999999998876

>PF09379 FERM_N: FERM N-terminal domain ; InterPro: IPR018979 This domain is the N-terminal ubiquitin-like structural domain of the FERM domain

Probab=94.16  E-value=0.11  Score=29.66  Aligned_cols=55  Identities=13%  Similarity=0.071  Sum_probs=40.8

Q ss_pred             EECCCCCEEEEeecCCCcHHHhhcccc--------------C----C--CeeCCCCCcccccccCCCCEEEEEEe
Q 042212           41 VKTSTGKTITLEVESSDMIDNASRGSS--------------S----P--AGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        41 vk~~~g~~~~l~v~~~~tV~~lK~~I~--------------~----~--gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      |+.++|...+++++++.|+.++=+.|+              +    +  ..-|+.+++|.++...++....+.+|
T Consensus         1 V~llD~~~~~~~v~~~~t~~~l~~~v~~~l~l~e~~~FgL~~~~~~~~~~~wL~~~k~l~~q~~~~~~~~~l~fr   75 (80)
T PF09379_consen    1 VRLLDGTTKTFEVDPKTTGQDLLEQVCDKLGLKEKEYFGLQYQVDKDGEHHWLDLDKKLKKQLKKNNPPFTLYFR   75 (80)
T ss_dssp             EEESSEEEEEEEEETTSBHHHHHHHHHHHHTTSSGGGEEEEE-EBTTSSEEEE-SSSBGGGSTBTSSSSEEEEEE
T ss_pred             CCCcCCCcEEEEEcCCCcHHHHHHHHHHHcCCCCccEEEEEEeecCCCcceeccCcccHHHHcCCCCCCEEEEEE
Confidence            567899999999999999999999988              4    2  24468888999998873444444333

The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane. Ezrin, a component of the undercoat of the microvilli plasma membrane. Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane. Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction. Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts. Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis. Merlin (or schwannomin). Protein NBL4. Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness. Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins. Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptors for cytokines or polypeptidic hormones. Non-receptor tyrosine-protein kinase TYK2. Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton. Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E. Caenorhabditis elegans protein phosphatase ptp-1. Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signalling pathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure []. The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].; PDB: 1EF1_B 1SGH_A 1E5W_A 2KC2_A 2KMA_A 3IVF_A 1H4R_B 3U8Z_A 1ISN_A 3BIN_A ....

>cd01788 ElonginB Ubiquitin-like domain of Elongin B

Probab=93.76  E-value=0.073  Score=33.47  Aligned_cols=32  Identities=41%  Similarity=0.473  Sum_probs=23.9

Q ss_pred             CCCCceEEEecCccc-----cccccc-------cCCCcceeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNI-------QKESTLHLVAR   32 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i-------~~~s~i~l~~~   32 (97)
                      .|++.|+|+-.+..|     |+|||+       ++-.++=|.+|
T Consensus        37 ~pp~dQrL~kd~qvLeD~kTL~d~g~t~~~akaq~pA~vgLa~r   80 (119)
T cd01788          37 RPPEDQRLYKDDQLLDDGKTLGDCGFTSQTARPQAPATVGLAFR   80 (119)
T ss_pred             CChhHheeecCceeecccccHHHcCccccccccCCCCeEEEEEe
Confidence            389999999444445     999999       55666666666

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.

>PF14453 ThiS-like: ThiS-like ubiquitin

Probab=93.15  E-value=0.31  Score=26.91  Aligned_cols=49  Identities=14%  Similarity=0.208  Sum_probs=35.5

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      |+|+|.   |+  .++++.+.|..++|.++.       ++|-+..++.     -+++|+.|.+.-|
T Consensus         1 M~I~vN---~k--~~~~~~~~tl~~lr~~~k~~~DI~I~NGF~~~~d~-----~L~e~D~v~~Ikk   56 (57)
T PF14453_consen    1 MKIKVN---EK--EIETEENTTLFELRKESKPDADIVILNGFPTKEDI-----ELKEGDEVFLIKK   56 (57)
T ss_pred             CEEEEC---CE--EEEcCCCcCHHHHHHhhCCCCCEEEEcCcccCCcc-----ccCCCCEEEEEeC
Confidence            566663   44  467778889999999988       7787776664     4567888877543

>PLN02560 enoyl-CoA reductase

Probab=92.01  E-value=0.12  Score=37.53  Aligned_cols=28  Identities=32%  Similarity=0.465  Sum_probs=22.6

Q ss_pred             CCCceEEEec---Cc----cc-----cccccccCCCccee
Q 042212            2 PLEQQRLVFA---DK----SL-----LADYNIQKESTLHL   29 (97)
Q Consensus         2 p~~~q~L~~~---~~----~L-----l~~y~i~~~s~i~l   29 (97)
                      |+++|||.+.   |+    .|     |+|||+++||++++
T Consensus        41 ~~~RqRL~~~~~~gk~~g~~L~d~ktL~d~gv~~gstLy~   80 (308)
T PLN02560         41 YPSRQRLTLPLPPGKTRPTVLDDSKSLKDYGLGDGGTVVF   80 (308)
T ss_pred             ChhheEEEEecCCCCcCccccCCCCCHHhcCCCCCceEEE
Confidence            6899999983   33    44     99999999998665

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

Probab=91.99  E-value=0.2  Score=38.31  Aligned_cols=56  Identities=18%  Similarity=0.162  Sum_probs=48.2

Q ss_pred             eeEEECCCCCEEEEe-ecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEE
Q 042212           38 QIFVKTSTGKTITLE-VESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        38 ~i~vk~~~g~~~~l~-v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      .+.||- .|+.+.++ ++.++|+..+|+++.             +.|+.+.|+--....+|+++.+++++-
T Consensus         5 ~v~VKW-~gk~y~v~~l~~d~t~~vlKaqlf~LTgV~PeRQKv~vKGg~a~dd~~~~al~iKpn~~lmMmG   74 (473)
T KOG1872|consen    5 TVIVKW-GGKKYPVETLSTDETPSVLKAQLFALTGVPPERQKVMVKGGLAKDDVDWGALQIKPNETLMMMG   74 (473)
T ss_pred             eEeeee-cCccccceeccCCCchHHHHHHHHHhcCCCccceeEEEecccccccccccccccCCCCEEEeec
Confidence            355655 47888887 999999999999998             889999999888899999999999874

>cd00196 UBQ Ubiquitin-like proteins

Probab=91.74  E-value=0.15  Score=26.00  Aligned_cols=31  Identities=48%  Similarity=0.700  Sum_probs=25.7

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVA   31 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~   31 (97)
                      +|++.|.|+++|..+     +.+|++.+++++++..
T Consensus        33 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~   68 (69)
T cd00196          33 LPPEQQRLLVNGKILPDSLTLEDYGLQDGDELVLVP   68 (69)
T ss_pred             cChHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEe
Confidence            367889999999887     4489999999998764

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.

>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain

Probab=91.41  E-value=0.86  Score=27.20  Aligned_cols=30  Identities=13%  Similarity=0.196  Sum_probs=27.7

Q ss_pred             eeEEECCCCCEEEEeecCCCcHHHhhcccc
Q 042212           38 QIFVKTSTGKTITLEVESSDMIDNASRGSS   67 (97)
Q Consensus        38 ~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~   67 (97)
                      .+.++++.|+++.+.+.|++.+.+|++.|.
T Consensus         2 ~FK~~~~~GrvhRf~~~~s~~~~~L~~~I~   31 (86)
T cd06409           2 AFKFKDPKGRVHRFRLRPSESLEELRTLIS   31 (86)
T ss_pred             cEEeeCCCCCEEEEEecCCCCHHHHHHHHH
Confidence            467889999999999999999999999998

The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. 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 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid 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

>KOG0013 consensus Uncharacterized conserved protein [Function unknown]

Probab=90.82  E-value=0.32  Score=33.75  Aligned_cols=49  Identities=16%  Similarity=0.157  Sum_probs=42.6

Q ss_pred             CCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEE
Q 042212           45 TGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        45 ~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~   93 (97)
                      +++.+.+.+...+|+.++|..+.             |+|+.+-|...|..|++++|.-..+-
T Consensus       155 T~~d~~lta~~~Dtv~eik~~L~Aaeg~D~~sQrif~Sg~~l~dkt~LeEc~iekg~rYvlq  216 (231)
T KOG0013|consen  155 TREDFWLTAPHYDTVGEIKRALRAAEGVDPLSQRIFFSGGVLVDKTDLEECKIEKGQRYVLQ  216 (231)
T ss_pred             hhhheeecccCcCcHHHHHHHHHHhhccchhhheeeccCCceeccccceeeeecCCCEEEEE
Confidence            56778899999999999998887             99999999999999999999554443

>PF10209 DUF2340: Uncharacterized conserved protein (DUF2340); InterPro: IPR018794 This entry consists of small proteins of approximately 150 amino acids whose function is unknown

Probab=90.63  E-value=0.2  Score=31.76  Aligned_cols=23  Identities=17%  Similarity=0.336  Sum_probs=19.6

Q ss_pred             eeC---CCCCcccccccCCCCEEEEE
Q 042212           71 GNF---EDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        71 k~L---~d~~tL~~y~I~~~sti~l~   93 (97)
                      ..|   +++.+|.++||.+.+.|.+.
T Consensus        81 ~iL~~~~~~~tL~~~gv~nETEiSfF  106 (122)
T PF10209_consen   81 WILDVSDDDKTLKELGVENETEISFF  106 (122)
T ss_pred             eeeecCCCCCcHHHcCCCccceeeee
Confidence            567   78899999999999988764

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

Probab=90.36  E-value=0.2  Score=37.00  Aligned_cols=47  Identities=11%  Similarity=0.168  Sum_probs=37.5

Q ss_pred             CeeeEEECCCC--CEEEEeecCCCcHHHhhcccc---------------CCCeeCCCCCccccc
Q 042212           36 RMQIFVKTSTG--KTITLEVESSDMIDNASRGSS---------------SPAGNFEDGWTQADY   82 (97)
Q Consensus        36 ~m~i~vk~~~g--~~~~l~v~~~~tV~~lK~~I~---------------~~gk~L~d~~tL~~y   82 (97)
                      +..+++|..+.  +..++..+..+||.+||..++               |.||.|.|...+.|.
T Consensus         9 ~v~lliks~Nq~y~dl~i~~dl~wtv~~Lk~hls~VyPskpl~~dqrliYsgkllld~qcl~d~   72 (391)
T KOG4583|consen    9 PVTLLIKSPNQSYKDLSISLDLKWTVGDLKVHLSQVYPSKPLELDQRLIYSGKLLLDHQCLTDW   72 (391)
T ss_pred             ceEEEecCCCccccceeeehhhhhhHHHHhhhHhhcCCCCCchhhHHHHhhccccccchhHHHH
Confidence            35677777765  457778889999999999988               889988888777664

>smart00295 B41 Band 4

Probab=90.32  E-value=1.7  Score=28.62  Aligned_cols=33  Identities=21%  Similarity=0.179  Sum_probs=29.6

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS   67 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~   67 (97)
                      .++.+.|..++|.+..+.++++.|++++-..++
T Consensus         2 ~~~~~~V~l~dg~~~~~~~~~~~t~~ev~~~v~   34 (207)
T smart00295        2 KPRVLKVYLLDGTTLEFEVDSSTTAEELLETVC   34 (207)
T ss_pred             CcEEEEEEecCCCEEEEEECCCCCHHHHHHHHH
Confidence            356788888999999999999999999999988

1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.

>KOG2086 consensus Protein tyrosine phosphatase SHP1/Cofactor for p97 ATPase-mediated vesicle membrane fusion [Nuclear structure]

Probab=89.66  E-value=0.27  Score=36.78  Aligned_cols=55  Identities=13%  Similarity=0.209  Sum_probs=46.7

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc----------------CCCeeCCC-CCcccccccCCCCEE
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS----------------SPAGNFED-GWTQADYNIQKESTL   90 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~----------------~~gk~L~d-~~tL~~y~I~~~sti   90 (97)
                      +-.|-||..+|+.....++.+.||.+++.-|.                |--|.|.| +.||.+.|+.+...+
T Consensus       305 tTsIQIRLanG~RlV~~fN~sHTv~DIR~fI~~aRp~~~~~~F~L~~~FPpk~l~D~sqTle~AgL~Nsvlv  376 (380)
T KOG2086|consen  305 TTSIQIRLANGTRLVLKFNHSHTVSDIREFIDTARPGDSSTYFILMMAFPPKPLSDDSQTLEEAGLLNSVLV  376 (380)
T ss_pred             cceEEEEecCCceeeeeccCcccHHHHHHHHHhcCCCCcCCceeeeecCCCcccCCcchhHHhccchhhhhh
Confidence            46788888999999999999999999999998                66788855 689999999876544

>KOG3206 consensus Alpha-tubulin folding cofactor B [Posttranslational modification, protein turnover, chaperones]

Probab=89.44  E-value=0.55  Score=32.59  Aligned_cols=45  Identities=7%  Similarity=0.099  Sum_probs=35.9

Q ss_pred             EEEeecCCCcHHHhhcccc--------------CCC-----eeC-CCCCcccccccCCCCEEEEE
Q 042212           49 ITLEVESSDMIDNASRGSS--------------SPA-----GNF-EDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        49 ~~l~v~~~~tV~~lK~~I~--------------~~g-----k~L-~d~~tL~~y~I~~~sti~l~   93 (97)
                      ..-..+++.|++++|.|++              |.|     ..| +++..|..|+..+|..||++
T Consensus        15 ~Ekr~~~~ltl~q~K~KLe~~~G~~~~~M~l~l~~~~d~~~~~lsn~d~~lg~~~~~Dg~rihvi   79 (234)
T KOG3206|consen   15 TEKRLSNSLTLAQFKDKLELLTGTEAESMELELYDGDDKKVSALSNEDADLGFYKVEDGLRIHVI   79 (234)
T ss_pred             hhhhcCCcCcHHHHHhhhhhhhCCCccceEEEEEcCCCceeeeccCCcccccccCCCCceEEEEE
Confidence            4456678999999999999              333     345 55789999999999999985

>PRK06437 hypothetical protein; Provisional

Probab=88.98  E-value=1.9  Score=24.23  Aligned_cols=44  Identities=14%  Similarity=0.200  Sum_probs=33.6

Q ss_pred             CCCEEEEeecCCCcHHHhhcccc---------CCCeeCCCCCcccccccCCCCEEEEE
Q 042212           45 TGKTITLEVESSDMIDNASRGSS---------SPAGNFEDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        45 ~g~~~~l~v~~~~tV~~lK~~I~---------~~gk~L~d~~tL~~y~I~~~sti~l~   93 (97)
                      .++...++++...||++|-+.+.         .+|+.+.     .++-+++|+.+.++
T Consensus         9 g~~~~~~~i~~~~tv~dLL~~Lgi~~~~vaV~vNg~iv~-----~~~~L~dgD~Veiv   61 (67)
T PRK06437          9 GHINKTIEIDHELTVNDIIKDLGLDEEEYVVIVNGSPVL-----EDHNVKKEDDVLIL   61 (67)
T ss_pred             CCcceEEEcCCCCcHHHHHHHcCCCCccEEEEECCEECC-----CceEcCCCCEEEEE
Confidence            44667788888899998877666         6777776     55677889988876

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

Probab=88.26  E-value=0.77  Score=27.82  Aligned_cols=55  Identities=9%  Similarity=0.195  Sum_probs=44.8

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEE
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLH   91 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~   91 (97)
                      +.+.|-..+|..+.+.+..+.+.+.|..--+             |+|+.++.++|-++++.++++.|.
T Consensus        25 inLkvv~qd~telfFkiKktT~f~klm~af~~rqGK~m~slRfL~dG~rI~~dqTP~dldmEdnd~iE   92 (103)
T COG5227          25 INLKVVDQDGTELFFKIKKTTTFKKLMDAFSRRQGKNMSSLRFLFDGKRIDLDQTPGDLDMEDNDEIE   92 (103)
T ss_pred             cceEEecCCCCEEEEEEeccchHHHHHHHHHHHhCcCcceeEEEEcceecCCCCChhhcCCccchHHH
Confidence            5566666678889999999998887765444             999999999999999999887654

>TIGR02958 sec_mycoba_snm4 secretion protein snm4

Probab=86.63  E-value=1.9  Score=33.02  Aligned_cols=57  Identities=7%  Similarity=0.107  Sum_probs=43.0

Q ss_pred             eeEEECCCCCEEEEeecCCCcHHHhhcccc--------------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           38 QIFVKTSTGKTITLEVESSDMIDNASRGSS--------------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        38 ~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~--------------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      ++.|...+ +...+-+..+..+.++-..|.                    -+|.+|+.++||++.+|.||+++++..+
T Consensus         4 RVtV~~~~-~~~DlaLPa~~PvaellP~ll~~~~~~~~~~~~~~~w~L~r~gG~pL~~~~sL~~~gV~DG~~L~L~p~   80 (452)
T TIGR02958         4 RVTVLAGR-RAVDVALPADVPVAELIPDLVDLLDDRGAAELGAVRWALARAGGSPLDPDASLAEAGVRDGELLVLVPA   80 (452)
T ss_pred             EEEEeeCC-eeeeeecCCCCcHHHHHHHHHHHhCcccccCCCCcceEEecCCCCCCCCCCCHHHcCCCCCCeEEEeeC
Confidence            45565543 345666667777777665554                    6788999999999999999999999754

Members of this family are the 12-transmembrane domain protein snm4, where snm stands for secretion in mycocbacteria. This system acts on Mycobacterium tuberculosis related pair of virulence factors ESAT-6 and CFP-10 and on other homologs. The system is conserved in many Actinobacteria, including the non-pathogenic Mycobacterium smegmatis.

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

Probab=85.72  E-value=0.61  Score=34.45  Aligned_cols=31  Identities=29%  Similarity=0.653  Sum_probs=28.0

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVA   31 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~   31 (97)
                      ||+++.+.||+|++|     +..+.+...|.+|.++
T Consensus        39 vp~D~L~viFaGKeLs~~ttv~~cDL~qqs~~hi~~   74 (446)
T KOG0006|consen   39 VPADQLRVIFAGKELSNDTTVQNCDLSQQSATHIML   74 (446)
T ss_pred             CChhheEEEEeccccccCceeecccccccchhhhhc
Confidence            699999999999999     8888888999999873

>PRK08364 sulfur carrier protein ThiS; Provisional

Probab=85.40  E-value=4.8  Score=22.62  Aligned_cols=51  Identities=10%  Similarity=0.084  Sum_probs=35.6

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc---------CCCeeCCCCCcccccccCCCCEEEEE
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS---------SPAGNFEDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~---------~~gk~L~d~~tL~~y~I~~~sti~l~   93 (97)
                      |+|.+... +....+++++..|++++-+.+.         .+|....     .++-+++|+.+.+.
T Consensus         5 m~v~vng~-~~~~~~~~~~~~tv~~ll~~l~~~~~~v~v~vNg~iv~-----~~~~l~~gD~Veii   64 (70)
T PRK08364          5 IRVKVIGR-GIEKEIEWRKGMKVADILRAVGFNTESAIAKVNGKVAL-----EDDPVKDGDYVEVI   64 (70)
T ss_pred             EEEEEecc-ccceEEEcCCCCcHHHHHHHcCCCCccEEEEECCEECC-----CCcCcCCCCEEEEE
Confidence            55666332 2356778888899999998776         5666664     35667889988875

>PRK06488 sulfur carrier protein ThiS; Validated

Probab=84.89  E-value=2.9  Score=23.02  Aligned_cols=51  Identities=14%  Similarity=0.244  Sum_probs=32.5

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc---------CCCeeCCCCCcccccccCCCCEEEEEE
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS---------SPAGNFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~---------~~gk~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      |+|.+   +|+.+.+  ++ .|+.+|.+.+.         .++..+.. ..-++.-+++|+.|.++-
T Consensus         1 m~i~~---Ng~~~~~--~~-~tl~~Ll~~l~~~~~~vavavN~~iv~~-~~~~~~~L~dgD~Ieiv~   60 (65)
T PRK06488          1 MKLFV---NGETLQT--EA-TTLALLLAELDYEGNWLATAVNGELVHK-EARAQFVLHEGDRIEILS   60 (65)
T ss_pred             CEEEE---CCeEEEc--Cc-CcHHHHHHHcCCCCCeEEEEECCEEcCH-HHcCccccCCCCEEEEEE
Confidence            44555   5677666  33 58998887766         44554432 233466788999988763

>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=83.04  E-value=3.1  Score=24.90  Aligned_cols=48  Identities=10%  Similarity=0.087  Sum_probs=33.1

Q ss_pred             EEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           48 TITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        48 ~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      .+...++-.+++..||..++             ....+|+++++|-+.|++-..++.+.+-
T Consensus         4 vI~q~mDI~epl~~Lk~lLe~Rl~~~L~~~~f~LQD~~L~~~k~L~dQcVqgeGlVQlnvQ   64 (88)
T PF11620_consen    4 VIMQHMDIREPLSTLKKLLERRLGISLSDYEFWLQDIQLEPHKSLVDQCVQGEGLVQLNVQ   64 (88)
T ss_dssp             EEEEEEESSSBGGGHHHHSHHHH-S--SS-EEEETTEE--TTSBTTTSS----SEEEEEEE
T ss_pred             eEEEEEecCCcHHHHHHHHHHhhCCCcCCCeEEeccceecCCccHHHhhccccCEEEEEEE
Confidence            34557778888999998887             3355699999999999998888888764

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.

>PF02824 TGS: TGS domain; InterPro: IPR004095 The TGS domain is present in a number of enzymes, for example, in threonyl-tRNA synthetase (ThrRS), GTPase, and guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (SpoT) []

Probab=81.67  E-value=4.1  Score=22.22  Aligned_cols=48  Identities=6%  Similarity=0.054  Sum_probs=33.0

Q ss_pred             eEEECCCCCEEEEeecCCCcHHHhhcccc-----------CCCeeCCCCCcccccccCCCCEEEEE
Q 042212           39 IFVKTSTGKTITLEVESSDMIDNASRGSS-----------SPAGNFEDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        39 i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-----------~~gk~L~d~~tL~~y~I~~~sti~l~   93 (97)
                      |.|.+++|+...  ++...|+.++=+.|.           .+|+..+-+     |-+++|+++.+.
T Consensus         1 I~v~lpdG~~~~--~~~g~T~~d~A~~I~~~l~~~~~~A~Vng~~vdl~-----~~L~~~d~v~ii   59 (60)
T PF02824_consen    1 IRVYLPDGSIKE--LPEGSTVLDVAYSIHSSLAKRAVAAKVNGQLVDLD-----HPLEDGDVVEII   59 (60)
T ss_dssp             EEEEETTSCEEE--EETTBBHHHHHHHHSHHHHHCEEEEEETTEEEETT-----SBB-SSEEEEEE
T ss_pred             CEEECCCCCeee--CCCCCCHHHHHHHHCHHHHhheeEEEEcCEECCCC-----CCcCCCCEEEEE
Confidence            345568888766  668889999988888           666655554     445677777664

The TGS domain is also present at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role []. ; PDB: 1WXQ_A 1NYR_B 1NYQ_B 2KMM_A 1WWT_A 1TKE_A 1TKG_A 1TJE_A 1QF6_A 1TKY_A ....

>PF11069 DUF2870: Protein of unknown function (DUF2870); InterPro: IPR021298 This is a eukaryotic family of proteins with unknown function

Probab=80.98  E-value=1.4  Score=26.95  Aligned_cols=29  Identities=21%  Similarity=0.368  Sum_probs=21.2

Q ss_pred             cCCCeeCCCCCcccccccCCCCEEEEEEee
Q 042212           67 SSPAGNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        67 ~~~gk~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      -|+||+|..+.+|++| +..+..-.+++++
T Consensus         5 W~aGK~l~~~k~l~dy-~GkNEKtKiivKl   33 (98)
T PF11069_consen    5 WWAGKELQRGKKLSDY-IGKNEKTKIIVKL   33 (98)
T ss_pred             EeccccccCCCcHHHh-cCCCcceeEEEEe
Confidence            3899999999999999 5444444555443

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

Probab=80.93  E-value=1.5  Score=33.66  Aligned_cols=33  Identities=18%  Similarity=0.316  Sum_probs=30.0

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARL   33 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~   33 (97)
                      +|++.|+++..|+.+     ...-+|++|.+++|+-..
T Consensus        39 V~PeRQKv~vKGg~a~dd~~~~al~iKpn~~lmMmGt~   76 (473)
T KOG1872|consen   39 VPPERQKVMVKGGLAKDDVDWGALQIKPNETLMMMGTA   76 (473)
T ss_pred             CCccceeEEEecccccccccccccccCCCCEEEeeccc
Confidence            589999999999999     888999999999998764

>PRK07440 hypothetical protein; Provisional

Probab=80.52  E-value=5.4  Score=22.56  Aligned_cols=52  Identities=13%  Similarity=0.120  Sum_probs=34.7

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc---------CCCeeCCCCCcccccccCCCCEEEEE
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS---------SPAGNFEDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~---------~~gk~L~d~~tL~~y~I~~~sti~l~   93 (97)
                      .|.|.+   +|+.  .++....||.+|-+.+.         .+|..+.-+ .-+++-+++|+.+.++
T Consensus         4 ~m~i~v---NG~~--~~~~~~~tl~~lL~~l~~~~~~vav~~N~~iv~r~-~w~~~~L~~gD~IEIv   64 (70)
T PRK07440          4 PITLQV---NGET--RTCSSGTSLPDLLQQLGFNPRLVAVEYNGEILHRQ-FWEQTQVQPGDRLEIV   64 (70)
T ss_pred             ceEEEE---CCEE--EEcCCCCCHHHHHHHcCCCCCeEEEEECCEEeCHH-HcCceecCCCCEEEEE
Confidence            467766   5665  45557788998877665         666666422 3455667888888775

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	97
2y5b_B	152	Structure Of Usp21 In Complex With Linear Diubiquit		3e-29
3b08_A	152	Crystal Structure Of The Mouse Hoil1-L-Nzf In Compl		6e-29
2zvn_A	154	Nemo Cozi Domain Incomplex With Diubiquitin In P212		6e-29
2w9n_A	152	Crystal Structure Of Linear Di-Ubiquitin Length = 1		6e-29
3u30_A	172	Crystal Structure Of A Linear-Specific Ubiquitin Fa		6e-29
3u5e_m	128	The Structure Of The Eukaryotic Ribosome At 3.0 A R		2e-15
3u5g_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		5e-15
1otr_B	76	Solution Structure Of A Cue-Ubiquitin Complex Lengt		5e-15
3olm_D	79	Structure And Function Of A Ubiquitin Binding Site		5e-15
4ii3_B	96	Crystal Structure Of S. Pombe Ubiquitin Activating		7e-15
4hcn_B	98	Crystal Structure Of Burkholderia Pseudomallei Effe		7e-15
1zw7_A	82	Elimination Of The C-Cap In Ubiquitin Structure, Dy		8e-15
3l0w_B	169	Structure Of Split Monoubiquitinated Pcna With Ubiq		1e-14
4ii2_B	83	Crystal Structure Of Ubiquitin Activating Enzyme 1		1e-14
2jwz_A	76	Mutations In The Hydrophobic Core Of Ubiquitin Diff		1e-14
2k25_A	103	Automated Nmr Structure Of The Ubb By Fapsy Length		2e-14
3jvz_X	81	E2~ubiquitin-Hect Length = 81		3e-14
3ai5_A	307	Crystal Structure Of Yeast Enhanced Green Fluoresce		3e-14
3ldz_F	73	Crystal Structure Of Human Stam1 Vhs Domain In Comp		4e-14
3rul_A	79	New Strategy To Analyze Structures Of Glycopeptide-		4e-14
2zcb_A	76	Crystal Structure Of Ubiquitin P37aP38A Length = 76		4e-14
2k6d_B	76	Cin85 Sh3-C Domain In Complex With Ubiquitin Length		4e-14
1xd3_B	75	Crystal Structure Of Uchl3-Ubvme Complex Length = 7		5e-14
1cmx_B	76	Structural Basis For The Specificity Of Ubiquitin C		5e-14
2xk5_B	76	Crystal Structure Of K6-Linked Diubiquitin Length =		5e-14
1yx5_B	98	Solution Structure Of S5a Uim-1UBIQUITIN COMPLEX Le		5e-14
4a18_K	129	T.Thermophila 60s Ribosomal Subunit In Complex With		5e-14
1aar_A	76	Structure Of A Diubiquitin Conjugate And A Model Fo		5e-14
1zgu_B	76	Solution Structure Of The Human Mms2-Ubiquitin Comp		5e-14
2znv_C	77	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		6e-14
3nob_A	78	Structure Of K11-Linked Di-Ubiquitin Length = 78		6e-14
4ap4_C	80	Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Le		6e-14
2ld9_A	77	Backbone Structure Of Ubiquitin Determined Using Ba		6e-14
2khw_B	79	Solution Structure Of The Human Polymerase Iota Ubm		7e-14
3k9o_B	96	The Crystal Structure Of E2-25k And Ubb+1 Complex L		8e-14
3dvg_X	80	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		8e-14
2kdi_A	114	Solution Structure Of A UbiquitinUIM FUSION PROTEIN		8e-14
3zf7_s	128	High-resolution Cryo-electron Microscopy Structure		8e-14
2o6v_D	76	Crystal Structure And Solution Nmr Studies Of Lys48		1e-13
2znv_B	76	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		1e-13
2o6v_B	76	Crystal Structure And Solution Nmr Studies Of Lys48		1e-13
3ons_A	72	Crystal Structure Of Human Ubiquitin In A New Cryst		1e-13
1yiw_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		1e-13
3vdz_A	111	Tailoring Encodable Lanthanide-Binding Tags As Mri		1e-13
3dvg_Y	79	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		1e-13
3v6e_B	91	Crystal Structure Of Usp2 And A Mutant Form Of Ubiq		2e-13
3u5c_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		2e-13
2fcs_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		2e-13
1yj1_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		3e-13
1s1q_B	76	Tsg101(Uev) Domain In Complex With Ubiquitin Length		3e-13
2gbr_A	81	Crystal Structure Of The 35-36 Moad Insertion Mutan		3e-13
2ojr_A	111	Structure Of Ubiquitin Solved By Sad Using The Lant		3e-13
3v6c_B	91	Crystal Structure Of Usp2 In Complex With Mutated U		4e-13
1ogw_A	76	Synthetic Ubiquitin With Fluoro-Leu At 50 And 67 Le		6e-13
3h7s_B	76	Crystal Structures Of K63-Linked Di- And Tri-Ubiqui		1e-12
4i6l_B	76	Crystal Structure Of Otub1 In Complex With Ubiquiti		2e-12
2gbm_A	84	Crystal Structure Of The 35-36 8 Glycine Insertion		2e-12
4gsw_A	80	Crystal Structure Of Ubiquitin From Entamoeba Histo		2e-12
3q3f_A	189	Engineering Domain-Swapped Binding Interfaces By Mu		2e-12
1ud7_A	76	Solution Structure Of The Designed Hydrophobic Core		4e-12
2gbk_A	83	Crystal Structure Of The 9-10 Moad Insertion Mutant		5e-12
1c3t_A	76	Rotamer Strain As A Determinant Of Protein Structur		1e-11
4hjk_A	77	U7ub7 Disulfide Variant Length = 77		2e-11
1sif_A	88	Crystal Structure Of A Multiple Hydrophobic Core Mu		2e-11
2gbj_A	84	Crystal Structure Of The 9-10 8 Glycine Insertion M		7e-11
4hk2_A	78	U7ub25.2540 Length = 78		2e-10
2jvc_A	82	Nmr Solution Structure Of Ubiquitin Like Protein Le		9e-10
3mtn_B	85	Usp21 In Complex With A Ubiquitin-based, Usp21-spec		4e-09
1gjz_A	53	Solution Structure Of A Dimeric N-Terminal Fragment		5e-06
3n3k_B	85	The Catalytic Domain Of Usp8 In Complex With A Usp8		8e-05
1bt0_A	76	Structure Of Ubiquitin-Like Protein, Rub1 Length =		3e-04
3dbh_I	88	Structural Dissection Of A Gating Mechanism Prevent		8e-04

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

Iteration: 1
 Score =  122 bits (307), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 68/114 (59%), Positives = 74/114 (64%), Gaps = 18/114 (15%)
Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P +QQRL+FA K L     L+DYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVE 
Sbjct: 36  IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGHMQIFVKTLTGKTITLEVEP 95
Query: 56  SDMIDNASRGSSSPAG-------------NFEDGWTQADYNIQKESTLHFVLRL 96
           SD I+N         G               EDG T +DYNIQKESTLH VLRL
Sbjct: 96  SDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL 149

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

Iteration: 1
 Score =  122 bits (305), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 68/114 (59%), Positives = 74/114 (64%), Gaps = 18/114 (15%)
Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P +QQRL+FA K L     L+DYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVE 
Sbjct: 36  IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEP 95
Query: 56  SDMIDNASRGSSSPAG-------------NFEDGWTQADYNIQKESTLHFVLRL 96
           SD I+N         G               EDG T +DYNIQKESTLH VLRL
Sbjct: 96  SDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL 149

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

Iteration: 1
 Score =  122 bits (305), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 68/114 (59%), Positives = 74/114 (64%), Gaps = 18/114 (15%)
Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P +QQRL+FA K L     L+DYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVE 
Sbjct: 38  IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEP 97
Query: 56  SDMIDNASRGSSSPAG-------------NFEDGWTQADYNIQKESTLHFVLRL 96
           SD I+N         G               EDG T +DYNIQKESTLH VLRL
Sbjct: 98  SDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL 151

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

Iteration: 1
 Score =  122 bits (305), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 68/114 (59%), Positives = 74/114 (64%), Gaps = 18/114 (15%)
Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P +QQRL+FA K L     L+DYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVE 
Sbjct: 36  IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEP 95
Query: 56  SDMIDNASRGSSSPAG-------------NFEDGWTQADYNIQKESTLHFVLRL 96
           SD I+N         G               EDG T +DYNIQKESTLH VLRL
Sbjct: 96  SDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL 149

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

Iteration: 1
 Score =  122 bits (305), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 68/114 (59%), Positives = 74/114 (64%), Gaps = 18/114 (15%)
Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P +QQRL+FA K L     L+DYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVE 
Sbjct: 56  IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEP 115
Query: 56  SDMIDNASRGSSSPAG-------------NFEDGWTQADYNIQKESTLHFVLRL 96
           SD I+N         G               EDG T +DYNIQKESTLH VLRL
Sbjct: 116 SDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL 169

>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 = 77.4 bits (189), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 43/73 (58%), Positives = 44/73 (60%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVESSD IDN         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

>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 = 75.9 bits (185), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 43/73 (58%), Positives = 44/73 (60%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVESSD IDN         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

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

Iteration: 1
 Score = 75.9 bits (185), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 43/73 (58%), Positives = 44/73 (60%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVESSD IDN         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

>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 = 75.9 bits (185), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 43/73 (58%), Positives = 44/73 (60%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVESSD IDN         G               EDG T +DYN
Sbjct: 4  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 63
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 64 IQKESTLHLVLRL 76

>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 = 75.5 bits (184), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 43/73 (58%), Positives = 44/73 (60%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVESSD IDN         G               EDG T +DYN
Sbjct: 21 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 80
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 81 IQKESTLHLVLRL 93

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

Iteration: 1
 Score = 75.5 bits (184), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 45/78 (57%), Positives = 47/78 (60%), Gaps = 14/78 (17%)
Query: 33 LRGR-MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWT 78
           +GR MQIFVKT TGKTITLEVESSD IDN         G               EDG T
Sbjct: 18 FQGRPMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRT 77
Query: 79 QADYNIQKESTLHFVLRL 96
           +DYNIQKESTLH VLRL
Sbjct: 78 LSDYNIQKESTLHLVLRL 95

>pdb|1ZW7|A Chain A, Elimination Of The C-Cap In Ubiquitin Structure, Dynamics And Thermodynamic Consequences Length = 82

Iteration: 1
 Score = 75.5 bits (184), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 45/73 (61%), Positives = 49/73 (67%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNA-SRGSSSP-----------AGN-FEDGWTQADYN 83
          MQIFVKT TG TITLEVESSD IDN  S+  ++P           AG   EDG T +DYN
Sbjct: 1  MQIFVKTLTGATITLEVESSDTIDNVKSKIQAAPGIPPDQQELIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

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

Iteration: 1
 Score = 75.1 bits (183), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 43/73 (58%), Positives = 44/73 (60%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVESSD IDN         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

>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 = 74.7 bits (182), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 44/73 (60%), Positives = 47/73 (64%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNA-----SRGSSSP-------AG-NFEDGWTQADYN 83
          MQIFV+T TG+TITLEVESSD IDN       R    P       AG   EDG T ADYN
Sbjct: 8  MQIFVRTLTGRTITLEVESSDTIDNVRARIQDREGIPPDQQRLIFAGRQLEDGRTLADYN 67
Query: 84 IQKESTLHFVLRL 96
          IQ+ESTLH VLRL
Sbjct: 68 IQRESTLHLVLRL 80

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

Iteration: 1
 Score = 74.3 bits (181), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 43/73 (58%), Positives = 44/73 (60%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVESSD IDN         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHSVLRL 73

>pdb|2K25|A Chain A, Automated Nmr Structure Of The Ubb By Fapsy Length = 103

Iteration: 1
 Score = 73.9 bits (180), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 42/76 (55%), Positives = 45/76 (59%), Gaps = 13/76 (17%)
Query: 34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQA 80
          RG MQIFVKT TGKTITLEVE SD I+N         G               EDG T +
Sbjct: 6  RGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLS 65
Query: 81 DYNIQKESTLHFVLRL 96
          +YNIQKESTLH VLRL
Sbjct: 66 EYNIQKESTLHLVLRL 81

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

Iteration: 1
 Score = 73.6 bits (179), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 42/75 (56%), Positives = 44/75 (58%), Gaps = 13/75 (17%)
Query: 35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQAD 81
          G MQIFVKT TGKTITLEVE SD I+N         G               EDG T +D
Sbjct: 4  GSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSD 63
Query: 82 YNIQKESTLHFVLRL 96
          YNIQKESTLH VLRL
Sbjct: 64 YNIQKESTLHLVLRL 78

>pdb|3AI5|A Chain A, Crystal Structure Of Yeast Enhanced Green Fluorescent Protein- Ubiquitin Fusion Protein Length = 307

Iteration: 1
 Score = 73.2 bits (178), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 43/79 (54%), Positives = 46/79 (58%), Gaps = 13/79 (16%)
Query: 31  ARLRGRMQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGW 77
           A + G MQIFVKT TGKTITLEVE SD I+N         G               EDG 
Sbjct: 228 AGITGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGR 287
Query: 78  TQADYNIQKESTLHFVLRL 96
           T +DYNIQKESTLH VLRL
Sbjct: 288 TLSDYNIQKESTLHLVLRL 306

>pdb|3LDZ|F Chain F, Crystal Structure Of Human Stam1 Vhs Domain In Complex With Ubiquitin Length = 73

Iteration: 1
 Score = 73.2 bits (178), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 41/73 (56%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

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

Iteration: 1
 Score = 72.8 bits (177), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 41/73 (56%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

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

Iteration: 1
 Score = 72.8 bits (177), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 41/73 (56%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIAADQQRLIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

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

Iteration: 1
 Score = 72.8 bits (177), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 41/73 (56%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

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

Iteration: 1
 Score = 72.8 bits (177), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 41/73 (56%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

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

Iteration: 1
 Score = 72.8 bits (177), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 41/73 (56%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

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

Iteration: 1
 Score = 72.8 bits (177), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 41/73 (56%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPQQQRLIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

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

Iteration: 1
 Score = 72.8 bits (177), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 41/73 (56%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

>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 = 72.8 bits (177), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 40/73 (54%), Positives = 44/73 (60%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITL+VE+SD I+N         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLDVEASDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

>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 = 72.8 bits (177), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 41/73 (56%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

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

Iteration: 1
 Score = 72.4 bits (176), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 41/73 (56%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGRQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

>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 = 72.4 bits (176), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 41/73 (56%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

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

Iteration: 1
 Score = 72.4 bits (176), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 41/73 (56%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 3  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 62
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 63 IQKESTLHLVLRL 75

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

Iteration: 1
 Score = 72.4 bits (176), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 41/73 (56%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 5  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 64
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 65 IQKESTLHLVLRL 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 = 72.4 bits (176), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 41/73 (56%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 2  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 61
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 62 IQKESTLHLVLRL 74

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

Iteration: 1
 Score = 72.4 bits (176), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 41/73 (56%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 63
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 64 IQKESTLHLVLRL 76

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

Iteration: 1
 Score = 72.0 bits (175), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 41/73 (56%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 2  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 61
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 62 IQKESTLHLVLRL 74

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

Iteration: 1
 Score = 72.0 bits (175), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 41/73 (56%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 63
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 64 IQKESTLHLVLRL 76

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

Iteration: 1
 Score = 72.0 bits (175), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 41/75 (54%), Positives = 43/75 (57%), Gaps = 13/75 (17%)
Query: 35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQAD 81
          G  QIF KT TGKTITLEVESSD IDN         G               EDG T +D
Sbjct: 8  GEFQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLEDGRTLSD 67
Query: 82 YNIQKESTLHFVLRL 96
          YNIQ+ESTLH VLRL
Sbjct: 68 YNIQRESTLHLVLRL 82

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

Iteration: 1
 Score = 72.0 bits (175), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 40/73 (54%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTI LEVE+SD I+N         G               E+G T ADYN
Sbjct: 1  MQIFVKTLTGKTIALEVEASDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEEGRTLADYN 60
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

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

Iteration: 1
 Score = 71.6 bits (174), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 40/73 (54%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGRQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQ+ESTLH VLRL
Sbjct: 61 IQRESTLHLVLRL 73

>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 = 71.6 bits (174), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 40/73 (54%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQ+ESTLH VLRL
Sbjct: 61 IQRESTLHLVLRL 73

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

Iteration: 1
 Score = 71.2 bits (173), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 40/73 (54%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGXQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQ+ESTLH VLRL
Sbjct: 61 IQRESTLHLVLRL 73

>pdb|3ONS|A Chain A, Crystal Structure Of Human Ubiquitin In A New Crystal Form Length = 72

Iteration: 1
 Score = 71.2 bits (173), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 40/72 (55%), Positives = 42/72 (58%), Gaps = 13/72 (18%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLR 95
          IQKESTLH VLR
Sbjct: 61 IQKESTLHLVLR 72

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

Iteration: 1
 Score = 71.2 bits (173), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 40/73 (54%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          +QIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 1  LQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

>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 = 71.2 bits (173), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 41/73 (56%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37  MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
           MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 36  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 95
Query: 84  IQKESTLHFVLRL 96
           IQKESTLH VLRL
Sbjct: 96  IQKESTLHLVLRL 108

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

Iteration: 1
 Score = 71.2 bits (173), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 40/73 (54%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 63
Query: 84 IQKESTLHFVLRL 96
          IQ+ESTLH VLRL
Sbjct: 64 IQRESTLHLVLRL 76

>pdb|3V6E|B Chain B, Crystal Structure Of Usp2 And A Mutant Form Of Ubiquitin Length = 91

Iteration: 1
 Score = 70.5 bits (171), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 40/76 (52%), Positives = 43/76 (56%), Gaps = 13/76 (17%)
Query: 34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQA 80
          RG MQIFV T +GK ITLEVE SD I+N         G               EDG T +
Sbjct: 15 RGSMQIFVNTLSGKHITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLS 74
Query: 81 DYNIQKESTLHFVLRL 96
          DYNIQKESTLH VLRL
Sbjct: 75 DYNIQKESTLHLVLRL 90

>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 = 70.5 bits (171), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 40/70 (57%), Positives = 41/70 (58%), Gaps = 13/70 (18%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVESSD IDN         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFV 93
          IQKESTLH V
Sbjct: 61 IQKESTLHLV 70

>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 = 70.5 bits (171), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 42/73 (57%), Positives = 46/73 (63%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNAS-----RGSSSP-------AGN-FEDGWTQADYN 83
          +QIFVKT TGKTITLEVE SD I+N       +    P       AG   EDG T +DYN
Sbjct: 1  LQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEQIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

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

Iteration: 1
 Score = 70.5 bits (171), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 42/73 (57%), Positives = 46/73 (63%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNAS-----RGSSSP-------AGN-FEDGWTQADYN 83
          +QIFVKT TGKTITLEVE SD I+N       +    P       AG   EDG T +DYN
Sbjct: 1  LQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEXIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

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

Iteration: 1
 Score = 70.1 bits (170), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 40/72 (55%), Positives = 42/72 (58%), Gaps = 13/72 (18%)
Query: 38 QIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYNI 84
          QIFVKT TGKTITLEVE SD I+N         G               EDG T +DYNI
Sbjct: 2  QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNI 61
Query: 85 QKESTLHFVLRL 96
          QKESTLH VLRL
Sbjct: 62 QKESTLHLVLRL 73

>pdb|2GBR|A Chain A, Crystal Structure Of The 35-36 Moad Insertion Mutant Of Ubiquitin Length = 81

Iteration: 1
 Score = 70.1 bits (170), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 41/78 (52%), Positives = 44/78 (56%), Gaps = 18/78 (23%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAGNF------------------EDGWT 78
          MQIFVKT TGKTITLEVE SD I+N         G +                  EDG T
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGRWALAIPPDQQRLIFAGKQLEDGRT 60
Query: 79 QADYNIQKESTLHFVLRL 96
           +DYNIQKESTLH VLRL
Sbjct: 61 LSDYNIQKESTLHLVLRL 78

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

Iteration: 1
 Score = 70.1 bits (170), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 41/73 (56%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37  MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
           MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 36  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 95
Query: 84  IQKESTLHFVLRL 96
           IQKESTLH VLRL
Sbjct: 96  IQKESTLHLVLRL 108

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

Iteration: 1
 Score = 69.7 bits (169), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 40/76 (52%), Positives = 42/76 (55%), Gaps = 13/76 (17%)
Query: 34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQA 80
          RG MQIFV T TG  ITLEVE SD I+N         G               EDG T +
Sbjct: 15 RGSMQIFVNTLTGTHITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLS 74
Query: 81 DYNIQKESTLHFVLRL 96
          DYNIQKESTLH VLRL
Sbjct: 75 DYNIQKESTLHLVLRL 90

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

Iteration: 1
 Score = 69.3 bits (168), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 40/73 (54%), Positives = 42/73 (57%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQXEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQKEST H VLRL
Sbjct: 61 IQKESTXHLVLRL 73

>pdb|4I6L|B Chain B, Crystal Structure Of Otub1 In Complex With Ubiquitin Variant Length = 76

Iteration: 1
 Score = 67.8 bits (164), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 39/75 (52%), Positives = 42/75 (56%), Gaps = 13/75 (17%)
Query: 35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQAD 81
          G MQIFVKT TGKTITLEVE SD I+N         G               EDG T +D
Sbjct: 1  GSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQKLLFARKQLEDGRTLSD 60
Query: 82 YNIQKESTLHFVLRL 96
          YNI KES L+ VLRL
Sbjct: 61 YNIHKESFLYLVLRL 75

>pdb|2GBM|A Chain A, Crystal Structure Of The 35-36 8 Glycine Insertion Mutant Of Ubiquitin Length = 84

Iteration: 1
 Score = 67.8 bits (164), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 42/81 (51%), Positives = 44/81 (54%), Gaps = 21/81 (25%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSP--------------------AGN-FED 75
          MQIFVKT TGKTITLEVE SD I+N                            AG   ED
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGGGGGGGGGIPPDQQRLIFAGKQLED 60
Query: 76 GWTQADYNIQKESTLHFVLRL 96
          G T +DYNIQKESTLH VLRL
Sbjct: 61 GRTLSDYNIQKESTLHLVLRL 81

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

Iteration: 1
 Score = 67.4 bits (163), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 39/73 (53%), Positives = 42/73 (57%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE +D ID          G               E+G T +DYN
Sbjct: 4  MQIFVKTLTGKTITLEVEPNDSIDAIKAKIQEKEGIPPDQQRLIFAGKQLEEGKTLSDYN 63
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 64 IQKESTLHLVLRL 76

>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 = 40/72 (55%), Positives = 42/72 (58%), Gaps = 13/72 (18%)
Query: 38  QIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYNI 84
           QIFVKT TGKTITLEVE SD I+N         G               EDG T +DYNI
Sbjct: 107 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNI 166
Query: 85  QKESTLHFVLRL 96
           QKESTLH VLRL
Sbjct: 167 QKESTLHLVLRL 178

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

Iteration: 1
 Score = 66.2 bits (160), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 35/73 (47%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQ+F+KT TGKT+T+EVE SD ++N         G               EDG T +DYN
Sbjct: 1  MQVFLKTLTGKTVTIEVEPSDTVENFKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          IQKEST+H VLRL
Sbjct: 61 IQKESTIHLVLRL 73

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

Iteration: 1
 Score = 65.9 bits (159), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 41/80 (51%), Positives = 43/80 (53%), Gaps = 20/80 (25%)
Query: 37 MQIFVKTST-------GKTITLEVESSDMIDNASRGSSSPAG-------------NFEDG 76
          MQIFVKT T       GKTITLEVE SD I+N         G               EDG
Sbjct: 1  MQIFVKTLTQVRELVGGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDG 60
Query: 77 WTQADYNIQKESTLHFVLRL 96
           T +DYNIQKESTLH VLRL
Sbjct: 61 RTLSDYNIQKESTLHLVLRL 80

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

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 34/73 (46%), Positives = 43/73 (58%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQ+FVKT TGKT+T+E+E SD ++N         G               EDG T +DYN
Sbjct: 1  MQLFVKTLTGKTLTVELEPSDTVENLKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 84 IQKESTLHFVLRL 96
          +QKEST+H VLRL
Sbjct: 61 LQKESTIHLVLRL 73

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 38/73 (52%), Positives = 40/73 (54%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVK  TGKT TLEVE SD I+N         G               EDG T +DYN
Sbjct: 2  MQIFVKCLTGKTNTLEVEPSDTIENVKAKIQDKIGYPPDQQRLIFAGKQLEDGRTLSDYN 61
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH V RL
Sbjct: 62 IQKESTLHCVRRL 74

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

Iteration: 1
 Score = 63.9 bits (154), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 35/73 (47%), Positives = 42/73 (57%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          +Q+F+KT TGKT T+E+E SD I+N         G               EDG T +DYN
Sbjct: 10 LQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 69
Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 70 IQKESTLHLVLRL 82

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

Iteration: 1
 Score = 62.4 bits (150), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 41/81 (50%), Positives = 43/81 (53%), Gaps = 21/81 (25%)
Query: 37 MQIFVKTSTG--------KTITLEVESSDMIDNASRGSSSPAG-------------NFED 75
          MQIFVKT TG        KTITLEVE SD I+N         G               ED
Sbjct: 1  MQIFVKTLTGGGGGGGGGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLED 60
Query: 76 GWTQADYNIQKESTLHFVLRL 96
          G T +DYNIQKESTLH VLRL
Sbjct: 61 GRTLSDYNIQKESTLHLVLRL 81

>pdb|4HK2|A Chain A, U7ub25.2540 Length = 78

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 38/75 (50%), Positives = 40/75 (53%), Gaps = 13/75 (17%)
Query: 35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQAD 81
          G MQIFVK  TGKT TLEVE SD I+N         G               EDG T +D
Sbjct: 1  GSMQIFVKFRTGKTYTLEVEPSDTIENVKAKIQDKLGIPPDQQWLIFAGKRLEDGRTLSD 60
Query: 82 YNIQKESTLHFVLRL 96
          YNIQKESTL  V RL
Sbjct: 61 YNIQKESTLRGVRRL 75

>pdb|2JVC|A Chain A, Nmr Solution Structure Of Ubiquitin Like Protein Length = 82

Iteration: 1
 Score = 58.5 bits (140), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 33/75 (44%), Positives = 40/75 (53%), Gaps = 13/75 (17%)
Query: 35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQAD 81
          G MQIFVKT TGKTIT++V+ +D +           G               ED    +D
Sbjct: 4  GSMQIFVKTLTGKTITIDVDHADTVGAVKAKIYDKEGIPPDQQRLIFGGKQLEDSNAMSD 63
Query: 82 YNIQKESTLHFVLRL 96
          YN+QKESTLH VLRL
Sbjct: 64 YNVQKESTLHLVLRL 78

>pdb|3MTN|B Chain B, Usp21 In Complex With A Ubiquitin-based, Usp21-specific Inhibitor Length = 85

Iteration: 1
 Score = 56.6 bits (135), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 35/67 (52%), Positives = 37/67 (55%), Gaps = 13/67 (19%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 63
Query: 84 IQKESTL 90
          IQK STL
Sbjct: 64 IQKWSTL 70

>pdb|1GJZ|A Chain A, Solution Structure Of A Dimeric N-Terminal Fragment Of Human Ubiquitin Length = 53

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 22/28 (78%), Positives = 23/28 (82%)
Query: 35 GRMQIFVKTSTGKTITLEVESSDMIDNA 62
          G MQIFVKT TGKTITLEVE SD I+N 
Sbjct: 1  GSMQIFVKTLTGKTITLEVEPSDTIENV 28

>pdb|3N3K|B Chain B, The Catalytic Domain Of Usp8 In Complex With A Usp8 Specific Inhibitor Length = 85

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 26/65 (40%), Positives = 30/65 (46%), Gaps = 13/65 (20%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          M+I VKT  G+TI LEVE SD I+N         G               EDG T +DYN
Sbjct: 4  MRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 63
Query: 84 IQKES 88
          I   S
Sbjct: 64 IHNHS 68

>pdb|1BT0|A Chain A, Structure Of Ubiquitin-Like Protein, Rub1 Length = 76

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 31/73 (42%), Gaps = 13/73 (17%)
Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          M I VKT TGK I +++E +D ID          G                D  T  DYN
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLIYAGKQLADDKTAKDYN 60
Query: 84 IQKESTLHFVLRL 96
          I+  S LH VL L
Sbjct: 61 IEGGSVLHLVLAL 73

>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 = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 32/75 (42%), Gaps = 13/75 (17%)
Query: 35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQAD 81
          G M I VKT TGK I +++E +D ++          G                D  T AD
Sbjct: 11 GSMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAAD 70
Query: 82 YNIQKESTLHFVLRL 96
          Y I   S LH VLRL
Sbjct: 71 YKILGGSVLHLVLRL 85

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	97
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	4e-24
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	4e-13
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	3e-23
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	6e-18
3u5c_F	225	RP14, S2, YS8, 40S ribosomal protein S5; translati	5e-23
3u5c_F	225	RP14, S2, YS8, 40S ribosomal protein S5; translati	3e-14
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	2e-22
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	1e-14
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	2e-22
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	2e-14
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	2e-22
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	3e-12
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	3e-22
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	9e-16
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	4e-22
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	5e-14
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	5e-22
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	1e-11
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	5e-22
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	2e-12
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	6e-22
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	2e-13
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	8e-22
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	9e-14
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	1e-21
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	5e-13
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	1e-21
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	7e-14
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	2e-21
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	7e-14
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	2e-21
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	4e-11
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	2e-21
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	2e-13
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	2e-21
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	1e-13
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	3e-21
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	2e-15
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	5e-12
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	3e-21
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	9e-17
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	4e-21
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	8e-16
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	7e-12
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	1e-20
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	3e-14
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	5e-13
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	1e-19
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	1e-12
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	2e-18
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	5e-12
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	3e-18
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	2e-17
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	4e-04
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	3e-18
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	3e-10
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	4e-18
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	2e-15
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	7e-18
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	2e-09
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	2e-17
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	2e-14
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	6e-17
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	7e-09
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	8e-17
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	5e-06
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	1e-16
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	4e-09
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	2e-16
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	2e-09
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	4e-16
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	9e-13
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	3e-15
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	3e-11
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	5e-15
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	2e-11
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	2e-14
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	3e-13
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	2e-14
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	7e-13
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	6e-14
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	3e-07
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	9e-14
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	3e-13
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	3e-13
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	7e-11
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	3e-13
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	7e-12
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	5e-13
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	3e-09
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	7e-13
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	1e-10
1we6_A	111	Splicing factor, putative; structural genomics, ub	2e-12
1we6_A	111	Splicing factor, putative; structural genomics, ub	2e-08
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	6e-09
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	6e-04
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	1e-05
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	6e-05
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	2e-04
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	2e-04

>1sif_A Ubiquitin; hydrophobic mutants, folding, stability, structural protein; 2.18A {Homo sapiens} SCOP: d.15.1.1 Length = 88

 Score = 86.3 bits (214), Expect = 4e-24
 Identities = 36/82 (43%), Positives = 43/82 (52%), Gaps = 13/82 (15%)

Query: 28 HLVARLRGRMQIFVKTSTGKTITLEVESSDMIDNA----SRGSSSPAG---------NFE 74
          H        +Q+F+KT TGKT T+E+E SD I+N           P             E
Sbjct: 1  HHHHHHLQGLQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEGIPPDQQRLIFAGKQLE 60

Query: 75 DGWTQADYNIQKESTLHFVLRL 96
          DG T +DYNIQKESTLH VLRL
Sbjct: 61 DGRTLSDYNIQKESTLHLVLRL 82

>1sif_A Ubiquitin; hydrophobic mutants, folding, stability, structural protein; 2.18A {Homo sapiens} SCOP: d.15.1.1 Length = 88

 Score = 58.5 bits (142), Expect = 4e-13
 Identities = 27/40 (67%), Positives = 31/40 (77%), Gaps = 5/40 (12%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG 35
          +P +QQRL+FA K L     L+DYNIQKESTLHLV RLRG
Sbjct: 45 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG 84

>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion protein; ubiquitin interacting motif, UIM, protein domain interface; NMR {Saccharomyces cerevisiae} Length = 114

 Score = 84.9 bits (210), Expect = 3e-23
 Identities = 41/78 (52%), Positives = 43/78 (55%), Gaps = 13/78 (16%)

Query: 32 RLRGRMQIFVKTSTGKTITLEVESSDMIDNA----SRGSSSPAG---------NFEDGWT 78
             G  QIF KT TGKTITLEVESSD IDN           P             EDG T
Sbjct: 5  HHHGEFQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLEDGRT 64

Query: 79 QADYNIQKESTLHFVLRL 96
           +DYNIQ+ESTLH VLRL
Sbjct: 65 LSDYNIQRESTLHLVLRL 82

>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion protein; ubiquitin interacting motif, UIM, protein domain interface; NMR {Saccharomyces cerevisiae} Length = 114

 Score = 71.4 bits (175), Expect = 6e-18
 Identities = 29/65 (44%), Positives = 38/65 (58%), Gaps = 8/65 (12%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRM---QIFVKTSTGKTITLE 52
           +P +QQRL++A K L     L+DYNIQ+ESTLHLV RLRG         +    K I L 
Sbjct: 45  IPPDQQRLIWAGKQLEDGRTLSDYNIQRESTLHLVLRLRGGSMGGAADEEELIRKAIELS 104

Query: 53  VESSD 57
           ++ S 
Sbjct: 105 LKESR 109

>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 = 85.6 bits (212), Expect = 5e-23
 Identities = 5/73 (6%), Positives = 12/73 (16%), Gaps = 13/73 (17%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDN-----ASRGSSSP-------AGN-FEDGWTQADYN 83
          M         +     VE    +            +               +    +  +
Sbjct: 1  MSDTEAPVEVQEDFEVVEEFTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVD 60

Query: 84 IQKESTLHFVLRL 96
            +     FV   
Sbjct: 61 YVQVRQPIFVAHT 73

>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 = 5/43 (11%), Positives = 9/43 (20%), Gaps = 5/43 (11%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQ 38
             E +               +  +  +      VA   GR  
Sbjct: 36 AQTEIKLFNKWSFEEVEVKDASLVDYVQVRQPIFVAHTAGRYA 78

>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 = 81.9 bits (203), Expect = 2e-22
 Identities = 25/73 (34%), Positives = 33/73 (45%), Gaps = 13/73 (17%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDN-----ASRGSSSP-------AGN-FEDGWTQADYN 83
          M I VKT TGK I +++E +D ++        +    P       +G    D  T ADY 
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK 60

Query: 84 IQKESTLHFVLRL 96
          I   S LH VL L
Sbjct: 61 ILGGSVLHLVLAL 73

>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 = 61.9 bits (151), Expect = 1e-14
 Identities = 18/40 (45%), Positives = 24/40 (60%), Gaps = 5/40 (12%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG 35
          +P +QQRL+++ K +      ADY I   S LHLV  LRG
Sbjct: 36 IPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRG 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 = 81.6 bits (202), Expect = 2e-22
 Identities = 15/73 (20%), Positives = 30/73 (41%), Gaps = 13/73 (17%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDN-----ASRGSSSP-------AGNF-EDGWTQADYN 83
          M +FV+ ++     +EV+S   I       A +            AG    +  T  + +
Sbjct: 1  MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKQQGVPADQLRVIFAGKELPNHLTVQNCD 60

Query: 84 IQKESTLHFVLRL 96
          ++++S +H V R 
Sbjct: 61 LEQQSIVHIVQRP 73

>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 = 61.2 bits (149), Expect = 2e-14
 Identities = 13/41 (31%), Positives = 26/41 (63%), Gaps = 5/41 (12%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR 36
          +P +Q R++FA K L     + + +++++S +H+V R R R
Sbjct: 36 VPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRRR 76

>2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing, protein binding; 2.60A {Homo sapiens} Length = 111

 Score = 82.6 bits (204), Expect = 2e-22
 Identities = 44/101 (43%), Positives = 49/101 (48%), Gaps = 14/101 (13%)

Query: 10  FADKSLLAD-YNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVESSDMIDN----ASR 64
             D  +  D   I   +   +       MQIFVKT TGKTITLEVE SD I+N       
Sbjct: 8   NNDGWIEGDELYIDTNNDGWIEGDELLAMQIFVKTLTGKTITLEVEPSDTIENVKAKIQD 67

Query: 65  GSSSPAGN---------FEDGWTQADYNIQKESTLHFVLRL 96
               P             EDG T +DYNIQKESTLH VLRL
Sbjct: 68  KEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL 108

>2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing, protein binding; 2.60A {Homo sapiens} Length = 111

 Score = 56.8 bits (137), Expect = 3e-12
 Identities = 27/40 (67%), Positives = 31/40 (77%), Gaps = 5/40 (12%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG 35
           +P +QQRL+FA K L     L+DYNIQKESTLHLV RLRG
Sbjct: 71  IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG 110

>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 = 81.6 bits (202), Expect = 3e-22
 Identities = 25/73 (34%), Positives = 33/73 (45%), Gaps = 13/73 (17%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDN-----ASRGSSSP-------AGN-FEDGWTQADYN 83
          M I VKT TGK I +++E +D ++        +    P       +G    D  T ADY 
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK 60

Query: 84 IQKESTLHFVLRL 96
          I   S LH VL L
Sbjct: 61 ILGGSVLHLVLAL 73

>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 = 65.1 bits (159), Expect = 9e-16
 Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 5/52 (9%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGK 47
          +P +QQRL+++ K +      ADY I   S LHLV  LRG   +  K     
Sbjct: 36 IPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGGGGLRQKHHHHH 87

>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 = 81.3 bits (201), Expect = 4e-22
 Identities = 26/76 (34%), Positives = 33/76 (43%), Gaps = 13/76 (17%)

Query: 34 RGRMQIFVKTSTGKTITLEVESSDMIDN-----ASRGSSSPA--------GNFEDGWTQA 80
           G M I VKT TGK I +++E +D ++        +    P             D  T A
Sbjct: 10 GGSMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAA 69

Query: 81 DYNIQKESTLHFVLRL 96
          DY I   S LH VLRL
Sbjct: 70 DYKILGGSVLHLVLRL 85

>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 = 60.9 bits (148), Expect = 5e-14
 Identities = 19/40 (47%), Positives = 25/40 (62%), Gaps = 5/40 (12%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG 35
          +P +QQRL+++ K +      ADY I   S LHLV RLRG
Sbjct: 48 IPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLRLRG 87

