Citrus Sinensis ID: 040720

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70-------
Protein Sequence
RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVVR
Secondary Structure (PSIPRED)
cEEEEEEcccccHHHHHHHHHcccccccccccEEEEEEEEcccHHHHHHHHHHHHHcccccccEEEEcccccccccc
Secondary Structure Prediction (SSPRO)
cEEEEEEcccccHHHHHHHHHHHHcccHHHEEEEEEEEcccccEHHHHHHHHHHHHcccHHHEEEEEccEEccEEEc
Coil and Loop (DISEMBL)
rrlllmwkaptplinvkakiqdkegippdqQRLITtlevkssdtiNNVKSkiqdkegippdqQRLIFAGINLKLVVR
Flexible Loop (DISEMBL)
rrlllmwkaptplinvkakiqdkegippdQQRLIttlevkssdtinnvkskiqdkegippdqqrlifaginlklvvr
Low Complexity Region (SEG)
RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVVR
Disordered region (IsUnstruct)
***LLMWKAPTPLINVKA*********************************************RLIFAGINLKLV**
Disordered Region (DISOPRED)
RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKL***
Disordered Region (DISEMBL)
RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVVR
Disordered Region (DISPRO)
RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVVR
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVVR
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	77	2.2.26 [Sep-21-2011]
P0CG83	171	Polyubiquitin (Fragment)	N/A	no	0.766	0.345	0.504	6e-17
P0CG63	381	Polyubiquitin OS=Saccharo	yes	no	0.948	0.191	0.452	6e-17
P0CG84	377	Polyubiquitin (Fragment)	N/A	no	0.948	0.193	0.452	6e-17
P0CG75	381	Polyubiquitin OS=Kluyvero	yes	no	0.948	0.191	0.452	7e-17
P69315	305	Polyubiquitin (Fragment)	N/A	no	0.766	0.193	0.504	7e-17
Q8H159	457	Polyubiquitin 10 OS=Arabi	no	no	0.766	0.129	0.504	7e-17
P69322	381	Polyubiquitin OS=Pisum sa	N/A	no	0.766	0.154	0.504	7e-17
P0CG85	457	Polyubiquitin OS=Nicotian	N/A	no	0.766	0.129	0.504	7e-17
Q58G87	381	Polyubiquitin 3 OS=Oryza	yes	no	0.766	0.154	0.504	7e-17
P0CH32	382	Polyubiquitin 4 OS=Arabid	yes	no	0.766	0.154	0.504	7e-17

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

 Score = 86.3 bits (212), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 52/103 (50%), Positives = 56/103 (54%), Gaps = 44/103 (42%)

Query: 15  NVKAKIQDKEGIPPDQQRLI---------------------------------------- 34
           NVKAKIQDKEGIPPDQQRLI                                        
Sbjct: 43  NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTL 102

Query: 35  ----TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
                TLEV+SSDTI+NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 103 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE 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.
Hordeum vulgare (taxid: 4513)

>sp|P0CG63|UBI4P_YEAST Polyubiquitin OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=UBI4 PE=1 SV=1

 Score = 85.9 bits (211), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 53/117 (45%), Positives = 62/117 (52%), Gaps = 44/117 (37%)

Query: 1   RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLI-------------------------- 34
           + + L  ++   + NVK+KIQDKEGIPPDQQRLI                          
Sbjct: 11  KTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV 70

Query: 35  ------------------TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
                              TLEV+SSDTI+NVKSKIQDKEGIPPDQQRLIFAG  L+
Sbjct: 71  LRLRGGMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLE 127

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, 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.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

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

 Score = 85.9 bits (211), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 53/117 (45%), Positives = 62/117 (52%), Gaps = 44/117 (37%)

Query: 1   RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLI-------------------------- 34
           + + L  ++   + NVKAKIQDKEGIPPDQQRLI                          
Sbjct: 7   KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV 66

Query: 35  ------------------TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
                              TLEV+SSDTI+NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 67  LRLRGGMQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE 123

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|P0CG75|UBI4P_KLULA Polyubiquitin OS=Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) GN=ubi4 PE=1 SV=1

 Score = 85.9 bits (211), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 53/117 (45%), Positives = 62/117 (52%), Gaps = 44/117 (37%)

Query: 1   RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLI-------------------------- 34
           + + L  ++   + NVK+KIQDKEGIPPDQQRLI                          
Sbjct: 11  KTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV 70

Query: 35  ------------------TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
                              TLEV+SSDTI+NVKSKIQDKEGIPPDQQRLIFAG  L+
Sbjct: 71  LRLRGGMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLE 127

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, 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.

Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid: 284590)

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

 Score = 85.9 bits (211), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 52/103 (50%), Positives = 56/103 (54%), Gaps = 44/103 (42%)

Query: 15  NVKAKIQDKEGIPPDQQRLI---------------------------------------- 34
           NVKAKIQDKEGIPPDQQRLI                                        
Sbjct: 66  NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTL 125

Query: 35  ----TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
                TLEV+SSDTI+NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 126 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE 168

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

Linum usitatissimum (taxid: 4006)

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

 Score = 85.9 bits (211), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 52/103 (50%), Positives = 56/103 (54%), Gaps = 44/103 (42%)

Query: 15  NVKAKIQDKEGIPPDQQRLI---------------------------------------- 34
           NVKAKIQDKEGIPPDQQRLI                                        
Sbjct: 25  NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTL 84

Query: 35  ----TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
                TLEV+SSDTI+NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 85  TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE 127

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 = 85.9 bits (211), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 52/103 (50%), Positives = 56/103 (54%), Gaps = 44/103 (42%)

Query: 15  NVKAKIQDKEGIPPDQQRLI---------------------------------------- 34
           NVKAKIQDKEGIPPDQQRLI                                        
Sbjct: 25  NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTL 84

Query: 35  ----TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
                TLEV+SSDTI+NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 85  TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE 127

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

 Score = 85.9 bits (211), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 52/103 (50%), Positives = 56/103 (54%), Gaps = 44/103 (42%)

Query: 15  NVKAKIQDKEGIPPDQQRLI---------------------------------------- 34
           NVKAKIQDKEGIPPDQQRLI                                        
Sbjct: 25  NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTL 84

Query: 35  ----TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
                TLEV+SSDTI+NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 85  TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE 127

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

 Score = 85.9 bits (211), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 52/103 (50%), Positives = 56/103 (54%), Gaps = 44/103 (42%)

Query: 15  NVKAKIQDKEGIPPDQQRLI---------------------------------------- 34
           NVKAKIQDKEGIPPDQQRLI                                        
Sbjct: 25  NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTL 84

Query: 35  ----TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
                TLEV+SSDTI+NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 85  TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE 127

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

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score = 85.9 bits (211), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 52/103 (50%), Positives = 56/103 (54%), Gaps = 44/103 (42%)

Query: 15  NVKAKIQDKEGIPPDQQRLI---------------------------------------- 34
           NVKAKIQDKEGIPPDQQRLI                                        
Sbjct: 25  NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTL 84

Query: 35  ----TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
                TLEV+SSDTI+NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 85  TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE 127

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	77
149063235	163	rCG21224 [Rattus norvegicus]	0.766	0.361	0.796	1e-18
353237461	195	related to UBI4-Ubiquitin [Piriformospor	0.948	0.374	0.602	7e-18
388578851	701	ubiquitin [Wallemia sebi CBS 633.66]	0.766	0.084	0.653	1e-17
6118549	381	ubiquitin precursor [Hevea brasiliensis]	0.805	0.162	0.490	4e-16
400599610	212	Ubiquitin subgroup [Beauveria bassiana A	0.948	0.344	0.52	1e-15
16552475	388	unnamed protein product [Homo sapiens]	0.766	0.152	0.765	1e-15
297735960	204	unnamed protein product [Vitis vinifera]	0.649	0.245	0.762	1e-15
380446928	264	ubiquitin, partial [Trichoderma harzianu	0.896	0.261	0.466	1e-15
71020945	286	hypothetical protein UM04556.1 [Ustilago	0.766	0.206	0.504	1e-15
1332579	761	polyubiquitin [Pinus sylvestris]	0.948	0.095	0.461	1e-15

>gi|149063235|gb|EDM13558.1| rCG21224 [Rattus norvegicus]

 Score = 97.1 bits (240), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 51/64 (79%), Positives = 54/64 (84%), Gaps = 5/64 (7%)

Query: 15 NVKAKIQDKEGIPPDQQRLI-----TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG 69
          NVKAKIQDKEGIPPDQQRLI      TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG
Sbjct: 25 NVKAKIQDKEGIPPDQQRLIFAGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAG 84

Query: 70 INLK 73
            L+
Sbjct: 85 KQLE 88

Source: Rattus norvegicus

Species: Rattus norvegicus

Genus: Rattus

Family: Muridae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|353237461|emb|CCA69433.1| related to UBI4-Ubiquitin [Piriformospora indica DSM 11827]

 Score = 94.4 bits (233), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 50/83 (60%), Positives = 60/83 (72%), Gaps = 10/83 (12%)

Query: 1   RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRL----------ITTLEVKSSDTINNVKS 50
           + + L  ++   + NVK KIQDKEGIPPDQQR+            TLEV+SSDTI+NVK+
Sbjct: 87  KTITLEVESSDTIDNVKTKIQDKEGIPPDQQRMQIFVKTLTGKTITLEVESSDTIDNVKT 146

Query: 51  KIQDKEGIPPDQQRLIFAGINLK 73
           KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 147 KIQDKEGIPPDQQRLIFAGKQLE 169

Source: Piriformospora indica DSM 11827

Species: Piriformospora indica

Genus: Piriformospora

Family: Sebacinaceae

Order: Sebacinales

Class: Agaricomycetes

Phylum: Basidiomycota

Superkingdom: Eukaryota

>gi|388578851|gb|EIM19184.1| ubiquitin [Wallemia sebi CBS 633.66]

 Score = 93.6 bits (231), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 51/78 (65%), Positives = 55/78 (70%), Gaps = 19/78 (24%)

Query: 15  NVKAKIQDKEGIPPDQQRLI-------------------TTLEVKSSDTINNVKSKIQDK 55
           NVK KIQDKEGIPPDQQRLI                    TLEV+SSDTI+NVK+KIQDK
Sbjct: 177 NVKTKIQDKEGIPPDQQRLIFAGKQLEDGLFVKTLTGKTITLEVESSDTIDNVKTKIQDK 236

Query: 56  EGIPPDQQRLIFAGINLK 73
           EGIPPDQQRLIFAG  L+
Sbjct: 237 EGIPPDQQRLIFAGKQLE 254

Source: Wallemia sebi CBS 633.66

Species: Wallemia sebi

Genus: Wallemia

Order: Wallemiales

Class: Wallemiomycetes

Phylum: Basidiomycota

Superkingdom: Eukaryota

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

 Score = 88.6 bits (218), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 52/106 (49%), Positives = 58/106 (54%), Gaps = 44/106 (41%)

Query: 15  NVKAKIQDKEGIPPDQQRLI---------------------------------------- 34
           NVKAKIQDKEGIPPDQQR I                                        
Sbjct: 101 NVKAKIQDKEGIPPDQQRFIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTL 160

Query: 35  ----TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV 76
                TLEV+SSDTI+NVK+KIQDKEGIPPDQQRLIFAG +L++V 
Sbjct: 161 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGSSLRMVA 206

Source: Hevea brasiliensis

Species: Hevea brasiliensis

Genus: Hevea

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|400599610|gb|EJP67307.1| Ubiquitin subgroup [Beauveria bassiana ARSEF 2860]

 Score = 87.4 bits (215), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 52/100 (52%), Positives = 62/100 (62%), Gaps = 27/100 (27%)

Query: 1   RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLI--------------------TTLE-- 38
           + + L  ++   + NVK+KIQDKEGIPPDQQRLI                    +TL   
Sbjct: 87  KTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV 146

Query: 39  -----VKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
                V+SSDTI+NVKSKIQDKEGIPPDQQRLIFAG  L+
Sbjct: 147 LRLRGVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLE 186

Source: Beauveria bassiana ARSEF 2860

Species: Beauveria bassiana

Genus: Beauveria

Family: Cordycipitaceae

Order: Hypocreales

Class: Sordariomycetes

Phylum: Ascomycota

Superkingdom: Eukaryota

>gi|16552475|dbj|BAB71316.1| unnamed protein product [Homo sapiens]

 Score = 87.4 bits (215), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 49/64 (76%), Positives = 51/64 (79%), Gaps = 5/64 (7%)

Query: 15  NVKAKIQDKEGIPPDQQRLITT---LEVKS--SDTINNVKSKIQDKEGIPPDQQRLIFAG 69
           NVKAKIQDKEGIPPDQQRLI     LE     SDTI NVK+KIQDKEGIPPDQQRLIFAG
Sbjct: 299 NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDTIENVKAKIQDKEGIPPDQQRLIFAG 358

Query: 70  INLK 73
             L+
Sbjct: 359 KQLE 362

Source: Homo sapiens

Species: Homo sapiens

Genus: Homo

Family: Hominidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|297735960|emb|CBI23934.3| unnamed protein product [Vitis vinifera]

 Score = 87.4 bits (215), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 45/59 (76%), Positives = 48/59 (81%), Gaps = 9/59 (15%)

Query: 15 NVKAKIQDKEGIPPDQQRLITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          NVKAKIQDKEGIPPDQQ         SSDTI+NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 25 NVKAKIQDKEGIPPDQQ---------SSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE 74

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|380446928|gb|AFD53810.1| ubiquitin, partial [Trichoderma harzianum]

 Score = 87.0 bits (214), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 56/120 (46%), Positives = 61/120 (50%), Gaps = 51/120 (42%)

Query: 5   LMWKAPT-------PLINVKAKIQDKEGIPPDQQRLI----------------------- 34
           L WK  T        + NVK+KIQDKEGIPPDQQRLI                       
Sbjct: 89  LTWKTVTLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTL 148

Query: 35  ---------------------TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
                                 TLEV+SSDTI+NVKSKIQDKEGIPPDQQRLIFAG  L+
Sbjct: 149 HLVLRLRGGMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLE 208

Source: Trichoderma harzianum

Species: Trichoderma harzianum

Genus: Hypocrea

Family: Hypocreaceae

Order: Hypocreales

Class: Sordariomycetes

Phylum: Ascomycota

Superkingdom: Eukaryota

>gi|71020945|ref|XP_760703.1| hypothetical protein UM04556.1 [Ustilago maydis 521] gi|46100297|gb|EAK85530.1| hypothetical protein UM04556.1 [Ustilago maydis 521]

 Score = 87.0 bits (214), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 52/103 (50%), Positives = 56/103 (54%), Gaps = 44/103 (42%)

Query: 15  NVKAKIQDKEGIPPDQQRLI---------------------------------------- 34
           NVKAKIQDKEGIPPDQQRLI                                        
Sbjct: 83  NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTL 142

Query: 35  ----TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
                TLEV+SSDTI+NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 143 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE 185

Source: Ustilago maydis 521

Species: Ustilago maydis

Genus: Ustilago

Family: Ustilaginaceae

Order: Ustilaginales

Class: Ustilaginomycetes

Phylum: Basidiomycota

Superkingdom: Eukaryota

>gi|1332579|emb|CAA66667.1| polyubiquitin [Pinus sylvestris]

 Score = 87.0 bits (214), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 54/117 (46%), Positives = 62/117 (52%), Gaps = 44/117 (37%)

Query: 1   RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLI-------------------------- 34
           + + L  ++   + NVKAKIQDKEGIPPDQQRLI                          
Sbjct: 239 KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV 298

Query: 35  ------------------TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
                              TLEV+SSDTI+NVKSKIQDKEGIPPDQQRLIFAG  L+
Sbjct: 299 LRLRGGMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLE 355

Source: Pinus sylvestris

Species: Pinus sylvestris

Genus: Pinus

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

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	77
CGD|CAL0004945	229	UBI4 [Candida albicans (taxid:	0.493	0.165	0.868	4.1e-21
UNIPROTKB|Q5ADS0	229	UBI4 "Putative uncharacterized	0.493	0.165	0.868	4.1e-21
TAIR|locus:2138386	229	UBQ11 "AT4G05050" [Arabidopsis	0.493	0.165	0.842	4.1e-21
UNIPROTKB|F1PDG4	229	UBB "Uncharacterized protein"	0.493	0.165	0.815	1.4e-20
UNIPROTKB|J3QKN0	206	UBB "Ubiquitin" [Homo sapiens	0.493	0.184	0.815	1.4e-20
UNIPROTKB|P0CG47	229	UBB "Polyubiquitin-B" [Homo sa	0.493	0.165	0.815	1.4e-20
UNIPROTKB|A7U5U2	229	UBB "Uncharacterized protein"	0.493	0.165	0.815	1.4e-20
UNIPROTKB|F1NGE3	157	UBB "Polyubiquitin-B" [Gallus	0.493	0.242	0.815	1.4e-20
UNIPROTKB|Q91021	157	UBB "Ubiquitin" [Gallus gallus	0.493	0.242	0.815	1.4e-20
UNIPROTKB|F5GYU3	134	UBC "Polyubiquitin-C" [Homo sa	0.493	0.283	0.815	1.4e-20

CGD|CAL0004945 UBI4 [Candida albicans (taxid:5476)]

 Score = 163 (62.4 bits), Expect = 4.1e-21, Sum P(2) = 4.1e-21
 Identities = 33/38 (86%), Positives = 36/38 (94%)

Query:    36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
             TLEV+SSDTI+NVKSKIQDKEGIPPDQQRLIFAG  L+
Sbjct:   166 TLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLE 203

GO:0016567 "protein ubiquitination" evidence=IGI;ISS;IMP

GO:0009405 "pathogenesis" evidence=IMP

GO:0000902 "cell morphogenesis" evidence=IMP

GO:0005886 "plasma membrane" evidence=IDA

GO:0031386 "protein tag" evidence=IGI;ISS

GO:0030447 "filamentous growth" evidence=IMP

GO:0033554 "cellular response to stress" evidence=IEP;IMP

GO:0034605 "cellular response to heat" evidence=IMP

GO:0044182 "filamentous growth of a population of unicellular organisms" evidence=IMP

GO:0036166 "phenotypic switching" evidence=IMP

UNIPROTKB|Q5ADS0 UBI4 "Putative uncharacterized protein UBI4" [Candida albicans SC5314 (taxid:237561)]

 Score = 163 (62.4 bits), Expect = 4.1e-21, Sum P(2) = 4.1e-21
 Identities = 33/38 (86%), Positives = 36/38 (94%)

Query:    36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
             TLEV+SSDTI+NVKSKIQDKEGIPPDQQRLIFAG  L+
Sbjct:   166 TLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLE 203

GO:0000902 "cell morphogenesis" evidence=IMP

GO:0005886 "plasma membrane" evidence=IDA

GO:0009405 "pathogenesis" evidence=IMP

GO:0016567 "protein ubiquitination" evidence=IGI;ISS;IMP

GO:0030447 "filamentous growth" evidence=IMP

GO:0031386 "protein tag" evidence=IGI;ISS

GO:0033554 "cellular response to stress" evidence=IEP;IMP

GO:0034605 "cellular response to heat" evidence=IMP

GO:0036166 "phenotypic switching" evidence=IMP

GO:0044182 "filamentous growth of a population of unicellular organisms" evidence=IMP

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

 Score = 160 (61.4 bits), Expect = 4.1e-21, Sum P(2) = 4.1e-21
 Identities = 32/38 (84%), Positives = 36/38 (94%)

Query:    36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
             TLEV+SSDTI+NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct:   166 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE 203

GO:0005622 "intracellular" evidence=TAS

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

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

UNIPROTKB|F1PDG4 UBB "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 154 (59.3 bits), Expect = 1.4e-20, Sum P(2) = 1.4e-20
 Identities = 31/38 (81%), Positives = 34/38 (89%)

Query:    36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
             TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct:   166 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 203

GO:0097009 "energy homeostasis" evidence=IEA

GO:0072520 "seminiferous tubule development" evidence=IEA

GO:0060613 "fat pad development" evidence=IEA

GO:0021888 "hypothalamus gonadotrophin-releasing hormone neuron development" evidence=IEA

GO:0010992 "ubiquitin homeostasis" evidence=IEA

GO:0008585 "female gonad development" evidence=IEA

GO:0007144 "female meiosis I" evidence=IEA

GO:0007141 "male meiosis I" evidence=IEA

UNIPROTKB|J3QKN0 UBB "Ubiquitin" [Homo sapiens (taxid:9606)]

 Score = 154 (59.3 bits), Expect = 1.4e-20, Sum P(2) = 1.4e-20
 Identities = 31/38 (81%), Positives = 34/38 (89%)

Query:    36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
             TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct:   166 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 203

GO:0007141 "male meiosis I" evidence=IEA

GO:0007144 "female meiosis I" evidence=IEA

GO:0008585 "female gonad development" evidence=IEA

GO:0010992 "ubiquitin homeostasis" evidence=IEA

GO:0021888 "hypothalamus gonadotrophin-releasing hormone neuron development" evidence=IEA

GO:0060613 "fat pad development" evidence=IEA

GO:0072520 "seminiferous tubule development" evidence=IEA

GO:0097009 "energy homeostasis" evidence=IEA

UNIPROTKB|P0CG47 UBB "Polyubiquitin-B" [Homo sapiens (taxid:9606)]

 Score = 154 (59.3 bits), Expect = 1.4e-20, Sum P(2) = 1.4e-20
 Identities = 31/38 (81%), Positives = 34/38 (89%)

Query:    36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
             TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct:   166 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 203

GO:0000075 "cell cycle checkpoint" evidence=TAS

GO:0000080 "G1 phase of mitotic cell cycle" evidence=TAS

GO:0000082 "G1/S transition of mitotic cell cycle" evidence=TAS

GO:0000084 "S phase of mitotic cell cycle" evidence=TAS

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=TAS

GO:0000187 "activation of MAPK activity" evidence=TAS

GO:0000209 "protein polyubiquitination" evidence=TAS

GO:0000216 "M/G1 transition of mitotic cell cycle" evidence=TAS

GO:0000278 "mitotic cell cycle" evidence=TAS

GO:0002224 "toll-like receptor signaling pathway" evidence=TAS

GO:0002474 "antigen processing and presentation of peptide antigen via MHC class I" evidence=TAS

GO:0002479 "antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent" evidence=TAS

GO:0002755 "MyD88-dependent toll-like receptor signaling pathway" evidence=TAS

GO:0002756 "MyD88-independent toll-like receptor signaling pathway" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0005886 "plasma membrane" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

GO:0006351 "transcription, DNA-dependent" evidence=TAS

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=TAS

GO:0006915 "apoptotic process" evidence=TAS

GO:0006977 "DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest" evidence=TAS

GO:0007173 "epidermal growth factor receptor signaling pathway" evidence=TAS

GO:0007179 "transforming growth factor beta receptor signaling pathway" evidence=TAS

GO:0007219 "Notch signaling pathway" evidence=TAS

GO:0007220 "Notch receptor processing" evidence=TAS

GO:0007249 "I-kappaB kinase/NF-kappaB cascade" evidence=TAS

GO:0007254 "JNK cascade" evidence=TAS

GO:0008063 "Toll signaling pathway" evidence=TAS

GO:0008543 "fibroblast growth factor receptor signaling pathway" evidence=TAS

GO:0010008 "endosome membrane" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0016044 "cellular membrane organization" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0016197 "endosomal transport" evidence=TAS

GO:0019221 "cytokine-mediated signaling pathway" evidence=TAS

GO:0030512 "negative regulation of transforming growth factor beta receptor signaling pathway" evidence=TAS

GO:0030666 "endocytic vesicle membrane" evidence=TAS

GO:0031145 "anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process" evidence=TAS

GO:0032480 "negative regulation of type I interferon production" evidence=TAS

GO:0033554 "cellular response to stress" evidence=TAS

GO:0034130 "toll-like receptor 1 signaling pathway" evidence=TAS

GO:0034134 "toll-like receptor 2 signaling pathway" evidence=TAS

GO:0034138 "toll-like receptor 3 signaling pathway" evidence=TAS

GO:0034142 "toll-like receptor 4 signaling pathway" evidence=TAS

GO:0035666 "TRIF-dependent toll-like receptor signaling pathway" evidence=TAS

GO:0035872 "nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway" evidence=TAS

GO:0042059 "negative regulation of epidermal growth factor receptor signaling pathway" evidence=TAS

GO:0042590 "antigen processing and presentation of exogenous peptide antigen via MHC class I" evidence=TAS

GO:0042981 "regulation of apoptotic process" evidence=TAS

GO:0043123 "positive regulation of I-kappaB kinase/NF-kappaB cascade" evidence=TAS

GO:0045087 "innate immune response" evidence=TAS

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=TAS

GO:0046788 "egress of virus within host cell" evidence=TAS

GO:0048011 "neurotrophin TRK receptor signaling pathway" evidence=TAS

GO:0050852 "T cell receptor signaling pathway" evidence=TAS

GO:0051092 "positive regulation of NF-kappaB transcription factor activity" evidence=TAS

GO:0051403 "stress-activated MAPK cascade" evidence=TAS

GO:0051436 "negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle" evidence=TAS

GO:0051437 "positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle" evidence=TAS

GO:0051439 "regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle" evidence=TAS

GO:0061418 "regulation of transcription from RNA polymerase II promoter in response to hypoxia" evidence=TAS

GO:0070423 "nucleotide-binding oligomerization domain containing signaling pathway" evidence=TAS

GO:0071456 "cellular response to hypoxia" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|A7U5U2 UBB "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 154 (59.3 bits), Expect = 1.4e-20, Sum P(2) = 1.4e-20
 Identities = 31/38 (81%), Positives = 34/38 (89%)

Query:    36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
             TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct:   166 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 203

GO:0097009 "energy homeostasis" evidence=IEA

GO:0072520 "seminiferous tubule development" evidence=IEA

GO:0060613 "fat pad development" evidence=IEA

GO:0021888 "hypothalamus gonadotrophin-releasing hormone neuron development" evidence=IEA

GO:0010992 "ubiquitin homeostasis" evidence=IEA

GO:0008585 "female gonad development" evidence=IEA

GO:0007144 "female meiosis I" evidence=IEA

GO:0007141 "male meiosis I" evidence=IEA

UNIPROTKB|F1NGE3 UBB "Polyubiquitin-B" [Gallus gallus (taxid:9031)]

 Score = 154 (59.3 bits), Expect = 1.4e-20, Sum P(2) = 1.4e-20
 Identities = 31/38 (81%), Positives = 34/38 (89%)

Query:    36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
             TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct:    94 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 131

GO:0007141 "male meiosis I" evidence=IEA

GO:0007144 "female meiosis I" evidence=IEA

GO:0008585 "female gonad development" evidence=IEA

GO:0010992 "ubiquitin homeostasis" evidence=IEA

GO:0021888 "hypothalamus gonadotrophin-releasing hormone neuron development" evidence=IEA

GO:0060613 "fat pad development" evidence=IEA

GO:0072520 "seminiferous tubule development" evidence=IEA

GO:0097009 "energy homeostasis" evidence=IEA

UNIPROTKB|Q91021 UBB "Ubiquitin" [Gallus gallus (taxid:9031)]

 Score = 154 (59.3 bits), Expect = 1.4e-20, Sum P(2) = 1.4e-20
 Identities = 31/38 (81%), Positives = 34/38 (89%)

Query:    36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
             TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct:    94 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 131

GO:0007141 "male meiosis I" evidence=IEA

GO:0007144 "female meiosis I" evidence=IEA

GO:0008585 "female gonad development" evidence=IEA

GO:0010992 "ubiquitin homeostasis" evidence=IEA

GO:0021888 "hypothalamus gonadotrophin-releasing hormone neuron development" evidence=IEA

GO:0060613 "fat pad development" evidence=IEA

GO:0072520 "seminiferous tubule development" evidence=IEA

GO:0097009 "energy homeostasis" evidence=IEA

UNIPROTKB|F5GYU3 UBC "Polyubiquitin-C" [Homo sapiens (taxid:9606)]

 Score = 154 (59.3 bits), Expect = 1.4e-20, Sum P(2) = 1.4e-20
 Identities = 31/38 (81%), Positives = 34/38 (89%)

Query:    36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
             TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct:    90 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 127

GO:0007141 "male meiosis I" evidence=IEA

GO:0007144 "female meiosis I" evidence=IEA

GO:0008585 "female gonad development" evidence=IEA

GO:0010992 "ubiquitin homeostasis" evidence=IEA

GO:0021888 "hypothalamus gonadotrophin-releasing hormone neuron development" evidence=IEA

GO:0060613 "fat pad development" evidence=IEA

GO:0072520 "seminiferous tubule development" evidence=IEA

GO:0097009 "energy homeostasis" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	UM04556.1	hypothetical protein (286 aa)
		(Ustilago maydis)
Predicted Functional Partners:
	UM03237.1	40S ribosomal protein S20 (122 aa)				•	•	•			0.712
	UM04633.1	hypothetical protein (178 aa)				•	•	•			0.660
	UM02956.1	hypothetical protein (239 aa)				•	•	•	•		0.644
	UM04077.1	hypothetical protein (187 aa)				•	•	•			0.630
	RPS1	hypothetical protein (315 aa)				•	•	•	•		0.623
	UM01634.1	hypothetical protein (195 aa)				•	•	•			0.615
	UM02714.1	hypothetical protein (386 aa)				•	•	•	•		0.612
	UM03511.1	hypothetical protein (210 aa)				•	•	•	•		0.608
	UM00591.1	hypothetical protein (248 aa)				•	•	•	•		0.607
	UM00658.1	40S ribosomal protein S13 (151 aa)				•	•	•			0.604

---

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	77
cd01803	76	cd01803, Ubiquitin, Ubiquitin	3e-16
pfam00240	69	pfam00240, ubiquitin, Ubiquitin family	7e-12
smart00213	72	smart00213, UBQ, Ubiquitin homologues	4e-10
cd01769	69	cd01769, UBL, Ubiquitin-like domain of UBL	3e-09
cd01806	76	cd01806, Nedd8, Nebb8-like ubiquitin protein	3e-08
cd01803	76	cd01803, Ubiquitin, Ubiquitin	9e-08
cd01800	76	cd01800, SF3a120_C, Ubiquitin-like domain of Mamma	4e-06
cd01809	72	cd01809, Scythe_N, Ubiquitin-like domain of Scythe	5e-05
cd01793	74	cd01793, Fubi, Fubi ubiquitin-like protein	6e-05
cd01805	77	cd01805, RAD23_N, Ubiquitin-like domain of RAD23	1e-04
pfam00240	69	pfam00240, ubiquitin, Ubiquitin family	2e-04
cd01802	103	cd01802, AN1_N, ubiquitin-like domain of AN1	3e-04
cd01798	70	cd01798, parkin_N, amino-terminal ubiquitin-like o	3e-04
smart00213	72	smart00213, UBQ, Ubiquitin homologues	0.001
cd01769	69	cd01769, UBL, Ubiquitin-like domain of UBL	0.001
cd00196	69	cd00196, UBQ, Ubiquitin-like proteins	0.001
cd01806	76	cd01806, Nedd8, Nebb8-like ubiquitin protein	0.003
cd01802	103	cd01802, AN1_N, ubiquitin-like domain of AN1	0.004
pfam11976	72	pfam11976, Rad60-SLD, Ubiquitin-2 like Rad60 SUMO-	0.004

>gnl|CDD|176398 cd01803, Ubiquitin, Ubiquitin

 Score = 65.7 bits (160), Expect = 3e-16
 Identities = 31/38 (81%), Positives = 34/38 (89%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 51

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 = 54.5 bits (132), Expect = 7e-12
 Identities = 25/40 (62%), Positives = 31/40 (77%)

Query: 34 ITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
            TLEV  SDT++ +K KI+DKEGIP DQQRLIF+G  L+
Sbjct: 7  TITLEVDPSDTVSELKEKIEDKEGIPVDQQRLIFSGKVLE 46

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 = 50.3 bits (121), Expect = 4e-10
 Identities = 22/38 (57%), Positives = 29/38 (76%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEVK SDT++ +K KI +  GIPP+QQRLI+ G  L+
Sbjct: 14 TLEVKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVLE 51

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 = 48.0 bits (115), Expect = 3e-09
 Identities = 22/38 (57%), Positives = 28/38 (73%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
           LEV   DT+  +K+KI  KEG+PP+QQRLI+AG  LK
Sbjct: 11 ELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYAGKILK 48

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 = 45.2 bits (107), Expect = 3e-08
 Identities = 14/33 (42%), Positives = 27/33 (81%)

Query: 37 LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG 69
          ++++ +D +  +K ++++KEGIPP QQRLI++G
Sbjct: 15 IDIEPTDKVERIKERVEEKEGIPPQQQRLIYSG 47

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|176398 cd01803, Ubiquitin, Ubiquitin

 Score = 44.1 bits (104), Expect = 9e-08
 Identities = 20/20 (100%), Positives = 20/20 (100%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
          NVKAKIQDKEGIPPDQQRLI
Sbjct: 25 NVKAKIQDKEGIPPDQQRLI 44

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

>gnl|CDD|176395 cd01800, SF3a120_C, Ubiquitin-like domain of Mammalian splicing factor SF3a_120

 Score = 40.1 bits (94), Expect = 4e-06
 Identities = 16/45 (35%), Positives = 29/45 (64%), Gaps = 2/45 (4%)

Query: 29 DQQRLITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          + Q L  TL++  SD ++ +K KI ++ G+P  +Q+L + GI +K
Sbjct: 6  NGQMLNFTLQL--SDPVSVLKVKIHEETGMPAGKQKLQYEGIFIK 48

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. Length = 76

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

 Score = 37.2 bits (87), Expect = 5e-05
 Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 9/60 (15%)

Query: 14 INVKAKIQDKEGIPPDQQRLITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          I +K K  D +           T  V+   T+ ++K KI ++ GIP +QQRLI++G  LK
Sbjct: 1  IEIKVKTLDSQT---------HTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYSGRVLK 51

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|176388 cd01793, Fubi, Fubi ubiquitin-like protein

 Score = 36.7 bits (85), Expect = 6e-05
 Identities = 14/37 (37%), Positives = 24/37 (64%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINL 72
          TLEV   +T++++K+ +   EGI  + Q L+ AG+ L
Sbjct: 12 TLEVTGQETVSDIKAHVAGLEGIDVEDQVLLLAGVPL 48

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. Length = 74

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

 Score = 36.2 bits (84), Expect = 1e-04
 Identities = 17/40 (42%), Positives = 28/40 (70%), Gaps = 2/40 (5%)

Query: 36 TLEVKSSDTINNVKSKIQDKEG--IPPDQQRLIFAGINLK 73
           +EV   DT+  +K KI++++G   PP+QQ+LI++G  LK
Sbjct: 14 PIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKILK 53

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

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

 Score = 35.7 bits (83), Expect = 2e-04
 Identities = 15/20 (75%), Positives = 17/20 (85%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
           +K KI+DKEGIP DQQRLI
Sbjct: 20 ELKEKIEDKEGIPVDQQRLI 39

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|176397 cd01802, AN1_N, ubiquitin-like domain of AN1

 Score = 35.6 bits (82), Expect = 3e-04
 Identities = 17/37 (45%), Positives = 24/37 (64%)

Query: 37 LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          L V   +T+ +VK+KIQ  EGIP  QQ LI+  + L+
Sbjct: 42 LRVSPFETVISVKAKIQRLEGIPVAQQHLIWNNMELE 78

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. Length = 103

>gnl|CDD|176393 cd01798, parkin_N, amino-terminal ubiquitin-like of parkin protein

 Score = 34.7 bits (80), Expect = 3e-04
 Identities = 15/38 (39%), Positives = 23/38 (60%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
           +EV     I  +K  +  ++G+PPDQ R+IFAG  L+
Sbjct: 12 PVEVDPDTDIKQLKEVVAKRQGVPPDQLRVIFAGKELR 49

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. Length = 70

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

 Score = 33.4 bits (77), Expect = 0.001
 Identities = 13/27 (48%), Positives = 17/27 (62%)

Query: 8  KAPTPLINVKAKIQDKEGIPPDQQRLI 34
          K    +  +K KI +  GIPP+QQRLI
Sbjct: 18 KPSDTVSELKEKIAELTGIPPEQQRLI 44

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 = 33.8 bits (78), Expect = 0.001
 Identities = 14/24 (58%), Positives = 18/24 (75%)

Query: 11 TPLINVKAKIQDKEGIPPDQQRLI 34
            +  +KAKI  KEG+PP+QQRLI
Sbjct: 18 DTVAELKAKIAAKEGVPPEQQRLI 41

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|176352 cd00196, UBQ, Ubiquitin-like proteins

 Score = 33.7 bits (77), Expect = 0.001
 Identities = 16/39 (41%), Positives = 23/39 (58%)

Query: 35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
            L V S  T+ ++K K+  K G+PP+QQRL+  G  L 
Sbjct: 10 VELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGKILP 48

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. Length = 69

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

 Score = 32.4 bits (74), Expect = 0.003
 Identities = 12/19 (63%), Positives = 17/19 (89%)

Query: 16 VKAKIQDKEGIPPDQQRLI 34
          +K ++++KEGIPP QQRLI
Sbjct: 26 IKERVEEKEGIPPQQQRLI 44

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|176397 cd01802, AN1_N, ubiquitin-like domain of AN1

 Score = 32.5 bits (74), Expect = 0.004
 Identities = 17/36 (47%), Positives = 24/36 (66%), Gaps = 1/36 (2%)

Query: 13 LINVKAKIQDKEGIPPDQQRLI-TTLEVKSSDTINN 47
          +I+VKAKIQ  EGIP  QQ LI   +E++    +N+
Sbjct: 50 VISVKAKIQRLEGIPVAQQHLIWNNMELEDEYCLND 85

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. Length = 103

>gnl|CDD|192903 pfam11976, Rad60-SLD, Ubiquitin-2 like Rad60 SUMO-like

 Score = 32.1 bits (74), Expect = 0.004
 Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 10/57 (17%)

Query: 14 INVKAKIQDKEGIPPDQQRLITTLEVKSSDTINNVKSKIQDKEGIPPDQQ-RLIFAG 69
          I +K K +D + +          ++VK + T++ + +  + K GIP DQQ RLIF G
Sbjct: 1  IRIKLKGKDGKEV---------FIKVKPTTTLSKLINAYRKKRGIPADQQVRLIFDG 48

The small ubiquitin-related modifier SUMO-1 is a Ub/Ubl family member, and although SUMO-1 shares structural similarity to Ub, SUMO's cellular functions remain distinct insomuch as SUMO modification alters protein function through changes in activity, cellular localisation, or by protecting substrates from ubiquitination. Rad60 family members contain functionally enigmatic, integral SUMO-like domains (SLDs). Despite their divergence from SUMO, each Rad60 SLD interacts with a subset of SUMO pathway enzymes: SLD2 specifically binds the SUMO E2 conjugating enzyme (Ubc9)), whereas SLD1 binds the SUMO E1 (Fub2, also called Uba2) activating and E3 (Pli1, also called Siz1 and Siz2) specificity enzymes. Structural analysis of PDB:2uyz reveals a mechanistic basis for the near-synonymous roles of Rad60 and SUMO in survival of genotoxic stress and suggest unprecedented DNA-damage-response functions for SLDs in regulating SUMOylation. The Rad60 branch of this family is also known as RENi (Rad60-Esc2-Nip45), and biologically it should be two distinct families SUMO and RENi (Rad60-Esc2-Nip45). Length = 72

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	77
cd01794	70	DC_UbP_C dendritic cell derived ubiquitin-like pro	99.42
cd01793	74	Fubi Fubi ubiquitin-like protein. Fubi is a ubiqui	99.4
cd01791	73	Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also know	99.34
cd01807	74	GDX_N ubiquitin-like domain of GDX. GDX contains a	99.33
cd01810	74	ISG15_repeat2 ISG15 ubiquitin-like protein, second	99.3
KOG0005	70	consensus Ubiquitin-like protein [Cell cycle contr	99.29
cd01813	74	UBP_N UBP ubiquitin processing protease. The UBP (	99.29
cd01796	71	DDI1_N DNA damage inducible protein 1 ubiquitin-li	99.28
cd01798	70	parkin_N amino-terminal ubiquitin-like of parkin p	99.26
cd01802	103	AN1_N ubiquitin-like domain of AN1. AN1 (also know	99.24
PTZ00044	76	ubiquitin; Provisional	99.24
cd01790	79	Herp_N Homocysteine-responsive endoplasmic reticul	99.23
cd01794	70	DC_UbP_C dendritic cell derived ubiquitin-like pro	99.23
cd01793	74	Fubi Fubi ubiquitin-like protein. Fubi is a ubiqui	99.23
cd01800	76	SF3a120_C Ubiquitin-like domain of Mammalian splic	99.23
cd01799	75	Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HO	99.2
cd01807	74	GDX_N ubiquitin-like domain of GDX. GDX contains a	99.2
KOG0005	70	consensus Ubiquitin-like protein [Cell cycle contr	99.18
cd01796	71	DDI1_N DNA damage inducible protein 1 ubiquitin-li	99.17
PF00240	69	ubiquitin: Ubiquitin family; InterPro: IPR000626 U	99.16
cd01797	78	NIRF_N amino-terminal ubiquitin-like domain of Np9	99.15
cd01812	71	BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-ter	99.13
cd01805	77	RAD23_N Ubiquitin-like domain of RAD23. RAD23 belo	99.12
cd01798	70	parkin_N amino-terminal ubiquitin-like of parkin p	99.12
cd01804	78	midnolin_N Ubiquitin-like domain of midnolin. midn	99.11
cd01810	74	ISG15_repeat2 ISG15 ubiquitin-like protein, second	99.11
cd01803	76	Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40	99.1
cd01790	79	Herp_N Homocysteine-responsive endoplasmic reticul	99.09
cd01806	76	Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also kn	99.09
cd01797	78	NIRF_N amino-terminal ubiquitin-like domain of Np9	99.07
cd01791	73	Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also know	99.06
KOG0003	128	consensus Ubiquitin/60s ribosomal protein L40 fusi	99.04
PF00240	69	ubiquitin: Ubiquitin family; InterPro: IPR000626 U	99.03
cd01809	72	Scythe_N Ubiquitin-like domain of Scythe protein.	99.03
PTZ00044	76	ubiquitin; Provisional	99.03
cd01802	103	AN1_N ubiquitin-like domain of AN1. AN1 (also know	99.02
cd01792	80	ISG15_repeat1 ISG15 ubiquitin-like protein, first	99.01
cd01795	107	USP48_C USP ubiquitin-specific protease. The USP (	98.99
cd01800	76	SF3a120_C Ubiquitin-like domain of Mammalian splic	98.98
cd01808	71	hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC	98.98
KOG0004	156	consensus Ubiquitin/40S ribosomal protein S27a fus	98.96
smart00213	64	UBQ Ubiquitin homologues. Ubiquitin-mediated prote	98.96
cd01805	77	RAD23_N Ubiquitin-like domain of RAD23. RAD23 belo	98.95
cd01804	78	midnolin_N Ubiquitin-like domain of midnolin. midn	98.95
cd01808	71	hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC	98.91
cd01813	74	UBP_N UBP ubiquitin processing protease. The UBP (	98.89
cd01815	75	BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC	98.87
cd01803	76	Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40	98.86
cd01815	75	BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC	98.86
cd01812	71	BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-ter	98.85
cd01806	76	Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also kn	98.85
cd01809	72	Scythe_N Ubiquitin-like domain of Scythe protein.	98.84
cd01799	75	Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HO	98.84
cd01814	113	NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and AT	98.83
cd01763	87	Sumo Small ubiquitin-related modifier (SUMO). Smal	98.8
smart00213	64	UBQ Ubiquitin homologues. Ubiquitin-mediated prote	98.79
KOG0003	128	consensus Ubiquitin/60s ribosomal protein L40 fusi	98.79
KOG0004	156	consensus Ubiquitin/40S ribosomal protein S27a fus	98.76
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	98.75
cd01792	80	ISG15_repeat1 ISG15 ubiquitin-like protein, first	98.73
cd01769	69	UBL Ubiquitin-like domain of UBL. UBLs function by	98.7
cd01814	113	NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and AT	98.67
cd01795	107	USP48_C USP ubiquitin-specific protease. The USP (	98.67
KOG0011	340	consensus Nucleotide excision repair factor NEF2,	98.56
cd01769	69	UBL Ubiquitin-like domain of UBL. UBLs function by	98.55
cd01763	87	Sumo Small ubiquitin-related modifier (SUMO). Smal	98.52
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	98.49
KOG0010	493	consensus Ubiquitin-like protein [Posttranslationa	98.33
PF14560	87	Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2K	98.21
cd01789	84	Alp11_N Ubiquitin-like domain of Alp11 tubulin-fol	98.08
PF11976	72	Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; Inter	98.02
KOG0001	75	consensus Ubiquitin and ubiquitin-like proteins [P	98.0
KOG0011	340	consensus Nucleotide excision repair factor NEF2,	97.97
cd01788	119	ElonginB Ubiquitin-like domain of Elongin B. Elong	97.94
PF11976	72	Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; Inter	97.8
KOG0010	493	consensus Ubiquitin-like protein [Posttranslationa	97.77
PLN02560	308	enoyl-CoA reductase	97.76
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	97.73
cd01811	80	OASL_repeat1 2'-5' oligoadenylate synthetase-like	97.7
KOG0001	75	consensus Ubiquitin and ubiquitin-like proteins [P	97.69
cd01789	84	Alp11_N Ubiquitin-like domain of Alp11 tubulin-fol	97.66
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	97.5
PF11543	80	UN_NPL4: Nuclear pore localisation protein NPL4; I	97.45
cd00196	69	UBQ Ubiquitin-like proteins. Ubiquitin homologs; I	97.43
cd01788	119	ElonginB Ubiquitin-like domain of Elongin B. Elong	97.43
KOG4248	1143	consensus Ubiquitin-like protein, regulator of apo	97.34
cd00196	69	UBQ Ubiquitin-like proteins. Ubiquitin homologs; I	97.24
PF14560	87	Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2K	97.09
KOG4248	1143	consensus Ubiquitin-like protein, regulator of apo	96.94
PF13881	111	Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB	96.91
PF13881	111	Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB	96.67
PF10302	97	DUF2407: DUF2407 ubiquitin-like domain; InterPro:	96.66
cd06406	80	PB1_P67 A PB1 domain is present in p67 proteins wh	96.62
PLN02560	308	enoyl-CoA reductase	96.58
cd01801	77	Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-	96.28
cd01801	77	Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-	95.97
KOG4495	110	consensus RNA polymerase II transcription elongati	95.87
cd06411	78	PB1_p51 The PB1 domain is present in the p51 prote	95.85
KOG3493	73	consensus Ubiquitin-like protein [Posttranslationa	95.75
KOG1872	473	consensus Ubiquitin-specific protease [Posttransla	95.5
PF10302	97	DUF2407: DUF2407 ubiquitin-like domain; InterPro:	95.41
PF11470	65	TUG-UBL1: GLUT4 regulating protein TUG; InterPro:	95.39
KOG1872	473	consensus Ubiquitin-specific protease [Posttransla	95.38
PF11543	80	UN_NPL4: Nuclear pore localisation protein NPL4; I	95.1
PF11470	65	TUG-UBL1: GLUT4 regulating protein TUG; InterPro:	94.37
KOG1769	99	consensus Ubiquitin-like proteins [Posttranslation	94.01
smart00455	70	RBD Raf-like Ras-binding domain.	92.1
KOG3439	116	consensus Protein conjugation factor involved in a	92.01
PF13019	162	Telomere_Sde2: Telomere stability and silencing	91.82
PF14533	213	USP7_C2: Ubiquitin-specific protease C-terminal; P	90.87
cd01760	72	RBD Ubiquitin-like domain of RBD-like S/T kinases.	90.38
KOG4583	391	consensus Membrane-associated ER protein involved	90.34
PF14533	213	USP7_C2: Ubiquitin-specific protease C-terminal; P	90.07
cd01811	80	OASL_repeat1 2'-5' oligoadenylate synthetase-like	89.72
KOG0013	231	consensus Uncharacterized conserved protein [Funct	89.49
KOG1769	99	consensus Ubiquitin-like proteins [Posttranslation	89.21
cd06406	80	PB1_P67 A PB1 domain is present in p67 proteins wh	89.01
smart00666	81	PB1 PB1 domain. Phox and Bem1p domain, present in	88.49
PF04110	87	APG12: Ubiquitin-like autophagy protein Apg12 ; In	88.23
cd06409	86	PB1_MUG70 The MUG70 protein is a product of the me	86.95
cd01776	87	Rin1_RA Ubiquitin domain of RIN1 RAS effector. Rin	86.76
KOG4495	110	consensus RNA polymerase II transcription elongati	86.61
KOG4250	732	consensus TANK binding protein kinase TBK1 [Signal	86.21
cd06411	78	PB1_p51 The PB1 domain is present in the p51 prote	85.54
KOG3206	234	consensus Alpha-tubulin folding cofactor B [Posttr	85.28
PF02192	78	PI3K_p85B: PI3-kinase family, p85-binding domain;	85.26
COG5227	103	SMT3 Ubiquitin-like protein (sentrin) [Posttransla	84.28
KOG0013	231	consensus Uncharacterized conserved protein [Funct	84.25
PF15044	76	CLU_N: Mitochondrial function, CLU-N-term	82.47
KOG4250	732	consensus TANK binding protein kinase TBK1 [Signal	80.92
smart00143	78	PI3K_p85B PI3-kinase family, p85-binding domain. R	80.76
cd01612	87	APG12_C Ubiquitin-like domain of APG12. APG12_C Th	80.65

>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein

Probab=99.42  E-value=3.6e-13  Score=71.10  Aligned_cols=48  Identities=17%  Similarity=0.230  Sum_probs=43.2

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++++++|++++||++||++|++.+|+|+++|+|+|.+ .++++.++.++
T Consensus         9 ~~~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~Li~~G~~L~D~~~l~~~   57 (70)
T cd01794           9 KDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWFFSGKLLTDKTRLQET   57 (70)
T ss_pred             CEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEECCeECCCCCCHHHc
Confidence            4689999999999999999999999999999999986 56888888876

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.

>cd01793 Fubi Fubi ubiquitin-like protein

Probab=99.40  E-value=4.1e-13  Score=71.32  Aligned_cols=48  Identities=19%  Similarity=0.255  Sum_probs=43.2

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++++++|++++||++||++|++.+|+|+++|+|+|.+ .++++.+++++
T Consensus         9 ~~~~l~v~~~~tV~~lK~~i~~~~gip~~~q~Li~~Gk~L~D~~tL~~~   57 (74)
T cd01793           9 NTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVLLLAGVPLEDDATLGQC   57 (74)
T ss_pred             CEEEEEECCcCcHHHHHHHHHhhhCCCHHHEEEEECCeECCCCCCHHHc
Confidence            4688999999999999999999999999999999986 66888898887

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.

>cd01791 Ubl5 UBL5 ubiquitin-like modifier

Probab=99.34  E-value=4.8e-12  Score=67.29  Aligned_cols=47  Identities=13%  Similarity=0.176  Sum_probs=41.5

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      .+.++++|++||++||++|++..|+|+++|+|+|.+ -++++.++.++
T Consensus        13 ~~~~~v~~~~TV~~LK~~I~~~~~~~~~~qrLi~~Gk~L~D~~tL~~y   60 (73)
T cd01791          13 KVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFKDHISLGDY   60 (73)
T ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEeCCcCCCCCCCHHHc
Confidence            578899999999999999999999999999999987 44677788887

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.

>cd01807 GDX_N ubiquitin-like domain of GDX

Probab=99.33  E-value=6.4e-12  Score=66.68  Aligned_cols=48  Identities=17%  Similarity=0.277  Sum_probs=42.1

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++++++|++++||++||++|++..|+|+++|+|+|.+ .+.++.+++++
T Consensus        11 ~~~~l~v~~~~tV~~lK~~i~~~~gi~~~~q~L~~~G~~L~d~~~L~~~   59 (74)
T cd01807          11 RECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLLFKGKALADDKRLSDY   59 (74)
T ss_pred             CEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEECCCCCCHHHC
Confidence            3578899999999999999999999999999999986 66888888887

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

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

Probab=99.30  E-value=1.3e-11  Score=65.57  Aligned_cols=48  Identities=13%  Similarity=0.188  Sum_probs=43.0

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++++++++++||++||++|++..|+|+++|+|+|.+ .+.++.++.++
T Consensus         9 ~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~q~L~~~G~~L~D~~tL~~~   57 (74)
T cd01810           9 RSSIYEVQLTQTVATLKQQVSQRERVQADQFWLSFEGRPMEDEHPLGEY   57 (74)
T ss_pred             CEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEECCEECCCCCCHHHc
Confidence            4688999999999999999999999999999999986 56888888876

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.

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

Probab=99.29  E-value=2.8e-12  Score=65.18  Aligned_cols=48  Identities=27%  Similarity=0.481  Sum_probs=40.2

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNVK   49 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~lK   49 (77)
                      .+.++++|.|+|+.+|+++++++||||.+|||+|++ .+.++.|..+++
T Consensus        12 eIeidIep~DkverIKErvEEkeGIPp~qqrli~~gkqm~DD~tA~~Y~   60 (70)
T KOG0005|consen   12 EIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYAGKQMNDDKTAAHYN   60 (70)
T ss_pred             eEEEeeCcchHHHHHHHHhhhhcCCCchhhhhhhccccccccccHHHhh
Confidence            467888999999999999999999999999999986 666777777775

>cd01813 UBP_N UBP ubiquitin processing protease

Probab=99.29  E-value=1.2e-11  Score=65.87  Aligned_cols=47  Identities=15%  Similarity=0.268  Sum_probs=42.1

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEE---EE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLIT---TL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~---~~-~v~~~~tv~~l   48 (77)
                      ++.++|++++||++||++|++..|+|+++|+|+|   .+ .+.++.++.++
T Consensus        11 ~~~v~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~~~~~Gk~l~D~~~L~~~   61 (74)
T cd01813          11 EYSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLGLKVKGKPAEDDVKISAL   61 (74)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEeecccCCcCCCCcCHHHc
Confidence            6889999999999999999999999999999997   44 45778888887

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.

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

Probab=99.28  E-value=1.9e-11  Score=64.56  Aligned_cols=48  Identities=27%  Similarity=0.256  Sum_probs=38.6

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCC-ccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSS-DTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~-~tv~~l   48 (77)
                      +++++++++++||++||.+|++.+|+|+++|+|+|.+ .+.++ .+++++
T Consensus        10 ~~~~l~v~~~~TV~~lK~~I~~~~gip~~~q~Li~~Gk~L~D~~~~L~~~   59 (71)
T cd01796          10 TTFSLDVDPDLELENFKALCEAESGIPASQQQLIYNGRELVDNKRLLALY   59 (71)
T ss_pred             CEEEEEECCcCCHHHHHHHHHHHhCCCHHHeEEEECCeEccCCcccHHHc
Confidence            3578899999999999999999999999999999886 45554 466666

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.

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

Probab=99.26  E-value=9.5e-12  Score=65.33  Aligned_cols=48  Identities=25%  Similarity=0.456  Sum_probs=41.9

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++++++++++||++||.+|++..|+|+++|+|+|.+ .++++.+++++
T Consensus         9 ~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~q~Li~~G~~L~d~~~l~~~   57 (70)
T cd01798           9 HTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVIFAGKELRNTTTIQEC   57 (70)
T ss_pred             CEEEEEECCCChHHHHHHHHHHHHCCCHHHeEEEECCeECCCCCcHHHc
Confidence            3678999999999999999999999999999999986 66888888876

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.

>cd01802 AN1_N ubiquitin-like domain of AN1

Probab=99.24  E-value=1.3e-11  Score=69.46  Aligned_cols=48  Identities=38%  Similarity=0.388  Sum_probs=40.9

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++++++|++++||++||++|++.+|+|+++|+|+|.+ .+.++.+++++
T Consensus        38 ~~~~leV~~~~TV~~lK~kI~~~~gip~~~QrLi~~Gk~L~D~~tL~dy   86 (103)
T cd01802          38 TCFELRVSPFETVISVKAKIQRLEGIPVAQQHLIWNNMELEDEYCLNDY   86 (103)
T ss_pred             CEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEECCEECCCCCcHHHc
Confidence            3578899999999999999999999999999999886 56788888877

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.

>PTZ00044 ubiquitin; Provisional

Probab=99.24  E-value=1.6e-11  Score=65.19  Aligned_cols=48  Identities=23%  Similarity=0.350  Sum_probs=42.7

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++++++++++||++||.+|++..|+|++.|+|+|.+ .++++.+++++
T Consensus        11 ~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~L~d~~~l~~~   59 (76)
T PTZ00044         11 KKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYSGKQMSDDLKLSDY   59 (76)
T ss_pred             CEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEEccCCCcHHHc
Confidence            3688999999999999999999999999999999986 56778888877

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

Probab=99.23  E-value=1.7e-11  Score=66.01  Aligned_cols=51  Identities=14%  Similarity=0.016  Sum_probs=41.0

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhC--CCcccceEEEEEEe-cCCccHHHHHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEG--IPPDQQRLITTLEV-KSSDTINNVKSKI   52 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~g--i~~~~q~L~~~~~v-~~~~tv~~lK~~i   52 (77)
                      .|.+++++++||++||++|++..+  .|+++|+|||.+.+ .++.++.++...+
T Consensus        15 ~~~ve~~~~~TV~~lK~~i~~~~~~~~~~~~QrLIy~GKiLkD~~tL~~~~~~~   68 (79)
T cd01790          15 DQTVSCFLNWTVGELKTHLSRVYPSKPLEQDQRLIYSGKLLPDHLKLRDVLRKQ   68 (79)
T ss_pred             EEEEecCCcChHHHHHHHHHHhcCCCCChhHeEEEEcCeeccchhhHHHHhhcc
Confidence            477778999999999999998764  55799999999854 7888888885443

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.

>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein

Probab=99.23  E-value=2.3e-11  Score=64.11  Aligned_cols=42  Identities=36%  Similarity=0.502  Sum_probs=39.1

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      +.+++++++||.++|+.|++.+|+|+++|+|+|+|++|+|..
T Consensus        11 ~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~Li~~G~~L~D~~   52 (70)
T cd01794          11 VKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWFFSGKLLTDKT   52 (70)
T ss_pred             EEEEECCcChHHHHHHHHHHHhCCCHHHeEEEECCeECCCCC
Confidence            467899999999999999999999999999999999999864

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.

>cd01793 Fubi Fubi ubiquitin-like protein

Probab=99.23  E-value=2.9e-11  Score=64.18  Aligned_cols=42  Identities=33%  Similarity=0.545  Sum_probs=39.2

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      +.+++++++||+++|+.|++.+|+|+++|+|+|+|++|+|.-
T Consensus        11 ~~l~v~~~~tV~~lK~~i~~~~gip~~~q~Li~~Gk~L~D~~   52 (74)
T cd01793          11 HTLEVTGQETVSDIKAHVAGLEGIDVEDQVLLLAGVPLEDDA   52 (74)
T ss_pred             EEEEECCcCcHHHHHHHHHhhhCCCHHHEEEEECCeECCCCC
Confidence            467899999999999999999999999999999999999864

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.

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

Probab=99.23  E-value=2e-11  Score=65.18  Aligned_cols=48  Identities=23%  Similarity=0.372  Sum_probs=43.4

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++++++++++||++||++|++..|+|++.|+|+|.+ .++++.+++++
T Consensus         8 ~~~~l~v~~~~TV~~lK~~i~~~~gip~~~q~L~~~G~~L~d~~tL~~~   56 (76)
T cd01800           8 QMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQYEGIFIKDSNSLAYY   56 (76)
T ss_pred             eEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCEEcCCCCcHHHc
Confidence            4689999999999999999999999999999999986 56778888887

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.

>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1

Probab=99.20  E-value=8.5e-11  Score=62.77  Aligned_cols=47  Identities=19%  Similarity=0.287  Sum_probs=41.1

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-Ee-cCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EV-KSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v-~~~~tv~~l   48 (77)
                      .+++++|++++||++||++|++.+|||++.|+| |.+ .+ +++.+++++
T Consensus        13 ~t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL-~~G~~L~dD~~tL~~y   61 (75)
T cd01799          13 VTIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRW-VIGQRLARDQETLYSH   61 (75)
T ss_pred             CeEEEEECCCCcHHHHHHHHHHHHCcCHHHEEE-EcCCeeCCCcCCHHHc
Confidence            368899999999999999999999999999999 775 55 466788877

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.

>cd01807 GDX_N ubiquitin-like domain of GDX

Probab=99.20  E-value=4.7e-11  Score=63.32  Aligned_cols=42  Identities=26%  Similarity=0.493  Sum_probs=39.0

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      +.+++++++||.++|+.|+++.|+|+++|+|+|+|++|+|..
T Consensus        13 ~~l~v~~~~tV~~lK~~i~~~~gi~~~~q~L~~~G~~L~d~~   54 (74)
T cd01807          13 CSLQVSEKESVSTLKKLVSEHLNVPEEQQRLLFKGKALADDK   54 (74)
T ss_pred             EEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEECCCCC
Confidence            357889999999999999999999999999999999999864

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

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

Probab=99.18  E-value=1.1e-11  Score=63.04  Aligned_cols=41  Identities=37%  Similarity=0.786  Sum_probs=38.2

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+++++++.|+.+|..++++.|+||.+|+|+|.|++|.|+.
T Consensus        14 eidIep~DkverIKErvEEkeGIPp~qqrli~~gkqm~DD~   54 (70)
T KOG0005|consen   14 EIDIEPTDKVERIKERVEEKEGIPPQQQRLIYAGKQMNDDK   54 (70)
T ss_pred             EEeeCcchHHHHHHHHhhhhcCCCchhhhhhhccccccccc
Confidence            46789999999999999999999999999999999998865

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

Probab=99.17  E-value=6.9e-11  Score=62.36  Aligned_cols=41  Identities=32%  Similarity=0.473  Sum_probs=38.6

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      +.++++++.||.++|..|++.+|+|+++|+|+|+|++|+|.
T Consensus        12 ~~l~v~~~~TV~~lK~~I~~~~gip~~~q~Li~~Gk~L~D~   52 (71)
T cd01796          12 FSLDVDPDLELENFKALCEAESGIPASQQQLIYNGRELVDN   52 (71)
T ss_pred             EEEEECCcCCHHHHHHHHHHHhCCCHHHeEEEECCeEccCC
Confidence            46889999999999999999999999999999999999875

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.

