Citrus Sinensis ID: 040111

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130---
Protein Sequence
IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQESTLHLGWRADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIFCGCRVNFWNASLRFDPENVLWLLG
Secondary Structure (PSIPRED)
ccccccccccccEEEEccEEcccccccccccccccccccEEEEccccccccccEEEEEcccHHHHHHHHHHcccccccccccEEEEccccccccccccccccccccEEEEEEEEcccccEEEEcccccEEccc
Secondary Structure Prediction (SSPRO)
HHHHHcccHHHEEEEEccEEcccccEHHHHccccccHHHHHHHHEEEEccccEEEEEcccccEHHHHHHHHHHHHcccHcHcEEEEccccccccccccHcccccccHHHHHEEHHHHHHcccccHHHHHHHcc
Coil and Loop (DISEMBL)
iedkegippgqqrsifagkqledgrtlADYKIQESTLhlgwradfcknpdpqnitlevessdtiDNVKAKIqdkkripppaeadllkfpfffFEEVLSFFWFVVVGVIFCGCrvnfwnaslrfdpENVLWLLG
Flexible Loop (DISEMBL)
iedkegippgqqrsifagkqledGRTLADYKIQESTLHLGWRADFCKNPDPQNitlevessdtidNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIFCGCRVNFwnaslrfdpenvlwllg
Low Complexity Region (SEG)
IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQESTLHLGWRADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKfpffffeevlsffwfvvvGVIFCGCRVNFWNASLRFDPENVLWLLG
Disordered region (IsUnstruct)
************************RTLADYKIQESTLHLGWRADFCKN**********************************ADLLKFPFFFFEEVLSFFWFVVVGVIFCGCRVNFWNASLRFDPENVLWLL*
Disordered Region (DISOPRED)
IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQESTLHLGWRADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIFCGCRVNFWNASLRFDPENVLWLLG
Disordered Region (DISEMBL)
********PGQQRSIFAGKQLEDGRTLADYKIQESTLHLGWRADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIFCGCRVNFWNASLRFDPENVLWLLG
Disordered Region (DISPRO)
IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQESTLHLGWRADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIFCGCRVNFWNASLRFDPENVLWLLG
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQESTLHLGWRADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIFCGCRVNFWNASLRFDPENVLWLLG
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	133	2.2.26 [Sep-21-2011]
Q8H159	457	Polyubiquitin 10 OS=Arabi	yes	no	0.593	0.172	0.729	6e-26
P0CH05	458	Polyubiquitin OS=Petrosel	N/A	no	0.593	0.172	0.729	6e-26
P0CH04	458	Polyubiquitin OS=Petrosel	N/A	no	0.593	0.172	0.729	6e-26
P0CG85	457	Polyubiquitin OS=Nicotian	N/A	no	0.593	0.172	0.729	6e-26
P0CG83	171	Polyubiquitin (Fragment)	N/A	no	0.616	0.479	0.704	2e-25
Q1EC66	306	Polyubiquitin 3 OS=Arabid	no	no	0.616	0.267	0.704	2e-25
P69315	305	Polyubiquitin (Fragment)	N/A	no	0.616	0.268	0.704	2e-25
P0CH32	382	Polyubiquitin 4 OS=Arabid	no	no	0.616	0.214	0.704	2e-25
Q58G87	381	Polyubiquitin 3 OS=Oryza	no	no	0.616	0.215	0.704	2e-25
P69322	381	Polyubiquitin OS=Pisum sa	N/A	no	0.616	0.215	0.704	2e-25

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

 Score =  115 bits (289), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 62/85 (72%), Positives = 65/85 (76%), Gaps = 6/85 (7%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 55  TLEVESSDTIDNVKAKIQDKKRIPP 79
           TLEVESSDTIDNVKAKIQDK+ IPP
Sbjct: 90  TLEVESSDTIDNVKAKIQDKEGIPP 114

Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, and DNA-damage responses. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.
Arabidopsis thaliana (taxid: 3702)

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

 Score =  115 bits (289), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 62/85 (72%), Positives = 65/85 (76%), Gaps = 6/85 (7%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 55  TLEVESSDTIDNVKAKIQDKKRIPP 79
           TLEVESSDTIDNVKAKIQDK+ IPP
Sbjct: 90  TLEVESSDTIDNVKAKIQDKEGIPP 114

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

Petroselinum crispum (taxid: 4043)

>sp|P0CH04|UBI1P_PETCR Polyubiquitin OS=Petroselinum crispum GN=PCUBI4-1 PE=2 SV=1

 Score =  115 bits (289), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 62/85 (72%), Positives = 65/85 (76%), Gaps = 6/85 (7%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 55  TLEVESSDTIDNVKAKIQDKKRIPP 79
           TLEVESSDTIDNVKAKIQDK+ IPP
Sbjct: 90  TLEVESSDTIDNVKAKIQDKEGIPP 114

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

Petroselinum crispum (taxid: 4043)

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

 Score =  115 bits (289), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 62/85 (72%), Positives = 65/85 (76%), Gaps = 6/85 (7%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 55  TLEVESSDTIDNVKAKIQDKKRIPP 79
           TLEVESSDTIDNVKAKIQDK+ IPP
Sbjct: 90  TLEVESSDTIDNVKAKIQDKEGIPP 114

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

 Score =  114 bits (284), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 62/88 (70%), Positives = 66/88 (75%), Gaps = 6/88 (6%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct: 48  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 107

Query: 55  TLEVESSDTIDNVKAKIQDKKRIPPPAE 82
           TLEVESSDTIDNVKAKIQDK+ IPP  +
Sbjct: 108 TLEVESSDTIDNVKAKIQDKEGIPPDQQ 135

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

 Score =  114 bits (284), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 62/88 (70%), Positives = 66/88 (75%), Gaps = 6/88 (6%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 55  TLEVESSDTIDNVKAKIQDKKRIPPPAE 82
           TLEVESSDTIDNVKAKIQDK+ IPP  +
Sbjct: 90  TLEVESSDTIDNVKAKIQDKEGIPPDQQ 117

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

 Score =  114 bits (284), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 62/88 (70%), Positives = 66/88 (75%), Gaps = 6/88 (6%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct: 71  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 130

Query: 55  TLEVESSDTIDNVKAKIQDKKRIPPPAE 82
           TLEVESSDTIDNVKAKIQDK+ IPP  +
Sbjct: 131 TLEVESSDTIDNVKAKIQDKEGIPPDQQ 158

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

 Score =  114 bits (284), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 62/88 (70%), Positives = 66/88 (75%), Gaps = 6/88 (6%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 55  TLEVESSDTIDNVKAKIQDKKRIPPPAE 82
           TLEVESSDTIDNVKAKIQDK+ IPP  +
Sbjct: 90  TLEVESSDTIDNVKAKIQDKEGIPPDQQ 117

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  114 bits (284), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 62/88 (70%), Positives = 66/88 (75%), Gaps = 6/88 (6%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 55  TLEVESSDTIDNVKAKIQDKKRIPPPAE 82
           TLEVESSDTIDNVKAKIQDK+ IPP  +
Sbjct: 90  TLEVESSDTIDNVKAKIQDKEGIPPDQQ 117

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

 Score =  114 bits (284), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 62/88 (70%), Positives = 66/88 (75%), Gaps = 6/88 (6%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 55  TLEVESSDTIDNVKAKIQDKKRIPPPAE 82
           TLEVESSDTIDNVKAKIQDK+ IPP  +
Sbjct: 90  TLEVESSDTIDNVKAKIQDKEGIPPDQQ 117

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)

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	133
1332579	761	polyubiquitin [Pinus sylvestris]	0.593	0.103	0.729	3e-24
312160	534	ubiquitin [Solanum lycopersicum]	0.593	0.147	0.729	4e-24
357475981	533	Ubiquitin [Medicago truncatula] gi|35550	0.593	0.148	0.729	4e-24
902584	533	polyubiquitin containing 7 ubiquitin mon	0.593	0.148	0.729	4e-24
1684855	407	ubiquitin-like protein [Phaseolus vulgar	0.593	0.194	0.729	4e-24
2760347	456	ubiquitin [Arabidopsis thaliana]	0.593	0.173	0.729	4e-24
240255754	457	polyubiquitin 10 [Arabidopsis thaliana]	0.593	0.172	0.729	4e-24
115444401	457	Os02g0161900 [Oryza sativa Japonica Grou	0.593	0.172	0.729	4e-24
413935668	502	polyubiquitin-like protein [Zea mays]	0.593	0.157	0.729	4e-24
413926513	535	ubiquitin2 [Zea mays]	0.593	0.147	0.729	4e-24

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

 Score =  116 bits (290), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 62/85 (72%), Positives = 65/85 (76%), Gaps = 6/85 (7%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct: 638 IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTAKTI 697

Query: 55  TLEVESSDTIDNVKAKIQDKKRIPP 79
           TLEVESSDTIDNVKAKIQDK+ IPP
Sbjct: 698 TLEVESSDTIDNVKAKIQDKEGIPP 722

Source: Pinus sylvestris

Species: Pinus sylvestris

Genus: Pinus

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|312160|emb|CAA51679.1| ubiquitin [Solanum lycopersicum]

 Score =  115 bits (289), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 62/85 (72%), Positives = 65/85 (76%), Gaps = 6/85 (7%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct: 182 IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTRKTI 241

Query: 55  TLEVESSDTIDNVKAKIQDKKRIPP 79
           TLEVESSDTIDNVKAKIQDK+ IPP
Sbjct: 242 TLEVESSDTIDNVKAKIQDKEGIPP 266

Source: Solanum lycopersicum

Species: Solanum lycopersicum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357475981|ref|XP_003608276.1| Ubiquitin [Medicago truncatula] gi|355509331|gb|AES90473.1| Ubiquitin [Medicago truncatula]

 Score =  115 bits (289), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 62/85 (72%), Positives = 65/85 (76%), Gaps = 6/85 (7%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 55  TLEVESSDTIDNVKAKIQDKKRIPP 79
           TLEVESSDTIDNVKAKIQDK+ IPP
Sbjct: 90  TLEVESSDTIDNVKAKIQDKEGIPP 114

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  115 bits (289), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 62/85 (72%), Positives = 65/85 (76%), Gaps = 6/85 (7%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 55  TLEVESSDTIDNVKAKIQDKKRIPP 79
           TLEVESSDTIDNVKAKIQDK+ IPP
Sbjct: 90  TLEVESSDTIDNVKAKIQDKEGIPP 114

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|1684855|gb|AAB36545.1| ubiquitin-like protein [Phaseolus vulgaris]

 Score =  115 bits (289), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 62/85 (72%), Positives = 65/85 (76%), Gaps = 6/85 (7%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct: 132 IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 191

Query: 55  TLEVESSDTIDNVKAKIQDKKRIPP 79
           TLEVESSDTIDNVKAKIQDK+ IPP
Sbjct: 192 TLEVESSDTIDNVKAKIQDKEGIPP 216

Source: Phaseolus vulgaris

Species: Phaseolus vulgaris

Genus: Phaseolus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|2760347|gb|AAB95251.1| ubiquitin [Arabidopsis thaliana]

 Score =  115 bits (289), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 62/85 (72%), Positives = 65/85 (76%), Gaps = 6/85 (7%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 55  TLEVESSDTIDNVKAKIQDKKRIPP 79
           TLEVESSDTIDNVKAKIQDK+ IPP
Sbjct: 90  TLEVESSDTIDNVKAKIQDKEGIPP 114

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|240255754|ref|NP_849299.4| polyubiquitin 10 [Arabidopsis thaliana] gi|240255758|ref|NP_849301.4| polyubiquitin 10 [Arabidopsis thaliana] gi|297809731|ref|XP_002872749.1| hexameric polyubiquitin [Arabidopsis lyrata subsp. lyrata] gi|449454712|ref|XP_004145098.1| PREDICTED: polyubiquitin 10-like [Cucumis sativus] gi|449471945|ref|XP_004153450.1| PREDICTED: polyubiquitin 10-like [Cucumis sativus] gi|302595948|sp|P0CG85.1|UBI1P_NICSY RecName: Full=Polyubiquitin; Contains: RecName: Full=Ubiquitin; Flags: Precursor gi|302596003|sp|Q8H159.2|UBQ10_ARATH RecName: Full=Polyubiquitin 10; Contains: RecName: Full=Ubiquitin; Flags: Precursor gi|170352|gb|AAA34123.1| hexameric polyubiquitin [Nicotiana sylvestris] gi|870792|gb|AAA68878.1| polyubiquitin [Arabidopsis thaliana] gi|4115333|gb|AAD03341.1| ubiquitin [Pisum sativum] gi|4115335|gb|AAD03342.1| ubiquitin [Pisum sativum] gi|22655101|gb|AAM98141.1| polyubiquitin UBQ10 [Arabidopsis thaliana] gi|118481031|gb|ABK92469.1| unknown [Populus trichocarpa] gi|147805226|emb|CAN64480.1| hypothetical protein VITISV_002813 [Vitis vinifera] gi|241740189|gb|ACS68204.1| ubiquitin 10.1 [Brassica napus] gi|297318586|gb|EFH49008.1| hexameric polyubiquitin [Arabidopsis lyrata subsp. lyrata] gi|312282619|dbj|BAJ34175.1| unnamed protein product [Thellungiella halophila] gi|332657100|gb|AEE82500.1| polyubiquitin 10 [Arabidopsis thaliana] gi|332657102|gb|AEE82502.1| polyubiquitin 10 [Arabidopsis thaliana]

 Score =  115 bits (289), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 62/85 (72%), Positives = 65/85 (76%), Gaps = 6/85 (7%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 55  TLEVESSDTIDNVKAKIQDKKRIPP 79
           TLEVESSDTIDNVKAKIQDK+ IPP
Sbjct: 90  TLEVESSDTIDNVKAKIQDKEGIPP 114

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115444401|ref|NP_001045980.1| Os02g0161900 [Oryza sativa Japonica Group] gi|115469558|ref|NP_001058378.1| Os06g0681400 [Oryza sativa Japonica Group] gi|6013289|gb|AAF01315.1|AF184279_1 polyubiquitin [Oryza sativa Indica Group] gi|6013291|gb|AAF01316.1|AF184280_1 polyubiquitin [Oryza sativa Indica Group] gi|416038|emb|CAA53665.1| polyubiquitin [Oryza sativa Indica Group] gi|1574944|gb|AAC49806.1| polyubiquitin [Oryza sativa Indica Group] gi|49389251|dbj|BAD25213.1| polyubiquitin 6 [Oryza sativa Japonica Group] gi|113535511|dbj|BAF07894.1| Os02g0161900 [Oryza sativa Japonica Group] gi|113596418|dbj|BAF20292.1| Os06g0681400 [Oryza sativa Japonica Group] gi|215715366|dbj|BAG95117.1| unnamed protein product [Oryza sativa Japonica Group] gi|218190115|gb|EEC72542.1| hypothetical protein OsI_05955 [Oryza sativa Indica Group] gi|222622224|gb|EEE56356.1| hypothetical protein OsJ_05481 [Oryza sativa Japonica Group] gi|284431760|gb|ADB84621.1| polyubiquitin [Oryza sativa Japonica Group] gi|306415955|gb|ADM86852.1| polyubiquitin [Oryza sativa Japonica Group] gi|326504784|dbj|BAK06683.1| predicted protein [Hordeum vulgare subsp. vulgare] gi|332379898|gb|AEE65380.1| ubiquitin 2 [Panicum virgatum] gi|413926517|gb|AFW66449.1| ubiquitin2 [Zea mays]

 Score =  115 bits (289), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 62/85 (72%), Positives = 65/85 (76%), Gaps = 6/85 (7%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 55  TLEVESSDTIDNVKAKIQDKKRIPP 79
           TLEVESSDTIDNVKAKIQDK+ IPP
Sbjct: 90  TLEVESSDTIDNVKAKIQDKEGIPP 114

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  115 bits (289), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 62/85 (72%), Positives = 65/85 (76%), Gaps = 6/85 (7%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 55  TLEVESSDTIDNVKAKIQDKKRIPP 79
           TLEVESSDTIDNVKAKIQDK+ IPP
Sbjct: 90  TLEVESSDTIDNVKAKIQDKEGIPP 114

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413926513|gb|AFW66445.1| ubiquitin2 [Zea mays]

 Score =  115 bits (289), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 62/85 (72%), Positives = 65/85 (76%), Gaps = 6/85 (7%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct: 32  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 91

Query: 55  TLEVESSDTIDNVKAKIQDKKRIPP 79
           TLEVESSDTIDNVKAKIQDK+ IPP
Sbjct: 92  TLEVESSDTIDNVKAKIQDKEGIPP 116

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

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	133
TAIR|locus:2180434	382	UBQ4 "AT5G20620" [Arabidopsis	0.593	0.206	0.729	6.8e-24
TAIR|locus:2143548	306	UBQ3 "AT5G03240" [Arabidopsis	0.593	0.258	0.729	6.8e-24
TAIR|locus:2140200	305	UBQ14 "AT4G02890" [Arabidopsis	0.593	0.259	0.729	6.8e-24
TAIR|locus:2206310	319	UBQ13 "AT1G65350" [Arabidopsis	0.593	0.247	0.729	6.8e-24
TAIR|locus:2138386	229	UBQ11 "AT4G05050" [Arabidopsis	0.593	0.344	0.729	6.8e-24
TAIR|locus:2115663	457	UBQ10 "AT4G05320" [Arabidopsis	0.593	0.172	0.729	1.7e-23
POMBASE|SPBC337.08c	382	ubi4 "ubiquitin" [Schizosaccha	0.593	0.206	0.705	2.9e-23
SGD|S000003962	381	UBI4 "Ubiquitin" [Saccharomyce	0.593	0.207	0.705	2.9e-23
UNIPROTKB|G4MY63	305	MGG_01282 "Polyubiquitin" [Mag	0.593	0.259	0.705	2.9e-23
ASPGD|ASPL0000049163	305	ubi4 [Emericella nidulans (tax	0.593	0.259	0.705	2.9e-23

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

 Score = 274 (101.5 bits), Expect = 6.8e-24, P = 6.8e-24
 Identities = 62/85 (72%), Positives = 65/85 (76%)

Query:     1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
             I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct:   258 IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 317

Query:    55 TLEVESSDTIDNVKAKIQDKKRIPP 79
             TLEVESSDTIDNVKAKIQDK+ IPP
Sbjct:   318 TLEVESSDTIDNVKAKIQDKEGIPP 342

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

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

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

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

 Score = 274 (101.5 bits), Expect = 6.8e-24, P = 6.8e-24
 Identities = 62/85 (72%), Positives = 65/85 (76%)

Query:     1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
             I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct:   182 IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 241

Query:    55 TLEVESSDTIDNVKAKIQDKKRIPP 79
             TLEVESSDTIDNVKAKIQDK+ IPP
Sbjct:   242 TLEVESSDTIDNVKAKIQDKEGIPP 266

GO:0005622 "intracellular" evidence=TAS

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

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

GO:0005773 "vacuole" evidence=IDA

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

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

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

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

 Score = 274 (101.5 bits), Expect = 6.8e-24, P = 6.8e-24
 Identities = 62/85 (72%), Positives = 65/85 (76%)

Query:     1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
             I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct:   182 IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 241

Query:    55 TLEVESSDTIDNVKAKIQDKKRIPP 79
             TLEVESSDTIDNVKAKIQDK+ IPP
Sbjct:   242 TLEVESSDTIDNVKAKIQDKEGIPP 266

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

GO:0005773 "vacuole" evidence=IDA

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

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

 Score = 274 (101.5 bits), Expect = 6.8e-24, P = 6.8e-24
 Identities = 62/85 (72%), Positives = 65/85 (76%)

Query:     1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
             I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct:    30 IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query:    55 TLEVESSDTIDNVKAKIQDKKRIPP 79
             TLEVESSDTIDNVKAKIQDK+ IPP
Sbjct:    90 TLEVESSDTIDNVKAKIQDKEGIPP 114

GO:0005622 "intracellular" evidence=TAS

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

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

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

 Score = 274 (101.5 bits), Expect = 6.8e-24, P = 6.8e-24
 Identities = 62/85 (72%), Positives = 65/85 (76%)

Query:     1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
             I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct:   106 IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 165

Query:    55 TLEVESSDTIDNVKAKIQDKKRIPP 79
             TLEVESSDTIDNVKAKIQDK+ IPP
Sbjct:   166 TLEVESSDTIDNVKAKIQDKEGIPP 190

GO:0005622 "intracellular" evidence=TAS

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

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

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

 Score = 274 (101.5 bits), Expect = 1.7e-23, P = 1.7e-23
 Identities = 62/85 (72%), Positives = 65/85 (76%)

Query:     1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
             I+DKEGIPP QQR IFAGKQLEDGRTLADY IQ ESTLHL     G    F K    + I
Sbjct:   334 IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 393

Query:    55 TLEVESSDTIDNVKAKIQDKKRIPP 79
             TLEVESSDTIDNVKAKIQDK+ IPP
Sbjct:   394 TLEVESSDTIDNVKAKIQDKEGIPP 418

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

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

GO:0007568 "aging" evidence=IEP

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

 Score = 268 (99.4 bits), Expect = 2.9e-23, P = 2.9e-23
 Identities = 60/85 (70%), Positives = 65/85 (76%)

Query:     1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
             I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL     G    F K    + I
Sbjct:   258 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 317

Query:    55 TLEVESSDTIDNVKAKIQDKKRIPP 79
             TLEVESSDTIDNVK+KIQDK+ IPP
Sbjct:   318 TLEVESSDTIDNVKSKIQDKEGIPP 342

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0007126 "meiosis" evidence=IMP

GO:0016567 "protein ubiquitination" evidence=NAS

GO:0016579 "protein deubiquitination" evidence=NAS

GO:0031386 "protein tag" evidence=NAS

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

 Score = 268 (99.4 bits), Expect = 2.9e-23, P = 2.9e-23
 Identities = 60/85 (70%), Positives = 65/85 (76%)

Query:     1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
             I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL     G    F K    + I
Sbjct:   258 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 317

Query:    55 TLEVESSDTIDNVKAKIQDKKRIPP 79
             TLEVESSDTIDNVK+KIQDK+ IPP
Sbjct:   318 TLEVESSDTIDNVKSKIQDKEGIPP 342

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA;IC

GO:0006281 "DNA repair" evidence=IEA

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

GO:0016567 "protein ubiquitination" evidence=IMP

GO:0031386 "protein tag" evidence=ISS

GO:0006950 "response to stress" evidence=TAS

GO:0006513 "protein monoubiquitination" evidence=TAS

GO:0000209 "protein polyubiquitination" evidence=TAS

GO:0030437 "ascospore formation" evidence=TAS

GO:0016579 "protein deubiquitination" evidence=TAS

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

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

 Score = 268 (99.4 bits), Expect = 2.9e-23, P = 2.9e-23
 Identities = 60/85 (70%), Positives = 65/85 (76%)

Query:     1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
             I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL     G    F K    + I
Sbjct:   182 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 241

Query:    55 TLEVESSDTIDNVKAKIQDKKRIPP 79
             TLEVESSDTIDNVK+KIQDK+ IPP
Sbjct:   242 TLEVESSDTIDNVKSKIQDKEGIPP 266

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0043581 "mycelium development" evidence=IEP

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

 Score = 268 (99.4 bits), Expect = 2.9e-23, P = 2.9e-23
 Identities = 60/85 (70%), Positives = 65/85 (76%)

Query:     1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
             I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL     G    F K    + I
Sbjct:   106 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 165

Query:    55 TLEVESSDTIDNVKAKIQDKKRIPP 79
             TLEVESSDTIDNVK+KIQDK+ IPP
Sbjct:   166 TLEVESSDTIDNVKSKIQDKEGIPP 190

GO:0031386 "protein tag" evidence=ISA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8H159	UBQ10_ARATH	No assigned EC number	0.7294	0.5939	0.1728	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	133
cd01803	76	cd01803, Ubiquitin, Ubiquitin	2e-20
pfam00240	69	pfam00240, ubiquitin, Ubiquitin family	2e-15
smart00213	72	smart00213, UBQ, Ubiquitin homologues	4e-15
cd01806	76	cd01806, Nedd8, Nebb8-like ubiquitin protein	5e-14
cd01769	69	cd01769, UBL, Ubiquitin-like domain of UBL	7e-13
cd01803	76	cd01803, Ubiquitin, Ubiquitin	4e-11
cd01809	72	cd01809, Scythe_N, Ubiquitin-like domain of Scythe	3e-09
pfam00240	69	pfam00240, ubiquitin, Ubiquitin family	1e-07
PTZ00044	76	PTZ00044, PTZ00044, ubiquitin; Provisional	1e-07
cd01805	77	cd01805, RAD23_N, Ubiquitin-like domain of RAD23	2e-06
smart00213	72	smart00213, UBQ, Ubiquitin homologues	1e-05
pfam11976	72	pfam11976, Rad60-SLD, Ubiquitin-2 like Rad60 SUMO-	2e-05
cd01769	69	cd01769, UBL, Ubiquitin-like domain of UBL	4e-05
cd01797	78	cd01797, NIRF_N, amino-terminal ubiquitin-like dom	9e-05
cd01807	74	cd01807, GDX_N, ubiquitin-like domain of GDX	0.002
TIGR00601	378	TIGR00601, rad23, UV excision repair protein Rad23	0.002
cd01806	76	cd01806, Nedd8, Nebb8-like ubiquitin protein	0.004

>gnl|CDD|176398 cd01803, Ubiquitin, Ubiquitin

 Score = 78.8 bits (194), Expect = 2e-20
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72

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 = 65.3 bits (160), Expect = 2e-15
 Identities = 28/40 (70%), Positives = 32/40 (80%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQE-STLHL 39
          IEDKEGIP  QQR IF+GK LED  TL++Y IQ+ STLHL
Sbjct: 25 IEDKEGIPVDQQRLIFSGKVLEDDTTLSEYGIQDGSTLHL 64

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 = 64.6 bits (158), Expect = 4e-15
 Identities = 26/40 (65%), Positives = 29/40 (72%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          I +  GIPP QQR I+ GK LED RTLADY IQ  ST+HL
Sbjct: 30 IAELTGIPPEQQRLIYKGKVLEDDRTLADYGIQDGSTIHL 69

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

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

 Score = 62.1 bits (151), Expect = 5e-14
 Identities = 24/40 (60%), Positives = 32/40 (80%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQE-STLHL 39
          +E+KEGIPP QQR I++GKQ+ D +T ADYK++  S LHL
Sbjct: 30 VEEKEGIPPQQQRLIYSGKQMNDDKTAADYKLEGGSVLHL 69

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

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

 Score = 59.2 bits (144), Expect = 7e-13
 Identities = 26/40 (65%), Positives = 32/40 (80%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQE-STLHL 39
          I  KEG+PP QQR I+AGK L+D +TL+DY IQ+ STLHL
Sbjct: 27 IAAKEGVPPEQQRLIYAGKILKDDKTLSDYGIQDGSTLHL 66

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|176398 cd01803, Ubiquitin, Ubiquitin

 Score = 54.9 bits (132), Expect = 4e-11
 Identities = 24/35 (68%), Positives = 27/35 (77%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 38

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

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

 Score = 49.9 bits (120), Expect = 3e-09
 Identities = 18/40 (45%), Positives = 30/40 (75%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQES-TLHL 39
          I ++ GIP  QQR I++G+ L+D  TL++YK+++  T+HL
Sbjct: 30 IAEEVGIPVEQQRLIYSGRVLKDDETLSEYKVEDGHTIHL 69

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|215813 pfam00240, ubiquitin, Ubiquitin family

 Score = 45.3 bits (108), Expect = 1e-07
 Identities = 17/33 (51%), Positives = 23/33 (69%)

Query: 47 KNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          K  D + ITLEV+ SDT+  +K KI+DK+ IP 
Sbjct: 1  KTLDGKTITLEVDPSDTVSELKEKIEDKEGIPV 33

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|185411 PTZ00044, PTZ00044, ubiquitin; Provisional

 Score = 45.6 bits (108), Expect = 1e-07
 Identities = 18/40 (45%), Positives = 28/40 (70%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQE-STLHL 39
          +++KEGI   Q R I++GKQ+ D   L+DYK+   ST+H+
Sbjct: 30 LQEKEGIDVKQIRLIYSGKQMSDDLKLSDYKVVPGSTIHM 69

Length = 76

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

 Score = 42.3 bits (100), Expect = 2e-06
 Identities = 18/37 (48%), Positives = 26/37 (70%), Gaps = 2/37 (5%)

Query: 1  IEDKEG--IPPGQQRSIFAGKQLEDGRTLADYKIQES 35
          IE+++G   PP QQ+ I++GK L+D  TL +YKI E 
Sbjct: 30 IEEEKGCDYPPEQQKLIYSGKILKDDTTLEEYKIDEK 66

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|214563 smart00213, UBQ, Ubiquitin homologues

 Score = 40.3 bits (95), Expect = 1e-05
 Identities = 16/35 (45%), Positives = 21/35 (60%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
            K  D + ITLEV+ SDT+  +K KI +   IPP
Sbjct: 4  TVKTLDGKTITLEVKPSDTVSELKEKIAELTGIPP 38

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

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

 Score = 39.4 bits (93), Expect = 2e-05
 Identities = 17/39 (43%), Positives = 24/39 (61%), Gaps = 2/39 (5%)

Query: 3  DKEGIPPGQQ-RSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
           K GIP  QQ R IF G++L+   T+ADY I+   T+ +
Sbjct: 32 KKRGIPADQQVRLIFDGERLDPNDTVADYDIEDGDTIDV 70

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

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

 Score = 38.8 bits (91), Expect = 4e-05
 Identities = 13/35 (37%), Positives = 18/35 (51%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
            K    +   LEV   DT+  +KAKI  K+ +PP
Sbjct: 1  TVKTLTGKTFELEVSPDDTVAELKAKIAAKEGVPP 35

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|176392 cd01797, NIRF_N, amino-terminal ubiquitin-like domain of Np95 and NIRF

 Score = 38.3 bits (89), Expect = 9e-05
 Identities = 14/32 (43%), Positives = 20/32 (62%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKI 32
          I++   + P  QR  + GKQ+EDG TL DY +
Sbjct: 32 IQELFNVEPECQRLFYRGKQMEDGHTLFDYNV 63

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. Length = 78

>gnl|CDD|176402 cd01807, GDX_N, ubiquitin-like domain of GDX

 Score = 34.9 bits (80), Expect = 0.002
 Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKI-QESTLHL 39
          + +   +P  QQR +F GK L D + L+DY I   + L+L
Sbjct: 30 VSEHLNVPEEQQRLLFKGKALADDKRLSDYSIGPNAKLNL 69

GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown. Length = 74

>gnl|CDD|233045 TIGR00601, rad23, UV excision repair protein Rad23

 Score = 36.4 bits (84), Expect = 0.002
 Identities = 16/37 (43%), Positives = 25/37 (67%), Gaps = 3/37 (8%)

Query: 1  IEDKEG---IPPGQQRSIFAGKQLEDGRTLADYKIQE 34
          IE ++G    P  QQ+ I++GK L D +T+ +YKI+E
Sbjct: 30 IEAEQGKDAYPVAQQKLIYSGKILSDDKTVKEYKIKE 66

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) [DNA metabolism, DNA replication, recombination, and repair]. Length = 378

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

 Score = 33.6 bits (77), Expect = 0.004
 Identities = 8/27 (29%), Positives = 20/27 (74%)

Query: 54 ITLEVESSDTIDNVKAKIQDKKRIPPP 80
          I +++E +D ++ +K ++++K+ IPP 
Sbjct: 13 IEIDIEPTDKVERIKERVEEKEGIPPQ 39

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	133
cd01802	103	AN1_N ubiquitin-like domain of AN1. AN1 (also know	99.72
cd01807	74	GDX_N ubiquitin-like domain of GDX. GDX contains a	99.71
cd01810	74	ISG15_repeat2 ISG15 ubiquitin-like protein, second	99.71
cd01797	78	NIRF_N amino-terminal ubiquitin-like domain of Np9	99.69
cd01798	70	parkin_N amino-terminal ubiquitin-like of parkin p	99.69
cd01794	70	DC_UbP_C dendritic cell derived ubiquitin-like pro	99.69
cd01791	73	Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also know	99.67
cd01796	71	DDI1_N DNA damage inducible protein 1 ubiquitin-li	99.66
PTZ00044	76	ubiquitin; Provisional	99.65
cd01793	74	Fubi Fubi ubiquitin-like protein. Fubi is a ubiqui	99.65
cd01805	77	RAD23_N Ubiquitin-like domain of RAD23. RAD23 belo	99.62
PF00240	69	ubiquitin: Ubiquitin family; InterPro: IPR000626 U	99.61
KOG0004	156	consensus Ubiquitin/40S ribosomal protein S27a fus	99.61
cd01804	78	midnolin_N Ubiquitin-like domain of midnolin. midn	99.6
cd01806	76	Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also kn	99.59
cd01792	80	ISG15_repeat1 ISG15 ubiquitin-like protein, first	99.59
cd01803	76	Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40	99.59
cd01809	72	Scythe_N Ubiquitin-like domain of Scythe protein.	99.58
KOG0005	70	consensus Ubiquitin-like protein [Cell cycle contr	99.58
KOG0003	128	consensus Ubiquitin/60s ribosomal protein L40 fusi	99.58
cd01808	71	hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC	99.57
cd01800	76	SF3a120_C Ubiquitin-like domain of Mammalian splic	99.53
cd01812	71	BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-ter	99.5
cd01790	79	Herp_N Homocysteine-responsive endoplasmic reticul	99.49
cd01813	74	UBP_N UBP ubiquitin processing protease. The UBP (	99.46
smart00213	64	UBQ Ubiquitin homologues. Ubiquitin-mediated prote	99.44
cd01799	75	Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HO	99.43
cd01815	75	BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC	99.41
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	99.38
cd01763	87	Sumo Small ubiquitin-related modifier (SUMO). Smal	99.32
cd01769	69	UBL Ubiquitin-like domain of UBL. UBLs function by	99.3
cd01793	74	Fubi Fubi ubiquitin-like protein. Fubi is a ubiqui	99.25
cd01797	78	NIRF_N amino-terminal ubiquitin-like domain of Np9	99.23
KOG0011	340	consensus Nucleotide excision repair factor NEF2,	99.23
cd01807	74	GDX_N ubiquitin-like domain of GDX. GDX contains a	99.22
cd01814	113	NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and AT	99.22
KOG0004	156	consensus Ubiquitin/40S ribosomal protein S27a fus	99.17
cd01794	70	DC_UbP_C dendritic cell derived ubiquitin-like pro	99.16
cd01815	75	BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC	99.16
cd01795	107	USP48_C USP ubiquitin-specific protease. The USP (	99.14
cd01798	70	parkin_N amino-terminal ubiquitin-like of parkin p	99.13
KOG0005	70	consensus Ubiquitin-like protein [Cell cycle contr	99.12
cd01810	74	ISG15_repeat2 ISG15 ubiquitin-like protein, second	99.1
cd01802	103	AN1_N ubiquitin-like domain of AN1. AN1 (also know	99.07
KOG0003	128	consensus Ubiquitin/60s ribosomal protein L40 fusi	99.05
cd01791	73	Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also know	99.04
cd01808	71	hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC	99.02
PF00240	69	ubiquitin: Ubiquitin family; InterPro: IPR000626 U	99.02
PTZ00044	76	ubiquitin; Provisional	99.0
KOG0010	493	consensus Ubiquitin-like protein [Posttranslationa	99.0
cd01800	76	SF3a120_C Ubiquitin-like domain of Mammalian splic	98.95
cd01796	71	DDI1_N DNA damage inducible protein 1 ubiquitin-li	98.93
cd01805	77	RAD23_N Ubiquitin-like domain of RAD23. RAD23 belo	98.93
cd01809	72	Scythe_N Ubiquitin-like domain of Scythe protein.	98.93
cd01806	76	Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also kn	98.93
cd01804	78	midnolin_N Ubiquitin-like domain of midnolin. midn	98.89
cd01814	113	NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and AT	98.88
cd01803	76	Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40	98.87
cd01792	80	ISG15_repeat1 ISG15 ubiquitin-like protein, first	98.84
KOG0001	75	consensus Ubiquitin and ubiquitin-like proteins [P	98.84
PF11976	72	Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; Inter	98.79
cd01812	71	BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-ter	98.74
cd01790	79	Herp_N Homocysteine-responsive endoplasmic reticul	98.71
PLN02560	308	enoyl-CoA reductase	98.66
cd01789	84	Alp11_N Ubiquitin-like domain of Alp11 tubulin-fol	98.65
cd01763	87	Sumo Small ubiquitin-related modifier (SUMO). Smal	98.64
cd01788	119	ElonginB Ubiquitin-like domain of Elongin B. Elong	98.64
cd01813	74	UBP_N UBP ubiquitin processing protease. The UBP (	98.63
cd01799	75	Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HO	98.51
PF14560	87	Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2K	98.5
cd01795	107	USP48_C USP ubiquitin-specific protease. The USP (	98.48
KOG4248	1143	consensus Ubiquitin-like protein, regulator of apo	98.45
KOG0010	493	consensus Ubiquitin-like protein [Posttranslationa	98.39
smart00213	64	UBQ Ubiquitin homologues. Ubiquitin-mediated prote	98.39
cd01801	77	Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-	98.37
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	98.32
PF13881	111	Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB	98.32
cd00196	69	UBQ Ubiquitin-like proteins. Ubiquitin homologs; I	98.27
cd01769	69	UBL Ubiquitin-like domain of UBL. UBLs function by	98.23
KOG0001	75	consensus Ubiquitin and ubiquitin-like proteins [P	98.1
KOG0011	340	consensus Nucleotide excision repair factor NEF2,	97.84
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	97.84
PF11976	72	Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; Inter	97.82
cd01811	80	OASL_repeat1 2'-5' oligoadenylate synthetase-like	97.75
PF11543	80	UN_NPL4: Nuclear pore localisation protein NPL4; I	97.69
cd01789	84	Alp11_N Ubiquitin-like domain of Alp11 tubulin-fol	97.62
KOG4495	110	consensus RNA polymerase II transcription elongati	97.58
KOG4248	1143	consensus Ubiquitin-like protein, regulator of apo	97.4
KOG1872	473	consensus Ubiquitin-specific protease [Posttransla	97.34
PF10302	97	DUF2407: DUF2407 ubiquitin-like domain; InterPro:	97.34
PF13881	111	Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB	97.3
PF13019	162	Telomere_Sde2: Telomere stability and silencing	97.14
cd01801	77	Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-	96.87
smart00166	80	UBX Domain present in ubiquitin-regulatory protein	96.7
KOG3493	73	consensus Ubiquitin-like protein [Posttranslationa	96.68
cd01811	80	OASL_repeat1 2'-5' oligoadenylate synthetase-like	96.67
cd01788	119	ElonginB Ubiquitin-like domain of Elongin B. Elong	96.58
PF11470	65	TUG-UBL1: GLUT4 regulating protein TUG; InterPro:	96.56
PF00789	82	UBX: UBX domain; InterPro: IPR001012 The UBX domai	96.56
PF14560	87	Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2K	96.49
cd01767	77	UBX UBX (ubiquitin regulatory X) domain. The UBX (	96.16
cd01772	79	SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-subst	96.0
PLN02560	308	enoyl-CoA reductase	95.75
cd01770	79	p47_UBX p47-like ubiquitin domain. p47_UBX p47 is	95.67
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	95.55
KOG1769	99	consensus Ubiquitin-like proteins [Posttranslation	95.52
cd00196	69	UBQ Ubiquitin-like proteins. Ubiquitin homologs; I	95.42
cd01774	85	Faf1_like2_UBX Faf1 ike-2 UBX domain. Faf1_like2 i	95.21
KOG0013	231	consensus Uncharacterized conserved protein [Funct	95.01
cd01773	82	Faf1_like1_UBX Faf1 ike-1 UBX domain. Faf1_like1 i	94.7
smart00455	70	RBD Raf-like Ras-binding domain.	94.66
cd01760	72	RBD Ubiquitin-like domain of RBD-like S/T kinases.	94.31
PF08817	79	YukD: WXG100 protein secretion system (Wss), prote	94.26
cd01771	80	Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated fac	93.6
cd06406	80	PB1_P67 A PB1 domain is present in p67 proteins wh	93.56
cd06409	86	PB1_MUG70 The MUG70 protein is a product of the me	93.35
KOG1872	473	consensus Ubiquitin-specific protease [Posttransla	91.78
PF12754	309	Blt1: Cell-cycle control medial ring component; In	91.47
COG5227	103	SMT3 Ubiquitin-like protein (sentrin) [Posttransla	91.11
KOG4583	391	consensus Membrane-associated ER protein involved	90.88
PRK06437	67	hypothetical protein; Provisional	90.13
PF09379	80	FERM_N: FERM N-terminal domain ; InterPro: IPR0189	90.06
PF11620	88	GABP-alpha: GA-binding protein alpha chain; InterP	89.82
PRK08364	70	sulfur carrier protein ThiS; Provisional	89.64
cd01817	73	RGS12_RBD Ubiquitin domain of RGS12 and RGS14. RGS	89.44
PF02196	71	RBD: Raf-like Ras-binding domain; InterPro: IPR003	89.42
KOG1769	99	consensus Ubiquitin-like proteins [Posttranslation	89.24
PF10302	97	DUF2407: DUF2407 ubiquitin-like domain; InterPro:	88.24
KOG0007	341	consensus Splicing factor 3a, subunit 1 [RNA proce	87.54
cd00754	80	MoaD Ubiquitin domain of MoaD-like proteins. MoaD	87.19
KOG1639	297	consensus Steroid reductase required for elongatio	87.03
PF15044	76	CLU_N: Mitochondrial function, CLU-N-term	86.45
PF11543	80	UN_NPL4: Nuclear pore localisation protein NPL4; I	85.73
cd01818	77	TIAM1_RBD Ubiquitin domain of Tiam1 guanine nucleo	85.56
PF08817	79	YukD: WXG100 protein secretion system (Wss), prote	85.56
PF10790	76	DUF2604: Protein of Unknown function (DUF2604); In	84.61
cd06410	97	PB1_UP2 Uncharacterized protein 2. The PB1 domain	84.21
smart00666	81	PB1 PB1 domain. Phox and Bem1p domain, present in	83.94
cd01787	85	GRB7_RA RA (RAS-associated like) domain of Grb7. G	83.35
cd06407	82	PB1_NLP A PB1 domain is present in NIN like protei	81.9
cd06411	78	PB1_p51 The PB1 domain is present in the p51 prote	81.3
PF12436	249	USP7_ICP0_bdg: ICP0-binding domain of Ubiquitin-sp	80.64
cd00565	65	ThiS ThiaminS ubiquitin-like sulfur carrier protei	80.5
COG5417	81	Uncharacterized small protein [Function unknown]	80.18

>cd01802 AN1_N ubiquitin-like domain of AN1

Probab=99.72  E-value=5e-18  Score=114.98  Aligned_cols=80  Identities=19%  Similarity=0.085  Sum_probs=71.7

Q ss_pred             ccccc-cccccccccc-----cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCcccccccccc
Q 040111           29 DYKIQ-ESTLHLGWRA-----DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWF  102 (133)
Q Consensus        29 ~ygI~-~stl~L~~~~-----i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~  102 (133)
                      -|.+. -+++|+.++.     ++||+.+|+++.++|++++||++||++|+++.|+|+++|+|+|+|+.|+|+.+|++|+|
T Consensus         9 ~~~~~~~~~~~~~~~~~~~M~I~Vk~l~G~~~~leV~~~~TV~~lK~kI~~~~gip~~~QrLi~~Gk~L~D~~tL~dy~I   88 (103)
T cd01802           9 FFNEDNMGPFHYKLPFYDTMELFIETLTGTCFELRVSPFETVISVKAKIQRLEGIPVAQQHLIWNNMELEDEYCLNDYNI   88 (103)
T ss_pred             ccccCCcceeEEeeccCCCEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEECCEECCCCCcHHHcCC
Confidence            35566 6788887776     99999999999999999999999999999999999999999999999999999999998


Q ss_pred             EEeEEE
Q 040111          103 VVVGVI  108 (133)
Q Consensus       103 ~~~~~~  108 (133)
                      ...+.+
T Consensus        89 ~~~stL   94 (103)
T cd01802          89 SEGCTL   94 (103)
T ss_pred             CCCCEE
Confidence            655543

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

>cd01807 GDX_N ubiquitin-like domain of GDX

Probab=99.71  E-value=4.8e-18  Score=108.26  Aligned_cols=67  Identities=13%  Similarity=0.088  Sum_probs=62.4

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      .|+||+.+|+++.++|++++||++||++|++++|+|+++|+|+|+|++|+|+.+|++|++.+.+.+.
T Consensus         2 ~i~vk~~~G~~~~l~v~~~~tV~~lK~~i~~~~gi~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~l~   68 (74)
T cd01807           2 FLTVKLLQGRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLLFKGKALADDKRLSDYSIGPNAKLN   68 (74)
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEECCCCCCHHHCCCCCCCEEE
Confidence            3789999999999999999999999999999999999999999999999999999999997666543

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=99.71  E-value=6.6e-18  Score=107.66  Aligned_cols=66  Identities=14%  Similarity=0.099  Sum_probs=61.5

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      |+||++.|+++++++++++||++||++|+++.|+|+++|+|+|+|+.|+|+.+|++|+|.+...+.
T Consensus         1 i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~q~L~~~G~~L~D~~tL~~~~i~~~~tl~   66 (74)
T cd01810           1 ILVRNDKGRSSIYEVQLTQTVATLKQQVSQRERVQADQFWLSFEGRPMEDEHPLGEYGLKPGCTVF   66 (74)
T ss_pred             CEEECCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEECCEECCCCCCHHHcCCCCCCEEE
Confidence            689999999999999999999999999999999999999999999999999999999996555443

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.