>3phx_B Ubiquitin-like protein ISG15; OTU domain, DE-ubiquitinase, DE-isgylase, hydrolase-protein complex; 1.60A {Homo sapiens} Length = 79

 Score = 80.9 bits (200), Expect = 5e-22
 Identities = 15/73 (20%), Positives = 28/73 (38%), Gaps = 13/73 (17%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDN-----ASRGSSSP-------AGNF-EDGWTQADYN 83
          + I V+ + G++ T EV  +  + +     +               G   ED     +Y 
Sbjct: 5  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 64

Query: 84 IQKESTLHFVLRL 96
          ++  ST+   LRL
Sbjct: 65 LKPLSTVFMNLRL 77

>3phx_B Ubiquitin-like protein ISG15; OTU domain, DE-ubiquitinase, DE-isgylase, hydrolase-protein complex; 1.60A {Homo sapiens} Length = 79

 Score = 54.3 bits (131), Expect = 1e-11
 Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 5/37 (13%)

Query: 4  EQQRLVFADKSL-----LADYNIQKESTLHLVARLRG 35
          +   L F  K L     L +Y ++  ST+ +  RLRG
Sbjct: 43 DLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRG 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 = 80.8 bits (200), Expect = 5e-22
 Identities = 16/73 (21%), Positives = 31/73 (42%), Gaps = 13/73 (17%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDN-----ASRGSSSP-------AG-NFEDGWTQADYN 83
          MQ+ VK   G+  +L+V   +++       + + +           G    DG   +DY+
Sbjct: 8  MQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLNVPVRQQRLLFKGKALADGKRLSDYS 67

Query: 84 IQKESTLHFVLRL 96
          I   S L+ V++ 
Sbjct: 68 IGPNSKLNLVVKP 80

>2dzi_A Ubiquitin-like protein 4A; GDX, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 81

 Score = 56.2 bits (136), Expect = 2e-12
 Identities = 16/38 (42%), Positives = 24/38 (63%), Gaps = 5/38 (13%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARL 33
          +P+ QQRL+F  K+L     L+DY+I   S L+LV + 
Sbjct: 43 VPVRQQRLLFKGKALADGKRLSDYSIGPNSKLNLVVKP 80

>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 = 80.9 bits (200), Expect = 6e-22
 Identities = 13/75 (17%), Positives = 21/75 (28%), Gaps = 13/75 (17%)

Query: 35 GRMQIFVKTSTGKTITLEVESSDMIDN-----ASRGSSSP-------AGNF-EDGWTQAD 81
            +Q+FVK   G +    +  +  I         +             G   +D      
Sbjct: 6  SGIQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGLGI 65

Query: 82 YNIQKESTLHFVLRL 96
          Y IQ   TL    + 
Sbjct: 66 YGIQDSDTLILSKKK 80

>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 = 58.9 bits (143), Expect = 2e-13
 Identities = 13/40 (32%), Positives = 18/40 (45%), Gaps = 5/40 (12%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG 35
          +P +QQ+L F  + L     L  Y IQ   TL L  +   
Sbjct: 43 LPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKGS 82

>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 = 80.5 bits (199), Expect = 8e-22
 Identities = 15/73 (20%), Positives = 28/73 (38%), Gaps = 13/73 (17%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDN-----ASRGSSSP-------AGNF-EDGWTQADYN 83
          + I V+ + G++ T EV  +  + +     +               G   ED     +Y 
Sbjct: 5  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 64

Query: 84 IQKESTLHFVLRL 96
          ++  ST+   LRL
Sbjct: 65 LKPLSTVFMNLRL 77

>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 = 60.1 bits (146), Expect = 9e-14
 Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 5/44 (11%)

Query: 4  EQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVK 42
          +   L F  K L     L +Y ++  ST+ +  RLRG ++    
Sbjct: 43 DLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRGGLEHHHH 86

>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 = 80.9 bits (200), Expect = 1e-21
 Identities = 14/76 (18%), Positives = 28/76 (36%), Gaps = 13/76 (17%)

Query: 34 RGRMQIFVKTSTGKTITLEVESSDMIDN-----ASRGSSSP-------AGN-FEDGWTQA 80
              Q+ ++ STGK + L V S+D + +      +     P       +G    D     
Sbjct: 21 GYECQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKFE 80

Query: 81 DYNIQKESTLHFVLRL 96
          +  I K+  +  ++  
Sbjct: 81 ELKIPKDYVVQVIVSQ 96

>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 = 58.6 bits (142), Expect = 5e-13
 Identities = 7/47 (14%), Positives = 17/47 (36%), Gaps = 5/47 (10%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVK 42
           +    QR  F+ + L       +  I K+  + ++     +    V+
Sbjct: 59  VEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQPVQNPTPVE 105

>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 = 80.6 bits (199), Expect = 1e-21
 Identities = 41/73 (56%), Positives = 43/73 (58%), Gaps = 13/73 (17%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDNA----SRGSSSPAG---------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N           P             EDG T +DYN
Sbjct: 2  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 61

Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 62 IQKESTLHLVLRL 74

>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 = 60.5 bits (147), Expect = 7e-14
 Identities = 27/49 (55%), Positives = 32/49 (65%), Gaps = 5/49 (10%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTS 44
          +P +QQRL+FA K L     L+DYNIQKESTLHLV RLRG   +     
Sbjct: 37 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGYADLREDPD 85

>3n3k_B Ubiquitin; hydrolase, protease, thiol protease, DUB, zinc ribbon, inhibitor, ubiqu acetylation, cytoplasm, isopeptide bond, nucleus; 2.60A {Homo sapiens} Length = 85

 Score = 79.7 bits (197), Expect = 2e-21
 Identities = 29/73 (39%), Positives = 36/73 (49%), Gaps = 13/73 (17%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDNA----SRGSSSPAG---------NFEDGWTQADYN 83
          M+I VKT  G+TI LEVE SD I+N           P             EDG T +DYN
Sbjct: 4  MRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 63

Query: 84 IQKESTLHFVLRL 96
          I   S L+ +L+L
Sbjct: 64 IHNHSALYLLLKL 76

>3n3k_B Ubiquitin; hydrolase, protease, thiol protease, DUB, zinc ribbon, inhibitor, ubiqu acetylation, cytoplasm, isopeptide bond, nucleus; 2.60A {Homo sapiens} Length = 85

 Score = 60.1 bits (146), Expect = 7e-14
 Identities = 20/40 (50%), Positives = 27/40 (67%), Gaps = 5/40 (12%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG 35
          +P +QQRL+FA K L     L+DYNI   S L+L+ +LRG
Sbjct: 39 IPPDQQRLIFAGKQLEDGRTLSDYNIHNHSALYLLLKLRG 78

>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 = 17/98 (17%), Positives = 35/98 (35%), Gaps = 18/98 (18%)

Query: 12 DKSLLADYNIQKESTLHLVARLRGRMQIFVKTSTGK-TITLEVESSDMIDNA----SRGS 66
              ++DY+I     L+     +G M + +   +G+    + V     +       ++ +
Sbjct: 6  HHHPMSDYDIPTTENLYF----QGAMSLNIHIKSGQDKWEVNVAPESTVLQFKEAINKAN 61

Query: 67 SSPAGN---------FEDGWTQADYNIQKESTLHFVLR 95
            P  N          +D  T   Y+IQ   ++H V  
Sbjct: 62 GIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS 99

>3m63_B Ubiquitin domain-containing protein DSK2; armadillo-like repeats, UBL conjugation pathway, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} Length = 101

 Score = 53.5 bits (129), Expect = 4e-11
 Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 5/36 (13%)

Query: 2  PLEQQRLVFADKSL-----LADYNIQKESTLHLVAR 32
          P+  QRL+++ K L     +  Y+IQ   ++HLV  
Sbjct: 64 PVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS 99

>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 = 79.3 bits (196), Expect = 2e-21
 Identities = 42/73 (57%), Positives = 46/73 (63%), Gaps = 13/73 (17%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDN-----ASRGSSSP-------AG-NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N       +    P       AG   EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query: 84 IQKESTLHFVLRL 96
          IQ+ESTLH VLRL
Sbjct: 61 IQRESTLHLVLRL 73

>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 = 59.2 bits (144), Expect = 2e-13
 Identities = 26/40 (65%), Positives = 31/40 (77%), Gaps = 5/40 (12%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG 35
          +P +QQRL+FA K L     L+DYNIQ+ESTLHLV RLRG
Sbjct: 36 IPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRG 75

>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 = 79.3 bits (196), Expect = 2e-21
 Identities = 38/75 (50%), Positives = 41/75 (54%), Gaps = 13/75 (17%)

Query: 35 GRMQIFVKTSTGKTITLEVESSDMIDN----ASRGSSSPAG---------NFEDGWTQAD 81
            MQIFVKT TGKTITLEVE SD I+N           P             EDG T +D
Sbjct: 2  SHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSD 61

Query: 82 YNIQKESTLHFVLRL 96
          YNIQK STL  +LRL
Sbjct: 62 YNIQKWSTLFLLLRL 76

>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 = 59.3 bits (144), Expect = 1e-13
 Identities = 24/40 (60%), Positives = 29/40 (72%), Gaps = 5/40 (12%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG 35
          +P +QQRL+FA K L     L+DYNIQK STL L+ RLRG
Sbjct: 39 IPPDQQRLIFAGKQLEDGRTLSDYNIQKWSTLFLLLRLRG 78

>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 = 80.8 bits (199), Expect = 3e-21
 Identities = 69/114 (60%), Positives = 76/114 (66%), Gaps = 18/114 (15%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVES 55
           +P +QQRL+FA K L     L+DYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVE 
Sbjct: 36  IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEP 95

Query: 56  SDMIDN------------ASRGSSSPAG-NFEDGWTQADYNIQKESTLHFVLRL 96
           SD I+N              +     AG   EDG T +DYNIQKESTLH VLRL
Sbjct: 96  SDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL 149

>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 = 65.8 bits (160), Expect = 2e-15
 Identities = 37/70 (52%), Positives = 40/70 (57%), Gaps = 13/70 (18%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDN-------------ASRGSSSPAGNFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N               +         EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query: 84 IQKESTLHFV 93
          IQKESTLH V
Sbjct: 61 IQKESTLHLV 70

>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 = 57.3 bits (138), Expect = 5e-12
 Identities = 27/39 (69%), Positives = 30/39 (76%), Gaps = 5/39 (12%)

Query: 2   PLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG 35
           P +QQRL+FA K L     L+DYNIQKESTLHLV RLRG
Sbjct: 113 PPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG 151

>1yx5_B Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo sapiens} SCOP: d.15.1.1 PDB: 1yx6_B Length = 98

 Score = 79.4 bits (196), Expect = 3e-21
 Identities = 41/73 (56%), Positives = 43/73 (58%), Gaps = 13/73 (17%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDNA----SRGSSSPAG---------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N           P             EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

>1yx5_B Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo sapiens} SCOP: d.15.1.1 PDB: 1yx6_B Length = 98

 Score = 67.9 bits (166), Expect = 9e-17
 Identities = 29/59 (49%), Positives = 34/59 (57%), Gaps = 5/59 (8%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVE 54
          +P +QQRL+FA K L     L+DYNIQKESTLHLV RLRG       +       LE  
Sbjct: 36 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGRDPNSSSVDKLAAALEHH 94

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens} Length = 172

 Score = 81.3 bits (200), Expect = 4e-21
 Identities = 69/113 (61%), Positives = 75/113 (66%), Gaps = 18/113 (15%)

Query: 2   PLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVESS 56
           P +QQRL+FA K L     L+DYNIQKESTLHLV RLRG MQIFVKT TGKTITLEVE S
Sbjct: 57  PPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPS 116

Query: 57  DMIDN------------ASRGSSSPAG-NFEDGWTQADYNIQKESTLHFVLRL 96
           D I+N              +     AG   EDG T +DYNIQKESTLH VLRL
Sbjct: 117 DTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL 169

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens} Length = 172

 Score = 67.4 bits (164), Expect = 8e-16
 Identities = 39/90 (43%), Positives = 45/90 (50%), Gaps = 16/90 (17%)

Query: 17 ADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVESSDMIDN-------------AS 63
          + ++    S L         MQIFVKT TGKTITLEVE SD I+N               
Sbjct: 4  SHHHHHHSSGLVPRGS---HMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ 60

Query: 64 RGSSSPAGNFEDGWTQADYNIQKESTLHFV 93
          +         EDG T +DYNIQKESTLH V
Sbjct: 61 QRLIFAGKQLEDGRTLSDYNIQKESTLHLV 90

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens} Length = 172

 Score = 57.0 bits (137), Expect = 7e-12
 Identities = 27/39 (69%), Positives = 30/39 (76%), Gaps = 5/39 (12%)

Query: 2   PLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG 35
           P +QQRL+FA K L     L+DYNIQKESTLHLV RLRG
Sbjct: 133 PPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG 171

>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 = 79.2 bits (195), Expect = 1e-20
 Identities = 26/114 (22%), Positives = 42/114 (36%), Gaps = 21/114 (18%)

Query: 4   EQQRLVFA-------DKSLLADYNIQKESTLHLV-ARLRGRMQIFVKTSTGKTITLEVES 55
            QQRL          D+  LA   +   ST+ LV  +    + I V+ + G++ T EV  
Sbjct: 41  FQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDKSDEPLSILVRNNKGRSSTYEVRL 100

Query: 56  SDMIDNA-----SRGSSSP-------AGN-FEDGWTQADYNIQKESTLHFVLRL 96
           +  + +                     G   ED     +Y ++  ST+   LRL
Sbjct: 101 TQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRL 154

>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 = 63.0 bits (153), Expect = 3e-14
 Identities = 13/72 (18%), Positives = 22/72 (30%), Gaps = 15/72 (20%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDN--------------ASRGSSSPAGNF-EDGWTQAD 81
            + VK   G    + + SS  +                  R +  P+G   +D    A 
Sbjct: 3  WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLAS 62

Query: 82 YNIQKESTLHFV 93
            +   ST+  V
Sbjct: 63 QGLGPGSTVLLV 74

>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 = 60.0 bits (145), Expect = 5e-13
 Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 5/43 (11%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQ 38
           +  +   L F  K L     L +Y ++  ST+ +  RLRG  +
Sbjct: 117 VQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRGGGR 159

>2l7r_A Ubiquitin-like protein FUBI; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; NMR {Homo sapiens} Length = 93

 Score = 75.2 bits (185), Expect = 1e-19
 Identities = 20/85 (23%), Positives = 30/85 (35%), Gaps = 15/85 (17%)

Query: 25 STLHLVARLRGRMQIFVKTSTGKTITLEVESSDMIDN-----ASRGSSSP-------AGN 72
                   RG MQ+FV+    +  T EV   + +       AS    +P       AG 
Sbjct: 8  HHHSSGLVPRGSMQLFVRA--QELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAGA 65

Query: 73 -FEDGWTQADYNIQKESTLHFVLRL 96
            ED  T     ++  +TL    R+
Sbjct: 66 PLEDEATLGQCGVEALTTLEVAGRM 90

>2l7r_A Ubiquitin-like protein FUBI; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; NMR {Homo sapiens} Length = 93

 Score = 57.1 bits (138), Expect = 1e-12
 Identities = 9/40 (22%), Positives = 17/40 (42%), Gaps = 5/40 (12%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG 35
          +  E Q ++ A   L     L    ++  +TL +  R+ G
Sbjct: 53 IAPEDQVVLLAGAPLEDEATLGQCGVEALTTLEVAGRMLG 92

>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 = 71.2 bits (175), Expect = 2e-18
 Identities = 17/78 (21%), Positives = 27/78 (34%), Gaps = 15/78 (19%)

Query: 35 GRMQIFVKTSTGKTIT--LEVESSDMIDN-----ASRGSSSP-------AGN-FEDGWTQ 79
          G M I V+T  G+       +     ++             P        G   EDG T 
Sbjct: 1  GSMWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTL 60

Query: 80 ADYNIQKESTLHFVLRLS 97
           DY ++   T+  ++R S
Sbjct: 61 FDYEVRLNDTIQLLVRQS 78

>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 = 55.1 bits (133), Expect = 5e-12
 Identities = 10/38 (26%), Positives = 17/38 (44%), Gaps = 5/38 (13%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARL 33
          +    QRL +  K +     L DY ++   T+ L+ R 
Sbjct: 40 VEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLLVRQ 77

>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 = 73.8 bits (181), Expect = 3e-18
 Identities = 45/73 (61%), Positives = 47/73 (64%), Gaps = 13/73 (17%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDN-----ASRGSSSP-------AGN-FEDGWTQADYN 83
          MQIFVKT TGKTITLEVESSD IDN       +    P       AG   EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

>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 = 71.9 bits (176), Expect = 2e-17
 Identities = 34/120 (28%), Positives = 51/120 (42%), Gaps = 24/120 (20%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG---RMQIFVKTSTGKTITLE 52
           +P +QQRL+FA K L     L+DYNIQKESTLHLV RLRG       FV      + ++ 
Sbjct: 36  IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGGGETIKFVADGDIGSGSVI 95

Query: 53  VESSDMIDNASRGSSSPAG-------------NFEDGWTQAD---YNIQKESTLHFVLRL 96
           ++    +++                       +   G + +D     +  E+   F   L
Sbjct: 96  IKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDL 155

>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 = 36.5 bits (84), Expect = 4e-04
 Identities = 11/50 (22%), Positives = 18/50 (36%), Gaps = 12/50 (24%)

Query: 4   EQQRLVFADKSL--------LAD---YNIQKESTLHLVARLR-GRMQIFV 41
           +   L F  K L        L+D     +  E+       L+ G +Q F+
Sbjct: 115 QPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKSGFLQFFL 164

>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 = 71.6 bits (176), Expect = 3e-18
 Identities = 10/76 (13%), Positives = 29/76 (38%), Gaps = 16/76 (21%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDN------ASRGSSS-PAGN---------FEDGWTQA 80
          MQ+ +KT   +T  ++++  + +        + +G  + P              D     
Sbjct: 1  MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 60

Query: 81 DYNIQKESTLHFVLRL 96
          +Y I +++ +  ++  
Sbjct: 61 EYKIDEKNFVVVMVTK 76

>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 = 51.2 bits (123), Expect = 3e-10
 Identities = 9/39 (23%), Positives = 20/39 (51%), Gaps = 5/39 (12%)

Query: 2  PLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG 35
          P+  Q+L++A K L     L +Y I +++ + ++     
Sbjct: 40 PVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKPK 78

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens} Length = 189

 Score = 73.9 bits (181), Expect = 4e-18
 Identities = 42/108 (38%), Positives = 50/108 (46%), Gaps = 13/108 (12%)

Query: 2   PLEQQRLVFADKSLLADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVESSDMIDN 61
              +  + +      +D  +     L          QIFVKT TGKTITLEVE SD I+N
Sbjct: 71  TWREADINYTSGFRNSDRILYSSDWLIYKTTDHYGGQIFVKTLTGKTITLEVEPSDTIEN 130

Query: 62  -----ASRGSSSP--------AGNFEDGWTQADYNIQKESTLHFVLRL 96
                  +    P            EDG T +DYNIQKESTLH VLRL
Sbjct: 131 VKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL 178

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens} Length = 189

 Score = 66.9 bits (163), Expect = 2e-15
 Identities = 30/47 (63%), Positives = 34/47 (72%), Gaps = 5/47 (10%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVK 42
           +P +QQRL+FA K L     L+DYNIQKESTLHLV RLRG  Q F K
Sbjct: 141 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGGQTFTK 187

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens} Length = 88

 Score = 70.4 bits (173), Expect = 7e-18
 Identities = 15/88 (17%), Positives = 30/88 (34%), Gaps = 14/88 (15%)

Query: 21 IQKESTLHLVARLRGRMQIFVKTSTGKTITLEVESSDMIDN-----ASRGSSSP------ 69
          ++   +          +++ VKT   +T T  V +   +       A+  S         
Sbjct: 2  MEPNDSTSTAVEEPDSLEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLI 61

Query: 70 -AGNF-EDGWTQADYNIQKESTLHFVLR 95
            G   +D     +YN+  +  +H V R
Sbjct: 62 YQGRVLQDDKKLQEYNVGGK-VIHLVER 88

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens} Length = 88

 Score = 49.2 bits (118), Expect = 2e-09
 Identities = 13/36 (36%), Positives = 21/36 (58%), Gaps = 6/36 (16%)

Query: 2  PLEQQRLVFADKSL-----LADYNIQKESTLHLVAR 32
          P E+QRL++  + L     L +YN+  +  +HLV R
Sbjct: 54 PSEKQRLIYQGRVLQDDKKLQEYNVGGK-VIHLVER 88

>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 = 69.3 bits (170), Expect = 2e-17
 Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 15/75 (20%)

Query: 37 MQIFVKTSTG-KTITLE-VESSDMIDN-----ASRGSSSP-------AG-NFEDGWTQAD 81
          M I V+T  G KT T+E V     I+       +     P        G   E+G+T  D
Sbjct: 8  MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFD 67

Query: 82 YNIQKESTLHFVLRL 96
          Y++     +  ++R 
Sbjct: 68 YDVGLNDIIQLLVRP 82

>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 = 61.6 bits (150), Expect = 2e-14
 Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 5/40 (12%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG 35
          +  E QRL +  K L     L DY++     + L+ R   
Sbjct: 45 VRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVRPDS 84

>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana, uncharacterized putative protein, NESG, structural genomics; NMR {Arabidopsis thaliana} Length = 84

 Score = 68.0 bits (167), Expect = 6e-17
 Identities = 12/72 (16%), Positives = 20/72 (27%), Gaps = 14/72 (19%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDNA----SRGSSSPAGN----------FEDGWTQADY 82
          M+  V+   G +  LEV+  D +        R    P               +  T    
Sbjct: 11 MKFLVENLNGSSFELEVDYRDTLLVVKQKIERSQHIPVSKQTLIVDGIVILREDLTVEQC 70

Query: 83 NIQKESTLHFVL 94
           I   S +   +
Sbjct: 71 QIVPTSDIQLEV 82

>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana, uncharacterized putative protein, NESG, structural genomics; NMR {Arabidopsis thaliana} Length = 84

 Score = 47.2 bits (113), Expect = 7e-09
 Identities = 7/35 (20%), Positives = 12/35 (34%), Gaps = 6/35 (17%)

Query: 2  PLEQQRLVFADKSLL------ADYNIQKESTLHLV 30
          P+ +Q L+     +L          I   S + L 
Sbjct: 47 PVSKQTLIVDGIVILREDLTVEQCQIVPTSDIQLE 81

>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 = 68.9 bits (168), Expect = 8e-17
 Identities = 44/72 (61%), Positives = 45/72 (62%), Gaps = 13/72 (18%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDN------ASRGSSSP------AGN-FEDGWTQADYN 83
          MQIFVKT TGKTITLEVESSD IDN         G          AG   EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query: 84 IQKESTLHFVLR 95
          IQKESTLH VLR
Sbjct: 61 IQKESTLHLVLR 72

>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 = 40.8 bits (95), Expect = 5e-06
 Identities = 27/43 (62%), Positives = 32/43 (74%), Gaps = 5/43 (11%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQ 38
          +P +QQRL+FA K L     L+DYNIQKESTLHLV RLRG + 
Sbjct: 36 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGII 78

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9 Length = 189

 Score = 70.1 bits (171), Expect = 1e-16
 Identities = 12/72 (16%), Positives = 21/72 (29%), Gaps = 18/72 (25%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDN-----ASRGSSSP-------AGN-FEDGWTQADYN 83
          MQ+ VKT  G+T    +E    + +     +               G    +     D  
Sbjct: 1  MQVQVKTLEGETKIYTLEQGTSVLDLKSQISQDMGFEIDMMTLVNNGFIAPNTELVTDD- 59

Query: 84 IQKESTLHFVLR 95
               T +  L+
Sbjct: 60 ----VTYYLSLK 67

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9 Length = 189

 Score = 50.1 bits (119), Expect = 4e-09
 Identities = 8/48 (16%), Positives = 15/48 (31%)

Query: 1  MPLEQQRLVFADKSLLADYNIQKESTLHLVARLRGRMQIFVKTSTGKT 48
            ++   LV           +  + T +L  +L G  +   K S    
Sbjct: 36 FEIDMMTLVNNGFIAPNTELVTDDVTYYLSLKLLGGKKKKKKKSYTTK 83

>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 = 66.5 bits (163), Expect = 2e-16
 Identities = 12/75 (16%), Positives = 27/75 (36%), Gaps = 16/75 (21%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDN------ASRGSSS-PAGN---------FEDGWTQA 80
          + I +KT   +T  + +E  + +        A +G  + P              D     
Sbjct: 6  VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIR 65

Query: 81 DYNIQKESTLHFVLR 95
          DY I +++ +  ++ 
Sbjct: 66 DYRIDEKNFVVVMVT 80

>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 = 48.8 bits (117), Expect = 2e-09
 Identities = 10/41 (24%), Positives = 22/41 (53%), Gaps = 6/41 (14%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHL-VARLRG 35
           P+  Q+L++A K L     + DY I +++ + + V + + 
Sbjct: 44 FPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTKTKA 84

>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 = 66.1 bits (162), Expect = 4e-16
 Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 14/75 (18%)

Query: 35 GRMQIFVKTSTGKTITLEVESSDMIDN-----ASRGSSSP-------AGNF-EDGWTQAD 81
            +++ VKT   +T T  V +   +       A+  S           G   +D     +
Sbjct: 4  DSLEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQE 63

Query: 82 YNIQKESTLHFVLRL 96
          YN+  +  +H V R 
Sbjct: 64 YNVGGK-VIHLVERA 77

>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 = 57.7 bits (140), Expect = 9e-13
 Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 6/50 (12%)

Query: 2  PLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTG 46
          P E+QRL++  + L     L +YN+  +  +HLV R   +  +    S+G
Sbjct: 42 PSEKQRLIYQGRVLQDDKKLQEYNVGGK-VIHLVERAPPQTHLPSGASSG 90

>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 = 63.4 bits (155), Expect = 3e-15
 Identities = 12/73 (16%), Positives = 25/73 (34%), Gaps = 14/73 (19%)

Query: 37 MQIFVKTSTGK-TITLEVESSDMIDNA----SRGSSSPAGN---------FEDGWTQADY 82
          M + +   +G+    + V     +       ++ +  P  N          +D  T   Y
Sbjct: 3  MSLNIHIKSGQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESY 62

Query: 83 NIQKESTLHFVLR 95
          +IQ   ++H V  
Sbjct: 63 HIQDGHSVHLVKS 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 = 53.4 bits (129), Expect = 3e-11
 Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 5/36 (13%)

Query: 2  PLEQQRLVFADKSL-----LADYNIQKESTLHLVAR 32
          P+  QRL+++ K L     +  Y+IQ   ++HLV  
Sbjct: 40 PVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS 75

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens} Length = 101

 Score = 63.6 bits (155), Expect = 5e-15
 Identities = 17/92 (18%), Positives = 33/92 (35%), Gaps = 15/92 (16%)

Query: 18 DYNIQKESTLHLVARLRGR-MQIFVKTSTGKTITLEVESSDMIDN-----ASRGSSSP-- 69
           ++       +L  +   + M++ VKT   K     V  +  +       + R  S    
Sbjct: 6  HHHHHSSGRENLYFQGHPKIMKVTVKTPKEK-EEFAVPENSSVQQFKEEISKRFKSHTDQ 64

Query: 70 -----AGN-FEDGWTQADYNIQKESTLHFVLR 95
               AG   +D  T + + I    T+H V++
Sbjct: 65 LVLIFAGKILKDQDTLSQHGIHDGLTVHLVIK 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 = 54.7 bits (132), Expect = 2e-11
 Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 5/40 (12%)

Query: 2   PLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR 36
             +Q  L+FA K L     L+ + I    T+HLV + + R
Sbjct: 61  HTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQNR 100

>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 = 62.4 bits (152), Expect = 2e-14
 Identities = 12/73 (16%), Positives = 25/73 (34%), Gaps = 14/73 (19%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDNA----SRGSSSPAGN---------FEDGWTQADYN 83
          +++ VKT   K     V  +  I       S+   +              +D  + A   
Sbjct: 18 IKVTVKTPKDKE-DFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCG 76

Query: 84 IQKESTLHFVLRL 96
          ++   T+H V++ 
Sbjct: 77 VRDGLTVHLVIKR 89

>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 = 59.3 bits (144), Expect = 3e-13
 Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 5/52 (9%)

Query: 2   PLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKT 48
             +Q  L+FA K L     LA   ++   T+HLV + + R       ++G +
Sbjct: 53  HPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHRAMGNECPASGPS 104

>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 = 62.5 bits (152), Expect = 2e-14
 Identities = 11/40 (27%), Positives = 19/40 (47%), Gaps = 5/40 (12%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG 35
           MP  +Q+L +    +     LA YN+   + +HL  + R 
Sbjct: 71  MPAGKQKLQYEGIFIKDSNSLAYYNMASGAVIHLALKERS 110

>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 = 58.3 bits (141), Expect = 7e-13
 Identities = 11/93 (11%), Positives = 31/93 (33%), Gaps = 13/93 (13%)

Query: 17  ADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVESSDMIDNA----SRGSSSPAGN 72
            ++  + +  + +  ++            G+ +   +  +D +          +  PAG 
Sbjct: 16  EEFLRRNKGPVSIKVQVPNMQDKTEWKLNGQGLVFTLPLTDQVSVIKVKIHEATGMPAGK 75

Query: 73  ---------FEDGWTQADYNIQKESTLHFVLRL 96
                     +D  + A YN+   + +H  L+ 
Sbjct: 76  QKLQYEGIFIKDSNSLAYYNMASGAVIHLALKE 108

>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 = 60.9 bits (148), Expect = 6e-14
 Identities = 9/72 (12%), Positives = 26/72 (36%), Gaps = 13/72 (18%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDNA----SRGSSSPAGN---------FEDGWTQADYN 83
          + +  K    + + L++E S+ I       ++  S               +D  T ++  
Sbjct: 2  VSLTFKNFKKEKVPLDLEPSNTILETKTKLAQSISCEESQIKLIYSGKVLQDSKTVSECG 61

Query: 84 IQKESTLHFVLR 95
          ++    + F++ 
Sbjct: 62 LKDGDQVVFMVS 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 = 43.9 bits (104), Expect = 3e-07
 Identities = 4/34 (11%), Positives = 15/34 (44%), Gaps = 5/34 (14%)

Query: 2  PLEQQRLVFADKSL-----LADYNIQKESTLHLV 30
             Q +L+++ K L     +++  ++    +  +
Sbjct: 38 EESQIKLIYSGKVLQDSKTVSECGLKDGDQVVFM 71

>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 = 63.7 bits (154), Expect = 9e-14
 Identities = 26/38 (68%), Positives = 29/38 (76%), Gaps = 5/38 (13%)

Query: 2   PLEQQRLVFADKSL-----LADYNIQKESTLHLVARLR 34
           P +QQRL+FA K L     L+DYNIQKESTLHLV RLR
Sbjct: 270 PPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 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 = 62.5 bits (151), Expect = 3e-13
 Identities = 41/74 (55%), Positives = 43/74 (58%), Gaps = 13/74 (17%)

Query: 36  RMQIFVKTSTGKTITLEVESSDMIDNASRG----SSSPAGN---------FEDGWTQADY 82
            MQIFVKT TGKTITLEVE SD I+N           P             EDG T +DY
Sbjct: 233 SMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY 292

Query: 83  NIQKESTLHFVLRL 96
           NIQKESTLH VLRL
Sbjct: 293 NIQKESTLHLVLRL 306

>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 = 58.9 bits (143), Expect = 3e-13
 Identities = 12/74 (16%), Positives = 25/74 (33%), Gaps = 14/74 (18%)

Query: 35 GRMQIFVKTSTGKTITLEVESSDMIDNA----SRGSSSPAGN---------FEDGWTQAD 81
            +++ VKT   K     V  +  I       S+   +              +D  + A 
Sbjct: 21 HLIKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQ 79

Query: 82 YNIQKESTLHFVLR 95
            ++   T+H V++
Sbjct: 80 CGVRDGLTVHLVIK 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 = 53.1 bits (128), Expect = 7e-11
 Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 5/42 (11%)

Query: 2  PLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQ 38
            +Q  L+FA K L     LA   ++   T+HLV + + R  
Sbjct: 58 HPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHRAM 99

>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 = 58.9 bits (143), Expect = 3e-13
 Identities = 12/75 (16%), Positives = 22/75 (29%), Gaps = 14/75 (18%)

Query: 35 GRMQIFVKTSTGKTITLEVESSDMIDN----ASRGSSSPAGN---------FEDGWTQAD 81
            +++ VKT         +  +  +       S+     A             D    + 
Sbjct: 16 RIIRVSVKTPQDCH-EFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQDILSQ 74

Query: 82 YNIQKESTLHFVLRL 96
            I   ST+H V+R 
Sbjct: 75 RGILDGSTVHVVVRS 89

>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 = 55.5 bits (134), Expect = 7e-12
 Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 5/40 (12%)

Query: 2  PLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR 36
            ++  L+F  K L     L+   I   ST+H+V R    
Sbjct: 53 NADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVRSHSG 92

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} Length = 94

 Score = 58.2 bits (141), Expect = 5e-13
 Identities = 13/87 (14%), Positives = 29/87 (33%), Gaps = 15/87 (17%)

Query: 23 KESTLHLVARLRGRMQIFVKTSTGKTITLEVESSDMIDNA----SRGSSSPAGN------ 72
               H       ++ + VK    K  T+EV+ ++ + +         ++P         
Sbjct: 2  GHHHHHHSHAAVRKIHVTVKFP-SKQFTVEVDRTETVSSLKDKIHIVENTPIKRMQLYYS 60

Query: 73 ----FEDGWTQADYNIQKESTLHFVLR 95
               +D     +Y I + S +   L+
Sbjct: 61 GIELADDYRNLNEYGITEFSEIVVFLK 87

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} Length = 94

 Score = 48.5 bits (116), Expect = 3e-09
 Identities = 8/43 (18%), Positives = 20/43 (46%), Gaps = 6/43 (13%)

Query: 2  PLEQQRLVFADKSL------LADYNIQKESTLHLVARLRGRMQ 38
          P+++ +L ++   L      L +Y I + S + +  +   R +
Sbjct: 51 PIKRMQLYYSGIELADDYRNLNEYGITEFSEIVVFLKSINRAK 93

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 125

 Score = 58.7 bits (142), Expect = 7e-13
 Identities = 12/72 (16%), Positives = 22/72 (30%), Gaps = 14/72 (19%)

Query: 37  MQIFVKTSTGKTITLEVESSDMIDNASRG----SSSPAGN---------FEDGWTQADYN 83
           +++ VKT   K     V  +  +            S              +D  T   + 
Sbjct: 33  IKVTVKTPKEK-EEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLIQHG 91

Query: 84  IQKESTLHFVLR 95
           I    T+H V++
Sbjct: 92  IHDGLTVHLVIK 103

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 125

 Score = 52.9 bits (127), Expect = 1e-10
 Identities = 12/40 (30%), Positives = 17/40 (42%), Gaps = 5/40 (12%)

Query: 2   PLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR 36
             +Q  L+FA K L     L  + I    T+HLV +    
Sbjct: 68  QTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIKRDPN 107

>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 = 57.5 bits (139), Expect = 2e-12
 Identities = 12/40 (30%), Positives = 16/40 (40%), Gaps = 5/40 (12%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG 35
           +P  +Q+L      L     LA YN+     L L  R R 
Sbjct: 67  IPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLRERS 106

>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 = 47.1 bits (112), Expect = 2e-08
 Identities = 13/75 (17%), Positives = 27/75 (36%), Gaps = 15/75 (20%)

Query: 37  MQIFVKTST-GKTITLEVES-SDMIDNA----SRGSSSPAGN---------FEDGWTQAD 81
           +++       G+ + + V+S S+ + +     +     PA            +D  + A 
Sbjct: 30  IRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSLAH 89

Query: 82  YNIQKESTLHFVLRL 96
           YN+     L   LR 
Sbjct: 90  YNVGAGEILTLSLRE 104

>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 = 50.4 bits (119), Expect = 6e-09
 Identities = 11/75 (14%), Positives = 25/75 (33%), Gaps = 16/75 (21%)

Query: 37 MQIFVKTSTGKTITLEVESSD-------MIDNASRGSSSPAGN---------FEDGWTQA 80
          + I +KT   +T  + +E  +        I+      + P              D     
Sbjct: 8  VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIR 67

Query: 81 DYNIQKESTLHFVLR 95
          DY I +++ +  ++ 
Sbjct: 68 DYRIDEKNFVVVMVT 82

>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 = 36.1 bits (82), Expect = 6e-04
 Identities = 18/86 (20%), Positives = 31/86 (36%), Gaps = 6/86 (6%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHL-VARLRGRMQIFVKTSTGKTITLEVE 54
            P+  Q+L++A K L     + DY I +++ + + V + +             T   E  
Sbjct: 46  FPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTKTKAGQGTSAPPEASPTAAPESS 105

Query: 55  SSDMIDNASRGSSSPAGNFEDGWTQA 80
           +S      S  S  P    ED     
Sbjct: 106 TSFPPAPTSGMSHPPPAAREDKSPSE 131

>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 = 39.2 bits (92), Expect = 1e-05
 Identities = 8/34 (23%), Positives = 14/34 (41%), Gaps = 5/34 (14%)

Query: 2  PLEQQRLVFADKSL-----LADYNIQKESTLHLV 30
              Q+L+F  K L     L   ++   + L L+
Sbjct: 48 LPRGQKLIFKGKVLVETSTLKQSDVGSGAKLMLM 81

>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 = 37.3 bits (87), Expect = 6e-05
 Identities = 9/70 (12%), Positives = 20/70 (28%), Gaps = 14/70 (20%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          +++ VK   GK+I L V     + +                          +  T    +
Sbjct: 13 IKLTVKF-GGKSIPLSVSPDCTVKDLKSQLQPITNVLPRGQKLIFKGKVLVETSTLKQSD 71

Query: 84 IQKESTLHFV 93
          +   + L  +
Sbjct: 72 VGSGAKLMLM 81

>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 = 36.6 bits (84), Expect = 2e-04
 Identities = 10/75 (13%), Positives = 25/75 (33%), Gaps = 14/75 (18%)

Query: 34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSSS--------------PAGNFEDGWTQ 79
           GRM  F      + + + +E +  +    +   +                G+ ED    
Sbjct: 6  SGRMLDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGDVEDSTVL 65

Query: 80 ADYNIQKESTLHFVL 94
             ++ K ++L+ + 
Sbjct: 66 KSLHLPKNNSLYVLT 80

>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 = 36.5 bits (84), Expect = 2e-04
 Identities = 9/52 (17%), Positives = 25/52 (48%), Gaps = 6/52 (11%)

Query: 1  MPLEQQRLVFADKSL------LADYNIQKESTLHLVARLRGRMQIFVKTSTG 46
          +P E+ ++V+ ++ L      L  Y ++    + L+ +    ++   +T +G
Sbjct: 47 VPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVLLQKDNVGLRTPGRTPSG 98

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	99.97
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.96
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.95
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	99.83
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	99.82
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	99.78
3v6c_B	91	Ubiquitin; structural genomics, structural genomic	99.78
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	99.77
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	99.76
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	99.75
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	99.75
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	99.74
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	99.74
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	99.74
4hcn_B	98	Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidas	99.73
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	99.73
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	99.73
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	99.73
2uyz_B	79	Small ubiquitin-related modifier 1; sumoylation, c	99.73
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	99.73
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	99.72
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	99.72
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	99.57
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	99.72
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	99.72
1wyw_B	97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	99.72
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	99.72
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	99.71
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	99.71
3vdz_A	111	Ubiquitin-40S ribosomal protein S27A; gadolinium,	99.7
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	99.7
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	99.69
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	99.69
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	99.69
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	99.69
2lxa_A	87	Ubiquitin-like protein MDY2; ubiquitin-like domain	99.68
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	99.68
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	99.68
1se9_A	126	Ubiquitin family; ubiquitin-like, cell-free, wheat	99.68
4a20_A	98	Ubiquitin-like protein MDY2; protein binding, GET-	99.68
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	99.67
1we6_A	111	Splicing factor, putative; structural genomics, ub	99.67
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	99.66
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	99.66
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	99.65
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	99.65
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	99.65
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	99.65
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	99.65
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	99.64
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	99.64
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	99.64
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.64
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	99.64
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	99.63
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	99.62
1wju_A	100	NEDD8 ultimate buster-1; ubiquitin-like domain, st	99.62
3u5c_f	152	40S ribosomal protein S31; translation, ribosome,	99.62
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	99.61
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	99.61
4ajy_B	118	Transcription elongation factor B polypeptide 2; E	99.61
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	99.59
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.58
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	99.58
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	99.58
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	99.57
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.55
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	99.53
2dzj_A	88	Synaptic glycoprotein SC2; ubiquitin-like fold, st	99.49
2daf_A	118	FLJ35834 protein; hypothetical protein FLJ35834, u	99.48
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	99.48
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	99.46
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	99.45
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	99.44
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	99.43
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	99.43
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	99.43
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	99.41
1wxv_A	92	BAG-family molecular chaperone regulator-1; struct	99.4
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	99.37
4b6w_A	86	Tubulin-specific chaperone; CAP-Gly, ubiquitin-lik	99.35
1wf9_A	107	NPL4 family protein; beta-grAsp fold like domain,	99.34
2kjr_A	95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	99.33
2io1_B	94	Small ubiquitin-related modifier 3 precursor; SUMO	99.33
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	99.21
2kzr_A	86	Ubiquitin thioesterase OTU1; structural genomics,	99.2
2kj6_A	97	Tubulin folding cofactor B; methods development, N	99.19
2io0_B	91	Small ubiquitin-related modifier 2 precursor; SUMO	99.19
1v6e_A	95	Cytoskeleton-associated protein 1; tubulin-specifi	99.16
1wm3_A	72	Ubiquitin-like protein SMT3B; ubiquitin fold, half	99.14
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	99.13
2d07_B	93	Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Ho	99.13
1wz0_A	104	Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-li	99.09
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	99.07
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	99.06
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	99.05
2eke_C	106	Ubiquitin-like protein SMT3; UBC9, SUMO binding mo	99.05
4ajy_B	118	Transcription elongation factor B polypeptide 2; E	99.04
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	99.04
3a4r_A	79	Nfatc2-interacting protein; ubiquitin fold, coiled	99.03
1wju_A	100	NEDD8 ultimate buster-1; ubiquitin-like domain, st	99.01
2k8h_A	110	Small ubiquitin protein; SUMO, post-translational	99.0
2uyz_B	79	Small ubiquitin-related modifier 1; sumoylation, c	99.0
1wyw_B	97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	98.99
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	98.98
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	98.98
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	98.98
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	98.97
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	98.96
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	98.95
4hcn_B	98	Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidas	98.94
3v6c_B	91	Ubiquitin; structural genomics, structural genomic	98.93
2daf_A	118	FLJ35834 protein; hypothetical protein FLJ35834, u	98.93
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	98.93
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	98.92
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	98.91
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	98.91
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	98.91
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	98.91
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	98.9
3vdz_A	111	Ubiquitin-40S ribosomal protein S27A; gadolinium,	98.9
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	98.9
4a20_A	98	Ubiquitin-like protein MDY2; protein binding, GET-	98.9
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	98.9
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	98.89
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	98.88
2lxa_A	87	Ubiquitin-like protein MDY2; ubiquitin-like domain	98.88
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	98.88
1se9_A	126	Ubiquitin family; ubiquitin-like, cell-free, wheat	98.88
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	98.39
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	98.87
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	98.87
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	98.87
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	98.86
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	98.86
1we6_A	111	Splicing factor, putative; structural genomics, ub	98.86
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	98.85
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	98.83
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	98.83
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	98.8
4b6w_A	86	Tubulin-specific chaperone; CAP-Gly, ubiquitin-lik	98.79
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	98.79
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	98.77
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	98.76
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	98.75
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	98.74
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	98.74
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	98.73
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	98.73
3u5c_f	152	40S ribosomal protein S31; translation, ribosome,	98.72
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	98.7
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	98.7
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	98.69
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	98.69
1wjn_A	97	Tubulin-folding protein TBCE; ubiquitin-like domai	98.68
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	98.66
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	98.63
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	98.63
1wxv_A	92	BAG-family molecular chaperone regulator-1; struct	98.57
2kj6_A	97	Tubulin folding cofactor B; methods development, N	98.54
3kyd_D	115	Small ubiquitin-related modifier 1; SUMO, thioeste	98.53
2kjr_A	95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	98.51
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	98.5
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	98.46
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	98.45
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	98.4
2pjh_A	80	Protein NPL4, nuclear protein localization protein	98.38
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	98.37
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	98.33
1v6e_A	95	Cytoskeleton-associated protein 1; tubulin-specifi	98.32
3pge_A	200	SUMO-modified proliferating cell nuclear antigen;	98.31
2dzj_A	88	Synaptic glycoprotein SC2; ubiquitin-like fold, st	98.27
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	98.26
3tix_A	207	Ubiquitin-like protein SMT3, RNA-induced transcri	98.22
2io1_B	94	Small ubiquitin-related modifier 3 precursor; SUMO	98.21
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	98.17
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	98.13
2io0_B	91	Small ubiquitin-related modifier 2 precursor; SUMO	97.96
2d07_B	93	Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Ho	97.95
3v7o_A	227	Minor nucleoprotein VP30; ssgcid, seattle structur	97.93
1wf9_A	107	NPL4 family protein; beta-grAsp fold like domain,	97.86
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	97.84
1wm3_A	72	Ubiquitin-like protein SMT3B; ubiquitin fold, half	97.82
1wz0_A	104	Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-li	97.77
2eke_C	106	Ubiquitin-like protein SMT3; UBC9, SUMO binding mo	97.74
4e71_A	111	Plexin-B2, MM1; transmembrane, signaling, RBD, str	97.73
3goe_A	82	DNA repair protein RAD60; SUMO-like domain, sumoyl	97.72
2k8h_A	110	Small ubiquitin protein; SUMO, post-translational	97.67
2kc2_A	128	Talin-1, F1; FERM, adhesion, cell membrane, cell p	97.58
3a4r_A	79	Nfatc2-interacting protein; ubiquitin fold, coiled	97.57
2kzr_A	86	Ubiquitin thioesterase OTU1; structural genomics,	97.49
3qx1_A	84	FAS-associated factor 1; UBX, protein binding, P97	97.47
2jxx_A	97	Nfatc2-interacting protein; nuclear factor of acti	97.46
1wjn_A	97	Tubulin-folding protein TBCE; ubiquitin-like domai	97.46
3h6n_A	127	Plexin-D1; structural genomics consortium, SGC, me	97.44
2al3_A	90	TUG long isoform; TUG UBL1 insulin, endocytosis/ex	97.43
2r2o_A	138	Plexin-B1; effector domain, structural genomics, s	97.37
3ix6_A	360	TS, tsase, thymidylate synthase; niaid, ssgcid, se	97.35
2bps_A	81	YUKD protein; ubiquitin-like protein, ubiquitin; 2	97.33
4e74_A	117	Plexin-A4; RBD, structural genomics, structural ge	97.26
2dzk_A	109	UBX domain-containing protein 2; ubiquitin-like fo	97.06
3uf8_A	209	Ubiquitin-like protein SMT3, peptidyl-prolyl CIS-	97.02
3pge_A	200	SUMO-modified proliferating cell nuclear antigen;	96.94
1wj4_A	124	KIAA0794 protein; UBX domain, beta-grAsp fold, str	96.73
4da1_A	389	Protein phosphatase 1K, mitochondrial; metal-ION-a	96.69
2cr5_A	109	Reproduction 8; UBX domain, D0H8S2298E protein, st	96.63
3ivf_A	371	Talin-1; FERM domain, cell membrane, cell projecti	96.5
1s3s_G	127	P47 protein; AAA ATPase, protein-protein complex,	96.5
2l76_A	95	Nfatc2-interacting protein; ubiquitin-like domain,	96.44
3kuz_A	126	Plexin-C1; structural genomics, structural genomic	96.39
3kyd_D	115	Small ubiquitin-related modifier 1; SUMO, thioeste	96.21
3ig3_A	627	Plxna3 protein; plexin intracellular GAP RBD inact	96.14
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	95.83
3hm6_X	644	Plexin-B1; structural genomics consortium, SGC, me	95.82
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	95.76
3tix_A	207	Ubiquitin-like protein SMT3, RNA-induced transcri	95.41
3ivf_A	371	Talin-1; FERM domain, cell membrane, cell projecti	95.32
4efo_A	94	Serine/threonine-protein kinase TBK1; ubiquitin li	94.82
3v7o_A	227	Minor nucleoprotein VP30; ssgcid, seattle structur	94.52
2l32_A	74	Small archaeal modifier protein 2; protein BIN; NM	94.31
4efo_A	94	Serine/threonine-protein kinase TBK1; ubiquitin li	94.16
2daj_A	91	KIAA0977 protein, COBL-like 1; ubiquitin-like doma	93.76
3ix6_A	360	TS, tsase, thymidylate synthase; niaid, ssgcid, se	92.12
2kmm_A	73	Guanosine-3',5'-BIS(diphosphate) 3'- pyrophosphohy	91.5
1ef1_A	294	Moesin; membrane, FERM domain, tail domain, membra	91.5
3goe_A	82	DNA repair protein RAD60; SUMO-like domain, sumoyl	91.11
1h4r_A	314	Merlin; FERM, neurofibromatosis, NF2, structural p	90.17
1ryj_A	70	Unknown; beta/alpha protein, structural genomics,	89.87
2inc_C	83	TOUB protein; DIIRON, 4-helix bundle, carboxylate	88.39
2i1j_A	575	Moesin; FERM, coiled-coil, C-ermad, ERM, radixin,	87.63
2kmc_A	102	Fermitin family homolog 1; kindlin, cytoskeleton,	86.05
4da1_A	389	Protein phosphatase 1K, mitochondrial; metal-ION-a	85.86
3uf8_A	209	Ubiquitin-like protein SMT3, peptidyl-prolyl CIS-	85.78
3jyu_A	231	Ubiquitin carboxyl-terminal hydrolase; domain in u	85.13
3ge3_C	84	Toluene-4-monooxygenase system protein B; DIIRON h	84.7
2kl0_A	73	Putative thiamin biosynthesis THis; structural gen	84.5
1tyg_B	87	YJBS; alpha beta barrel, protein-protein complex,	84.4
3qij_A	296	Protein 4.1; cytoskeleton, structural genomics, st	83.93
1wgr_A	100	Growth factor receptor-bound protein 7; RA domain,	83.51
2juo_A	89	GA-binding protein alpha chain; OST, ubiquitin, tr	82.59
4a3p_A	217	Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {H	81.72
1vjk_A	98	Molybdopterin converting factor, subunit 1; struct	80.17

>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=99.97  E-value=1.3e-30  Score=169.70  Aligned_cols=97  Identities=27%  Similarity=0.347  Sum_probs=94.1

Q ss_pred             CCCCceEEE-e-cCccc-----cccccccCCCcceeeee-ecCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-----
Q 042212            1 MPLEQQRLV-F-ADKSL-----LADYNIQKESTLHLVAR-LRGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-----   67 (97)
Q Consensus         1 ip~~~q~L~-~-~~~~L-----l~~y~i~~~s~i~l~~~-~~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-----   67 (97)
                      ||+++|+|+ | +|++|     |++|||.+|+++||+++ ++++|+|+||+.+|++++++|++++||+++|++|+     
T Consensus        38 ip~~~QrL~~~~~g~~L~d~~tL~~y~i~~~~~l~l~~~~~~~~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi  117 (159)
T 3rt3_B           38 VHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDKSDEPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGV  117 (159)
T ss_dssp             CCGGGEEEEEETTCCBCCTTSCGGGGTCCTTCEEEEEECCCCCCEEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHTC
T ss_pred             CCHHHEEEEEcCCCCCCCCCCCHHHcCCCCCCEEEEEccCCCCcEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHHHHCC
Confidence            799999999 9 79999     99999999999999999 58999999999999999999999999999999998     


Q ss_pred             --------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           68 --------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        68 --------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                              |+|++|+|+.+|++|||++|+++|+++|+|
T Consensus       118 p~~~q~L~~~G~~L~d~~tL~~y~i~~g~~l~l~~rl~  155 (159)
T 3rt3_B          118 QDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLR  155 (159)
T ss_dssp             CGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCC
T ss_pred             CHHHEEEEECCeecCCCCCHHHcCCCCCCEEEEEEecC
Confidence                    999999999999999999999999999986

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}

Probab=99.96  E-value=7.5e-30  Score=168.19  Aligned_cols=97  Identities=69%  Similarity=0.933  Sum_probs=92.5

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc--------
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS--------   67 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~--------   67 (97)
                      ||+++|+|+|+|++|     |++|||.+|+++||+++.+++|+++|++.+|+++++++++++||.+||++|+        
T Consensus        56 ip~~~QrL~~~g~~L~d~~tL~~~~i~~~~~l~l~~~~~gg~~i~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~  135 (172)
T 3u30_A           56 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPD  135 (172)
T ss_dssp             CCGGGEEEEETTEECCTTCBTGGGTCCTTCEEEEEECCCCCEEEEEEESSCCEEEEEECTTCBHHHHHHHHHHHHCCCGG
T ss_pred             cChHHEEEEECCccccccCCHhHcCCcccceeeeeecccccccceeecccCcceeEEecCCCCHHHHHHHHHHHhCCCce
Confidence            799999999999999     9999999999999999999999999999999999999999999999999998        


Q ss_pred             -----CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           68 -----SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        68 -----~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                           |+|++|+|+.+|++|+|++|+++|+++|+|
T Consensus       136 ~q~L~~~g~~L~D~~tL~~y~i~~g~tl~l~~rlr  170 (172)
T 3u30_A          136 QQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR  170 (172)
T ss_dssp             GCCEEETTEECCTTSBSGGGTCCTTCEEEECC---
T ss_pred             eEEEEECCccCCCCCcHHHhCCCCCCEEEEEEecC
Confidence                 999999999999999999999999999986

>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=99.95  E-value=4.3e-28  Score=155.74  Aligned_cols=97  Identities=69%  Similarity=0.933  Sum_probs=94.4

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc--------
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS--------   67 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~--------   67 (97)
                      ||+++|+|+|+|+.|     |++|||.+|+++|++.+.+++|+|+|++.+|+++.+++++++||++||++|+        
T Consensus        36 ip~~~q~L~~~g~~L~d~~tL~~~~i~~~~~l~l~~~~~~~~~i~Vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~  115 (152)
T 3b08_A           36 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPD  115 (152)
T ss_dssp             CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCTTCEEEEEEESSSCEEEEEECTTCBHHHHHHHHHHHHCCCGG
T ss_pred             cChHHeEEEECCeECcCcccHHHhccCCCCeeEEEeecccccceeeeecCCCEEEEEeCCCCcHHHHHHHHHHHhCcChh
Confidence            699999999999999     9999999999999999999999999999999999999999999999999998        


Q ss_pred             -----CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           68 -----SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        68 -----~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                           |+|+.|+|+.+|++|||++|+++++++|+|
T Consensus       116 ~qrL~~~g~~L~d~~tL~~~~i~~~~~i~l~~r~~  150 (152)
T 3b08_A          116 QQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR  150 (152)
T ss_dssp             GEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCC
T ss_pred             hEEEEECCEECCCCCCHHHcCCCCCCEEEEEEecC
Confidence                 999999999999999999999999999986

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens}

Probab=99.83  E-value=5.7e-21  Score=113.21  Aligned_cols=75  Identities=16%  Similarity=0.228  Sum_probs=59.4

Q ss_pred             cccCCCcceeeeeecCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCC
Q 042212           20 NIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQK   86 (97)
Q Consensus        20 ~i~~~s~i~l~~~~~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~   86 (97)
                      |..++++++++++.+..|+|+||+.+|+++.++|++++||++||++|+             |+|+.|+|+.+|++||| +
T Consensus         1 g~~~~~~~~~~~~~~~~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i-~   79 (88)
T 4eew_A            1 GMEPNDSTSTAVEEPDSLEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYNV-G   79 (88)
T ss_dssp             --------------CCEEEEEEEETTSCEEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGGTC-T
T ss_pred             CCCCCCceEEeecCCCeEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEECCCCCcHHHcCC-C
Confidence            567899999999999999999999999999999999999999999999             99999999999999999 8


Q ss_pred             CCEEEEEEe
Q 042212           87 ESTLHFVLR   95 (97)
Q Consensus        87 ~sti~l~~r   95 (97)
                      |+++|+++|
T Consensus        80 g~~i~lv~R   88 (88)
T 4eew_A           80 GKVIHLVER   88 (88)
T ss_dssp             TEEEEEEEC
T ss_pred             CcEEEEEEC
Confidence            999999986

>3phx_B Ubiquitin-like protein ISG15; OTU domain, DE-ubiquitinase, DE-isgylase, hydrolase-protein complex; 1.60A {Homo sapiens}

Probab=99.82  E-value=2.9e-20  Score=108.05  Aligned_cols=64  Identities=23%  Similarity=0.370  Sum_probs=61.0

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      .++|+|+||+.+|+++.++|++++||+++|++|+             |+|+.|+|+.+|++|||++|+++++++|+|
T Consensus         2 ~~~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~l~l~~rl~   78 (79)
T 3phx_B            2 DEPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLR   78 (79)
T ss_dssp             -CCEEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCB
T ss_pred             CCCEEEEEEeCCCCEEEEEECCcChHHHHHHHHHhhcCCCHHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecC
Confidence            3679999999999999999999999999999998             999999999999999999999999999986

>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=99.78  E-value=2.6e-19  Score=107.59  Aligned_cols=64  Identities=17%  Similarity=0.311  Sum_probs=57.3

Q ss_pred             eeeecCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEE
Q 042212           30 VARLRGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        30 ~~~~~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~   93 (97)
                      +-..+..|+|+||+++|++++++|+|++||.+||++|+             |+|++|+|+.||++|+|++|+|++|.
T Consensus        15 ~~~~~~mIqI~Vk~~~Gkk~~v~v~p~DTI~~LK~~I~~k~Gip~~qQrLif~Gk~LkD~~TL~dY~I~dgstLhL~   91 (93)
T 3plu_A           15 VPRGSHMIEVVVNDRLGKKVRVKCLGEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLELY   91 (93)
T ss_dssp             -----CEEEEEEECTTSCEEEEEEETTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEE
T ss_pred             cCCCCceEEEEEECCCCCEEEEEECCcCHHHHHHHHHHHHhCCCHHHEEEEeCCEEccCcCCHHHcCCCCCCEEEEE
Confidence            33445669999999999999999999999999999999             99999999999999999999999985

>3v6c_B Ubiquitin; structural genomics, structural genomics consortium, SGC, UB protease, hydrolase-signaling protein complex; 1.70A {Homo sapiens} PDB: 3v6e_B

Probab=99.78  E-value=3.4e-19  Score=106.29  Aligned_cols=64  Identities=61%  Similarity=0.808  Sum_probs=61.4

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      ...|+|+||+.+|+++.++|++++||.+||++|+             |+|+.|+|+.+|++|||++|++|++++|+|
T Consensus        15 ~~~m~i~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~rlr   91 (91)
T 3v6c_B           15 RGSMQIFVNTLTGTHITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   91 (91)
T ss_dssp             CCSEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTCBTGGGTCCTTCEEEEECCCC
T ss_pred             CCeEEEEEEeCCCCEEEEEECCCCCHHHHHHHHHhhhCCChhhEEEEECCeECCCcCcHHHCCCCCCCEEEEEEecC
Confidence            3569999999999999999999999999999998             999999999999999999999999999987

>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=99.77  E-value=5.7e-19  Score=104.95  Aligned_cols=61  Identities=38%  Similarity=0.507  Sum_probs=59.3

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      |+|+||+.+|++++++|++++||++||++|+             |+|+.|+|+.+|++|+|++|+++++++|+|
T Consensus         1 M~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~l~l~~rl~   74 (88)
T 4fbj_B            1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALR   74 (88)
T ss_dssp             CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBTTTTTCCTTCEEEEECBCC
T ss_pred             CEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHCcChhHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEECC
Confidence            7999999999999999999999999999999             999999999999999999999999999986

>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=99.76  E-value=1.2e-18  Score=102.82  Aligned_cols=64  Identities=39%  Similarity=0.539  Sum_probs=61.3

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      ..+|+|+||+.+|+++.++|++++||.+||++|+             |+|+.|+|+.+|++|+|+++++|++++|+|
T Consensus        10 ~~~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~i~l~~rl~   86 (88)
T 3dbh_I           10 GGSMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLRLR   86 (88)
T ss_dssp             CCCEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCCEEETTEECCTTSBGGGGTCCTTCEEEECCCCC
T ss_pred             CCcEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHCcCHHHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEeCC
Confidence            4569999999999999999999999999999998             999999999999999999999999999986

>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=99.75  E-value=1.9e-18  Score=99.96  Aligned_cols=63  Identities=27%  Similarity=0.447  Sum_probs=58.9

Q ss_pred             CCeeeEEECCCCCEE-EEe-ecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           35 GRMQIFVKTSTGKTI-TLE-VESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~-~l~-v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      ++|+|+||+.+|+++ +++ +++++||++||++|+             |+|++|+|+.+|++|||++|+++++++|+.
T Consensus         1 g~m~i~Vk~~~g~~~~~l~~v~~~~tv~~lK~~i~~~~gip~~~qrL~~~g~~L~d~~tL~~~~i~~g~~i~l~~r~~   78 (78)
T 2faz_A            1 GSMWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLLVRQS   78 (78)
T ss_dssp             -CEEEEEEETTSSCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTTTTTCCTTCEEEEEECCC
T ss_pred             CcEEEEEEECCCCEEEEEeccCCCCCHHHHHHHHHHHHCcChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEeCC
Confidence            579999999999985 999 999999999999999             999999999999999999999999999863

>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=99.75  E-value=3.3e-18  Score=97.96  Aligned_cols=61  Identities=38%  Similarity=0.507  Sum_probs=59.0

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      |+|+||+.+|+++.+++++++||++||++|+             |+|+.|+|+.+|++|||++|+++++++|++
T Consensus         1 M~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~~i~~~~q~L~~~g~~L~d~~tL~~~~i~~g~~i~l~~~~~   74 (76)
T 1ndd_A            1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALR   74 (76)
T ss_dssp             CEEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCC
T ss_pred             CEEEEECCCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCC
Confidence            8999999999999999999999999999998             999999999999999999999999999975

>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=99.74  E-value=2.6e-18  Score=100.59  Aligned_cols=63  Identities=44%  Similarity=0.623  Sum_probs=59.4

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      ..|+|+||+.+|+++.+++++++||.+||++|+             |+|+.|+|+.+|++|+|+++++|++++|++
T Consensus         2 s~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~~ip~~~qrL~~~g~~L~d~~tL~~~~i~~~~~i~l~~rl~   77 (85)
T 3n3k_B            2 SHMRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIHNHSALYLLLKLR   77 (85)
T ss_dssp             --CEEEEECGGGCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETBEECCTTCBTTTTTCCTTCEEEEEECCC
T ss_pred             CeEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCeECCCCCCHHHCCCCCCCEEEEEEecc
Confidence            369999999999999999999999999999998             999999999999999999999999999985

>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=99.74  E-value=5.3e-18  Score=99.19  Aligned_cols=63  Identities=59%  Similarity=0.729  Sum_probs=60.0

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      .+|+|+|++.+|+++.+++++++||.+||++|+             |+|+.|+|+.+|++|+|++++++++++|++
T Consensus         2 s~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~~i~~~~qrL~~~g~~L~d~~tL~~~~i~~~~~l~l~~r~~   77 (85)
T 3mtn_B            2 SHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKWSTLFLLLRLR   77 (85)
T ss_dssp             -CEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBTGGGTCCTTCEEEEECCCC
T ss_pred             CeEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHCcChHHEEEEECCEECCCCCCHHHcCCCCCCEEEEEEECc
Confidence            469999999999999999999999999999999             999999999999999999999999999975