>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=99.16  E-value=9.6e-11  Score=61.05  Aligned_cols=47  Identities=32%  Similarity=0.528  Sum_probs=41.2

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.++|++++||++||.+|++..|+|++.|+|+|.+ .++++.++.++
T Consensus         7 ~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~~G~~L~d~~tL~~~   54 (69)
T PF00240_consen    7 TFTLEVDPDDTVADLKQKIAEETGIPPEQQRLIYNGKELDDDKTLSDY   54 (69)
T ss_dssp             EEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEETTEEESTTSBTGGG
T ss_pred             EEEEEECCCCCHHHhhhhcccccccccccceeeeeeecccCcCcHHHc
Confidence            578999999999999999999999999999999975 56888888887

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 ....

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

Probab=99.15  E-value=5.6e-11  Score=63.85  Aligned_cols=46  Identities=20%  Similarity=0.224  Sum_probs=39.8

Q ss_pred             EEEE-eeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            3 LLLM-WKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         3 ~~~~-v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++++ +++++||++||++|++..|+|+++|+|+|.+ .+.++.+++++
T Consensus        14 ~~l~~v~~~~TV~~lK~~i~~~~gi~~~~QrLi~~Gk~L~D~~tL~~y   61 (78)
T cd01797          14 RTVDSLSRLTKVEELREKIQELFNVEPECQRLFYRGKQMEDGHTLFDY   61 (78)
T ss_pred             EEeeccCCcCcHHHHHHHHHHHhCCCHHHeEEEeCCEECCCCCCHHHc
Confidence            5674 7889999999999999999999999999986 66888888887

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.

>cd01812 BAG1_N Ubiquitin-like domain of BAG1

Probab=99.13  E-value=2.6e-10  Score=59.63  Aligned_cols=47  Identities=19%  Similarity=0.246  Sum_probs=40.1

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.+++++++||++||++|++..|+|++.|+|+|.+ .+.++.++.++
T Consensus        11 ~~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~l~d~~~L~~~   58 (71)
T cd01812          11 SHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIFKGKERDDAETLDMS   58 (71)
T ss_pred             EEEEEECCCCcHHHHHHHHHHhhCCChHHeEEeeCCcccCccCcHHHc
Confidence            578899999999999999999999999999999885 45666677666

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).

>cd01805 RAD23_N Ubiquitin-like domain of RAD23

Probab=99.12  E-value=4.2e-10  Score=59.80  Aligned_cols=48  Identities=25%  Similarity=0.448  Sum_probs=41.6

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCC--CcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGI--PPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi--~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++.+++++++||++||++|++..|+  |+++|+|+|.+ .+.++.++.++
T Consensus        11 ~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~~~G~~L~d~~~L~~~   61 (77)
T cd01805          11 QTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKILKDDTTLEEY   61 (77)
T ss_pred             CEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEEECCEEccCCCCHHHc
Confidence            35789999999999999999999999  99999999986 56777788876

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).

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

Probab=99.12  E-value=1.8e-10  Score=60.38  Aligned_cols=42  Identities=36%  Similarity=0.672  Sum_probs=39.1

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      +.+++++++||.++|+.|+++.|+|+++|+|+|+|++|+|..
T Consensus        11 ~~~~v~~~~tV~~lK~~i~~~~gi~~~~q~Li~~G~~L~d~~   52 (70)
T cd01798          11 FPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVIFAGKELRNTT   52 (70)
T ss_pred             EEEEECCCChHHHHHHHHHHHHCCCHHHeEEEECCeECCCCC
Confidence            467889999999999999999999999999999999998864

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.

>cd01804 midnolin_N Ubiquitin-like domain of midnolin

Probab=99.11  E-value=2.6e-10  Score=61.16  Aligned_cols=47  Identities=15%  Similarity=0.287  Sum_probs=39.7

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++++++++++||++||.+|++..|+|+++|+|+|.+ .++++ ++.++
T Consensus        12 ~~~~l~v~~~~TV~~LK~~I~~~~~~~~~~qrL~~~Gk~L~d~-~L~~~   59 (78)
T cd01804          12 TRFDLSVPPDETVEGLKKRISQRLKVPKERLALLHRETRLSSG-KLQDL   59 (78)
T ss_pred             CEEEEEECCcCHHHHHHHHHHHHhCCChHHEEEEECCcCCCCC-cHHHc
Confidence            3578999999999999999999999999999999986 44555 77766

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.

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

Probab=99.11  E-value=2.2e-10  Score=60.73  Aligned_cols=42  Identities=24%  Similarity=0.372  Sum_probs=39.0

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      +.++++++.||.++|+.|++..|+|+++|+|+|+|++|+|..
T Consensus        11 ~~l~v~~~~tV~~lK~~I~~~~gi~~~~q~L~~~G~~L~D~~   52 (74)
T cd01810          11 SIYEVQLTQTVATLKQQVSQRERVQADQFWLSFEGRPMEDEH   52 (74)
T ss_pred             EEEEECCcChHHHHHHHHHHHhCCCHHHeEEEECCEECCCCC
Confidence            367889999999999999999999999999999999999863

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=99.10  E-value=1.6e-10  Score=61.03  Aligned_cols=48  Identities=46%  Similarity=0.659  Sum_probs=42.0

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++.+++++++||++||++|++..|+|++.|+|+|.+ .+.++.++.++
T Consensus        11 ~~~~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~~~g~~L~d~~~L~~~   59 (76)
T cd01803          11 KTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY   59 (76)
T ss_pred             CEEEEEECCcCcHHHHHHHHHHHhCCCHHHeEEEECCEECCCCCcHHHc
Confidence            3678999999999999999999999999999999985 56777777776

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

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

Probab=99.09  E-value=3.3e-10  Score=61.00  Aligned_cols=48  Identities=21%  Similarity=0.156  Sum_probs=40.0

Q ss_pred             ccceEEEEEEecCCccHHHHHHHHhhccC--CCccceEEEECCeEcCccc
Q 040720           29 DQQRLITTLEVKSSDTINNVKSKIQDKEG--IPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        29 ~~q~L~~~~~v~~~~tv~~lK~~i~~~~g--ip~~~q~l~~~g~~L~d~~   76 (77)
                      .+...-|.+++++++||.++|..|++..+  .|+++|+|+|+|+.|+|..
T Consensus        10 ~~~~~~~~ve~~~~~TV~~lK~~i~~~~~~~~~~~~QrLIy~GKiLkD~~   59 (79)
T cd01790          10 NQKYEDQTVSCFLNWTVGELKTHLSRVYPSKPLEQDQRLIYSGKLLPDHL   59 (79)
T ss_pred             CCCeEEEEEecCCcChHHHHHHHHHHhcCCCCChhHeEEEEcCeeccchh
Confidence            44555567778999999999999999874  4579999999999998863

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.

>cd01806 Nedd8 Nebb8-like ubiquitin protein

Probab=99.09  E-value=2.4e-10  Score=60.39  Aligned_cols=48  Identities=27%  Similarity=0.507  Sum_probs=41.8

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++.+++++++||++||++|++..|+|++.|+|+|.+ .+.++.++.++
T Consensus        11 ~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~~~g~~L~d~~tl~~~   59 (76)
T cd01806          11 KEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDDKTAADY   59 (76)
T ss_pred             CEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEEECCeEccCCCCHHHc
Confidence            3578899999999999999999999999999999886 56777888887

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.

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

Probab=99.07  E-value=3.6e-10  Score=60.73  Aligned_cols=42  Identities=21%  Similarity=0.401  Sum_probs=37.8

Q ss_pred             EEEE-ecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLE-VKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~-v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      +.++ ++++.||.++|..|++..|+|+++|+|+|+|+.|+|..
T Consensus        14 ~~l~~v~~~~TV~~lK~~i~~~~gi~~~~QrLi~~Gk~L~D~~   56 (78)
T cd01797          14 RTVDSLSRLTKVEELREKIQELFNVEPECQRLFYRGKQMEDGH   56 (78)
T ss_pred             EEeeccCCcCcHHHHHHHHHHHhCCCHHHeEEEeCCEECCCCC
Confidence            3553 68899999999999999999999999999999999864

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.

>cd01791 Ubl5 UBL5 ubiquitin-like modifier

Probab=99.06  E-value=3.3e-10  Score=60.18  Aligned_cols=41  Identities=22%  Similarity=0.238  Sum_probs=38.0

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+++++++||.++|..|++..|+|+++|+|+|+|+.|+|..
T Consensus        15 ~~~v~~~~TV~~LK~~I~~~~~~~~~~qrLi~~Gk~L~D~~   55 (73)
T cd01791          15 RVKCNPDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFKDHI   55 (73)
T ss_pred             EEEeCCCCcHHHHHHHHHHHhCCChHHEEEEeCCcCCCCCC
Confidence            45889999999999999999999999999999999998863

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.

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

Probab=99.04  E-value=4.2e-11  Score=67.38  Aligned_cols=48  Identities=46%  Similarity=0.643  Sum_probs=42.5

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +|.+++++|++||..||.+|+.++|||++.|+|+|+. .+.+..|++.+
T Consensus        11 KT~~le~EpS~ti~~vKA~i~~~~Gi~~~~~~L~~~~k~LED~~Tla~Y   59 (128)
T KOG0003|consen   11 KTITLEVEPSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADY   59 (128)
T ss_pred             ceEEEEecccchHHHHHHHhccccCCCHHHHHHHhcccccccCCccccc
Confidence            4789999999999999999999999999999999975 56777777665

>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=99.03  E-value=1e-09  Score=57.11  Aligned_cols=43  Identities=47%  Similarity=0.721  Sum_probs=39.8

Q ss_pred             EEEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           34 ITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        34 ~~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .|.+.+++++||.++|..|+...|+|++.|+|+|+|+.|+|..
T Consensus         7 ~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~~G~~L~d~~   49 (69)
T PF00240_consen    7 TFTLEVDPDDTVADLKQKIAEETGIPPEQQRLIYNGKELDDDK   49 (69)
T ss_dssp             EEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEETTEEESTTS
T ss_pred             EEEEEECCCCCHHHhhhhcccccccccccceeeeeeecccCcC
Confidence            4678999999999999999999999999999999999998753

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 ....

>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein

Probab=99.03  E-value=5e-10  Score=58.59  Aligned_cols=48  Identities=27%  Similarity=0.439  Sum_probs=40.6

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++++++++++||++||.+|++..|+|++.|+|+|.+ .++++.+++++
T Consensus        11 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~L~d~~~L~~~   59 (72)
T cd01809          11 QTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYSGRVLKDDETLSEY   59 (72)
T ss_pred             CEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCEECCCcCcHHHC
Confidence            3578899999999999999999999999999999886 45677777776

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.

>PTZ00044 ubiquitin; Provisional

Probab=99.03  E-value=7.6e-10  Score=58.70  Aligned_cols=42  Identities=31%  Similarity=0.532  Sum_probs=38.6

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      +.+.+++++||.++|+.|++..|+|+++|+|+|+|+.|+|..
T Consensus        13 ~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~L~d~~   54 (76)
T PTZ00044         13 QSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYSGKQMSDDL   54 (76)
T ss_pred             EEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEEccCCC
Confidence            356888999999999999999999999999999999998863

>cd01802 AN1_N ubiquitin-like domain of AN1

Probab=99.02  E-value=7.4e-10  Score=62.36  Aligned_cols=41  Identities=41%  Similarity=0.537  Sum_probs=38.3

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+++++||.++|++|++..|+|+++|+|+|+|+.|+|..
T Consensus        41 ~leV~~~~TV~~lK~kI~~~~gip~~~QrLi~~Gk~L~D~~   81 (103)
T cd01802          41 ELRVSPFETVISVKAKIQRLEGIPVAQQHLIWNNMELEDEY   81 (103)
T ss_pred             EEEeCCCCcHHHHHHHHHHHhCCChHHEEEEECCEECCCCC
Confidence            56889999999999999999999999999999999998863

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.

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

Probab=99.01  E-value=3.6e-10  Score=60.80  Aligned_cols=48  Identities=21%  Similarity=0.348  Sum_probs=41.1

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceE--EEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRL--ITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L--~~~~-~v~~~~tv~~l   48 (77)
                      +++.+++++++||++||++|++..|+|+++|+|  +|.+ .+.++.++.++
T Consensus        13 ~~~~~~v~~~~TV~~lK~~I~~~~~i~~~~qrL~~~~~G~~L~D~~tL~~~   63 (80)
T cd01792          13 NEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLAHLDSREVLQDGVPLVSQ   63 (80)
T ss_pred             CEEEEEcCCCCcHHHHHHHHHHHhCCCHHHEEEEeccCCCCCCCCCCHHHc
Confidence            457889999999999999999999999999999  6665 55777788877

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.

>cd01795 USP48_C USP ubiquitin-specific protease

Probab=98.99  E-value=2.1e-09  Score=59.92  Aligned_cols=60  Identities=22%  Similarity=0.263  Sum_probs=48.8

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEEE-e-cCCccHHHHHHHHhhccCCCccceEEEECCe
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTLE-V-KSSDTINNVKSKIQDKEGIPPDQQRLIFAGI   70 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~~-v-~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~   70 (77)
                      .+++|++++||++||.+|....|+||++|+|+|.+. + +++.|+.++        |+.++.-.++.-..
T Consensus        17 ~~L~V~~~~TVg~LK~lImQ~f~V~P~dQkL~~dG~~L~DDsrTLssy--------Gv~sgSvl~Llide   78 (107)
T cd01795          17 KALLVSANQTLKELKIQIMHAFSVAPFDQNLSIDGKILSDDCATLGTL--------GVIPESVILLKADE   78 (107)
T ss_pred             ceEEeCccccHHHHHHHHHHHhcCCcccceeeecCceeccCCccHHhc--------CCCCCCEEEEEecC
Confidence            578999999999999999999999999999999853 3 677888887        88776655444333

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,

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

Probab=98.98  E-value=1.4e-09  Score=57.94  Aligned_cols=43  Identities=28%  Similarity=0.522  Sum_probs=39.4

Q ss_pred             EEEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           34 ITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        34 ~~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+.+++++||.++|+.|+...|+|+++|+|+|+|+.|+|..
T Consensus         9 ~~~l~v~~~~TV~~lK~~i~~~~gip~~~q~L~~~G~~L~d~~   51 (76)
T cd01800           9 MLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQYEGIFIKDSN   51 (76)
T ss_pred             EEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCEEcCCCC
Confidence            3568889999999999999999999999999999999998863

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.

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

Probab=98.98  E-value=8.7e-10  Score=57.98  Aligned_cols=46  Identities=17%  Similarity=0.115  Sum_probs=37.0

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      .++++++++||++||++|++..|+|+++|+|+|.+ .+.++.++.++
T Consensus        12 ~~l~v~~~~TV~~lK~~I~~~~~i~~~~~~Li~~Gk~L~d~~tL~~~   58 (71)
T cd01808          12 EEIEIAEDASVKDFKEAVSKKFKANQEQLVLIFAGKILKDTDTLTQH   58 (71)
T ss_pred             EEEEECCCChHHHHHHHHHHHhCCCHHHEEEEECCeEcCCCCcHHHc
Confidence            36788888888888888888888888888888875 55777777776

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=98.96  E-value=2.8e-10  Score=67.59  Aligned_cols=48  Identities=48%  Similarity=0.657  Sum_probs=42.7

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++++++++++||..+|.+|++.+|||+++|+|+|+. .+.+..+++++
T Consensus        11 kti~~eve~~~ti~~~Kakiq~~egIp~dqqrlifag~qLedgrtlSDY   59 (156)
T KOG0004|consen   11 KTITLEVEANDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY   59 (156)
T ss_pred             cceeeeecccccHHHHHHhhhcccCCCchhhhhhhhhcccccCCccccc
Confidence            3688999999999999999999999999999999985 77777888877

>smart00213 UBQ Ubiquitin homologues

Probab=98.96  E-value=1.5e-09  Score=55.23  Aligned_cols=47  Identities=30%  Similarity=0.405  Sum_probs=34.3

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.+++++++||++||.+|++..|+|++.|+|+|.+ .+.++.++.++
T Consensus        11 ~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~~g~~L~d~~tL~~~   58 (64)
T smart00213       11 TITLEVKPSDTVSELKEKIAELTGIPVEQQRLIYKGKVLEDDRTLADY   58 (64)
T ss_pred             eEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCEECCCCCCHHHc
Confidence            456777788888888888888888887778887764 45556666665

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

>cd01805 RAD23_N Ubiquitin-like domain of RAD23

Probab=98.95  E-value=2.8e-09  Score=56.60  Aligned_cols=42  Identities=40%  Similarity=0.690  Sum_probs=38.7

Q ss_pred             EEEEecCCccHHHHHHHHhhccCC--CccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGI--PPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gi--p~~~q~l~~~g~~L~d~~   76 (77)
                      |.+.+++++||.++|+.|++..|+  |+++|+|+|+|++|+|..
T Consensus        13 ~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~~~G~~L~d~~   56 (77)
T cd01805          13 FPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKILKDDT   56 (77)
T ss_pred             EEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEEECCEEccCCC
Confidence            467889999999999999999999  999999999999998863

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).

>cd01804 midnolin_N Ubiquitin-like domain of midnolin

Probab=98.95  E-value=1.6e-09  Score=58.14  Aligned_cols=41  Identities=20%  Similarity=0.349  Sum_probs=38.5

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      +.++++++.||.++|..|+++.++|+++|+|+|+|+.|+|.
T Consensus        14 ~~l~v~~~~TV~~LK~~I~~~~~~~~~~qrL~~~Gk~L~d~   54 (78)
T cd01804          14 FDLSVPPDETVEGLKKRISQRLKVPKERLALLHRETRLSSG   54 (78)
T ss_pred             EEEEECCcCHHHHHHHHHHHHhCCChHHEEEEECCcCCCCC
Confidence            46789999999999999999999999999999999999885

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.

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

Probab=98.91  E-value=2.9e-09  Score=55.97  Aligned_cols=41  Identities=27%  Similarity=0.338  Sum_probs=38.1

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .++++++.||.++|+.|++..|+|+++|+|+|+|+.|+|.-
T Consensus        13 ~l~v~~~~TV~~lK~~I~~~~~i~~~~~~Li~~Gk~L~d~~   53 (71)
T cd01808          13 EIEIAEDASVKDFKEAVSKKFKANQEQLVLIFAGKILKDTD   53 (71)
T ss_pred             EEEECCCChHHHHHHHHHHHhCCCHHHEEEEECCeEcCCCC
Confidence            57888999999999999999999999999999999998863

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.

>cd01813 UBP_N UBP ubiquitin processing protease

Probab=98.89  E-value=4.2e-09  Score=56.03  Aligned_cols=42  Identities=26%  Similarity=0.336  Sum_probs=38.6

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEE---CCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIF---AGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~---~g~~L~d~~   76 (77)
                      |.+++++++|+.++|+.|++..|+|+++|+|+|   +|+.+.|..
T Consensus        12 ~~v~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~~~~~Gk~l~D~~   56 (74)
T cd01813          12 YSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLGLKVKGKPAEDDV   56 (74)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEeecccCCcCCCCc
Confidence            578899999999999999999999999999996   999998753

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.

>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP

Probab=98.87  E-value=2.5e-09  Score=57.07  Aligned_cols=39  Identities=21%  Similarity=0.332  Sum_probs=25.8

Q ss_pred             CCcHHHHHHHhhhh--hCCC-cccceEEEEE-EecCCccHHHH
Q 040720           10 PTPLINVKAKIQDK--EGIP-PDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus        10 ~~tv~~lK~~i~~~--~gi~-~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++||++||++|++.  +|++ +++|+|+|.+ .+.++.++.++
T Consensus        20 ~~TV~~LK~kI~~~~~egi~~~dqQrLIy~GKiL~D~~TL~dy   62 (75)
T cd01815          20 GYQVSTLKQLIAAQLPDSLPDPELIDLIHCGRKLKDDQTLDFY   62 (75)
T ss_pred             cCcHHHHHHHHHHhhccCCCChHHeEEEeCCcCCCCCCcHHHc
Confidence            46777777777777  3453 6777777765 44666677666

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.

>cd01803 Ubiquitin Ubiquitin

Probab=98.86  E-value=7.2e-09  Score=54.67  Aligned_cols=41  Identities=76%  Similarity=0.986  Sum_probs=38.1

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.++++.||.++|+.|+...|+|++.|+|+|+|+.|+|.-
T Consensus        14 ~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~~~g~~L~d~~   54 (76)
T cd01803          14 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGR   54 (76)
T ss_pred             EEEECCcCcHHHHHHHHHHHhCCCHHHeEEEECCEECCCCC
Confidence            56888999999999999999999999999999999998863

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

>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP

Probab=98.86  E-value=6.4e-09  Score=55.48  Aligned_cols=37  Identities=24%  Similarity=0.332  Sum_probs=32.7

Q ss_pred             cCCccHHHHHHHHhhcc--CCC-ccceEEEECCeEcCccc
Q 040720           40 KSSDTINNVKSKIQDKE--GIP-PDQQRLIFAGINLKLVV   76 (77)
Q Consensus        40 ~~~~tv~~lK~~i~~~~--gip-~~~q~l~~~g~~L~d~~   76 (77)
                      +.++||.++|++|+++.  |++ +++|+|+|+|++|+|.-
T Consensus        18 ~~~~TV~~LK~kI~~~~~egi~~~dqQrLIy~GKiL~D~~   57 (75)
T cd01815          18 PGGYQVSTLKQLIAAQLPDSLPDPELIDLIHCGRKLKDDQ   57 (75)
T ss_pred             CccCcHHHHHHHHHHhhccCCCChHHeEEEeCCcCCCCCC
Confidence            56889999999999995  575 99999999999999864

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.

>cd01812 BAG1_N Ubiquitin-like domain of BAG1

Probab=98.85  E-value=6.5e-09  Score=54.28  Aligned_cols=41  Identities=27%  Similarity=0.459  Sum_probs=38.0

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      +.+.++++.||.++|+.|+..+|+|++.|+|.|+|+.|+|.
T Consensus        12 ~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~l~d~   52 (71)
T cd01812          12 HDLSISSQATFGDLKKMLAPVTGVEPRDQKLIFKGKERDDA   52 (71)
T ss_pred             EEEEECCCCcHHHHHHHHHHhhCCChHHeEEeeCCcccCcc
Confidence            46788999999999999999999999999999999999875

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).

>cd01806 Nedd8 Nebb8-like ubiquitin protein

Probab=98.85  E-value=1.1e-08  Score=53.97  Aligned_cols=41  Identities=34%  Similarity=0.776  Sum_probs=37.8

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.++++.||.++|+.|+...|+|++.|+|+|+|+.|+|..
T Consensus        14 ~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~~~g~~L~d~~   54 (76)
T cd01806          14 EIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDDK   54 (76)
T ss_pred             EEEECCCCCHHHHHHHHhHhhCCChhhEEEEECCeEccCCC
Confidence            46788999999999999999999999999999999998763

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.

>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein

Probab=98.84  E-value=1e-08  Score=53.56  Aligned_cols=42  Identities=40%  Similarity=0.541  Sum_probs=38.4

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      +.+.++++.+|.++|..|++..|+|++.|+|+|+|+.|+|..
T Consensus        13 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~L~d~~   54 (72)
T cd01809          13 HTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYSGRVLKDDE   54 (72)
T ss_pred             EEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCEECCCcC
Confidence            357888999999999999999999999999999999998863

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.

>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1

Probab=98.84  E-value=6.1e-09  Score=55.56  Aligned_cols=38  Identities=32%  Similarity=0.412  Sum_probs=35.1

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKL   74 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d   74 (77)
                      .+.++++.||.++|.+|++.+|+|+++|+| |+|+.|.|
T Consensus        16 ~l~v~~~~TV~~lK~kI~~~~gip~~~QrL-~~G~~L~d   53 (75)
T cd01799          16 WLTVRPDMTVAQLKDKVFLDYGFPPAVQRW-VIGQRLAR   53 (75)
T ss_pred             EEEECCCCcHHHHHHHHHHHHCcCHHHEEE-EcCCeeCC
Confidence            568899999999999999999999999999 99999853

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.

>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4

Probab=98.83  E-value=2.2e-09  Score=61.01  Aligned_cols=48  Identities=25%  Similarity=0.360  Sum_probs=39.2

Q ss_pred             EEeeCCCcHHHHHHHhh-----hhhCCC--cccceEEEEEE-ecCCccHHHHHHHH
Q 040720            5 LMWKAPTPLINVKAKIQ-----DKEGIP--PDQQRLITTLE-VKSSDTINNVKSKI   52 (77)
Q Consensus         5 ~~v~~~~tv~~lK~~i~-----~~~gi~--~~~q~L~~~~~-v~~~~tv~~lK~~i   52 (77)
                      ..+.+++||++||++|+     .++|+|  +++|+|||++. +.++.|+++++..+
T Consensus        20 ~~~~~sdTV~~lKekI~~~~p~~ke~~P~~~~~qKLIysGKiLeD~~TL~d~~~p~   75 (113)
T cd01814          20 KRYPAATTVDFLKERVVSQWPKDKEVGPKTVNEVKLISAGKILENSKTVGECRSPV   75 (113)
T ss_pred             cccChhhHHHHHHHHHHHhcccccccCCCCHHHeEEEeCCeecCCCCcHHHhCCcc
Confidence            45678999999999999     555666  99999999984 58889999996443

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

>cd01763 Sumo Small ubiquitin-related modifier (SUMO)

Probab=98.80  E-value=1.4e-08  Score=55.45  Aligned_cols=47  Identities=15%  Similarity=0.333  Sum_probs=40.3

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      .+.++|.+++|+..||.++++..|+|+++|+|+|.+ .+.++.|+.++
T Consensus        23 ~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f~G~~L~~~~T~~~l   70 (87)
T cd01763          23 EVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLFDGQRIRDNQTPDDL   70 (87)
T ss_pred             EEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEECCeECCCCCCHHHc
Confidence            567888889999999999999999998999998885 77888888887

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.

>smart00213 UBQ Ubiquitin homologues

Probab=98.79  E-value=1.9e-08  Score=51.12  Aligned_cols=41  Identities=51%  Similarity=0.699  Sum_probs=38.1

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      +.+.++++.||.++|..|+...|+|++.|+|+|+|+.|+|.
T Consensus        12 ~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~~g~~L~d~   52 (64)
T smart00213       12 ITLEVKPSDTVSELKEKIAELTGIPVEQQRLIYKGKVLEDD   52 (64)
T ss_pred             EEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCEECCCC
Confidence            46788999999999999999999999999999999999875

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

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

Probab=98.79  E-value=1e-09  Score=61.87  Aligned_cols=40  Identities=78%  Similarity=1.038  Sum_probs=37.7

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      .+++.++++|.++|+.|+.+.|+|+++|+|+|+|++|+|.
T Consensus        14 ~le~EpS~ti~~vKA~i~~~~Gi~~~~~~L~~~~k~LED~   53 (128)
T KOG0003|consen   14 TLEVEPSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDG   53 (128)
T ss_pred             EEEecccchHHHHHHHhccccCCCHHHHHHHhcccccccC
Confidence            4678999999999999999999999999999999999985

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

Probab=98.76  E-value=3.7e-09  Score=62.86  Aligned_cols=40  Identities=75%  Similarity=1.033  Sum_probs=37.4

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      ..++..+++|..+|+.|++.+|||++||+|+|.|++|+|-
T Consensus        14 ~~eve~~~ti~~~Kakiq~~egIp~dqqrlifag~qLedg   53 (156)
T KOG0004|consen   14 TLEVEANDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDG   53 (156)
T ss_pred             eeeecccccHHHHHHhhhcccCCCchhhhhhhhhcccccC
Confidence            4578899999999999999999999999999999999984

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=98.75  E-value=2.8e-08  Score=66.74  Aligned_cols=48  Identities=21%  Similarity=0.348  Sum_probs=42.9

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhC---CCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEG---IPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~g---i~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++.|+|++++||.+||.+|++..|   +|+++|+|+|.+ -+.++.++.++
T Consensus        11 ~~~~IeV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLIy~GkiL~Dd~tL~dy   62 (378)
T TIGR00601        11 QKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVREY   62 (378)
T ss_pred             CEEEEEeCCcChHHHHHHHHHHhhCCCCCChhHeEEEECCEECCCCCcHHHc
Confidence            4688999999999999999999998   999999999997 45778888887

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).

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

Probab=98.73  E-value=1.5e-08  Score=54.51  Aligned_cols=40  Identities=30%  Similarity=0.360  Sum_probs=37.1

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEE--EECCeEcCcc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRL--IFAGINLKLV   75 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l--~~~g~~L~d~   75 (77)
                      .+.++++.||.++|..|++..|+|+++|+|  +|+|+.|+|.
T Consensus        16 ~~~v~~~~TV~~lK~~I~~~~~i~~~~qrL~~~~~G~~L~D~   57 (80)
T cd01792          16 LVSLRDSMTVSELKQQIAQKIGVPAFQQRLAHLDSREVLQDG   57 (80)
T ss_pred             EEEcCCCCcHHHHHHHHHHHhCCCHHHEEEEeccCCCCCCCC
Confidence            467889999999999999999999999999  8999999875

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.

>cd01769 UBL Ubiquitin-like domain of UBL

Probab=98.70  E-value=8.3e-08  Score=49.33  Aligned_cols=47  Identities=36%  Similarity=0.512  Sum_probs=38.2

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      .+.+++.+++||++||.+|++..|+|++.|+|+|.+ .++++.++.++
T Consensus         9 ~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l~~~g~~l~d~~~l~~~   56 (69)
T cd01769           9 TFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYAGKILKDDKTLSDY   56 (69)
T ss_pred             EEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCcCCCCcCCHHHC
Confidence            567888899999999999999999999999998875 45666666654

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.

>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4

Probab=98.67  E-value=2e-08  Score=57.15  Aligned_cols=40  Identities=28%  Similarity=0.305  Sum_probs=34.2

Q ss_pred             EEecCCccHHHHHHHHh-----hccCCC--ccceEEEECCeEcCccc
Q 040720           37 LEVKSSDTINNVKSKIQ-----DKEGIP--PDQQRLIFAGINLKLVV   76 (77)
Q Consensus        37 ~~v~~~~tv~~lK~~i~-----~~~gip--~~~q~l~~~g~~L~d~~   76 (77)
                      ..+.+++||.++|+.|+     .++++|  +++|+|+|+|++|+|.-
T Consensus        20 ~~~~~sdTV~~lKekI~~~~p~~ke~~P~~~~~qKLIysGKiLeD~~   66 (113)
T cd01814          20 KRYPAATTVDFLKERVVSQWPKDKEVGPKTVNEVKLISAGKILENSK   66 (113)
T ss_pred             cccChhhHHHHHHHHHHHhcccccccCCCCHHHeEEEeCCeecCCCC
Confidence            35678999999999999     455566  99999999999999864

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

>cd01795 USP48_C USP ubiquitin-specific protease

Probab=98.67  E-value=4.8e-08  Score=54.51  Aligned_cols=42  Identities=24%  Similarity=0.248  Sum_probs=38.7

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcccC
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVVR   77 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~~   77 (77)
                      ++.+.+++||.++|.+|...+++||.+|+|+|+|+.|.|+-|
T Consensus        18 ~L~V~~~~TVg~LK~lImQ~f~V~P~dQkL~~dG~~L~DDsr   59 (107)
T cd01795          18 ALLVSANQTLKELKIQIMHAFSVAPFDQNLSIDGKILSDDCA   59 (107)
T ss_pred             eEEeCccccHHHHHHHHHHHhcCCcccceeeecCceeccCCc
Confidence            567999999999999999999999999999999999988743

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,

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

Probab=98.56  E-value=7.8e-08  Score=63.20  Aligned_cols=48  Identities=29%  Similarity=0.452  Sum_probs=44.4

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhC--CCcccceEEEEE-EecCCccHHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEG--IPPDQQRLITTL-EVKSSDTINNVK   49 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~g--i~~~~q~L~~~~-~v~~~~tv~~lK   49 (77)
                      +|++++.|++||.++|.+|+...|  +|++.|+|||.+ .+.++.++.++|
T Consensus        12 ~F~iev~Pe~tV~evK~kIet~~g~dyP~~~QkLIy~GkiL~D~~tv~Eyk   62 (340)
T KOG0011|consen   12 TFTIEVKPEDTVVEVKKKIETEKGPDYPAEQQKLIYSGKILKDETTVGEYK   62 (340)
T ss_pred             eeEeecCcchhHHHHHHHHHhccCCCCchhhheeeecceeccCCcchhhhc
Confidence            689999999999999999999999  999999999997 458899999885

>cd01769 UBL Ubiquitin-like domain of UBL

Probab=98.55  E-value=2.2e-07  Score=47.70  Aligned_cols=41  Identities=54%  Similarity=0.780  Sum_probs=37.3

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.++++.|+.++|..|+...|+|++.|+|+|+|+.|+|..
T Consensus        11 ~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l~~~g~~l~d~~   51 (69)
T cd01769          11 ELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYAGKILKDDK   51 (69)
T ss_pred             EEEECCCChHHHHHHHHHHHHCcChHHEEEEECCcCCCCcC
Confidence            45678899999999999999999999999999999998754

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.

>cd01763 Sumo Small ubiquitin-related modifier (SUMO)

Probab=98.52  E-value=3.5e-07  Score=49.88  Aligned_cols=41  Identities=15%  Similarity=0.355  Sum_probs=38.1

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+..++++..++..++++.|+|+++|+|+|+|+.|++.-
T Consensus        25 ~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f~G~~L~~~~   65 (87)
T cd01763          25 FFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLFDGQRIRDNQ   65 (87)
T ss_pred             EEEEcCCCHHHHHHHHHHHHhCCCccceEEEECCeECCCCC
Confidence            46789999999999999999999999999999999998764

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.

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=98.49  E-value=2.8e-07  Score=62.01  Aligned_cols=42  Identities=29%  Similarity=0.514  Sum_probs=39.0

Q ss_pred             EEEEecCCccHHHHHHHHhhccC---CCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEG---IPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~g---ip~~~q~l~~~g~~L~d~~   76 (77)
                      |.+.+++++||.++|.+|+...|   +|+++|+|+|+|++|+|..
T Consensus        13 ~~IeV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLIy~GkiL~Dd~   57 (378)
T TIGR00601        13 FKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDK   57 (378)
T ss_pred             EEEEeCCcChHHHHHHHHHHhhCCCCCChhHeEEEECCEECCCCC
Confidence            56789999999999999999998   9999999999999999864

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).

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

Probab=98.33  E-value=4.9e-07  Score=62.09  Aligned_cols=42  Identities=36%  Similarity=0.437  Sum_probs=36.7

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      |.+.|.++.+|.++|..|...+++|+++++|+|+||+|+|..
T Consensus        27 ~~~~V~~~ssV~qlKE~I~~~f~a~~dqlvLIfaGrILKD~d   68 (493)
T KOG0010|consen   27 YEVNVASDSSVLQLKELIAQRFGAPPDQLVLIYAGRILKDDD   68 (493)
T ss_pred             eeEecccchHHHHHHHHHHHhcCCChhHeeeeecCccccChh
Confidence            467788899999999999999999999999999999998754

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

Probab=98.21  E-value=4.7e-06  Score=45.29  Aligned_cols=35  Identities=23%  Similarity=0.392  Sum_probs=30.7

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEE
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITT   36 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~   36 (77)
                      .....++++.||++||.+|+...|+|++.|+|.+.
T Consensus        15 ~~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~   49 (87)
T PF14560_consen   15 SVEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLK   49 (87)
T ss_dssp             EEEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEE
Confidence            45678999999999999999999999999999874

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

Probab=98.08  E-value=9e-06  Score=44.09  Aligned_cols=32  Identities=19%  Similarity=0.223  Sum_probs=27.9

Q ss_pred             EEEeeCCCcHHHHHHHhhhhhCCCcccceEEE
Q 040720            4 LLMWKAPTPLINVKAKIQDKEGIPPDQQRLIT   35 (77)
Q Consensus         4 ~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~   35 (77)
                      ...++++.||.+||++++...|+||..|+|.+
T Consensus        16 ekr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l   47 (84)
T cd01789          16 EKKYSRGLTIAELKKKLELVVGTPASSMRLQL   47 (84)
T ss_pred             eEecCCCCcHHHHHHHHHHHHCCCccceEEEE
Confidence            34488999999999999999999999999964

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

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

Probab=98.02  E-value=1.6e-05  Score=41.52  Aligned_cols=47  Identities=28%  Similarity=0.422  Sum_probs=37.0

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCc-ccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPP-DQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~-~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      .+.+.|.+++++..|++++++..|+|+ +..+|+|.+ .++++.|+.++
T Consensus        12 ~~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~fdG~~L~~~~T~~~~   60 (72)
T PF11976_consen   12 EIKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLIFDGKRLDPNDTPEDL   60 (72)
T ss_dssp             EEEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEEETTEEE-TTSCHHHH
T ss_pred             EEEEEECCCCcHHHHHHHHHHhhCCCccceEEEEECCEEcCCCCCHHHC
Confidence            466778888888888888888888888 888888874 67888888877

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 ....

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

Probab=98.00  E-value=3.2e-05  Score=39.35  Aligned_cols=48  Identities=40%  Similarity=0.517  Sum_probs=40.1

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEE-EEecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITT-LEVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~-~~v~~~~tv~~l   48 (77)
                      +++.+++.++++|..+|.+|+...|+|+..|++.+. ..+.++.++.++
T Consensus        10 k~~~~~~~~~~~i~~~k~~i~~~~~~~~~~q~~~~~~~~l~d~~~l~~~   58 (75)
T KOG0001|consen   10 KTITLEVSPSDTIEVVKAKIRDKEGIPVDQQRLIFGGKPLEDGRTLADY   58 (75)
T ss_pred             CEEEEEecCCCHHHHHHHHHHhhcCCCCeeEEEEECCEECcCCCcHHHh
Confidence            357789999999999999999999999999998886 456667777776

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

Probab=97.97  E-value=1.1e-05  Score=53.31  Aligned_cols=42  Identities=45%  Similarity=0.657  Sum_probs=39.4

Q ss_pred             EEEEecCCccHHHHHHHHhhccC--CCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEG--IPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~g--ip~~~q~l~~~g~~L~d~~   76 (77)
                      |.+.+.++++|.++|..|+...|  .|..+|+|+|+|+.|.|..
T Consensus        13 F~iev~Pe~tV~evK~kIet~~g~dyP~~~QkLIy~GkiL~D~~   56 (340)
T KOG0011|consen   13 FTIEVKPEDTVVEVKKKIETEKGPDYPAEQQKLIYSGKILKDET   56 (340)
T ss_pred             eEeecCcchhHHHHHHHHHhccCCCCchhhheeeecceeccCCc
Confidence            57899999999999999999999  9999999999999999864

>cd01788 ElonginB Ubiquitin-like domain of Elongin B

Probab=97.94  E-value=2.6e-05  Score=44.57  Aligned_cols=67  Identities=19%  Similarity=0.255  Sum_probs=49.3

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEEE-ecCCccHHHHHHHHhhccCCCccceEEEEC
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTLE-VKSSDTINNVKSKIQDKEGIPPDQQRLIFA   68 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~~-v~~~~tv~~lK~~i~~~~gip~~~q~l~~~   68 (77)
                      |+-+++.++.||-+||.+|+.....||++|+|+-.-. ++++.|+.+++.-.+....-.+...-|.|.
T Consensus        13 TiF~dakes~tVlelK~~iegI~k~pp~dQrL~kd~qvLeD~kTL~d~g~t~~~akaq~pA~vgLa~r   80 (119)
T cd01788          13 TIFTDAKESTTVYELKRIVEGILKRPPEDQRLYKDDQLLDDGKTLGDCGFTSQTARPQAPATVGLAFR   80 (119)
T ss_pred             EEEeecCCcccHHHHHHHHHHHhcCChhHheeecCceeecccccHHHcCccccccccCCCCeEEEEEe
Confidence            4668899999999999999999999999999984334 688999999854332222223444445555

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.

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

Probab=97.80  E-value=8.2e-05  Score=38.74  Aligned_cols=42  Identities=36%  Similarity=0.585  Sum_probs=37.3

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCc-cceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPP-DQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~-~~q~l~~~g~~L~d~~   76 (77)
                      +.+.+..++++..+...++.+.|+|+ +..+|.|+|+.|+++-
T Consensus        13 ~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~fdG~~L~~~~   55 (72)
T PF11976_consen   13 IKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLIFDGKRLDPND   55 (72)
T ss_dssp             EEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEEETTEEE-TTS
T ss_pred             EEEEECCCCcHHHHHHHHHHhhCCCccceEEEEECCEEcCCCC
Confidence            45688899999999999999999999 9999999999998764

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 ....

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

Probab=97.77  E-value=2.3e-05  Score=54.08  Aligned_cols=46  Identities=26%  Similarity=0.385  Sum_probs=41.1

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEEEe-cCCccHHHH
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTLEV-KSSDTINNV   48 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~~v-~~~~tv~~l   48 (77)
                      ..+.|....||.++|+.|+...++|+++++|||++.+ ++.+|+..+
T Consensus        27 ~~~~V~~~ssV~qlKE~I~~~f~a~~dqlvLIfaGrILKD~dTL~~~   73 (493)
T KOG0010|consen   27 YEVNVASDSSVLQLKELIAQRFGAPPDQLVLIYAGRILKDDDTLKQY   73 (493)
T ss_pred             eeEecccchHHHHHHHHHHHhcCCChhHeeeeecCccccChhhHHHc
Confidence            4678899999999999999999999999999999854 788888776

>PLN02560 enoyl-CoA reductase

Probab=97.76  E-value=5.4e-05  Score=49.90  Aligned_cols=45  Identities=20%  Similarity=0.290  Sum_probs=36.7

Q ss_pred             EEEeeCCCcHHHHHHHhhhhhCC-CcccceEEEEE--------EecCCccHHHH
Q 040720            4 LLMWKAPTPLINVKAKIQDKEGI-PPDQQRLITTL--------EVKSSDTINNV   48 (77)
Q Consensus         4 ~~~v~~~~tv~~lK~~i~~~~gi-~~~~q~L~~~~--------~v~~~~tv~~l   48 (77)
                      ++++++++||++||.+|++..|+ ++++|+|.+..        .++++.++.++
T Consensus        17 ~lev~~~aTV~dLK~~Isk~~~~~~~~RqRL~~~~~~gk~~g~~L~d~ktL~d~   70 (308)
T PLN02560         17 GLEVPDSATVADLKKAIHKRKKKYYPSRQRLTLPLPPGKTRPTVLDDSKSLKDY   70 (308)
T ss_pred             eEEcCCCCcHHHHHHHHHHHcCCCChhheEEEEecCCCCcCccccCCCCCHHhc
Confidence            68999999999999999999987 89999999841        33555566655

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

Probab=97.73  E-value=6e-05  Score=50.03  Aligned_cols=45  Identities=24%  Similarity=0.434  Sum_probs=36.2

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTIN   46 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~   46 (77)
                      .++++|+.+..|.+||+-++...|+|+++.+.+|++ +++++++|.
T Consensus        15 ~l~v~v~~~t~I~~lke~Vak~~gvp~D~L~viFaGKeLs~~ttv~   60 (446)
T KOG0006|consen   15 GLPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELSNDTTVQ   60 (446)
T ss_pred             ceeEEEecCCCHHHHHHHHHHhhCCChhheEEEEeccccccCceee
Confidence            467888888888888888888888888888888875 777777777

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

Probab=97.70  E-value=8.9e-05  Score=39.43  Aligned_cols=45  Identities=20%  Similarity=0.259  Sum_probs=36.5

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE------EecCCccHHHH
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL------EVKSSDTINNV   48 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~------~v~~~~tv~~l   48 (77)
                      .++.|+|..+|.++|++|+...|++ ..|||.|.-      -++...+++++
T Consensus        13 l~l~vnPy~pI~k~K~kI~~~~~~~-g~qrLsfQepgg~rqlL~s~~sLA~y   63 (80)
T cd01811          13 WILRVNPYSPIRKIKEKIRRSRNCS-GLQRLSFQEPGGERQLLSSRKSLADY   63 (80)
T ss_pred             eEEEeCCcchHHHHHHHHHHhhCcc-cceEEEeecCCcccccccccccHhhh
Confidence            6789999999999999999999999 599999831      23455566655

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.

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

Probab=97.69  E-value=0.00021  Score=36.19  Aligned_cols=40  Identities=68%  Similarity=0.851  Sum_probs=36.9

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      ...+....++..+|.+|+...|+|+++|++.++|+.|+|.
T Consensus        13 ~~~~~~~~~i~~~k~~i~~~~~~~~~~q~~~~~~~~l~d~   52 (75)
T KOG0001|consen   13 TLEVSPSDTIEVVKAKIRDKEGIPVDQQRLIFGGKPLEDG   52 (75)
T ss_pred             EEEecCCCHHHHHHHHHHhhcCCCCeeEEEEECCEECcCC
Confidence            4677889999999999999999999999999999999875

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

Probab=97.66  E-value=0.00012  Score=39.63  Aligned_cols=35  Identities=29%  Similarity=0.348  Sum_probs=31.9

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEE-ECCe
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLI-FAGI   70 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~-~~g~   70 (77)
                      ...++++.||.++|.+++..+|+|+..|+|. |.|+
T Consensus        16 ekr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~~~~   51 (84)
T cd01789          16 EKKYSRGLTIAELKKKLELVVGTPASSMRLQLFDGD   51 (84)
T ss_pred             eEecCCCCcHHHHHHHHHHHHCCCccceEEEEEcCC
Confidence            3568999999999999999999999999994 8888

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.

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

Probab=97.50  E-value=0.00016  Score=48.09  Aligned_cols=41  Identities=37%  Similarity=0.587  Sum_probs=38.1

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      ++++++.+.+|.++|..++...|+|+++.+++|.||.|++.
T Consensus        16 l~v~v~~~t~I~~lke~Vak~~gvp~D~L~viFaGKeLs~~   56 (446)
T KOG0006|consen   16 LPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELSND   56 (446)
T ss_pred             eeEEEecCCCHHHHHHHHHHhhCCChhheEEEEeccccccC
Confidence            46788899999999999999999999999999999999875

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

Probab=97.45  E-value=0.00022  Score=38.43  Aligned_cols=33  Identities=24%  Similarity=0.300  Sum_probs=23.2

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEE
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLI   34 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~   34 (77)
                      ++-+++++++|+++|+++|++..++|...|.|+
T Consensus        15 ~~Rie~~~~~t~~~L~~kI~~~l~~~~~~~~L~   47 (80)
T PF11543_consen   15 MKRIEVSPSSTLSDLKEKISEQLSIPDSSQSLS   47 (80)
T ss_dssp             EEEEEE-TTSBHHHHHHHHHHHS---TTT---B
T ss_pred             CEEEEcCCcccHHHHHHHHHHHcCCCCcceEEE
Confidence            356899999999999999999999999888775

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.

>cd00196 UBQ Ubiquitin-like proteins

Probab=97.43  E-value=0.00037  Score=33.54  Aligned_cols=35  Identities=34%  Similarity=0.571  Sum_probs=27.9

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL   37 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~   37 (77)
                      ..+.+.++.|+++++.+|+++.|++++.+.|++..
T Consensus        10 ~~~~~~~~~tv~~l~~~i~~~~~~~~~~~~l~~~~   44 (69)
T cd00196          10 VELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNG   44 (69)
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHCcChHHeEEEECC
Confidence            45677778888888888888888888888887764

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

>cd01788 ElonginB Ubiquitin-like domain of Elongin B

Probab=97.43  E-value=0.00033  Score=40.10  Aligned_cols=48  Identities=21%  Similarity=0.199  Sum_probs=41.8

Q ss_pred             ccceEEEEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           29 DQQRLITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        29 ~~q~L~~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+++..|...+.++.+|.++|..|+.-...|+..|+|+-.+..|+|.-
T Consensus         8 rR~KTTiF~dakes~tVlelK~~iegI~k~pp~dQrL~kd~qvLeD~k   55 (119)
T cd01788           8 RRHKTTIFTDAKESTTVYELKRIVEGILKRPPEDQRLYKDDQLLDDGK   55 (119)
T ss_pred             EecceEEEeecCCcccHHHHHHHHHHHhcCChhHheeecCceeecccc
Confidence            356666778999999999999999999999999999997778888863

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.

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

Probab=97.34  E-value=0.00028  Score=52.56  Aligned_cols=48  Identities=23%  Similarity=0.342  Sum_probs=40.3

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEEEe-cCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTLEV-KSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~~v-~~~~tv~~l   48 (77)
                      |++++.+...+||.++|++|+++.+|+.+.|||||.+.| .++.+|..+
T Consensus        13 r~~t~~ig~q~ti~~~~d~~r~~~ni~s~~qr~i~~grvl~~~k~vq~~   61 (1143)
T KOG4248|consen   13 RTRTFIIGAQMTIKEFKDHIRASVNIPSEKQRLIYQGRVLQDDKKVQEY   61 (1143)
T ss_pred             ceeEEEechHHHHHHHHHHHHHhcccccccceeeecceeeccchhhhhc
Confidence            467778888899999999999999999999999998754 667777666

>cd00196 UBQ Ubiquitin-like proteins

Probab=97.24  E-value=0.0009  Score=32.12  Aligned_cols=39  Identities=41%  Similarity=0.600  Sum_probs=34.9

Q ss_pred             EEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           37 LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        37 ~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      +.++...++.+++..+..+.|++++.+.|.++|..+++.
T Consensus        12 ~~~~~~~tv~~l~~~i~~~~~~~~~~~~l~~~~~~~~~~   50 (69)
T cd00196          12 LLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGKILPDS   50 (69)
T ss_pred             EEcCCCCcHHHHHHHHHHHHCcChHHeEEEECCeECCCC
Confidence            456689999999999999999999999999999988654

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.

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

Probab=97.09  E-value=0.0018  Score=34.99  Aligned_cols=34  Identities=29%  Similarity=0.485  Sum_probs=29.9

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEEC
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFA   68 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~   68 (77)
                      ....++.+.||.+||.+++..+|+|++.|+|.+.
T Consensus        16 ~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~   49 (87)
T PF14560_consen   16 VEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLK   49 (87)
T ss_dssp             EEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE
T ss_pred             EEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEE
Confidence            3568899999999999999999999999999865

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

Probab=96.94  E-value=0.001  Score=49.70  Aligned_cols=41  Identities=32%  Similarity=0.439  Sum_probs=37.2

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+....||.++|.+|.++.+|+.+.|||+|+|+.|.|+.
T Consensus        16 t~~ig~q~ti~~~~d~~r~~~ni~s~~qr~i~~grvl~~~k   56 (1143)
T KOG4248|consen   16 TFIIGAQMTIKEFKDHIRASVNIPSEKQRLIYQGRVLQDDK   56 (1143)
T ss_pred             EEEechHHHHHHHHHHHHHhcccccccceeeecceeeccch
Confidence            45677889999999999999999999999999999998863

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

Probab=96.91  E-value=0.0039  Score=35.55  Aligned_cols=46  Identities=20%  Similarity=0.309  Sum_probs=23.7

Q ss_pred             EEEEeeCCCcHHHHHHHhhhh-----h--CCCcccceEEEEEE-ecCCccHHHH
Q 040720            3 LLLMWKAPTPLINVKAKIQDK-----E--GIPPDQQRLITTLE-VKSSDTINNV   48 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~-----~--gi~~~~q~L~~~~~-v~~~~tv~~l   48 (77)
                      .++.+++++||++||++|...     .  -..+...||+|.+. +.++.++.++
T Consensus        16 ~~~~~~~~~TV~~lKe~i~~~WP~d~~~~p~s~~~lRLI~~GriL~d~~tL~~~   69 (111)
T PF13881_consen   16 GPFRFDPSTTVADLKERIWAEWPEDWEERPKSPSDLRLIYAGRILEDNKTLSDC   69 (111)
T ss_dssp             EEEEE-TTSBHHHHHHHHHHSSSTTSSSTT-SGGGEEEEETTEEE-SSSBTGGG
T ss_pred             cccccCccChHHHHHHHHHHHCccccccCCCChhhEEEEeCCeecCCcCcHHHh
Confidence            456677777777777777642     1  01234455555542 2455555554

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

Probab=96.67  E-value=0.0017  Score=37.04  Aligned_cols=41  Identities=27%  Similarity=0.343  Sum_probs=31.2

Q ss_pred             EEEecCCccHHHHHHHHhhcc-------CCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKE-------GIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~-------gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+..++++||.++|+.|...-       ...++..+|+|.|+.|+|.-
T Consensus        17 ~~~~~~~~TV~~lKe~i~~~WP~d~~~~p~s~~~lRLI~~GriL~d~~   64 (111)
T PF13881_consen   17 PFRFDPSTTVADLKERIWAEWPEDWEERPKSPSDLRLIYAGRILEDNK   64 (111)
T ss_dssp             EEEE-TTSBHHHHHHHHHHSSSTTSSSTT-SGGGEEEEETTEEE-SSS
T ss_pred             ccccCccChHHHHHHHHHHHCccccccCCCChhhEEEEeCCeecCCcC
Confidence            456678999999999998763       12467899999999999863

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

Probab=96.66  E-value=0.0036  Score=34.88  Aligned_cols=34  Identities=26%  Similarity=0.319  Sum_probs=15.2

Q ss_pred             CCccHHHHHHHHhhccC--CCccceEEEECCeEcCc
Q 040720           41 SSDTINNVKSKIQDKEG--IPPDQQRLIFAGINLKL   74 (77)
Q Consensus        41 ~~~tv~~lK~~i~~~~g--ip~~~q~l~~~g~~L~d   74 (77)
                      .+.|+..||..|.+.-+  .....++|+|+|+.|.|
T Consensus        22 ~~~Tv~~LK~lIR~~~p~~~s~~rLRlI~~Gr~L~d   57 (97)
T PF10302_consen   22 NTTTVAWLKQLIRERLPPEPSRRRLRLIYAGRLLND   57 (97)
T ss_pred             CcccHHHHHHHHHhhcCCCCccccEEeeecCcccCc
Confidence            34444445544444441  22234445555555444

They contain a characteristic GFDRL sequence motif.

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

Probab=96.62  E-value=0.0068  Score=32.70  Aligned_cols=35  Identities=14%  Similarity=0.152  Sum_probs=32.7

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEE
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITT   36 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~   36 (77)
                      ++.|.|.++-+-.+|.++|+++.++|++..+|.|.
T Consensus        12 tIaIrvp~~~~y~~L~~ki~~kLkl~~e~i~LsYk   46 (80)
T cd06406          12 TVAIQVARGLSYATLLQKISSKLELPAEHITLSYK   46 (80)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCchhcEEEec
Confidence            68899999999999999999999999999999984

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

>PLN02560 enoyl-CoA reductase

Probab=96.58  E-value=0.005  Score=40.73  Aligned_cols=33  Identities=33%  Similarity=0.491  Sum_probs=29.9

Q ss_pred             EEEEecCCccHHHHHHHHhhccCC-CccceEEEE
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGI-PPDQQRLIF   67 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gi-p~~~q~l~~   67 (77)
                      ..+++++++||+++|..|+++.++ ++++|+|.+
T Consensus        16 ~~lev~~~aTV~dLK~~Isk~~~~~~~~RqRL~~   49 (308)
T PLN02560         16 GGLEVPDSATVADLKKAIHKRKKKYYPSRQRLTL   49 (308)
T ss_pred             eeEEcCCCCcHHHHHHHHHHHcCCCChhheEEEE
Confidence            357889999999999999999986 899999998

>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13

Probab=96.28  E-value=0.0082  Score=31.75  Aligned_cols=41  Identities=17%  Similarity=0.257  Sum_probs=28.4

Q ss_pred             eCCCcHHHHHHHhhhhhC-CCcccceEEEE--E-EecCCccHHHH
Q 040720            8 KAPTPLINVKAKIQDKEG-IPPDQQRLITT--L-EVKSSDTINNV   48 (77)
Q Consensus         8 ~~~~tv~~lK~~i~~~~g-i~~~~q~L~~~--~-~v~~~~tv~~l   48 (77)
                      +++.||++||..|++..+ +++++|+|.+.  + .+.++.++.++
T Consensus        20 ~~~aTV~dlk~~i~~~~~~~~~~Rqrl~~~~~g~~L~d~~tL~~~   64 (77)
T cd01801          20 SGDATIADLKKLIAKSSPQLTVNRQSLRLEPKGKSLKDDDTLVDL   64 (77)
T ss_pred             CCCccHHHHHHHHHHHcCCCCcceeEEEeCCCCcccCCcccHhhc
Confidence            477899999999988765 57888888642  2 34555555554

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.

>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13

Probab=95.97  E-value=0.0098  Score=31.43  Aligned_cols=36  Identities=25%  Similarity=0.238  Sum_probs=30.8

Q ss_pred             cCCccHHHHHHHHhhccC-CCccceEEE--ECCeEcCcc
Q 040720           40 KSSDTINNVKSKIQDKEG-IPPDQQRLI--FAGINLKLV   75 (77)
Q Consensus        40 ~~~~tv~~lK~~i~~~~g-ip~~~q~l~--~~g~~L~d~   75 (77)
                      +++.||.++|..|+...+ .++++|+|.  +.|+.|.|.
T Consensus        20 ~~~aTV~dlk~~i~~~~~~~~~~Rqrl~~~~~g~~L~d~   58 (77)
T cd01801          20 SGDATIADLKKLIAKSSPQLTVNRQSLRLEPKGKSLKDD   58 (77)
T ss_pred             CCCccHHHHHHHHHHHcCCCCcceeEEEeCCCCcccCCc
Confidence            678899999999999876 589999985  889988765

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

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

Probab=95.87  E-value=0.014  Score=32.54  Aligned_cols=47  Identities=17%  Similarity=0.261  Sum_probs=37.2

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEE---EEecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITT---LEVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~---~~v~~~~tv~~l   48 (77)
                      ++-++.+++.||-+||.+++....=|++.|+|+--   --+.++.++++.
T Consensus        13 tif~da~es~tV~elK~~l~gi~~~Pvn~qrL~kmd~eqlL~D~ktL~d~   62 (110)
T KOG4495|consen   13 TIFTDAKESSTVFELKRKLEGILKRPVNEQRLYKMDTEQLLDDGKTLGDC   62 (110)
T ss_pred             eEEeecCccccHHHHHHHHHHHHhCCCcchheeecCHHHHhhccchhhhc
Confidence            46688999999999999999999999999999751   123556666655

>cd06411 PB1_p51 The PB1 domain is present in the p51 protein, a homolog of the p67 protein

Probab=95.85  E-value=0.028  Score=30.21  Aligned_cols=35  Identities=9%  Similarity=0.023  Sum_probs=33.0

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEE
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITT   36 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~   36 (77)
                      |+.|.+.++.+..+|..+|+++.+.+++.-+|.|.
T Consensus         8 TVai~v~~g~~y~~L~~~ls~kL~l~~~~~~LSY~   42 (78)
T cd06411           8 TVALRAPRGADVSSLRALLSQALPQQAQRGQLSYR   42 (78)
T ss_pred             EEEEEccCCCCHHHHHHHHHHHhcCChhhcEEEec
Confidence            68899999999999999999999999999999984

p51 plays an important role in NADPH oxidase activation during phagosytosis. The PB1 domain is a modular domain mediating specific protein-protein interaction 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 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain mo

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

Probab=95.75  E-value=0.0065  Score=31.56  Aligned_cols=31  Identities=16%  Similarity=0.267  Sum_probs=27.0

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceE
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRL   33 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L   33 (77)
                      .-+...+.|||+++|.-|+...|..++..+|
T Consensus        14 VRvKCn~dDtiGD~KKliaaQtGT~~~kivl   44 (73)
T KOG3493|consen   14 VRVKCNTDDTIGDLKKLIAAQTGTRPEKIVL   44 (73)
T ss_pred             EEEEeCCcccccCHHHHHHHhhCCChhHhHH
Confidence            4578889999999999999999998887765

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

Probab=95.50  E-value=0.021  Score=39.70  Aligned_cols=37  Identities=16%  Similarity=0.292  Sum_probs=28.2

Q ss_pred             EEE-eeCCCcHHHHHHHhhhhhCCCcccceEEEEEEec
Q 040720            4 LLM-WKAPTPLINVKAKIQDKEGIPPDQQRLITTLEVK   40 (77)
Q Consensus         4 ~~~-v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~~v~   40 (77)
                      +++ +++++|+..+|+++...+|+||++|++.+.+...
T Consensus        16 ~v~~l~~d~t~~vlKaqlf~LTgV~PeRQKv~vKGg~a   53 (473)
T KOG1872|consen   16 PVETLSTDETPSVLKAQLFALTGVPPERQKVMVKGGLA   53 (473)
T ss_pred             cceeccCCCchHHHHHHHHHhcCCCccceeEEEecccc
Confidence            344 7778888888888888888888888877766443

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

Probab=95.41  E-value=0.036  Score=30.89  Aligned_cols=44  Identities=18%  Similarity=0.152  Sum_probs=32.8

Q ss_pred             EEEEee--CCCcHHHHHHHhhhhhC--CCcccceEEEEEEe-cCCccHH
Q 040720            3 LLLMWK--APTPLINVKAKIQDKEG--IPPDQQRLITTLEV-KSSDTIN   46 (77)
Q Consensus         3 ~~~~v~--~~~tv~~lK~~i~~~~g--i~~~~q~L~~~~~v-~~~~tv~   46 (77)
                      +.+++.  .+.||..||..|.+..+  .+...+||+|++.+ .++..+.
T Consensus        14 l~L~I~~~~~~Tv~~LK~lIR~~~p~~~s~~rLRlI~~Gr~L~d~t~l~   62 (97)
T PF10302_consen   14 LPLDIPSPNTTTVAWLKQLIRERLPPEPSRRRLRLIYAGRLLNDHTDLS   62 (97)
T ss_pred             ceeecCCCCcccHHHHHHHHHhhcCCCCccccEEeeecCcccCccchhh
Confidence            456666  88999999999999873  34567889998754 5555544

They contain a characteristic GFDRL sequence motif.