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

Probab=99.69  E-value=1.4e-17  Score=107.54  Aligned_cols=68  Identities=12%  Similarity=0.068  Sum_probs=62.3

Q ss_pred             ccccCCCCCCC-ceee-ccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEEe
Q 040111           43 ADFCKNPDPQN-ITLE-VESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        43 ~i~Vk~~~g~~-~~l~-V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~~  110 (133)
                      +|+||+.+|+. +.++ +++++||+++|++|++++|+|+++|+|+|+|+.|+|+.+|++|++...++|.+
T Consensus         2 ~I~vk~~~G~~~~~l~~v~~~~TV~~lK~~i~~~~gi~~~~QrLi~~Gk~L~D~~tL~~y~i~~~~~i~l   71 (78)
T cd01797           2 WIQVRTMDGKETRTVDSLSRLTKVEELREKIQELFNVEPECQRLFYRGKQMEDGHTLFDYNVGLNDIIQL   71 (78)
T ss_pred             EEEEEcCCCCEEEEeeccCCcCcHHHHHHHHHHHhCCCHHHeEEEeCCEECCCCCCHHHcCCCCCCEEEE
Confidence            47899999997 6885 89999999999999999999999999999999999999999999987776654

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.

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

Probab=99.69  E-value=1.4e-17  Score=104.91  Aligned_cols=67  Identities=9%  Similarity=0.151  Sum_probs=62.6

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEEe
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~~  110 (133)
                      |+||+++|+++.+++++++||+++|++|+++.|+|+++|+|+|+|++|+|+.+|++|++...+.+..
T Consensus         1 i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~q~Li~~G~~L~d~~~l~~~~i~~~stl~l   67 (70)
T cd01798           1 VYVRTNTGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVIFAGKELRNTTTIQECDLGQQSILHA   67 (70)
T ss_pred             CEEEcCCCCEEEEEECCCChHHHHHHHHHHHHCCCHHHeEEEECCeECCCCCcHHHcCCCCCCEEEE
Confidence            5789999999999999999999999999999999999999999999999999999999987766543

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.

>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein

Probab=99.69  E-value=1.7e-17  Score=105.05  Aligned_cols=65  Identities=15%  Similarity=0.107  Sum_probs=59.8

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      +.||.++|+++++++++++||+++|++|++++|+|+++|+|+|+|++|+|+.+|++|++....+|
T Consensus         1 ~~vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~Li~~G~~L~D~~~l~~~~i~~~~tv   65 (70)
T cd01794           1 LKVRLSTGKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWFFSGKLLTDKTRLQETKIQKDYVV   65 (70)
T ss_pred             CeEEcCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEECCeECCCCCCHHHcCCCCCCEE
Confidence            35789999999999999999999999999999999999999999999999999999998654444

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.

>cd01791 Ubl5 UBL5 ubiquitin-like modifier

Probab=99.67  E-value=5.2e-17  Score=103.62  Aligned_cols=66  Identities=14%  Similarity=0.078  Sum_probs=61.6

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      |+|++..|+.+.+++++++||++||++|+++.|+|+++|||+|+|+.|+|+.+|++|++.+.+.|.
T Consensus         4 i~vkt~~Gk~~~~~v~~~~TV~~LK~~I~~~~~~~~~~qrLi~~Gk~L~D~~tL~~ygi~~~stv~   69 (73)
T cd01791           4 VVCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFKDHISLGDYEIHDGMNLE   69 (73)
T ss_pred             EEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEeCCcCCCCCCCHHHcCCCCCCEEE
Confidence            788999999999999999999999999999999999999999999999999999999997666553

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.

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

Probab=99.66  E-value=4.2e-17  Score=103.35  Aligned_cols=68  Identities=12%  Similarity=0.128  Sum_probs=62.1

Q ss_pred             cccCCC-CCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCcc-ccccccccEEeEEEEeC
Q 040111           44 DFCKNP-DPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFE-EVLSFFWFVVVGVIFCG  111 (133)
Q Consensus        44 i~Vk~~-~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~-~tL~dy~~~~~~~~~~~  111 (133)
                      ++|++. +|+++.+++++++||+++|++|++++|+|+++|+|+|+|++|+|+ .+|++|++.+..+++.+
T Consensus         1 l~v~~~~~g~~~~l~v~~~~TV~~lK~~I~~~~gip~~~q~Li~~Gk~L~D~~~~L~~~gi~~~~~l~l~   70 (71)
T cd01796           1 ITVYTARSETTFSLDVDPDLELENFKALCEAESGIPASQQQLIYNGRELVDNKRLLALYGVKDGDLVVLR   70 (71)
T ss_pred             CEEEECCCCCEEEEEECCcCCHHHHHHHHHHHhCCCHHHeEEEECCeEccCCcccHHHcCCCCCCEEEEe
Confidence            468888 899999999999999999999999999999999999999999997 68999999887776653

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.

>PTZ00044 ubiquitin; Provisional

Probab=99.65  E-value=7.7e-17  Score=102.81  Aligned_cols=64  Identities=17%  Similarity=0.081  Sum_probs=60.3

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVG  106 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~  106 (133)
                      +|+||+++|+++++++++++||+++|++|++++|+|+++|+|+|+|+.|+|+.+|++|++....
T Consensus         2 ~i~vk~~~G~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~L~d~~~l~~~~i~~~~   65 (76)
T PTZ00044          2 QILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYSGKQMSDDLKLSDYKVVPGS   65 (76)
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEEccCCCcHHHcCCCCCC
Confidence            3789999999999999999999999999999999999999999999999999999999985444

>cd01793 Fubi Fubi ubiquitin-like protein

Probab=99.65  E-value=1e-16  Score=102.19  Aligned_cols=63  Identities=19%  Similarity=0.130  Sum_probs=56.9

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGV  107 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~  107 (133)
                      +|+||+.  ++++++|++++||+++|++|++++|+|+++|+|+|+|++|+|+.+|++|++.+.+.
T Consensus         2 qi~vk~~--~~~~l~v~~~~tV~~lK~~i~~~~gip~~~q~Li~~Gk~L~D~~tL~~~~i~~~~t   64 (74)
T cd01793           2 QLFVRAQ--NTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVLLLAGVPLEDDATLGQCGVEELCT   64 (74)
T ss_pred             EEEEECC--CEEEEEECCcCcHHHHHHHHHhhhCCCHHHEEEEECCeECCCCCCHHHcCCCCCCE
Confidence            3678873  67899999999999999999999999999999999999999999999999955443

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.

>cd01805 RAD23_N Ubiquitin-like domain of RAD23

Probab=99.62  E-value=3e-16  Score=100.23  Aligned_cols=67  Identities=19%  Similarity=0.243  Sum_probs=62.1

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCC--CCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRI--PPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gI--p~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      .++|++.+|+.+.+++++++||++||++|++++|+  |+++|+|+|+|+.|+|+.+|++|++...+.++
T Consensus         2 ~i~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~i~   70 (77)
T cd01805           2 KITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKILKDDTTLEEYKIDEKDFVV   70 (77)
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEEECCEEccCCCCHHHcCCCCCCEEE
Confidence            37899999999999999999999999999999999  99999999999999999999999998766444

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).

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

Probab=99.61  E-value=3.7e-16  Score=97.75  Aligned_cols=64  Identities=25%  Similarity=0.275  Sum_probs=59.6

Q ss_pred             CCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEEe
Q 040111           47 KNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        47 k~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~~  110 (133)
                      |+++|+.+.+++++++||.+||++|+++.|+|++.|+|+|+|+.|+|+.+|++|++.+.++|++
T Consensus         1 k~~~g~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~~G~~L~d~~tL~~~~i~~~~~I~l   64 (69)
T PF00240_consen    1 KTLSGKTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLIYNGKELDDDKTLSDYGIKDGSTIHL   64 (69)
T ss_dssp             EETTSEEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEETTEEESTTSBTGGGTTSTTEEEEE
T ss_pred             CCCCCcEEEEEECCCCCHHHhhhhcccccccccccceeeeeeecccCcCcHHHcCCCCCCEEEE
Confidence            4678899999999999999999999999999999999999999999999999999988776654

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 ....

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

Probab=99.61  E-value=4.3e-16  Score=110.96  Aligned_cols=72  Identities=38%  Similarity=0.355  Sum_probs=64.7

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEe-----EEEEeCcee
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVV-----GVIFCGCRV  114 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~-----~~~~~~~~~  114 (133)
                      +|||+++.++++..++++++||..+|++|++.+|||+++|||+|+|++|+|+.+||||+|...     .+...||+.
T Consensus         2 ~ifVk~l~~kti~~eve~~~ti~~~Kakiq~~egIp~dqqrlifag~qLedgrtlSDY~Iqkestl~l~l~l~Gg~k   78 (156)
T KOG0004|consen    2 QIFVKTLTGKTITLEVEANDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGAK   78 (156)
T ss_pred             ccchhhccccceeeeecccccHHHHHHhhhcccCCCchhhhhhhhhcccccCCccccccccccceEEEEEEecCCcc
Confidence            489999999999999999999999999999999999999999999999999999999999443     355566654

>cd01804 midnolin_N Ubiquitin-like domain of midnolin

Probab=99.60  E-value=6.7e-16  Score=99.50  Aligned_cols=65  Identities=14%  Similarity=0.084  Sum_probs=60.0

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      .|+|++..|+.+.+++++++||++||++|+++.|+|+++|+|+|+|+.|+|+ +|++|++.+.+++
T Consensus         3 ~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~~~~~~~qrL~~~Gk~L~d~-~L~~~gi~~~~~i   67 (78)
T cd01804           3 NLNIHSTTGTRFDLSVPPDETVEGLKKRISQRLKVPKERLALLHRETRLSSG-KLQDLGLGDGSKL   67 (78)
T ss_pred             EEEEEECCCCEEEEEECCcCHHHHHHHHHHHHhCCChHHEEEEECCcCCCCC-cHHHcCCCCCCEE
Confidence            4789999999999999999999999999999999999999999999999999 9999999665544

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.

>cd01806 Nedd8 Nebb8-like ubiquitin protein

Probab=99.59  E-value=9.2e-16  Score=97.36  Aligned_cols=66  Identities=15%  Similarity=0.250  Sum_probs=61.3

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      |+|++.+|+++.+++++++||++||++|+++.|+|++.|+|+|+|+.|.|+.+|++|++...+++.
T Consensus         3 i~v~~~~g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~~~g~~L~d~~tl~~~~i~~g~~i~   68 (76)
T cd01806           3 IKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDDKTAADYKLEGGSVLH   68 (76)
T ss_pred             EEEEeCCCCEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEEECCeEccCCCCHHHcCCCCCCEEE
Confidence            789999999999999999999999999999999999999999999999999999999987655443

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.

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

Probab=99.59  E-value=6.8e-16  Score=99.82  Aligned_cols=66  Identities=14%  Similarity=-0.025  Sum_probs=61.3

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEE--EeCCcccCccccccccccEEeEEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEAD--LLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L--~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      .++|++.+|+++.+++++++||++||++|+++.|+|+++|+|  +|+|+.|+|+.+|++|++.+.+++
T Consensus         4 ~i~Vk~~~G~~~~~~v~~~~TV~~lK~~I~~~~~i~~~~qrL~~~~~G~~L~D~~tL~~~gi~~gs~l   71 (80)
T cd01792           4 DLKVKMLGGNEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLAHLDSREVLQDGVPLVSQGLGPGSTV   71 (80)
T ss_pred             EEEEEeCCCCEEEEEcCCCCcHHHHHHHHHHHhCCCHHHEEEEeccCCCCCCCCCCHHHcCCCCCCEE
Confidence            478999999999999999999999999999999999999999  899999999999999999765544

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.

>cd01803 Ubiquitin Ubiquitin

Probab=99.59  E-value=7.9e-16  Score=97.66  Aligned_cols=66  Identities=39%  Similarity=0.406  Sum_probs=61.1

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      +|+|++.+|+.+.+++++++||++||++|++++|+|++.|+|+|+|+.|+|+.+|++|++...+.+
T Consensus         2 ~i~v~~~~g~~~~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~i   67 (76)
T cd01803           2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTL   67 (76)
T ss_pred             EEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCHHHeEEEECCEECCCCCcHHHcCCCCCCEE
Confidence            378999999999999999999999999999999999999999999999999999999998655443

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

>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein

Probab=99.58  E-value=9.9e-16  Score=96.26  Aligned_cols=66  Identities=24%  Similarity=0.140  Sum_probs=61.7

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      ++||+++|+++.+++++++||+++|++|++.+|+|++.|+|+|+|+.|+|+.+|++|++...+.+.
T Consensus         3 i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~l~   68 (72)
T cd01809           3 IKVKTLDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYSGRVLKDDETLSEYKVEDGHTIH   68 (72)
T ss_pred             EEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCEECCCcCcHHHCCCCCCCEEE
Confidence            789999999999999999999999999999999999999999999999999999999997666543

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.

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

Probab=99.58  E-value=5e-16  Score=94.20  Aligned_cols=63  Identities=14%  Similarity=0.269  Sum_probs=59.1

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVG  106 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~  106 (133)
                      |.|++++|+.+.++++|+++|..+|.+|++++||||.+|||+|+|++|.|+.+-++|++--.+
T Consensus         3 iKvktLt~KeIeidIep~DkverIKErvEEkeGIPp~qqrli~~gkqm~DD~tA~~Y~~~~GS   65 (70)
T KOG0005|consen    3 IKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYAGKQMNDDKTAAHYNLLGGS   65 (70)
T ss_pred             eeEeeeccceEEEeeCcchHHHHHHHHhhhhcCCCchhhhhhhccccccccccHHHhhhccce
Confidence            678999999999999999999999999999999999999999999999999999999875333

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

Probab=99.58  E-value=1.4e-16  Score=107.25  Aligned_cols=64  Identities=41%  Similarity=0.408  Sum_probs=60.4

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVG  106 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~  106 (133)
                      .++++++.|+++.++++|++||.++|++|++++||||++|+|+|+|++|+|+.||++|+|...+
T Consensus         2 ~~~~~~~~GKT~~le~EpS~ti~~vKA~i~~~~Gi~~~~~~L~~~~k~LED~~Tla~Y~i~~~~   65 (128)
T KOG0003|consen    2 QIFVKTLTGKTITLEVEPSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKES   65 (128)
T ss_pred             cEEEEEeeCceEEEEecccchHHHHHHHhccccCCCHHHHHHHhcccccccCCcccccCccchh
Confidence            4788999999999999999999999999999999999999999999999999999999986554

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

Probab=99.57  E-value=1.5e-15  Score=95.93  Aligned_cols=64  Identities=9%  Similarity=0.051  Sum_probs=58.8

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      |+||+.+|+ ..+++++++||++||++|+++.|+|+++|+|+|+|+.|+|+.+|++|++.+.+++
T Consensus         3 i~vk~~~g~-~~l~v~~~~TV~~lK~~I~~~~~i~~~~~~Li~~Gk~L~d~~tL~~~~i~~~stl   66 (71)
T cd01808           3 VTVKTPKDK-EEIEIAEDASVKDFKEAVSKKFKANQEQLVLIFAGKILKDTDTLTQHNIKDGLTV   66 (71)
T ss_pred             EEEEcCCCC-EEEEECCCChHHHHHHHHHHHhCCCHHHEEEEECCeEcCCCCcHHHcCCCCCCEE
Confidence            678899887 5899999999999999999999999999999999999999999999999766544

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

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

Probab=99.53  E-value=6.3e-15  Score=94.38  Aligned_cols=61  Identities=16%  Similarity=0.233  Sum_probs=56.1

Q ss_pred             CCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           49 PDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        49 ~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      ++|+++++++++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++|++.+...+.
T Consensus         5 l~g~~~~l~v~~~~TV~~lK~~i~~~~gip~~~q~L~~~G~~L~d~~tL~~~~i~~g~~l~   65 (76)
T cd01800           5 LNGQMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQYEGIFIKDSNSLAYYNLANGTIIH   65 (76)
T ss_pred             cCCeEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCEEcCCCCcHHHcCCCCCCEEE
Confidence            4688999999999999999999999999999999999999999999999999986655443

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.

>cd01812 BAG1_N Ubiquitin-like domain of BAG1

Probab=99.50  E-value=1.2e-14  Score=91.25  Aligned_cols=64  Identities=14%  Similarity=0.016  Sum_probs=58.0

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      |.||+. |+.+.+++++++||++||++|++.+|+|++.|+|+|+|+.|.|+.+|++|++.....+
T Consensus         3 i~vk~~-g~~~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~l~d~~~L~~~~i~~g~~l   66 (71)
T cd01812           3 VRVKHG-GESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIFKGKERDDAETLDMSGVKDGSKV   66 (71)
T ss_pred             EEEEEC-CEEEEEEECCCCcHHHHHHHHHHhhCCChHHeEEeeCCcccCccCcHHHcCCCCCCEE
Confidence            567776 8889999999999999999999999999999999999999999999999998755433

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).

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

Probab=99.49  E-value=1.8e-14  Score=93.03  Aligned_cols=58  Identities=10%  Similarity=-0.041  Sum_probs=51.9

Q ss_pred             cccCCCCCCC--ceeeccccCcHHHHHHHhhhhcC--CCCCceEEEeCCcccCccccccccc
Q 040111           44 DFCKNPDPQN--ITLEVESSDTIDNVKAKIQDKKR--IPPPAEADLLKFPFFFFEEVLSFFW  101 (133)
Q Consensus        44 i~Vk~~~g~~--~~l~V~~~~tV~~LK~~I~~~~g--Ip~~~q~L~~~gk~L~d~~tL~dy~  101 (133)
                      ++||+++++.  +.+++++++||++||++|++..+  .|+++|||+|+||.|+|+.+|++|.
T Consensus         4 l~IK~~~~~~~~~~ve~~~~~TV~~lK~~i~~~~~~~~~~~~QrLIy~GKiLkD~~tL~~~~   65 (79)
T cd01790           4 LLIKSPNQKYEDQTVSCFLNWTVGELKTHLSRVYPSKPLEQDQRLIYSGKLLPDHLKLRDVL   65 (79)
T ss_pred             EEEECCCCCeEEEEEecCCcChHHHHHHHHHHhcCCCCChhHeEEEEcCeeccchhhHHHHh
Confidence            6899999998  55566899999999999999875  5689999999999999999999994

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

>cd01813 UBP_N UBP ubiquitin processing protease

Probab=99.46  E-value=4.3e-14  Score=90.29  Aligned_cols=59  Identities=19%  Similarity=0.012  Sum_probs=54.1

Q ss_pred             CCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEe---CCcccCccccccccccEEeEEE
Q 040111           50 DPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLL---KFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        50 ~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~---~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      .|+.+.+++++++||++||++|++.+|+||++|+|+|   +|+.+.|+.+|++|++.....|
T Consensus         8 ~g~~~~v~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~~~~~Gk~l~D~~~L~~~~i~~g~~i   69 (74)
T cd01813           8 GGQEYSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLGLKVKGKPAEDDVKISALKLKPNTKI   69 (74)
T ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEeecccCCcCCCCcCHHHcCCCCCCEE
Confidence            5778899999999999999999999999999999996   9999999999999998765533

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.

>smart00213 UBQ Ubiquitin homologues

Probab=99.44  E-value=5.1e-14  Score=86.01  Aligned_cols=60  Identities=28%  Similarity=0.257  Sum_probs=56.1

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVV  104 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~  104 (133)
                      |+||+.+ +.+.+++++++||++||++|++.+|+|++.|+|+|+|+.|.|+.+|++|++..
T Consensus         3 i~vk~~~-~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~~g~~L~d~~tL~~~~i~~   62 (64)
T smart00213        3 LTVKTLD-GTITLEVKPSDTVSELKEKIAELTGIPVEQQRLIYKGKVLEDDRTLADYNIQD   62 (64)
T ss_pred             EEEEECC-ceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCEECCCCCCHHHcCCcC
Confidence            6788887 68899999999999999999999999999999999999999999999998864

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

>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1

Probab=99.43  E-value=8.8e-14  Score=89.12  Aligned_cols=58  Identities=19%  Similarity=0.101  Sum_probs=52.5

Q ss_pred             CCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccC-ccccccccccEEeE
Q 040111           48 NPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFF-FEEVLSFFWFVVVG  106 (133)
Q Consensus        48 ~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~-d~~tL~dy~~~~~~  106 (133)
                      ...|.++.+++++++||++||++|++++|+||++|+| |+|+.|. |+.+|++|++...|
T Consensus         9 ~~~~~t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL-~~G~~L~dD~~tL~~ygi~~~g   67 (75)
T cd01799           9 QSHTVTIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRW-VIGQRLARDQETLYSHGIRTNG   67 (75)
T ss_pred             ccCCCeEEEEECCCCcHHHHHHHHHHHHCcCHHHEEE-EcCCeeCCCcCCHHHcCCCCCC
Confidence            4567889999999999999999999999999999999 9999996 66899999997554

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.

>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP

Probab=99.41  E-value=1.3e-13  Score=88.08  Aligned_cols=50  Identities=14%  Similarity=0.110  Sum_probs=44.7

Q ss_pred             ccCcHHHHHHHhhhhc--CCC-CCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           60 SSDTIDNVKAKIQDKK--RIP-PPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        60 ~~~tV~~LK~~I~~~~--gIp-~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      .++||.+||++|+++.  |++ +++|||+|+|+.|+|++||++|+|...+++.
T Consensus        19 ~~~TV~~LK~kI~~~~~egi~~~dqQrLIy~GKiL~D~~TL~dygI~~gstlh   71 (75)
T cd01815          19 GGYQVSTLKQLIAAQLPDSLPDPELIDLIHCGRKLKDDQTLDFYGIQSGSTIH   71 (75)
T ss_pred             ccCcHHHHHHHHHHhhccCCCChHHeEEEeCCcCCCCCCcHHHcCCCCCCEEE
Confidence            5799999999999995  575 9999999999999999999999998766554

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.

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=99.38  E-value=2.3e-13  Score=110.42  Aligned_cols=65  Identities=12%  Similarity=0.163  Sum_probs=61.2

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcC---CCCCceEEEeCCcccCccccccccccEEeEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKR---IPPPAEADLLKFPFFFFEEVLSFFWFVVVGV  107 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~g---Ip~~~q~L~~~gk~L~d~~tL~dy~~~~~~~  107 (133)
                      +|+||++.|+++.++|++++||.+||++|++..|   +|+++|+|+|+|+.|+|+.+|++|+|....+
T Consensus         2 kItVKtl~g~~~~IeV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLIy~GkiL~Dd~tL~dy~I~e~~~   69 (378)
T TIGR00601         2 TLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVREYKIKEKDF   69 (378)
T ss_pred             EEEEEeCCCCEEEEEeCCcChHHHHHHHHHHhhCCCCCChhHeEEEECCEECCCCCcHHHcCCCCCCE
Confidence            4789999999999999999999999999999998   9999999999999999999999999976653

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).

>cd01763 Sumo Small ubiquitin-related modifier (SUMO)

Probab=99.32  E-value=1.6e-12  Score=85.33  Aligned_cols=65  Identities=8%  Similarity=-0.040  Sum_probs=61.1

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      |+|++.+|+.+.++|.++++++.||.+++++.|+|+++|+|+|+|+.|+++.|+++|++....+|
T Consensus        14 I~v~~~~g~~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f~G~~L~~~~T~~~l~m~d~d~I   78 (87)
T cd01763          14 LKVKGQDGNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLFDGQRIRDNQTPDDLGMEDGDEI   78 (87)
T ss_pred             EEEECCCCCEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEECCeECCCCCCHHHcCCCCCCEE
Confidence            88999999999999999999999999999999999999999999999999999999998665544

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.

>cd01769 UBL Ubiquitin-like domain of UBL

Probab=99.30  E-value=2.8e-12  Score=79.20  Aligned_cols=64  Identities=23%  Similarity=0.277  Sum_probs=58.3

Q ss_pred             cCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           46 CKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        46 Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      |+..+|+.+.+++++++||.+||++|++..|+|++.|+|+|+|+.|+|+.+|++|++...+.|+
T Consensus         2 v~~~~~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l~~~g~~l~d~~~l~~~~v~~~~~i~   65 (69)
T cd01769           2 VKTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYAGKILKDDKTLSDYGIQDGSTLH   65 (69)
T ss_pred             eEccCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCcCCCCcCCHHHCCCCCCCEEE
Confidence            5666788999999999999999999999999999999999999999999999999997666544

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.

>cd01793 Fubi Fubi ubiquitin-like protein

Probab=99.25  E-value=1.8e-12  Score=82.47  Aligned_cols=43  Identities=33%  Similarity=0.407  Sum_probs=39.8

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|||+++|+|+|+|++|+|+.+|++|||. ++++|+.++.
T Consensus        28 i~~~~gip~~~q~Li~~Gk~L~D~~tL~~~~i~~~~tl~l~~~l   71 (74)
T cd01793          28 VAGLEGIDVEDQVLLLAGVPLEDDATLGQCGVEELCTLEVAGRL   71 (74)
T ss_pred             HHhhhCCCHHHEEEEECCeECCCCCCHHHcCCCCCCEEEEEEec
Confidence            467899999999999999999999999999999 9999987763

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.

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

Probab=99.23  E-value=1.9e-12  Score=83.49  Aligned_cols=43  Identities=37%  Similarity=0.600  Sum_probs=40.1

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|||+++|+|+|+|++|+|+.+|++|||. +++|+|++++
T Consensus        32 i~~~~gi~~~~QrLi~~Gk~L~D~~tL~~y~i~~~~~i~l~~~~   75 (78)
T cd01797          32 IQELFNVEPECQRLFYRGKQMEDGHTLFDYNVGLNDIIQLLVRQ   75 (78)
T ss_pred             HHHHhCCCHHHeEEEeCCEECCCCCCHHHcCCCCCCEEEEEEec
Confidence            457789999999999999999999999999999 9999998875

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.

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

Probab=99.23  E-value=6.4e-12  Score=99.13  Aligned_cols=68  Identities=22%  Similarity=0.186  Sum_probs=64.1

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcC--CCCCceEEEeCCcccCccccccccccEEeEEEEe
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKR--IPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~g--Ip~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~~  110 (133)
                      .++||++.++++.+++.|++||.++|.+|+...|  .|+++|+|+|+||.|.|+.++.+|++....+|++
T Consensus         2 ~lt~KtL~q~~F~iev~Pe~tV~evK~kIet~~g~dyP~~~QkLIy~GkiL~D~~tv~Eykv~E~~fiVv   71 (340)
T KOG0011|consen    2 KLTVKTLKQQTFTIEVKPEDTVVEVKKKIETEKGPDYPAEQQKLIYSGKILKDETTVGEYKVKEKKFIVV   71 (340)
T ss_pred             eeEeeeccCceeEeecCcchhHHHHHHHHHhccCCCCchhhheeeecceeccCCcchhhhccccCceEEE
Confidence            3789999999999999999999999999999999  9999999999999999999999999988886654

>cd01807 GDX_N ubiquitin-like domain of GDX

Probab=99.22  E-value=2.1e-12  Score=82.03  Aligned_cols=43  Identities=37%  Similarity=0.644  Sum_probs=39.8

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+|+++|+|+|+|++|+|+.+|++|||. +++++|++++
T Consensus        30 i~~~~gi~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~l~l~~~~   73 (74)
T cd01807          30 VSEHLNVPEEQQRLLFKGKALADDKRLSDYSIGPNAKLNLVVRP   73 (74)
T ss_pred             HHHHHCCCHHHeEEEECCEECCCCCCHHHCCCCCCCEEEEEEcC
Confidence            467889999999999999999999999999999 9999998764

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

>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4

Probab=99.22  E-value=9.5e-12  Score=84.83  Aligned_cols=58  Identities=10%  Similarity=-0.016  Sum_probs=49.6

Q ss_pred             cccCCCCCCCc-eeeccccCcHHHHHHHhhhh-----cCCC--CCceEEEeCCcccCccccccccc
Q 040111           44 DFCKNPDPQNI-TLEVESSDTIDNVKAKIQDK-----KRIP--PPAEADLLKFPFFFFEEVLSFFW  101 (133)
Q Consensus        44 i~Vk~~~g~~~-~l~V~~~~tV~~LK~~I~~~-----~gIp--~~~q~L~~~gk~L~d~~tL~dy~  101 (133)
                      |.+|..+|.-+ +..+++++||++||++|++.     +|+|  +++|+|+|+||.|+|++||++|+
T Consensus         7 ~kfrl~dg~digp~~~~~sdTV~~lKekI~~~~p~~ke~~P~~~~~qKLIysGKiLeD~~TL~d~~   72 (113)
T cd01814           7 IKFRLYDGSDIGPKRYPAATTVDFLKERVVSQWPKDKEVGPKTVNEVKLISAGKILENSKTVGECR   72 (113)
T ss_pred             EEEEccCCCccCccccChhhHHHHHHHHHHHhcccccccCCCCHHHeEEEeCCeecCCCCcHHHhC
Confidence            55677777543 66788999999999999944     4566  99999999999999999999999

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

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

Probab=99.17  E-value=4.8e-12  Score=90.35  Aligned_cols=43  Identities=81%  Similarity=1.161  Sum_probs=41.4

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      ||.++|||+++|||||.|++|+|..+|+||+|+ .+||||+++.
T Consensus        30 iq~~egIp~dqqrlifag~qLedgrtlSDY~Iqkestl~l~l~l   73 (156)
T KOG0004|consen   30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL   73 (156)
T ss_pred             hhcccCCCchhhhhhhhhcccccCCccccccccccceEEEEEEe
Confidence            688999999999999999999999999999999 9999999886

>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein

Probab=99.16  E-value=5.9e-12  Score=79.55  Aligned_cols=41  Identities=34%  Similarity=0.498  Sum_probs=38.4

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGW   41 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~   41 (133)
                      |++++|+|+++|+|+|+|++|+|+.+|.+|+|. ++++||++
T Consensus        28 I~~~~gi~~~~q~Li~~G~~L~D~~~l~~~~i~~~~tv~~~~   69 (70)
T cd01794          28 LQAAEGVDPCCQRWFFSGKLLTDKTRLQETKIQKDYVVQVIV   69 (70)
T ss_pred             HHHHhCCCHHHeEEEECCeECCCCCCHHHcCCCCCCEEEEEe
Confidence            467889999999999999999999999999999 99999875

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.

>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP

Probab=99.16  E-value=5.7e-12  Score=80.54  Aligned_cols=40  Identities=35%  Similarity=0.558  Sum_probs=35.5

Q ss_pred             Ccc--cCCC-CCCeEEEeCCEECCCCCCccccccc-cccccccc
Q 040111            2 EDK--EGIP-PGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGW   41 (133)
Q Consensus         2 ~~~--~gip-~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~   41 (133)
                      +++  +|+| +++|||||+||+|+|+.||++|||. +++|||+.
T Consensus        31 ~~~~~egi~~~dqQrLIy~GKiL~D~~TL~dygI~~gstlhLv~   74 (75)
T cd01815          31 AAQLPDSLPDPELIDLIHCGRKLKDDQTLDFYGIQSGSTIHILR   74 (75)
T ss_pred             HHhhccCCCChHHeEEEeCCcCCCCCCcHHHcCCCCCCEEEEEe
Confidence            445  4675 9999999999999999999999999 99999864

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.

>cd01795 USP48_C USP ubiquitin-specific protease

Probab=99.14  E-value=6.6e-11  Score=78.98  Aligned_cols=59  Identities=15%  Similarity=0.106  Sum_probs=51.7

Q ss_pred             CCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCc-cccccccccEEeEEEEe
Q 040111           52 QNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFF-EEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        52 ~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d-~~tL~dy~~~~~~~~~~  110 (133)
                      ...+++|++++||.+||.+|.+..++||.+|+|++.|+.|.| .+||++|++..-++++.
T Consensus        15 ~~~~L~V~~~~TVg~LK~lImQ~f~V~P~dQkL~~dG~~L~DDsrTLssyGv~sgSvl~L   74 (107)
T cd01795          15 GEKALLVSANQTLKELKIQIMHAFSVAPFDQNLSIDGKILSDDCATLGTLGVIPESVILL   74 (107)
T ss_pred             CCceEEeCccccHHHHHHHHHHHhcCCcccceeeecCceeccCCccHHhcCCCCCCEEEE
Confidence            356788999999999999999999999999999999999997 57999999875555543

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,

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

Probab=99.13  E-value=1.2e-11  Score=77.75  Aligned_cols=42  Identities=38%  Similarity=0.711  Sum_probs=38.8

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |++++|+|+++|+|+|+|++|+|+.+|++|||. ++++||+.|
T Consensus        28 i~~~~gi~~~~q~Li~~G~~L~d~~~l~~~~i~~~stl~l~~~   70 (70)
T cd01798          28 VAKRQGVPPDQLRVIFAGKELRNTTTIQECDLGQQSILHAVRR   70 (70)
T ss_pred             HHHHHCCCHHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEeC
Confidence            467889999999999999999999999999999 999998754

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.

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

Probab=99.12  E-value=7.1e-12  Score=76.13  Aligned_cols=40  Identities=58%  Similarity=0.918  Sum_probs=37.9

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLG   40 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~   40 (133)
                      |++++|||+.+|||+|.||++.|+.|-++|++. ||++|++
T Consensus        30 vEEkeGIPp~qqrli~~gkqm~DD~tA~~Y~~~~GSVlHlv   70 (70)
T KOG0005|consen   30 VEEKEGIPPQQQRLIYAGKQMNDDKTAAHYNLLGGSVLHLV   70 (70)
T ss_pred             hhhhcCCCchhhhhhhccccccccccHHHhhhccceeEeeC
Confidence            578999999999999999999999999999999 9999974

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

Probab=99.10  E-value=2.2e-11  Score=77.38  Aligned_cols=43  Identities=23%  Similarity=0.483  Sum_probs=39.2

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|||+++|+|+|+|++|+|+.+|++|||. +++++|.++.
T Consensus        28 I~~~~gi~~~~q~L~~~G~~L~D~~tL~~~~i~~~~tl~l~~~l   71 (74)
T cd01810          28 VSQRERVQADQFWLSFEGRPMEDEHPLGEYGLKPGCTVFMNLRL   71 (74)
T ss_pred             HHHHhCCCHHHeEEEECCEECCCCCCHHHcCCCCCCEEEEEEEc
Confidence            467789999999999999999999999999999 9999987653

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.

>cd01802 AN1_N ubiquitin-like domain of AN1

Probab=99.07  E-value=3.6e-11  Score=81.37  Aligned_cols=42  Identities=43%  Similarity=0.571  Sum_probs=39.2

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |++++|||+++|+|+|+|++|+|+.+|++|+|. +++|||.++
T Consensus        57 I~~~~gip~~~QrLi~~Gk~L~D~~tL~dy~I~~~stL~l~~~   99 (103)
T cd01802          57 IQRLEGIPVAQQHLIWNNMELEDEYCLNDYNISEGCTLKLVLA   99 (103)
T ss_pred             HHHHhCCChHHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEe
Confidence            467899999999999999999999999999999 999998765

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.

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

Probab=99.05  E-value=9.5e-12  Score=83.91  Aligned_cols=43  Identities=84%  Similarity=1.171  Sum_probs=39.9

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|||+++|+|+|+|++|+|..|+++|||+ .+|||+..+.
T Consensus        30 i~~~~Gi~~~~~~L~~~~k~LED~~Tla~Y~i~~~~Tl~~~~rL   73 (128)
T KOG0003|consen   30 IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (128)
T ss_pred             hccccCCCHHHHHHHhcccccccCCcccccCccchhhhhhhHHH
Confidence            678999999999999999999999999999999 9999976554

>cd01791 Ubl5 UBL5 ubiquitin-like modifier

Probab=99.04  E-value=3.7e-11  Score=76.55  Aligned_cols=41  Identities=24%  Similarity=0.274  Sum_probs=37.4

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGW   41 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~   41 (133)
                      |+++.|+|+++|||+|+|++|+|+.+|++|||. ++++||..
T Consensus        31 I~~~~~~~~~~qrLi~~Gk~L~D~~tL~~ygi~~~stv~l~~   72 (73)
T cd01791          31 IAAQTGTRPEKIVLKKWYTIFKDHISLGDYEIHDGMNLELYY   72 (73)
T ss_pred             HHHHhCCChHHEEEEeCCcCCCCCCCHHHcCCCCCCEEEEEe
Confidence            356779999999999999999999999999999 99999853

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.

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

Probab=99.02  E-value=5.6e-11  Score=74.90  Aligned_cols=42  Identities=36%  Similarity=0.376  Sum_probs=38.3

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |++++|+|+++|+|+|.|++|+|+.+|++|||. ++++||+++
T Consensus        29 I~~~~~i~~~~~~Li~~Gk~L~d~~tL~~~~i~~~stl~l~~~   71 (71)
T cd01808          29 VSKKFKANQEQLVLIFAGKILKDTDTLTQHNIKDGLTVHLVIK   71 (71)
T ss_pred             HHHHhCCCHHHEEEEECCeEcCCCCcHHHcCCCCCCEEEEEEC
Confidence            356779999999999999999999999999999 999998764

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.

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

Probab=99.02  E-value=8.2e-11  Score=73.32  Aligned_cols=43  Identities=51%  Similarity=0.886  Sum_probs=39.0

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++..++|+++|+|+|+|++|+|+.+|.+|||. +++|+|.+++
T Consensus        25 i~~~~~~~~~~~~L~~~G~~L~d~~tL~~~~i~~~~~I~l~~k~   68 (69)
T PF00240_consen   25 IAEETGIPPEQQRLIYNGKELDDDKTLSDYGIKDGSTIHLVIKP   68 (69)
T ss_dssp             HHHHHTSTGGGEEEEETTEEESTTSBTGGGTTSTTEEEEEEESS
T ss_pred             cccccccccccceeeeeeecccCcCcHHHcCCCCCCEEEEEEec
Confidence            356789999999999999999999999999999 9999987763

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 ....

>PTZ00044 ubiquitin; Provisional

Probab=99.00  E-value=7.6e-11  Score=74.92  Aligned_cols=42  Identities=43%  Similarity=0.700  Sum_probs=38.9

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |++++|+|+++|+|+|+|++|+|+.+|++|++. ++++|+.++
T Consensus        30 i~~~~gi~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~   72 (76)
T PTZ00044         30 LQEKEGIDVKQIRLIYSGKQMSDDLKLSDYKVVPGSTIHMVLQ   72 (76)
T ss_pred             HHHHHCCCHHHeEEEECCEEccCCCcHHHcCCCCCCEEEEEEE
Confidence            467889999999999999999999999999999 999998765

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

Probab=99.00  E-value=3.2e-10  Score=93.56  Aligned_cols=60  Identities=15%  Similarity=0.156  Sum_probs=56.7

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFV  103 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~  103 (133)
                      .|.||+.++ ...+.|..+.||.+||+.|+.+.++++++++|+|+||.|+|+.+|..|+|.
T Consensus        17 rV~Vkt~~d-k~~~~V~~~ssV~qlKE~I~~~f~a~~dqlvLIfaGrILKD~dTL~~~gI~   76 (493)
T KOG0010|consen   17 RVTVKTPKD-KYEVNVASDSSVLQLKELIAQRFGAPPDQLVLIYAGRILKDDDTLKQYGIQ   76 (493)
T ss_pred             EEEEecCCc-ceeEecccchHHHHHHHHHHHhcCCChhHeeeeecCccccChhhHHHcCCC
Confidence            388999988 778999999999999999999999999999999999999999999999984

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

Probab=98.95  E-value=1.5e-10  Score=73.91  Aligned_cols=43  Identities=28%  Similarity=0.631  Sum_probs=39.1

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |+..+|||+++|+|+|+|+.|+|+.+|++|+|. +++|+|+++.
T Consensus        27 i~~~~gip~~~q~L~~~G~~L~d~~tL~~~~i~~g~~l~v~~~~   70 (76)
T cd01800          27 IHEETGMPAGKQKLQYEGIFIKDSNSLAYYNLANGTIIHLQLKE   70 (76)
T ss_pred             HHHHHCCCHHHEEEEECCEEcCCCCcHHHcCCCCCCEEEEEEec
Confidence            456789999999999999999999999999999 9999987653

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

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

Probab=98.93  E-value=2e-10  Score=72.53  Aligned_cols=40  Identities=38%  Similarity=0.606  Sum_probs=36.3

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCC-CCccccccc-ccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDG-RTLADYKIQ-ESTLHLG   40 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~-~tL~~ygI~-~stl~L~   40 (133)
                      |++++|+|+++|+|+|+|++|+|+ .+|++|||. +++++|.
T Consensus        29 I~~~~gip~~~q~Li~~Gk~L~D~~~~L~~~gi~~~~~l~l~   70 (71)
T cd01796          29 CEAESGIPASQQQLIYNGRELVDNKRLLALYGVKDGDLVVLR   70 (71)
T ss_pred             HHHHhCCCHHHeEEEECCeEccCCcccHHHcCCCCCCEEEEe
Confidence            467899999999999999999987 689999999 9999874

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.

>cd01805 RAD23_N Ubiquitin-like domain of RAD23

Probab=98.93  E-value=2.7e-10  Score=72.44  Aligned_cols=43  Identities=40%  Similarity=0.667  Sum_probs=38.6

Q ss_pred             CCcccCC--CCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGI--PPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gi--p~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+  |+++|+|+|+|++|+|+.+|++|||. +++++++++.
T Consensus        30 i~~~~~i~~~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~i~~~~~~   75 (77)
T cd01805          30 IEEEKGCDYPPEQQKLIYSGKILKDDTTLEEYKIDEKDFVVVMVSK   75 (77)
T ss_pred             HHHhhCCCCChhHeEEEECCEEccCCCCHHHcCCCCCCEEEEEEec
Confidence            3567888  99999999999999999999999999 9999987653

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

>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein

Probab=98.93  E-value=2.3e-10  Score=71.62  Aligned_cols=42  Identities=45%  Similarity=0.764  Sum_probs=38.2

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |++.+|+|+++|+|+|+|++|+|+.+|++||+. ++++|+..+
T Consensus        30 i~~~~gi~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~l~l~~~   72 (72)
T cd01809          30 IAEEVGIPVEQQRLIYSGRVLKDDETLSEYKVEDGHTIHLVKR   72 (72)
T ss_pred             HHHHHCcCHHHeEEEECCEECCCcCcHHHCCCCCCCEEEEEeC
Confidence            356789999999999999999999999999999 999998754

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.

>cd01806 Nedd8 Nebb8-like ubiquitin protein

Probab=98.93  E-value=3.7e-10  Score=71.35  Aligned_cols=42  Identities=57%  Similarity=0.933  Sum_probs=38.9

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |+++.|+|+++|+|+|+|+.|+|+.+|++|++. +++||+.++
T Consensus        30 i~~~~g~~~~~qrL~~~g~~L~d~~tl~~~~i~~g~~i~l~~~   72 (76)
T cd01806          30 VEEKEGIPPQQQRLIYSGKQMNDDKTAADYKLEGGSVLHLVLA   72 (76)
T ss_pred             HhHhhCCChhhEEEEECCeEccCCCCHHHcCCCCCCEEEEEEE
Confidence            467789999999999999999999999999999 999998765

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.

>cd01804 midnolin_N Ubiquitin-like domain of midnolin

Probab=98.89  E-value=3.6e-10  Score=72.67  Aligned_cols=42  Identities=21%  Similarity=0.277  Sum_probs=37.7

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |+++.++|+++|+|+|.|++|+|+ +|++|||. +++|+|+...
T Consensus        31 I~~~~~~~~~~qrL~~~Gk~L~d~-~L~~~gi~~~~~i~l~~~~   73 (78)
T cd01804          31 ISQRLKVPKERLALLHRETRLSSG-KLQDLGLGDGSKLTLVPTV   73 (78)
T ss_pred             HHHHhCCChHHEEEEECCcCCCCC-cHHHcCCCCCCEEEEEeec
Confidence            456779999999999999999999 99999999 9999987653

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.

>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4

Probab=98.88  E-value=9.7e-10  Score=75.02  Aligned_cols=51  Identities=25%  Similarity=0.345  Sum_probs=42.6

Q ss_pred             cccCCC--CCCeEEEeCCEECCCCCCccccc------cc-cccccccccccccCCCCCCC
Q 040111            3 DKEGIP--PGQQRSIFAGKQLEDGRTLADYK------IQ-ESTLHLGWRADFCKNPDPQN   53 (133)
Q Consensus         3 ~~~gip--~~~Q~Li~~gk~L~D~~tL~~yg------I~-~stl~L~~~~i~Vk~~~g~~   53 (133)
                      .++++|  +++|+|||+||+|+|+.||++|+      +. .+|+|++++.-.-+...++.
T Consensus        42 ~ke~~P~~~~~qKLIysGKiLeD~~TL~d~~~p~g~~~~~~~TmHvvlr~~~~~~~~~k~  101 (113)
T cd01814          42 DKEVGPKTVNEVKLISAGKILENSKTVGECRSPVGDIAGGVITMHVVVQPPLADKKTEKK  101 (113)
T ss_pred             ccccCCCCHHHeEEEeCCeecCCCCcHHHhCCcccccCCCceEEEEEecCCCCCcccccc
Confidence            467888  99999999999999999999999      66 79999998886555544443

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

>cd01803 Ubiquitin Ubiquitin

Probab=98.87  E-value=5.5e-10  Score=70.57  Aligned_cols=42  Identities=83%  Similarity=1.199  Sum_probs=38.8

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |++++|+|+++|+|+|+|+.|+|+.+|++||+. ++++++.++
T Consensus        30 i~~~~g~~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~i~l~~~   72 (76)
T cd01803          30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR   72 (76)
T ss_pred             HHHHhCCCHHHeEEEECCEECCCCCcHHHcCCCCCCEEEEEEE
Confidence            467789999999999999999999999999999 999998765

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

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

Probab=98.84  E-value=4.2e-10  Score=72.59  Aligned_cols=43  Identities=33%  Similarity=0.356  Sum_probs=39.2

Q ss_pred             CCcccCCCCCCeEE--EeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRS--IFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~L--i~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+|+++|+|  +|.|+.|+|+.+|++|||. +++|+|++++
T Consensus        32 I~~~~~i~~~~qrL~~~~~G~~L~D~~tL~~~gi~~gs~l~l~~~~   77 (80)
T cd01792          32 IAQKIGVPAFQQRLAHLDSREVLQDGVPLVSQGLGPGSTVLLVVQN   77 (80)
T ss_pred             HHHHhCCCHHHEEEEeccCCCCCCCCCCHHHcCCCCCCEEEEEEEc
Confidence            45678999999999  8999999999999999999 9999988764

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.