>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=99.74  E-value=3.9e-18  Score=101.28  Aligned_cols=63  Identities=19%  Similarity=0.256  Sum_probs=59.6

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      +..|+|+||+.+|+++.++|++++||.+||++|+             |+|+.|+|+.+|++|+| +|++||+++|++
T Consensus         3 ~~~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~d~~tL~~~~i-~g~~i~l~~~~~   78 (90)
T 4dwf_A            3 PDSLEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVIHLVERAP   78 (90)
T ss_dssp             CCEEEEEEEETTCCEEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGGTC-TTEEEEEEECCC
T ss_pred             CcEEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCeECCCCCCHHHcCC-CCcEEEEEecCC
Confidence            3569999999999999999999999999999999             99999999999999999 899999999863

>4hcn_B Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidase, NEDD8, protein binding; 2.60A {Saccharomyces cerevisiae}

Probab=99.73  E-value=3.6e-18  Score=103.25  Aligned_cols=64  Identities=66%  Similarity=0.800  Sum_probs=60.2

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      ...|+|+||+.+|+++.++|++++||.+||++|+             |+|+.|+|+.+|++|+|++|++|++++|+|
T Consensus        20 ~~~m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~i~l~~rl~   96 (98)
T 4hcn_B           20 GRPMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   96 (98)
T ss_dssp             --CCEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTCBSGGGTCCTTEEEEEECBCS
T ss_pred             CCeEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecC
Confidence            3569999999999999999999999999999998             999999999999999999999999999986

>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=99.73  E-value=5.8e-18  Score=101.52  Aligned_cols=62  Identities=65%  Similarity=0.813  Sum_probs=59.2

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      +|+|+||+.+|+++.++|++++||.+||++|+             |+|+.|+|+.+|++|+|++|++|++++|++
T Consensus         1 gm~i~vk~~~g~~~~~~v~~~~TV~~LK~~i~~~~gip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~i~l~~r~~   75 (96)
T 3k9o_B            1 GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   75 (96)
T ss_dssp             -CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCC
T ss_pred             CcEEEEEeCCCCEEEEEECCCCCHHHHHHHHHhhhCCChhHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEEcC
Confidence            48999999999999999999999999999998             999999999999999999999999999975

>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=99.73  E-value=4.3e-18  Score=104.55  Aligned_cols=63  Identities=17%  Similarity=0.300  Sum_probs=58.9

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc----------------------------CCCeeCC-CCCcccccccC
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS----------------------------SPAGNFE-DGWTQADYNIQ   85 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~----------------------------~~gk~L~-d~~tL~~y~I~   85 (97)
                      ..|+|+|++++|++++++|++++||++||++|+                            |+|++|. |+.||++|||+
T Consensus         6 ~~M~I~Vk~l~g~~~~v~V~~~~TV~dLK~~I~~~~~i~~~~q~g~~~isw~~~w~q~~Li~~Gk~L~dD~~tL~dygI~   85 (105)
T 1v2y_A            6 SGMTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLRDYGIR   85 (105)
T ss_dssp             CSEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHHHHHHHTTCCCCCCHHHHHTTEEEESSSCEECCSSSBHHHHTCC
T ss_pred             CcEEEEEEecCCCEEEEEECCCChHHHHHHHHHHHhCCCcccccCcceeeeeecceeEEEEeCCcCccCCcCCHHHcCCC
Confidence            459999999999999999999999999999987                            7899996 67999999999


Q ss_pred             CCCEEEEEEeeC
Q 042212           86 KESTLHFVLRLS   97 (97)
Q Consensus        86 ~~sti~l~~rl~   97 (97)
                      +|++|||++++|
T Consensus        86 ~g~~l~lv~~lr   97 (105)
T 1v2y_A           86 NRDEVSFIKKLG   97 (105)
T ss_dssp             SSEEEEEEECSC
T ss_pred             CCCEEEEEehhc
Confidence            999999999986

>2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing, protein binding; 2.60A {Homo sapiens}

Probab=99.73  E-value=8.7e-18  Score=103.74  Aligned_cols=80  Identities=51%  Similarity=0.598  Sum_probs=72.3

Q ss_pred             cccccCCCcceeeeeec--------CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCC
Q 042212           18 DYNIQKESTLHLVARLR--------GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDG   76 (97)
Q Consensus        18 ~y~i~~~s~i~l~~~~~--------~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~   76 (97)
                      .-++.+|.++++.....        ..|+|+||+.+|+++.++|++++||++||++|+             |+|+.|+|+
T Consensus         9 ~~~~~~~~~~~~~~~~~~~~~g~~~~~m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~   88 (111)
T 2ojr_A            9 NDGWIEGDELYIDTNNDGWIEGDELLAMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDG   88 (111)
T ss_dssp             CSSSCCGGGBCCCTTCSSSCCGGGSSCEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHCCCTTTEEEEETTEECCSS
T ss_pred             CCceecCCEEEEeecccccccCCCCCeEEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHHHCcCcccEEEEECCEECCCC
Confidence            34677888888877632        469999999999999999999999999999998             999999999


Q ss_pred             CcccccccCCCCEEEEEEeeC
Q 042212           77 WTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        77 ~tL~~y~I~~~sti~l~~rl~   97 (97)
                      .+|++|+|++|++|++++|+|
T Consensus        89 ~tL~~~gI~~gs~I~l~~rl~  109 (111)
T 2ojr_A           89 RTLSDYNIQKESTLHLVLRLR  109 (111)
T ss_dssp             CBTTTTTCCTTCEEEEEECCC
T ss_pred             CcHHHcCCCCCCEEEEEEeCC
Confidence            999999999999999999986

>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=99.73  E-value=4e-18  Score=98.94  Aligned_cols=62  Identities=10%  Similarity=0.174  Sum_probs=59.8

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      .|+|+|++.+|+++.++|++++||+++|++|+             |+|++|+|+.||++|+|++|++|++++|++
T Consensus         3 ~m~i~vk~~~g~~~~~~v~~~~tv~~lk~~i~~~~gi~~~~qrL~~~G~~L~d~~tl~~~~i~~~~~i~l~~~~~   77 (79)
T 2uyz_B            3 YIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQT   77 (79)
T ss_dssp             EEEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCHHHHTCCTTEEEEEEECCC
T ss_pred             eEEEEEECCCCCEEEEEECCCChHHHHHHHHHHHHCCCcccEEEEECCEEeCCCCCHHHcCCCCCCEEEEEEecc
Confidence            59999999999999999999999999999998             999999999999999999999999999875

>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure, northeast structural genomics consortium, protein structure initiative, NESG; NMR {Homo sapiens}

Probab=99.73  E-value=4.3e-18  Score=101.06  Aligned_cols=63  Identities=24%  Similarity=0.377  Sum_probs=58.9

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      .+|+|+||+.+|+++.++|++++||++||++|+             |+|++|+|+.+|++|||++|++|+++++++
T Consensus         3 ~~m~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~~I~~g~~i~l~~~~~   78 (88)
T 2hj8_A            3 EPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLR   78 (88)
T ss_dssp             CEEEEEEEETTSCEEEEEEESSSBHHHHHHHHHHHTCSCTTTEEEESSSSCCCTTSBHHHHHCSTTCEEEEEEC--
T ss_pred             ccEEEEEECCCCCEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEEcC
Confidence            569999999999999999999999999999998             999999999999999999999999999864

>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=99.72  E-value=4.6e-18  Score=100.23  Aligned_cols=64  Identities=19%  Similarity=0.246  Sum_probs=61.0

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      ++.|+|+||+.+|+++.+++++++||.+||++|+             |+|+.|+|+.+|++|+|+++++|++++|++
T Consensus         5 ~~~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~qrL~~~Gk~L~d~~tL~~~~i~~g~~i~l~~~~~   81 (87)
T 1wh3_A            5 SSGIQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKG   81 (87)
T ss_dssp             SSSEEEEEEETTTEEEEEEECSSSBHHHHHHHHHHHTCCCTTTEEEEETTEECCSSSBHHHHTCCTTEEEEEEECSC
T ss_pred             CCCEEEEEEcCCCCEEEEEeCCCChHHHHHHHHHHHhCCChHHEEEEECCEEccCCCCHHHCCCCCCCEEEEEEecc
Confidence            4679999999999999999999999999999998             999999999999999999999999999975

>1sif_A Ubiquitin; hydrophobic mutants, folding, stability, structural protein; 2.18A {Homo sapiens} SCOP: d.15.1.1

Probab=99.72  E-value=7.1e-18  Score=100.16  Aligned_cols=63  Identities=54%  Similarity=0.736  Sum_probs=57.1

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      .+|+|+|++.+|+++.+++++++||++||++|+             |+|+.|+|+.+|++|||++|++|++++|++
T Consensus         8 ~~~~i~v~~~~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~r~~   83 (88)
T 1sif_A            8 QGLQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   83 (88)
T ss_dssp             --CEEEEEETTSCEEEEECCTTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBSGGGTCCTTCEEEEEC---
T ss_pred             cceEEEEEeCCCCEEEEEECCCChHHHHHHHHHHHHCcChhhEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCC
Confidence            469999999999999999999999999999998             999999999999999999999999999875

>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=99.57  E-value=3e-19  Score=102.88  Aligned_cols=61  Identities=20%  Similarity=0.291  Sum_probs=59.1

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      |+|+||+.+|+++.+++++++||++||++|+             |+|+.|+|+.+|++|||++|+++++++|+|
T Consensus         1 M~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~rlr   74 (76)
T 3b1l_X            1 MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKQQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPR   74 (76)
Confidence            8999999999999999999999999999999             999999999999999999999999999986

>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=99.72  E-value=1e-17  Score=95.89  Aligned_cols=61  Identities=64%  Similarity=0.829  Sum_probs=58.8

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      |+|+||+.+|+++.+++++++||++||++|+             |+|+.|+|+.+|++|||++|+++++++|++
T Consensus         1 M~i~vk~~~g~~~~i~v~~~~tv~~lK~~i~~~~~i~~~~q~L~~~g~~L~d~~tL~~~~i~~g~~i~l~~~~~   74 (76)
T 3a9j_A            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLR   74 (76)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTGGGTCCTTCEEEEEECCC
T ss_pred             CEEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEEeCC
Confidence            8999999999999999999999999999998             999999999999999999999999999975

>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana, uncharacterized putative protein, NESG, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.72  E-value=4.7e-18  Score=100.39  Aligned_cols=62  Identities=16%  Similarity=0.217  Sum_probs=59.2

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCee-CCCCCcccccccCCCCEEEEEEee
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGN-FEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~-L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      .-|+|+|++.+|++++++|++++||++||++|+             |+|++ |+|+.+|++|||++|++|++++|.
T Consensus         9 ~~~~i~vk~l~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~lL~D~~tL~~y~I~~gs~i~lv~~p   84 (84)
T 2kk8_A            9 SHMKFLVENLNGSSFELEVDYRDTLLVVKQKIERSQHIPVSKQTLIVDGIVILREDLTVEQCQIVPTSDIQLEVSS   84 (84)
T ss_dssp             CCEEEEEEETTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCCSSSBHHHHTCCTTSCEEEEECC
T ss_pred             CceEEEEEecCCcEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCEEecCCcCCHHHcCCCCCCEEEEEEcC
Confidence            459999999999999999999999999999999             99999 999999999999999999999874

>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=99.72  E-value=6.2e-18  Score=102.18  Aligned_cols=64  Identities=9%  Similarity=0.159  Sum_probs=61.0

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      +..|+|+||+.+|+++.++|++++||.+||++|+             |+|++|+|+.||++|+|+++++|++++|+|
T Consensus        19 ~~~m~I~Vk~~~g~~~~l~v~~~~tv~~lK~~i~~~~gip~~~qrLif~Gk~L~d~~tl~dy~i~~g~~I~l~~~~~   95 (97)
T 1wyw_B           19 GEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQT   95 (97)
T ss_dssp             CCEEEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCHHHHTCCTTCEEEEEESSS
T ss_pred             CCcEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCChhhEEEEECCeEcCCCCCHHHCCCCCCCEEEEEEecC
Confidence            3459999999999999999999999999999998             999999999999999999999999999975

>2dzi_A Ubiquitin-like protein 4A; GDX, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=7.6e-18  Score=97.81  Aligned_cols=64  Identities=25%  Similarity=0.377  Sum_probs=60.5

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      +..|+|+|++.+|+++.+++++++||++||++|+             |+|+.|+|+.+|++|||++|+++++++|++
T Consensus         5 ~~~m~i~vk~~~g~~~~~~v~~~~tV~~LK~~i~~~~~i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~~~   81 (81)
T 2dzi_A            5 SSGMQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLNVPVRQQRLLFKGKALADGKRLSDYSIGPNSKLNLVVKPL   81 (81)
T ss_dssp             SSSEEEEEEETTSCEEEEEECSSCBHHHHHHHHHHHTCCCTTTCEEEETTEECCTTSBGGGGTCCSSBCCEEECCCC
T ss_pred             CCcEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEeCC
Confidence            3569999999999999999999999999999998             999999999999999999999999999875

>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=99.71  E-value=7.3e-18  Score=102.67  Aligned_cols=58  Identities=17%  Similarity=0.308  Sum_probs=56.2

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEE
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      |+|+||++.|++++++|+|++||.+||++|+             |+|++|+|+.||++|||+++++|+|+.
T Consensus        29 m~I~VKtl~Gk~i~lev~p~dTV~~lK~~Ia~k~Gip~~qQrLi~~Gk~L~D~~TL~dygI~~gstlhL~~   99 (100)
T 1uh6_A           29 IEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLELYY   99 (100)
T ss_dssp             EEEEEECSSSSCEEEEEETTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCSSCBHHHHTCCTTEEEEEEC
T ss_pred             EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhCCCHHHEEEEECCEECCCCCCHHHcCCCCCCEEEEEe
Confidence            9999999999999999999999999999999             999999999999999999999999863

>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=99.71  E-value=1.8e-17  Score=98.10  Aligned_cols=63  Identities=25%  Similarity=0.396  Sum_probs=59.6

Q ss_pred             CCeeeEEECCCC-CEEEE-eecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           35 GRMQIFVKTSTG-KTITL-EVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        35 ~~m~i~vk~~~g-~~~~l-~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      ..|+|+||+.+| +++.+ +|++++||.+||++|+             |+|+.|+|+.+|++|+|+++++|++++|++
T Consensus         6 ~~m~i~Vk~~~g~~~~~l~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~~~   83 (89)
T 1wy8_A            6 SGMWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVRPD   83 (89)
T ss_dssp             SCEEEEEEETTCSCEEEEEEECTTCBHHHHHHHHHHHSCCCTTTEEEEETTEECCSSSBHHHHTCCTTCEEEEEECCC
T ss_pred             CcEEEEEEECCCCceEEEEecCCCCCHHHHHHHHHHHHCcChhhEEEEECCeECCCCCCHHHCCCCCCCEEEEEEeCC
Confidence            569999999999 79999 5999999999999998             999999999999999999999999999875

>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=99.70  E-value=3.6e-17  Score=101.04  Aligned_cols=63  Identities=63%  Similarity=0.779  Sum_probs=60.6

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      ..|+|+||+.+|+++.++|++++||.+||++|+             |+|+.|+|+.+|++|+|+++++|++++|+|
T Consensus        34 ~~m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~gI~~gs~I~l~~rl~  109 (111)
T 3vdz_A           34 LAMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR  109 (111)
T ss_dssp             GCEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTTTTTCCTTCEEEEEECCC
T ss_pred             ccEEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHhCCChHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecC
Confidence            359999999999999999999999999999998             999999999999999999999999999986

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.70  E-value=2.1e-17  Score=99.42  Aligned_cols=64  Identities=16%  Similarity=0.231  Sum_probs=60.1

Q ss_pred             ecCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCC-CcccccccCCCCEEEEEEeeC
Q 042212           33 LRGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDG-WTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        33 ~~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~-~tL~~y~I~~~sti~l~~rl~   97 (97)
                      ...+|+|+||+..| +++++|++++||++||++|+             |+|++|+|+ .+|++|||++|++|++++|++
T Consensus        12 ~~~~~~I~Vk~~~~-~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~~tL~~ygI~~gstl~lv~r~~   89 (94)
T 2kan_A           12 AVRKIHVTVKFPSK-QFTVEVDRTETVSSLKDKIHIVENTPIKRMQLYYSGIELADDYRNLNEYGITEFSEIVVFLKSI   89 (94)
T ss_dssp             SSCCEEEEEECSSC-EEEEEECTTCBHHHHHHHHHHHSSSCTTTEEEEETTEEECCTTSBHHHHTCCTTEEEEEEECCC
T ss_pred             CCCCEEEEEEcCCc-EEEEEECCCCcHHHHHHHHHHHHCcCHHHEEEEECCEECCCCcccHHHCCCCCCCEEEEEEeCC
Confidence            35679999999988 89999999999999999999             999999999 999999999999999999975

>3m63_B Ubiquitin domain-containing protein DSK2; armadillo-like repeats, UBL conjugation pathway, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=99.69  E-value=5e-18  Score=103.43  Aligned_cols=77  Identities=19%  Similarity=0.276  Sum_probs=55.4

Q ss_pred             cccccccCCCcceeeeeecCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCccccc
Q 042212           16 LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADY   82 (97)
Q Consensus        16 l~~y~i~~~s~i~l~~~~~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y   82 (97)
                      .+||.|  ++|.++.++....|.|+|++ +|+++.++|++++||++||++|+             |+|+.|+|+.+|++|
T Consensus        10 ~~~~~~--~~t~~l~l~~~m~i~I~Vk~-~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~   86 (101)
T 3m63_B           10 MSDYDI--PTTENLYFQGAMSLNIHIKS-GQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESY   86 (101)
T ss_dssp             ---------------------CCEEEEC-SSCCCCBCCCTTSBHHHHHHHHHHHHSCCSTTCCEEETTEECCTTSBTTTT
T ss_pred             ccccCC--CcceeecccCCcEEEEEEEE-CCEEEEEEeCCCCCHHHHHHHHHHHHCcChHHEEEEECCEECCCcCcHHHC
Confidence            578888  45667777766778899998 89999999999999999999998             999999999999999


Q ss_pred             ccCCCCEEEEEEe
Q 042212           83 NIQKESTLHFVLR   95 (97)
Q Consensus        83 ~I~~~sti~l~~r   95 (97)
                      ||++|++|+++.+
T Consensus        87 gI~~g~tI~lv~~   99 (101)
T 3m63_B           87 HIQDGHSVHLVKS   99 (101)
T ss_dssp             TCCTTEEEEECCC
T ss_pred             CCCCCCEEEEEeC
Confidence            9999999999865

>2l7r_A Ubiquitin-like protein FUBI; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=99.69  E-value=2e-17  Score=99.21  Aligned_cols=62  Identities=24%  Similarity=0.345  Sum_probs=57.2

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      +..|+|+||+  |+++.++|++++||++||++|+             |+|++|+|+.+|++|+|+++++|++++|+|
T Consensus        17 ~~~m~I~Vk~--g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~y~I~~gstI~lv~rl~   91 (93)
T 2l7r_A           17 RGSMQLFVRA--QELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAGAPLEDEATLGQCGVEALTTLEVAGRML   91 (93)
T ss_dssp             ---CEEEEES--SSEEEEECCSSCBHHHHHHHHHHHHTCCGGGCEEEETTEECCTTSBHHHHTCCSSCEEEEECCCC
T ss_pred             CCcEEEEEEC--CCEEEEEeCCCCcHHHHHHHHHHHhCcChhHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecC
Confidence            3569999998  8999999999999999999998             999999999999999999999999999986

>3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=99.69  E-value=3.1e-17  Score=100.57  Aligned_cols=59  Identities=14%  Similarity=0.243  Sum_probs=56.6

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      |+|+||+.+|+++.++|++++||.+||++|+             |+|+.|+|+.+|++|||++|++|+++++
T Consensus         2 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~~i~~g~~i~lv~~   73 (106)
T 3m62_B            2 VSLTFKNFKKEKVPLDLEPSNTILETKTKLAQSISCEESQIKLIYSGKVLQDSKTVSECGLKDGDQVVFMVS   73 (106)
T ss_dssp             -CEEEECTTCCEEEECCCTTSBHHHHHHHHHHTTTSCGGGCEEEETTEECCTTSBTTTTTCCTTCEEEEECC
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCChhhEEEEECCEECCCcCCHHHcCCCCCCEEEEEEc
Confidence            8999999999999999999999999999998             9999999999999999999999999986

>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=99.69  E-value=7e-17  Score=94.61  Aligned_cols=63  Identities=14%  Similarity=0.182  Sum_probs=58.0

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc----------------CCCeeCCCCCcccccccCCCCEEEEEEee
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS----------------SPAGNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~----------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      +..|+|+||+.+|+++.++|++++||++||++|+                |+|+.|+|+.+|++|||++|++++++.+.
T Consensus         3 ~~~m~i~vk~~~g~~~~~~v~~~~TV~~lK~~i~~~~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~i~l~~~~   81 (85)
T 2wyq_A            3 PMAVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTK   81 (85)
T ss_dssp             -CCEEEEEEETTSCEEEEEECTTSBHHHHHHHHHHHHCTTTCCGGGEEEEETTEECCTTSBGGGGCCCTTSEEEEEEC-
T ss_pred             CceEEEEEEECCCCEEEEEECCCCCHHHHHHHHHhhccccCCCHHHeEEEECCEECcCCCCHHHcCCCCCCEEEEEEcC
Confidence            4679999999999999999999999999999875                89999999999999999999999999863

>2lxa_A Ubiquitin-like protein MDY2; ubiquitin-like domain, protein-protein interaction, SGT2 BIN domain, GET pathway, protein binding; NMR {Saccharomyces cerevisiae}

Probab=99.68  E-value=1.1e-17  Score=99.55  Aligned_cols=60  Identities=17%  Similarity=0.239  Sum_probs=56.2

Q ss_pred             eeeEEECCCCCEEEEeec--CCCcHHHhhccc-c-------------CCCeeCCCCCccccccc-CCCCEEEEEEee
Q 042212           37 MQIFVKTSTGKTITLEVE--SSDMIDNASRGS-S-------------SPAGNFEDGWTQADYNI-QKESTLHFVLRL   96 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~--~~~tV~~lK~~I-~-------------~~gk~L~d~~tL~~y~I-~~~sti~l~~rl   96 (97)
                      |+|+||+++|++++++|+  +++||.++|++| +             |+|++|+|+.+|++|+| ++|++++++++.
T Consensus         2 mqI~VKtl~g~~~~i~v~v~~~~TV~~lK~~I~~~~~gip~~~QrLi~~Gk~L~D~~tL~~y~I~~~~stl~v~~~~   78 (87)
T 2lxa_A            2 VHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKP   78 (87)
T ss_dssp             CEEEEEECSSSCEECCEECCTTCBHHHHHHHHHHTTSCSSSTTEEEEETTEECCTTCBHHHHCCCGGGCEEEEEECC
T ss_pred             EEEEEEcCCCCEEEEEEcCCCCCcHHHHHHHHHHHhcCCChHHEEEEECCEECcCcCCHHHcCCCCCCCEEEEEcCC
Confidence            899999999999999866  999999999999 5             99999999999999999 799999998863

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B

Probab=99.68  E-value=6.4e-17  Score=106.54  Aligned_cols=61  Identities=69%  Similarity=0.855  Sum_probs=59.4

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      |+|+||+.+|+++.++|++++||.+||++|+             |+|++|+|+.+|++|+|++|+++|+++|+|
T Consensus         1 MqI~Vk~~~Gk~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~y~I~~gstI~Lvlrl~   74 (169)
T 3l0w_B            1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   74 (169)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHCCCTTTEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCC
T ss_pred             CEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHHCcCHHHEEEEECCccccCcCcHHHcCCCCCCEEEEEEEec
Confidence            8999999999999999999999999999998             999999999999999999999999999975

>1yx5_B Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo sapiens} SCOP: d.15.1.1 PDB: 1yx6_B

Probab=99.68  E-value=8.3e-17  Score=97.05  Aligned_cols=61  Identities=66%  Similarity=0.832  Sum_probs=58.5

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      |+|+||+.+|+++.++|++++||++||++|+             |+|+.|+|+.+|++|||++|++|+++++++
T Consensus         1 M~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~gi~~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~   74 (98)
T 1yx5_B            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   74 (98)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHTCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCC
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEeCC
Confidence            8999999999999999999999999999998             999999999999999999999999998864

>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=99.68  E-value=8e-17  Score=101.62  Aligned_cols=70  Identities=19%  Similarity=0.320  Sum_probs=61.2

Q ss_pred             eeeeeecCCeeeEEECCCCCEE-EEeecCCCcHHHhhccc-----c---------------CCCeeCCCCCcccccccCC
Q 042212           28 HLVARLRGRMQIFVKTSTGKTI-TLEVESSDMIDNASRGS-----S---------------SPAGNFEDGWTQADYNIQK   86 (97)
Q Consensus        28 ~l~~~~~~~m~i~vk~~~g~~~-~l~v~~~~tV~~lK~~I-----~---------------~~gk~L~d~~tL~~y~I~~   86 (97)
                      ||.......|+|+||+.+|+.+ +++++|++||++||++|     +               |+||+|+|+.||++|+|++
T Consensus         8 ~~~~~~~~~~~i~~kt~~G~~i~~l~v~psdTV~~lK~kI~~~~p~dkegiP~~~~qQrLIy~GK~LeD~~TLsdy~I~~   87 (126)
T 1se9_A            8 HLEAEVHNQLEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSKTVKDYRSPV   87 (126)
T ss_dssp             --CCSSCCCEEEEEEETTSCEEEEEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEEETTEECCTTSBGGGGSCCT
T ss_pred             hhhhhhcccEEEEEEECCCCEEEeeecCccCHHHHHHHHHHhhcccccccCCCChhhEEEEECCeECcCCCcHHHcCCCc
Confidence            3333344679999999999988 79999999999999999     2               9999999999999999999


Q ss_pred             C------CEEEEEEeeC
Q 042212           87 E------STLHFVLRLS   97 (97)
Q Consensus        87 ~------sti~l~~rl~   97 (97)
                      +      +|+||++|++
T Consensus        88 ~~~~~~v~tmhlVlrl~  104 (126)
T 1se9_A           88 SNLAGAVTTMHVIIQAP  104 (126)
T ss_dssp             TSCTTCCEEEEEEECCC
T ss_pred             CCccCCcEEEEEEeccC
Confidence            8      7899999975

>4a20_A Ubiquitin-like protein MDY2; protein binding, GET-pathway, tail-anchored proteins; 1.78A {Saccharomyces cerevisiae} PDB: 2lxc_A 4goc_A

Probab=99.68  E-value=6.3e-17  Score=98.25  Aligned_cols=62  Identities=15%  Similarity=0.238  Sum_probs=56.6

Q ss_pred             cCCeeeEEECCCCCEEEE--eecCCCcHHHhhccc-c-------------CCCeeCCCCCccccccc-CCCCEEEEEEe
Q 042212           34 RGRMQIFVKTSTGKTITL--EVESSDMIDNASRGS-S-------------SPAGNFEDGWTQADYNI-QKESTLHFVLR   95 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l--~v~~~~tV~~lK~~I-~-------------~~gk~L~d~~tL~~y~I-~~~sti~l~~r   95 (97)
                      .++|+|+||+++|+++++  +|++++||.+||++| +             |+|++|+|+.+|++|+| ++|++|+++++
T Consensus        17 ~~~m~I~VKtl~g~~~~i~v~v~~~~TV~~lK~~I~~~~~gip~~~QrLi~~Gk~L~D~~tL~dy~I~~~g~ti~lmvs   95 (98)
T 4a20_A           17 NAAVHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIK   95 (98)
T ss_dssp             -CCEEEEEEECSSSCEEEEEEECTTCBHHHHHHHHHHTTSCSCGGGEEEEETTEEECTTCBGGGSCCBTTBCEEEEEEC
T ss_pred             CCCEEEEEEcCCCCEEEEEEecCCCChHHHHHHHHHHHhcCCChhhEEEEECCEECcCcCCHHHcCcCCCCCEEEEEEe
Confidence            467999999999998777  566999999999999 4             99999999999999999 99999999986

>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=99.67  E-value=1.1e-16  Score=99.79  Aligned_cols=65  Identities=12%  Similarity=0.130  Sum_probs=58.2

Q ss_pred             ecCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc---------------------CCCeeCCCCCcccccccCCC--CE
Q 042212           33 LRGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS---------------------SPAGNFEDGWTQADYNIQKE--ST   89 (97)
Q Consensus        33 ~~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~---------------------~~gk~L~d~~tL~~y~I~~~--st   89 (97)
                      ....|+|+||+++|++++++|++++||++||++|+                     |+|++|+|+.||++|+|+.+  ++
T Consensus        13 ~~~~m~I~vKtl~G~t~~lev~~s~TV~~lK~kI~~~~p~dwke~~p~p~~qqrLIy~GK~LeD~~TL~~y~I~~~~~~t   92 (116)
T 1wgh_A           13 PADMINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTV   92 (116)
T ss_dssp             CSSSEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEEETTEEECSSCBTTTTTCCSSCEEE
T ss_pred             CCCeEEEEEEeCCCCEEEEEECCcCHHHHHHHHHHHhcccccccCCCCChHHEEEEECCcCCCCCCcHHHcCCCCCCceE
Confidence            34569999999999999999999999999999875                     78999999999999999766  67


Q ss_pred             EEEEEeeC
Q 042212           90 LHFVLRLS   97 (97)
Q Consensus        90 i~l~~rl~   97 (97)
                      +||++|+.
T Consensus        93 lhLvlr~~  100 (116)
T 1wgh_A           93 MHLVARET  100 (116)
T ss_dssp             EEEEECSS
T ss_pred             EEEEccCC
Confidence            99998863

>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=99.67  E-value=9.5e-17  Score=99.00  Aligned_cols=65  Identities=25%  Similarity=0.349  Sum_probs=61.4

Q ss_pred             ecCCeeeEEECC---CCCEEEEeecC-CCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           33 LRGRMQIFVKTS---TGKTITLEVES-SDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        33 ~~~~m~i~vk~~---~g~~~~l~v~~-~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      .++.|+|+|+++   +|+++.++|++ ++||.+||++|+             |+|+.|+|+.+|++|+|++|++|++++|
T Consensus        24 ~~~~i~i~Vk~~~~~~g~~~~l~v~~l~~TV~~LK~~I~~~~gip~~~QrL~~~Gk~L~D~~tL~~y~I~~g~~l~l~~r  103 (111)
T 1we6_A           24 HPGPATIRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLR  103 (111)
T ss_dssp             CCSCEEEEECCTTCSSSCCEEEEESCSSSBHHHHHHHHHHHTTCCTTTSEEECSSSBCCTTSBTTTTTCSSSCEEEEECS
T ss_pred             CCCcEEEEEEecccCCCcEEEEEecCCCCcHHHHHHHHHHHHCCCHHHeEEEECCEECCCCCcHHHCCCCCCCEEEEEEE
Confidence            457899999998   89999999998 999999999999             9999999999999999999999999999


Q ss_pred             eC
Q 042212           96 LS   97 (97)
Q Consensus        96 l~   97 (97)
                      +|
T Consensus       104 ~~  105 (111)
T 1we6_A          104 ER  105 (111)
T ss_dssp             SC
T ss_pred             cC
Confidence            75

>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion protein; ubiquitin interacting motif, UIM, protein domain interface; NMR {Saccharomyces cerevisiae}

Probab=99.66  E-value=1.7e-16  Score=98.50  Aligned_cols=64  Identities=63%  Similarity=0.818  Sum_probs=61.2

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      .++++|+|++++|+++.++|++++||++||++|+             |+|++|+|+.+|++|+|++|++|++++|++
T Consensus         7 ~~~~~i~vk~l~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~ygI~~gstI~l~~~~~   83 (114)
T 2kdi_A            7 HGEFQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLEDGRTLSDYNIQRESTLHLVLRLR   83 (114)
T ss_dssp             CCCCEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTTTTTCCSSCEEEEEECCC
T ss_pred             CCcEEEEEEeCCCcEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEEcC
Confidence            4789999999999999999999999999999998             999999999999999999999999999875

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens}

Probab=99.66  E-value=1.9e-16  Score=106.04  Aligned_cols=62  Identities=63%  Similarity=0.771  Sum_probs=60.0

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      .|+|+||+++|++++++|++++||.+||++|+             |+|++|+|+.+|++|+|+++++|+|++|++
T Consensus       105 eMqI~VKtl~Gkt~~l~V~~s~TV~~LK~kI~~~~gIp~~~QrLi~~Gk~L~D~~tL~dygI~~gstI~Lvlrlr  179 (189)
T 3q3f_A          105 GGQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR  179 (189)
T ss_dssp             CEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCCEEETTEECCTTCBGGGGTCCTTCEEEECCCCC
T ss_pred             ceeeeeecCCCCEEEEEeCCCCcHHHHHHHHHhccCCCHHHEEEEECCEECCCCCCHHHCCCCCCCEEEEEEEcC
Confidence            49999999999999999999999999999999             999999999999999999999999999975

>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling proteins; 1.15A {Saccharomyces cerevisiae} SCOP: d.15.1.1 PDB: 2bwe_S

Probab=99.65  E-value=2.7e-16  Score=90.35  Aligned_cols=58  Identities=17%  Similarity=0.263  Sum_probs=55.8

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      |+|+|++ +|+++.+++++++||.+||++|+             |+|+.|+|+.+|++|||++|++++++.+
T Consensus         5 m~i~vk~-~g~~~~~~v~~~~tV~~LK~~i~~~~~i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~   75 (77)
T 2bwf_A            5 LNIHIKS-GQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS   75 (77)
T ss_dssp             EEEEEEE-TTEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEEC
T ss_pred             EEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHhCCCHHHEEEEECCeEcCCCCCHHHcCCCCCCEEEEEEc
Confidence            8999999 89999999999999999999998             9999999999999999999999999875

>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=99.65  E-value=1.1e-16  Score=95.70  Aligned_cols=63  Identities=16%  Similarity=0.185  Sum_probs=58.5

Q ss_pred             CCeeeEEECCCCC--EEEEeecCCCcHHHhhcccc---------------CCCeeCCCCCccccc--ccCCCCEEEEEEe
Q 042212           35 GRMQIFVKTSTGK--TITLEVESSDMIDNASRGSS---------------SPAGNFEDGWTQADY--NIQKESTLHFVLR   95 (97)
Q Consensus        35 ~~m~i~vk~~~g~--~~~l~v~~~~tV~~lK~~I~---------------~~gk~L~d~~tL~~y--~I~~~sti~l~~r   95 (97)
                      ..|+|+||+.+|+  ++.+++++++||.+||++|+               |+|++|+|+.+|++|  +|+++++|||+++
T Consensus         6 ~~m~i~Vk~~~~~~~~~~v~v~~~~TV~~lK~~I~~~~~~~i~~~~QrLi~~Gk~L~D~~tL~~~~~~i~~~~~i~lv~~   85 (93)
T 1wgd_A            6 SGVTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVCN   85 (93)
T ss_dssp             CCCEEEEECSSSSCCCEEEECCTTSCHHHHHHHHHHHSTTCCCTTTCEEEETTEECCSSSCHHHHSCSSSCSEEEEEECC
T ss_pred             cEEEEEEEeCCCCeEEEEEecCCCCcHHHHHHHHHHHhcCCCChHHeEEEECCEECcCcCCHHHHhcCCCCCCEEEEEeC
Confidence            5699999999998  77888889999999999997               899999999999999  9999999999998


Q ss_pred             eC
Q 042212           96 LS   97 (97)
Q Consensus        96 l~   97 (97)
                      +|
T Consensus        86 ~~   87 (93)
T 1wgd_A           86 VK   87 (93)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=99.65  E-value=3.4e-16  Score=95.19  Aligned_cols=65  Identities=18%  Similarity=0.175  Sum_probs=59.4

Q ss_pred             eecCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           32 RLRGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        32 ~~~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      .....|+|+|++. |+++.++|++++||++||++|+             |+|+.|+|+.+|++|||++|++|+++.+++
T Consensus        21 ~~~~~m~I~Vk~~-g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~gI~~g~~I~l~~~~~   98 (101)
T 2klc_A           21 GHPKIMKVTVKTP-KEKEEFAVPENSSVQQFKEEISKRFKSHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQ   98 (101)
T ss_dssp             --CCCEEEEEECS-SCEEEEEECSCCCHHHHHHHHHHHHTCCGGGEEEEETTEEECTTCCTGGGTCCTTCEEEEEECCS
T ss_pred             CCCCeEEEEEEeC-CcEEEEEECCCCCHHHHHHHHHHHHCcChhhEEEEECCEECCCcCcHHHcCCCCCCEEEEEEcCC
Confidence            3456799999998 8999999999999999999998             999999999999999999999999998864

>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=99.65  E-value=1.4e-16  Score=97.53  Aligned_cols=63  Identities=21%  Similarity=0.252  Sum_probs=59.5

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEee
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      ...|+|+||+.+|+++.++|++++||.+||++|+             |+|+.|+|+.+|++|||++|++||++++.
T Consensus        21 ~~~m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~ygI~~g~ti~lv~~~   96 (106)
T 1ttn_A           21 GYECQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQ   96 (106)
T ss_dssp             CCSEEEEEEETTTEEEEEEECTTSHHHHHHHHHHHTTCCCSTTCEEEETTEECCTTSHHHHCCCSSSCEEEEECCC
T ss_pred             CCeEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHHCcCcccEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            3569999999999999999999999999999998             99999999999999999999999999874

>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=99.65  E-value=1.8e-16  Score=96.34  Aligned_cols=64  Identities=19%  Similarity=0.192  Sum_probs=59.3

Q ss_pred             ecCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           33 LRGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        33 ~~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      .+..|+|+|++.+|+ +.++|++++||.+||++|+             |+|+.|+|+.+|++|||++|++|++++|++
T Consensus        19 ~~~~m~I~Vk~~~g~-~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~ygI~~gstI~l~~r~~   95 (100)
T 1yqb_A           19 SPHLIKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQ   95 (100)
T ss_dssp             CTTEEEEEEECSSCE-EEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBHHHHTCCTTCEEEEEECCC
T ss_pred             CCCeEEEEEEcCCCc-EEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEECCCcCcHHHCCCCCCCEEEEEEcCC
Confidence            346699999999886 7999999999999999998             999999999999999999999999999874

>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=99.64  E-value=3.2e-16  Score=94.17  Aligned_cols=60  Identities=13%  Similarity=0.265  Sum_probs=56.7

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc----------------CCCeeCCCCCcccccccCCCCEEEEEEee
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS----------------SPAGNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~----------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      |+|+||+.+|+++.++|++++||++||++|+                |+|+.|+|+.+|++|||++|++|+++++.
T Consensus         1 M~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~~~~gip~~~qrLi~~Gk~L~D~~tL~~ygI~~g~~i~l~~~~   76 (95)
T 1uel_A            1 MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTK   76 (95)
T ss_dssp             CEEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEETTEECCTTSBGGGGTCCSSSEEEEEESS
T ss_pred             CEEEEEeCCCCEEEEEECCCCHHHHHHHHHHhhcccCCCChhhEEEEECCEECCCcCcHHHCCCCCCCEEEEEEeC
Confidence            8999999999999999999999999999886                89999999999999999999999998863

>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=99.64  E-value=1.4e-17  Score=105.17  Aligned_cols=61  Identities=69%  Similarity=0.855  Sum_probs=0.0

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      |+|+|++.+|+++.++|++++||++||++|+             |+|++|+|+.+|++|||++|++|++++|++
T Consensus         1 M~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~~I~~gsti~l~~rl~   74 (128)
T 3u5e_m            1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   74 (128)
T ss_dssp             --------------------------------------------------------------------------
T ss_pred             CEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHhCcChHHEEEEECCEECCCCCchhhhccCCCCEEEEEEEcC
Confidence            7999999999999999999999999999999             999999999999999999999999999874

>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=99.64  E-value=3.8e-16  Score=93.65  Aligned_cols=62  Identities=11%  Similarity=0.064  Sum_probs=58.6

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc----------CCCeeCCCC-CcccccccCCCCEEEEEEee
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS----------SPAGNFEDG-WTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~----------~~gk~L~d~-~tL~~y~I~~~sti~l~~rl   96 (97)
                      ..|+|+||+.+|+.+.++|++++||.+||++|+          |+|+.|+|+ .+|++|||++|++||++++.
T Consensus         6 ~~m~i~Vk~~~g~~~~~~v~~~~TV~~LK~~i~~~~~~~qrLi~~Gk~L~D~~~tL~~y~i~~g~~i~l~~~~   78 (95)
T 1wia_A            6 SGINVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRSP   78 (95)
T ss_dssp             CSEEEEEEETTTEEEEEEECSSSBHHHHHHHHSSSTTTTCEEEETTEECCCSSCBTTTTTCCTTEEEEEECCC
T ss_pred             CeEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHhhCcCcEEEEECCEEccCCcCCHHHcCCCCCCEEEEEECC
Confidence            569999999999999999999999999999987          999999999 99999999999999999874

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}

Probab=99.64  E-value=3.9e-16  Score=102.43  Aligned_cols=64  Identities=63%  Similarity=0.793  Sum_probs=60.2

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      ...|+|+||+.+|+++.++|++++||.+||++|+             |+|+.|+|+.+|++|||+++++++++++++
T Consensus        18 ~~~m~i~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~QrL~~~g~~L~d~~tL~~~~i~~~~~l~l~~~~~   94 (172)
T 3u30_A           18 GSHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   94 (172)
T ss_dssp             -CCEEEEEEETTTEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTGGGTCCTTCEEEEEECCC
T ss_pred             CCcEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCccccccCCHhHcCCcccceeeeeeccc
Confidence            3569999999999999999999999999999999             999999999999999999999999998864

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens}

Probab=99.64  E-value=4.1e-16  Score=98.35  Aligned_cols=64  Identities=13%  Similarity=0.136  Sum_probs=57.9

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc---------------------CCCeeCCCCCcccccccCCCC--EE
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS---------------------SPAGNFEDGWTQADYNIQKES--TL   90 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~---------------------~~gk~L~d~~tL~~y~I~~~s--ti   90 (97)
                      ...|.|+||+++|++++++|++++||++||++|+                     |+||+|+|+.||++|+|++++  ++
T Consensus        15 ~~~m~I~vktl~G~~~~lev~~s~TV~~lK~~I~~~~p~dwke~ip~~~~~qrLIy~GK~LeD~~TL~~y~I~~~~~~tl   94 (125)
T 2gow_A           15 ADMINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVM   94 (125)
T ss_dssp             TTCEEEEEECTTSCEEEEEECTTSBHHHHHHHHHSSCCCSCCCCTTCCGGGEEEESSSSEEESSCBTGGGCCCTTSEEEE
T ss_pred             CCeEEEEEEeCCCCEEEEEeCCccHHHHHHHHHHHHCCcccccCCCCChHHEEEEECCcCCCCCCcHHHcCCCCCCceEE
Confidence            3459999999999999999999999999999876                     799999999999999999776  78


Q ss_pred             EEEEeeC
Q 042212           91 HFVLRLS   97 (97)
Q Consensus        91 ~l~~rl~   97 (97)
                      |+++|++
T Consensus        95 hlv~r~~  101 (125)
T 2gow_A           95 HLVARET  101 (125)
T ss_dssp             EEEECSC
T ss_pred             EEEecCC
Confidence            9998864

>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=99.63  E-value=1.4e-16  Score=95.59  Aligned_cols=62  Identities=18%  Similarity=0.136  Sum_probs=58.7

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      ..|+|+|++. |+++.++|++++||.+||++|+             |+|+.|+|+.+|++|+|+++++||+++|++
T Consensus        16 ~~m~i~Vk~~-g~~~~~~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~   90 (96)
T 1wx8_A           16 RIIRVSVKTP-QDCHEFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVRSH   90 (96)
T ss_dssp             CEEEEEEECS-SSEEEEEEETTCCHHHHHHHHHHHTCSCTTTBCCEETTEECCTTSCHHHHTCCTTEEEECCBCCS
T ss_pred             CcEEEEEEEC-CeEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEECCCcCCHHHCCCCCCCEEEEEEeCC
Confidence            4599999998 9999999999999999999998             999999999999999999999999998864

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens}

Probab=99.62  E-value=2e-16  Score=96.16  Aligned_cols=60  Identities=13%  Similarity=0.102  Sum_probs=55.0

Q ss_pred             cCCeeeEEECCCCC--EEEEeecCCCcHHHhhcccc---------------CCCeeCCCCCccccc--ccCCCCEEEEE
Q 042212           34 RGRMQIFVKTSTGK--TITLEVESSDMIDNASRGSS---------------SPAGNFEDGWTQADY--NIQKESTLHFV   93 (97)
Q Consensus        34 ~~~m~i~vk~~~g~--~~~l~v~~~~tV~~lK~~I~---------------~~gk~L~d~~tL~~y--~I~~~sti~l~   93 (97)
                      .++|+|+||+++|+  +++++|++++||.+||++|+               |+|++|+|+.+|++|  +|+++++|||+
T Consensus        21 ~~~m~I~VK~~~g~~~~i~l~v~~~~TV~~LK~~I~~~~~g~pp~~~QrLIy~Gk~L~D~~tL~~y~~~I~~~~tihLv   99 (99)
T 2kdb_A           21 GHPVTLIIKAPNQKYSDQTISCFLNWTVGKLKTHLSNVYPSKPLTKDQRLVYSGRLLPDHLQLKDILRKQDEYHMVHLV   99 (99)
T ss_dssp             --CEEEEEECTTSSSCCEEEEECTTSBHHHHHHHHHHHSTTCCCTTTCCEEETTEEECTTSBTHHHHTTTCSEEEEEEC
T ss_pred             CCeEEEEEEcCCCCEEEEEEEcCCCCHHHHHHHHHHHHhcCCCChhhEEEEECCEECCCCCCHHHHhcCCCCCCEEEeC
Confidence            35699999999998  67999999999999999998               999999999999999  99999999984

>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=99.62  E-value=3.1e-16  Score=95.44  Aligned_cols=59  Identities=15%  Similarity=0.057  Sum_probs=52.3

Q ss_pred             eeEEECCC----CCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           38 QIFVKTST----GKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        38 ~i~vk~~~----g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      .|.|+..+    |++++++|++++||++||++|+             |+||+|+|+.||++|+|++|++| +++++|
T Consensus        17 ti~V~~~~~~~~~~~~~lev~~~~TV~~lK~kI~~k~gip~~qQrLI~~GKiL~D~~TL~~y~I~~gsti-~vl~lr   92 (100)
T 1wju_A           17 TIEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFGLQENYIKIVINKKQLQLGKTLEEQGVAHNVKA-MVLELK   92 (100)
T ss_dssp             EEEEECCTTTCCSSSEEEEEESSSBHHHHHHHHHHHTTCCSTTCEEEETTEECCTTSBHHHHTCCSSEEE-EEECCC
T ss_pred             EEEEEecCCCCCCcEEEEEeCCcCHHHHHHHHHHHHHCcCHHHeEEEeCCeECCCCCcHHHcCCCCCCEE-EEEEEC
Confidence            45555555    7899999999999999999999             99999999999999999999999 777765

>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=99.62  E-value=3.5e-17  Score=106.32  Aligned_cols=61  Identities=69%  Similarity=0.855  Sum_probs=0.0

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      |+|+|++++|+++.++|++++||.+||++|+             |+|++|+|+.+|++|+|++|++|++++|++
T Consensus         1 MqI~VK~l~G~~~~l~V~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~dygI~~gstL~Lvlrl~   74 (152)
T 3u5c_f            1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   74 (152)
T ss_dssp             --------------------------------------------------------------------------
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEEccccCcHHHcCCCCCCEEEEEeecc
Confidence            8999999999999999999999999999999             999999999999999999999999999975

>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=99.61  E-value=2.4e-16  Score=98.42  Aligned_cols=59  Identities=20%  Similarity=0.273  Sum_probs=53.6

Q ss_pred             eeeEEECCCCC-EEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccC-------CCCEEEEEEe
Q 042212           37 MQIFVKTSTGK-TITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQ-------KESTLHFVLR   95 (97)
Q Consensus        37 m~i~vk~~~g~-~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~-------~~sti~l~~r   95 (97)
                      |++|++...|+ ++.++|++++||.+||++|+             |+|++|+|++||++|||+       +++|+||++|
T Consensus         1 M~mfl~ir~~ktti~lev~~sdTV~~lK~kI~~~egIP~~qQrLi~~Gk~LeD~~TLsdy~I~~~~a~~q~~stL~L~lr   80 (118)
T 2fnj_B            1 MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPEEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFR   80 (118)
T ss_dssp             CEEEEEEEEBTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBHHHHTCCTTTSBTTBCEEEEEEEB
T ss_pred             CcEEEEEecCCEEEEEEeCCcChHHHHHHHHHHHhCCCHHHeEEEECCeECCCCCCHHHcCcccccccCCCCCEEEEEec
Confidence            56667666676 58999999999999999999             999999999999999999       7999999998

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.61  E-value=1e-15  Score=96.47  Aligned_cols=62  Identities=18%  Similarity=0.187  Sum_probs=57.7

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      ..|+|+||+. |+++.++|++++||.+||++|+             |+|+.|+|+.+|++|||++|++|+++++++
T Consensus        31 ~~m~I~Vk~~-g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~dygI~~gstI~lv~~~~  105 (125)
T 1j8c_A           31 KIIKVTVKTP-KEKEEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIKRD  105 (125)
T ss_dssp             CCEEEEEECS-SCEEEEEECTTCCHHHHHHHHHHHHCSCSSSEEEEETTEEESTTSCGGGTTCSSSEEEEEEEC--
T ss_pred             CcEEEEEEeC-CeEEEEEECCCCcHHHHHHHHHHHHCcCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEEeccC
Confidence            5699999999 9999999999999999999998             999999999999999999999999998864

>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=99.61  E-value=4.4e-16  Score=97.13  Aligned_cols=60  Identities=20%  Similarity=0.265  Sum_probs=55.4

Q ss_pred             eeeEEECCCCC-EEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCC-------CCEEEEEEe
Q 042212           37 MQIFVKTSTGK-TITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQK-------ESTLHFVLR   95 (97)
Q Consensus        37 m~i~vk~~~g~-~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~-------~sti~l~~r   95 (97)
                      |.+|++...++ ++.+++++++||.+||++|+             |+|++|+|++||++|||++       ++||||++|
T Consensus         1 m~vFl~Ikr~ktTI~ldve~sdTV~~lK~kI~~~~giPp~qQrLI~~Gk~LeD~kTL~dy~I~~~ta~~q~~atl~Lvlr   80 (118)
T 4ajy_B            1 MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFR   80 (118)
T ss_dssp             CEEEEEEEEBTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTTTTTCCGGGSBTTBCEEEEEEEC
T ss_pred             CceEEEEecCCEEEEEEcCCCChHHHHHHHHHHHHCCCHHHeEEEeCCeECCCcCCHHHcCCCcCcccCCCCCEEEEEEe
Confidence            66788777776 78889999999999999999             9999999999999999999       999999998


Q ss_pred             e
Q 042212           96 L   96 (97)
Q Consensus        96 l   96 (97)
                      .
T Consensus        81 ~   81 (118)
T 4ajy_B           81 A   81 (118)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.59  E-value=9e-16  Score=93.83  Aligned_cols=62  Identities=19%  Similarity=0.214  Sum_probs=57.8

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      ..|+|+||..+|+ +.++|++++||.+||++|+             |+|+.|+|+.+|++|+|+++++|++++|++
T Consensus        16 ~~m~I~Vk~~~g~-~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~   90 (106)
T 1wx7_A           16 HLIKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQ   90 (106)
T ss_dssp             SEEEEEEECSSCE-EEEEEETTCCHHHHHHHHHHHHTCCTTTEEEEETTEECCTTSCHHHHTCCTTEEEEEEECCC
T ss_pred             ceEEEEEEeCCCc-EEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEECCCcCcHHHcCCCCCCEEEEEEcCC
Confidence            4599999999886 7999999999999999998             999999999999999999999999999864

>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=99.58  E-value=2.2e-15  Score=97.51  Aligned_cols=60  Identities=17%  Similarity=0.178  Sum_probs=57.2

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc--------------C-CCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS--------------S-PAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~--------------~-~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      .|+|+||+.+|++++++|++++||+++|++|+              | +|++|+|+.+|++|||++|++++++++
T Consensus         2 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~QrL~~~~~g~~L~d~~tL~~y~i~~~~~l~l~~~   76 (159)
T 3rt3_B            2 GWDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVD   76 (159)
T ss_dssp             -CEEEEEETTSCEEEEECCTTCCHHHHHHHHHHHHCCCGGGEEEEEETTCCBCCTTSCGGGGTCCTTCEEEEEEC
T ss_pred             ceEEEEEECCCCEEEEEeCCCCcHHHHHHHHHHHhCCCHHHEEEEEcCCCCCCCCCCCHHHcCCCCCCEEEEEcc
Confidence            38999999999999999999999999999999              5 899999999999999999999999987

>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=99.58  E-value=1.5e-15  Score=94.11  Aligned_cols=64  Identities=17%  Similarity=0.267  Sum_probs=57.8

Q ss_pred             cCCeeeEEECC----------CCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEE
Q 042212           34 RGRMQIFVKTS----------TGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTL   90 (97)
Q Consensus        34 ~~~m~i~vk~~----------~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti   90 (97)
                      +++++|.|+.+          +|+++.++|++++||.+||++|+             |+|+.|+|+.+|++|+|++|++|
T Consensus        23 ~~~i~l~V~~p~~~~~~~~~L~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrL~~~Gk~L~D~~tL~~y~i~~g~~i  102 (115)
T 1we7_A           23 KGPVSIKVQVPNMQDKTEWKLNGQGLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMASGAVI  102 (115)
T ss_dssp             CSCEEEEEEECCCSSSCSSCCSSEEEEEEECSCSBTHHHHHHHHHHSSCCTTTEEEEETTEEECTTSBHHHHTCCSSCEE
T ss_pred             CCCEEEEEEcCCCccccccccCCeEEEEEECCCCCHHHHHHHHHHHHCCChHHEEEEECCEECCCCCCHHHCCCCCCCEE
Confidence            45677777765          47899999999999999999998             99999999999999999999999


Q ss_pred             EEEEeeC
Q 042212           91 HFVLRLS   97 (97)
Q Consensus        91 ~l~~rl~   97 (97)
                      |+++|+|
T Consensus       103 ~lv~rl~  109 (115)
T 1we7_A          103 HLALKER  109 (115)
T ss_dssp             EEEECCC
T ss_pred             EEEEEcC
Confidence            9999986

>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=99.58  E-value=1.4e-15  Score=92.44  Aligned_cols=63  Identities=14%  Similarity=0.112  Sum_probs=57.2

Q ss_pred             CCeeeEEECCCC----CEEEEeecCCCcHHHhhcccc-------------CCCeeCCCC-CcccccccCCCCEEEEEEee
Q 042212           35 GRMQIFVKTSTG----KTITLEVESSDMIDNASRGSS-------------SPAGNFEDG-WTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        35 ~~m~i~vk~~~g----~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~-~tL~~y~I~~~sti~l~~rl   96 (97)
                      ..|+|+|++.++    +++.++|++++||++||++|+             |+|++|+|+ .+|++|+|++|++|+++.+.
T Consensus         6 ~~m~I~Vk~~~~~~~~~~~~i~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~gk~L~D~~~tL~~ygI~~g~~l~l~~~~   85 (102)
T 1v5o_A            6 SGMLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVLLQKD   85 (102)
T ss_dssp             CCEEEEEEECCCCCCCCEEEEEECTTCBHHHHHHHHHHHTCCCGGGBCEEETTEEECCSSSBHHHHTCCTTEEEEECBCC
T ss_pred             CeEEEEEEECCCCcCceEEEEEcCCCCCHHHHHHHHHHHHCcChHHeEEEECCEECCCCcccHHHCCCCCCCEEEEEECC
Confidence            459999999754    799999999999999999999             999999988 79999999999999999876


Q ss_pred             C
Q 042212           97 S   97 (97)
Q Consensus        97 ~   97 (97)
                      |
T Consensus        86 ~   86 (102)
T 1v5o_A           86 N   86 (102)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B*

Probab=99.57  E-value=4.5e-15  Score=105.60  Aligned_cols=64  Identities=64%  Similarity=0.825  Sum_probs=59.1

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      ++.|+|+||+++|+++.++|++++||++||++|+             |+|++|+|+.+|++|+|+++++|++++|+|
T Consensus       231 ~~~MqI~VKtl~Gk~~~leV~~s~TV~dLK~kI~~~~GIp~~~QRLi~~Gk~L~D~~TLsdygI~~gstL~LvlRLr  307 (307)
T 3ai5_A          231 TGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR  307 (307)
T ss_dssp             CCCEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBTGGGTCCTTCEEEEEC---
T ss_pred             CCeEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEeCCeecCCCCCHHHcCCCCCCEEEEEEeCC
Confidence            4679999999999999999999999999999998             999999999999999999999999999987

>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=99.55  E-value=7.7e-15  Score=93.64  Aligned_cols=60  Identities=67%  Similarity=0.847  Sum_probs=57.5

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEee
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      |+|+|++.+|+++++++++++||++||++|+             |+|+.|+|+.+|++|||++|++++++.+.
T Consensus         1 M~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gip~~~q~L~~~g~~L~d~~tL~~~~i~~~~~l~l~~~~   73 (152)
T 3b08_A            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL   73 (152)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHHHHHCcChHHeEEEECCeECcCcccHHHhccCCCCeeEEEeec
Confidence            8999999999999999999999999999998             99999999999999999999999999874

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A

Probab=99.53  E-value=1.6e-14  Score=88.48  Aligned_cols=60  Identities=17%  Similarity=0.027  Sum_probs=55.2

Q ss_pred             CeeeEEECCCC--CEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCccccccc-CCCCEEEEEEe
Q 042212           36 RMQIFVKTSTG--KTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNI-QKESTLHFVLR   95 (97)
Q Consensus        36 ~m~i~vk~~~g--~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I-~~~sti~l~~r   95 (97)
                      .|+++|++..+  .+++++|+|++||.+||++|+             |+|+.++|++||++||| ++|+++||++.
T Consensus        24 ~l~v~v~d~~s~~~~i~l~V~ps~TV~~LK~~I~~k~Gipp~~QRli~ggkll~D~~TL~~ygI~~~G~t~hL~l~   99 (105)
T 4dbg_A           24 RLWVSVEDAQMHTVTIWLTVRPDMTVASLKDMVFLDYGFPPVLQQWVIGQRLARDQETLHSHGVRQNGDSAYLYLL   99 (105)
T ss_dssp             EEEEEEEESSSCCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEEECTTCBTGGGTCCSTTCEEEEEEC
T ss_pred             EEEEEEEccCCCCceEEEEECCcChHHHHHHHHHHHhCCCHHHEEEeccCeEccCcCcHHHcCCCCCCCEEEEEEE
Confidence            39999999875  689999999999999999999             89999999999999999 69999999874

>2dzj_A Synaptic glycoprotein SC2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.49  E-value=2.1e-14  Score=85.41  Aligned_cols=57  Identities=14%  Similarity=0.148  Sum_probs=51.7

Q ss_pred             CeeeEEECCCCCEE--EE-eecCCCcHHHhhcccc----------------CCCeeCCCCCcccccccCCCCEEEE
Q 042212           36 RMQIFVKTSTGKTI--TL-EVESSDMIDNASRGSS----------------SPAGNFEDGWTQADYNIQKESTLHF   92 (97)
Q Consensus        36 ~m~i~vk~~~g~~~--~l-~v~~~~tV~~lK~~I~----------------~~gk~L~d~~tL~~y~I~~~sti~l   92 (97)
                      .|+|+|+++.|+.+  ++ +|+|++||++||++|+                ++|++|+|+.||++|||.++++|++
T Consensus        10 ~M~I~Vk~~~g~~~~~~l~~v~~~~TV~~lK~~I~~~~~~i~~~~QrL~~~~~Gk~L~D~~tL~~y~i~~~stl~~   85 (88)
T 2dzj_A           10 HYEVEILDAKTREKLCFLDKVEPHATIAEIKNLFTKTHPQWYPARQSLRLDPKGKSLKDEDVLQKLPVGTTATLYF   85 (88)
T ss_dssp             CEEEEEEESSSCCCCEEEEEECSSCBHHHHHHHHHHHCSSSCTTTCCEESSTTSCCCCTTCBTTTSSCCSEEEEEE
T ss_pred             EEEEEEECCCCCEEeeEEeEcCCCCcHHHHHHHHHHHhcCCChHHeEEEecCCCcCcCCCCCHHHcCCCCCCEEEE
Confidence            39999999998775  58 9999999999999998                4599999999999999999999876

>2daf_A FLJ35834 protein; hypothetical protein FLJ35834, ubiquitin-like domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.48  E-value=4.6e-14  Score=87.77  Aligned_cols=61  Identities=8%  Similarity=0.099  Sum_probs=56.5

Q ss_pred             CCeeeEEE-CCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           35 GRMQIFVK-TSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        35 ~~m~i~vk-~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      ..+.|.|+ ...|+.++++++++.||++||+.++             |+||.|+|+.||++|||++|.||||+.+
T Consensus        14 ~~itvkv~l~~~~~k~tv~v~~d~TV~dLKe~ls~~~~iP~e~qrLIy~GKiLKD~eTL~~~gIk~g~TIhLvi~   88 (118)
T 2daf_A           14 SLATVKVVLIPVGQEIVIPFKVDTILKYLKDHFSHLLGIPHSVLQIRYSGKILKNNETLVQHGVKPQEIVQVEIF   88 (118)
T ss_dssp             SCEEEEEEETTTCCEEEEEECSSSCSHHHHHHHHHHHTCCTTTEEEEETTEEECSSCCHHHHSCCSSCEEEEEEE
T ss_pred             ccEEEEEEEcCCCcEEEEEeCCCCcHHHHHHHHHhhhCCChHHEEEEECCeEcCCcchHHHcCCCCCCEEEEEEe
Confidence            34778887 6778999999999999999999999             9999999999999999999999999986

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9

Probab=99.48  E-value=3e-15  Score=100.08  Aligned_cols=56  Identities=21%  Similarity=0.135  Sum_probs=0.0

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      |+|+|++++|++++++|++++||.+||++|+             |+|++|+|+.||+     +++||||++|+|
T Consensus         1 MqI~VKtL~GktitLeV~~sdTV~~LK~kI~~keGIP~~qQRLIf~GK~LeD~~TLs-----~~STLhLvlRLr   69 (189)
T 2xzm_9            1 MQVQVKTLEGETKIYTLEQGTSVLDLKSQISQDMGFEIDMMTLVNNGFIAPNTELVT-----DDVTYYLSLKLL   69 (189)
T ss_dssp             --------------------------------------------------------------------------
T ss_pred             CEEEEEcCCCCEEEEEECCcChHHHHHHHHHHHhCcChhHEEEEecCeECCCCCccc-----CCCEEEEEEecC
Confidence            8999999999999999999999999999999             9999999999999     999999999985

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.46  E-value=5.6e-14  Score=82.84  Aligned_cols=57  Identities=12%  Similarity=0.106  Sum_probs=51.9

Q ss_pred             eEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           39 IFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        39 i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      +++++.+|+++.+++++++||++||++|+             |+|++|+|+.+|++|||++|++|+++..
T Consensus        14 ~~~~~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~l~l~~s   83 (85)
T 2kd0_A           14 KLTVKFGGKSIPLSVSPDCTVKDLKSQLQPITNVLPRGQKLIFKGKVLVETSTLKQSDVGSGAKLMLMAS   83 (85)
T ss_dssp             EEEEEETTEEEEEEECTTSBHHHHHHHHHHHHCCCTTTCEEEETTEECCTTCBTTTTTCCTTEEEEEECC
T ss_pred             EEEEEECCEEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCeECCCcCCHHHCCCCCCCEEEEEEe
Confidence            34556689999999999999999999998             9999999999999999999999999864