>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=95.39  E-value=0.077  Score=27.48  Aligned_cols=37  Identities=24%  Similarity=0.319  Sum_probs=15.4

Q ss_pred             EEecCCccHHHHHHHHhhccCCCccceEEEECCeEcC
Q 040720           37 LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK   73 (77)
Q Consensus        37 ~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~   73 (77)
                      +.+.+++++.++-.....++|+.+++..|.|+++.|+
T Consensus        11 vkvtp~~~l~~VL~eac~k~~l~~~~~~L~h~~k~ld   47 (65)
T PF11470_consen   11 VKVTPNTTLNQVLEEACKKFGLDPSSYDLKHNNKPLD   47 (65)
T ss_dssp             E---TTSBHHHHHHHHHHHTT--GGG-EEEETTEEES
T ss_pred             EEECCCCCHHHHHHHHHHHcCCCccceEEEECCEEec
Confidence            3444444555444444444555555555555555544

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.

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

Probab=95.38  E-value=0.041  Score=38.34  Aligned_cols=44  Identities=23%  Similarity=0.350  Sum_probs=39.1

Q ss_pred             EEEEEE-ecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           33 LITTLE-VKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        33 L~~~~~-v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      =.|... ++.+++...+|+++-...|+||+.|++.+.|..+.|++
T Consensus        13 k~y~v~~l~~d~t~~vlKaqlf~LTgV~PeRQKv~vKGg~a~dd~   57 (473)
T KOG1872|consen   13 KKYPVETLSTDETPSVLKAQLFALTGVPPERQKVMVKGGLAKDDV   57 (473)
T ss_pred             ccccceeccCCCchHHHHHHHHHhcCCCccceeEEEecccccccc
Confidence            346654 88999999999999999999999999999999998874

>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=95.10  E-value=0.037  Score=29.71  Aligned_cols=31  Identities=35%  Similarity=0.559  Sum_probs=21.8

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEE
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLI   66 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~   66 (77)
                      -+++++++|+.++++.|++..++|...|.|.
T Consensus        17 Rie~~~~~t~~~L~~kI~~~l~~~~~~~~L~   47 (80)
T PF11543_consen   17 RIEVSPSSTLSDLKEKISEQLSIPDSSQSLS   47 (80)
T ss_dssp             EEEE-TTSBHHHHHHHHHHHS---TTT---B
T ss_pred             EEEcCCcccHHHHHHHHHHHcCCCCcceEEE
Confidence            4688999999999999999999999988764

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.

>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=94.37  E-value=0.32  Score=25.15  Aligned_cols=48  Identities=21%  Similarity=0.144  Sum_probs=33.0

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEE-EEecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITT-LEVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~-~~v~~~~tv~~l   48 (77)
                      |.+.+.+.|+.|+.+|=+....+.|++++.-.|.|. -.++.+..+.-.
T Consensus         7 rr~~vkvtp~~~l~~VL~eac~k~~l~~~~~~L~h~~k~ldlslp~R~s   55 (65)
T PF11470_consen    7 RRFKVKVTPNTTLNQVLEEACKKFGLDPSSYDLKHNNKPLDLSLPFRLS   55 (65)
T ss_dssp             -EEEE---TTSBHHHHHHHHHHHTT--GGG-EEEETTEEESSS-BHHHH
T ss_pred             cEEEEEECCCCCHHHHHHHHHHHcCCCccceEEEECCEEeccccceeec
Confidence            568899999999999999999999999998888886 456666665543

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.

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

Probab=94.01  E-value=0.19  Score=28.15  Aligned_cols=39  Identities=13%  Similarity=0.427  Sum_probs=31.0

Q ss_pred             EEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           37 LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        37 ~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      +.+..++.+.-|...-..+.|++-.+.|++|+|+.++..
T Consensus        35 Fkikr~t~LkKLM~aYc~r~Gl~~~s~RFlFdG~rI~~~   73 (99)
T KOG1769|consen   35 FKIKRHTPLKKLMKAYCERQGLSMNSLRFLFDGQRIRET   73 (99)
T ss_pred             EEeecCChHHHHHHHHHHHcCCccceEEEEECCcCcCCC
Confidence            456677788888888888888888888888888887654

>smart00455 RBD Raf-like Ras-binding domain

Probab=92.10  E-value=0.5  Score=24.63  Aligned_cols=35  Identities=17%  Similarity=0.206  Sum_probs=30.0

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEE
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITT   36 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~   36 (77)
                      ...+.+.|+.|+.++=.++.++.|+.++.-.++..
T Consensus        11 ~~~V~vrpg~tl~e~L~~~~~kr~l~~~~~~v~~~   45 (70)
T smart00455       11 RTVVKVRPGKTVRDALAKALKKRGLNPECCVVRLR   45 (70)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEc
Confidence            45788999999999999999999999888777663

>KOG3439 consensus Protein conjugation factor involved in autophagy [Posttranslational modification, protein turnover, chaperones]

Probab=92.01  E-value=0.43  Score=27.30  Aligned_cols=46  Identities=4%  Similarity=0.072  Sum_probs=39.0

Q ss_pred             EEEeeCCCcHHHHHHHhhhhhCCCcccceEEE---EEEecCCccHHHHH
Q 040720            4 LLMWKAPTPLINVKAKIQDKEGIPPDQQRLIT---TLEVKSSDTINNVK   49 (77)
Q Consensus         4 ~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~---~~~v~~~~tv~~lK   49 (77)
                      ...|++++|++.+-..|....++++.+|-+.|   ++.-+++++|..|=
T Consensus        48 k~~i~~t~tfa~vi~Flkk~Lkl~as~slflYVN~sFAPsPDq~v~~Ly   96 (116)
T KOG3439|consen   48 KFKINPTQTFAKVILFLKKFLKLQASDSLFLYVNNSFAPSPDQIVGNLY   96 (116)
T ss_pred             eEEeCcchhhHHHHHHHHHHhCCcccCeEEEEEcCccCCCchhHHHHHH
Confidence            46789999999999999999999999998877   35567888888773

>PF13019 Telomere_Sde2: Telomere stability and silencing

Probab=91.82  E-value=0.38  Score=29.26  Aligned_cols=30  Identities=23%  Similarity=0.399  Sum_probs=27.3

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccc
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQ   31 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q   31 (77)
                      ++.+.++++.||.+|+.+|.+..++|+..|
T Consensus        16 tl~~~lp~~ttv~dL~~~l~~~~~~~~~~~   45 (162)
T PF13019_consen   16 TLSLSLPSTTTVSDLKDRLSERLPIPSSSQ   45 (162)
T ss_pred             eEEeeCCCCCcHHHHHHHHHhhcCCCccce
Confidence            678889999999999999999999998886

>PF14533 USP7_C2: Ubiquitin-specific protease C-terminal; PDB: 2YLM_A

Probab=90.87  E-value=0.39  Score=30.12  Aligned_cols=27  Identities=19%  Similarity=0.391  Sum_probs=19.8

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCc
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPP   28 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~   28 (77)
                      .|.+-|.+++|.+++|.+|+++.|++.
T Consensus       134 PF~f~v~~gE~f~~tK~Rl~~rlgv~~  160 (213)
T PF14533_consen  134 PFLFVVKPGETFSDTKERLQKRLGVSD  160 (213)
T ss_dssp             EEEEEEETT--HHHHHHHHHHHH---H
T ss_pred             CEEEEeeCCCcHHHHHHHHHHHhCCCh
Confidence            477889999999999999999999985

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

Probab=90.38  E-value=0.93  Score=23.85  Aligned_cols=35  Identities=17%  Similarity=0.168  Sum_probs=30.5

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL   37 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~   37 (77)
                      -.+.+.|+.||.++=.++.++.|+.++.--+++..
T Consensus        12 t~V~vrpg~ti~d~L~~~c~kr~l~~~~~~v~~~~   46 (72)
T cd01760          12 TVVPVRPGMSVRDVLAKACKKRGLNPECCDVFLLG   46 (72)
T ss_pred             EEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEec
Confidence            46889999999999999999999998888776654

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

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

Probab=90.34  E-value=0.14  Score=34.63  Aligned_cols=41  Identities=22%  Similarity=0.246  Sum_probs=30.8

Q ss_pred             EEEecCCccHHHHHHHHhhccCC-C-ccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGI-P-PDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gi-p-~~~q~l~~~g~~L~d~~   76 (77)
                      .+..+..++|.++|..++..+.- | +..|||+|.|+.|.|.+
T Consensus        25 ~i~~dl~wtv~~Lk~hls~VyPskpl~~dqrliYsgkllld~q   67 (391)
T KOG4583|consen   25 SISLDLKWTVGDLKVHLSQVYPSKPLELDQRLIYSGKLLLDHQ   67 (391)
T ss_pred             eeehhhhhhHHHHhhhHhhcCCCCCchhhHHHHhhccccccch
Confidence            45667888999999888877642 3 35688999999887764

>PF14533 USP7_C2: Ubiquitin-specific protease C-terminal; PDB: 2YLM_A

Probab=90.07  E-value=1.9  Score=27.04  Aligned_cols=28  Identities=14%  Similarity=0.246  Sum_probs=16.9

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcc
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPD   29 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~   29 (77)
                      .+.+-|+.+.||++|-+.++.+.+++.+
T Consensus        35 ~~~~~vpk~~tV~Dll~~l~~k~~~~~~   62 (213)
T PF14533_consen   35 EYELLVPKTGTVSDLLEELQKKVGFSEE   62 (213)
T ss_dssp             EEEE--BTT-BHHHHHHHHHTT----TT
T ss_pred             EEEEEECCCCCHHHHHHHHHHHcCCCcC
Confidence            4677888889999999998888887654

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

Probab=89.72  E-value=0.98  Score=24.17  Aligned_cols=32  Identities=31%  Similarity=0.423  Sum_probs=28.5

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEEC
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFA   68 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~   68 (77)
                      .+.+.+...|..+|.+|....|++- +|+|.|.
T Consensus        14 ~l~vnPy~pI~k~K~kI~~~~~~~g-~qrLsfQ   45 (80)
T cd01811          14 ILRVNPYSPIRKIKEKIRRSRNCSG-LQRLSFQ   45 (80)
T ss_pred             EEEeCCcchHHHHHHHHHHhhCccc-ceEEEee
Confidence            4678899999999999999999887 8999885

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.

>KOG0013 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.49  E-value=0.54  Score=29.88  Aligned_cols=32  Identities=22%  Similarity=0.308  Sum_probs=15.5

Q ss_pred             EEeeCCCcHHHHHHHhhhhhCCCcccceEEEE
Q 040720            5 LMWKAPTPLINVKAKIQDKEGIPPDQQRLITT   36 (77)
Q Consensus         5 ~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~   36 (77)
                      +.+...||+.++|.++++.+|+.+-.|+.+|+
T Consensus       161 lta~~~Dtv~eik~~L~Aaeg~D~~sQrif~S  192 (231)
T KOG0013|consen  161 LTAPHYDTVGEIKRALRAAEGVDPLSQRIFFS  192 (231)
T ss_pred             ecccCcCcHHHHHHHHHHhhccchhhheeecc
Confidence            33444455555555555555555444444444

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

Probab=89.21  E-value=1.5  Score=24.57  Aligned_cols=46  Identities=15%  Similarity=0.315  Sum_probs=41.2

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ..+.|..+.+...|+..-++..|++....|+.|.+ .+....|.++|
T Consensus        33 ~~Fkikr~t~LkKLM~aYc~r~Gl~~~s~RFlFdG~rI~~~~TP~~L   79 (99)
T KOG1769|consen   33 VVFKIKRHTPLKKLMKAYCERQGLSMNSLRFLFDGQRIRETHTPADL   79 (99)
T ss_pred             EEEEeecCChHHHHHHHHHHHcCCccceEEEEECCcCcCCCCChhhh
Confidence            45678889999999999999999999999999986 78888888887

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

Probab=89.01  E-value=1.5  Score=23.65  Aligned_cols=36  Identities=17%  Similarity=0.275  Sum_probs=32.2

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeE
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGIN   71 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~   71 (77)
                      ++.+++..+..++..+|.++.++|++...|.|....
T Consensus        14 aIrvp~~~~y~~L~~ki~~kLkl~~e~i~LsYkde~   49 (80)
T cd06406          14 AIQVARGLSYATLLQKISSKLELPAEHITLSYKSEA   49 (80)
T ss_pred             EEEcCCCCCHHHHHHHHHHHhCCCchhcEEEeccCC
Confidence            567899999999999999999999999999997654

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

>smart00666 PB1 PB1 domain

Probab=88.49  E-value=1.9  Score=22.44  Aligned_cols=34  Identities=12%  Similarity=0.119  Sum_probs=28.2

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEE
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLIT   35 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~   35 (77)
                      ++.+.++++.|-.+|+.+|+++.+.+.....|-|
T Consensus        12 ~~~~~~~~~~s~~dL~~~i~~~~~~~~~~~~l~Y   45 (81)
T smart00666       12 TRRLSVPRDISFEDLRSKVAKRFGLDNQSFTLKY   45 (81)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHhCCCCCCeEEEE
Confidence            4567788899999999999999998876777766

Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.

>PF04110 APG12: Ubiquitin-like autophagy protein Apg12 ; InterPro: IPR007242 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells

Probab=88.23  E-value=2.7  Score=22.97  Aligned_cols=50  Identities=12%  Similarity=0.177  Sum_probs=33.2

Q ss_pred             EEEeeCCCcHHHHHHHhhhhhCCCcccceEEEE---EEecCCccHHHHHHHHh
Q 040720            4 LLMWKAPTPLINVKAKIQDKEGIPPDQQRLITT---LEVKSSDTINNVKSKIQ   53 (77)
Q Consensus         4 ~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~---~~v~~~~tv~~lK~~i~   53 (77)
                      ...+++++|++.|-.-++...++.+.+....|-   +.-.+++++++|=....
T Consensus        19 k~kI~~~~~f~~vi~fLrk~Lk~~~~~slFlYin~sFaPspDe~vg~L~~~f~   71 (87)
T PF04110_consen   19 KFKISASQTFATVIAFLRKKLKLKPSDSLFLYINNSFAPSPDETVGDLYRCFG   71 (87)
T ss_dssp             EEEEETTSBTHHHHHHHHHHCT----SS-EEEEEEEE---TTSBHHHHHHHH-
T ss_pred             EEEECCCCchHHHHHHHHHHhCCccCCeEEEEEcCccCCCchhHHHHHHHHhC
Confidence            467899999999999999999998766655552   45578999999865543

In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. This entry represents Apg12, which is covalently bound to Apg5 [].; GO: 0000045 autophagic vacuole assembly, 0005737 cytoplasm; PDB: 1WZ3_B.

>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=86.95  E-value=2.7  Score=22.95  Aligned_cols=35  Identities=14%  Similarity=0.054  Sum_probs=28.8

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcc---cceEEE
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPD---QQRLIT   35 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~---~q~L~~   35 (77)
                      |++-+.+.|+..+.+|++.|+++.|+...   .-.|.|
T Consensus        11 rvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~~~~~~L~Y   48 (86)
T cd06409          11 RVHRFRLRPSESLEELRTLISQRLGDDDFETHLYALSY   48 (86)
T ss_pred             CEEEEEecCCCCHHHHHHHHHHHhCCccccCCcccEEE
Confidence            46778888999999999999999999863   556656

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

>cd01776 Rin1_RA Ubiquitin domain of RIN1 RAS effector

Probab=86.76  E-value=1.9  Score=23.50  Aligned_cols=53  Identities=11%  Similarity=0.164  Sum_probs=39.3

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCC-cccceEEEE-----EEecCCccHHHHHHHHhhc
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIP-PDQQRLITT-----LEVKSSDTINNVKSKIQDK   55 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~-~~~q~L~~~-----~~v~~~~tv~~lK~~i~~~   55 (77)
                      -++-|.|+.|+.+|-..++.+.++. |+.-.|++-     ..+.++.-...+|..+..+
T Consensus        16 KTL~V~P~~tt~~vc~lcA~Kf~V~qPe~y~LFl~vdg~~~qLadd~~Pq~ika~L~~~   74 (87)
T cd01776          16 KTLLVRPYITTEDVCQLCAEKFKVTQPEEYSLFLFVEETWQQLAPDTYPQRIKAELHSR   74 (87)
T ss_pred             eeeecCCCCcHHHHHHHHHHHhccCChhheeEEEEECCcEEEcCcccccceechhhccC
Confidence            3677899999999999999999994 888888763     2455666555666554433

Rin1_RA RIN1 is a RAS effector that binds with specificity and high affinity to activated RAS via its carboxy-terminal RA (RAS-associated) domain. RIN1 competes directly with RAF1 for RAS binding and is thought to divert signaling away from RAF and the MAPK pathway while also shunting RAS signals through alternate pathways. In addition, Rin1 and Rin2 are Rab5-binding proteins, binding preferentially to the GTP-bound form, that enhance the GDP-GTP exchange reaction on Rab5 that regulate the docking and fusion processes of endocytic vesicles. In addition to the RA domain, RIN1 and RIN2 have an SH2 (Src homology 2) domain, a proline-rich SH3 domain, and a Vps9 domain.

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

Probab=86.61  E-value=1.1  Score=25.12  Aligned_cols=34  Identities=26%  Similarity=0.285  Sum_probs=29.6

Q ss_pred             EEEEEecCCccHHHHHHHHhhccCCCccceEEEE
Q 040720           34 ITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIF   67 (77)
Q Consensus        34 ~~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~   67 (77)
                      .+....+++.+|.++|..+..-..-|++.|+|+.
T Consensus        13 tif~da~es~tV~elK~~l~gi~~~Pvn~qrL~k   46 (110)
T KOG4495|consen   13 TIFTDAKESSTVFELKRKLEGILKRPVNEQRLYK   46 (110)
T ss_pred             eEEeecCccccHHHHHHHHHHHHhCCCcchheee
Confidence            3456788999999999999999999999999875

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

Probab=86.21  E-value=1.2  Score=32.97  Aligned_cols=35  Identities=23%  Similarity=0.279  Sum_probs=30.7

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL   37 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~   37 (77)
                      +.+-++++.|+..+.+.|...+|||.+.|.|+|..
T Consensus       327 ~~~~~~~~ntl~~~~~~I~~~Tgipe~~qeLL~e~  361 (732)
T KOG4250|consen  327 HEYYVHADNTLHSLIERISKQTGIPEGKQELLFEG  361 (732)
T ss_pred             EEEecChhhhHHHHHHHHHHhhCCCCccceeeeec
Confidence            56778888999999999999999999999999863

>cd06411 PB1_p51 The PB1 domain is present in the p51 protein, a homolog of the p67 protein

Probab=85.54  E-value=3.6  Score=22.08  Aligned_cols=36  Identities=6%  Similarity=0.183  Sum_probs=31.6

Q ss_pred             EEEEEecCCccHHHHHHHHhhccCCCccceEEEECC
Q 040720           34 ITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG   69 (77)
Q Consensus        34 ~~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g   69 (77)
                      .+++.++......++...|.++...+++.-.|.|.-
T Consensus         8 TVai~v~~g~~y~~L~~~ls~kL~l~~~~~~LSY~~   43 (78)
T cd06411           8 TVALRAPRGADVSSLRALLSQALPQQAQRGQLSYRA   43 (78)
T ss_pred             EEEEEccCCCCHHHHHHHHHHHhcCChhhcEEEecC
Confidence            345678999999999999999999999999998864

p51 plays an important role in NADPH oxidase activation during phagosytosis. The PB1 domain is a modular domain mediating specific protein-protein interaction 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 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain mo

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

Probab=85.28  E-value=1.2  Score=28.28  Aligned_cols=30  Identities=17%  Similarity=0.148  Sum_probs=26.9

Q ss_pred             EeeCCCcHHHHHHHhhhhhCCCcccceEEE
Q 040720            6 MWKAPTPLINVKAKIQDKEGIPPDQQRLIT   35 (77)
Q Consensus         6 ~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~   35 (77)
                      +.+++.|++++|.+++-..|.+++.+.|..
T Consensus        18 r~~~~ltl~q~K~KLe~~~G~~~~~M~l~l   47 (234)
T KOG3206|consen   18 RLSNSLTLAQFKDKLELLTGTEAESMELEL   47 (234)
T ss_pred             hcCCcCcHHHHHhhhhhhhCCCccceEEEE
Confidence            457889999999999999999999998864

>PF02192 PI3K_p85B: PI3-kinase family, p85-binding domain; InterPro: IPR003113 This is the region of the p110 phosphatidylinositol 3-kinase (PI3-Kinase) that binds the p85 subunit

Probab=85.26  E-value=1.8  Score=23.15  Aligned_cols=21  Identities=14%  Similarity=0.229  Sum_probs=17.7

Q ss_pred             EEEEeeCCCcHHHHHHHhhhh
Q 040720            3 LLLMWKAPTPLINVKAKIQDK   23 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~   23 (77)
                      ++++++.++|+.++|+.+.+.
T Consensus         2 i~l~~~~~~Tl~~iK~~lw~~   22 (78)
T PF02192_consen    2 IPLRVSRDATLSEIKEELWEE   22 (78)
T ss_dssp             EEEEEETT-BHHHHHHHHHHH
T ss_pred             eEEEccCcCcHHHHHHHHHHH
Confidence            578999999999999998765

; GO: 0046934 phosphatidylinositol-4,5-bisphosphate 3-kinase activity, 0007165 signal transduction, 0005942 phosphatidylinositol 3-kinase complex; PDB: 3HIZ_A 3HHM_A 2RD0_A 4A55_A 2Y3A_A 2V1Y_A.

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

Probab=84.28  E-value=4.6  Score=22.42  Aligned_cols=40  Identities=18%  Similarity=0.386  Sum_probs=28.8

Q ss_pred             EEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           37 LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        37 ~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      +++..+++...+-.....+.|=.-+..|++|+|+.++..+
T Consensus        39 FkiKktT~f~klm~af~~rqGK~m~slRfL~dG~rI~~dq   78 (103)
T COG5227          39 FKIKKTTTFKKLMDAFSRRQGKNMSSLRFLFDGKRIDLDQ   78 (103)
T ss_pred             EEEeccchHHHHHHHHHHHhCcCcceeEEEEcceecCCCC
Confidence            4556677777777777777777777788888888766543

>KOG0013 consensus Uncharacterized conserved protein [Function unknown]

Probab=84.25  E-value=1.3  Score=28.23  Aligned_cols=41  Identities=29%  Similarity=0.397  Sum_probs=36.3

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      |...++..+++.++|..+.++.|+.+..|+++|+|..+-|.
T Consensus       159 ~~lta~~~Dtv~eik~~L~Aaeg~D~~sQrif~Sg~~l~dk  199 (231)
T KOG0013|consen  159 FWLTAPHYDTVGEIKRALRAAEGVDPLSQRIFFSGGVLVDK  199 (231)
T ss_pred             eeecccCcCcHHHHHHHHHHhhccchhhheeeccCCceecc
Confidence            45667889999999999999999999999999999998665

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

Probab=82.47  E-value=2.2  Score=22.59  Aligned_cols=42  Identities=5%  Similarity=0.022  Sum_probs=22.0

Q ss_pred             eeCCCcHHHHHHHhhhhhCC-CcccceEEEEE-EecCCccHHHH
Q 040720            7 WKAPTPLINVKAKIQDKEGI-PPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         7 v~~~~tv~~lK~~i~~~~gi-~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      |.++++|.+|++-+...... .-....|.+.+ .+++...+.++
T Consensus         1 v~~~d~v~dvrq~L~~~~~t~~~Tn~~L~~~g~~L~~~~el~~i   44 (76)
T PF15044_consen    1 VSPTDTVQDVRQVLAESPETCYLTNFSLEHNGQRLDDFVELSEI   44 (76)
T ss_pred             CChhhHHHHHHHHHHhCccccceeEEEEEECCCccCCchhhhhh
Confidence            46778888888887765332 22333333332 34444444444

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

Probab=80.92  E-value=3.1  Score=30.85  Aligned_cols=37  Identities=27%  Similarity=0.506  Sum_probs=32.8

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeE
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGIN   71 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~   71 (77)
                      +.+.++.+.++..++..|....|+|...|-|+|.|..
T Consensus       327 ~~~~~~~~ntl~~~~~~I~~~Tgipe~~qeLL~e~~~  363 (732)
T KOG4250|consen  327 HEYYVHADNTLHSLIERISKQTGIPEGKQELLFEGGL  363 (732)
T ss_pred             EEEecChhhhHHHHHHHHHHhhCCCCccceeeeecCc
Confidence            3567889999999999999999999999999998653

>smart00143 PI3K_p85B PI3-kinase family, p85-binding domain

Probab=80.76  E-value=2.5  Score=22.68  Aligned_cols=25  Identities=16%  Similarity=0.251  Sum_probs=20.4

Q ss_pred             EEEEeeCCCcHHHHHHHhhhh-hCCC
Q 040720            3 LLLMWKAPTPLINVKAKIQDK-EGIP   27 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~-~gi~   27 (77)
                      +++.|+.++|+.++|+.+.+. ...|
T Consensus         2 i~l~v~~~aTl~~IK~~lw~~A~~~P   27 (78)
T smart00143        2 VTLRVLREATLSTIKHELFKQARKMP   27 (78)
T ss_pred             eeEEccccccHHHHHHHHHHHHHhCC
Confidence            578999999999999999765 4444

Region of p110 PI3K that binds the p85 subunit.

>cd01612 APG12_C Ubiquitin-like domain of APG12

Probab=80.65  E-value=5.1  Score=21.78  Aligned_cols=47  Identities=6%  Similarity=0.089  Sum_probs=32.6

Q ss_pred             EEeeCCCcHHHHHHHhhhhhCCCcccceEEEEEEe---cCCccHHHHHHH
Q 040720            5 LMWKAPTPLINVKAKIQDKEGIPPDQQRLITTLEV---KSSDTINNVKSK   51 (77)
Q Consensus         5 ~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~~v---~~~~tv~~lK~~   51 (77)
                      .-|+.+.|++++..-|+...++++++-...|-.+.   .++++++++=..
T Consensus        20 flv~~~~tv~~~~~~lrk~L~l~~~~slflyvnn~f~p~~d~~~g~LY~~   69 (87)
T cd01612          20 FKISATQSFQAVIDFLRKRLKLKASDSLFLYINNSFAPSPDENVGNLYRC   69 (87)
T ss_pred             EEeCCCCCHHHHHHHHHHHhCCCccCeEEEEECCccCCCchhHHHHHHHh
Confidence            34788999999999999999998665443343332   345677776444

APG12_C The carboxy-terminal ubiquitin-like domain of APG12. Autophagy is a process in which cytoplasmic components are delivered to the lysosome/vacuole for degradation. Autophagy requires a ubiquitin-like protein conjugation system, in which APG12 is covalently bound to APG5.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	77
2y5b_B	152	Structure Of Usp21 In Complex With Linear Diubiquit		7e-17
3u30_A	172	Crystal Structure Of A Linear-Specific Ubiquitin Fa		7e-17
3b08_A	152	Crystal Structure Of The Mouse Hoil1-L-Nzf In Compl		8e-17
2zvn_A	154	Nemo Cozi Domain Incomplex With Diubiquitin In P212		8e-17
2w9n_A	152	Crystal Structure Of Linear Di-Ubiquitin Length = 1		8e-17
3u5c_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		4e-13
3u5g_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		4e-13
3u5e_m	128	The Structure Of The Eukaryotic Ribosome At 3.0 A R		6e-13
2jwz_A	76	Mutations In The Hydrophobic Core Of Ubiquitin Diff		7e-13
4ii3_B	96	Crystal Structure Of S. Pombe Ubiquitin Activating		7e-13
1otr_B	76	Solution Structure Of A Cue-Ubiquitin Complex Lengt		7e-13
3olm_D	79	Structure And Function Of A Ubiquitin Binding Site		8e-13
4hcn_B	98	Crystal Structure Of Burkholderia Pseudomallei Effe		8e-13
3l0w_B	169	Structure Of Split Monoubiquitinated Pcna With Ubiq		9e-13
2kdi_A	114	Solution Structure Of A UbiquitinUIM FUSION PROTEIN		4e-12
4ii2_B	83	Crystal Structure Of Ubiquitin Activating Enzyme 1		6e-12
2o6v_B	76	Crystal Structure And Solution Nmr Studies Of Lys48		9e-12
3ai5_A	307	Crystal Structure Of Yeast Enhanced Green Fluoresce		9e-12
3zf7_s	128	High-resolution Cryo-electron Microscopy Structure		9e-12
4a18_K	129	T.Thermophila 60s Ribosomal Subunit In Complex With		1e-11
2k25_A	103	Automated Nmr Structure Of The Ubb By Fapsy Length		1e-11
3v6c_B	91	Crystal Structure Of Usp2 In Complex With Mutated U		1e-11
3dvg_Y	79	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		1e-11
3v6e_B	91	Crystal Structure Of Usp2 And A Mutant Form Of Ubiq		1e-11
4ap4_C	80	Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Le		1e-11
2gbk_A	83	Crystal Structure Of The 9-10 Moad Insertion Mutant		1e-11
3ons_A	72	Crystal Structure Of Human Ubiquitin In A New Cryst		2e-11
3k9o_B	96	The Crystal Structure Of E2-25k And Ubb+1 Complex L		2e-11
2khw_B	79	Solution Structure Of The Human Polymerase Iota Ubm		2e-11
1xd3_B	75	Crystal Structure Of Uchl3-Ubvme Complex Length = 7		2e-11
1cmx_B	76	Structural Basis For The Specificity Of Ubiquitin C		2e-11
3nob_A	78	Structure Of K11-Linked Di-Ubiquitin Length = 78		2e-11
3h7s_A	76	Crystal Structures Of K63-Linked Di- And Tri-Ubiqui		2e-11
2gbj_A	84	Crystal Structure Of The 9-10 8 Glycine Insertion M		2e-11
3ldz_F	73	Crystal Structure Of Human Stam1 Vhs Domain In Comp		2e-11
1yx5_B	98	Solution Structure Of S5a Uim-1UBIQUITIN COMPLEX Le		2e-11
2k6d_B	76	Cin85 Sh3-C Domain In Complex With Ubiquitin Length		2e-11
2o6v_D	76	Crystal Structure And Solution Nmr Studies Of Lys48		2e-11
3rul_A	79	New Strategy To Analyze Structures Of Glycopeptide-		2e-11
3jvz_X	81	E2~ubiquitin-Hect Length = 81		2e-11
2znv_B	76	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		2e-11
2ld9_A	77	Backbone Structure Of Ubiquitin Determined Using Ba		2e-11
3dvg_X	80	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		2e-11
1aar_A	76	Structure Of A Diubiquitin Conjugate And A Model Fo		2e-11
1zgu_B	76	Solution Structure Of The Human Mms2-Ubiquitin Comp		2e-11
1s1q_B	76	Tsg101(Uev) Domain In Complex With Ubiquitin Length		2e-11
1yiw_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		2e-11
1gjz_A	53	Solution Structure Of A Dimeric N-Terminal Fragment		2e-11
2znv_C	77	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		2e-11
3q3f_A	189	Engineering Domain-Swapped Binding Interfaces By Mu		2e-11
3mtn_B	85	Usp21 In Complex With A Ubiquitin-based, Usp21-spec		2e-11
3vdz_A	111	Tailoring Encodable Lanthanide-Binding Tags As Mri		2e-11
1ogw_A	76	Synthetic Ubiquitin With Fluoro-Leu At 50 And 67 Le		2e-11
2ojr_A	111	Structure Of Ubiquitin Solved By Sad Using The Lant		3e-11
3n3k_B	85	The Catalytic Domain Of Usp8 In Complex With A Usp8		6e-11
2xk5_B	76	Crystal Structure Of K6-Linked Diubiquitin Length =		1e-10
1ud7_A	76	Solution Structure Of The Designed Hydrophobic Core		1e-10
1yj1_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		2e-10
2fcs_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		2e-10
1sif_A	88	Crystal Structure Of A Multiple Hydrophobic Core Mu		2e-10
1c3t_A	76	Rotamer Strain As A Determinant Of Protein Structur		3e-10
2zcb_A	76	Crystal Structure Of Ubiquitin P37aP38A Length = 76		5e-10
4i6l_B	76	Crystal Structure Of Otub1 In Complex With Ubiquiti		6e-10
4hjk_A	77	U7ub7 Disulfide Variant Length = 77		6e-10
1zw7_A	82	Elimination Of The C-Cap In Ubiquitin Structure, Dy		8e-10
2gbr_A	81	Crystal Structure Of The 35-36 Moad Insertion Mutan		1e-09
4hk2_A	78	U7ub25.2540 Length = 78		2e-09
4gsw_A	80	Crystal Structure Of Ubiquitin From Entamoeba Histo		3e-09
2jvc_A	82	Nmr Solution Structure Of Ubiquitin Like Protein Le		1e-08
2gbm_A	84	Crystal Structure Of The 35-36 8 Glycine Insertion		3e-08
1bt0_A	76	Structure Of Ubiquitin-Like Protein, Rub1 Length =		8e-06
4hcp_B	78	Crystal Structure Of Burkholderia Pseudomallei Effe		1e-04
1ndd_B	76	Structure Of Nedd8 Length = 76		1e-04
3gzn_I	82	Structure Of Nedd8-Activating Enzyme In Complex Wit		1e-04
2bkr_B	77	Nedd8 Nedp1 Complex Length = 77		1e-04
4f8c_B	88	Structure Of The Cif:nedd8 Complex - Yersinia Pseud		1e-04
3dbh_I	88	Structural Dissection Of A Gating Mechanism Prevent		1e-04
3dbl_I	88	Structural Dissection Of A Gating Mechanism Prevent		1e-04
2nvu_I	81	Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C1		1e-04
3dqv_A	81	Structural Insights Into Nedd8 Activation Of Cullin		1e-04

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

Iteration: 1
 Score = 82.4 bits (202), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 51/103 (49%), Positives = 54/103 (52%), Gaps = 44/103 (42%)
Query: 15  NVKAKIQDKEGIPPDQQRLI---------------------------------------- 34
           NVKAKIQDKEGIPPDQQRLI                                        
Sbjct: 25  NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGHMQIFVKTL 84
Query: 35  ----TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
                TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 85  TGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 127

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

Iteration: 1
 Score = 82.0 bits (201), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 51/103 (49%), Positives = 54/103 (52%), Gaps = 44/103 (42%)
Query: 15  NVKAKIQDKEGIPPDQQRLI---------------------------------------- 34
           NVKAKIQDKEGIPPDQQRLI                                        
Sbjct: 45  NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTL 104
Query: 35  ----TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
                TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 105 TGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 147

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

Iteration: 1
 Score = 82.0 bits (201), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 51/103 (49%), Positives = 54/103 (52%), Gaps = 44/103 (42%)
Query: 15  NVKAKIQDKEGIPPDQQRLI---------------------------------------- 34
           NVKAKIQDKEGIPPDQQRLI                                        
Sbjct: 25  NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTL 84
Query: 35  ----TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
                TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 85  TGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 127

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

Iteration: 1
 Score = 82.0 bits (201), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 51/103 (49%), Positives = 54/103 (52%), Gaps = 44/103 (42%)
Query: 15  NVKAKIQDKEGIPPDQQRLI---------------------------------------- 34
           NVKAKIQDKEGIPPDQQRLI                                        
Sbjct: 27  NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTL 86
Query: 35  ----TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
                TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 87  TGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 129

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

Iteration: 1
 Score = 82.0 bits (201), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 51/103 (49%), Positives = 54/103 (52%), Gaps = 44/103 (42%)
Query: 15  NVKAKIQDKEGIPPDQQRLI---------------------------------------- 34
           NVKAKIQDKEGIPPDQQRLI                                        
Sbjct: 25  NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTL 84
Query: 35  ----TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
                TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 85  TGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 127

>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 = 69.7 bits (169), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 33/38 (86%), Positives = 36/38 (94%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+SSDTI+NVKSKIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLE 51

>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 = 69.7 bits (169), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 33/38 (86%), Positives = 36/38 (94%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+SSDTI+NVKSKIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLE 51

>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 = 69.3 bits (168), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 33/38 (86%), Positives = 36/38 (94%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+SSDTI+NVKSKIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLE 51

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

Iteration: 1
 Score = 68.9 bits (167), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 33/38 (86%), Positives = 36/38 (94%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+SSDTI+NVKSKIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLE 51

>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 = 68.9 bits (167), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 33/38 (86%), Positives = 36/38 (94%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+SSDTI+NVKSKIQDKEGIPPDQQRLIFAG  L+
Sbjct: 34 TLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLE 71

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

Iteration: 1
 Score = 68.9 bits (167), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 33/38 (86%), Positives = 36/38 (94%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+SSDTI+NVKSKIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLE 51

>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 = 68.9 bits (167), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 33/38 (86%), Positives = 36/38 (94%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+SSDTI+NVKSKIQDKEGIPPDQQRLIFAG  L+
Sbjct: 17 TLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLE 54

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

Iteration: 1
 Score = 68.6 bits (166), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 33/38 (86%), Positives = 36/38 (94%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+SSDTI+NVKSKIQDKEGIPPDQQRLIFAG  L+
Sbjct: 36 TLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLE 73

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

Iteration: 1
 Score = 68.6 bits (166), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 33/38 (86%), Positives = 36/38 (94%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+SSDTI+NVKSKIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLE 51

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

Iteration: 1
 Score = 66.6 bits (161), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 32/38 (84%), Positives = 36/38 (94%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+SSDTI+NVKSKIQDKEGIPPDQQRLI+AG  L+
Sbjct: 23 TLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLE 60

>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 = 65.9 bits (159), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 29/38 (76%), Positives = 36/38 (94%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+SSDTI+NV+++IQD+EGIPPDQQRLIFAG  L+
Sbjct: 21 TLEVESSDTIDNVRARIQDREGIPPDQQRLIFAGRQLE 58

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

Iteration: 1
 Score = 65.1 bits (157), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGXQLE 51

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

Iteration: 1
 Score = 65.1 bits (157), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36  TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
           TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 247 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 284

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

Iteration: 1
 Score = 65.1 bits (157), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 30/38 (78%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
           LEV++SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 ALEVEASDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 51

>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 = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 30/38 (78%), Positives = 35/38 (92%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TL+V++SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLDVEASDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 51

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

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 22 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 59

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 31 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 68

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 17 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 54

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 31 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 68

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 18 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 55

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 21 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 58

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 51

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 15 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 52

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 17 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 54

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 51

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 51

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 16 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 53

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 51

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 22 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 59

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 51

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 51

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 51

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGRQLE 51

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 51

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 19 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 56

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 51

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 15 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 52

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 17 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 54

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 51

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGRQLE 51

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 51

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 51

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 16 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 53

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 51

>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 = 63.9 bits (154), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36  TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
           TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 119 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 156

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

Iteration: 1
 Score = 63.9 bits (154), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 17 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 54

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

Iteration: 1
 Score = 63.9 bits (154), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 49 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 86

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

Iteration: 1
 Score = 63.9 bits (154), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 30/34 (88%), Positives = 32/34 (94%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG 69
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAG 47

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

Iteration: 1
 Score = 63.2 bits (152), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 49 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 86

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

Iteration: 1
 Score = 62.4 bits (150), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 30/37 (81%), Positives = 33/37 (89%)
Query: 37 LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          LEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 18 LEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 54

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

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 30/38 (78%), Positives = 33/38 (86%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPP QQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGIPPQQQRLIFAGKQLE 51

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

Iteration: 1
 Score = 61.2 bits (147), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 28/38 (73%), Positives = 33/38 (86%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          T+EV+ SDT+ N K+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TIEVEPSDTVENFKAKIQDKEGIPPDQQRLIFAGKQLE 51

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

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 30/38 (78%), Positives = 33/38 (86%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKE IPPDQQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEXIPPDQQRLIFAGKQLE 51

>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 = 60.8 bits (146), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 30/38 (78%), Positives = 33/38 (86%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKE IPPDQQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEQIPPDQQRLIFAGKQLE 51

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

Iteration: 1
 Score = 60.5 bits (145), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 28/38 (73%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          T+E++ SDTI N+K+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 23 TVEMEPSDTIENLKAKIQDKEGIPPDQQRLIFAGKQLE 60

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

Iteration: 1
 Score = 60.1 bits (144), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 27/38 (71%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          T+E++ SDT+ N+K+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TVELEPSDTVENLKAKIQDKEGIPPDQQRLIFAGKQLE 51

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

Iteration: 1
 Score = 59.7 bits (143), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 29/38 (76%), Positives = 32/38 (84%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGI  DQQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGIAADQQRLIFAGKQLE 51

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

Iteration: 1
 Score = 58.9 bits (141), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 27/33 (81%), Positives = 31/33 (93%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFA 68
          TLEV+ SDTI NVK+KIQDKEGIPPDQQ+L+FA
Sbjct: 16 TLEVEPSDTIENVKAKIQDKEGIPPDQQKLLFA 48

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

Iteration: 1
 Score = 58.9 bits (141), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 29/38 (76%), Positives = 32/38 (84%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDK G PPDQQRLIFAG  L+
Sbjct: 15 TLEVEPSDTIENVKAKIQDKIGYPPDQQRLIFAGKQLE 52

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 29/38 (76%), Positives = 32/38 (84%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+SSDTI+NVKSKIQ   GIPPDQQ LIFAG  L+
Sbjct: 14 TLEVESSDTIDNVKSKIQAAPGIPPDQQELIFAGKQLE 51

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 31/43 (72%), Positives = 34/43 (79%), Gaps = 5/43 (11%)
Query: 36 TLEVKSSDTINNVKSKIQDKEG-----IPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEG     IPPDQQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGRWALAIPPDQQRLIFAGKQLE 56

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 29/38 (76%), Positives = 32/38 (84%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDK GIPPDQQ LIFAG  L+
Sbjct: 16 TLEVEPSDTIENVKAKIQDKLGIPPDQQWLIFAGKRLE 53

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

Iteration: 1
 Score = 57.0 bits (136), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 26/38 (68%), Positives = 34/38 (89%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ +D+I+ +K+KIQ+KEGIPPDQQRLIFAG  L+
Sbjct: 17 TLEVEPNDSIDAIKAKIQEKEGIPPDQQRLIFAGKQLE 54

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 24/38 (63%), Positives = 30/38 (78%)
Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          T++V  +DT+  VK+KI DKEGIPPDQQRLIF G  L+
Sbjct: 19 TIDVDHADTVGAVKAKIYDKEGIPPDQQRLIFGGKQLE 56

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 31/46 (67%), Positives = 34/46 (73%), Gaps = 8/46 (17%)
Query: 36 TLEVKSSDTINNVKSKIQDKE--------GIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKE        GIPPDQQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGGGGGGGGGIPPDQQRLIFAGKQLE 59

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 18/36 (50%), Positives = 30/36 (83%)
Query: 37 LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINL 72
          ++++ +DTI+ +K ++++KEGIPP QQRLI+AG  L
Sbjct: 15 IDIEPTDTIDRIKERVEEKEGIPPVQQRLIYAGKQL 50

>pdb|4HCP|B Chain B, Crystal Structure Of Burkholderia Pseudomallei Effector Protein Chbp In Complex With Nedd8 Length = 78

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 14/33 (42%), Positives = 27/33 (81%)
Query: 37 LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG 69
          ++++ +D +  +K ++++KEGIPP QQRLI++G
Sbjct: 17 IDIEPTDKVERIKERVEEKEGIPPQQQRLIYSG 49

>pdb|1NDD|B Chain B, Structure Of Nedd8 Length = 76

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 14/33 (42%), Positives = 27/33 (81%)
Query: 37 LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG 69
          ++++ +D +  +K ++++KEGIPP QQRLI++G
Sbjct: 15 IDIEPTDKVERIKERVEEKEGIPPQQQRLIYSG 47

>pdb|3GZN|I Chain I, Structure Of Nedd8-Activating Enzyme In Complex With Nedd8 And Mln4924 Length = 82

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 14/33 (42%), Positives = 27/33 (81%)
Query: 37 LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG 69
          ++++ +D +  +K ++++KEGIPP QQRLI++G
Sbjct: 21 IDIEPTDKVERIKERVEEKEGIPPQQQRLIYSG 53

>pdb|2BKR|B Chain B, Nedd8 Nedp1 Complex Length = 77

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 14/33 (42%), Positives = 27/33 (81%)
Query: 37 LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG 69
          ++++ +D +  +K ++++KEGIPP QQRLI++G
Sbjct: 16 IDIEPTDKVERIKERVEEKEGIPPQQQRLIYSG 48

>pdb|4F8C|B Chain B, Structure Of The Cif:nedd8 Complex - Yersinia Pseudotuberculosis Cycle Inhibiting Factor In Complex With Human Nedd8 Length = 88

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 14/33 (42%), Positives = 27/33 (81%)
Query: 37 LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG 69
          ++++ +D +  +K ++++KEGIPP QQRLI++G
Sbjct: 15 IDIEPTDKVERIKERVEEKEGIPPQQQRLIYSG 47

>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 = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 14/33 (42%), Positives = 27/33 (81%)
Query: 37 LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG 69
          ++++ +D +  +K ++++KEGIPP QQRLI++G
Sbjct: 27 IDIEPTDKVERIKERVEEKEGIPPQQQRLIYSG 59

>pdb|3DBL|I Chain I, Structural Dissection Of A Gating Mechanism Preventing Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1- Uba3arg190wt-Nedd8ala72gln) Length = 88

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 14/33 (42%), Positives = 27/33 (81%)
Query: 37 LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG 69
          ++++ +D +  +K ++++KEGIPP QQRLI++G
Sbjct: 27 IDIEPTDKVERIKERVEEKEGIPPQQQRLIYSG 59

>pdb|2NVU|I Chain I, Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C111a), A Trapped Ubiquitin-Like Protein Activation Complex Length = 81

Iteration: 1
 Score = 41.2 bits (95), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 14/33 (42%), Positives = 27/33 (81%)
Query: 37 LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG 69
          ++++ +D +  +K ++++KEGIPP QQRLI++G
Sbjct: 20 IDIEPTDKVERIKERVEEKEGIPPQQQRLIYSG 52

>pdb|3DQV|A Chain A, Structural Insights Into Nedd8 Activation Of Cullin-Ring Ligases: Conformational Control Of Conjugation Length = 81

Iteration: 1
 Score = 41.2 bits (95), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 14/33 (42%), Positives = 27/33 (81%)
Query: 37 LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG 69
          ++++ +D +  +K ++++KEGIPP QQRLI++G
Sbjct: 20 IDIEPTDKVERIKERVEEKEGIPPQQQRLIYSG 52

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	77
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	2e-19
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	6e-11
3u5c_F	225	RP14, S2, YS8, 40S ribosomal protein S5; translati	2e-17
3u5c_F	225	RP14, S2, YS8, 40S ribosomal protein S5; translati	3e-07
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	4e-17
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	1e-08
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	5e-17
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	7e-09
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	7e-17
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	1e-08
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	7e-17
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	3e-07
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	8e-17
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	1e-08
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	2e-16
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	2e-08
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	3e-16
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	3e-07
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	6e-16
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	5e-07
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	1e-15
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	1e-07
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	2e-15
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	9e-08
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	2e-15
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	3e-06
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	3e-15
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	2e-06
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	4e-15
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	1e-07
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	6e-15
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	1e-06
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	9e-15
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	1e-05
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	1e-14
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	8e-06
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	1e-14
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	6e-07
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	1e-14
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	2e-06
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	1e-14
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	1e-05
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	1e-14
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	1e-05
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	2e-14
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	2e-05
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	2e-14
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	3e-07
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	2e-14
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	1e-06
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	3e-14
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	1e-05
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	3e-14
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	3e-05
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	4e-14
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	2e-05
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	5e-14
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	3e-12
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	6e-14
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	2e-06
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	9e-14
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	7e-05
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	1e-13
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	6e-05
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	2e-13
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	4e-11
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	2e-13
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	6e-06
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	2e-13
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	8e-05
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	3e-13
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	2e-05
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	3e-13
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	8e-05
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	3e-13
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	2e-11
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	4e-13
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	1e-05
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	4e-13
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	2e-04
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	5e-13
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	4e-05
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	2e-12
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	4e-12
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	5e-12
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	7e-07
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	9e-12
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	2e-05
1we6_A	111	Splicing factor, putative; structural genomics, ub	1e-10
1we6_A	111	Splicing factor, putative; structural genomics, ub	3e-06
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	3e-10
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	4e-10
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	3e-08
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	1e-06
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	4e-06
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	1e-05
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	2e-05
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	3e-05
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	4e-05
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	9e-05
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	5e-04

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens} Length = 189

 Score = 76.2 bits (187), Expect = 2e-19
 Identities = 35/98 (35%), Positives = 42/98 (42%), Gaps = 39/98 (39%)

Query: 15  NVKAKIQDKEGIPPDQQRLI---------------------------------------T 35
           N + K+  K G    +  +                                         
Sbjct: 59  NREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYGGQIFVKTLTGKTI 118

Query: 36  TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
           TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 119 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 156

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens} Length = 189

 Score = 54.2 bits (130), Expect = 6e-11
 Identities = 9/52 (17%), Positives = 16/52 (30%), Gaps = 2/52 (3%)

Query: 23 KEGIPPDQQRLITTLEVKS--SDTINNVKSKIQDKEGIPPDQQRLIFAGINL 72
            G    +  L      KS   D  +N + K+  K G    +  + +     
Sbjct: 33 ALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFR 84

>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 = 70.2 bits (172), Expect = 2e-17
 Identities = 1/38 (2%), Positives = 8/38 (21%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
             V+    +       ++ +    + +          
Sbjct: 14 FEVVEEFTPVVLATPIPEEVQQAQTEIKLFNKWSFEEV 51

>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 = 43.6 bits (103), Expect = 3e-07
 Identities = 0/20 (0%), Positives = 5/20 (25%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
                ++ +    + +   
Sbjct: 25 LATPIPEEVQQAQTEIKLFN 44

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens} Length = 88

 Score = 67.7 bits (166), Expect = 4e-17
 Identities = 12/38 (31%), Positives = 18/38 (47%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          T  V +   +   K  I     IP ++QRLI+ G  L+
Sbjct: 31 TFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQ 68

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens} Length = 88

 Score = 45.7 bits (109), Expect = 1e-08
 Identities = 8/20 (40%), Positives = 10/20 (50%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
            K  I     IP ++QRLI
Sbjct: 42 EFKEHIAASVSIPSEKQRLI 61

>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 = 67.7 bits (166), Expect = 5e-17
 Identities = 12/38 (31%), Positives = 18/38 (47%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          T  V +   +   K  I     IP ++QRLI+ G  L+
Sbjct: 19 TFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQ 56

>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 = 46.9 bits (112), Expect = 7e-09
 Identities = 8/20 (40%), Positives = 10/20 (50%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
            K  I     IP ++QRLI
Sbjct: 30 EFKEHIAASVSIPSEKQRLI 49

>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana, uncharacterized putative protein, NESG, structural genomics; NMR {Arabidopsis thaliana} Length = 84

 Score = 66.9 bits (164), Expect = 7e-17
 Identities = 15/34 (44%), Positives = 19/34 (55%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG 69
           LEV   DT+  VK KI+  + IP  +Q LI  G
Sbjct: 24 ELEVDYRDTLLVVKQKIERSQHIPVSKQTLIVDG 57

>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana, uncharacterized putative protein, NESG, structural genomics; NMR {Arabidopsis thaliana} Length = 84

 Score = 46.1 bits (110), Expect = 1e-08
 Identities = 9/20 (45%), Positives = 12/20 (60%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
           VK KI+  + IP  +Q LI
Sbjct: 35 VVKQKIERSQHIPVSKQTLI 54

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9 Length = 189

 Score = 69.8 bits (170), Expect = 7e-17
 Identities = 7/37 (18%), Positives = 15/37 (40%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINL 72
             ++   ++ ++KS+I    G   D   L+  G   
Sbjct: 14 IYTLEQGTSVLDLKSQISQDMGFEIDMMTLVNNGFIA 50

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9 Length = 189

 Score = 44.3 bits (104), Expect = 3e-07
 Identities = 5/20 (25%), Positives = 10/20 (50%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
          ++K++I    G   D   L+
Sbjct: 25 DLKSQISQDMGFEIDMMTLV 44

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

 Score = 67.4 bits (165), Expect = 8e-17
 Identities = 14/39 (35%), Positives = 18/39 (46%)

Query: 35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
            + V    T+   K  I    GIP   QRLI++G  LK
Sbjct: 40 WEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILK 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 = 46.6 bits (111), Expect = 1e-08
 Identities = 9/20 (45%), Positives = 9/20 (45%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
            K  I    GIP   QRLI
Sbjct: 52 QFKEAINKANGIPVANQRLI 71

>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 = 65.7 bits (161), Expect = 2e-16
 Identities = 14/38 (36%), Positives = 18/38 (47%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
           + V    T+   K  I    GIP   QRLI++G  LK
Sbjct: 17 EVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILK 54

>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 = 45.3 bits (108), Expect = 2e-08
 Identities = 9/20 (45%), Positives = 9/20 (45%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
            K  I    GIP   QRLI
Sbjct: 28 QFKEAINKANGIPVANQRLI 47

>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 = 65.3 bits (160), Expect = 3e-16
 Identities = 14/38 (36%), Positives = 28/38 (73%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
           ++++ +D +  +K ++++KEGIPP QQRLI++G  + 
Sbjct: 14 EIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMN 51

>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 = 42.2 bits (100), Expect = 3e-07
 Identities = 12/20 (60%), Positives = 17/20 (85%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
           +K ++++KEGIPP QQRLI
Sbjct: 25 RIKERVEEKEGIPPQQQRLI 44

>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 = 64.7 bits (158), Expect = 6e-16
 Identities = 14/38 (36%), Positives = 28/38 (73%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
           ++++ +D +  +K ++++KEGIPP QQRLI++G  + 
Sbjct: 14 EIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMN 51

>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 = 41.9 bits (99), Expect = 5e-07
 Identities = 12/20 (60%), Positives = 17/20 (85%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
           +K ++++KEGIPP QQRLI
Sbjct: 25 RIKERVEEKEGIPPQQQRLI 44

>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 = 64.7 bits (158), Expect = 1e-15
 Identities = 15/39 (38%), Positives = 19/39 (48%)

Query: 35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
              V  + TI  +K +I  +    PDQ  LIFAG  LK
Sbjct: 29 EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILK 67

>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 = 44.3 bits (105), Expect = 1e-07
 Identities = 7/20 (35%), Positives = 10/20 (50%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
           +K +I  +    PDQ  LI
Sbjct: 41 QLKEEISQRFKAHPDQLVLI 60

>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 = 63.5 bits (155), Expect = 2e-15
 Identities = 15/39 (38%), Positives = 19/39 (48%)

Query: 35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
              V  + TI  +K +I  +    PDQ  LIFAG  LK
Sbjct: 34 EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILK 72

>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 = 44.3 bits (105), Expect = 9e-08
 Identities = 7/20 (35%), Positives = 10/20 (50%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
           +K +I  +    PDQ  LI
Sbjct: 46 QLKEEISQRFKAHPDQLVLI 65

>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 = 63.2 bits (154), Expect = 2e-15
 Identities = 14/38 (36%), Positives = 28/38 (73%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
           ++++ +D +  +K ++++KEGIPP QQRLI++G  + 
Sbjct: 26 EIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMN 63

>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 = 40.1 bits (94), Expect = 3e-06
 Identities = 12/22 (54%), Positives = 18/22 (81%)

Query: 15 NVKAKIQDKEGIPPDQQRLITT 36
           +K ++++KEGIPP QQRLI +
Sbjct: 37 RIKERVEEKEGIPPQQQRLIYS 58

>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 = 62.7 bits (153), Expect = 3e-15
 Identities = 31/38 (81%), Positives = 34/38 (89%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 51

>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 = 40.0 bits (94), Expect = 2e-06
 Identities = 20/20 (100%), Positives = 20/20 (100%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
          NVKAKIQDKEGIPPDQQRLI
Sbjct: 25 NVKAKIQDKEGIPPDQQRLI 44

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens} Length = 101

 Score = 62.8 bits (153), Expect = 4e-15
 Identities = 12/38 (31%), Positives = 17/38 (44%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
             V  + ++   K +I  +     DQ  LIFAG  LK
Sbjct: 38 EFAVPENSSVQQFKEEISKRFKSHTDQLVLIFAGKILK 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 = 43.9 bits (104), Expect = 1e-07
 Identities = 6/20 (30%), Positives = 8/20 (40%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
            K +I  +     DQ  LI
Sbjct: 49 QFKEEISKRFKSHTDQLVLI 68

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} Length = 94

 Score = 62.4 bits (152), Expect = 6e-15
 Identities = 13/38 (34%), Positives = 24/38 (63%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          T+EV  ++T++++K KI   E  P  + +L ++GI L 
Sbjct: 28 TVEVDRTETVSSLKDKIHIVENTPIKRMQLYYSGIELA 65

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} Length = 94

 Score = 40.8 bits (96), Expect = 1e-06
 Identities = 6/20 (30%), Positives = 10/20 (50%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
          ++K KI   E  P  + +L 
Sbjct: 39 SLKDKIHIVENTPIKRMQLY 58

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

 Score = 61.6 bits (150), Expect = 9e-15
 Identities = 30/38 (78%), Positives = 33/38 (86%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
           LEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 17 ILEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 54

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

 Score = 38.5 bits (90), Expect = 1e-05
 Identities = 20/20 (100%), Positives = 20/20 (100%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
          NVKAKIQDKEGIPPDQQRLI
Sbjct: 28 NVKAKIQDKEGIPPDQQRLI 47

>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 = 62.1 bits (151), Expect = 1e-14
 Identities = 14/38 (36%), Positives = 23/38 (60%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
           L V+S+DT+ ++K ++   EG+ P  QR  F+G  L 
Sbjct: 37 KLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLT 74

>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 = 39.3 bits (92), Expect = 8e-06
 Identities = 6/20 (30%), Positives = 11/20 (55%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
          ++K ++   EG+ P  QR  
Sbjct: 48 HMKRRLHAAEGVEPGSQRWF 67

>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 = 61.6 bits (150), Expect = 1e-14
 Identities = 8/39 (20%), Positives = 14/39 (35%)

Query: 35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
              +  +  +   K +I        D+  LIF G  L+
Sbjct: 29 HEFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILR 67

>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 = 42.0 bits (99), Expect = 6e-07
 Identities = 5/20 (25%), Positives = 7/20 (35%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
            K +I        D+  LI
Sbjct: 41 RFKKQISKYLHCNADRLVLI 60

>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 = 1e-14
 Identities = 10/39 (25%), Positives = 18/39 (46%)

Query: 34 ITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINL 72
           T  +V    TI  ++ ++     + P+ QRL + G  L
Sbjct: 21 CTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQL 59

>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 = 40.8 bits (96), Expect = 2e-06
 Identities = 4/20 (20%), Positives = 10/20 (50%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
           ++ ++     + P+ QRL 
Sbjct: 34 ELRERVWALFDVRPECQRLF 53

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

 Score = 61.2 bits (149), Expect = 1e-14
 Identities = 12/38 (31%), Positives = 22/38 (57%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          +L+V   + ++ +K  + +K  +P  QQRL+F G  L 
Sbjct: 21 SLQVPEDELVSTLKQLVSEKLNVPVRQQRLLFKGKALA 58

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

 Score = 38.4 bits (90), Expect = 1e-05
 Identities = 7/20 (35%), Positives = 12/20 (60%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
           +K  + +K  +P  QQRL+
Sbjct: 32 TLKQLVSEKLNVPVRQQRLL 51

>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 = 61.2 bits (149), Expect = 1e-14
 Identities = 31/38 (81%), Positives = 34/38 (89%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 17 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 54

>3mtn_B UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquitin-specific protease activity, hydrolase, ubiquitin B structural genomics consortium, SGC; 2.70A {Homo sapiens} Length = 85

 Score = 38.5 bits (90), Expect = 1e-05
 Identities = 20/21 (95%), Positives = 20/21 (95%)

Query: 15 NVKAKIQDKEGIPPDQQRLIT 35
          NVKAKIQDKEGIPPDQQRLI 
Sbjct: 28 NVKAKIQDKEGIPPDQQRLIF 48

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

 Score = 61.3 bits (149), Expect = 2e-14
 Identities = 13/37 (35%), Positives = 21/37 (56%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINL 72
          T EV   +T+  +K+ +   EGI P+ Q ++ AG  L
Sbjct: 31 TFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAGAPL 67

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

 Score = 38.2 bits (89), Expect = 2e-05
 Identities = 7/20 (35%), Positives = 12/20 (60%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
           +KA +   EGI P+ Q ++
Sbjct: 42 QIKAHVASLEGIAPEDQVVL 61

>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 = 61.7 bits (150), Expect = 2e-14
 Identities = 11/38 (28%), Positives = 22/38 (57%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
             +  +D ++ +K KI +  G+P  +Q+L + GI +K
Sbjct: 49 VFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIK 86

>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 = 43.3 bits (102), Expect = 3e-07
 Identities = 7/24 (29%), Positives = 13/24 (54%)