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

Probab=98.84  E-value=3.3e-09  Score=65.03  Aligned_cols=63  Identities=35%  Similarity=0.306  Sum_probs=57.4

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVG  106 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~  106 (133)
                      +++++..|+.+.+++.+..+|..+|.+|+...|+|+++|++.++|+.|+|+.++++|+|...+
T Consensus         2 ~~~~~~~gk~~~~~~~~~~~i~~~k~~i~~~~~~~~~~q~~~~~~~~l~d~~~l~~~~i~~~~   64 (75)
T KOG0001|consen    2 IFVKTLDGKTITLEVSPSDTIEVVKAKIRDKEGIPVDQQRLIFGGKPLEDGRTLADYNIQEGS   64 (75)
T ss_pred             EEEEecCCCEEEEEecCCCHHHHHHHHHHhhcCCCCeeEEEEECCEECcCCCcHHHhCCCCCC
Confidence            356678899999999999999999999999999999999999999999999999999975444

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

Probab=98.79  E-value=2.4e-09  Score=67.30  Aligned_cols=63  Identities=16%  Similarity=0.113  Sum_probs=56.3

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCC-CceEEEeCCcccCccccccccccEEeE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP-PAEADLLKFPFFFFEEVLSFFWFVVVG  106 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~-~~q~L~~~gk~L~d~~tL~dy~~~~~~  106 (133)
                      |+|+..+|+.+.+.|.+++++..|++..+++.|+|+ +..+|+|.|+.|.++.|+++|++....
T Consensus         3 i~v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~fdG~~L~~~~T~~~~~ied~d   66 (72)
T PF11976_consen    3 IKVRSQDGKEIKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLIFDGKRLDPNDTPEDLGIEDGD   66 (72)
T ss_dssp             EEEEETTSEEEEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEEETTEEE-TTSCHHHHT-STTE
T ss_pred             EEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCccceEEEEECCEEcCCCCCHHHCCCCCCC
Confidence            577888899999999999999999999999999999 999999999999999999999985433

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 ....

>cd01812 BAG1_N Ubiquitin-like domain of BAG1

Probab=98.74  E-value=2.1e-09  Score=67.12  Aligned_cols=41  Identities=29%  Similarity=0.413  Sum_probs=37.6

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGW   41 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~   41 (133)
                      |++.+|+|+++|+|+|+|+.|+|+.+|++|||. +++|+++.
T Consensus        29 i~~~~gi~~~~q~L~~~g~~l~d~~~L~~~~i~~g~~l~v~~   70 (71)
T cd01812          29 LAPVTGVEPRDQKLIFKGKERDDAETLDMSGVKDGSKVMLLE   70 (71)
T ss_pred             HHHhhCCChHHeEEeeCCcccCccCcHHHcCCCCCCEEEEec
Confidence            467789999999999999999999999999999 99998764

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).

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

Probab=98.71  E-value=2.9e-09  Score=68.76  Aligned_cols=35  Identities=31%  Similarity=0.295  Sum_probs=32.1

Q ss_pred             CCCCCeEEEeCCEECCCCCCccccc--cc-cccccccc
Q 040111            7 IPPGQQRSIFAGKQLEDGRTLADYK--IQ-ESTLHLGW   41 (133)
Q Consensus         7 ip~~~Q~Li~~gk~L~D~~tL~~yg--I~-~stl~L~~   41 (133)
                      .|+++|||||+||+|+|+.||++|+  +. +.++||+.
T Consensus        41 ~~~~~QrLIy~GKiLkD~~tL~~~~~~~~~~~tiHLV~   78 (79)
T cd01790          41 PLEQDQRLIYSGKLLPDHLKLRDVLRKQDEYHMVHLVC   78 (79)
T ss_pred             CChhHeEEEEcCeeccchhhHHHHhhcccCCceEEEEe
Confidence            5579999999999999999999996  99 99999864

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.

>PLN02560 enoyl-CoA reductase

Probab=98.66  E-value=2.8e-08  Score=79.01  Aligned_cols=67  Identities=19%  Similarity=0.143  Sum_probs=56.5

Q ss_pred             cccCCCCCCCc---eeeccccCcHHHHHHHhhhhcCC-CCCceEEEeC---C----cccCccccccccccEEeEEEEe
Q 040111           44 DFCKNPDPQNI---TLEVESSDTIDNVKAKIQDKKRI-PPPAEADLLK---F----PFFFFEEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        44 i~Vk~~~g~~~---~l~V~~~~tV~~LK~~I~~~~gI-p~~~q~L~~~---g----k~L~d~~tL~dy~~~~~~~~~~  110 (133)
                      |.|+..+|+.+   ++++++++||++||++|+++.++ ++++|||.+.   |    +.|.|+++|+||++...+.++.
T Consensus         3 I~Vk~~~Gk~i~~~~lev~~~aTV~dLK~~Isk~~~~~~~~RqRL~~~~~~gk~~g~~L~d~ktL~d~gv~~gstLy~   80 (308)
T PLN02560          3 VTVVSRSGREIIKGGLEVPDSATVADLKKAIHKRKKKYYPSRQRLTLPLPPGKTRPTVLDDSKSLKDYGLGDGGTVVF   80 (308)
T ss_pred             EEEEcCCCCeecceeEEcCCCCcHHHHHHHHHHHcCCCChhheEEEEecCCCCcCccccCCCCCHHhcCCCCCceEEE
Confidence            56777778776   79999999999999999999986 8999999973   4    4889999999999976665554

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

Probab=98.65  E-value=4.8e-08  Score=63.67  Aligned_cols=56  Identities=13%  Similarity=-0.049  Sum_probs=46.7

Q ss_pred             CceeeccccCcHHHHHHHhhhhcCCCCCceEEE-eCCc-----cc-CccccccccccEEeEEE
Q 040111           53 NITLEVESSDTIDNVKAKIQDKKRIPPPAEADL-LKFP-----FF-FFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        53 ~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~-~~gk-----~L-~d~~tL~dy~~~~~~~~  108 (133)
                      .....++++.||.+||++++..+|+||+.|+|. |.|+     .| .|+++|++|++.....|
T Consensus        14 ~~ekr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~~~~~~~~~~l~~d~~~L~~y~~~dg~~I   76 (84)
T cd01789          14 SFEKKYSRGLTIAELKKKLELVVGTPASSMRLQLFDGDDKLVSKLDDDDALLGSYPVDDGCRI   76 (84)
T ss_pred             eeeEecCCCCcHHHHHHHHHHHHCCCccceEEEEEcCCCCeEeecCCCccEeeeccCCCCCEE
Confidence            345569999999999999999999999999995 8888     46 56789999998655443

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.

>cd01763 Sumo Small ubiquitin-related modifier (SUMO)

Probab=98.64  E-value=1.1e-08  Score=66.97  Aligned_cols=42  Identities=17%  Similarity=0.381  Sum_probs=38.7

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      +++.|+|+++|+|+|+|+.|+|+.|+.+|++. +++|++.+++
T Consensus        42 ~~~~gi~~~~~rf~f~G~~L~~~~T~~~l~m~d~d~I~v~l~l   84 (87)
T cd01763          42 CQRQGLSMNSVRFLFDGQRIRDNQTPDDLGMEDGDEIEVMLEQ   84 (87)
T ss_pred             HHHhCCCccceEEEECCeECCCCCCHHHcCCCCCCEEEEEEec
Confidence            46789999999999999999999999999999 9999987654

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.

>cd01788 ElonginB Ubiquitin-like domain of Elongin B

Probab=98.64  E-value=2e-08  Score=68.53  Aligned_cols=52  Identities=15%  Similarity=0.105  Sum_probs=47.9

Q ss_pred             CceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEE
Q 040111           53 NITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVV  104 (133)
Q Consensus        53 ~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~  104 (133)
                      ++-++..+++||.+||++|+.....||++|+|+-.+..|+|++||+||++++
T Consensus        13 TiF~dakes~tVlelK~~iegI~k~pp~dQrL~kd~qvLeD~kTL~d~g~t~   64 (119)
T cd01788          13 TIFTDAKESTTVYELKRIVEGILKRPPEDQRLYKDDQLLDDGKTLGDCGFTS   64 (119)
T ss_pred             EEEeecCCcccHHHHHHHHHHHhcCChhHheeecCceeecccccHHHcCccc
Confidence            4667899999999999999999999999999997888899999999999954

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.

>cd01813 UBP_N UBP ubiquitin processing protease

Probab=98.63  E-value=6e-09  Score=66.43  Aligned_cols=41  Identities=22%  Similarity=0.363  Sum_probs=37.2

Q ss_pred             CCcccCCCCCCeEEEe---CCEECCCCCCccccccc-cccccccc
Q 040111            1 IEDKEGIPPGQQRSIF---AGKQLEDGRTLADYKIQ-ESTLHLGW   41 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~---~gk~L~D~~tL~~ygI~-~stl~L~~   41 (133)
                      |++.+|+|+++|+|+|   .|++|+|+.+|++|+|. +++++|+.
T Consensus        29 i~~~tgvp~~~QKLi~~~~~Gk~l~D~~~L~~~~i~~g~~i~lmG   73 (74)
T cd01813          29 IKTLTGVLPERQKLLGLKVKGKPAEDDVKISALKLKPNTKIMMMG   73 (74)
T ss_pred             HHHHHCCCHHHEEEEeecccCCcCCCCcCHHHcCCCCCCEEEEEe
Confidence            4677899999999996   89999999999999999 99998864

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.

>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1

Probab=98.51  E-value=1.9e-08  Score=64.32  Aligned_cols=40  Identities=30%  Similarity=0.343  Sum_probs=34.6

Q ss_pred             CCcccCCCCCCeEEEeCCEECC-CCCCccccccc--cccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLE-DGRTLADYKIQ--ESTLHLGW   41 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~-D~~tL~~ygI~--~stl~L~~   41 (133)
                      |++++|||+++|+| |.|+.|. |+.+|++||+.  |++++|.+
T Consensus        32 I~~~~gip~~~QrL-~~G~~L~dD~~tL~~ygi~~~g~~~~l~~   74 (75)
T cd01799          32 VFLDYGFPPAVQRW-VIGQRLARDQETLYSHGIRTNGDSAFLYI   74 (75)
T ss_pred             HHHHHCcCHHHEEE-EcCCeeCCCcCCHHHcCCCCCCCEEEEEe
Confidence            46789999999999 9999884 77999999998  68998753

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

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

Probab=98.50  E-value=8e-08  Score=62.74  Aligned_cols=58  Identities=19%  Similarity=0.106  Sum_probs=45.1

Q ss_pred             CCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeC----C---ccc-CccccccccccEEeEEEE
Q 040111           52 QNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLK----F---PFF-FFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        52 ~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~----g---k~L-~d~~tL~dy~~~~~~~~~  109 (133)
                      ......++++.||.+||.+|+..+|+||+.|+|.+.    +   ..+ .|+++|++|++.....|.
T Consensus        14 ~~~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~~~~~~~~~~~~~dd~~~L~~y~~~dg~~i~   79 (87)
T PF14560_consen   14 RSVEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLKSDKDDSKIEELDDDDATLGSYGIKDGMRIH   79 (87)
T ss_dssp             SEEEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE-TSSSSEEEESSGSSSBCCHHT-STTEEEE
T ss_pred             eeEEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEEecCCCccccccCCCccEeecCCCCCCCEEE
Confidence            456778999999999999999999999999999976    1   123 457899999987655443

>cd01795 USP48_C USP ubiquitin-specific protease

Probab=98.48  E-value=4.5e-08  Score=65.49  Aligned_cols=42  Identities=29%  Similarity=0.256  Sum_probs=37.2

Q ss_pred             CCcccCCCCCCeEEEeCCEECC-CCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLE-DGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~-D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |++++++|+.+|+|+|.|+.|. |..||++|||. +|++.|.++
T Consensus        34 ImQ~f~V~P~dQkL~~dG~~L~DDsrTLssyGv~sgSvl~Llid   77 (107)
T cd01795          34 IMHAFSVAPFDQNLSIDGKILSDDCATLGTLGVIPESVILLKAD   77 (107)
T ss_pred             HHHHhcCCcccceeeecCceeccCCccHHhcCCCCCCEEEEEec
Confidence            5678999999999999999995 56999999999 999997643

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

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

Probab=98.45  E-value=1e-07  Score=84.45  Aligned_cols=59  Identities=15%  Similarity=0.151  Sum_probs=57.6

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCcccccccccc
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWF  102 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~  102 (133)
                      +.||+++.++.++.+...+||.++|..|.++.+|+.+.|||+|+|+.|.|++++.+|++
T Consensus         5 v~vktld~r~~t~~ig~q~ti~~~~d~~r~~~ni~s~~qr~i~~grvl~~~k~vq~~~v   63 (1143)
T KOG4248|consen    5 VLVKTLDSRTRTFIIGAQMTIKEFKDHIRASVNIPSEKQRLIYQGRVLQDDKKVQEYNV   63 (1143)
T ss_pred             eeeeecccceeEEEechHHHHHHHHHHHHHhcccccccceeeecceeeccchhhhhccC
Confidence            78999999999999999999999999999999999999999999999999999999987

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

Probab=98.39  E-value=6e-08  Score=80.34  Aligned_cols=43  Identities=42%  Similarity=0.642  Sum_probs=39.3

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |.++.++|+++|+|||.||+|+|+.||..|||. +.|+||+++.
T Consensus        44 I~~~f~a~~dqlvLIfaGrILKD~dTL~~~gI~Dg~TvHLVik~   87 (493)
T KOG0010|consen   44 IAQRFGAPPDQLVLIYAGRILKDDDTLKQYGIQDGHTVHLVIKS   87 (493)
T ss_pred             HHHhcCCChhHeeeeecCccccChhhHHHcCCCCCcEEEEEecc
Confidence            356789999999999999999999999999999 9999987665

>smart00213 UBQ Ubiquitin homologues

Probab=98.39  E-value=8.7e-08  Score=58.04  Aligned_cols=35  Identities=63%  Similarity=0.881  Sum_probs=31.5

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ES   35 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~s   35 (133)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|||. ++
T Consensus        29 i~~~~~~~~~~~~L~~~g~~L~d~~tL~~~~i~~~~   64 (64)
T smart00213       29 IAELTGIPVEQQRLIYKGKVLEDDRTLADYNIQDGS   64 (64)
T ss_pred             HHHHHCCCHHHEEEEECCEECCCCCCHHHcCCcCCC
Confidence            356789999999999999999999999999998 54

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

>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13

Probab=98.37  E-value=7e-07  Score=57.04  Aligned_cols=52  Identities=12%  Similarity=0.015  Sum_probs=44.9

Q ss_pred             cccCcHHHHHHHhhhhcC-CCCCceEEE--eCCcccCccccccccccEEeEEEEe
Q 040111           59 ESSDTIDNVKAKIQDKKR-IPPPAEADL--LKFPFFFFEEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        59 ~~~~tV~~LK~~I~~~~g-Ip~~~q~L~--~~gk~L~d~~tL~dy~~~~~~~~~~  110 (133)
                      +++.||.+||..|++..+ +++++|+|.  +.|+.|.|+.+|++|++...+.++.
T Consensus        20 ~~~aTV~dlk~~i~~~~~~~~~~Rqrl~~~~~g~~L~d~~tL~~~gv~~g~~lyv   74 (77)
T cd01801          20 SGDATIADLKKLIAKSSPQLTVNRQSLRLEPKGKSLKDDDTLVDLGVGAGATLYV   74 (77)
T ss_pred             CCCccHHHHHHHHHHHcCCCCcceeEEEeCCCCcccCCcccHhhcCCCCCCEEEE
Confidence            588999999999999976 689999995  8999999999999999976555554

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.

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=98.32  E-value=1.7e-07  Score=76.43  Aligned_cols=44  Identities=32%  Similarity=0.512  Sum_probs=39.0

Q ss_pred             CcccC---CCCCCeEEEeCCEECCCCCCccccccc-cccccccccccc
Q 040111            2 EDKEG---IPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRADF   45 (133)
Q Consensus         2 ~~~~g---ip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~i~   45 (133)
                      ++..|   +|+++|+|||+||+|+|+.+|++|||. +++|++++++-.
T Consensus        31 ~~~~g~~~ip~~~QkLIy~GkiL~Dd~tL~dy~I~e~~~Ivvmv~k~k   78 (378)
T TIGR00601        31 EAEQGKDAYPVAQQKLIYSGKILSDDKTVREYKIKEKDFVVVMVSKPK   78 (378)
T ss_pred             HHhhCCCCCChhHeEEEECCEECCCCCcHHHcCCCCCCEEEEEeccCC
Confidence            34556   999999999999999999999999999 999999888743

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).

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

Probab=98.32  E-value=5.2e-07  Score=61.86  Aligned_cols=56  Identities=14%  Similarity=0.042  Sum_probs=44.2

Q ss_pred             CCCCC-CceeeccccCcHHHHHHHhhhhc-------CCCCCceEEEeCCcccCccccccccccE
Q 040111           48 NPDPQ-NITLEVESSDTIDNVKAKIQDKK-------RIPPPAEADLLKFPFFFFEEVLSFFWFV  103 (133)
Q Consensus        48 ~~~g~-~~~l~V~~~~tV~~LK~~I~~~~-------gIp~~~q~L~~~gk~L~d~~tL~dy~~~  103 (133)
                      ..+|. ..++..++++||.+||+.|...+       -..++..||+|.||.|+|+.+|+++++.
T Consensus         9 l~~G~d~~~~~~~~~~TV~~lKe~i~~~WP~d~~~~p~s~~~lRLI~~GriL~d~~tL~~~~~~   72 (111)
T PF13881_consen    9 LADGKDIGPFRFDPSTTVADLKERIWAEWPEDWEERPKSPSDLRLIYAGRILEDNKTLSDCRLP   72 (111)
T ss_dssp             ETTS-EEEEEEE-TTSBHHHHHHHHHHSSSTTSSSTT-SGGGEEEEETTEEE-SSSBTGGGT--
T ss_pred             EeCCCcccccccCccChHHHHHHHHHHHCccccccCCCChhhEEEEeCCeecCCcCcHHHhCCC
Confidence            34777 78889999999999999999775       1357899999999999999999999753

>cd00196 UBQ Ubiquitin-like proteins

Probab=98.27  E-value=1.2e-06  Score=50.71  Aligned_cols=59  Identities=20%  Similarity=0.184  Sum_probs=51.1

Q ss_pred             CCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeE
Q 040111           48 NPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVG  106 (133)
Q Consensus        48 ~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~  106 (133)
                      ..++....+.+.++.|+.++|++|+++.|++++.|.|++.|..+.+...+.+|.+....
T Consensus         4 ~~~~~~~~~~~~~~~tv~~l~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~   62 (69)
T cd00196           4 LNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGKILPDSLTLEDYGLQDGD   62 (69)
T ss_pred             ecCCCEEEEEcCCCCcHHHHHHHHHHHHCcChHHeEEEECCeECCCCCcHHHcCCCCCC
Confidence            34677788899999999999999999999999999999999999998877777665444

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

>cd01769 UBL Ubiquitin-like domain of UBL

Probab=98.23  E-value=2.8e-07  Score=56.48  Aligned_cols=41  Identities=63%  Similarity=0.929  Sum_probs=36.6

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGW   41 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~   41 (133)
                      |++..|+|+++|+|+|+|+.|+|..+|.+|++. +++|++..
T Consensus        27 i~~~~~~~~~~~~l~~~g~~l~d~~~l~~~~v~~~~~i~v~~   68 (69)
T cd01769          27 IAAKEGVPPEQQRLIYAGKILKDDKTLSDYGIQDGSTLHLVL   68 (69)
T ss_pred             HHHHHCcChHHEEEEECCcCCCCcCCHHHCCCCCCCEEEEEE
Confidence            346689999999999999999999999999999 99988753

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.

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

Probab=98.10  E-value=1.9e-06  Score=52.51  Aligned_cols=42  Identities=74%  Similarity=1.013  Sum_probs=37.6

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |+...|+|.++|++.+.|+.|+|+.++.+|+|. ++++++..+
T Consensus        29 i~~~~~~~~~~q~~~~~~~~l~d~~~l~~~~i~~~~~~~l~~~   71 (75)
T KOG0001|consen   29 IRDKEGIPVDQQRLIFGGKPLEDGRTLADYNIQEGSTLHLVLS   71 (75)
T ss_pred             HHhhcCCCCeeEEEEECCEECcCCCcHHHhCCCCCCEEEEEEe
Confidence            345679999999999999999999999999999 999997654

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

Probab=97.84  E-value=5.7e-06  Score=65.81  Aligned_cols=39  Identities=31%  Similarity=0.520  Sum_probs=36.7

Q ss_pred             CCCCCeEEEeCCEECCCCCCccccccc-cccccccccccc
Q 040111            7 IPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRADF   45 (133)
Q Consensus         7 ip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~i~   45 (133)
                      .|+++|.|||+||+|.|+.|+.+|+|. +..+.+++++-.
T Consensus        38 yP~~~QkLIy~GkiL~D~~tv~Eykv~E~~fiVvMlsK~k   77 (340)
T KOG0011|consen   38 YPAEQQKLIYSGKILKDETTVGEYKVKEKKFIVVMLSKDK   77 (340)
T ss_pred             CchhhheeeecceeccCCcchhhhccccCceEEEEEecCc
Confidence            999999999999999999999999999 999998888754

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

Probab=97.84  E-value=2.4e-05  Score=62.35  Aligned_cols=72  Identities=13%  Similarity=0.206  Sum_probs=55.7

Q ss_pred             CCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCcccccccccc--EEeEEEEeCceeeeeecccccCc
Q 040111           51 PQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWF--VVVGVIFCGCRVNFWNASLRFDP  125 (133)
Q Consensus        51 g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~--~~~~~~~~~~~~~~~~~~~~~~~  125 (133)
                      ...++++|+.+.+|.+||+.++.+.|+|+++.+++|+||+|.++.++..+++  +...-|+   ..+=|.|--+|+.
T Consensus        13 ~h~l~v~v~~~t~I~~lke~Vak~~gvp~D~L~viFaGKeLs~~ttv~~cDL~qqs~~hi~---~lRP~~~~qk~ns   86 (446)
T KOG0006|consen   13 SHGLPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELSNDTTVQNCDLSQQSATHIM---LLRPWRKGQKFNS   86 (446)
T ss_pred             cCceeEEEecCCCHHHHHHHHHHhhCCChhheEEEEeccccccCceeecccccccchhhhh---ccCcccccccccc
Confidence            3457889999999999999999999999999999999999999999996654  3222222   2444555555544

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

Probab=97.82  E-value=7.4e-06  Score=51.18  Aligned_cols=38  Identities=39%  Similarity=0.643  Sum_probs=33.4

Q ss_pred             cccCCCC-CCeEEEeCCEECCCCCCccccccc-ccccccc
Q 040111            3 DKEGIPP-GQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLG   40 (133)
Q Consensus         3 ~~~gip~-~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~   40 (133)
                      ++.|+|+ +..+|+|.|+.|+++.|++++|+. +++|++.
T Consensus        32 ~~~~i~~~~~~~l~fdG~~L~~~~T~~~~~ied~d~Idv~   71 (72)
T PF11976_consen   32 EKKGIPPEESIRLIFDGKRLDPNDTPEDLGIEDGDTIDVI   71 (72)
T ss_dssp             HHHTTTT-TTEEEEETTEEE-TTSCHHHHT-STTEEEEEE
T ss_pred             HhhCCCccceEEEEECCEEcCCCCCHHHCCCCCCCEEEEE
Confidence            5679999 999999999999999999999999 9999875

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 ....

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

Probab=97.75  E-value=8.8e-05  Score=47.18  Aligned_cols=59  Identities=12%  Similarity=0.100  Sum_probs=49.6

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeC-----CcccCccccccccccE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLK-----FPFFFFEEVLSFFWFV  103 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~-----gk~L~d~~tL~dy~~~  103 (133)
                      +.|+........+.|+|.++|..+|++|....|++- +|||.|.     -+.|.+..+|++|+|=
T Consensus         3 VtV~q~g~~dl~l~vnPy~pI~k~K~kI~~~~~~~g-~qrLsfQepgg~rqlL~s~~sLA~yGiF   66 (80)
T cd01811           3 VTVEQTGYSDWILRVNPYSPIRKIKEKIRRSRNCSG-LQRLSFQEPGGERQLLSSRKSLADYGIF   66 (80)
T ss_pred             EEeeecCCCceEEEeCCcchHHHHHHHHHHhhCccc-ceEEEeecCCcccccccccccHhhhcce
Confidence            566777777788999999999999999999999887 9999983     2456688999999974

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.

>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=97.69  E-value=1.7e-05  Score=51.30  Aligned_cols=65  Identities=18%  Similarity=0.164  Sum_probs=38.8

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeC---Cccc--CccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLK---FPFF--FFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~---gk~L--~d~~tL~dy~~~~~~~~~  109 (133)
                      |.|++.+| ...+++++++|+.+|+++|++..++|++.|.|...   ...+  .++++|+++++.-...+|
T Consensus         7 lRvrS~dG-~~Rie~~~~~t~~~L~~kI~~~l~~~~~~~~L~~~~~~~~~l~s~~~~tl~~lglkHGdmly   76 (80)
T PF11543_consen    7 LRVRSKDG-MKRIEVSPSSTLSDLKEKISEQLSIPDSSQSLSKDRNNKEELKSSDSKTLSSLGLKHGDMLY   76 (80)
T ss_dssp             EEEE-SSE-EEEEEE-TTSBHHHHHHHHHHHS---TTT---BSSGGGGGCSSS-TT-CCCCT---TT-EEE
T ss_pred             EEEECCCC-CEEEEcCCcccHHHHHHHHHHHcCCCCcceEEEecCCCCcccccCCcCCHHHcCCCCccEEE
Confidence            56777665 45689999999999999999999999999998632   2344  357899999987544444

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.

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

Probab=97.62  E-value=2.2e-05  Score=51.02  Aligned_cols=39  Identities=28%  Similarity=0.524  Sum_probs=33.3

Q ss_pred             CcccCCCCCCeEE-EeCCE-----EC-CCCCCccccccc-ccccccc
Q 040111            2 EDKEGIPPGQQRS-IFAGK-----QL-EDGRTLADYKIQ-ESTLHLG   40 (133)
Q Consensus         2 ~~~~gip~~~Q~L-i~~gk-----~L-~D~~tL~~ygI~-~stl~L~   40 (133)
                      +...|+|++.|+| +|.|+     .| +|+.+|+.||+. +.+||+.
T Consensus        33 ~~~~G~~~~~mrL~l~~~~~~~~~~l~~d~~~L~~y~~~dg~~IhVv   79 (84)
T cd01789          33 ELVVGTPASSMRLQLFDGDDKLVSKLDDDDALLGSYPVDDGCRIHVI   79 (84)
T ss_pred             HHHHCCCccceEEEEEcCCCCeEeecCCCccEeeeccCCCCCEEEEE
Confidence            4568999999999 58888     46 788999999999 9999964

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.

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

Probab=97.58  E-value=5e-05  Score=50.54  Aligned_cols=53  Identities=15%  Similarity=0.082  Sum_probs=46.2

Q ss_pred             CCceeeccccCcHHHHHHHhhhhcCCCCCceEEEe-CC-cccCccccccccccEE
Q 040111           52 QNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLL-KF-PFFFFEEVLSFFWFVV  104 (133)
Q Consensus        52 ~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~-~g-k~L~d~~tL~dy~~~~  104 (133)
                      .++-++.+++.||.+||.+++....-|++.|+|+- .. ..|+|.++|+|++|+.
T Consensus        12 ttif~da~es~tV~elK~~l~gi~~~Pvn~qrL~kmd~eqlL~D~ktL~d~gfts   66 (110)
T KOG4495|consen   12 TTIFTDAKESSTVFELKRKLEGILKRPVNEQRLYKMDTEQLLDDGKTLGDCGFTS   66 (110)
T ss_pred             eeEEeecCccccHHHHHHHHHHHHhCCCcchheeecCHHHHhhccchhhhccccc
Confidence            34667889999999999999999999999999986 33 6788999999999864

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

Probab=97.40  E-value=5.6e-05  Score=67.61  Aligned_cols=43  Identities=30%  Similarity=0.598  Sum_probs=39.8

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccccccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~~stl~L~~~~   43 (133)
                      |.++.+||.+.|||||+|++|.|++++.+|+|.|-+|||+-|.
T Consensus        32 ~r~~~ni~s~~qr~i~~grvl~~~k~vq~~~vdgk~~hlverp   74 (1143)
T KOG4248|consen   32 IRASVNIPSEKQRLIYQGRVLQDDKKVQEYNVDGKVIHLVERP   74 (1143)
T ss_pred             HHHhcccccccceeeecceeeccchhhhhccCCCeEEEeeccC
Confidence            3467899999999999999999999999999999999999886

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

Probab=97.34  E-value=0.00027  Score=58.66  Aligned_cols=64  Identities=11%  Similarity=0.063  Sum_probs=56.4

Q ss_pred             CCCCceee-ccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEEeCce
Q 040111           50 DPQNITLE-VESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIFCGCR  113 (133)
Q Consensus        50 ~g~~~~l~-V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~~~~~  113 (133)
                      .|+..+++ ++.++|+..+|+++...+|+||+.|++++.|..+.|+-.+....|.++..++.+|-
T Consensus        11 ~gk~y~v~~l~~d~t~~vlKaqlf~LTgV~PeRQKv~vKGg~a~dd~~~~al~iKpn~~lmMmGt   75 (473)
T KOG1872|consen   11 GGKKYPVETLSTDETPSVLKAQLFALTGVPPERQKVMVKGGLAKDDVDWGALQIKPNETLMMMGT   75 (473)
T ss_pred             cCccccceeccCCCchHHHHHHHHHhcCCCccceeEEEecccccccccccccccCCCCEEEeecc
Confidence            46667776 99999999999999999999999999999999999998888888888887776654

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

Probab=97.34  E-value=0.00033  Score=46.90  Aligned_cols=47  Identities=13%  Similarity=0.034  Sum_probs=39.5

Q ss_pred             ceeecc--ccCcHHHHHHHhhhhcC--CCCCceEEEeCCcccCcccccccc
Q 040111           54 ITLEVE--SSDTIDNVKAKIQDKKR--IPPPAEADLLKFPFFFFEEVLSFF  100 (133)
Q Consensus        54 ~~l~V~--~~~tV~~LK~~I~~~~g--Ip~~~q~L~~~gk~L~d~~tL~dy  100 (133)
                      ..+++.  .+.||..||++|.+..+  ..-..+||+|+|+.|.|+..|+.-
T Consensus        14 l~L~I~~~~~~Tv~~LK~lIR~~~p~~~s~~rLRlI~~Gr~L~d~t~l~~~   64 (97)
T PF10302_consen   14 LPLDIPSPNTTTVAWLKQLIRERLPPEPSRRRLRLIYAGRLLNDHTDLSSE   64 (97)
T ss_pred             ceeecCCCCcccHHHHHHHHHhhcCCCCccccEEeeecCcccCccchhhhh
Confidence            456666  78999999999999983  667788999999999998877654

They contain a characteristic GFDRL sequence motif.

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

Probab=97.30  E-value=0.00015  Score=49.73  Aligned_cols=36  Identities=39%  Similarity=0.676  Sum_probs=27.1

Q ss_pred             CCCCeEEEeCCEECCCCCCccccccc-cc------cccccccc
Q 040111            8 PPGQQRSIFAGKQLEDGRTLADYKIQ-ES------TLHLGWRA   43 (133)
Q Consensus         8 p~~~Q~Li~~gk~L~D~~tL~~ygI~-~s------tl~L~~~~   43 (133)
                      .++..||||.||.|+|+.||.++++. +.      ++||+++.
T Consensus        47 s~~~lRLI~~GriL~d~~tL~~~~~~~~~~~~~~~vmHlvvrp   89 (111)
T PF13881_consen   47 SPSDLRLIYAGRILEDNKTLSDCRLPSGETPGGPTVMHLVVRP   89 (111)
T ss_dssp             SGGGEEEEETTEEE-SSSBTGGGT--TTSETT--EEEEEEE-S
T ss_pred             ChhhEEEEeCCeecCCcCcHHHhCCCCCCCCCCCEEEEEEecC
Confidence            34679999999999999999999987 44      78877765

>PF13019 Telomere_Sde2: Telomere stability and silencing

Probab=97.14  E-value=0.0012  Score=48.02  Aligned_cols=73  Identities=16%  Similarity=0.241  Sum_probs=56.0

Q ss_pred             cccCCCCC----CCceeeccccCcHHHHHHHhhhhcCCCCCce-EEEe-CCccc--Cccccccccc-------c--EEeE
Q 040111           44 DFCKNPDP----QNITLEVESSDTIDNVKAKIQDKKRIPPPAE-ADLL-KFPFF--FFEEVLSFFW-------F--VVVG  106 (133)
Q Consensus        44 i~Vk~~~g----~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q-~L~~-~gk~L--~d~~tL~dy~-------~--~~~~  106 (133)
                      |+|++++|    .++.+.+++++||.+|+..|.+..++|+..| .|.+ .++.+  .++.+++++.       +  ..+.
T Consensus         3 Vlvss~~g~~lp~tl~~~lp~~ttv~dL~~~l~~~~~~~~~~~~~L~~~~n~~l~~~~~~~~s~l~~~~~~~~~~~l~l~   82 (162)
T PF13019_consen    3 VLVSSFDGLTLPPTLSLSLPSTTTVSDLKDRLSERLPIPSSSQLYLTTNSNGQLSPSSDIPLSSLLSSSQDSDFITLRLS   82 (162)
T ss_pred             EEEecCCCCCCCCeEEeeCCCCCcHHHHHHHHHhhcCCCccceeEEEEeCCCeeCCCccccHHhhccCcCCCCceEEEEE
Confidence            78899988    5778889999999999999999999998884 4555 45555  3455666553       2  3456


Q ss_pred             EEEeCceeee
Q 040111          107 VIFCGCRVNF  116 (133)
Q Consensus       107 ~~~~~~~~~~  116 (133)
                      +-+|||.+-|
T Consensus        83 ~rl~GGKGGF   92 (162)
T PF13019_consen   83 LRLRGGKGGF   92 (162)
T ss_pred             EeccCCCccH
Confidence            7789998877

>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13

Probab=96.87  E-value=0.00058  Score=43.41  Aligned_cols=34  Identities=29%  Similarity=0.337  Sum_probs=29.6

Q ss_pred             CCCCCCeEEE--eCCEECCCCCCccccccc-cccccc
Q 040111            6 GIPPGQQRSI--FAGKQLEDGRTLADYKIQ-ESTLHL   39 (133)
Q Consensus         6 gip~~~Q~Li--~~gk~L~D~~tL~~ygI~-~stl~L   39 (133)
                      .+|+++|||.  +.|+.|.|+.+|.+||+. ++++++
T Consensus        38 ~~~~~Rqrl~~~~~g~~L~d~~tL~~~gv~~g~~lyv   74 (77)
T cd01801          38 QLTVNRQSLRLEPKGKSLKDDDTLVDLGVGAGATLYV   74 (77)
T ss_pred             CCCcceeEEEeCCCCcccCCcccHhhcCCCCCCEEEE
Confidence            4688999995  779999999999999999 988764

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.

>smart00166 UBX Domain present in ubiquitin-regulatory proteins

Probab=96.70  E-value=0.0043  Score=39.59  Aligned_cols=67  Identities=13%  Similarity=-0.013  Sum_probs=54.9

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEE--eCCcccCc---cccccccccEEeEEEEe
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADL--LKFPFFFF---EEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~--~~gk~L~d---~~tL~dy~~~~~~~~~~  110 (133)
                      |.||.++|+.+.....+++|++++.+-+....+.......|+  |..+.+.+   +.||.+.++...++++.
T Consensus         7 I~iRlPdG~ri~~~F~~~~tl~~v~~~v~~~~~~~~~~f~L~t~~Prk~l~~~d~~~tL~e~gL~p~~~l~v   78 (80)
T smart00166        7 LQIRLPDGSRLVRRFPSSDTLRTVYEFVSAALTDGNDPFTLNSPFPRRTFTKDDYSKTLLELALLPSSTLVL   78 (80)
T ss_pred             EEEEcCCCCEEEEEeCCCCcHHHHHHHHHHcccCCCCCEEEEeCCCCcCCccccccCCHHHCCCCCceEEEE
Confidence            778999999999999999999999999977667666677776  67777864   36899999877776654

Present in FAF1 and Shp1p.

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

Probab=96.68  E-value=0.00041  Score=42.99  Aligned_cols=58  Identities=16%  Similarity=0.127  Sum_probs=50.0

Q ss_pred             cCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccE
Q 040111           46 CKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFV  103 (133)
Q Consensus        46 Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~  103 (133)
                      +...-|+...+.-.+++||.++|..|+..+|-.++.-.|---+..++|.-+|++|.|-
T Consensus         6 ~nDrLGKKVRvKCn~dDtiGD~KKliaaQtGT~~~kivl~k~~~i~kd~I~L~dyeih   63 (73)
T KOG3493|consen    6 LNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFKDHITLSDYEIH   63 (73)
T ss_pred             hhhhcCceEEEEeCCcccccCHHHHHHHhhCCChhHhHHHhhhhhhhcccceeeEEec
Confidence            3444577778888899999999999999999999988888788888999999999874

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

Probab=96.67  E-value=0.00064  Score=43.27  Aligned_cols=39  Identities=33%  Similarity=0.490  Sum_probs=31.7

Q ss_pred             CCcccCCCCCCeEEEeC---CE--ECCCCCCccccccc-ccccccc
Q 040111            1 IEDKEGIPPGQQRSIFA---GK--QLEDGRTLADYKIQ-ESTLHLG   40 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~---gk--~L~D~~tL~~ygI~-~stl~L~   40 (133)
                      |++..|++ ..|||.|+   |+  .|++..+|++|||+ +..|.|+
T Consensus        30 I~~~~~~~-g~qrLsfQepgg~rqlL~s~~sLA~yGiFs~~~i~ll   74 (80)
T cd01811          30 IRRSRNCS-GLQRLSFQEPGGERQLLSSRKSLADYGIFSKTNICLL   74 (80)
T ss_pred             HHHhhCcc-cceEEEeecCCcccccccccccHhhhcceeccEEEEE
Confidence            34567888 69999998   54  37999999999999 8887764

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.

>cd01788 ElonginB Ubiquitin-like domain of Elongin B

Probab=96.58  E-value=0.00094  Score=45.85  Aligned_cols=60  Identities=27%  Similarity=0.371  Sum_probs=39.8

Q ss_pred             cccCCCCCCeEEEeCCEECCCCCCcccccc-------c-cccccccccccccCCCCCCCceeeccccCcHHHH
Q 040111            3 DKEGIPPGQQRSIFAGKQLEDGRTLADYKI-------Q-ESTLHLGWRADFCKNPDPQNITLEVESSDTIDNV   67 (133)
Q Consensus         3 ~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI-------~-~stl~L~~~~i~Vk~~~g~~~~l~V~~~~tV~~L   67 (133)
                      .-...|++.|||+-.+.+|+|..||+|||+       + .+++=|.+     |..+|..-.+++.+-.+--+|
T Consensus        33 gI~k~pp~dQrL~kd~qvLeD~kTL~d~g~t~~~akaq~pA~vgLa~-----r~~d~~fE~l~I~p~S~pp~l  100 (119)
T cd01788          33 GILKRPPEDQRLYKDDQLLDDGKTLGDCGFTSQTARPQAPATVGLAF-----RSSDDTFEPLRIEPFSSPPEL  100 (119)
T ss_pred             HHhcCChhHheeecCceeecccccHHHcCccccccccCCCCeEEEEE-----ecCCCCccceeeeeCCCCCCc
Confidence            335679999999966678999999999999       5 55555433     334455445555554443333

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.

>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=96.56  E-value=0.0019  Score=40.16  Aligned_cols=58  Identities=9%  Similarity=-0.039  Sum_probs=41.3

Q ss_pred             CCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEe
Q 040111           48 NPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVV  105 (133)
Q Consensus        48 ~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~  105 (133)
                      ..+++...+.+.|++++.++-+....+.|+++++..|.|+++.++-+.+...-++.++
T Consensus         3 ~~~~rr~~vkvtp~~~l~~VL~eac~k~~l~~~~~~L~h~~k~ldlslp~R~snL~n~   60 (65)
T PF11470_consen    3 CYNFRRFKVKVTPNTTLNQVLEEACKKFGLDPSSYDLKHNNKPLDLSLPFRLSNLPNN   60 (65)
T ss_dssp             -TTS-EEEE---TTSBHHHHHHHHHHHTT--GGG-EEEETTEEESSS-BHHHH---SS
T ss_pred             ccCCcEEEEEECCCCCHHHHHHHHHHHcCCCccceEEEECCEEeccccceeecCCCCC
Confidence            3567888999999999999999999999999999999999999988888877766543

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.

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

Probab=96.56  E-value=0.004  Score=39.70  Aligned_cols=67  Identities=12%  Similarity=0.060  Sum_probs=55.5

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCc-eEEE--eCCcccCcc--ccccccccEEeEEEEe
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPA-EADL--LKFPFFFFE--EVLSFFWFVVVGVIFC  110 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~-q~L~--~~gk~L~d~--~tL~dy~~~~~~~~~~  110 (133)
                      |-||.++|+.+.-...+++|+.+|.+-|......+... ..|+  |..+.+.++  .+|++.++...+.+++
T Consensus         9 I~vRlpdG~~l~~~F~~~~tl~~l~~~v~~~~~~~~~~~f~L~~~~Pr~~l~~~~~~tl~e~~l~p~~~l~v   80 (82)
T PF00789_consen    9 IQVRLPDGSRLQRRFPKSDTLQDLYDFVESQLFSPEESDFELITAFPRRELTDEDSKTLEEAGLLPSATLIV   80 (82)
T ss_dssp             EEEEETTSTEEEEEEETTSBHHHHHHHHHHHHHCTTTSSEEEEESSSTEECCSTTTSBTCCCTTSSCEEEEE
T ss_pred             EEEECCCCCEEEEEECCcchHHHHHHHHHHhcCCCCCccEEEEeCCCCcCCCccccccHHHhcCCCCeEEEE
Confidence            77899999999889999999999999999887766654 7776  677888764  5999998877776654

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

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

Probab=96.49  E-value=0.00061  Score=44.23  Aligned_cols=39  Identities=33%  Similarity=0.579  Sum_probs=29.5

Q ss_pred             CcccCCCCCCeEEEeC----CE---EC-CCCCCccccccc-ccccccc
Q 040111            2 EDKEGIPPGQQRSIFA----GK---QL-EDGRTLADYKIQ-ESTLHLG   40 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~----gk---~L-~D~~tL~~ygI~-~stl~L~   40 (133)
                      +...|+|++.|+|.+.    +.   .+ +|..+|.+||+. +.+||+.
T Consensus        34 ~~~~Gi~~~~m~L~l~~~~~~~~~~~~~dd~~~L~~y~~~dg~~i~V~   81 (87)
T PF14560_consen   34 EKLTGIPPSDMRLQLKSDKDDSKIEELDDDDATLGSYGIKDGMRIHVV   81 (87)
T ss_dssp             HHHHTS-TTTEEEEEE-TSSSSEEEESSGSSSBCCHHT-STTEEEEEE
T ss_pred             HHHhCCCcccEEEEEEecCCCccccccCCCccEeecCCCCCCCEEEEE
Confidence            4568999999999876    22   24 578999999999 9999863

>cd01767 UBX UBX (ubiquitin regulatory X) domain

Probab=96.16  E-value=0.016  Score=36.66  Aligned_cols=64  Identities=13%  Similarity=0.036  Sum_probs=50.4

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEE--eCCcccCc---cccccccccEEeEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADL--LKFPFFFF---EEVLSFFWFVVVGVI  108 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~--~~gk~L~d---~~tL~dy~~~~~~~~  108 (133)
                      |.||.++|+.+.-....++|+.+|.+-|.....- .....|+  |..+.+.+   +.||.+.++...+++
T Consensus         5 i~iRlpdG~~~~~~F~~~~tl~~l~~fv~~~~~~-~~~f~L~t~~Pr~~~~~~~~~~TL~e~gL~~s~~~   73 (77)
T cd01767           5 IQIRLPDGKRLEQRFNSTHKLSDVRDFVESNGPP-AEPFTLMTSFPRRVLTDLDYELTLQEAGLVNEVVF   73 (77)
T ss_pred             EEEEcCCCCEEEEEeCCCCCHHHHHHHHHHcCCC-CCCEEEEeCCCCccCCCCCccCcHHHcCCccceEE
Confidence            6789999999888999999999999999875432 5556676  66777754   679999998755544

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

>cd01772 SAKS1_UBX SAKS1-like UBX domain

Probab=96.00  E-value=0.018  Score=36.79  Aligned_cols=66  Identities=11%  Similarity=0.023  Sum_probs=52.5

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEE--eCCcccCc---cccccccccEEeEEEEe
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADL--LKFPFFFF---EEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~--~~gk~L~d---~~tL~dy~~~~~~~~~~  110 (133)
                      |.||.++|+.+.-....++|++++.+-|+...+-+ ....|+  |-.+.+.+   +.||.+.++.+.+++++
T Consensus         7 i~iRlp~G~~~~~~F~~~~tl~~v~~fV~~~~~~~-~~f~L~t~fPrk~~~~~d~~~TL~elgL~Psa~L~v   77 (79)
T cd01772           7 IQIRLLDGTTLKQTFKAREQLAAVRLFVELNTGNG-GPFTLMTPFPRKVFTEDDMEKPLQELGLVPSAVLIV   77 (79)
T ss_pred             EEEECCCCCEEEEEeCCCChHHHHHHHHHHcCCCC-CCEEEEeCCCCeECCcccccCCHHHCCCCCceEEEE
Confidence            67899999998888999999999999998755432 446666  77888864   47999999887776654

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

>PLN02560 enoyl-CoA reductase

Probab=95.75  E-value=0.0042  Score=49.57  Aligned_cols=38  Identities=26%  Similarity=0.500  Sum_probs=30.9

Q ss_pred             CcccCC-CCCCeEEEeC---C----EECCCCCCccccccc-cccccc
Q 040111            2 EDKEGI-PPGQQRSIFA---G----KQLEDGRTLADYKIQ-ESTLHL   39 (133)
Q Consensus         2 ~~~~gi-p~~~Q~Li~~---g----k~L~D~~tL~~ygI~-~stl~L   39 (133)
                      +++.++ ++++|||.+.   |    +.|+|+.+|.+||+. ++++++
T Consensus        34 sk~~~~~~~~RqRL~~~~~~gk~~g~~L~d~ktL~d~gv~~gstLy~   80 (308)
T PLN02560         34 HKRKKKYYPSRQRLTLPLPPGKTRPTVLDDSKSLKDYGLGDGGTVVF   80 (308)
T ss_pred             HHHcCCCChhheEEEEecCCCCcCccccCCCCCHHhcCCCCCceEEE
Confidence            456665 8999999983   3    378999999999999 988663

>cd01770 p47_UBX p47-like ubiquitin domain

Probab=95.67  E-value=0.035  Score=35.58  Aligned_cols=65  Identities=9%  Similarity=-0.005  Sum_probs=51.5

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCC-CCCceEEE--eCCcccCc-cccccccccEEeEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRI-PPPAEADL--LKFPFFFF-EEVLSFFWFVVVGV  107 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gI-p~~~q~L~--~~gk~L~d-~~tL~dy~~~~~~~  107 (133)
                      .|.||.++|+.+......++||++|.+-|....+- ......|+  |-.+.|.| +.||.|.++.+..+
T Consensus         6 ~iqiRlpdG~r~~~rF~~~~tv~~l~~~v~~~~~~~~~~~f~L~t~fP~k~l~~~~~Tl~eagL~~s~v   74 (79)
T cd01770           6 SIQIRLADGKRLVQKFNSSHRVSDVRDFIVNARPEFAARPFTLMTAFPVKELSDESLTLKEANLLNAVI   74 (79)
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHHhCCCCCCCCEEEecCCCCcccCCCCCcHHHCCCcCcEE
Confidence            37799999999999999999999999999986542 33556676  77888876 67999998875443

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

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

Probab=95.55  E-value=0.0087  Score=48.01  Aligned_cols=40  Identities=33%  Similarity=0.631  Sum_probs=36.1

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGW   41 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~   41 (133)
                      +++.|+|+++.++||.||.|+|+.|+..+.+. -+.+|.+.
T Consensus        34 ak~~gvp~D~L~viFaGKeLs~~ttv~~cDL~qqs~~hi~~   74 (446)
T KOG0006|consen   34 AKRQGVPADQLRVIFAGKELSNDTTVQNCDLSQQSATHIML   74 (446)
T ss_pred             HHhhCCChhheEEEEeccccccCceeecccccccchhhhhc
Confidence            56799999999999999999999999999988 88888763

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

Probab=95.52  E-value=0.034  Score=37.26  Aligned_cols=59  Identities=5%  Similarity=-0.038  Sum_probs=52.2

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCcccccccccc
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWF  102 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~  102 (133)
                      +.|+.-++....+.|..+++...|+..-+++.|++.+..|++|.|+.+...+|-++.++
T Consensus        23 LKV~gqd~~~~~Fkikr~t~LkKLM~aYc~r~Gl~~~s~RFlFdG~rI~~~~TP~~L~m   81 (99)
T KOG1769|consen   23 LKVKGQDGSVVVFKIKRHTPLKKLMKAYCERQGLSMNSLRFLFDGQRIRETHTPADLEM   81 (99)
T ss_pred             EEEecCCCCEEEEEeecCChHHHHHHHHHHHcCCccceEEEEECCcCcCCCCChhhhCC
Confidence            44555456667889999999999999999999999999999999999999999998886

>cd00196 UBQ Ubiquitin-like proteins

Probab=95.42  E-value=0.0058  Score=34.65  Aligned_cols=39  Identities=46%  Similarity=0.644  Sum_probs=33.8

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLG   40 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~   40 (133)
                      .++.|+|++.|.|+++|..+++...+.+|++. ++++++.
T Consensus        28 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~   67 (69)
T cd00196          28 AKKLGLPPEQQRLLVNGKILPDSLTLEDYGLQDGDELVLV   67 (69)
T ss_pred             HHHHCcChHHeEEEECCeECCCCCcHHHcCCCCCCEEEEE
Confidence            34567899999999999999998888899999 8888864

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.