>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=99.45  E-value=6.4e-14  Score=101.79  Aligned_cols=63  Identities=16%  Similarity=0.229  Sum_probs=58.1

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc----------------CCCeeCCCCCcccccccCCCCEE-EEEEeeC
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS----------------SPAGNFEDGWTQADYNIQKESTL-HFVLRLS   97 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~----------------~~gk~L~d~~tL~~y~I~~~sti-~l~~rl~   97 (97)
                      ..|+|+||+++|+++.++|++++||.+||++|+                |+||+|+|+.+|++|||++|++| +++.|++
T Consensus         6 ~~M~I~VKtl~Gk~~~leV~~~~TV~~LK~~I~~~~~~~gip~~~QrLiy~GK~L~D~~tL~dygI~~gstIv~lv~k~~   85 (368)
T 1oqy_A            6 SAVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTKTK   85 (368)
T ss_dssp             CCCCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSSEECSSSBTTTTCCCTTSCEEEEEECCC
T ss_pred             ceEEEEEEeCCCCEEEEEeCCCChHHHHHHHHHHHhCcCCCChhheEEEECCeecCCcCCHHHcCCCCCCEEEEEEecCC
Confidence            469999999999999999999999999999887                99999999999999999999998 7776653

>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion protein; ubiquitin interacting motif, UIM, protein domain interface; NMR {Saccharomyces cerevisiae}

Probab=99.44  E-value=8.1e-16  Score=95.42  Aligned_cols=61  Identities=48%  Similarity=0.617  Sum_probs=56.8

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCCeeeEEE---CCCCCEEEEeecCCCcHHH
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVK---TSTGKTITLEVESSDMIDN   61 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~m~i~vk---~~~g~~~~l~v~~~~tV~~   61 (97)
                      ||+++|+|+|+|++|     |++|||.+|++|+|+++++++++++++   +.+|++++++|++++||.+
T Consensus        45 ip~~~qrLi~~Gk~L~D~~tL~~ygI~~gstI~l~~~~~GG~~~~~~~~~~~~g~~~~~~v~~~~~~~~  113 (114)
T 2kdi_A           45 IPPDQQRLIWAGKQLEDGRTLSDYNIQRESTLHLVLRLRGGSMGGAADEEELIRKAIELSLKESRNSGG  113 (114)
T ss_dssp             CCGGGEEEEETTEECCTTCBTTTTTCCSSCEEEEEECCCSSCCCSSCSSSHHHHHHHHSSSHHHHHGGG
T ss_pred             cChHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEEcCCCceeeccccccccCceEEEEeccccccCC
Confidence            799999999999999     999999999999999999999999998   4578999999999999864

>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=99.43  E-value=1.1e-13  Score=84.74  Aligned_cols=62  Identities=19%  Similarity=0.120  Sum_probs=55.1

Q ss_pred             CCeeeEEECCCC---CEEEEe--------ecCC-CcHHHhhcccc----------------CCCeeCCCCCcccccccCC
Q 042212           35 GRMQIFVKTSTG---KTITLE--------VESS-DMIDNASRGSS----------------SPAGNFEDGWTQADYNIQK   86 (97)
Q Consensus        35 ~~m~i~vk~~~g---~~~~l~--------v~~~-~tV~~lK~~I~----------------~~gk~L~d~~tL~~y~I~~   86 (97)
                      ..|+|+||+.+|   +++.++        |+++ +||.+||++|+                |+|+.|+|+.+|++|+|++
T Consensus        11 ~~~~i~Vk~~~~~~~~~~~l~v~~~~~~~v~~~~~TV~~LK~~i~~~~~~gip~~~~qrLi~~Gk~L~D~~tL~~y~i~~   90 (107)
T 1x1m_A           11 SDWHLAVKLADQPLAPKSILQLPETELGEYSLGGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDFYGIQP   90 (107)
T ss_dssp             CSCCEEEEETTCTTSCCEEECCCCCSSCSSCCCCCBHHHHHHHHHHHCTTTCCCSSSEEEEETTEECCTTCBHHHHTCCT
T ss_pred             CceEEEEEeCCCCCccEEEEEecCccccccCcccCCHHHHHHHHHHHhccCCChhhcEEEEECCeECCCCCcHHHcCCCC
Confidence            469999999998   899999        4454 99999998774                7899999999999999999


Q ss_pred             CCEEEEEEee
Q 042212           87 ESTLHFVLRL   96 (97)
Q Consensus        87 ~sti~l~~rl   96 (97)
                      |++||++++.
T Consensus        91 g~~i~lv~~~  100 (107)
T 1x1m_A           91 GSTVHVLRKS  100 (107)
T ss_dssp             TCEEEEEESS
T ss_pred             CCEEEEEeCC
Confidence            9999999874

>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=99.43  E-value=7.6e-14  Score=83.01  Aligned_cols=60  Identities=10%  Similarity=0.138  Sum_probs=55.2

Q ss_pred             CCeeeEEECCCCCEEEE-eecCCCcHHHhhcccc----------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           35 GRMQIFVKTSTGKTITL-EVESSDMIDNASRGSS----------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l-~v~~~~tV~~lK~~I~----------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      ..|+|+||. .|+++.+ ++++++||.+||++|+                |+|++|+|+.+|++|+|++|++|+|+..
T Consensus         6 ~~m~i~Vk~-~g~~~~i~~v~~~~TV~~lK~~I~~~~gip~~~QkLi~~k~~Gk~L~D~~~L~~~~i~~g~~l~l~~~   82 (90)
T 1v5t_A            6 SGLPIIVKW-GGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMGT   82 (90)
T ss_dssp             CSCCEEEEE-TTEEEEECSCCSSSBHHHHHHHHHHHTCCCTTTCEEESCEETTEECCTTSBHHHHTCCTTEEEEEECC
T ss_pred             ceEEEEEEE-CCEEEEEEEeCCCCCHHHHHHHHHHHHCcCHHHeEEEeeccCCcCcCCCCCHHHcCCCCCCEEEEEec
Confidence            459999996 7899999 9999999999999999                5799999999999999999999999854

>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=99.43  E-value=9.3e-14  Score=83.70  Aligned_cols=59  Identities=10%  Similarity=0.081  Sum_probs=54.0

Q ss_pred             CCeeeEEECCCCCEE-EEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           35 GRMQIFVKTSTGKTI-TLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~-~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      ..|+|+||. .|+++ .+++++++||.+||++|+             |+|++|+|+ +|++|||+++++|+|+..
T Consensus         6 ~~m~i~Vk~-~g~~~~~l~v~~~~TV~~lK~~I~~~tgip~~~QkLi~~Gk~L~D~-tL~~~~I~~g~~i~l~~~   78 (96)
T 1wgg_A            6 SGYSVTVKW-GKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLKDD-DWGNIKMKNGMTVLMMGS   78 (96)
T ss_dssp             CEEEEEEEE-TTEEEEEEEEESSSCHHHHHHHHHHHTCCCTTTSCCEETTEECCSS-CCCSCCCCSSCEEECCCC
T ss_pred             cEEEEEEEE-CCEEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCcCCCCC-CHHHCCCCCCCEEEEEec
Confidence            359999996 68999 699999999999999999             999999999 999999999999998754

>2dzm_A FAS-associated factor 1; ubiquitin-like domain, HFAF1, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.41  E-value=1.1e-13  Score=84.16  Aligned_cols=59  Identities=14%  Similarity=0.170  Sum_probs=54.0

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------C--CCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------S--PAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~--~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      +|+++++...|+++++++++++||++||++|+             |  +|+ |+|+.+|++|+|++|+++|++++
T Consensus         8 ~m~~~~vk~~Gk~~~v~v~~~~TV~~LK~~I~~~tgIpp~~QkLi~~~~gk-L~D~~tLs~~~I~~gstL~lvl~   81 (100)
T 2dzm_A            8 RMLDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGD-VEDSTVLKSLHLPKNNSLYVLTP   81 (100)
T ss_dssp             CEEEEEEECSSCEEEEEEETTSBHHHHHHHHHHHHCCCTTTCCEECCSSSC-CCTTSBHHHHCCCSEEEEEECCS
T ss_pred             ceEEEEEEeCCeEEEEEECCCCcHHHHHHHHHHHHCCChhHeEEEccCCCC-CCCcCCHHHcCCCCCCEEEEEec
Confidence            58999988999999999999999999999998             3  455 99999999999999999999875

>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=99.40  E-value=3e-13  Score=80.45  Aligned_cols=60  Identities=10%  Similarity=0.170  Sum_probs=54.5

Q ss_pred             CCeeeEEECCCCCEEEEeecCC-----CcHHHhhcccc-------------CCCeeCCC-CCcccccccCCCCEEEEEEe
Q 042212           35 GRMQIFVKTSTGKTITLEVESS-----DMIDNASRGSS-------------SPAGNFED-GWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~-----~tV~~lK~~I~-------------~~gk~L~d-~~tL~~y~I~~~sti~l~~r   95 (97)
                      ..|+|+|+. .|+++.++++++     +||.+||++|+             |+|+.|+| +.+|++|+|++|++|+++.+
T Consensus         6 ~~~~v~Vk~-~~~~~~i~v~~~~~~~~~TV~~LK~~i~~~~gip~~~qrL~~~Gk~L~D~~~~L~~~~i~~g~~i~l~~~   84 (92)
T 1wxv_A            6 SGLTVTVTH-SNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVMLIGK   84 (92)
T ss_dssp             SSEEEEEEC-SSSEEEEEECCCSSSSSCBHHHHHHHHHHHTCCCTTTCEEEETTEEECCSSSBHHHHTCCSSEEEEEESC
T ss_pred             CeEEEEEEE-CCEEEEEEECCCcCcccCcHHHHHHHHHHHHCcCHHHEEEEECCeecCCCcccHHHCCCCCCCEEEEEec
Confidence            469999999 588999999995     99999999998             99999998 66899999999999999865

>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=99.37  E-value=3.1e-13  Score=81.18  Aligned_cols=59  Identities=7%  Similarity=-0.069  Sum_probs=52.6

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      ..|+|+|+. .|+++.+++++++||.+||++|+             |+|++|+ +.+|++|+|+++++|+|+.+
T Consensus        16 ~~~~i~Vk~-~g~~~~i~v~~~~TV~~LK~~I~~~tgip~~~QrL~~~Gk~Ld-d~tL~~~~i~~g~~i~lv~~   87 (95)
T 1v86_A           16 ELVDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGLVPE-DKTLREIKVTSGAKIMVVGS   87 (95)
T ss_dssp             CCEEEEEEE-TTEEEEEEECTTSBHHHHHHHHHHHHCSCSTTCCCBSSSBCCS-SSBHHHHCCCTTEEEEECCS
T ss_pred             ceEEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCeeCC-cCcHHHCCCCCCCEEEEEec
Confidence            358999984 68999999999999999999999             9999994 45999999999999999753

>4b6w_A Tubulin-specific chaperone; CAP-Gly, ubiquitin-like; HET: MSE; 2.35A {Trypanosoma brucei brucei strain 927}

Probab=99.35  E-value=9.4e-13  Score=77.94  Aligned_cols=53  Identities=13%  Similarity=0.085  Sum_probs=47.0

Q ss_pred             CCCCCEEEEeecCCCcHHHhhcccc--------------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           43 TSTGKTITLEVESSDMIDNASRGSS--------------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        43 ~~~g~~~~l~v~~~~tV~~lK~~I~--------------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      ....+.+...+++++||++||++|+                    |.|+.|+|+++|++|||++|++||++-+
T Consensus        11 ~~~~~~~E~r~~~s~TI~~lK~ki~~~~Gip~~~QrLi~~~~~~~~~g~~l~d~~tL~~Y~i~~g~~ihlvd~   83 (86)
T 4b6w_A           11 ASRMRVPEKRYGLAQTIESIKENVFTHFATPPEYMQLQLIDDRGITIEKNMANDKQLGYYQCRDEFVIHVVDL   83 (86)
T ss_dssp             TCSCCEEEEEEETTSBHHHHHHHHHTTSCCCGGGEEEEEECTTSCEEESSCCTTSBGGGGTCCTTCEEEEEEC
T ss_pred             CCCCeEEEEEcCccCcHHHHHHHHHHHHCCCHHHEEEEEecCCCCceeeEcCCCCCHHHCCCCCCCEEEEEeC
Confidence            3455678899999999999999999                    3689999999999999999999999853

>1wf9_A NPL4 family protein; beta-grAsp fold like domain, hypothetical protein, structural genomics, NPPSFA; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=99.34  E-value=1e-12  Score=80.45  Aligned_cols=58  Identities=9%  Similarity=0.106  Sum_probs=51.8

Q ss_pred             CeeeEEECCCCCEEEEeec-CCCcHHHhhcccc-------------CCCe-----------e----CCCCCcccccccCC
Q 042212           36 RMQIFVKTSTGKTITLEVE-SSDMIDNASRGSS-------------SPAG-----------N----FEDGWTQADYNIQK   86 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~-~~~tV~~lK~~I~-------------~~gk-----------~----L~d~~tL~~y~I~~   86 (97)
                      .|.|+||+.+|+. .++|+ +++||.+||++|+             |+|+           .    ++|+.+|++|||++
T Consensus         7 ~M~irvrs~~G~~-~v~v~~~~~Tv~~LK~kI~~~~gip~~~QrL~~~~~~~~~k~~~~~~~l~~~l~d~~tL~~~gi~~   85 (107)
T 1wf9_A            7 GTMLRVRSRDGLE-RVSVDGPHITVSQLKTLIQDQLQIPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLAH   85 (107)
T ss_dssp             CEEEEEECSSCEE-EEEECCTTSBHHHHHHHHHHHSCCCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTCCCT
T ss_pred             eEEEEEECCCCCE-EEEECCCCCcHHHHHHHHHHHhCcCcccCEEEECCccccccCccccccccccCCCCCCHHHCCCCC
Confidence            4999999999966 79999 9999999999999             6666           4    58999999999999


Q ss_pred             CCEEEEEE
Q 042212           87 ESTLHFVL   94 (97)
Q Consensus        87 ~sti~l~~   94 (97)
                      |++|||..
T Consensus        86 G~~L~l~~   93 (107)
T 1wf9_A           86 GSMVYLAY   93 (107)
T ss_dssp             TCEEECCC
T ss_pred             CCEEEEEe
Confidence            99999864

>2kjr_A CG11242; UBL, ubiquitin, ubiquitin-like, structural genomics, PSI-2, protein structure initiative; NMR {Drosophila melanogaster}

Probab=99.33  E-value=1.3e-12  Score=78.67  Aligned_cols=60  Identities=10%  Similarity=0.093  Sum_probs=51.2

Q ss_pred             cCCeeeEEECCCCC--EEEEeecCCCcHHHhhcccc-------------CC--Ce---eC-CCCCcccccccCCCCEEEE
Q 042212           34 RGRMQIFVKTSTGK--TITLEVESSDMIDNASRGSS-------------SP--AG---NF-EDGWTQADYNIQKESTLHF   92 (97)
Q Consensus        34 ~~~m~i~vk~~~g~--~~~l~v~~~~tV~~lK~~I~-------------~~--gk---~L-~d~~tL~~y~I~~~sti~l   92 (97)
                      .+.+.|+|+...++  ++++++++++||++||++|+             |+  |+   .| +|+++|++|||++|++|++
T Consensus        13 ~~~v~l~It~s~~~~~~~~~~v~~~~TV~~LK~kI~~~~GiP~~~QrL~~~~~g~~~~~L~~D~~tL~~Y~i~~gstihl   92 (95)
T 2kjr_A           13 SDFIKVNVSNSHNDAVAFEVKLAKDLTVAQLKTKLEILTGGCAGTMKVQVFKGDTCVSTMDNNDAQLGYYANSDGLRLHV   92 (95)
T ss_dssp             CCEEEEEEEESSCSCEEEEEEEETTCBHHHHHHHHHHHHCSCTTTEEEEEEETTEEEEECCCTTSBHHHHCCSSSCEEEE
T ss_pred             CCeEEEEEEECCCCceEEEEEeCccCHHHHHHHHHHHHHCcCHHHeEEEEecCCcccceeCCCCCCHhHCCcCCCCEEEE
Confidence            34578888876654  88999999999999999999             55  55   45 8999999999999999998


Q ss_pred             E
Q 042212           93 V   93 (97)
Q Consensus        93 ~   93 (97)
                      +
T Consensus        93 v   93 (95)
T 2kjr_A           93 V   93 (95)
T ss_dssp             E
T ss_pred             E
Confidence            6

>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=99.33  E-value=2.6e-12  Score=77.22  Aligned_cols=63  Identities=10%  Similarity=0.199  Sum_probs=59.4

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      ..|+|+|++.+|+.+.+.|+++++++.|++.++             |.|+.|+++.|+++|++++|++|+++++++
T Consensus         6 ~~i~ikVk~~~g~~i~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~~~   81 (94)
T 2io1_B            6 DHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQT   81 (94)
T ss_dssp             CEEEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCTTTTTCCTTCEEEEEECCE
T ss_pred             CeEEEEEECCCCCEEEEEECCCCHHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEecc
Confidence            459999999999999999999999999999988             999999999999999999999999998764

>1yx5_B Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo sapiens} SCOP: d.15.1.1 PDB: 1yx6_B

Probab=99.21  E-value=8e-12  Score=74.96  Aligned_cols=52  Identities=56%  Similarity=0.752  Sum_probs=35.0

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCCeeeEEECCCCCEEEEe
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLE   52 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~m~i~vk~~~g~~~~l~   52 (97)
                      ||+++|+|+|+|+.|     |++|||.+|++|+|+.+..++.+++.++.+|+.-.++
T Consensus        36 i~~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~gG~~i~~~~v~~~~~~~~   92 (98)
T 1yx5_B           36 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGRDPNSSSVDKLAAALE   92 (98)
T ss_dssp             CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCCCC----------------
T ss_pred             cChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEeCCCCCcCccccCCCchhhhh
Confidence            699999999999999     9999999999999999999999999999998765443

>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative, hydrolase; NMR {Mus musculus}

Probab=99.20  E-value=1.1e-11  Score=72.96  Aligned_cols=56  Identities=18%  Similarity=0.200  Sum_probs=49.2

Q ss_pred             eeeEEECCCCCEEEEe-ecCCCcHHHhhcccc---------------CCCeeCC---CCCcccccccCCCCEEEEE
Q 042212           37 MQIFVKTSTGKTITLE-VESSDMIDNASRGSS---------------SPAGNFE---DGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~-v~~~~tV~~lK~~I~---------------~~gk~L~---d~~tL~~y~I~~~sti~l~   93 (97)
                      |+|+||+.+|+. .++ +++++||.+||++|+               |.+++|+   |+.+|++|||.+|++|++.
T Consensus         1 m~i~vr~~~G~~-~v~~l~~~~Tv~~Lk~~I~~~~gi~~~~qrL~~~~p~k~l~l~~~~~tL~~~gl~~g~~l~v~   75 (86)
T 2kzr_A            1 WRVRCKAKGGTH-LLQGLSSRTRLRELQGQIAAITGIAPGSQRILVGYPPECLDLSDRDITLGDLPIQSGDMLIVE   75 (86)
T ss_dssp             CCEEEEETTEEE-EECSCCTTCBHHHHHHHHHHHTCCCTTTCCCEESSCCCCCCCCCSSCBTTTSSCCTTCEEECC
T ss_pred             CEEEEEcCCCCE-EeeecCCCCCHHHHHHHHHHHhCCCccceEEEeCCCCcccccCCCCCCHHHcCCCCCCEEEEE
Confidence            789999999965 477 999999999999999               4468884   6889999999999999875

>2kj6_A Tubulin folding cofactor B; methods development, NESG, solution PSI-2, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.19  E-value=1.1e-11  Score=74.79  Aligned_cols=60  Identities=5%  Similarity=-0.001  Sum_probs=49.6

Q ss_pred             CCeeeEEECCCC--CEEEEeecCCCcHHHhhcccc-------------CCC---ee----CCCCCcccccccCCCCEEEE
Q 042212           35 GRMQIFVKTSTG--KTITLEVESSDMIDNASRGSS-------------SPA---GN----FEDGWTQADYNIQKESTLHF   92 (97)
Q Consensus        35 ~~m~i~vk~~~g--~~~~l~v~~~~tV~~lK~~I~-------------~~g---k~----L~d~~tL~~y~I~~~sti~l   92 (97)
                      +.+.++|.....  +.+++++++++||++||++|+             |+|   +.    ++|+++|++|+|++|++|++
T Consensus        13 ~~v~l~It~s~~~~~~~e~~v~~~~TV~~LK~kIe~~~Gip~~~QrLi~~g~~g~~~~~L~~D~~tL~~Y~I~~g~~Ihl   92 (97)
T 2kj6_A           13 DSVHLHITHANLKSFSADARFSPQMSVEAVKEKLWKKCGTSVNSMALELYDDSGSKVAVLSDDSRPLGFFSPFDGFRLHI   92 (97)
T ss_dssp             CCEEEEEEETTSSCCCEEEEECTTCCHHHHHHHHHHHHCCCTTSEEEEEECSSSCBCCCSSGGGSCHHHHCCCSCCEEEE
T ss_pred             ceEEEEEEECCCCceEEEEEeCCCChHHHHHHHHHHHHCcCHHHeEEEEecCCCcccceecCCcCCHHHCCCCCCCEEEE
Confidence            346677766444  578999999999999999999             666   43    48999999999999999998


Q ss_pred             EE
Q 042212           93 VL   94 (97)
Q Consensus        93 ~~   94 (97)
                      +=
T Consensus        93 vd   94 (97)
T 2kj6_A           93 ID   94 (97)
T ss_dssp             EE
T ss_pred             Ee
Confidence            73

>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=99.19  E-value=3.8e-11  Score=71.69  Aligned_cols=63  Identities=10%  Similarity=0.199  Sum_probs=59.1

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      ..|+|+|++.+|+.+.+.|+++++++.|++..+             |.|+.|.++.|.++|++++|++|+++++++
T Consensus         4 ~~i~ikVk~~~g~~v~~~vk~~t~l~kl~~~y~~~~gi~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~q~   79 (91)
T 2io0_B            4 DHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQT   79 (91)
T ss_dssp             CEEEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHTTCCSTTEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCC
T ss_pred             CeEEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEecc
Confidence            458999999999999999999999999999888             999999999999999999999999998764

>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=99.16  E-value=3.6e-11  Score=71.95  Aligned_cols=57  Identities=11%  Similarity=0.089  Sum_probs=48.0

Q ss_pred             eeeEEECCCCC-EEEEeecCCCcHHHhhcccc-------------CCC---ee----CCCCCcccccccCCCCEEEEE
Q 042212           37 MQIFVKTSTGK-TITLEVESSDMIDNASRGSS-------------SPA---GN----FEDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        37 m~i~vk~~~g~-~~~l~v~~~~tV~~lK~~I~-------------~~g---k~----L~d~~tL~~y~I~~~sti~l~   93 (97)
                      +.++|+..... .+++++++++||++||++|+             |+|   +.    ++|+++|++|||++|++||++
T Consensus         8 v~l~I~~~~~~~~~~~~v~~~~TV~~lK~ki~~~~gip~~~qrL~~~~~~g~~~~~l~~D~~tL~~y~i~~g~~l~v~   85 (95)
T 1v6e_A            8 VMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVGSPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIHVI   85 (95)
T ss_dssp             EEEEEEETTSSSCEEEEECTTSBHHHHHHHHHHHTCSCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCEEEEB
T ss_pred             EEEEEEECCCCeeEEEEcCccCHHHHHHHHHHHHHCCCHHHeEEEEeCCCCccccccCCCcCCHhHCCCCCCCEEEEE
Confidence            66777765442 68999999999999999999             554   54    589999999999999999986

>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=99.14  E-value=9.9e-11  Score=66.84  Aligned_cols=57  Identities=11%  Similarity=0.217  Sum_probs=54.5

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEE
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~   93 (97)
                      |+|+|++.+|+.+.+.|+++++++.|++..+             |.|+.|.++.|.++|++++|++|++.
T Consensus         2 i~lkV~~~~g~~v~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~~l~~~~Tp~~l~medgD~Idv~   71 (72)
T 1wm3_A            2 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVF   71 (72)
T ss_dssp             EEEEEECTTSCEEEEEECTTSCTHHHHHHHHHHHTCCTTTCEEEETTEECCTTCCTTTTTCCTTEEEEEE
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEE
Confidence            7899999999999999999999999999888             99999999999999999999999986

>3phx_B Ubiquitin-like protein ISG15; OTU domain, DE-ubiquitinase, DE-isgylase, hydrolase-protein complex; 1.60A {Homo sapiens}

Probab=99.13  E-value=3.3e-11  Score=69.35  Aligned_cols=35  Identities=34%  Similarity=0.526  Sum_probs=33.0

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++|+|+|+|++|     |++|||++|++|||+++++|
T Consensus        40 ip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~l~l~~rl~G   79 (79)
T 3phx_B           40 VQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRG   79 (79)
T ss_dssp             CCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCBC
T ss_pred             CCHHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCC
Confidence            799999999999999     99999999999999999764

>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=99.13  E-value=1.3e-10  Score=69.51  Aligned_cols=63  Identities=10%  Similarity=0.199  Sum_probs=58.6

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      ..|.|+|++.+|+.+.+.|++++++..|+...+             |.|+.|.++.|.++|++++|++|+++++++
T Consensus        16 ~~i~ikV~~~~g~~i~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~~l~~~~Tp~dl~medgD~Idv~~~q~   91 (93)
T 2d07_B           16 DHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQT   91 (93)
T ss_dssp             CEEEEEEECTTSCEEEEEEETTSCHHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECC-
T ss_pred             CeEEEEEECCCCCEEEEEEccCCHHHHHHHHHHHHhCCCccceEEEECCEEcCCCCCHHHcCCCCCCEEEEEeecc
Confidence            459999999999999999999999999999888             999999999999999999999999998764

>1wz0_A Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-like molecule, structural genomics, sentrin2, NPPFSA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.09  E-value=2e-10  Score=70.15  Aligned_cols=63  Identities=10%  Similarity=0.199  Sum_probs=59.0

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      ..|+|+|++.+|+.+.+.|++++++..|+...+             |.|+.|.++.|.++|++++|++|+++++++
T Consensus        23 ~~I~IkVk~~~g~~i~~kVk~~t~l~kL~~~y~ek~gi~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~q~   98 (104)
T 1wz0_A           23 DHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQT   98 (104)
T ss_dssp             CCEEEEEECSSSCEEEEEECTTSCHHHHHHHHHHHHTCCTTTSCEESSSSBCCTTSCTTTTTCCTTEEEEECCCCC
T ss_pred             CeEEEEEECCCCCEEEEEEcCCChHHHHHHHHHHHhCCCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEecc
Confidence            469999999999999999999999999999888             999999999999999999999999988764

>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=99.07  E-value=1.3e-10  Score=72.53  Aligned_cols=60  Identities=7%  Similarity=0.060  Sum_probs=49.7

Q ss_pred             CCeeeEEECCCCC-EEEEeecCCCcHHHhhcccc-------------CCC---e---e-CCCCCcccccccCCCCEEEEE
Q 042212           35 GRMQIFVKTSTGK-TITLEVESSDMIDNASRGSS-------------SPA---G---N-FEDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        35 ~~m~i~vk~~~g~-~~~l~v~~~~tV~~lK~~I~-------------~~g---k---~-L~d~~tL~~y~I~~~sti~l~   93 (97)
                      +.+.|+|+...+. .+++++++++||++||++|+             |.|   +   + ++|+++|++|||++|++||++
T Consensus         5 ~~v~l~V~~~~~~~~~e~~v~~~~TV~~lK~ki~~~~Gip~~~qrL~~~g~~~~~~~~l~~D~~tL~~y~i~~g~~ihvv   84 (122)
T 1t0y_A            5 EVYDLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHAV   84 (122)
T ss_dssp             CEEEEEEEESSCCSCEEEEEETTSBHHHHHHHHHHHHCCCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEEEEE
T ss_pred             CEEEEEEEECCCCccEEEEeCCCCcHHHHHHHHHHHhCCCHHHeEEEEecCCCccccccCCCcCCHHHCCCCCCCEEEEE
Confidence            3467778775443 68899999999999999999             554   4   3 489999999999999999997


Q ss_pred             E
Q 042212           94 L   94 (97)
Q Consensus        94 ~   94 (97)
                      .
T Consensus        85 d   85 (122)
T 1t0y_A           85 D   85 (122)
T ss_dssp             E
T ss_pred             e
Confidence            4

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster}

Probab=99.06  E-value=1.9e-10  Score=82.25  Aligned_cols=59  Identities=14%  Similarity=0.162  Sum_probs=52.0

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc----------------CCCeeCCCCCcccccccCCCCEEEEEE
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS----------------SPAGNFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~----------------~~gk~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      ..|.|.||. +|+++++++++++||++||++|+                |+|++|+|+.+|++|||++|++|+|+-
T Consensus         4 ~~i~i~Vk~-~g~~~~v~v~~~~Tv~~lK~~I~~~tgVpp~~QkLi~~k~~Gk~l~D~~~L~~~~ik~g~~l~L~g   78 (320)
T 3shq_A            4 KEVVVIVKW-SGKEYPVDLTDQDTVEVLRHEIFRKTQVRPERQKLLNLKYKGKTAADNVKISALELKPNFKLMMVG   78 (320)
T ss_dssp             CEEEEEEEE-TTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGCEETTCBSSSSBCCTTSBTTSSCCC--CEEEEEC
T ss_pred             ceEEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEeecccCCcccCccccHHHcCCCCCCEEEEEc
Confidence            347888986 79999999999999999999998                479999999999999999999999974

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B

Probab=99.05  E-value=1.8e-10  Score=75.58  Aligned_cols=61  Identities=48%  Similarity=0.648  Sum_probs=45.8

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCCeeeEEECC-CC--CEEEEeecCCCcHHH
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTS-TG--KTITLEVESSDMIDN   61 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~m~i~vk~~-~g--~~~~l~v~~~~tV~~   61 (97)
                      ||+++|||+|+|++|     |++|||++|++|||+++++++++-.|+.. .|  .+-.+.++++.++.+
T Consensus        36 ip~~~QrLi~~Gk~L~D~~tL~~y~I~~gstI~Lvlrl~GG~k~~vkfs~~Gd~g~~~i~l~~~~~~~~  104 (169)
T 3l0w_B           36 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGGGETIKFVADGDIGSGSVIIKPFVDMEH  104 (169)
T ss_dssp             CCTTTEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCCC---CCEEEEEECSSCEEEEEECCBCCSSC
T ss_pred             cCHHHEEEEECCccccCcCcHHHcCCCCCCEEEEEEEecccccccccccccCcccceeEEEecCCCCCC
Confidence            799999999999999     99999999999999999988766666543 22  244566666655543

>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=99.05  E-value=3.2e-10  Score=69.46  Aligned_cols=62  Identities=6%  Similarity=0.082  Sum_probs=57.7

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      ..|+|+|++ +|+.+.+.|++++++..|+...+             |.|+.|.++.|.++|++++|++|+++++++
T Consensus        30 ~~I~IkV~~-~g~~i~fkIk~tt~l~kL~~ay~ek~gi~~~~~rF~FdG~rl~~~~Tp~dl~medgD~Idv~~~q~  104 (106)
T 2eke_C           30 THINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQI  104 (106)
T ss_dssp             SEEEEEEEC-SSCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECC-
T ss_pred             CeEEEEEec-CCcEEEEEeCCCCHHHHHHHHHHHHhCCCcccEEEEECCeEcCCCCCHHHcCCCCCCEEEEEeecc
Confidence            449999999 99999999999999999999888             999999999999999999999999998764

>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=99.04  E-value=1e-10  Score=72.84  Aligned_cols=35  Identities=29%  Similarity=0.378  Sum_probs=33.1

Q ss_pred             CCCCceEEEecCccc-----cccccccC-------CCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQK-------ESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~-------~s~i~l~~~~~~   35 (97)
                      ||+++|||+|+|++|     |++|||++       +++|||++|.++
T Consensus        37 iPp~qQrLI~~Gk~LeD~kTL~dy~I~~~ta~~q~~atl~Lvlr~~~   83 (118)
T 4ajy_B           37 RPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADD   83 (118)
T ss_dssp             CCGGGEEEEETTEECCTTSBTTTTTCCGGGSBTTBCEEEEEEECCSS
T ss_pred             CCHHHeEEEeCCeECCCcCCHHHcCCCcCcccCCCCCEEEEEEecCC
Confidence            799999999999999     99999999       999999999754

>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=99.04  E-value=9.6e-11  Score=69.08  Aligned_cols=37  Identities=49%  Similarity=0.746  Sum_probs=33.0

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCCe
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRM   37 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~m   37 (97)
                      ||+++|+|+|+|+.|     |++|||.+|++|+|+++++++.
T Consensus        36 ip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~l~l~~rl~Gg~   77 (88)
T 4fbj_B           36 IPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGGG   77 (88)
T ss_dssp             CCGGGCEEEETTEECCTTSBTTTTTCCTTCEEEEECBCC---
T ss_pred             cChhHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEECCCCC
Confidence            799999999999999     9999999999999999988764

>3a4r_A Nfatc2-interacting protein; ubiquitin fold, coiled coil, cytoplasm, methylation, nucleus, transcription; 1.00A {Mus musculus} PDB: 3a4s_C 3rd2_A

Probab=99.03  E-value=6.1e-10  Score=64.68  Aligned_cols=60  Identities=5%  Similarity=0.064  Sum_probs=55.7

Q ss_pred             cCCeeeEEECCCCC-EEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEE
Q 042212           34 RGRMQIFVKTSTGK-TITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        34 ~~~m~i~vk~~~g~-~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~   93 (97)
                      +..|+|+|++.+|+ .+.+.|+++++++.|+...+             |.|+.|.++.|.++|++++|++|++.
T Consensus         5 ~~~i~ikV~~~~g~~~i~~~i~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~~l~~~~Tp~~l~medgD~Idv~   78 (79)
T 3a4r_A            5 SQELRLRVQGKEKHQMLEISLSPDSPLKVLMSHYEEAMGLSGHKLSFFFDGTKLSGKELPADLGLESGDLIEVW   78 (79)
T ss_dssp             CCCEEEEEECSSTTCEEEEEECTTSCHHHHHHHHHHHHTCTTCCCEEEETTEECCSCCCHHHHTCCTTCEEEEE
T ss_pred             CCEEEEEEEeCCCCEEEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEe
Confidence            35599999999996 89999999999999999888             99999999999999999999999985

>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=99.01  E-value=9.6e-11  Score=71.09  Aligned_cols=34  Identities=18%  Similarity=0.329  Sum_probs=30.5

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++|+|||+|++|     |++|||++|++| +++++++
T Consensus        55 ip~~qQrLI~~GKiL~D~~TL~~y~I~~gsti-~vl~lrg   93 (100)
T 1wju_A           55 LQENYIKIVINKKQLQLGKTLEEQGVAHNVKA-MVLELKQ   93 (100)
T ss_dssp             CCSTTCEEEETTEECCTTSBHHHHTCCSSEEE-EEECCCC
T ss_pred             cCHHHeEEEeCCeECCCCCcHHHcCCCCCCEE-EEEEECC
Confidence            799999999999999     999999999999 6666554

>2k8h_A Small ubiquitin protein; SUMO, post-translational modifier, signaling protein; NMR {Trypanosoma brucei}

Probab=99.00  E-value=2.6e-10  Score=70.29  Aligned_cols=64  Identities=6%  Similarity=0.156  Sum_probs=59.4

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      ...|+|+|++.+|+.+.+.|+++++++.|+...+             |.|+.|.++.|.++|++++|++|++++.++
T Consensus        24 ~~~I~IkVk~~~g~~i~fkVk~~t~l~kL~~ay~ek~gi~~~~~rfiFdG~~L~~~~Tp~dl~mEDgD~Idv~~~q~  100 (110)
T 2k8h_A           24 TALVAVKVVNADGAEMFFRIKSRTALKKLIDTYCKKQGISRNSVRFLFDGTPIDETKTPEELGMEDDDVIDAMVEQT  100 (110)
T ss_dssp             CCCEEEEEEETTSCCEEEEECTTSSHHHHHHHHHHHHTCCSSSCEEESSSCBCCSSSHHHHHHCSSEEEEEEECCCC
T ss_pred             CCeEEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEccc
Confidence            3459999999999999999999999999999888             999999999999999999999999998753

>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=99.00  E-value=1.3e-10  Score=66.85  Aligned_cols=35  Identities=14%  Similarity=0.477  Sum_probs=33.1

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++|+|+|+|++|     |++|||.+|++||++++..+
T Consensus        39 i~~~~qrL~~~G~~L~d~~tl~~~~i~~~~~i~l~~~~~G   78 (79)
T 2uyz_B           39 VPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTG   78 (79)
T ss_dssp             CCGGGEEEEETTEECCTTCCHHHHTCCTTEEEEEEECCCC
T ss_pred             CCcccEEEEECCEEeCCCCCHHHcCCCCCCEEEEEEeccC
Confidence            799999999999999     99999999999999998765

>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=98.99  E-value=1.6e-10  Score=69.36  Aligned_cols=36  Identities=14%  Similarity=0.455  Sum_probs=33.6

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|||+|+|++|     |++|||.+|++|||++++.++
T Consensus        57 ip~~~qrLif~Gk~L~d~~tl~dy~i~~g~~I~l~~~~~GG   97 (97)
T 1wyw_B           57 VPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGG   97 (97)
T ss_dssp             CCGGGEEEEETTEECCTTCCHHHHTCCTTCEEEEEESSSCC
T ss_pred             CChhhEEEEECCeEcCCCCCHHHCCCCCCCEEEEEEecCCC
Confidence            799999999999999     999999999999999987653

>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=98.98  E-value=3.1e-10  Score=65.00  Aligned_cols=34  Identities=29%  Similarity=0.520  Sum_probs=31.9

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeec
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLR   34 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~   34 (97)
                      ||+++|+|+|+|++|     |++|||.+|++|||+++++
T Consensus        40 ip~~~qrL~~~g~~L~d~~tL~~~~i~~g~~i~l~~r~~   78 (78)
T 2faz_A           40 VEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLLVRQS   78 (78)
T ss_dssp             CCGGGEEEEETTEECCTTCBTTTTTCCTTCEEEEEECCC
T ss_pred             cChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEeCC
Confidence            799999999999999     9999999999999998853

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens}

Probab=98.98  E-value=1.1e-10  Score=78.03  Aligned_cols=43  Identities=70%  Similarity=0.988  Sum_probs=40.6

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCCeeeEEEC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKT   43 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~m~i~vk~   43 (97)
                      ||+++|+|+|+|++|     |++|||++|++|||++++.++..+|||.
T Consensus       141 Ip~~~QrLi~~Gk~L~D~~tL~dygI~~gstI~LvlrlrGG~~~fvk~  188 (189)
T 3q3f_A          141 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGGQTFTKI  188 (189)
T ss_dssp             CCGGGCCEEETTEECCTTCBGGGGTCCTTCEEEECCCCCCCCCCCCCC
T ss_pred             CCHHHEEEEECCEECCCCCCHHHCCCCCCCEEEEEEEcCCCCcceEec
Confidence            799999999999999     9999999999999999999999998864

>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=98.98  E-value=2.8e-10  Score=68.14  Aligned_cols=31  Identities=23%  Similarity=0.317  Sum_probs=29.4

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVA   31 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~   31 (97)
                      ||+++|||+|+|++|     |++|||++|++|||..
T Consensus        57 ip~~qQrLif~Gk~LkD~~TL~dY~I~dgstLhL~~   92 (93)
T 3plu_A           57 TQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLELYY   92 (93)
T ss_dssp             CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEE
T ss_pred             CCHHHEEEEeCCEEccCcCCHHHcCCCCCCEEEEEe
Confidence            799999999999999     9999999999999964

>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=98.97  E-value=3.7e-10  Score=63.95  Aligned_cols=35  Identities=51%  Similarity=0.831  Sum_probs=32.5

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++|+|+|+|+.|     |++|||.+|++||+++++++
T Consensus        36 i~~~~q~L~~~g~~L~d~~tL~~~~i~~g~~i~l~~~~~G   75 (76)
T 1ndd_A           36 IPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRG   75 (76)
T ss_dssp             CCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCC-
T ss_pred             cChHHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCC
Confidence            699999999999999     99999999999999998765

>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=98.96  E-value=2.3e-10  Score=71.31  Aligned_cols=35  Identities=31%  Similarity=0.382  Sum_probs=32.4

Q ss_pred             CCCCceEEEecCccc-----ccccccc-------CCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQ-------KESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~-------~~s~i~l~~~~~~   35 (97)
                      ||+++|||+|+|++|     |++|||+       ++|+|||+++.++
T Consensus        37 IP~~qQrLi~~Gk~LeD~~TLsdy~I~~~~a~~q~~stL~L~lr~~g   83 (118)
T 2fnj_B           37 RPPEEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADD   83 (118)
T ss_dssp             CCGGGEEEEETTEECCTTSBHHHHTCCTTTSBTTBCEEEEEEEBSSS
T ss_pred             CCHHHeEEEECCeECCCCCCHHHcCcccccccCCCCCEEEEEecCCC
Confidence            799999999999999     9999999       7999999999444

>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=98.95  E-value=2.4e-10  Score=66.74  Aligned_cols=36  Identities=53%  Similarity=0.848  Sum_probs=33.6

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|+.|     |++|||++|++|||+++++++
T Consensus        48 ip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~i~l~~rl~GG   88 (88)
T 3dbh_I           48 IPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLRLRGG   88 (88)
T ss_dssp             CCGGGCCEEETTEECCTTSBGGGGTCCTTCEEEECCCCCCC
T ss_pred             cCHHHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEeCCCC
Confidence            799999999999999     999999999999999998753

>4hcn_B Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidase, NEDD8, protein binding; 2.60A {Saccharomyces cerevisiae}

Probab=98.94  E-value=3.7e-10  Score=67.75  Aligned_cols=36  Identities=75%  Similarity=1.104  Sum_probs=33.7

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|+.|     |++|||++|++|||+++++++
T Consensus        58 ip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~i~l~~rl~GG   98 (98)
T 4hcn_B           58 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   98 (98)
T ss_dssp             CCGGGCEEEETTEECCTTCBSGGGTCCTTEEEEEECBCSCC
T ss_pred             CChhHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCCC
Confidence            799999999999999     999999999999999998763

>3v6c_B Ubiquitin; structural genomics, structural genomics consortium, SGC, UB protease, hydrolase-signaling protein complex; 1.70A {Homo sapiens} PDB: 3v6e_B

Probab=98.93  E-value=4.2e-10  Score=66.50  Aligned_cols=34  Identities=76%  Similarity=1.114  Sum_probs=32.0

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeec
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLR   34 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~   34 (97)
                      ||+++|+|+|+|+.|     |++|||.+|++|||+++++
T Consensus        53 ip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~rlr   91 (91)
T 3v6c_B           53 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   91 (91)
T ss_dssp             CCGGGCEEEETTEECCTTCBTGGGTCCTTCEEEEECCCC
T ss_pred             CChhhEEEEECCeECCCcCcHHHCCCCCCCEEEEEEecC
Confidence            799999999999999     9999999999999999863

>2daf_A FLJ35834 protein; hypothetical protein FLJ35834, ubiquitin-like domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.93  E-value=3.5e-10  Score=70.28  Aligned_cols=47  Identities=13%  Similarity=0.168  Sum_probs=40.2

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCCeeeEEECCCCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFVKTSTGK   47 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~m~i~vk~~~g~   47 (97)
                      ||+++|+|+|+||.|     |++|||++|.+|||+.+...+-..=+|...|.
T Consensus        52 iP~e~qrLIy~GKiLKD~eTL~~~gIk~g~TIhLvi~s~~p~~~p~~~~~~~  103 (118)
T 2daf_A           52 IPHSVLQIRYSGKILKNNETLVQHGVKPQEIVQVEIFSTNPDLYPVRRIDGL  103 (118)
T ss_dssp             CCTTTEEEEETTEEECSSCCHHHHSCCSSCEEEEEEEESCTTTSCCCCCCSC
T ss_pred             CChHHEEEEECCeEcCCcchHHHcCCCCCCEEEEEEecCCCccCcceeccCc
Confidence            799999999999999     99999999999999999876655555555443

>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=98.93  E-value=6.4e-10  Score=66.06  Aligned_cols=40  Identities=68%  Similarity=0.986  Sum_probs=33.8

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCCeeeE
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIF   40 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~m~i~   40 (97)
                      ||+++|+|+|+|+.|     |++|||.+|++|||++++.+++...
T Consensus        37 ip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~i~l~~r~~gG~~~~   81 (96)
T 3k9o_B           37 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGYADLR   81 (96)
T ss_dssp             CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCCC-----
T ss_pred             CChhHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEEcCCCCccc
Confidence            799999999999999     9999999999999999998876643

>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana, uncharacterized putative protein, NESG, structural genomics; NMR {Arabidopsis thaliana}

Probab=98.92  E-value=4.2e-10  Score=65.96  Aligned_cols=32  Identities=22%  Similarity=0.386  Sum_probs=30.6

Q ss_pred             CCCCceEEEecCcc-c-----cccccccCCCcceeeee
Q 042212            1 MPLEQQRLVFADKS-L-----LADYNIQKESTLHLVAR   32 (97)
Q Consensus         1 ip~~~q~L~~~~~~-L-----l~~y~i~~~s~i~l~~~   32 (97)
                      ||+++|+|+|+|++ |     |++|||.+|++|+|+++
T Consensus        46 ip~~~QrLi~~Gk~lL~D~~tL~~y~I~~gs~i~lv~~   83 (84)
T 2kk8_A           46 IPVSKQTLIVDGIVILREDLTVEQCQIVPTSDIQLEVS   83 (84)
T ss_dssp             CCGGGEEEEETTEECCCSSSBHHHHTCCTTSCEEEEEC
T ss_pred             cChHHEEEEECCEEecCCcCCHHHcCCCCCCEEEEEEc
Confidence            79999999999999 8     99999999999999886

>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=98.91  E-value=6.6e-10  Score=64.38  Aligned_cols=36  Identities=56%  Similarity=0.912  Sum_probs=32.6

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|+.|     |++|||+++++||++++++++
T Consensus        39 ip~~~qrL~~~g~~L~d~~tL~~~~i~~~~~i~l~~rl~GG   79 (85)
T 3n3k_B           39 IPPDQQRLIFAGKQLEDGRTLSDYNIHNHSALYLLLKLRGG   79 (85)
T ss_dssp             CCGGGEEEEETBEECCTTCBTTTTTCCTTCEEEEEECCC--
T ss_pred             CCHHHEEEEECCeECCCCCCHHHCCCCCCCEEEEEEeccCC
Confidence            799999999999999     999999999999999997653

>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=98.91  E-value=9.2e-10  Score=62.26  Aligned_cols=36  Identities=72%  Similarity=1.100  Sum_probs=33.4

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|+.|     |++|||.+|++||++++++++
T Consensus        36 i~~~~q~L~~~g~~L~d~~tL~~~~i~~g~~i~l~~~~~GG   76 (76)
T 3a9j_A           36 IPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRGG   76 (76)
T ss_dssp             CCGGGEEEEETTEECCTTCBTGGGTCCTTCEEEEEECCCCC
T ss_pred             cCHHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEEeCCCC
Confidence            699999999999999     999999999999999987653

>2l7r_A Ubiquitin-like protein FUBI; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=98.91  E-value=3.9e-10  Score=67.17  Aligned_cols=36  Identities=25%  Similarity=0.431  Sum_probs=33.6

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|++|     |++|||.+|++|+|+++++++
T Consensus        53 ip~~~qrLi~~Gk~L~D~~tL~~y~I~~gstI~lv~rl~GG   93 (93)
T 2l7r_A           53 IAPEDQVVLLAGAPLEDEATLGQCGVEALTTLEVAGRMLGG   93 (93)
T ss_dssp             CCGGGCEEEETTEECCTTSBHHHHTCCSSCEEEEECCCCCC
T ss_pred             cChhHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCCC
Confidence            799999999999999     999999999999999998763

>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=98.91  E-value=7e-10  Score=65.23  Aligned_cols=35  Identities=37%  Similarity=0.728  Sum_probs=31.8

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|||+|+|+.|     |++||| +|++|||+++.++.
T Consensus        41 ip~~~qrLi~~Gk~L~d~~tL~~~~i-~g~~i~l~~~~~~~   80 (90)
T 4dwf_A           41 IPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVIHLVERAPPQ   80 (90)
T ss_dssp             CCGGGEEEEETTEECCTTSBGGGGTC-TTEEEEEEECCCC-
T ss_pred             CCHHHEEEEECCeECCCCCCHHHcCC-CCcEEEEEecCCCC
Confidence            799999999999999     999999 89999999987643

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens}

Probab=98.90  E-value=7e-10  Score=64.99  Aligned_cols=31  Identities=42%  Similarity=0.845  Sum_probs=29.4

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVAR   32 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~   32 (97)
                      ||+++|+|+|+|+.|     |++||| +|++|||++|
T Consensus        53 ip~~~qrLi~~Gk~L~D~~tL~~~~i-~g~~i~lv~R   88 (88)
T 4eew_A           53 IPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVIHLVER   88 (88)
T ss_dssp             CCGGGEEEEETTEECCTTSBGGGGTC-TTEEEEEEEC
T ss_pred             CCHHHEEEEECCEECCCCCcHHHcCC-CCcEEEEEEC
Confidence            799999999999999     999999 8999999875

>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=98.90  E-value=9e-10  Score=67.59  Aligned_cols=36  Identities=75%  Similarity=1.104  Sum_probs=33.3

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|||+|+|+.|     |++|||++|++|||+++++++
T Consensus        71 ip~~~QrLi~~Gk~L~D~~tL~~~gI~~gs~I~l~~rl~GG  111 (111)
T 3vdz_A           71 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  111 (111)
T ss_dssp             CCGGGEEEEETTEECCTTSBTTTTTCCTTCEEEEEECCCC-
T ss_pred             CChHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCCC
Confidence            799999999999999     999999999999999998753

>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure, northeast structural genomics consortium, protein structure initiative, NESG; NMR {Homo sapiens}

Probab=98.90  E-value=4.8e-10  Score=65.97  Aligned_cols=36  Identities=33%  Similarity=0.502  Sum_probs=31.1

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|++|     |++|||.+|++|+|+.+..++
T Consensus        40 ip~~~qrL~~~Gk~L~D~~tL~~~~I~~g~~i~l~~~~~gg   80 (88)
T 2hj8_A           40 VQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRGG   80 (88)
T ss_dssp             SCTTTEEEESSSSCCCTTSBHHHHHCSTTCEEEEEEC----
T ss_pred             CChhHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEEcCCC
Confidence            799999999999999     999999999999999987653

>4a20_A Ubiquitin-like protein MDY2; protein binding, GET-pathway, tail-anchored proteins; 1.78A {Saccharomyces cerevisiae} PDB: 2lxc_A 4goc_A

Probab=98.90  E-value=8.2e-10  Score=66.69  Aligned_cols=34  Identities=21%  Similarity=0.405  Sum_probs=31.7

Q ss_pred             CCCCceEEEecCccc-----cccccc-cCCCcceeeeeec
Q 042212            1 MPLEQQRLVFADKSL-----LADYNI-QKESTLHLVARLR   34 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i-~~~s~i~l~~~~~   34 (97)
                      ||+++|||+|+|++|     |++||| ++|++|+|+++.+
T Consensus        58 ip~~~QrLi~~Gk~L~D~~tL~dy~I~~~g~ti~lmvskp   97 (98)
T 4a20_A           58 SHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKPN   97 (98)
T ss_dssp             SCGGGEEEEETTEEECTTCBGGGSCCBTTBCEEEEEECCC
T ss_pred             CChhhEEEEECCEECcCcCCHHHcCcCCCCCEEEEEEeCC
Confidence            699999999999999     999999 9999999998743

>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=98.90  E-value=4.4e-10  Score=66.70  Aligned_cols=36  Identities=36%  Similarity=0.547  Sum_probs=33.3

Q ss_pred             CCCCceEEEecCccc-----cccc--cccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADY--NIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y--~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|||+|+|+.|     |++|  ||.++++|||+++++++
T Consensus        47 i~~~~QrLi~~Gk~L~D~~tL~~~~~~i~~~~~i~lv~~~~gg   89 (93)
T 1wgd_A           47 PRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVCNVKSG   89 (93)
T ss_dssp             CCTTTCEEEETTEECCSSSCHHHHSCSSSCSEEEEEECCCCCC
T ss_pred             CChHHeEEEECCEECcCcCCHHHHhcCCCCCCEEEEEeCCCCC
Confidence            689999999999999     9999  99999999999987653

>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=98.89  E-value=8.1e-10  Score=64.77  Aligned_cols=36  Identities=31%  Similarity=0.480  Sum_probs=33.8

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|+.|     |++|||.+|++|||+++++++
T Consensus        45 ip~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~~~gG   85 (89)
T 1wy8_A           45 VRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVRPDSG   85 (89)
T ss_dssp             CCTTTEEEEETTEECCSSSBHHHHTCCTTCEEEEEECCCCS
T ss_pred             cChhhEEEEECCeECCCCCCHHHCCCCCCCEEEEEEeCCCC
Confidence            799999999999999     999999999999999998765

>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=98.88  E-value=1e-09  Score=68.17  Aligned_cols=35  Identities=26%  Similarity=0.341  Sum_probs=30.8

Q ss_pred             CCCCceEEEecCccc-----cccccccCC--CcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKE--STLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~--s~i~l~~~~~~   35 (97)
                      ||+++|||||+|++|     |++|+|..+  +++||++++..
T Consensus        60 ~p~~qqrLIy~GK~LeD~~TL~~y~I~~~~~~tlhLvlr~~~  101 (116)
T 1wgh_A           60 SSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLVARETL  101 (116)
T ss_dssp             CCTTTEEEEETTEEECSSCBTTTTTCCSSCEEEEEEEECSSC
T ss_pred             CChHHEEEEECCcCCCCCCcHHHcCCCCCCceEEEEEccCCC
Confidence            479999999999999     999999866  78999998753

>2lxa_A Ubiquitin-like protein MDY2; ubiquitin-like domain, protein-protein interaction, SGT2 BIN domain, GET pathway, protein binding; NMR {Saccharomyces cerevisiae}

Probab=98.88  E-value=5.8e-10  Score=65.98  Aligned_cols=33  Identities=21%  Similarity=0.414  Sum_probs=31.1

Q ss_pred             CCCCceEEEecCccc-----cccccc-cCCCcceeeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNI-QKESTLHLVARL   33 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i-~~~s~i~l~~~~   33 (97)
                      ||+++|||+|+|++|     |++||| ++|++|+|..+.
T Consensus        40 ip~~~QrLi~~Gk~L~D~~tL~~y~I~~~~stl~v~~~~   78 (87)
T 2lxa_A           40 SHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKP   78 (87)
T ss_dssp             SSSTTEEEEETTEECCTTCBHHHHCCCGGGCEEEEEECC
T ss_pred             CChHHEEEEECCEECcCcCCHHHcCCCCCCCEEEEEcCC
Confidence            699999999999999     999999 799999999874

>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=98.88  E-value=1.2e-09  Score=63.32  Aligned_cols=34  Identities=26%  Similarity=0.562  Sum_probs=30.7

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeec
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLR   34 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~   34 (97)
                      ||+++|+|+|+|+.|     |++|||.+|++|||+.+.+
T Consensus        44 ip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~i~l~~~~~   82 (85)
T 2wyq_A           44 FPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTKT   82 (85)
T ss_dssp             CCGGGEEEEETTEECCTTSBGGGGCCCTTSEEEEEEC--
T ss_pred             CCHHHeEEEECCEECcCCCCHHHcCCCCCCEEEEEEcCC
Confidence            689999999999999     9999999999999998754

>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=98.88  E-value=1.1e-09  Score=68.84  Aligned_cols=36  Identities=25%  Similarity=0.396  Sum_probs=32.1

Q ss_pred             CCC--CceEEEecCccc-----cccccccCC------CcceeeeeecCC
Q 042212            1 MPL--EQQRLVFADKSL-----LADYNIQKE------STLHLVARLRGR   36 (97)
Q Consensus         1 ip~--~~q~L~~~~~~L-----l~~y~i~~~------s~i~l~~~~~~~   36 (97)
                      ||+  ++|||||+||+|     |++|+|++|      +++||+++++++
T Consensus        58 iP~~~~qQrLIy~GK~LeD~~TLsdy~I~~~~~~~~v~tmhlVlrl~g~  106 (126)
T 1se9_A           58 GPKTVKEVKLISAGKVLENSKTVKDYRSPVSNLAGAVTTMHVIIQAPVT  106 (126)
T ss_dssp             SCCSGGGEEEEETTEECCTTSBGGGGSCCTTSCTTCCEEEEEEECCCSS
T ss_pred             CCCChhhEEEEECCeECcCCCcHHHcCCCcCCccCCcEEEEEEeccCCc
Confidence            565  899999999999     999999999      789999998754

>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=98.39  E-value=2e-10  Score=65.40  Aligned_cols=35  Identities=34%  Similarity=0.695  Sum_probs=33.0

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++|+|+|+|+.|     |++|||.+|++|||++++++
T Consensus        36 i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~rlrg   75 (76)
T 3b1l_X           36 VPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRR   75 (76)
Confidence            699999999999999     99999999999999999765

>1sif_A Ubiquitin; hydrophobic mutants, folding, stability, structural protein; 2.18A {Homo sapiens} SCOP: d.15.1.1

Probab=98.87  E-value=9.3e-10  Score=64.78  Aligned_cols=36  Identities=75%  Similarity=1.104  Sum_probs=30.2

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|+.|     |++|||.+|++|+|+++++++
T Consensus        45 ip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~r~~GG   85 (88)
T 1sif_A           45 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   85 (88)
T ss_dssp             CCGGGCEEEETTEECCTTSBSGGGTCCTTCEEEEEC-----
T ss_pred             cChhhEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCCC
Confidence            799999999999999     999999999999999987754

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=98.87  E-value=8.3e-10  Score=65.95  Aligned_cols=36  Identities=22%  Similarity=0.437  Sum_probs=33.5

Q ss_pred             CCCCceEEEecCccc------cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL------LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L------l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|++|      |++|||++|++|+|+++++++
T Consensus        50 ip~~~QrLi~~Gk~L~D~~~tL~~ygI~~gstl~lv~r~~gg   91 (94)
T 2kan_A           50 TPIKRMQLYYSGIELADDYRNLNEYGITEFSEIVVFLKSINR   91 (94)
T ss_dssp             SCTTTEEEEETTEEECCTTSBHHHHTCCTTEEEEEEECCCSS
T ss_pred             cCHHHEEEEECCEECCCCcccHHHCCCCCCCEEEEEEeCCCC
Confidence            799999999999988      999999999999999998764

>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=98.87  E-value=8.7e-10  Score=64.32  Aligned_cols=36  Identities=36%  Similarity=0.488  Sum_probs=33.8

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|+.|     |++|||.++++|||++++.++
T Consensus        43 i~~~~qrL~~~Gk~L~d~~tL~~~~i~~g~~i~l~~~~~GG   83 (87)
T 1wh3_A           43 LPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKGSG   83 (87)
T ss_dssp             CCTTTEEEEETTEECCSSSBHHHHTCCTTEEEEEEECSCCC
T ss_pred             CChHHEEEEECCEEccCCCCHHHCCCCCCCEEEEEEeccCC
Confidence            799999999999999     999999999999999998765

>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=98.86  E-value=1e-09  Score=67.65  Aligned_cols=36  Identities=31%  Similarity=0.519  Sum_probs=33.9

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|+.|     |++|||.+|++|||+++++++
T Consensus        71 ip~~~QrL~~~Gk~L~D~~tL~~y~i~~g~~i~lv~rl~GG  111 (115)
T 1we7_A           71 MPAGKQKLQYEGIFIKDSNSLAYYNMASGAVIHLALKERSG  111 (115)
T ss_dssp             CCTTTEEEEETTEEECTTSBHHHHTCCSSCEEEEEECCCSC
T ss_pred             CChHHEEEEECCEECCCCCCHHHCCCCCCCEEEEEEEcCCC
Confidence            799999999999999     999999999999999998765

>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=98.86  E-value=1.3e-09  Score=63.07  Aligned_cols=36  Identities=67%  Similarity=0.960  Sum_probs=33.5

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|+.|     |++|||.++++|||+++++++
T Consensus        39 i~~~~qrL~~~g~~L~d~~tL~~~~i~~~~~l~l~~r~~GG   79 (85)
T 3mtn_B           39 IPPDQQRLIFAGKQLEDGRTLSDYNIQKWSTLFLLLRLRGG   79 (85)
T ss_dssp             CCGGGCEEEETTEECCTTSBTGGGTCCTTCEEEEECCCCCC
T ss_pred             cChHHEEEEECCEECCCCCCHHHcCCCCCCEEEEEEECcCC
Confidence            799999999999999     999999999999999997653

>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=98.86  E-value=1.2e-09  Score=66.92  Aligned_cols=36  Identities=33%  Similarity=0.411  Sum_probs=33.7

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|+.|     |++|||.+|++|||+++++++
T Consensus        67 ip~~~QrL~~~Gk~L~D~~tL~~y~I~~g~~l~l~~r~~GG  107 (111)
T 1we6_A           67 IPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLRERSG  107 (111)
T ss_dssp             CCTTTSEEECSSSBCCTTSBTTTTTCSSSCEEEEECSSCCS
T ss_pred             CCHHHeEEEECCEECCCCCcHHHCCCCCCCEEEEEEEcCCC
Confidence            799999999999999     999999999999999997764

>2dzi_A Ubiquitin-like protein 4A; GDX, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.85  E-value=1.4e-09  Score=62.37  Aligned_cols=33  Identities=48%  Similarity=0.803  Sum_probs=31.3

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARL   33 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~   33 (97)
                      ||+++|+|+|+|+.|     |++|||.+|++||+++++
T Consensus        43 i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~~   80 (81)
T 2dzi_A           43 VPVRQQRLLFKGKALADGKRLSDYSIGPNSKLNLVVKP   80 (81)
T ss_dssp             CCTTTCEEEETTEECCTTSBGGGGTCCSSBCCEEECCC
T ss_pred             cCHHHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            699999999999999     999999999999999875

>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=98.83  E-value=2.7e-09  Score=63.59  Aligned_cols=34  Identities=26%  Similarity=0.555  Sum_probs=31.7

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeec
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLR   34 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~   34 (97)
                      ||+++|+|+|+|+.|     |++|||.+|++|+|+++.+
T Consensus        39 ip~~~qrLi~~Gk~L~D~~tL~~ygI~~g~~i~l~~~~~   77 (95)
T 1uel_A           39 FPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKP   77 (95)
T ss_dssp             CCTTTEEEEETTEECCTTSBGGGGTCCSSSEEEEEESSC
T ss_pred             CChhhEEEEECCEECCCcCcHHHCCCCCCCEEEEEEeCC
Confidence            699999999999999     9999999999999998754

>3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=98.83  E-value=1.5e-09  Score=66.11  Aligned_cols=35  Identities=11%  Similarity=0.310  Sum_probs=31.6

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++|||+|+|+.|     |++|||++|++|+|+++.+.
T Consensus        37 ip~~~QrLi~~Gk~L~D~~tL~~~~i~~g~~i~lv~~~~~   76 (106)
T 3m62_B           37 CEESQIKLIYSGKVLQDSKTVSECGLKDGDQVVFMVSQKK   76 (106)
T ss_dssp             SCGGGCEEEETTEECCTTSBTTTTTCCTTCEEEEECCC--
T ss_pred             CChhhEEEEECCEECCCcCCHHHcCCCCCCEEEEEEcCCC
Confidence            699999999999999     99999999999999998543