Query: 11 TPLINVKAKIQDKEGIPPDQQRLI 34
            +  +K KI +  G+P  +Q+L 
Sbjct: 56 DQVSVIKVKIHEATGMPAGKQKLQ 79

>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 = 62.7 bits (152), Expect = 2e-14
 Identities = 32/34 (94%), Positives = 34/34 (100%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG 69
          TLEV+SSDTI+NVKSKIQDKEGIPPDQQRLIFAG
Sbjct: 14 TLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAG 47

>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 = 42.3 bits (99), Expect = 1e-06
 Identities = 25/102 (24%), Positives = 34/102 (33%), Gaps = 50/102 (49%)

Query: 15  NVKAKIQDKEGIPPDQQRLITT-------------------------------------- 36
           NVK+KIQDKEGIPPDQQRLI                                        
Sbjct: 25  NVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGGGETIKFV 84

Query: 37  ---------LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG 69
                    + +K    + + ++ I+ +   P D   L F  
Sbjct: 85  ADGDIGSGSVIIKPFVDMEHPETSIKLEMDQPVD---LTFGA 123

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

 Score = 60.5 bits (147), Expect = 3e-14
 Identities = 28/38 (73%), Positives = 34/38 (89%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          T+E++ SDTI N+K+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 23 TVEMEPSDTIENLKAKIQDKEGIPPDQQRLIFAGKQLE 60

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

 Score = 38.1 bits (89), Expect = 1e-05
 Identities = 19/20 (95%), Positives = 20/20 (100%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
          N+KAKIQDKEGIPPDQQRLI
Sbjct: 34 NLKAKIQDKEGIPPDQQRLI 53

>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 = 60.5 bits (147), Expect = 3e-14
 Identities = 12/38 (31%), Positives = 22/38 (57%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
             +  +  I  +K +I+D++G+P  QQ+L F G  L+
Sbjct: 21 AYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQ 58

>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 = 37.8 bits (88), Expect = 3e-05
 Identities = 8/20 (40%), Positives = 15/20 (75%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
           +K +I+D++G+P  QQ+L 
Sbjct: 32 GLKQQIEDQQGLPKKQQQLE 51

>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 = 60.0 bits (146), Expect = 4e-14
 Identities = 15/38 (39%), Positives = 23/38 (60%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
           +EV S  +I  +K  +  ++G+P DQ R+IFAG  L 
Sbjct: 14 PVEVDSDTSILQLKEVVAKQQGVPADQLRVIFAGKELP 51

>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 = 37.7 bits (88), Expect = 2e-05
 Identities = 7/20 (35%), Positives = 13/20 (65%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
           +K  +  ++G+P DQ R+I
Sbjct: 25 QLKEVVAKQQGVPADQLRVI 44

>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 = 61.5 bits (149), Expect = 5e-14
 Identities = 21/105 (20%), Positives = 33/105 (31%), Gaps = 47/105 (44%)

Query: 15  NVKAKIQDKEGIPPDQQRLI---------------------------------------- 34
            +KA+I  K G+   QQRL                                         
Sbjct: 27  ELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDKSDEPLSILV 86

Query: 35  -------TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINL 72
                  +T EV+ + T+ ++K ++   EG+  D   L F G  L
Sbjct: 87  RNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPL 131

>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 = 56.9 bits (137), Expect = 3e-12
 Identities = 11/39 (28%), Positives = 21/39 (53%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKL 74
           + + SS +++ +K++I  K G+   QQRL      + L
Sbjct: 16 QVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVAL 54

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 125

 Score = 60.6 bits (147), Expect = 6e-14
 Identities = 10/34 (29%), Positives = 14/34 (41%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG 69
             V  + ++   K  I  +     DQ  LIFAG
Sbjct: 45 EFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAG 78

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 125

 Score = 41.0 bits (96), Expect = 2e-06
 Identities = 6/20 (30%), Positives = 7/20 (35%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
            K  I  +     DQ  LI
Sbjct: 56 QFKEAISKRFKSQTDQLVLI 75

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

 Score = 59.8 bits (145), Expect = 9e-14
 Identities = 32/38 (84%), Positives = 36/38 (94%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+SSDTI+NVKSKIQDKEGIPPDQQRLI+AG  L+
Sbjct: 23 TLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLE 60

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

 Score = 37.1 bits (86), Expect = 7e-05
 Identities = 19/20 (95%), Positives = 20/20 (100%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
          NVK+KIQDKEGIPPDQQRLI
Sbjct: 34 NVKSKIQDKEGIPPDQQRLI 53

>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 = 59.4 bits (144), Expect = 1e-13
 Identities = 31/38 (81%), Positives = 34/38 (89%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 15 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 52

>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 = 36.7 bits (85), Expect = 6e-05
 Identities = 20/20 (100%), Positives = 20/20 (100%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
          NVKAKIQDKEGIPPDQQRLI
Sbjct: 26 NVKAKIQDKEGIPPDQQRLI 45

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

 Score = 60.8 bits (147), Expect = 2e-13
 Identities = 51/102 (50%), Positives = 53/102 (51%), Gaps = 44/102 (43%)

Query: 15  NVKAKIQDKEGIPPDQQRLIT--------------------------------------- 35
           NVKAKIQDKEGIPPDQQRLI                                        
Sbjct: 45  NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTL 104

Query: 36  -----TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINL 72
                TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L
Sbjct: 105 TGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQL 146

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

 Score = 54.3 bits (130), Expect = 4e-11
 Identities = 31/37 (83%), Positives = 33/37 (89%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINL 72
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L
Sbjct: 34 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQL 70

>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 = 58.9 bits (143), Expect = 2e-13
 Identities = 11/38 (28%), Positives = 21/38 (55%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
           L+++ S+TI   K+K+         Q +LI++G  L+
Sbjct: 15 PLDLEPSNTILETKTKLAQSISCEESQIKLIYSGKVLQ 52

>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 = 39.7 bits (93), Expect = 6e-06
 Identities = 9/49 (18%), Positives = 16/49 (32%), Gaps = 12/49 (24%)

Query: 15 NVKAKIQDKEGIPPDQQRLI---------TTLE---VKSSDTINNVKSK 51
            K K+         Q +LI          T+    +K  D +  + S+
Sbjct: 26 ETKTKLAQSISCEESQIKLIYSGKVLQDSKTVSECGLKDGDQVVFMVSQ 74

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

 Score = 58.6 bits (142), Expect = 2e-13
 Identities = 31/38 (81%), Positives = 34/38 (89%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 51

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

 Score = 36.7 bits (85), Expect = 8e-05
 Identities = 20/20 (100%), Positives = 20/20 (100%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
          NVKAKIQDKEGIPPDQQRLI
Sbjct: 25 NVKAKIQDKEGIPPDQQRLI 44

>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 = 58.1 bits (141), Expect = 3e-13
 Identities = 12/41 (29%), Positives = 23/41 (56%), Gaps = 3/41 (7%)

Query: 36 TLEVKSSDTINNVKSKIQDKEG---IPPDQQRLIFAGINLK 73
           +++   +T+  +K KI+ ++G    P   Q+LI+AG  L 
Sbjct: 14 KIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILN 54

>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 = 38.1 bits (89), Expect = 2e-05
 Identities = 8/23 (34%), Positives = 13/23 (56%), Gaps = 3/23 (13%)

Query: 15 NVKAKIQDKEG---IPPDQQRLI 34
           +K KI+ ++G    P   Q+LI
Sbjct: 25 ALKEKIESEKGKDAFPVAGQKLI 47

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

 Score = 58.7 bits (142), Expect = 3e-13
 Identities = 31/38 (81%), Positives = 34/38 (89%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L+
Sbjct: 49 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 86

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

 Score = 36.8 bits (85), Expect = 8e-05
 Identities = 20/20 (100%), Positives = 20/20 (100%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
          NVKAKIQDKEGIPPDQQRLI
Sbjct: 60 NVKAKIQDKEGIPPDQQRLI 79

>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 = 59.6 bits (144), Expect = 3e-13
 Identities = 51/102 (50%), Positives = 53/102 (51%), Gaps = 44/102 (43%)

Query: 15  NVKAKIQDKEGIPPDQQRLI---------------------------------------- 34
           NVKAKIQDKEGIPPDQQRLI                                        
Sbjct: 25  NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTL 84

Query: 35  ----TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINL 72
                TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L
Sbjct: 85  TGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQL 126

>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 = 54.6 bits (131), Expect = 2e-11
 Identities = 31/37 (83%), Positives = 33/37 (89%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINL 72
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQL 50

>2faz_A Ubiquitin-like containing PHD and ring finger DOM protein 1; cell cycle, DNA damage, DNA repair, DNA-binding, ligase, Met binding, nuclear protein; 2.00A {Homo sapiens} SCOP: d.15.1.1 Length = 78

 Score = 57.4 bits (139), Expect = 4e-13
 Identities = 9/40 (22%), Positives = 18/40 (45%)

Query: 34 ITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
           T   +     +  ++ KIQ+   + P  QRL + G  ++
Sbjct: 16 HTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQME 55

>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 = 38.5 bits (90), Expect = 1e-05
 Identities = 7/20 (35%), Positives = 11/20 (55%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
           ++ KIQ+   + P  QRL 
Sbjct: 29 ELRRKIQELFHVEPGLQRLF 48

>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 = 58.5 bits (141), Expect = 4e-13
 Identities = 33/38 (86%), Positives = 36/38 (94%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          TLEV+SSDTI+NVKSKIQDKEGIPPDQQRLIFAG  L+
Sbjct: 14 TLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLE 51

>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 = 36.2 bits (83), Expect = 2e-04
 Identities = 19/20 (95%), Positives = 20/20 (100%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
          NVK+KIQDKEGIPPDQQRLI
Sbjct: 25 NVKSKIQDKEGIPPDQQRLI 44

>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 = 57.3 bits (139), Expect = 5e-13
 Identities = 12/41 (29%), Positives = 23/41 (56%), Gaps = 3/41 (7%)

Query: 36 TLEVKSSDTINNVKSKIQDKEG---IPPDQQRLIFAGINLK 73
           + ++  +T+  +K KI+ ++G    P   Q+LI+AG  L 
Sbjct: 19 KIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILS 59

>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 = 36.8 bits (86), Expect = 4e-05
 Identities = 8/23 (34%), Positives = 13/23 (56%), Gaps = 3/23 (13%)

Query: 15 NVKAKIQDKEG---IPPDQQRLI 34
           +K KI+ ++G    P   Q+LI
Sbjct: 30 VLKEKIEAEKGRDAFPVAGQKLI 52

>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 = 55.9 bits (135), Expect = 2e-12
 Identities = 12/38 (31%), Positives = 21/38 (55%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          T EV+ + T+ ++K ++   EG+  D   L F G  L+
Sbjct: 18 TYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLE 55

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

 Score = 54.7 bits (132), Expect = 4e-12
 Identities = 12/38 (31%), Positives = 21/38 (55%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          T EV+ + T+ ++K ++   EG+  D   L F G  L+
Sbjct: 18 TYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLE 55

>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 = 57.9 bits (139), Expect = 5e-12
 Identities = 30/36 (83%), Positives = 32/36 (88%)

Query: 37  LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINL 72
           LEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG  L
Sbjct: 248 LEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQL 283

>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 = 43.6 bits (102), Expect = 7e-07
 Identities = 20/20 (100%), Positives = 20/20 (100%)

Query: 15  NVKAKIQDKEGIPPDQQRLI 34
           NVKAKIQDKEGIPPDQQRLI
Sbjct: 258 NVKAKIQDKEGIPPDQQRLI 277

>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 = 54.2 bits (131), Expect = 9e-12
 Identities = 13/38 (34%), Positives = 20/38 (52%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
           L V    T+ ++KS++Q    + P  Q+LIF G  L 
Sbjct: 25 PLSVSPDCTVKDLKSQLQPITNVLPRGQKLIFKGKVLV 62

>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 = 37.7 bits (88), Expect = 2e-05
 Identities = 6/24 (25%), Positives = 14/24 (58%)

Query: 11 TPLINVKAKIQDKEGIPPDQQRLI 34
            + ++K+++Q    + P  Q+LI
Sbjct: 32 CTVKDLKSQLQPITNVLPRGQKLI 55

>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 = 52.1 bits (125), Expect = 1e-10
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 26 IPPDQQRLITTLEVKS-SDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
           P +       + V+S S+ + ++K KI  +  IP ++Q+L      LK
Sbjct: 34 KPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLK 82

>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 = 40.6 bits (95), Expect = 3e-06
 Identities = 7/24 (29%), Positives = 14/24 (58%)

Query: 11 TPLINVKAKIQDKEGIPPDQQRLI 34
            + ++K KI  +  IP ++Q+L 
Sbjct: 52 ENVGSLKEKIAGEIQIPANKQKLS 75

>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 = 50.8 bits (121), Expect = 3e-10
 Identities = 7/48 (14%), Positives = 23/48 (47%)

Query: 26 IPPDQQRLITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          +  D   +  +L+V     ++N +   + + G+P ++ ++++    L 
Sbjct: 15 VRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLT 62

>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 = 52.7 bits (125), Expect = 4e-10
 Identities = 12/41 (29%), Positives = 23/41 (56%), Gaps = 3/41 (7%)

Query: 36 TLEVKSSDTINNVKSKIQDKEG---IPPDQQRLIFAGINLK 73
           + ++  +T+  +K KI+ ++G    P   Q+LI+AG  L 
Sbjct: 21 KIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILS 61

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A Length = 105

 Score = 45.4 bits (107), Expect = 3e-08
 Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 5/60 (8%)

Query: 10 PTPLINVKAKIQDKEGIPPDQQRLITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG 69
          PT  I +   ++D +        +   L V+   T+ ++K  +    G PP  Q+ +   
Sbjct: 19 PTQDIRLWVSVEDAQM-----HTVTIWLTVRPDMTVASLKDMVFLDYGFPPVLQQWVIGQ 73

>1v86_A DNA segment, CHR 7, wayne state university 128, expressed; ubiquitin fold, structural genomics, D7WSU128E protein; HET: DNA; NMR {Mus musculus} SCOP: d.15.1.1 Length = 95

 Score = 40.9 bits (96), Expect = 1e-06
 Identities = 10/35 (28%), Positives = 20/35 (57%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGI 70
           ++V    T + +K KI    G+PP  Q++++ G+
Sbjct: 30 DVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGL 64

>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 Length = 96

 Score = 39.8 bits (93), Expect = 4e-06
 Identities = 8/44 (18%), Positives = 21/44 (47%)

Query: 30 QQRLITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
           +     +E+ + +     K+++    G+ P +Q+++  G  LK
Sbjct: 15 GKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLK 58

>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 = 38.9 bits (90), Expect = 1e-05
 Identities = 5/33 (15%), Positives = 16/33 (48%)

Query: 34 ITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLI 66
             + ++ + T+  +K  ++++  IP  +  L 
Sbjct: 20 NVDVVLEDTCTVGEIKQILENELQIPVSKMLLK 52

>1wgd_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; ENDPLASMIC reticulum stress, UBL domain; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 93

 Score = 38.0 bits (88), Expect = 2e-05
 Identities = 12/48 (25%), Positives = 23/48 (47%), Gaps = 2/48 (4%)

Query: 28 PDQQRLITTLEVKSSDTINNVKSKIQDK--EGIPPDQQRLIFAGINLK 73
          P+Q+     L      ++ ++K+ +     E   P+ QRLI++G  L 
Sbjct: 15 PNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLL 62

>1t0y_A Tubulin folding cofactor B; ubiquitin-like, cytoskeleton, microtubule, CESG, structural genomics, protein structure initiative, PSI; NMR {Caenorhabditis elegans} SCOP: d.15.1.1 Length = 122

 Score = 38.0 bits (88), Expect = 3e-05
 Identities = 6/29 (20%), Positives = 14/29 (48%)

Query: 39 VKSSDTINNVKSKIQDKEGIPPDQQRLIF 67
            +  ++N++K K++   G   D  R+  
Sbjct: 24 YPAGMSLNDLKKKLELVVGTTVDSMRIQL 52

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens} Length = 99

 Score = 37.6 bits (87), Expect = 4e-05
 Identities = 10/48 (20%), Positives = 22/48 (45%), Gaps = 2/48 (4%)

Query: 28 PDQQRLITTLEVKSSDTINNVKSKIQDK--EGIPPDQQRLIFAGINLK 73
          P+Q+    T+    + T+  +K+ + +          QRL+++G  L 
Sbjct: 31 PNQKYSDQTISCFLNWTVGKLKTHLSNVYPSKPLTKDQRLVYSGRLLP 78

>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 Length = 118

 Score = 36.9 bits (85), Expect = 9e-05
 Identities = 10/37 (27%), Positives = 17/37 (45%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINL 72
            + K S T+  +K  ++     PP++QRL      L
Sbjct: 15 FTDAKESSTVFELKRIVEGILKRPPEEQRLYKDDQLL 51

>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 Length = 93

 Score = 34.2 bits (78), Expect = 5e-04
 Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 2/44 (4%)

Query: 32 RLITTLEVK--SSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          RL   + VK    D++ + K  +  + G  P++  L   G  LK
Sbjct: 29 RLGKKVRVKCLGEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLK 72

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	77
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.84
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.84
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.79
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	99.44
1wju_A	100	NEDD8 ultimate buster-1; ubiquitin-like domain, st	99.44
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	99.39
2lxa_A	87	Ubiquitin-like protein MDY2; ubiquitin-like domain	99.38
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	99.37
4ajy_B	118	Transcription elongation factor B polypeptide 2; E	99.33
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	99.31
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	99.31
1wju_A	100	NEDD8 ultimate buster-1; ubiquitin-like domain, st	99.29
2kjr_A	95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	99.27
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	99.27
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	99.25
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	99.24
2uyz_B	79	Small ubiquitin-related modifier 1; sumoylation, c	99.23
2kj6_A	97	Tubulin folding cofactor B; methods development, N	99.22
2lxa_A	87	Ubiquitin-like protein MDY2; ubiquitin-like domain	99.22
4ajy_B	118	Transcription elongation factor B polypeptide 2; E	99.22
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	99.21
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	99.21
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	99.2
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	99.2
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	99.2
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	99.19
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	99.19
1wyw_B	97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	99.19
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	99.19
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	99.18
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	99.17
3v6c_B	91	Ubiquitin; structural genomics, structural genomic	99.17
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	99.16
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	99.16
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	99.16
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	99.16
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	99.16
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	99.16
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	99.15
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	99.15
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	99.14
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	99.14
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	99.14
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	99.14
4a20_A	98	Ubiquitin-like protein MDY2; protein binding, GET-	99.13
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	99.13
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	99.13
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	99.13
4a20_A	98	Ubiquitin-like protein MDY2; protein binding, GET-	99.12
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	99.12
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	99.12
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	99.12
4b6w_A	86	Tubulin-specific chaperone; CAP-Gly, ubiquitin-lik	99.12
4hcn_B	98	Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidas	99.11
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	99.11
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	99.11
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	99.1
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	99.1
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	99.1
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	99.1
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	99.09
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	99.09
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	99.09
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	99.09
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	99.07
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	99.07
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	99.07
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	99.06
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	99.06
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	99.06
1se9_A	126	Ubiquitin family; ubiquitin-like, cell-free, wheat	99.06
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	99.06
2uyz_B	79	Small ubiquitin-related modifier 1; sumoylation, c	99.05
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	99.05
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	99.05
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	99.05
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	99.05
3v6c_B	91	Ubiquitin; structural genomics, structural genomic	99.04
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	99.04
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	99.04
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	99.04
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	99.04
3vdz_A	111	Ubiquitin-40S ribosomal protein S27A; gadolinium,	99.03
1v6e_A	95	Cytoskeleton-associated protein 1; tubulin-specifi	99.03
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.03
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	98.6
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	99.03
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	99.02
4hcn_B	98	Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidas	99.02
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	99.01
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	99.01
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	99.01
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	99.0
1wxv_A	92	BAG-family molecular chaperone regulator-1; struct	99.0
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	99.0
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	99.0
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	99.0
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	99.0
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	98.99
1wyw_B	97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	98.99
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	98.99
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	98.99
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	98.99
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	98.99
1we6_A	111	Splicing factor, putative; structural genomics, ub	98.98
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	98.98
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	98.97
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	98.97
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	98.97
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	98.96
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	98.96
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	98.96
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	98.95
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	98.95
3vdz_A	111	Ubiquitin-40S ribosomal protein S27A; gadolinium,	98.95
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	98.94
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	98.94
1se9_A	126	Ubiquitin family; ubiquitin-like, cell-free, wheat	98.94
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	98.94
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	98.93
2daf_A	118	FLJ35834 protein; hypothetical protein FLJ35834, u	98.93
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	98.93
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	98.92
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	98.92
3u5c_f	152	40S ribosomal protein S31; translation, ribosome,	98.92
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	98.91
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	98.91
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	98.91
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	98.91
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	98.9
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	98.9
1wxv_A	92	BAG-family molecular chaperone regulator-1; struct	98.9
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	98.89
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	98.89
2daf_A	118	FLJ35834 protein; hypothetical protein FLJ35834, u	98.88
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	98.88
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	98.87
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	98.86
1we6_A	111	Splicing factor, putative; structural genomics, ub	98.84
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	98.84
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	98.83
2dzj_A	88	Synaptic glycoprotein SC2; ubiquitin-like fold, st	98.82
4b6w_A	86	Tubulin-specific chaperone; CAP-Gly, ubiquitin-lik	98.81
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	98.81
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	98.8
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	98.26
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	98.77
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	98.76
2kjr_A	95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	98.74
2kj6_A	97	Tubulin folding cofactor B; methods development, N	98.74
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	98.72
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	98.72
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	98.71
2dzj_A	88	Synaptic glycoprotein SC2; ubiquitin-like fold, st	98.69
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	98.69
4efo_A	94	Serine/threonine-protein kinase TBK1; ubiquitin li	98.68
3u5c_f	152	40S ribosomal protein S31; translation, ribosome,	98.68
4efo_A	94	Serine/threonine-protein kinase TBK1; ubiquitin li	98.67
1wf9_A	107	NPL4 family protein; beta-grAsp fold like domain,	98.65
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	98.59
1v6e_A	95	Cytoskeleton-associated protein 1; tubulin-specifi	98.57
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	98.55
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	98.54
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	98.53
2io1_B	94	Small ubiquitin-related modifier 3 precursor; SUMO	98.47
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	98.46
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	98.46
2kzr_A	86	Ubiquitin thioesterase OTU1; structural genomics,	98.44
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	98.43
3a4r_A	79	Nfatc2-interacting protein; ubiquitin fold, coiled	98.41
1wm3_A	72	Ubiquitin-like protein SMT3B; ubiquitin fold, half	98.4
1wjn_A	97	Tubulin-folding protein TBCE; ubiquitin-like domai	98.39
2io0_B	91	Small ubiquitin-related modifier 2 precursor; SUMO	98.32
2io1_B	94	Small ubiquitin-related modifier 3 precursor; SUMO	98.24
2k8h_A	110	Small ubiquitin protein; SUMO, post-translational	98.22
2d07_B	93	Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Ho	98.2
1wm3_A	72	Ubiquitin-like protein SMT3B; ubiquitin fold, half	98.19
3a4r_A	79	Nfatc2-interacting protein; ubiquitin fold, coiled	98.14
2io0_B	91	Small ubiquitin-related modifier 2 precursor; SUMO	98.11
1wz0_A	104	Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-li	98.07
2eke_C	106	Ubiquitin-like protein SMT3; UBC9, SUMO binding mo	98.06
1wf9_A	107	NPL4 family protein; beta-grAsp fold like domain,	98.05
2d07_B	93	Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Ho	98.0
2kzr_A	86	Ubiquitin thioesterase OTU1; structural genomics,	97.91
2eke_C	106	Ubiquitin-like protein SMT3; UBC9, SUMO binding mo	97.88
2k8h_A	110	Small ubiquitin protein; SUMO, post-translational	97.86
1wz0_A	104	Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-li	97.84
1wjn_A	97	Tubulin-folding protein TBCE; ubiquitin-like domai	97.74
3kyd_D	115	Small ubiquitin-related modifier 1; SUMO, thioeste	97.36
3pge_A	200	SUMO-modified proliferating cell nuclear antigen;	97.35
2pjh_A	80	Protein NPL4, nuclear protein localization protein	97.32
3kyd_D	115	Small ubiquitin-related modifier 1; SUMO, thioeste	97.28
3pge_A	200	SUMO-modified proliferating cell nuclear antigen;	97.14
3goe_A	82	DNA repair protein RAD60; SUMO-like domain, sumoyl	96.89
3tix_A	207	Ubiquitin-like protein SMT3, RNA-induced transcri	96.83
3tix_A	207	Ubiquitin-like protein SMT3, RNA-induced transcri	96.81
3goe_A	82	DNA repair protein RAD60; SUMO-like domain, sumoyl	96.75
1oey_A	83	P67-PHOX, neutrophil cytosol factor 2; immune syst	96.46
3uf8_A	209	Ubiquitin-like protein SMT3, peptidyl-prolyl CIS-	96.45
2kvr_A	130	Ubiquitin carboxyl-terminal hydrolase 7; USP7, ubi	96.35
3v7o_A	227	Minor nucleoprotein VP30; ssgcid, seattle structur	96.28
2jxx_A	97	Nfatc2-interacting protein; nuclear factor of acti	96.2
3uf8_A	209	Ubiquitin-like protein SMT3, peptidyl-prolyl CIS-	96.19
3v7o_A	227	Minor nucleoprotein VP30; ssgcid, seattle structur	95.77
2kc2_A	128	Talin-1, F1; FERM, adhesion, cell membrane, cell p	95.65
2jxx_A	97	Nfatc2-interacting protein; nuclear factor of acti	95.65
2ylm_A	530	Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70	95.64
2al3_A	90	TUG long isoform; TUG UBL1 insulin, endocytosis/ex	94.88
2pjh_A	80	Protein NPL4, nuclear protein localization protein	94.73
3ix6_A	360	TS, tsase, thymidylate synthase; niaid, ssgcid, se	94.36
2l76_A	95	Nfatc2-interacting protein; ubiquitin-like domain,	93.82
2l76_A	95	Nfatc2-interacting protein; ubiquitin-like domain,	93.8
2al3_A	90	TUG long isoform; TUG UBL1 insulin, endocytosis/ex	93.7
2kvr_A	130	Ubiquitin carboxyl-terminal hydrolase 7; USP7, ubi	93.45
4da1_A	389	Protein phosphatase 1K, mitochondrial; metal-ION-a	92.84
4da1_A	389	Protein phosphatase 1K, mitochondrial; metal-ION-a	92.81
4a3p_A	217	Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {H	92.79
3ix6_A	360	TS, tsase, thymidylate synthase; niaid, ssgcid, se	92.65
4eut_A	396	Serine/threonine-protein kinase TBK1; ATP binding,	92.15
2r2o_A	138	Plexin-B1; effector domain, structural genomics, s	91.6
3jyu_A	231	Ubiquitin carboxyl-terminal hydrolase; domain in u	90.28
4e74_A	117	Plexin-A4; RBD, structural genomics, structural ge	90.27
3qa8_A	676	MGC80376 protein; kinase ubiquitin-like domain, ph	89.72
4e71_A	111	Plexin-B2, MM1; transmembrane, signaling, RBD, str	89.38
3h6n_A	127	Plexin-D1; structural genomics consortium, SGC, me	88.39
3kuz_A	126	Plexin-C1; structural genomics, structural genomic	88.12
1oey_A	83	P67-PHOX, neutrophil cytosol factor 2; immune syst	86.93
2ylm_A	530	Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70	84.18
4eut_A	396	Serine/threonine-protein kinase TBK1; ATP binding,	82.37

>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=99.84  E-value=2.7e-20  Score=110.01  Aligned_cols=76  Identities=28%  Similarity=0.390  Sum_probs=70.9

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEE-E--------------------------------------------
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLI-T--------------------------------------------   35 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~-~--------------------------------------------   35 (77)
                      ++++++|++++||++||.+|++..|+|+++|+|+ |                                            
T Consensus        13 ~~~~l~v~~~~tV~~lK~~I~~~~gip~~~QrL~~~~~g~~L~d~~tL~~y~i~~~~~l~l~~~~~~~~m~i~vk~~~g~   92 (159)
T 3rt3_B           13 NEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDKSDEPLSILVRNNKGR   92 (159)
T ss_dssp             CEEEEECCTTCCHHHHHHHHHHHHCCCGGGEEEEEETTCCBCCTTSCGGGGTCCTTCEEEEEECCCCCCEEEEEECTTSC
T ss_pred             CEEEEEeCCCCcHHHHHHHHHHHhCCCHHHEEEEEcCCCCCCCCCCCHHHcCCCCCCEEEEEccCCCCcEEEEEECCCCC
Confidence            4689999999999999999999999999999999 7                                            


Q ss_pred             --EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 --TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 --~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                        .+++++++||.++|..|++..|+|+++|+|+|+|+.|+|..
T Consensus        93 ~~~~~v~~~~tV~~lK~~i~~~~gip~~~q~L~~~G~~L~d~~  135 (159)
T 3rt3_B           93 SSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQL  135 (159)
T ss_dssp             EEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTS
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHCCCHHHEEEEECCeecCCCC
Confidence              35788899999999999999999999999999999999863

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

Probab=99.84  E-value=1.8e-20  Score=112.16  Aligned_cols=75  Identities=69%  Similarity=0.910  Sum_probs=70.8

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEE--------------------------------------------EE
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLIT--------------------------------------------TL   37 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~--------------------------------------------~~   37 (77)
                      ++.++|++++||++||.+|++..|+|+++|+|+|                                            .+
T Consensus        32 ~~~l~v~~~~tV~~lK~~I~~~~gip~~~QrL~~~g~~L~d~~tL~~~~i~~~~~l~l~~~~~gg~~i~Vk~~~g~~~~l  111 (172)
T 3u30_A           32 TITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITL  111 (172)
T ss_dssp             EEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTGGGTCCTTCEEEEEECCCCCEEEEEEESSCCEEEE
T ss_pred             EEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCccccccCCHhHcCCcccceeeeeecccccccceeecccCcceeE
Confidence            5889999999999999999999999999999999                                            45


Q ss_pred             EecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           38 EVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        38 ~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+++++||.++|.+|+...|+|+++|+|+|+|+.|+|..
T Consensus       112 ~v~~~~tV~~lK~~I~~~~gip~~~q~L~~~g~~L~D~~  150 (172)
T 3u30_A          112 EVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGR  150 (172)
T ss_dssp             EECTTCBHHHHHHHHHHHHCCCGGGCCEEETTEECCTTS
T ss_pred             EecCCCCHHHHHHHHHHHhCCCceeEEEEECCccCCCCC
Confidence            788999999999999999999999999999999999863

>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=99.79  E-value=1.1e-18  Score=101.84  Aligned_cols=75  Identities=69%  Similarity=0.931  Sum_probs=70.2

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEE--------------------------------------------E
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLIT--------------------------------------------T   36 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~--------------------------------------------~   36 (77)
                      +++.++|++++||++||.+|++..|+|++.|+|+|                                            .
T Consensus        11 ~~~~~~v~~~~tv~~lK~~i~~~~gip~~~q~L~~~g~~L~d~~tL~~~~i~~~~~l~l~~~~~~~~~i~Vk~~~g~~~~   90 (152)
T 3b08_A           11 KTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTIT   90 (152)
T ss_dssp             CEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCTTCEEEEEEESSSCEEE
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHCcChHHeEEEECCeECcCcccHHHhccCCCCeeEEEeecccccceeeeecCCCEEE
Confidence            36789999999999999999999999999999999                                            3


Q ss_pred             EEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           37 LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        37 ~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      +.+++++||.++|..|+...|+|+++|+|+|+|+.|+|.
T Consensus        91 ~~v~~~~tv~~lK~~i~~~~gi~~~~qrL~~~g~~L~d~  129 (152)
T 3b08_A           91 LEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDG  129 (152)
T ss_dssp             EEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTT
T ss_pred             EEeCCCCcHHHHHHHHHHHhCcChhhEEEEECCEECCCC
Confidence            567889999999999999999999999999999999875

>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=99.44  E-value=2.2e-13  Score=74.53  Aligned_cols=48  Identities=10%  Similarity=0.120  Sum_probs=37.9

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++.++++|+|||++||++|++++|+|+++|+|+|.+ .+++..|+.++
T Consensus        32 kk~~v~v~p~DTI~~LK~~I~~k~Gip~~qQrLif~Gk~LkD~~TL~dY   80 (93)
T 3plu_A           32 KKVRVKCLGEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHISLEDY   80 (93)
T ss_dssp             CEEEEEEETTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBTGGG
T ss_pred             CEEEEEECCcCHHHHHHHHHHHHhCCCHHHEEEEeCCEEccCcCCHHHc
Confidence            4577888888888888888888888888888888875 55777777776

>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=99.44  E-value=3.3e-13  Score=74.83  Aligned_cols=57  Identities=12%  Similarity=0.278  Sum_probs=48.7

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHHHHHHhhccCCCccceEEE
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNVKSKIQDKEGIPPDQQRLI   66 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~lK~~i~~~~gip~~~q~l~   66 (77)
                      +++++|++++||++||++|++++|+|+++|+|+|.+ .+.++.|+.++        ++......++
T Consensus        31 ~~~lev~~~~TV~~lK~kI~~k~gip~~qQrLI~~GKiL~D~~TL~~y--------~I~~gsti~v   88 (100)
T 1wju_A           31 KNLLETRLHITGRELRSKIAETFGLQENYIKIVINKKQLQLGKTLEEQ--------GVAHNVKAMV   88 (100)
T ss_dssp             SEEEEEESSSBHHHHHHHHHHHTTCCSTTCEEEETTEECCTTSBHHHH--------TCCSSEEEEE
T ss_pred             EEEEEeCCcCHHHHHHHHHHHHHCcCHHHeEEEeCCeECCCCCcHHHc--------CCCCCCEEEE
Confidence            688999999999999999999999999999999986 56888899988        6666555444

>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=99.39  E-value=4.3e-13  Score=74.35  Aligned_cols=48  Identities=10%  Similarity=0.108  Sum_probs=43.1

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++.++|+|++||++||++|++++|+|+++|+|+|.+ .++++.++.++
T Consensus        39 k~i~lev~p~dTV~~lK~~Ia~k~Gip~~qQrLi~~Gk~L~D~~TL~dy   87 (100)
T 1uh6_A           39 KKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSLGDY   87 (100)
T ss_dssp             SCEEEEEETTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCSSCBHHHH
T ss_pred             CEEEEEeCCCCcHHHHHHHHHHHhCCCHHHEEEEECCEECCCCCCHHHc
Confidence            3588999999999999999999999999999999986 55788899988

>2lxa_A Ubiquitin-like protein MDY2; ubiquitin-like domain, protein-protein interaction, SGT2 BIN domain, GET pathway, protein binding; NMR {Saccharomyces cerevisiae}

Probab=99.38  E-value=5.2e-13  Score=72.36  Aligned_cols=47  Identities=4%  Similarity=0.198  Sum_probs=41.5

Q ss_pred             eEEEEee--CCCcHHHHHHHh-hhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWK--APTPLINVKAKI-QDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~--~~~tv~~lK~~i-~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++++|+  +++||++||++| ++.+|+|+++|+|+|.+ .+.++.+++++
T Consensus        13 ~~~i~v~v~~~~TV~~lK~~I~~~~~gip~~~QrLi~~Gk~L~D~~tL~~y   63 (87)
T 2lxa_A           13 KFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFLSDL   63 (87)
T ss_dssp             CEECCEECCTTCBHHHHHHHHHHTTSCSSSTTEEEEETTEECCTTCBHHHH
T ss_pred             EEEEEEcCCCCCcHHHHHHHHHHHhcCCChHHEEEEECCEECcCcCCHHHc
Confidence            4677766  999999999999 99999999999999986 56888999988

>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=99.37  E-value=5.9e-13  Score=75.70  Aligned_cols=47  Identities=17%  Similarity=0.273  Sum_probs=44.0

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.++|++++||++||.+|++++|||+++|+|+|.+ .++++.++.++
T Consensus        13 ti~lev~~sdTV~~lK~kI~~~egIP~~qQrLi~~Gk~LeD~~TLsdy   60 (118)
T 2fnj_B           13 TIFTDAKESSTVFELKRIVEGILKRPPEEQRLYKDDQLLDDGKTLGEC   60 (118)
T ss_dssp             EEEEEEETTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBHHHH
T ss_pred             EEEEEeCCcChHHHHHHHHHHHhCCCHHHeEEEECCeECCCCCCHHHc
Confidence            588999999999999999999999999999999986 66889999998

>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=99.33  E-value=6.3e-13  Score=75.50  Aligned_cols=48  Identities=19%  Similarity=0.274  Sum_probs=43.9

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNVK   49 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~lK   49 (77)
                      ++.+++++++||.+||.+|++++|||+++|+|+|.+ .++++.|+.+++
T Consensus        13 TI~ldve~sdTV~~lK~kI~~~~giPp~qQrLI~~Gk~LeD~kTL~dy~   61 (118)
T 4ajy_B           13 TIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECG   61 (118)
T ss_dssp             EEEEEEETTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTTTTT
T ss_pred             EEEEEcCCCChHHHHHHHHHHHHCCCHHHeEEEeCCeECCCcCCHHHcC
Confidence            678899999999999999999999999999999986 568899999883

>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=99.31  E-value=3.9e-12  Score=69.58  Aligned_cols=41  Identities=20%  Similarity=0.263  Sum_probs=39.0

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+.+++||.++|+.|+++.|+|+++|+|+|+|++|+|..
T Consensus        35 ~v~v~p~DTI~~LK~~I~~k~Gip~~qQrLif~Gk~LkD~~   75 (93)
T 3plu_A           35 RVKCLGEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHI   75 (93)
T ss_dssp             EEEEETTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTS
T ss_pred             EEEECCcCHHHHHHHHHHHHhCCCHHHEEEEeCCEEccCcC
Confidence            57889999999999999999999999999999999999975

>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana, uncharacterized putative protein, NESG, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.31  E-value=3.2e-12  Score=68.65  Aligned_cols=48  Identities=25%  Similarity=0.280  Sum_probs=42.8

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-E-ecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-E-VKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~-v~~~~tv~~l   48 (77)
                      +++.++|++++||++||++|++..|+|+++|+|+|.+ . ++++.+++++
T Consensus        21 ~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~lL~D~~tL~~y   70 (84)
T 2kk8_A           21 SSFELEVDYRDTLLVVKQKIERSQHIPVSKQTLIVDGIVILREDLTVEQC   70 (84)
T ss_dssp             CEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCCSSSBHHHH
T ss_pred             cEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCEEecCCcCCHHHc
Confidence            4688999999999999999999999999999999986 4 5788888888

>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=99.29  E-value=5.8e-12  Score=69.79  Aligned_cols=42  Identities=21%  Similarity=0.270  Sum_probs=39.2

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      +.+++++++||.++|+.|++++|+|+++|+|+|+|++|+|.-
T Consensus        32 ~~lev~~~~TV~~lK~kI~~k~gip~~qQrLI~~GKiL~D~~   73 (100)
T 1wju_A           32 NLLETRLHITGRELRSKIAETFGLQENYIKIVINKKQLQLGK   73 (100)
T ss_dssp             EEEEEESSSBHHHHHHHHHHHTTCCSTTCEEEETTEECCTTS
T ss_pred             EEEEeCCcCHHHHHHHHHHHHHCcCHHHeEEEeCCeECCCCC
Confidence            467899999999999999999999999999999999999863

>2kjr_A CG11242; UBL, ubiquitin, ubiquitin-like, structural genomics, PSI-2, protein structure initiative; NMR {Drosophila melanogaster}

Probab=99.27  E-value=1.6e-11  Score=67.44  Aligned_cols=47  Identities=6%  Similarity=0.041  Sum_probs=41.9

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE------Ee-cCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL------EV-KSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~------~v-~~~~tv~~l   48 (77)
                      ++.+++++++||++||++|+..+|||+++|+|+|..      .+ +++.++.++
T Consensus        29 ~~~~~v~~~~TV~~LK~kI~~~~GiP~~~QrL~~~~~g~~~~~L~~D~~tL~~Y   82 (95)
T 2kjr_A           29 AFEVKLAKDLTVAQLKTKLEILTGGCAGTMKVQVFKGDTCVSTMDNNDAQLGYY   82 (95)
T ss_dssp             EEEEEEETTCBHHHHHHHHHHHHCSCTTTEEEEEEETTEEEEECCCTTSBHHHH
T ss_pred             EEEEEeCccCHHHHHHHHHHHHHCcCHHHeEEEEecCCcccceeCCCCCCHhHC
Confidence            578999999999999999999999999999999973      34 678888887

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

Probab=99.27  E-value=3.5e-12  Score=67.26  Aligned_cols=48  Identities=13%  Similarity=0.129  Sum_probs=39.2

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++.++|++++||++||.+|++..|+|+++|+|+|.+ .++++.++.++
T Consensus        15 ~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~G~~L~d~~tL~~~   63 (79)
T 3phx_B           15 RSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEY   63 (79)
T ss_dssp             CEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGG
T ss_pred             CEEEEEECCcChHHHHHHHHHhhcCCCHHHEEEEECCEECCCCCcHHHC
Confidence            3577888888888888888888888888888888875 56777777776

>2dzm_A FAS-associated factor 1; ubiquitin-like domain, HFAF1, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.25  E-value=1.4e-11  Score=68.24  Aligned_cols=48  Identities=17%  Similarity=0.253  Sum_probs=42.6

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEE--EEEecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLIT--TLEVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~--~~~v~~~~tv~~l   48 (77)
                      +++++++++++||++||++|++++||||++|+|+|  ...+.++.++.++
T Consensus        19 k~~~v~v~~~~TV~~LK~~I~~~tgIpp~~QkLi~~~~gkL~D~~tLs~~   68 (100)
T 2dzm_A           19 RNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGDVEDSTVLKSL   68 (100)
T ss_dssp             CEEEEEEETTSBHHHHHHHHHHHHCCCTTTCCEECCSSSCCCTTSBHHHH
T ss_pred             eEEEEEECCCCcHHHHHHHHHHHHCCChhHeEEEccCCCCCCCcCCHHHc
Confidence            46889999999999999999999999999999986  3457778888888

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A

Probab=99.24  E-value=5.2e-12  Score=70.50  Aligned_cols=47  Identities=15%  Similarity=0.280  Sum_probs=40.7

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEEEe-cCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTLEV-KSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~~v-~~~~tv~~l   48 (77)
                      +++++|+|++||++||++|++++|||++.|||+|...+ +++.|+.++
T Consensus        38 ~i~l~V~ps~TV~~LK~~I~~k~Gipp~~QRli~ggkll~D~~TL~~y   85 (105)
T 4dbg_A           38 TIWLTVRPDMTVASLKDMVFLDYGFPPVLQQWVIGQRLARDQETLHSH   85 (105)
T ss_dssp             EEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEEECTTCBTGGG
T ss_pred             eEEEEECCcChHHHHHHHHHHHhCCCHHHEEEeccCeEccCcCcHHHc
Confidence            57899999999999999999999999999998887644 678888887

>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=99.23  E-value=1.3e-11  Score=65.02  Aligned_cols=48  Identities=17%  Similarity=0.279  Sum_probs=42.4

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++.++|++++||++||++|++..|+|+++|+|+|.+ .+.++.|+.++
T Consensus        14 ~~~~~~v~~~~tv~~lk~~i~~~~gi~~~~qrL~~~G~~L~d~~tl~~~   62 (79)
T 2uyz_B           14 SEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKEL   62 (79)
T ss_dssp             CEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCHHHH
T ss_pred             CEEEEEECCCChHHHHHHHHHHHHCCCcccEEEEECCEEeCCCCCHHHc
Confidence            3578899999999999999999999999999999985 67888899888

>2kj6_A Tubulin folding cofactor B; methods development, NESG, solution PSI-2, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.22  E-value=2e-11  Score=67.26  Aligned_cols=47  Identities=15%  Similarity=0.067  Sum_probs=41.0

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEEE--------ecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTLE--------VKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~~--------v~~~~tv~~l   48 (77)
                      .+.+++++++||++||++|+..+|||+++|+|+|...        .+++.++.++
T Consensus        28 ~~e~~v~~~~TV~~LK~kIe~~~Gip~~~QrLi~~g~~g~~~~~L~~D~~tL~~Y   82 (97)
T 2kj6_A           28 SADARFSPQMSVEAVKEKLWKKCGTSVNSMALELYDDSGSKVAVLSDDSRPLGFF   82 (97)
T ss_dssp             CEEEEECTTCCHHHHHHHHHHHHCCCTTSEEEEEECSSSCBCCCSSGGGSCHHHH
T ss_pred             EEEEEeCCCChHHHHHHHHHHHHCcCHHHeEEEEecCCCcccceecCCcCCHHHC
Confidence            5789999999999999999999999999999999752        2667788877

>2lxa_A Ubiquitin-like protein MDY2; ubiquitin-like domain, protein-protein interaction, SGT2 BIN domain, GET pathway, protein binding; NMR {Saccharomyces cerevisiae}

Probab=99.22  E-value=2.1e-11  Score=66.00  Aligned_cols=40  Identities=20%  Similarity=0.307  Sum_probs=36.4

Q ss_pred             EEecCCccHHHHHHHH-hhccCCCccceEEEECCeEcCccc
Q 040720           37 LEVKSSDTINNVKSKI-QDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        37 ~~v~~~~tv~~lK~~i-~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      +++++++||.++|+.| ++..|+|+++|+|+|+|++|+|..
T Consensus        18 v~v~~~~TV~~lK~~I~~~~~gip~~~QrLi~~Gk~L~D~~   58 (87)
T 2lxa_A           18 HDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNL   58 (87)
T ss_dssp             EECCTTCBHHHHHHHHHHTTSCSSSTTEEEEETTEECCTTC
T ss_pred             EcCCCCCcHHHHHHHHHHHhcCCChHHEEEEECCEECcCcC
Confidence            3455999999999999 999999999999999999999863

>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=99.22  E-value=2.5e-11  Score=68.92  Aligned_cols=45  Identities=24%  Similarity=0.228  Sum_probs=40.9

Q ss_pred             ceEEEEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           31 QRLITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        31 q~L~~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      ++..+.+++.+++||.++|..|+...|+|+++|+|+|+|++|+|.
T Consensus        10 ~ktTI~ldve~sdTV~~lK~kI~~~~giPp~qQrLI~~Gk~LeD~   54 (118)
T 4ajy_B           10 HKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDG   54 (118)
T ss_dssp             BTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTT
T ss_pred             CCEEEEEEcCCCChHHHHHHHHHHHHCCCHHHeEEEeCCeECCCc
Confidence            445556789999999999999999999999999999999999885

>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure, northeast structural genomics consortium, protein structure initiative, NESG; NMR {Homo sapiens}

Probab=99.21  E-value=1.4e-11  Score=66.35  Aligned_cols=48  Identities=13%  Similarity=0.129  Sum_probs=42.4

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++.++|++++||++||.+|++..|+|+++|+|+|.+ .++++.++.++
T Consensus        15 ~~~~~~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~   63 (88)
T 2hj8_A           15 RSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEY   63 (88)
T ss_dssp             CEEEEEEESSSBHHHHHHHHHHHTCSCTTTEEEESSSSCCCTTSBHHHH
T ss_pred             CEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEECCEECCCCCcHHHc
Confidence            3578999999999999999999999999999999986 56788888888

>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=99.21  E-value=2.2e-11  Score=65.63  Aligned_cols=48  Identities=27%  Similarity=0.505  Sum_probs=41.4

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++.++|++++||++||.+|++..|+|+++|+|+|.+ .++++.++.++
T Consensus        11 ~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~   59 (88)
T 4fbj_B           11 KEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADY   59 (88)
T ss_dssp             CEEEEECCTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBTTTT
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHCcChhHEEEEECCeECCCCCcHHHc
Confidence            3678899999999999999999999999999999975 56778888876

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.20  E-value=5.7e-11  Score=64.89  Aligned_cols=47  Identities=17%  Similarity=0.214  Sum_probs=40.1

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCC-ccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSS-DTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~-~tv~~l   48 (77)
                      ++.++|++++||++||.+|++..|+|+++|+|+|.+ .+.++ .++.++
T Consensus        26 ~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~~tL~~y   74 (94)
T 2kan_A           26 QFTVEVDRTETVSSLKDKIHIVENTPIKRMQLYYSGIELADDYRNLNEY   74 (94)
T ss_dssp             EEEEEECTTCBHHHHHHHHHHHSSSCTTTEEEEETTEEECCTTSBHHHH
T ss_pred             EEEEEECCCCcHHHHHHHHHHHHCcCHHHEEEEECCEECCCCcccHHHC
Confidence            577899999999999999999999999999999875 56677 788887

>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=99.20  E-value=3.4e-11  Score=68.41  Aligned_cols=44  Identities=23%  Similarity=0.175  Sum_probs=40.1

Q ss_pred             EEEEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           33 LITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        33 L~~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      ..+.+++++++||.++|..|+.+.|+|+++|+|+|+|++|+|.-
T Consensus        12 tti~lev~~sdTV~~lK~kI~~~egIP~~qQrLi~~Gk~LeD~~   55 (118)
T 2fnj_B           12 TTIFTDAKESSTVFELKRIVEGILKRPPEEQRLYKDDQLLDDGK   55 (118)
T ss_dssp             EEEEEEEETTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTS
T ss_pred             EEEEEEeCCcChHHHHHHHHHHHhCCCHHHeEEEECCeECCCCC
Confidence            34567899999999999999999999999999999999999863

>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=99.20  E-value=3.1e-11  Score=66.83  Aligned_cols=41  Identities=22%  Similarity=0.144  Sum_probs=38.5

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+++++++||.++|+.|++++|+|+++|+|+|+|++|+|..
T Consensus        42 ~lev~p~dTV~~lK~~Ia~k~Gip~~qQrLi~~Gk~L~D~~   82 (100)
T 1uh6_A           42 RVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHV   82 (100)
T ss_dssp             EEEEETTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCSSC
T ss_pred             EEEeCCCCcHHHHHHHHHHHhCCCHHHEEEEECCEECCCCC
Confidence            57889999999999999999999999999999999999863

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens}

Probab=99.19  E-value=1.8e-11  Score=65.76  Aligned_cols=47  Identities=19%  Similarity=0.257  Sum_probs=28.5

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.++|++++||++||.+|++..|+|+++|+|+|.+ .+.++.++.++
T Consensus        29 ~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~D~~tL~~~   76 (88)
T 4eew_A           29 TRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEY   76 (88)
T ss_dssp             EEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGG
T ss_pred             EEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEECCCCCcHHHc
Confidence            355666666666666666666666666666666653 34555555554

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

Probab=99.19  E-value=8.2e-11  Score=64.06  Aligned_cols=48  Identities=17%  Similarity=0.282  Sum_probs=41.0

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++.++|++++||++||.+|++..|+|+++|+|+|.+ .++++.++.++
T Consensus        28 ~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~y   76 (93)
T 2l7r_A           28 ELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAGAPLEDEATLGQC   76 (93)
T ss_dssp             SEEEEECCSSCBHHHHHHHHHHHHTCCGGGCEEEETTEECCTTSBHHHH
T ss_pred             CEEEEEeCCCCcHHHHHHHHHHHhCcChhHEEEEECCEECCCCCcHHHC
Confidence            3578899999999999999999999999999999875 56778888887

>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=99.19  E-value=7.5e-11  Score=64.65  Aligned_cols=47  Identities=17%  Similarity=0.286  Sum_probs=39.1

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.++|.+++||++||.+|++..|+|+++|+|+|.+ .+.++.|+.++
T Consensus        33 ~~~l~v~~~~tv~~lK~~i~~~~gip~~~qrLif~Gk~L~d~~tl~dy   80 (97)
T 1wyw_B           33 EIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKEL   80 (97)
T ss_dssp             EEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCHHHH
T ss_pred             EEEEEECCCCcHHHHHHHHHHHHCCChhhEEEEECCeEcCCCCCHHHC
Confidence            577888888888888888888888888888888875 56778888887

>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=99.19  E-value=1.9e-11  Score=65.87  Aligned_cols=48  Identities=19%  Similarity=0.262  Sum_probs=40.8

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++.++|++++||++||.+|++..|+|+++|+|+|.+ .++++.++.++
T Consensus        16 ~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~d~~tL~~~   64 (90)
T 4dwf_A           16 QTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEY   64 (90)
T ss_dssp             CEEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGG
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCeECCCCCCHHHc
Confidence            3578899999999999999999999999999999875 56777788877

>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=99.18  E-value=3.3e-11  Score=68.34  Aligned_cols=48  Identities=15%  Similarity=0.234  Sum_probs=41.7

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhh------hhCC--CcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQD------KEGI--PPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~------~~gi--~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++++++|++++||++||++|++      ++|+  |+++|+|+|++ .+.++.++.++
T Consensus        27 ~t~~lev~~s~TV~~lK~kI~~~~p~dwke~~p~p~~qqrLIy~GK~LeD~~TL~~y   83 (116)
T 1wgh_A           27 KTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGAL   83 (116)
T ss_dssp             CEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEEETTEEECSSCBTTTT
T ss_pred             CEEEEEECCcCHHHHHHHHHHHhcccccccCCCCChHHEEEEECCcCCCCCCcHHHc
Confidence            4689999999999999999998      6786  58999999986 66888898887

>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=99.17  E-value=5.1e-11  Score=63.71  Aligned_cols=47  Identities=28%  Similarity=0.497  Sum_probs=37.8

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.++|++++||++||.+|++..|+|++.|+|+|.+ .++++.++.++
T Consensus        24 ~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~G~~L~d~~tL~~~   71 (88)
T 3dbh_I           24 EIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADY   71 (88)
T ss_dssp             EEEEEECTTCBHHHHHHHHHHHHCCCGGGCCEEETTEECCTTSBGGGG
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHCcCHHHEEEEECCeECCCCCcHHHc
Confidence            577888888888888888888888888888888874 55677777776

>3v6c_B Ubiquitin; structural genomics, structural genomics consortium, SGC, UB protease, hydrolase-signaling protein complex; 1.70A {Homo sapiens} PDB: 3v6e_B

Probab=99.17  E-value=7.2e-11  Score=63.85  Aligned_cols=47  Identities=47%  Similarity=0.660  Sum_probs=35.4

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.++|++++||++||.+|++..|+|++.|+|+|.+ .++++.++.++
T Consensus        29 ~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~   76 (91)
T 3v6c_B           29 HITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY   76 (91)
T ss_dssp             EEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTCBTGGG
T ss_pred             EEEEEECCCCCHHHHHHHHHhhhCCChhhEEEEECCeECCCcCcHHHC
Confidence            567778888888888888888888888888888764 45666676665

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens}

Probab=99.16  E-value=3.5e-11  Score=69.00  Aligned_cols=48  Identities=15%  Similarity=0.218  Sum_probs=42.7

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhh------hhCCC--cccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQD------KEGIP--PDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~------~~gi~--~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++++++|++++||++||++|++      ++|+|  +++|+|+|++ -+.++.+++++
T Consensus        28 ~~~~lev~~s~TV~~lK~~I~~~~p~dwke~ip~~~~~qrLIy~GK~LeD~~TL~~y   84 (125)
T 2gow_A           28 KTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGAL   84 (125)
T ss_dssp             CEEEEEECTTSBHHHHHHHHHSSCCCSCCCCTTCCGGGEEEESSSSEEESSCBTGGG
T ss_pred             CEEEEEeCCccHHHHHHHHHHHHCCcccccCCCCChHHEEEEECCcCCCCCCcHHHc
Confidence            4689999999999999999998      78984  8999999987 66888999987

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

Probab=99.16  E-value=8.6e-11  Score=61.82  Aligned_cols=42  Identities=29%  Similarity=0.440  Sum_probs=38.7

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      +.+.+++++||.++|..|++..|+|+++|+|+|+|+.|+|..
T Consensus        17 ~~~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~G~~L~d~~   58 (79)
T 3phx_B           17 STYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQL   58 (79)
T ss_dssp             EEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTS
T ss_pred             EEEEECCcChHHHHHHHHHhhcCCCHHHEEEEECCEECCCCC
Confidence            357889999999999999999999999999999999998863

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.16  E-value=4.9e-11  Score=64.03  Aligned_cols=47  Identities=17%  Similarity=0.231  Sum_probs=38.1

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.+++++++||++||.+|++..|+|+++|+|+|.+ .++++.++.++
T Consensus        23 ~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~   70 (85)
T 2kd0_A           23 SIPLSVSPDCTVKDLKSQLQPITNVLPRGQKLIFKGKVLVETSTLKQS   70 (85)
T ss_dssp             EEEEEECTTSBHHHHHHHHHHHHCCCTTTCEEEETTEECCTTCBTTTT
T ss_pred             EEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCeECCCcCCHHHC
Confidence            567888888999999999988889988889988875 45667777666

>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=99.16  E-value=8.5e-11  Score=61.02  Aligned_cols=47  Identities=28%  Similarity=0.497  Sum_probs=40.1

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.+++++++||++||.+|++..|+|++.|+|+|.+ .++++.++.++
T Consensus        12 ~~~~~v~~~~tv~~lK~~i~~~~~i~~~~q~L~~~g~~L~d~~tL~~~   59 (76)
T 1ndd_A           12 EIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADY   59 (76)
T ss_dssp             EEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBGGGG
T ss_pred             EEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCEECCCCCcHHHc
Confidence            578899999999999999999999999999999875 55777777776

>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling proteins; 1.15A {Saccharomyces cerevisiae} SCOP: d.15.1.1 PDB: 2bwe_S

Probab=99.16  E-value=6.2e-11  Score=61.86  Aligned_cols=47  Identities=23%  Similarity=0.349  Sum_probs=38.7

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.+++++++||++||.+|++..|+|++.|+|+|.+ .+.++.++.++
T Consensus        15 ~~~~~v~~~~tV~~LK~~i~~~~~i~~~~qrL~~~gk~L~d~~tL~~~   62 (77)
T 2bwf_A           15 KWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESY   62 (77)
T ss_dssp             EEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGG
T ss_pred             EEEEEECCCCcHHHHHHHHHHHhCCCHHHEEEEECCeEcCCCCCHHHc
Confidence            567888899999999999999999999999998875 55677777776

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

Probab=99.16  E-value=7e-11  Score=63.68  Aligned_cols=48  Identities=42%  Similarity=0.639  Sum_probs=41.4

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++.++|++++||++||.+|++..|+|++.|+|+|.+ .+.++.++.++
T Consensus        20 ~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~   68 (88)
T 1sif_A           20 KTFTVEMEPSDTIENLKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY   68 (88)
T ss_dssp             CEEEEECCTTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBSGGG
T ss_pred             CEEEEEECCCChHHHHHHHHHHHHCcChhhEEEEECCEECCCCCcHHHc
Confidence            4678999999999999999999999999999999975 56777787776

>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=99.15  E-value=7.9e-11  Score=62.51  Aligned_cols=47  Identities=47%  Similarity=0.683  Sum_probs=39.5

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.+++++++||++||++|++..|+|++.|+|+|.. .++++.++.++
T Consensus        15 ~~~~~v~~~~tV~~lK~~i~~~~~ip~~~qrL~~~g~~L~d~~tL~~~   62 (85)
T 3n3k_B           15 TIILEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY   62 (85)
T ss_dssp             EEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETBEECCTTCBTTTT
T ss_pred             EEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCeECCCCCCHHHC
Confidence            578889999999999999999999999999999875 56777777776

>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=99.15  E-value=4.9e-11  Score=63.76  Aligned_cols=47  Identities=17%  Similarity=0.223  Sum_probs=40.5

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.++|++++||++||.+|++..|+|++.|+|+|.. .++++.++.++
T Consensus        19 ~~~~~v~~~~tV~~lK~~i~~~~gi~~~~qrL~~~Gk~L~d~~tL~~~   66 (87)
T 1wh3_A           19 SYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGLGIY   66 (87)
T ss_dssp             EEEEEECSSSBHHHHHHHHHHHTCCCTTTEEEEETTEECCSSSBHHHH
T ss_pred             EEEEEeCCCChHHHHHHHHHHHhCCChHHEEEEECCEEccCCCCHHHC
Confidence            578889999999999999999999999999999875 56778888887

>3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=99.14  E-value=5.7e-11  Score=66.13  Aligned_cols=48  Identities=17%  Similarity=0.261  Sum_probs=39.7

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++.++|++++||++||.+|++..|+|+++|+|+|.+ .++++.++.++
T Consensus        12 ~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~   60 (106)
T 3m62_B           12 EKVPLDLEPSNTILETKTKLAQSISCEESQIKLIYSGKVLQDSKTVSEC   60 (106)
T ss_dssp             CEEEECCCTTSBHHHHHHHHHHTTTSCGGGCEEEETTEECCTTSBTTTT
T ss_pred             CEEEEEECCCCcHHHHHHHHHHHHCCChhhEEEEECCEECCCcCCHHHc
Confidence            3578888999999999999999999999999998875 55777777776

>1v5t_A 8430435I17RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 PDB: 2kx3_A

Probab=99.14  E-value=2e-10  Score=62.15  Aligned_cols=47  Identities=11%  Similarity=0.285  Sum_probs=41.3

Q ss_pred             eEEE-EeeCCCcHHHHHHHhhhhhCCCcccceEE---EEE-EecCCccHHHH
Q 040720            2 RLLL-MWKAPTPLINVKAKIQDKEGIPPDQQRLI---TTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~-~v~~~~tv~~lK~~i~~~~gi~~~~q~L~---~~~-~v~~~~tv~~l   48 (77)
                      ++.+ ++++++||++||++|++.+|+|+++|+|+   |.+ .+.++.++.++
T Consensus        18 ~~~i~~v~~~~TV~~lK~~I~~~~gip~~~QkLi~~k~~Gk~L~D~~~L~~~   69 (90)
T 1v5t_A           18 EYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGAL   69 (90)
T ss_dssp             EEEECSCCSSSBHHHHHHHHHHHTCCCTTTCEEESCEETTEECCTTSBHHHH
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHHHCcCHHHeEEEeeccCCcCcCCCCCHHHc
Confidence            5778 99999999999999999999999999999   864 55777888887