>cd01774 Faf1_like2_UBX Faf1 ike-2 UBX domain

Probab=95.21  E-value=0.053  Score=35.25  Aligned_cols=66  Identities=11%  Similarity=0.025  Sum_probs=53.4

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCC--cccC--------ccccccccccEEeEEEEe
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKF--PFFF--------FEEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~g--k~L~--------d~~tL~dy~~~~~~~~~~  110 (133)
                      |.+|.++|+.+.-....++|+++|.+-|.. .+-.++...|+.+-  +.+.        .+.||.+-|+...++.|+
T Consensus         7 I~iRlp~G~Rl~rrF~~~~tl~~l~~fv~~-~~~~~~~f~L~t~FPrr~~~~~~~~~~~~~~TL~eaGL~~s~~L~V   82 (85)
T cd01774           7 IVFKLPNGTRVERRFLFTQSLRVIHDFLFS-LKETPEKFQIVTNFPRRVLPCLPSEGDPPPPTLLEAGLSNSEVLFV   82 (85)
T ss_pred             EEEECCCCCEEEEEeCCCCcHHHHHHHHHh-CCCCCCcEEEecCCCCccccccccccCcCCCCHHHcCCCCccEEEE
Confidence            678999999988888899999999999964 55677889999666  8885        257999999876666553

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

>KOG0013 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.01  E-value=0.032  Score=42.26  Aligned_cols=56  Identities=11%  Similarity=0.072  Sum_probs=51.3

Q ss_pred             CCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEe
Q 040111           50 DPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVV  105 (133)
Q Consensus        50 ~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~  105 (133)
                      +++.+.+.+...+|+.++|.++..+.|+.+-.|++.|+|+.+-|...|..+++-..
T Consensus       155 T~~d~~lta~~~Dtv~eik~~L~Aaeg~D~~sQrif~Sg~~l~dkt~LeEc~iekg  210 (231)
T KOG0013|consen  155 TREDFWLTAPHYDTVGEIKRALRAAEGVDPLSQRIFFSGGVLVDKTDLEECKIEKG  210 (231)
T ss_pred             hhhheeecccCcCcHHHHHHHHHHhhccchhhheeeccCCceeccccceeeeecCC
Confidence            56778888999999999999999999999999999999999999999999987544

>cd01773 Faf1_like1_UBX Faf1 ike-1 UBX domain

Probab=94.70  E-value=0.087  Score=34.17  Aligned_cols=67  Identities=12%  Similarity=0.072  Sum_probs=55.6

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEE--eCCcccCc---cccccccccEEeEEEEe
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADL--LKFPFFFF---EEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~--~~gk~L~d---~~tL~dy~~~~~~~~~~  110 (133)
                      .|.||.++|+...-....++++++|-.-++. .|.+++...|+  |--+.+..   +.||.+.++..-.++|+
T Consensus         7 ~i~vRlP~G~r~~rrF~~~~~L~~v~~fv~~-~g~~~~~f~L~t~FPRr~~~~~d~~~TL~e~GL~P~~~LfV   78 (82)
T cd01773           7 RLMLRYPDGKREQIALPEQAKLLALVRHVQS-KGYPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFV   78 (82)
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-cCCCCCCEEEecCCCCcccCCcccCCCHHHcCCCCCcEEEE
Confidence            4789999999998888899999999999888 68899999998  66677642   47999999877666654

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

>smart00455 RBD Raf-like Ras-binding domain

Probab=94.66  E-value=0.058  Score=33.82  Aligned_cols=48  Identities=21%  Similarity=0.185  Sum_probs=41.7

Q ss_pred             ccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCC--cccC
Q 040111           45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKF--PFFF   92 (133)
Q Consensus        45 ~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~g--k~L~   92 (133)
                      .|..++|+...+.+.|+.|+.++-..+.++.|+.++...+...|  ++|.
T Consensus         3 ~v~LP~~~~~~V~vrpg~tl~e~L~~~~~kr~l~~~~~~v~~~g~~k~ld   52 (70)
T smart00455        3 KVHLPDNQRTVVKVRPGKTVRDALAKALKKRGLNPECCVVRLRGEKKPLD   52 (70)
T ss_pred             EEECCCCCEEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEcCCCccee
Confidence            35578999999999999999999999999999999999998855  4444

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

Probab=94.31  E-value=0.055  Score=34.20  Aligned_cols=44  Identities=20%  Similarity=0.175  Sum_probs=39.8

Q ss_pred             ccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCC
Q 040111           45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKF   88 (133)
Q Consensus        45 ~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~g   88 (133)
                      .|..++|+...+.+.|.+|+.++-.++.++.|+.|+...+...|
T Consensus         3 ~V~LPng~~t~V~vrpg~ti~d~L~~~c~kr~l~~~~~~v~~~~   46 (72)
T cd01760           3 RVYLPNGQRTVVPVRPGMSVRDVLAKACKKRGLNPECCDVFLLG   46 (72)
T ss_pred             EEECcCCCeEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEec
Confidence            45678999999999999999999999999999999999988654

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.

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

Probab=94.26  E-value=0.027  Score=35.87  Aligned_cols=62  Identities=8%  Similarity=-0.007  Sum_probs=42.6

Q ss_pred             ccCCCCCCCceeeccccCcHHHHHHHhhhhcCCC---CC---ceEEE-eCCcccCccccccccccEEeE
Q 040111           45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIP---PP---AEADL-LKFPFFFFEEVLSFFWFVVVG  106 (133)
Q Consensus        45 ~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp---~~---~q~L~-~~gk~L~d~~tL~dy~~~~~~  106 (133)
                      .|...+|+.+.+.++.+.+|++|...|.+..+.+   +.   ..+|. -+|..|.++.+|++|++....
T Consensus         6 tv~~~~~~~~Dl~lP~~vpv~~li~~l~~~~~~~~~~~~~~~~~~L~~~~g~~L~~~~tL~~~gV~dGd   74 (79)
T PF08817_consen    6 TVDAGNGRQVDLALPADVPVAELIPELVELLGLPGDDPPGHGQWVLARAGGRPLDPDQTLADAGVRDGD   74 (79)
T ss_dssp             EEE-TT--EEEEEEETTSBTTHHHHHHHHHS---S---TT-E-EEEG-GGTEEEETTSBCGGGT--TT-
T ss_pred             EEEcCCCcEEEEEcCCCCcHHHHHHHHHHHhCCccCCCCCcceEEEEecCCcccCCcCcHhHcCCCCCC
Confidence            3444446788899999999999999999987753   23   35666 789999999999999986443

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

>cd01771 Faf1_UBX Faf1 UBX domain

Probab=93.60  E-value=0.19  Score=32.20  Aligned_cols=66  Identities=8%  Similarity=-0.092  Sum_probs=54.2

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEE--eCCcccC--c-cccccccccEEeEEEEe
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADL--LKFPFFF--F-EEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~--~~gk~L~--d-~~tL~dy~~~~~~~~~~  110 (133)
                      |.+|.++|+...-....++++++|-.-+.. .|.++...+|+  |--+.+.  | +.||.+.++...+++|+
T Consensus         7 i~iRlP~G~r~~rrF~~t~~L~~l~~fv~~-~~~~~~~f~L~t~fPRk~~~~~d~~~TL~e~gL~p~~~L~V   77 (80)
T cd01771           7 LRVRTPSGDFLERRFLGDTPLQVLLNFVAS-KGYPIDEYKLLSSWPRRDLTQLDPNFTLLELKLYPQETLIL   77 (80)
T ss_pred             EEEECCCCCEEEEEeCCCCcHHHHHHHHHh-cCCCCCCEEEecCCCCCCCcCCCCCCcHHHcCCCCCcEEEE
Confidence            678999999988889999999999999976 48888889998  7778774  2 56999998876666554

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

>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=93.56  E-value=0.061  Score=34.76  Aligned_cols=47  Identities=17%  Similarity=0.078  Sum_probs=38.6

Q ss_pred             CceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccc
Q 040111           53 NITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSF   99 (133)
Q Consensus        53 ~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~d   99 (133)
                      ++.+.+++.-+..+|.++|.++.++|+++..|.|....=.+--+|+|
T Consensus        12 tIaIrvp~~~~y~~L~~ki~~kLkl~~e~i~LsYkde~s~~~v~l~d   58 (80)
T cd06406          12 TVAIQVARGLSYATLLQKISSKLELPAEHITLSYKSEASGEDVILSD   58 (80)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCchhcEEEeccCCCCCccCcCh
Confidence            78899999999999999999999999999999997655433333433

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

>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=93.35  E-value=0.15  Score=33.39  Aligned_cols=42  Identities=12%  Similarity=0.131  Sum_probs=36.2

Q ss_pred             ccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCC---CceEEEe
Q 040111           45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP---PAEADLL   86 (133)
Q Consensus        45 ~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~---~~q~L~~   86 (133)
                      .++++.|+.+.+.+.++..+.+|++.|+++.|+..   +...|.|
T Consensus         4 K~~~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~~~~~~L~Y   48 (86)
T cd06409           4 KFKDPKGRVHRFRLRPSESLEELRTLISQRLGDDDFETHLYALSY   48 (86)
T ss_pred             EeeCCCCCEEEEEecCCCCHHHHHHHHHHHhCCccccCCcccEEE
Confidence            46788999999999999999999999999999876   4556644

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

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

Probab=91.78  E-value=0.099  Score=43.81  Aligned_cols=41  Identities=24%  Similarity=0.381  Sum_probs=37.9

Q ss_pred             cccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            3 DKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         3 ~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      ..+|+||++|++.+.|..+.|+-.+..-+|+ +.+++|+.+.
T Consensus        35 ~LTgV~PeRQKv~vKGg~a~dd~~~~al~iKpn~~lmMmGt~   76 (473)
T KOG1872|consen   35 ALTGVPPERQKVMVKGGLAKDDVDWGALQIKPNETLMMMGTA   76 (473)
T ss_pred             HhcCCCccceeEEEecccccccccccccccCCCCEEEeeccc
Confidence            4589999999999999999999999999999 9999998876

>PF12754 Blt1: Cell-cycle control medial ring component; InterPro: IPR024737 During size-dependent cell cycle transitions controlled by the ubiquitous cyclin-dependent kinase Cdk1, Blt1 has been shown to co-localise with Cdr2 in the medial interphase nodes, as well as with Mid1 which was previously shown to localise to similar interphase structures

Probab=91.47  E-value=0.056  Score=43.11  Aligned_cols=73  Identities=16%  Similarity=0.144  Sum_probs=0.0

Q ss_pred             cccCCCCCCCceeec--c-c--cCcHHHHHHHhhh----------hcCCCCCceE-----EEeCCcccCccccccccc--
Q 040111           44 DFCKNPDPQNITLEV--E-S--SDTIDNVKAKIQD----------KKRIPPPAEA-----DLLKFPFFFFEEVLSFFW--  101 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V--~-~--~~tV~~LK~~I~~----------~~gIp~~~q~-----L~~~gk~L~d~~tL~dy~--  101 (133)
                      |.+|.+-+....+.+  . +  +.+|.++|..+++          .+++|.+..+     |.|+-+++.|.++|.+..  
T Consensus        81 V~Lks~rnp~l~i~L~~~~plattSv~dlk~~v~~rv~~~~~~~~~~~vp~dKik~~~~~lL~~kkPv~~~ktl~e~l~~  160 (309)
T PF12754_consen   81 VHLKSLRNPPLDISLPNVPPLATTSVQDLKDAVQQRVHPSQATYDETRVPLDKIKNFRCRLLYKKKPVGDSKTLAEVLAD  160 (309)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EEeecCCCCCceeEeCCCCcCCcCcHHHHHHHHHhhhcccccccccccCCHHHhhhhhhhheecCccCCCcCcHHHHHhc
Confidence            445555444433322  2 2  6899999999999          8899999999     999999998888877663  


Q ss_pred             ----------cEEeEEEEeCceeee
Q 040111          102 ----------FVVVGVIFCGCRVNF  116 (133)
Q Consensus       102 ----------~~~~~~~~~~~~~~~  116 (133)
                                =.+.|+.+.||+.-.
T Consensus       161 ~~~~l~~~~~~vE~gvMVlGGa~~~  185 (309)
T PF12754_consen  161 SESRLLSGGKEVEFGVMVLGGAAVI  185 (309)
T ss_dssp             -------------------------
T ss_pred             ccchhccCCceEEEEEEEECCcccC
Confidence                      145566666776544

Physical interactions between Blt1-Mid1, Blt1-Cdr2 and Cdr2-Mid1 were detected, indicating that medial cortical nodes are formed by the ordered, Cdr2-dependent assembly of multiple interacting proteins during interphase[].; PDB: 2LO0_A.

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

Probab=91.11  E-value=0.57  Score=31.02  Aligned_cols=55  Identities=5%  Similarity=0.007  Sum_probs=49.7

Q ss_pred             CCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccE
Q 040111           49 PDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFV  103 (133)
Q Consensus        49 ~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~  103 (133)
                      -+|.++.+.+..+++-..|....+.+.|=..+..|++|.|+.++-++|-.|+++-
T Consensus        32 qd~telfFkiKktT~f~klm~af~~rqGK~m~slRfL~dG~rI~~dqTP~dldmE   86 (103)
T COG5227          32 QDGTELFFKIKKTTTFKKLMDAFSRRQGKNMSSLRFLFDGKRIDLDQTPGDLDME   86 (103)
T ss_pred             CCCCEEEEEEeccchHHHHHHHHHHHhCcCcceeEEEEcceecCCCCChhhcCCc
Confidence            3566778899999999999999999999999999999999999999999998863

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

Probab=90.88  E-value=0.084  Score=42.67  Aligned_cols=58  Identities=9%  Similarity=0.092  Sum_probs=46.0

Q ss_pred             cccCCCCCCCc--eeeccccCcHHHHHHHhhhhcC--CCCCceEEEeCCcccCccccccccc
Q 040111           44 DFCKNPDPQNI--TLEVESSDTIDNVKAKIQDKKR--IPPPAEADLLKFPFFFFEEVLSFFW  101 (133)
Q Consensus        44 i~Vk~~~g~~~--~l~V~~~~tV~~LK~~I~~~~g--Ip~~~q~L~~~gk~L~d~~tL~dy~  101 (133)
                      +++|.++.+..  ++..+..-||.+||..+....-  =-..+|||+|.||.|.|...|+|.-
T Consensus        12 lliks~Nq~y~dl~i~~dl~wtv~~Lk~hls~VyPskpl~~dqrliYsgkllld~qcl~d~l   73 (391)
T KOG4583|consen   12 LLIKSPNQSYKDLSISLDLKWTVGDLKVHLSQVYPSKPLELDQRLIYSGKLLLDHQCLTDWL   73 (391)
T ss_pred             EEecCCCccccceeeehhhhhhHHHHhhhHhhcCCCCCchhhHHHHhhccccccchhHHHHH
Confidence            56788776654  4555678899999999988763  3467899999999999998888764

>PRK06437 hypothetical protein; Provisional

Probab=90.13  E-value=1.4  Score=27.13  Aligned_cols=49  Identities=8%  Similarity=-0.038  Sum_probs=39.0

Q ss_pred             CCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCcccccccccc
Q 040111           50 DPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWF  102 (133)
Q Consensus        50 ~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~  102 (133)
                      .++...++++...|+++|-+.    .|++++...+..+|+.+..+..|++=+=
T Consensus         9 g~~~~~~~i~~~~tv~dLL~~----Lgi~~~~vaV~vNg~iv~~~~~L~dgD~   57 (67)
T PRK06437          9 GHINKTIEIDHELTVNDIIKD----LGLDEEEYVVIVNGSPVLEDHNVKKEDD   57 (67)
T ss_pred             CCcceEEEcCCCCcHHHHHHH----cCCCCccEEEEECCEECCCceEcCCCCE
Confidence            445567888888999988755    5899998889999999998777877543

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

Probab=90.06  E-value=0.26  Score=30.81  Aligned_cols=56  Identities=14%  Similarity=0.082  Sum_probs=40.9

Q ss_pred             cCCCCCCCceeeccccCcHHHHHHHhhhhcCCC-CCceEEEe----C--CcccCccccccccc
Q 040111           46 CKNPDPQNITLEVESSDTIDNVKAKIQDKKRIP-PPAEADLL----K--FPFFFFEEVLSFFW  101 (133)
Q Consensus        46 Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp-~~~q~L~~----~--gk~L~d~~tL~dy~  101 (133)
                      |+.++|....+++++++|+.++-.+|++..|+. .+-.-|.+    .  ..-|+.+++|.++.
T Consensus         1 V~llD~~~~~~~v~~~~t~~~l~~~v~~~l~l~e~~~FgL~~~~~~~~~~~wL~~~k~l~~q~   63 (80)
T PF09379_consen    1 VRLLDGTTKTFEVDPKTTGQDLLEQVCDKLGLKEKEYFGLQYQVDKDGEHHWLDLDKKLKKQL   63 (80)
T ss_dssp             EEESSEEEEEEEEETTSBHHHHHHHHHHHHTTSSGGGEEEEE-EBTTSSEEEE-SSSBGGGST
T ss_pred             CCCcCCCcEEEEEcCCCcHHHHHHHHHHHcCCCCccEEEEEEeecCCCcceeccCcccHHHHc
Confidence            456788889999999999999999999999974 44555666    1  22345556666653

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

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

Probab=89.82  E-value=0.67  Score=30.29  Aligned_cols=55  Identities=11%  Similarity=0.016  Sum_probs=39.4

Q ss_pred             ceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           54 ITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        54 ~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      +...++-.+++..||..++.+.|++.+...+...+..|+.+++|-|=.+.-.|.|
T Consensus         5 I~q~mDI~epl~~Lk~lLe~Rl~~~L~~~~f~LQD~~L~~~k~L~dQcVqgeGlV   59 (88)
T PF11620_consen    5 IMQHMDIREPLSTLKKLLERRLGISLSDYEFWLQDIQLEPHKSLVDQCVQGEGLV   59 (88)
T ss_dssp             EEEEEESSSBGGGHHHHSHHHH-S--SS-EEEETTEE--TTSBTTTSS----SEE
T ss_pred             EEEEEecCCcHHHHHHHHHHhhCCCcCCCeEEeccceecCCccHHHhhccccCEE
Confidence            4556777889999999999999999999999999988999999999987555554

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

>PRK08364 sulfur carrier protein ThiS; Provisional

Probab=89.64  E-value=1.6  Score=27.02  Aligned_cols=55  Identities=7%  Similarity=0.015  Sum_probs=38.8

Q ss_pred             CceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEEeC
Q 040111           53 NITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIFCG  111 (133)
Q Consensus        53 ~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~~~  111 (133)
                      ...+++++..|++++-+.+    ++++..-.+..+|.....+..|++=+-..+--.++|
T Consensus        15 ~~~~~~~~~~tv~~ll~~l----~~~~~~v~v~vNg~iv~~~~~l~~gD~Veii~~V~G   69 (70)
T PRK08364         15 EKEIEWRKGMKVADILRAV----GFNTESAIAKVNGKVALEDDPVKDGDYVEVIPVVSG   69 (70)
T ss_pred             ceEEEcCCCCcHHHHHHHc----CCCCccEEEEECCEECCCCcCcCCCCEEEEEccccC
Confidence            4567778888999988764    777777777788888877777777764333333344

>cd01817 RGS12_RBD Ubiquitin domain of RGS12 and RGS14

Probab=89.44  E-value=0.69  Score=29.36  Aligned_cols=44  Identities=16%  Similarity=0.154  Sum_probs=38.4

Q ss_pred             cCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCc
Q 040111           46 CKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFP   89 (133)
Q Consensus        46 Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk   89 (133)
                      |..++|+...+.+.|..||.++-.+..++.|+.++.--++..|.
T Consensus         4 V~LPdg~~T~V~vrpG~ti~d~L~kllekRgl~~~~~~vf~~g~   47 (73)
T cd01817           4 VILPDGSTTVVPTRPGESIRDLLSGLCEKRGINYAAVDLFLVGG   47 (73)
T ss_pred             EECCCCCeEEEEecCCCCHHHHHHHHHHHcCCChhHEEEEEecC
Confidence            34578999999999999999999999999999999888876553

RGS12 (regulator of G signalling 12), and RGS14, are members of a family of GTPase-activating proteins (GAP's) specific for the G-alpha subunit, which act as key inhibitors of G-protein-mediated cell responses in eukaryotes. Their domain architecture includes tandem RBD domains as well as PDZ , PTB, and RGS, and GoLoco domains.

>PF02196 RBD: Raf-like Ras-binding domain; InterPro: IPR003116 This is the Ras-binding domain found in proteins related to Ras

Probab=89.42  E-value=0.33  Score=30.41  Aligned_cols=44  Identities=20%  Similarity=0.178  Sum_probs=35.2

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeC
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLK   87 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~   87 (133)
                      +.|..++|+...+.+.+..|+.+.-.++.++.|+.++...+...
T Consensus         3 ~~v~LP~~q~t~V~vrpg~ti~d~L~~~~~kr~L~~~~~~V~~~   46 (71)
T PF02196_consen    3 CRVHLPNGQRTVVQVRPGMTIRDALSKACKKRGLNPECCDVRLV   46 (71)
T ss_dssp             EEEEETTTEEEEEEE-TTSBHHHHHHHHHHTTT--CCCEEEEEE
T ss_pred             EEEECCCCCEEEEEEcCCCCHHHHHHHHHHHcCCCHHHEEEEEc
Confidence            34566889999999999999999999999999999997777643

It is found in association with the PE-bind and pkinase domains.; GO: 0005057 receptor signaling protein activity, 0007165 signal transduction; PDB: 1RFA_A 1C1Y_B 3KUD_B 1GUA_B 3KUC_B 2L05_A 3NY5_D 1RRB_A 1WFY_A 1WXM_A.

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

Probab=89.24  E-value=0.28  Score=32.87  Aligned_cols=40  Identities=18%  Similarity=0.431  Sum_probs=36.0

Q ss_pred             cccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccccc
Q 040111            3 DKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         3 ~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      ++.|++...-|++|.|+.+.+..|-.+.+.. +..|.+...
T Consensus        52 ~r~Gl~~~s~RFlFdG~rI~~~~TP~~L~mEd~D~Iev~~~   92 (99)
T KOG1769|consen   52 ERQGLSMNSLRFLFDGQRIRETHTPADLEMEDGDEIEVVQE   92 (99)
T ss_pred             HHcCCccceEEEEECCcCcCCCCChhhhCCcCCcEEEEEee
Confidence            5789999999999999999999999999999 999886543

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

Probab=88.24  E-value=0.27  Score=32.83  Aligned_cols=21  Identities=33%  Similarity=0.529  Sum_probs=17.4

Q ss_pred             CCCCeEEEeCCEECCCCCCcc
Q 040111            8 PPGQQRSIFAGKQLEDGRTLA   28 (133)
Q Consensus         8 p~~~Q~Li~~gk~L~D~~tL~   28 (133)
                      .-.++||||+|+.|.|+..|.
T Consensus        42 s~~rLRlI~~Gr~L~d~t~l~   62 (97)
T PF10302_consen   42 SRRRLRLIYAGRLLNDHTDLS   62 (97)
T ss_pred             ccccEEeeecCcccCccchhh
Confidence            345699999999999988774

They contain a characteristic GFDRL sequence motif.

>KOG0007 consensus Splicing factor 3a, subunit 1 [RNA processing and modification]

Probab=87.54  E-value=0.27  Score=39.68  Aligned_cols=51  Identities=25%  Similarity=0.300  Sum_probs=45.1

Q ss_pred             CCCCCCceeecc-ccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCcccccc
Q 040111           48 NPDPQNITLEVE-SSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLS   98 (133)
Q Consensus        48 ~~~g~~~~l~V~-~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~   98 (133)
                      ..+|+.+.+.+. .++.+..+|.++.+..+|+++.|++.+.|..+.|+.+++
T Consensus       289 ~~dg~~~~~~~~~~~~~~~~~k~k~~~~~~i~~~~q~~~~~~~~l~d~~~~~  340 (341)
T KOG0007|consen  289 PADGQVIKITVQSLSENVASLKEKIADESQIPANKQKLRGEGAFLKDNRSLA  340 (341)
T ss_pred             CCCCceeeeccccccccccccccccccccccchhheeeccCCcccCcccccc
Confidence            567888888777 789999999999999999999999999999999985543

>cd00754 MoaD Ubiquitin domain of MoaD-like proteins

Probab=87.19  E-value=1.8  Score=26.86  Aligned_cols=50  Identities=8%  Similarity=-0.084  Sum_probs=36.7

Q ss_pred             CceeeccccCcHHHHHHHhhhhcCC----CCCceEEEeCCcccCcccccccccc
Q 040111           53 NITLEVESSDTIDNVKAKIQDKKRI----PPPAEADLLKFPFFFFEEVLSFFWF  102 (133)
Q Consensus        53 ~~~l~V~~~~tV~~LK~~I~~~~gI----p~~~q~L~~~gk~L~d~~tL~dy~~  102 (133)
                      ...++++...|+.+|.+.+.++.+-    ......+..+|+....+..|++-+-
T Consensus        17 ~~~~~~~~~~tv~~ll~~l~~~~~~~~~~~~~~~~v~vNg~~v~~~~~l~~gD~   70 (80)
T cd00754          17 EEELELPEGATVGELLDALEARYPGLLEELLARVRIAVNGEYVRLDTPLKDGDE   70 (80)
T ss_pred             eEEEECCCCCcHHHHHHHHHHHCchHHHhhhhcEEEEECCeEcCCCcccCCCCE
Confidence            3567777789999999999987542    3345566678888887777777653

MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.

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

Probab=87.03  E-value=0.63  Score=36.34  Aligned_cols=54  Identities=20%  Similarity=0.097  Sum_probs=39.2

Q ss_pred             eeccccCcHHHHHHHhhhh-cCCCCCceEEE----eCCcccCccccccccccEEeEEEE
Q 040111           56 LEVESSDTIDNVKAKIQDK-KRIPPPAEADL----LKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        56 l~V~~~~tV~~LK~~I~~~-~gIp~~~q~L~----~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      .+.+..+|+.|++..|..+ ..+.+..+|+.    -+|+++.|+.+|++|+.-+...|+
T Consensus        17 ~~~s~~~ti~d~~~~~~~~~~k~~~~~~r~tlr~e~kgkpl~~~s~l~e~~~~s~~~i~   75 (297)
T KOG1639|consen   17 KDLSGSETIDDLLKAISAKNLKITPYRIRLTLRVEPKGKPLIDNSKLQEYGDGSGATIY   75 (297)
T ss_pred             ecCCCCCcHHHHHHHHHHhhhccCccchhheeeccCCCccccchhHHHHhccCCCCEEE
Confidence            5567889999999766665 46777544443    589999999999999765443333

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

Probab=86.45  E-value=0.79  Score=29.07  Aligned_cols=43  Identities=14%  Similarity=-0.068  Sum_probs=37.0

Q ss_pred             ccccCcHHHHHHHhhhhcC-CCCCceEEEeCCcccCcccccccc
Q 040111           58 VESSDTIDNVKAKIQDKKR-IPPPAEADLLKFPFFFFEEVLSFF  100 (133)
Q Consensus        58 V~~~~tV~~LK~~I~~~~g-Ip~~~q~L~~~gk~L~d~~tL~dy  100 (133)
                      |.++++|.++++-+.+... ..-....|.++|+.|.+...|+++
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            5688999999999999865 677888899999999888888877

>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=85.73  E-value=0.15  Score=32.78  Aligned_cols=40  Identities=25%  Similarity=0.359  Sum_probs=19.0

Q ss_pred             CCcccCCCCCCeEEEeC--C-EEC--CCCCCccccccc-ccccccc
Q 040111            1 IEDKEGIPPGQQRSIFA--G-KQL--EDGRTLADYKIQ-ESTLHLG   40 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~--g-k~L--~D~~tL~~ygI~-~stl~L~   40 (133)
                      |++..++|.+.|.|+.+  + ..|  .++.+|+++||+ |+.+.|.
T Consensus        33 I~~~l~~~~~~~~L~~~~~~~~~l~s~~~~tl~~lglkHGdmlyL~   78 (80)
T PF11543_consen   33 ISEQLSIPDSSQSLSKDRNNKEELKSSDSKTLSSLGLKHGDMLYLK   78 (80)
T ss_dssp             HHHHS---TTT---BSSGGGGGCSSS-TT-CCCCT---TT-EEE--
T ss_pred             HHHHcCCCCcceEEEecCCCCcccccCCcCCHHHcCCCCccEEEEe
Confidence            34567899999988755  2 245  578999999999 9988763

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.

>cd01818 TIAM1_RBD Ubiquitin domain of Tiam1 guanine nucleotide exchange factor

Probab=85.56  E-value=1.2  Score=28.41  Aligned_cols=49  Identities=16%  Similarity=0.141  Sum_probs=41.1

Q ss_pred             cCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCcc
Q 040111           46 CKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFE   94 (133)
Q Consensus        46 Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~   94 (133)
                      |-.++|+...+.+.+++|+.++-+....+.++.|....|-..-..++|.
T Consensus         4 V~lPn~~~~~v~vrp~~tv~dvLe~aCk~~~ldp~eh~Lrlk~~~~e~~   52 (77)
T cd01818           4 VCLPDNQPVLTYLRPGMSVEDFLESACKRKQLDPMEHYLRLKFLRMENH   52 (77)
T ss_pred             EECCCCceEEEEECCCCCHHHHHHHHHHhcCCChhHheeEEEEEecCCc
Confidence            5568899999999999999999999999999999988876544445554

Tiam1 (T lymphoma invasion and metastasis 1) a guanine nucleotide exchange factor that activates Rac, is an important regulator of Rho GTPase functions in tumor cells including regulation of cell shape and invasiveness in epithelial cells and fibroblasts. TIAM1 has an RBD (Ras-binding domain) similar to that of Raf kinase as well as PH (pleckstrin homology), PDZ, and RhoGEF domains.

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

Probab=85.56  E-value=0.37  Score=30.51  Aligned_cols=24  Identities=33%  Similarity=0.494  Sum_probs=18.6

Q ss_pred             eCCEECCCCCCccccccc-cccccc
Q 040111           16 FAGKQLEDGRTLADYKIQ-ESTLHL   39 (133)
Q Consensus        16 ~~gk~L~D~~tL~~ygI~-~stl~L   39 (133)
                      -.|..|+++.||+++||. |+.++|
T Consensus        54 ~~g~~L~~~~tL~~~gV~dGd~L~L   78 (79)
T PF08817_consen   54 AGGRPLDPDQTLADAGVRDGDVLVL   78 (79)
T ss_dssp             GGTEEEETTSBCGGGT--TT-EEEE
T ss_pred             cCCcccCCcCcHhHcCCCCCCEEEe
Confidence            458899999999999999 998876

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

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

Probab=84.61  E-value=2.8  Score=26.06  Aligned_cols=61  Identities=16%  Similarity=0.133  Sum_probs=47.2

Q ss_pred             CCCCceeeccccCcHHHHHHHhhhhc---CCCCCceEEE-eCCcccCccccccccccEEeEEEEe
Q 040111           50 DPQNITLEVESSDTIDNVKAKIQDKK---RIPPPAEADL-LKFPFFFFEEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        50 ~g~~~~l~V~~~~tV~~LK~~I~~~~---gIp~~~q~L~-~~gk~L~d~~tL~dy~~~~~~~~~~  110 (133)
                      +|++..++..++....-+.++--+..   |-|++..-|- -+|..|+-++.+.||+|+...-.|.
T Consensus         4 NGqPv~VEANvnaPLh~v~akALe~sgNvgQP~ENWElkDe~G~vlD~~kKveD~GftngvkLFL   68 (76)
T PF10790_consen    4 NGQPVQVEANVNAPLHPVRAKALEQSGNVGQPPENWELKDESGQVLDVNKKVEDFGFTNGVKLFL   68 (76)
T ss_pred             CCCceeeecCCCCcchHHHHHHHhhccccCCCcccceeeccCCcEeeccchhhhccccccceEEE
Confidence            68888888888887777776655554   4788888887 5788888899999999987665543

>cd06410 PB1_UP2 Uncharacterized protein 2

Probab=84.21  E-value=3.5  Score=27.42  Aligned_cols=40  Identities=8%  Similarity=-0.004  Sum_probs=33.9

Q ss_pred             CCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeC
Q 040111           47 KNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLK   87 (133)
Q Consensus        47 k~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~   87 (133)
                      +...|++..+.|+.+.+-.+|+.++.+..+++.. ..|-|.
T Consensus        18 ~Y~GG~tr~i~V~r~~s~~el~~kl~~~~~~~~~-~~lky~   57 (97)
T cd06410          18 RYVGGETRIVSVDRSISFKELVSKLSELFGAGVV-VTLKYQ   57 (97)
T ss_pred             EEcCCceEEEEEcCCCCHHHHHHHHHHHhCCCCc-eEEEEE
Confidence            3446889999999999999999999999999876 666653

The PB1 domain is a modular domain mediating specific protein-protein interaction 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 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.

>smart00666 PB1 PB1 domain

Probab=83.94  E-value=2.4  Score=26.42  Aligned_cols=40  Identities=8%  Similarity=0.076  Sum_probs=34.8

Q ss_pred             CCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCc
Q 040111           50 DPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFP   89 (133)
Q Consensus        50 ~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk   89 (133)
                      ++..+.+.++++.|-.+|+.+|+++.+++....+|-|...
T Consensus         9 ~~~~~~~~~~~~~s~~dL~~~i~~~~~~~~~~~~l~Y~De   48 (81)
T smart00666        9 GGETRRLSVPRDISFEDLRSKVAKRFGLDNQSFTLKYQDE   48 (81)
T ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHhCCCCCCeEEEEECC
Confidence            4567888999999999999999999999888888988743

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.

>cd01787 GRB7_RA RA (RAS-associated like) domain of Grb7

Probab=83.35  E-value=2.8  Score=27.35  Aligned_cols=57  Identities=18%  Similarity=0.141  Sum_probs=42.9

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCC-CCCceEEEeCCcccCcccccccc
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRI-PPPAEADLLKFPFFFFEEVLSFF  100 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gI-p~~~q~L~~~gk~L~d~~tL~dy  100 (133)
                      +.|-..+|.+..+.|+..+|+.++-+.++++... +.....|+=.-..|.-++.+.|.
T Consensus         5 vkv~~~Dg~sK~l~V~~~~Ta~dV~~~L~~K~h~~~~~~W~LvE~~P~l~lER~~EDH   62 (85)
T cd01787           5 VKVYSEDGASKSLEVDERMTARDVCQLLVDKNHCQDDSSWTLVEHLPHLQLERLFEDH   62 (85)
T ss_pred             EEEEecCCCeeEEEEcCCCcHHHHHHHHHHHhCCCCCCCeEEEEecchhhhhhhccch
Confidence            4556678999999999999999999999999985 55556666555555555555554

Grb7_RA The RA (RAS-associated like) domain of Grb7. Grb7 is an adaptor molecule that mediates signal transduction from multiple cell surface receptors to various downstream signaling pathways. Grb7 and its related family members Grb10 and Grb14 share a conserved domain architecture that includes an amino-terminal proline-rich region, a central segment termed the GM region (for Grb and Mig) which includes the RA, PIR, and PH domains, and a carboxyl-terminal SH2 domain. Grb7/10/14 family proteins are phosphorylated on serine/threonine as well as tyrosine residues and are mainly localized to the cytoplasm.

>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium)

Probab=81.90  E-value=3.1  Score=26.73  Aligned_cols=41  Identities=12%  Similarity=0.021  Sum_probs=33.1

Q ss_pred             CCCCceeeccccCcHHHHHHHhhhhcCCCC-CceEEEeCCcc
Q 040111           50 DPQNITLEVESSDTIDNVKAKIQDKKRIPP-PAEADLLKFPF   90 (133)
Q Consensus        50 ~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~-~~q~L~~~gk~   90 (133)
                      +|..+.+.++++.+..+|++.|+++.++.. ....|-|-.-.
T Consensus         8 ~~d~~r~~l~~~~~~~~L~~~i~~r~~~~~~~~f~LkY~Dde   49 (82)
T cd06407           8 GEEKIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKYLDDD   49 (82)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEEECCC
Confidence            566788999999999999999999999865 56667664443

The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like 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-inte

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

Probab=81.30  E-value=2.4  Score=27.27  Aligned_cols=38  Identities=8%  Similarity=0.099  Sum_probs=33.4

Q ss_pred             CceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcc
Q 040111           53 NITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPF   90 (133)
Q Consensus        53 ~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~   90 (133)
                      ++.+.+.+..+..+|..+|.++...+++.-+|.|.-..
T Consensus         8 TVai~v~~g~~y~~L~~~ls~kL~l~~~~~~LSY~~~~   45 (78)
T cd06411           8 TVALRAPRGADVSSLRALLSQALPQQAQRGQLSYRAPG   45 (78)
T ss_pred             EEEEEccCCCCHHHHHHHHHHHhcCChhhcEEEecCCC
Confidence            45678889999999999999999999999999986543

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

>PF12436 USP7_ICP0_bdg: ICP0-binding domain of Ubiquitin-specific protease 7; InterPro: IPR024729 This domain is found in eukaryotes, and is approximately 40 amino acids in length

Probab=80.64  E-value=2  Score=33.18  Aligned_cols=83  Identities=16%  Similarity=0.307  Sum_probs=53.2

Q ss_pred             cccCCCCCCeEEEeC----CE--ECCCCCCccccccc-cccccccccc-------------------------ccc---C
Q 040111            3 DKEGIPPGQQRSIFA----GK--QLEDGRTLADYKIQ-ESTLHLGWRA-------------------------DFC---K   47 (133)
Q Consensus         3 ~~~gip~~~Q~Li~~----gk--~L~D~~tL~~ygI~-~stl~L~~~~-------------------------i~V---k   47 (133)
                      ++-|+|++..-++|.    ++  .++...|+....+. |+.|..-...                         |.+   .
T Consensus       106 ~~~g~p~~t~l~lyEEi~~~~ie~i~~~~t~~~~el~~GdIi~fQ~~~~~~~~~~~~~~~v~~Yy~~l~nrv~V~f~~~~  185 (249)
T PF12436_consen  106 ERAGLPPDTPLLLYEEIKPNMIEPIDPNQTFEKAELQDGDIICFQRAPSEDLDKSSRYPDVKEYYDFLYNRVEVEFKPKD  185 (249)
T ss_dssp             HHHT--TT--EEEEEEEETTEEEE--SSSBHHHTT--TTEEEEEEE--GG--GGGSSS-SHHHHHHHHHHEEEEEEEETT
T ss_pred             HHcCCCCCCceEEEEEeccceeeEcCCCCchhhcccCCCCEEEEEeccccccccccCCCCHHHHHHHHhCeEEEEEEECC
Confidence            457889888888776    55  37889999999999 8877655421                         111   1


Q ss_pred             CCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEE
Q 040111           48 NPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADL   85 (133)
Q Consensus        48 ~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~   85 (133)
                      .+.+..+.+.+...+|-.++-++|++..|++|...||.
T Consensus       186 ~~~~~~F~l~ls~~~tY~~la~~Va~~l~~dP~~lr~~  223 (249)
T PF12436_consen  186 NPNDPEFTLWLSKKMTYDQLAEKVAEHLNVDPEHLRFF  223 (249)
T ss_dssp             STT---EEEEEETT--HHHHHHHHHHHHTS-GGGEEEE
T ss_pred             CCCCCCEEEEECCCCCHHHHHHHHHHHHCCChHHEEEE
Confidence            34455789999999999999999999999999999887

It is found in proteins of the peptidase C19 family, which contains contains ubiquitinyl hydrolases like ubiquitin-specific protease 7 (USP7). USP7 regulates the turnover of p53 [].; PDB: 2KVR_A 2YLM_A.

>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein

Probab=80.50  E-value=8.4  Score=23.12  Aligned_cols=53  Identities=17%  Similarity=0.025  Sum_probs=35.4

Q ss_pred             eeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCcc----ccccccccEEeEEEEeCc
Q 040111           56 LEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFE----EVLSFFWFVVVGVIFCGC  112 (133)
Q Consensus        56 l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~----~tL~dy~~~~~~~~~~~~  112 (133)
                      ++++...|+.+|.+++    +++++...+..+|+....+    ..|.+=+-..+--.++||
T Consensus         9 ~~~~~~~tv~~ll~~l----~~~~~~i~V~vNg~~v~~~~~~~~~L~~gD~V~ii~~v~GG   65 (65)
T cd00565           9 REVEEGATLAELLEEL----GLDPRGVAVALNGEIVPRSEWASTPLQDGDRIEIVTAVGGG   65 (65)
T ss_pred             EEcCCCCCHHHHHHHc----CCCCCcEEEEECCEEcCHHHcCceecCCCCEEEEEEeccCC
Confidence            4556678999988764    5778888888899888765    566665544333444443

ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.