>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=98.80  E-value=2.1e-09  Score=64.87  Aligned_cols=35  Identities=34%  Similarity=0.445  Sum_probs=32.8

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++|+|+|+|+.|     |++|||.+|++|+|+++.++
T Consensus        57 ip~~~QrLi~~Gk~L~D~~tL~~ygI~~gstI~l~~r~~~   96 (100)
T 1yqb_A           57 AHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQH   96 (100)
T ss_dssp             CCGGGEEEEETTEECCTTSBHHHHTCCTTCEEEEEECCCC
T ss_pred             cChhhEEEEECCEECCCcCcHHHCCCCCCCEEEEEEcCCC
Confidence            799999999999999     99999999999999998764

>4b6w_A Tubulin-specific chaperone; CAP-Gly, ubiquitin-like; HET: MSE; 2.35A {Trypanosoma brucei brucei strain 927}

Probab=98.79  E-value=3e-09  Score=62.71  Aligned_cols=34  Identities=26%  Similarity=0.406  Sum_probs=29.8

Q ss_pred             CCCCceEEEe-------cCccc-----cccccccCCCcceeeeeec
Q 042212            1 MPLEQQRLVF-------ADKSL-----LADYNIQKESTLHLVARLR   34 (97)
Q Consensus         1 ip~~~q~L~~-------~~~~L-----l~~y~i~~~s~i~l~~~~~   34 (97)
                      ||+++|||+|       +|++|     |++|||++|++|||+-+.|
T Consensus        40 ip~~~QrLi~~~~~~~~~g~~l~d~~tL~~Y~i~~g~~ihlvd~~P   85 (86)
T 4b6w_A           40 TPPEYMQLQLIDDRGITIEKNMANDKQLGYYQCRDEFVIHVVDLQP   85 (86)
T ss_dssp             CCGGGEEEEEECTTSCEEESSCCTTSBGGGGTCCTTCEEEEEECCC
T ss_pred             CCHHHEEEEEecCCCCceeeEcCCCCCHHHCCCCCCCEEEEEeCCC
Confidence            7999999996       57777     9999999999999987643

>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling proteins; 1.15A {Saccharomyces cerevisiae} SCOP: d.15.1.1 PDB: 2bwe_S

Probab=98.79  E-value=4e-09  Score=59.94  Aligned_cols=32  Identities=38%  Similarity=0.754  Sum_probs=30.3

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVAR   32 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~   32 (97)
                      ||+++|+|+|+|+.|     |++|||.+|++||++.+
T Consensus        39 i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~   75 (77)
T 2bwf_A           39 IPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS   75 (77)
T ss_dssp             CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEEC
T ss_pred             CCHHHEEEEECCeEcCCCCCHHHcCCCCCCEEEEEEc
Confidence            699999999999999     99999999999999875

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=98.77  E-value=5e-09  Score=63.22  Aligned_cols=35  Identities=34%  Similarity=0.451  Sum_probs=32.5

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++|+|+|+|+.|     |++|||.+|++|+|+.+.++
T Consensus        60 ip~~~qrLi~~Gk~L~D~~tL~~~gI~~g~~I~l~~~~~~   99 (101)
T 2klc_A           60 SHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQN   99 (101)
T ss_dssp             CCGGGEEEEETTEEECTTCCTGGGTCCTTCEEEEEECCSS
T ss_pred             cChhhEEEEECCEECCCcCcHHHcCCCCCCEEEEEEcCCC
Confidence            799999999999999     99999999999999998654

>2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing, protein binding; 2.60A {Homo sapiens}

Probab=98.76  E-value=5.3e-09  Score=64.03  Aligned_cols=35  Identities=77%  Similarity=1.145  Sum_probs=33.1

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++|+|+|+|+.|     |++|||.+|++|||++++++
T Consensus        71 ip~~~qrLi~~Gk~L~D~~tL~~~gI~~gs~I~l~~rl~G  110 (111)
T 2ojr_A           71 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG  110 (111)
T ss_dssp             CCTTTEEEEETTEECCSSCBTTTTTCCTTCEEEEEECCCC
T ss_pred             cCcccEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCC
Confidence            699999999999999     99999999999999999765

>3m63_B Ubiquitin domain-containing protein DSK2; armadillo-like repeats, UBL conjugation pathway, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=98.75  E-value=2.3e-09  Score=64.79  Aligned_cols=33  Identities=36%  Similarity=0.715  Sum_probs=30.9

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARL   33 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~   33 (97)
                      ||+++|+|+|+|+.|     |++|||++|++|+|+.+.
T Consensus        63 ip~~~QrLi~~Gk~L~D~~tL~~~gI~~g~tI~lv~~~  100 (101)
T 3m63_B           63 IPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKSQ  100 (101)
T ss_dssp             CCSTTCCEEETTEECCTTSBTTTTTCCTTEEEEECCCC
T ss_pred             cChHHEEEEECCEECCCcCcHHHCCCCCCCEEEEEeCC
Confidence            799999999999999     999999999999998763

>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=98.74  E-value=1.1e-09  Score=68.66  Aligned_cols=36  Identities=75%  Similarity=1.104  Sum_probs=0.0

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|++|     |++|||.+|++|||+++++++
T Consensus        36 ip~~~QrLi~~Gk~L~D~~tL~~~~I~~gsti~l~~rl~GG   76 (128)
T 3u5e_m           36 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   76 (128)
T ss_dssp             -----------------------------------------
T ss_pred             cChHHEEEEECCEECCCCCchhhhccCCCCEEEEEEEcCCC
Confidence            699999999999999     999999999999999998765

>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=98.74  E-value=4.6e-09  Score=63.83  Aligned_cols=34  Identities=18%  Similarity=0.383  Sum_probs=31.9

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeec
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLR   34 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~   34 (97)
                      ||+++|+|+|+|++|     |++|||.+|++|||+++.+
T Consensus        59 ip~~~qrLi~~Gk~L~D~~tL~~ygI~~g~ti~lv~~~~   97 (106)
T 1ttn_A           59 VEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQP   97 (106)
T ss_dssp             CCSTTCEEEETTEECCTTSHHHHCCCSSSCEEEEECCCS
T ss_pred             cCcccEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCC
Confidence            799999999999999     9999999999999999754

>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=98.73  E-value=1.5e-09  Score=64.65  Aligned_cols=36  Identities=31%  Similarity=0.417  Sum_probs=33.3

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|+.|     |++|||.+|++|||+++..++
T Consensus        52 ip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~~g   92 (96)
T 1wx8_A           52 CNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVRSHSG   92 (96)
T ss_dssp             SCTTTBCCEETTEECCTTSCHHHHTCCTTEEEECCBCCSSC
T ss_pred             CCHHHEEEEECCEECCCcCCHHHCCCCCCCEEEEEEeCCCC
Confidence            699999999999999     999999999999999987653

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=98.73  E-value=6.3e-09  Score=65.19  Aligned_cols=36  Identities=33%  Similarity=0.388  Sum_probs=31.0

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|+.|     |++|||.+|++|+|+.+..++
T Consensus        67 ip~~~QrLi~~Gk~L~D~~tL~dygI~~gstI~lv~~~~gg  107 (125)
T 1j8c_A           67 SQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIKRDPN  107 (125)
T ss_dssp             SCSSSEEEEETTEEESTTSCGGGTTCSSSEEEEEEEC----
T ss_pred             cCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEEeccCCC
Confidence            699999999999999     999999999999999987653

>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=98.72  E-value=1.3e-09  Score=70.52  Aligned_cols=36  Identities=75%  Similarity=1.104  Sum_probs=0.0

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|++|     |++|||.+|++|||++++.++
T Consensus        36 ip~~~QrLi~~Gk~L~D~~tL~dygI~~gstL~Lvlrl~GG   76 (152)
T 3u5c_f           36 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   76 (152)
T ss_dssp             -----------------------------------------
T ss_pred             CCHHHEEEEECCEEccccCcHHHcCCCCCCEEEEEeeccCC
Confidence            799999999999999     999999999999999998754

>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=98.70  E-value=5.9e-09  Score=63.25  Aligned_cols=36  Identities=36%  Similarity=0.476  Sum_probs=33.1

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|+.|     |++|||.+|++|||+++..+.
T Consensus        52 ip~~~qrLi~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~~~   92 (106)
T 1wx7_A           52 AHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHR   92 (106)
T ss_dssp             CCTTTEEEEETTEECCTTSCHHHHTCCTTEEEEEEECCCCC
T ss_pred             cChhhEEEEECCEECCCcCcHHHcCCCCCCEEEEEEcCCCC
Confidence            689999999999999     999999999999999987643

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens}

Probab=98.70  E-value=9e-09  Score=64.64  Aligned_cols=34  Identities=26%  Similarity=0.351  Sum_probs=30.1

Q ss_pred             CCCceEEEecCccc-----cccccccCCC--cceeeeeecC
Q 042212            2 PLEQQRLVFADKSL-----LADYNIQKES--TLHLVARLRG   35 (97)
Q Consensus         2 p~~~q~L~~~~~~L-----l~~y~i~~~s--~i~l~~~~~~   35 (97)
                      |+++|||||+|++|     |++|||++++  ++||++++.+
T Consensus        62 ~~~~qrLIy~GK~LeD~~TL~~y~I~~~~~~tlhlv~r~~~  102 (125)
T 2gow_A           62 SPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLVARETL  102 (125)
T ss_dssp             CGGGEEEESSSSEEESSCBTGGGCCCTTSEEEEEEEECSCC
T ss_pred             ChHHEEEEECCcCCCCCCcHHHcCCCCCCceEEEEEecCCC
Confidence            58999999999999     9999999665  7899998754

>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=98.69  E-value=8.5e-09  Score=62.77  Aligned_cols=34  Identities=29%  Similarity=0.501  Sum_probs=31.7

Q ss_pred             CCCCc-eEEEecCccc-----cccccccCCCcceeeeeec
Q 042212            1 MPLEQ-QRLVFADKSL-----LADYNIQKESTLHLVARLR   34 (97)
Q Consensus         1 ip~~~-q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~   34 (97)
                      ||+++ |+|+|+|+.|     |++|||.+|++|||+.+..
T Consensus        62 ip~~~~qrLi~~Gk~L~D~~tL~~y~i~~g~~i~lv~~~~  101 (107)
T 1x1m_A           62 VPDPELIDLIYCGRKLKDDQTLDFYGIQPGSTVHVLRKSW  101 (107)
T ss_dssp             CCCSSSEEEEETTEECCTTCBHHHHTCCTTCEEEEEESSC
T ss_pred             CChhhcEEEEECCeECCCCCcHHHcCCCCCCEEEEEeCCC
Confidence            68999 9999999999     9999999999999998754

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana}

Probab=98.69  E-value=8e-09  Score=60.46  Aligned_cols=32  Identities=28%  Similarity=0.415  Sum_probs=30.2

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVAR   32 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~   32 (97)
                      ||+++|+|+|+|++|     |++|||.+|++|+|+.+
T Consensus        47 ip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~l~l~~s   83 (85)
T 2kd0_A           47 VLPRGQKLIFKGKVLVETSTLKQSDVGSGAKLMLMAS   83 (85)
T ss_dssp             CCTTTCEEEETTEECCTTCBTTTTTCCTTEEEEEECC
T ss_pred             cChHHEEEEECCeECCCcCCHHHCCCCCCCEEEEEEe
Confidence            799999999999999     99999999999999865

>1wjn_A Tubulin-folding protein TBCE; ubiquitin-like domain, progressive motor neuropathy, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=98.68  E-value=4.4e-08  Score=58.50  Aligned_cols=58  Identities=10%  Similarity=0.071  Sum_probs=46.9

Q ss_pred             eeeEEEC---CCCCEEEEeecCCCcHHHhhcccc-------------CC-------CeeC-CCCCcccccccCCCCEEEE
Q 042212           37 MQIFVKT---STGKTITLEVESSDMIDNASRGSS-------------SP-------AGNF-EDGWTQADYNIQKESTLHF   92 (97)
Q Consensus        37 m~i~vk~---~~g~~~~l~v~~~~tV~~lK~~I~-------------~~-------gk~L-~d~~tL~~y~I~~~sti~l   92 (97)
                      +.+.|+.   .+|+.+...+.+++||.+||.+|+             |.       ...| +|.++|++|++.+|++||+
T Consensus        10 v~l~I~~~~~~~~~~~e~~l~~~~TV~~LK~~i~~~~gip~~~q~L~~~~~~~~~~~~~L~~d~~~L~~y~i~~G~~I~V   89 (97)
T 1wjn_A           10 LTLKIKCSNQPERQILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCLLV   89 (97)
T ss_dssp             EEEEEEESSCSSSCCEEEEEETTSBHHHHHHHHHTTTTCCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTCCTTCEEEE
T ss_pred             EEEEEEecCCCCCcEEEEECCCCCCHHHHHHHHHHHHCCChhHeEEEEEcCCCCceeeccCCCcccHhhcCCCCCCEEEE
Confidence            5555653   467899999999999999999999             22       1225 7788999999999999998


Q ss_pred             EE
Q 042212           93 VL   94 (97)
Q Consensus        93 ~~   94 (97)
                      ..
T Consensus        90 ~d   91 (97)
T 1wjn_A           90 RW   91 (97)
T ss_dssp             EC
T ss_pred             Ee
Confidence            75

>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=98.66  E-value=4.3e-09  Score=64.27  Aligned_cols=33  Identities=24%  Similarity=0.460  Sum_probs=30.4

Q ss_pred             CceEEEecCccc------cccccccCCCcceeeeeecCC
Q 042212            4 EQQRLVFADKSL------LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         4 ~~q~L~~~~~~L------l~~y~i~~~s~i~l~~~~~~~   36 (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            679999999998      999999999999999998764

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A

Probab=98.63  E-value=1.9e-08  Score=61.37  Aligned_cols=33  Identities=18%  Similarity=0.162  Sum_probs=30.1

Q ss_pred             CCCCceEEEecCccc-----cccccc-cCCCcceeeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNI-QKESTLHLVARL   33 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i-~~~s~i~l~~~~   33 (97)
                      ||+++|||+|+|+.+     |++||| ++|+++||++..
T Consensus        62 ipp~~QRli~ggkll~D~~TL~~ygI~~~G~t~hL~l~~  100 (105)
T 4dbg_A           62 FPPVLQQWVIGQRLARDQETLHSHGVRQNGDSAYLYLLS  100 (105)
T ss_dssp             CCGGGEEEEETTEEECTTCBTGGGTCCSTTCEEEEEECC
T ss_pred             CCHHHEEEeccCeEccCcCcHHHcCCCCCCCEEEEEEEe
Confidence            799999999999976     999999 599999999864

>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=98.63  E-value=6.2e-09  Score=62.85  Aligned_cols=36  Identities=19%  Similarity=0.450  Sum_probs=32.9

Q ss_pred             CCCCceEEEecCccc------cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL------LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L------l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|++|      |++|||++|++|||+.+.+++
T Consensus        47 ip~~~qrL~~~gk~L~D~~~tL~~ygI~~g~~l~l~~~~~gg   88 (102)
T 1v5o_A           47 VPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVLLQKDNVG   88 (102)
T ss_dssp             CCGGGBCEEETTEEECCSSSBHHHHTCCTTEEEEECBCCCCC
T ss_pred             cChHHeEEEECCEECCCCcccHHHCCCCCCCEEEEEECCCCC
Confidence            799999999999998      999999999999999987543

>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=98.57  E-value=1.8e-08  Score=59.52  Aligned_cols=34  Identities=32%  Similarity=0.533  Sum_probs=31.3

Q ss_pred             CCCCceEEEecCccc------cccccccCCCcceeeeeec
Q 042212            1 MPLEQQRLVFADKSL------LADYNIQKESTLHLVARLR   34 (97)
Q Consensus         1 ip~~~q~L~~~~~~L------l~~y~i~~~s~i~l~~~~~   34 (97)
                      ||+++|+|+|+|+.|      |++|||.+|++|||+.+..
T Consensus        47 ip~~~qrL~~~Gk~L~D~~~~L~~~~i~~g~~i~l~~~~~   86 (92)
T 1wxv_A           47 VPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVMLIGKKN   86 (92)
T ss_dssp             CCTTTCEEEETTEEECCSSSBHHHHTCCSSEEEEEESCCS
T ss_pred             cCHHHEEEEECCeecCCCcccHHHCCCCCCCEEEEEecCC
Confidence            799999999999998      9999999999999988654

>2kj6_A Tubulin folding cofactor B; methods development, NESG, solution PSI-2, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=98.54  E-value=3.2e-08  Score=59.53  Aligned_cols=32  Identities=19%  Similarity=0.232  Sum_probs=27.8

Q ss_pred             CCCCceEEEecCc------cc------cccccccCCCcceeeee
Q 042212            1 MPLEQQRLVFADK------SL------LADYNIQKESTLHLVAR   32 (97)
Q Consensus         1 ip~~~q~L~~~~~------~L------l~~y~i~~~s~i~l~~~   32 (97)
                      ||+++|||+|.|+      +|      |++|||++|++|||+=.
T Consensus        52 ip~~~QrLi~~g~~g~~~~~L~~D~~tL~~Y~I~~g~~Ihlvd~   95 (97)
T 2kj6_A           52 TSVNSMALELYDDSGSKVAVLSDDSRPLGFFSPFDGFRLHIIDL   95 (97)
T ss_dssp             CCTTSEEEEEECSSSCBCCCSSGGGSCHHHHCCCSCCEEEEEEC
T ss_pred             cCHHHeEEEEecCCCcccceecCCcCCHHHCCCCCCCEEEEEeC
Confidence            7999999999883      34      99999999999998753

>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=98.53  E-value=2.6e-07  Score=57.19  Aligned_cols=61  Identities=10%  Similarity=0.173  Sum_probs=56.6

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      ..+.|+|+..+|+.+.+.|.+++++..|+...+             |.|+.|.++.|.+++++++|++|++.+.
T Consensus        39 ~~I~LKV~~qdg~ev~fkIk~tt~L~KLm~aY~er~Gl~~~~irFlFDG~rI~~~~TP~dL~MEDgD~IdV~~~  112 (115)
T 3kyd_D           39 EYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQE  112 (115)
T ss_dssp             CEEEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHHTCCTTSEEEEETTEECCTTCCTTTTTCCTTCEEEEEEC
T ss_pred             CeEEEEEEcCCCCEEEEEEccCChHHHHHHHHHHHhCCChhhEEEEECCeECCCCCCHHHcCCCCCCEEEEEee
Confidence            348999999999999999999999999998877             9999999999999999999999999875

>2kjr_A CG11242; UBL, ubiquitin, ubiquitin-like, structural genomics, PSI-2, protein structure initiative; NMR {Drosophila melanogaster}

Probab=98.51  E-value=3.9e-08  Score=58.88  Aligned_cols=30  Identities=20%  Similarity=0.218  Sum_probs=26.6

Q ss_pred             CCCCceEEEec--Cc---cc------cccccccCCCcceee
Q 042212            1 MPLEQQRLVFA--DK---SL------LADYNIQKESTLHLV   30 (97)
Q Consensus         1 ip~~~q~L~~~--~~---~L------l~~y~i~~~s~i~l~   30 (97)
                      ||+++|||+|+  |+   +|      |++|||++|++|||+
T Consensus        53 iP~~~QrL~~~~~g~~~~~L~~D~~tL~~Y~i~~gstihlv   93 (95)
T 2kjr_A           53 GCAGTMKVQVFKGDTCVSTMDNNDAQLGYYANSDGLRLHVV   93 (95)
T ss_dssp             SCTTTEEEEEEETTEEEEECCCTTSBHHHHCCSSSCEEEEE
T ss_pred             cCHHHeEEEEecCCcccceeCCCCCCHhHCCcCCCCEEEEE
Confidence            79999999998  44   44      999999999999986

>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=98.50  E-value=6.4e-08  Score=60.21  Aligned_cols=61  Identities=20%  Similarity=0.325  Sum_probs=30.3

Q ss_pred             CCCCceEEEecC---c---cc------cccccccCCCcceeeeeecCCeeeEEECCCCCEEEEeecCC------CcHHHh
Q 042212            1 MPLEQQRLVFAD---K---SL------LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVESS------DMIDNA   62 (97)
Q Consensus         1 ip~~~q~L~~~~---~---~L------l~~y~i~~~s~i~l~~~~~~~m~i~vk~~~g~~~~l~v~~~------~tV~~l   62 (97)
                      ||+++|||+|.|   +   +|      |++|||++|++|||+...+.. .-+ .. ....-.++++..      +||...
T Consensus        43 ip~~~qrL~~~g~~~~~~~~l~~D~~tL~~y~i~~g~~ihvvd~~p~~-~~~-~d-~s~v~ky~~~~e~Y~~r~~tv~~~  119 (122)
T 1t0y_A           43 TTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHAVDVTGGN-EDF-KD-ESMVEKYEMSDDTYGKRTDSVRAW  119 (122)
T ss_dssp             CCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEEEEEECTTCC-CC-----------------------------
T ss_pred             CCHHHeEEEEecCCCccccccCCCcCCHHHCCCCCCCEEEEEeCCCCC-CCc-cc-cccceeeecCHHHHhcchhHHHHH
Confidence            799999999987   3   34      999999999999999854432 111 11 112223444444      677777


Q ss_pred             hc
Q 042212           63 SR   64 (97)
Q Consensus        63 K~   64 (97)
                      |+
T Consensus       120 k~  121 (122)
T 1t0y_A          120 KK  121 (122)
T ss_dssp             --
T ss_pred             hh
Confidence            65

>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=98.46  E-value=7.5e-08  Score=57.08  Aligned_cols=33  Identities=24%  Similarity=0.421  Sum_probs=30.0

Q ss_pred             CCceEEEecCccc------cccccccCCCcceeeeeecC
Q 042212            3 LEQQRLVFADKSL------LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         3 ~~~q~L~~~~~~L------l~~y~i~~~s~i~l~~~~~~   35 (97)
                      +++|||+|+|+.|      |++|||.+|++|||+++.+.
T Consensus        42 ~~~qrLi~~Gk~L~D~~~tL~~y~i~~g~~i~l~~~~~~   80 (95)
T 1wia_A           42 ESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRSPPG   80 (95)
T ss_dssp             TTTCEEEETTEECCCSSCBTTTTTCCTTEEEEEECCCCC
T ss_pred             cCcEEEEECCEEccCCcCCHHHcCCCCCCEEEEEECCCC
Confidence            4789999999998      99999999999999998654

>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=98.45  E-value=3.9e-08  Score=58.81  Aligned_cols=34  Identities=9%  Similarity=0.236  Sum_probs=31.5

Q ss_pred             CCCCceEEEecCccc----cccccccCCCcceeeeeec
Q 042212            1 MPLEQQRLVFADKSL----LADYNIQKESTLHLVARLR   34 (97)
Q Consensus         1 ip~~~q~L~~~~~~L----l~~y~i~~~s~i~l~~~~~   34 (97)
                      ||+++|+|+|+|++|    |++|||.+|++|+|+....
T Consensus        43 ip~~~QkLi~~Gk~L~D~tL~~~~I~~g~~i~l~~~~~   80 (96)
T 1wgg_A           43 VQPARQKVMVKGGTLKDDDWGNIKMKNGMTVLMMGSAD   80 (96)
T ss_dssp             CCTTTSCCEETTEECCSSCCCSCCCCSSCEEECCCCCC
T ss_pred             cCHHHeEEEECCcCCCCCCHHHCCCCCCCEEEEEecch
Confidence            799999999999999    9999999999999988654

>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=98.40  E-value=8.3e-08  Score=56.60  Aligned_cols=33  Identities=15%  Similarity=0.312  Sum_probs=30.8

Q ss_pred             CCCCceEEE---ecCccc-----cccccccCCCcceeeeee
Q 042212            1 MPLEQQRLV---FADKSL-----LADYNIQKESTLHLVARL   33 (97)
Q Consensus         1 ip~~~q~L~---~~~~~L-----l~~y~i~~~s~i~l~~~~   33 (97)
                      ||+++|+|+   |+|++|     |++|||.+|++|+|+...
T Consensus        43 ip~~~QkLi~~k~~Gk~L~D~~~L~~~~i~~g~~l~l~~~~   83 (90)
T 1v5t_A           43 VLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMGTR   83 (90)
T ss_dssp             CCTTTCEEESCEETTEECCTTSBHHHHTCCTTEEEEEECCC
T ss_pred             cCHHHeEEEeeccCCcCcCCCCCHHHcCCCCCCEEEEEecC
Confidence            799999999   999998     999999999999998764

>2pjh_A Protein NPL4, nuclear protein localization protein 4 homolog; UFD1, NPL4, AAA, protein binding, transport protein; NMR {Mus musculus}

Probab=98.38  E-value=2.4e-07  Score=53.76  Aligned_cols=58  Identities=10%  Similarity=0.139  Sum_probs=47.1

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc---------------CCC-eeC--CCCCcccccccCCCCEEEEE
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS---------------SPA-GNF--EDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~---------------~~g-k~L--~d~~tL~~y~I~~~sti~l~   93 (97)
                      ..|.|.||+.+| ++.+++++++|+.+|+++|+               +.- +.|  .++.+|+++|+++|+++++.
T Consensus         3 ~~m~lRvrs~~G-~~Ri~v~~~~t~~~L~~~I~~~~~i~~~~~~l~~~~~p~~~l~~~~~~~l~~lgl~hGd~l~l~   78 (80)
T 2pjh_A            3 ESIIIRVQSPDG-VKRITATKRETAATFLKKVAKEFGFQNNGFSVYINRNKTGEITASSSKSLHLLKIKHGDLLFLF   78 (80)
T ss_dssp             CCCCCEEECSSE-EEECCCCSSCCHHHHHHHHHHHTCCCTTTCCCCCSCCGGGGSSSCCCCTTTTTCCCTTCCEEC-
T ss_pred             CcEEEEEECCCC-CEEEEcCCcChHHHHHHHHHHHcCCCCCcceEEecCCCCCcccCCCCCCHHHcCCCCCCEEEEe
Confidence            458999999988 66789999999999999999               111 223  47789999999999999875

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B*

Probab=98.37  E-value=1.5e-07  Score=66.90  Aligned_cols=33  Identities=76%  Similarity=1.101  Sum_probs=30.2

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARL   33 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~   33 (97)
                      ||+++|+|+|+|++|     |++|||.++++|||++++
T Consensus       269 Ip~~~QRLi~~Gk~L~D~~TLsdygI~~gstL~LvlRL  306 (307)
T 3ai5_A          269 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  306 (307)
T ss_dssp             CCGGGCEEEETTEECCTTSBTGGGTCCTTCEEEEEC--
T ss_pred             cChHHEEEEeCCeecCCCCCHHHcCCCCCCEEEEEEeC
Confidence            799999999999999     999999999999999985

>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=98.33  E-value=4.8e-08  Score=58.24  Aligned_cols=33  Identities=12%  Similarity=0.313  Sum_probs=30.7

Q ss_pred             CCCCceEEEecCccc----cccccccCCCcceeeeee
Q 042212            1 MPLEQQRLVFADKSL----LADYNIQKESTLHLVARL   33 (97)
Q Consensus         1 ip~~~q~L~~~~~~L----l~~y~i~~~s~i~l~~~~   33 (97)
                      ||+++|+|+|.|++|    |++|||.+|++|||+.+.
T Consensus        52 ip~~~QrL~~~Gk~Ldd~tL~~~~i~~g~~i~lv~~~   88 (95)
T 1v86_A           52 LPPAMQKVMYKGLVPEDKTLREIKVTSGAKIMVVGST   88 (95)
T ss_dssp             SCSTTCCCBSSSBCCSSSBHHHHCCCTTEEEEECCSS
T ss_pred             cCHHHeEEEECCeeCCcCcHHHCCCCCCCEEEEEecc
Confidence            799999999999999    999999999999998753

>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=98.32  E-value=1.6e-07  Score=55.91  Aligned_cols=32  Identities=22%  Similarity=0.428  Sum_probs=27.9

Q ss_pred             CCCCceEEEecC---c---cc------cccccccCCCcceeeee
Q 042212            1 MPLEQQRLVFAD---K---SL------LADYNIQKESTLHLVAR   32 (97)
Q Consensus         1 ip~~~q~L~~~~---~---~L------l~~y~i~~~s~i~l~~~   32 (97)
                      ||+++|||+|+|   +   +|      |++|||++|++|||+-.
T Consensus        44 ip~~~qrL~~~~~~g~~~~~l~~D~~tL~~y~i~~g~~l~v~d~   87 (95)
T 1v6e_A           44 SPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIHVIDH   87 (95)
T ss_dssp             SCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCEEEEBCC
T ss_pred             CCHHHeEEEEeCCCCccccccCCCcCCHhHCCCCCCCEEEEEEC
Confidence            799999999987   3   24      99999999999998764

>3pge_A SUMO-modified proliferating cell nuclear antigen; DNA replication, DNA binding protein; 2.80A {Saccharomyces cerevisiae}

Probab=98.31  E-value=1.3e-06  Score=58.71  Aligned_cols=61  Identities=7%  Similarity=0.093  Sum_probs=55.9

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEee
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      .-++|+|+. +|+.+.+.|.+++++..|+...+             |.|+.|.++.|.+++++++|++|++++.+
T Consensus        28 ~~I~LkV~~-~g~~v~fkIk~~t~l~kL~~ay~er~Gi~~~~~RF~FdG~rI~~~~TP~dL~MEdgD~Idv~~~q  101 (200)
T 3pge_A           28 THINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQ  101 (200)
T ss_dssp             CCEEEEEEC-SSCEEEEEECTTSCTHHHHHHHHHHHSSCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECC
T ss_pred             CeEEEEEec-CCCEEEEEEecCCHHHHHHHHHHHHhCCChhhEEEEECCEEcCCCCCHHHcCCCCCCEEEEEecc
Confidence            348888974 89999999999999999998877             99999999999999999999999999875

>2dzj_A Synaptic glycoprotein SC2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.27  E-value=1.9e-07  Score=55.08  Aligned_cols=29  Identities=28%  Similarity=0.274  Sum_probs=26.6

Q ss_pred             CCCCceEEEec--Cccc-----cccccccCCCccee
Q 042212            1 MPLEQQRLVFA--DKSL-----LADYNIQKESTLHL   29 (97)
Q Consensus         1 ip~~~q~L~~~--~~~L-----l~~y~i~~~s~i~l   29 (97)
                      ||+++|||+|.  |++|     |++|||.+|++||+
T Consensus        50 i~~~~QrL~~~~~Gk~L~D~~tL~~y~i~~~stl~~   85 (88)
T 2dzj_A           50 WYPARQSLRLDPKGKSLKDEDVLQKLPVGTTATLYF   85 (88)
T ss_dssp             SCTTTCCEESSTTSCCCCTTCBTTTSSCCSEEEEEE
T ss_pred             CChHHeEEEecCCCcCcCCCCCHHHcCCCCCCEEEE
Confidence            68999999987  8899     99999999999876

>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=98.26  E-value=5.2e-07  Score=65.54  Aligned_cols=35  Identities=29%  Similarity=0.645  Sum_probs=31.2

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcc-eeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTL-HLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i-~l~~~~~~   35 (97)
                      ||+++|||+|+|+.|     |++|||.+|++| ||+.+.++
T Consensus        46 ip~~~QrLiy~GK~L~D~~tL~dygI~~gstIv~lv~k~~~   86 (368)
T 1oqy_A           46 FPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTKTKA   86 (368)
T ss_dssp             CCSTEEEEESSSSEECSSSBTTTTCCCTTSCEEEEEECCCS
T ss_pred             CChhheEEEECCeecCCcCCHHHcCCCCCCEEEEEEecCCC
Confidence            689999999999999     999999999999 77776643

>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=98.22  E-value=1.7e-06  Score=57.97  Aligned_cols=60  Identities=7%  Similarity=0.104  Sum_probs=54.9

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEee
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      .+.|+|+. +|..+.+.|.+++++..|+...+             |.|+.|.++.|.+++++++|++|++++..
T Consensus        57 ~InLKVk~-dG~eV~FKIKrtTpL~KLmeAYcERqGL~~~sIRFLFDGqRI~~ddTPeDLdMEDGDtIDV~leQ  129 (207)
T 3tix_A           57 HINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLTFLYDGIEIQADQTPEDLDMEDNDIIEAHREQ  129 (207)
T ss_dssp             EEEEEEEC-SSCEEEEEEETTSCTHHHHHHHHHHTTCCGGGSCEEETTEECCSSCCTTTTTCCTTEEEEECCCC
T ss_pred             cEEEEEec-CCCEEEEEEccCChHHHHHHHHHHHhCCCcccEEEEECCeecCCCCCHHHcCCCCCCEEEEEEec
Confidence            48888874 89999999999999999998877             99999999999999999999999998764

>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=98.21  E-value=8.4e-07  Score=52.91  Aligned_cols=36  Identities=19%  Similarity=0.434  Sum_probs=33.3

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|||+|+|++|     .++|++++|++|+++++..++
T Consensus        43 i~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~~~GG   83 (94)
T 2io1_B           43 LSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGG   83 (94)
T ss_dssp             CCGGGEEEEETTEECCTTCCTTTTTCCTTCEEEEEECCEES
T ss_pred             CCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEeccCC
Confidence            689999999999999     999999999999999987654

>2dzm_A FAS-associated factor 1; ubiquitin-like domain, HFAF1, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.17  E-value=2.5e-07  Score=55.94  Aligned_cols=32  Identities=16%  Similarity=0.272  Sum_probs=28.1

Q ss_pred             CCCCceEEEe--cCccc-----cccccccCCCcceeeeee
Q 042212            1 MPLEQQRLVF--ADKSL-----LADYNIQKESTLHLVARL   33 (97)
Q Consensus         1 ip~~~q~L~~--~~~~L-----l~~y~i~~~s~i~l~~~~   33 (97)
                      ||+++|+|+|  +|+ |     |++|+|++|+++||++..
T Consensus        44 Ipp~~QkLi~~~~gk-L~D~~tLs~~~I~~gstL~lvl~~   82 (100)
T 2dzm_A           44 IPVSKMLLKGWKTGD-VEDSTVLKSLHLPKNNSLYVLTPD   82 (100)
T ss_dssp             CCTTTCCEECCSSSC-CCTTSBHHHHCCCSEEEEEECCSS
T ss_pred             CChhHeEEEccCCCC-CCCcCCHHHcCCCCCCEEEEEecC
Confidence            7999999996  554 7     999999999999998863

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9

Probab=98.13  E-value=3.2e-07  Score=61.22  Aligned_cols=36  Identities=17%  Similarity=0.108  Sum_probs=0.0

Q ss_pred             CCCCceEEEecCccccccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSLLADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~Ll~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|++|=.+.-|.++|+|||+++++++
T Consensus        36 IP~~qQRLIf~GK~LeD~~TLs~~STLhLvlRLrGG   71 (189)
T 2xzm_9           36 FEIDMMTLVNNGFIAPNTELVTDDVTYYLSLKLLGG   71 (189)
T ss_dssp             ------------------------------------
T ss_pred             cChhHEEEEecCeECCCCCcccCCCEEEEEEecCCC
Confidence            799999999999999111122299999999998765

>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=97.96  E-value=6.5e-06  Score=48.77  Aligned_cols=36  Identities=19%  Similarity=0.434  Sum_probs=33.0

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++||++|+|++|     .++|++.+|++|+++++..++
T Consensus        41 i~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~q~gg   81 (91)
T 2io0_B           41 LSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGG   81 (91)
T ss_dssp             CCSTTEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCCCC
T ss_pred             CCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEeccCC
Confidence            688999999999999     999999999999999987654

>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=97.95  E-value=5e-06  Score=49.36  Aligned_cols=35  Identities=20%  Similarity=0.456  Sum_probs=31.2

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++||++|.|++|     .++|++.+|.+|+++++..+
T Consensus        53 i~~~~~rf~fdG~~l~~~~Tp~dl~medgD~Idv~~~q~G   92 (93)
T 2d07_B           53 LSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTG   92 (93)
T ss_dssp             CCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECC--
T ss_pred             CCccceEEEECCEEcCCCCCHHHcCCCCCCEEEEEeeccC
Confidence            688999999999999     99999999999999998654

>3v7o_A Minor nucleoprotein VP30; ssgcid, seattle structural genomics center for infectious disease, SMT, transcription; 2.25A {Reston ebolavirus}

Probab=97.93  E-value=1.3e-06  Score=59.29  Aligned_cols=62  Identities=6%  Similarity=0.104  Sum_probs=0.0

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEee
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      ...|.|+| ..+|+.+.+.|++++++..|++..+             |.|+.+.++.|.+++++++|++|++++..
T Consensus        19 ~e~InLKV-~qdGseV~FKIKrtTpL~KLM~AYcERqGLs~~siRFLFDGqRI~dddTPadL~MEDGDtIDV~leQ   93 (227)
T 3v7o_A           19 ETHINLKV-SDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQ   93 (227)
T ss_dssp             ----------------------------------------------------------------------------
T ss_pred             CCeEEEEE-eCCCCEEEEEEccCChHHHHHHHHHHHhCCCccceEEEECCEecCCCCCHHHcCCCCCCEEEEEecc
Confidence            34588999 7799999999999999999998887             99999999999999999999999998764

>1wf9_A NPL4 family protein; beta-grAsp fold like domain, hypothetical protein, structural genomics, NPPSFA; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=97.86  E-value=2.6e-06  Score=51.70  Aligned_cols=33  Identities=18%  Similarity=0.275  Sum_probs=29.5

Q ss_pred             CCCCceEEEecCc-----------c----c-----cccccccCCCcceeeeee
Q 042212            1 MPLEQQRLVFADK-----------S----L-----LADYNIQKESTLHLVARL   33 (97)
Q Consensus         1 ip~~~q~L~~~~~-----------~----L-----l~~y~i~~~s~i~l~~~~   33 (97)
                      ||+++|+|+|.++           +    +     |++|||.+|++|||+...
T Consensus        43 ip~~~QrL~~~~~~~~~k~~~~~~~l~~~l~d~~tL~~~gi~~G~~L~l~~~~   95 (107)
T 1wf9_A           43 IPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLAHGSMVYLAYEG   95 (107)
T ss_dssp             CCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTCCCTTCEEECCCSS
T ss_pred             cCcccCEEEECCccccccCccccccccccCCCCCCHHHCCCCCCCEEEEEeCC
Confidence            7999999999888           4    4     999999999999998764

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster}

Probab=97.84  E-value=4.4e-06  Score=59.62  Aligned_cols=35  Identities=17%  Similarity=0.365  Sum_probs=29.6

Q ss_pred             CCCCceEEE---ecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLV---FADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~---~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++|+|+   |+|++|     |++|||++|++|+|+-+...
T Consensus        40 Vpp~~QkLi~~k~~Gk~l~D~~~L~~~~ik~g~~l~L~gs~~~   82 (320)
T 3shq_A           40 VRPERQKLLNLKYKGKTAADNVKISALELKPNFKLMMVGSTEA   82 (320)
T ss_dssp             CCGGGCEETTCBSSSSBCCTTSBTTSSCCC--CEEEEECCCC-
T ss_pred             cCHHHeEEeecccCCcccCccccHHHcCCCCCCEEEEEccchh
Confidence            799999999   999999     99999999999999876544

>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=97.82  E-value=1e-05  Score=45.67  Aligned_cols=31  Identities=19%  Similarity=0.447  Sum_probs=28.7

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVA   31 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~   31 (97)
                      ||+++||++|+|++|     .++|++.+|++|++++
T Consensus        37 i~~~~~rf~fdG~~l~~~~Tp~~l~medgD~Idv~~   72 (72)
T 1wm3_A           37 LSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQ   72 (72)
T ss_dssp             CCTTTCEEEETTEECCTTCCTTTTTCCTTEEEEEEC
T ss_pred             CCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEEC
Confidence            688999999999999     9999999999999863

>1wz0_A Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-like molecule, structural genomics, sentrin2, NPPFSA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=97.77  E-value=8.5e-06  Score=49.41  Aligned_cols=36  Identities=17%  Similarity=0.377  Sum_probs=32.7

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|||+|.|++|     .++|++.+|.+|+++++..++
T Consensus        60 i~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~q~GG  100 (104)
T 1wz0_A           60 LSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTSG  100 (104)
T ss_dssp             CCTTTSCEESSSSBCCTTSCTTTTTCCTTEEEEECCCCCCC
T ss_pred             CCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEeccCC
Confidence            688999999999999     999999999999999986553

>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=97.74  E-value=1.8e-05  Score=48.15  Aligned_cols=35  Identities=9%  Similarity=0.274  Sum_probs=31.1

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++||++|+|++|     .++|++.+|++|+++++..+
T Consensus        66 i~~~~~rF~FdG~rl~~~~Tp~dl~medgD~Idv~~~q~G  105 (106)
T 2eke_C           66 KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIG  105 (106)
T ss_dssp             CCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECC--
T ss_pred             CCcccEEEEECCeEcCCCCCHHHcCCCCCCEEEEEeeccc
Confidence            688999999999999     99999999999999987654

>4e71_A Plexin-B2, MM1; transmembrane, signaling, RBD, structural genomics consortium, SGC, signaling protein; 2.26A {Homo sapiens}

Probab=97.73  E-value=5.3e-05  Score=46.42  Aligned_cols=50  Identities=24%  Similarity=0.204  Sum_probs=41.1

Q ss_pred             CCEEEEeecCCCcHHHhhcccc-------------------------CCCeeCCCC-------------CcccccccCCC
Q 042212           46 GKTITLEVESSDMIDNASRGSS-------------------------SPAGNFEDG-------------WTQADYNIQKE   87 (97)
Q Consensus        46 g~~~~l~v~~~~tV~~lK~~I~-------------------------~~gk~L~d~-------------~tL~~y~I~~~   87 (97)
                      +..+++.|-..|||.++|+||-                         -.|+.|.|.             .||++|+|.+|
T Consensus        23 ~~~i~vkVLdCDTItQvKeKiLd~vyk~~pyS~rP~~~~~dLEwr~g~~~~iL~D~D~ts~~~~~wkrLNTL~HY~V~dg  102 (111)
T 4e71_A           23 VDAIPVKVLNCDTISQVKEKIIDQVYRGQPCSCWPRPDSVVLEWRPGSTAQILSDLDLTSQREGRWKRVNTLMHYNVRDG  102 (111)
T ss_dssp             CCCEEEEEETTCBHHHHHHHHHHHHTC---------CCSEEEEEC--CCCEECCSSCTTSCC---CCCCCBHHHHTCCTT
T ss_pred             CCceeeeeeccCcHHHHHHHHHHHHHcCCccccCCCCCceeeEEecCCCCccccccCccceecCcceEecchhhcCCCCC
Confidence            4668888989999999999998                         334566552             48999999999


Q ss_pred             CEEEEEEe
Q 042212           88 STLHFVLR   95 (97)
Q Consensus        88 sti~l~~r   95 (97)
                      +++.++.+
T Consensus       103 atl~l~~~  110 (111)
T 4e71_A          103 ATLILSKV  110 (111)
T ss_dssp             CEEEEEEC
T ss_pred             CEEEEEeC
Confidence            99999865

>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=97.72  E-value=0.00011  Score=42.47  Aligned_cols=58  Identities=9%  Similarity=0.184  Sum_probs=47.9

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc--------------CCCeeCCCCCcccccccCCCCEEEEEE
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS--------------SPAGNFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~--------------~~gk~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      +.+..+......+.+.+.++.+|.++-+.-.              |.|..|+++.++++|++++|+.|.+++
T Consensus        10 ~~~~~~~~~~~dl~f~I~~~t~v~kLi~ayc~~~~I~~~~~IrllFDGdRLdp~~tp~DlemeD~D~IDvmL   81 (82)
T 3goe_A           10 ITLLLRSSKSEDLRLSIPVDFTVKDLIKRYCTEVKISFHERIRLEFEGEWLDPNDQVQSTELEDEDQVSVVL   81 (82)
T ss_dssp             EEEEEEESSSCCEEEEEETTSBHHHHHHHHHHHHTCCCCTTCEEEETTEECCTTSBGGGSSCCTTCEEEEEC
T ss_pred             HHHhhhccCCCCeEEEecCCCCHHHHHHHHHHHcCCCcCceEEEEEcCcccCccCChhhhCCcCCceeeeee
Confidence            4455666666778899999999998754333              999999999999999999999999875

>2k8h_A Small ubiquitin protein; SUMO, post-translational modifier, signaling protein; NMR {Trypanosoma brucei}

Probab=97.67  E-value=1.1e-05  Score=49.38  Aligned_cols=37  Identities=8%  Similarity=0.346  Sum_probs=33.5

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCCe
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRM   37 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~m   37 (97)
                      ||+++||++|.|++|     .++|++.+|.+|++++...+++
T Consensus        62 i~~~~~rfiFdG~~L~~~~Tp~dl~mEDgD~Idv~~~q~Gg~  103 (110)
T 2k8h_A           62 ISRNSVRFLFDGTPIDETKTPEELGMEDDDVIDAMVEQTGGL  103 (110)
T ss_dssp             CCSSSCEEESSSCBCCSSSHHHHHHCSSEEEEEEECCCCCC-
T ss_pred             CCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEcccCcc
Confidence            688999999999999     9999999999999999877653

>2kc2_A Talin-1, F1; FERM, adhesion, cell membrane, cell projection, cytoplasm, cytoskeleton, membrane, phosphoprotein, structural protein; NMR {Mus musculus}

Probab=97.58  E-value=0.00011  Score=46.12  Aligned_cols=58  Identities=14%  Similarity=0.205  Sum_probs=49.2

Q ss_pred             eeEEECCCCCEEEEeecCCCcHHHhhcccc-------C------------------------------------------
Q 042212           38 QIFVKTSTGKTITLEVESSDMIDNASRGSS-------S------------------------------------------   68 (97)
Q Consensus        38 ~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------~------------------------------------------   68 (97)
                      .+.|+.++|+..++.|+.+.+|.+++..|+       +                                          
T Consensus        13 ~LkV~llDg~~ktl~VD~S~~V~~lv~~Ic~kigI~n~~ey~L~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~k~kL~   92 (128)
T 2kc2_A           13 PLKIRMLDGTVKTIMVDDSKTVTDMLMTICARIGITNHDEYSLVRELMEEKKDEGTGTLRKDKTLLRDEKKMEKLKQKLH   92 (128)
T ss_dssp             EEEEECTTSCEEEEEEEECSSHHHHHHHHHHHHTCCCCSSEEEEEECCCCCCCCCSSCCSSSSSCSCCSCCSCSSCCSCC
T ss_pred             cEEEEcCCCCEEEEEeCCCcCHHHHHHHHHHHhCCCCcccccccccccccccccCchhhccccccccchhHHHHHHHHhc
Confidence            588999999999999999999999999988       2                                          


Q ss_pred             ---CCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           69 ---PAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        69 ---~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                         ++..|++++||.++||.+++++-|-.+
T Consensus        93 ~dd~~~WLD~srtL~EQGI~e~~tllLRrK  122 (128)
T 2kc2_A           93 TDDELNWLDHGRTLREQGVEEHETLLLRRK  122 (128)
T ss_dssp             CSSSEEEECSSSCHHHHTCCTTSEEEEEES
T ss_pred             ccCCCCcccCCCcHHHcCCCCCCEEEEEEE
Confidence               014567799999999999999776543

>3a4r_A Nfatc2-interacting protein; ubiquitin fold, coiled coil, cytoplasm, methylation, nucleus, transcription; 1.00A {Mus musculus} PDB: 3a4s_C 3rd2_A

Probab=97.57  E-value=3.2e-05  Score=44.45  Aligned_cols=30  Identities=13%  Similarity=0.253  Sum_probs=28.0

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLV   30 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~   30 (97)
                      ||+++||++|.|++|     .++|++.+|.+|++.
T Consensus        44 i~~~~~rf~fdG~~l~~~~Tp~~l~medgD~Idv~   78 (79)
T 3a4r_A           44 LSGHKLSFFFDGTKLSGKELPADLGLESGDLIEVW   78 (79)
T ss_dssp             CTTCCCEEEETTEECCSCCCHHHHTCCTTCEEEEE
T ss_pred             CCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEe
Confidence            688999999999999     999999999999975

>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative, hydrolase; NMR {Mus musculus}

Probab=97.49  E-value=3.4e-05  Score=44.77  Aligned_cols=33  Identities=24%  Similarity=0.294  Sum_probs=27.7

Q ss_pred             CCCCceEEEecC--ccc--------cccccccCCCcceeeeee
Q 042212            1 MPLEQQRLVFAD--KSL--------LADYNIQKESTLHLVARL   33 (97)
Q Consensus         1 ip~~~q~L~~~~--~~L--------l~~y~i~~~s~i~l~~~~   33 (97)
                      ||+++|+|+|+.  ++|        |++|||.+|++||+....
T Consensus        36 i~~~~qrL~~~~p~k~l~l~~~~~tL~~~gl~~g~~l~v~~~~   78 (86)
T 2kzr_A           36 IAPGSQRILVGYPPECLDLSDRDITLGDLPIQSGDMLIVEEDQ   78 (86)
T ss_dssp             CCTTTCCCEESSCCCCCCCCCSSCBTTTSSCCTTCEEECCCCS
T ss_pred             CCccceEEEeCCCCcccccCCCCCCHHHcCCCCCCEEEEEeCC
Confidence            689999999874  554        999999999999988653

>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=97.47  E-value=0.00036  Score=40.28  Aligned_cols=60  Identities=10%  Similarity=0.109  Sum_probs=50.9

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc--------------CCCeeC---CCCCcccccccCCCCEEEEEE
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS--------------SPAGNF---EDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~--------------~~gk~L---~d~~tL~~y~I~~~sti~l~~   94 (97)
                      +...|.||.++|+.+.-....++||.+|.+-|.              |-.+.+   +.+.||.+.|+.+.+++.+--
T Consensus         6 ~~~~i~iRlpdG~r~~~~F~~~~tl~~v~~fv~~~~~~~~~f~L~t~fPrk~l~~~d~~~TL~e~gL~p~a~L~ve~   82 (84)
T 3qx1_A            6 PVSKLRIRTPSGEFLERRFLASNKLQIVFDFVASKGFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLEA   82 (84)
T ss_dssp             CEEEEEEECTTSCEEEEEEETTSBHHHHHHHHHHTTCCTTTEEEECSSSCCBGGGSCTTSBTTTTTCCSEEEEEEEE
T ss_pred             CeEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHHcCCCCCCeEEEeCCCCCCCcCCCCCCCHHHCCCCCCCEEEEEe
Confidence            346789999999998889999999999998776              667878   347899999999999988754

>2jxx_A Nfatc2-interacting protein; nuclear factor of activated T-cells, cytoplasmic 2- interacting protein, ubiquitin like homologue; NMR {Homo sapiens}

Probab=97.46  E-value=0.00019  Score=42.93  Aligned_cols=59  Identities=8%  Similarity=0.101  Sum_probs=51.5

Q ss_pred             CCeeeEEECCCCC-EEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEE
Q 042212           35 GRMQIFVKTSTGK-TITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        35 ~~m~i~vk~~~g~-~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~   93 (97)
                      ..+.|.|+..+|. .+.+.|.++.+...|...-+             |.|..|.++.|.++.++++|++|.+.
T Consensus        24 ~~I~LkV~~~dg~~~v~fkIk~~t~l~kLm~aY~~~~g~~~~~vrF~FDG~rI~~~~TP~dLdMEDgD~IDv~   96 (97)
T 2jxx_A           24 QQLQLRVQGKEKHQTLEVSLSRDSPLKTLMSHYEEAMGLSGRKLSFFFDGTKLSGRELPADLGMESGDLIEVW   96 (97)
T ss_dssp             SEEEEEEEESSSSCEEEEEEETTSCHHHHHHHHHHHTTCSSSCCEEEETTEECCSCSCHHHHTCCTTEEEEEE
T ss_pred             CeEEEEEEcCCCCEEEEEEECCCChHHHHHHHHHHHHCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEe
Confidence            4488888888884 88999999999888876655             99999999999999999999999874

>1wjn_A Tubulin-folding protein TBCE; ubiquitin-like domain, progressive motor neuropathy, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=97.46  E-value=6.5e-05  Score=44.48  Aligned_cols=34  Identities=18%  Similarity=0.253  Sum_probs=28.0

Q ss_pred             CCCCceEEEecCc------c-c------cccccccCCCcceeeeeec
Q 042212            1 MPLEQQRLVFADK------S-L------LADYNIQKESTLHLVARLR   34 (97)
Q Consensus         1 ip~~~q~L~~~~~------~-L------l~~y~i~~~s~i~l~~~~~   34 (97)
                      +|+.+|+|+|.+.      . |      |++|||.+|++||+....+
T Consensus        48 ip~~~q~L~~~~~~~~~~~~~L~~d~~~L~~y~i~~G~~I~V~d~~p   94 (97)
T 1wjn_A           48 VPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCLLVRWSGP   94 (97)
T ss_dssp             CCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTCCTTCEEEEECCSS
T ss_pred             CChhHeEEEEEcCCCCceeeccCCCcccHhhcCCCCCCEEEEEecCC
Confidence            6999999998741      1 4      9999999999999987543

>3h6n_A Plexin-D1; structural genomics consortium, SGC, membrane, transmembrane, receptor, alternative splicing, cell membrane, glycoprotein, polymorphism; 2.00A {Homo sapiens}

Probab=97.44  E-value=0.00052  Score=42.87  Aligned_cols=51  Identities=18%  Similarity=0.201  Sum_probs=40.7

Q ss_pred             CCCEEEEeecCCCcHHHhhcccc-------------------------CCCe-eCCCC-------------CcccccccC
Q 042212           45 TGKTITLEVESSDMIDNASRGSS-------------------------SPAG-NFEDG-------------WTQADYNIQ   85 (97)
Q Consensus        45 ~g~~~~l~v~~~~tV~~lK~~I~-------------------------~~gk-~L~d~-------------~tL~~y~I~   85 (97)
                      ++..+++.|-..|||.++|+||-                         -.|+ .|.|.             .||++|+|.
T Consensus        15 ~~~~i~VkVLdCDTItQvKeKiLd~vyk~~p~S~rP~~~~~dLEwr~g~~~~~iL~D~D~ts~~~~~~krLNTL~HY~V~   94 (127)
T 3h6n_A           15 GMDSLSVRAMDTDTLTQVKEKILEAFCKNVPYSQWPRAEDVDLEWFASSTQSYILRDLDDTSVVEDGRKKLNTLAHYKIP   94 (127)
T ss_dssp             CCCCEEEEEETTSBHHHHHHHHHHHHSTTSCGGGSCCGGGEEEEEECSSSCEEECCSSSTTSCEETTEECCCBTTTTTCC
T ss_pred             CCCceeeeeeccCchhhhhHHHHHHHhccCCcccCCCCcccceEEecCCCCceEeecCCCcceecCceeEeccccccCCC
Confidence            45678888989999999999998                         2233 35542             589999999


Q ss_pred             CCCEEEEEEe
Q 042212           86 KESTLHFVLR   95 (97)
Q Consensus        86 ~~sti~l~~r   95 (97)
                      +|+++.++.+
T Consensus        95 dgatv~l~~~  104 (127)
T 3h6n_A           95 EGASLAMSLI  104 (127)
T ss_dssp             TTCEEEEEEC
T ss_pred             CCCEEEEEEc
Confidence            9999999865

>2al3_A TUG long isoform; TUG UBL1 insulin, endocytosis/exocytosis complex; NMR {Mus musculus} SCOP: d.15.1.2

Probab=97.43  E-value=0.00022  Score=42.14  Aligned_cols=62  Identities=15%  Similarity=0.129  Sum_probs=52.5

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      +++|.+.|-..+|+..++.|.|+.++.++-+.-.             |+++.|+-..++.-.|+.+|+.+.++-.
T Consensus         7 ~~~m~v~Vl~~n~rr~~VKvtp~t~L~~VL~eaC~K~gl~~~~~~Lkh~~k~lDLSlpfRlsgLpnnAkLELv~~   81 (90)
T 2al3_A            7 GGGSAVSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQDFNPSEYDLKFQRTVLDLSLQWRFANLPNNAKLEMVPV   81 (90)
T ss_dssp             ---CCEEEECTTSCEEEECCCTTSBHHHHHHHHHHHTTCCGGGCEEEETTEEESSSCBHHHHCCCSSCEEEEECS
T ss_pred             CCccEEEEEcCCCcEEEEEECCCCCHHHHHHHHHHHhCCChhhCeEEeCCEeccccceeEecCCCCCCEEEEEEc
Confidence            4568999999999999999999999999744333             8999999999999999999999999754

>2r2o_A Plexin-B1; effector domain, structural genomics, structural GEN consortium, SGC, glycoprotein, membrane, phosphorylation, R secreted, transmembrane; 2.00A {Homo sapiens} PDB: 2rex_A* 2jph_A

Probab=97.37  E-value=0.00031  Score=44.47  Aligned_cols=50  Identities=20%  Similarity=0.237  Sum_probs=40.3

Q ss_pred             CEEEEeecCCCcHHHhhcccc-------------------------CCCe-eCCCC-------------CcccccccCCC
Q 042212           47 KTITLEVESSDMIDNASRGSS-------------------------SPAG-NFEDG-------------WTQADYNIQKE   87 (97)
Q Consensus        47 ~~~~l~v~~~~tV~~lK~~I~-------------------------~~gk-~L~d~-------------~tL~~y~I~~~   87 (97)
                      ..+++.|-..|||.++|+||-                         -+|+ .|.|.             .||+.|+|.+|
T Consensus        41 ~~i~VkVLdCDTItQvKeKiLDavYk~~PySqRP~~~d~dLEwr~g~~g~liL~D~D~tS~~~~~wkrLNTL~HY~V~Dg  120 (138)
T 2r2o_A           41 QGVPVKVLDCDTISQAKEKMLDQLYKGVPLTQRPDPRTLDVEWRSGVAGHLILSDEDVTSEVQGLWRRLNTLQHYKVPDG  120 (138)
T ss_dssp             CCEEEEEETTCBHHHHHHHHHHHHTTTSCGGGCCCGGGEEEEEECSSSCEEEECSSSTTCCEETTEEECCBHHHHTCCTT
T ss_pred             CceeEEEeccccHHHHHHHHHHHHHcCCccccCCCccceeEEEecCCcCceEeeccCCcccccCCceeecchhccCCCCC
Confidence            578899999999999999998                         2243 36553             38999999999


Q ss_pred             CEEEEEEee
Q 042212           88 STLHFVLRL   96 (97)
Q Consensus        88 sti~l~~rl   96 (97)
                      +++.++.+.
T Consensus       121 a~l~l~~~~  129 (138)
T 2r2o_A          121 ATVALVPCL  129 (138)
T ss_dssp             CEEEEEEC-
T ss_pred             CEEEEEECC
Confidence            999998763

>3ix6_A TS, tsase, thymidylate synthase; niaid, ssgcid, seattle structural center for infectious DISE brucellosis, orchitis, epididymitis, mastitis; 2.20A {Brucella melitensis}

Probab=97.35  E-value=2.8e-05  Score=56.33  Aligned_cols=62  Identities=6%  Similarity=0.094  Sum_probs=0.0

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEee
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      ...+.|+|+. +|+.+.+.|.++++.+.|+...+             |.|+.+.++.|.+++++++|++|++....
T Consensus        19 ~~~I~LKV~~-~g~~v~FkIk~~t~l~kLm~aY~~r~G~~~~~~rFlFdG~rI~~~~TP~~L~MEDgD~Idv~~~Q   93 (360)
T 3ix6_A           19 ETHINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQ   93 (360)
T ss_dssp             ----------------------------------------------------------------------------
T ss_pred             CCeEEEEEec-CCcEEEEEEecCChHHHHHHHHHHHhCCCcceEEEEECCeECCCCCChHHcCCCccchhhhhhcc
Confidence            3458888887 68888999999999999999888             99999999999999999999999998764

>2bps_A YUKD protein; ubiquitin-like protein, ubiquitin; 2.7A {Bacillus subtilis}

Probab=97.33  E-value=0.00044  Score=40.07  Aligned_cols=49  Identities=12%  Similarity=0.146  Sum_probs=42.8

Q ss_pred             CCCCEEEEeecCCCcHHHhhcccc------------------CCCeeCCCCCcccccccCCCCEEEE
Q 042212           44 STGKTITLEVESSDMIDNASRGSS------------------SPAGNFEDGWTQADYNIQKESTLHF   92 (97)
Q Consensus        44 ~~g~~~~l~v~~~~tV~~lK~~I~------------------~~gk~L~d~~tL~~y~I~~~sti~l   92 (97)
                      -.|+++-+.++...||+.|++.+.                  -.+..|.++.+|++|+|++|+.+.+
T Consensus        14 y~~~~~DLRIP~~~tvK~Li~~l~ea~~l~~~~~~~~~irv~NK~~~L~~~~~L~d~~ItnGD~Lei   80 (81)
T 2bps_A           14 YNGSVFDLRLSDYHPVKKVIDIAWQAQSVSMPPREGHWIRVVNKDKVFSGECKLSDCGITNGDRLEI   80 (81)
T ss_dssp             TTCCEEEEEEETTSBTTHHHHHHHHHSCCCSCCCTTCEEEEGGGTEEEETTSBTGGGTCCTTCEEEE
T ss_pred             cCCceEEEECCCchhHHHHHHHHHHHhCCCcCCCCCCEEEEecCCEEEcCCCEEeeCCcCCCCEEEE
Confidence            478999999999999999988766                  4467789999999999999999875

>4e74_A Plexin-A4; RBD, structural genomics, structural genomics consor SGC, signaling protein; 1.58A {Homo sapiens} PDB: 3q3j_A*

Probab=97.26  E-value=0.00043  Score=42.75  Aligned_cols=50  Identities=20%  Similarity=0.260  Sum_probs=39.2

Q ss_pred             CCEEEEeecCCCcHHHhhcccc-------------------------CCCe-eCCCC-------------CcccccccCC
Q 042212           46 GKTITLEVESSDMIDNASRGSS-------------------------SPAG-NFEDG-------------WTQADYNIQK   86 (97)
Q Consensus        46 g~~~~l~v~~~~tV~~lK~~I~-------------------------~~gk-~L~d~-------------~tL~~y~I~~   86 (97)
                      ...+++.|-..|||.++|+||-                         -+|+ .|.|.             .||++|+|.+
T Consensus        26 ~~~i~VkVLdCDTItQvKeKiLd~vyk~~p~S~rP~~~~~dLEwr~g~~~~~iL~D~D~ts~~~~~wkrLNTL~HY~V~d  105 (117)
T 4e74_A           26 SPEVPVKILNCDTITQVKEKILDAIFKNVPCSHRPKAADMDLEWRQGSGARMILQDEDITTKIENDWKRLNTLAHYQVPD  105 (117)
T ss_dssp             CCCEEEEEETTSBHHHHHHHHHHHHTTTSCGGGSCCGGGEEEEEECTTSCEEEECSSSTTCCC---CCCCCBHHHHTCCT
T ss_pred             CCceEeeeecCCchHHHHHHHHHHHhcCCCcccCCCCCceeEEEecCCCCceEeecCCCccEecCcceEeccccccCCCC
Confidence            4568888889999999999998                         1223 24441             4899999999


Q ss_pred             CCEEEEEEe
Q 042212           87 ESTLHFVLR   95 (97)
Q Consensus        87 ~sti~l~~r   95 (97)
                      |+++.++.|
T Consensus       106 gatl~l~~~  114 (117)
T 4e74_A          106 GSVVALVSK  114 (117)
T ss_dssp             TCEEEEEEC
T ss_pred             CCEEEEEeC
Confidence            999999876