>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=99.14  E-value=1.1e-10  Score=62.05  Aligned_cols=47  Identities=17%  Similarity=0.229  Sum_probs=39.5

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhh---hCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDK---EGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~---~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.++|++++||++||++|++.   +|+|+++|+|+|.+ .++++.++.++
T Consensus        17 ~~~~~v~~~~TV~~lK~~i~~~~~~~gip~~~qrLi~~Gk~L~D~~tL~~~   67 (85)
T 2wyq_A           17 TFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDY   67 (85)
T ss_dssp             EEEEEECTTSBHHHHHHHHHHHHCTTTCCGGGEEEEETTEECCTTSBGGGG
T ss_pred             EEEEEECCCCCHHHHHHHHHhhccccCCCHHHeEEEECCEECcCCCCHHHc
Confidence            5788999999999999999987   88999999999875 55677787776

>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=99.14  E-value=2.3e-10  Score=61.41  Aligned_cols=47  Identities=11%  Similarity=0.135  Sum_probs=41.7

Q ss_pred             eEEE-EeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLL-MWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~-~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.+ +|++++||++||.+|++..|+|+++|+|+|.. .+.++.++.++
T Consensus        20 ~~~l~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~gk~L~d~~tL~~~   68 (89)
T 1wy8_A           20 TCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDY   68 (89)
T ss_dssp             EEEEEEECTTCBHHHHHHHHHHHSCCCTTTEEEEETTEECCSSSBHHHH
T ss_pred             eEEEEecCCCCCHHHHHHHHHHHHCcChhhEEEEECCeECCCCCCHHHC
Confidence            6788 49999999999999999999999999999975 56788888888

>4a20_A Ubiquitin-like protein MDY2; protein binding, GET-pathway, tail-anchored proteins; 1.78A {Saccharomyces cerevisiae} PDB: 2lxc_A 4goc_A

Probab=99.13  E-value=3e-11  Score=66.64  Aligned_cols=43  Identities=5%  Similarity=0.197  Sum_probs=29.6

Q ss_pred             EeeCCCcHHHHHHHh-hhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            6 MWKAPTPLINVKAKI-QDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         6 ~v~~~~tv~~lK~~i-~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +|++++||++||++| ++..|+|+++|+|+|.+ .+.++.++.++
T Consensus        37 ~v~~~~TV~~lK~~I~~~~~gip~~~QrLi~~Gk~L~D~~tL~dy   81 (98)
T 4a20_A           37 DFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFLSDL   81 (98)
T ss_dssp             EECTTCBHHHHHHHHHHTTSCSCGGGEEEEETTEEECTTCBGGGS
T ss_pred             ecCCCChHHHHHHHHHHHhcCCChhhEEEEECCEECcCcCCHHHc
Confidence            455777777777777 66677777777777764 45666666665

>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=99.13  E-value=2.5e-10  Score=60.50  Aligned_cols=48  Identities=46%  Similarity=0.659  Sum_probs=40.3

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++.+++++++||.+||++|++..|+|++.|+|+|.. .++++.++.++
T Consensus        14 ~~~~~~v~~~~tV~~lK~~i~~~~~i~~~~qrL~~~g~~L~d~~tL~~~   62 (85)
T 3mtn_B           14 KTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY   62 (85)
T ss_dssp             CEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBTGGG
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHCcChHHEEEEECCEECCCCCCHHHc
Confidence            3578899999999999999999999999999999874 56777777776

>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana, uncharacterized putative protein, NESG, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.13  E-value=1.5e-10  Score=62.05  Aligned_cols=40  Identities=43%  Similarity=0.512  Sum_probs=37.9

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeE-cCcc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGIN-LKLV   75 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~-L~d~   75 (77)
                      .+++++++||.++|..|++..|+|+++|+|+|+|++ |+|.
T Consensus        24 ~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~lL~D~   64 (84)
T 2kk8_A           24 ELEVDYRDTLLVVKQKIERSQHIPVSKQTLIVDGIVILRED   64 (84)
T ss_dssp             EEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCCSS
T ss_pred             EEEECCCChHHHHHHHHHHHHCcChHHEEEEECCEEecCCc
Confidence            578899999999999999999999999999999999 9875

>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=99.13  E-value=6.7e-11  Score=64.23  Aligned_cols=47  Identities=19%  Similarity=0.155  Sum_probs=37.1

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhh--CCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKE--GIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~--gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.+++++++||++||++|++..  |+|+++|+|+|.+ .+.++.++.++
T Consensus        21 ~~~v~v~~~~TV~~lK~~I~~~~~~~i~~~~QrLi~~Gk~L~D~~tL~~~   70 (93)
T 1wgd_A           21 DLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDL   70 (93)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHSTTCCCTTTCEEEETTEECCSSSCHHHH
T ss_pred             EEEEecCCCCcHHHHHHHHHHHhcCCCChHHeEEEECCEECcCcCCHHHH
Confidence            45667778888888888888887  8888888888875 55677777776

>4a20_A Ubiquitin-like protein MDY2; protein binding, GET-pathway, tail-anchored proteins; 1.78A {Saccharomyces cerevisiae} PDB: 2lxc_A 4goc_A

Probab=99.12  E-value=2.1e-10  Score=63.22  Aligned_cols=41  Identities=20%  Similarity=0.298  Sum_probs=36.9

Q ss_pred             EEEecCCccHHHHHHHH-hhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKI-QDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i-~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+++++++||.++|+.| ++..|+|+++|+|+|+|++|+|..
T Consensus        35 ~v~v~~~~TV~~lK~~I~~~~~gip~~~QrLi~~Gk~L~D~~   76 (98)
T 4a20_A           35 EHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNL   76 (98)
T ss_dssp             EEEECTTCBHHHHHHHHHHTTSCSCGGGEEEEETTEEECTTC
T ss_pred             EEecCCCChHHHHHHHHHHHhcCCChhhEEEEECCEECcCcC
Confidence            44667999999999999 888899999999999999998863

>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=99.12  E-value=1e-10  Score=61.35  Aligned_cols=46  Identities=20%  Similarity=0.196  Sum_probs=37.1

Q ss_pred             EEEE-eeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            3 LLLM-WKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         3 ~~~~-v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +.++ |++++||++||.+|++..|+|+++|+|+|.+ .++++.++.++
T Consensus        16 ~~l~~v~~~~tv~~lK~~i~~~~gip~~~qrL~~~g~~L~d~~tL~~~   63 (78)
T 2faz_A           16 HTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFDY   63 (78)
T ss_dssp             EEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTTTT
T ss_pred             EEEeccCCCCCHHHHHHHHHHHHCcChhhEEEEECCEECCCCCCHHHc
Confidence            3788 8888888888888888888888888888874 45667777766

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

Probab=99.12  E-value=1.2e-10  Score=61.27  Aligned_cols=47  Identities=17%  Similarity=0.214  Sum_probs=36.3

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.+++++++||++||.+|++..|+|++.|+|+|.+ .++++.++.++
T Consensus        19 ~~~~~v~~~~tV~~LK~~i~~~~~i~~~~qrL~~~gk~L~d~~tL~~~   66 (81)
T 2dzi_A           19 ECSLQVPEDELVSTLKQLVSEKLNVPVRQQRLLFKGKALADGKRLSDY   66 (81)
T ss_dssp             EEEEEECSSCBHHHHHHHHHHHTCCCTTTCEEEETTEECCTTSBGGGG
T ss_pred             EEEEEECCCCcHHHHHHHHHHHHCcCHHHEEEEECCeECCCCCcHHHc
Confidence            467788888888888888888888888888888864 45666677665

>1v5o_A 1700011N24RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.12  E-value=1e-10  Score=64.60  Aligned_cols=47  Identities=11%  Similarity=0.200  Sum_probs=40.5

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCC-ccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSS-DTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~-~tv~~l   48 (77)
                      ++.++|++++||++||++|++..|+|+++|+|+|.+ .+.++ .++.++
T Consensus        23 ~~~i~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~gk~L~D~~~tL~~y   71 (102)
T 1v5o_A           23 TFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLTDDHCSLGSY   71 (102)
T ss_dssp             EEEEEECTTCBHHHHHHHHHHHTCCCGGGBCEEETTEEECCSSSBHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHCcChHHeEEEECCEECCCCcccHHHC
Confidence            678999999999999999999999999999999974 55555 578887

>4b6w_A Tubulin-specific chaperone; CAP-Gly, ubiquitin-like; HET: MSE; 2.35A {Trypanosoma brucei brucei strain 927}

Probab=99.12  E-value=7.5e-11  Score=63.62  Aligned_cols=47  Identities=9%  Similarity=0.111  Sum_probs=39.4

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEE-------EE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLIT-------TL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~-------~~-~v~~~~tv~~l   48 (77)
                      .+.+.+++++||++||++|+..+||||++|+|+|       .+ ..+++.++.++
T Consensus        16 ~~E~r~~~s~TI~~lK~ki~~~~Gip~~~QrLi~~~~~~~~~g~~l~d~~tL~~Y   70 (86)
T 4b6w_A           16 VPEKRYGLAQTIESIKENVFTHFATPPEYMQLQLIDDRGITIEKNMANDKQLGYY   70 (86)
T ss_dssp             EEEEEEETTSBHHHHHHHHHTTSCCCGGGEEEEEECTTSCEEESSCCTTSBGGGG
T ss_pred             EEEEEcCccCcHHHHHHHHHHHHCCCHHHEEEEEecCCCCceeeEcCCCCCHHHC
Confidence            3567899999999999999999999999999997       34 34677787776

>4hcn_B Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidase, NEDD8, protein binding; 2.60A {Saccharomyces cerevisiae}

Probab=99.11  E-value=1.3e-10  Score=63.73  Aligned_cols=47  Identities=45%  Similarity=0.643  Sum_probs=34.3

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.++|++++||++||.+|++..|+|++.|+|+|.+ .++++.++.++
T Consensus        34 ~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~   81 (98)
T 4hcn_B           34 TITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY   81 (98)
T ss_dssp             EEEEECCTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTCBSGGG
T ss_pred             EEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEECCEECCCCCcHHHC
Confidence            467777777778888877777777777777777764 45666666665

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens}

Probab=99.11  E-value=1.9e-10  Score=61.69  Aligned_cols=41  Identities=29%  Similarity=0.402  Sum_probs=38.2

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+++++||.++|..|++..|+|+++|+|+|+|+.|+|..
T Consensus        31 ~~~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~D~~   71 (88)
T 4eew_A           31 TFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDK   71 (88)
T ss_dssp             EEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTS
T ss_pred             EEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEECCCCC
Confidence            56788999999999999999999999999999999998853

>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=99.11  E-value=1.9e-10  Score=59.68  Aligned_cols=47  Identities=47%  Similarity=0.654  Sum_probs=39.6

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.+++++++||++||.+|++..|+|++.|+|+|.+ .++++.++.++
T Consensus        12 ~~~i~v~~~~tv~~lK~~i~~~~~i~~~~q~L~~~g~~L~d~~tL~~~   59 (76)
T 3a9j_A           12 TITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY   59 (76)
T ss_dssp             EEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTGGG
T ss_pred             EEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCeECCCCCcHHHc
Confidence            578889999999999999999999999999999875 55677777776

>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=99.10  E-value=1.7e-10  Score=62.09  Aligned_cols=42  Identities=33%  Similarity=0.760  Sum_probs=38.8

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      |.+.+++++||.++|..|++..|+|+++|+|+|+|+.|+|..
T Consensus        13 ~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~   54 (88)
T 4fbj_B           13 IEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEK   54 (88)
T ss_dssp             EEEECCTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTS
T ss_pred             EEEEECCCCCHHHHHHHHHHHHCcChhHEEEEECCeECCCCC
Confidence            467889999999999999999999999999999999998863

>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=99.10  E-value=1.5e-10  Score=63.12  Aligned_cols=48  Identities=15%  Similarity=0.250  Sum_probs=41.4

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhh---hCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDK---EGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~---~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++.++|++++||++||.+|++.   +|+|+++|+|+|.+ .++++.++.++
T Consensus        11 ~~~~~~v~~~~TV~~LK~~I~~~~~~~gip~~~qrLi~~Gk~L~D~~tL~~y   62 (95)
T 1uel_A           11 QTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEY   62 (95)
T ss_dssp             CEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEETTEECCTTSBGGGG
T ss_pred             CEEEEEECCCCHHHHHHHHHHhhcccCCCChhhEEEEECCEECCCcCcHHHC
Confidence            35789999999999999999998   88999999999985 56777788776

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.10  E-value=2.6e-10  Score=62.26  Aligned_cols=41  Identities=32%  Similarity=0.472  Sum_probs=38.7

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      +.+.+++++||.++|..|++..|+|+++|+|+|+|++|+|.
T Consensus        27 ~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~   67 (94)
T 2kan_A           27 FTVEVDRTETVSSLKDKIHIVENTPIKRMQLYYSGIELADD   67 (94)
T ss_dssp             EEEEECTTCBHHHHHHHHHHHSSSCTTTEEEEETTEEECCT
T ss_pred             EEEEECCCCcHHHHHHHHHHHHCcCHHHEEEEECCEECCCC
Confidence            56789999999999999999999999999999999999886

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=99.10  E-value=2.3e-10  Score=63.16  Aligned_cols=47  Identities=19%  Similarity=0.139  Sum_probs=36.5

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.++|++++||++||.+|++..|+|++.|+|+|.+ .++++.++.++
T Consensus        36 ~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~   83 (101)
T 2klc_A           36 KEEFAVPENSSVQQFKEEISKRFKSHTDQLVLIFAGKILKDQDTLSQH   83 (101)
T ss_dssp             EEEEEECSCCCHHHHHHHHHHHHTCCGGGEEEEETTEEECTTCCTGGG
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHCcChhhEEEEECCEECCCcCcHHHc
Confidence            467788888888888888888888888888888864 45666777766

>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=99.09  E-value=1.2e-10  Score=63.47  Aligned_cols=48  Identities=15%  Similarity=0.081  Sum_probs=41.5

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++.++|++++||++||.+|++..|+|++.|+|+|.. .++++.++.++
T Consensus        27 ~~~~~~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~   75 (96)
T 1wx8_A           27 DCHEFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQDILSQR   75 (96)
T ss_dssp             SEEEEEEETTCCHHHHHHHHHHHTCSCTTTBCCEETTEECCTTSCHHHH
T ss_pred             eEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEECCCcCCHHHC
Confidence            3578899999999999999999999999999999975 56778888887

>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=99.09  E-value=2e-10  Score=62.40  Aligned_cols=48  Identities=46%  Similarity=0.659  Sum_probs=41.9

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++.++|++++||++||.+|++..|+|++.|+|+|.+ .+.++.++.++
T Consensus        12 ~~~~~~v~~~~TV~~LK~~i~~~~gip~~~qrL~~~G~~L~d~~tL~~~   60 (96)
T 3k9o_B           12 KTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY   60 (96)
T ss_dssp             CEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGG
T ss_pred             CEEEEEECCCCCHHHHHHHHHhhhCCChhHEEEEECCEECCCCCcHHHc
Confidence            3578999999999999999999999999999999975 56778888887

>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=99.09  E-value=2.5e-10  Score=61.44  Aligned_cols=41  Identities=29%  Similarity=0.402  Sum_probs=38.2

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+++++||.++|..|++..|+|+++|+|+|+|+.|+|..
T Consensus        19 ~~~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~d~~   59 (90)
T 4dwf_A           19 TFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDK   59 (90)
T ss_dssp             EEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTS
T ss_pred             EEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCeECCCCC
Confidence            56888999999999999999999999999999999998863

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens}

Probab=99.09  E-value=1.1e-10  Score=64.50  Aligned_cols=46  Identities=11%  Similarity=0.123  Sum_probs=29.0

Q ss_pred             EEEEeeCCCcHHHHHHHhhhh-hCCC-cccceEEEEE-EecCCccHHHH
Q 040720            3 LLLMWKAPTPLINVKAKIQDK-EGIP-PDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~-~gi~-~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++++|++++||++||++|++. .|+| +++|||+|.+ .+.++.++.++
T Consensus        38 i~l~v~~~~TV~~LK~~I~~~~~g~pp~~~QrLIy~Gk~L~D~~tL~~y   86 (99)
T 2kdb_A           38 QTISCFLNWTVGKLKTHLSNVYPSKPLTKDQRLVYSGRLLPDHLQLKDI   86 (99)
T ss_dssp             EEEEECTTSBHHHHHHHHHHHSTTCCCTTTCCEEETTEEECTTSBTHHH
T ss_pred             EEEEcCCCCHHHHHHHHHHHHhcCCCChhhEEEEECCEECCCCCCHHHH
Confidence            566667777777777777764 4554 3667777664 44566666655

>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=99.07  E-value=5.5e-10  Score=61.57  Aligned_cols=46  Identities=20%  Similarity=0.186  Sum_probs=39.5

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +.++|++++||++||.+|++..|+|+++|+|+|.+ .++++.++.++
T Consensus        34 ~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~y   80 (100)
T 1yqb_A           34 EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQC   80 (100)
T ss_dssp             EEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBHHHH
T ss_pred             EEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEECCCcCcHHHC
Confidence            57889999999999999999999999999999875 56778888887

>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=99.07  E-value=1.4e-10  Score=65.37  Aligned_cols=47  Identities=21%  Similarity=0.334  Sum_probs=40.7

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.++|++++||++||.+|++..|+|++.|+|+|.+ .+.++.++.++
T Consensus        47 ~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrL~~~Gk~L~D~~tL~~y   94 (115)
T 1we7_A           47 GLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYY   94 (115)
T ss_dssp             EEEEEECSCSBTHHHHHHHHHHSSCCTTTEEEEETTEEECTTSBHHHH
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHCCChHHEEEEECCEECCCCCCHHHC
Confidence            578899999999999999999999999999999875 56778888887

>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=99.07  E-value=8.9e-10  Score=58.77  Aligned_cols=40  Identities=30%  Similarity=0.493  Sum_probs=37.7

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      .+.+++++||.++|..|++..|+|+++|+|+|+|+.|+|.
T Consensus        21 ~~~v~~~~tV~~lK~~i~~~~gi~~~~qrL~~~Gk~L~d~   60 (87)
T 1wh3_A           21 AYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDW   60 (87)
T ss_dssp             EEEECSSSBHHHHHHHHHHHTCCCTTTEEEEETTEECCSS
T ss_pred             EEEeCCCChHHHHHHHHHHHhCCChHHEEEEECCEEccCC
Confidence            5688999999999999999999999999999999999875

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

Probab=99.06  E-value=5.1e-11  Score=65.90  Aligned_cols=46  Identities=24%  Similarity=0.337  Sum_probs=27.4

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +.++|++++||++||++|++..|+|+++|+|+|.+ .++++.++.++
T Consensus        40 ~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~   86 (101)
T 3m63_B           40 WEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESY   86 (101)
T ss_dssp             CCBCCCTTSBHHHHHHHHHHHHSCCSTTCCEEETTEECCTTSBTTTT
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHCcChHHEEEEECCEECCCcCcHHHC
Confidence            44556666666666666666666666666666653 34555555554

>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=99.06  E-value=1.6e-10  Score=63.16  Aligned_cols=47  Identities=19%  Similarity=0.268  Sum_probs=38.8

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEEEecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTLEVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~~v~~~~tv~~l   48 (77)
                      ++.+++++++||.+||++|++..|+|+++|+|+|....-++.++.++
T Consensus        28 ~~~i~v~~~~TV~~LK~~I~~~tgip~~~QrL~~~Gk~Ldd~tL~~~   74 (95)
T 1v86_A           28 KHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGLVPEDKTLREI   74 (95)
T ss_dssp             EEEEEECTTSBHHHHHHHHHHHHCSCSTTCCCBSSSBCCSSSBHHHH
T ss_pred             EEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCeeCCcCcHHHC
Confidence            57889999999999999999999999999999987533244477777

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

Probab=99.06  E-value=2.4e-10  Score=64.38  Aligned_cols=48  Identities=44%  Similarity=0.639  Sum_probs=42.1

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++.++|++++||++||.+|++..|+|++.|+|+|.+ .++++.++.++
T Consensus        20 ~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~y   68 (114)
T 2kdi_A           20 KTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLEDGRTLSDY   68 (114)
T ss_dssp             CEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTTTT
T ss_pred             cEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCEECCCCCcHHHC
Confidence            3678999999999999999999999999999999975 56777788776

>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=99.06  E-value=6.7e-11  Score=67.89  Aligned_cols=46  Identities=20%  Similarity=0.337  Sum_probs=39.9

Q ss_pred             EEEeeCCCcHHHHHHHh-----hhhhCCCc--ccceEEEEE-EecCCccHHHHH
Q 040720            4 LLMWKAPTPLINVKAKI-----QDKEGIPP--DQQRLITTL-EVKSSDTINNVK   49 (77)
Q Consensus         4 ~~~v~~~~tv~~lK~~i-----~~~~gi~~--~~q~L~~~~-~v~~~~tv~~lK   49 (77)
                      ++++++++||++||++|     ++.+|+|+  ++|+|+|++ .+.++.|+++++
T Consensus        31 ~l~v~psdTV~~lK~kI~~~~p~dkegiP~~~~qQrLIy~GK~LeD~~TLsdy~   84 (126)
T 1se9_A           31 PKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSKTVKDYR   84 (126)
T ss_dssp             EEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEEETTEECCTTSBGGGGS
T ss_pred             eeecCccCHHHHHHHHHHhhcccccccCCCChhhEEEEECCeECcCCCcHHHcC
Confidence            68999999999999999     56789986  899999986 568889999873

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

Probab=99.06  E-value=3.4e-10  Score=61.90  Aligned_cols=47  Identities=47%  Similarity=0.654  Sum_probs=41.8

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.++|++++||++||.+|++..|+|++.|+|+|.+ .+.++.++.++
T Consensus        12 ~~~~~v~~~~TV~~LK~~I~~~~gi~~~~qrL~~~Gk~L~D~~tL~~~   59 (98)
T 1yx5_B           12 TITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY   59 (98)
T ss_dssp             EEEEECCTTCBHHHHHHHHHHHTCCCGGGEEEEETTEECCTTSBTGGG
T ss_pred             EEEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEECCCCCCHHHc
Confidence            578999999999999999999999999999999975 56778888877

>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=99.05  E-value=3.5e-10  Score=59.47  Aligned_cols=42  Identities=19%  Similarity=0.414  Sum_probs=38.7

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      +.+.++++++|..+|..++++.|+|+++|+|+|+|++|+|.-
T Consensus        16 ~~~~v~~~~tv~~lk~~i~~~~gi~~~~qrL~~~G~~L~d~~   57 (79)
T 2uyz_B           16 IHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNH   57 (79)
T ss_dssp             EEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTC
T ss_pred             EEEEECCCChHHHHHHHHHHHHCCCcccEEEEECCEEeCCCC
Confidence            356888999999999999999999999999999999998864

>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=99.05  E-value=9.1e-10  Score=62.37  Aligned_cols=41  Identities=24%  Similarity=0.387  Sum_probs=36.6

Q ss_pred             EEEecCCccHHHHHHHHhh------ccCC--CccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQD------KEGI--PPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~------~~gi--p~~~q~l~~~g~~L~d~~   76 (77)
                      .+++++++||.++|+.|++      ++++  |+++|+|+|+|++|+|..
T Consensus        30 ~lev~~s~TV~~lK~kI~~~~p~dwke~~p~p~~qqrLIy~GK~LeD~~   78 (116)
T 1wgh_A           30 EFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNV   78 (116)
T ss_dssp             EEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEEETTEEECSSC
T ss_pred             EEEECCcCHHHHHHHHHHHhcccccccCCCCChHHEEEEECCcCCCCCC
Confidence            5789999999999999999      5675  699999999999999863

>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=99.05  E-value=4.7e-10  Score=60.84  Aligned_cols=42  Identities=21%  Similarity=0.243  Sum_probs=37.9

Q ss_pred             EEEEecCCccHHHHHHHHhhcc--CCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKE--GIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~--gip~~~q~l~~~g~~L~d~~   76 (77)
                      +.+.+++++||.++|..|++..  ++|+++|+|+|+|+.|+|..
T Consensus        22 ~~v~v~~~~TV~~lK~~I~~~~~~~i~~~~QrLi~~Gk~L~D~~   65 (93)
T 1wgd_A           22 LELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQ   65 (93)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHSTTCCCTTTCEEEETTEECCSSS
T ss_pred             EEEecCCCCcHHHHHHHHHHHhcCCCChHHeEEEECCEECcCcC
Confidence            4556779999999999999998  99999999999999998863

>3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=99.05  E-value=3.2e-10  Score=63.06  Aligned_cols=42  Identities=26%  Similarity=0.362  Sum_probs=38.9

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      |.+.+++++||.++|..|++..|+|+++|+|+|+|+.|+|..
T Consensus        14 ~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~   55 (106)
T 3m62_B           14 VPLDLEPSNTILETKTKLAQSISCEESQIKLIYSGKVLQDSK   55 (106)
T ss_dssp             EEECCCTTSBHHHHHHHHHHTTTSCGGGCEEEETTEECCTTS
T ss_pred             EEEEECCCCcHHHHHHHHHHHHCCChhhEEEEECCEECCCcC
Confidence            467889999999999999999999999999999999998863

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.05  E-value=5.2e-10  Score=59.95  Aligned_cols=41  Identities=32%  Similarity=0.441  Sum_probs=38.1

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      |.+.+++++||.++|..|++..|+|+++|+|+|+|+.|+|.
T Consensus        24 ~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~   64 (85)
T 2kd0_A           24 IPLSVSPDCTVKDLKSQLQPITNVLPRGQKLIFKGKVLVET   64 (85)
T ss_dssp             EEEEECTTSBHHHHHHHHHHHHCCCTTTCEEEETTEECCTT
T ss_pred             EEEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCeECCCc
Confidence            35688999999999999999999999999999999999875

>3v6c_B Ubiquitin; structural genomics, structural genomics consortium, SGC, UB protease, hydrolase-signaling protein complex; 1.70A {Homo sapiens} PDB: 3v6e_B

Probab=99.04  E-value=5.2e-10  Score=60.41  Aligned_cols=41  Identities=76%  Similarity=0.986  Sum_probs=38.3

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+++++||.++|..|++..|+|+++|+|+|+|+.|+|..
T Consensus        31 ~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~   71 (91)
T 3v6c_B           31 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGR   71 (91)
T ss_dssp             EEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTC
T ss_pred             EEEECCCCCHHHHHHHHHhhhCCChhhEEEEECCeECCCcC
Confidence            56889999999999999999999999999999999998863

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A

Probab=99.04  E-value=4.8e-10  Score=62.53  Aligned_cols=40  Identities=20%  Similarity=0.210  Sum_probs=37.2

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      .+++.+++||.++|++|++++|+|+++|||+|+|+.++|.
T Consensus        40 ~l~V~ps~TV~~LK~~I~~k~Gipp~~QRli~ggkll~D~   79 (105)
T 4dbg_A           40 WLTVRPDMTVASLKDMVFLDYGFPPVLQQWVIGQRLARDQ   79 (105)
T ss_dssp             EEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEEECTT
T ss_pred             EEEECCcChHHHHHHHHHHHhCCCHHHEEEeccCeEccCc
Confidence            5678899999999999999999999999999999998775

>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=99.04  E-value=3.4e-10  Score=62.90  Aligned_cols=47  Identities=17%  Similarity=0.355  Sum_probs=36.8

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.++|.+++||++||.+|++..|+|+++|+|+|.+ .+.++.++.++
T Consensus        35 ~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~y   82 (106)
T 1ttn_A           35 DLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKFEEL   82 (106)
T ss_dssp             EEEEEECTTSHHHHHHHHHHHTTCCCSTTCEEEETTEECCTTSHHHHC
T ss_pred             EEEEEeCCCCcHHHHHHHHHHHHCcCcccEEEEECCEECCCCCcHHHc
Confidence            467888888888888888888888888888888875 45666677766

>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=99.04  E-value=4.2e-10  Score=60.06  Aligned_cols=41  Identities=34%  Similarity=0.784  Sum_probs=38.3

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+++++||.++|..|++..|+|+++|+|+|+|+.|+|..
T Consensus        26 ~~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~G~~L~d~~   66 (88)
T 3dbh_I           26 EIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEK   66 (88)
T ss_dssp             EEEECTTCBHHHHHHHHHHHHCCCGGGCCEEETTEECCTTS
T ss_pred             EEEECCCCCHHHHHHHHHHHHCcCHHHEEEEECCeECCCCC
Confidence            57889999999999999999999999999999999998853

>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=99.04  E-value=5.6e-10  Score=58.46  Aligned_cols=41  Identities=22%  Similarity=0.394  Sum_probs=38.1

Q ss_pred             EEEE-ecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLE-VKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~-v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      +.++ +++++||.++|..|++..|+|+++|+|+|+|++|+|.
T Consensus        16 ~~l~~v~~~~tv~~lK~~i~~~~gip~~~qrL~~~g~~L~d~   57 (78)
T 2faz_A           16 HTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDG   57 (78)
T ss_dssp             EEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTT
T ss_pred             EEEeccCCCCCHHHHHHHHHHHHCcChhhEEEEECCEECCCC
Confidence            3577 9999999999999999999999999999999999875

>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=99.03  E-value=4.1e-10  Score=63.08  Aligned_cols=47  Identities=47%  Similarity=0.654  Sum_probs=30.0

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.++|.+++||++||.+|++..|+|++.|+|+|.+ .+.++.++.++
T Consensus        47 ~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~   94 (111)
T 3vdz_A           47 TITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY   94 (111)
T ss_dssp             EEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTTTT
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHhCCChHHEEEEECCEECCCCCcHHHC
Confidence            456666666777777777776667776667766653 44555555554

>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=99.03  E-value=1.9e-10  Score=62.80  Aligned_cols=47  Identities=13%  Similarity=0.116  Sum_probs=39.6

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-------Ee-cCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-------EV-KSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-------~v-~~~~tv~~l   48 (77)
                      .+.+++++++||++||++|+..+|+|+++|+|+|..       .+ +++.++.++
T Consensus        20 ~~~~~v~~~~TV~~lK~ki~~~~gip~~~qrL~~~~~~g~~~~~l~~D~~tL~~y   74 (95)
T 1v6e_A           20 RSEKRYSRSLTIAEFKCKLELVVGSPASCMELELYGADDKFYSKLDQEDALLGSY   74 (95)
T ss_dssp             CEEEEECTTSBHHHHHHHHHHHTCSCTTTCBCEEECSSSCEEEECCCSSSBTTSS
T ss_pred             eEEEEcCccCHHHHHHHHHHHHHCCCHHHeEEEEeCCCCccccccCCCcCCHhHC
Confidence            478899999999999999999999999999999974       23 566677665

>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=99.03  E-value=1.8e-10  Score=67.63  Aligned_cols=48  Identities=13%  Similarity=0.129  Sum_probs=43.9

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++++++|++++||++||.+|++..|+|+++|+|+|.+ .++++.++.++
T Consensus        92 ~~~~~~v~~~~tV~~lK~~i~~~~gip~~~q~L~~~G~~L~d~~tL~~y  140 (159)
T 3rt3_B           92 RSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEY  140 (159)
T ss_dssp             CEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGG
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHHCCCHHHEEEEECCeecCCCCCHHHc
Confidence            4688999999999999999999999999999999985 66888898887

>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=98.60  E-value=2.6e-11  Score=63.35  Aligned_cols=47  Identities=23%  Similarity=0.394  Sum_probs=40.8

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.+++++++||++||.+|++..|+|++.|+|+|.+ .++++.++.++
T Consensus        12 ~~~~~v~~~~tV~~lK~~i~~~~gi~~~~qrL~~~gk~L~d~~tL~~~   59 (76)
T 3b1l_X           12 GFPVEVDSDTSILQLKEVVAKQQGVPADQLRVIFAGKELPNHLTVQNC   59 (76)
Confidence            567899999999999999999999999999999986 55677777776

>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling proteins; 1.15A {Saccharomyces cerevisiae} SCOP: d.15.1.1 PDB: 2bwe_S

Probab=99.03  E-value=7.9e-10  Score=57.58  Aligned_cols=41  Identities=34%  Similarity=0.454  Sum_probs=38.3

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      +.+.+++++||.++|..|++..|+|++.|+|+|+|+.|+|.
T Consensus        16 ~~~~v~~~~tV~~LK~~i~~~~~i~~~~qrL~~~gk~L~d~   56 (77)
T 2bwf_A           16 WEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDD   56 (77)
T ss_dssp             EEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTT
T ss_pred             EEEEECCCCcHHHHHHHHHHHhCCCHHHEEEEECCeEcCCC
Confidence            46788999999999999999999999999999999999875

>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure, northeast structural genomics consortium, protein structure initiative, NESG; NMR {Homo sapiens}

Probab=99.02  E-value=4.6e-10  Score=60.36  Aligned_cols=40  Identities=30%  Similarity=0.434  Sum_probs=37.7

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      .+.+++++||.++|..|++..|+|+++|+|+|+|++|+|.
T Consensus        18 ~~~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~   57 (88)
T 2hj8_A           18 TYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQ   57 (88)
T ss_dssp             EEEEESSSBHHHHHHHHHHHTCSCTTTEEEESSSSCCCTT
T ss_pred             EEEECCCCcHHHHHHHHHHHhCCChhHEEEEECCEECCCC
Confidence            5688899999999999999999999999999999999875

>4hcn_B Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidase, NEDD8, protein binding; 2.60A {Saccharomyces cerevisiae}

Probab=99.02  E-value=6.2e-10  Score=60.99  Aligned_cols=41  Identities=80%  Similarity=1.020  Sum_probs=38.3

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+++++||.++|..|++..|+|+++|+|+|+|+.|+|..
T Consensus        36 ~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~   76 (98)
T 4hcn_B           36 TLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGR   76 (98)
T ss_dssp             EEECCTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTC
T ss_pred             EEEECCCCcHHHHHHHHHHHhCCChhHEEEEECCEECCCCC
Confidence            56889999999999999999999999999999999998863

>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=99.01  E-value=6.8e-10  Score=58.83  Aligned_cols=42  Identities=71%  Similarity=0.934  Sum_probs=38.8

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      +.+.+++++||.++|..|++..++|+++|+|+|+|+.|+|..
T Consensus        16 ~~~~v~~~~tV~~lK~~i~~~~~ip~~~qrL~~~g~~L~d~~   57 (85)
T 3n3k_B           16 IILEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGR   57 (85)
T ss_dssp             EEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETBEECCTTC
T ss_pred             EEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCeECCCCC
Confidence            467889999999999999999999999999999999998863

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9

Probab=99.01  E-value=3.1e-11  Score=73.39  Aligned_cols=46  Identities=13%  Similarity=0.254  Sum_probs=0.0

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTIN   46 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~   46 (77)
                      ++++++|++++||.+||.+|++.+|||+++|+|+|.+ .+.++.++.
T Consensus        11 ktitLeV~~sdTV~~LK~kI~~keGIP~~qQRLIf~GK~LeD~~TLs   57 (189)
T 2xzm_9           11 ETKIYTLEQGTSVLDLKSQISQDMGFEIDMMTLVNNGFIAPNTELVT   57 (189)
T ss_dssp             -----------------------------------------------
T ss_pred             CEEEEEECCcChHHHHHHHHHHHhCcChhHEEEEecCeECCCCCccc
Confidence            3578999999999999999999999999999999986 556666665

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

Probab=99.01  E-value=7.8e-10  Score=60.14  Aligned_cols=42  Identities=31%  Similarity=0.553  Sum_probs=38.7

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      +.+++++++||.++|..|++..|+|+++|+|+|+|++|+|..
T Consensus        30 ~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~   71 (93)
T 2l7r_A           30 HTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAGAPLEDEA   71 (93)
T ss_dssp             EEEECCSSCBHHHHHHHHHHHHTCCGGGCEEEETTEECCTTS
T ss_pred             EEEEeCCCCcHHHHHHHHHHHhCcChhHEEEEECCEECCCCC
Confidence            357889999999999999999999999999999999998753

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.00  E-value=7.5e-10  Score=63.33  Aligned_cols=47  Identities=19%  Similarity=0.108  Sum_probs=38.9

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.++|++++||.+||.+|++..|+|+++|+|+|.+ .++++.++.++
T Consensus        43 ~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~dy   90 (125)
T 1j8c_A           43 KEEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLIQH   90 (125)
T ss_dssp             EEEEEECTTCCHHHHHHHHHHHHCSCSSSEEEEETTEEESTTSCGGGT
T ss_pred             EEEEEECCCCcHHHHHHHHHHHHCcCcceEEEEECCEEcCCCCCHHHc
Confidence            577888888999999999999899999999998874 55677777776

>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=99.00  E-value=2.3e-09  Score=57.93  Aligned_cols=47  Identities=15%  Similarity=0.241  Sum_probs=38.2

Q ss_pred             eEEEEeeCC-----CcHHHHHHHhhhhhCCCcccceEEEEE-EecC-CccHHHH
Q 040720            2 RLLLMWKAP-----TPLINVKAKIQDKEGIPPDQQRLITTL-EVKS-SDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~-----~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~-~~tv~~l   48 (77)
                      ++.++++++     +||++||++|++..|+|+++|+|+|.+ .+.+ +.++.++
T Consensus        18 ~~~i~v~~~~~~~~~TV~~LK~~i~~~~gip~~~qrL~~~Gk~L~D~~~~L~~~   71 (92)
T 1wxv_A           18 KHDLHVTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLKEMETPLSAL   71 (92)
T ss_dssp             EEEEEECCCSSSSSCBHHHHHHHHHHHTCCCTTTCEEEETTEEECCSSSBHHHH
T ss_pred             EEEEEECCCcCcccCcHHHHHHHHHHHHCcCHHHEEEEECCeecCCCcccHHHC
Confidence            567888885     999999999999999999999999874 4555 4578777

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

Probab=99.00  E-value=8.2e-10  Score=59.41  Aligned_cols=41  Identities=68%  Similarity=0.939  Sum_probs=38.1

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      +.+.+++++||.++|..|++..|+|++.|+|+|+|+.|+|.
T Consensus        22 ~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~   62 (88)
T 1sif_A           22 FTVEMEPSDTIENLKAKIQDKEGIPPDQQRLIFAGKQLEDG   62 (88)
T ss_dssp             EEEECCTTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCTT
T ss_pred             EEEEECCCChHHHHHHHHHHHHCcChhhEEEEECCEECCCC
Confidence            35788999999999999999999999999999999999875

>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=99.00  E-value=1e-09  Score=58.10  Aligned_cols=42  Identities=74%  Similarity=0.958  Sum_probs=38.7

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      +.+.+++++||.++|..|++..++|++.|+|+|+|+.|+|..
T Consensus        16 ~~~~v~~~~tV~~lK~~i~~~~~i~~~~qrL~~~g~~L~d~~   57 (85)
T 3mtn_B           16 ITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGR   57 (85)
T ss_dssp             EEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTS
T ss_pred             EEEEECCCCCHHHHHHHHHHHHCcChHHEEEEECCEECCCCC
Confidence            467889999999999999999999999999999999998863

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B

Probab=99.00  E-value=2.8e-10  Score=68.00  Aligned_cols=48  Identities=44%  Similarity=0.648  Sum_probs=42.9

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++.++|++++||++||.+|++..|+|+++|+|+|.+ .++++.++.++
T Consensus        11 k~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~y   59 (169)
T 3l0w_B           11 KTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY   59 (169)
T ss_dssp             CEEEEECCTTCBHHHHHHHHHHHHCCCTTTEEEEETTEECCTTSBGGGG
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHHCcCHHHEEEEECCccccCcCcHHHc
Confidence            4688999999999999999999999999999999985 66788888887

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens}

Probab=99.00  E-value=7.6e-10  Score=61.07  Aligned_cols=41  Identities=22%  Similarity=0.336  Sum_probs=35.7

Q ss_pred             EEEecCCccHHHHHHHHhhc-cCCC-ccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDK-EGIP-PDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~-~gip-~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+++++||.++|+.|+++ .|+| +++|+|+|+|++|+|..
T Consensus        39 ~l~v~~~~TV~~LK~~I~~~~~g~pp~~~QrLIy~Gk~L~D~~   81 (99)
T 2kdb_A           39 TISCFLNWTVGKLKTHLSNVYPSKPLTKDQRLVYSGRLLPDHL   81 (99)
T ss_dssp             EEEECTTSBHHHHHHHHHHHSTTCCCTTTCCEEETTEEECTTS
T ss_pred             EEEcCCCCHHHHHHHHHHHHhcCCCChhhEEEEECCEECCCCC
Confidence            56779999999999999986 5665 59999999999999863

>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=98.99  E-value=3.2e-10  Score=62.13  Aligned_cols=46  Identities=17%  Similarity=0.332  Sum_probs=36.2

Q ss_pred             eE-EEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RL-LLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~-~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++ .+++++++||++||++|++.+|+|+++|+|+|.+ .+.++ ++.++
T Consensus        18 ~~~~l~v~~~~TV~~lK~~I~~~tgip~~~QkLi~~Gk~L~D~-tL~~~   65 (96)
T 1wgg_A           18 KFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLKDD-DWGNI   65 (96)
T ss_dssp             EEEEEEEESSSCHHHHHHHHHHHTCCCTTTSCCEETTEECCSS-CCCSC
T ss_pred             EEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCcCCCCC-CHHHC
Confidence            46 4888889999999999999999999999998874 44555 66655

>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=8.9e-10  Score=60.33  Aligned_cols=41  Identities=20%  Similarity=0.429  Sum_probs=38.3

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+.++++|..+|..|+++.|+|+++|+|+|+|++|+|.-
T Consensus        35 ~l~v~~~~tv~~lK~~i~~~~gip~~~qrLif~Gk~L~d~~   75 (97)
T 1wyw_B           35 HFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNH   75 (97)
T ss_dssp             EEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTC
T ss_pred             EEEECCCCcHHHHHHHHHHHHCCChhhEEEEECCeEcCCCC
Confidence            57889999999999999999999999999999999998863

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

Probab=98.99  E-value=1.4e-09  Score=57.12  Aligned_cols=41  Identities=29%  Similarity=0.477  Sum_probs=38.0

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      +.+.+++++||.++|..|++..|+|++.|+|+|+|+.|+|.
T Consensus        20 ~~~~v~~~~tV~~LK~~i~~~~~i~~~~qrL~~~gk~L~d~   60 (81)
T 2dzi_A           20 CSLQVPEDELVSTLKQLVSEKLNVPVRQQRLLFKGKALADG   60 (81)
T ss_dssp             EEEEECSSCBHHHHHHHHHHHTCCCTTTCEEEETTEECCTT
T ss_pred             EEEEECCCCcHHHHHHHHHHHHCcCHHHEEEEECCeECCCC
Confidence            35688999999999999999999999999999999999875

>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=98.99  E-value=9.2e-10  Score=60.75  Aligned_cols=41  Identities=15%  Similarity=0.293  Sum_probs=38.1

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      |.+++++++||.++|..|++..|+|+++|+|+|+|++|+|.
T Consensus        24 ~~i~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~gk~L~D~   64 (102)
T 1v5o_A           24 FSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLTDD   64 (102)
T ss_dssp             EEEEECTTCBHHHHHHHHHHHTCCCGGGBCEEETTEEECCS
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHCcChHHeEEEECCEECCCC
Confidence            45788999999999999999999999999999999999875

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens}

Probab=98.99  E-value=3.2e-10  Score=69.00  Aligned_cols=48  Identities=46%  Similarity=0.659  Sum_probs=42.4

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++++++|++++||.+||++|++.+|+|+++|+|+|.+ .++++.++.++
T Consensus       116 kt~~l~V~~s~TV~~LK~kI~~~~gIp~~~QrLi~~Gk~L~D~~tL~dy  164 (189)
T 3q3f_A          116 KTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY  164 (189)
T ss_dssp             CEEEEEECTTCBHHHHHHHHHHHHCCCGGGCCEEETTEECCTTCBGGGG
T ss_pred             CEEEEEeCCCCcHHHHHHHHHhccCCCHHHEEEEECCEECCCCCCHHHC
Confidence            3688999999999999999999999999999999985 66788888887

>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=98.99  E-value=1.3e-09  Score=56.48  Aligned_cols=41  Identities=34%  Similarity=0.793  Sum_probs=38.1

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      +.+.+++++||.++|..|++..|+|++.|+|+|+|+.|+|.
T Consensus        13 ~~~~v~~~~tv~~lK~~i~~~~~i~~~~q~L~~~g~~L~d~   53 (76)
T 1ndd_A           13 IEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDE   53 (76)
T ss_dssp             EEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTT
T ss_pred             EEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCEECCCC
Confidence            35688899999999999999999999999999999999875

>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=98.98  E-value=5.5e-10  Score=62.46  Aligned_cols=47  Identities=17%  Similarity=0.220  Sum_probs=35.8

Q ss_pred             eEEEEeeC-CCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKA-PTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~-~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.++|++ ++||++||.+|++..|+|++.|+|+|.+ .++++.++.++
T Consensus        42 ~~~l~v~~l~~TV~~LK~~I~~~~gip~~~QrL~~~Gk~L~D~~tL~~y   90 (111)
T 1we6_A           42 FMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSLAHY   90 (111)
T ss_dssp             CEEEEESCSSSBHHHHHHHHHHHTTCCTTTSEEECSSSBCCTTSBTTTT
T ss_pred             EEEEEecCCCCcHHHHHHHHHHHHCCCHHHeEEEECCEECCCCCcHHHC
Confidence            46778887 8888888888888888888888888765 44566666665

>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=98.98  E-value=2e-09  Score=59.70  Aligned_cols=46  Identities=20%  Similarity=0.186  Sum_probs=39.2

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +.++|++++||.+||.+|++..|+|++.|+|+|.+ .+.++.++.++
T Consensus        29 ~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~   75 (106)
T 1wx7_A           29 EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQC   75 (106)
T ss_dssp             EEEEEETTCCHHHHHHHHHHHHTCCTTTEEEEETTEECCTTSCHHHH
T ss_pred             EEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEECCCcCcHHHc
Confidence            57888999999999999999999999999998875 56777888887

>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=98.97  E-value=8.1e-10  Score=60.50  Aligned_cols=40  Identities=20%  Similarity=0.326  Sum_probs=37.6

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      .+++++++||.++|..|++..|+|+++|+|+|+|++|+|.
T Consensus        21 ~l~v~~~~TV~~lK~~I~~~tgip~~~QkLi~~Gk~L~D~   60 (96)
T 1wgg_A           21 GVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLKDD   60 (96)
T ss_dssp             EEEEESSSCHHHHHHHHHHHTCCCTTTSCCEETTEECCSS
T ss_pred             EEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCcCCCCC
Confidence            4788999999999999999999999999999999999875

>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=98.97  E-value=1.4e-09  Score=59.01  Aligned_cols=42  Identities=74%  Similarity=0.958  Sum_probs=38.8

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      |.+.+++++||.++|..|++..|+|++.|+|+|+|+.|+|..
T Consensus        14 ~~~~v~~~~TV~~LK~~i~~~~gip~~~qrL~~~G~~L~d~~   55 (96)
T 3k9o_B           14 ITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGR   55 (96)
T ss_dssp             EEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTS
T ss_pred             EEEEECCCCCHHHHHHHHHhhhCCChhHEEEEECCEECCCCC
Confidence            467889999999999999999999999999999999998863

>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=98.97  E-value=1.9e-09  Score=57.17  Aligned_cols=41  Identities=27%  Similarity=0.450  Sum_probs=37.6

Q ss_pred             EEEEecCCccHHHHHHHHhhc---cCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDK---EGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~---~gip~~~q~l~~~g~~L~d~   75 (77)
                      |.+.+++++||.++|..|++.   .|+|+++|+|+|+|+.|+|.
T Consensus        18 ~~~~v~~~~TV~~lK~~i~~~~~~~gip~~~qrLi~~Gk~L~D~   61 (85)
T 2wyq_A           18 FKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDD   61 (85)
T ss_dssp             EEEEECTTSBHHHHHHHHHHHHCTTTCCGGGEEEEETTEECCTT
T ss_pred             EEEEECCCCCHHHHHHHHHhhccccCCCHHHeEEEECCEECcCC
Confidence            357889999999999999998   89999999999999999875

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=98.96  E-value=1.7e-09  Score=59.62  Aligned_cols=42  Identities=29%  Similarity=0.305  Sum_probs=38.6

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      +.+.+++++||.++|..|++..|+|++.|+|+|+|+.|+|..
T Consensus        37 ~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~   78 (101)
T 2klc_A           37 EEFAVPENSSVQQFKEEISKRFKSHTDQLVLIFAGKILKDQD   78 (101)
T ss_dssp             EEEEECSCCCHHHHHHHHHHHHTCCGGGEEEEETTEEECTTC
T ss_pred             EEEEECCCCCHHHHHHHHHHHHCcChhhEEEEECCEECCCcC
Confidence            457889999999999999999999999999999999998753

>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=98.96  E-value=2.3e-09  Score=57.43  Aligned_cols=41  Identities=24%  Similarity=0.421  Sum_probs=38.0

Q ss_pred             EEE-EecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTL-EVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~-~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      |.+ ++++++||.++|..|++..|+|+++|+|+|+|+.|+|.
T Consensus        21 ~~l~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~gk~L~d~   62 (89)
T 1wy8_A           21 CTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENG   62 (89)
T ss_dssp             EEEEEECTTCBHHHHHHHHHHHSCCCTTTEEEEETTEECCSS
T ss_pred             EEEEecCCCCCHHHHHHHHHHHHCcChhhEEEEECCeECCCC
Confidence            467 58999999999999999999999999999999999875

>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=98.96  E-value=1.5e-09  Score=59.83  Aligned_cols=40  Identities=38%  Similarity=0.431  Sum_probs=37.8

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      .+++++++||.++|..|++..|+|+++|+|+|+|+.|+|.
T Consensus        35 ~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~   74 (100)
T 1yqb_A           35 DFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDP   74 (100)
T ss_dssp             EEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTT
T ss_pred             EEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEECCCc
Confidence            5788999999999999999999999999999999999875

>3u5e_m 60S ribosomal protein L40; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3u5i_m 4b6a_m 4a18_K 4a19_K 4a1b_K 4a1d_K 4adx_5 3izc_p 3izs_p 3iz5_p 3izr_p

Probab=98.95  E-value=7.3e-11  Score=67.63  Aligned_cols=47  Identities=45%  Similarity=0.643  Sum_probs=0.0

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.++|++++||++||.+|++..|+|++.|+|+|.+ .++++.++.++
T Consensus        12 ~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~   59 (128)
T 3u5e_m           12 TITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY   59 (128)
T ss_dssp             ------------------------------------------------
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHhCcChHHEEEEECCEECCCCCchhhh
Confidence            578999999999999999999999999999999986 56778888877

>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=98.95  E-value=2.2e-09  Score=58.48  Aligned_cols=41  Identities=27%  Similarity=0.500  Sum_probs=37.9

Q ss_pred             EEEEecCCccHHHHHHHHhhc---cCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDK---EGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~---~gip~~~q~l~~~g~~L~d~   75 (77)
                      |.+.+++++||.++|..|++.   .|+|+++|+|+|+|+.|+|.
T Consensus        13 ~~~~v~~~~TV~~LK~~I~~~~~~~gip~~~qrLi~~Gk~L~D~   56 (95)
T 1uel_A           13 FKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDD   56 (95)
T ss_dssp             EEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEETTEECCTT
T ss_pred             EEEEECCCCHHHHHHHHHHhhcccCCCChhhEEEEECCEECCCc
Confidence            467889999999999999999   78999999999999999875

>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=98.95  E-value=2e-09  Score=60.26  Aligned_cols=41  Identities=76%  Similarity=0.986  Sum_probs=38.2

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+++++||.++|..|+...|+|+++|+|+|+|+.|+|..
T Consensus        49 ~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~   89 (111)
T 3vdz_A           49 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGR   89 (111)
T ss_dssp             EEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTS
T ss_pred             EEEeCCCCCHHHHHHHHHHHhCCChHHEEEEECCEECCCCC
Confidence            56889999999999999999999999999999999998853

>1t0y_A Tubulin folding cofactor B; ubiquitin-like, cytoskeleton, microtubule, CESG, structural genomics, protein structure initiative, PSI; NMR {Caenorhabditis elegans} SCOP: d.15.1.1

Probab=98.94  E-value=1.1e-09  Score=62.29  Aligned_cols=47  Identities=17%  Similarity=0.222  Sum_probs=40.3

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-------Ee-cCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-------EV-KSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-------~v-~~~~tv~~l   48 (77)
                      .+.+++++++||++||.+|+...|||+++|+|+|..       .+ +++.++.++
T Consensus        19 ~~e~~v~~~~TV~~lK~ki~~~~Gip~~~qrL~~~g~~~~~~~~l~~D~~tL~~y   73 (122)
T 1t0y_A           19 PMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDL   73 (122)
T ss_dssp             CEEEEEETTSBHHHHHHHHHHHHCCCTTTEEEEEECSSSSEEEECCCCSSBTTTT
T ss_pred             cEEEEeCCCCcHHHHHHHHHHHhCCCHHHeEEEEecCCCccccccCCCcCCHHHC
Confidence            478899999999999999999999999999999965       23 566677776

>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=98.94  E-value=2.3e-09  Score=55.45  Aligned_cols=41  Identities=76%  Similarity=0.998  Sum_probs=38.0

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      +.+.+++++||.++|..|++..|+|++.|+|+|+|+.|+|.
T Consensus        13 ~~i~v~~~~tv~~lK~~i~~~~~i~~~~q~L~~~g~~L~d~   53 (76)
T 3a9j_A           13 ITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDG   53 (76)
T ss_dssp             EEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTT
T ss_pred             EEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCeECCCC
Confidence            35688899999999999999999999999999999999875

>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=98.94  E-value=1.7e-09  Score=62.03  Aligned_cols=41  Identities=24%  Similarity=0.330  Sum_probs=36.1

Q ss_pred             EEEecCCccHHHHHHHH-----hhccCCCc--cceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKI-----QDKEGIPP--DQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i-----~~~~gip~--~~q~l~~~g~~L~d~~   76 (77)
                      .+.+++++||.++|+.|     ++.+|+|+  ++|+|+|+|++|+|.-
T Consensus        31 ~l~v~psdTV~~lK~kI~~~~p~dkegiP~~~~qQrLIy~GK~LeD~~   78 (126)
T 1se9_A           31 PKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSK   78 (126)
T ss_dssp             EEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEEETTEECCTTS
T ss_pred             eeecCccCHHHHHHHHHHhhcccccccCCCChhhEEEEECCeECcCCC
Confidence            46788999999999999     66788986  8999999999999863

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens}

Probab=98.94  E-value=1.3e-09  Score=62.42  Aligned_cols=41  Identities=24%  Similarity=0.387  Sum_probs=37.0

Q ss_pred             EEEecCCccHHHHHHHHhh------ccCC--CccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQD------KEGI--PPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~------~~gi--p~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+++++||.++|+.|++      ++|+  |+++|+|+|+|++|+|.-
T Consensus        31 ~lev~~s~TV~~lK~~I~~~~p~dwke~ip~~~~~qrLIy~GK~LeD~~   79 (125)
T 2gow_A           31 EFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNV   79 (125)
T ss_dssp             EEEECTTSBHHHHHHHHHSSCCCSCCCCTTCCGGGEEEESSSSEEESSC
T ss_pred             EEEeCCccHHHHHHHHHHHHCCcccccCCCCChHHEEEEECCcCCCCCC
Confidence            6789999999999999999      7788  489999999999999863

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

Probab=98.93  E-value=1.8e-09  Score=60.34  Aligned_cols=47  Identities=47%  Similarity=0.654  Sum_probs=31.4

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.++|++++||++||.+|++..|+|++.|+|+|.. .+.++.++.++
T Consensus        47 ~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~   94 (111)
T 2ojr_A           47 TITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY   94 (111)
T ss_dssp             EEEEEECTTCBHHHHHHHHHHHHCCCTTTEEEEETTEECCSSCBTTTT
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHCcCcccEEEEECCEECCCCCcHHHc
Confidence            456677777777777777777777777777777653 44555566555

>2daf_A FLJ35834 protein; hypothetical protein FLJ35834, ubiquitin-like domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.93  E-value=8.8e-10  Score=62.43  Aligned_cols=46  Identities=20%  Similarity=0.247  Sum_probs=33.9

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++++++++.||++||+++++..++|++.|+|+|.+ -+.+++|+.++
T Consensus        29 ~tv~v~~d~TV~dLKe~ls~~~~iP~e~qrLIy~GKiLKD~eTL~~~   75 (118)
T 2daf_A           29 IVIPFKVDTILKYLKDHFSHLLGIPHSVLQIRYSGKILKNNETLVQH   75 (118)
T ss_dssp             EEEEECSSSCSHHHHHHHHHHHTCCTTTEEEEETTEEECSSCCHHHH
T ss_pred             EEEEeCCCCcHHHHHHHHHhhhCCChHHEEEEECCeEcCCcchHHHc
Confidence            56777777777777777777777777777777775 45677777776

>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=98.93  E-value=1.7e-09  Score=58.44  Aligned_cols=41  Identities=20%  Similarity=0.377  Sum_probs=38.1

Q ss_pred             EEE-EecCCccHHHHHHHHhhccCCCccceEEE---ECCeEcCcc
Q 040720           35 TTL-EVKSSDTINNVKSKIQDKEGIPPDQQRLI---FAGINLKLV   75 (77)
Q Consensus        35 ~~~-~v~~~~tv~~lK~~i~~~~gip~~~q~l~---~~g~~L~d~   75 (77)
                      |.+ ++++++||.++|..|++..|+|+++|+|+   |+|++|+|.
T Consensus        19 ~~i~~v~~~~TV~~lK~~I~~~~gip~~~QkLi~~k~~Gk~L~D~   63 (90)
T 1v5t_A           19 YSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAEND   63 (90)
T ss_dssp             EEECSCCSSSBHHHHHHHHHHHTCCCTTTCEEESCEETTEECCTT
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHCcCHHHeEEEeeccCCcCcCCC
Confidence            357 88999999999999999999999999999   999999875

>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=98.92  E-value=2e-09  Score=58.58  Aligned_cols=41  Identities=20%  Similarity=0.205  Sum_probs=38.1

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+++++||.++|..|+...|+|+++|+|+|+|+.|+|..
T Consensus        30 ~~~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~   70 (96)
T 1wx8_A           30 EFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQD   70 (96)
T ss_dssp             EEEEETTCCHHHHHHHHHHHTCSCTTTBCCEETTEECCTTS
T ss_pred             EEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEECCCcC
Confidence            56888999999999999999999999999999999998863

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

Probab=98.92  E-value=2.7e-09  Score=60.06  Aligned_cols=40  Identities=80%  Similarity=1.034  Sum_probs=37.8

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      .+.+++++||.++|..|++..|+|+++|+|+|+|+.|+|.
T Consensus        23 ~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~   62 (114)
T 2kdi_A           23 TLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLEDG   62 (114)
T ss_dssp             EEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTT
T ss_pred             EEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCEECCCC
Confidence            5788999999999999999999999999999999999875

>3u5c_f 40S ribosomal protein S31; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3u5g_f

Probab=98.92  E-value=1.2e-10  Score=68.68  Aligned_cols=47  Identities=45%  Similarity=0.643  Sum_probs=0.0

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.++|++++||++||++|++..|+|+++|+|+|.+ .++++.++.++
T Consensus        12 ~~~l~V~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~dy   59 (152)
T 3u5c_f           12 TITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY   59 (152)
T ss_dssp             ------------------------------------------------
T ss_pred             EEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEEccccCcHHHc
Confidence            578899999999999999999999999999999986 56778888877

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

Probab=98.91  E-value=8.6e-10  Score=60.91  Aligned_cols=41  Identities=34%  Similarity=0.470  Sum_probs=37.8

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+++++||.++|..|++..|+|+++|+|+|+|+.|+|..
T Consensus        41 ~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~   81 (101)
T 3m63_B           41 EVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQ   81 (101)
T ss_dssp             CBCCCTTSBHHHHHHHHHHHHSCCSTTCCEEETTEECCTTS
T ss_pred             EEEeCCCCCHHHHHHHHHHHHCcChHHEEEEECCEECCCcC
Confidence            45788999999999999999999999999999999998863

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

Probab=98.91  E-value=7.7e-10  Score=65.83  Aligned_cols=48  Identities=46%  Similarity=0.659  Sum_probs=43.8

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++++++|++++||.+||.+|+..+|+|+++|+|+|.+ .++++.++.++
T Consensus       107 ~~~~l~v~~~~tV~~lK~~I~~~~gip~~~q~L~~~g~~L~D~~tL~~y  155 (172)
T 3u30_A          107 KTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY  155 (172)
T ss_dssp             CEEEEEECTTCBHHHHHHHHHHHHCCCGGGCCEEETTEECCTTSBSGGG
T ss_pred             cceeEEecCCCCHHHHHHHHHHHhCCCceeEEEEECCccCCCCCcHHHh
Confidence            4688999999999999999999999999999999985 67888888887

>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=98.91  E-value=3e-09  Score=59.84  Aligned_cols=41  Identities=27%  Similarity=0.515  Sum_probs=38.4

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      +.+.+++++||.++|..|+...|+|+++|+|+|+|+.|+|.
T Consensus        48 ~~l~v~~~~TV~~LK~~I~~~~gip~~~QrL~~~Gk~L~D~   88 (115)
T 1we7_A           48 LVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDS   88 (115)
T ss_dssp             EEEEECSCSBTHHHHHHHHHHSSCCTTTEEEEETTEEECTT
T ss_pred             EEEEECCCCCHHHHHHHHHHHHCCChHHEEEEECCEECCCC
Confidence            46788999999999999999999999999999999999875