>COG5417 Uncharacterized small protein [Function unknown]

Probab=80.18  E-value=3  Score=26.62  Aligned_cols=58  Identities=10%  Similarity=-0.009  Sum_probs=47.1

Q ss_pred             CCCCCCCceeeccccCcHHHHHHHhhhhcCC--C---CCceEEEeCCcccCccccccccccEE
Q 040111           47 KNPDPQNITLEVESSDTIDNVKAKIQDKKRI--P---PPAEADLLKFPFFFFEEVLSFFWFVV  104 (133)
Q Consensus        47 k~~~g~~~~l~V~~~~tV~~LK~~I~~~~gI--p---~~~q~L~~~gk~L~d~~tL~dy~~~~  104 (133)
                      +.-+|.++.+.++...++..+-..+.+...+  +   -.+.+.+-.++.|.++..|+||+|++
T Consensus        12 t~y~g~~yDLrl~d~~pikklIdivwe~~kis~~~reg~~Ikv~nKa~llsgd~kL~d~~Iad   74 (81)
T COG5417          12 TNYNGGTYDLRLPDYLPIKKLIDIVWESLKISIFDREGTQIKVMNKAQLLSGDDKLIDYQIAD   74 (81)
T ss_pred             EecCCceEEEeccccchHHHHHHHHHHHhhccccccCCCEEEEeccceEecCCceEEeccccC
Confidence            3446888999999999999988888777653  2   24567889999999999999999874

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	133
2y5b_B	152	Structure Of Usp21 In Complex With Linear Diubiquit		2e-24
3b08_A	152	Crystal Structure Of The Mouse Hoil1-L-Nzf In Compl		2e-24
2zvn_A	154	Nemo Cozi Domain Incomplex With Diubiquitin In P212		2e-24
3u30_A	172	Crystal Structure Of A Linear-Specific Ubiquitin Fa		2e-24
2w9n_A	152	Crystal Structure Of Linear Di-Ubiquitin Length = 1		2e-24
3k9o_B	96	The Crystal Structure Of E2-25k And Ubb+1 Complex L		2e-14
3k9o_B	96	The Crystal Structure Of E2-25k And Ubb+1 Complex L		1e-06
1yx5_B	98	Solution Structure Of S5a Uim-1UBIQUITIN COMPLEX Le		3e-14
1yx5_B	98	Solution Structure Of S5a Uim-1UBIQUITIN COMPLEX Le		1e-06
2k25_A	103	Automated Nmr Structure Of The Ubb By Fapsy Length		7e-14
2k25_A	103	Automated Nmr Structure Of The Ubb By Fapsy Length		1e-06
2k6d_B	76	Cin85 Sh3-C Domain In Complex With Ubiquitin Length		1e-13
2k6d_B	76	Cin85 Sh3-C Domain In Complex With Ubiquitin Length		1e-06
3ldz_F	73	Crystal Structure Of Human Stam1 Vhs Domain In Comp		2e-13
3ldz_F	73	Crystal Structure Of Human Stam1 Vhs Domain In Comp		1e-06
3olm_D	79	Structure And Function Of A Ubiquitin Binding Site		2e-13
3olm_D	79	Structure And Function Of A Ubiquitin Binding Site		1e-07
3ons_A	72	Crystal Structure Of Human Ubiquitin In A New Cryst		2e-13
3ons_A	72	Crystal Structure Of Human Ubiquitin In A New Cryst		1e-06
3v6c_B	91	Crystal Structure Of Usp2 In Complex With Mutated U		2e-13
3v6c_B	91	Crystal Structure Of Usp2 In Complex With Mutated U		4e-06
3rul_A	79	New Strategy To Analyze Structures Of Glycopeptide-		2e-13
3rul_A	79	New Strategy To Analyze Structures Of Glycopeptide-		1e-06
1otr_B	76	Solution Structure Of A Cue-Ubiquitin Complex Lengt		2e-13
1otr_B	76	Solution Structure Of A Cue-Ubiquitin Complex Lengt		1e-07
3v6e_B	91	Crystal Structure Of Usp2 And A Mutant Form Of Ubiq		2e-13
3v6e_B	91	Crystal Structure Of Usp2 And A Mutant Form Of Ubiq		2e-06
1xd3_B	75	Crystal Structure Of Uchl3-Ubvme Complex Length = 7		2e-13
1xd3_B	75	Crystal Structure Of Uchl3-Ubvme Complex Length = 7		1e-06
1cmx_B	76	Structural Basis For The Specificity Of Ubiquitin C		2e-13
1cmx_B	76	Structural Basis For The Specificity Of Ubiquitin C		1e-06
2gbj_A	84	Crystal Structure Of The 9-10 8 Glycine Insertion M		2e-13
2gbj_A	84	Crystal Structure Of The 9-10 8 Glycine Insertion M		8e-06
3l0w_B	169	Structure Of Split Monoubiquitinated Pcna With Ubiq		3e-13
3l0w_B	169	Structure Of Split Monoubiquitinated Pcna With Ubiq		1e-07
3u5e_m	128	The Structure Of The Eukaryotic Ribosome At 3.0 A R		3e-13
3u5e_m	128	The Structure Of The Eukaryotic Ribosome At 3.0 A R		5e-07
3u5g_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		3e-13
3u5g_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		2e-07
2znv_C	77	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		3e-13
2znv_C	77	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		1e-06
2xk5_B	76	Crystal Structure Of K6-Linked Diubiquitin Length =		3e-13
2xk5_B	76	Crystal Structure Of K6-Linked Diubiquitin Length =		9e-07
1aar_A	76	Structure Of A Diubiquitin Conjugate And A Model Fo		3e-13
1aar_A	76	Structure Of A Diubiquitin Conjugate And A Model Fo		9e-07
3nob_A	78	Structure Of K11-Linked Di-Ubiquitin Length = 78		3e-13
3nob_A	78	Structure Of K11-Linked Di-Ubiquitin Length = 78		9e-07
2gbk_A	83	Crystal Structure Of The 9-10 Moad Insertion Mutant		3e-13
2gbk_A	83	Crystal Structure Of The 9-10 Moad Insertion Mutant		7e-06
1yiw_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		3e-13
1yiw_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		1e-06
4a18_K	129	T.Thermophila 60s Ribosomal Subunit In Complex With		3e-13
4a18_K	129	T.Thermophila 60s Ribosomal Subunit In Complex With		4e-06
2znv_B	76	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		3e-13
2znv_B	76	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		1e-06
3h7s_B	76	Crystal Structures Of K63-Linked Di- And Tri-Ubiqui		3e-13
3h7s_A	76	Crystal Structures Of K63-Linked Di- And Tri-Ubiqui		1e-06
1s1q_B	76	Tsg101(Uev) Domain In Complex With Ubiquitin Length		3e-13
1s1q_B	76	Tsg101(Uev) Domain In Complex With Ubiquitin Length		1e-06
4ii3_B	96	Crystal Structure Of S. Pombe Ubiquitin Activating		4e-13
4ii3_B	96	Crystal Structure Of S. Pombe Ubiquitin Activating		8e-08
4ap4_C	80	Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Le		4e-13
4ap4_C	80	Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Le		6e-07
2khw_B	79	Solution Structure Of The Human Polymerase Iota Ubm		4e-13
2khw_B	79	Solution Structure Of The Human Polymerase Iota Ubm		8e-07
3vdz_A	111	Tailoring Encodable Lanthanide-Binding Tags As Mri		4e-13
3vdz_A	111	Tailoring Encodable Lanthanide-Binding Tags As Mri		1e-06
2ld9_A	77	Backbone Structure Of Ubiquitin Determined Using Ba		4e-13
2ld9_A	77	Backbone Structure Of Ubiquitin Determined Using Ba		8e-07
4ii2_B	83	Crystal Structure Of Ubiquitin Activating Enzyme 1		4e-13
4ii2_B	83	Crystal Structure Of Ubiquitin Activating Enzyme 1		3e-07
3dvg_Y	79	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		4e-13
3dvg_Y	79	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		8e-07
3dvg_X	80	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		4e-13
3dvg_X	80	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		9e-07
3ai5_A	307	Crystal Structure Of Yeast Enhanced Green Fluoresce		4e-13
3ai5_A	307	Crystal Structure Of Yeast Enhanced Green Fluoresce		1e-06
4hcn_B	98	Crystal Structure Of Burkholderia Pseudomallei Effe		4e-13
4hcn_B	98	Crystal Structure Of Burkholderia Pseudomallei Effe		9e-08
3jvz_X	81	E2~ubiquitin-Hect Length = 81		4e-13
3jvz_X	81	E2~ubiquitin-Hect Length = 81		7e-07
1sif_A	88	Crystal Structure Of A Multiple Hydrophobic Core Mu		5e-13
1sif_A	88	Crystal Structure Of A Multiple Hydrophobic Core Mu		3e-05
3zf7_s	128	High-resolution Cryo-electron Microscopy Structure		5e-13
3zf7_s	128	High-resolution Cryo-electron Microscopy Structure		2e-06
3u5c_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		5e-13
3u5c_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		2e-07
1ud7_A	76	Solution Structure Of The Designed Hydrophobic Core		6e-13
1ud7_A	76	Solution Structure Of The Designed Hydrophobic Core		2e-05
1zgu_B	76	Solution Structure Of The Human Mms2-Ubiquitin Comp		6e-13
1zgu_B	76	Solution Structure Of The Human Mms2-Ubiquitin Comp		1e-06
2o6v_D	76	Crystal Structure And Solution Nmr Studies Of Lys48		7e-13
2o6v_D	76	Crystal Structure And Solution Nmr Studies Of Lys48		9e-07
3q3f_A	189	Engineering Domain-Swapped Binding Interfaces By Mu		9e-13
3q3f_A	189	Engineering Domain-Swapped Binding Interfaces By Mu		5e-08
1c3t_A	76	Rotamer Strain As A Determinant Of Protein Structur		1e-12
1c3t_A	76	Rotamer Strain As A Determinant Of Protein Structur		3e-05
2ojr_A	111	Structure Of Ubiquitin Solved By Sad Using The Lant		1e-12
2ojr_A	111	Structure Of Ubiquitin Solved By Sad Using The Lant		1e-06
2o6v_B	76	Crystal Structure And Solution Nmr Studies Of Lys48		1e-12
2o6v_B	76	Crystal Structure And Solution Nmr Studies Of Lys48		9e-07
2jwz_A	76	Mutations In The Hydrophobic Core Of Ubiquitin Diff		1e-12
2jwz_A	76	Mutations In The Hydrophobic Core Of Ubiquitin Diff		1e-07
1yj1_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		2e-12
1yj1_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		7e-07
2fcs_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		2e-12
2fcs_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		4e-07
2kdi_A	114	Solution Structure Of A UbiquitinUIM FUSION PROTEIN		4e-12
2kdi_A	114	Solution Structure Of A UbiquitinUIM FUSION PROTEIN		5e-08
4gsw_A	80	Crystal Structure Of Ubiquitin From Entamoeba Histo		7e-12
4gsw_A	80	Crystal Structure Of Ubiquitin From Entamoeba Histo		7e-05
1ogw_A	76	Synthetic Ubiquitin With Fluoro-Leu At 50 And 67 Le		7e-12
1ogw_A	76	Synthetic Ubiquitin With Fluoro-Leu At 50 And 67 Le		1e-06
2zcb_A	76	Crystal Structure Of Ubiquitin P37aP38A Length = 76		8e-12
2zcb_A	76	Crystal Structure Of Ubiquitin P37aP38A Length = 76		2e-05
2gbr_A	81	Crystal Structure Of The 35-36 Moad Insertion Mutan		4e-11
2gbr_A	81	Crystal Structure Of The 35-36 Moad Insertion Mutan		5e-05
4hjk_A	77	U7ub7 Disulfide Variant Length = 77		1e-10
4hjk_A	77	U7ub7 Disulfide Variant Length = 77		3e-04
3mtn_B	85	Usp21 In Complex With A Ubiquitin-based, Usp21-spec		1e-10
3mtn_B	85	Usp21 In Complex With A Ubiquitin-based, Usp21-spec		1e-06
1zw7_A	82	Elimination Of The C-Cap In Ubiquitin Structure, Dy		3e-10
1zw7_A	82	Elimination Of The C-Cap In Ubiquitin Structure, Dy		1e-05
3n3k_B	85	The Catalytic Domain Of Usp8 In Complex With A Usp8		3e-10
3n3k_B	85	The Catalytic Domain Of Usp8 In Complex With A Usp8		4e-05
2gbm_A	84	Crystal Structure Of The 35-36 8 Glycine Insertion		3e-10
2gbm_A	84	Crystal Structure Of The 35-36 8 Glycine Insertion		8e-05
2jvc_A	82	Nmr Solution Structure Of Ubiquitin Like Protein Le		7e-10
2jvc_A	82	Nmr Solution Structure Of Ubiquitin Like Protein Le		5e-04
4i6l_B	76	Crystal Structure Of Otub1 In Complex With Ubiquiti		1e-09
4i6l_B	76	Crystal Structure Of Otub1 In Complex With Ubiquiti		1e-06
4hk2_A	78	U7ub25.2540 Length = 78		1e-08
4hk2_A	78	U7ub25.2540 Length = 78		2e-05
3dbh_I	88	Structural Dissection Of A Gating Mechanism Prevent		9e-08
4hcp_B	78	Crystal Structure Of Burkholderia Pseudomallei Effe		1e-07
2bkr_B	77	Nedd8 Nedp1 Complex Length = 77		1e-07
1ndd_B	76	Structure Of Nedd8 Length = 76		1e-07
3gzn_I	82	Structure Of Nedd8-Activating Enzyme In Complex Wit		1e-07
3dbl_I	88	Structural Dissection Of A Gating Mechanism Prevent		1e-07
2nvu_I	81	Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C1		1e-07
4f8c_B	88	Structure Of The Cif:nedd8 Complex - Yersinia Pseud		2e-07
1bt0_A	76	Structure Of Ubiquitin-Like Protein, Rub1 Length =		3e-07
3dqv_A	81	Structural Insights Into Nedd8 Activation Of Cullin		4e-07
1gjz_A	53	Solution Structure Of A Dimeric N-Terminal Fragment		1e-06

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

Iteration: 1
 Score =  107 bits (268), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 59/85 (69%), Positives = 64/85 (75%), Gaps = 6/85 (7%)
Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL     G    F K    + I
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGHMQIFVKTLTGKTI 89
Query: 55  TLEVESSDTIDNVKAKIQDKKRIPP 79
           TLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 90  TLEVEPSDTIENVKAKIQDKEGIPP 114

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

Iteration: 1
 Score =  107 bits (267), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 59/85 (69%), Positives = 64/85 (75%), Gaps = 6/85 (7%)
Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRAD-----FCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R       F K    + I
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89
Query: 55  TLEVESSDTIDNVKAKIQDKKRIPP 79
           TLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 90  TLEVEPSDTIENVKAKIQDKEGIPP 114

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

Iteration: 1
 Score =  107 bits (267), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 59/85 (69%), Positives = 64/85 (75%), Gaps = 6/85 (7%)
Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL     G    F K    + I
Sbjct: 32  IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 91
Query: 55  TLEVESSDTIDNVKAKIQDKKRIPP 79
           TLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 92  TLEVEPSDTIENVKAKIQDKEGIPP 116

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

Iteration: 1
 Score =  107 bits (266), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 59/85 (69%), Positives = 64/85 (75%), Gaps = 6/85 (7%)
Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL     G    F K    + I
Sbjct: 50  IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 109
Query: 55  TLEVESSDTIDNVKAKIQDKKRIPP 79
           TLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 110 TLEVEPSDTIENVKAKIQDKEGIPP 134

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

Iteration: 1
 Score =  107 bits (266), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 59/85 (69%), Positives = 64/85 (75%), Gaps = 6/85 (7%)
Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRAD-----FCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R       F K    + I
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89
Query: 55  TLEVESSDTIDNVKAKIQDKKRIPP 79
           TLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 90  TLEVEPSDTIENVKAKIQDKEGIPP 114

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

Iteration: 1
 Score = 73.9 bits (180), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 40/58 (68%), Positives = 45/58 (77%), Gaps = 5/58 (8%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR----ADFCKNPDPQN 53
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R    AD  ++PD Q+
Sbjct: 31 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGYADLREDPDRQD 88

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 5  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 39

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

Iteration: 1
 Score = 73.6 bits (179), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 36/55 (65%), Positives = 43/55 (78%), Gaps = 1/55 (1%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRADFCKNPDPQNI 54
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R    ++P+  ++
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGRDPNSSSV 84

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 38

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

Iteration: 1
 Score = 72.4 bits (176), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 39/58 (67%), Positives = 45/58 (77%), Gaps = 5/58 (8%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR----ADFCKNPDPQN 53
          I+DKEGIPP QQR IFAGKQLEDGRTL++Y IQ ESTLHL  R    AD  ++PD Q+
Sbjct: 38 IQDKEGIPPDQQRLIFAGKQLEDGRTLSEYNIQKESTLHLVLRLRGYADLREDPDRQD 95

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 12 FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 46

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

Iteration: 1
 Score = 72.0 bits (175), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 36/47 (76%), Positives = 38/47 (80%), Gaps = 1/47 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRADFC 46
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R   C
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGC 76

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 38

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

Iteration: 1
 Score = 70.9 bits (172), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 38

>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 = 70.9 bits (172), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 33 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 75

>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 = 52.0 bits (123), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/35 (71%), Positives = 28/35 (80%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVESSDTIDNVK+KIQDK+ IPP
Sbjct: 7  FVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPP 41

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

Iteration: 1
 Score = 70.9 bits (172), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 38

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

Iteration: 1
 Score = 70.9 bits (172), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 47 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 89

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 24/40 (60%), Positives = 27/40 (67%)
Query: 40 GWRADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          G    F       +ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 16 GSMQIFVNTLTGTHITLEVEPSDTIENVKAKIQDKEGIPP 55

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

Iteration: 1
 Score = 70.5 bits (171), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 38

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

Iteration: 1
 Score = 70.5 bits (171), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/35 (71%), Positives = 28/35 (80%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVESSDTIDNVK+KIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPP 38

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

Iteration: 1
 Score = 70.5 bits (171), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 47 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 89

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/40 (60%), Positives = 28/40 (70%)
Query: 40 GWRADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          G    F      ++ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 16 GSMQIFVNTLSGKHITLEVEPSDTIENVKAKIQDKEGIPP 55

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

Iteration: 1
 Score = 70.5 bits (171), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 38

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

Iteration: 1
 Score = 70.5 bits (171), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 38

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

Iteration: 1
 Score = 70.5 bits (171), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 38 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 80

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 22/28 (78%), Positives = 25/28 (89%)
Query: 52 QNITLEVESSDTIDNVKAKIQDKKRIPP 79
          + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 19 KTITLEVEPSDTIENVKAKIQDKEGIPP 46

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

Iteration: 1
 Score = 70.5 bits (171), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/35 (71%), Positives = 28/35 (80%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVESSDTIDNVK+KIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPP 38

>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 = 70.5 bits (171), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72

>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 = 49.7 bits (117), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 25/35 (71%), Positives = 28/35 (80%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVESSDTIDNVK+KIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPP 38

>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 = 70.5 bits (171), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72

>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 = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/35 (71%), Positives = 28/35 (80%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVESSDTIDNVK+KIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPP 38

>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 = 70.5 bits (171), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72

>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 = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 38

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

Iteration: 1
 Score = 70.1 bits (170), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQDKEGIPPQQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 38

>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 = 70.1 bits (170), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72

>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 = 48.5 bits (114), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 38

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

Iteration: 1
 Score = 70.1 bits (170), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 32 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 74

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 6  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 40

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

Iteration: 1
 Score = 70.1 bits (170), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 37 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 79

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 22/28 (78%), Positives = 25/28 (89%)
Query: 52 QNITLEVESSDTIDNVKAKIQDKKRIPP 79
          + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 18 KTITLEVEPSDTIENVKAKIQDKEGIPP 45

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

Iteration: 1
 Score = 70.1 bits (170), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 38

>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 = 70.1 bits (170), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72

>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 = 46.6 bits (109), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 23/35 (65%), Positives = 28/35 (80%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITL+VE+SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLDVEASDTIENVKAKIQDKEGIPP 38

>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 = 70.1 bits (170), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLR 72

>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 = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 38

>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 = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 38

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

Iteration: 1
 Score = 70.1 bits (170), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 38

>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 = 70.1 bits (170), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 50 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 92

>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 = 52.4 bits (124), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 25/35 (71%), Positives = 28/35 (80%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVESSDTIDNVK+KIQDK+ IPP
Sbjct: 24 FVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPP 58

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

Iteration: 1
 Score = 70.1 bits (170), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 34 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 76

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 8  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 42

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

Iteration: 1
 Score = 70.1 bits (170), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 33 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 75

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 7  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 41

>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 = 70.1 bits (170), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
           I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 65  IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 107

>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 = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 39 FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 73

>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 = 70.1 bits (170), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 31 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 73

>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 = 48.9 bits (115), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 5  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 39

>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 = 70.1 bits (170), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 34/43 (79%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+D+EGIPP QQR IFAG+QLEDGRTLADY IQ ESTLHL  R
Sbjct: 37 IQDREGIPPDQQRLIFAGRQLEDGRTLADYNIQRESTLHLVLR 79

>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 = 50.4 bits (119), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 22/35 (62%), Positives = 28/35 (80%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F +    + ITLEVESSDTIDNV+A+IQD++ IPP
Sbjct: 11 FVRTLTGRTITLEVESSDTIDNVRARIQDREGIPP 45

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

Iteration: 1
 Score = 70.1 bits (170), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 33 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLR 75

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 7  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 41

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

Iteration: 1
 Score = 70.1 bits (170), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 33 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 75

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 7  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 41

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

Iteration: 1
 Score = 69.7 bits (169), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
           I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 263 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 305

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45  FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
           F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 237 FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 271

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

Iteration: 1
 Score = 69.7 bits (169), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 52 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 94

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 25/35 (71%), Positives = 28/35 (80%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVESSDTIDNVK+KIQDK+ IPP
Sbjct: 26 FVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPP 60

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

Iteration: 1
 Score = 69.7 bits (169), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 35 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 77

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 9  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 43

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

Iteration: 1
 Score = 69.7 bits (169), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 39 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 81

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/35 (57%), Positives = 26/35 (74%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    +  T+E+E SDTI+N+KAKIQDK+ IPP
Sbjct: 13 FIKTLTGKTFTVEMEPSDTIENLKAKIQDKEGIPP 47

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

Iteration: 1
 Score = 69.7 bits (169), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLE+GRTLADY IQ ESTLHL  R
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEEGRTLADYNIQKESTLHLVLR 72

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/35 (65%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + I LEVE+SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTIALEVEASDTIENVKAKIQDKEGIPP 38

>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 = 5e-13,   Method: Compositional matrix adjust.
 Identities = 34/40 (85%), Positives = 36/40 (90%), Gaps = 1/40 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHL 69

>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 = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/35 (71%), Positives = 28/35 (80%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVESSDTIDNVK+KIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPP 38

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

Iteration: 1
 Score = 69.3 bits (168), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 34/43 (79%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ EST+HL  R
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTIHLVLR 72

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/35 (57%), Positives = 26/35 (74%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + +T+EVE SDT++N KAKIQDK+ IPP
Sbjct: 4  FLKTLTGKTVTIEVEPSDTVENFKAKIQDKEGIPP 38

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

Iteration: 1
 Score = 69.3 bits (168), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 34/43 (79%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAG+QLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQDKEGIPPDQQRLIFAGRQLEDGRTLSDYNIQKESTLHLVLR 72

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 38

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

Iteration: 1
 Score = 68.9 bits (167), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 34/43 (79%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAG+QLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQDKEGIPPDQQRLIFAGRQLEDGRTLSDYNIQRESTLHLVLR 72

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 38

>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 = 68.6 bits (166), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
           I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 135 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 177

>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 = 53.1 bits (126), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 29/52 (55%), Positives = 37/52 (71%), Gaps = 1/52 (1%)
Query: 28  ADYKIQESTLHLGWRADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
           +D+ I ++T H G +  F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 93  SDWLIYKTTDHYGGQI-FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 143

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

Iteration: 1
 Score = 68.6 bits (166), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 33/43 (76%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY +Q EST+HL  R
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNLQKESTIHLVLR 72

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 19/35 (54%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + +T+E+E SDT++N+KAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTLTVELEPSDTVENLKAKIQDKEGIPP 38

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
           I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 65  IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 107

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 39 FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 73

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/43 (79%), Positives = 36/43 (83%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAG QLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQDKEGIPPDQQRLIFAGXQLEDGRTLSDYNIQRESTLHLVLR 72

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 38

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/43 (79%), Positives = 36/43 (83%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLH   R
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHSVLR 72

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/35 (71%), Positives = 28/35 (80%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVESSDTIDNVK+KIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPP 38

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

Iteration: 1
 Score = 67.4 bits (163), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 34/43 (79%), Positives = 36/43 (83%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKE IPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQDKEXIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEXIPP 38

>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 = 67.4 bits (163), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 34/43 (79%), Positives = 36/43 (83%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKE IPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQDKEQIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72

>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 = 49.7 bits (117), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 28/35 (80%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK++IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEQIPP 38

>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 = 34/43 (79%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR I+AGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 39 IQDKEGIPPDQQRLIWAGKQLEDGRTLSDYNIQRESTLHLVLR 81

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 25/35 (71%), Positives = 28/35 (80%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVESSDTIDNVK+KIQDK+ IPP
Sbjct: 13 FAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPP 47

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

Iteration: 1
 Score = 65.9 bits (159), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 32/43 (74%), Positives = 37/43 (86%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I++KEGIPP QQR IFAGKQLE+G+TL+DY IQ ESTLHL  R
Sbjct: 33 IQEKEGIPPDQQRLIFAGKQLEEGKTLSDYNIQKESTLHLVLR 75

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 20/35 (57%), Positives = 26/35 (74%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE +D+ID +KAKIQ+K+ IPP
Sbjct: 7  FVKTLTGKTITLEVEPNDSIDAIKAKIQEKEGIPP 41

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

Iteration: 1
 Score = 65.9 bits (159), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 33/43 (76%), Positives = 35/43 (81%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGIPP QQR IFAGKQ EDGRTL+DY IQ EST HL  R
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQXEDGRTLSDYNIQKESTXHLVLR 72

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 38

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

Iteration: 1
 Score = 65.5 bits (158), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 33/43 (76%), Positives = 35/43 (81%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEGI   QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQDKEGIAADQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/35 (62%), Positives = 25/35 (71%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ I  
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIAA 38

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

Iteration: 1
 Score = 63.2 bits (152), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 35/48 (72%), Positives = 37/48 (77%), Gaps = 6/48 (12%)
Query: 1  IEDKEG-----IPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DKEG     IPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQDKEGRWALAIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 77

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 24/40 (60%), Positives = 27/40 (67%), Gaps = 5/40 (12%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKK-----RIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+      IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGRWALAIPP 43

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

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 32/43 (74%), Positives = 34/43 (79%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+DK G PP QQR IFAGKQLEDGRTL+DY IQ ESTLH   R
Sbjct: 31 IQDKIGYPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHCVRR 73

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/35 (62%), Positives = 24/35 (68%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    +  TLEVE SDTI+NVKAKIQDK   PP
Sbjct: 5  FVKCLTGKTNTLEVEPSDTIENVKAKIQDKIGYPP 39

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

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 34/38 (89%), Gaps = 1/38 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQE-STL 37
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ+ STL
Sbjct: 33 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKWSTL 70

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/35 (68%), Positives = 27/35 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 7  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 41

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

Iteration: 1
 Score = 60.5 bits (145), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 31/43 (72%), Positives = 33/43 (76%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I+   GIPP QQ  IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 30 IQAAPGIPPDQQELIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/35 (65%), Positives = 24/35 (68%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K      ITLEVESSDTIDNVK+KIQ    IPP
Sbjct: 4  FVKTLTGATITLEVESSDTIDNVKSKIQAAPGIPP 38

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

Iteration: 1
 Score = 60.5 bits (145), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 27/36 (75%), Positives = 30/36 (83%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQEST 36
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY I   +
Sbjct: 33 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIHNHS 68

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/28 (75%), Positives = 24/28 (85%)
Query: 52 QNITLEVESSDTIDNVKAKIQDKKRIPP 79
          + I LEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 14 RTIILEVEPSDTIENVKAKIQDKEGIPP 41

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

Iteration: 1
 Score = 60.5 bits (145), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 30/37 (81%), Positives = 31/37 (83%), Gaps = 1/37 (2%)
Query: 7  IPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          IPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 44 IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 80

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 21/31 (67%), Positives = 24/31 (77%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKK 75
          F K    + ITLEVE SDTI+NVKAKIQDK+
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKE 34

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

Iteration: 1
 Score = 58.9 bits (141), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 29/43 (67%), Positives = 32/43 (74%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I DKEGIPP QQR IF GKQLED   ++DY +Q ESTLHL  R
Sbjct: 35 IYDKEGIPPDQQRLIFGGKQLEDSNAMSDYNVQKESTLHLVLR 77

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

Iteration: 1
 Score = 39.7 bits (91), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 19/41 (46%), Positives = 26/41 (63%)
Query: 39 LGWRADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          LG    F K    + IT++V+ +DT+  VKAKI DK+ IPP
Sbjct: 3  LGSMQIFVKTLTGKTITIDVDHADTVGAVKAKIYDKEGIPP 43

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 29/43 (67%), Positives = 35/43 (81%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKI-QESTLHLGWR 42
          I+DKEGIPP QQ+ +FA KQLEDGRTL+DY I +ES L+L  R
Sbjct: 32 IQDKEGIPPDQQKLLFARKQLEDGRTLSDYNIHKESFLYLVLR 74

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/40 (62%), Positives = 28/40 (70%)
Query: 40 GWRADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          G    F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 1  GSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 40

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 29/39 (74%), Positives = 32/39 (82%), Gaps = 1/39 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLH 38
          I+DK GIPP QQ  IFAGK+LEDGRTL+DY IQ ESTL 
Sbjct: 32 IQDKLGIPPDQQWLIFAGKRLEDGRTLSDYNIQKESTLR 70

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/35 (65%), Positives = 25/35 (71%)
Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    +  TLEVE SDTI+NVKAKIQDK  IPP
Sbjct: 6  FVKFRTGKTYTLEVEPSDTIENVKAKIQDKLGIPP 40

>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 = 52.0 bits (123), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 26/43 (60%), Positives = 32/43 (74%), Gaps = 1/43 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKI-QESTLHLGWR 42
          +E+KEGIPP QQR I++GKQ+ D +T ADYKI   S LHL  R
Sbjct: 42 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLR 84

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/40 (62%), Positives = 31/40 (77%), Gaps = 1/40 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKI-QESTLHL 39
          +E+KEGIPP QQR I++GKQ+ D +T ADYKI   S LHL
Sbjct: 32 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHL 71

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/40 (62%), Positives = 31/40 (77%), Gaps = 1/40 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKI-QESTLHL 39
          +E+KEGIPP QQR I++GKQ+ D +T ADYKI   S LHL
Sbjct: 31 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHL 70

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/40 (62%), Positives = 31/40 (77%), Gaps = 1/40 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKI-QESTLHL 39
          +E+KEGIPP QQR I++GKQ+ D +T ADYKI   S LHL
Sbjct: 30 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHL 69

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/40 (62%), Positives = 31/40 (77%), Gaps = 1/40 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKI-QESTLHL 39
          +E+KEGIPP QQR I++GKQ+ D +T ADYKI   S LHL
Sbjct: 36 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHL 75

>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 = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/40 (62%), Positives = 31/40 (77%), Gaps = 1/40 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKI-QESTLHL 39
          +E+KEGIPP QQR I++GKQ+ D +T ADYKI   S LHL
Sbjct: 42 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHL 81

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/40 (62%), Positives = 31/40 (77%), Gaps = 1/40 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKI-QESTLHL 39
          +E+KEGIPP QQR I++GKQ+ D +T ADYKI   S LHL
Sbjct: 35 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHL 74

>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 = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/40 (62%), Positives = 31/40 (77%), Gaps = 1/40 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKI-QESTLHL 39
          +E+KEGIPP QQR I++GKQ+ D +T ADYKI   S LHL
Sbjct: 30 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHL 69

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 25/40 (62%), Positives = 30/40 (75%), Gaps = 1/40 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          +E+KEGIPP QQR I+AGKQL D +T  DY I+  S LHL
Sbjct: 30 VEEKEGIPPVQQRLIYAGKQLADDKTAKDYNIEGGSVLHL 69

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

Iteration: 1
 Score = 50.1 bits (118), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 25/40 (62%), Positives = 30/40 (75%), Gaps = 1/40 (2%)
Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          +E+KEGIPP QQR I++GKQ  D +T ADYKI   S LHL
Sbjct: 35 VEEKEGIPPQQQRLIYSGKQXNDEKTAADYKIXGGSVLHL 74

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/40 (62%), Positives = 28/40 (70%)
Query: 40 GWRADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          G    F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 1  GSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 40

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	133
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	1e-24
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	8e-12
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	2e-24
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	9e-12
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	1e-23
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	1e-17
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	1e-09
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	1e-23
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	8e-17
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	4e-07
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	5e-23
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	2e-17
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	9e-10
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	1e-22
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	6e-19
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	1e-22
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	2e-16
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	5e-09
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	3e-22
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	5e-10
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	8e-22
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	7e-10
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	7e-06
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	1e-21
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	8e-11
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	1e-21
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	3e-07
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	2e-21
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	5e-11
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	2e-21
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	3e-08
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	2e-21
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	9e-09
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	3e-21
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	1e-04
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	4e-21
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	3e-07
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	4e-21
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	4e-08
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	5e-21
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	9e-07
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	3e-20
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	3e-08
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	8e-20
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	6e-09
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	9e-20
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	6e-07
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	1e-19
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	7e-11
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	1e-19
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	4e-11
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	2e-19
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	3e-10
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	3e-19
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	2e-10
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	3e-19
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	2e-10
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	3e-19
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	8e-10
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	3e-19
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	3e-10
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	4e-19
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	8e-11
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	4e-19
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	1e-10
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	5e-19
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	7e-11
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	6e-19
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	1e-10
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	8e-19
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	2e-11
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	1e-18
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	2e-11
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	1e-18
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	9e-10
1we6_A	111	Splicing factor, putative; structural genomics, ub	1e-18
1we6_A	111	Splicing factor, putative; structural genomics, ub	9e-05
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	1e-18
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	1e-10
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	2e-18
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	2e-10
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	6e-18
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	2e-09
3u5c_F	225	RP14, S2, YS8, 40S ribosomal protein S5; translati	3e-17
3u5c_F	225	RP14, S2, YS8, 40S ribosomal protein S5; translati	5e-10
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	1e-16
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	4e-10
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	1e-16
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	1e-09
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	5e-16
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	4e-10
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	1e-15
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	4e-08
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	2e-15
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	4e-06
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	9e-15
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	9e-11
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	1e-10
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	4e-07
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	2e-09
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	4e-06
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	2e-08
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	2e-07
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	6e-06
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	1e-05
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	2e-04
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	2e-05
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	3e-05
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	3e-05
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	4e-05
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	6e-05
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	1e-04
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	2e-04
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	2e-04

>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 = 88.9 bits (221), Expect = 1e-24
 Identities = 15/43 (34%), Positives = 23/43 (53%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQESTLHLGWRA 43
          I     IP  +QR I+ G+ L+D + L +Y +    +HL  RA
Sbjct: 35 IAASVSIPSEKQRLIYQGRVLQDDKKLQEYNVGGKVIHLVERA 77

>4dwf_A HLA-B-associated transcript 3; ubiquitin-like domain, BAT3 protein, PF00240, structural GEN joint center for structural genomics, JCSG; 1.80A {Homo sapiens} PDB: 1wx9_A Length = 90

 Score = 56.1 bits (136), Expect = 8e-12
 Identities = 9/35 (25%), Positives = 11/35 (31%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
            K  D Q  T  V +   +   K  I     IP 
Sbjct: 9  LVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPS 43

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

 Score = 88.9 bits (221), Expect = 2e-24
 Identities = 14/42 (33%), Positives = 22/42 (52%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQESTLHLGWR 42
          I     IP  +QR I+ G+ L+D + L +Y +    +HL  R
Sbjct: 47 IAASVSIPSEKQRLIYQGRVLQDDKKLQEYNVGGKVIHLVER 88

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

 Score = 56.1 bits (136), Expect = 9e-12
 Identities = 9/35 (25%), Positives = 11/35 (31%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
            K  D Q  T  V +   +   K  I     IP 
Sbjct: 21 LVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPS 55

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

 Score = 89.0 bits (220), Expect = 1e-23
 Identities = 58/86 (67%), Positives = 64/86 (74%), Gaps = 6/86 (6%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQE-STLHL-----GWRADFCKNPDPQNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ+ STLHL     G    F K    + I
Sbjct: 50  IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 109

Query: 55  TLEVESSDTIDNVKAKIQDKKRIPPP 80
           TLEVE SDTI+NVKAKIQDK+ IPP 
Sbjct: 110 TLEVEPSDTIENVKAKIQDKEGIPPD 135

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

 Score = 73.6 bits (180), Expect = 1e-17
 Identities = 34/40 (85%), Positives = 36/40 (90%), Gaps = 1/40 (2%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
           I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL
Sbjct: 126 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHL 165

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

 Score = 52.7 bits (126), Expect = 1e-09
 Identities = 24/36 (66%), Positives = 27/36 (75%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPP 80
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP 
Sbjct: 24 FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPD 59

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

 Score = 89.3 bits (221), Expect = 1e-23
 Identities = 33/81 (40%), Positives = 43/81 (53%), Gaps = 3/81 (3%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLA--DYKIQESTLHLGWRADFCKNPDPQNITLEV 58
           +  K G    +    +        R L   D+ I ++T H G +  F K    + ITLEV
Sbjct: 64  LPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYGGQI-FVKTLTGKTITLEV 122

Query: 59  ESSDTIDNVKAKIQDKKRIPP 79
           E SDTI+NVKAKIQDK+ IPP
Sbjct: 123 EPSDTIENVKAKIQDKEGIPP 143

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

 Score = 71.9 bits (176), Expect = 8e-17
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
           I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 135 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 177

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

 Score = 45.7 bits (108), Expect = 4e-07
 Identities = 17/67 (25%), Positives = 23/67 (34%), Gaps = 4/67 (5%)

Query: 21 LEDGRTLADYKIQES-TLHLGWRADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          L+    L D  I +S    LGW A   K         +    D   N + K+  K     
Sbjct: 15 LQTYHKLPDNYITKSEAQALGWVAS--KGNLADVAPGKSIGGDIFSNREGKLPGKSGRTW 72

Query: 80 PAEADLL 86
            EAD+ 
Sbjct: 73 R-EADIN 78

>3b08_A Polyubiquitin-C, ubiquitin; protein complex, signaling protein-metal binding protein COM; HET: TRE; 1.70A {Homo sapiens} PDB: 2w9n_A* 3b0a_A* 3axc_A 2zvn_A 2zvo_A 2y5b_B Length = 152

 Score = 87.0 bits (215), Expect = 5e-23
 Identities = 56/86 (65%), Positives = 62/86 (72%), Gaps = 6/86 (6%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQE-STLHLGWRADFCKNPDP-----QNI 54
           I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ+ STLHL  R              + I
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTI 89

Query: 55  TLEVESSDTIDNVKAKIQDKKRIPPP 80
           TLEVE SDTI+NVKAKIQDK+ IPP 
Sbjct: 90  TLEVEPSDTIENVKAKIQDKEGIPPD 115

>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 = 72.4 bits (177), Expect = 2e-17
 Identities = 34/40 (85%), Positives = 36/40 (90%), Gaps = 1/40 (2%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
           I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL
Sbjct: 106 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHL 145

>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 = 52.3 bits (125), Expect = 9e-10
 Identities = 24/35 (68%), Positives = 27/35 (77%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 38

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

 Score = 84.3 bits (209), Expect = 1e-22
 Identities = 17/40 (42%), Positives = 24/40 (60%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          I    GIP   QR I++GK L+D +T+  Y IQ   ++HL
Sbjct: 57 INKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHL 96

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

 Score = 75.1 bits (185), Expect = 6e-19
 Identities = 12/65 (18%), Positives = 18/65 (27%), Gaps = 5/65 (7%)

Query: 19 KQLEDGRTLADYKIQ-ESTLHLGWRAD---FCKNPDPQNITLEVESSDTIDNVKAKIQDK 74
          K       ++DY I     L+           K+       + V    T+   K  I   
Sbjct: 2  KHHHHHHPMSDYDIPTTENLYFQGAMSLNIHIKSGQ-DKWEVNVAPESTVLQFKEAINKA 60

Query: 75 KRIPP 79
            IP 
Sbjct: 61 NGIPV 65

>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 = 86.2 bits (213), Expect = 1e-22
 Identities = 20/88 (22%), Positives = 36/88 (40%), Gaps = 9/88 (10%)

Query: 1   IEDKEGIPPGQQRSIF--AGKQLEDGRTLADYKIQ-ESTLHLGWRAD------FCKNPDP 51
           I  K G+   QQR     +G  L+D   LA   +   ST+ L             +N   
Sbjct: 32  ITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDKSDEPLSILVRNNKG 91

Query: 52  QNITLEVESSDTIDNVKAKIQDKKRIPP 79
           ++ T EV  + T+ ++K ++   + +  
Sbjct: 92  RSSTYEVRLTQTVAHLKQQVSGLEGVQD 119

>3rt3_B Ubiquitin-like protein ISG15; ubiquitin-like domain, isgylation, antiviral protein-viral P complex; 2.01A {Homo sapiens} PDB: 3sdl_C 3r66_C 3pse_B 1z2m_A Length = 159

 Score = 70.0 bits (171), Expect = 2e-16
 Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 1/40 (2%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
           +   EG+        F GK LED   L +Y ++  ST+ +
Sbjct: 111 VSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFM 150

>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 = 50.7 bits (121), Expect = 5e-09
 Identities = 7/35 (20%), Positives = 14/35 (40%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
            K        + + SS ++  +KA+I  K  +  
Sbjct: 6  TVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHA 40

>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 = 82.6 bits (205), Expect = 3e-22
 Identities = 17/40 (42%), Positives = 24/40 (60%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          I    GIP   QR I++GK L+D +T+  Y IQ   ++HL
Sbjct: 33 INKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHL 72

>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 = 51.4 bits (124), Expect = 5e-10
 Identities = 6/28 (21%), Positives = 8/28 (28%)

Query: 52 QNITLEVESSDTIDNVKAKIQDKKRIPP 79
              + V    T+   K  I     IP 
Sbjct: 14 DKWEVNVAPESTVLQFKEAINKANGIPV 41

>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 = 84.2 bits (208), Expect = 8e-22
 Identities = 39/88 (44%), Positives = 53/88 (60%), Gaps = 9/88 (10%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL--------GWRADFCKNPDP 51
           I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL        G    F  + D 
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGGGETIKFVADGDI 89

Query: 52  QNITLEVESSDTIDNVKAKIQDKKRIPP 79
            + ++ ++    +++ +  I+ +   P 
Sbjct: 90  GSGSVIIKPFVDMEHPETSIKLEMDQPV 117

>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 = 53.0 bits (127), Expect = 7e-10
 Identities = 25/35 (71%), Positives = 28/35 (80%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVESSDTIDNVK+KIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPP 38

>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 = 7e-06
 Identities = 10/49 (20%), Positives = 18/49 (36%), Gaps = 10/49 (20%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLED---GRTLAD---YKIQ-ESTLHLGWR 42
           I+ +   P       F  K L D   G +L+D    ++  E+     + 
Sbjct: 109 IKLEMDQPVDL---TFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFD 154

>1ndd_A NEDD8, protein (ubiquitin-like protein NEDD8); proteolysis, signaling protei; 1.60A {Homo sapiens} SCOP: d.15.1.1 PDB: 1r4m_I 1r4n_I* 1xt9_B 2ko3_A 3gzn_I* 2bkr_B 2nvu_I* 3dqv_A 1bt0_A Length = 76

 Score = 81.1 bits (201), Expect = 1e-21
 Identities = 25/40 (62%), Positives = 31/40 (77%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          +E+KEGIPP QQR I++GKQ+ D +T ADYKI   S LHL
Sbjct: 30 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHL 69

>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 = 53.4 bits (129), Expect = 8e-11
 Identities = 9/36 (25%), Positives = 22/36 (61%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPP 80
            K    + I +++E +D ++ +K ++++K+ IPP 
Sbjct: 4  KVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQ 39

>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 = 80.9 bits (200), Expect = 1e-21
 Identities = 18/43 (41%), Positives = 27/43 (62%), Gaps = 1/43 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I++   + PG QR  + GKQ+EDG TL DY+++   T+ L  R
Sbjct: 34 IQELFHVEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLLVR 76

>2faz_A Ubiquitin-like containing PHD and ring finger DOM protein 1; cell cycle, DNA damage, DNA repair, DNA-binding, ligase, Met binding, nuclear protein; 2.00A {Homo sapiens} SCOP: d.15.1.1 Length = 78

 Score = 43.9 bits (104), Expect = 3e-07
 Identities = 4/26 (15%), Positives = 11/26 (42%)

Query: 54 ITLEVESSDTIDNVKAKIQDKKRIPP 79
              +     ++ ++ KIQ+   + P
Sbjct: 17 TVDSLSRLTKVEELRRKIQELFHVEP 42

>4fbj_B NEDD8; effector-HOST target complex, glutamine deamidase, deamidati bacterial effector, cell cycle-protein binding complex; 1.60A {Homo sapiens} PDB: 4f8c_B Length = 88

 Score = 81.2 bits (201), Expect = 2e-21
 Identities = 25/40 (62%), Positives = 31/40 (77%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          +E+KEGIPP QQR I++GKQ+ D +T ADYKI   S LHL
Sbjct: 30 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHL 69

>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 = 54.3 bits (131), Expect = 5e-11
 Identities = 9/36 (25%), Positives = 22/36 (61%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPP 80
            K    + I +++E +D ++ +K ++++K+ IPP 
Sbjct: 4  KVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQ 39

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens} Length = 101

 Score = 81.3 bits (201), Expect = 2e-21
 Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 1/44 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA 43
          I  +      Q   IFAGK L+D  TL+ + I    T+HL  + 
Sbjct: 54 ISKRFKSHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKT 97

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens} Length = 101

 Score = 47.4 bits (113), Expect = 3e-08
 Identities = 3/28 (10%), Positives = 10/28 (35%)

Query: 52 QNITLEVESSDTIDNVKAKIQDKKRIPP 79
          +     V  + ++   K +I  + +   
Sbjct: 35 EKEEFAVPENSSVQQFKEEISKRFKSHT 62

>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 = 81.2 bits (201), Expect = 2e-21
 Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          I  +    P Q   IFAGK L+D  +LA   ++   T+HL
Sbjct: 51 ISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHL 90

>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 = 48.5 bits (116), Expect = 9e-09
 Identities = 8/35 (22%), Positives = 13/35 (37%), Gaps = 1/35 (2%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
            K P        V  + TI  +K +I  + +  P
Sbjct: 26 TVKTPK-DKEDFSVTDTCTIQQLKEEISQRFKAHP 59

>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 = 85.6 bits (211), Expect = 3e-21
 Identities = 35/43 (81%), Positives = 37/43 (86%), Gaps = 1/43 (2%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
           I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R
Sbjct: 263 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 305

>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 = 39.0 bits (90), Expect = 1e-04
 Identities = 24/90 (26%), Positives = 32/90 (35%), Gaps = 11/90 (12%)

Query: 2   EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQESTLHLGWRADFCKNPDPQN-------- 53
             +          +     L     L+    ++    +                      
Sbjct: 183 YQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITGSMQIFVKTLT 242

Query: 54  ---ITLEVESSDTIDNVKAKIQDKKRIPPP 80
              ITLEVE SDTI+NVKAKIQDK+ IPP 
Sbjct: 243 GKTITLEVEPSDTIENVKAKIQDKEGIPPD 272

>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 = 81.0 bits (200), Expect = 4e-21
 Identities = 12/43 (27%), Positives = 24/43 (55%), Gaps = 1/43 (2%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
           I +  G+P G+Q+  + G  ++D  +LA Y +   + +HL  +
Sbjct: 65  IHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMASGAVIHLALK 107