>2dzk_A UBX domain-containing protein 2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} PDB: 2kxj_A

Probab=97.06  E-value=0.0021  Score=38.97  Aligned_cols=60  Identities=13%  Similarity=0.179  Sum_probs=51.6

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc---------------CCCeeCC---CCCcccccccCCCCEEEEEE
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS---------------SPAGNFE---DGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~---------------~~gk~L~---d~~tL~~y~I~~~sti~l~~   94 (97)
                      +...|.||.++|+.+.-....++||.+|.+-|.               |-.+.+.   .+.||.+.|+.+.+++.+..
T Consensus        12 ~~t~IqIRlpdG~rl~~rF~~~~tl~~v~~fV~~~~~~~~~~f~L~t~fPrk~l~~~d~~~TL~elgL~psa~L~v~~   89 (109)
T 2dzk_A           12 TIARIQFRLPDGSSFTNQFPSDAPLEEARQFAAQTVGNTYGNFSLATMFPRREFTREDYKRRLLDLELAPSASVVLLP   89 (109)
T ss_dssp             CCEEEEEECSSSCEEEEEECTTSBHHHHHHHHHHHHTTSSCSCEEECSSSCCBCCTTTTTSBTGGGTCSSEEEEEEEC
T ss_pred             CcEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHhccCCCCCceEEEcCCCCcCCcccccCCCHHHCCCCCceEEEEEE
Confidence            357899999999999999999999999998886               6677785   36899999999998888754

>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=97.02  E-value=0.0013  Score=44.11  Aligned_cols=64  Identities=6%  Similarity=0.102  Sum_probs=55.8

Q ss_pred             eeecCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           31 ARLRGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        31 ~~~~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      +.....+.|+|+. +|+.+.+.+..+++...|+...+             |.|+.+.++.|..+.+.+++++|++...
T Consensus        16 ~~~~~~i~ikv~~-~~~~v~~~i~~~~~l~kl~~~y~~~~g~~~~~~~f~fdG~~i~~~~Tpk~L~~ed~d~I~~~~e   92 (209)
T 3uf8_A           16 VKPETHINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHRE   92 (209)
T ss_dssp             --CCSEEEEEEEC-SSCEEEEEEETTSCTHHHHHHHHHHHTCCGGGCEEEETTEECCTTCCTTTTTCCTTEEEEEECS
T ss_pred             eCCCCcEEEEEEc-CCCEEEEEEeeCCHHHHHHHHHHHhhCCChheEEEEECCEeccCCCChHHhhhcccccchhhcc
Confidence            3344568888987 78888999999999999999888             9999999999999999999999998765

>3pge_A SUMO-modified proliferating cell nuclear antigen; DNA replication, DNA binding protein; 2.80A {Saccharomyces cerevisiae}

Probab=96.94  E-value=0.0019  Score=43.31  Aligned_cols=55  Identities=7%  Similarity=0.238  Sum_probs=42.0

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC----CeeeEEECCCCCEEEEeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG----RMQIFVKTSTGKTITLEVESS   56 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~----~m~i~vk~~~g~~~~l~v~~~   56 (97)
                      +|.+++|++|.|+.+     ..++++.+|.+|++++...+    ++.+..+.-.| +..+.++++
T Consensus        64 i~~~~~RF~FdG~rI~~~~TP~dL~MEdgD~Idv~~~q~gg~kd~v~Fs~~GD~G-~~~i~l~~~  127 (200)
T 3pge_A           64 KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGGGETIKFVADGDIG-SGSVIIKPF  127 (200)
T ss_dssp             SCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCSCCC-CCEEEEEECSSC-EEEEEECCB
T ss_pred             CChhhEEEEECCEEcCCCCCHHHcCCCCCCEEEEEeccCcCcCceEEEEeeccCC-eEEEEEecC
Confidence            588999999999999     99999999999999998653    36666655444 334445443

>1wj4_A KIAA0794 protein; UBX domain, beta-grAsp fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: d.15.1.2

Probab=96.73  E-value=0.0037  Score=38.71  Aligned_cols=60  Identities=12%  Similarity=0.159  Sum_probs=51.4

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc--------------CCCeeC--CC-CCcccccccCCCCEEEEE
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS--------------SPAGNF--ED-GWTQADYNIQKESTLHFV   93 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~--------------~~gk~L--~d-~~tL~~y~I~~~sti~l~   93 (97)
                      .+...|.||.++|+.+.-....++||.+|..-|.              |-.+.|  +| +.||.+.|+.+.+++.+.
T Consensus        41 ~~~t~IqIRlPdG~rl~~rF~~~~tl~~V~~fV~~~~~~~~~F~L~t~fPrk~l~~~d~~~TL~e~gL~psa~Liv~  117 (124)
T 1wj4_A           41 GPKAQLMLRYPDGKREQITLPEQAKLLALVKHVQSKGYPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQ  117 (124)
T ss_dssp             SCEEEEEEECTTSCEEEEEEETTSCHHHHHHHHHHHHCCTTTEEEECSSSCCEETSSCSSSCTTTTTCCSSBCCEEE
T ss_pred             CCcEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHhcCCCCCCeEEecCCCCcCCccCCCCCCHHHCCCCCceEEEEE
Confidence            3458999999999999999999999999998876              677888  33 789999999998887765

>4da1_A Protein phosphatase 1K, mitochondrial; metal-ION-assisted catalysis, dehydrogenase phosphatase, hydrolase; 2.38A {Homo sapiens} PDB: 3qht_A 1l2n_A

Probab=96.69  E-value=0.00026  Score=51.21  Aligned_cols=60  Identities=5%  Similarity=0.090  Sum_probs=0.0

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEee
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      .+.|+|+. +|..+.+.|.++++.+.|+...+             |.|+.+.++.|.++.++++|++|++.+..
T Consensus        30 ~i~lkv~~-~~~~~~~~i~~~~~~~~l~~~y~~~~g~~~~~~~f~f~G~~i~~~~Tp~~l~med~d~i~~~~~q  102 (389)
T 4da1_A           30 HINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQAPEDLDMEDNDIIEAHREQ  102 (389)
T ss_dssp             --------------------------------------------------------------------------
T ss_pred             cEEEEEec-CCcEEEEEECCCChHHHHHHHHHHHhCCCcceEEEEECCEEcCCCCCHHHcCCCCCCEeeeeecc
Confidence            37777877 77888899999999999998887             99999999999999999999999987653

>2cr5_A Reproduction 8; UBX domain, D0H8S2298E protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.15.1.2

Probab=96.63  E-value=0.0039  Score=37.64  Aligned_cols=60  Identities=13%  Similarity=0.088  Sum_probs=50.8

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc--------------CCCeeCC--CCCcccccccCCCCEEEEEE
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS--------------SPAGNFE--DGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~--------------~~gk~L~--d~~tL~~y~I~~~sti~l~~   94 (97)
                      +..+|.||.++|+.+.-....++||.+|..-|.              |-.+.|.  .+.||.+.|+.+.+++.+.-
T Consensus        22 ~~~~IqiRlpdG~r~~rrF~~~~tl~~v~~fv~~~~~~~~~f~L~t~fPrk~l~~d~~~TL~e~gL~p~a~L~Ve~   97 (109)
T 2cr5_A           22 EVVTVALRCPNGRVLRRRFFKSWNSQVLLDWMMKVGYHKSLYRLSTSFPRRALEVEGGSSLEDIGITVDTVLNVEE   97 (109)
T ss_dssp             SEEEEEEECTTSCEEEEEEESSSBTHHHHHHHHHHTCCTTTEEEECSSSCCBCCCCSSCBHHHHTCSSCEEEEEEE
T ss_pred             CcEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHhcCCCCCCeEEEeCCCCcCCCCCCCCCHHHcCCCCCeEEEEEe
Confidence            348899999999998889999999999988776              6677785  47899999999999887753

>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=96.50  E-value=0.014  Score=41.68  Aligned_cols=77  Identities=14%  Similarity=0.229  Sum_probs=61.0

Q ss_pred             cccccccCCCcceeeeeecCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc--------------CC---------Cee
Q 042212           16 LADYNIQKESTLHLVARLRGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS--------------SP---------AGN   72 (97)
Q Consensus        16 l~~y~i~~~s~i~l~~~~~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~--------------~~---------gk~   72 (97)
                      |..|++++|..++..-+   .+.+.|..++|....+.++++.|+.++-+.|+              +.         -..
T Consensus        68 l~~y~~~~~~~l~~~~~---~~~~~V~l~dg~~~~~~vd~~tt~~el~~~v~~~l~L~e~~~FgL~~~~~~~~~~~~~~w  144 (371)
T 3ivf_A           68 LDYYMLRNGDTMEYRKK---QRPLKIRMLDGTVKTIMVDDSKTVTDMLMTICARIGITNHDEYSLVRELMEEKKDDELNW  144 (371)
T ss_dssp             GGGGTCCTTCEEEEEEC---EEEEEEECTTSCEEEEEEETTSBHHHHHHHHHHHTTCSCGGGEEEECCC----------C
T ss_pred             HHHhCCCCCceeeccCc---eeEEEEECcCCCEEEEEECCCCCHHHHHHHHHHHcCCCCccccEEEEEecccccchHHHH
Confidence            99999999998887665   58899999999999999999999999988877              11         134


Q ss_pred             CCCCCcccccccCCCCEEEEEEe
Q 042212           73 FEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        73 L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      |+.++++.+.+.....++.+..|
T Consensus       145 L~~~k~l~~q~~~~~~~l~frvK  167 (371)
T 3ivf_A          145 LDHGRTLREQGVEEHETLLLRRK  167 (371)
T ss_dssp             CCTTSBTGGGTCCTTCEEEEEEC
T ss_pred             HhcCchhHhhCCCCCceEEEEEE
Confidence            56677788777766777666544

>1s3s_G P47 protein; AAA ATPase, protein-protein complex, UBX domain, protein binding; HET: ADP; 2.90A {Rattus norvegicus} SCOP: d.15.1.2 PDB: 1i42_A 1jru_A

Probab=96.50  E-value=0.0039  Score=38.73  Aligned_cols=56  Identities=14%  Similarity=0.156  Sum_probs=47.7

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc----------------CCCeeCCC-CCcccccccCCCCEE
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS----------------SPAGNFED-GWTQADYNIQKESTL   90 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~----------------~~gk~L~d-~~tL~~y~I~~~sti   90 (97)
                      ....|.||..+|+.+.-....++||.+|.+-|.                |-.+.++| +.||.+.|+.+.+++
T Consensus        51 ~~t~IqIRlpdG~rl~~rF~~~~tl~~v~~fV~~~~~~~~~~~f~L~t~fPrk~l~d~~~TL~eagL~psavl  123 (127)
T 1s3s_G           51 PTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFPNKELADENQTLKEANLLNAVIV  123 (127)
T ss_dssp             CCCCEEEEETTTTEEEEECCSSCBHHHHHHHHHHHCSGGGTSCEEEEETTTTEECCSTTCBHHHHTCSSCEEE
T ss_pred             CcEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHHhCcCCCCCCeEEecCCCCCCCCCCCCcHHHCCCcCceEE
Confidence            358899999999999999999999999988876                66788865 689999999985544

>2l76_A Nfatc2-interacting protein; ubiquitin-like domain, structural genomics, PSI-biology, Pro structure initiative; NMR {Homo sapiens}

Probab=96.44  E-value=0.0081  Score=35.68  Aligned_cols=58  Identities=7%  Similarity=0.101  Sum_probs=50.8

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEE
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      .+.|.|+. +|..+.+.+..++..+.|..-.+             |.|..+.++.|-++.+++++++|.+++
T Consensus        21 ~IniKV~~-~g~ev~FkIK~tt~l~KL~~aYc~r~gv~~~sirFlfDG~rI~~~~TP~~L~meD~DiID~~~   91 (95)
T 2l76_A           21 LFPLKIRC-RADLVRLPLRMSEPLQSVVDHMATHLGVSPSRILLLFGETELSPTATPRTLKLGVADIIDCVV   91 (95)
T ss_dssp             CEEEEEEC-SSSEEEEEECSSSCTHHHHHHHHHHHTSCGGGEEEEETTEECCTTSCHHHHTCCSSCEEEEEE
T ss_pred             eEEEEEEc-CCcEEEEEEecCChHHHHHHHHHhhcCCChhhEEEEECCcCCCCCCCHhHcCCCCCCEEEEEE
Confidence            38888884 78899999999998888776655             999999999999999999999998875

>3kuz_A Plexin-C1; structural genomics, structural genomics consortium, SGC; 2.30A {Homo sapiens}

Probab=96.39  E-value=0.0091  Score=37.17  Aligned_cols=48  Identities=27%  Similarity=0.338  Sum_probs=36.6

Q ss_pred             CEEEEeecCCCcHHHhhcccc---C-------C---------------CeeC----------CCC----CcccccccCCC
Q 042212           47 KTITLEVESSDMIDNASRGSS---S-------P---------------AGNF----------EDG----WTQADYNIQKE   87 (97)
Q Consensus        47 ~~~~l~v~~~~tV~~lK~~I~---~-------~---------------gk~L----------~d~----~tL~~y~I~~~   87 (97)
                      ..+++.|-..|||.++|+||-   |       +               |..|          +++    .||+.|+|.+|
T Consensus        39 ~~v~VkVLdCDTItQVKEKILdavYk~k~~pys~r~~d~dLEwr~g~~~~~L~D~D~tS~~~e~~wkrLNTL~HY~V~Dg  118 (126)
T 3kuz_A           39 RNISVNVLDCDTIGQAKEKIFQAFLSKNGSPYGLQLNEIGLELQMGTRQKELLDIDSSSVILEDGITKLNTIGHYEISNG  118 (126)
T ss_dssp             CEEEEEEETTCBHHHHHHHHHHHHHHHHSSCCSSCGGGEEEEEEETTEEEEECSSCTTCCBCTTSCBCCCBTGGGTCCTT
T ss_pred             CceEeeeecCCcHHHHHHHHHHHHhccCCCcCCCCccccceEEecCCCcceeeccCCcceEecCCeeEeccccccCCCCC
Confidence            568888989999999999998   3       1               1222          222    47889999999


Q ss_pred             CEEEEEE
Q 042212           88 STLHFVL   94 (97)
Q Consensus        88 sti~l~~   94 (97)
                      +++.++-
T Consensus       119 atlal~k  125 (126)
T 3kuz_A          119 STIKVFK  125 (126)
T ss_dssp             CEEEEEE
T ss_pred             CEEEEee
Confidence            9998863

>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=96.21  E-value=0.0046  Score=37.98  Aligned_cols=32  Identities=13%  Similarity=0.472  Sum_probs=29.8

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVAR   32 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~   32 (97)
                      +|.+++|++|.|+.|     ..++++.+|.+|++++.
T Consensus        76 l~~~~irFlFDG~rI~~~~TP~dL~MEDgD~IdV~~~  112 (115)
T 3kyd_D           76 VPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQE  112 (115)
T ss_dssp             CCTTSEEEEETTEECCTTCCTTTTTCCTTCEEEEEEC
T ss_pred             CChhhEEEEECCeECCCCCCHHHcCCCCCCEEEEEee
Confidence            588999999999999     99999999999999875

>3ig3_A Plxna3 protein; plexin intracellular GAP RBD inactive, membrane, transmembra membrane protein, signaling protein; 1.99A {Mus musculus} PDB: 3ryt_A*

Probab=96.14  E-value=0.013  Score=44.97  Aligned_cols=59  Identities=17%  Similarity=0.217  Sum_probs=42.9

Q ss_pred             eeeEEECCC---CCEEEEeecCCCcHHHhhcccc-------------------------CCCe-eCCCC-----------
Q 042212           37 MQIFVKTST---GKTITLEVESSDMIDNASRGSS-------------------------SPAG-NFEDG-----------   76 (97)
Q Consensus        37 m~i~vk~~~---g~~~~l~v~~~~tV~~lK~~I~-------------------------~~gk-~L~d~-----------   76 (97)
                      +.+.+-..+   ...+.+.|-..|||.++|+||-                         -+|+ .|.|.           
T Consensus       234 ltL~v~~~~~~~~~~i~vkVLdCDTItQVKeKiLdavYk~~pyS~rP~~~~~dLEwr~g~~g~~iL~D~D~ts~~~~~wk  313 (627)
T 3ig3_A          234 LTLHCVCPESEGSAQVPVKVLNCDSITQAKDKLLDTVYKGIPYSQRPKAEDMDLEWRQGRMARIILQDEDITTKIECDWK  313 (627)
T ss_dssp             EEEEEECTTTC--CEEEEEEETTCBHHHHHHHHHHHHTTTSCGGGSCCGGGEEEEEESCSSCEEEECSSSTTCCEETTEE
T ss_pred             EEEEEeccCCCCCCceeeEeeccCcHHHHHHHHHHHHHcCCCcccCCCCCccceeEeeCCCCceeeccCCccccccCcee
Confidence            444454333   3678889999999999999998                         1222 34441           


Q ss_pred             --CcccccccCCCCEEEEEEe
Q 042212           77 --WTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        77 --~tL~~y~I~~~sti~l~~r   95 (97)
                        .||++|+|.+|+++.++.|
T Consensus       314 rLNTL~HY~V~Dga~v~L~p~  334 (627)
T 3ig3_A          314 RVNSLAHYQVTDGSLVALVPK  334 (627)
T ss_dssp             ECCBTTTTTCCTTCEEEEEEC
T ss_pred             EecchhhcCCCCCceEEEEec
Confidence              4899999999999998765

>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=95.83  E-value=0.0031  Score=37.80  Aligned_cols=15  Identities=7%  Similarity=-0.237  Sum_probs=14.1

Q ss_pred             CCCCceEEEecCccc
Q 042212            1 MPLEQQRLVFADKSL   15 (97)
Q Consensus         1 ip~~~q~L~~~~~~L   15 (97)
                      ||+++|||+|+|++|
T Consensus        64 ip~~qQrLi~~Gk~L   78 (100)
T 1uh6_A           64 TRWNKIVLKKWYTIF   78 (100)
T ss_dssp             CCGGGCEEEETTEEC
T ss_pred             CCHHHEEEEECCEEC
Confidence            799999999999987

>3hm6_X Plexin-B1; structural genomics consortium, SGC, membrane, transmembrane receptor, cell membrane, glycoprotein, phosphoprotein; 2.40A {Homo sapiens} PDB: 3sua_D* 3su8_X*

Probab=95.82  E-value=0.019  Score=44.25  Aligned_cols=49  Identities=18%  Similarity=0.215  Sum_probs=39.1

Q ss_pred             CEEEEeecCCCcHHHhhcccc-------------------------CCCe-eCCCC-------------CcccccccCCC
Q 042212           47 KTITLEVESSDMIDNASRGSS-------------------------SPAG-NFEDG-------------WTQADYNIQKE   87 (97)
Q Consensus        47 ~~~~l~v~~~~tV~~lK~~I~-------------------------~~gk-~L~d~-------------~tL~~y~I~~~   87 (97)
                      ..+.+.|-..|||.++|+||-                         ..|+ .|.|.             .||++|+|.+|
T Consensus       274 ~~i~VkVLdCDTItQVKeKiLDavYk~~pyS~rP~~~~~dLEwr~g~~g~~iL~D~D~ts~~~~~wkrLNTL~HY~V~dg  353 (644)
T 3hm6_X          274 QGVPVKVLDCDTISQAKEKMLDQLYKGVPLTQRPDPRTLDVEWRSGVAGHLILSDEDVTSEVQGLWRRLNTLQHYKVPDG  353 (644)
T ss_dssp             CCEEEEEETTSBHHHHHHHHHHHHTTTSCGGGSCCGGGEEEEEECSSSCEEEECSSSTTCCEETTEEECCBTTTTTCCTT
T ss_pred             CceeeEeeccCcHHHHHHHHHHHHHcCCCcccCCCCCCcceEEeeCCCCceeecccCccceecCcceeecchhhcCCCCC
Confidence            468888999999999999998                         2233 35552             48999999999


Q ss_pred             CEEEEEEe
Q 042212           88 STLHFVLR   95 (97)
Q Consensus        88 sti~l~~r   95 (97)
                      +++.++.+
T Consensus       354 a~v~L~p~  361 (644)
T 3hm6_X          354 ATVALVPC  361 (644)
T ss_dssp             CEEEEEEC
T ss_pred             cEEEEEec
Confidence            99998765

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens}

Probab=95.76  E-value=0.0028  Score=37.78  Aligned_cols=14  Identities=36%  Similarity=0.577  Sum_probs=12.5

Q ss_pred             CCCceEEEecCccc
Q 042212            2 PLEQQRLVFADKSL   15 (97)
Q Consensus         2 p~~~q~L~~~~~~L   15 (97)
                      |+++|||+|+|++|
T Consensus        64 p~~~QrLIy~Gk~L   77 (99)
T 2kdb_A           64 LTKDQRLVYSGRLL   77 (99)
T ss_dssp             CTTTCCEEETTEEE
T ss_pred             ChhhEEEEECCEEC
Confidence            45999999999987

>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=95.41  E-value=0.0057  Score=40.92  Aligned_cols=36  Identities=6%  Similarity=0.216  Sum_probs=32.9

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      +|+++++++|.|+.+     ..++++.+|.+|++++...++
T Consensus        92 L~~~sIRFLFDGqRI~~ddTPeDLdMEDGDtIDV~leQ~GG  132 (207)
T 3tix_A           92 KEMDSLTFLYDGIEIQADQTPEDLDMEDNDIIEAHREQIGG  132 (207)
T ss_dssp             CCGGGSCEEETTEECCSSCCTTTTTCCTTEEEEECCCCCTT
T ss_pred             CCcccEEEEECCeecCCCCCHHHcCCCCCCEEEEEEeccCC
Confidence            688999999999999     999999999999999987655

>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=95.32  E-value=0.042  Score=39.22  Aligned_cols=57  Identities=18%  Similarity=0.219  Sum_probs=44.2

Q ss_pred             eeEEECCCCCEEEEeecCCCcHHHhhcccc-----------------------CCCeeCCCCCcccccccCCCCEEEEEE
Q 042212           38 QIFVKTSTGKTITLEVESSDMIDNASRGSS-----------------------SPAGNFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        38 ~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-----------------------~~gk~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      .+.|... +.+-++.++|+.||.++-.+|.                       -.|+-|++.+||+.|++++|+.++..-
T Consensus         5 ~~~~~~~-~~~~~~~f~~~~~v~~~~~~i~e~~~~~~~~~~~~y~l~~~~~~~~~~~Wl~~~~~l~~y~~~~~~~l~~~~   83 (371)
T 3ivf_A            5 SLKISIG-NVVKTMQFEPSTMVYDACRMIRERIPEALAGPPNDFGLFLSDDDPKKGIWLEAGKALDYYMLRNGDTMEYRK   83 (371)
T ss_dssp             EEEEEET-TEEEEEEECTTCBHHHHHHHHHTTCGGGGSSCGGGEEEEECCSSGGGCEECCTTSBGGGGTCCTTCEEEEEE
T ss_pred             EEEEEec-ceeEEEEECCCCCHHHHHHHHHHhcccccCCCHHHCeEeccCCCCCcCEeccCCCCHHHhCCCCCceeeccC
Confidence            3344444 6778899999999999877764                       135668999999999999999998764


Q ss_pred             e
Q 042212           95 R   95 (97)
Q Consensus        95 r   95 (97)
                      +
T Consensus        84 ~   84 (371)
T 3ivf_A           84 K   84 (371)
T ss_dssp             C
T ss_pred             c
Confidence            3

>4efo_A Serine/threonine-protein kinase TBK1; ubiquitin like domain, transferase; 1.77A {Homo sapiens}

Probab=94.82  E-value=0.012  Score=34.89  Aligned_cols=15  Identities=20%  Similarity=0.459  Sum_probs=14.3

Q ss_pred             CCCCceEEEecCccc
Q 042212            1 MPLEQQRLVFADKSL   15 (97)
Q Consensus         1 ip~~~q~L~~~~~~L   15 (97)
                      ||+++|+|+|+|++|
T Consensus        49 Ip~~~Q~LL~eg~~l   63 (94)
T 4efo_A           49 IISSNQELIYEGRRL   63 (94)
T ss_dssp             CCGGGEEEEETTEEE
T ss_pred             CCHHHHHHHhCCCcc
Confidence            899999999999998

>3v7o_A Minor nucleoprotein VP30; ssgcid, seattle structural genomics center for infectious disease, SMT, transcription; 2.25A {Reston ebolavirus}

Probab=94.52  E-value=0.0068  Score=41.11  Aligned_cols=36  Identities=8%  Similarity=0.257  Sum_probs=0.5

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      +|++++|++|+|+.+     -+++++.+|.+|++++...++
T Consensus        56 Ls~~siRFLFDGqRI~dddTPadL~MEDGDtIDV~leQ~GG   96 (227)
T 3v7o_A           56 KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGG   96 (227)
T ss_dssp             ----------------------------------------C
T ss_pred             CCccceEEEECCEecCCCCCHHHcCCCCCCEEEEEecccCC
Confidence            578899999999999     999999999999999987655

>2l32_A Small archaeal modifier protein 2; protein BIN; NMR {Haloferax volcanii}

Probab=94.31  E-value=0.16  Score=28.38  Aligned_cols=51  Identities=10%  Similarity=0.124  Sum_probs=37.0

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc---------CCCeeCCCCCcccccccCCCCEEEEE
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS---------SPAGNFEDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~---------~~gk~L~d~~tL~~y~I~~~sti~l~   93 (97)
                      |+|.|+........+++++..||+++-+.+.         .||+....+.      +.+|+.+.++
T Consensus         1 M~v~Vkl~g~~~~~~ev~~g~Tv~dLL~~Lgl~~~~VvV~vNG~~v~~d~------~l~GD~VeIv   60 (74)
T 2l32_A            1 MNVTVEVVGEETSEVAVDDDGTYADLVRAVDLSPHEVTVLVDGRPVPEDQ------SVEVDRVKVL   60 (74)
T ss_dssp             CEEEEECSSSSEEEEECSTTCSHHHHHHTTCCCSSCCCEECCCCCCCTTS------SSCCCCEEEC
T ss_pred             CEEEEEEeCccceeEEcCCCCcHHHHHHHcCCCcceEEEEECCEECCHHH------CCCCCEEEEE
Confidence            6788877744556689999999999998888         6777765554      2347776653

>4efo_A Serine/threonine-protein kinase TBK1; ubiquitin like domain, transferase; 1.77A {Homo sapiens}

Probab=94.16  E-value=0.069  Score=31.55  Aligned_cols=42  Identities=7%  Similarity=-0.040  Sum_probs=33.3

Q ss_pred             CCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeC--CCCCccccccc
Q 042212           43 TSTGKTITLEVESSDMIDNASRGSS-------------SPAGNF--EDGWTQADYNI   84 (97)
Q Consensus        43 ~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L--~d~~tL~~y~I   84 (97)
                      ...++.+.+.+++++|+..+|++|+             |+|+.|  +...+...|--
T Consensus        20 ~~~a~~h~v~I~~~etv~~~ke~V~eqTgIp~~~Q~LL~eg~~l~l~p~~~a~~~p~   76 (94)
T 4efo_A           20 LQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLVLEPGRLAQHFPK   76 (94)
T ss_dssp             TTTTEEEEEEEETTCBHHHHHHHHHHHHCCCGGGEEEEETTEEECCCTTCBGGGSCC
T ss_pred             cccceEEEEEeccchHHHHHHHHHHHHhCCCHHHHHHHhCCCccccCCCCccccCCC
Confidence            4467889999999999999999999             999775  45555556543

>2daj_A KIAA0977 protein, COBL-like 1; ubiquitin-like domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=93.76  E-value=0.047  Score=31.83  Aligned_cols=52  Identities=4%  Similarity=0.085  Sum_probs=43.5

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc----------------CCCeeCCCCCcccccccCC
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS----------------SPAGNFEDGWTQADYNIQK   86 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~----------------~~gk~L~d~~tL~~y~I~~   86 (97)
                      .++++.|+....+...+.|+|.-+..++-.-|.                -++.+|+-+++|.||||++
T Consensus         9 ~TvRLvVNy~~tQKtVvRVSP~vpL~ellp~IC~Kcefdp~~~~Ll~d~~~~e~LdLskSLndlgirE   76 (91)
T 2daj_A            9 KTVRVVINFKKTQKTIVRVSPHASLQELAPIICSKCEFDPLHTLLLKDYQSQEPLDLTKSLNDLGLRE   76 (91)
T ss_dssp             SCEEEEEEETTTEEEEEEECSSSCTTTHHHHHHHHTTCCTTSEEEESCSSCCCBCCTTSCHHHHTCSE
T ss_pred             cEEEEEEeecCcceeEEEeCCCCcHHHHHHHHhhcccCChhhEEEecCCCCCcccchhcchhhhhhhh
Confidence            346677777766788889999999999988887                5678899999999999986

>3ix6_A TS, tsase, thymidylate synthase; niaid, ssgcid, seattle structural center for infectious DISE brucellosis, orchitis, epididymitis, mastitis; 2.20A {Brucella melitensis}

Probab=92.12  E-value=0.024  Score=41.06  Aligned_cols=38  Identities=11%  Similarity=0.294  Sum_probs=0.9

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCCee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQ   38 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~m~   38 (97)
                      +|++++|+.|.|+.+     -+++++++|.+|+++....++|+
T Consensus        56 ~~~~~~rFlFdG~rI~~~~TP~~L~MEDgD~Idv~~~Q~g~~~   98 (360)
T 3ix6_A           56 KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGMR   98 (360)
T ss_dssp             -----------------------------------------CH
T ss_pred             CCcceEEEEECCeECCCCCChHHcCCCccchhhhhhccCchHH
Confidence            477899999999998     99999999999999998766644

>2kmm_A Guanosine-3',5'-BIS(diphosphate) 3'- pyrophosphohydrolase; methods development, TGS domain, predominantly beta-sheet structure; NMR {Porphyromonas gingivalis}

Probab=91.50  E-value=0.59  Score=25.24  Aligned_cols=50  Identities=10%  Similarity=0.102  Sum_probs=34.4

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-----------CCCeeCCCCCcccccccCCCCEEEEE
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-----------SPAGNFEDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-----------~~gk~L~d~~tL~~y~I~~~sti~l~   93 (97)
                      |.+.|..++|+..  +++...|+.++-+.+.           .+|+..+-+     +-+++|+.|.++
T Consensus         1 m~i~i~~p~g~~~--~~~~g~T~~dla~~i~~~l~~~~vaa~vNg~lvdl~-----~~L~~~~~Veiv   61 (73)
T 2kmm_A            1 MEVMVFTPKGEIK--RLPQGATALDFAYSLHSDLGDHCIGAKVNHKLVPLS-----YVLNSGDQVEVL   61 (73)
T ss_dssp             CCEEEECTTCCEE--EECTTCBHHHHHHHHCSHHHHTEEEEEETTEECCTT-----CBCCSSSBEEEE
T ss_pred             CeEEEEcCCCCEE--EcCCCCcHHHHHHHHhhccccceEEEEECCEEeCCC-----cCcCCCCEEEEE
Confidence            6778887788864  5557788988876663           677765544     445567777665

>1ef1_A Moesin; membrane, FERM domain, tail domain, membrane protein; 1.90A {Homo sapiens} SCOP: a.11.2.1 b.55.1.5 d.15.1.4 PDB: 1sgh_A 1j19_A 2emt_A 2ems_A 2d10_A 2d11_A 2yvc_A 2d2q_A 2zpy_A 1gc7_A 1gc6_A 1ni2_A

Probab=91.50  E-value=0.49  Score=32.37  Aligned_cols=60  Identities=13%  Similarity=0.145  Sum_probs=45.3

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc-----------------CCC--eeCCCCCcccccccCCCCEEEEEEee
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS-----------------SPA--GNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-----------------~~g--k~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      ++.+.|..++| +..+.++++.|+.++-+.|.                 .+|  ..|+.+.++.+.++..+....+.+|.
T Consensus         1 ~i~~~V~l~d~-~~~~~v~~~tt~~el~~~v~~~l~L~e~~~FgL~~~~~~~~~~wLd~~~~l~~q~~~~~~~~~l~fr~   79 (294)
T 1ef1_A            1 TISVRVTTMDA-ELEFAIQPNTTGKQLFDQVVKTIGLREVWFFGLQYQDTKGFSTWLKLNKKVTAQDVRKESPLLFKFRA   79 (294)
T ss_dssp             CEEEEEEETTE-EEEEEECTTCBHHHHHHHHHHHHTCCCGGGEEEEEEBTTSCEEECCSSSBGGGSCBCCCSSEEEEEEE
T ss_pred             CEEEEEEECCc-eEEEEECCCCcHHHHHHHHHHHcCCCCcceeEEEEECCCCceeecccccCHHhhccCCCCCEEEEEEE
Confidence            36778888888 78899999999999988877                 133  24677888888877666666666553

>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=91.11  E-value=0.22  Score=28.55  Aligned_cols=31  Identities=19%  Similarity=0.394  Sum_probs=27.3

Q ss_pred             CCCC-ceEEEecCccc-----cccccccCCCcceeee
Q 042212            1 MPLE-QQRLVFADKSL-----LADYNIQKESTLHLVA   31 (97)
Q Consensus         1 ip~~-~q~L~~~~~~L-----l~~y~i~~~s~i~l~~   31 (97)
                      ||.+ .-+|.|.|.-|     +.||++.+|.-|.+++
T Consensus        45 I~~~~~IrllFDGdRLdp~~tp~DlemeD~D~IDvmL   81 (82)
T 3goe_A           45 ISFHERIRLEFEGEWLDPNDQVQSTELEDEDQVSVVL   81 (82)
T ss_dssp             CCCCTTCEEEETTEECCTTSBGGGSSCCTTCEEEEEC
T ss_pred             CCcCceEEEEEcCcccCccCChhhhCCcCCceeeeee
Confidence            5677 78999999999     9999999999988765

>1h4r_A Merlin; FERM, neurofibromatosis, NF2, structural protein, cytoskeleton, anti-oncogene; 1.8A {Homo sapiens} SCOP: a.11.2.1 b.55.1.5 d.15.1.4 PDB: 1isn_A 3u8z_A

Probab=90.17  E-value=0.71  Score=31.95  Aligned_cols=62  Identities=10%  Similarity=0.004  Sum_probs=47.6

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc--------------C--CC--eeCCCCCcccccccCCCCEEEEEEe
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS--------------S--PA--GNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~--------------~--~g--k~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      +.++.+.|..++| ++.+.++++.|+.++-+.|.              |  +|  ..|+.+.++.+.+++.+....+.+|
T Consensus        20 ~~~~~~~V~lldg-~~~~~v~~~t~~~el~~~v~~~l~L~e~~~FgL~~~~~~~~~wL~~~~~i~~q~~~~~~~~~l~fr   98 (314)
T 1h4r_A           20 PKTFTVRIVTMDA-EMEFNCEMKWKGKDLFDLVCRTLGLRETWFFGLQYTIKDTVAWLKMDKKVLDHDVSKEEPVTFHFL   98 (314)
T ss_dssp             -CEEEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHTCCCGGGEEEEEEETTEEEECCTTSBGGGSSCCCSSSEEEEEE
T ss_pred             CCeeEEEEEeCCc-eEEEEeCCCCcHHHHHHHHHHHhCCCCCccceEEEEeCCcCeeCCCccCHHHcCCCCCCCEEEEEE
Confidence            4568889999999 88899999999999988877              1  22  2478888999988776666666655


Q ss_pred             e
Q 042212           96 L   96 (97)
Q Consensus        96 l   96 (97)
                      .
T Consensus        99 ~   99 (314)
T 1h4r_A           99 A   99 (314)
T ss_dssp             E
T ss_pred             E
Confidence            3

>1ryj_A Unknown; beta/alpha protein, structural genomics, protein structure initiative, OCSP, NESG, PSI; NMR {Methanothermococcusthermolithotrophicus} SCOP: d.15.3.2

Probab=89.87  E-value=1.4  Score=23.89  Aligned_cols=53  Identities=17%  Similarity=0.110  Sum_probs=38.2

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc---------CCCeeCCCCCcccccccCCCCEEEEEE
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS---------SPAGNFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~---------~~gk~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      .|+|.|+...+ ...++++...|+.+|.+.+.         .+|.....+.     -+++|+.|.+.-
T Consensus         4 ~m~i~vNg~~~-~~~~~~~~~~tv~~Ll~~l~~~~~~v~vavN~~~v~~~~-----~L~~gD~V~ii~   65 (70)
T 1ryj_A            4 GMKFTVITDDG-KKILESGAPRRIKDVLGELEIPIETVVVKKNGQIVIDEE-----EIFDGDIIEVIR   65 (70)
T ss_dssp             CEEEEEEETTE-EEEEEESSCCBHHHHHHHTTCCTTTEEEEETTEECCTTS-----BCCTTCEEEEEE
T ss_pred             eEEEEEeCccC-ceeEECCCCCcHHHHHHHhCCCCCCEEEEECCEECCCcc-----cCCCCCEEEEEe
Confidence            48888866432 34567777789999998875         6777766554     578899888764

>2inc_C TOUB protein; DIIRON, 4-helix bundle, carboxylate bridge, metalloenzyme, oxidoreductase; HET: P6G; 1.85A {Pseudomonas stutzeri} SCOP: d.15.12.1 PDB: 2ind_C* 3n20_C* 1t0r_C 1t0s_C 1t0q_C* 3n1x_C 3n1y_C* 3n1z_C* 2rdb_C* 3rn9_C* 3rna_C 3rnb_C 3rnc_C 3rne_C 3rnf_C* 3rng_C

Probab=88.39  E-value=0.89  Score=26.12  Aligned_cols=46  Identities=17%  Similarity=0.325  Sum_probs=39.9

Q ss_pred             EEEeecCCCcHHHhhcccc-------------------CCC--eeCCCCCcccccccCCCCEEEEEE
Q 042212           49 ITLEVESSDMIDNASRGSS-------------------SPA--GNFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        49 ~~l~v~~~~tV~~lK~~I~-------------------~~g--k~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      .-+.|+..+|+.++-++++                   ++|  +.+..+.|+++-||.+-..+.+..
T Consensus        15 ~LV~VDt~dTmdqVA~kvA~HsVGrRV~p~p~~~~rVr~~G~~~~~pr~~tvae~gl~P~e~vev~~   81 (83)
T 2inc_C           15 QLVPVDTEDTMDQVAEKCAYHSINRRVHPQPEKILRVRRHEDGTLFPRGMIVSDAGLRPTETLDIIF   81 (83)
T ss_dssp             EEEEECTTCBHHHHHHHHHTTTBTTTBCCCTTSEEEEEETTTCCEECTTCBGGGSCCCTTCEEEEEE
T ss_pred             EEEEecCCCcHHHHHHHHhhhhcceecCCCCCCeEEEEecCCccCCCCCCEeeccCCCCceEEEEEE
Confidence            4468899999999999988                   666  889999999999999999988765

>2i1j_A Moesin; FERM, coiled-coil, C-ermad, ERM, radixin, ezrin, MER actin binding, masking, regulation, SELF-inhibition, cell A membrane protein; 2.10A {Spodoptera frugiperda} PDB: 2i1k_A 1e5w_A

Probab=87.63  E-value=1.5  Score=33.36  Aligned_cols=62  Identities=13%  Similarity=0.107  Sum_probs=46.6

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc--------------C---CC--eeCCCCCcccccccCCCCEEEEEE
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS--------------S---PA--GNFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~--------------~---~g--k~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      +.++.+.|..++| ++.+.|+++.|+.++-..|.              |   .|  ..|+.+.++.+.++..+....+.+
T Consensus         2 ~k~i~v~V~llDg-t~e~~vd~~tt~~ell~~V~~~LgL~e~~~FGL~~~d~~~~~~WLd~~k~i~~q~~~~~~~~~L~F   80 (575)
T 2i1j_A            2 PKSMNVRVTTMDA-ELEFAIQQTTTGKQLFDQVVKTIGLREVWFFGLQYTDSKGDLTWIKLYKKVMQQDVKKENPLQFKF   80 (575)
T ss_dssp             -CEEEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHTCCCGGGEEEEEEBTTSCEEECCTTSBGGGSCBCCCSSEEEEE
T ss_pred             CceEEEEEEeCCC-eEEEEECCCCCHHHHHHHHHHHcCCCCccceeEEEEecCcchhHhhccccHHHhcccCCCCeEEEE
Confidence            3457888889998 78899999999999988877              1   12  356778888888777777766666


Q ss_pred             ee
Q 042212           95 RL   96 (97)
Q Consensus        95 rl   96 (97)
                      |.
T Consensus        81 Rv   82 (575)
T 2i1j_A           81 RA   82 (575)
T ss_dssp             EE
T ss_pred             EE
Confidence            54

>2kmc_A Fermitin family homolog 1; kindlin, cytoskeleton, integrin, N-terminal, talin, cell adhesion, cell junction, cell membrane, cell projection; NMR {Mus musculus}

Probab=86.05  E-value=1.6  Score=25.95  Aligned_cols=60  Identities=20%  Similarity=0.268  Sum_probs=45.6

Q ss_pred             CeeeEEECCCC---CEEEEeecCCCcHHHhhcccc------------------CCCeeCCCCCcccccccCCCCEEEEEE
Q 042212           36 RMQIFVKTSTG---KTITLEVESSDMIDNASRGSS------------------SPAGNFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        36 ~m~i~vk~~~g---~~~~l~v~~~~tV~~lK~~I~------------------~~gk~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      +..|+|...+.   ..+++.|..+.-|..+-.++-                  -+-..+.-..||..|||+.++.+++..
T Consensus        19 eL~V~V~d~~~~~~~~~~lrV~GdlHIGGvmlklVEki~i~~dWSDhaLWW~~k~~WLlkt~~tLDkygiqADa~L~ftp   98 (102)
T 2kmc_A           19 ELVVRVDHANGEQQTEITLRVSGDLHIGGVMLKLVEQMNIAQDWSDYALWWEQKRCWLLKTHWTLDKCGVQADANLLFTP   98 (102)
T ss_dssp             EEEEEEECTTSSCEEEEEEEECSCCBHHHHHHHHHHHHCCSSCCSSEEEEETTTTEEECCTTSBHHHHTCCTTSCEEEEE
T ss_pred             EEEEEEecCCcccCccEEEEEeeccccchhhhhhhhhcccccchHHhhhhhhhhchhhhhhhhhhhhhceeeeeeeeccC
Confidence            47788888654   568889998888887766554                  223456888999999999999998865


Q ss_pred             e
Q 042212           95 R   95 (97)
Q Consensus        95 r   95 (97)
                      .
T Consensus        99 ~   99 (102)
T 2kmc_A           99 Q   99 (102)
T ss_dssp             C
T ss_pred             C
Confidence            3

>4da1_A Protein phosphatase 1K, mitochondrial; metal-ION-assisted catalysis, dehydrogenase phosphatase, hydrolase; 2.38A {Homo sapiens} PDB: 3qht_A 1l2n_A

Probab=85.86  E-value=0.15  Score=36.67  Aligned_cols=41  Identities=7%  Similarity=0.280  Sum_probs=0.0

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCCeeeEE
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGRMQIFV   41 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~m~i~v   41 (97)
                      +|.+++++.|.|+.+     -.++|+.+|.+|+++....++....+
T Consensus        65 ~~~~~~~f~f~G~~i~~~~Tp~~l~med~d~i~~~~~q~gg~n~~~  110 (389)
T 4da1_A           65 KEMDSLRFLYDGIRIQADQAPEDLDMEDNDIIEAHREQIGGENLYF  110 (389)
T ss_dssp             ----------------------------------------------
T ss_pred             CCcceEEEEECCEEcCCCCCHHHcCCCCCCEeeeeeccccccccce
Confidence            478899999999999     99999999999999998665544433

>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=85.78  E-value=1.7  Score=28.66  Aligned_cols=35  Identities=9%  Similarity=0.274  Sum_probs=30.8

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      +|.+++|++|.|+.+     -.+.++.++.+|.+.....+
T Consensus        56 ~~~~~~~f~fdG~~i~~~~Tpk~L~~ed~d~I~~~~eq~G   95 (209)
T 3uf8_A           56 KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIG   95 (209)
T ss_dssp             CCGGGCEEEETTEECCTTCCTTTTTCCTTEEEEEECSCTT
T ss_pred             CChheEEEEECCEeccCCCChHHhhhcccccchhhccccc
Confidence            588999999999998     88999999999999887544

>3jyu_A Ubiquitin carboxyl-terminal hydrolase; domain in ubiquitin-specific peptidases (DUSP), proto- oncogene, ubiquitin-fold, UBL, protease, thioesterase; HET: 1PS; 2.37A {Mus musculus}

Probab=85.13  E-value=1.3  Score=29.76  Aligned_cols=48  Identities=10%  Similarity=0.087  Sum_probs=38.4

Q ss_pred             EEEEeecCCCcHHHhhcccc---------------CC----CeeCCC-CCcccccccCCCCEEEEEEe
Q 042212           48 TITLEVESSDMIDNASRGSS---------------SP----AGNFED-GWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        48 ~~~l~v~~~~tV~~lK~~I~---------------~~----gk~L~d-~~tL~~y~I~~~sti~l~~r   95 (97)
                      .+++.++..+||.++++++.               |.    ...|.| +.||.++++.++..|.+-.|
T Consensus       153 ~~~~~~Sk~~ti~~l~~~~~~~~~i~~~~~~RLW~~~~~~~~~~L~~~~~tl~d~~L~~~Q~illE~r  220 (231)
T 3jyu_A          153 VLSCHFSKADTIATIEKEMRKLFNIPAERETRLWNKYMSNTYEQLSKLDNTIQDAGLYQGQVLVIEPQ  220 (231)
T ss_dssp             EEEEEECTTCBHHHHHHHHHHHTTCCTTSCEEEEECSSSSSCEECCCTTSBTTTTTCCTTEEEEEEEC
T ss_pred             eEEEEecccCcHHHHHHHHHHHhCCCCCCeEEEEEecCCCCHhhhcCCCCCHHHhCCCCCCEEEEEEe
Confidence            35577899999999998887               22    345665 58999999999999988776

>3ge3_C Toluene-4-monooxygenase system protein B; DIIRON hydroxylase, effector protein, T201A, aromatic hydrocarbons catabolism, FAD, flavoprotein; 1.52A {Pseudomonas mendocina} SCOP: d.15.12.0 PDB: 3dhh_C* 3dhg_C* 3dhi_C 3ge8_C 3i5j_C 3i63_C 3q14_C 3q2a_C* 3q3m_C* 3q3n_C* 3q3o_C* 3rmk_C* 3ri7_C*

Probab=84.70  E-value=0.88  Score=26.18  Aligned_cols=46  Identities=15%  Similarity=0.247  Sum_probs=39.8

Q ss_pred             EEEeecCCCcHHHhhcccc------------------CCCee--CCCCCcccccccCCCCEEEEEE
Q 042212           49 ITLEVESSDMIDNASRGSS------------------SPAGN--FEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        49 ~~l~v~~~~tV~~lK~~I~------------------~~gk~--L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      .-+.|+..+|+.++-++++                  .+|..  +..+.|+++-||++-..+.+..
T Consensus        17 ~Lv~VDt~dtmdqVA~k~A~h~VGrrv~p~pg~lrVr~~G~~~~~Pr~mtVaeaGl~Pme~vev~~   82 (84)
T 3ge3_C           17 QLVVVDLNDSMDQVAEKVAYHCVNRRVAPREGVMRVRKHRSTELFPRDMTIAESGLNPTEVIDVVF   82 (84)
T ss_dssp             EEEEEETTCBHHHHHHHHHHTTBTTTBCCCSSCEEEEETTCSCBCCTTCBHHHHCCCTTCEEEEEE
T ss_pred             EEEEecCCCcHHHHHHHHhhhhcceeeCCCCCcEEEEECCCcccCCCCCEeeccCCCcceEEEEEE
Confidence            4468899999999999988                  66776  8999999999999999998765

>1tyg_B YJBS; alpha beta barrel, protein-protein complex, THis, BIOS protein; 3.15A {Bacillus subtilis} SCOP: d.15.3.2

Probab=84.40  E-value=1.1  Score=25.83  Aligned_cols=54  Identities=11%  Similarity=0.169  Sum_probs=34.3

Q ss_pred             CCeeeEEECCCCCEEEEeecCC-CcHHHhhcccc---------CCCeeCCCCCcccccccCCCCEEEEEE
Q 042212           35 GRMQIFVKTSTGKTITLEVESS-DMIDNASRGSS---------SPAGNFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~-~tV~~lK~~I~---------~~gk~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      ..|+|.|   +|+.  ++++.. .||.+|.+.+.         .||..+..+ ..++.-+++|+.|.++-
T Consensus        19 ~~M~I~v---NGe~--~el~~~~~Tv~dLL~~L~~~~~~vaVavNg~iV~~~-~~~~~~L~dGD~Vei~~   82 (87)
T 1tyg_B           19 GRHMLQL---NGKD--VKWKKDTGTIQDLLASYQLENKIVIVERNKEIIGKE-RYHEVELCDRDVIEIVH   82 (87)
T ss_dssp             ---CEEE---TTEE--ECCSSSCCBHHHHHHHTTCTTSCCEEEETTEEECGG-GTTTSBCCSSSEEEEEE
T ss_pred             cceEEEE---CCEE--EECCCCCCcHHHHHHHhCCCCCCEEEEECCEECChh-hcCCcCCCCCCEEEEEc
Confidence            4587777   4554  455666 89999988876         445544322 33456789999998864

>3qij_A Protein 4.1; cytoskeleton, structural genomics, structural genomics conso SGC; 1.80A {Homo sapiens} PDB: 1gg3_A 3bin_A 2he7_A 2rq1_A

Probab=83.93  E-value=1.8  Score=29.89  Aligned_cols=60  Identities=7%  Similarity=-0.106  Sum_probs=42.3

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-----------------CCC--eeCCCCCcccccccCCCCEEEEEE
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-----------------SPA--GNFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-----------------~~g--k~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      ..+.+.|..++|...++.+++..|+.++-..|.                 -+|  ..|+.+.++.+.......++.+.+
T Consensus        16 ~~~~~~V~lldgt~~~~~vd~~tt~~el~~~v~~~l~L~e~~~FgL~~~~~~~~~~wLd~~k~i~~q~~~~~~~l~frv   94 (296)
T 3qij_A           16 FQGHCKVSLLDDTVYECVVEKHAKGQDLLKRVCEHLNLLEEDYFGLAIWDNATSKTWLDSAKEIKKQVRGVPWNFTFNV   94 (296)
T ss_dssp             -CCEEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHTCSSGGGEEEEEEEETTEEEECCTTSBHHHHC---CCEEEEEE
T ss_pred             ceEEEEEEccCCCEEEEEECCCCCHHHHHHHHHHHcCCCCcceeEEEEEcCCCccchhccchhHHHhcCCCCcEEEEEE
Confidence            458899999999999999999999999988887                 112  346777777766544444454443

>1wgr_A Growth factor receptor-bound protein 7; RA domain, GRB7, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.15.1.5

Probab=83.51  E-value=2.5  Score=25.03  Aligned_cols=33  Identities=12%  Similarity=0.067  Sum_probs=27.7

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS   67 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~   67 (97)
                      +..-|.|-..+|...++.|++++|+.++=+.+.
T Consensus         8 ~k~vvkvf~~Dgssksi~V~~~~Ta~dv~~~L~   40 (100)
T 1wgr_A            8 RPHVVKVYSEDGACRSVEVAAGATARHVCEMLV   40 (100)
T ss_dssp             SCEEEEEEETTSCEEEEEECTTCCHHHHHHHHH
T ss_pred             CCEEEEEEecCCCEEEEEECCCCcHHHHHHHHH
Confidence            445666667899999999999999999988877

>2juo_A GA-binding protein alpha chain; OST, ubiquitin, transcription factor, ensemble, DNA-binding, nucleus, transcription regulation; NMR {Mus musculus}

Probab=82.59  E-value=3.1  Score=24.02  Aligned_cols=47  Identities=9%  Similarity=0.187  Sum_probs=37.8

Q ss_pred             EEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           49 ITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        49 ~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      +.-.++-.+++..||..++             ..+.+|+++.+|.+.+++-...+.+.+-
T Consensus         5 i~qhmDI~epL~~Lk~LLe~Rl~i~L~~y~f~LQd~~L~~~k~LvdQcVqgeGlVQinvq   64 (89)
T 2juo_A            5 VSQAIDINEPIGNLKKLLEPRLQCSLDAHEICLQDIQLDPDRSLFDQGVKTDGTVQLSVQ   64 (89)
T ss_dssp             EEEEEESSSBGGGHHHHSHHHHCSCCSSCEEEETTEECCTTSBTTTSSCCCCSEEEEEEE
T ss_pred             hhhhccccCcHHHHHHHHHHHhcCCcccCeEEeeccccCCCccHHHhhcccccEEEEEEE
Confidence            3446777888899998888             3456699999999999998888888764

>4a3p_A Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {Homo sapiens} PDB: 4a3o_A 3pv1_A 3ppa_A* 3t9l_A 3lmn_A

Probab=81.72  E-value=1.4  Score=29.26  Aligned_cols=48  Identities=15%  Similarity=0.140  Sum_probs=38.5

Q ss_pred             EEEEeecCCCcHHHhhcccc----------------C---CCeeCCC-CCcccccccCCCCEEEEEEe
Q 042212           48 TITLEVESSDMIDNASRGSS----------------S---PAGNFED-GWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        48 ~~~l~v~~~~tV~~lK~~I~----------------~---~gk~L~d-~~tL~~y~I~~~sti~l~~r   95 (97)
                      ..++.++..+||.++++++.                +   ....|+| +.||.++++.++..|.+-+|
T Consensus       141 ~~~~~~Sk~~ti~~l~~~~~~~~~i~~~~~~RlW~~~~~~~~~~L~~~~~tl~~~~l~~~Q~illE~r  208 (217)
T 4a3p_A          141 VVTRRFSKADTIDTIEKEIRKIFSIPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLVIEQK  208 (217)
T ss_dssp             EEEEEECTTSBHHHHHHHHHHHTTCCTTSCEEEEEEEETTEEEECCCTTSBHHHHTCCTTCEEEEEEC
T ss_pred             ceEEEEcccchHHHHHHHHHHHhCCCCCCceEEEEecCCCCeeecCCCCCCHHHhCCCCCCEEEEEEe
Confidence            35678899999999998887                1   1245665 57999999999999988776

>1vjk_A Molybdopterin converting factor, subunit 1; structural genomics, PSI, protein structure INI southeast collaboratory for structural genomics; 1.51A {Pyrococcus furiosus} SCOP: d.15.3.1

Probab=80.17  E-value=6.3  Score=22.54  Aligned_cols=61  Identities=13%  Similarity=0.140  Sum_probs=38.1

Q ss_pred             cCCeeeEEECCC------C-CEEEEeecCCCcHHHhhcccc--CC--------------Ce--eCCCCCc-ccccccCCC
Q 042212           34 RGRMQIFVKTST------G-KTITLEVESSDMIDNASRGSS--SP--------------AG--NFEDGWT-QADYNIQKE   87 (97)
Q Consensus        34 ~~~m~i~vk~~~------g-~~~~l~v~~~~tV~~lK~~I~--~~--------------gk--~L~d~~t-L~~y~I~~~   87 (97)
                      .++|+|.|+..-      | ....+++....||.+|.+.+.  |.              ..  .+-|+.- -.++-+++|
T Consensus         7 ~~~~~v~V~~FA~lre~~g~~~~~~e~~~~~Tv~~Ll~~L~~~~p~l~~~l~~~~g~~~~~v~v~VNg~~v~~~~~L~dG   86 (98)
T 1vjk_A            7 HGSVKVKVKYFARFRQLAGVDEEEIELPEGARVRDLIEEIKKRHEKFKEEVFGEGYDEDADVNIAVNGRYVSWDEELKDG   86 (98)
T ss_dssp             --CEEEEEEECTHHHHHHSSSEEEEEECTTCBHHHHHHHHHHHCGGGGGSCBCSSSCTTSSBEEEETTBCCCTTCBCCTT
T ss_pred             cCcEEEEEEEhHHHHHHhCCCeEEEECCCCCCHHHHHHHHHhHChhHHHHhhccccccCCcEEEEECCEECCCCCCCCCC
Confidence            467888888753      4 466788877889999988876  21              10  1112111 136678899


Q ss_pred             CEEEEEE
Q 042212           88 STLHFVL   94 (97)
Q Consensus        88 sti~l~~   94 (97)
                      +.|.+..
T Consensus        87 DeV~i~p   93 (98)
T 1vjk_A           87 DVVGVFP   93 (98)
T ss_dssp             CEEEEES
T ss_pred             CEEEEEC
Confidence            9988763

---

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
d1ogwa_	76	d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [Tax	3e-18
d1ogwa_	76	d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [Tax	1e-09
d1bt0a_	73	d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis t	4e-18
d1bt0a_	73	d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis t	7e-08
d1z2ma2	76	d.15.1.1 (A:79-154) Interferon-induced 15 kDa prot	8e-18
d1z2ma2	76	d.15.1.1 (A:79-154) Interferon-induced 15 kDa prot	2e-06
d1wh3a_	87	d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like	7e-17
d1wh3a_	87	d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like	7e-08
d2zeqa1	78	d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin	2e-16
d2zeqa1	78	d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin	2e-10
d1ttna1	80	d.15.1.1 (A:21-100) Dendritic cell-derived ubiquit	1e-15
d1ttna1	80	d.15.1.1 (A:21-100) Dendritic cell-derived ubiquit	0.002
d1uela_	95	d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homol	4e-15
d1uela_	95	d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homol	8e-06
d2faza1	76	d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING fing	6e-15
d2faza1	76	d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING fing	1e-06
d1wx9a1	73	d.15.1.1 (A:8-80) Large proline-rich protein BAT3	2e-14
d1wx9a1	73	d.15.1.1 (A:8-80) Large proline-rich protein BAT3	4e-04
d1uh6a_	100	d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mous	2e-13
d1uh6a_	100	d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mous	2e-04
d1z2ma1	76	d.15.1.1 (A:3-78) Interferon-induced 15 kDa protei	5e-13
d1z2ma1	76	d.15.1.1 (A:3-78) Interferon-induced 15 kDa protei	1e-04
d1oqya4	77	d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 h	3e-12
d1oqya4	77	d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 h	9e-05
d1wy8a1	76	d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING fing	6e-12
d1wy8a1	76	d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING fing	2e-05
d1zkha1	86	d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-t	4e-11
d1zkha1	86	d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-t	1e-10
d1m94a_	73	d.15.1.1 (A:) Ubiquitin-like modifier protein hub1	5e-11
d2c9wb1	103	d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens)	2e-10
d2c9wb1	103	d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens)	3e-06
d1j8ca_	103	d.15.1.1 (A:) Ubiquitin-like N-terminal domain of	9e-10
d1j8ca_	103	d.15.1.1 (A:) Ubiquitin-like N-terminal domain of	0.001
d1wiaa_	95	d.15.1.1 (A:) Ubiquitin-like protein bab25500 (201	1e-09
d1wiaa_	95	d.15.1.1 (A:) Ubiquitin-like protein bab25500 (201	2e-05
d2bwfa1	73	d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyc	1e-09
d2bwfa1	73	d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyc	2e-05
d1v5oa_	102	d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus mu	1e-09
d1v5oa_	102	d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus mu	2e-07
d1v2ya_	105	d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik	1e-09
d1v2ya_	105	d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik	4e-06
d1yqba1	84	d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapien	4e-09
d1yqba1	84	d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapien	6e-04
d1wx8a1	83	d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus muscul	6e-09
d1wx8a1	83	d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus muscul	2e-04
d1x1ma1	94	d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse	4e-08
d1x1ma1	94	d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse	3e-05
d1wgha_	116	d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mous	5e-08
d1wgha_	116	d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mous	6e-05
d1wjua_	100	d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human	8e-08
d1wgda_	93	d.15.1.1 (A:) Homocysteine-responsive endoplasmic	5e-07
d1wgda_	93	d.15.1.1 (A:) Homocysteine-responsive endoplasmic	7e-07
d1we6a_	111	d.15.1.1 (A:) Splicing factor 3 subunit 1, C-termi	5e-07
d1we6a_	111	d.15.1.1 (A:) Splicing factor 3 subunit 1, C-termi	4e-06
d1euvb_	79	d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yea	9e-07
d1euvb_	79	d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yea	0.001
d1wgga_	96	d.15.1.1 (A:) Ubiquitin carboxyl-terminal hydrolas	2e-06
d1v5ta_	90	d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus mu	2e-06
d1t0ya_	90	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	1e-05
d1wxva1	81	d.15.1.1 (A:7-87) Bag-family molecular chaperone r	1e-05
d1v86a_	95	d.15.1.1 (A:) hypothetical D7wsu128e protein {Mous	2e-05
d1v86a_	95	d.15.1.1 (A:) hypothetical D7wsu128e protein {Mous	0.004
d1se9a_	101	d.15.1.1 (A:) Hypothetical protein At3g01050 {Thal	6e-05
d1se9a_	101	d.15.1.1 (A:) Hypothetical protein At3g01050 {Thal	3e-04
d1v6ea_	95	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	2e-04
d1v6ea_	95	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	0.004
d2uyzb1	77	d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human	5e-04

>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 = 69.9 bits (171), Expect = 3e-18
 Identities = 41/73 (56%), Positives = 43/73 (58%), Gaps = 13/73 (17%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          MQIFVKT TGKTITLEVE SD I+N         G               EDG T +DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query: 84 IQKESTLHFVLRL 96
          IQKESTLH VLRL
Sbjct: 61 IQKESTLHLVLRL 73

>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 = 48.4 bits (115), Expect = 1e-09
 Identities = 26/40 (65%), Positives = 30/40 (75%), Gaps = 5/40 (12%)

Query: 1  MPLEQQRLVFA-----DKSLLADYNIQKESTLHLVARLRG 35
          +P +QQRL+FA     D   L+DYNIQKESTLHLV RLRG
Sbjct: 36 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG 75

>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 = 69.5 bits (170), Expect = 4e-18
 Identities = 26/73 (35%), Positives = 31/73 (42%), Gaps = 13/73 (17%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRG----SSSPAGNF---------EDGWTQADYN 83
          M I VKT TGK I +++E +D ID            P              D  T  DYN
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLIYAGKQLADDKTAKDYN 60

Query: 84 IQKESTLHFVLRL 96
          I+  S LH VL L
Sbjct: 61 IEGGSVLHLVLAL 73

>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 = 43.3 bits (102), Expect = 7e-08
 Identities = 18/38 (47%), Positives = 22/38 (57%), Gaps = 5/38 (13%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARL 33
          +P  QQRL++A K L       DYNI+  S LHLV  L
Sbjct: 36 IPPVQQRLIYAGKQLADDKTAKDYNIEGGSVLHLVLAL 73

>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 = 68.8 bits (168), Expect = 8e-18
 Identities = 14/73 (19%), Positives = 27/73 (36%), Gaps = 13/73 (17%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDN-------------ASRGSSSPAGNFEDGWTQADYN 83
          + I V+ + G++ T EV  +  + +                  +      ED     +Y 
Sbjct: 4  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 63

Query: 84 IQKESTLHFVLRL 96
          ++  ST+   LRL
Sbjct: 64 LKPLSTVFMNLRL 76

>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 = 39.5 bits (92), Expect = 2e-06
 Identities = 10/38 (26%), Positives = 17/38 (44%), Gaps = 5/38 (13%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARL 33
          +  +   L F  K L     L +Y ++  ST+ +  RL
Sbjct: 39 VQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRL 76

>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 = 66.9 bits (163), Expect = 7e-17
 Identities = 12/79 (15%), Positives = 21/79 (26%), Gaps = 13/79 (16%)

Query: 31 ARLRGRMQIFVKTSTGKTITLEVESSDMIDN-------------ASRGSSSPAGNFEDGW 77
          +     +Q+FVK   G +    +  +  I                 +         +D  
Sbjct: 2  SSGSSGIQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWL 61