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

Probab=98.91  E-value=3.6e-09  Score=57.77  Aligned_cols=41  Identities=76%  Similarity=0.998  Sum_probs=38.2

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      +.+.+++++||.++|..|++..|+|++.|+|+|+|+.|+|.
T Consensus        13 ~~~~v~~~~TV~~LK~~I~~~~gi~~~~qrL~~~Gk~L~D~   53 (98)
T 1yx5_B           13 ITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDG   53 (98)
T ss_dssp             EEEECCTTCBHHHHHHHHHHHTCCCGGGEEEEETTEECCTT
T ss_pred             EEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEECCCC
Confidence            36788999999999999999999999999999999999875

>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=98.90  E-value=3.6e-09  Score=58.73  Aligned_cols=40  Identities=35%  Similarity=0.577  Sum_probs=37.6

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      .+.+++++||.++|..|+...|+|+++|+|+|+|+.|+|.
T Consensus        37 ~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~   76 (106)
T 1ttn_A           37 KLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDK   76 (106)
T ss_dssp             EEEECTTSHHHHHHHHHHHTTCCCSTTCEEEETTEECCTT
T ss_pred             EEEeCCCCcHHHHHHHHHHHHCcCcccEEEEECCEECCCC
Confidence            4688999999999999999999999999999999999875

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=98.90  E-value=4.7e-09  Score=60.00  Aligned_cols=42  Identities=29%  Similarity=0.299  Sum_probs=38.6

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      |.+.+++++||.+||..|+...|+|+++|+|+|+|+.|+|..
T Consensus        44 ~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~   85 (125)
T 1j8c_A           44 EEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQD   85 (125)
T ss_dssp             EEEEECTTCCHHHHHHHHHHHHCSCSSSEEEEETTEEESTTS
T ss_pred             EEEEECCCCcHHHHHHHHHHHHCcCcceEEEEECCEEcCCCC
Confidence            357889999999999999999999999999999999998763

>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=98.90  E-value=4.5e-09  Score=56.77  Aligned_cols=39  Identities=31%  Similarity=0.543  Sum_probs=35.9

Q ss_pred             EEEecCC-----ccHHHHHHHHhhccCCCccceEEEECCeEcCc
Q 040720           36 TLEVKSS-----DTINNVKSKIQDKEGIPPDQQRLIFAGINLKL   74 (77)
Q Consensus        36 ~~~v~~~-----~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d   74 (77)
                      .+.++++     .||.+||..|++..|+|+++|+|+|+|+.|+|
T Consensus        20 ~i~v~~~~~~~~~TV~~LK~~i~~~~gip~~~qrL~~~Gk~L~D   63 (92)
T 1wxv_A           20 DLHVTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLKE   63 (92)
T ss_dssp             EEEECCCSSSSSCBHHHHHHHHHHHTCCCTTTCEEEETTEEECC
T ss_pred             EEEECCCcCcccCcHHHHHHHHHHHHCcCHHHEEEEECCeecCC
Confidence            5677774     99999999999999999999999999999987

>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=98.89  E-value=1.1e-09  Score=61.07  Aligned_cols=48  Identities=8%  Similarity=0.169  Sum_probs=39.8

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcc---------------cceEEEEE-Ee-cCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPD---------------QQRLITTL-EV-KSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~---------------~q~L~~~~-~v-~~~~tv~~l   48 (77)
                      ++++++|++++||++||++|++..|+|+.               +|+|+|.+ .+ +++.++.++
T Consensus        18 ~~~~v~V~~~~TV~dLK~~I~~~~~i~~~~q~g~~~isw~~~w~q~~Li~~Gk~L~dD~~tL~dy   82 (105)
T 1v2y_A           18 EVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLRDY   82 (105)
T ss_dssp             CEEEEEECTTCBHHHHHHHHHHHHHHHHHHTTCCCCCCHHHHHTTEEEESSSCEECCSSSBHHHH
T ss_pred             CEEEEEECCCChHHHHHHHHHHHhCCCcccccCcceeeeeecceeEEEEeCCcCccCCcCCHHHc
Confidence            46899999999999999999999999884               45888875 44 456788887

>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=98.89  E-value=4.7e-09  Score=58.16  Aligned_cols=41  Identities=37%  Similarity=0.397  Sum_probs=38.2

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.++.++||.+||..|++..|+|+++|+|+|+|+.|+|..
T Consensus        30 ~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~   70 (106)
T 1wx7_A           30 DFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPD   70 (106)
T ss_dssp             EEEEETTCCHHHHHHHHHHHHTCCTTTEEEEETTEECCTTS
T ss_pred             EEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEECCCcC
Confidence            57888999999999999999999999999999999998863

>2daf_A FLJ35834 protein; hypothetical protein FLJ35834, ubiquitin-like domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.88  E-value=3.5e-09  Score=59.96  Aligned_cols=42  Identities=19%  Similarity=0.266  Sum_probs=38.9

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      +.+.++++.+|.+||..++...++|+++|+|+|+|+.|.|.-
T Consensus        29 ~tv~v~~d~TV~dLKe~ls~~~~iP~e~qrLIy~GKiLKD~e   70 (118)
T 2daf_A           29 IVIPFKVDTILKYLKDHFSHLLGIPHSVLQIRYSGKILKNNE   70 (118)
T ss_dssp             EEEEECSSSCSHHHHHHHHHHHTCCTTTEEEEETTEEECSSC
T ss_pred             EEEEeCCCCcHHHHHHHHHhhhCCChHHEEEEECCeEcCCcc
Confidence            367789999999999999999999999999999999998864

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B

Probab=98.88  E-value=4e-09  Score=62.98  Aligned_cols=42  Identities=79%  Similarity=0.991  Sum_probs=38.9

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      +.+.+++++||.++|..|++..|+|+++|+|+|+|++|+|..
T Consensus        13 ~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~   54 (169)
T 3l0w_B           13 ITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGR   54 (169)
T ss_dssp             EEEECCTTCBHHHHHHHHHHHHCCCTTTEEEEETTEECCTTS
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHCcCHHHEEEEECCccccCcC
Confidence            357889999999999999999999999999999999998863

>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=98.87  E-value=4.8e-09  Score=60.67  Aligned_cols=48  Identities=46%  Similarity=0.659  Sum_probs=43.2

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++.+++++++||++||.+|++..|+|++.|+|+|.+ .++++.++.++
T Consensus        87 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~qrL~~~g~~L~d~~tL~~~  135 (152)
T 3b08_A           87 KTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY  135 (152)
T ss_dssp             CEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGG
T ss_pred             CEEEEEeCCCCcHHHHHHHHHHHhCcChhhEEEEECCEECCCCCCHHHc
Confidence            3678999999999999999999999999999999985 66788888877

>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=98.86  E-value=1.7e-09  Score=59.06  Aligned_cols=40  Identities=25%  Similarity=0.467  Sum_probs=37.1

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKL   74 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d   74 (77)
                      |.+.++++.||.+||..|++..|+|+++|+|+|+|++|+|
T Consensus        29 ~~i~v~~~~TV~~LK~~I~~~tgip~~~QrL~~~Gk~Ldd   68 (95)
T 1v86_A           29 HDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGLVPED   68 (95)
T ss_dssp             EEEEECTTSBHHHHHHHHHHHHCSCSTTCCCBSSSBCCSS
T ss_pred             EEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCeeCCc
Confidence            3578899999999999999999999999999999999955

>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=98.84  E-value=4.5e-09  Score=58.69  Aligned_cols=41  Identities=29%  Similarity=0.328  Sum_probs=37.9

Q ss_pred             EEEEecC-CccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKS-SDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~-~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      +.+.+++ ++||.++|..|+...|+|+++|+|+|+|+.|+|.
T Consensus        43 ~~l~v~~l~~TV~~LK~~I~~~~gip~~~QrL~~~Gk~L~D~   84 (111)
T 1we6_A           43 MEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDN   84 (111)
T ss_dssp             EEEEESCSSSBHHHHHHHHHHHTTCCTTTSEEECSSSBCCTT
T ss_pred             EEEEecCCCCcHHHHHHHHHHHHCCCHHHeEEEECCEECCCC
Confidence            3578887 9999999999999999999999999999999875

>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=98.84  E-value=3.7e-09  Score=58.77  Aligned_cols=47  Identities=19%  Similarity=0.236  Sum_probs=39.4

Q ss_pred             eEEEE--------eeCC-CcHHHHHHHhhhhh--CCCccc-ceEEEEE-EecCCccHHHH
Q 040720            2 RLLLM--------WKAP-TPLINVKAKIQDKE--GIPPDQ-QRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~--------v~~~-~tv~~lK~~i~~~~--gi~~~~-q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.++        |+++ +||++||++|++..  |+|++. |+|+|.+ .+.++.++.++
T Consensus        27 ~~~l~v~~~~~~~v~~~~~TV~~LK~~i~~~~~~gip~~~~qrLi~~Gk~L~D~~tL~~y   86 (107)
T 1x1m_A           27 KSILQLPETELGEYSLGGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDFY   86 (107)
T ss_dssp             CEEECCCCCSSCSSCCCCCBHHHHHHHHHHHCTTTCCCSSSEEEEETTEECCTTCBHHHH
T ss_pred             EEEEEecCccccccCcccCCHHHHHHHHHHHhccCCChhhcEEEEECCeECCCCCcHHHc
Confidence            46677        4454 99999999999999  999999 9999975 56788888888

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9

Probab=98.83  E-value=3.8e-10  Score=68.59  Aligned_cols=41  Identities=17%  Similarity=0.244  Sum_probs=0.0

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      +.+++++++||.++|..|+..+|+|+++|+|+|+|++|+|.
T Consensus        13 itLeV~~sdTV~~LK~kI~~keGIP~~qQRLIf~GK~LeD~   53 (189)
T 2xzm_9           13 KIYTLEQGTSVLDLKSQISQDMGFEIDMMTLVNNGFIAPNT   53 (189)
T ss_dssp             -----------------------------------------
T ss_pred             EEEEECCcChHHHHHHHHHHHhCcChhHEEEEecCeECCCC
Confidence            35788899999999999999999999999999999999985

>2dzj_A Synaptic glycoprotein SC2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.82  E-value=5.4e-10  Score=60.43  Aligned_cols=45  Identities=16%  Similarity=0.217  Sum_probs=32.0

Q ss_pred             EE-EeeCCCcHHHHHHHhhhh-hCCCcccceEEEE--E-EecCCccHHHH
Q 040720            4 LL-MWKAPTPLINVKAKIQDK-EGIPPDQQRLITT--L-EVKSSDTINNV   48 (77)
Q Consensus         4 ~~-~v~~~~tv~~lK~~i~~~-~gi~~~~q~L~~~--~-~v~~~~tv~~l   48 (77)
                      .+ +|+|++||++||++|++. .|+|+++|+|+|.  + .+.++.++.++
T Consensus        26 ~l~~v~~~~TV~~lK~~I~~~~~~i~~~~QrL~~~~~Gk~L~D~~tL~~y   75 (88)
T 2dzj_A           26 FLDKVEPHATIAEIKNLFTKTHPQWYPARQSLRLDPKGKSLKDEDVLQKL   75 (88)
T ss_dssp             EEEEECSSCBHHHHHHHHHHHCSSSCTTTCCEESSTTSCCCCTTCBTTTS
T ss_pred             EEeEcCCCCcHHHHHHHHHHHhcCCChHHeEEEecCCCcCcCCCCCHHHc
Confidence            46 788888888888888873 7888888888764  3 34556666665

>4b6w_A Tubulin-specific chaperone; CAP-Gly, ubiquitin-like; HET: MSE; 2.35A {Trypanosoma brucei brucei strain 927}

Probab=98.81  E-value=5.7e-09  Score=56.16  Aligned_cols=40  Identities=18%  Similarity=0.218  Sum_probs=36.0

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEE-------CCeEcCcc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIF-------AGINLKLV   75 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~-------~g~~L~d~   75 (77)
                      ...+++++||.++|.+|+..+|+|+++|+|+|       .|+.|+|.
T Consensus        18 E~r~~~s~TI~~lK~ki~~~~Gip~~~QrLi~~~~~~~~~g~~l~d~   64 (86)
T 4b6w_A           18 EKRYGLAQTIESIKENVFTHFATPPEYMQLQLIDDRGITIEKNMAND   64 (86)
T ss_dssp             EEEEETTSBHHHHHHHHHTTSCCCGGGEEEEEECTTSCEEESSCCTT
T ss_pred             EEEcCccCcHHHHHHHHHHHHCCCHHHEEEEEecCCCCceeeEcCCC
Confidence            56789999999999999999999999999996       57778775

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

Probab=98.81  E-value=1.3e-08  Score=56.80  Aligned_cols=40  Identities=78%  Similarity=1.027  Sum_probs=37.5

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      .+.+++++||.++|..|++..|+|++.|+|+|+|+.|+|.
T Consensus        49 ~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~   88 (111)
T 2ojr_A           49 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDG   88 (111)
T ss_dssp             EEEECTTCBHHHHHHHHHHHHCCCTTTEEEEETTEECCSS
T ss_pred             EEEeCCCCCHHHHHHHHHHHHCcCcccEEEEECCEECCCC
Confidence            5678899999999999999999999999999999999875

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens}

Probab=98.80  E-value=7.3e-09  Score=62.97  Aligned_cols=41  Identities=76%  Similarity=0.986  Sum_probs=38.3

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+++++||.++|..|++..|+|+++|+|+|+|++|+|..
T Consensus       119 ~l~V~~s~TV~~LK~kI~~~~gIp~~~QrLi~~Gk~L~D~~  159 (189)
T 3q3f_A          119 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGR  159 (189)
T ss_dssp             EEEECTTCBHHHHHHHHHHHHCCCGGGCCEEETTEECCTTC
T ss_pred             EEEeCCCCcHHHHHHHHHhccCCCHHHEEEEECCEECCCCC
Confidence            57889999999999999999999999999999999998853

>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=98.26  E-value=7.2e-10  Score=57.72  Aligned_cols=40  Identities=38%  Similarity=0.605  Sum_probs=37.2

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      .+.+++++||.++|..|++..|+|++.|+|+|+|+.|+|.
T Consensus        14 ~~~v~~~~tV~~lK~~i~~~~gi~~~~qrL~~~gk~L~d~   53 (76)
T 3b1l_X           14 PVEVDSDTSILQLKEVVAKQQGVPADQLRVIFAGKELPNH   53 (76)
Confidence            5678899999999999999999999999999999999875

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster}

Probab=98.77  E-value=3.5e-09  Score=68.73  Aligned_cols=47  Identities=13%  Similarity=0.183  Sum_probs=41.2

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEE---EEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLI---TTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~---~~~-~v~~~~tv~~l   48 (77)
                      ++++++++++||++||++|++.+|||+++|+|+   |.+ .+.++.++.++
T Consensus        16 ~~~v~v~~~~Tv~~lK~~I~~~tgVpp~~QkLi~~k~~Gk~l~D~~~L~~~   66 (320)
T 3shq_A           16 EYPVDLTDQDTVEVLRHEIFRKTQVRPERQKLLNLKYKGKTAADNVKISAL   66 (320)
T ss_dssp             EEEEEEETTSBHHHHHHHHHHHHCCCGGGCEETTCBSSSSBCCTTSBTTSS
T ss_pred             EEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEeecccCCcccCccccHHHc
Confidence            588999999999999999999999999999999   665 55677777776

>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=98.76  E-value=1.7e-08  Score=56.08  Aligned_cols=38  Identities=26%  Similarity=0.281  Sum_probs=34.1

Q ss_pred             ecC-CccHHHHHHHHhhcc--CCCccc-eEEEECCeEcCccc
Q 040720           39 VKS-SDTINNVKSKIQDKE--GIPPDQ-QRLIFAGINLKLVV   76 (77)
Q Consensus        39 v~~-~~tv~~lK~~i~~~~--gip~~~-q~l~~~g~~L~d~~   76 (77)
                      +++ ++||.++|..|+...  |+|+++ |+|+|+|+.|+|..
T Consensus        40 v~~~~~TV~~LK~~i~~~~~~gip~~~~qrLi~~Gk~L~D~~   81 (107)
T 1x1m_A           40 YSLGGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQ   81 (107)
T ss_dssp             SCCCCCBHHHHHHHHHHHCTTTCCCSSSEEEEETTEECCTTC
T ss_pred             cCcccCCHHHHHHHHHHHhccCCChhhcEEEEECCeECCCCC
Confidence            444 499999999999999  999999 99999999998863

>2kjr_A CG11242; UBL, ubiquitin, ubiquitin-like, structural genomics, PSI-2, protein structure initiative; NMR {Drosophila melanogaster}

Probab=98.74  E-value=2.4e-08  Score=54.62  Aligned_cols=42  Identities=10%  Similarity=0.071  Sum_probs=36.0

Q ss_pred             EEEEEecCCccHHHHHHHHhhccCCCccceEEEEC--Ce---Ec-Ccc
Q 040720           34 ITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFA--GI---NL-KLV   75 (77)
Q Consensus        34 ~~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~--g~---~L-~d~   75 (77)
                      .+.+.+++++||.++|.+|+..+|+|+++|+|+|+  |+   +| +|.
T Consensus        29 ~~~~~v~~~~TV~~LK~kI~~~~GiP~~~QrL~~~~~g~~~~~L~~D~   76 (95)
T 2kjr_A           29 AFEVKLAKDLTVAQLKTKLEILTGGCAGTMKVQVFKGDTCVSTMDNND   76 (95)
T ss_dssp             EEEEEEETTCBHHHHHHHHHHHHCSCTTTEEEEEEETTEEEEECCCTT
T ss_pred             EEEEEeCccCHHHHHHHHHHHHHCcCHHHeEEEEecCCcccceeCCCC
Confidence            34678899999999999999999999999999997  55   45 554

>2kj6_A Tubulin folding cofactor B; methods development, NESG, solution PSI-2, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=98.74  E-value=1.9e-08  Score=55.27  Aligned_cols=36  Identities=17%  Similarity=0.154  Sum_probs=33.5

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCe
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGI   70 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~   70 (77)
                      +...+++++||.++|.+|+..+|+|+++|+|+|.|+
T Consensus        29 ~e~~v~~~~TV~~LK~kIe~~~Gip~~~QrLi~~g~   64 (97)
T 2kj6_A           29 ADARFSPQMSVEAVKEKLWKKCGTSVNSMALELYDD   64 (97)
T ss_dssp             EEEEECTTCCHHHHHHHHHHHHCCCTTSEEEEEECS
T ss_pred             EEEEeCCCChHHHHHHHHHHHHCcCHHHeEEEEecC
Confidence            467899999999999999999999999999999884

>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=98.72  E-value=1.3e-09  Score=62.33  Aligned_cols=42  Identities=79%  Similarity=0.991  Sum_probs=0.0

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      |.+.+++++||.++|..|++..|+|+++|+|+|+|+.|+|..
T Consensus        13 ~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~   54 (128)
T 3u5e_m           13 ITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGR   54 (128)
T ss_dssp             ------------------------------------------
T ss_pred             EEEEeCCCCCHHHHHHHHHHHhCcChHHEEEEECCEECCCCC
Confidence            356788999999999999999999999999999999998863

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B*

Probab=98.72  E-value=9.4e-09  Score=66.48  Aligned_cols=47  Identities=47%  Similarity=0.654  Sum_probs=35.0

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.++|++++||++||++|++..|+|+++|+|+|.+ .++++.++.++
T Consensus       245 ~~~leV~~s~TV~dLK~kI~~~~GIp~~~QRLi~~Gk~L~D~~TLsdy  292 (307)
T 3ai5_A          245 TITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY  292 (307)
T ss_dssp             EEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBTGGG
T ss_pred             EEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEeCCeecCCCCCHHHc
Confidence            467778888888888888888888888888887764 45666666665

>2dzm_A FAS-associated factor 1; ubiquitin-like domain, HFAF1, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.71  E-value=1.7e-08  Score=55.75  Aligned_cols=39  Identities=15%  Similarity=0.205  Sum_probs=34.7

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEE--CCeEcCcc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIF--AGINLKLV   75 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~--~g~~L~d~   75 (77)
                      .+.+++++||.++|.+|++++|||+++|+|+|  +|+ |+|.
T Consensus        22 ~v~v~~~~TV~~LK~~I~~~tgIpp~~QkLi~~~~gk-L~D~   62 (100)
T 2dzm_A           22 DVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGD-VEDS   62 (100)
T ss_dssp             EEEEETTSBHHHHHHHHHHHHCCCTTTCCEECCSSSC-CCTT
T ss_pred             EEEECCCCcHHHHHHHHHHHHCCChhHeEEEccCCCC-CCCc
Confidence            56789999999999999999999999999986  666 7764

>2dzj_A Synaptic glycoprotein SC2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.69  E-value=2.1e-08  Score=54.10  Aligned_cols=41  Identities=27%  Similarity=0.296  Sum_probs=36.7

Q ss_pred             EEE-EecCCccHHHHHHHHhh-ccCCCccceEEEEC--CeEcCcc
Q 040720           35 TTL-EVKSSDTINNVKSKIQD-KEGIPPDQQRLIFA--GINLKLV   75 (77)
Q Consensus        35 ~~~-~v~~~~tv~~lK~~i~~-~~gip~~~q~l~~~--g~~L~d~   75 (77)
                      +.+ ++++++||.++|+.|++ ..|+|+++|+|+|.  |++|+|.
T Consensus        25 ~~l~~v~~~~TV~~lK~~I~~~~~~i~~~~QrL~~~~~Gk~L~D~   69 (88)
T 2dzj_A           25 CFLDKVEPHATIAEIKNLFTKTHPQWYPARQSLRLDPKGKSLKDE   69 (88)
T ss_dssp             EEEEEECSSCBHHHHHHHHHHHCSSSCTTTCCEESSTTSCCCCTT
T ss_pred             eEEeEcCCCCcHHHHHHHHHHHhcCCChHHeEEEecCCCcCcCCC
Confidence            457 89999999999999999 48999999999976  9999775

>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=98.69  E-value=8.7e-09  Score=57.40  Aligned_cols=39  Identities=23%  Similarity=0.198  Sum_probs=35.1

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCc---------------cceEEEECCeEcCc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPP---------------DQQRLIFAGINLKL   74 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~---------------~~q~l~~~g~~L~d   74 (77)
                      .+.+++++||.+||+.|++++++|+               ++|+|+|+|++|.|
T Consensus        21 ~v~V~~~~TV~dLK~~I~~~~~i~~~~q~g~~~isw~~~w~q~~Li~~Gk~L~d   74 (105)
T 1v2y_A           21 PVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEKLTE   74 (105)
T ss_dssp             EEEECTTCBHHHHHHHHHHHHHHHHHHTTCCCCCCHHHHHTTEEEESSSCEECC
T ss_pred             EEEECCCChHHHHHHHHHHHhCCCcccccCcceeeeeecceeEEEEeCCcCccC
Confidence            6789999999999999999999987               46799999999964

>4efo_A Serine/threonine-protein kinase TBK1; ubiquitin like domain, transferase; 1.77A {Homo sapiens}

Probab=98.68  E-value=4.9e-08  Score=53.34  Aligned_cols=34  Identities=12%  Similarity=0.045  Sum_probs=23.2

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEE
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITT   36 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~   36 (77)
                      +.+.+.+.+|+..+|++|++.+|||+++|+|+|.
T Consensus        26 h~v~I~~~etv~~~ke~V~eqTgIp~~~Q~LL~e   59 (94)
T 4efo_A           26 HKIYIHSYNTATIFHELVYKQTKIISSNQELIYE   59 (94)
T ss_dssp             EEEEEETTCBHHHHHHHHHHHHCCCGGGEEEEET
T ss_pred             EEEEeccchHHHHHHHHHHHHhCCCHHHHHHHhC
Confidence            5566667777777777777777777777777664

>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=98.68  E-value=2.2e-09  Score=63.29  Aligned_cols=42  Identities=79%  Similarity=0.991  Sum_probs=0.0

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      +.+.+++++||.++|..|++..|+|+++|+|+|+|++|+|..
T Consensus        13 ~~l~V~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~   54 (152)
T 3u5c_f           13 ITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGR   54 (152)
T ss_dssp             ------------------------------------------
T ss_pred             EEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEEccccC
Confidence            356788999999999999999999999999999999998863

>4efo_A Serine/threonine-protein kinase TBK1; ubiquitin like domain, transferase; 1.77A {Homo sapiens}

Probab=98.67  E-value=4.5e-08  Score=53.51  Aligned_cols=39  Identities=21%  Similarity=0.279  Sum_probs=36.3

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcC
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK   73 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~   73 (77)
                      +.+.+.+++++..+|..|++++|||+++|+|+|+|+.|.
T Consensus        26 h~v~I~~~etv~~~ke~V~eqTgIp~~~Q~LL~eg~~l~   64 (94)
T 4efo_A           26 HKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLV   64 (94)
T ss_dssp             EEEEEETTCBHHHHHHHHHHHHCCCGGGEEEEETTEEEC
T ss_pred             EEEEeccchHHHHHHHHHHHHhCCCHHHHHHHhCCCccc
Confidence            467888999999999999999999999999999998875

>1wf9_A NPL4 family protein; beta-grAsp fold like domain, hypothetical protein, structural genomics, NPPSFA; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=98.65  E-value=6.4e-09  Score=57.88  Aligned_cols=35  Identities=26%  Similarity=0.201  Sum_probs=31.5

Q ss_pred             EEEEee-CCCcHHHHHHHhhhhhCCCcccceEEEEE
Q 040720            3 LLLMWK-APTPLINVKAKIQDKEGIPPDQQRLITTL   37 (77)
Q Consensus         3 ~~~~v~-~~~tv~~lK~~i~~~~gi~~~~q~L~~~~   37 (77)
                      ..++|+ +++||.+||++|++..|+|++.|+|+|..
T Consensus        19 ~~v~v~~~~~Tv~~LK~kI~~~~gip~~~QrL~~~~   54 (107)
T 1wf9_A           19 ERVSVDGPHITVSQLKTLIQDQLQIPIHNQTLSTNR   54 (107)
T ss_dssp             EEEEECCTTSBHHHHHHHHHHHSCCCTTTCCCBSSG
T ss_pred             EEEEECCCCCcHHHHHHHHHHHhCcCcccCEEEECC
Confidence            468899 99999999999999999999999998754

>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=98.59  E-value=8.4e-09  Score=68.10  Aligned_cols=47  Identities=17%  Similarity=0.240  Sum_probs=39.9

Q ss_pred             eEEEEeeCCCcHHHHHHHhhh---hhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQD---KEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~---~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.++|++++||.+||.+|++   ++|||+++|+|+|.+ .+.++.++.++
T Consensus        19 ~~~leV~~~~TV~~LK~~I~~~~~~~gip~~~QrLiy~GK~L~D~~tL~dy   69 (368)
T 1oqy_A           19 TFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDY   69 (368)
T ss_dssp             EEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSSEECSSSBTTTT
T ss_pred             EEEEEeCCCChHHHHHHHHHHHhCcCCCChhheEEEECCeecCCcCCHHHc
Confidence            578899999999999999998   677999999999986 56777788776

>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=98.57  E-value=7.4e-08  Score=52.38  Aligned_cols=36  Identities=25%  Similarity=0.213  Sum_probs=33.5

Q ss_pred             EEEEEecCCccHHHHHHHHhhccCCCccceEEEECC
Q 040720           34 ITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG   69 (77)
Q Consensus        34 ~~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g   69 (77)
                      .+.+.+++++||.++|.+|+..+|+|+++|+|+|.|
T Consensus        20 ~~~~~v~~~~TV~~lK~ki~~~~gip~~~qrL~~~~   55 (95)
T 1v6e_A           20 RSEKRYSRSLTIAEFKCKLELVVGSPASCMELELYG   55 (95)
T ss_dssp             CEEEEECTTSBHHHHHHHHHHHTCSCTTTCBCEEEC
T ss_pred             eEEEEcCccCHHHHHHHHHHHHHCCCHHHeEEEEeC
Confidence            356789999999999999999999999999999986

>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=98.55  E-value=6.1e-08  Score=52.51  Aligned_cols=44  Identities=16%  Similarity=0.160  Sum_probs=28.6

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCC-ccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSS-DTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~-~tv~~l   48 (77)
                      ++.++|++++||++||.+|++..   +++|+|+|.+ .+.++ .++.++
T Consensus        19 ~~~~~v~~~~TV~~LK~~i~~~~---~~~qrLi~~Gk~L~D~~~tL~~y   64 (95)
T 1wia_A           19 EELAVARPEDTVGTLKSKYFPGQ---ESQMKLIYQGRLLQDPARTLSSL   64 (95)
T ss_dssp             EEEEEECSSSBHHHHHHHHSSST---TTTCEEEETTEECCCSSCBTTTT
T ss_pred             EEEEEECCCCcHHHHHHHHHhhC---cCcEEEEECCEEccCCcCCHHHc
Confidence            35667777777777777777665   5677777764 44555 566555

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B*

Probab=98.54  E-value=1.5e-07  Score=60.87  Aligned_cols=40  Identities=78%  Similarity=1.027  Sum_probs=37.8

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      .+.+++++||.++|..|++..|+|+++|+|+|+|++|+|.
T Consensus       247 ~leV~~s~TV~dLK~kI~~~~GIp~~~QRLi~~Gk~L~D~  286 (307)
T 3ai5_A          247 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDG  286 (307)
T ss_dssp             EEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTT
T ss_pred             EEEECCCCcHHHHHHHHHHHHCcChHHEEEEeCCeecCCC
Confidence            5788999999999999999999999999999999999875

>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=98.53  E-value=2e-07  Score=50.46  Aligned_cols=38  Identities=26%  Similarity=0.311  Sum_probs=34.7

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      +.+.++++++|.++|..|+...   +++|+|+|+|+.|+|.
T Consensus        20 ~~~~v~~~~TV~~LK~~i~~~~---~~~qrLi~~Gk~L~D~   57 (95)
T 1wia_A           20 ELAVARPEDTVGTLKSKYFPGQ---ESQMKLIYQGRLLQDP   57 (95)
T ss_dssp             EEEEECSSSBHHHHHHHHSSST---TTTCEEEETTEECCCS
T ss_pred             EEEEECCCCcHHHHHHHHHhhC---cCcEEEEECCEEccCC
Confidence            3578899999999999999998   8999999999999876

>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=98.47  E-value=1.1e-07  Score=51.93  Aligned_cols=47  Identities=19%  Similarity=0.234  Sum_probs=38.8

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      .+.++|.+++++..|+++++++.|+|+++++|+|.+ .+.++.|+.++
T Consensus        19 ~i~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~FdG~~l~~~~Tp~dl   66 (94)
T 2io1_B           19 VVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQL   66 (94)
T ss_dssp             EEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCTTTT
T ss_pred             EEEEEECCCCHHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHc
Confidence            467888888888888888888888888888888874 67788888777

>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=98.46  E-value=1.7e-07  Score=61.85  Aligned_cols=41  Identities=27%  Similarity=0.462  Sum_probs=37.3

Q ss_pred             EEEEecCCccHHHHHHHHhh---ccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQD---KEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~---~~gip~~~q~l~~~g~~L~d~   75 (77)
                      |.+.++.++||.++|..|+.   +.|+|+++|+|+|+|+.|+|.
T Consensus        20 ~~leV~~~~TV~~LK~~I~~~~~~~gip~~~QrLiy~GK~L~D~   63 (368)
T 1oqy_A           20 FKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDD   63 (368)
T ss_dssp             EEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSSEECSS
T ss_pred             EEEEeCCCChHHHHHHHHHHHhCcCCCChhheEEEECCeecCCc
Confidence            35788999999999999999   678999999999999999875

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster}

Probab=98.46  E-value=1e-07  Score=61.90  Aligned_cols=41  Identities=20%  Similarity=0.417  Sum_probs=38.4

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEE---ECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLI---FAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~---~~g~~L~d~   75 (77)
                      |.+.+++++||.++|+.|++.+|+|+++|+|+   |+|++|+|.
T Consensus        17 ~~v~v~~~~Tv~~lK~~I~~~tgVpp~~QkLi~~k~~Gk~l~D~   60 (320)
T 3shq_A           17 YPVDLTDQDTVEVLRHEIFRKTQVRPERQKLLNLKYKGKTAADN   60 (320)
T ss_dssp             EEEEEETTSBHHHHHHHHHHHHCCCGGGCEETTCBSSSSBCCTT
T ss_pred             EEEEECCCCcHHHHHHHHHHHHCcCHHHeEEeecccCCcccCcc
Confidence            46789999999999999999999999999999   899999885

>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative, hydrolase; NMR {Mus musculus}

Probab=98.44  E-value=2.3e-07  Score=49.51  Aligned_cols=45  Identities=24%  Similarity=0.395  Sum_probs=36.4

Q ss_pred             EEE-eeCCCcHHHHHHHhhhhhCCCcccceEEEEE---Ee--c-CCccHHHH
Q 040720            4 LLM-WKAPTPLINVKAKIQDKEGIPPDQQRLITTL---EV--K-SSDTINNV   48 (77)
Q Consensus         4 ~~~-v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~---~v--~-~~~tv~~l   48 (77)
                      .++ +++++||++||++|++..|+|++.|+|+|.+   .+  . ++.++.++
T Consensus        13 ~v~~l~~~~Tv~~Lk~~I~~~~gi~~~~qrL~~~~p~k~l~l~~~~~tL~~~   64 (86)
T 2kzr_A           13 LLQGLSSRTRLRELQGQIAAITGIAPGSQRILVGYPPECLDLSDRDITLGDL   64 (86)
T ss_dssp             EECSCCTTCBHHHHHHHHHHHTCCCTTTCCCEESSCCCCCCCCCSSCBTTTS
T ss_pred             EeeecCCCCCHHHHHHHHHHHhCCCccceEEEeCCCCcccccCCCCCCHHHc
Confidence            466 8999999999999999999999999999853   12  2 45566666

>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=98.43  E-value=3.9e-07  Score=51.67  Aligned_cols=36  Identities=17%  Similarity=0.203  Sum_probs=33.2

Q ss_pred             EEEEEecCCccHHHHHHHHhhccCCCccceEEEECC
Q 040720           34 ITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG   69 (77)
Q Consensus        34 ~~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g   69 (77)
                      .+...+++++||.++|.+|+...|+|+++|+|+|.|
T Consensus        19 ~~e~~v~~~~TV~~lK~ki~~~~Gip~~~qrL~~~g   54 (122)
T 1t0y_A           19 PMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFD   54 (122)
T ss_dssp             CEEEEEETTSBHHHHHHHHHHHHCCCTTTEEEEEEC
T ss_pred             cEEEEeCCCCcHHHHHHHHHHHhCCCHHHeEEEEec
Confidence            356788999999999999999999999999999987

>3a4r_A Nfatc2-interacting protein; ubiquitin fold, coiled coil, cytoplasm, methylation, nucleus, transcription; 1.00A {Mus musculus} PDB: 3a4s_C 3rd2_A

Probab=98.41  E-value=1.9e-06  Score=45.41  Aligned_cols=47  Identities=9%  Similarity=0.164  Sum_probs=39.3

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      .+.+.|.+++++..|+.++++..|+++++++|+|.+ .+.++.|+.++
T Consensus        20 ~i~~~i~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~~l~~~~Tp~~l   67 (79)
T 3a4r_A           20 MLEISLSPDSPLKVLMSHYEEAMGLSGHKLSFFFDGTKLSGKELPADL   67 (79)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHTCTTCCCEEEETTEECCSCCCHHHH
T ss_pred             EEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHc
Confidence            467888888888888888888888888888888875 77888888887

>1wm3_A Ubiquitin-like protein SMT3B; ubiquitin fold, half-open barrel, two helices, protein transport; 1.20A {Homo sapiens} SCOP: d.15.1.1 PDB: 1wm2_A 3uin_B 3uio_B 2ckh_B

Probab=98.40  E-value=2.1e-07  Score=48.30  Aligned_cols=47  Identities=19%  Similarity=0.234  Sum_probs=32.8

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      .+.+.|.++++++.|+.++++..|+|+..++|+|.+ .+.++.|+.++
T Consensus        13 ~v~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~~l~~~~Tp~~l   60 (72)
T 1wm3_A           13 VVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQL   60 (72)
T ss_dssp             EEEEEECTTSCTHHHHHHHHHHHTCCTTTCEEEETTEECCTTCCTTTT
T ss_pred             EEEEEECCCChHHHHHHHHHHHhCCCcceEEEEECCEEcCCCCCHHHc
Confidence            356677777777777777777777777777777764 56666666665

>1wjn_A Tubulin-folding protein TBCE; ubiquitin-like domain, progressive motor neuropathy, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=98.39  E-value=6.2e-07  Score=48.79  Aligned_cols=47  Identities=13%  Similarity=0.045  Sum_probs=37.4

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEE-------E-Ee-cCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITT-------L-EV-KSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~-------~-~v-~~~~tv~~l   48 (77)
                      .+.+.+.++.||++||.+|+...|+|+..|+|+|.       . .+ ++..++..+
T Consensus        24 ~~e~~l~~~~TV~~LK~~i~~~~gip~~~q~L~~~~~~~~~~~~~L~~d~~~L~~y   79 (97)
T 1wjn_A           24 ILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQFY   79 (97)
T ss_dssp             CEEEEEETTSBHHHHHHHHHTTTTCCTTTCEEEEECTTSCSCEEECCCSSSBSGGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCChhHeEEEEEcCCCCceeeccCCCcccHhhc
Confidence            35677889999999999999999999999999886       1 23 455566665

>2io0_B Small ubiquitin-related modifier 2 precursor; SUMO, SENP, ULP, complex, protein binding, hydrolase; 2.30A {Homo sapiens} SCOP: d.15.1.1

Probab=98.32  E-value=3.9e-07  Score=49.42  Aligned_cols=47  Identities=19%  Similarity=0.234  Sum_probs=36.9

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      .+.+.|.+++++..|+..+++..|+|+.+++|+|.+ .+.+++|+.++
T Consensus        17 ~v~~~vk~~t~l~kl~~~y~~~~gi~~~~~rf~FdG~~l~~~~Tp~dl   64 (91)
T 2io0_B           17 VVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQL   64 (91)
T ss_dssp             EEEEEEETTSCTHHHHHHHHHHTTCCSTTEEEEETTEECCTTCCTTTT
T ss_pred             EEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHc
Confidence            466778888888888888888888888888888874 67777777776

>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=98.24  E-value=2.3e-06  Score=46.59  Aligned_cols=41  Identities=15%  Similarity=0.314  Sum_probs=37.9

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+..++++..++..++++.|+|+++++|+|+|+.|++.-
T Consensus        21 ~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~FdG~~l~~~~   61 (94)
T 2io1_B           21 QFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETD   61 (94)
T ss_dssp             EEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTC
T ss_pred             EEEECCCCHHHHHHHHHHHHhCCCcccEEEEECCEEcCCCC
Confidence            46788999999999999999999999999999999998764

>2k8h_A Small ubiquitin protein; SUMO, post-translational modifier, signaling protein; NMR {Trypanosoma brucei}

Probab=98.22  E-value=1.3e-06  Score=48.85  Aligned_cols=47  Identities=17%  Similarity=0.265  Sum_probs=37.1

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      .+.+.|.+++++..|+..+++..|+|+++++|+|.+ .+.++.|+.++
T Consensus        38 ~i~fkVk~~t~l~kL~~ay~ek~gi~~~~~rfiFdG~~L~~~~Tp~dl   85 (110)
T 2k8h_A           38 EMFFRIKSRTALKKLIDTYCKKQGISRNSVRFLFDGTPIDETKTPEEL   85 (110)
T ss_dssp             CEEEEECTTSSHHHHHHHHHHHHTCCSSSCEEESSSCBCCSSSHHHHH
T ss_pred             EEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHc
Confidence            356778888888888888888888888888888875 67777788777

>2d07_B Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Homo sapiens} SCOP: d.15.1.1 PDB: 2rpq_A 2awt_A 2io3_B 2iyd_B 1u4a_A 2k1f_A

Probab=98.20  E-value=1.2e-06  Score=47.52  Aligned_cols=38  Identities=16%  Similarity=0.364  Sum_probs=18.9

Q ss_pred             EEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCc
Q 040720           37 LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKL   74 (77)
Q Consensus        37 ~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d   74 (77)
                      +.+..++++..++..++++.|+++++++|+|+|+.|.+
T Consensus        32 ~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~~l~~   69 (93)
T 2d07_B           32 FKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINE   69 (93)
T ss_dssp             EEEETTSCHHHHHHHHHHHHTCCGGGEEEEETTEECCT
T ss_pred             EEEccCCHHHHHHHHHHHHhCCCccceEEEECCEEcCC
Confidence            34444445555555555555555555555555555443

>1wm3_A Ubiquitin-like protein SMT3B; ubiquitin fold, half-open barrel, two helices, protein transport; 1.20A {Homo sapiens} SCOP: d.15.1.1 PDB: 1wm2_A 3uin_B 3uio_B 2ckh_B

Probab=98.19  E-value=3.8e-06  Score=43.41  Aligned_cols=41  Identities=15%  Similarity=0.314  Sum_probs=37.8

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+..++++..++...+++.|+|+++++++|+|+.|++.-
T Consensus        15 ~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~~l~~~~   55 (72)
T 1wm3_A           15 QFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETD   55 (72)
T ss_dssp             EEEECTTSCTHHHHHHHHHHHTCCTTTCEEEETTEECCTTC
T ss_pred             EEEECCCChHHHHHHHHHHHhCCCcceEEEEECCEEcCCCC
Confidence            56788999999999999999999999999999999998764

>3a4r_A Nfatc2-interacting protein; ubiquitin fold, coiled coil, cytoplasm, methylation, nucleus, transcription; 1.00A {Mus musculus} PDB: 3a4s_C 3rd2_A

Probab=98.14  E-value=7.2e-06  Score=43.14  Aligned_cols=41  Identities=12%  Similarity=0.271  Sum_probs=37.6

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+..++++..++...+++.|+++++++++|+|+.|.+.-
T Consensus        22 ~~~i~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~~l~~~~   62 (79)
T 3a4r_A           22 EISLSPDSPLKVLMSHYEEAMGLSGHKLSFFFDGTKLSGKE   62 (79)
T ss_dssp             EEEECTTSCHHHHHHHHHHHHTCTTCCCEEEETTEECCSCC
T ss_pred             EEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEEcCCCC
Confidence            46788999999999999999999999999999999998764

>2io0_B Small ubiquitin-related modifier 2 precursor; SUMO, SENP, ULP, complex, protein binding, hydrolase; 2.30A {Homo sapiens} SCOP: d.15.1.1

Probab=98.11  E-value=7.3e-06  Score=44.34  Aligned_cols=41  Identities=15%  Similarity=0.314  Sum_probs=37.7

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+..++++..++...+++.|+|+++++++|+|+.|++.-
T Consensus        19 ~~~vk~~t~l~kl~~~y~~~~gi~~~~~rf~FdG~~l~~~~   59 (91)
T 2io0_B           19 QFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETD   59 (91)
T ss_dssp             EEEEETTSCTHHHHHHHHHHTTCCSTTEEEEETTEECCTTC
T ss_pred             EEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEEcCCCC
Confidence            56788999999999999999999999999999999998764

>1wz0_A Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-like molecule, structural genomics, sentrin2, NPPFSA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=98.07  E-value=1.7e-06  Score=47.98  Aligned_cols=46  Identities=20%  Similarity=0.253  Sum_probs=26.2

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +.+.|.+++++..|+.++++..|+++..++|+|.+ .+.++.|+.++
T Consensus        37 i~~kVk~~t~l~kL~~~y~ek~gi~~~~~rf~FdG~~l~~~~Tp~dl   83 (104)
T 1wz0_A           37 VQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQL   83 (104)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHTCCTTTSCEESSSSBCCTTSCTTTT
T ss_pred             EEEEEcCCChHHHHHHHHHHHhCCCcceEEEEECCEEcCCCCCHHHc
Confidence            44555556666666666666666665555665554 44555555554

>2eke_C Ubiquitin-like protein SMT3; UBC9, SUMO binding motif, SBM, ligase/protein binding complex; 1.90A {Saccharomyces cerevisiae} SCOP: d.15.1.1

Probab=98.06  E-value=2.9e-06  Score=47.23  Aligned_cols=47  Identities=17%  Similarity=0.321  Sum_probs=29.8

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      .+.+.|.+++++..|+..+++..|+++..++|+|.+ .+.++.|..++
T Consensus        42 ~i~fkIk~tt~l~kL~~ay~ek~gi~~~~~rF~FdG~rl~~~~Tp~dl   89 (106)
T 2eke_C           42 EIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDL   89 (106)
T ss_dssp             EEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCTTTT
T ss_pred             EEEEEeCCCCHHHHHHHHHHHHhCCCcccEEEEECCeEcCCCCCHHHc
Confidence            345666666666666666666666666666666653 55666666555

>1wf9_A NPL4 family protein; beta-grAsp fold like domain, hypothetical protein, structural genomics, NPPSFA; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=98.05  E-value=1.6e-06  Score=48.02  Aligned_cols=35  Identities=29%  Similarity=0.300  Sum_probs=32.6

Q ss_pred             EEEec-CCccHHHHHHHHhhccCCCccceEEEECCe
Q 040720           36 TLEVK-SSDTINNVKSKIQDKEGIPPDQQRLIFAGI   70 (77)
Q Consensus        36 ~~~v~-~~~tv~~lK~~i~~~~gip~~~q~l~~~g~   70 (77)
                      .++++ +++||.+||.+|++..|+|+++|+|+|.|+
T Consensus        20 ~v~v~~~~~Tv~~LK~kI~~~~gip~~~QrL~~~~~   55 (107)
T 1wf9_A           20 RVSVDGPHITVSQLKTLIQDQLQIPIHNQTLSTNRN   55 (107)
T ss_dssp             EEEECCTTSBHHHHHHHHHHHSCCCTTTCCCBSSGG
T ss_pred             EEEECCCCCcHHHHHHHHHHHhCcCcccCEEEECCc
Confidence            46788 999999999999999999999999999988

>2d07_B Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Homo sapiens} SCOP: d.15.1.1 PDB: 2rpq_A 2awt_A 2io3_B 2iyd_B 1u4a_A 2k1f_A

Probab=98.00  E-value=1.7e-05  Score=42.94  Aligned_cols=47  Identities=19%  Similarity=0.234  Sum_probs=43.5

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      .+.+.|.+++++..|+..+++..|++++.++|+|.+ .+.++.|+.++
T Consensus        29 ~i~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~~l~~~~Tp~dl   76 (93)
T 2d07_B           29 VVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQL   76 (93)
T ss_dssp             EEEEEEETTSCHHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCTTTT
T ss_pred             EEEEEEccCCHHHHHHHHHHHHhCCCccceEEEECCEEcCCCCCHHHc
Confidence            477899999999999999999999999999999985 78899999887

>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative, hydrolase; NMR {Mus musculus}

Probab=97.91  E-value=7.5e-06  Score=43.51  Aligned_cols=35  Identities=23%  Similarity=0.407  Sum_probs=31.6

Q ss_pred             ecCCccHHHHHHHHhhccCCCccceEEEECC--eEcC
Q 040720           39 VKSSDTINNVKSKIQDKEGIPPDQQRLIFAG--INLK   73 (77)
Q Consensus        39 v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g--~~L~   73 (77)
                      +++++||.++|..|+++.|+|+++|+|+|++  ++|+
T Consensus        17 l~~~~Tv~~Lk~~I~~~~gi~~~~qrL~~~~p~k~l~   53 (86)
T 2kzr_A           17 LSSRTRLRELQGQIAAITGIAPGSQRILVGYPPECLD   53 (86)
T ss_dssp             CCTTCBHHHHHHHHHHHTCCCTTTCCCEESSCCCCCC
T ss_pred             cCCCCCHHHHHHHHHHHhCCCccceEEEeCCCCcccc
Confidence            7889999999999999999999999999874  6663

>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=97.88  E-value=2.8e-05  Score=43.19  Aligned_cols=41  Identities=15%  Similarity=0.384  Sum_probs=37.3

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+..++++..++..++++.|+++++++++|+|+.|.+.-
T Consensus        44 ~fkIk~tt~l~kL~~ay~ek~gi~~~~~rF~FdG~rl~~~~   84 (106)
T 2eke_C           44 FFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQ   84 (106)
T ss_dssp             EEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTC
T ss_pred             EEEeCCCCHHHHHHHHHHHHhCCCcccEEEEECCeEcCCCC
Confidence            46788899999999999999999999999999999998753

>2k8h_A Small ubiquitin protein; SUMO, post-translational modifier, signaling protein; NMR {Trypanosoma brucei}

Probab=97.86  E-value=1.8e-05  Score=44.26  Aligned_cols=40  Identities=20%  Similarity=0.409  Sum_probs=37.3

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      .+.+..++++..++..++++.|+|+++++|+|+|+.|.+.
T Consensus        40 ~fkVk~~t~l~kL~~ay~ek~gi~~~~~rfiFdG~~L~~~   79 (110)
T 2k8h_A           40 FFRIKSRTALKKLIDTYCKKQGISRNSVRFLFDGTPIDET   79 (110)
T ss_dssp             EEEECTTSSHHHHHHHHHHHHTCCSSSCEEESSSCBCCSS
T ss_pred             EEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEEcCCC
Confidence            5678899999999999999999999999999999999875

>1wz0_A Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-like molecule, structural genomics, sentrin2, NPPFSA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=97.84  E-value=2e-05  Score=43.58  Aligned_cols=41  Identities=15%  Similarity=0.314  Sum_probs=37.7

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+..++++..++..++++.|+++++++|+|+|+.|.+.-
T Consensus        38 ~~kVk~~t~l~kL~~~y~ek~gi~~~~~rf~FdG~~l~~~~   78 (104)
T 1wz0_A           38 QFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETD   78 (104)
T ss_dssp             EEEECTTSCHHHHHHHHHHHHTCCTTTSCEESSSSBCCTTS
T ss_pred             EEEEcCCChHHHHHHHHHHHhCCCcceEEEEECCEEcCCCC
Confidence            46788999999999999999999999999999999998763

>1wjn_A Tubulin-folding protein TBCE; ubiquitin-like domain, progressive motor neuropathy, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=97.74  E-value=7e-05  Score=40.51  Aligned_cols=34  Identities=18%  Similarity=0.238  Sum_probs=30.9

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECC
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG   69 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g   69 (77)
                      ...++.+.||.+||..|+..+|+|+..|+|.|.+
T Consensus        26 e~~l~~~~TV~~LK~~i~~~~gip~~~q~L~~~~   59 (97)
T 1wjn_A           26 EKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYES   59 (97)
T ss_dssp             EEEEETTSBHHHHHHHHHTTTTCCTTTCEEEEEC
T ss_pred             EEECCCCCCHHHHHHHHHHHHCCChhHeEEEEEc
Confidence            4577899999999999999999999999999873

>3kyd_D Small ubiquitin-related modifier 1; SUMO, thioester, adenylation, inhibitor, TETR intermediate, ligase, nucleus, phosphoprotein; HET: VMX; 2.61A {Homo sapiens} SCOP: d.15.1.1

Probab=97.36  E-value=0.00046  Score=38.80  Aligned_cols=41  Identities=20%  Similarity=0.429  Sum_probs=34.9

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+..++++..|+...+++.|+++.+++++|+|+.|.+..
T Consensus        54 ~fkIk~tt~L~KLm~aY~er~Gl~~~~irFlFDG~rI~~~~   94 (115)
T 3kyd_D           54 HFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNH   94 (115)
T ss_dssp             EEEEETTSCTHHHHHHHHHHHTCCTTSEEEEETTEECCTTC
T ss_pred             EEEEccCChHHHHHHHHHHHhCCChhhEEEEECCeECCCCC
Confidence            45778888899999999999999999999999999987754

>3pge_A SUMO-modified proliferating cell nuclear antigen; DNA replication, DNA binding protein; 2.80A {Saccharomyces cerevisiae}

Probab=97.35  E-value=0.00036  Score=42.68  Aligned_cols=41  Identities=15%  Similarity=0.384  Sum_probs=30.9

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+..++.+..|+...+++.|+|+.++|++|+|+.|.+..
T Consensus        42 ~fkIk~~t~l~kL~~ay~er~Gi~~~~~RF~FdG~rI~~~~   82 (200)
T 3pge_A           42 FFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQ   82 (200)
T ss_dssp             EEEECTTSCTHHHHHHHHHHHSSCGGGEEEEETTEECCTTC
T ss_pred             EEEEecCCHHHHHHHHHHHHhCCChhhEEEEECCEEcCCCC
Confidence            45667777788888888888888888888888888776653

>2pjh_A Protein NPL4, nuclear protein localization protein 4 homolog; UFD1, NPL4, AAA, protein binding, transport protein; NMR {Mus musculus}

Probab=97.32  E-value=0.00013  Score=38.44  Aligned_cols=36  Identities=6%  Similarity=-0.045  Sum_probs=30.7

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL   37 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~   37 (77)
                      ++-+++++++|+.+|+++|++..+++++.|.+.+..
T Consensus        15 ~~Ri~v~~~~t~~~L~~~I~~~~~i~~~~~~l~~~~   50 (80)
T 2pjh_A           15 VKRITATKRETAATFLKKVAKEFGFQNNGFSVYINR   50 (80)
T ss_dssp             EEECCCCSSCCHHHHHHHHHHHTCCCTTTCCCCCSC
T ss_pred             CEEEEcCCcChHHHHHHHHHHHcCCCCCcceEEecC
Confidence            456789999999999999999999998888776543

>3kyd_D Small ubiquitin-related modifier 1; SUMO, thioester, adenylation, inhibitor, TETR intermediate, ligase, nucleus, phosphoprotein; HET: VMX; 2.61A {Homo sapiens} SCOP: d.15.1.1

Probab=97.28  E-value=0.00022  Score=40.13  Aligned_cols=47  Identities=17%  Similarity=0.286  Sum_probs=42.8

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      .+.+.|.+++++..|+...++..|+++..++|+|.+ .+.++.|..++
T Consensus        52 ev~fkIk~tt~L~KLm~aY~er~Gl~~~~irFlFDG~rI~~~~TP~dL   99 (115)
T 3kyd_D           52 EIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKEL   99 (115)
T ss_dssp             EEEEEEETTSCTHHHHHHHHHHHTCCTTSEEEEETTEECCTTCCTTTT
T ss_pred             EEEEEEccCChHHHHHHHHHHHhCCChhhEEEEECCeECCCCCCHHHc
Confidence            367889999999999999999999999999999985 78888898887

>3pge_A SUMO-modified proliferating cell nuclear antigen; DNA replication, DNA binding protein; 2.80A {Saccharomyces cerevisiae}

Probab=97.14  E-value=0.00028  Score=43.16  Aligned_cols=47  Identities=17%  Similarity=0.321  Sum_probs=42.6

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      .+.+.|.+++++..|+...++..|+|+.++||+|.+ .+.++.|..++
T Consensus        40 ~v~fkIk~~t~l~kL~~ay~er~Gi~~~~~RF~FdG~rI~~~~TP~dL   87 (200)
T 3pge_A           40 EIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDL   87 (200)
T ss_dssp             EEEEEECTTSCTHHHHHHHHHHHSSCGGGEEEEETTEECCTTCCTTTT
T ss_pred             EEEEEEecCCHHHHHHHHHHHHhCCChhhEEEEECCEEcCCCCCHHHc
Confidence            467899999999999999999999999999999975 78888888877

>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=96.89  E-value=0.0013  Score=34.71  Aligned_cols=45  Identities=11%  Similarity=0.024  Sum_probs=25.3

Q ss_pred             EEEeeCCCcHHHHHHHhhhhhCCCcc-cceEEEEE-EecCCccHHHH
Q 040720            4 LLMWKAPTPLINVKAKIQDKEGIPPD-QQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         4 ~~~v~~~~tv~~lK~~i~~~~gi~~~-~q~L~~~~-~v~~~~tv~~l   48 (77)
                      -++|.++.||.++-...+...|||++ ..+|.|.+ .++++.++.++
T Consensus        23 ~f~I~~~t~v~kLi~ayc~~~~I~~~~~IrllFDGdRLdp~~tp~Dl   69 (82)
T 3goe_A           23 RLSIPVDFTVKDLIKRYCTEVKISFHERIRLEFEGEWLDPNDQVQST   69 (82)
T ss_dssp             EEEEETTSBHHHHHHHHHHHHTCCCCTTCEEEETTEECCTTSBGGGS
T ss_pred             EEEecCCCCHHHHHHHHHHHcCCCcCceEEEEEcCcccCccCChhhh
Confidence            34555566666666666666666555 55555554 45555555543

>3tix_A Ubiquitin-like protein SMT3, RNA-induced transcri silencing complex protein TAS3; PIN, rossmann fold, SPOC, alpha-helical hairpin, heterochrom silencing, RITS, RNAI, argonaute; 2.90A {Saccharomyces cerevisiae}

Probab=96.83  E-value=0.00083  Score=41.06  Aligned_cols=39  Identities=13%  Similarity=0.399  Sum_probs=23.5

Q ss_pred             EEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           37 LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        37 ~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      +.+..++.+..|+....++.|+++.+++++|+|+.|.+.
T Consensus        71 FKIKrtTpL~KLmeAYcERqGL~~~sIRFLFDGqRI~~d  109 (207)
T 3tix_A           71 FKIKKTTPLRRLMEAFAKRQGKEMDSLTFLYDGIEIQAD  109 (207)
T ss_dssp             EEEETTSCTHHHHHHHHHHTTCCGGGSCEEETTEECCSS
T ss_pred             EEEccCChHHHHHHHHHHHhCCCcccEEEEECCeecCCC
Confidence            455556666666666666666666666666666665543

>3tix_A Ubiquitin-like protein SMT3, RNA-induced transcri silencing complex protein TAS3; PIN, rossmann fold, SPOC, alpha-helical hairpin, heterochrom silencing, RITS, RNAI, argonaute; 2.90A {Saccharomyces cerevisiae}

Probab=96.81  E-value=0.0019  Score=39.49  Aligned_cols=47  Identities=17%  Similarity=0.309  Sum_probs=43.4

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      .+.+.|.+++++..|+...++..|+++..++|+|.+ .+.++.|..++
T Consensus        68 eV~FKIKrtTpL~KLmeAYcERqGL~~~sIRFLFDGqRI~~ddTPeDL  115 (207)
T 3tix_A           68 EIFFKIKKTTPLRRLMEAFAKRQGKEMDSLTFLYDGIEIQADQTPEDL  115 (207)
T ss_dssp             EEEEEEETTSCTHHHHHHHHHHTTCCGGGSCEEETTEECCSSCCTTTT
T ss_pred             EEEEEEccCChHHHHHHHHHHHhCCCcccEEEEECCeecCCCCCHHHc
Confidence            467899999999999999999999999999999985 88999999888

>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=96.75  E-value=0.0058  Score=32.17  Aligned_cols=41  Identities=20%  Similarity=0.154  Sum_probs=37.0

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCcc-ceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPD-QQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~-~q~l~~~g~~L~d~~   76 (77)
                      .+.++.+.++..+-.....+.|||++ ..+|+|.|..|+...
T Consensus        23 ~f~I~~~t~v~kLi~ayc~~~~I~~~~~IrllFDGdRLdp~~   64 (82)
T 3goe_A           23 RLSIPVDFTVKDLIKRYCTEVKISFHERIRLEFEGEWLDPND   64 (82)
T ss_dssp             EEEEETTSBHHHHHHHHHHHHTCCCCTTCEEEETTEECCTTS
T ss_pred             EEEecCCCCHHHHHHHHHHHcCCCcCceEEEEEcCcccCccC
Confidence            56788999999999999999999998 999999999987653

>1oey_A P67-PHOX, neutrophil cytosol factor 2; immune system, PB1 heterodimer/complex, NADPH oxidase, PB1 D heterodimerization; 2.0A {Homo sapiens} SCOP: d.15.2.2

Probab=96.46  E-value=0.0075  Score=31.99  Aligned_cols=34  Identities=12%  Similarity=0.208  Sum_probs=32.2

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEE
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLIT   35 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~   35 (77)
                      |+.|.|+++.+..+|.++|+++.++|++.-+|.|
T Consensus        15 tvairvp~~~~y~~L~~~l~~kL~l~~~~~~LsY   48 (83)
T 1oey_A           15 TVVMKTQPGLPYSQVRDMVSKKLELRLEHTKLSY   48 (83)
T ss_dssp             EEEEEECTTCCHHHHHHHHHHHTTCCGGGCCEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCcceeEEEe
Confidence            6889999999999999999999999999999988

>3uf8_A Ubiquitin-like protein SMT3, peptidyl-prolyl CIS- isomerase; ssgcid, seattle structural genomics center for in disease; HET: FK5; 1.50A {Burkholderia pseudomallei} PDB: 4ggq_C* 3vaw_A* 3uqa_A* 4g50_A* 4fn2_A* 3uqb_A* 4giv_A* 1euv_B 3v60_A 3v61_A 3v62_A*

Probab=96.45  E-value=0.0052  Score=37.49  Aligned_cols=39  Identities=15%  Similarity=0.435  Sum_probs=23.5

Q ss_pred             EEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           37 LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        37 ~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      +.+..++.+..|+...+++.|+|+++++++|.|+.+.+.
T Consensus        35 ~~i~~~~~l~kl~~~y~~~~g~~~~~~~f~fdG~~i~~~   73 (209)
T 3uf8_A           35 FKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQAD   73 (209)
T ss_dssp             EEEETTSCTHHHHHHHHHHHTCCGGGCEEEETTEECCTT
T ss_pred             EEEeeCCHHHHHHHHHHHhhCCChheEEEEECCEeccCC
Confidence            445556666666666666666666666666666665443