>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 = 44.8 bits (106), Expect = 3e-07
 Identities = 6/28 (21%), Positives = 13/28 (46%)

Query: 52 QNITLEVESSDTIDNVKAKIQDKKRIPP 79
          Q +   +  +D +  +K KI +   +P 
Sbjct: 46 QGLVFTLPLTDQVSVIKVKIHEATGMPA 73

>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 = 80.5 bits (199), Expect = 4e-21
 Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          I  +    P Q   IFAGK L+D  +LA   ++   T+HL
Sbjct: 46 ISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHL 85

>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 = 47.0 bits (112), Expect = 4e-08
 Identities = 8/35 (22%), Positives = 13/35 (37%), Gaps = 1/35 (2%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
            K P        V  + TI  +K +I  + +  P
Sbjct: 21 TVKTPK-DKEDFSVTDTCTIQQLKEEISQRFKAHP 54

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 125

 Score = 81.0 bits (200), Expect = 5e-21
 Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 1/40 (2%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
           I  +      Q   IFAGK L+D  TL  + I    T+HL
Sbjct: 61  ISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHL 100

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 125

 Score = 44.1 bits (104), Expect = 9e-07
 Identities = 5/35 (14%), Positives = 11/35 (31%), Gaps = 1/35 (2%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
            K P  +     V  + ++   K  I  + +   
Sbjct: 36 TVKTPKEK-EEFAVPENSSVQQFKEAISKRFKSQT 69

>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 = 77.8 bits (192), Expect = 3e-20
 Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          +     + P  QR  + GKQLE+G TL DY +     + L
Sbjct: 39 VWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQL 78

>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 = 47.0 bits (112), Expect = 3e-08
 Identities = 7/37 (18%), Positives = 16/37 (43%), Gaps = 2/37 (5%)

Query: 45 FCKNPD-PQNITLE-VESSDTIDNVKAKIQDKKRIPP 79
            +  D  +  T+E V    TI+ ++ ++     + P
Sbjct: 11 QVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRP 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 = 77.5 bits (191), Expect = 8e-20
 Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          +   EG+ PG QR  F+G+ L D     + KI  +  + +
Sbjct: 53 LHAAEGVEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQV 92

>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 = 49.4 bits (118), Expect = 6e-09
 Identities = 7/35 (20%), Positives = 19/35 (54%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
            +    +++ L V S+DT+ ++K ++   + + P
Sbjct: 27 RLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEP 61

>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 = 77.0 bits (190), Expect = 9e-20
 Identities = 12/40 (30%), Positives = 16/40 (40%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          I         +   IF GK L D   L+   I   ST+H+
Sbjct: 46 ISKYLHCNADRLVLIFTGKILRDQDILSQRGILDGSTVHV 85

>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 = 43.9 bits (104), Expect = 6e-07
 Identities = 2/28 (7%), Positives = 6/28 (21%)

Query: 52 QNITLEVESSDTIDNVKAKIQDKKRIPP 79
                +  +  +   K +I        
Sbjct: 27 DCHEFFLAENSNVRRFKKQISKYLHCNA 54

>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 = 76.2 bits (188), Expect = 1e-19
 Identities = 34/40 (85%), Positives = 36/40 (90%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHL 69

>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 = 53.5 bits (129), Expect = 7e-11
 Identities = 24/35 (68%), Positives = 27/35 (77%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 38

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

 Score = 76.1 bits (188), Expect = 1e-19
 Identities = 12/41 (29%), Positives = 18/41 (43%), Gaps = 2/41 (4%)

Query: 1  IEDKEGIPPGQQRSIFAGKQ-LEDGRTLADYKIQE-STLHL 39
          IE  + IP  +Q  I  G   L +  T+   +I   S + L
Sbjct: 40 IERSQHIPVSKQTLIVDGIVILREDLTVEQCQIVPTSDIQL 80

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

 Score = 54.2 bits (131), Expect = 4e-11
 Identities = 11/28 (39%), Positives = 16/28 (57%)

Query: 52 QNITLEVESSDTIDNVKAKIQDKKRIPP 79
           +  LEV+  DT+  VK KI+  + IP 
Sbjct: 21 SSFELEVDYRDTLLVVKQKIERSQHIPV 48

>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 = 76.3 bits (188), Expect = 2e-19
 Identities = 12/73 (16%), Positives = 32/73 (43%), Gaps = 4/73 (5%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQE-STLHLGWRADFCKNPDPQNITLEVE 59
           +         Q + I++GK L+D +T+++  +++   +         K      +T    
Sbjct: 31  LAQSISCEESQIKLIYSGKVLQDSKTVSECGLKDGDQVVFMVSQ---KKSTKTKVTERDP 87

Query: 60  SSDTIDNVKAKIQ 72
           +S ++D + A ++
Sbjct: 88  NSSSVDKLAAALE 100

>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 = 52.4 bits (126), Expect = 3e-10
 Identities = 9/35 (25%), Positives = 15/35 (42%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
            KN   + + L++E S+TI   K K+        
Sbjct: 5  TFKNFKKEKVPLDLEPSNTILETKTKLAQSISCEE 39

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

 Score = 75.0 bits (185), Expect = 3e-19
 Identities = 18/40 (45%), Positives = 25/40 (62%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          + +K  +P  QQR +F GK L DG+ L+DY I   S L+L
Sbjct: 37 VSEKLNVPVRQQRLLFKGKALADGKRLSDYSIGPNSKLNL 76

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

 Score = 52.3 bits (126), Expect = 2e-10
 Identities = 6/35 (17%), Positives = 15/35 (42%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
            K    +  +L+V   + +  +K  + +K  +P 
Sbjct: 11 TVKALQGRECSLQVPEDELVSTLKQLVSEKLNVPV 45

>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 = 75.0 bits (185), Expect = 3e-19
 Identities = 13/40 (32%), Positives = 26/40 (65%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          +  ++G+P  Q R IFAGK+L +  T+ +  ++ +S +H+
Sbjct: 30 VAKQQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHI 69

>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 = 52.3 bits (126), Expect = 2e-10
 Identities = 7/35 (20%), Positives = 16/35 (45%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F +        +EV+S  +I  +K  +  ++ +P 
Sbjct: 4  FVRFNSSYGFPVEVDSDTSILQLKEVVAKQQGVPA 38

>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 = 75.4 bits (186), Expect = 3e-19
 Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 4/43 (9%)

Query: 1  IEDKEG---IPPGQQRSIFAGKQLEDGRTLADYKIQE-STLHL 39
          IE ++G    P   Q+ I+AGK L D   L +YKI E + + +
Sbjct: 30 IESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVV 72

>1uel_A HHR23B, UV excision repair protein RAD23 homolog B; UBL, UIM, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 95

 Score = 51.2 bits (123), Expect = 8e-10
 Identities = 8/38 (21%), Positives = 17/38 (44%), Gaps = 3/38 (7%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKK---RIPP 79
            K    Q   ++++  +T+  +K KI+ +K     P 
Sbjct: 4  TLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPV 41

>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 = 75.1 bits (185), Expect = 3e-19
 Identities = 32/40 (80%), Positives = 34/40 (85%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ  STL L
Sbjct: 33 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKWSTLFL 72

>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 = 52.4 bits (126), Expect = 3e-10
 Identities = 24/35 (68%), Positives = 27/35 (77%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 7  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 41

>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 = 75.1 bits (185), Expect = 4e-19
 Identities = 25/40 (62%), Positives = 31/40 (77%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          +E+KEGIPP QQR I++GKQ+ D +T ADYKI   S LHL
Sbjct: 42 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHL 81

>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 = 53.5 bits (129), Expect = 8e-11
 Identities = 9/36 (25%), Positives = 22/36 (61%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPP 80
            K    + I +++E +D ++ +K ++++K+ IPP 
Sbjct: 16 KVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQ 51

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

 Score = 75.6 bits (186), Expect = 4e-19
 Identities = 37/71 (52%), Positives = 44/71 (61%), Gaps = 9/71 (12%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL--------GWRADFCKNPDP 51
           I+DKEGIPP QQR I+AGKQLEDGRTL+DY IQ ESTLHL           A   +    
Sbjct: 39  IQDKEGIPPDQQRLIWAGKQLEDGRTLSDYNIQRESTLHLVLRLRGGSMGGAADEEELIR 98

Query: 52  QNITLEVESSD 62
           + I L ++ S 
Sbjct: 99  KAIELSLKESR 109

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

 Score = 53.7 bits (129), Expect = 1e-10
 Identities = 25/35 (71%), Positives = 28/35 (80%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVESSDTIDNVK+KIQDK+ IPP
Sbjct: 13 FAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPP 47

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

 Score = 74.7 bits (184), Expect = 5e-19
 Identities = 34/40 (85%), Positives = 36/40 (90%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL
Sbjct: 39 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHL 78

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

 Score = 53.9 bits (130), Expect = 7e-11
 Identities = 20/35 (57%), Positives = 26/35 (74%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    +  T+E+E SDTI+N+KAKIQDK+ IPP
Sbjct: 13 FIKTLTGKTFTVEMEPSDTIENLKAKIQDKEGIPP 47

>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 = 74.8 bits (184), Expect = 6e-19
 Identities = 40/58 (68%), Positives = 45/58 (77%), Gaps = 5/58 (8%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR----ADFCKNPDPQN 53
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL  R    AD  ++PD Q+
Sbjct: 31 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGYADLREDPDRQD 88

>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 = 53.6 bits (129), Expect = 1e-10
 Identities = 24/35 (68%), Positives = 27/35 (77%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 5  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 39

>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 = 74.3 bits (183), Expect = 8e-19
 Identities = 18/40 (45%), Positives = 24/40 (60%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          IED++G+P  QQ+  F G+ L+D   L  Y IQ   TL L
Sbjct: 37 IEDQQGLPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLIL 76

>1wh3_A 59 kDa 2'-5'-oligoadenylate synthetase like protein; P59 OASL, ubiquitin family, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 87

 Score = 55.5 bits (134), Expect = 2e-11
 Identities = 10/35 (28%), Positives = 19/35 (54%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F KNPD  +    +  +  I  +K +I+D++ +P 
Sbjct: 11 FVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPK 45

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

 Score = 74.9 bits (184), Expect = 1e-18
 Identities = 34/40 (85%), Positives = 36/40 (90%), Gaps = 1/40 (2%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
           I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL
Sbjct: 65  IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHL 104

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

 Score = 55.6 bits (134), Expect = 2e-11
 Identities = 26/67 (38%), Positives = 32/67 (47%), Gaps = 4/67 (5%)

Query: 16 FAGKQLEDGRTLADYKIQESTLHLGWRAD---FCKNPDPQNITLEVESSDTIDNVKAKIQ 72
               +E      D    +  +          F K    + ITLEVE SDTI+NVKAKIQ
Sbjct: 8  NNDGWIEGDELYIDTN-NDGWIEGDELLAMQIFVKTLTGKTITLEVEPSDTIENVKAKIQ 66

Query: 73 DKKRIPP 79
          DK+ IPP
Sbjct: 67 DKEGIPP 73

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

 Score = 74.0 bits (182), Expect = 1e-18
 Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          +   EGI P  Q  + AG  LED  TL    ++  +TL +
Sbjct: 47 VASLEGIAPEDQVVLLAGAPLEDEATLGQCGVEALTTLEV 86

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

 Score = 50.9 bits (122), Expect = 9e-10
 Identities = 8/28 (28%), Positives = 14/28 (50%)

Query: 52 QNITLEVESSDTIDNVKAKIQDKKRIPP 79
          +  T EV   +T+  +KA +   + I P
Sbjct: 28 ELHTFEVTGQETVAQIKAHVASLEGIAP 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 = 74.5 bits (183), Expect = 1e-18
 Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 1/43 (2%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
           I  +  IP  +Q+       L+D  +LA Y +     L L  R
Sbjct: 61  IAGEIQIPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLR 103

>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 = 38.3 bits (89), Expect = 9e-05
 Identities = 10/32 (31%), Positives = 19/32 (59%), Gaps = 1/32 (3%)

Query: 49 PDPQNITLEVES-SDTIDNVKAKIQDKKRIPP 79
           D Q + + V+S S+ + ++K KI  + +IP 
Sbjct: 38 NDGQFMEITVQSLSENVGSLKEKIAGEIQIPA 69

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

 Score = 74.1 bits (182), Expect = 1e-18
 Identities = 39/65 (60%), Positives = 42/65 (64%), Gaps = 6/65 (9%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL-----GWRADFCKNPDPQNI 54
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL     G R     + D    
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGRDPNSSSVDKLAA 89

Query: 55 TLEVE 59
           LE  
Sbjct: 90 ALEHH 94

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

 Score = 53.3 bits (128), Expect = 1e-10
 Identities = 24/35 (68%), Positives = 27/35 (77%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 38

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

 Score = 73.2 bits (180), Expect = 2e-18
 Identities = 30/40 (75%), Positives = 33/40 (82%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY I   S L+L
Sbjct: 33 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIHNHSALYL 72

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

 Score = 52.4 bits (126), Expect = 2e-10
 Identities = 22/35 (62%), Positives = 25/35 (71%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
            K    + I LEVE SDTI+NVKAKIQDK+ IPP
Sbjct: 7  VVKTLMGRTIILEVEPSDTIENVKAKIQDKEGIPP 41

>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 = 71.9 bits (177), Expect = 6e-18
 Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 4/43 (9%)

Query: 1  IEDKEG---IPPGQQRSIFAGKQLEDGRTLADYKIQE-STLHL 39
          IE ++G    P   Q+ I+AGK L D   + DY+I E + + +
Sbjct: 35 IEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVV 77

>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 = 49.6 bits (119), Expect = 2e-09
 Identities = 9/38 (23%), Positives = 16/38 (42%), Gaps = 3/38 (7%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKK---RIPP 79
            K    Q   + +E  +T+  +K KI+ +K     P 
Sbjct: 9  TLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPV 46

>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 = 72.1 bits (177), Expect = 3e-17
 Identities = 1/43 (2%), Positives = 8/43 (18%), Gaps = 1/43 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
           E+ +      +       +  + +  +               
Sbjct: 30 PEEVQQAQTEIKLFNKWSFEEVEVKDASLVDYVQVRQPIFVAH 72

>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 = 53.3 bits (128), Expect = 5e-10
 Identities = 3/35 (8%), Positives = 9/35 (25%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
               + Q     VE    +       ++ ++   
Sbjct: 4  TEAPVEVQEDFEVVEEFTPVVLATPIPEEVQQAQT 38

>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 = 69.0 bits (169), Expect = 1e-16
 Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          +   EG+        F GK LED   L +Y ++  ST+ +
Sbjct: 34 VSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFM 73

>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 = 52.0 bits (125), Expect = 4e-10
 Identities = 6/35 (17%), Positives = 17/35 (48%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
            +N   ++ T EV  + T+ ++K ++   + +  
Sbjct: 8  LVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQD 42

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} Length = 94

 Score = 69.0 bits (169), Expect = 1e-16
 Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 2/41 (4%)

Query: 1  IEDKEGIPPGQQRSIFAGKQL-EDGRTLADYKIQE-STLHL 39
          I   E  P  + +  ++G +L +D R L +Y I E S + +
Sbjct: 44 IHIVENTPIKRMQLYYSGIELADDYRNLNEYGITEFSEIVV 84

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} Length = 94

 Score = 50.9 bits (122), Expect = 1e-09
 Identities = 8/28 (28%), Positives = 17/28 (60%)

Query: 52 QNITLEVESSDTIDNVKAKIQDKKRIPP 79
          +  T+EV+ ++T+ ++K KI   +  P 
Sbjct: 25 KQFTVEVDRTETVSSLKDKIHIVENTPI 52

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

 Score = 67.0 bits (164), Expect = 5e-16
 Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          +   EG+        F GK LED   L +Y ++  ST+ +
Sbjct: 34 VSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFM 73

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

 Score = 51.6 bits (124), Expect = 4e-10
 Identities = 6/35 (17%), Positives = 17/35 (48%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
            +N   ++ T EV  + T+ ++K ++   + +  
Sbjct: 8  LVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQD 42

>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 = 67.4 bits (164), Expect = 1e-15
 Identities = 36/81 (44%), Positives = 43/81 (53%), Gaps = 3/81 (3%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLH--LGWRADFCKNPDPQNITLE 57
           I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLH  L  R    +       +  
Sbjct: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGIIEPSLKALASKY 89

Query: 58  VESSDTIDNVKAKIQDKKRIP 78
                      A++  +    
Sbjct: 90  NCDKSVCRKCYARLPPRATNC 110

>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 = 47.7 bits (113), Expect = 4e-08
 Identities = 25/35 (71%), Positives = 28/35 (80%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F K    + ITLEVESSDTIDNVK+KIQDK+ IPP
Sbjct: 4  FVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPP 38

>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 = 65.4 bits (160), Expect = 2e-15
 Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQE-STLHL 39
          ++    + P  Q+ IF GK L +  TL    +   + L L
Sbjct: 41 LQPITNVLPRGQKLIFKGKVLVETSTLKQSDVGSGAKLML 80

>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 = 41.5 bits (98), Expect = 4e-06
 Identities = 7/28 (25%), Positives = 16/28 (57%)

Query: 52 QNITLEVESSDTIDNVKAKIQDKKRIPP 79
          ++I L V    T+ ++K+++Q    + P
Sbjct: 22 KSIPLSVSPDCTVKDLKSQLQPITNVLP 49

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

 Score = 66.3 bits (161), Expect = 9e-15
 Identities = 10/88 (11%), Positives = 25/88 (28%), Gaps = 5/88 (5%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQESTLHLGWRA-DFCKNPDPQNITLEVE 59
           I    G        +  G    +   + D      T +L  +     K    ++ T + +
Sbjct: 30  ISQDMGFEIDMMTLVNNGFIAPNTELVTDD----VTYYLSLKLLGGKKKKKKKSYTTKKK 85

Query: 60  SSDTIDNVKAKIQDKKRIPPPAEADLLK 87
           +     + K       ++    +  L +
Sbjct: 86  TKHRHVHTKLGALAFYKLENNGKVSLQQ 113

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

 Score = 55.9 bits (134), Expect = 9e-11
 Identities = 4/35 (11%), Positives = 13/35 (37%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
            K  + +     +E   ++ ++K++I        
Sbjct: 4  QVKTLEGETKIYTLEQGTSVLDLKSQISQDMGFEI 38

>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 = 56.5 bits (135), Expect = 1e-10
 Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 4/43 (9%)

Query: 1  IEDKEG---IPPGQQRSIFAGKQLEDGRTLADYKIQE-STLHL 39
          IE ++G    P   Q+ I+AGK L D   + DY+I E + + +
Sbjct: 37 IEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVV 79

>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 = 46.5 bits (109), Expect = 4e-07
 Identities = 11/45 (24%), Positives = 19/45 (42%), Gaps = 1/45 (2%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKK-RIPPPAEADLLKF 88
            K    Q   + +E  +T+  +K KI+ +K R   P     L +
Sbjct: 11 TLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIY 55

>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 = 50.4 bits (120), Expect = 2e-09
 Identities = 8/41 (19%), Positives = 21/41 (51%), Gaps = 2/41 (4%)

Query: 1  IEDKEGIPPGQQRSIFAGKQL-EDGRTLADYKIQE-STLHL 39
           E + G+P  + + ++  + L +D  +L  Y +++   + L
Sbjct: 41 CELESGVPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVL 81

>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 = 41.9 bits (98), Expect = 4e-06
 Identities = 6/37 (16%), Positives = 14/37 (37%), Gaps = 2/37 (5%)

Query: 45 FCKNPDPQN--ITLEVESSDTIDNVKAKIQDKKRIPP 79
          +C   D      +L+V     + N +   + +  +P 
Sbjct: 13 YCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPA 49

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A Length = 105

 Score = 47.7 bits (113), Expect = 2e-08
 Identities = 8/41 (19%), Positives = 19/41 (46%), Gaps = 2/41 (4%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQES--TLHL 39
          +    G PP  Q+ +   +   D  TL  + ++++  + +L
Sbjct: 56 VFLDYGFPPVLQQWVIGQRLARDQETLHSHGVRQNGDSAYL 96

>1x1m_A Ubiquitin-like protein SB132; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.15.1.1 Length = 107

 Score = 45.2 bits (106), Expect = 2e-07
 Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 1/34 (2%)

Query: 7  IPPGQQRSIFAGKQLEDGRTLADYKIQE-STLHL 39
            P     I+ G++L+D +TL  Y IQ  ST+H+
Sbjct: 63 PDPELIDLIYCGRKLKDDQTLDFYGIQPGSTVHV 96

>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 = 41.8 bits (98), Expect = 6e-06
 Identities = 10/69 (14%), Positives = 21/69 (30%), Gaps = 15/69 (21%)

Query: 1  IEDKEGIPPGQQR-------SIFAGKQLEDGRTLADYKIQE-STLHLGWRADFCKNPDPQ 52
          +E   G      R           G+  +  ++L D  +++   +H         +    
Sbjct: 37 LELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIH-------AVDVTGG 89

Query: 53 NITLEVESS 61
          N   + ES 
Sbjct: 90 NEDFKDESM 98

>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 = 40.8 bits (95), Expect = 1e-05
 Identities = 7/41 (17%), Positives = 18/41 (43%), Gaps = 2/41 (4%)

Query: 1  IEDKEGIPPGQQRSI-FAGKQLEDGRTLADYKIQ-ESTLHL 39
          +E++  IP  +     +    +ED   L    +   ++L++
Sbjct: 38 LENELQIPVSKMLLKGWKTGDVEDSTVLKSLHLPKNNSLYV 78

>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 = 37.4 bits (86), Expect = 2e-04
 Identities = 6/28 (21%), Positives = 18/28 (64%)

Query: 52 QNITLEVESSDTIDNVKAKIQDKKRIPP 79
          +N+ + +E + T+  +K  ++++ +IP 
Sbjct: 19 RNVDVVLEDTCTVGEIKQILENELQIPV 46

>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 = 39.6 bits (92), Expect = 2e-05
 Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 3/41 (7%)

Query: 2  EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQES---TLHL 39
             E   P  QR I++GK L D + L D   ++     LHL
Sbjct: 42 VYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHL 82

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens} Length = 125

 Score = 40.0 bits (93), Expect = 3e-05
 Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 3/46 (6%)

Query: 2   EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQE---STLHLGWRAD 44
           E+++   P   R I+ G+ L    TL   K+     + +HL  R  
Sbjct: 56  EEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLVARET 101

>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 = 40.0 bits (93), Expect = 3e-05
 Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 8/52 (15%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQEST--------LHLGWRAD 44
          +E     PP +QR     + L+DG+TL +      T        + L +RAD
Sbjct: 31 VEGILKRPPEEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRAD 82

>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 = 39.0 bits (91), Expect = 4e-05
 Identities = 9/40 (22%), Positives = 21/40 (52%), Gaps = 2/40 (5%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQE-STLHL 39
          I    G+PP  Q+ ++ G  + + +TL + K+   + + +
Sbjct: 46 IHSITGLPPAMQKVMYKGL-VPEDKTLREIKVTSGAKIMV 84

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens} Length = 99

 Score = 38.8 bits (90), Expect = 6e-05
 Identities = 11/41 (26%), Positives = 16/41 (39%), Gaps = 3/41 (7%)

Query: 2  EDKEGIPPGQQRSIFAGKQLEDGRTLAD--YKIQES-TLHL 39
                    QR +++G+ L D   L D   K  E   +HL
Sbjct: 58 VYPSKPLTKDQRLVYSGRLLPDHLQLKDILRKQDEYHMVHL 98

>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 Length = 116

 Score = 38.1 bits (88), Expect = 1e-04
 Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 3/46 (6%)

Query: 2   EDKEGIPPGQQRSIFAGKQLEDGRTLADYKI---QESTLHLGWRAD 44
           E+++   P   R I+ G+ L    TL   K+   + + +HL  R  
Sbjct: 55  EEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLVARET 100

>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 = 37.2 bits (86), Expect = 2e-04
 Identities = 8/40 (20%), Positives = 19/40 (47%), Gaps = 2/40 (5%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQE-STLHL 39
          +    G+ P +Q+ +  G  L+D     + K++   T+ +
Sbjct: 37 LFALTGVQPARQKVMVKGGTLKDD-DWGNIKMKNGMTVLM 75

>1wia_A Hypothetical ubiquitin-like protein (riken cDNA 2010008E23); 'structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 Length = 95

 Score = 36.9 bits (85), Expect = 2e-04
 Identities = 11/59 (18%), Positives = 18/59 (30%), Gaps = 7/59 (11%)

Query: 7  IPPGQQRSIFAGKQL-EDGRTLADYKIQE-STLHLGWRADFCKNPDPQNITLEVESSDT 63
              Q + I+ G+ L +  RTL+   I     +H          P          S  +
Sbjct: 40 GQESQMKLIYQGRLLQDPARTLSSLNITNNCVIHC-----HRSPPGAAVSGPSASSGPS 93

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	133
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.95
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.95
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.94
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	99.75
2lxa_A	87	Ubiquitin-like protein MDY2; ubiquitin-like domain	99.73
1wju_A	100	NEDD8 ultimate buster-1; ubiquitin-like domain, st	99.72
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	99.71
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	99.7
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	99.7
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	99.67
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	99.67
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	99.66
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	99.65
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	99.65
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	99.65
4a20_A	98	Ubiquitin-like protein MDY2; protein binding, GET-	99.64
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	99.64
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	99.64
3v6c_B	91	Ubiquitin; structural genomics, structural genomic	99.64
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	99.64
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	99.64
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	99.64
2uyz_B	79	Small ubiquitin-related modifier 1; sumoylation, c	99.64
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	99.64
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	99.62
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	99.62
4hcn_B	98	Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidas	99.62
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	99.62
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	99.61
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	99.61
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	99.61
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	99.61
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	99.4
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	99.61
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	99.6
1wyw_B	97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	99.6
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	99.6
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	99.59
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	99.59
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	99.59
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	99.58
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	99.58
4ajy_B	118	Transcription elongation factor B polypeptide 2; E	99.58
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	99.58
1we6_A	111	Splicing factor, putative; structural genomics, ub	99.57
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	99.57
3vdz_A	111	Ubiquitin-40S ribosomal protein S27A; gadolinium,	99.57
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	99.56
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	99.56
1se9_A	126	Ubiquitin family; ubiquitin-like, cell-free, wheat	99.56
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	99.56
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	99.55
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	99.55
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	99.54
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	99.54
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	99.54
2dzj_A	88	Synaptic glycoprotein SC2; ubiquitin-like fold, st	99.54
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.53
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	99.52
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	99.52
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	99.51
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	99.51
3u5c_f	152	40S ribosomal protein S31; translation, ribosome,	99.51
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	99.51
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	99.5
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	99.5
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.5
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	99.5
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	99.47
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	99.47
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	99.46
1wxv_A	92	BAG-family molecular chaperone regulator-1; struct	99.46
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.46
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	99.45
2kjr_A	95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	99.45
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	99.44
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	99.42
4b6w_A	86	Tubulin-specific chaperone; CAP-Gly, ubiquitin-lik	99.42
2kj6_A	97	Tubulin folding cofactor B; methods development, N	99.4
2daf_A	118	FLJ35834 protein; hypothetical protein FLJ35834, u	99.4
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	99.36
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	99.35
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	99.34
1v6e_A	95	Cytoskeleton-associated protein 1; tubulin-specifi	99.33
1wf9_A	107	NPL4 family protein; beta-grAsp fold like domain,	99.29
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	99.25
1wju_A	100	NEDD8 ultimate buster-1; ubiquitin-like domain, st	99.24
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	99.24
2lxa_A	87	Ubiquitin-like protein MDY2; ubiquitin-like domain	99.23
2kzr_A	86	Ubiquitin thioesterase OTU1; structural genomics,	99.22
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	99.22
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	99.21
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	99.16
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	99.15
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	99.15
4a20_A	98	Ubiquitin-like protein MDY2; protein binding, GET-	99.14
2uyz_B	79	Small ubiquitin-related modifier 1; sumoylation, c	99.13
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	99.12
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	99.12
3v6c_B	91	Ubiquitin; structural genomics, structural genomic	99.11
1se9_A	126	Ubiquitin family; ubiquitin-like, cell-free, wheat	99.1
2io1_B	94	Small ubiquitin-related modifier 3 precursor; SUMO	99.1
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	99.09
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	99.09
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	99.09
4ajy_B	118	Transcription elongation factor B polypeptide 2; E	99.09
1wyw_B	97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	99.08
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	99.08
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	99.08
2daf_A	118	FLJ35834 protein; hypothetical protein FLJ35834, u	99.08
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	99.07
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	98.64
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	99.06
1wm3_A	72	Ubiquitin-like protein SMT3B; ubiquitin fold, half	99.06
4hcn_B	98	Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidas	99.06
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	99.05
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	99.05
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	99.05
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	99.05
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	99.05
2io0_B	91	Small ubiquitin-related modifier 2 precursor; SUMO	99.04
4b6w_A	86	Tubulin-specific chaperone; CAP-Gly, ubiquitin-lik	99.04
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	99.04
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	99.04
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	99.03
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	99.02
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	99.02
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	99.02
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	99.02
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	99.02
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	99.01
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	99.01
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	99.01
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	98.99
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	98.99
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	98.99
3vdz_A	111	Ubiquitin-40S ribosomal protein S27A; gadolinium,	98.98
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	98.97
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	98.97
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	98.97
1we6_A	111	Splicing factor, putative; structural genomics, ub	98.96
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	98.96
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	98.96
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	98.95
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	98.94
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	98.93
3a4r_A	79	Nfatc2-interacting protein; ubiquitin fold, coiled	98.93
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	98.93
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	98.93
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	98.92
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	98.92
3u5c_f	152	40S ribosomal protein S31; translation, ribosome,	98.91
2d07_B	93	Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Ho	98.88
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	98.88
1wxv_A	92	BAG-family molecular chaperone regulator-1; struct	98.88
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	98.87
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	98.87
1wz0_A	104	Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-li	98.86
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	98.85
2k8h_A	110	Small ubiquitin protein; SUMO, post-translational	98.84
1wjn_A	97	Tubulin-folding protein TBCE; ubiquitin-like domai	98.84
2eke_C	106	Ubiquitin-like protein SMT3; UBC9, SUMO binding mo	98.79
2kjr_A	95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	98.79
2kj6_A	97	Tubulin folding cofactor B; methods development, N	98.74
2dzj_A	88	Synaptic glycoprotein SC2; ubiquitin-like fold, st	98.73
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	98.71
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	98.7
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	98.68
1v6e_A	95	Cytoskeleton-associated protein 1; tubulin-specifi	98.67
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	98.64
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	98.57
4efo_A	94	Serine/threonine-protein kinase TBK1; ubiquitin li	98.51
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	98.46
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	98.46
2io1_B	94	Small ubiquitin-related modifier 3 precursor; SUMO	98.43
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	98.35
1wm3_A	72	Ubiquitin-like protein SMT3B; ubiquitin fold, half	98.31
3kyd_D	115	Small ubiquitin-related modifier 1; SUMO, thioeste	98.3
1wf9_A	107	NPL4 family protein; beta-grAsp fold like domain,	98.28
2io0_B	91	Small ubiquitin-related modifier 2 precursor; SUMO	98.27
2d07_B	93	Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Ho	98.18
2kzr_A	86	Ubiquitin thioesterase OTU1; structural genomics,	98.11
3pge_A	200	SUMO-modified proliferating cell nuclear antigen;	98.1
3a4r_A	79	Nfatc2-interacting protein; ubiquitin fold, coiled	98.09
2pjh_A	80	Protein NPL4, nuclear protein localization protein	98.07
1wz0_A	104	Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-li	98.05
2eke_C	106	Ubiquitin-like protein SMT3; UBC9, SUMO binding mo	98.05
2k8h_A	110	Small ubiquitin protein; SUMO, post-translational	97.92
3goe_A	82	DNA repair protein RAD60; SUMO-like domain, sumoyl	97.91
3tix_A	207	Ubiquitin-like protein SMT3, RNA-induced transcri	97.89
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	97.87
3v7o_A	227	Minor nucleoprotein VP30; ssgcid, seattle structur	97.74
1wjn_A	97	Tubulin-folding protein TBCE; ubiquitin-like domai	97.72
3kyd_D	115	Small ubiquitin-related modifier 1; SUMO, thioeste	97.46
3pge_A	200	SUMO-modified proliferating cell nuclear antigen;	97.37
3uf8_A	209	Ubiquitin-like protein SMT3, peptidyl-prolyl CIS-	97.33
2kc2_A	128	Talin-1, F1; FERM, adhesion, cell membrane, cell p	97.25
3qx1_A	84	FAS-associated factor 1; UBX, protein binding, P97	97.16
3ix6_A	360	TS, tsase, thymidylate synthase; niaid, ssgcid, se	97.12
2jxx_A	97	Nfatc2-interacting protein; nuclear factor of acti	97.11
2dzk_A	109	UBX domain-containing protein 2; ubiquitin-like fo	97.04
3tix_A	207	Ubiquitin-like protein SMT3, RNA-induced transcri	97.01
3v7o_A	227	Minor nucleoprotein VP30; ssgcid, seattle structur	96.79
2al3_A	90	TUG long isoform; TUG UBL1 insulin, endocytosis/ex	96.78
4efo_A	94	Serine/threonine-protein kinase TBK1; ubiquitin li	96.76
4da1_A	389	Protein phosphatase 1K, mitochondrial; metal-ION-a	96.68
2l76_A	95	Nfatc2-interacting protein; ubiquitin-like domain,	95.98
1wj4_A	124	KIAA0794 protein; UBX domain, beta-grAsp fold, str	95.91
3ivf_A	371	Talin-1; FERM domain, cell membrane, cell projecti	95.83
3goe_A	82	DNA repair protein RAD60; SUMO-like domain, sumoyl	95.6
3ix6_A	360	TS, tsase, thymidylate synthase; niaid, ssgcid, se	95.18
2bps_A	81	YUKD protein; ubiquitin-like protein, ubiquitin; 2	95.13
2cr5_A	109	Reproduction 8; UBX domain, D0H8S2298E protein, st	95.12
3uf8_A	209	Ubiquitin-like protein SMT3, peptidyl-prolyl CIS-	95.06
1s3s_G	127	P47 protein; AAA ATPase, protein-protein complex,	94.73
2daj_A	91	KIAA0977 protein, COBL-like 1; ubiquitin-like doma	94.65
4da1_A	389	Protein phosphatase 1K, mitochondrial; metal-ION-a	94.49
2jxx_A	97	Nfatc2-interacting protein; nuclear factor of acti	93.57
2kvr_A	130	Ubiquitin carboxyl-terminal hydrolase 7; USP7, ubi	92.76
4e71_A	111	Plexin-B2, MM1; transmembrane, signaling, RBD, str	92.42
2juo_A	89	GA-binding protein alpha chain; OST, ubiquitin, tr	90.55
2l76_A	95	Nfatc2-interacting protein; ubiquitin-like domain,	90.39
2pjh_A	80	Protein NPL4, nuclear protein localization protein	88.89
3h6n_A	127	Plexin-D1; structural genomics consortium, SGC, me	88.84
1oey_A	83	P67-PHOX, neutrophil cytosol factor 2; immune syst	88.76
3qa8_A	676	MGC80376 protein; kinase ubiquitin-like domain, ph	88.68
2l32_A	74	Small archaeal modifier protein 2; protein BIN; NM	87.34
4eut_A	396	Serine/threonine-protein kinase TBK1; ATP binding,	86.82
2r2o_A	138	Plexin-B1; effector domain, structural genomics, s	86.45
3jyu_A	231	Ubiquitin carboxyl-terminal hydrolase; domain in u	85.19
1ryj_A	70	Unknown; beta/alpha protein, structural genomics,	84.11
2ylm_A	530	Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70	83.06
3ivf_A	371	Talin-1; FERM domain, cell membrane, cell projecti	80.86
2juo_A	89	GA-binding protein alpha chain; OST, ubiquitin, tr	80.85

>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=99.95  E-value=2.7e-29  Score=179.48  Aligned_cols=106  Identities=20%  Similarity=0.123  Sum_probs=100.0

Q ss_pred             CCcccCCCCCCeEEE-e-CCEECCCCCCccccccc-cccccccccc------cccCCCCCCCceeeccccCcHHHHHHHh
Q 040111            1 IEDKEGIPPGQQRSI-F-AGKQLEDGRTLADYKIQ-ESTLHLGWRA------DFCKNPDPQNITLEVESSDTIDNVKAKI   71 (133)
Q Consensus         1 I~~~~gip~~~Q~Li-~-~gk~L~D~~tL~~ygI~-~stl~L~~~~------i~Vk~~~g~~~~l~V~~~~tV~~LK~~I   71 (133)
                      |++.+|||+++|+|+ | +|++|+|+.+|++|||. +++++|+++.      ++|++.+|+++.+++++++||++||++|
T Consensus        32 I~~~~gip~~~QrL~~~~~g~~L~d~~tL~~y~i~~~~~l~l~~~~~~~~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i  111 (159)
T 3rt3_B           32 ITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDKSDEPLSILVRNNKGRSSTYEVRLTQTVAHLKQQV  111 (159)
T ss_dssp             HHHHHCCCGGGEEEEEETTCCBCCTTSCGGGGTCCTTCEEEEEECCCCCCEEEEEECTTSCEEEEEECTTSBHHHHHHHH
T ss_pred             HHHHhCCCHHHEEEEEcCCCCCCCCCCCHHHcCCCCCCEEEEEccCCCCcEEEEEECCCCCEEEEEeCCCCCHHHHHHHH
Confidence            456789999999999 9 79999999999999999 9999999983      8999999999999999999999999999


Q ss_pred             hhhcCCCCCceEEEeCCcccCccccccccccEEeE
Q 040111           72 QDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVG  106 (133)
Q Consensus        72 ~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~  106 (133)
                      ++++|+|+++|+|+|+|+.|+|+.+|++|+|...+
T Consensus       112 ~~~~gip~~~q~L~~~G~~L~d~~tL~~y~i~~g~  146 (159)
T 3rt3_B          112 SGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLS  146 (159)
T ss_dssp             HHHHTCCGGGEEEEETTEECCTTSBGGGGTCCTTC
T ss_pred             HHHHCCCHHHEEEEECCeecCCCCCHHHcCCCCCC
Confidence            99999999999999999999999999999985444

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

Probab=99.95  E-value=9.9e-29  Score=178.99  Aligned_cols=109  Identities=56%  Similarity=0.704  Sum_probs=102.0

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc-----cccCCCCCCCceeeccccCcHHHHHHHhhhh
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA-----DFCKNPDPQNITLEVESSDTIDNVKAKIQDK   74 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~-----i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~   74 (133)
                      |++++|||+++|+|+|+|++|+|+.+|++|||. +++|+|+++.     ++|++.+|+++.+++++++||.+||++|+++
T Consensus        50 I~~~~gip~~~QrL~~~g~~L~d~~tL~~~~i~~~~~l~l~~~~~gg~~i~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~  129 (172)
T 3u30_A           50 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDK  129 (172)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTCBTGGGTCCTTCEEEEEECCCCCEEEEEEESSCCEEEEEECTTCBHHHHHHHHHHH
T ss_pred             HHHHHCcChHHEEEEECCccccccCCHhHcCCcccceeeeeecccccccceeecccCcceeEEecCCCCHHHHHHHHHHH
Confidence            456789999999999999999999999999999 9999999886     8999999999999999999999999999999


Q ss_pred             cCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           75 KRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        75 ~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      +|+|+++|+|+|+|+.|+|+.+|++|++...+.+.
T Consensus       130 ~gip~~~q~L~~~g~~L~D~~tL~~y~i~~g~tl~  164 (172)
T 3u30_A          130 EGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLH  164 (172)
T ss_dssp             HCCCGGGCCEEETTEECCTTSBSGGGTCCTTCEEE
T ss_pred             hCCCceeEEEEECCccCCCCCcHHHhCCCCCCEEE
Confidence            99999999999999999999999999986555443

>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=99.94  E-value=2.3e-27  Score=167.25  Aligned_cols=108  Identities=56%  Similarity=0.711  Sum_probs=100.3

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc-----cccCCCCCCCceeeccccCcHHHHHHHhhhh
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA-----DFCKNPDPQNITLEVESSDTIDNVKAKIQDK   74 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~-----i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~   74 (133)
                      |++++|+|+++|+|+|+|++|+|+.+|++|||. ++++++..+.     ++|++.+|+++.+++++++||++||++|+++
T Consensus        30 i~~~~gip~~~q~L~~~g~~L~d~~tL~~~~i~~~~~l~l~~~~~~~~~i~Vk~~~g~~~~~~v~~~~tv~~lK~~i~~~  109 (152)
T 3b08_A           30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDK  109 (152)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCTTCEEEEEEESSSCEEEEEECTTCBHHHHHHHHHHH
T ss_pred             HHHHHCcChHHeEEEECCeECcCcccHHHhccCCCCeeEEEeecccccceeeeecCCCEEEEEeCCCCcHHHHHHHHHHH
Confidence            356789999999999999999999999999999 9999999875     8899999999999999999999999999999


Q ss_pred             cCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           75 KRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        75 ~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      .|+|+++|+|+|+|+.|+|+.+|++|++...+.+
T Consensus       110 ~gi~~~~qrL~~~g~~L~d~~tL~~~~i~~~~~i  143 (152)
T 3b08_A          110 EGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTL  143 (152)
T ss_dssp             HCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEE
T ss_pred             hCcChhhEEEEECCEECCCCCCHHHcCCCCCCEE
Confidence            9999999999999999999999999998654433

>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=99.75  E-value=5.4e-19  Score=116.38  Aligned_cols=63  Identities=6%  Similarity=-0.086  Sum_probs=60.6

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVG  106 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~  106 (133)
                      |+||+++|+++.++++|++||.+||++|++++|+||++|||+|+|++|+|+.+|+||+|...+
T Consensus        24 I~Vk~~~Gkk~~v~v~p~DTI~~LK~~I~~k~Gip~~qQrLif~Gk~LkD~~TL~dY~I~dgs   86 (93)
T 3plu_A           24 VVVNDRLGKKVRVKCLGEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHISLEDYEVHDQT   86 (93)
T ss_dssp             EEEECTTSCEEEEEEETTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBTGGGTCCTTC
T ss_pred             EEEECCCCCEEEEEECCcCHHHHHHHHHHHHhCCCHHHEEEEeCCEEccCcCCHHHcCCCCCC
Confidence            999999999999999999999999999999999999999999999999999999999997544

>2lxa_A Ubiquitin-like protein MDY2; ubiquitin-like domain, protein-protein interaction, SGT2 BIN domain, GET pathway, protein binding; NMR {Saccharomyces cerevisiae}

Probab=99.73  E-value=7.9e-19  Score=114.58  Aligned_cols=75  Identities=20%  Similarity=0.085  Sum_probs=65.8

Q ss_pred             cccccCCCCCCCceeecc--ccCcHHHHHHHh-hhhcCCCCCceEEEeCCcccCcccccccccc-EEeEEEEeCceeee
Q 040111           42 RADFCKNPDPQNITLEVE--SSDTIDNVKAKI-QDKKRIPPPAEADLLKFPFFFFEEVLSFFWF-VVVGVIFCGCRVNF  116 (133)
Q Consensus        42 ~~i~Vk~~~g~~~~l~V~--~~~tV~~LK~~I-~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~-~~~~~~~~~~~~~~  116 (133)
                      .+|+||+++|++++++++  +++||.++|++| ++++|+|+++|||+|+|+.|+|+.+|++|+| ...+.+.+-+..|+
T Consensus         2 mqI~VKtl~g~~~~i~v~v~~~~TV~~lK~~I~~~~~gip~~~QrLi~~Gk~L~D~~tL~~y~I~~~~stl~v~~~~~~   80 (87)
T 2lxa_A            2 VHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKPNL   80 (87)
T ss_dssp             CEEEEEECSSSCEECCEECCTTCBHHHHHHHHHHTTSCSSSTTEEEEETTEECCTTCBHHHHCCCGGGCEEEEEECCCC
T ss_pred             EEEEEEcCCCCEEEEEEcCCCCCcHHHHHHHHHHHhcCCChHHEEEEECCEECcCcCCHHHcCCCCCCCEEEEEcCCCc
Confidence            358999999999988866  999999999999 9999999999999999999999999999999 46666666555554

>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=99.72  E-value=4.5e-18  Score=113.60  Aligned_cols=59  Identities=10%  Similarity=-0.068  Sum_probs=55.3

Q ss_pred             CCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           51 PQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        51 g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      ++.+.++|++++||.+||++|++++|+||++|+|+|+|++|+|+.||++|+|...+.|+
T Consensus        29 ~~~~~lev~~~~TV~~lK~kI~~k~gip~~qQrLI~~GKiL~D~~TL~~y~I~~gsti~   87 (100)
T 1wju_A           29 DRKNLLETRLHITGRELRSKIAETFGLQENYIKIVINKKQLQLGKTLEEQGVAHNVKAM   87 (100)
T ss_dssp             SSSEEEEEESSSBHHHHHHHHHHHTTCCSTTCEEEETTEECCTTSBHHHHTCCSSEEEE
T ss_pred             CcEEEEEeCCcCHHHHHHHHHHHHHCcCHHHeEEEeCCeECCCCCcHHHcCCCCCCEEE
Confidence            67899999999999999999999999999999999999999999999999998766554

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

Probab=99.71  E-value=4.3e-18  Score=110.27  Aligned_cols=74  Identities=16%  Similarity=0.107  Sum_probs=60.0

Q ss_pred             cccccccccc-----cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           34 ESTLHLGWRA-----DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        34 ~stl~L~~~~-----i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      +++++++++.     ++||+.+|+++.+++++++||++||++|++++|+|+++|+|+|+|+.|+|+.+|++|++ ..+.+
T Consensus         5 ~~~~~~~~~~~~~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i-~g~~i   83 (88)
T 4eew_A            5 NDSTSTAVEEPDSLEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVI   83 (88)
T ss_dssp             ----------CCEEEEEEEETTSCEEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGGTC-TTEEE
T ss_pred             CCceEEeecCCCeEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEECCCCCcHHHcCC-CCcEE
Confidence            5566665543     89999999999999999999999999999999999999999999999999999999998 44433

>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=99.70  E-value=5e-18  Score=113.37  Aligned_cols=65  Identities=12%  Similarity=0.028  Sum_probs=61.2