Query: 78 TQADYNIQKESTLHFVLRL 96
              Y IQ   TL    + 
Sbjct: 62 GLGIYGIQDSDTLILSKKK 80

>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 = 13/40 (32%), Positives = 18/40 (45%), Gaps = 5/40 (12%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG 35
          +P +QQ+L F  + L     L  Y IQ   TL L  +   
Sbjct: 43 LPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKGS 82

>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 = 65.3 bits (159), Expect = 2e-16
 Identities = 14/73 (19%), Positives = 30/73 (41%), Gaps = 13/73 (17%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDN----ASRGSSSPAGNF---------EDGWTQADYN 83
          M +FV+ ++     +EV+S   I       ++    PA             +  T  + +
Sbjct: 3  MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVIFAGKELPNHLTVQNCD 62

Query: 84 IQKESTLHFVLRL 96
          ++++S +H V R 
Sbjct: 63 LEQQSIVHIVQRP 75

>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 = 50.3 bits (120), Expect = 2e-10
 Identities = 13/41 (31%), Positives = 26/41 (63%), Gaps = 5/41 (12%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR 36
          +P +Q R++FA K L     + + +++++S +H+V R R R
Sbjct: 38 VPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRRR 78

>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 = 63.4 bits (154), Expect = 1e-15
 Identities = 12/73 (16%), Positives = 25/73 (34%), Gaps = 13/73 (17%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDNAS-------------RGSSSPAGNFEDGWTQADYN 83
           Q+ ++ STGK + L V S+D + +               +          D     +  
Sbjct: 4  CQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKFEELK 63

Query: 84 IQKESTLHFVLRL 96
          I K+  +  ++  
Sbjct: 64 IPKDYVVQVIVSQ 76

>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 = 32.2 bits (73), Expect = 0.002
 Identities = 6/35 (17%), Positives = 13/35 (37%), Gaps = 5/35 (14%)

Query: 4  EQQRLVFADKSL-----LADYNIQKESTLHLVARL 33
            QR  F+ + L       +  I K+  + ++   
Sbjct: 42 GSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQ 76

>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 = 62.4 bits (151), Expect = 4e-15
 Identities = 10/75 (13%), Positives = 28/75 (37%), Gaps = 16/75 (21%)

Query: 37 MQIFVKTSTGKTITLEVESSD-------MIDNASRGSSSPAGNF---------EDGWTQA 80
          MQ+ +KT   +T  ++++  +        I++     + P              D     
Sbjct: 1  MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 60

Query: 81 DYNIQKESTLHFVLR 95
          +Y I +++ +  ++ 
Sbjct: 61 EYKIDEKNFVVVMVT 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 = 38.9 bits (90), Expect = 8e-06
 Identities = 9/36 (25%), Positives = 20/36 (55%), Gaps = 5/36 (13%)

Query: 2  PLEQQRLVFADKSL-----LADYNIQKESTLHLVAR 32
          P+  Q+L++A K L     L +Y I +++ + ++  
Sbjct: 40 PVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVT 75

>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 = 61.4 bits (149), Expect = 6e-15
 Identities = 17/76 (22%), Positives = 29/76 (38%), Gaps = 15/76 (19%)

Query: 37 MQIFVKTSTGK-TITLEVESSDM--------------IDNASRGSSSPAGNFEDGWTQAD 81
          M I V+T  G+ T T++  S                 ++   +         EDG T  D
Sbjct: 1  MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFD 60

Query: 82 YNIQKESTLHFVLRLS 97
          Y ++   T+  ++R S
Sbjct: 61 YEVRLNDTIQLLVRQS 76

>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 = 40.3 bits (94), Expect = 1e-06
 Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 5/38 (13%)

Query: 1  MPLEQQRLVF-----ADKSLLADYNIQKESTLHLVARL 33
          +    QRL +      D   L DY ++   T+ L+ R 
Sbjct: 38 VEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLLVRQ 75

>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 = 60.2 bits (146), Expect = 2e-14
 Identities = 13/72 (18%), Positives = 25/72 (34%), Gaps = 14/72 (19%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDN------------ASRGSSSPAGN-FEDGWTQADYN 83
          +++ VKT   +T T  V +   +              + +      G   +D     +YN
Sbjct: 1  LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYN 60

Query: 84 IQKESTLHFVLR 95
          +     +H V R
Sbjct: 61 VGG-KVIHLVER 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 = 33.7 bits (77), Expect = 4e-04
 Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 6/37 (16%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVAR 32
          +P E+QRL++  + L     L +YN+     +HLV R
Sbjct: 36 IPSEKQRLIYQGRVLQDDKKLQEYNVGG-KVIHLVER 71

>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 = 58.5 bits (141), Expect = 2e-13
 Identities = 13/96 (13%), Positives = 30/96 (31%), Gaps = 17/96 (17%)

Query: 17  ADYNIQKESTLHLVARLR----GRMQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAGN 72
           + ++    S   LV R        +++      GK + ++  + D I +  +  ++  G 
Sbjct: 5   SHHHHHHSSGASLVPRGSEGAATMIEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGT 64

Query: 73  FED-------------GWTQADYNIQKESTLHFVLR 95
             +               +  DY I     L    +
Sbjct: 65  RWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLELYYQ 100

>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 = 35.3 bits (81), Expect = 2e-04
 Identities = 7/34 (20%), Positives = 9/34 (26%), Gaps = 5/34 (14%)

Query: 4   EQQRLVFADKSL-----LADYNIQKESTLHLVAR 32
            +  L            L DY I     L L  +
Sbjct: 67  NKIVLKKWYTIFKDHVSLGDYEIHDGMNLELYYQ 100

>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 = 56.8 bits (137), Expect = 5e-13
 Identities = 11/75 (14%), Positives = 20/75 (26%), Gaps = 15/75 (20%)

Query: 38 QIFVKTSTGKTITLEVESSDMIDNASRGSS---------------SPAGNFEDGWTQADY 82
           + VK   G    + + SS  +       +                     +D    A  
Sbjct: 2  DLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQ 61

Query: 83 NIQKESTLHFVLRLS 97
           +   ST+  V+  S
Sbjct: 62 GLGPGSTVLLVVDKS 76

>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 = 35.3 bits (81), Expect = 1e-04
 Identities = 11/36 (30%), Positives = 14/36 (38%), Gaps = 7/36 (19%)

Query: 4  EQQRLVFA-------DKSLLADYNIQKESTLHLVAR 32
           QQRL          D+  LA   +   ST+ LV  
Sbjct: 39 FQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVD 74

>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 = 54.5 bits (131), Expect = 3e-12
 Identities = 11/74 (14%), Positives = 25/74 (33%), Gaps = 16/74 (21%)

Query: 37 MQIFVKTSTGKTITLEVESSD-------MIDNASRGSSSPAGNF---------EDGWTQA 80
          + I +KT   +T  + +E  +        I+      + P              D     
Sbjct: 3  VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIR 62

Query: 81 DYNIQKESTLHFVL 94
          DY I +++ +  ++
Sbjct: 63 DYRIDEKNFVVVMV 76

>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 = 35.6 bits (82), Expect = 9e-05
 Identities = 9/34 (26%), Positives = 20/34 (58%), Gaps = 5/34 (14%)

Query: 2  PLEQQRLVFADKSL-----LADYNIQKESTLHLV 30
          P+  Q+L++A K L     + DY I +++ + ++
Sbjct: 42 PVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVM 75

>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 = 53.8 bits (129), Expect = 6e-12
 Identities = 17/74 (22%), Positives = 28/74 (37%), Gaps = 15/74 (20%)

Query: 37 MQIFVKTSTG-KTITLE-VESSDMIDN-------------ASRGSSSPAGNFEDGWTQAD 81
          M I V+T  G KT T+E V     I+                +         E+G+T  D
Sbjct: 1  MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFD 60

Query: 82 YNIQKESTLHFVLR 95
          Y++     +  ++R
Sbjct: 61 YDVGLNDIIQLLVR 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 = 37.2 bits (86), Expect = 2e-05
 Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 5/37 (13%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVAR 32
          +  E QRL +  K L     L DY++     + L+ R
Sbjct: 38 VRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVR 74

>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 = 52.2 bits (125), Expect = 4e-11
 Identities = 10/65 (15%), Positives = 22/65 (33%), Gaps = 13/65 (20%)

Query: 45 TGKTITLEVESSDMIDN----ASRGSSSPA---------GNFEDGWTQADYNIQKESTLH 91
           G+ +   +  +D +          +  PA            +D  + A YN+   + +H
Sbjct: 20 NGQVLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMANGAVIH 79

Query: 92 FVLRL 96
            L+ 
Sbjct: 80 LALKE 84

>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 = 51.0 bits (122), Expect = 1e-10
 Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 5/40 (12%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG 35
          MP  +Q+L +    +     LA YN+   + +HL  + RG
Sbjct: 47 MPAGKQKLQYEGIFIKDSNSLAYYNMANGAVIHLALKERG 86

>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 = 51.6 bits (123), Expect = 5e-11
 Identities = 9/68 (13%), Positives = 24/68 (35%), Gaps = 13/68 (19%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSS-------------PAGNFEDGWTQADYN 83
          +++ V    GK + ++  + D + +  +  S                   +D  +  DY 
Sbjct: 2  IEVVVNDRLGKKVRVKCLAEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHISLEDYE 61

Query: 84 IQKESTLH 91
          +  ++ L 
Sbjct: 62 VHDQTNLE 69

>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 = 50.6 bits (121), Expect = 2e-10
 Identities = 13/81 (16%), Positives = 22/81 (27%), Gaps = 21/81 (25%)

Query: 38 QIFVKTSTGK-TITLEVESSDMIDNASRG----SSSPAGNF---------EDGWTQADYN 83
           +F+     K TI  + + S  +    R        P             +DG T  +  
Sbjct: 1  DVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECG 60

Query: 84 I-------QKESTLHFVLRLS 97
                  Q  +T+    R  
Sbjct: 61 FTSQTARPQAPATVGLAFRAD 81

>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 = 39.8 bits (93), Expect = 3e-06
 Identities = 11/54 (20%), Positives = 18/54 (33%), Gaps = 12/54 (22%)

Query: 2  PLEQQRLVFADKSL-----LADYNI-------QKESTLHLVARLRGRMQIFVKT 43
          P ++QRL   D+ L     L +          Q  +T+ L  R     +     
Sbjct: 37 PPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALCIE 90

>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 = 49.2 bits (117), Expect = 9e-10
 Identities = 11/72 (15%), Positives = 21/72 (29%), Gaps = 14/72 (19%)

Query: 37  MQIFVKTSTGKTITLEVESSDMIDN-------------ASRGSSSPAGNFEDGWTQADYN 83
           +++ VKT   K     V  +  +                           +D  T   + 
Sbjct: 33  IKVTVKTPKEK-EEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLIQHG 91

Query: 84  IQKESTLHFVLR 95
           I    T+H V++
Sbjct: 92  IHDGLTVHLVIK 103

>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 = 33.0 bits (75), Expect = 0.001
 Identities = 7/23 (30%), Positives = 11/23 (47%)

Query: 10  FADKSLLADYNIQKESTLHLVAR 32
             D+  L  + I    T+HLV +
Sbjct: 81  LKDQDTLIQHGIHDGLTVHLVIK 103

>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 = 48.7 bits (116), Expect = 1e-09
 Identities = 7/70 (10%), Positives = 15/70 (21%), Gaps = 11/70 (15%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDN-ASRGSSSPAG----------NFEDGWTQADYNIQ 85
          + + +K              D +    S+                   +   T +  NI 
Sbjct: 8  INVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQESQMKLIYQGRLLQDPARTLSSLNIT 67

Query: 86 KESTLHFVLR 95
              +H    
Sbjct: 68 NNCVIHCHRS 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 = 37.6 bits (87), Expect = 2e-05
 Identities = 7/41 (17%), Positives = 12/41 (29%), Gaps = 6/41 (14%)

Query: 1  MPLEQQRLVFA------DKSLLADYNIQKESTLHLVARLRG 35
              Q +L++           L+  NI     +H      G
Sbjct: 40 GQESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRSPPG 80

>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 = 47.8 bits (114), Expect = 1e-09
 Identities = 11/72 (15%), Positives = 20/72 (27%), Gaps = 14/72 (19%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDN-----ASRGSSSPAGN--------FEDGWTQADYN 83
          + I +K+       + V     +               A           +D  T   Y+
Sbjct: 2  LNIHIKSG-QDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYH 60

Query: 84 IQKESTLHFVLR 95
          IQ   ++H V  
Sbjct: 61 IQDGHSVHLVKS 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 = 37.4 bits (87), Expect = 2e-05
 Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 5/36 (13%)

Query: 2  PLEQQRLVFADKSL-----LADYNIQKESTLHLVAR 32
          P+  QRL+++ K L     +  Y+IQ   ++HLV  
Sbjct: 37 PVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS 72

>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 = 48.5 bits (115), Expect = 1e-09
 Identities = 11/79 (13%), Positives = 24/79 (30%), Gaps = 18/79 (22%)

Query: 37 MQIFV----KTSTGKTITLEVESSDMIDNASRGSSSPAGNF--------------EDGWT 78
          M I V    +  T  T +L+V     + N        +G                +D  +
Sbjct: 8  MLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLTDDHCS 67

Query: 79 QADYNIQKESTLHFVLRLS 97
             Y ++    +  + + +
Sbjct: 68 LGSYGLKDGDMVVLLQKDN 86

>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 = 43.1 bits (101), Expect = 2e-07
 Identities = 9/52 (17%), Positives = 25/52 (48%), Gaps = 6/52 (11%)

Query: 1  MPLEQQRLVFADKSL------LADYNIQKESTLHLVARLRGRMQIFVKTSTG 46
          +P E+ ++V+ ++ L      L  Y ++    + L+ +    ++   +T +G
Sbjct: 47 VPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVLLQKDNVGLRTPGRTPSG 98

>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 = 48.5 bits (115), Expect = 1e-09
 Identities = 12/90 (13%), Positives = 24/90 (26%), Gaps = 29/90 (32%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDN-------------------ASRGSSSPAGNF---- 73
          M + V    G+ + + V  +  + +                        S     +    
Sbjct: 8  MTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTS 67

Query: 74 ------EDGWTQADYNIQKESTLHFVLRLS 97
                ED     DY I+    + F+ +L 
Sbjct: 68 AGEKLTEDRKKLRDYGIRNRDEVSFIKKLG 97

>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 = 39.7 bits (92), Expect = 4e-06
 Identities = 8/38 (21%), Positives = 14/38 (36%), Gaps = 6/38 (15%)

Query: 5  QQRLVFADKSL------LADYNIQKESTLHLVARLRGR 36
             L  A + L      L DY I+    +  + +L  +
Sbjct: 62 TYHLTSAGEKLTEDRKKLRDYGIRNRDEVSFIKKLGQK 99

>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 = 46.9 bits (111), Expect = 4e-09
 Identities = 12/74 (16%), Positives = 23/74 (31%), Gaps = 14/74 (18%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQADYN 83
          +++ VKT   K     V  +  I       S                   +D  + A   
Sbjct: 8  IKVTVKTPKDKE-DFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCG 66

Query: 84 IQKESTLHFVLRLS 97
          ++   T+H V++  
Sbjct: 67 VRDGLTVHLVIKRQ 80

>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 = 33.4 bits (76), Expect = 6e-04
 Identities = 10/41 (24%), Positives = 17/41 (41%), Gaps = 5/41 (12%)

Query: 1  MPLEQQRL-----VFADKSLLADYNIQKESTLHLVARLRGR 36
             +Q  L     +  D   LA   ++   T+HLV + + R
Sbjct: 42 AHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHR 82

>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 = 46.5 bits (110), Expect = 6e-09
 Identities = 11/74 (14%), Positives = 21/74 (28%), Gaps = 14/74 (18%)

Query: 35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAG-------------NFEDGWTQAD 81
            +++ VKT         +  +  +    +  S                    D    + 
Sbjct: 9  RIIRVSVKTPQDCH-EFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQDILSQ 67

Query: 82 YNIQKESTLHFVLR 95
            I   ST+H V+R
Sbjct: 68 RGILDGSTVHVVVR 81

>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 = 34.6 bits (79), Expect = 2e-04
 Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 5/37 (13%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVAR 32
             ++  L+F  K L     L+   I   ST+H+V R
Sbjct: 45 CNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVR 81

>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 = 44.5 bits (105), Expect = 4e-08
 Identities = 10/34 (29%), Positives = 17/34 (50%), Gaps = 5/34 (14%)

Query: 4  EQQRLVFADKSL-----LADYNIQKESTLHLVAR 32
          E   L++  + L     L  Y IQ  ST+H++ +
Sbjct: 59 ELIDLIYCGRKLKDDQTLDFYGIQPGSTVHVLRK 92

>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 = 37.1 bits (86), Expect = 3e-05
 Identities = 18/90 (20%), Positives = 28/90 (31%), Gaps = 18/90 (20%)

Query: 24 ESTLHLVARLRGRMQI------FVKTSTGKTITLEVESSD---MIDNASRGSSSP----- 69
           S  HL  +L  +           +T  G+        S    +I    + S        
Sbjct: 3  LSDWHLAVKLADQPLAPKSILQLPETELGEYSLGGYSISFLKQLIAGKLQESVPDPELID 62

Query: 70 ---AGN-FEDGWTQADYNIQKESTLHFVLR 95
              G   +D  T   Y IQ  ST+H + +
Sbjct: 63 LIYCGRKLKDDQTLDFYGIQPGSTVHVLRK 92

>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 = 44.6 bits (105), Expect = 5e-08
 Identities = 11/83 (13%), Positives = 18/83 (21%), Gaps = 21/83 (25%)

Query: 35 GRMQIFVKTSTGKTITLEVESSDMIDN-------------ASRGSSSP-------AGN-F 73
            + + +   +GKT       +D   +                  SSP        G   
Sbjct: 15 DMINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFL 74

Query: 74 EDGWTQADYNIQKESTLHFVLRL 96
              T     +    T    L  
Sbjct: 75 HGNVTLGALKLPFGKTTVMHLVA 97

>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 = 36.9 bits (85), Expect = 6e-05
 Identities = 5/42 (11%), Positives = 10/42 (23%), Gaps = 5/42 (11%)

Query: 1   MPLEQQRLVFA-----DKSLLADYNIQKESTLHLVARLRGRM 37
                 RL++          L    +    T  +    R  +
Sbjct: 60  SSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLVARETL 101

>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 = 43.8 bits (103), Expect = 8e-08
 Identities = 5/74 (6%), Positives = 16/74 (21%), Gaps = 15/74 (20%)

Query: 37 MQIFV--KTSTGKTITLEVESSDMIDN----ASRGSSSPAGNF---------EDGWTQAD 81
          +++F+  +    +   LE              +                   + G T  +
Sbjct: 18 IEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFGLQENYIKIVINKKQLQLGKTLEE 77

Query: 82 YNIQKESTLHFVLR 95
            +        +  
Sbjct: 78 QGVAHNVKAMVLEL 91

>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 = 41.8 bits (98), Expect = 5e-07
 Identities = 13/41 (31%), Positives = 20/41 (48%), Gaps = 7/41 (17%)

Query: 2  PLEQQRLVFADKSL-----LADYNIQKES--TLHLVARLRG 35
            E QRL+++ K L     L D   ++E    LHLV  ++ 
Sbjct: 48 RPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVCNVKS 88

>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 = 41.4 bits (97), Expect = 7e-07
 Identities = 9/80 (11%), Positives = 21/80 (26%), Gaps = 19/80 (23%)

Query: 37 MQIFVKTSTGK--TITLEVESSDMIDN------ASRGSSSPAGNF---------EDGWTQ 79
          + + VK+   +   + L  +    + +                +           D    
Sbjct: 8  VTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCL 67

Query: 80 ADYNIQKES--TLHFVLRLS 97
           D   ++E    LH V  + 
Sbjct: 68 RDLLPKQEKRHVLHLVCNVK 87

>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 = 42.3 bits (99), Expect = 5e-07
 Identities = 14/76 (18%), Positives = 29/76 (38%), Gaps = 15/76 (19%)

Query: 36  RMQIFVKT-STGKTITLEVES-SDMIDN-------------ASRGSSSPAGNFEDGWTQA 80
            +++     + G+ + + V+S S+ + +               +  S  AG  +D  + A
Sbjct: 29  TIRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSLA 88

Query: 81  DYNIQKESTLHFVLRL 96
            YN+     L   LR 
Sbjct: 89  HYNVGAGEILTLSLRE 104

>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 = 39.6 bits (92), Expect = 4e-06
 Identities = 12/40 (30%), Positives = 16/40 (40%), Gaps = 5/40 (12%)

Query: 1   MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG 35
           +P  +Q+L      L     LA YN+     L L  R R 
Sbjct: 67  IPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLRERS 106

>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 = 40.6 bits (95), Expect = 9e-07
 Identities = 3/40 (7%), Positives = 12/40 (30%), Gaps = 5/40 (12%)

Query: 1  MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG 35
            ++  R ++    +       D +++    +       G
Sbjct: 39 KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIG 78

>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 = 32.5 bits (74), Expect = 0.001
 Identities = 2/23 (8%), Positives = 7/23 (30%)

Query: 74 EDGWTQADYNIQKESTLHFVLRL 96
          +   T  D +++    +      
Sbjct: 54 QADQTPEDLDMEDNDIIEAHREQ 76

>d1wgga_ d.15.1.1 (A:) Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (Mus musculus) [TaxId: 10090]} Length = 96

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]

 Score = 40.4 bits (94), Expect = 2e-06
 Identities = 6/69 (8%), Positives = 17/69 (24%), Gaps = 12/69 (17%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDNASRGSSSPAGNFEDGW------------TQADYNI 84
            + VK    K   +E+ + +          +  G                     +  +
Sbjct: 8  YSVTVKWGKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLKDDDWGNIKM 67

Query: 85 QKESTLHFV 93
          +   T+  +
Sbjct: 68 KNGMTVLMM 76

>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 = 40.0 bits (93), Expect = 2e-06
 Identities = 6/75 (8%), Positives = 18/75 (24%), Gaps = 16/75 (21%)

Query: 37 MQIFVKTSTGKTITLEVESSDMIDN-----ASRGSSSP-----------AGNFEDGWTQA 80
          + I VK    +     +   D + +      +     P               E+     
Sbjct: 8  LPIIVKWGGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLG 67

Query: 81 DYNIQKESTLHFVLR 95
             ++  + +  +  
Sbjct: 68 ALKLKPNTKIMMMGT 82

>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 = 38.3 bits (89), Expect = 1e-05
 Identities = 7/48 (14%), Positives = 13/48 (27%), Gaps = 12/48 (25%)

Query: 1  MPLEQQRLVFADK------------SLLADYNIQKESTLHLVARLRGR 36
            ++  R+   D               L D  ++    +H V    G 
Sbjct: 41 TTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHAVDVTGGN 88

>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 = 37.9 bits (88), Expect = 1e-05
 Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 6/38 (15%)

Query: 1  MPLEQQRLVFADKSL------LADYNIQKESTLHLVAR 32
          +P   Q+L+F  KSL      L+   IQ    + L+ +
Sbjct: 41 VPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVMLIGK 78

>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 = 37.6 bits (87), Expect = 2e-05
 Identities = 6/74 (8%), Positives = 17/74 (22%), Gaps = 13/74 (17%)

Query: 35 GRMQIFVKTST-GKTITLEVESSDMIDN------------ASRGSSSPAGNFEDGWTQAD 81
          G+  + +K         ++V                     +       G   +  T  +
Sbjct: 14 GKELVDLKIIWNKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGLVPEDKTLRE 73

Query: 82 YNIQKESTLHFVLR 95
            +   + +  V  
Sbjct: 74 IKVTSGAKIMVVGS 87

>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 = 31.5 bits (71), Expect = 0.004
 Identities = 3/36 (8%), Positives = 13/36 (36%), Gaps = 4/36 (11%)

Query: 4  EQQRLVFA----DKSLLADYNIQKESTLHLVARLRG 35
            Q++++     +   L +  +   + + +V     
Sbjct: 55 AMQKVMYKGLVPEDKTLREIKVTSGAKIMVVGSTIS 90

>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 = 36.4 bits (84), Expect = 6e-05
 Identities = 8/40 (20%), Positives = 18/40 (45%), Gaps = 11/40 (27%)

Query: 4  EQQRLVFADKSL-----LADYNI------QKESTLHLVAR 32
          ++ +L+ A K L     + 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 = 34.9 bits (80), Expect = 3e-04
 Identities = 10/88 (11%), Positives = 22/88 (25%), Gaps = 27/88 (30%)

Query: 37 MQIFVKTSTGKTIT-LEVESSDMIDN-----ASRGSSSPAGN---------------FED 75
          ++I  + + G  I       +  +        S                         E+
Sbjct: 8  LEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLEN 67

Query: 76 GWTQADYNI------QKESTLHFVLRLS 97
            T  DY           +T+H +++  
Sbjct: 68 SKTVKDYRSPVSNLAGAVTTMHVIIQAP 95

>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 = 34.9 bits (80), Expect = 2e-04
 Identities = 6/43 (13%), Positives = 10/43 (23%), Gaps = 12/43 (27%)

Query: 2  PLEQQRLVFADKS------------LLADYNIQKESTLHLVAR 32
          P     L                  LL  Y +     +H++  
Sbjct: 45 PASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIHVIDH 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 = 31.4 bits (71), Expect = 0.004
 Identities = 6/80 (7%), Positives = 16/80 (20%), Gaps = 21/80 (26%)

Query: 37 MQIFVKTS-TGKTITLEVESSDMIDN--------------------ASRGSSSPAGNFED 75
          + +F+ +S            S  I                              +   ++
Sbjct: 8  VMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVGSPASCMELELYGADDKFYSKLDQE 67

Query: 76 GWTQADYNIQKESTLHFVLR 95
                Y +     +H +  
Sbjct: 68 DALLGSYPVDDGCRIHVIDH 87

>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 = 33.6 bits (77), Expect = 5e-04
 Identities = 8/74 (10%), Positives = 22/74 (29%), Gaps = 13/74 (17%)

Query: 36 RMQIFVKTSTGKTITLEVESSDMIDN------ASRGSSSPAGNF-------EDGWTQADY 82
           +++ V       I  +V+ +  +          +G    +  F        D  T  + 
Sbjct: 2  YIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKEL 61

Query: 83 NIQKESTLHFVLRL 96
           +++E  +      
Sbjct: 62 GMEEEDVIEVYQEQ 75

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	97
d1bt0a_	73	Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxI	99.86
d2zeqa1	78	Ubiquitin-like domain of parkin {Mouse (Mus muscul	99.86
d1z2ma2	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.85
d1ogwa_	76	Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}	99.85
d1wh3a_	87	2'-5'-oligoadenylate synthetase-like protein, OASL	99.82
d2faza1	76	Ubiquitin-like PHD and RING finger domain-containi	99.8
d1ttna1	80	Dendritic cell-derived ubiquitin-like protein {Hum	99.8
d1wy8a1	76	Ubiquitin-like PHD and RING finger domain-containi	99.77
d1uela_	95	Ubiquitin-like domain of Rad23 homolog B (Hhr23B)	99.77
d1wx9a1	73	Large proline-rich protein BAT3 {Human (Homo sapie	99.77
d1uh6a_	100	Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculu	99.75
d1m94a_	73	Ubiquitin-like modifier protein hub1 {Baker's yeas	99.75
d1oqya4	77	Ubiquitin-like domain of Rad23 homolog A (Hhr23a)	99.74
d1z2ma1	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.73
d1wiaa_	95	Ubiquitin-like protein bab25500 (2010008E23Rik) {M	99.71
d1yqba1	84	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	99.71
d1zkha1	86	Splicing factor 3 subunit 1, C-terminal domain {Hu	99.71
d2bwfa1	73	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.71
d1v2ya_	105	Ubiquitin-like protein 3300001g02rik {Mouse (Mus m	99.7
d1j8ca_	103	Ubiquitin-like N-terminal domain of PLIC-2 {Human	99.67
d1wx8a1	83	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	99.66
d1we6a_	111	Splicing factor 3 subunit 1, C-terminal domain {Th	99.65
d1se9a_	101	Hypothetical protein At3g01050 {Thale cress (Arabi	99.64
d1wgha_	116	Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculu	99.62
d1v5oa_	102	1700011n24rik protein {Mouse (Mus musculus) [TaxId	99.59
d1wjua_	100	NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens	99.53
d1wgda_	93	Homocysteine-responsive endoplasmic reticulum-resi	99.5
d1wgga_	96	Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (M	99.49
d2c9wb1	103	Elongin B {Human (Homo sapiens) [TaxId: 9606]}	99.44
d1v5ta_	90	8430435i17rik protein {Mouse (Mus musculus) [TaxId	99.4
d1v86a_	95	hypothetical D7wsu128e protein {Mouse (Mus musculu	99.38
d1x1ma1	94	Ubiquitin-like protein 7 {Mouse (Mus musculus) [Ta	99.38
d1wxva1	81	Bag-family molecular chaperone regulator-1 {Human	99.33
d2zeqa1	78	Ubiquitin-like domain of parkin {Mouse (Mus muscul	99.31
d1euvb_	79	SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomy	99.24
d1bt0a_	73	Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxI	99.24
d1z2ma2	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.23
d2faza1	76	Ubiquitin-like PHD and RING finger domain-containi	99.23
d1ogwa_	76	Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}	99.22
d1v6ea_	95	Ubiquitin-like domain of tubulin folding cofactor	99.2
d1wh3a_	87	2'-5'-oligoadenylate synthetase-like protein, OASL	99.18
d1wy8a1	76	Ubiquitin-like PHD and RING finger domain-containi	99.17
d2bwfa1	73	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.15
d1we6a_	111	Splicing factor 3 subunit 1, C-terminal domain {Th	99.14
d1ttna1	80	Dendritic cell-derived ubiquitin-like protein {Hum	99.14
d1zkha1	86	Splicing factor 3 subunit 1, C-terminal domain {Hu	99.12
d2uyzb1	77	SUMO-1 (smt3 homologue) {Human (Homo sapiens) [Tax	99.11
d1yqba1	84	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	99.09
d1z2ma1	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.07
d1x1ma1	94	Ubiquitin-like protein 7 {Mouse (Mus musculus) [Ta	99.04
d1uela_	95	Ubiquitin-like domain of Rad23 homolog B (Hhr23B)	99.03
d1wjna_	97	Tubulin-folding protein TbcE {Mouse (Mus musculus)	99.01
d1wx9a1	73	Large proline-rich protein BAT3 {Human (Homo sapie	99.0
d1oqya4	77	Ubiquitin-like domain of Rad23 homolog A (Hhr23a)	99.0
d1wx8a1	83	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	98.99
d1m94a_	73	Ubiquitin-like modifier protein hub1 {Baker's yeas	98.96
d1se9a_	101	Hypothetical protein At3g01050 {Thale cress (Arabi	98.96
d1wiaa_	95	Ubiquitin-like protein bab25500 (2010008E23Rik) {M	98.8
d1v5oa_	102	1700011n24rik protein {Mouse (Mus musculus) [TaxId	98.78
d1wgha_	116	Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculu	98.77
d1wxva1	81	Bag-family molecular chaperone regulator-1 {Human	98.76
d1t0ya_	90	Ubiquitin-like domain of tubulin folding cofactor	98.72
d1wgga_	96	Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (M	98.68
d1wjua_	100	NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens	98.61
d2c9wb1	103	Elongin B {Human (Homo sapiens) [TaxId: 9606]}	98.56
d1v2ya_	105	Ubiquitin-like protein 3300001g02rik {Mouse (Mus m	98.56
d1wgda_	93	Homocysteine-responsive endoplasmic reticulum-resi	98.55
d1euvb_	79	SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomy	98.55
d1v5ta_	90	8430435i17rik protein {Mouse (Mus musculus) [TaxId	98.46
d1v86a_	95	hypothetical D7wsu128e protein {Mouse (Mus musculu	98.37
d1v6ea_	95	Ubiquitin-like domain of tubulin folding cofactor	98.36
d1wjna_	97	Tubulin-folding protein TbcE {Mouse (Mus musculus)	98.28
d1wm3a_	72	SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}	98.2
d1t0ya_	90	Ubiquitin-like domain of tubulin folding cofactor	98.11
d1wf9a1	94	NPL4-like protein 1 {Thale cress (Arabidopsis thal	97.97
d2uyzb1	77	SUMO-1 (smt3 homologue) {Human (Homo sapiens) [Tax	97.88
d1h8ca_	82	Fas-associated factor 1, Faf1 {Human (Homo sapiens	97.36
d2cr5a1	96	UBX domain-containing protein 6 (Reproduction 8) {	97.24
d1i42a_	89	p47 {Rat (Rattus norvegicus) [TaxId: 10116]}	97.17
d2al3a1	76	Tether containing UBX domain for GLUT4 (Tug) {Mous	96.91
d1wj4a_	124	Hypothetical protein KIAA0794 {Human (Homo sapiens	96.81
d1uh6a_	100	Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculu	95.31
d1wf9a1	94	NPL4-like protein 1 {Thale cress (Arabidopsis thal	95.17
d1j8ca_	103	Ubiquitin-like N-terminal domain of PLIC-2 {Human	95.15
d1ef1a3	84	Moesin {Human (Homo sapiens) [TaxId: 9606]}	93.36
d1wm3a_	72	SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}	93.12
d1vjka_	88	Molybdopterin synthase subunit MoaD {Pyrococcus fu	91.21
d2incc1	83	Toluene, o-xylene monooxygenase oxygenase subunit	90.46
d1h4ra3	84	Merlin {Human (Homo sapiens) [TaxId: 9606]}	88.65
d1gg3a3	81	Erythroid membrane protein 4.1R {Human (Homo sapie	87.27

>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=99.86  E-value=2.3e-22  Score=114.82  Aligned_cols=60  Identities=42%  Similarity=0.558  Sum_probs=58.9

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEee
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      |+|+||+++|++++++|++++||+++|++|+             |+|++|+|+.||++|||++|++||+++||
T Consensus         1 M~I~Vk~~~G~~~~l~V~~~~tV~~lK~~i~~~~gi~~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lvlrL   73 (73)
T d1bt0a_           1 MLIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLIYAGKQLADDKTAKDYNIEGGSVLHLVLAL   73 (73)
T ss_dssp             CEEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhCCChHHEEEEECCeEcCCCCcHHHcCCCCCCEEEEEeeC
Confidence            8999999999999999999999999999999             99999999999999999999999999996

>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=99.86  E-value=3.5e-22  Score=115.54  Aligned_cols=62  Identities=19%  Similarity=0.281  Sum_probs=60.5

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      +|+||||+.+|++++++|++++||+++|++|+             |+|++|+|+.+|++|+|+++++||+++|+|
T Consensus         2 ~M~I~Vk~~~g~t~~l~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lv~R~r   76 (78)
T d2zeqa1           2 GMIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPR   76 (78)
T ss_dssp             CEEEEEESSSSSCEEEEECTTCBHHHHHHHHHHHHTCCGGGEEEEETTEEECTTCBGGGSSCCTTCEEEEEESSC
T ss_pred             ceEEEEEcCCCCEEEEEEcccccHHHHHHHHHHHHCcChhHeEEEEeeeEcCCCCCHHHcCCCCCCEEEEEeccC
Confidence            59999999999999999999999999999998             999999999999999999999999999986

>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=99.85  E-value=9e-22  Score=113.04  Aligned_cols=62  Identities=24%  Similarity=0.384  Sum_probs=60.2

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEee
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      ..|+|+||+.+|++++++|++++||+++|++|+             |+|++|+|+.||++|||++|++||+++||
T Consensus         2 ~~~qi~Vk~~~G~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~qrL~~~gk~L~d~~tL~~y~I~~~sti~l~lRL   76 (76)
T d1z2ma2           2 EPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRL   76 (76)
T ss_dssp             CCEEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECC
T ss_pred             CCEEEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHhcCChhHeEEEECCeECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            469999999999999999999999999999999             99999999999999999999999999996

>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=99.85  E-value=5.8e-22  Score=113.92  Aligned_cols=61  Identities=66%  Similarity=0.832  Sum_probs=59.8

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      |+|+||+++|++++++|++++||++||++|+             |+|++|+|+.||++|||++|++|+|++|+|
T Consensus         1 MqI~Vk~l~G~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~qrL~~~Gk~L~d~~tL~~y~i~~~s~I~L~~rlr   74 (76)
T d1ogwa_           1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   74 (76)
T ss_dssp             CEEEEEETTSCEEEEECCTTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECTT
T ss_pred             CEEEEEcCCCCEEEEEECCCCcHHHHHHhhhhhcCCChHHEEeEECCeEcCCCCCHHHcCCCCCCEEEEEEecC
Confidence            8999999999999999999999999999999             999999999999999999999999999986

>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=99.82  E-value=4.8e-21  Score=112.64  Aligned_cols=64  Identities=19%  Similarity=0.246  Sum_probs=61.3

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      ...|+|+||+++|++++++|++++||.+||++|+             |+|++|+|+++|++|+|+++++|||+.|++
T Consensus         5 s~~mqI~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~~tL~~y~I~~~stl~l~~r~~   81 (87)
T d1wh3a_           5 SSGIQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKG   81 (87)
T ss_dssp             SSSEEEEEEETTTEEEEEEECSSSBHHHHHHHHHHHTCCCTTTEEEEETTEECCSSSBHHHHTCCTTEEEEEEECSC
T ss_pred             CCcEEEEEECCCCCEEEEEECCcCcHHHHHHHHHHHHCcChHHeEEEeeceEcCCCCcHHHcCCCCCCEEEEEecCC
Confidence            4679999999999999999999999999999999             999999999999999999999999999864

>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=99.80  E-value=3.5e-20  Score=106.51  Aligned_cols=60  Identities=27%  Similarity=0.426  Sum_probs=57.4

Q ss_pred             eeeEEECCCCC-EEEEe-ecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEee
Q 042212           37 MQIFVKTSTGK-TITLE-VESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        37 m~i~vk~~~g~-~~~l~-v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      |+|+||+++|+ +++++ +++++||+++|++|+             |+|++|+|+.+|++|||++|++||+++|+
T Consensus         1 M~I~Vktl~Gk~t~~l~~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~y~I~~~sti~lv~r~   75 (76)
T d2faza1           1 MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLLVRQ   75 (76)
T ss_dssp             EEEEEEETTSSCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTTTTTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCcEEEEecCCCCCCHHHHHHHHHHHHCcChHHeEEEEeeEeccCCCcHHHcCCCCCCEEEEEEEc
Confidence            89999999996 88885 899999999999999             99999999999999999999999999996

>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=99.80  E-value=2e-20  Score=108.37  Aligned_cols=62  Identities=21%  Similarity=0.262  Sum_probs=59.6

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEee
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      .+|+|+||+.+|++++++|++++||+++|++|+             |+|++|+|++||++|||++|++|||+++.
T Consensus         2 ~e~qi~Vk~~~G~~~~l~V~~~~tV~~lK~~I~~~~~ip~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lvi~~   76 (80)
T d1ttna1           2 YECQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQ   76 (80)
T ss_dssp             CSEEEEEEETTTEEEEEEECTTSHHHHHHHHHHHTTCCCSTTCEEEETTEECCTTSHHHHCCCSSSCEEEEECCC
T ss_pred             CeEEEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCcccEEEEECceEcCCCCcHHHcCCCCCCEEEEEecC
Confidence            469999999999999999999999999999999             99999999999999999999999999874

>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=99.77  E-value=1.6e-19  Score=103.72  Aligned_cols=60  Identities=27%  Similarity=0.417  Sum_probs=57.0

Q ss_pred             eeeEEECCCC-CEEEE-eecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEee
Q 042212           37 MQIFVKTSTG-KTITL-EVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        37 m~i~vk~~~g-~~~~l-~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      |+|+||+++| +++++ +|++++||++||++|+             |+|++|+|+.||++|||++|++||+++|.
T Consensus         1 M~I~Vk~l~G~~t~~~~~v~~~~TV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~~tL~~y~I~~~s~i~lv~rp   75 (76)
T d1wy8a1           1 MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVRP   75 (76)
T ss_dssp             EEEEEEETTCSCEEEEEEECTTCBHHHHHHHHHHHSCCCTTTEEEEETTEECCSSSBHHHHTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCceEEEeccCCCChHHHHHHHHHHHHCCCchhcEEEEEeeEecCCCCHHHcCCCCCCEEEEEEcc
Confidence            8999999999 57887 6999999999999999             99999999999999999999999999985

>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=99.77  E-value=2.1e-19  Score=106.95  Aligned_cols=59  Identities=14%  Similarity=0.281  Sum_probs=57.2

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc----------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS----------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~----------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      |+|+||+++|++++++|++++||.++|++|+                |+|+.|+|+.+|++|||++|++|+++++
T Consensus         1 M~I~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~~~~i~~~~qrLi~~Gk~L~d~~tL~~y~I~~~s~i~lv~~   75 (95)
T d1uela_           1 MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVT   75 (95)
T ss_dssp             CEEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEETTEECCTTSBGGGGTCCSSSEEEEEES
T ss_pred             CEEEEEeCCCCEEEEEECCCccHHHHHHHHHhhhcccCCCccceEEEECCeEccCCCcHHHcCCCCCCEEEEEEC
Confidence            8999999999999999999999999999986                9999999999999999999999999886

>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=99.77  E-value=5.7e-20  Score=104.80  Aligned_cols=59  Identities=20%  Similarity=0.277  Sum_probs=56.5

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEee
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      |+|+||+++|++++++|++++||+++|++|+             |+|++|+|+++|++|+| +++++||++|.
T Consensus         1 m~I~Vk~~~g~~~~l~V~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~~tL~dy~i-~~~ti~lv~r~   72 (73)
T d1wx9a1           1 LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVIHLVERA   72 (73)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHCCCTTTCCCEETTEECCSSSBHHHHTC-TTEEEBCCCSS
T ss_pred             CEEEEEcCCCCEEEEEECCCChHHHHHHHHHHHhCCChHHEEEEECCeEccCCCCHHHhCC-CCCEEEEEecC
Confidence            8999999999999999999999999999999             99999999999999999 58999999875

>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=99.75  E-value=5.5e-19  Score=106.25  Aligned_cols=79  Identities=18%  Similarity=0.255  Sum_probs=68.9

Q ss_pred             ccccccCCCcceeeeeecC----CeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcc
Q 042212           17 ADYNIQKESTLHLVARLRG----RMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQ   79 (97)
Q Consensus        17 ~~y~i~~~s~i~l~~~~~~----~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL   79 (97)
                      ++|.....|.-..+-+...    .++|+|++..|+++.++|+|++||.+||++|+             |+|++|+|+.+|
T Consensus         5 ~~~~~~~ss~~~~~p~~~~~~~~~i~V~V~~~~Gk~~~v~V~p~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL   84 (100)
T d1uh6a_           5 SHHHHHHSSGASLVPRGSEGAATMIEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSL   84 (100)
T ss_dssp             CCCCCCCCCCCSSCCCCCSSCCCEEEEEEECSSSSCEEEEEETTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCSSCBH
T ss_pred             cccccccCCcccccCCCCCCCCceEEEEEECCCCCEEEEEECCcChHHHHHHHHHHHHCCCcceEEEEEEeecccCcCCH
Confidence            4667777777666665432    27999999999999999999999999999999             999999999999


Q ss_pred             cccccCCCCEEEEEEe
Q 042212           80 ADYNIQKESTLHFVLR   95 (97)
Q Consensus        80 ~~y~I~~~sti~l~~r   95 (97)
                      ++|||++|++|+|..+
T Consensus        85 ~dygI~~GstI~L~~~  100 (100)
T d1uh6a_          85 GDYEIHDGMNLELYYQ  100 (100)
T ss_dssp             HHHTCCTTEEEEEECC
T ss_pred             HHcCCCCCCEEEEEEC
Confidence            9999999999999764

>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=99.75  E-value=5e-19  Score=100.83  Aligned_cols=58  Identities=16%  Similarity=0.343  Sum_probs=55.9

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEE
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      |+|+||+..|++++++|+|++||+++|++|+             |+|+.|+|+.||++|||++|++++|..
T Consensus         2 i~i~vk~~~Gk~~~v~V~~~~tV~~lK~~I~~~~~i~~~~q~Li~~Gk~L~d~~tL~~y~I~~gstl~L~~   72 (73)
T d1m94a_           2 IEVVVNDRLGKKVRVKCLAEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLELYY   72 (73)
T ss_dssp             EEEEEEETTTEEEEEEECTTSBHHHHHHHHHHHHCCTTTSEEEESSSCEECTTSBHHHHTCCTTEEEEEEE
T ss_pred             eEEEEECCCCCEEEEEECCcCcHHHHHHHHHHhhcccccEEEEEEEeEEecccCcHHHcCCCCCCEEEEEE
Confidence            7899999999999999999999999999999             999999999999999999999999863

>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=99.74  E-value=8.9e-19  Score=100.60  Aligned_cols=59  Identities=15%  Similarity=0.232  Sum_probs=56.7

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc----------------CCCeeCCCCCcccccccCCCCEEEEEE
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS----------------SPAGNFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~----------------~~gk~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      +|+|+||+++|++++++|+|++||+++|++|+                |+|++|+|+.+|++|||++|++|++++
T Consensus         2 ~~~i~vk~l~g~~~~l~v~~~~TV~~lK~~i~~~~g~~~i~~~~qrLi~~Gk~L~D~~tL~~y~I~~~s~i~~~v   76 (77)
T d1oqya4           2 AVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMV   76 (77)
T ss_dssp             CCCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSSEECSSSBTTTTCCCTTSCEEEEE
T ss_pred             cEEEEEECCCCCEEEEEECCCCcHHHHHHHHHHhcCCCCCChHHEEeEECCcCccCCCcHHHcCCCCCCEEEEEE
Confidence            68999999999999999999999999999986                999999999999999999999999886

>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=99.73  E-value=2.2e-18  Score=98.84  Aligned_cols=60  Identities=17%  Similarity=0.168  Sum_probs=56.8

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------C--CCeeCCCCCcccccccCCCCEEEEEEee
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------S--PAGNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~--~gk~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      .+|.||+++|++++++|++++||+++|++|+             |  +|+.|+|+.+|++|||++|++|+|+++-
T Consensus         1 ~~l~Vk~l~G~~~~v~V~~~~tV~~lK~~I~~~~gip~~~QrLi~~~~Gk~L~D~~tL~~y~i~~g~~i~lv~~~   75 (76)
T d1z2ma1           1 WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDK   75 (76)
T ss_dssp             CEEEEEESSSCEEEEECCSSCCHHHHHHHHHHHHCCCGGGEEEEEETTCCBCCSSSCSGGGTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhccCCccEEEEEcCCCeeccCCCcHHHcCCCCCCEEEEEEEC
Confidence            4789999999999999999999999999999             6  7999999999999999999999999873

>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=99.71  E-value=5.9e-18  Score=100.83  Aligned_cols=63  Identities=10%  Similarity=0.045  Sum_probs=58.7

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc----------CCCeeCC-CCCcccccccCCCCEEEEEEee
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS----------SPAGNFE-DGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~----------~~gk~L~-d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      ..+|+|+||+++|+.+.++|++++||.+||++|+          |+|++|. |.++|++|+|++|++||++++.
T Consensus         5 ~s~m~i~vK~l~~~~~~v~v~~~~TV~~lK~~i~~~~~~~qrLi~~Gk~L~dd~~tL~~y~i~~g~~v~l~~~~   78 (95)
T d1wiaa_           5 SSGINVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRSP   78 (95)
T ss_dssp             CCSEEEEEEETTTEEEEEEECSSSBHHHHHHHHSSSTTTTCEEEETTEECCCSSCBTTTTTCCTTEEEEEECCC
T ss_pred             CCcEEEEEEcCCCCEEEEEECCcCcHHHHHHHHhcCCcceeEEEECCEEcccCCCCHHHcCCCCCCEEEEEEcC
Confidence            4579999999999999999999999999999999          9999996 5689999999999999999864

>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=99.71  E-value=4.6e-18  Score=99.11  Aligned_cols=61  Identities=18%  Similarity=0.201  Sum_probs=56.9

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEee
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      ..|+|+||+.+ .+++++|++++||++||++|+             |+|++|+|+.+|++|||++|++|||++|.
T Consensus         6 ~~i~I~Vkt~~-~~~~~~V~~~~tV~~lK~~i~~~~gi~~~~qrL~~~Gk~L~D~~tL~~y~i~~gsti~lv~r~   79 (84)
T d1yqba1           6 HLIKVTVKTPK-DKEDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKR   79 (84)
T ss_dssp             TEEEEEEECSS-CEEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBHHHHTCCTTCEEEEEECC
T ss_pred             CEEEEEEEcCC-CcEEEEECCCCcHHHHHHHHHHHHCcCchhEEEEEeeeeccccCcHHHcCCCCCCEEEEEECC
Confidence            45999999975 468999999999999999999             99999999999999999999999999985

>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=99.71  E-value=5.9e-18  Score=99.14  Aligned_cols=54  Identities=15%  Similarity=0.215  Sum_probs=52.5

Q ss_pred             CCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           44 STGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        44 ~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      ++|++++++|++++||++||++|+             |+|+.|+|+.||++|||++|++|||++|+|
T Consensus        19 L~G~~~~l~v~~~~tV~~lK~~I~~~~~ip~~~q~Li~~Gk~L~D~~tL~dY~I~~gsti~l~~r~R   85 (86)
T d1zkha1          19 LNGQVLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMANGAVIHLALKER   85 (86)
T ss_dssp             CSSCEEEEEECTTSBHHHHHHHHHHHTCCCTTTEEEEETTEEECTTSBHHHHTCCTTEEEEEEESCC
T ss_pred             cCCeEEEEEECCCChHHHHHHHHHhhhcCChHHEEEEeCCcCcCCCCCHHHcCCCCCCEEEEEEecC
Confidence            689999999999999999999999             999999999999999999999999999987

>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=99.71  E-value=9.6e-18  Score=95.34  Aligned_cols=59  Identities=17%  Similarity=0.266  Sum_probs=55.0

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      +|+|+||+. +++++++|++++||++||++|+             |+|+.|+|+.+|++|||++|++|||+.|
T Consensus         1 si~I~Vk~~-~~~~~i~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~I~~g~~i~lV~~   72 (73)
T d2bwfa1           1 SLNIHIKSG-QDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS   72 (73)
T ss_dssp             EEEEEEEET-TEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEEC
T ss_pred             CEEEEEEeC-CeEEEEEECCCChHHHHHHHHHHHHCcChHHeEEEECCeEccCCCcHHHCCCCCCCEEEEEee
Confidence            488999985 5679999999999999999999             9999999999999999999999999875

>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=99.70  E-value=8e-18  Score=101.85  Aligned_cols=64  Identities=16%  Similarity=0.290  Sum_probs=59.1

Q ss_pred             cCCeeeEEECCCCCEEEEeecCCCcHHHhhcccc----------------------------CCCeeCCCC-Cccccccc
Q 042212           34 RGRMQIFVKTSTGKTITLEVESSDMIDNASRGSS----------------------------SPAGNFEDG-WTQADYNI   84 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~----------------------------~~gk~L~d~-~tL~~y~I   84 (97)
                      ...|+|+|++.+|++++++|++++||++||++|+                            |+|+.|.|+ .||++|||
T Consensus         5 ss~M~v~Vk~~~G~~~~v~V~~~~TV~~LK~~I~~~~~ip~~~Qr~~~~~~~~~~~~~~~Li~~G~~L~d~~~tL~~~gI   84 (105)
T d1v2ya_           5 SSGMTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLRDYGI   84 (105)
T ss_dssp             CCSEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHHHHHHHTTCCCCCCHHHHHTTEEEESSSCEECCSSSBHHHHTC
T ss_pred             CCcEEEEEEeCCCCEEEEEECCCChHHHHHHHHHHHHCcCHHHhcccccccccccccceEEEECCEECcccCCCHHHcCC
Confidence            3569999999999999999999999999999986                            899999765 59999999


Q ss_pred             CCCCEEEEEEeeC
Q 042212           85 QKESTLHFVLRLS   97 (97)
Q Consensus        85 ~~~sti~l~~rl~   97 (97)
                      ++|++|||+.|+|
T Consensus        85 ~~g~~l~lv~r~~   97 (105)
T d1v2ya_          85 RNRDEVSFIKKLG   97 (105)
T ss_dssp             CSSEEEEEEECSC
T ss_pred             CCCCEEEEEEecC
Confidence            9999999999875

>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=99.67  E-value=3.1e-17  Score=98.77  Aligned_cols=59  Identities=19%  Similarity=0.208  Sum_probs=55.7

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      .|+|+||+.++ +++++|++++||.+||++|+             |+|++|+|+.+|++|||++|++|||++|
T Consensus        32 ~i~V~Vk~~~~-~~~i~V~~~~tV~~LK~~I~~~~gi~~~~qrLi~~Gk~L~D~~tL~~~~I~~g~~I~lvlr  103 (103)
T d1j8ca_          32 IIKVTVKTPKE-KEEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIK  103 (103)
T ss_dssp             CEEEEEECSSC-EEEEEECTTCCHHHHHHHHHHHHCSCSSSEEEEETTEEESTTSCGGGTTCSSSEEEEEEEC
T ss_pred             eEEEEEECCCc-cEEEEECCCChHHHHHHHHHHHHCcCHHHeeeeeeeecccCCCcHHHcCCCCCCEEEEEEC
Confidence            49999999765 67999999999999999999             9999999999999999999999999986

>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=99.66  E-value=1.3e-17  Score=96.88  Aligned_cols=60  Identities=18%  Similarity=0.157  Sum_probs=55.7

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      ..|+|+||+.++ .++++|++++||.+||++|+             |+|+.|+|+.+|++|||++|++|||++|
T Consensus         9 ~~i~v~Vk~~~~-~~~i~v~~~~tV~~lK~~I~~~~~v~~~~qrL~f~Gk~L~d~~tL~~~gI~~gs~I~lv~r   81 (83)
T d1wx8a1           9 RIIRVSVKTPQD-CHEFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVR   81 (83)
T ss_dssp             CEEEEEEECSSS-EEEEEEETTCCHHHHHHHHHHHTCSCTTTBCCEETTEECCTTSCHHHHTCCTTEEEECCBC
T ss_pred             CeEEEEEEcCCC-cEEEEECCCChHHHHHHHHHHHhCCChhHEEEEEEhhccccCCcHHHcCCCCCCEEEEEEe
Confidence            459999999754 56899999999999999999             9999999999999999999999999887

>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=99.65  E-value=1.1e-16  Score=97.62  Aligned_cols=61  Identities=21%  Similarity=0.348  Sum_probs=54.7

Q ss_pred             eeeEEECC-CCCEEEEeecC-CCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           37 MQIFVKTS-TGKTITLEVES-SDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        37 m~i~vk~~-~g~~~~l~v~~-~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      ++|++++. +|++++++|.+ ++||++||++|+             |+|+.|+|+.||++|||++|++|||++|+|
T Consensus        30 i~V~v~~~~~G~~i~l~v~~~sdtV~~lK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~ynI~~gsti~L~lr~r  105 (111)
T d1we6a_          30 IRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLRER  105 (111)
T ss_dssp             EEECCTTCSSSCCEEEEESCSSSBHHHHHHHHHHHTTCCTTTSEEECSSSBCCTTSBTTTTTCSSSCEEEEECSSC
T ss_pred             EEEEcccCCCCeEEEEEecCCccHHHHHHHHHHHHHCCCccceEEEEeeEEccccCCHHHcCCCCCCEEEEEeeCC
Confidence            44444443 69999999987 999999999999             999999999999999999999999999987

>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=99.64  E-value=2e-16  Score=94.87  Aligned_cols=63  Identities=16%  Similarity=0.274  Sum_probs=58.3

Q ss_pred             cCCeeeEEECCCCCEE-EEeecCCCcHHHhhcccc--------------------CCCeeCCCCCcccccccCCCC----
Q 042212           34 RGRMQIFVKTSTGKTI-TLEVESSDMIDNASRGSS--------------------SPAGNFEDGWTQADYNIQKES----   88 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~-~l~v~~~~tV~~lK~~I~--------------------~~gk~L~d~~tL~~y~I~~~s----   88 (97)
                      ..+|.|++|+.+|+.+ .+.+++++||.+||++|+                    |+||+|+|++||++|+|.+|+    
T Consensus         5 ~~~i~I~~r~~~G~~i~~~~v~~s~TV~~lK~~I~~~~~~~k~~iP~~~~~qRLIf~Gk~L~D~~tL~dy~i~~g~~~~~   84 (101)
T d1se9a_           5 HNQLEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSKTVKDYRSPVSNLAGA   84 (101)
T ss_dssp             CCCEEEEEEETTSCEEEEEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEEETTEECCTTSBGGGGSCCTTSCTTC
T ss_pred             cceEEEEEEeCCCCeecceecCccCHHHHHHHHHHHhccccccCCCCCcccEEEEECCeEecCCCCHHHcCCCCCCcCCC
Confidence            4579999999999977 699999999999999983                    999999999999999999998    


Q ss_pred             --EEEEEEee
Q 042212           89 --TLHFVLRL   96 (97)
Q Consensus        89 --ti~l~~rl   96 (97)
                        ++||++|.
T Consensus        85 ~~tmHlVvrp   94 (101)
T d1se9a_          85 VTTMHVIIQA   94 (101)
T ss_dssp             CEEEEEEECC
T ss_pred             ceEEEEEeCC
Confidence              99999984

>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=99.62  E-value=6.9e-16  Score=94.70  Aligned_cols=63  Identities=14%  Similarity=0.158  Sum_probs=57.3

Q ss_pred             ecCCeeeEEECCCCCEEEEeecCCCcHHHhhccc--------c-------------CCCeeCCCCCcccccccCCCCE--
Q 042212           33 LRGRMQIFVKTSTGKTITLEVESSDMIDNASRGS--------S-------------SPAGNFEDGWTQADYNIQKEST--   89 (97)
Q Consensus        33 ~~~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I--------~-------------~~gk~L~d~~tL~~y~I~~~st--   89 (97)
                      ....|+|+|++++|+++++.|+|++||.+||++|        +             |+||.|+|+.+|++|+|.+|++  
T Consensus        13 ~~~~i~i~v~~l~Gk~~~~~v~p~~TV~~lK~~I~~~~p~~~~e~~~~~~~~qRLiy~Gk~L~D~~tL~~~~i~~g~~~~   92 (116)
T d1wgha_          13 PADMINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTV   92 (116)
T ss_dssp             CSSSEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEEETTEEECSSCBTTTTTCCSSCEEE
T ss_pred             CCCeEEEEEEEcCCCEEEEEECCcchHHHHHHHHHhhcccccccccCCChHHeEEEECCEEecCCCCHHHcCCCCCCEEE
Confidence            4466999999999999999999999999999999        2             9999999999999999999987  


Q ss_pred             EEEEEe
Q 042212           90 LHFVLR   95 (97)
Q Consensus        90 i~l~~r   95 (97)
                      +||++|
T Consensus        93 lhlv~r   98 (116)
T d1wgha_          93 MHLVAR   98 (116)
T ss_dssp             EEEEEC
T ss_pred             EEEEeC
Confidence            666655

>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=99.59  E-value=4.8e-16  Score=93.49  Aligned_cols=62  Identities=16%  Similarity=0.139  Sum_probs=56.8

Q ss_pred             CCeeeEE----ECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCC-CCCcccccccCCCCEEEEEEee
Q 042212           35 GRMQIFV----KTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFE-DGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        35 ~~m~i~v----k~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~-d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      .+|.|+|    |..+|.+++++|++++||.+||++|+             |+|+.|. |..||++|||++|++|+|+.|.
T Consensus         6 ~~m~itV~~~~~~~~~~t~~l~V~~~~tV~~LK~~Ie~~~gip~~~Q~Li~~Gk~L~dd~~tL~~~gI~~g~~i~l~~r~   85 (102)
T d1v5oa_           6 SGMLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVLLQKD   85 (102)
T ss_dssp             CCEEEEEEECCCCCCCCEEEEEECTTCBHHHHHHHHHHHTCCCGGGBCEEETTEEECCSSSBHHHHTCCTTEEEEECBCC
T ss_pred             CCEEEEEEecccCCCCCEEEEEECCcccHHHHHHHHHHHhCCCcceEEEEeCCeEeecccCCHHHcCCCCCCEEEEEECC
Confidence            4699999    88899999999999999999999999             9999995 5679999999999999998764

>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=99.53  E-value=1.6e-15  Score=90.87  Aligned_cols=60  Identities=8%  Similarity=0.057  Sum_probs=54.7

Q ss_pred             CeeeEE--ECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           36 RMQIFV--KTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        36 ~m~i~v--k~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      +|+|++  +...|++++++|++++||++||++|+             |+|++|+|+.||++|||+++++|+++.+
T Consensus        17 ti~V~~~~~~~~g~~~~lev~~~~TV~~LK~~I~~~~gi~~~~qkLi~~Gk~L~d~~tL~~~gI~~~s~i~vi~~   91 (100)
T d1wjua_          17 TIEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFGLQENYIKIVINKKQLQLGKTLEEQGVAHNVKAMVLEL   91 (100)
T ss_dssp             EEEEECCTTTCCSSSEEEEEESSSBHHHHHHHHHHHTTCCSTTCEEEETTEECCTTSBHHHHTCCSSEEEEEECC
T ss_pred             EEEEEEeeccCCCeEEEEEECCCcHHHHHHHHHHHHHCCCCeeEEEEEcccCcCCCcCHHHcCCCCCCEEEEEEc
Confidence            477777  66789999999999999999999999             9999999999999999999999987743

>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=99.50  E-value=1.1e-14  Score=86.00  Aligned_cols=63  Identities=16%  Similarity=0.168  Sum_probs=54.9

Q ss_pred             CCeeeEEECCCCC--EEEEeecCCCcHHHhhcccc---------------CCCeeCCCCCcccccccCCC--CEEEEEEe
Q 042212           35 GRMQIFVKTSTGK--TITLEVESSDMIDNASRGSS---------------SPAGNFEDGWTQADYNIQKE--STLHFVLR   95 (97)
Q Consensus        35 ~~m~i~vk~~~g~--~~~l~v~~~~tV~~lK~~I~---------------~~gk~L~d~~tL~~y~I~~~--sti~l~~r   95 (97)
                      .+|+|+||+++++  .+++++++++||.+||++|+               |+|++|+|+.+|++|+...+  .+|||+++
T Consensus         6 ~~i~l~Ik~~~~~~~~~~~~v~~~~TV~~LK~~I~~~~~~~~~~~~qrLIy~Gk~L~D~~~L~d~~~~~~~~~viHLV~~   85 (93)
T d1wgda_           6 SGVTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVCN   85 (93)
T ss_dssp             CCCEEEEECSSSSCCCEEEECCTTSCHHHHHHHHHHHSTTCCCTTTCEEEETTEECCSSSCHHHHSCSSSCSEEEEEECC
T ss_pred             CcEEEEEECCCCCceeEEEEcCCCCcHHHHHHHHHHHcCCCCChHHEEEEECCeEccCCCCHHHhCcccCCCCEEEEEec
Confidence            4599999998775  48899999999999999998               99999999999999976544  59999987


Q ss_pred             eC
Q 042212           96 LS   97 (97)
Q Consensus        96 l~   97 (97)
                      .+
T Consensus        86 ~~   87 (93)
T d1wgda_          86 VK   87 (93)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.49  E-value=7.3e-15  Score=87.26  Aligned_cols=59  Identities=12%  Similarity=0.071  Sum_probs=55.1