>2kvr_A Ubiquitin carboxyl-terminal hydrolase 7; USP7, ubiquitin-like domain, UBL, ubiquitin specific protease, HOST-virus interaction, nucleus, protease; NMR {Homo sapiens}

Probab=96.35  E-value=0.0066  Score=34.64  Aligned_cols=32  Identities=22%  Similarity=0.316  Sum_probs=28.2

Q ss_pred             EEEeeCCCcHHHHHHHhhhhhCCCcccceEEE
Q 040720            4 LLMWKAPTPLINVKAKIQDKEGIPPDQQRLIT   35 (77)
Q Consensus         4 ~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~   35 (77)
                      ++.|..++|+.+++..|++..|+|++.|||..
T Consensus        59 ~~rv~k~~~~~~~~~~va~~lg~~~~~~RlW~   90 (130)
T 2kvr_A           59 VFKVLKNSSLAEFVQSLSQTMGFPQDQIRLWP   90 (130)
T ss_dssp             EEECCTTSBHHHHHHHHHHHHCCCGGGCEEEE
T ss_pred             eEEEeccCcHHHHHHHHHHHhCCCcccEEEEE
Confidence            56788889999999999999999999999886

>3v7o_A Minor nucleoprotein VP30; ssgcid, seattle structural genomics center for infectious disease, SMT, transcription; 2.25A {Reston ebolavirus}

Probab=96.28  E-value=0.00067  Score=41.98  Aligned_cols=45  Identities=18%  Similarity=0.311  Sum_probs=0.0

Q ss_pred             EEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            4 LLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         4 ~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      .+.|.++++...|+...++..|+++..++++|.+ .+.+++|..++
T Consensus        34 ~FKIKrtTpL~KLM~AYcERqGLs~~siRFLFDGqRI~dddTPadL   79 (227)
T 3v7o_A           34 FFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDL   79 (227)
T ss_dssp             ----------------------------------------------
T ss_pred             EEEEccCChHHHHHHHHHHHhCCCccceEEEECCEecCCCCCHHHc
Confidence            3455556666666666666666666666666654 45555555554

>2jxx_A Nfatc2-interacting protein; nuclear factor of activated T-cells, cytoplasmic 2- interacting protein, ubiquitin like homologue; NMR {Homo sapiens}

Probab=96.20  E-value=0.04  Score=29.89  Aligned_cols=46  Identities=9%  Similarity=0.179  Sum_probs=27.3

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +.+.|.++++...|....++..|+++...+++|.+ .+.+++|..++
T Consensus        39 v~fkIk~~t~l~kLm~aY~~~~g~~~~~vrF~FDG~rI~~~~TP~dL   85 (97)
T 2jxx_A           39 LEVSLSRDSPLKTLMSHYEEAMGLSGRKLSFFFDGTKLSGRELPADL   85 (97)
T ss_dssp             EEEEEETTSCHHHHHHHHHHHTTCSSSCCEEEETTEECCSCSCHHHH
T ss_pred             EEEEECCCChHHHHHHHHHHHHCCCcccEEEEECCEEcCCCCCHHHc
Confidence            44555666666666666666666666666665553 55556666555

>3uf8_A Ubiquitin-like protein SMT3, peptidyl-prolyl CIS- isomerase; ssgcid, seattle structural genomics center for in disease; HET: FK5; 1.50A {Burkholderia pseudomallei} PDB: 4ggq_C* 3vaw_A* 3uqa_A* 4g50_A* 4fn2_A* 3uqb_A* 4giv_A* 1euv_B 3v60_A 3v61_A 3v62_A*

Probab=96.19  E-value=0.0041  Score=37.98  Aligned_cols=47  Identities=17%  Similarity=0.321  Sum_probs=39.8

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHHH
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNVK   49 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~lK   49 (77)
                      +.+.+..+++...|+...++..|+|+++++|+|.+ .+.+++|..++.
T Consensus        33 v~~~i~~~~~l~kl~~~y~~~~g~~~~~~~f~fdG~~i~~~~Tpk~L~   80 (209)
T 3uf8_A           33 IFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLD   80 (209)
T ss_dssp             EEEEEETTSCTHHHHHHHHHHHTCCGGGCEEEETTEECCTTCCTTTTT
T ss_pred             EEEEEeeCCHHHHHHHHHHHhhCCChheEEEEECCEeccCCCChHHhh
Confidence            56889999999999999999999999999999963 566666666553

>3v7o_A Minor nucleoprotein VP30; ssgcid, seattle structural genomics center for infectious disease, SMT, transcription; 2.25A {Reston ebolavirus}

Probab=95.77  E-value=0.0016  Score=40.31  Aligned_cols=41  Identities=15%  Similarity=0.384  Sum_probs=0.0

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+..++.+..++...+++.|+++.+++++|+|+.+.+.-
T Consensus        34 ~FKIKrtTpL~KLM~AYcERqGLs~~siRFLFDGqRI~ddd   74 (227)
T 3v7o_A           34 FFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQ   74 (227)
T ss_dssp             -----------------------------------------
T ss_pred             EEEEccCChHHHHHHHHHHHhCCCccceEEEECCEecCCCC
Confidence            45778899999999999999999999999999999997653

>2kc2_A Talin-1, F1; FERM, adhesion, cell membrane, cell projection, cytoplasm, cytoskeleton, membrane, phosphoprotein, structural protein; NMR {Mus musculus}

Probab=95.65  E-value=0.085  Score=30.02  Aligned_cols=28  Identities=14%  Similarity=0.165  Sum_probs=25.3

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcc
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPD   29 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~   29 (77)
                      ..++.|+.+.||.+++..|+.+.||+..
T Consensus        23 ~ktl~VD~S~~V~~lv~~Ic~kigI~n~   50 (128)
T 2kc2_A           23 VKTIMVDDSKTVTDMLMTICARIGITNH   50 (128)
T ss_dssp             EEEEEEEECSSHHHHHHHHHHHHTCCCC
T ss_pred             EEEEEeCCCcCHHHHHHHHHHHhCCCCc
Confidence            4688999999999999999999999844

>2jxx_A Nfatc2-interacting protein; nuclear factor of activated T-cells, cytoplasmic 2- interacting protein, ubiquitin like homologue; NMR {Homo sapiens}

Probab=95.65  E-value=0.045  Score=29.66  Aligned_cols=41  Identities=12%  Similarity=0.272  Sum_probs=36.1

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+..++.+..|....+++.|+++...+++|+|..|...-
T Consensus        40 ~fkIk~~t~l~kLm~aY~~~~g~~~~~vrF~FDG~rI~~~~   80 (97)
T 2jxx_A           40 EVSLSRDSPLKTLMSHYEEAMGLSGRKLSFFFDGTKLSGRE   80 (97)
T ss_dssp             EEEEETTSCHHHHHHHHHHHTTCSSSCCEEEETTEECCSCS
T ss_pred             EEEECCCChHHHHHHHHHHHHCCCcccEEEEECCEEcCCCC
Confidence            35677889999999999999999999999999999997653

>2ylm_A Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70A {Homo sapiens}

Probab=95.64  E-value=0.068  Score=36.75  Aligned_cols=33  Identities=21%  Similarity=0.293  Sum_probs=30.7

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEE
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLIT   35 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~   35 (77)
                      .++.|..++|+.+++.+|++..|+|++.|||+.
T Consensus        38 ~~~rv~k~~~~~~l~~~va~~lg~~~~~~RlW~   70 (530)
T 2ylm_A           38 TVFKVLKNSSLAEFVQSLSQTMGFPQDQIRLWP   70 (530)
T ss_dssp             EEEEEETTSBHHHHHHHHHHHHTSCGGGEEEEE
T ss_pred             ceEEEcCcCCHHHHHHHHHHHhCcCcccEEEEE
Confidence            367899999999999999999999999999986

>2al3_A TUG long isoform; TUG UBL1 insulin, endocytosis/exocytosis complex; NMR {Mus musculus} SCOP: d.15.1.2

Probab=94.88  E-value=0.086  Score=28.28  Aligned_cols=38  Identities=21%  Similarity=0.301  Sum_probs=21.3

Q ss_pred             EEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCc
Q 040720           37 LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKL   74 (77)
Q Consensus        37 ~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d   74 (77)
                      +.+.++.++.++=..-..++|+.+++..|.|++++|+.
T Consensus        24 VKvtp~t~L~~VL~eaC~K~gl~~~~~~Lkh~~k~lDL   61 (90)
T 2al3_A           24 VKVTPSTVLLQVLEDTCRRQDFNPSEYDLKFQRTVLDL   61 (90)
T ss_dssp             ECCCTTSBHHHHHHHHHHHTTCCGGGCEEEETTEEESS
T ss_pred             EEECCCCCHHHHHHHHHHHhCCChhhCeEEeCCEeccc
Confidence            44555555555555555555555555555566655543

>2pjh_A Protein NPL4, nuclear protein localization protein 4 homolog; UFD1, NPL4, AAA, protein binding, transport protein; NMR {Mus musculus}

Probab=94.73  E-value=0.015  Score=30.33  Aligned_cols=36  Identities=8%  Similarity=0.122  Sum_probs=29.9

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeE
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGIN   71 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~   71 (77)
                      -+++++++++.+++..|++..+++++.|.+.++..+
T Consensus        17 Ri~v~~~~t~~~L~~~I~~~~~i~~~~~~l~~~~~p   52 (80)
T 2pjh_A           17 RITATKRETAATFLKKVAKEFGFQNNGFSVYINRNK   52 (80)
T ss_dssp             ECCCCSSCCHHHHHHHHHHHTCCCTTTCCCCCSCCG
T ss_pred             EEEcCCcChHHHHHHHHHHHcCCCCCcceEEecCCC
Confidence            356789999999999999999999888877665544

>3ix6_A TS, tsase, thymidylate synthase; niaid, ssgcid, seattle structural center for infectious DISE brucellosis, orchitis, epididymitis, mastitis; 2.20A {Brucella melitensis}

Probab=94.36  E-value=0.0073  Score=39.87  Aligned_cols=36  Identities=17%  Similarity=0.491  Sum_probs=0.0

Q ss_pred             EecCCccHHHHHHHHhhccCCCccceEEEECCeEcC
Q 040720           38 EVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK   73 (77)
Q Consensus        38 ~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~   73 (77)
                      .+..++.+..++...+++.|+++++++++|+|+.+.
T Consensus        36 kIk~~t~l~kLm~aY~~r~G~~~~~~rFlFdG~rI~   71 (360)
T 3ix6_A           36 KIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQ   71 (360)
T ss_dssp             ------------------------------------
T ss_pred             EEecCChHHHHHHHHHHHhCCCcceEEEEECCeECC
Confidence            334444444444444444444444444445444443

>2l76_A Nfatc2-interacting protein; ubiquitin-like domain, structural genomics, PSI-biology, Pro structure initiative; NMR {Homo sapiens}

Probab=93.82  E-value=0.2  Score=27.14  Aligned_cols=37  Identities=19%  Similarity=0.416  Sum_probs=18.9

Q ss_pred             EecCCccHHHHHHHHhhccCCCccceEEEECCeEcCc
Q 040720           38 EVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKL   74 (77)
Q Consensus        38 ~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d   74 (77)
                      .+..++.+..+....+.+.|++++..+++|+|..+.+
T Consensus        36 kIK~tt~l~KL~~aYc~r~gv~~~sirFlfDG~rI~~   72 (95)
T 2l76_A           36 PLRMSEPLQSVVDHMATHLGVSPSRILLLFGETELSP   72 (95)
T ss_dssp             EECSSSCTHHHHHHHHHHHTSCGGGEEEEETTEECCT
T ss_pred             EEecCChHHHHHHHHHhhcCCChhhEEEEECCcCCCC
Confidence            3444445555555555555555555555555555443

>2l76_A Nfatc2-interacting protein; ubiquitin-like domain, structural genomics, PSI-biology, Pro structure initiative; NMR {Homo sapiens}

Probab=93.80  E-value=0.15  Score=27.62  Aligned_cols=46  Identities=20%  Similarity=0.302  Sum_probs=41.5

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +-+.+..++....|....++..|+++...++.|.+ .+.+++|..+|
T Consensus        33 v~FkIK~tt~l~KL~~aYc~r~gv~~~sirFlfDG~rI~~~~TP~~L   79 (95)
T 2l76_A           33 VRLPLRMSEPLQSVVDHMATHLGVSPSRILLLFGETELSPTATPRTL   79 (95)
T ss_dssp             EEEEECSSSCTHHHHHHHHHHHTSCGGGEEEEETTEECCTTSCHHHH
T ss_pred             EEEEEecCChHHHHHHHHHhhcCCChhhEEEEECCcCCCCCCCHhHc
Confidence            45677888999999999999999999999999984 89999999998

>2al3_A TUG long isoform; TUG UBL1 insulin, endocytosis/exocytosis complex; NMR {Mus musculus} SCOP: d.15.1.2

Probab=93.70  E-value=0.4  Score=25.65  Aligned_cols=48  Identities=17%  Similarity=0.102  Sum_probs=39.0

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEE-EEecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITT-LEVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~-~~v~~~~tv~~l   48 (77)
                      |...+.|.|+.|+.+|=+.-.++.|+.+++-.|.|. -.++.+....-.
T Consensus        20 rr~~VKvtp~t~L~~VL~eaC~K~gl~~~~~~Lkh~~k~lDLSlpfRls   68 (90)
T 2al3_A           20 RRHTVKVTPSTVLLQVLEDTCRRQDFNPSEYDLKFQRTVLDLSLQWRFA   68 (90)
T ss_dssp             CEEEECCCTTSBHHHHHHHHHHHTTCCGGGCEEEETTEEESSSCBHHHH
T ss_pred             cEEEEEECCCCCHHHHHHHHHHHhCCChhhCeEEeCCEeccccceeEec
Confidence            467899999999999999999999999999988886 356666554443

>2kvr_A Ubiquitin carboxyl-terminal hydrolase 7; USP7, ubiquitin-like domain, UBL, ubiquitin specific protease, HOST-virus interaction, nucleus, protease; NMR {Homo sapiens}

Probab=93.45  E-value=0.094  Score=29.80  Aligned_cols=31  Identities=23%  Similarity=0.421  Sum_probs=28.3

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEE
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLI   66 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~   66 (77)
                      .+.+..+.++.+++..|+...|+|++++||-
T Consensus        59 ~~rv~k~~~~~~~~~~va~~lg~~~~~~RlW   89 (130)
T 2kvr_A           59 VFKVLKNSSLAEFVQSLSQTMGFPQDQIRLW   89 (130)
T ss_dssp             EEECCTTSBHHHHHHHHHHHHCCCGGGCEEE
T ss_pred             eEEEeccCcHHHHHHHHHHHhCCCcccEEEE
Confidence            4688889999999999999999999999964

>4da1_A Protein phosphatase 1K, mitochondrial; metal-ION-assisted catalysis, dehydrogenase phosphatase, hydrolase; 2.38A {Homo sapiens} PDB: 3qht_A 1l2n_A

Probab=92.84  E-value=0.019  Score=37.71  Aligned_cols=43  Identities=16%  Similarity=0.281  Sum_probs=0.0

Q ss_pred             EEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHH
Q 040720            5 LMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINN   47 (77)
Q Consensus         5 ~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~   47 (77)
                      +.|.++++...|+...+++.|+++.++++.|.+ .+.++.|..+
T Consensus        44 ~~i~~~~~~~~l~~~y~~~~g~~~~~~~f~f~G~~i~~~~Tp~~   87 (389)
T 4da1_A           44 FKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQAPED   87 (389)
T ss_dssp             --------------------------------------------
T ss_pred             EEECCCChHHHHHHHHHHHhCCCcceEEEEECCEEcCCCCCHHH
Confidence            444455555555555555555555555555543 3344444433

>4da1_A Protein phosphatase 1K, mitochondrial; metal-ION-assisted catalysis, dehydrogenase phosphatase, hydrolase; 2.38A {Homo sapiens} PDB: 3qht_A 1l2n_A

Probab=92.81  E-value=0.02  Score=37.68  Aligned_cols=41  Identities=15%  Similarity=0.384  Sum_probs=0.0

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+..++.+..|+....++.|+++.++++.|+|+.+.+..
T Consensus        43 ~~~i~~~~~~~~l~~~y~~~~g~~~~~~~f~f~G~~i~~~~   83 (389)
T 4da1_A           43 FFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQ   83 (389)
T ss_dssp             -----------------------------------------
T ss_pred             EEEECCCChHHHHHHHHHHHhCCCcceEEEEECCEEcCCCC
Confidence            46778899999999999999999999999999999987653

>4a3p_A Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {Homo sapiens} PDB: 4a3o_A 3pv1_A 3ppa_A* 3t9l_A 3lmn_A

Probab=92.79  E-value=0.97  Score=27.47  Aligned_cols=59  Identities=17%  Similarity=0.293  Sum_probs=43.4

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcc-cceEEEE-----E-Eec-CCccHHHHHHHHhhccCCCccceEEE-ECC
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPD-QQRLITT-----L-EVK-SSDTINNVKSKIQDKEGIPPDQQRLI-FAG   69 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~-~q~L~~~-----~-~v~-~~~tv~~lK~~i~~~~gip~~~q~l~-~~g   69 (77)
                      +++.++..+||.+|+.++....++|++ .-||...     . .+. .+.|+.++        ++..+|+.|+ +.+
T Consensus       142 ~~~~~Sk~~ti~~l~~~~~~~~~i~~~~~~RlW~~~~~~~~~~L~~~~~tl~~~--------~l~~~Q~illE~r~  209 (217)
T 4a3p_A          142 VTRRFSKADTIDTIEKEIRKIFSIPDEKETRLWNKYMSNTFEPLNKPDSTIQDA--------GLYQGQVLVIEQKN  209 (217)
T ss_dssp             EEEEECTTSBHHHHHHHHHHHTTCCTTSCEEEEEEEETTEEEECCCTTSBHHHH--------TCCTTCEEEEEECC
T ss_pred             eEEEEcccchHHHHHHHHHHHhCCCCCCceEEEEecCCCCeeecCCCCCCHHHh--------CCCCCCEEEEEEec
Confidence            467789999999999999999999987 6888641     2 233 35688887        6666666654 444

>3ix6_A TS, tsase, thymidylate synthase; niaid, ssgcid, seattle structural center for infectious DISE brucellosis, orchitis, epididymitis, mastitis; 2.20A {Brucella melitensis}

Probab=92.65  E-value=0.021  Score=37.69  Aligned_cols=47  Identities=17%  Similarity=0.321  Sum_probs=0.0

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHHH
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNVK   49 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~lK   49 (77)
                      +.+.|.++++...|+...++..|++++.+++.|.+ .+.+++|..++.
T Consensus        33 v~FkIk~~t~l~kLm~aY~~r~G~~~~~~rFlFdG~rI~~~~TP~~L~   80 (360)
T 3ix6_A           33 IFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLD   80 (360)
T ss_dssp             ------------------------------------------------
T ss_pred             EEEEEecCChHHHHHHHHHHHhCCCcceEEEEECCeECCCCCChHHcC
Confidence            56788999999999999999999999999999986 789999999984

>4eut_A Serine/threonine-protein kinase TBK1; ATP binding, phosphorylation, transferase-transferas inhibitor complex; HET: BX7; 2.60A {Homo sapiens}

Probab=92.15  E-value=0.21  Score=32.28  Aligned_cols=32  Identities=13%  Similarity=0.068  Sum_probs=17.7

Q ss_pred             EEEeeCCCcHHHHHHHhhhhhCCCcccceEEE
Q 040720            4 LLMWKAPTPLINVKAKIQDKEGIPPDQQRLIT   35 (77)
Q Consensus         4 ~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~   35 (77)
                      .+.+.+.+|+.++++++++..|++++.|.|.+
T Consensus       325 ~~~~~~~~~~~~~~~~~~~~t~i~~~~q~~l~  356 (396)
T 4eut_A          325 KIYIHSYNTATIFHELVYKQTKIISSNQELIY  356 (396)
T ss_dssp             EEEECTTCBHHHHHHHHHHHHCCCSTTEEEES
T ss_pred             EEEcCchhHHHHHHHHHHHhcCCChhhhHHHh
Confidence            34445555555555555555555555555554

>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=91.60  E-value=0.31  Score=28.09  Aligned_cols=27  Identities=19%  Similarity=0.278  Sum_probs=22.0

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhh--hCCCc
Q 040720            2 RLLLMWKAPTPLINVKAKIQDK--EGIPP   28 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~--~gi~~   28 (77)
                      .+++.|-.+|||.++|+||-+.  .|+|.
T Consensus        42 ~i~VkVLdCDTItQvKeKiLDavYk~~Py   70 (138)
T 2r2o_A           42 GVPVKVLDCDTISQAKEKMLDQLYKGVPL   70 (138)
T ss_dssp             CEEEEEETTCBHHHHHHHHHHHHTTTSCG
T ss_pred             ceeEEEeccccHHHHHHHHHHHHHcCCcc
Confidence            3678888999999999999765  66664

>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=90.28  E-value=1.1  Score=27.56  Aligned_cols=33  Identities=15%  Similarity=0.335  Sum_probs=28.0

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcc-cceEEE
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPD-QQRLIT   35 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~-~q~L~~   35 (77)
                      ++..++..+||.+|+.++....+|+++ .-||..
T Consensus       154 ~~~~~Sk~~ti~~l~~~~~~~~~i~~~~~~RLW~  187 (231)
T 3jyu_A          154 LSCHFSKADTIATIEKEMRKLFNIPAERETRLWN  187 (231)
T ss_dssp             EEEEECTTCBHHHHHHHHHHHTTCCTTSCEEEEE
T ss_pred             EEEEecccCcHHHHHHHHHHHhCCCCCCeEEEEE
Confidence            456678899999999999999999987 588865

>4e74_A Plexin-A4; RBD, structural genomics, structural genomics consor SGC, signaling protein; 1.58A {Homo sapiens} PDB: 3q3j_A*

Probab=90.27  E-value=0.49  Score=26.49  Aligned_cols=27  Identities=22%  Similarity=0.271  Sum_probs=21.6

Q ss_pred             EEEEeeCCCcHHHHHHHhhhh--hCCCcc
Q 040720            3 LLLMWKAPTPLINVKAKIQDK--EGIPPD   29 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~--~gi~~~   29 (77)
                      +++.|-.+|||.++|+||-..  .|.|..
T Consensus        29 i~VkVLdCDTItQvKeKiLd~vyk~~p~S   57 (117)
T 4e74_A           29 VPVKILNCDTITQVKEKILDAIFKNVPCS   57 (117)
T ss_dssp             EEEEEETTSBHHHHHHHHHHHHTTTSCGG
T ss_pred             eEeeeecCCchHHHHHHHHHHHhcCCCcc
Confidence            678888999999999999654  566643

>3qa8_A MGC80376 protein; kinase ubiquitin-like domain, phosphorylation, kinase domain ubiquitin-like domain, kinase, substrate binding; 3.60A {Xenopus laevis} PDB: 3qad_A* 3rzf_A*

Probab=89.72  E-value=0.28  Score=34.77  Aligned_cols=45  Identities=22%  Similarity=0.347  Sum_probs=33.7

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE--EecCCccHHH
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL--EVKSSDTINN   47 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~--~v~~~~tv~~   47 (77)
                      +.+.+.+..|+.+++..|++.+|||++.|.+++..  .+.++....+
T Consensus       324 ~~~~i~~~~tl~~l~~~i~~~T~i~~~~q~~~~~~~~~~~p~~~~~~  370 (676)
T 3qa8_A          324 HTYPVTENENLQNLKSWLQQDTGIPEEEQELLQASGLALNSAQPLTQ  370 (676)
T ss_dssp             CEEECCTTCCHHHHHHHHHTTSCCCSTTCEEESSSSCCCCTTSCGGG
T ss_pred             ceeecCCCccHHHHHHHHHHHhCCCHHHHHHHhccCCCCCCCcchhh
Confidence            45678889999999999999999999999988752  3344444333

>4e71_A Plexin-B2, MM1; transmembrane, signaling, RBD, structural genomics consortium, SGC, signaling protein; 2.26A {Homo sapiens}

Probab=89.38  E-value=0.39  Score=26.64  Aligned_cols=27  Identities=26%  Similarity=0.283  Sum_probs=18.9

Q ss_pred             EEEEeeCCCcHHHHHHHhhhh--hCCCcc
Q 040720            3 LLLMWKAPTPLINVKAKIQDK--EGIPPD   29 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~--~gi~~~   29 (77)
                      +++.|-.+|||.++|+||-..  .|.|..
T Consensus        26 i~vkVLdCDTItQvKeKiLd~vyk~~pyS   54 (111)
T 4e71_A           26 IPVKVLNCDTISQVKEKIIDQVYRGQPCS   54 (111)
T ss_dssp             EEEEEETTCBHHHHHHHHHHHHTC-----
T ss_pred             eeeeeeccCcHHHHHHHHHHHHHcCCccc
Confidence            678888999999999999654  566643

>3h6n_A Plexin-D1; structural genomics consortium, SGC, membrane, transmembrane, receptor, alternative splicing, cell membrane, glycoprotein, polymorphism; 2.00A {Homo sapiens}

Probab=88.39  E-value=0.8  Score=25.98  Aligned_cols=26  Identities=27%  Similarity=0.318  Sum_probs=21.1

Q ss_pred             EEEEeeCCCcHHHHHHHhhhh--hCCCc
Q 040720            3 LLLMWKAPTPLINVKAKIQDK--EGIPP   28 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~--~gi~~   28 (77)
                      +++.|-.+|||.++|+||-+.  .|.|.
T Consensus        19 i~VkVLdCDTItQvKeKiLd~vyk~~p~   46 (127)
T 3h6n_A           19 LSVRAMDTDTLTQVKEKILEAFCKNVPY   46 (127)
T ss_dssp             EEEEEETTSBHHHHHHHHHHHHSTTSCG
T ss_pred             eeeeeeccCchhhhhHHHHHHHhccCCc
Confidence            678888999999999999655  56654

>3kuz_A Plexin-C1; structural genomics, structural genomics consortium, SGC; 2.30A {Homo sapiens}

Probab=88.12  E-value=0.58  Score=26.53  Aligned_cols=28  Identities=18%  Similarity=0.125  Sum_probs=22.3

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhh----hCCCcc
Q 040720            2 RLLLMWKAPTPLINVKAKIQDK----EGIPPD   29 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~----~gi~~~   29 (77)
                      .+++.|-.+|||.++|+||-..    .|+|..
T Consensus        40 ~v~VkVLdCDTItQVKEKILdavYk~k~~pys   71 (126)
T 3kuz_A           40 NISVNVLDCDTIGQAKEKIFQAFLSKNGSPYG   71 (126)
T ss_dssp             EEEEEEETTCBHHHHHHHHHHHHHHHHSSCCS
T ss_pred             ceEeeeecCCcHHHHHHHHHHHHhccCCCcCC
Confidence            3678889999999999999543    488753

>1oey_A P67-PHOX, neutrophil cytosol factor 2; immune system, PB1 heterodimer/complex, NADPH oxidase, PB1 D heterodimerization; 2.0A {Homo sapiens} SCOP: d.15.2.2

Probab=86.93  E-value=1.6  Score=22.85  Aligned_cols=36  Identities=8%  Similarity=0.194  Sum_probs=32.3

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCe
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGI   70 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~   70 (77)
                      +++.++.+.+..++..+|.++.++|++.-.|.|...
T Consensus        16 vairvp~~~~y~~L~~~l~~kL~l~~~~~~LsYk~~   51 (83)
T 1oey_A           16 VVMKTQPGLPYSQVRDMVSKKLELRLEHTKLSYRPR   51 (83)
T ss_dssp             EEEEECTTCCHHHHHHHHHHHTTCCGGGCCEEECCT
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCCcceeEEEeeCC
Confidence            467899999999999999999999999888998764

>2ylm_A Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70A {Homo sapiens}

Probab=84.18  E-value=1.1  Score=30.73  Aligned_cols=31  Identities=23%  Similarity=0.421  Sum_probs=28.4

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEE
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLI   66 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~   66 (77)
                      .+.+..+.++.+++..|++..|+|+++|||-
T Consensus        39 ~~rv~k~~~~~~l~~~va~~lg~~~~~~RlW   69 (530)
T 2ylm_A           39 VFKVLKNSSLAEFVQSLSQTMGFPQDQIRLW   69 (530)
T ss_dssp             EEEEETTSBHHHHHHHHHHHHTSCGGGEEEE
T ss_pred             eEEEcCcCCHHHHHHHHHHHhCcCcccEEEE
Confidence            4688899999999999999999999999964

>4eut_A Serine/threonine-protein kinase TBK1; ATP binding, phosphorylation, transferase-transferas inhibitor complex; HET: BX7; 2.60A {Homo sapiens}

Probab=82.37  E-value=2.6  Score=27.06  Aligned_cols=35  Identities=20%  Similarity=0.289  Sum_probs=31.5

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCe
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGI   70 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~   70 (77)
                      .+.+.+..++.+++..++...+++++.|.+++.+.
T Consensus       325 ~~~~~~~~~~~~~~~~~~~~t~i~~~~q~~l~~~~  359 (396)
T 4eut_A          325 KIYIHSYNTATIFHELVYKQTKIISSNQELIYEGR  359 (396)
T ss_dssp             EEEECTTCBHHHHHHHHHHHHCCCSTTEEEESSSS
T ss_pred             EEEcCchhHHHHHHHHHHHhcCCChhhhHHHhcCC
Confidence            45677889999999999999999999999999983

---

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	77
d1wjna_	97	d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse	8e-12
d2c9wb1	103	d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens)	5e-11
d2c9wb1	103	d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens)	0.002
d1uh6a_	100	d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mous	2e-10
d1uh6a_	100	d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mous	0.001
d1zkha1	86	d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-t	5e-10
d1ogwa_	76	d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [Tax	9e-10
d1wgha_	116	d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mous	1e-09
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	0.003
d1wgda_	93	d.15.1.1 (A:) Homocysteine-responsive endoplasmic	1e-09
d1wxva1	81	d.15.1.1 (A:7-87) Bag-family molecular chaperone r	2e-09
d1wxva1	81	d.15.1.1 (A:7-87) Bag-family molecular chaperone r	1e-04
d1wx9a1	73	d.15.1.1 (A:8-80) Large proline-rich protein BAT3	4e-09
d1wy8a1	76	d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING fing	5e-09
d1wy8a1	76	d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING fing	0.003
d2zeqa1	78	d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin	5e-09
d1wh3a_	87	d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like	7e-09
d2faza1	76	d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING fing	7e-09
d2faza1	76	d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING fing	8e-04
d1bt0a_	73	d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis t	8e-09
d1v2ya_	105	d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik	4e-08
d1v6ea_	95	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	6e-08
d1v6ea_	95	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	3e-04
d1t0ya_	90	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	7e-08
d1t0ya_	90	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	3e-04
d1z2ma2	76	d.15.1.1 (A:79-154) Interferon-induced 15 kDa prot	8e-08
d1oqya4	77	d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 h	1e-07
d1v5oa_	102	d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus mu	1e-07
d1wx8a1	83	d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus muscul	3e-07
d1v5ta_	90	d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus mu	3e-07
d1wiaa_	95	d.15.1.1 (A:) Ubiquitin-like protein bab25500 (201	3e-07
d1z2ma1	76	d.15.1.1 (A:3-78) Interferon-induced 15 kDa protei	3e-07
d1wjua_	100	d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human	5e-07
d1v86a_	95	d.15.1.1 (A:) hypothetical D7wsu128e protein {Mous	6e-07
d1euvb_	79	d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yea	1e-06
d1j8ca_	103	d.15.1.1 (A:) Ubiquitin-like N-terminal domain of	1e-06
d1uela_	95	d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homol	1e-06
d1se9a_	101	d.15.1.1 (A:) Hypothetical protein At3g01050 {Thal	2e-06
d1ttna1	80	d.15.1.1 (A:21-100) Dendritic cell-derived ubiquit	4e-06
d2uyzb1	77	d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human	5e-06
d1yqba1	84	d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapien	7e-06
d1x1ma1	94	d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse	5e-05
d1m94a_	73	d.15.1.1 (A:) Ubiquitin-like modifier protein hub1	4e-04
d1wgga_	96	d.15.1.1 (A:) Ubiquitin carboxyl-terminal hydrolas	0.002
d1we6a_	111	d.15.1.1 (A:) Splicing factor 3 subunit 1, C-termi	0.003

>d1wjna_ d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Tubulin-folding protein TbcE
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.4 bits (128), Expect = 8e-12
 Identities = 8/52 (15%), Positives = 17/52 (32%)

Query: 26 IPPDQQRLITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVVR 77
               +R I   ++  S T+  VK  +     +P  +  L +    +     
Sbjct: 16 CSNQPERQILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSKMPGREI 67

>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 = 51.4 bits (123), Expect = 5e-11
 Identities = 11/43 (25%), Positives = 18/43 (41%)

Query: 31 QRLITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
           +     + K S T+  +K  ++     PPD+QRL      L 
Sbjct: 9  HKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLD 51

>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 = 31.7 bits (72), Expect = 0.002
 Identities = 7/20 (35%), Positives = 11/20 (55%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
           +K  ++     PPD+QRL 
Sbjct: 25 ELKRIVEGILKRPPDEQRLY 44

>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 = 50.0 bits (119), Expect = 2e-10
 Identities = 8/38 (21%), Positives = 16/38 (42%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
           ++  + DTI ++K  I  + G   ++  L       K
Sbjct: 42 RVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFK 79

>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 = 32.3 bits (73), Expect = 0.001
 Identities = 4/20 (20%), Positives = 9/20 (45%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
          ++K  I  + G   ++  L 
Sbjct: 53 DLKKLIAAQTGTRWNKIVLK 72

>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 = 48.3 bits (115), Expect = 5e-10
 Identities = 13/60 (21%), Positives = 29/60 (48%), Gaps = 1/60 (1%)

Query: 14 INVKAKIQDKEGIPPDQQRLITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          I V+      +       +++    +  +D ++ +K KI +  G+P  +Q+L + GI +K
Sbjct: 4  IKVQVPNMQDKTEWKLNGQVLV-FTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIK 62

>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 = 47.6 bits (113), Expect = 9e-10
 Identities = 30/34 (88%), Positives = 32/34 (94%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG 69
          TLEV+ SDTI NVK+KIQDKEGIPPDQQRLIFAG
Sbjct: 14 TLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAG 47

>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 = 48.4 bits (115), Expect = 1e-09
 Identities = 10/73 (13%), Positives = 27/73 (36%), Gaps = 17/73 (23%)

Query: 9  APTPLINVKAKIQDKEGIPPDQQRLITTLEVKSSDTINNVKSKI--------QDKEGIPP 60
           P  +IN++  +   +                 +D+ +++   +        ++++   P
Sbjct: 12 VPADMINLRLILVSGKTK---------EFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSP 62

Query: 61 DQQRLIFAGINLK 73
          +  RLI+ G  L 
Sbjct: 63 NILRLIYQGRFLH 75

>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 = 47.1 bits (112), Expect = 1e-09
 Identities = 14/38 (36%), Positives = 18/38 (47%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
           + V    T+   K  I    GIP   QRLI++G  LK
Sbjct: 14 EVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILK 51

>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 = 30.9 bits (70), Expect = 0.003
 Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 12/49 (24%)

Query: 15 NVKAKIQDKEGIPPDQQRLI---------TTLE---VKSSDTINNVKSK 51
            K  I    GIP   QRLI          T+E   ++   +++ VKS+
Sbjct: 25 QFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKSQ 73

>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 = 47.5 bits (113), Expect = 1e-09
 Identities = 11/48 (22%), Positives = 22/48 (45%), Gaps = 2/48 (4%)

Query: 28 PDQQRLITTLEVKSSDTINNVKSKIQDKEG--IPPDQQRLIFAGINLK 73
          P+Q+     L      ++ ++K+ +         P+ QRLI++G  L 
Sbjct: 15 PNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLL 62

>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 = 46.8 bits (111), Expect = 2e-09
 Identities = 11/40 (27%), Positives = 23/40 (57%)

Query: 34 ITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          +T+ +  S   + ++   +++  G+P   Q+LIF G +LK
Sbjct: 17 VTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLK 56

>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 = 34.5 bits (79), Expect = 1e-04
 Identities = 5/20 (25%), Positives = 12/20 (60%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
          ++   +++  G+P   Q+LI
Sbjct: 30 DLAQVVEEVIGVPQSFQKLI 49

>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 = 46.0 bits (109), Expect = 4e-09
 Identities = 12/38 (31%), Positives = 18/38 (47%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          T  V +   +   K  I     IP ++QRLI+ G  L+
Sbjct: 14 TFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQ 51

>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 = 45.7 bits (108), Expect = 5e-09
 Identities = 11/44 (25%), Positives = 20/44 (45%)

Query: 29 DQQRLITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINL 72
          D  +  T  +V    TI  ++ ++     + P+ QRL + G  L
Sbjct: 9  DGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQL 52

>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 = 31.0 bits (70), Expect = 0.003
 Identities = 4/20 (20%), Positives = 10/20 (50%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
           ++ ++     + P+ QRL 
Sbjct: 27 ELRERVWALFDVRPECQRLF 46

>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 = 45.7 bits (108), Expect = 5e-09
 Identities = 15/38 (39%), Positives = 23/38 (60%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
           +EV S  +I  +K  +  ++G+P DQ R+IFAG  L 
Sbjct: 16 PVEVDSDTSILQLKEVVAKRQGVPADQLRVIFAGKELP 53

>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 = 45.7 bits (108), Expect = 7e-09
 Identities = 12/38 (31%), Positives = 22/38 (57%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
             +  +  I  +K +I+D++G+P  QQ+L F G  L+
Sbjct: 21 AYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQ 58

>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 = 45.3 bits (107), Expect = 7e-09
 Identities = 9/39 (23%), Positives = 18/39 (46%)

Query: 29 DQQRLITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIF 67
          D ++  T   +     +  ++ KIQ+   + P  QRL +
Sbjct: 9  DGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFY 47

>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 = 32.6 bits (74), Expect = 8e-04
 Identities = 7/20 (35%), Positives = 11/20 (55%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
           ++ KIQ+   + P  QRL 
Sbjct: 27 ELRRKIQELFHVEPGLQRLF 46

>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 = 45.2 bits (107), Expect = 8e-09
 Identities = 18/38 (47%), Positives = 30/38 (78%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
           ++++ +DTI+ +K ++++KEGIPP QQRLI+AG  L 
Sbjct: 14 EIDIEPTDTIDRIKERVEEKEGIPPVQQRLIYAGKQLA 51

>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 = 44.3 bits (104), Expect = 4e-08
 Identities = 9/52 (17%), Positives = 18/52 (34%), Gaps = 15/52 (28%)

Query: 37 LEVKSSDTINNVKSKIQDKEGIPPDQQR---------------LIFAGINLK 73
          + V  + T+ ++K  IQ    +  +++                L  AG  L 
Sbjct: 22 VVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEKLT 73

>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 = 43.4 bits (102), Expect = 6e-08
 Identities = 10/41 (24%), Positives = 14/41 (34%)

Query: 35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV 75
          +      S TI   K K++   G P     L   G + K  
Sbjct: 21 SEKRYSRSLTIAEFKCKLELVVGSPASCMELELYGADDKFY 61

>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 = 34.1 bits (78), Expect = 3e-04
 Identities = 5/23 (21%), Positives = 8/23 (34%)

Query: 12 PLINVKAKIQDKEGIPPDQQRLI 34
           +   K K++   G P     L 
Sbjct: 30 TIAEFKCKLELVVGSPASCMELE 52

>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 = 43.3 bits (102), Expect = 7e-08
 Identities = 7/37 (18%), Positives = 17/37 (45%)

Query: 39 VKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV 75
            +  ++N++K K++   G   D  R+     + +L 
Sbjct: 22 YPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLK 58

>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 = 33.7 bits (77), Expect = 3e-04
 Identities = 5/20 (25%), Positives = 10/20 (50%)

Query: 15 NVKAKIQDKEGIPPDQQRLI 34
          ++K K++   G   D  R+ 
Sbjct: 30 DLKKKLELVVGTTVDSMRIQ 49

>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 = 42.6 bits (100), Expect = 8e-08
 Identities = 12/38 (31%), Positives = 21/38 (55%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          T EV+ + T+ ++K ++   EG+  D   L F G  L+
Sbjct: 17 TYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLE 54

>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 = 42.2 bits (99), Expect = 1e-07
 Identities = 12/41 (29%), Positives = 23/41 (56%), Gaps = 3/41 (7%)

Query: 36 TLEVKSSDTINNVKSKIQDKEG---IPPDQQRLIFAGINLK 73
           + ++  +T+  +K KI+ ++G    P   Q+LI+AG  L 
Sbjct: 16 KIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILS 56

>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 = 42.7 bits (100), Expect = 1e-07
 Identities = 5/34 (14%), Positives = 19/34 (55%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG 69
          +L+V     ++N +   + + G+P ++ ++++  
Sbjct: 25 SLQVNPDFELSNFRVLCELESGVPAEEAQIVYME 58

>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 = 41.5 bits (97), Expect = 3e-07
 Identities = 8/39 (20%), Positives = 14/39 (35%)

Query: 35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
              +  +  +   K +I        D+  LIF G  L+
Sbjct: 22 HEFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILR 60

>d1v5ta_ d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 90

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 8430435i17rik protein
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.5 bits (97), Expect = 3e-07
 Identities = 8/41 (19%), Positives = 21/41 (51%)

Query: 34 ITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKL 74
           +   +   DT+ ++K  ++   G+ P++Q+L+   +  K 
Sbjct: 19 YSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKP 59

>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 = 41.8 bits (98), Expect = 3e-07
 Identities = 9/34 (26%), Positives = 15/34 (44%), Gaps = 3/34 (8%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG 69
              +  DT+  +KSK    +     Q +LI+ G
Sbjct: 21 LAVARPEDTVGTLKSKYFPGQ---ESQMKLIYQG 51

>d1z2ma1 d.15.1.1 (A:3-78) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.0 bits (96), Expect = 3e-07
 Identities = 10/32 (31%), Positives = 19/32 (59%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIF 67
           + + SS +++ +K++I  K G+   QQRL  
Sbjct: 14 QVSLSSSMSVSELKAQITQKIGVHAFQQRLAV 45

>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 = 41.1 bits (96), Expect = 5e-07
 Identities = 8/37 (21%), Positives = 17/37 (45%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINL 72
           LE +   T   ++SKI +  G+  +  +++     L
Sbjct: 33 LLETRLHITGRELRSKIAETFGLQENYIKIVINKKQL 69

>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 = 40.7 bits (95), Expect = 6e-07
 Identities = 10/36 (27%), Positives = 20/36 (55%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGIN 71
           ++V    T + +K KI    G+PP  Q++++ G+ 
Sbjct: 30 DVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGLV 65

>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 = 39.8 bits (93), Expect = 1e-06
 Identities = 11/64 (17%), Positives = 23/64 (35%), Gaps = 10/64 (15%)

Query: 10 PTPLINVKAKIQDKEGIPPDQQRLITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAG 69
          P   IN+K      E             ++K +  +  +      ++G   D  R ++ G
Sbjct: 1  PETHINLKVSDGSSE----------IFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDG 50

Query: 70 INLK 73
          I ++
Sbjct: 51 IRIQ 54

>d1j8ca_ d.15.1.1 (A:) Ubiquitin-like N-terminal domain of PLIC-2 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like N-terminal domain of PLIC-2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.0 bits (93), Expect = 1e-06
 Identities = 14/60 (23%), Positives = 21/60 (35%), Gaps = 12/60 (20%)

Query: 9  APTPLINVKAK-IQDKEGIPPDQQRLITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIF 67
          A   +I V  K  ++KE              V  + ++   K  I  +     DQ  LIF
Sbjct: 28 AEPKIIKVTVKTPKEKE-----------EFAVPENSSVQQFKEAISKRFKSQTDQLVLIF 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 = 40.0 bits (93), Expect = 1e-06
 Identities = 11/41 (26%), Positives = 22/41 (53%), Gaps = 3/41 (7%)

Query: 36 TLEVKSSDTINNVKSKIQDK---EGIPPDQQRLIFAGINLK 73
           +++   +T+  +K KI+ +   +  P   Q+LI+AG  L 
Sbjct: 14 KIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILN 54

>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 = 39.9 bits (93), Expect = 2e-06
 Identities = 10/43 (23%), Positives = 17/43 (39%), Gaps = 7/43 (16%)

Query: 34 ITTLEVKSSDTINNVKSKIQD-----KEGIP--PDQQRLIFAG 69
          I       + T++ +K  +       KE  P    + +LI AG
Sbjct: 20 IGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAG 62

>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 = 38.4 bits (89), Expect = 4e-06
 Identities = 14/38 (36%), Positives = 23/38 (60%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
           L V+S+DT+ ++K ++   EG+ P  QR  F+G  L 
Sbjct: 17 KLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLT 54

>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 = 38.2 bits (89), Expect = 5e-06
 Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 9/60 (15%)

Query: 14 INVKAKIQDKEGIPPDQQRLITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
          I +K   QD   I           +VK +  +  +K     ++G+P +  R +F G  + 
Sbjct: 3  IKLKVIGQDSSEI---------HFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIA 53

>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 = 38.1 bits (88), Expect = 7e-06
 Identities = 11/33 (33%), Positives = 15/33 (45%)

Query: 35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIF 67
              V  + TI  +K +I  +    PDQ  LIF
Sbjct: 19 EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIF 51

>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 = 36.0 bits (83), Expect = 5e-05
 Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 3/38 (7%)

Query: 39 VKSSDTINNVKSKIQDK--EGIP-PDQQRLIFAGINLK 73
               +I+ +K  I  K  E +P P+   LI+ G  LK
Sbjct: 34 SLGGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLK 71

>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 = 33.1 bits (75), Expect = 4e-04
 Identities = 5/32 (15%), Positives = 15/32 (46%)

Query: 36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIF 67
           ++  + D++ + K  +  + G  P++  L  
Sbjct: 15 RVKCLAEDSVGDFKKVLSLQIGTQPNKIVLQK 46

>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 = 31.9 bits (72), Expect = 0.002
 Identities = 8/40 (20%), Positives = 20/40 (50%)

Query: 34 ITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLK 73
             +E+ + +     K+++    G+ P +Q+++  G  LK
Sbjct: 19 FEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLK 58

>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 = 31.5 bits (71), Expect = 0.003
 Identities = 10/36 (27%), Positives = 20/36 (55%), Gaps = 1/36 (2%)

Query: 34 ITTLEVKS-SDTINNVKSKIQDKEGIPPDQQRLIFA 68
             + V+S S+ + ++K KI  +  IP ++Q+L   
Sbjct: 42 FMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGK 77

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	77
d1wx9a1	73	Large proline-rich protein BAT3 {Human (Homo sapie	99.42
d2zeqa1	78	Ubiquitin-like domain of parkin {Mouse (Mus muscul	99.41
d1m94a_	73	Ubiquitin-like modifier protein hub1 {Baker's yeas	99.38
d1bt0a_	73	Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxI	99.38
d1wh3a_	87	2'-5'-oligoadenylate synthetase-like protein, OASL	99.38
d1z2ma2	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.35
d1ogwa_	76	Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}	99.34
d1uh6a_	100	Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculu	99.32
d2bwfa1	73	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.32
d1ttna1	80	Dendritic cell-derived ubiquitin-like protein {Hum	99.31
d2c9wb1	103	Elongin B {Human (Homo sapiens) [TaxId: 9606]}	99.3
d1zkha1	86	Splicing factor 3 subunit 1, C-terminal domain {Hu	99.3
d1z2ma1	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.3
d2bwfa1	73	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.29
d1wy8a1	76	Ubiquitin-like PHD and RING finger domain-containi	99.29
d1yqba1	84	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	99.28
d1oqya4	77	Ubiquitin-like domain of Rad23 homolog A (Hhr23a)	99.27
d1wh3a_	87	2'-5'-oligoadenylate synthetase-like protein, OASL	99.26
d1bt0a_	73	Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxI	99.26
d2zeqa1	78	Ubiquitin-like domain of parkin {Mouse (Mus muscul	99.26
d1wx9a1	73	Large proline-rich protein BAT3 {Human (Homo sapie	99.25
d1v86a_	95	hypothetical D7wsu128e protein {Mouse (Mus musculu	99.25
d1wjua_	100	NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens	99.25
d2faza1	76	Ubiquitin-like PHD and RING finger domain-containi	99.25
d1z2ma2	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.23
d1v5oa_	102	1700011n24rik protein {Mouse (Mus musculus) [TaxId	99.22
d1m94a_	73	Ubiquitin-like modifier protein hub1 {Baker's yeas	99.21
d1ogwa_	76	Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}	99.19
d1wgha_	116	Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculu	99.18
d1ttna1	80	Dendritic cell-derived ubiquitin-like protein {Hum	99.17
d1uela_	95	Ubiquitin-like domain of Rad23 homolog B (Hhr23B)	99.16
d2faza1	76	Ubiquitin-like PHD and RING finger domain-containi	99.15
d1uh6a_	100	Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculu	99.15
d2c9wb1	103	Elongin B {Human (Homo sapiens) [TaxId: 9606]}	99.14
d1yqba1	84	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	99.14
d1oqya4	77	Ubiquitin-like domain of Rad23 homolog A (Hhr23a)	99.13
d1z2ma1	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.13
d1wy8a1	76	Ubiquitin-like PHD and RING finger domain-containi	99.13
d1wx8a1	83	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	99.13
d1zkha1	86	Splicing factor 3 subunit 1, C-terminal domain {Hu	99.13
d1v5oa_	102	1700011n24rik protein {Mouse (Mus musculus) [TaxId	99.12
d1wgda_	93	Homocysteine-responsive endoplasmic reticulum-resi	99.11
d1we6a_	111	Splicing factor 3 subunit 1, C-terminal domain {Th	99.1
d1j8ca_	103	Ubiquitin-like N-terminal domain of PLIC-2 {Human	99.09
d1wgda_	93	Homocysteine-responsive endoplasmic reticulum-resi	99.09
d1wx8a1	83	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	99.07
d1wgha_	116	Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculu	99.06
d1wgga_	96	Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (M	99.06
d1wjua_	100	NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens	99.05
d1wgga_	96	Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (M	99.05
d1j8ca_	103	Ubiquitin-like N-terminal domain of PLIC-2 {Human	99.03
d1wxva1	81	Bag-family molecular chaperone regulator-1 {Human	99.03
d1uela_	95	Ubiquitin-like domain of Rad23 homolog B (Hhr23B)	99.02
d1se9a_	101	Hypothetical protein At3g01050 {Thale cress (Arabi	99.0
d1se9a_	101	Hypothetical protein At3g01050 {Thale cress (Arabi	98.96
d1we6a_	111	Splicing factor 3 subunit 1, C-terminal domain {Th	98.96
d1v5ta_	90	8430435i17rik protein {Mouse (Mus musculus) [TaxId	98.94
d1wxva1	81	Bag-family molecular chaperone regulator-1 {Human	98.94
d1v86a_	95	hypothetical D7wsu128e protein {Mouse (Mus musculu	98.87
d1v2ya_	105	Ubiquitin-like protein 3300001g02rik {Mouse (Mus m	98.81
d1v5ta_	90	8430435i17rik protein {Mouse (Mus musculus) [TaxId	98.79
d1v6ea_	95	Ubiquitin-like domain of tubulin folding cofactor	98.7
d1wjna_	97	Tubulin-folding protein TbcE {Mouse (Mus musculus)	98.69
d1v2ya_	105	Ubiquitin-like protein 3300001g02rik {Mouse (Mus m	98.65
d1wiaa_	95	Ubiquitin-like protein bab25500 (2010008E23Rik) {M	98.53
d1wiaa_	95	Ubiquitin-like protein bab25500 (2010008E23Rik) {M	98.48
d1x1ma1	94	Ubiquitin-like protein 7 {Mouse (Mus musculus) [Ta	98.43
d1t0ya_	90	Ubiquitin-like domain of tubulin folding cofactor	98.42
d1wjna_	97	Tubulin-folding protein TbcE {Mouse (Mus musculus)	98.34
d1euvb_	79	SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomy	98.34
d1v6ea_	95	Ubiquitin-like domain of tubulin folding cofactor	98.33
d1euvb_	79	SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomy	98.32
d2uyzb1	77	SUMO-1 (smt3 homologue) {Human (Homo sapiens) [Tax	98.27
d2uyzb1	77	SUMO-1 (smt3 homologue) {Human (Homo sapiens) [Tax	98.02
d1x1ma1	94	Ubiquitin-like protein 7 {Mouse (Mus musculus) [Ta	98.02
d1t0ya_	90	Ubiquitin-like domain of tubulin folding cofactor	98.02
d1wf9a1	94	NPL4-like protein 1 {Thale cress (Arabidopsis thal	97.52
d1wm3a_	72	SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}	96.94
d1wm3a_	72	SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}	96.32
d1wf9a1	94	NPL4-like protein 1 {Thale cress (Arabidopsis thal	96.32
d1oeya_	82	Neutrophil cytosol factor 2 (p67phox component of	96.12
d2al3a1	76	Tether containing UBX domain for GLUT4 (Tug) {Mous	95.24
d2al3a1	76	Tether containing UBX domain for GLUT4 (Tug) {Mous	94.85
d1wxma1	73	A-Raf proto-oncogene serine/threonine-protein kina	86.46
d1oeya_	82	Neutrophil cytosol factor 2 (p67phox component of	84.85
d1c1yb_	77	c-Raf1 RBD {Human (Homo sapiens) [TaxId: 9606]}	84.55

>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=99.42  E-value=8.7e-14  Score=71.85  Aligned_cols=48  Identities=19%  Similarity=0.262  Sum_probs=43.9

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++++++|++++||++||++|++..|+|+++|+|+|.+ .+.++.++.++
T Consensus        11 ~~~~l~V~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~~tL~dy   59 (73)
T d1wx9a1          11 QTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEY   59 (73)
T ss_dssp             CEEEEEECTTSBHHHHHHHHHHHHCCCTTTCCCEETTEECCSSSBHHHH
T ss_pred             CEEEEEECCCChHHHHHHHHHHHhCCChHHEEEEECCeEccCCCCHHHh
Confidence            4689999999999999999999999999999999986 67888899987

>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=99.41  E-value=1.1e-13  Score=72.32  Aligned_cols=48  Identities=23%  Similarity=0.382  Sum_probs=43.1

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++++++|++++||++||++|++.+|||+++|+|+|.+ .+.++.+++++
T Consensus        13 ~t~~l~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~d~~tL~~y   61 (78)
T d2zeqa1          13 YGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVIFAGKELPNHLTVQNC   61 (78)
T ss_dssp             SCEEEEECTTCBHHHHHHHHHHHHTCCGGGEEEEETTEEECTTCBGGGS
T ss_pred             CEEEEEEcccccHHHHHHHHHHHHCcChhHeEEEEeeeEcCCCCCHHHc
Confidence            4689999999999999999999999999999999985 67888888876

>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=99.38  E-value=4.8e-13  Score=68.99  Aligned_cols=48  Identities=13%  Similarity=0.133  Sum_probs=43.0

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++.++|+|++||++||.+|++..|+|+++|+|+|.+ .+.++.+++++
T Consensus        12 k~~~v~V~~~~tV~~lK~~I~~~~~i~~~~q~Li~~Gk~L~d~~tL~~y   60 (73)
T d1m94a_          12 KKVRVKCLAEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHISLEDY   60 (73)
T ss_dssp             EEEEEEECTTSBHHHHHHHHHHHHCCTTTSEEEESSSCEECTTSBHHHH
T ss_pred             CEEEEEECCcCcHHHHHHHHHHhhcccccEEEEEEEeEEecccCcHHHc
Confidence            3688999999999999999999999999999999986 67888899887

>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=99.38  E-value=1.1e-13  Score=71.34  Aligned_cols=48  Identities=27%  Similarity=0.479  Sum_probs=41.5

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++++++|++++||+++|++|++..|+|+++|+|+|.+ .+.++.+++++
T Consensus        11 ~~~~l~V~~~~tV~~lK~~i~~~~gi~~~~qrLi~~Gk~L~d~~tL~~y   59 (73)
T d1bt0a_          11 KEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLIYAGKQLADDKTAKDY   59 (73)
T ss_dssp             CEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGG
T ss_pred             CEEEEEECCCCcHHHHHHHHHHHhCCChHHEEEEECCeEcCCCCcHHHc
Confidence            4688999999999999999999999999999999985 66788888876

>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=99.38  E-value=2.6e-13  Score=72.08  Aligned_cols=48  Identities=17%  Similarity=0.211  Sum_probs=42.4

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++++++|++++||.+||++|++++|||+++|+|+|.+ .+.++.++.++
T Consensus        18 ~~~~l~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~~tL~~y   66 (87)
T d1wh3a_          18 GSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGLGIY   66 (87)
T ss_dssp             EEEEEEECSSSBHHHHHHHHHHHTCCCTTTEEEEETTEECCSSSBHHHH
T ss_pred             CEEEEEECCcCcHHHHHHHHHHHHCcChHHeEEEeeceEcCCCCcHHHc
Confidence            3588999999999999999999999999999999985 66888898887

>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=99.35  E-value=3e-13  Score=70.14  Aligned_cols=48  Identities=13%  Similarity=0.129  Sum_probs=40.5

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++++++|++++||++||.+|++..|+|+++|+|+|.+ .+.++.+++++
T Consensus        14 ~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~qrL~~~gk~L~d~~tL~~y   62 (76)
T d1z2ma2          14 RSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEY   62 (76)
T ss_dssp             CEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGG
T ss_pred             CEEEEEECCCCcHHHHHHHHHHHhcCChhHeEEEECCeECCCCCcHHHc
Confidence            4688889999999999999999999999999998875 66778888776

>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=99.34  E-value=1.1e-12  Score=68.02  Aligned_cols=48  Identities=46%  Similarity=0.659  Sum_probs=43.1

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++++++|++++||++||++|++..|+|++.|+|+|.+ .+.++.+++++
T Consensus        11 ~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~qrL~~~Gk~L~d~~tL~~y   59 (76)
T d1ogwa_          11 KTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY   59 (76)
T ss_dssp             CEEEEECCTTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBGGGG
T ss_pred             CEEEEEECCCCcHHHHHHhhhhhcCCChHHEEeEECCeEcCCCCCHHHc
Confidence            4789999999999999999999999999999999985 66888888887

>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=99.32  E-value=2.8e-12  Score=69.76  Aligned_cols=48  Identities=10%  Similarity=0.108  Sum_probs=42.6

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++.++|.|++||++||++|++..|+|+++|+|+|.+ .+.++.++.++
T Consensus        39 k~~~v~V~p~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~dy   87 (100)
T d1uh6a_          39 KKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSLGDY   87 (100)
T ss_dssp             SCEEEEEETTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCSSCBHHHH
T ss_pred             CEEEEEECCcChHHHHHHHHHHHHCCCcceEEEEEEeecccCcCCHHHc
Confidence            4688999999999999999999999999999999975 66888889888

>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=99.32  E-value=5.6e-13  Score=68.68  Aligned_cols=47  Identities=23%  Similarity=0.349  Sum_probs=35.7

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.++|++++||.+||++|++..|+|+++|+|+|.+ .+.++.++.++
T Consensus        12 ~~~i~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~   59 (73)
T d2bwfa1          12 KWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESY   59 (73)
T ss_dssp             EEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGG
T ss_pred             EEEEEECCCChHHHHHHHHHHHHCcChHHeEEEECCeEccCCCcHHHC
Confidence            467788888888888888888888888888888775 55677777766

>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=99.31  E-value=1.7e-12  Score=67.88  Aligned_cols=48  Identities=17%  Similarity=0.366  Sum_probs=41.6

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++++++|++++||++||.+|++..|+|+++|+|+|.+ .+.++.+++++
T Consensus        14 ~~~~l~V~~~~tV~~lK~~I~~~~~ip~~~qrLi~~Gk~L~d~~tL~~y   62 (80)
T d1ttna1          14 KDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKFEEL   62 (80)
T ss_dssp             EEEEEEECTTSHHHHHHHHHHHTTCCCSTTCEEEETTEECCTTSHHHHC
T ss_pred             CEEEEEECCcCcHHHHHHHHHHHhCCCcccEEEEECceEcCCCCcHHHc
Confidence            3678999999999999999999999999999999985 66788888886

>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=99.30  E-value=1.3e-12  Score=71.44  Aligned_cols=47  Identities=19%  Similarity=0.287  Sum_probs=43.9

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.++|++++||.+||.+|++.+|||+++|+|+|.+ .+.++.++.++
T Consensus        12 Ti~l~v~~~~TV~~lK~~I~~~~gip~~~QrLi~~Gk~L~D~~TL~dY   59 (103)
T d2c9wb1          12 TIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC   59 (103)
T ss_dssp             EEEEEECTTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBHHHH
T ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHc
Confidence            678999999999999999999999999999999985 77899999998

>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=99.30  E-value=2.2e-12  Score=68.45  Aligned_cols=48  Identities=21%  Similarity=0.331  Sum_probs=40.7

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++++++|++++||++||++|++..|+|++.|+|+|.+ .+.++.+++++
T Consensus        22 ~~~~l~v~~~~tV~~lK~~I~~~~~ip~~~q~Li~~Gk~L~D~~tL~dY   70 (86)
T d1zkha1          22 QVLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYY   70 (86)
T ss_dssp             CEEEEEECTTSBHHHHHHHHHHHTCCCTTTEEEEETTEEECTTSBHHHH
T ss_pred             eEEEEEECCCChHHHHHHHHHhhhcCChHHEEEEeCCcCcCCCCCHHHc
Confidence            3578889999999999999999999999999998874 66788888887

>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=99.30  E-value=2.7e-12  Score=66.57  Aligned_cols=48  Identities=19%  Similarity=0.232  Sum_probs=42.0