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGV  107 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~  107 (133)
                      .|+||+++|+++.+++++++||.+||++|++++|+|+++|||+|+|++|+|+.+|++|+|...+.
T Consensus        30 ~I~VKtl~Gk~i~lev~p~dTV~~lK~~Ia~k~Gip~~qQrLi~~Gk~L~D~~TL~dygI~~gst   94 (100)
T 1uh6_A           30 EVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSLGDYEIHDGMN   94 (100)
T ss_dssp             EEEEECSSSSCEEEEEETTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCSSCBHHHHTCCTTEE
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhCCCHHHEEEEECCEECCCCCCHHHcCCCCCCE
Confidence            39999999999999999999999999999999999999999999999999999999999865543

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

Probab=99.70  E-value=7.6e-18  Score=106.96  Aligned_cols=67  Identities=12%  Similarity=0.067  Sum_probs=62.1

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      .|+||+.+|+++.+++++++||++||++|++++|+|+++|+|+|+|+.|+|+.+|++|++...+.+.
T Consensus         6 ~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~l~   72 (79)
T 3phx_B            6 SILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVF   72 (79)
T ss_dssp             EEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEE
T ss_pred             EEEEEeCCCCEEEEEECCcChHHHHHHHHHhhcCCCHHHEEEEECCEECCCCCcHHHCCCCCCCEEE
Confidence            3899999999999999999999999999999999999999999999999999999999987655443

>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=99.67  E-value=2.1e-17  Score=107.42  Aligned_cols=66  Identities=17%  Similarity=0.263  Sum_probs=61.0

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      .|+|++.+|+++.+++++++||++||++|++++|+|+++|+|+|+|+.|+|+.+|++|+|...+.+
T Consensus         2 ~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~l   67 (88)
T 4fbj_B            2 LIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVL   67 (88)
T ss_dssp             EEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBTTTTTCCTTCEE
T ss_pred             EEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHCcChhHEEEEECCeECCCCCcHHHcCCCCCCEE
Confidence            378999999999999999999999999999999999999999999999999999999998655433

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

Probab=99.67  E-value=1.1e-17  Score=108.15  Aligned_cols=66  Identities=21%  Similarity=0.180  Sum_probs=61.5

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcc-cCccccccccccEEeEEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPF-FFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~-L~d~~tL~dy~~~~~~~~  108 (133)
                      +|+|++.+|+++.+++++++||++||++|++++|+|+++|+|+|+|++ |+|+.+|++|++...+.+
T Consensus        12 ~i~vk~l~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~lL~D~~tL~~y~I~~gs~i   78 (84)
T 2kk8_A           12 KFLVENLNGSSFELEVDYRDTLLVVKQKIERSQHIPVSKQTLIVDGIVILREDLTVEQCQIVPTSDI   78 (84)
T ss_dssp             EEEEEETTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCCSSSBHHHHTCCTTSCE
T ss_pred             EEEEEecCCcEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCEEecCCcCCHHHcCCCCCCEE
Confidence            489999999999999999999999999999999999999999999999 999999999998655543

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

Probab=99.66  E-value=4e-17  Score=109.01  Aligned_cols=85  Identities=13%  Similarity=0.139  Sum_probs=60.2

Q ss_pred             CCCccccccc-cccccccccc---cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccc
Q 040111           24 GRTLADYKIQ-ESTLHLGWRA---DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSF   99 (133)
Q Consensus        24 ~~tL~~ygI~-~stl~L~~~~---i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~d   99 (133)
                      +...++|.|. -..+.+....   |+|++ +|+.+.+++++++||++||++|++++|+|+++|+|+|+|+.|+|+.+|++
T Consensus         7 ~~~~~~~~~~~t~~l~l~~~m~i~I~Vk~-~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~   85 (101)
T 3m63_B            7 HHPMSDYDIPTTENLYFQGAMSLNIHIKS-GQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVES   85 (101)
T ss_dssp             ----------------------CCEEEEC-SSCCCCBCCCTTSBHHHHHHHHHHHHSCCSTTCCEEETTEECCTTSBTTT
T ss_pred             cCCccccCCCcceeecccCCcEEEEEEEE-CCEEEEEEeCCCCCHHHHHHHHHHHHCcChHHEEEEECCEECCCcCcHHH
Confidence            3456788877 4444433332   78887 88999999999999999999999999999999999999999999999999


Q ss_pred             cccEEeEEEE
Q 040111          100 FWFVVVGVIF  109 (133)
Q Consensus       100 y~~~~~~~~~  109 (133)
                      |++...+.|.
T Consensus        86 ~gI~~g~tI~   95 (101)
T 3m63_B           86 YHIQDGHSVH   95 (101)
T ss_dssp             TTCCTTEEEE
T ss_pred             CCCCCCCEEE
Confidence            9997665544

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

Probab=99.65  E-value=5.3e-17  Score=105.56  Aligned_cols=71  Identities=34%  Similarity=0.344  Sum_probs=62.2

Q ss_pred             cccccccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           38 HLGWRADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        38 ~L~~~~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      ||....++|++.+|+++.+++++++||++||++|++++|+|+++|+|+|+|+.|+|+.+|++|++.+.+.+
T Consensus         6 ~~~~~~i~v~~~~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i   76 (88)
T 1sif_A            6 HLQGLQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTL   76 (88)
T ss_dssp             ----CEEEEEETTSCEEEEECCTTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBSGGGTCCTTCEE
T ss_pred             cccceEEEEEeCCCCEEEEEECCCChHHHHHHHHHHHHCcChhhEEEEECCEECCCCCcHHHcCCCCCCEE
Confidence            34455699999999999999999999999999999999999999999999999999999999998655443

>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=99.65  E-value=7.5e-17  Score=104.75  Aligned_cols=65  Identities=18%  Similarity=0.130  Sum_probs=60.4

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      .|+||+.+|+++.++|++++||.+||++|++++|+|+++|+|+|+|+.|+|+.+|++|++ ..+.+
T Consensus         7 ~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~d~~tL~~~~i-~g~~i   71 (90)
T 4dwf_A            7 EVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVI   71 (90)
T ss_dssp             EEEEEETTCCEEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGGTC-TTEEE
T ss_pred             EEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCeECCCCCCHHHcCC-CCcEE
Confidence            389999999999999999999999999999999999999999999999999999999998 44443

>3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=99.65  E-value=6.6e-17  Score=108.71  Aligned_cols=67  Identities=15%  Similarity=0.038  Sum_probs=62.3

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      .|+||+.+|+.+.++|++++||.+||++|++++|+|+++|+|+|+|+.|+|+.+|++|+|...+.|.
T Consensus         3 ~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~~i~~g~~i~   69 (106)
T 3m62_B            3 SLTFKNFKKEKVPLDLEPSNTILETKTKLAQSISCEESQIKLIYSGKVLQDSKTVSECGLKDGDQVV   69 (106)
T ss_dssp             CEEEECTTCCEEEECCCTTSBHHHHHHHHHHTTTSCGGGCEEEETTEECCTTSBTTTTTCCTTCEEE
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCChhhEEEEECCEECCCcCCHHHcCCCCCCEEE
Confidence            4889999999999999999999999999999999999999999999999999999999997665443

>4a20_A Ubiquitin-like protein MDY2; protein binding, GET-pathway, tail-anchored proteins; 1.78A {Saccharomyces cerevisiae} PDB: 2lxc_A 4goc_A

Probab=99.64  E-value=6.7e-17  Score=107.56  Aligned_cols=64  Identities=19%  Similarity=0.087  Sum_probs=57.9

Q ss_pred             cccCCCCCCCcee--eccccCcHHHHHHHh-hhhcCCCCCceEEEeCCcccCcccccccccc-EEeEE
Q 040111           44 DFCKNPDPQNITL--EVESSDTIDNVKAKI-QDKKRIPPPAEADLLKFPFFFFEEVLSFFWF-VVVGV  107 (133)
Q Consensus        44 i~Vk~~~g~~~~l--~V~~~~tV~~LK~~I-~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~-~~~~~  107 (133)
                      |+||+++|+.+++  ++++++||.+||++| ++..|+|+++|||+|+|+.|+|+.+|++|+| ...+.
T Consensus        22 I~VKtl~g~~~~i~v~v~~~~TV~~lK~~I~~~~~gip~~~QrLi~~Gk~L~D~~tL~dy~I~~~g~t   89 (98)
T 4a20_A           22 LTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANST   89 (98)
T ss_dssp             EEEEECSSSCEEEEEEECTTCBHHHHHHHHHHTTSCSCGGGEEEEETTEEECTTCBGGGSCCBTTBCE
T ss_pred             EEEEcCCCCEEEEEEecCCCChHHHHHHHHHHHhcCCChhhEEEEECCEECcCcCCHHHcCcCCCCCE
Confidence            8999999998777  455999999999999 8888999999999999999999999999999 54443

>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure, northeast structural genomics consortium, protein structure initiative, NESG; NMR {Homo sapiens}

Probab=99.64  E-value=5.1e-17  Score=105.57  Aligned_cols=66  Identities=11%  Similarity=0.033  Sum_probs=60.9

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      .|+|++.+|+++.+++++++||++||++|++++|+|+++|+|+|+|+.|+|+.+|++|+|...+.+
T Consensus         6 ~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~~I~~g~~i   71 (88)
T 2hj8_A            6 SILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTV   71 (88)
T ss_dssp             EEEEEETTSCEEEEEEESSSBHHHHHHHHHHHTCSCTTTEEEESSSSCCCTTSBHHHHHCSTTCEE
T ss_pred             EEEEECCCCCEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEECCEECCCCCcHHHcCCCCCCEE
Confidence            388999999999999999999999999999999999999999999999999999999998655444

>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=99.64  E-value=1e-16  Score=100.20  Aligned_cols=67  Identities=16%  Similarity=0.258  Sum_probs=61.3

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      .|+|++.+|+++.+++++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++|++.+.+.+.
T Consensus         2 ~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~~i~~~~q~L~~~g~~L~d~~tL~~~~i~~g~~i~   68 (76)
T 1ndd_A            2 LIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLH   68 (76)
T ss_dssp             EEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEE
T ss_pred             EEEEECCCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCEECCCCCcHHHcCCCCCCEEE
Confidence            3789999999999999999999999999999999999999999999999999999999986555443

>3v6c_B Ubiquitin; structural genomics, structural genomics consortium, SGC, UB protease, hydrolase-signaling protein complex; 1.70A {Homo sapiens} PDB: 3v6e_B

Probab=99.64  E-value=9e-17  Score=104.83  Aligned_cols=66  Identities=38%  Similarity=0.390  Sum_probs=61.9

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      |+||+.+|+++.+++++++||.+||++|++++|+|+++|+|+|+|+.|+|+.+|++|+|...+.+.
T Consensus        20 i~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~   85 (91)
T 3v6c_B           20 IFVNTLTGTHITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLH   85 (91)
T ss_dssp             EEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTCBTGGGTCCTTCEEE
T ss_pred             EEEEeCCCCEEEEEECCCCCHHHHHHHHHhhhCCChhhEEEEECCeECCCcCcHHHCCCCCCCEEE
Confidence            899999999999999999999999999999999999999999999999999999999997655444

>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=99.64  E-value=7.5e-17  Score=103.96  Aligned_cols=67  Identities=16%  Similarity=0.257  Sum_probs=62.4

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEEe
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~~  110 (133)
                      |+|++.+|+++.+++++++||.+||++|++++|+|+++|+|+|+|+.|+|+.+|++|+|...+.+.+
T Consensus        15 i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~i~l   81 (88)
T 3dbh_I           15 IKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHL   81 (88)
T ss_dssp             EEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCCEEETTEECCTTSBGGGGTCCTTCEEEE
T ss_pred             EEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHCcCHHHEEEEECCeECCCCCcHHHcCCCCCCEEEE
Confidence            8999999999999999999999999999999999999999999999999999999999876655543

>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=99.64  E-value=9.2e-17  Score=101.55  Aligned_cols=66  Identities=12%  Similarity=0.071  Sum_probs=60.4

Q ss_pred             ccccCCCCCCCc-eee-ccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           43 ADFCKNPDPQNI-TLE-VESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        43 ~i~Vk~~~g~~~-~l~-V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      .|+|++.+|+++ .++ +++++||++||++|++++|+|+++|+|+|+|+.|+|+.+|++|++...+.+
T Consensus         4 ~i~Vk~~~g~~~~~l~~v~~~~tv~~lK~~i~~~~gip~~~qrL~~~g~~L~d~~tL~~~~i~~g~~i   71 (78)
T 2faz_A            4 WIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTI   71 (78)
T ss_dssp             EEEEEETTSSCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTTTTTCCTTCEE
T ss_pred             EEEEEECCCCEEEEEeccCCCCCHHHHHHHHHHHHCcChhhEEEEECCEECCCCCCHHHcCCCCCCEE
Confidence            378999999985 999 999999999999999999999999999999999999999999998655444

>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=99.64  E-value=1.2e-16  Score=102.22  Aligned_cols=65  Identities=40%  Similarity=0.409  Sum_probs=60.6

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      |+|++.+|+++.+++++++||.+||++|++++++|+++|+|+|+|+.|+|+.+|++|++...+.+
T Consensus         6 i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~~i~~~~qrL~~~g~~L~d~~tL~~~~i~~~~~l   70 (85)
T 3mtn_B            6 IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKWSTL   70 (85)
T ss_dssp             EEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBTGGGTCCTTCEE
T ss_pred             EEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHCcChHHEEEEECCEECCCCCCHHHcCCCCCCEE
Confidence            88999999999999999999999999999999999999999999999999999999998654433

>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=99.64  E-value=8e-17  Score=102.16  Aligned_cols=66  Identities=12%  Similarity=0.043  Sum_probs=61.3

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      .|+|++.+|+++.++|++++||.+||++|+++.|+|+++|+|+|+|++|+|+.||++|++.....|
T Consensus         5 ~i~vk~~~g~~~~~~v~~~~tv~~lk~~i~~~~gi~~~~qrL~~~G~~L~d~~tl~~~~i~~~~~i   70 (79)
T 2uyz_B            5 KLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVI   70 (79)
T ss_dssp             EEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCHHHHTCCTTEEE
T ss_pred             EEEEECCCCCEEEEEECCCChHHHHHHHHHHHHCCCcccEEEEECCEEeCCCCCHHHcCCCCCCEE
Confidence            388999999999999999999999999999999999999999999999999999999998655543

>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=99.64  E-value=7.3e-17  Score=103.28  Aligned_cols=63  Identities=38%  Similarity=0.337  Sum_probs=59.4

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVG  106 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~  106 (133)
                      |+|++.+|+++.+++++++||.+||++|++++++|+++|+|+|+|+.|+|+.+|++|++...+
T Consensus         6 i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~~ip~~~qrL~~~g~~L~d~~tL~~~~i~~~~   68 (85)
T 3n3k_B            6 IVVKTLMGRTIILEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIHNHS   68 (85)
T ss_dssp             EEEECGGGCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETBEECCTTCBTTTTTCCTTC
T ss_pred             EEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCeECCCCCCHHHCCCCCCC
Confidence            889999999999999999999999999999999999999999999999999999999985444

>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=99.62  E-value=2.7e-16  Score=103.53  Aligned_cols=68  Identities=12%  Similarity=0.174  Sum_probs=62.2

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhh---cCCCCCceEEEeCCcccCccccccccccEEeEEEEe
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDK---KRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~---~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~~  110 (133)
                      .|+||+.+|+.+.+++++++||++||++|++.   +|+|+++|+|+|+|+.|+|+.+|++|+|...+.+.+
T Consensus         2 ~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~~~~gip~~~qrLi~~Gk~L~D~~tL~~ygI~~g~~i~l   72 (95)
T 1uel_A            2 QVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVV   72 (95)
T ss_dssp             EEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEETTEECCTTSBGGGGTCCSSSEEEE
T ss_pred             EEEEEeCCCCEEEEEECCCCHHHHHHHHHHhhcccCCCChhhEEEEECCEECCCcCcHHHCCCCCCCEEEE
Confidence            37899999999999999999999999999999   899999999999999999999999999976665543

>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=99.62  E-value=1.8e-16  Score=101.60  Aligned_cols=67  Identities=12%  Similarity=0.132  Sum_probs=61.3

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhh---cCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDK---KRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~---~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      .|+|++.+|+.+.+++++++||++||++|+++   +|+|+++|+|+|+|+.|+|+.+|++|++...+.+.
T Consensus         7 ~i~vk~~~g~~~~~~v~~~~TV~~lK~~i~~~~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~i~   76 (85)
T 2wyq_A            7 TITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVV   76 (85)
T ss_dssp             EEEEEETTSCEEEEEECTTSBHHHHHHHHHHHHCTTTCCGGGEEEEETTEECCTTSBGGGGCCCTTSEEE
T ss_pred             EEEEEECCCCEEEEEECCCCCHHHHHHHHHhhccccCCCHHHeEEEECCEECcCCCCHHHcCCCCCCEEE
Confidence            38899999999999999999999999999998   89999999999999999999999999987655443

>4hcn_B Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidase, NEDD8, protein binding; 2.60A {Saccharomyces cerevisiae}

Probab=99.62  E-value=2.1e-16  Score=104.61  Aligned_cols=66  Identities=41%  Similarity=0.419  Sum_probs=61.7

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      |+||+.+|+.+.++|++++||.+||++|++++|+|+++|+|+|+|+.|+|+.+|++|+|...+.|.
T Consensus        25 I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~i~   90 (98)
T 4hcn_B           25 IFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLH   90 (98)
T ss_dssp             EEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTCBSGGGTCCTTEEEE
T ss_pred             EEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEECCEECCCCCcHHHCCCCCCCEEE
Confidence            899999999999999999999999999999999999999999999999999999999987655444

>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=99.62  E-value=2.1e-16  Score=101.88  Aligned_cols=64  Identities=17%  Similarity=0.173  Sum_probs=59.8

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGV  107 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~  107 (133)
                      |+|++.+|+++.+++++++||++||++|++++|+|+++|+|+|+|+.|+|+.+|++|++...+.
T Consensus        10 i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~qrL~~~Gk~L~d~~tL~~~~i~~g~~   73 (87)
T 1wh3_A           10 VFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGLGIYGIQDSDT   73 (87)
T ss_dssp             EEEEETTTEEEEEEECSSSBHHHHHHHHHHHTCCCTTTEEEEETTEECCSSSBHHHHTCCTTEE
T ss_pred             EEEEcCCCCEEEEEeCCCChHHHHHHHHHHHhCCChHHEEEEECCEEccCCCCHHHCCCCCCCE
Confidence            8899999999999999999999999999999999999999999999999999999999854443

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.61  E-value=2.6e-16  Score=103.71  Aligned_cols=64  Identities=19%  Similarity=0.125  Sum_probs=59.1

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCcc-ccccccccEEeEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFE-EVLSFFWFVVVGVI  108 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~-~tL~dy~~~~~~~~  108 (133)
                      |+||++++ ++.++|++++||.+||++|++++|+|+++|+|+|+|+.|+|+ .+|++|++...+.+
T Consensus        18 I~Vk~~~~-~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~~tL~~ygI~~gstl   82 (94)
T 2kan_A           18 VTVKFPSK-QFTVEVDRTETVSSLKDKIHIVENTPIKRMQLYYSGIELADDYRNLNEYGITEFSEI   82 (94)
T ss_dssp             EEEECSSC-EEEEEECTTCBHHHHHHHHHHHSSSCTTTEEEEETTEEECCTTSBHHHHTCCTTEEE
T ss_pred             EEEEcCCc-EEEEEECCCCcHHHHHHHHHHHHCcCHHHEEEEECCEECCCCcccHHHCCCCCCCEE
Confidence            88999877 889999999999999999999999999999999999999999 99999998655544

>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=99.61  E-value=2.5e-16  Score=98.46  Aligned_cols=67  Identities=39%  Similarity=0.398  Sum_probs=61.1

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      .++|++.+|+++.+++++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++|++...+.+.
T Consensus         2 ~i~vk~~~g~~~~i~v~~~~tv~~lK~~i~~~~~i~~~~q~L~~~g~~L~d~~tL~~~~i~~g~~i~   68 (76)
T 3a9j_A            2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLH   68 (76)
T ss_dssp             EEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTGGGTCCTTCEEE
T ss_pred             EEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCeECCCCCcHHHcCCCCCCEEE
Confidence            3788999999999999999999999999999999999999999999999999999999986555443

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

Probab=99.61  E-value=2.6e-16  Score=99.80  Aligned_cols=66  Identities=15%  Similarity=0.086  Sum_probs=60.7

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      ++|++.+|+.+.+++++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++|++...+.+.
T Consensus        10 i~vk~~~g~~~~~~v~~~~tV~~LK~~i~~~~~i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~   75 (81)
T 2dzi_A           10 LTVKALQGRECSLQVPEDELVSTLKQLVSEKLNVPVRQQRLLFKGKALADGKRLSDYSIGPNSKLN   75 (81)
T ss_dssp             EEEEETTSCEEEEEECSSCBHHHHHHHHHHHTCCCTTTCEEEETTEECCTTSBGGGGTCCSSBCCE
T ss_pred             EEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHEEEEECCeECCCCCcHHHcCCCCCCEEE
Confidence            788888899999999999999999999999999999999999999999999999999997655443

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

Probab=99.61  E-value=3.1e-16  Score=103.57  Aligned_cols=77  Identities=36%  Similarity=0.343  Sum_probs=62.9

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE-----eCceeeee
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF-----CGCRVNFW  117 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~-----~~~~~~~~  117 (133)
                      .|+|++++|+++.+++++++||++||++|++..|+|+++|+|+|+|+.|+|+.+|++|++.+.+.|.     .||.--+|
T Consensus         2 ~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~gi~~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~gG~~i~~   81 (98)
T 1yx5_B            2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGRDPNS   81 (98)
T ss_dssp             EEEEEETTSCEEEEECCTTCBHHHHHHHHHHHTCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCCCC-----
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEeCCCCCcCcc
Confidence            3789999999999999999999999999999999999999999999999999999999986555443     56666777


Q ss_pred             ec
Q 040111          118 NA  119 (133)
Q Consensus       118 ~~  119 (133)
                      .-
T Consensus        82 ~~   83 (98)
T 1yx5_B           82 SS   83 (98)
T ss_dssp             --
T ss_pred             cc
Confidence            53

>3b1l_X E3 ubiquitin-protein ligase parkin; proteasome, ALFA-beta-protein; 1.85A {Mus musculus} PDB: 1mg8_A 2zeq_A 2knb_A 1iyf_A

Probab=99.40  E-value=4.9e-17  Score=102.25  Aligned_cols=68  Identities=10%  Similarity=0.073  Sum_probs=63.1

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEEe
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~~  110 (133)
                      +|+|++.+|+++.+++++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++|++...+.+.+
T Consensus         2 ~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l   69 (76)
T 3b1l_X            2 IVFVRFNSSYGFPVEVDSDTSILQLKEVVAKQQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHI   69 (76)
Confidence            47899999999999999999999999999999999999999999999999999999999987765544

>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=99.61  E-value=3.2e-16  Score=102.78  Aligned_cols=64  Identities=41%  Similarity=0.404  Sum_probs=59.7

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVG  106 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~  106 (133)
                      .|+|++.+|+++.+++++++||.+||++|++++|+|+++|+|+|+|+.|+|+.+|++|++...+
T Consensus         3 ~i~vk~~~g~~~~~~v~~~~TV~~LK~~i~~~~gip~~~qrL~~~G~~L~d~~tL~~~~i~~~~   66 (96)
T 3k9o_B            3 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKES   66 (96)
T ss_dssp             EEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTC
T ss_pred             EEEEEeCCCCEEEEEECCCCCHHHHHHHHHhhhCCChhHEEEEECCEECCCCCcHHHcCCCCCC
Confidence            3789999999999999999999999999999999999999999999999999999999985443

>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling proteins; 1.15A {Saccharomyces cerevisiae} SCOP: d.15.1.1 PDB: 2bwe_S

Probab=99.60  E-value=2.5e-16  Score=98.96  Aligned_cols=66  Identities=11%  Similarity=0.086  Sum_probs=60.5

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      .++|++ +|+.+.+++++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++|++...+.+.
T Consensus         6 ~i~vk~-~g~~~~~~v~~~~tV~~LK~~i~~~~~i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~   71 (77)
T 2bwf_A            6 NIHIKS-GQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVH   71 (77)
T ss_dssp             EEEEEE-TTEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEE
T ss_pred             EEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHhCCCHHHEEEEECCeEcCCCCCHHHcCCCCCCEEE
Confidence            478888 888999999999999999999999999999999999999999999999999997665544

>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=99.60  E-value=2.7e-16  Score=104.04  Aligned_cols=65  Identities=12%  Similarity=0.046  Sum_probs=60.8

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      |+|++.+|+++.++|++++||.+||++|+++.|+|+++|+|+|+|+.|+|+.+|++|+|.....|
T Consensus        24 I~Vk~~~g~~~~l~v~~~~tv~~lK~~i~~~~gip~~~qrLif~Gk~L~d~~tl~dy~i~~g~~I   88 (97)
T 1wyw_B           24 LKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVI   88 (97)
T ss_dssp             EEEECTTCCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCHHHHTCCTTCEE
T ss_pred             EEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCChhhEEEEECCeEcCCCCCHHHCCCCCCCEE
Confidence            89999999999999999999999999999999999999999999999999999999998654433

>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=99.60  E-value=6.9e-16  Score=105.57  Aligned_cols=60  Identities=8%  Similarity=0.016  Sum_probs=56.6

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhh------hcCC--CCCceEEEeCCcccCccccccccccE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQD------KKRI--PPPAEADLLKFPFFFFEEVLSFFWFV  103 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~------~~gI--p~~~q~L~~~gk~L~d~~tL~dy~~~  103 (133)
                      |+||+++|++++++|++++||++||++|++      ++|+  |+++|||+|+|++|+|+.+|++|+|.
T Consensus        19 I~vKtl~G~t~~lev~~s~TV~~lK~kI~~~~p~dwke~~p~p~~qqrLIy~GK~LeD~~TL~~y~I~   86 (116)
T 1wgh_A           19 LRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLP   86 (116)
T ss_dssp             EEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEEETTEEECSSCBTTTTTCC
T ss_pred             EEEEeCCCCEEEEEECCcCHHHHHHHHHHHhcccccccCCCCChHHEEEEECCcCCCCCCcHHHcCCC
Confidence            899999999999999999999999999999      6675  69999999999999999999999974

>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=99.59  E-value=5.7e-16  Score=100.28  Aligned_cols=64  Identities=11%  Similarity=0.065  Sum_probs=59.0

Q ss_pred             cccCCCCC-CCcee-eccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEE
Q 040111           44 DFCKNPDP-QNITL-EVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGV  107 (133)
Q Consensus        44 i~Vk~~~g-~~~~l-~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~  107 (133)
                      |+|++.+| +++.+ ++++++||.+||++|++++|+|+++|+|+|+|+.|+|+.+|++|++...+.
T Consensus        10 i~Vk~~~g~~~~~l~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~gk~L~d~~tL~~~~i~~g~~   75 (89)
T 1wy8_A           10 IQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDI   75 (89)
T ss_dssp             EEEEETTCSCEEEEEEECTTCBHHHHHHHHHHHSCCCTTTEEEEETTEECCSSSBHHHHTCCTTCE
T ss_pred             EEEEECCCCceEEEEecCCCCCHHHHHHHHHHHHCcChhhEEEEECCeECCCCCCHHHCCCCCCCE
Confidence            88999989 68999 599999999999999999999999999999999999999999999854443

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens}

Probab=99.59  E-value=8.8e-16  Score=102.30  Aligned_cols=65  Identities=11%  Similarity=0.013  Sum_probs=57.3

Q ss_pred             cccCCCCCC--CceeeccccCcHHHHHHHhhhh-cCCC-CCceEEEeCCcccCcccccccc--ccEEeEEE
Q 040111           44 DFCKNPDPQ--NITLEVESSDTIDNVKAKIQDK-KRIP-PPAEADLLKFPFFFFEEVLSFF--WFVVVGVI  108 (133)
Q Consensus        44 i~Vk~~~g~--~~~l~V~~~~tV~~LK~~I~~~-~gIp-~~~q~L~~~gk~L~d~~tL~dy--~~~~~~~~  108 (133)
                      |+||+++++  .+++++++++||.+||++|+++ .|+| +++|||+|+|++|+|+.+|++|  +|.....+
T Consensus        26 I~VK~~~g~~~~i~l~v~~~~TV~~LK~~I~~~~~g~pp~~~QrLIy~Gk~L~D~~tL~~y~~~I~~~~ti   96 (99)
T 2kdb_A           26 LIIKAPNQKYSDQTISCFLNWTVGKLKTHLSNVYPSKPLTKDQRLVYSGRLLPDHLQLKDILRKQDEYHMV   96 (99)
T ss_dssp             EEEECTTSSSCCEEEEECTTSBHHHHHHHHHHHSTTCCCTTTCCEEETTEEECTTSBTHHHHTTTCSEEEE
T ss_pred             EEEEcCCCCEEEEEEEcCCCCHHHHHHHHHHHHhcCCCChhhEEEEECCEECCCCCCHHHHhcCCCCCCEE
Confidence            899999988  5688899999999999999996 5666 5999999999999999999999  98755544

>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=99.59  E-value=1.1e-15  Score=99.99  Aligned_cols=65  Identities=14%  Similarity=0.154  Sum_probs=57.7

Q ss_pred             cccCCCCCC--CceeeccccCcHHHHHHHhhhhc--CCCCCceEEEeCCcccCcccccccc--ccEEeEEE
Q 040111           44 DFCKNPDPQ--NITLEVESSDTIDNVKAKIQDKK--RIPPPAEADLLKFPFFFFEEVLSFF--WFVVVGVI  108 (133)
Q Consensus        44 i~Vk~~~g~--~~~l~V~~~~tV~~LK~~I~~~~--gIp~~~q~L~~~gk~L~d~~tL~dy--~~~~~~~~  108 (133)
                      |+||+.+++  .+.+++++++||.+||++|++++  |+|+++|+|+|+|+.|+|+.+|++|  ++.....+
T Consensus        10 i~Vk~~~~~~~~~~v~v~~~~TV~~lK~~I~~~~~~~i~~~~QrLi~~Gk~L~D~~tL~~~~~~i~~~~~i   80 (93)
T 1wgd_A           10 LLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVL   80 (93)
T ss_dssp             EEEECSSSSCCCEEEECCTTSCHHHHHHHHHHHSTTCCCTTTCEEEETTEECCSSSCHHHHSCSSSCSEEE
T ss_pred             EEEEeCCCCeEEEEEecCCCCcHHHHHHHHHHHhcCCCChHHeEEEECCEECcCcCCHHHHhcCCCCCCEE
Confidence            889999888  56667779999999999999998  9999999999999999999999999  88654433

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.58  E-value=6.9e-16  Score=99.82  Aligned_cols=66  Identities=14%  Similarity=0.113  Sum_probs=59.8

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      .++++.+|+.+.+++++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++|++...+.++
T Consensus        14 ~~~~~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~l~   79 (85)
T 2kd0_A           14 KLTVKFGGKSIPLSVSPDCTVKDLKSQLQPITNVLPRGQKLIFKGKVLVETSTLKQSDVGSGAKLM   79 (85)
T ss_dssp             EEEEEETTEEEEEEECTTSBHHHHHHHHHHHHCCCTTTCEEEETTEECCTTCBTTTTTCCTTEEEE
T ss_pred             EEEEEECCEEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCeECCCcCCHHHCCCCCCCEEE
Confidence            456677899999999999999999999999999999999999999999999999999997666444

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

Probab=99.58  E-value=7.8e-16  Score=104.76  Aligned_cols=65  Identities=42%  Similarity=0.413  Sum_probs=60.7

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      |+|++.+|+++.+++++++||++||++|++++|+|+++|+|+|+|+.|+|+.+|++|++...+.+
T Consensus        12 i~vk~l~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~ygI~~gstI   76 (114)
T 2kdi_A           12 IFAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLEDGRTLSDYNIQRESTL   76 (114)
T ss_dssp             EEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTTTTTCCSSCEE
T ss_pred             EEEEeCCCcEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCEECCCCCcHHHCCCCCCCEE
Confidence            88999999999999999999999999999999999999999999999999999999998554433

>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=99.58  E-value=4.7e-16  Score=106.42  Aligned_cols=61  Identities=15%  Similarity=0.074  Sum_probs=54.9

Q ss_pred             cccCCCCCC-CceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEE
Q 040111           44 DFCKNPDPQ-NITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVV  104 (133)
Q Consensus        44 i~Vk~~~g~-~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~  104 (133)
                      +|++...++ ++.+++++++||.+||++|++++|+||++|||+|+|+.|+|++||++|+|..
T Consensus         3 vFl~Ikr~ktTI~ldve~sdTV~~lK~kI~~~~giPp~qQrLI~~Gk~LeD~kTL~dy~I~~   64 (118)
T 4ajy_B            3 VFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTS   64 (118)
T ss_dssp             EEEEEEEBTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTTTTTCCG
T ss_pred             eEEEEecCCEEEEEEcCCCChHHHHHHHHHHHHCCCHHHeEEEeCCeECCCcCCHHHcCCCc
Confidence            445555555 6888999999999999999999999999999999999999999999999976

>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=99.58  E-value=4.8e-16  Score=106.54  Aligned_cols=60  Identities=15%  Similarity=0.082  Sum_probs=54.3

Q ss_pred             cccCCCCCC-CceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccE
Q 040111           44 DFCKNPDPQ-NITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFV  103 (133)
Q Consensus        44 i~Vk~~~g~-~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~  103 (133)
                      ++++...++ ++.++|++++||++||++|++++|||+++|||+|+|++|+|+++|++|+|.
T Consensus         3 mfl~ir~~ktti~lev~~sdTV~~lK~kI~~~egIP~~qQrLi~~Gk~LeD~~TLsdy~I~   63 (118)
T 2fnj_B            3 VFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPEEQRLYKDDQLLDDGKTLGECGFT   63 (118)
T ss_dssp             EEEEEEEBTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBHHHHTCC
T ss_pred             EEEEEecCCEEEEEEeCCcChHHHHHHHHHHHhCCCHHHeEEEECCeECCCCCCHHHcCcc
Confidence            345554555 588999999999999999999999999999999999999999999999998

>1we6_A Splicing factor, putative; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=99.57  E-value=2.4e-15  Score=101.65  Aligned_cols=65  Identities=22%  Similarity=0.226  Sum_probs=59.9

Q ss_pred             cccCCC---CCCCceeeccc-cCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           44 DFCKNP---DPQNITLEVES-SDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        44 i~Vk~~---~g~~~~l~V~~-~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      |+|+++   +|+.+.+++++ ++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+|...+.+
T Consensus        30 i~Vk~~~~~~g~~~~l~v~~l~~TV~~LK~~I~~~~gip~~~QrL~~~Gk~L~D~~tL~~y~I~~g~~l   98 (111)
T 1we6_A           30 IRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSLAHYNVGAGEIL   98 (111)
T ss_dssp             EEECCTTCSSSCCEEEEESCSSSBHHHHHHHHHHHTTCCTTTSEEECSSSBCCTTSBTTTTTCSSSCEE
T ss_pred             EEEEecccCCCcEEEEEecCCCCcHHHHHHHHHHHHCCCHHHeEEEECCEECCCCCcHHHCCCCCCCEE
Confidence            889988   88999999998 999999999999999999999999999999999999999998655433

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens}

Probab=99.57  E-value=1.2e-15  Score=105.63  Aligned_cols=62  Identities=8%  Similarity=0.001  Sum_probs=57.8

Q ss_pred             cccccCCCCCCCceeeccccCcHHHHHHHhhh------hcCC--CCCceEEEeCCcccCccccccccccE
Q 040111           42 RADFCKNPDPQNITLEVESSDTIDNVKAKIQD------KKRI--PPPAEADLLKFPFFFFEEVLSFFWFV  103 (133)
Q Consensus        42 ~~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~------~~gI--p~~~q~L~~~gk~L~d~~tL~dy~~~  103 (133)
                      ..|+||+++|+++++++++++||++||++|++      ++|+  |+++|||+|+|++|+|+.+|++|+|.
T Consensus        18 m~I~vktl~G~~~~lev~~s~TV~~lK~~I~~~~p~dwke~ip~~~~~qrLIy~GK~LeD~~TL~~y~I~   87 (125)
T 2gow_A           18 INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLP   87 (125)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHSSCCCSCCCCTTCCGGGEEEESSSSEEESSCBTGGGCCC
T ss_pred             EEEEEEeCCCCEEEEEeCCccHHHHHHHHHHHHCCcccccCCCCChHHEEEEECCcCCCCCCcHHHcCCC
Confidence            34899999999999999999999999999999      7788  49999999999999999999999985

>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=99.57  E-value=1.2e-15  Score=103.28  Aligned_cols=67  Identities=39%  Similarity=0.399  Sum_probs=61.7

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      .|+||+.+|+++.+++++++||.+||++|++++|+|+++|+|+|+|+.|+|+.+|++|+|...+.|.
T Consensus        37 ~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~gI~~gs~I~  103 (111)
T 3vdz_A           37 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLH  103 (111)
T ss_dssp             EEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTTTTTCCTTCEEE
T ss_pred             EEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHhCCChHHEEEEECCEECCCCCcHHHCCCCCCCEEE
Confidence            3899999999999999999999999999999999999999999999999999999999986554443

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

Probab=99.56  E-value=1e-15  Score=100.54  Aligned_cols=64  Identities=20%  Similarity=0.180  Sum_probs=58.8

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      |+|++  |+++.+++++++||++||++|++++|+|+++|+|+|+|+.|+|+.+|++|++...+.+.
T Consensus        22 I~Vk~--g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~y~I~~gstI~   85 (93)
T 2l7r_A           22 LFVRA--QELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAGAPLEDEATLGQCGVEALTTLE   85 (93)
T ss_dssp             EEEES--SSEEEEECCSSCBHHHHHHHHHHHHTCCGGGCEEEETTEECCTTSBHHHHTCCSSCEEE
T ss_pred             EEEEC--CCEEEEEeCCCCcHHHHHHHHHHHhCcChhHEEEEECCEECCCCCcHHHCCCCCCCEEE
Confidence            78888  78899999999999999999999999999999999999999999999999986555443

>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=99.56  E-value=9.3e-16  Score=102.93  Aligned_cols=66  Identities=12%  Similarity=0.039  Sum_probs=61.2

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      |+||+.+|+.+.++|++++||.+||++|++++|+|+++|+|+|+|+.|+|+.+|++|+|...+.+.
T Consensus        26 I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~ygI~~g~ti~   91 (106)
T 1ttn_A           26 LRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQ   91 (106)
T ss_dssp             EEEEETTTEEEEEEECTTSHHHHHHHHHHHTTCCCSTTCEEEETTEECCTTSHHHHCCCSSSCEEE
T ss_pred             EEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHHCcCcccEEEEECCEECCCCCcHHHcCCCCCCEEE
Confidence            899999999999999999999999999999999999999999999999999999999997555443

>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=99.56  E-value=1.7e-15  Score=104.86  Aligned_cols=62  Identities=11%  Similarity=0.055  Sum_probs=56.9

Q ss_pred             ccccCCCCCCCc-eeeccccCcHHHHHHHh-----hhhcCCCC--CceEEEeCCcccCccccccccccEE
Q 040111           43 ADFCKNPDPQNI-TLEVESSDTIDNVKAKI-----QDKKRIPP--PAEADLLKFPFFFFEEVLSFFWFVV  104 (133)
Q Consensus        43 ~i~Vk~~~g~~~-~l~V~~~~tV~~LK~~I-----~~~~gIp~--~~q~L~~~gk~L~d~~tL~dy~~~~  104 (133)
                      .|++|+.+|+.+ ++++++++||++||++|     ++++|+|+  ++|||+|+|++|+|+.||++|+|..
T Consensus        18 ~i~~kt~~G~~i~~l~v~psdTV~~lK~kI~~~~p~dkegiP~~~~qQrLIy~GK~LeD~~TLsdy~I~~   87 (126)
T 1se9_A           18 EIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSKTVKDYRSPV   87 (126)
T ss_dssp             EEEEEETTSCEEEEEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEEETTEECCTTSBGGGGSCCT
T ss_pred             EEEEEECCCCEEEeeecCccCHHHHHHHHHHhhcccccccCCCChhhEEEEECCeECcCCCcHHHcCCCc
Confidence            389999999888 79999999999999999     56778997  8999999999999999999999864

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

Probab=99.56  E-value=3.7e-15  Score=100.73  Aligned_cols=66  Identities=39%  Similarity=0.406  Sum_probs=60.9

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      |+|++.+|+.+.+++++++||++||++|++++|+|+++|+|+|+|+.|+|+.+|++|++...+.|.
T Consensus        38 I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~gI~~gs~I~  103 (111)
T 2ojr_A           38 IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLH  103 (111)
T ss_dssp             EEEECSSSCEEEEEECTTCBHHHHHHHHHHHHCCCTTTEEEEETTEECCSSCBTTTTTCCTTCEEE
T ss_pred             EEEEcCCCCEEEEEeCCCCCHHHHHHHHHHHHCcCcccEEEEECCEECCCCCcHHHcCCCCCCEEE
Confidence            889999999999999999999999999999999999999999999999999999999986555443

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=99.55  E-value=2e-15  Score=100.61  Aligned_cols=65  Identities=11%  Similarity=0.043  Sum_probs=59.4

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      |+|++. |+.+.+++++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++|++...+.|.
T Consensus        28 I~Vk~~-g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~gI~~g~~I~   92 (101)
T 2klc_A           28 VTVKTP-KEKEEFAVPENSSVQQFKEEISKRFKSHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVH   92 (101)
T ss_dssp             EEEECS-SCEEEEEECSCCCHHHHHHHHHHHHTCCGGGEEEEETTEEECTTCCTGGGTCCTTCEEE
T ss_pred             EEEEeC-CcEEEEEECCCCCHHHHHHHHHHHHCcChhhEEEEECCEECCCcCcHHHcCCCCCCEEE
Confidence            788888 78899999999999999999999999999999999999999999999999987555443

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B

Probab=99.55  E-value=4.6e-15  Score=107.34  Aligned_cols=62  Identities=44%  Similarity=0.438  Sum_probs=58.9

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVV  104 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~  104 (133)
                      +|+||+.+|+++.+++++++||.+||++|++++|+|+++|+|+|+|+.|+|+.+|++|++..
T Consensus         2 qI~Vk~~~Gk~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~y~I~~   63 (169)
T 3l0w_B            2 QIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQK   63 (169)
T ss_dssp             EEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHCCCTTTEEEEETTEECCTTSBGGGGTCCT
T ss_pred             EEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHHCcCHHHEEEEECCccccCcCcHHHcCCCC
Confidence            37899999999999999999999999999999999999999999999999999999999743

>3u5e_m 60S ribosomal protein L40; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3u5i_m 4b6a_m 4a18_K 4a19_K 4a1b_K 4a1d_K 4adx_5 3izc_p 3izs_p 3iz5_p 3izr_p

Probab=99.54  E-value=4.6e-16  Score=107.75  Aligned_cols=66  Identities=41%  Similarity=0.418  Sum_probs=0.0

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      .|+|++.+|+++.++|++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+|...+.+
T Consensus         2 ~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~~I~~gsti   67 (128)
T 3u5e_m            2 QIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTL   67 (128)
T ss_dssp             ------------------------------------------------------------------
T ss_pred             EEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHhCcChHHEEEEECCEECCCCCchhhhccCCCCEE
Confidence            378999999999999999999999999999999999999999999999999999999998665543

>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=99.54  E-value=1.8e-15  Score=99.40  Aligned_cols=65  Identities=9%  Similarity=0.010  Sum_probs=60.2

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      |+|++. |+.+.+++++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|++.....|.
T Consensus        20 i~Vk~~-g~~~~~~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~   84 (96)
T 1wx8_A           20 VSVKTP-QDCHEFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQDILSQRGILDGSTVH   84 (96)
T ss_dssp             EEEECS-SSEEEEEEETTCCHHHHHHHHHHHTCSCTTTBCCEETTEECCTTSCHHHHTCCTTEEEE
T ss_pred             EEEEEC-CeEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEECCCcCCHHHCCCCCCCEEE
Confidence            788888 88999999999999999999999999999999999999999999999999997665554

>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=99.54  E-value=2e-15  Score=100.47  Aligned_cols=65  Identities=14%  Similarity=0.063  Sum_probs=59.2

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      |+|++.+|+ +.+++++++||.+||++|++++|+|+++|+|+|+|+.|+|+.+|++|++...+.+.
T Consensus        25 I~Vk~~~g~-~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~ygI~~gstI~   89 (100)
T 1yqb_A           25 VTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVH   89 (100)
T ss_dssp             EEEECSSCE-EEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBHHHHTCCTTCEEE
T ss_pred             EEEEcCCCc-EEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEECCCcCcHHHCCCCCCCEEE
Confidence            889998886 68999999999999999999999999999999999999999999999987555443

>2dzj_A Synaptic glycoprotein SC2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=5.1e-15  Score=96.51  Aligned_cols=69  Identities=16%  Similarity=0.080  Sum_probs=61.3

Q ss_pred             cccccCCCCCCCc--ee-eccccCcHHHHHHHhhhh-cCCCCCceEEEeC--CcccCccccccccccEEeEEEEe
Q 040111           42 RADFCKNPDPQNI--TL-EVESSDTIDNVKAKIQDK-KRIPPPAEADLLK--FPFFFFEEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        42 ~~i~Vk~~~g~~~--~l-~V~~~~tV~~LK~~I~~~-~gIp~~~q~L~~~--gk~L~d~~tL~dy~~~~~~~~~~  110 (133)
                      ..|+|++..|+.+  .+ +|++++||++||++|+++ .|+||++|+|+|.  |+.|+|+.+|++|++...+.+++
T Consensus        11 M~I~Vk~~~g~~~~~~l~~v~~~~TV~~lK~~I~~~~~~i~~~~QrL~~~~~Gk~L~D~~tL~~y~i~~~stl~~   85 (88)
T 2dzj_A           11 YEVEILDAKTREKLCFLDKVEPHATIAEIKNLFTKTHPQWYPARQSLRLDPKGKSLKDEDVLQKLPVGTTATLYF   85 (88)
T ss_dssp             EEEEEEESSSCCCCEEEEEECSSCBHHHHHHHHHHHCSSSCTTTCCEESSTTSCCCCTTCBTTTSSCCSEEEEEE
T ss_pred             EEEEEECCCCCEEeeEEeEcCCCCcHHHHHHHHHHHhcCCChHHeEEEecCCCcCcCCCCCHHHcCCCCCCEEEE
Confidence            4589999988775  47 999999999999999995 8999999999976  99999999999999987777665