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEE
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      ..|+|.||..+++.+.++|++++||.+||++|+             |+|+.|+|+ +|++|||++|++|+|+.
T Consensus         6 ~~~~I~VK~~~~~~~~v~v~~~~tV~~lK~~i~~~~gvp~~~QkLi~~Gk~L~d~-tL~~~gi~~g~~i~lv~   77 (96)
T d1wgga_           6 SGYSVTVKWGKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLKDD-DWGNIKMKNGMTVLMMG   77 (96)
T ss_dssp             CEEEEEEEETTEEEEEEEEESSSCHHHHHHHHHHHTCCCTTTSCCEETTEECCSS-CCCSCCCCSSCEEECCC
T ss_pred             CceEEEEEeCCCCEEEEEECCCCcHHHHHHHhhhhcCccceeeEEeecCcccCCC-cHHHCCCCCCCEEEEEe
Confidence            569999999988888999999999999999999             999999986 89999999999999974

>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=99.44  E-value=3.1e-14  Score=85.53  Aligned_cols=59  Identities=19%  Similarity=0.242  Sum_probs=50.4

Q ss_pred             eeEEECCCCC-EEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccC-------CCCEEEEEEee
Q 042212           38 QIFVKTSTGK-TITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQ-------KESTLHFVLRL   96 (97)
Q Consensus        38 ~i~vk~~~g~-~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~-------~~sti~l~~rl   96 (97)
                      +|||+...++ ++.++|++++||.+||++|+             |+|++|+|++||++|||.       ..+++++.++.
T Consensus         1 qifv~i~~~k~Ti~l~v~~~~TV~~lK~~I~~~~gip~~~QrLi~~Gk~L~D~~TL~dYgI~~~~~~~~~~~~~~l~~~~   80 (103)
T d2c9wb1           1 DVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRA   80 (103)
T ss_dssp             CEEEEEEEBTEEEEEEECTTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBHHHHTCCTTTSBTTBCEEEEEEEEE
T ss_pred             CEEEEEeCCCEEEEEEeCCCCcHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCcccccccCCcEEEEEEec
Confidence            4677766664 78899999999999999999             999999999999999995       44588887764

>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=99.40  E-value=4.3e-14  Score=82.81  Aligned_cols=61  Identities=10%  Similarity=0.135  Sum_probs=54.5

Q ss_pred             cCCeeeEEECCCCCEEEE-eecCCCcHHHhhcccc----------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           34 RGRMQIFVKTSTGKTITL-EVESSDMIDNASRGSS----------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        34 ~~~m~i~vk~~~g~~~~l-~v~~~~tV~~lK~~I~----------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      ...|.|+||. .|+.+.+ +|++++||.+||++|+                |.|+.|+|+.+|++|+|++|++|+|+.+
T Consensus         5 s~~~~i~Vk~-~~~~~~i~~v~~~~tV~~LK~~i~~~t~vp~~~QkLi~~~~~Gk~L~D~~tL~~~~i~~g~~i~lv~s   82 (90)
T d1v5ta_           5 SSGLPIIVKW-GGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMGT   82 (90)
T ss_dssp             CCSCCEEEEE-TTEEEEECSCCSSSBHHHHHHHHHHHTCCCTTTCEEESCEETTEECCTTSBHHHHTCCTTEEEEEECC
T ss_pred             CCcEEEEEEE-CCeEEEEEEeCCCCcHHHHHHHHHHHHcCCHHHhhhhhhccCCcCCCCcCcHHHcCCCCCCEEEEEee
Confidence            3569999997 5677777 7999999999999999                4899999999999999999999999865

>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=99.38  E-value=1e-13  Score=82.07  Aligned_cols=58  Identities=5%  Similarity=-0.039  Sum_probs=53.3

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEe
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLR   95 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~r   95 (97)
                      .|.|.|+. +++++.++|++++||.+||++|+             |+|+ |+|+.+|++|+|++|++|+|+.+
T Consensus        17 ~i~v~V~~-~~k~~~i~v~~~~TV~~LK~~I~~~tgvp~~~q~Li~~g~-l~D~~tL~~~~I~~gs~i~lvgs   87 (95)
T d1v86a_          17 LVDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGL-VPEDKTLREIKVTSGAKIMVVGS   87 (95)
T ss_dssp             CEEEEEEE-TTEEEEEEECTTSBHHHHHHHHHHHHCSCSTTCCCBSSSB-CCSSSBHHHHCCCTTEEEEECCS
T ss_pred             EEEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEeccc-ccCCCcHHHCCCCCCCEEEEEec
Confidence            48888885 78999999999999999999999             9987 99999999999999999999864

>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=99.38  E-value=7e-14  Score=82.66  Aligned_cols=73  Identities=18%  Similarity=0.103  Sum_probs=57.1

Q ss_pred             CCCcceeeeeecCC---eeeEEECCCCCEEEEeecCCCcHHHhhcccc----------------CCCeeCCCCCcccccc
Q 042212           23 KESTLHLVARLRGR---MQIFVKTSTGKTITLEVESSDMIDNASRGSS----------------SPAGNFEDGWTQADYN   83 (97)
Q Consensus        23 ~~s~i~l~~~~~~~---m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~----------------~~gk~L~d~~tL~~y~   83 (97)
                      ..|+.|+.+++.++   -...++..+.+. ...+..++||.++|++|+                |+|++|+|+.+|++||
T Consensus         2 ~~s~~~~~~~l~~~p~~pk~~i~~p~~~~-~~~~~~~~tV~~lK~~i~~~~~~~~P~p~~~rLIy~Gk~L~D~~tL~~y~   80 (94)
T d1x1ma1           2 SLSDWHLAVKLADQPLAPKSILQLPETEL-GEYSLGGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDFYG   80 (94)
T ss_dssp             CCCSCCEEEEETTCTTSCCEEECCCCCSS-CSSCCCCCBHHHHHHHHHHHCTTTCCCSSSEEEEETTEECCTTCBHHHHT
T ss_pred             CcccceEEEEEccCCCCCcceEECCCCcc-CccCCCccCHHHHHHHHHHHcccCCCChhheEEEECCeEECCCccHHHcC
Confidence            35788999987654   345555554322 123345789999999996                9999999999999999


Q ss_pred             cCCCCEEEEEEee
Q 042212           84 IQKESTLHFVLRL   96 (97)
Q Consensus        84 I~~~sti~l~~rl   96 (97)
                      |++|+||||+.|-
T Consensus        81 I~~gstihLV~r~   93 (94)
T d1x1ma1          81 IQPGSTVHVLRKS   93 (94)
T ss_dssp             CCTTCEEEEEESS
T ss_pred             CCCCCEEEEEEeC
Confidence            9999999999873

>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=99.33  E-value=6.3e-13  Score=76.44  Aligned_cols=60  Identities=10%  Similarity=0.126  Sum_probs=52.0

Q ss_pred             CeeeEEECCCCCEEEEee-----cCCCcHHHhhcccc-------------CCCeeCC-CCCcccccccCCCCEEEEEEee
Q 042212           36 RMQIFVKTSTGKTITLEV-----ESSDMIDNASRGSS-------------SPAGNFE-DGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v-----~~~~tV~~lK~~I~-------------~~gk~L~-d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      +|+|.|+. .++.+.+++     ++++||++||++|+             |+|+.|. |+.+|++|||++|++|+|+.|.
T Consensus         1 gi~i~V~~-~~~~~~i~v~~~~~~~~~Tv~~LK~~I~~~tgvp~~~QkL~~~G~~L~~d~~tL~~~gi~~g~~i~lv~~~   79 (81)
T d1wxva1           1 GLTVTVTH-SNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVMLIGKK   79 (81)
T ss_dssp             SEEEEEEC-SSSEEEEEECCCSSSSSCBHHHHHHHHHHHTCCCTTTCEEEETTEEECCSSSBHHHHTCCSSEEEEEESCC
T ss_pred             CEEEEEEE-CCeeEEEEEecCCCCCccHHHHHHHHHHHHHCcCHHHEEeeecCeEeCcCCCChHHCCCCCCCEEEEEEec
Confidence            47888976 567888887     46889999999999             9999995 6789999999999999998763

>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=99.31  E-value=6e-13  Score=76.00  Aligned_cols=35  Identities=34%  Similarity=0.695  Sum_probs=33.6

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++|+|+|+|++|     |++|||.++|+|||+.|+++
T Consensus        38 ip~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lv~R~rg   77 (78)
T d2zeqa1          38 VPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRR   77 (78)
T ss_dssp             CCGGGEEEEETTEEECTTCBGGGSSCCTTCEEEEEESSCC
T ss_pred             cChhHeEEEEeeeEcCCCCCHHHcCCCCCCEEEEEeccCC
Confidence            799999999999999     99999999999999999876

>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=99.24  E-value=6.3e-12  Score=71.71  Aligned_cols=60  Identities=7%  Similarity=0.087  Sum_probs=55.0

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEeeC
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRLS   97 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl~   97 (97)
                      +.|.|+. +|+.+.+.|+++++++.||+.++             |+|+.|+++.|+++|++++|++|++++|++
T Consensus         5 I~ikv~~-~~~~~~f~v~~~~~~~~l~~~~~~~~~i~~~~~~l~f~G~~l~~~~T~~~~~i~dgd~I~v~~~q~   77 (79)
T d1euvb_           5 INLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQI   77 (79)
T ss_dssp             EEEEEES-SSCEEEEEEETTSCTHHHHHHHHHHTTCCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCB
T ss_pred             EEEEECC-CCeEEEEEECCCCcHHHHHHHHHHHhCCChHhEEEEECCEEeCCCCCHHHCCCCCCCEEEEEEecc
Confidence            6677776 67888899999999999999888             999999999999999999999999999864

>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=99.24  E-value=1.9e-12  Score=72.83  Aligned_cols=33  Identities=55%  Similarity=0.792  Sum_probs=31.6

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARL   33 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~   33 (97)
                      ||+++|+|+|+|++|     |++|||++||+|||++|+
T Consensus        36 i~~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lvlrL   73 (73)
T d1bt0a_          36 IPPVQQRLIYAGKQLADDKTAKDYNIEGGSVLHLVLAL   73 (73)
T ss_dssp             CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECC
T ss_pred             CChHHEEEEECCeEcCCCCcHHHcCCCCCCEEEEEeeC
Confidence            799999999999999     999999999999999984

>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=99.23  E-value=2.5e-12  Score=72.79  Aligned_cols=33  Identities=30%  Similarity=0.443  Sum_probs=31.6

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARL   33 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~   33 (97)
                      ||+++|+|+|+|++|     |++|||++||+|||++|+
T Consensus        39 i~~~~qrL~~~gk~L~d~~tL~~y~I~~~sti~l~lRL   76 (76)
T d1z2ma2          39 VQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRL   76 (76)
T ss_dssp             CCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECC
T ss_pred             CChhHeEEEECCeECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            799999999999999     999999999999999874

>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=99.23  E-value=2.7e-12  Score=72.96  Aligned_cols=33  Identities=30%  Similarity=0.538  Sum_probs=31.8

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARL   33 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~   33 (97)
                      ||+++|||+|+|++|     |++|||++||+|||++|.
T Consensus        38 ip~~~qrLi~~Gk~L~D~~tL~~y~I~~~sti~lv~r~   75 (76)
T d2faza1          38 VEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLLVRQ   75 (76)
T ss_dssp             CCGGGEEEEETTEECCTTCBTTTTTCCTTCEEEEEECC
T ss_pred             cChHHeEEEEeeEeccCCCcHHHcCCCCCCEEEEEEEc
Confidence            799999999999999     999999999999999985

>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=99.22  E-value=3.2e-12  Score=72.43  Aligned_cols=36  Identities=75%  Similarity=1.104  Sum_probs=33.9

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|++|     |++|||++||+|||+++++++
T Consensus        36 i~~~~qrL~~~Gk~L~d~~tL~~y~i~~~s~I~L~~rlrgG   76 (76)
T d1ogwa_          36 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   76 (76)
T ss_dssp             CCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECTTCC
T ss_pred             CChHHEEeEECCeEcCCCCCHHHcCCCCCCEEEEEEecCCC
Confidence            799999999999999     999999999999999998763

>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=99.20  E-value=8.2e-12  Score=73.69  Aligned_cols=61  Identities=10%  Similarity=0.062  Sum_probs=52.8

Q ss_pred             CCeeeEEECC-CCCEEEEeecCCCcHHHhhcccc-------------CCCe-------eCCCCCcccccccCCCCEEEEE
Q 042212           35 GRMQIFVKTS-TGKTITLEVESSDMIDNASRGSS-------------SPAG-------NFEDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        35 ~~m~i~vk~~-~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk-------~L~d~~tL~~y~I~~~sti~l~   93 (97)
                      ..|.|+|++. ++...+..+++++||.+||++|+             |.|+       .++|+.+|++|+|.+|++||++
T Consensus         6 s~v~v~I~s~~~~~~~E~r~~~~~TV~~LK~kle~~tGip~~~qrL~~~~~~~~~~~~l~~d~~~L~~y~i~dg~~ihlv   85 (95)
T d1v6ea_           6 SGVMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVGSPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIHVI   85 (95)
T ss_dssp             CCEEEEEEETTSSSCEEEEECTTSBHHHHHHHHHHHTCSCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCEEEEB
T ss_pred             CcEEEEEEECCCCcEEEEEeCCCCCHHHHHHHHHHHhCcCchhEEEEEeCCCCceeecccCCcCCHHHCCCCCCCEEEEE
Confidence            4588999874 66678899999999999999999             5555       5789999999999999999998


Q ss_pred             Ee
Q 042212           94 LR   95 (97)
Q Consensus        94 ~r   95 (97)
                      -+
T Consensus        86 d~   87 (95)
T d1v6ea_          86 DH   87 (95)
T ss_dssp             CC
T ss_pred             eC
Confidence            65

>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=99.18  E-value=4e-12  Score=73.80  Aligned_cols=35  Identities=37%  Similarity=0.511  Sum_probs=33.2

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++|+|+|+|++|     |++|||.++|+|||+.+.++
T Consensus        43 ip~~~qrLi~~Gk~L~d~~tL~~y~I~~~stl~l~~r~~~   82 (87)
T d1wh3a_          43 LPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKGS   82 (87)
T ss_dssp             CCTTTEEEEETTEECCSSSBHHHHTCCTTEEEEEEECSCC
T ss_pred             cChHHeEEEeeceEcCCCCcHHHcCCCCCCEEEEEecCCC
Confidence            799999999999999     99999999999999998764

>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=99.17  E-value=5e-12  Score=71.78  Aligned_cols=33  Identities=33%  Similarity=0.532  Sum_probs=31.7

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARL   33 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~   33 (97)
                      ||+++|+|+|+|++|     |++|||.+||+|||++|+
T Consensus        38 ip~~~qrLi~~Gk~L~d~~tL~~y~I~~~s~i~lv~rp   75 (76)
T d1wy8a1          38 VRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVRP   75 (76)
T ss_dssp             CCTTTEEEEETTEECCSSSBHHHHTCCTTCEEEEEECC
T ss_pred             CCchhcEEEEEeeEecCCCCHHHcCCCCCCEEEEEEcc
Confidence            799999999999999     999999999999999985

>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=99.15  E-value=1.1e-11  Score=69.72  Aligned_cols=32  Identities=38%  Similarity=0.754  Sum_probs=30.6

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVAR   32 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~   32 (97)
                      ||+++|+|+|+|++|     |++|||.+|++|||+.+
T Consensus        36 ip~~~qrLi~~Gk~L~D~~tL~~~~I~~g~~i~lV~~   72 (73)
T d2bwfa1          36 IPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS   72 (73)
T ss_dssp             CCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEEC
T ss_pred             cChHHeEEEECCeEccCCCcHHHCCCCCCCEEEEEee
Confidence            799999999999999     99999999999999875

>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=8.8e-12  Score=75.52  Aligned_cols=36  Identities=33%  Similarity=0.411  Sum_probs=34.3

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|+.|     |++|||++|++|||++|++++
T Consensus        67 ip~~~QrLi~~Gk~L~D~~tL~~ynI~~gsti~L~lr~rGG  107 (111)
T d1we6a_          67 IPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLRERSG  107 (111)
T ss_dssp             CCTTTSEEECSSSBCCTTSBTTTTTCSSSCEEEEECSSCCS
T ss_pred             CCccceEEEEeeEEccccCCHHHcCCCCCCEEEEEeeCCCC
Confidence            799999999999999     999999999999999998864

>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=99.14  E-value=8.7e-12  Score=71.27  Aligned_cols=35  Identities=17%  Similarity=0.340  Sum_probs=32.7

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++|+|+|+|++|     |++|||++||+|||+++.+.
T Consensus        39 ip~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lvi~~p~   78 (80)
T d1ttna1          39 VEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQPV   78 (80)
T ss_dssp             CCSTTCEEEETTEECCTTSHHHHCCCSSSCEEEEECCCSS
T ss_pred             CCcccEEEEECceEcCCCCcHHHcCCCCCCEEEEEecCCC
Confidence            799999999999999     99999999999999998653

>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=8.5e-12  Score=72.39  Aligned_cols=35  Identities=34%  Similarity=0.609  Sum_probs=33.1

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++|+|+|+|+.|     |++|||.+||+|||+++.+|
T Consensus        47 ip~~~q~Li~~Gk~L~D~~tL~dY~I~~gsti~l~~r~RG   86 (86)
T d1zkha1          47 MPAGKQKLQYEGIFIKDSNSLAYYNMANGAVIHLALKERG   86 (86)
T ss_dssp             CCTTTEEEEETTEEECTTSBHHHHTCCTTEEEEEEESCCC
T ss_pred             CChHHEEEEeCCcCcCCCCCHHHcCCCCCCEEEEEEecCC
Confidence            799999999999999     99999999999999998764

>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=99.11  E-value=4.7e-11  Score=67.69  Aligned_cols=61  Identities=10%  Similarity=0.169  Sum_probs=57.4

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEEee
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      .+.|.|++.+|+.+.+.|.++.++..|+...+             |+|+.|.++.|++++++++|++|+++++.
T Consensus         2 ~I~ikv~~~dg~~v~f~v~~~t~l~kl~~~y~~~~~~~~~~~~f~fdG~~l~~~~T~~~l~~edgD~Idv~~~q   75 (77)
T d2uyzb1           2 YIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQ   75 (77)
T ss_dssp             EEEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCHHHHTCCTTEEEEEEECC
T ss_pred             EEEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCChhHEEEEECCEECCCCCCHHHcCCCCCCEEEEEEec
Confidence            37899999999999999999999999999887             99999999999999999999999999874

>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=99.09  E-value=1.9e-11  Score=70.42  Aligned_cols=35  Identities=34%  Similarity=0.445  Sum_probs=32.8

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++|+|+|+|++|     |++|||.+|++|||+++.+.
T Consensus        42 i~~~~qrL~~~Gk~L~D~~tL~~y~i~~gsti~lv~r~~~   81 (84)
T d1yqba1          42 AHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQH   81 (84)
T ss_dssp             CCGGGEEEEETTEECCTTSBHHHHTCCTTCEEEEEECCCC
T ss_pred             cCchhEEEEEeeeeccccCcHHHcCCCCCCEEEEEECCCC
Confidence            799999999999999     99999999999999998654

>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=99.07  E-value=4.3e-11  Score=67.72  Aligned_cols=33  Identities=33%  Similarity=0.305  Sum_probs=30.8

Q ss_pred             CCCCceEEEe--cCccc-----cccccccCCCcceeeeee
Q 042212            1 MPLEQQRLVF--ADKSL-----LADYNIQKESTLHLVARL   33 (97)
Q Consensus         1 ip~~~q~L~~--~~~~L-----l~~y~i~~~s~i~l~~~~   33 (97)
                      ||+++|+|+|  +|++|     |++|||++|++|||+++.
T Consensus        36 ip~~~QrLi~~~~Gk~L~D~~tL~~y~i~~g~~i~lv~~~   75 (76)
T d1z2ma1          36 VHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDK   75 (76)
T ss_dssp             CCGGGEEEEEETTCCBCCSSSCSGGGTCCTTCEEEEEECC
T ss_pred             cCCccEEEEEcCCCeeccCCCcHHHcCCCCCCEEEEEEEC
Confidence            7999999999  69999     999999999999999863

>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=99.04  E-value=3.9e-11  Score=70.63  Aligned_cols=31  Identities=32%  Similarity=0.494  Sum_probs=29.1

Q ss_pred             CCceEEEecCccc-----cccccccCCCcceeeeee
Q 042212            3 LEQQRLVFADKSL-----LADYNIQKESTLHLVARL   33 (97)
Q Consensus         3 ~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~   33 (97)
                      +++|||+|+|++|     |++|||++|++|||+.|.
T Consensus        58 p~~~rLIy~Gk~L~D~~tL~~y~I~~gstihLV~r~   93 (94)
T d1x1ma1          58 PELIDLIYCGRKLKDDQTLDFYGIQPGSTVHVLRKS   93 (94)
T ss_dssp             SSSEEEEETTEECCTTCBHHHHTCCTTCEEEEEESS
T ss_pred             hhheEEEECCeEECCCccHHHcCCCCCCEEEEEEeC
Confidence            5899999999999     999999999999999873

>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=99.03  E-value=8.2e-11  Score=69.03  Aligned_cols=35  Identities=26%  Similarity=0.528  Sum_probs=32.2

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++|||+|+|+.|     |++|||.+|++|||+++.+.
T Consensus        39 i~~~~qrLi~~Gk~L~d~~tL~~y~I~~~s~i~lv~~~~~   78 (95)
T d1uela_          39 FPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKPK   78 (95)
T ss_dssp             CCTTTEEEEETTEECCTTSBGGGGTCCSSSEEEEEESSCC
T ss_pred             CCccceEEEECCeEccCCCcHHHcCCCCCCEEEEEECCCC
Confidence            689999999999999     99999999999999997543

>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=99.01  E-value=1.9e-10  Score=67.86  Aligned_cols=57  Identities=12%  Similarity=0.127  Sum_probs=47.1

Q ss_pred             eeeEEEC---CCCCEEEEeecCCCcHHHhhcccc-------------CCCee-------CC-CCCcccccccCCCCEEEE
Q 042212           37 MQIFVKT---STGKTITLEVESSDMIDNASRGSS-------------SPAGN-------FE-DGWTQADYNIQKESTLHF   92 (97)
Q Consensus        37 m~i~vk~---~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~-------L~-d~~tL~~y~I~~~sti~l   92 (97)
                      ++|.|+.   .+++.+++++++++||.+||.+|+             |.|+.       |+ |+++|++|||++|++|++
T Consensus        10 iti~i~~~~~~~~~~~~~kv~~~~TV~~LK~~i~~~~gip~~~qrL~y~~~~~~~~~~~l~~d~~tL~~YgI~dg~~I~V   89 (97)
T d1wjna_          10 LTLKIKCSNQPERQILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCLLV   89 (97)
T ss_dssp             EEEEEEESSCSSSCCEEEEEETTSBHHHHHHHHHTTTTCCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTCCTTCEEEE
T ss_pred             EEEEEEeCCCCCCceEEEEcCCCCCHHHHHHHHHHHHCcChHHeEEEecCCCCCcccceecCCCcCHhhccCCCCCEEEE
Confidence            4555554   457889999999999999999999             66653       43 789999999999999997


Q ss_pred             E
Q 042212           93 V   93 (97)
Q Consensus        93 ~   93 (97)
                      .
T Consensus        90 ~   90 (97)
T d1wjna_          90 R   90 (97)
T ss_dssp             E
T ss_pred             E
Confidence            5

>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=99.00  E-value=1.4e-11  Score=69.30  Aligned_cols=33  Identities=39%  Similarity=0.773  Sum_probs=30.3

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeec
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLR   34 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~   34 (97)
                      ||+++|||+|+|++|     |++||| +++++||+.+.|
T Consensus        36 ip~~~qrLi~~Gk~L~d~~tL~dy~i-~~~ti~lv~r~P   73 (73)
T d1wx9a1          36 IPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVIHLVERAP   73 (73)
T ss_dssp             CCTTTCCCEETTEECCSSSBHHHHTC-TTEEEBCCCSSC
T ss_pred             CChHHEEEEECCeEccCCCCHHHhCC-CCCEEEEEecCC
Confidence            799999999999999     999999 589999998753

>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=99.00  E-value=1.1e-10  Score=65.98  Aligned_cols=32  Identities=28%  Similarity=0.621  Sum_probs=30.0

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVAR   32 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~   32 (97)
                      ||+++|||+|+|+.|     |++|||++|++|++++.
T Consensus        41 i~~~~qrLi~~Gk~L~D~~tL~~y~I~~~s~i~~~vs   77 (77)
T d1oqya4          41 FPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVT   77 (77)
T ss_dssp             CCSTEEEEESSSSEECSSSBTTTTCCCTTSCEEEEEE
T ss_pred             CChHHEEeEECCcCccCCCcHHHcCCCCCCEEEEEEC
Confidence            699999999999999     99999999999998863

>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=98.99  E-value=2.2e-11  Score=70.03  Aligned_cols=33  Identities=33%  Similarity=0.455  Sum_probs=31.4

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARL   33 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~   33 (97)
                      ||+++|+|+|+|+.|     |++|||.+||+|||++|.
T Consensus        45 v~~~~qrL~f~Gk~L~d~~tL~~~gI~~gs~I~lv~r~   82 (83)
T d1wx8a1          45 CNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVRS   82 (83)
T ss_dssp             SCTTTBCCEETTEECCTTSCHHHHTCCTTEEEECCBCC
T ss_pred             CChhHEEEEEEhhccccCCcHHHcCCCCCCEEEEEEeC
Confidence            699999999999999     999999999999999874

>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=98.96  E-value=8.5e-11  Score=65.99  Aligned_cols=31  Identities=23%  Similarity=0.317  Sum_probs=29.4

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVA   31 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~   31 (97)
                      ||+++|+|+|+|++|     |++|||++||+|||..
T Consensus        37 i~~~~q~Li~~Gk~L~d~~tL~~y~I~~gstl~L~~   72 (73)
T d1m94a_          37 TQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLELYY   72 (73)
T ss_dssp             CTTTSEEEESSSCEECTTSBHHHHTCCTTEEEEEEE
T ss_pred             ccccEEEEEEEeEEecccCcHHHcCCCCCCEEEEEE
Confidence            799999999999999     9999999999999974

>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=98.96  E-value=2.1e-10  Score=68.19  Aligned_cols=35  Identities=26%  Similarity=0.440  Sum_probs=31.6

Q ss_pred             CC--CCceEEEecCccc-----cccccccCCC------cceeeeeecC
Q 042212            1 MP--LEQQRLVFADKSL-----LADYNIQKES------TLHLVARLRG   35 (97)
Q Consensus         1 ip--~~~q~L~~~~~~L-----l~~y~i~~~s------~i~l~~~~~~   35 (97)
                      ||  +++|||+|+||+|     |++|+|.+|+      ++||++|.+.
T Consensus        49 iP~~~~~qRLIf~Gk~L~D~~tL~dy~i~~g~~~~~~~tmHlVvrpp~   96 (101)
T d1se9a_          49 GPKTVKEVKLISAGKVLENSKTVKDYRSPVSNLAGAVTTMHVIIQAPV   96 (101)
T ss_dssp             SCCSGGGEEEEETTEECCTTSBGGGGSCCTTSCTTCCEEEEEEECCCS
T ss_pred             CCCCcccEEEEECCeEecCCCCHHHcCCCCCCcCCCceEEEEEeCCCC
Confidence            56  7799999999999     9999999997      9999998754

>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=98.80  E-value=1e-09  Score=64.54  Aligned_cols=35  Identities=23%  Similarity=0.362  Sum_probs=31.8

Q ss_pred             CCCCceEEEecCccc------cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL------LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L------l~~y~i~~~s~i~l~~~~~~   35 (97)
                      +|.++|||+|+|+.|      |++|||.+|++|||+++.++
T Consensus        40 ~~~~~qrLi~~Gk~L~dd~~tL~~y~i~~g~~v~l~~~~~~   80 (95)
T d1wiaa_          40 GQESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRSPPG   80 (95)
T ss_dssp             STTTTCEEEETTEECCCSSCBTTTTTCCTTEEEEEECCCCC
T ss_pred             CCcceeEEEECCEEcccCCCCHHHcCCCCCCEEEEEEcCCC
Confidence            478999999999999      99999999999999987654

>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=98.78  E-value=4.9e-10  Score=66.67  Aligned_cols=36  Identities=19%  Similarity=0.450  Sum_probs=33.0

Q ss_pred             CCCCceEEEecCccc------cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL------LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L------l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      ||+++|+|+|+|++|      |++|||.+|++|+|+.+....
T Consensus        47 ip~~~Q~Li~~Gk~L~dd~~tL~~~gI~~g~~i~l~~r~~~~   88 (102)
T d1v5oa_          47 VPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVLLQKDNVG   88 (102)
T ss_dssp             CCGGGBCEEETTEEECCSSSBHHHHTCCTTEEEEECBCCCCC
T ss_pred             CCcceEEEEeCCeEeecccCCHHHcCCCCCCEEEEEECCCCC
Confidence            799999999999999      999999999999999886544

>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=98.77  E-value=2.4e-09  Score=65.00  Aligned_cols=33  Identities=30%  Similarity=0.419  Sum_probs=29.5

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCc--ceeeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKEST--LHLVARL   33 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~--i~l~~~~   33 (97)
                      +|+++|||+|+||.|     |++|+|.+|++  +||+++.
T Consensus        60 ~~~~~qRLiy~Gk~L~D~~tL~~~~i~~g~~~~lhlv~r~   99 (116)
T d1wgha_          60 SSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLVARE   99 (116)
T ss_dssp             CCTTTEEEEETTEEECSSCBTTTTTCCSSCEEEEEEEECS
T ss_pred             CChHHeEEEECCEEecCCCCHHHcCCCCCCEEEEEEEeCC
Confidence            589999999999999     99999999987  7777764

>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=98.76  E-value=9.8e-10  Score=62.71  Aligned_cols=34  Identities=32%  Similarity=0.533  Sum_probs=31.6

Q ss_pred             CCCCceEEEecCccc------cccccccCCCcceeeeeec
Q 042212            1 MPLEQQRLVFADKSL------LADYNIQKESTLHLVARLR   34 (97)
Q Consensus         1 ip~~~q~L~~~~~~L------l~~y~i~~~s~i~l~~~~~   34 (97)
                      ||+++|+|+|+|+.|      |++|||.+|++|+|+.+..
T Consensus        41 vp~~~QkL~~~G~~L~~d~~tL~~~gi~~g~~i~lv~~~~   80 (81)
T d1wxva1          41 VPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVMLIGKKN   80 (81)
T ss_dssp             CCTTTCEEEETTEEECCSSSBHHHHTCCSSEEEEEESCCS
T ss_pred             cCHHHEEeeecCeEeCcCCCChHHCCCCCCCEEEEEEecC
Confidence            799999999999998      9999999999999998743

>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=98.72  E-value=7.3e-09  Score=60.07  Aligned_cols=57  Identities=11%  Similarity=0.099  Sum_probs=44.7

Q ss_pred             eeEEEC-CCCCEEEEeecCCCcHHHhhcccc-------------CCCe-------eCCCCCcccccccCCCCEEEEEE
Q 042212           38 QIFVKT-STGKTITLEVESSDMIDNASRGSS-------------SPAG-------NFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        38 ~i~vk~-~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk-------~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      .+.|.+ .++..+...+++++||.+||++|+             |.|+       ..+|+++|++|||.+|++||++=
T Consensus         6 ~l~it~~~t~~~~E~r~~~~~TV~~LK~kle~~~Gip~~~q~L~~~~~~~~~~~~l~dd~~~L~~ygi~dG~~Ihvvd   83 (90)
T d1t0ya_           6 DLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHAVD   83 (90)
T ss_dssp             EEEEEESSCCSCEEEEEETTSBHHHHHHHHHHHHCCCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEEEEEE
T ss_pred             EEEEEECCCccEEEEecCCCCCHHHHHHHHHHHHCCChhheEEEEeCCCCCcccccccCCCCHHHCCCCCCCEEEEEe
Confidence            344433 344557788899999999999999             4443       45789999999999999999963

>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=98.68  E-value=1.8e-09  Score=63.46  Aligned_cols=32  Identities=9%  Similarity=0.266  Sum_probs=30.5

Q ss_pred             CCCCceEEEecCccc----cccccccCCCcceeeee
Q 042212            1 MPLEQQRLVFADKSL----LADYNIQKESTLHLVAR   32 (97)
Q Consensus         1 ip~~~q~L~~~~~~L----l~~y~i~~~s~i~l~~~   32 (97)
                      ||+++|+|+|+|++|    |++|||.+|++|+|+.+
T Consensus        43 vp~~~QkLi~~Gk~L~d~tL~~~gi~~g~~i~lv~t   78 (96)
T d1wgga_          43 VQPARQKVMVKGGTLKDDDWGNIKMKNGMTVLMMGS   78 (96)
T ss_dssp             CCTTTSCCEETTEECCSSCCCSCCCCSSCEEECCCC
T ss_pred             ccceeeEEeecCcccCCCcHHHCCCCCCCEEEEEee
Confidence            799999999999999    99999999999999865

>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=98.61  E-value=5.9e-09  Score=61.65  Aligned_cols=33  Identities=12%  Similarity=0.207  Sum_probs=30.5

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARL   33 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~   33 (97)
                      ||+++|+|+|+|+.|     |++|||.++++|+++...
T Consensus        55 i~~~~qkLi~~Gk~L~d~~tL~~~gI~~~s~i~vi~~~   92 (100)
T d1wjua_          55 LQENYIKIVINKKQLQLGKTLEEQGVAHNVKAMVLELK   92 (100)
T ss_dssp             CCSTTCEEEETTEECCTTSBHHHHTCCSSEEEEEECCC
T ss_pred             CCCeeEEEEEcccCcCCCcCHHHcCCCCCCEEEEEEcC
Confidence            699999999999999     999999999999887653

>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=98.56  E-value=1.2e-08  Score=60.71  Aligned_cols=35  Identities=29%  Similarity=0.403  Sum_probs=28.5

Q ss_pred             CCCCceEEEecCccc-----cccccccCCC-------cceeeeeecC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKES-------TLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s-------~i~l~~~~~~   35 (97)
                      ||+++|||+|+|++|     |++|||.+++       +++|.++..+
T Consensus        36 ip~~~QrLi~~Gk~L~D~~TL~dYgI~~~~~~~~~~~~~~l~~~~~~   82 (103)
T d2c9wb1          36 RPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADD   82 (103)
T ss_dssp             CCGGGEEEEETTEECCTTSBHHHHTCCTTTSBTTBCEEEEEEEEETT
T ss_pred             CCcccEEEEECCEEcCCCCCHHHcCCCcccccccCCcEEEEEEecCC
Confidence            799999999999999     9999996655       5666665544

>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=98.56  E-value=1.3e-09  Score=65.03  Aligned_cols=28  Identities=29%  Similarity=0.536  Sum_probs=25.9

Q ss_pred             EEEecCccc------cccccccCCCcceeeeeec
Q 042212            7 RLVFADKSL------LADYNIQKESTLHLVARLR   34 (97)
Q Consensus         7 ~L~~~~~~L------l~~y~i~~~s~i~l~~~~~   34 (97)
                      +|+|+|+.|      |.+|||.+|++|||+.+++
T Consensus        64 ~Li~~G~~L~d~~~tL~~~gI~~g~~l~lv~r~~   97 (105)
T d1v2ya_          64 HLTSAGEKLTEDRKKLRDYGIRNRDEVSFIKKLG   97 (105)
T ss_dssp             EEESSSCEECCSSSBHHHHTCCSSEEEEEEECSC
T ss_pred             EEEECCEECcccCCCHHHcCCCCCCEEEEEEecC
Confidence            399999999      9999999999999999864

>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=98.55  E-value=1.3e-08  Score=59.39  Aligned_cols=34  Identities=38%  Similarity=0.556  Sum_probs=29.1

Q ss_pred             CCCCceEEEecCccc-----cccccccCCC--cceeeeeec
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKES--TLHLVARLR   34 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s--~i~l~~~~~   34 (97)
                      +|+++|||+|+|++|     |++|++..++  +|||+.+..
T Consensus        47 ~~~~~qrLIy~Gk~L~D~~~L~d~~~~~~~~~viHLV~~~~   87 (93)
T d1wgda_          47 PRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVCNVK   87 (93)
T ss_dssp             CCTTTCEEEETTEECCSSSCHHHHSCSSSCSEEEEEECCCC
T ss_pred             CChHHEEEEECCeEccCCCCHHHhCcccCCCCEEEEEecCC
Confidence            589999999999999     9999766554  999998754

>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=98.55  E-value=2.2e-08  Score=56.48  Aligned_cols=36  Identities=8%  Similarity=0.257  Sum_probs=33.1

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeecCC
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLRGR   36 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~~~   36 (97)
                      +|+++|+|+|+|+.|     +++|||++|++|+++++..|+
T Consensus        39 i~~~~~~l~f~G~~l~~~~T~~~~~i~dgd~I~v~~~q~GG   79 (79)
T d1euvb_          39 KEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGG   79 (79)
T ss_dssp             CCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCBCC
T ss_pred             CChHhEEEEECCEEeCCCCCHHHCCCCCCCEEEEEEeccCC
Confidence            588999999999999     999999999999999987653

>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=98.46  E-value=2.6e-08  Score=57.55  Aligned_cols=33  Identities=15%  Similarity=0.312  Sum_probs=30.5

Q ss_pred             CCCCceEEE---ecCccc-----cccccccCCCcceeeeee
Q 042212            1 MPLEQQRLV---FADKSL-----LADYNIQKESTLHLVARL   33 (97)
Q Consensus         1 ip~~~q~L~---~~~~~L-----l~~y~i~~~s~i~l~~~~   33 (97)
                      ||+++|+|+   |.|+.|     |++|||++|++|||+.+.
T Consensus        43 vp~~~QkLi~~~~~Gk~L~D~~tL~~~~i~~g~~i~lv~s~   83 (90)
T d1v5ta_          43 VLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMGTR   83 (90)
T ss_dssp             CCTTTCEEESCEETTEECCTTSBHHHHTCCTTEEEEEECCC
T ss_pred             CCHHHhhhhhhccCCcCCCCcCcHHHcCCCCCCEEEEEeeC
Confidence            799999999   689999     999999999999998764

>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=98.37  E-value=1.8e-08  Score=58.87  Aligned_cols=32  Identities=13%  Similarity=0.375  Sum_probs=29.3

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARL   33 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~   33 (97)
                      ||+++|+|+|+|+ |     |++|||.+|++|+|+.+.
T Consensus        52 vp~~~q~Li~~g~-l~D~~tL~~~~I~~gs~i~lvgs~   88 (95)
T d1v86a_          52 LPPAMQKVMYKGL-VPEDKTLREIKVTSGAKIMVVGST   88 (95)
T ss_dssp             SCSTTCCCBSSSB-CCSSSBHHHHCCCTTEEEEECCSS
T ss_pred             CChhHEEEEeccc-ccCCCcHHHCCCCCCCEEEEEecC
Confidence            7999999999987 6     999999999999998764

>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=98.36  E-value=5.8e-08  Score=56.70  Aligned_cols=35  Identities=17%  Similarity=0.336  Sum_probs=31.1

Q ss_pred             CCCCceEEEecCcc------c------cccccccCCCcceeeeeecC
Q 042212            1 MPLEQQRLVFADKS------L------LADYNIQKESTLHLVARLRG   35 (97)
Q Consensus         1 ip~~~q~L~~~~~~------L------l~~y~i~~~s~i~l~~~~~~   35 (97)
                      ||+++|+|+|.|++      |      |++|||.+|++|||+.+.+.
T Consensus        44 ip~~~qrL~~~~~~~~~~~~l~~d~~~L~~y~i~dg~~ihlvd~~p~   90 (95)
T d1v6ea_          44 SPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIHVIDHSGS   90 (95)
T ss_dssp             SCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCEEEEBCCSCC
T ss_pred             cCchhEEEEEeCCCCceeecccCCcCCHHHCCCCCCCEEEEEeCCCC
Confidence            79999999998984      3      99999999999999987654

>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=98.28  E-value=2.4e-07  Score=54.07  Aligned_cols=32  Identities=19%  Similarity=0.343  Sum_probs=28.1

Q ss_pred             CCCCceEEEecCcc-------c------cccccccCCCcceeeee
Q 042212            1 MPLEQQRLVFADKS-------L------LADYNIQKESTLHLVAR   32 (97)
Q Consensus         1 ip~~~q~L~~~~~~-------L------l~~y~i~~~s~i~l~~~   32 (97)
                      ||+++|+|+|.|+.       |      |.+|||++|++|++.-.
T Consensus        48 ip~~~qrL~y~~~~~~~~~~~l~~d~~tL~~YgI~dg~~I~V~~~   92 (97)
T d1wjna_          48 VPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCLLVRWS   92 (97)
T ss_dssp             CCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTCCTTCEEEEECC
T ss_pred             cChHHeEEEecCCCCCcccceecCCCcCHhhccCCCCCEEEEEeC
Confidence            79999999999974       3      99999999999997643

>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=98.20  E-value=1.8e-06  Score=47.62  Aligned_cols=57  Identities=11%  Similarity=0.217  Sum_probs=51.4

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEE
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~   93 (97)
                      +.|.|+..+|+.+.+.|.++.+...|...-+             |+|..+.++.|.+++++++|++|.+.
T Consensus         2 I~lkv~~~~g~~v~f~vk~~t~l~kl~~~y~~~~~~~~~~~~f~fdG~~i~~~~Tp~~l~med~D~Idv~   71 (72)
T d1wm3a_           2 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVF   71 (72)
T ss_dssp             EEEEEECTTSCEEEEEECTTSCTHHHHHHHHHHHTCCTTTCEEEETTEECCTTCCTTTTTCCTTEEEEEE
T ss_pred             EEEEEECCCCCEEEEEEcCCChHHHHHHHHHHHhCCCccceEEEECCEEcCCCCCHHHcCCCCCCEEEEE
Confidence            4677888899999999999999999987766             99999999999999999999999863

>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=98.11  E-value=8.8e-07  Score=50.96  Aligned_cols=34  Identities=21%  Similarity=0.338  Sum_probs=29.4

Q ss_pred             CCCCceEEEecCcc------c------cccccccCCCcceeeeeec
Q 042212            1 MPLEQQRLVFADKS------L------LADYNIQKESTLHLVARLR   34 (97)
Q Consensus         1 ip~~~q~L~~~~~~------L------l~~y~i~~~s~i~l~~~~~   34 (97)
                      ||+++|+|+|.|+.      |      |++|||.+|++||++=..+
T Consensus        41 ip~~~q~L~~~~~~~~~~~~l~dd~~~L~~ygi~dG~~Ihvvd~~~   86 (90)
T d1t0ya_          41 TTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHAVDVTG   86 (90)
T ss_dssp             CCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEEEEEECTT
T ss_pred             CChhheEEEEeCCCCCcccccccCCCCHHHCCCCCCCEEEEEeCCC
Confidence            79999999998874      3      9999999999999976543

>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=97.97  E-value=7e-06  Score=47.24  Aligned_cols=54  Identities=11%  Similarity=0.135  Sum_probs=41.3

Q ss_pred             eEEECCCCCEEEEeec-CCCcHHHhhcccc--------------------------C-CCeeCCC-CCcccccccCCCCE
Q 042212           39 IFVKTSTGKTITLEVE-SSDMIDNASRGSS--------------------------S-PAGNFED-GWTQADYNIQKEST   89 (97)
Q Consensus        39 i~vk~~~g~~~~l~v~-~~~tV~~lK~~I~--------------------------~-~gk~L~d-~~tL~~y~I~~~st   89 (97)
                      |.||+.+| +-.++|+ ++.|+.+||.+|+                          + +-.-|.| ..+|+++||.+||.
T Consensus         3 iRiRsrdG-~eRv~v~~~~~Tl~~LK~~Ie~~L~VPv~~Q~LSl~~~llL~k~P~~~~~~~~l~d~~~~L~sl~i~hGsi   81 (94)
T d1wf9a1           3 LRVRSRDG-LERVSVDGPHITVSQLKTLIQDQLQIPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLAHGSM   81 (94)
T ss_dssp             EEEECSSC-EEEEEECCTTSBHHHHHHHHHHHSCCCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTCCCTTCE
T ss_pred             EEEEecCC-ceEEEecCCCCcHHHHHHHHHHHhCCCcccceeecChhhhccCCccccchhhhccCCccCHHHcCccCceE
Confidence            66888887 4467885 4789999999999                          1 1223544 56799999999999


Q ss_pred             EEEE
Q 042212           90 LHFV   93 (97)
Q Consensus        90 i~l~   93 (97)
                      |++.
T Consensus        82 vyL~   85 (94)
T d1wf9a1          82 VYLA   85 (94)
T ss_dssp             EECC
T ss_pred             EEEE
Confidence            9975

>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=97.88  E-value=2.7e-06  Score=47.38  Aligned_cols=34  Identities=12%  Similarity=0.427  Sum_probs=31.2

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceeeeeec
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLVARLR   34 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~~~~~   34 (97)
                      +|+++++|+|+|+.|     ++++|+++|.+|+++++..
T Consensus        38 ~~~~~~~f~fdG~~l~~~~T~~~l~~edgD~Idv~~~q~   76 (77)
T d2uyzb1          38 VPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQT   76 (77)
T ss_dssp             CCGGGEEEEETTEECCTTCCHHHHTCCTTEEEEEEECCC
T ss_pred             CChhHEEEEECCEECCCCCCHHHcCCCCCCEEEEEEecC
Confidence            688999999999999     9999999999999998643

>d1h8ca_ d.15.1.2 (A:) Fas-associated factor 1, Faf1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: Fas-associated factor 1, Faf1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.36  E-value=0.00019  Score=39.97  Aligned_cols=58  Identities=10%  Similarity=0.113  Sum_probs=50.2

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc--------------CCCeeCC---CCCcccccccCCCCEEEEE
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS--------------SPAGNFE---DGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~--------------~~gk~L~---d~~tL~~y~I~~~sti~l~   93 (97)
                      ..+|.||.++|+.+.-...+++|+.+|.+-+.              |-.+.+.   ++.||++.|+.+.+++++-
T Consensus         5 ~~~i~iRlPdG~~~~~~F~~~~tl~~v~~~v~~~~~~~~~~~l~~~~Pr~~l~~~d~~~TL~e~gL~p~~~L~vq   79 (82)
T d1h8ca_           5 VSKLRIRTPSGEFLERRFLASNKLQIVFDFVASKGFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLE   79 (82)
T ss_dssp             CEEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHTCCSSSEEEEETTTTEETTTCCTTSBHHHHCCCSEEEEEEE
T ss_pred             cEEEEEECCCCCEEEEEECCCCcHHHHHHHHHhcCCCCCceEEEecCcccccccccccCCHHHCCCCCCCEEEEE
Confidence            35789999999999999999999999998887              7777773   4689999999999988864

>d2cr5a1 d.15.1.2 (A:8-103) UBX domain-containing protein 6 (Reproduction 8) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: UBX domain-containing protein 6 (Reproduction 8)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.24  E-value=0.00022  Score=40.69  Aligned_cols=59  Identities=14%  Similarity=0.106  Sum_probs=49.8

Q ss_pred             CCeeeEEECCCCCEEEEeecCCCcHHHhhcccc--------------CCCeeCC--CCCcccccccCCCCEEEEE
Q 042212           35 GRMQIFVKTSTGKTITLEVESSDMIDNASRGSS--------------SPAGNFE--DGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        35 ~~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~--------------~~gk~L~--d~~tL~~y~I~~~sti~l~   93 (97)
                      +..+|.||.++|+.+.-...+++||.+|..-+.              |-.+.+.  .+.||++.|+.+.+++++-
T Consensus        15 ~~~~i~iRlPdG~r~~r~F~~~dtl~~l~~fv~~~~~~~~~f~l~~~~Pr~~~~~d~~~TL~e~gl~p~~~L~v~   89 (96)
T d2cr5a1          15 EVVTVALRCPNGRVLRRRFFKSWNSQVLLDWMMKVGYHKSLYRLSTSFPRRALEVEGGSSLEDIGITVDTVLNVE   89 (96)
T ss_dssp             SEEEEEEECTTSCEEEEEEESSSBTHHHHHHHHHHTCCTTTEEEECSSSCCBCCCCSSCBHHHHTCSSCEEEEEE
T ss_pred             CeEEEEEECCCCCEEEEEECCcccHHHHHHHHHHhccCcccceeecCCCceecCccCCCcHHHCCCCCCCEEEEe
Confidence            448899999999999999999999999998887              4456663  3689999999999888774

>d1i42a_ d.15.1.2 (A:) p47 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: p47
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.17  E-value=0.00042  Score=39.14  Aligned_cols=52  Identities=13%  Similarity=0.181  Sum_probs=44.5

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc----------------CCCeeC-CCCCcccccccCCC
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS----------------SPAGNF-EDGWTQADYNIQKE   87 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~----------------~~gk~L-~d~~tL~~y~I~~~   87 (97)
                      ...|.||.++|+.+...+.+++||.+|.+-+.                |--+.+ +++.||.+.|+.+.
T Consensus        14 ~t~I~iRlPdG~~~~~~F~~~~tl~dv~~~v~~~~~~~~~~~f~L~t~~Prr~l~d~~~TL~e~gL~~s   82 (89)
T d1i42a_          14 TTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFPNKELADENQTLKEANLLNA   82 (89)
T ss_dssp             CEEEEEEETTTCCEEEEECSSSCGGGHHHHHHHHCTTTSSCCEEEEETTTTEECCCCSSCSGGGTTCCS
T ss_pred             cEEEEEEcCCCCEEEEEECCchhHHHHHHHHHHhCccCCCCCEEEecCCCCcccCCCcCcHHHCCCcCc
Confidence            46788999999999999999999999998875                566778 45789999999864

>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=96.91  E-value=0.00079  Score=37.13  Aligned_cols=56  Identities=14%  Similarity=0.136  Sum_probs=49.9

Q ss_pred             eEEECCCCCEEEEeecCCCcHHHhhcccc-------------CCCeeCCCCCcccccccCCCCEEEEEE
Q 042212           39 IFVKTSTGKTITLEVESSDMIDNASRGSS-------------SPAGNFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        39 i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-------------~~gk~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      +.|=.++|+..++.|.|+.|+.++-+...             |+++.++-..++.-.|+.+|+.+.|+-
T Consensus         3 V~Vl~~~~rR~~VKvtP~t~l~~VL~eaC~k~~~~~~~~~Lkh~~k~ldLsl~~R~sgLpnnakLELv~   71 (76)
T d2al3a1           3 VSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQDFNPSEYDLKFQRTVLDLSLQWRFANLPNNAKLEMVP   71 (76)
T ss_dssp             EEEECTTSCEEEECCCTTSBHHHHHHHHHHHTTCCGGGCEEEETTEEESSSCBHHHHCCCSSCEEEEEC
T ss_pred             EEEECCCCcEEEEEeCCCcCHHHHHHHHHHHhCCChhHceeeeCCEEcCccceeeecCCCCCCEEEEEE
Confidence            56678899999999999999998876665             889999999999999999999999874

>d1wj4a_ d.15.1.2 (A:) Hypothetical protein KIAA0794 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: Hypothetical protein KIAA0794
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.81  E-value=0.00086  Score=40.03  Aligned_cols=58  Identities=10%  Similarity=0.153  Sum_probs=49.9

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc--------------CCCeeCC---CCCcccccccCCCCEEEEE
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS--------------SPAGNFE---DGWTQADYNIQKESTLHFV   93 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~--------------~~gk~L~---d~~tL~~y~I~~~sti~l~   93 (97)
                      ..+|.||.++|+.+.-.+..++||.+|.+-+.              |--+.|.   .+.||.+.|+.+.++|++-
T Consensus        43 ~~~l~iRlPdG~r~~r~F~~~~tl~~l~~~v~~~~~~~~~~~L~~~fPr~~l~~~d~~~TL~e~gL~P~~~L~ve  117 (124)
T d1wj4a_          43 KAQLMLRYPDGKREQITLPEQAKLLALVKHVQSKGYPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQ  117 (124)
T ss_dssp             EEEEEEECTTSCEEEEEEETTSCHHHHHHHHHHHHCCTTTEEEECSSSCCEETSSCSSSCTTTTTCCSSBCCEEE
T ss_pred             ceEEEEECCCCCEEEEEeCCCCcHHHHHHHHHhcccCCcceEEeecccccccccccccCcHHHcCCCCCCEEEEE
Confidence            37899999999999999999999999999887              6667773   4689999999998888763

>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=95.31  E-value=0.0029  Score=36.39  Aligned_cols=15  Identities=7%  Similarity=-0.237  Sum_probs=14.0

Q ss_pred             CCCCceEEEecCccc
Q 042212            1 MPLEQQRLVFADKSL   15 (97)
Q Consensus         1 ip~~~q~L~~~~~~L   15 (97)
                      ||+++|+|+|+|++|
T Consensus        64 ip~~~qrLi~~Gk~L   78 (100)
T d1uh6a_          64 TRWNKIVLKKWYTIF   78 (100)
T ss_dssp             CCGGGCEEEETTEEC
T ss_pred             CCcceEEEEEEeecc
Confidence            799999999999987

>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=95.17  E-value=0.0023  Score=36.44  Aligned_cols=32  Identities=19%  Similarity=0.322  Sum_probs=25.0

Q ss_pred             CCCCceEEEec-------------Cc-cc------cccccccCCCcceeeee
Q 042212            1 MPLEQQRLVFA-------------DK-SL------LADYNIQKESTLHLVAR   32 (97)
Q Consensus         1 ip~~~q~L~~~-------------~~-~L------l~~y~i~~~s~i~l~~~   32 (97)
                      ||.++|+|..+             .- .|      |+++||.+||.+||...
T Consensus        36 VPv~~Q~LSl~~~llL~k~P~~~~~~~~l~d~~~~L~sl~i~hGsivyL~y~   87 (94)
T d1wf9a1          36 IPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLAHGSMVYLAYE   87 (94)
T ss_dssp             CCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTCCCTTCEEECCCS
T ss_pred             CCcccceeecChhhhccCCccccchhhhccCCccCHHHcCccCceEEEEEee
Confidence            79999999543             11 12      99999999999999764

>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=95.15  E-value=0.0044  Score=35.50  Aligned_cols=15  Identities=40%  Similarity=0.465  Sum_probs=14.0

Q ss_pred             CCCCceEEEecCccc
Q 042212            1 MPLEQQRLVFADKSL   15 (97)
Q Consensus         1 ip~~~q~L~~~~~~L   15 (97)
                      ||+++|+|+|+|++|
T Consensus        67 i~~~~qrLi~~Gk~L   81 (103)
T d1j8ca_          67 SQTDQLVLIFAGKIL   81 (103)
T ss_dssp             SCSSSEEEEETTEEE
T ss_pred             cCHHHeeeeeeeecc
Confidence            799999999999987

>d1ef1a3 d.15.1.4 (A:4-87) Moesin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: First domain of FERM
domain: Moesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.36  E-value=0.12  Score=28.30  Aligned_cols=60  Identities=13%  Similarity=0.145  Sum_probs=46.6

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc-----------------CCC--eeCCCCCcccccccCCCCEEEEEEee
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS-----------------SPA--GNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~-----------------~~g--k~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      +|++.|..+++ ++++.+++..+..++-.++.                 ..|  .-|+.+..+..+..+.+....+.+|.
T Consensus         1 t~~v~V~~LD~-~~~~~v~~~a~G~~l~~~Vc~~l~L~E~dYFGL~y~d~~~~~~WLd~~k~l~kq~~~~~~~~~l~F~V   79 (84)
T d1ef1a3           1 TISVRVTTMDA-ELEFAIQPNTTGKQLFDQVVKTIGLREVWFFGLQYQDTKGFSTWLKLNKKVTAQDVRKESPLLFKFRA   79 (84)
T ss_dssp             CEEEEEEETTE-EEEEEECTTCBHHHHHHHHHHHHTCCCGGGEEEEEEBTTSCEEECCSSSBGGGSCBCCCSSEEEEEEE
T ss_pred             CEEEEEEEcCC-EEEEEEcCCChHHHHHHHHHHHcCCcccccceEEEECCCCCeEeccCCCchhhhccCCCCCEEEEEEE
Confidence            47899999997 58999999999999988888                 222  34788899999877777766665553

>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=93.12  E-value=0.033  Score=29.65  Aligned_cols=30  Identities=20%  Similarity=0.464  Sum_probs=26.7

Q ss_pred             CCCCceEEEecCccc-----cccccccCCCcceee
Q 042212            1 MPLEQQRLVFADKSL-----LADYNIQKESTLHLV   30 (97)
Q Consensus         1 ip~~~q~L~~~~~~L-----l~~y~i~~~s~i~l~   30 (97)
                      +|+++.+++|+|+.+     -+++|+++|..|.+.
T Consensus        37 ~~~~~~~f~fdG~~i~~~~Tp~~l~med~D~Idv~   71 (72)
T d1wm3a_          37 LSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVF   71 (72)
T ss_dssp             CCTTTCEEEETTEECCTTCCTTTTTCCTTEEEEEE
T ss_pred             CCccceEEEECCEEcCCCCCHHHcCCCCCCEEEEE
Confidence            477889999999998     999999999998764

>d1vjka_ d.15.3.1 (A:) Molybdopterin synthase subunit MoaD {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: MoaD/ThiS
family: MoaD
domain: Molybdopterin synthase subunit MoaD
species: Pyrococcus furiosus [TaxId: 2261]

Probab=91.21  E-value=0.42  Score=25.62  Aligned_cols=59  Identities=8%  Similarity=0.090  Sum_probs=38.1

Q ss_pred             CeeeEEECCC------C-CEEEEeecCCCcHHHhhcccc--CCC---ee-------------C-CCCCcccccccCCCCE
Q 042212           36 RMQIFVKTST------G-KTITLEVESSDMIDNASRGSS--SPA---GN-------------F-EDGWTQADYNIQKEST   89 (97)
Q Consensus        36 ~m~i~vk~~~------g-~~~~l~v~~~~tV~~lK~~I~--~~g---k~-------------L-~d~~tL~~y~I~~~st   89 (97)
                      +|+|.|+...      | ....+++....||.++.+.+.  |.+   ..             . .+...=.++-+++|+.
T Consensus         1 smkI~v~~Fa~lre~~G~~~~~~~~~~~~Tv~~l~~~L~~~~~~~~~~l~~~~~~~~~~i~iavN~~~~~~d~~L~~gDe   80 (88)
T d1vjka_           1 SVKVKVKYFARFRQLAGVDEEEIELPEGARVRDLIEEIKKRHEKFKEEVFGEGYDEDADVNIAVNGRYVSWDEELKDGDV   80 (88)
T ss_dssp             CEEEEEEECTHHHHHHSSSEEEEEECTTCBHHHHHHHHHHHCGGGGGSCBCSSSCTTSSBEEEETTBCCCTTCBCCTTCE
T ss_pred             CeEEEEEEhHHHHHHhCCCeEEEECCCCCCHHHHHHHHHHHChHHHHHhhhccccccccEEEEEcceEcCCCcCcCCCCE
Confidence            4778887753      4 467889988999999998886  211   11             0 1111123566888998


Q ss_pred             EEEEE
Q 042212           90 LHFVL   94 (97)
Q Consensus        90 i~l~~   94 (97)
                      |.+..
T Consensus        81 vai~P   85 (88)
T d1vjka_          81 VGVFP   85 (88)
T ss_dssp             EEEES
T ss_pred             EEEeC
Confidence            88764

>d2incc1 d.15.12.1 (C:3-85) Toluene, o-xylene monooxygenase oxygenase subunit TouB {Pseudomonas stutzeri [TaxId: 316]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: TmoB-like
family: TmoB-like
domain: Toluene, o-xylene monooxygenase oxygenase subunit TouB
species: Pseudomonas stutzeri [TaxId: 316]

Probab=90.46  E-value=0.27  Score=26.80  Aligned_cols=45  Identities=18%  Similarity=0.356  Sum_probs=39.2

Q ss_pred             EEeecCCCcHHHhhcccc---------------------CCCeeCCCCCcccccccCCCCEEEEEE
Q 042212           50 TLEVESSDMIDNASRGSS---------------------SPAGNFEDGWTQADYNIQKESTLHFVL   94 (97)
Q Consensus        50 ~l~v~~~~tV~~lK~~I~---------------------~~gk~L~d~~tL~~y~I~~~sti~l~~   94 (97)
                      -+.|+.++|+.++-++++                     .+|..+..+.++++-||++-..+.+..
T Consensus        16 LVaVDt~dtmdqVA~k~A~HsVGRRv~p~P~~~~rvr~~~~ge~~pr~~tv~~~gi~P~e~iev~f   81 (83)
T d2incc1          16 LVPVDTEDTMDQVAEKCAYHSINRRVHPQPEKILRVRRHEDGTLFPRGMIVSDAGLRPTETLDIIF   81 (83)
T ss_dssp             EEEECTTCBHHHHHHHHHTTTBTTTBCCCTTSEEEEEETTTCCEECTTCBGGGSCCCTTCEEEEEE
T ss_pred             EEEEcCCCcHHHHHHHHHHHhhccccCCCCCCccEEEEcCCCcCCCCCCChhhcCCCCceEEEEEE
Confidence            357899999999999988                     578889999999999999999888754

>d1h4ra3 d.15.1.4 (A:20-103) Merlin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: First domain of FERM
domain: Merlin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.65  E-value=0.65  Score=25.13  Aligned_cols=60  Identities=10%  Similarity=0.004  Sum_probs=46.1

Q ss_pred             CeeeEEECCCCCEEEEeecCCCcHHHhhcccc---------CCC---------eeCCCCCcccccccCCCCEEEEEEee
Q 042212           36 RMQIFVKTSTGKTITLEVESSDMIDNASRGSS---------SPA---------GNFEDGWTQADYNIQKESTLHFVLRL   96 (97)
Q Consensus        36 ~m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~---------~~g---------k~L~d~~tL~~y~I~~~sti~l~~rl   96 (97)
                      .+.+.|..++++ +++++++..+-.++-.++.         |=|         .-|+.+.++..+.+..++.+.+.+|.
T Consensus         2 ~~~v~V~lLD~~-le~~v~~~a~G~~L~d~Vc~~L~L~E~~YFGL~y~~~~~~~WLd~~k~l~kq~~~~~~~~~~~F~V   79 (84)
T d1h4ra3           2 TFTVRIVTMDAE-MEFNCEMKWKGKDLFDLVCRTLGLRETWFFGLQYTIKDTVAWLKMDKKVLDHDVSKEEPVTFHFLA   79 (84)
T ss_dssp             EEEEEEECSSCE-EEEEEETTCBHHHHHHHHHHHHTCCCGGGEEEEEEETTEEEECCTTSBGGGSSCCCSSSEEEEEEE
T ss_pred             eEEEEEEEcCCc-EEEEEcCCChHHHHHHHHHHHcCCcccccceEEEecCCceEEccCCCchhhhccCCCCCEEEEEEE
Confidence            367889999974 7999999999999988888         111         34677889998887777776666553

>d1gg3a3 d.15.1.4 (A:1-81) Erythroid membrane protein 4.1R {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: First domain of FERM
domain: Erythroid membrane protein 4.1R
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.27  E-value=0.85  Score=24.47  Aligned_cols=31  Identities=13%  Similarity=-0.014  Sum_probs=28.2

Q ss_pred             eeeEEECCCCCEEEEeecCCCcHHHhhcccc
Q 042212           37 MQIFVKTSTGKTITLEVESSDMIDNASRGSS   67 (97)
Q Consensus        37 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~   67 (97)
                      |...|..++|+.+.+.+++..+..++-+++.
T Consensus         1 ~~C~V~lLD~~~~~~~v~~~~~G~~l~~~Vc   31 (81)
T d1gg3a3           1 MHCKVSLLDDTVYECVVEKHAKGQDLLKRVC   31 (81)
T ss_dssp             CEEEEECTTSCEEEEECCTTCCHHHHHHHHH
T ss_pred             CEEEEEecCCCEEEEEECCCCcHHHHHHHHH
Confidence            5678899999999999999999999988888