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEE--E-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITT--L-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~--~-~v~~~~tv~~l   48 (77)
                      +++.++|++++||.+||.+|++..|+|+++|+|+|.  + .+.++.+++++
T Consensus        11 ~~~~v~V~~~~tV~~lK~~I~~~~gip~~~QrLi~~~~Gk~L~D~~tL~~y   61 (76)
T d1z2ma1          11 NEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQ   61 (76)
T ss_dssp             CEEEEECCSSCCHHHHHHHHHHHHCCCGGGEEEEEETTCCBCCSSSCSGGG
T ss_pred             CEEEEEECCCCcHHHHHHHHHHHhccCCccEEEEEcCCCeeccCCCcHHHc
Confidence            468899999999999999999999999999999993  4 56788888877

>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=99.29  E-value=3.3e-12  Score=65.72  Aligned_cols=42  Identities=33%  Similarity=0.431  Sum_probs=39.4

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      |.+++++++||.++|+.|+...|+|+++|+|+|+|+.|+|.-
T Consensus        13 ~~i~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~D~~   54 (73)
T d2bwfa1          13 WEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQ   54 (73)
T ss_dssp             EEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTS
T ss_pred             EEEEECCCChHHHHHHHHHHHHCcChHHeEEEECCeEccCCC
Confidence            578899999999999999999999999999999999998863

>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=99.29  E-value=2.1e-12  Score=67.06  Aligned_cols=47  Identities=11%  Similarity=0.135  Sum_probs=40.2

Q ss_pred             eEEE-EeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLL-MWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~-~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++++ .|++++||++||.+|++..|||++.|+|+|.+ .++++.+++++
T Consensus        13 t~~~~~v~~~~TV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~~tL~~y   61 (76)
T d1wy8a1          13 TCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDY   61 (76)
T ss_dssp             EEEEEEECTTCBHHHHHHHHHHHSCCCTTTEEEEETTEECCSSSBHHHH
T ss_pred             eEEEeccCCCChHHHHHHHHHHHHCCCchhcEEEEEeeEecCCCCHHHc
Confidence            5666 48999999999999999999999999999985 66888888887

>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=99.28  E-value=2.4e-12  Score=67.86  Aligned_cols=47  Identities=19%  Similarity=0.201  Sum_probs=41.8

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++++|++++||++||.+|++..|+|++.|+|+|.+ .+.++.+++++
T Consensus        18 ~~~~~V~~~~tV~~lK~~i~~~~gi~~~~qrL~~~Gk~L~D~~tL~~y   65 (84)
T d1yqba1          18 KEDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQC   65 (84)
T ss_dssp             EEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBHHHH
T ss_pred             cEEEEECCCCcHHHHHHHHHHHHCcCchhEEEEEeeeeccccCcHHHc
Confidence            478899999999999999999999999999999985 66888898887

>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=99.27  E-value=1.5e-12  Score=67.66  Aligned_cols=47  Identities=19%  Similarity=0.262  Sum_probs=37.3

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhC---CCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEG---IPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~g---i~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++++|+|++||++||++|++..|   +|+++|+|+|.+ .+.++.++.++
T Consensus        14 ~~~l~v~~~~TV~~lK~~i~~~~g~~~i~~~~qrLi~~Gk~L~D~~tL~~y   64 (77)
T d1oqya4          14 TFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDY   64 (77)
T ss_dssp             EEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSSEECSSSBTTTT
T ss_pred             EEEEEECCCCcHHHHHHHHHHhcCCCCCChHHEEeEECCcCccCCCcHHHc
Confidence            578888888888888888888777   788888888876 56777777776

>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=99.26  E-value=7.5e-12  Score=66.30  Aligned_cols=42  Identities=29%  Similarity=0.469  Sum_probs=39.1

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      |.+++++++||.++|..|+.+.|+|+++|+|+|+|++|+|.-
T Consensus        20 ~~l~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~~   61 (87)
T d1wh3a_          20 YAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWL   61 (87)
T ss_dssp             EEEEECSSSBHHHHHHHHHHHTCCCTTTEEEEETTEECCSSS
T ss_pred             EEEEECCcCcHHHHHHHHHHHHCcChHHeEEEeeceEcCCCC
Confidence            367899999999999999999999999999999999999864

>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=99.26  E-value=6e-12  Score=64.65  Aligned_cols=42  Identities=43%  Similarity=0.769  Sum_probs=39.4

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      |.++++++++|.++|+.|+++.|+|+++|+|+|+|++|+|..
T Consensus        13 ~~l~V~~~~tV~~lK~~i~~~~gi~~~~qrLi~~Gk~L~d~~   54 (73)
T d1bt0a_          13 IEIDIEPTDTIDRIKERVEEKEGIPPVQQRLIYAGKQLADDK   54 (73)
T ss_dssp             EEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTS
T ss_pred             EEEEECCCCcHHHHHHHHHHHhCCChHHEEEEECCeEcCCCC
Confidence            578899999999999999999999999999999999999864

>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=99.26  E-value=5.7e-12  Score=65.62  Aligned_cols=41  Identities=37%  Similarity=0.582  Sum_probs=38.8

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      |.+++++++||.++|..|+++.|+|+++|+|+|+|+.|+|.
T Consensus        15 ~~l~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~d~   55 (78)
T d2zeqa1          15 FPVEVDSDTSILQLKEVVAKRQGVPADQLRVIFAGKELPNH   55 (78)
T ss_dssp             EEEEECTTCBHHHHHHHHHHHHTCCGGGEEEEETTEEECTT
T ss_pred             EEEEEcccccHHHHHHHHHHHHCcChhHeEEEEeeeEcCCC
Confidence            46789999999999999999999999999999999999885

>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=99.25  E-value=4.2e-12  Score=65.34  Aligned_cols=41  Identities=29%  Similarity=0.414  Sum_probs=38.8

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      |.+.+++++||.++|+.|+++.|+|+++|+|+|+|+.|+|.
T Consensus        13 ~~l~V~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~   53 (73)
T d1wx9a1          13 RTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDD   53 (73)
T ss_dssp             EEEEECTTSBHHHHHHHHHHHHCCCTTTCCCEETTEECCSS
T ss_pred             EEEEECCCChHHHHHHHHHHHhCCChHHEEEEECCeEccCC
Confidence            56789999999999999999999999999999999999985

>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=99.25  E-value=2.9e-12  Score=69.04  Aligned_cols=47  Identities=19%  Similarity=0.268  Sum_probs=43.7

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEEEecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTLEVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~~v~~~~tv~~l   48 (77)
                      ++.++|++++||.+||++|++.+|+|+++|+|+|...+.++.++.++
T Consensus        28 ~~~i~v~~~~TV~~LK~~I~~~tgvp~~~q~Li~~g~l~D~~tL~~~   74 (95)
T d1v86a_          28 KHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGLVPEDKTLREI   74 (95)
T ss_dssp             EEEEEECTTSBHHHHHHHHHHHHCSCSTTCCCBSSSBCCSSSBHHHH
T ss_pred             EEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEecccccCCCcHHHC
Confidence            68999999999999999999999999999999998778888899888

>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=99.25  E-value=1e-11  Score=67.48  Aligned_cols=56  Identities=14%  Similarity=0.275  Sum_probs=48.3

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHHHHHHhhccCCCccceE
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNVKSKIQDKEGIPPDQQR   64 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~lK~~i~~~~gip~~~q~   64 (77)
                      +++.++|++++||.+||.+|++..|+|+++|+|+|.+ .+.++.++.++        ||......
T Consensus        30 ~~~~lev~~~~TV~~LK~~I~~~~gi~~~~qkLi~~Gk~L~d~~tL~~~--------gI~~~s~i   86 (100)
T d1wjua_          30 RKNLLETRLHITGRELRSKIAETFGLQENYIKIVINKKQLQLGKTLEEQ--------GVAHNVKA   86 (100)
T ss_dssp             SSEEEEEESSSBHHHHHHHHHHHTTCCSTTCEEEETTEECCTTSBHHHH--------TCCSSEEE
T ss_pred             eEEEEEECCCcHHHHHHHHHHHHHCCCCeeEEEEEcccCcCCCcCHHHc--------CCCCCCEE
Confidence            4689999999999999999999999999999999985 66888999998        77665544

>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=99.25  E-value=1.7e-12  Score=67.38  Aligned_cols=47  Identities=19%  Similarity=0.191  Sum_probs=35.1

Q ss_pred             eEEEE-eeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLM-WKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~-v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++++ +++++||++||++|++..|+|++.|+|+|.+ .++++.++.++
T Consensus        13 t~~l~~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~y   61 (76)
T d2faza1          13 THTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFDY   61 (76)
T ss_dssp             EEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTTTT
T ss_pred             EEEEecCCCCCCHHHHHHHHHHHHCcChHHeEEEEeeEeccCCCcHHHc
Confidence            46664 7777888888888888888888888888775 56777777766

>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=1.2e-11  Score=63.89  Aligned_cols=42  Identities=29%  Similarity=0.440  Sum_probs=39.2

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      +.+++++++||.++|..|+++.|+|+++|+|+|+|+.|+|..
T Consensus        16 ~~l~v~~~~tV~~lK~~I~~~~gi~~~~qrL~~~gk~L~d~~   57 (76)
T d1z2ma2          16 STYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQL   57 (76)
T ss_dssp             EEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTS
T ss_pred             EEEEECCCCcHHHHHHHHHHHhcCChhHeEEEECCeECCCCC
Confidence            468899999999999999999999999999999999998863

>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=99.22  E-value=1.8e-11  Score=66.70  Aligned_cols=47  Identities=11%  Similarity=0.195  Sum_probs=41.2

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-Eec-CCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVK-SSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~-~~~tv~~l   48 (77)
                      +++++|++++||.+||..|+.+.|||+++|+|+|.+ .+. +..++.++
T Consensus        23 t~~l~V~~~~tV~~LK~~Ie~~~gip~~~Q~Li~~Gk~L~dd~~tL~~~   71 (102)
T d1v5oa_          23 TFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLTDDHCSLGSY   71 (102)
T ss_dssp             EEEEEECTTCBHHHHHHHHHHHTCCCGGGBCEEETTEEECCSSSBHHHH
T ss_pred             EEEEEECCcccHHHHHHHHHHHhCCCcceEEEEeCCeEeecccCCHHHc
Confidence            688999999999999999999999999999999985 564 56788888

>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=99.21  E-value=1.2e-11  Score=63.67  Aligned_cols=42  Identities=19%  Similarity=0.262  Sum_probs=39.4

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      +.+.+.+++||.++|..|+.+.|+|+++|+|+|+|+.|+|..
T Consensus        14 ~~v~V~~~~tV~~lK~~I~~~~~i~~~~q~Li~~Gk~L~d~~   55 (73)
T d1m94a_          14 VRVKCLAEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHI   55 (73)
T ss_dssp             EEEEECTTSBHHHHHHHHHHHHCCTTTSEEEESSSCEECTTS
T ss_pred             EEEEECCcCcHHHHHHHHHHhhcccccEEEEEEEeEEecccC
Confidence            468899999999999999999999999999999999999864

>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=99.19  E-value=2.4e-11  Score=62.75  Aligned_cols=42  Identities=74%  Similarity=0.958  Sum_probs=39.2

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      |.+++++++||.++|..|+...|+|+++|+|+|+|++|+|..
T Consensus        13 ~~l~v~~~~tV~~lK~~I~~~~gi~~~~qrL~~~Gk~L~d~~   54 (76)
T d1ogwa_          13 ITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGR   54 (76)
T ss_dssp             EEEECCTTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTS
T ss_pred             EEEEECCCCcHHHHHHhhhhhcCCChHHEEeEECCeEcCCCC
Confidence            467899999999999999999999999999999999999864

>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=99.18  E-value=1.2e-11  Score=68.79  Aligned_cols=48  Identities=10%  Similarity=0.214  Sum_probs=41.3

Q ss_pred             CeEEEEeeCCCcHHHHHHHh--------hhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKI--------QDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i--------~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++.++|+|++||.+||++|        ++..|+|+++|||+|.+ .+.++.++.++
T Consensus        27 k~~~~~v~p~~TV~~lK~~I~~~~p~~~~e~~~~~~~~qRLiy~Gk~L~D~~tL~~~   83 (116)
T d1wgha_          27 KTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGAL   83 (116)
T ss_dssp             CEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEEETTEEECSSCBTTTT
T ss_pred             CEEEEEECCcchHHHHHHHHHhhcccccccccCCChHHeEEEECCEEecCCCCHHHc
Confidence            46788999999999999999        57789999999999985 66888888887

>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=99.17  E-value=3.5e-11  Score=62.73  Aligned_cols=41  Identities=34%  Similarity=0.553  Sum_probs=38.7

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      |.+.+++++||.++|..|+++.|+|+++|+|+|+|+.|+|.
T Consensus        16 ~~l~V~~~~tV~~lK~~I~~~~~ip~~~qrLi~~Gk~L~d~   56 (80)
T d1ttna1          16 LKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDK   56 (80)
T ss_dssp             EEEEECTTSHHHHHHHHHHHTTCCCSTTCEEEETTEECCTT
T ss_pred             EEEEECCcCcHHHHHHHHHHHhCCCcccEEEEECceEcCCC
Confidence            46789999999999999999999999999999999999885

>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=99.16  E-value=3.1e-11  Score=64.73  Aligned_cols=48  Identities=17%  Similarity=0.282  Sum_probs=41.8

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhC---CCcccceEEEEE-EecCCccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEG---IPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~g---i~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++++++|++++||++||++|++..|   +|+++|+|+|.+ .+.++.++.++
T Consensus        11 ~~~~l~v~~~~TV~~lK~~i~~~~~~~~i~~~~qrLi~~Gk~L~d~~tL~~y   62 (95)
T d1uela_          11 QTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEY   62 (95)
T ss_dssp             CEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEETTEECCTTSBGGGG
T ss_pred             CEEEEEECCCccHHHHHHHHHhhhcccCCCccceEEEECCeEccCCCcHHHc
Confidence            4689999999999999999998865   889999999986 66888888887

>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=99.15  E-value=2.7e-11  Score=62.77  Aligned_cols=41  Identities=22%  Similarity=0.360  Sum_probs=37.8

Q ss_pred             EE-EecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TL-EVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~-~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+ .++++++|.++|..|+++.|+|+++|+|+|+|+.|+|..
T Consensus        15 ~l~~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~D~~   56 (76)
T d2faza1          15 TVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGH   56 (76)
T ss_dssp             EEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTC
T ss_pred             EEecCCCCCCHHHHHHHHHHHHCcChHHeEEEEeeEeccCCC
Confidence            44 588999999999999999999999999999999999864

>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=99.15  E-value=3.6e-11  Score=65.28  Aligned_cols=41  Identities=22%  Similarity=0.144  Sum_probs=39.0

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+.+++||.++|.+|+++.|+|+++|+|+|+|++|+|..
T Consensus        42 ~v~V~p~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~   82 (100)
T d1uh6a_          42 RVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHV   82 (100)
T ss_dssp             EEEEETTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCSSC
T ss_pred             EEEECCcChHHHHHHHHHHHHCCCcceEEEEEEeecccCcC
Confidence            67899999999999999999999999999999999999864

>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=99.14  E-value=4.7e-11  Score=65.12  Aligned_cols=43  Identities=26%  Similarity=0.205  Sum_probs=39.6

Q ss_pred             EEEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           34 ITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        34 ~~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+++++++||.++|..|++..|+|+++|+|+|+|++|+|.-
T Consensus        12 Ti~l~v~~~~TV~~lK~~I~~~~gip~~~QrLi~~Gk~L~D~~   54 (103)
T d2c9wb1          12 TIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGK   54 (103)
T ss_dssp             EEEEEECTTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTS
T ss_pred             EEEEEeCCCCcHHHHHHHHHHHhCCCcccEEEEECCEEcCCCC
Confidence            3467899999999999999999999999999999999999863

>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=99.14  E-value=4.4e-11  Score=62.89  Aligned_cols=42  Identities=36%  Similarity=0.387  Sum_probs=38.9

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      |.+.++++++|.++|..|++.+|+|+++|+|+|+|+.|+|.-
T Consensus        19 ~~~~V~~~~tV~~lK~~i~~~~gi~~~~qrL~~~Gk~L~D~~   60 (84)
T d1yqba1          19 EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPD   60 (84)
T ss_dssp             EEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTS
T ss_pred             EEEEECCCCcHHHHHHHHHHHHCcCchhEEEEEeeeeccccC
Confidence            367899999999999999999999999999999999998863

>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=99.13  E-value=3.1e-11  Score=62.52  Aligned_cols=42  Identities=31%  Similarity=0.502  Sum_probs=38.6

Q ss_pred             EEEEecCCccHHHHHHHHhhccC---CCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEG---IPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~g---ip~~~q~l~~~g~~L~d~~   76 (77)
                      |.+++++++||.++|+.|+++.|   +|+++|+|+|+|+.|+|..
T Consensus        15 ~~l~v~~~~TV~~lK~~i~~~~g~~~i~~~~qrLi~~Gk~L~D~~   59 (77)
T d1oqya4          15 FKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDV   59 (77)
T ss_dssp             EEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSSEECSSS
T ss_pred             EEEEECCCCcHHHHHHHHHHhcCCCCCChHHEEeEECCcCccCCC
Confidence            57789999999999999999887   8999999999999999864

>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=99.13  E-value=5.7e-11  Score=61.42  Aligned_cols=42  Identities=31%  Similarity=0.427  Sum_probs=38.8

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEE--CCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIF--AGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~--~g~~L~d~~   76 (77)
                      |.+.+++++||.++|..|+.+.|+|+++|+|+|  +|+.|+|.-
T Consensus        13 ~~v~V~~~~tV~~lK~~I~~~~gip~~~QrLi~~~~Gk~L~D~~   56 (76)
T d1z2ma1          13 FQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRV   56 (76)
T ss_dssp             EEEECCSSCCHHHHHHHHHHHHCCCGGGEEEEEETTCCBCCSSS
T ss_pred             EEEEECCCCcHHHHHHHHHHHhccCCccEEEEEcCCCeeccCCC
Confidence            467899999999999999999999999999999  799999863

>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=99.13  E-value=4.9e-11  Score=61.75  Aligned_cols=39  Identities=23%  Similarity=0.377  Sum_probs=37.0

Q ss_pred             EEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           37 LEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        37 ~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      ..+++++||.++|..|+++.|+|+++|+|+|+|++|+|.
T Consensus        17 ~~v~~~~TV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~   55 (76)
T d1wy8a1          17 EDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENG   55 (76)
T ss_dssp             EEECTTCBHHHHHHHHHHHSCCCTTTEEEEETTEECCSS
T ss_pred             eccCCCChHHHHHHHHHHHHCCCchhcEEEEEeeEecCC
Confidence            368999999999999999999999999999999999885

>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=99.13  E-value=3.4e-11  Score=63.22  Aligned_cols=46  Identities=15%  Similarity=0.102  Sum_probs=36.1

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++++|++++||.+||.+|++..|+|+++|+|+|.+ .+.++.+++++
T Consensus        22 ~~i~v~~~~tV~~lK~~I~~~~~v~~~~qrL~f~Gk~L~d~~tL~~~   68 (83)
T d1wx8a1          22 HEFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQDILSQR   68 (83)
T ss_dssp             EEEEEETTCCHHHHHHHHHHHTCSCTTTBCCEETTEECCTTSCHHHH
T ss_pred             EEEEECCCChHHHHHHHHHHHhCCChhHEEEEEEhhccccCCcHHHc
Confidence            56788888888888888888888888888888875 45677777776

>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=99.13  E-value=8.5e-11  Score=62.12  Aligned_cols=41  Identities=27%  Similarity=0.515  Sum_probs=38.9

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      |.++++++++|.++|..|+++.|+|+++|+|+|+|+.|+|.
T Consensus        24 ~~l~v~~~~tV~~lK~~I~~~~~ip~~~q~Li~~Gk~L~D~   64 (86)
T d1zkha1          24 LVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDS   64 (86)
T ss_dssp             EEEEECTTSBHHHHHHHHHHHTCCCTTTEEEEETTEEECTT
T ss_pred             EEEEECCCChHHHHHHHHHhhhcCChHHEEEEeCCcCcCCC
Confidence            57889999999999999999999999999999999999885

>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=99.12  E-value=5.5e-11  Score=64.69  Aligned_cols=41  Identities=15%  Similarity=0.311  Sum_probs=38.5

Q ss_pred             EEEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCc
Q 040720           34 ITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKL   74 (77)
Q Consensus        34 ~~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d   74 (77)
                      .|.++++++.+|.+||+.|+.+.|+|+++|+|+|+|+.|.|
T Consensus        23 t~~l~V~~~~tV~~LK~~Ie~~~gip~~~Q~Li~~Gk~L~d   63 (102)
T d1v5oa_          23 TFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLTD   63 (102)
T ss_dssp             EEEEEECTTCBHHHHHHHHHHHTCCCGGGBCEEETTEEECC
T ss_pred             EEEEEECCcccHHHHHHHHHHHhCCCcceEEEEeCCeEeec
Confidence            57889999999999999999999999999999999999953

>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=99.11  E-value=4.9e-11  Score=63.90  Aligned_cols=47  Identities=19%  Similarity=0.150  Sum_probs=36.5

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhC--CCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEG--IPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~g--i~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      .+.+++++++||.+||++|++..|  +|+++|||+|.+ .+.++.++.++
T Consensus        21 ~~~~~v~~~~TV~~LK~~I~~~~~~~~~~~~qrLIy~Gk~L~D~~~L~d~   70 (93)
T d1wgda_          21 DLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDL   70 (93)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHSTTCCCTTTCEEEETTEECCSSSCHHHH
T ss_pred             eEEEEcCCCCcHHHHHHHHHHHcCCCCChHHEEEEECCeEccCCCCHHHh
Confidence            367788888888888888887754  788888888875 55777788877

>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=99.10  E-value=1.3e-11  Score=68.15  Aligned_cols=47  Identities=17%  Similarity=0.220  Sum_probs=28.7

Q ss_pred             eEEEEeeC-CCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKA-PTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~-~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +++++|.+ ++||.+||++|++..|+|++.|+|+|.+ .+.++.+++++
T Consensus        42 ~i~l~v~~~sdtV~~lK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~y   90 (111)
T d1we6a_          42 FMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSLAHY   90 (111)
T ss_dssp             CEEEEESCSSSBHHHHHHHHHHHTTCCTTTSEEECSSSBCCTTSBTTTT
T ss_pred             EEEEEecCCccHHHHHHHHHHHHHCCCccceEEEEeeEEccccCCHHHc
Confidence            45566655 5666666666666666666666666654 44555565555

>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=99.09  E-value=3.3e-11  Score=65.55  Aligned_cols=46  Identities=20%  Similarity=0.091  Sum_probs=27.7

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +.++|++++||.+||.+|++..|+|++.|+|+|.+ .+.++.++.++
T Consensus        44 ~~i~V~~~~tV~~LK~~I~~~~gi~~~~qrLi~~Gk~L~D~~tL~~~   90 (103)
T d1j8ca_          44 EEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLIQH   90 (103)
T ss_dssp             EEEEECTTCCHHHHHHHHHHHHCSCSSSEEEEETTEEESTTSCGGGT
T ss_pred             EEEEECCCChHHHHHHHHHHHHCcCHHHeeeeeeeecccCCCcHHHc
Confidence            45566666666666666666666666666666653 44555555554

>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=99.09  E-value=1.1e-10  Score=62.52  Aligned_cols=43  Identities=21%  Similarity=0.204  Sum_probs=38.5

Q ss_pred             EEEEEecCCccHHHHHHHHhhccC--CCccceEEEECCeEcCccc
Q 040720           34 ITTLEVKSSDTINNVKSKIQDKEG--IPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        34 ~~~~~v~~~~tv~~lK~~i~~~~g--ip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+++++++||.++|..|++..+  +|+++|+|+|+|+.|+|..
T Consensus        21 ~~~~~v~~~~TV~~LK~~I~~~~~~~~~~~~qrLIy~Gk~L~D~~   65 (93)
T d1wgda_          21 DLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQ   65 (93)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHSTTCCCTTTCEEEETTEECCSSS
T ss_pred             eEEEEcCCCCcHHHHHHHHHHHcCCCCChHHEEEEECCeEccCCC
Confidence            356788999999999999999865  8999999999999999864

>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=99.07  E-value=1e-10  Score=61.32  Aligned_cols=41  Identities=20%  Similarity=0.205  Sum_probs=38.5

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+++++||.++|..|++..|+|+++|+|+|+|+.|+|.-
T Consensus        23 ~i~v~~~~tV~~lK~~I~~~~~v~~~~qrL~f~Gk~L~d~~   63 (83)
T d1wx8a1          23 EFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQD   63 (83)
T ss_dssp             EEEEETTCCHHHHHHHHHHHTCSCTTTBCCEETTEECCTTS
T ss_pred             EEEECCCChHHHHHHHHHHHhCCChhHEEEEEEhhccccCC
Confidence            57889999999999999999999999999999999998863

>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=99.06  E-value=3.4e-10  Score=62.81  Aligned_cols=41  Identities=20%  Similarity=0.364  Sum_probs=37.5

Q ss_pred             EEEecCCccHHHHHHHH--------hhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKI--------QDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i--------~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+++++||.++|.+|        +++.++|+++|||+|+|+.|+|..
T Consensus        30 ~~~v~p~~TV~~lK~~I~~~~p~~~~e~~~~~~~~qRLiy~Gk~L~D~~   78 (116)
T d1wgha_          30 EFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNV   78 (116)
T ss_dssp             EEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEEETTEEECSSC
T ss_pred             EEEECCcchHHHHHHHHHhhcccccccccCCChHHeEEEECCEEecCCC
Confidence            57899999999999999        577899999999999999999864

>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=99.06  E-value=1.1e-10  Score=62.78  Aligned_cols=45  Identities=20%  Similarity=0.310  Sum_probs=34.0

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEEE-ecCCccHHHH
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTLE-VKSSDTINNV   48 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~~-v~~~~tv~~l   48 (77)
                      +.++|++++||.+||++|++..|+|+++|+|+|.+. +.+ +++.++
T Consensus        20 ~~v~v~~~~tV~~lK~~i~~~~gvp~~~QkLi~~Gk~L~d-~tL~~~   65 (96)
T d1wgga_          20 EGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLKD-DDWGNI   65 (96)
T ss_dssp             EEEEEESSSCHHHHHHHHHHHTCCCTTTSCCEETTEECCS-SCCCSC
T ss_pred             EEEEECCCCcHHHHHHHhhhhcCccceeeEEeecCcccCC-CcHHHC
Confidence            568888888888888888888888888888888753 443 344443

>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=99.05  E-value=2e-10  Score=62.18  Aligned_cols=42  Identities=21%  Similarity=0.270  Sum_probs=39.4

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      |.+++++++||.+||..|+++.|+|+++|+|+|+|+.|+|.-
T Consensus        32 ~~lev~~~~TV~~LK~~I~~~~gi~~~~qkLi~~Gk~L~d~~   73 (100)
T d1wjua_          32 NLLETRLHITGRELRSKIAETFGLQENYIKIVINKKQLQLGK   73 (100)
T ss_dssp             EEEEEESSSBHHHHHHHHHHHTTCCSTTCEEEETTEECCTTS
T ss_pred             EEEEECCCcHHHHHHHHHHHHHCCCCeeEEEEEcccCcCCCc
Confidence            468999999999999999999999999999999999999864

>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=99.05  E-value=4.3e-11  Score=64.43  Aligned_cols=41  Identities=20%  Similarity=0.317  Sum_probs=38.5

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      +.++++++++|.++|..|++..|+|+++|+|+|+|+.|+|.
T Consensus        20 ~~v~v~~~~tV~~lK~~i~~~~gvp~~~QkLi~~Gk~L~d~   60 (96)
T d1wgga_          20 EGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLKDD   60 (96)
T ss_dssp             EEEEEESSSCHHHHHHHHHHHTCCCTTTSCCEETTEECCSS
T ss_pred             EEEEECCCCcHHHHHHHhhhhcCccceeeEEeecCcccCCC
Confidence            46889999999999999999999999999999999999874

>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=99.03  E-value=3e-10  Score=61.65  Aligned_cols=41  Identities=29%  Similarity=0.307  Sum_probs=38.5

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+++++||.+||..|+..+|+|+++|+|+|+|+.|+|..
T Consensus        45 ~i~V~~~~tV~~LK~~I~~~~gi~~~~qrLi~~Gk~L~D~~   85 (103)
T d1j8ca_          45 EFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQD   85 (103)
T ss_dssp             EEEECTTCCHHHHHHHHHHHHCSCSSSEEEEETTEEESTTS
T ss_pred             EEEECCCChHHHHHHHHHHHHCcCHHHeeeeeeeecccCCC
Confidence            57899999999999999999999999999999999998853

>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=99.03  E-value=1.4e-09  Score=56.66  Aligned_cols=47  Identities=13%  Similarity=0.213  Sum_probs=37.3

Q ss_pred             eEEEEe-----eCCCcHHHHHHHhhhhhCCCcccceEEEEE-Ee-cCCccHHHH
Q 040720            2 RLLLMW-----KAPTPLINVKAKIQDKEGIPPDQQRLITTL-EV-KSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v-----~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v-~~~~tv~~l   48 (77)
                      .+.++|     ++++||++||++|++..|+|+++|+|+|.+ .+ +++.++.++
T Consensus        12 ~~~i~v~~~~~~~~~Tv~~LK~~I~~~tgvp~~~QkL~~~G~~L~~d~~tL~~~   65 (81)
T d1wxva1          12 KHDLHVTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLKEMETPLSAL   65 (81)
T ss_dssp             EEEEEECCCSSSSSCBHHHHHHHHHHHTCCCTTTCEEEETTEEECCSSSBHHHH
T ss_pred             eEEEEEecCCCCCccHHHHHHHHHHHHHCcCHHHEEeeecCeEeCcCCCChHHC
Confidence            356666     467899999999999999999999999875 55 456788887

>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=99.02  E-value=3.5e-10  Score=60.49  Aligned_cols=42  Identities=29%  Similarity=0.525  Sum_probs=38.1

Q ss_pred             EEEEecCCccHHHHHHHHhhccC---CCccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEG---IPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~g---ip~~~q~l~~~g~~L~d~~   76 (77)
                      |.+++++++||.++|+.|+++.|   +|+++|+|+|+|+.|+|..
T Consensus        13 ~~l~v~~~~TV~~lK~~i~~~~~~~~i~~~~qrLi~~Gk~L~d~~   57 (95)
T d1uela_          13 FKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDT   57 (95)
T ss_dssp             EEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEETTEECCTTS
T ss_pred             EEEEECCCccHHHHHHHHHhhhcccCCCccceEEEECCeEccCCC
Confidence            57789999999999999998865   8999999999999999864

>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=99.00  E-value=4.7e-10  Score=60.85  Aligned_cols=45  Identities=18%  Similarity=0.259  Sum_probs=25.8

Q ss_pred             EEEeeCCCcHHHHHHHhhhh-----hCCC--cccceEEEEE-EecCCccHHHH
Q 040720            4 LLMWKAPTPLINVKAKIQDK-----EGIP--PDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         4 ~~~v~~~~tv~~lK~~i~~~-----~gi~--~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      ++.+++++||.+||++|++.     +|+|  +++|||+|.+ .+.++.++.++
T Consensus        22 ~~~v~~s~TV~~lK~~I~~~~~~~k~~iP~~~~~qRLIf~Gk~L~D~~tL~dy   74 (101)
T d1se9a_          22 PKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSKTVKDY   74 (101)
T ss_dssp             EEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEEETTEECCTTSBGGGG
T ss_pred             ceecCccCHHHHHHHHHHHhccccccCCCCCcccEEEEECCeEecCCCCHHHc
Confidence            45666666666666666543     5555  4566666654 34555555555

>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=1.8e-10  Score=62.53  Aligned_cols=42  Identities=21%  Similarity=0.244  Sum_probs=37.1

Q ss_pred             EEEEecCCccHHHHHHHHhhc-----cCCC--ccceEEEECCeEcCccc
Q 040720           35 TTLEVKSSDTINNVKSKIQDK-----EGIP--PDQQRLIFAGINLKLVV   76 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~-----~gip--~~~q~l~~~g~~L~d~~   76 (77)
                      ..+.+++++||.++|..|++.     .|+|  +++|||+|+|++|+|.-
T Consensus        21 ~~~~v~~s~TV~~lK~~I~~~~~~~k~~iP~~~~~qRLIf~Gk~L~D~~   69 (101)
T d1se9a_          21 GPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSK   69 (101)
T ss_dssp             EEEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEEETTEECCTTS
T ss_pred             cceecCccCHHHHHHHHHHHhccccccCCCCCcccEEEEECCeEecCCC
Confidence            357899999999999999875     6888  78999999999999864

>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=98.96  E-value=4.2e-10  Score=61.99  Aligned_cols=41  Identities=29%  Similarity=0.346  Sum_probs=37.3

Q ss_pred             EEEecC-CccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKS-SDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~-~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+.+ ++||.++|.+|+++.|+|+++|+|+|+|+.|+|..
T Consensus        44 ~l~v~~~sdtV~~lK~~I~~~~gip~~~QrLi~~Gk~L~D~~   85 (111)
T d1we6a_          44 EITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNM   85 (111)
T ss_dssp             EEEESCSSSBHHHHHHHHHHHTTCCTTTSEEECSSSBCCTTS
T ss_pred             EEEecCCccHHHHHHHHHHHHHCCCccceEEEEeeEEccccC
Confidence            567764 89999999999999999999999999999999864

>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=98.94  E-value=9.8e-10  Score=58.22  Aligned_cols=46  Identities=11%  Similarity=0.296  Sum_probs=39.0

Q ss_pred             EEE-EeeCCCcHHHHHHHhhhhhCCCcccceEEE---E-EEecCCccHHHH
Q 040720            3 LLL-MWKAPTPLINVKAKIQDKEGIPPDQQRLIT---T-LEVKSSDTINNV   48 (77)
Q Consensus         3 ~~~-~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~---~-~~v~~~~tv~~l   48 (77)
                      +.+ +|++++||.+||++|++..|+|+++|+|+|   . ..+.++.++.++
T Consensus        19 ~~i~~v~~~~tV~~LK~~i~~~t~vp~~~QkLi~~~~~Gk~L~D~~tL~~~   69 (90)
T d1v5ta_          19 YSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGAL   69 (90)
T ss_dssp             EEECSCCSSSBHHHHHHHHHHHTCCCTTTCEEESCEETTEECCTTSBHHHH
T ss_pred             EEEEEeCCCCcHHHHHHHHHHHHcCCHHHhhhhhhccCCcCCCCcCcHHHc
Confidence            555 689999999999999999999999999985   4 356788898888

>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=98.94  E-value=1.2e-09  Score=57.01  Aligned_cols=35  Identities=29%  Similarity=0.530  Sum_probs=32.8

Q ss_pred             cCCccHHHHHHHHhhccCCCccceEEEECCeEcCc
Q 040720           40 KSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKL   74 (77)
Q Consensus        40 ~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d   74 (77)
                      ++++||.+||+.|++..|+|+++|+|+|+|+.|.|
T Consensus        23 ~~~~Tv~~LK~~I~~~tgvp~~~QkL~~~G~~L~~   57 (81)
T d1wxva1          23 SSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLKE   57 (81)
T ss_dssp             SSSCBHHHHHHHHHHHTCCCTTTCEEEETTEEECC
T ss_pred             CCccHHHHHHHHHHHHHCcCHHHEEeeecCeEeCc
Confidence            57889999999999999999999999999999953

>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=98.87  E-value=7.9e-10  Score=59.23  Aligned_cols=40  Identities=25%  Similarity=0.490  Sum_probs=36.8

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~   75 (77)
                      |.+++++++||.+||..|+..+|+|+++|+|+|+|+ |.|.
T Consensus        29 ~~i~v~~~~TV~~LK~~I~~~tgvp~~~q~Li~~g~-l~D~   68 (95)
T d1v86a_          29 HDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGL-VPED   68 (95)
T ss_dssp             EEEEECTTSBHHHHHHHHHHHHCSCSTTCCCBSSSB-CCSS
T ss_pred             EEEEECCCCcHHHHHHHHHHHhCCChhHEEEEeccc-ccCC
Confidence            468899999999999999999999999999999997 7665

>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=98.81  E-value=4.5e-10  Score=61.26  Aligned_cols=48  Identities=8%  Similarity=0.182  Sum_probs=39.0

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccce---------------EEEEE-EecC-CccHHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQR---------------LITTL-EVKS-SDTINNV   48 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~---------------L~~~~-~v~~-~~tv~~l   48 (77)
                      ++++++|++++||.+||.+|++..|+|+++|+               |+|.+ .+.+ ..++.++
T Consensus        18 ~~~~v~V~~~~TV~~LK~~I~~~~~ip~~~Qr~~~~~~~~~~~~~~~Li~~G~~L~d~~~tL~~~   82 (105)
T d1v2ya_          18 EVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLRDY   82 (105)
T ss_dssp             CEEEEEECTTCBHHHHHHHHHHHHHHHHHHTTCCCCCCHHHHHTTEEEESSSCEECCSSSBHHHH
T ss_pred             CEEEEEECCCChHHHHHHHHHHHHCcCHHHhcccccccccccccceEEEECCEECcccCCCHHHc
Confidence            46899999999999999999999999999998               66664 4433 3466666

>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=98.79  E-value=4.5e-09  Score=55.57  Aligned_cols=41  Identities=22%  Similarity=0.420  Sum_probs=37.2

Q ss_pred             EE-EecCCccHHHHHHHHhhccCCCccceEEE---ECCeEcCccc
Q 040720           36 TL-EVKSSDTINNVKSKIQDKEGIPPDQQRLI---FAGINLKLVV   76 (77)
Q Consensus        36 ~~-~v~~~~tv~~lK~~i~~~~gip~~~q~l~---~~g~~L~d~~   76 (77)
                      .+ +++++.+|.+||+.|++.+|+|+++|+|+   |.|+.|+|.-
T Consensus        20 ~i~~v~~~~tV~~LK~~i~~~t~vp~~~QkLi~~~~~Gk~L~D~~   64 (90)
T d1v5ta_          20 SVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDV   64 (90)
T ss_dssp             EECSCCSSSBHHHHHHHHHHHTCCCTTTCEEESCEETTEECCTTS
T ss_pred             EEEEeCCCCcHHHHHHHHHHHHcCCHHHhhhhhhccCCcCCCCcC
Confidence            44 68999999999999999999999999999   6999998863

>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=98.70  E-value=4.8e-09  Score=56.12  Aligned_cols=46  Identities=11%  Similarity=0.042  Sum_probs=36.6

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEEE--------ecCCccHHHH
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTLE--------VKSSDTINNV   48 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~~--------v~~~~tv~~l   48 (77)
                      ....++++.||.+||++|+...|+|++.|+|+|...        .+++.++.++
T Consensus        21 ~E~r~~~~~TV~~LK~kle~~tGip~~~qrL~~~~~~~~~~~~l~~d~~~L~~y   74 (95)
T d1v6ea_          21 SEKRYSRSLTIAEFKCKLELVVGSPASCMELELYGADDKFYSKLDQEDALLGSY   74 (95)
T ss_dssp             EEEEECTTSBHHHHHHHHHHHTCSCTTTCBCEEECSSSCEEEECCCSSSBTTSS
T ss_pred             EEEEeCCCCCHHHHHHHHHHHhCcCchhEEEEEeCCCCceeecccCCcCCHHHC
Confidence            456789999999999999999999999999998542        3556666655

>d1wjna_ d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Tubulin-folding protein TbcE
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.69  E-value=1.6e-08  Score=54.19  Aligned_cols=47  Identities=11%  Similarity=0.029  Sum_probs=38.7

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEEE--------ec-CCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTLE--------VK-SSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~~--------v~-~~~tv~~l   48 (77)
                      ++.+++++++||.+||.+|+...|+|++.|+|+|...        ++ ++.++..+
T Consensus        24 ~~~~kv~~~~TV~~LK~~i~~~~gip~~~qrL~y~~~~~~~~~~~l~~d~~tL~~Y   79 (97)
T d1wjna_          24 ILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQFY   79 (97)
T ss_dssp             CEEEEEETTSBHHHHHHHHHTTTTCCTTTCEEEEECTTSCSCEEECCCSSSBSGGG
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHHCcChHHeEEEecCCCCCcccceecCCCcCHhhc
Confidence            4788999999999999999999999999999998542        33 56677776

>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=98.65  E-value=2.3e-09  Score=58.34  Aligned_cols=41  Identities=22%  Similarity=0.212  Sum_probs=37.4

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceE---------------EEECCeEcCcc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQR---------------LIFAGINLKLV   75 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~---------------l~~~g~~L~d~   75 (77)
                      |.+.|+++.||.++|..|+...++|+++|+               |+|+|+.|.|.
T Consensus        20 ~~v~V~~~~TV~~LK~~I~~~~~ip~~~Qr~~~~~~~~~~~~~~~Li~~G~~L~d~   75 (105)
T d1v2ya_          20 MPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEKLTED   75 (105)
T ss_dssp             EEEEECTTCBHHHHHHHHHHHHHHHHHHTTCCCCCCHHHHHTTEEEESSSCEECCS
T ss_pred             EEEEECCCChHHHHHHHHHHHHCcCHHHhcccccccccccccceEEEECCEECccc
Confidence            467899999999999999999999999997               99999999653

>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=98.53  E-value=1.2e-07  Score=50.60  Aligned_cols=44  Identities=16%  Similarity=0.124  Sum_probs=26.9

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-Eec-CCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVK-SSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~-~~~tv~~l   48 (77)
                      .+.++|++++||++||.+|+.   +++++|+|+|.+ .+. +..++.++
T Consensus        19 ~~~v~v~~~~TV~~lK~~i~~---~~~~~qrLi~~Gk~L~dd~~tL~~y   64 (95)
T d1wiaa_          19 EELAVARPEDTVGTLKSKYFP---GQESQMKLIYQGRLLQDPARTLSSL   64 (95)
T ss_dssp             EEEEEECSSSBHHHHHHHHSS---STTTTCEEEETTEECCCSSCBTTTT
T ss_pred             EEEEEECCcCcHHHHHHHHhc---CCcceeEEEECCEEcccCCCCHHHc
Confidence            356677777777777776653   355667777764 332 44566655

>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=98.48  E-value=2.2e-08  Score=53.49  Aligned_cols=37  Identities=27%  Similarity=0.280  Sum_probs=32.3

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCc
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKL   74 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d   74 (77)
                      |.+.+++++||.++|++|+   .+++++|+|+|+|+.|.|
T Consensus        20 ~~v~v~~~~TV~~lK~~i~---~~~~~~qrLi~~Gk~L~d   56 (95)
T d1wiaa_          20 ELAVARPEDTVGTLKSKYF---PGQESQMKLIYQGRLLQD   56 (95)
T ss_dssp             EEEEECSSSBHHHHHHHHS---SSTTTTCEEEETTEECCC
T ss_pred             EEEEECCcCcHHHHHHHHh---cCCcceeEEEECCEEccc
Confidence            3578999999999999886   457899999999999964

>d1x1ma1 d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 7
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.43  E-value=1.7e-07  Score=49.87  Aligned_cols=37  Identities=30%  Similarity=0.376  Sum_probs=26.9

Q ss_pred             cCCccHHHHHHHHhhcc--CCC-ccceEEEECCeEcCccc
Q 040720           40 KSSDTINNVKSKIQDKE--GIP-PDQQRLIFAGINLKLVV   76 (77)
Q Consensus        40 ~~~~tv~~lK~~i~~~~--gip-~~~q~l~~~g~~L~d~~   76 (77)
                      ..+.+|.++|+.|+++.  ++| +++|+|+|+|+.|+|..
T Consensus        35 ~~~~tV~~lK~~i~~~~~~~~P~p~~~rLIy~Gk~L~D~~   74 (94)
T d1x1ma1          35 LGGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQ   74 (94)
T ss_dssp             CCCCBHHHHHHHHHHHCTTTCCCSSSEEEEETTEECCTTC
T ss_pred             CCccCHHHHHHHHHHHcccCCCChhheEEEECCeEECCCc
Confidence            34667888888887775  344 57888888888887753

>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=98.42  E-value=2.3e-07  Score=48.87  Aligned_cols=46  Identities=15%  Similarity=0.202  Sum_probs=36.2

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEEE-------e-cCCccHHHH
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTLE-------V-KSSDTINNV   48 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~~-------v-~~~~tv~~l   48 (77)
                      +...++++.||.+||.+|+...|+|+..|+|+|...       + +++.++..+
T Consensus        18 ~E~r~~~~~TV~~LK~kle~~~Gip~~~q~L~~~~~~~~~~~~l~dd~~~L~~y   71 (90)
T d1t0ya_          18 MEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDL   71 (90)
T ss_dssp             EEEEEETTSBHHHHHHHHHHHHCCCTTTEEEEEECSSSSEEEECCCCSSBTTTT
T ss_pred             EEEecCCCCCHHHHHHHHHHHHCCChhheEEEEeCCCCCcccccccCCCCHHHC
Confidence            345679999999999999999999999999998532       2 455566655

>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=98.34  E-value=5e-07  Score=48.13  Aligned_cols=37  Identities=16%  Similarity=0.198  Sum_probs=34.3

Q ss_pred             EEEEecCCccHHHHHHHHhhccCCCccceEEEECCeE
Q 040720           35 TTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGIN   71 (77)
Q Consensus        35 ~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~   71 (77)
                      +...++.+.||..||..|+..+|+|+++|+|+|.|+.
T Consensus        25 ~~~kv~~~~TV~~LK~~i~~~~gip~~~qrL~y~~~~   61 (97)
T d1wjna_          25 LEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSK   61 (97)
T ss_dssp             EEEEEETTSBHHHHHHHHHTTTTCCTTTCEEEEECTT
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHCcChHHeEEEecCCC
Confidence            3678999999999999999999999999999999874

>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=98.34  E-value=4.6e-07  Score=46.49  Aligned_cols=44  Identities=18%  Similarity=0.303  Sum_probs=21.3

Q ss_pred             EEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            5 LMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         5 ~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +.|.+++++..|++.+++..|+|++.++|+|.+ .++++.|+.++
T Consensus        18 f~v~~~~~~~~l~~~~~~~~~i~~~~~~l~f~G~~l~~~~T~~~~   62 (79)
T d1euvb_          18 FKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDL   62 (79)
T ss_dssp             EEEETTSCTHHHHHHHHHHTTCCGGGEEEEETTEECCTTCCTTTT
T ss_pred             EEECCCCcHHHHHHHHHHHhCCChHhEEEEECCEEeCCCCCHHHC
Confidence            444455555555555555555555555555442 34444444444

>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=98.33  E-value=2.5e-07  Score=49.21  Aligned_cols=35  Identities=26%  Similarity=0.220  Sum_probs=32.6

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCe
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGI   70 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~   70 (77)
                      ...++.+.||.+||++++..+|+|+.+|+|+|.|+
T Consensus        22 E~r~~~~~TV~~LK~kle~~tGip~~~qrL~~~~~   56 (95)
T d1v6ea_          22 EKRYSRSLTIAEFKCKLELVVGSPASCMELELYGA   56 (95)
T ss_dssp             EEEECTTSBHHHHHHHHHHHTCSCTTTCBCEEECS
T ss_pred             EEEeCCCCCHHHHHHHHHHHhCcCchhEEEEEeCC
Confidence            45789999999999999999999999999999887

>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=98.32  E-value=1.8e-07  Score=48.03  Aligned_cols=41  Identities=15%  Similarity=0.384  Sum_probs=38.0

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+..++++..++..++++.|+|+++++|+|+|+.|.++-
T Consensus        17 ~f~v~~~~~~~~l~~~~~~~~~i~~~~~~l~f~G~~l~~~~   57 (79)
T d1euvb_          17 FFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQ   57 (79)
T ss_dssp             EEEEETTSCTHHHHHHHHHHTTCCGGGEEEEETTEECCTTC
T ss_pred             EEEECCCCcHHHHHHHHHHHhCCChHhEEEEECCEEeCCCC
Confidence            46788999999999999999999999999999999998764

>d2uyzb1 d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-1 (smt3 homologue)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.27  E-value=7.9e-07  Score=45.38  Aligned_cols=47  Identities=17%  Similarity=0.286  Sum_probs=36.5

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      .+.+.|.+++++..|+..+++..|+|+..++|+|.+ .+.++.|+.++
T Consensus        14 ~v~f~v~~~t~l~kl~~~y~~~~~~~~~~~~f~fdG~~l~~~~T~~~l   61 (77)
T d2uyzb1          14 EIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKEL   61 (77)
T ss_dssp             EEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCHHHH
T ss_pred             EEEEEECCCChHHHHHHHHHHHhCCChhHEEEEECCEECCCCCCHHHc
Confidence            456777888888888888888888888888888774 66777787777

>d2uyzb1 d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-1 (smt3 homologue)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.02  E-value=7.6e-06  Score=41.55  Aligned_cols=41  Identities=20%  Similarity=0.429  Sum_probs=37.7

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+..++++..++...+++.|+|+++++|+|+|+.|.++-
T Consensus        16 ~f~v~~~t~l~kl~~~y~~~~~~~~~~~~f~fdG~~l~~~~   56 (77)
T d2uyzb1          16 HFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNH   56 (77)
T ss_dssp             EEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTC
T ss_pred             EEEECCCChHHHHHHHHHHHhCCChhHEEEEECCEECCCCC
Confidence            46788999999999999999999999999999999998763

>d1x1ma1 d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 7
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.02  E-value=7.7e-06  Score=43.30  Aligned_cols=40  Identities=23%  Similarity=0.273  Sum_probs=34.1

Q ss_pred             CCCcHHHHHHHhhhhh--CCC-cccceEEEEE-EecCCccHHHH
Q 040720            9 APTPLINVKAKIQDKE--GIP-PDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         9 ~~~tv~~lK~~i~~~~--gi~-~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      .+.||.+||++|++..  ++| +++|+|+|.+ .+.++.++.++
T Consensus        36 ~~~tV~~lK~~i~~~~~~~~P~p~~~rLIy~Gk~L~D~~tL~~y   79 (94)
T d1x1ma1          36 GGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDFY   79 (94)
T ss_dssp             CCCBHHHHHHHHHHHCTTTCCCSSSEEEEETTEECCTTCBHHHH
T ss_pred             CccCHHHHHHHHHHHcccCCCChhheEEEECCeEECCCccHHHc
Confidence            4679999999998874  455 6999999996 77999999998

>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=98.02  E-value=3.9e-06  Score=43.97  Aligned_cols=36  Identities=17%  Similarity=0.211  Sum_probs=32.5

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeE
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGIN   71 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~   71 (77)
                      ...++.+.||.++|..++..+|+|+..|+|+|.|+.
T Consensus        19 E~r~~~~~TV~~LK~kle~~~Gip~~~q~L~~~~~~   54 (90)
T d1t0ya_          19 EKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGD   54 (90)
T ss_dssp             EEEEETTSBHHHHHHHHHHHHCCCTTTEEEEEECSS
T ss_pred             EEecCCCCCHHHHHHHHHHHHCCChhheEEEEeCCC
Confidence            346789999999999999999999999999998873

>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=97.52  E-value=3.8e-05  Score=40.29  Aligned_cols=33  Identities=27%  Similarity=0.232  Sum_probs=28.3

Q ss_pred             EEEEeeC-CCcHHHHHHHhhhhhCCCcccceEEE
Q 040720            3 LLLMWKA-PTPLINVKAKIQDKEGIPPDQQRLIT   35 (77)
Q Consensus         3 ~~~~v~~-~~tv~~lK~~i~~~~gi~~~~q~L~~   35 (77)
                      --++|+. +-|+++||.+|++..++|.+.|.|+.
T Consensus        12 eRv~v~~~~~Tl~~LK~~Ie~~L~VPv~~Q~LSl   45 (94)
T d1wf9a1          12 ERVSVDGPHITVSQLKTLIQDQLQIPIHNQTLST   45 (94)
T ss_dssp             EEEEECCTTSBHHHHHHHHHHHSCCCTTTCCCBS
T ss_pred             eEEEecCCCCcHHHHHHHHHHHhCCCcccceeec
Confidence            3467754 67999999999999999999999964

>d1wm3a_ d.15.1.1 (A:) SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.94  E-value=0.00036  Score=34.67  Aligned_cols=46  Identities=20%  Similarity=0.253  Sum_probs=27.9

Q ss_pred             EEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEEE-EecCCccHHHH
Q 040720            3 LLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITTL-EVKSSDTINNV   48 (77)
Q Consensus         3 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~~-~v~~~~tv~~l   48 (77)
                      +.+.|.++++...|....++..|+++...+|+|.+ .+++++|..++
T Consensus        14 v~f~vk~~t~l~kl~~~y~~~~~~~~~~~~f~fdG~~i~~~~Tp~~l   60 (72)
T d1wm3a_          14 VQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQL   60 (72)
T ss_dssp             EEEEECTTSCTHHHHHHHHHHHTCCTTTCEEEETTEECCTTCCTTTT
T ss_pred             EEEEEcCCChHHHHHHHHHHHhCCCccceEEEECCEEcCCCCCHHHc
Confidence            45556666666666666666666666666666653 45555565554

>d1wm3a_ d.15.1.1 (A:) SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.32  E-value=0.0048  Score=30.34  Aligned_cols=41  Identities=15%  Similarity=0.314  Sum_probs=36.7

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+..++++..+....+.+.|+++...+++|+|..+..+-
T Consensus        15 ~f~vk~~t~l~kl~~~y~~~~~~~~~~~~f~fdG~~i~~~~   55 (72)
T d1wm3a_          15 QFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETD   55 (72)
T ss_dssp             EEEECTTSCTHHHHHHHHHHHTCCTTTCEEEETTEECCTTC
T ss_pred             EEEEcCCChHHHHHHHHHHHhCCCccceEEEECCEEcCCCC
Confidence            46788999999999999999999999999999999987653

>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=96.32  E-value=0.0015  Score=34.05  Aligned_cols=33  Identities=30%  Similarity=0.356  Sum_probs=28.0

Q ss_pred             EEEecC-CccHHHHHHHHhhccCCCccceEEEEC
Q 040720           36 TLEVKS-SDTINNVKSKIQDKEGIPPDQQRLIFA   68 (77)
Q Consensus        36 ~~~v~~-~~tv~~lK~~i~~~~gip~~~q~l~~~   68 (77)
                      -+.++. +.|+.+||..|++..++|.+.|.|.-+
T Consensus        13 Rv~v~~~~~Tl~~LK~~Ie~~L~VPv~~Q~LSl~   46 (94)
T d1wf9a1          13 RVSVDGPHITVSQLKTLIQDQLQIPIHNQTLSTN   46 (94)
T ss_dssp             EEEECCTTSBHHHHHHHHHHHSCCCTTTCCCBSS
T ss_pred             EEEecCCCCcHHHHHHHHHHHhCCCcccceeecC
Confidence            456754 679999999999999999999998543

>d1oeya_ d.15.2.2 (A:) Neutrophil cytosol factor 2 (p67phox component of NADPH oxidase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: CAD & PB1 domains
family: PB1 domain
domain: Neutrophil cytosol factor 2 (p67phox component of NADPH oxidase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.12  E-value=0.0072  Score=30.70  Aligned_cols=35  Identities=11%  Similarity=0.200  Sum_probs=33.1

Q ss_pred             eEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEE
Q 040720            2 RLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITT   36 (77)
Q Consensus         2 ~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~   36 (77)
                      |+.|++.++...++|.++|+++.+.+++.-+|.|.
T Consensus        15 TVal~v~~G~~y~~L~~lvs~KL~l~~~~~~LSY~   49 (82)
T d1oeya_          15 TVVMKTQPGLPYSQVRDMVSKKLELRLEHTKLSYR   49 (82)
T ss_dssp             EEEEEECTTCCHHHHHHHHHHHTTCCGGGCCEEEC
T ss_pred             EEEEEccCCCCHHHHHHHHHHHhCCChhheEEEec
Confidence            68899999999999999999999999999999994

>d2al3a1 d.15.1.2 (A:10-85) Tether containing UBX domain for GLUT4 (Tug) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: Tether containing UBX domain for GLUT4 (Tug)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.24  E-value=0.063  Score=26.70  Aligned_cols=47  Identities=17%  Similarity=0.103  Sum_probs=31.1

Q ss_pred             CeEEEEeeCCCcHHHHHHHhhhhhCCCcccceEEEE-EEecCCccHHH
Q 040720            1 RRLLLMWKAPTPLINVKAKIQDKEGIPPDQQRLITT-LEVKSSDTINN   47 (77)
Q Consensus         1 ~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~-~~v~~~~tv~~   47 (77)
                      |..++.|.|++|+-+|-+...++.|+.+++-.|.|. -.++.+....-
T Consensus        11 rR~~VKvtP~t~l~~VL~eaC~k~~~~~~~~~Lkh~~k~ldLsl~~R~   58 (76)
T d2al3a1          11 RRHTVKVTPSTVLLQVLEDTCRRQDFNPSEYDLKFQRTVLDLSLQWRF   58 (76)
T ss_dssp             CEEEECCCTTSBHHHHHHHHHHHTTCCGGGCEEEETTEEESSSCBHHH
T ss_pred             cEEEEEeCCCcCHHHHHHHHHHHhCCChhHceeeeCCEEcCccceeee
Confidence            346677777777777777777777777777777665 34555544433

>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=94.85  E-value=0.039  Score=27.48  Aligned_cols=41  Identities=22%  Similarity=0.306  Sum_probs=37.1

Q ss_pred             EEEecCCccHHHHHHHHhhccCCCccceEEEECCeEcCccc
Q 040720           36 TLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFAGINLKLVV   76 (77)
Q Consensus        36 ~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~g~~L~d~~   76 (77)
                      .+.+.+++++.++-.....++|+.+++..|.|++++|+..+
T Consensus        14 ~VKvtP~t~l~~VL~eaC~k~~~~~~~~~Lkh~~k~ldLsl   54 (76)
T d2al3a1          14 TVKVTPSTVLLQVLEDTCRRQDFNPSEYDLKFQRTVLDLSL   54 (76)
T ss_dssp             EECCCTTSBHHHHHHHHHHHTTCCGGGCEEEETTEEESSSC
T ss_pred             EEEeCCCcCHHHHHHHHHHHhCCChhHceeeeCCEEcCccc
Confidence            56788999999999999999999999999999999998654

>d1wxma1 d.15.1.5 (A:8-80) A-Raf proto-oncogene serine/threonine-protein kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ras-binding domain, RBD
domain: A-Raf proto-oncogene serine/threonine-protein kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.46  E-value=0.55  Score=22.86  Aligned_cols=31  Identities=10%  Similarity=0.090  Sum_probs=27.1

Q ss_pred             EEEeeCCCcHHHHHHHhhhhhCCCcccceEE
Q 040720            4 LLMWKAPTPLINVKAKIQDKEGIPPDQQRLI   34 (77)
Q Consensus         4 ~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~   34 (77)
                      .+.|.|+.||.++=.++-++.|++++.-.++
T Consensus        14 ~V~vrpG~tir~~L~k~l~kRgl~~~~~~V~   44 (73)
T d1wxma1          14 VVTVRDGMSVYDSLDKALKVRGLNQDCCVVY   44 (73)
T ss_dssp             EEECCSSCBSHHHHHHHHHTTTCCSSSEEEE
T ss_pred             EEEecCCCCHHHHHHHHHHHcCCCHHHEEEE
Confidence            4889999999999999999999998876664

>d1oeya_ d.15.2.2 (A:) Neutrophil cytosol factor 2 (p67phox component of NADPH oxidase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: CAD & PB1 domains
family: PB1 domain
domain: Neutrophil cytosol factor 2 (p67phox component of NADPH oxidase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.85  E-value=0.89  Score=22.62  Aligned_cols=35  Identities=9%  Similarity=0.232  Sum_probs=31.7

Q ss_pred             EEEEEecCCccHHHHHHHHhhccCCCccceEEEEC
Q 040720           34 ITTLEVKSSDTINNVKSKIQDKEGIPPDQQRLIFA   68 (77)
Q Consensus        34 ~~~~~v~~~~tv~~lK~~i~~~~gip~~~q~l~~~   68 (77)
                      .+++.+++.....++...|.++...+++.-.|.|.
T Consensus        15 TVal~v~~G~~y~~L~~lvs~KL~l~~~~~~LSY~   49 (82)
T d1oeya_          15 TVVMKTQPGLPYSQVRDMVSKKLELRLEHTKLSYR   49 (82)
T ss_dssp             EEEEEECTTCCHHHHHHHHHHHTTCCGGGCCEEEC
T ss_pred             EEEEEccCCCCHHHHHHHHHHHhCCChhheEEEec
Confidence            34678899999999999999999999999999996

>d1c1yb_ d.15.1.5 (B:) c-Raf1 RBD {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ras-binding domain, RBD
domain: c-Raf1 RBD
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.55  E-value=0.96  Score=22.16  Aligned_cols=32  Identities=13%  Similarity=0.182  Sum_probs=28.2

Q ss_pred             EEEeeCCCcHHHHHHHhhhhhCCCcccceEEE
Q 040720            4 LLMWKAPTPLINVKAKIQDKEGIPPDQQRLIT   35 (77)
Q Consensus         4 ~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~   35 (77)
                      .+.|.|+.||.++=.++-++.|++++.-.++.
T Consensus        15 ~V~vrpG~tird~L~k~l~kRgl~~~~c~V~~   46 (77)
T d1c1yb_          15 VVNVRNGMSLHDCLMKALKVRGLQPECCAVFR   46 (77)
T ss_dssp             EEECCTTCBHHHHHHHHHHTTTCCGGGEEEEE
T ss_pred             EEEecCCCCHHHHHHHHHHHcCCCHHHEEEEE
Confidence            48899999999999999999999988877754