>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=99.53  E-value=4.1e-15  Score=105.65  Aligned_cols=64  Identities=13%  Similarity=-0.088  Sum_probs=59.8

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEE-e-CCcccCccccccccccEEeE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADL-L-KFPFFFFEEVLSFFWFVVVG  106 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~-~-~gk~L~d~~tL~dy~~~~~~  106 (133)
                      .|+||+.+|+++++++++++||++||++|++.+|+||++|+|+ | +|+.|+|+.+|++|+|...+
T Consensus         4 ~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~QrL~~~~~g~~L~d~~tL~~y~i~~~~   69 (159)
T 3rt3_B            4 DLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGS   69 (159)
T ss_dssp             EEEEEETTSCEEEEECCTTCCHHHHHHHHHHHHCCCGGGEEEEEETTCCBCCTTSCGGGGTCCTTC
T ss_pred             EEEEEECCCCEEEEEeCCCCcHHHHHHHHHHHhCCCHHHEEEEEcCCCCCCCCCCCHHHcCCCCCC
Confidence            4889999999999999999999999999999999999999999 9 89999999999999985443

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.52  E-value=7.4e-15  Score=101.50  Aligned_cols=65  Identities=9%  Similarity=0.019  Sum_probs=59.7

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      |+|++. |+.+.+++++++||.+||++|++++|+|+++|+|+|+|+.|+|+.+|++|+|...+.|.
T Consensus        35 I~Vk~~-g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~dygI~~gstI~   99 (125)
T 1j8c_A           35 VTVKTP-KEKEEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVH   99 (125)
T ss_dssp             EEEECS-SCEEEEEECTTCCHHHHHHHHHHHHCSCSSSEEEEETTEEESTTSCGGGTTCSSSEEEE
T ss_pred             EEEEeC-CeEEEEEECCCCcHHHHHHHHHHHHCcCcceEEEEECCEEcCCCCCHHHcCCCCCCEEE
Confidence            888888 88899999999999999999999999999999999999999999999999986555443

>1v2y_A 3300001G02RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.52  E-value=1.7e-15  Score=101.99  Aligned_cols=64  Identities=11%  Similarity=-0.094  Sum_probs=58.4

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCC---------------CceEEEeCCcccC-ccccccccccEEeE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP---------------PAEADLLKFPFFF-FEEVLSFFWFVVVG  106 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~---------------~~q~L~~~gk~L~-d~~tL~dy~~~~~~  106 (133)
                      .|+|++++|++++++|++++||++||++|++++|+|+               ++|+|+|+|+.|. |+.+|++|+|.+.+
T Consensus         9 ~I~Vk~l~g~~~~v~V~~~~TV~dLK~~I~~~~~i~~~~q~g~~~isw~~~w~q~~Li~~Gk~L~dD~~tL~dygI~~g~   88 (105)
T 1v2y_A            9 TVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLRDYGIRNRD   88 (105)
T ss_dssp             EEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHHHHHHHTTCCCCCCHHHHHTTEEEESSSCEECCSSSBHHHHTCCSSE
T ss_pred             EEEEEecCCCEEEEEECCCChHHHHHHHHHHHhCCCcccccCcceeeeeecceeEEEEeCCcCccCCcCCHHHcCCCCCC
Confidence            3899999999999999999999999999999999988               4679999999997 56999999997655

>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=99.51  E-value=4.8e-15  Score=96.71  Aligned_cols=68  Identities=15%  Similarity=0.088  Sum_probs=60.0

Q ss_pred             cccCCCCCCCcee-eccccCcHHHHHHHhhhhcCCCCCceEEE---eCCcccCccccccccccEEeE-EEEeCc
Q 040111           44 DFCKNPDPQNITL-EVESSDTIDNVKAKIQDKKRIPPPAEADL---LKFPFFFFEEVLSFFWFVVVG-VIFCGC  112 (133)
Q Consensus        44 i~Vk~~~g~~~~l-~V~~~~tV~~LK~~I~~~~gIp~~~q~L~---~~gk~L~d~~tL~dy~~~~~~-~~~~~~  112 (133)
                      |+|+. .|+++.+ ++++++||.+||++|++++|+|+++|+|+   |+|++|+|+.+|++|+|.... +.+.|.
T Consensus        10 i~Vk~-~g~~~~i~~v~~~~TV~~lK~~I~~~~gip~~~QkLi~~k~~Gk~L~D~~~L~~~~i~~g~~l~l~~~   82 (90)
T 1v5t_A           10 IIVKW-GGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMGT   82 (90)
T ss_dssp             EEEEE-TTEEEEECSCCSSSBHHHHHHHHHHHTCCCTTTCEEESCEETTEECCTTSBHHHHTCCTTEEEEEECC
T ss_pred             EEEEE-CCEEEEEEEeCCCCCHHHHHHHHHHHHCcCHHHeEEEeeccCCcCcCCCCCHHHcCCCCCCEEEEEec
Confidence            67775 6888999 99999999999999999999999999999   999999999999999986555 444444

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

Probab=99.51  E-value=5.1e-15  Score=108.95  Aligned_cols=65  Identities=40%  Similarity=0.413  Sum_probs=61.0

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      |+||+.+|+++.++|++++||.+||++|++++|+|+++|+|+|+|+.|+|+.+|++|+|...+.+
T Consensus       108 I~VKtl~Gkt~~l~V~~s~TV~~LK~kI~~~~gIp~~~QrLi~~Gk~L~D~~tL~dygI~~gstI  172 (189)
T 3q3f_A          108 IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTL  172 (189)
T ss_dssp             EEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCCEEETTEECCTTCBGGGGTCCTTCEE
T ss_pred             eeeecCCCCEEEEEeCCCCcHHHHHHHHHhccCCCHHHEEEEECCEECCCCCCHHHCCCCCCCEE
Confidence            89999999999999999999999999999999999999999999999999999999998554443

>3u5c_f 40S ribosomal protein S31; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3u5g_f

Probab=99.51  E-value=1.1e-15  Score=109.05  Aligned_cols=72  Identities=39%  Similarity=0.391  Sum_probs=0.0

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE-----EeCcee
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI-----FCGCRV  114 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~-----~~~~~~  114 (133)
                      +|+|++++|+++.++|++++||++||++|++.+|+|+++|+|+|+|++|+|+.+|++|+|...+.+     +.||+-
T Consensus         2 qI~VK~l~G~~~~l~V~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~dygI~~gstL~Lvlrl~GGgK   78 (152)
T 3u5c_f            2 QIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGGK   78 (152)
T ss_dssp             -----------------------------------------------------------------------------
T ss_pred             EEEEEeCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEEccccCcHHHcCCCCCCEEEEEeeccCCCc
Confidence            378999999999999999999999999999999999999999999999999999999998655533     356643

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A

Probab=99.51  E-value=1e-14  Score=98.02  Aligned_cols=60  Identities=15%  Similarity=0.040  Sum_probs=55.6

Q ss_pred             cccCCCCC--CCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccE
Q 040111           44 DFCKNPDP--QNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFV  103 (133)
Q Consensus        44 i~Vk~~~g--~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~  103 (133)
                      ++|++..+  .+++++|++++||++||++|++++||||++|||+|+|+.++|+.+|++|+|.
T Consensus        27 v~v~d~~s~~~~i~l~V~ps~TV~~LK~~I~~k~Gipp~~QRli~ggkll~D~~TL~~ygI~   88 (105)
T 4dbg_A           27 VSVEDAQMHTVTIWLTVRPDMTVASLKDMVFLDYGFPPVLQQWVIGQRLARDQETLHSHGVR   88 (105)
T ss_dssp             EEEEESSSCCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEEECTTCBTGGGTCC
T ss_pred             EEEEccCCCCceEEEEECCcChHHHHHHHHHHHhCCCHHHEEEeccCeEccCcCcHHHcCCC
Confidence            77888764  5788999999999999999999999999999999999999999999999993

>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=99.50  E-value=5e-15  Score=98.71  Aligned_cols=67  Identities=7%  Similarity=-0.004  Sum_probs=58.6

Q ss_pred             cccCCCCC----CCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCcc-ccccccccEEeEEEEe
Q 040111           44 DFCKNPDP----QNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFE-EVLSFFWFVVVGVIFC  110 (133)
Q Consensus        44 i~Vk~~~g----~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~-~tL~dy~~~~~~~~~~  110 (133)
                      |+|++.++    +.+.++|++++||++||++|++++|+|+++|+|+|+|+.|+|+ .+|++|+|.....+++
T Consensus        10 I~Vk~~~~~~~~~~~~i~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~gk~L~D~~~tL~~ygI~~g~~l~l   81 (102)
T 1v5o_A           10 ITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVL   81 (102)
T ss_dssp             EEEEECCCCCCCCEEEEEECTTCBHHHHHHHHHHHTCCCGGGBCEEETTEEECCSSSBHHHHTCCTTEEEEE
T ss_pred             EEEEECCCCcCceEEEEEcCCCCCHHHHHHHHHHHHCcChHHeEEEECCEECCCCcccHHHCCCCCCCEEEE
Confidence            67777544    6889999999999999999999999999999999999999988 6999999976665443

>1wx7_A Ubiquilin 3; ubiquitin-like domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.50  E-value=9e-15  Score=97.96  Aligned_cols=66  Identities=14%  Similarity=0.055  Sum_probs=59.3

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEEe
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~~  110 (133)
                      |+|+..+++ +.+++++++||.+||++|++++|+|+++|+|+|+|+.|+|+.+|++|+|.....|.+
T Consensus        20 I~Vk~~~g~-~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~gi~~g~~i~l   85 (106)
T 1wx7_A           20 VTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHL   85 (106)
T ss_dssp             EEEECSSCE-EEEEEETTCCHHHHHHHHHHHHTCCTTTEEEEETTEECCTTSCHHHHTCCTTEEEEE
T ss_pred             EEEEeCCCc-EEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEECCCcCcHHHcCCCCCCEEEE
Confidence            788888776 689999999999999999999999999999999999999999999999865554443

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

Probab=99.50  E-value=6.7e-15  Score=106.05  Aligned_cols=62  Identities=42%  Similarity=0.425  Sum_probs=59.1

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVV  104 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~  104 (133)
                      .|+|++.+|+++.++|++++||.+||++|++++|+|+++|+|+|+|+.|+|+.+|++|+|..
T Consensus        22 ~i~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~QrL~~~g~~L~d~~tL~~~~i~~   83 (172)
T 3u30_A           22 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQK   83 (172)
T ss_dssp             EEEEEETTTEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTGGGTCCT
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCccccccCCHhHcCCcc
Confidence            38999999999999999999999999999999999999999999999999999999999844

>1wgg_A Ubiquitin carboxyl-terminal hydrolase 14; ubiquitin specific protease 14, USP14, ubiquitin-like fold, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.50  E-value=5.9e-15  Score=97.55  Aligned_cols=68  Identities=10%  Similarity=0.010  Sum_probs=59.0

Q ss_pred             cccCCCCCCCc-eeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEE-EEeCce
Q 040111           44 DFCKNPDPQNI-TLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGV-IFCGCR  113 (133)
Q Consensus        44 i~Vk~~~g~~~-~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~-~~~~~~  113 (133)
                      |+||. .|+.+ .+++++++||.+||++|++++|+|+++|+|+|+|+.|+|+ +|++|+|..... .+.|..
T Consensus        10 i~Vk~-~g~~~~~l~v~~~~TV~~lK~~I~~~tgip~~~QkLi~~Gk~L~D~-tL~~~~I~~g~~i~l~~~~   79 (96)
T 1wgg_A           10 VTVKW-GKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLKDD-DWGNIKMKNGMTVLMMGSA   79 (96)
T ss_dssp             EEEEE-TTEEEEEEEEESSSCHHHHHHHHHHHTCCCTTTSCCEETTEECCSS-CCCSCCCCSSCEEECCCCC
T ss_pred             EEEEE-CCEEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCcCCCCC-CHHHCCCCCCCEEEEEecc
Confidence            67774 57888 6999999999999999999999999999999999999999 999999976653 344443

>2dzm_A FAS-associated factor 1; ubiquitin-like domain, HFAF1, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.47  E-value=1.9e-14  Score=95.95  Aligned_cols=65  Identities=15%  Similarity=0.138  Sum_probs=57.5

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEe--CCcccCccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLL--KFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~--~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      +++++.+|+++.+++++++||++||++|++++||||++|+|++  +|+ |+|+.+|++|++...+.+.
T Consensus        11 ~~~vk~~Gk~~~v~v~~~~TV~~LK~~I~~~tgIpp~~QkLi~~~~gk-L~D~~tLs~~~I~~gstL~   77 (100)
T 2dzm_A           11 DFRVEYRDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGD-VEDSTVLKSLHLPKNNSLY   77 (100)
T ss_dssp             EEEEECSSCEEEEEEETTSBHHHHHHHHHHHHCCCTTTCCEECCSSSC-CCTTSBHHHHCCCSEEEEE
T ss_pred             EEEEEeCCeEEEEEECCCCcHHHHHHHHHHHHCCChhHeEEEccCCCC-CCCcCCHHHcCCCCCCEEE
Confidence            5667778999999999999999999999999999999999996  666 9999999999997655443

>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=99.47  E-value=3e-14  Score=96.79  Aligned_cols=58  Identities=14%  Similarity=0.212  Sum_probs=53.3

Q ss_pred             CCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeE
Q 040111           49 PDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVG  106 (133)
Q Consensus        49 ~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~  106 (133)
                      ++|+++.++|++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|++...+
T Consensus        43 L~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrL~~~Gk~L~D~~tL~~y~i~~g~  100 (115)
T 1we7_A           43 LNGQGLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMASGA  100 (115)
T ss_dssp             CSSEEEEEEECSCSBTHHHHHHHHHHSSCCTTTEEEEETTEEECTTSBHHHHTCCSSC
T ss_pred             cCCeEEEEEECCCCCHHHHHHHHHHHHCCChHHEEEEECCEECCCCCCHHHCCCCCCC
Confidence            3578899999999999999999999999999999999999999999999999984433

>1x1m_A Ubiquitin-like protein SB132; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.46  E-value=3.8e-14  Score=95.22  Aligned_cols=66  Identities=17%  Similarity=0.100  Sum_probs=57.9

Q ss_pred             ccccCCCCC---CCceeecc--------c-cCcHHHHHHHhhhhc--CCCCCc-eEEEeCCcccCccccccccccEEeEE
Q 040111           43 ADFCKNPDP---QNITLEVE--------S-SDTIDNVKAKIQDKK--RIPPPA-EADLLKFPFFFFEEVLSFFWFVVVGV  107 (133)
Q Consensus        43 ~i~Vk~~~g---~~~~l~V~--------~-~~tV~~LK~~I~~~~--gIp~~~-q~L~~~gk~L~d~~tL~dy~~~~~~~  107 (133)
                      .|+||+.++   +.+.++++        + ++||.+||++|++++  |+|+++ |+|+|+|+.|+|+.+|++|++.....
T Consensus        14 ~i~Vk~~~~~~~~~~~l~v~~~~~~~v~~~~~TV~~LK~~i~~~~~~gip~~~~qrLi~~Gk~L~D~~tL~~y~i~~g~~   93 (107)
T 1x1m_A           14 HLAVKLADQPLAPKSILQLPETELGEYSLGGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDFYGIQPGST   93 (107)
T ss_dssp             CEEEEETTCTTSCCEEECCCCCSSCSSCCCCCBHHHHHHHHHHHCTTTCCCSSSEEEEETTEECCTTCBHHHHTCCTTCE
T ss_pred             EEEEEeCCCCCccEEEEEecCccccccCcccCCHHHHHHHHHHHhccCCChhhcEEEEECCeECCCCCcHHHcCCCCCCE
Confidence            388898888   78888844        4 499999999999999  999999 99999999999999999999865554


Q ss_pred             E
Q 040111          108 I  108 (133)
Q Consensus       108 ~  108 (133)
                      +
T Consensus        94 i   94 (107)
T 1x1m_A           94 V   94 (107)
T ss_dssp             E
T ss_pred             E
Confidence            3

>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=99.46  E-value=4.1e-14  Score=92.28  Aligned_cols=65  Identities=12%  Similarity=0.062  Sum_probs=57.1

Q ss_pred             cccCCCCCCCceeecccc-----CcHHHHHHHhhhhcCCCCCceEEEeCCcccCc-cccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESS-----DTIDNVKAKIQDKKRIPPPAEADLLKFPFFFF-EEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~-----~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d-~~tL~dy~~~~~~~~~  109 (133)
                      |+|+. .++.+.++++++     +||.+||++|++.+|+|+++|+|+|+|+.|+| +.+|++|++.....|+
T Consensus        10 v~Vk~-~~~~~~i~v~~~~~~~~~TV~~LK~~i~~~~gip~~~qrL~~~Gk~L~D~~~~L~~~~i~~g~~i~   80 (92)
T 1wxv_A           10 VTVTH-SNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVM   80 (92)
T ss_dssp             EEEEC-SSSEEEEEECCCSSSSSCBHHHHHHHHHHHTCCCTTTCEEEETTEEECCSSSBHHHHTCCSSEEEE
T ss_pred             EEEEE-CCEEEEEEECCCcCcccCcHHHHHHHHHHHHCcCHHHEEEEECCeecCCCcccHHHCCCCCCCEEE
Confidence            77887 477889999985     99999999999999999999999999999999 5689999997655443

>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=99.46  E-value=2.9e-14  Score=99.82  Aligned_cols=65  Identities=40%  Similarity=0.398  Sum_probs=59.9

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGV  107 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~  107 (133)
                      .|+|++.+|+++.+++++++||++||++|++++|+|+++|+|+|+|+.|+|+.+|++|++...+.
T Consensus         2 ~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gip~~~q~L~~~g~~L~d~~tL~~~~i~~~~~   66 (152)
T 3b08_A            2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKEST   66 (152)
T ss_dssp             EEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCE
T ss_pred             EEEEEeCCCCEEEEEECCCCCHHHHHHHHHHHHCcChHHeEEEECCeECcCcccHHHhccCCCCe
Confidence            37889999999999999999999999999999999999999999999999999999999854443

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

Probab=99.45  E-value=5.9e-15  Score=108.49  Aligned_cols=73  Identities=8%  Similarity=-0.040  Sum_probs=2.2

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEEeCceee
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIFCGCRVN  115 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~~~~~~~  115 (133)
                      +|+|++++|++++++|++++||.+||++|++.+|||+++|+|+|+|++|+|+.+|++-....+.+.+.||.++
T Consensus         2 qI~VKtL~GktitLeV~~sdTV~~LK~kI~~keGIP~~qQRLIf~GK~LeD~~TLs~~STLhLvlRLrGG~~k   74 (189)
T 2xzm_9            2 QVQVKTLEGETKIYTLEQGTSVLDLKSQISQDMGFEIDMMTLVNNGFIAPNTELVTDDVTYYLSLKLLGGKKK   74 (189)
T ss_dssp             ----------------------------------------------------------------------CCC
T ss_pred             EEEEEcCCCCEEEEEECCcChHHHHHHHHHHHhCcChhHEEEEecCeECCCCCcccCCCEEEEEEecCCCccc
Confidence            4899999999999999999999999999999999999999999999999999999943344555677898875

>2kjr_A CG11242; UBL, ubiquitin, ubiquitin-like, structural genomics, PSI-2, protein structure initiative; NMR {Drosophila melanogaster}

Probab=99.45  E-value=2.8e-14  Score=94.29  Aligned_cols=65  Identities=8%  Similarity=-0.081  Sum_probs=54.1

Q ss_pred             cccCCCCCC--CceeeccccCcHHHHHHHhhhhcCCCCCceEEEeC--Cc---cc-CccccccccccEEeEEE
Q 040111           44 DFCKNPDPQ--NITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLK--FP---FF-FFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        44 i~Vk~~~g~--~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~--gk---~L-~d~~tL~dy~~~~~~~~  108 (133)
                      ++|+..+++  .+.+++++++||++||++|++++||||++|||+|+  |+   .| +|+++|++|++...+.+
T Consensus        18 l~It~s~~~~~~~~~~v~~~~TV~~LK~kI~~~~GiP~~~QrL~~~~~g~~~~~L~~D~~tL~~Y~i~~gsti   90 (95)
T 2kjr_A           18 VNVSNSHNDAVAFEVKLAKDLTVAQLKTKLEILTGGCAGTMKVQVFKGDTCVSTMDNNDAQLGYYANSDGLRL   90 (95)
T ss_dssp             EEEEESSCSCEEEEEEEETTCBHHHHHHHHHHHHCSCTTTEEEEEEETTEEEEECCCTTSBHHHHCCSSSCEE
T ss_pred             EEEEECCCCceEEEEEeCccCHHHHHHHHHHHHHCcCHHHeEEEEecCCcccceeCCCCCCHhHCCcCCCCEE
Confidence            556655543  68899999999999999999999999999999997  45   45 88999999998755443

>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=99.44  E-value=1.6e-14  Score=95.17  Aligned_cols=63  Identities=16%  Similarity=0.036  Sum_probs=55.5

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      |+|+ ..++++.+++++++||.+||++|++++|+|+++|+|+|.|+.| |+.+|++|+|.....|
T Consensus        20 i~Vk-~~g~~~~i~v~~~~TV~~LK~~I~~~tgip~~~QrL~~~Gk~L-dd~tL~~~~i~~g~~i   82 (95)
T 1v86_A           20 LKII-WNKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGLVP-EDKTLREIKVTSGAKI   82 (95)
T ss_dssp             EEEE-ETTEEEEEEECTTSBHHHHHHHHHHHHCSCSTTCCCBSSSBCC-SSSBHHHHCCCTTEEE
T ss_pred             EEEE-ECCEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCeeC-CcCcHHHCCCCCCCEE
Confidence            6676 3578899999999999999999999999999999999999999 5559999999765543

>1wia_A Hypothetical ubiquitin-like protein (riken cDNA 2010008E23); 'structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.42  E-value=5.4e-14  Score=92.21  Aligned_cols=64  Identities=16%  Similarity=0.037  Sum_probs=58.1

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCcc-ccccccccEEeEEEEe
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFE-EVLSFFWFVVVGVIFC  110 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~-~tL~dy~~~~~~~~~~  110 (133)
                      |+|++.+|+.+.++|++++||.+||++|++++   +++|+|+|+|+.|+|+ .+|++|++.....|.+
T Consensus        10 i~Vk~~~g~~~~~~v~~~~TV~~LK~~i~~~~---~~~qrLi~~Gk~L~D~~~tL~~y~i~~g~~i~l   74 (95)
T 1wia_A           10 VRLKFLNDTEELAVARPEDTVGTLKSKYFPGQ---ESQMKLIYQGRLLQDPARTLSSLNITNNCVIHC   74 (95)
T ss_dssp             EEEEETTTEEEEEEECSSSBHHHHHHHHSSST---TTTCEEEETTEECCCSSCBTTTTTCCTTEEEEE
T ss_pred             EEEEeCCCCEEEEEECCCCcHHHHHHHHHhhC---cCcEEEEECCEEccCCcCCHHHcCCCCCCEEEE
Confidence            78888889999999999999999999999988   9999999999999999 9999999976664443

>4b6w_A Tubulin-specific chaperone; CAP-Gly, ubiquitin-like; HET: MSE; 2.35A {Trypanosoma brucei brucei strain 927}

Probab=99.42  E-value=9.7e-14  Score=90.09  Aligned_cols=61  Identities=15%  Similarity=0.047  Sum_probs=52.4

Q ss_pred             CCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEe-------CCcccCccccccccccEEeEEE
Q 040111           48 NPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLL-------KFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        48 ~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~-------~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      ....+...+.+++++||++||++|++++|+||++|||+|       .|+.++|+++|++|+|...+.+
T Consensus        11 ~~~~~~~E~r~~~s~TI~~lK~ki~~~~Gip~~~QrLi~~~~~~~~~g~~l~d~~tL~~Y~i~~g~~i   78 (86)
T 4b6w_A           11 ASRMRVPEKRYGLAQTIESIKENVFTHFATPPEYMQLQLIDDRGITIEKNMANDKQLGYYQCRDEFVI   78 (86)
T ss_dssp             TCSCCEEEEEEETTSBHHHHHHHHHTTSCCCGGGEEEEEECTTSCEEESSCCTTSBGGGGTCCTTCEE
T ss_pred             CCCCeEEEEEcCccCcHHHHHHHHHHHHCCCHHHEEEEEecCCCCceeeEcCCCCCHHHCCCCCCCEE
Confidence            334455678899999999999999999999999999996       5899999999999998654433

>2kj6_A Tubulin folding cofactor B; methods development, NESG, solution PSI-2, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.40  E-value=1.9e-13  Score=90.63  Aligned_cols=58  Identities=16%  Similarity=-0.085  Sum_probs=50.3

Q ss_pred             CCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCc---c----cCccccccccccEEeEEE
Q 040111           51 PQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFP---F----FFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        51 g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk---~----L~d~~tL~dy~~~~~~~~  108 (133)
                      +..+.+++++++||++||++|++++||||++|||+|.|+   .    ++|+++|++|++...+.|
T Consensus        26 ~~~~e~~v~~~~TV~~LK~kIe~~~Gip~~~QrLi~~g~~g~~~~~L~~D~~tL~~Y~I~~g~~I   90 (97)
T 2kj6_A           26 SFSADARFSPQMSVEAVKEKLWKKCGTSVNSMALELYDDSGSKVAVLSDDSRPLGFFSPFDGFRL   90 (97)
T ss_dssp             CCCEEEEECTTCCHHHHHHHHHHHHCCCTTSEEEEEECSSSCBCCCSSGGGSCHHHHCCCSCCEE
T ss_pred             ceEEEEEeCCCChHHHHHHHHHHHHCcCHHHeEEEEecCCCcccceecCCcCCHHHCCCCCCCEE
Confidence            457889999999999999999999999999999999883   3    488999999998755433

>2daf_A FLJ35834 protein; hypothetical protein FLJ35834, ubiquitin-like domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.40  E-value=3.3e-13  Score=92.00  Aligned_cols=77  Identities=14%  Similarity=-0.005  Sum_probs=64.3

Q ss_pred             cccC-CCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCcccccccccc----EEeEEEEeCceeeeee
Q 040111           44 DFCK-NPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWF----VVVGVIFCGCRVNFWN  118 (133)
Q Consensus        44 i~Vk-~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~----~~~~~~~~~~~~~~~~  118 (133)
                      +.|+ .+.++.+.++++++.||++||+.+++..++|+++|+|+|+||.|+|+.||++|++    +.+-+++.---.+|=-
T Consensus        18 vkv~l~~~~~k~tv~v~~d~TV~dLKe~ls~~~~iP~e~qrLIy~GKiLKD~eTL~~~gIk~g~TIhLvi~s~~p~~~p~   97 (118)
T 2daf_A           18 VKVVLIPVGQEIVIPFKVDTILKYLKDHFSHLLGIPHSVLQIRYSGKILKNNETLVQHGVKPQEIVQVEIFSTNPDLYPV   97 (118)
T ss_dssp             EEEEETTTCCEEEEEECSSSCSHHHHHHHHHHHTCCTTTEEEEETTEEECSSCCHHHHSCCSSCEEEEEEEESCTTTSCC
T ss_pred             EEEEEcCCCcEEEEEeCCCCcHHHHHHHHHhhhCCChHHEEEEECCeEcCCcchHHHcCCCCCCEEEEEEecCCCccCcc
Confidence            5555 6678889999999999999999999999999999999999999999999999998    5555665544444443


Q ss_pred             cc
Q 040111          119 AS  120 (133)
Q Consensus       119 ~~  120 (133)
                      |.
T Consensus        98 ~~   99 (118)
T 2daf_A           98 RR   99 (118)
T ss_dssp             CC
T ss_pred             ee
Confidence            33

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B*

Probab=99.36  E-value=3.4e-13  Score=105.68  Aligned_cols=66  Identities=39%  Similarity=0.406  Sum_probs=61.5

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      |+||+++|+++.+++++++||++||++|++++|+|+++|+|+|+|+.|+|+.+|++|+|...+.+.
T Consensus       236 I~VKtl~Gk~~~leV~~s~TV~dLK~kI~~~~GIp~~~QRLi~~Gk~L~D~~TLsdygI~~gstL~  301 (307)
T 3ai5_A          236 IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLH  301 (307)
T ss_dssp             EEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBTGGGTCCTTCEEE
T ss_pred             EEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEeCCeecCCCCCHHHcCCCCCCEEE
Confidence            899999999999999999999999999999999999999999999999999999999987655443

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

Probab=99.35  E-value=2.1e-14  Score=97.61  Aligned_cols=66  Identities=56%  Similarity=0.753  Sum_probs=57.7

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc-----cccC---CCCCCCceeeccccCcHHH
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA-----DFCK---NPDPQNITLEVESSDTIDN   66 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~-----i~Vk---~~~g~~~~l~V~~~~tV~~   66 (133)
                      |++++|||+++|+|+|+|++|+|+.+|++|||. +++|+|..+.     ++++   +..|+++++++++++||.+
T Consensus        39 I~~~~gip~~~qrLi~~Gk~L~D~~tL~~ygI~~gstI~l~~~~~GG~~~~~~~~~~~~g~~~~~~v~~~~~~~~  113 (114)
T 2kdi_A           39 IQDKEGIPPDQQRLIWAGKQLEDGRTLSDYNIQRESTLHLVLRLRGGSMGGAADEEELIRKAIELSLKESRNSGG  113 (114)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTCBTTTTTCCSSCEEEEEECCCSSCCCSSCSSSHHHHHHHHSSSHHHHHGGG
T ss_pred             HHHHHCcChHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEEcCCCceeeccccccccCceEEEEeccccccCC
Confidence            356789999999999999999999999999999 9999999886     6777   3467888899999888864

>1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair, proteasome-mediated degradation, protein- protein interaction, replication; NMR {Homo sapiens} SCOP: a.5.2.1 a.5.2.1 a.189.1.1 d.15.1.1 PDB: 1qze_A 1tp4_A

Probab=99.34  E-value=2.2e-13  Score=109.21  Aligned_cols=66  Identities=12%  Similarity=0.141  Sum_probs=60.5

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhh---hcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQD---KKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~---~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      .|+||+.+|+++.++|++++||.+||.+|++   ++|||+++|||+|+|+.|+|+++|++|+|...+.|
T Consensus         9 ~I~VKtl~Gk~~~leV~~~~TV~~LK~~I~~~~~~~gip~~~QrLiy~GK~L~D~~tL~dygI~~gstI   77 (368)
T 1oqy_A            9 TITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFV   77 (368)
T ss_dssp             CEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSSEECSSSBTTTTCCCTTSCE
T ss_pred             EEEEEeCCCCEEEEEeCCCChHHHHHHHHHHHhCcCCCChhheEEEECCeecCCcCCHHHcCCCCCCEE
Confidence            3899999999999999999999999999999   67899999999999999999999999998655533

>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=99.33  E-value=4.8e-13  Score=87.96  Aligned_cols=65  Identities=17%  Similarity=-0.057  Sum_probs=53.0

Q ss_pred             cccCCCCC-CCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCC---cc----cCccccccccccEEeEEE
Q 040111           44 DFCKNPDP-QNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKF---PF----FFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        44 i~Vk~~~g-~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~g---k~----L~d~~tL~dy~~~~~~~~  108 (133)
                      ++|+.... ..+.+++++++||++||++|++++|+||++|||+|+|   +.    ++|+++|++|++...+.+
T Consensus        10 l~I~~~~~~~~~~~~v~~~~TV~~lK~ki~~~~gip~~~qrL~~~~~~g~~~~~l~~D~~tL~~y~i~~g~~l   82 (95)
T 1v6e_A           10 VFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVGSPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRI   82 (95)
T ss_dssp             EEEEETTSSSCEEEEECTTSBHHHHHHHHHHHTCSCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCEE
T ss_pred             EEEEECCCCeeEEEEcCccCHHHHHHHHHHHHHCCCHHHeEEEEeCCCCccccccCCCcCCHhHCCCCCCCEE
Confidence            44444333 2678899999999999999999999999999999986   43    589999999998755543

>1wf9_A NPL4 family protein; beta-grAsp fold like domain, hypothetical protein, structural genomics, NPPSFA; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=99.29  E-value=8e-13  Score=88.79  Aligned_cols=67  Identities=15%  Similarity=0.065  Sum_probs=58.1

Q ss_pred             ccccCCCCCCCceeecc-ccCcHHHHHHHhhhhcCCCCCceEEEeCCc-----------c----cCccccccccccEEeE
Q 040111           43 ADFCKNPDPQNITLEVE-SSDTIDNVKAKIQDKKRIPPPAEADLLKFP-----------F----FFFEEVLSFFWFVVVG  106 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~-~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk-----------~----L~d~~tL~dy~~~~~~  106 (133)
                      .|+||+.+|+. .++|+ +++||.+||++|++++|+|+++|+|++.|+           .    ++|+.+|++|++....
T Consensus         9 ~irvrs~~G~~-~v~v~~~~~Tv~~LK~kI~~~~gip~~~QrL~~~~~~~~~k~~~~~~~l~~~l~d~~tL~~~gi~~G~   87 (107)
T 1wf9_A            9 MLRVRSRDGLE-RVSVDGPHITVSQLKTLIQDQLQIPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLAHGS   87 (107)
T ss_dssp             EEEEECSSCEE-EEEECCTTSBHHHHHHHHHHHSCCCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTCCCTTC
T ss_pred             EEEEECCCCCE-EEEECCCCCcHHHHHHHHHHHhCcCcccCEEEECCccccccCccccccccccCCCCCCHHHCCCCCCC
Confidence            38899999876 78999 999999999999999999999999999888           4    5789999999987554


Q ss_pred             EEEe
Q 040111          107 VIFC  110 (133)
Q Consensus       107 ~~~~  110 (133)
                      .++.
T Consensus        88 ~L~l   91 (107)
T 1wf9_A           88 MVYL   91 (107)
T ss_dssp             EEEC
T ss_pred             EEEE
Confidence            4443

>1t0y_A Tubulin folding cofactor B; ubiquitin-like, cytoskeleton, microtubule, CESG, structural genomics, protein structure initiative, PSI; NMR {Caenorhabditis elegans} SCOP: d.15.1.1

Probab=99.25  E-value=5.2e-12  Score=86.66  Aligned_cols=65  Identities=8%  Similarity=-0.204  Sum_probs=52.9

Q ss_pred             cccCCCCCC-CceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCC---c---c-cCccccccccccEEeEEE
Q 040111           44 DFCKNPDPQ-NITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKF---P---F-FFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        44 i~Vk~~~g~-~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~g---k---~-L~d~~tL~dy~~~~~~~~  108 (133)
                      ++|+...+. .+.+++++++||++||++|++.+||||++|||+|.|   +   . ++|+++|++|++...+.|
T Consensus         9 l~V~~~~~~~~~e~~v~~~~TV~~lK~ki~~~~Gip~~~qrL~~~g~~~~~~~~l~~D~~tL~~y~i~~g~~i   81 (122)
T 1t0y_A            9 LEITTNATDFPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRI   81 (122)
T ss_dssp             EEEEESSCCSCEEEEEETTSBHHHHHHHHHHHHCCCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEE
T ss_pred             EEEEECCCCccEEEEeCCCCcHHHHHHHHHHHhCCCHHHeEEEEecCCCccccccCCCcCCHHHCCCCCCCEE
Confidence            445444333 678899999999999999999999999999999987   4   3 478999999999665544

>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=99.24  E-value=1.3e-12  Score=87.05  Aligned_cols=39  Identities=21%  Similarity=0.322  Sum_probs=36.5

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL   39 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L   39 (133)
                      |++++|+|+++|+|||+||+|+|+.||++|+|. +++|++
T Consensus        49 I~~k~gip~~qQrLI~~GKiL~D~~TL~~y~I~~gsti~v   88 (100)
T 1wju_A           49 IAETFGLQENYIKIVINKKQLQLGKTLEEQGVAHNVKAMV   88 (100)
T ss_dssp             HHHHTTCCSTTCEEEETTEECCTTSBHHHHTCCSSEEEEE
T ss_pred             HHHHHCcCHHHeEEEeCCeECCCCCcHHHcCCCCCCEEEE
Confidence            567899999999999999999999999999999 999954

>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=99.24  E-value=1.5e-12  Score=85.55  Aligned_cols=40  Identities=25%  Similarity=0.379  Sum_probs=37.7

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLG   40 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~   40 (133)
                      |++++|+|+++|||+|+|++|+|+.||++|+|+ +++|+|.
T Consensus        51 I~~k~Gip~~qQrLif~Gk~LkD~~TL~dY~I~dgstLhL~   91 (93)
T 3plu_A           51 LSLQIGTQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLELY   91 (93)
T ss_dssp             HHHHHTCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEE
T ss_pred             HHHHhCCCHHHEEEEeCCEEccCcCCHHHcCCCCCCEEEEE
Confidence            467899999999999999999999999999999 9999985

>2lxa_A Ubiquitin-like protein MDY2; ubiquitin-like domain, protein-protein interaction, SGT2 BIN domain, GET pathway, protein binding; NMR {Saccharomyces cerevisiae}

Probab=99.23  E-value=2.3e-12  Score=83.74  Aligned_cols=42  Identities=21%  Similarity=0.338  Sum_probs=39.2

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCcccccc-c-cccccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKI-Q-ESTLHLGWRA   43 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI-~-~stl~L~~~~   43 (133)
                      ++++|+|+++|||+|+|++|+|+.+|++|+| . +++|+|.+++
T Consensus        35 ~~~~gip~~~QrLi~~Gk~L~D~~tL~~y~I~~~~stl~v~~~~   78 (87)
T 2lxa_A           35 SEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKP   78 (87)
T ss_dssp             HTTSCSSSTTEEEEETTEECCTTCBHHHHCCCGGGCEEEEEECC
T ss_pred             HHhcCCChHHEEEEECCEECcCcCCHHHcCCCCCCCEEEEEcCC
Confidence            6778999999999999999999999999999 7 9999998775

>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative, hydrolase; NMR {Mus musculus}

Probab=99.22  E-value=2.6e-12  Score=82.92  Aligned_cols=67  Identities=13%  Similarity=0.187  Sum_probs=56.9

Q ss_pred             cccCCCCCCCceee-ccccCcHHHHHHHhhhhcCCCCCceEEEeCC--cccC---ccccccccccEEeEEEEeC
Q 040111           44 DFCKNPDPQNITLE-VESSDTIDNVKAKIQDKKRIPPPAEADLLKF--PFFF---FEEVLSFFWFVVVGVIFCG  111 (133)
Q Consensus        44 i~Vk~~~g~~~~l~-V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~g--k~L~---d~~tL~dy~~~~~~~~~~~  111 (133)
                      |.||+.+|+.. ++ +++++||.+||++|++++|+|+++|+|+|++  ++|.   |+.+|++|++...+.+++.
T Consensus         3 i~vr~~~G~~~-v~~l~~~~Tv~~Lk~~I~~~~gi~~~~qrL~~~~p~k~l~l~~~~~tL~~~gl~~g~~l~v~   75 (86)
T 2kzr_A            3 VRCKAKGGTHL-LQGLSSRTRLRELQGQIAAITGIAPGSQRILVGYPPECLDLSDRDITLGDLPIQSGDMLIVE   75 (86)
T ss_dssp             EEEEETTEEEE-ECSCCTTCBHHHHHHHHHHHTCCCTTTCCCEESSCCCCCCCCCSSCBTTTSSCCTTCEEECC
T ss_pred             EEEEcCCCCEE-eeecCCCCCHHHHHHHHHHHhCCCccceEEEeCCCCcccccCCCCCCHHHcCCCCCCEEEEE
Confidence            67899999654 66 9999999999999999999999999999874  7874   6789999999766555544

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster}

Probab=99.22  E-value=3.8e-12  Score=100.26  Aligned_cols=70  Identities=14%  Similarity=0.108  Sum_probs=60.5

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEE---eCCcccCccccccccccEEeE-EEEeCcee
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADL---LKFPFFFFEEVLSFFWFVVVG-VIFCGCRV  114 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~---~~gk~L~d~~tL~dy~~~~~~-~~~~~~~~  114 (133)
                      +.|+. +|+.+.+++++++||++||++|++++||||++|+|+   |+|+.|+|+.+|++|+|...+ +.+.|...
T Consensus         8 i~Vk~-~g~~~~v~v~~~~Tv~~lK~~I~~~tgVpp~~QkLi~~k~~Gk~l~D~~~L~~~~ik~g~~l~L~gs~~   81 (320)
T 3shq_A            8 VIVKW-SGKEYPVDLTDQDTVEVLRHEIFRKTQVRPERQKLLNLKYKGKTAADNVKISALELKPNFKLMMVGSTE   81 (320)
T ss_dssp             EEEEE-TTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGCEETTCBSSSSBCCTTSBTTSSCCC--CEEEEECCCC
T ss_pred             EEEEE-CCEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEeecccCCcccCccccHHHcCCCCCCEEEEEccch
Confidence            55664 688899999999999999999999999999999999   899999999999999997665 55667654

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

Probab=99.21  E-value=2.5e-12  Score=81.15  Aligned_cols=43  Identities=30%  Similarity=0.458  Sum_probs=39.5

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+|+++|+|+|+|++|+|+.+|++|||. +++|+|+++.
T Consensus        34 i~~~~gip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~l~l~~rl   77 (79)
T 3phx_B           34 VSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRL   77 (79)
T ss_dssp             HHHHHTCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECC
T ss_pred             HHhhcCCCHHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEec
Confidence            356789999999999999999999999999999 9999988764

>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=99.16  E-value=7.4e-12  Score=78.70  Aligned_cols=43  Identities=42%  Similarity=0.696  Sum_probs=39.5

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+|+++|+|+|+|++|+|+.+|++|||. +++|||.+++
T Consensus        34 i~~~~gip~~~qrL~~~g~~L~d~~tL~~~~i~~g~~i~l~~r~   77 (78)
T 2faz_A           34 IQELFHVEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLLVRQ   77 (78)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTCBTTTTTCCTTCEEEEEECC
T ss_pred             HHHHHCcChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEeC
Confidence            356789999999999999999999999999999 9999988764

>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=99.15  E-value=3.9e-12  Score=84.71  Aligned_cols=41  Identities=22%  Similarity=0.185  Sum_probs=38.2

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGW   41 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~   41 (133)
                      |++++|||+++|||+|+|++|+|+.||++|||. +++|+|..
T Consensus        58 Ia~k~Gip~~qQrLi~~Gk~L~D~~TL~dygI~~gstlhL~~   99 (100)
T 1uh6_A           58 IAAQTGTRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLELYY   99 (100)
T ss_dssp             HHHHHCCCGGGCEEEETTEECCSSCBHHHHTCCTTEEEEEEC
T ss_pred             HHHHhCCCHHHEEEEECCEECCCCCCHHHcCCCCCCEEEEEe
Confidence            467899999999999999999999999999999 99999864

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

Probab=99.15  E-value=4.7e-12  Score=81.53  Aligned_cols=43  Identities=28%  Similarity=0.373  Sum_probs=39.4

Q ss_pred             CCcccCCCCCCeEEEeCCEE-CCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQ-LEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~-L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+|+++|+|+|+|++ |+|+.+|++|||. +++|+|++++
T Consensus        40 I~~~~gip~~~QrLi~~Gk~lL~D~~tL~~y~I~~gs~i~lv~~p   84 (84)
T 2kk8_A           40 IERSQHIPVSKQTLIVDGIVILREDLTVEQCQIVPTSDIQLEVSS   84 (84)
T ss_dssp             HHHHHTCCGGGEEEEETTEECCCSSSBHHHHTCCTTSCEEEEECC
T ss_pred             HHHHHCcChHHEEEEECCEEecCCcCCHHHcCCCCCCEEEEEEcC
Confidence            45678999999999999999 9999999999999 9999988763

>4a20_A Ubiquitin-like protein MDY2; protein binding, GET-pathway, tail-anchored proteins; 1.78A {Saccharomyces cerevisiae} PDB: 2lxc_A 4goc_A

Probab=99.14  E-value=1.1e-11  Score=82.27  Aligned_cols=42  Identities=21%  Similarity=0.338  Sum_probs=39.0

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCcccccc-c-cccccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKI-Q-ESTLHLGWRA   43 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI-~-~stl~L~~~~   43 (133)
                      ++++|+|+++|||+|+|++|+|+.+|++|+| . +++|+|++++
T Consensus        53 ~~~~gip~~~QrLi~~Gk~L~D~~tL~dy~I~~~g~ti~lmvsk   96 (98)
T 4a20_A           53 SEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKP   96 (98)
T ss_dssp             HTTSCSCGGGEEEEETTEEECTTCBGGGSCCBTTBCEEEEEECC
T ss_pred             HHhcCCChhhEEEEECCEECcCcCCHHHcCcCCCCCEEEEEEeC
Confidence            5678999999999999999999999999999 9 9999998764

>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=99.13  E-value=7.3e-12  Score=78.98  Aligned_cols=43  Identities=19%  Similarity=0.416  Sum_probs=39.1

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+|+++|+|+|+|++|+|+.||++|+|. +++|++.++.
T Consensus        33 i~~~~gi~~~~qrL~~~G~~L~d~~tl~~~~i~~~~~i~l~~~~   76 (79)
T 2uyz_B           33 YCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQ   76 (79)
T ss_dssp             HHHHHTCCGGGEEEEETTEECCTTCCHHHHTCCTTEEEEEEECC
T ss_pred             HHHHHCCCcccEEEEECCEEeCCCCCHHHcCCCCCCEEEEEEec
Confidence            356789999999999999999999999999999 9999987653

>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=99.12  E-value=1.1e-11  Score=80.09  Aligned_cols=43  Identities=58%  Similarity=0.879  Sum_probs=38.9

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+|+++|+|+|+|++|+|+.+|++|||. +++|+|+++.
T Consensus        30 I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~l~l~~rl   73 (88)
T 4fbj_B           30 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLAL   73 (88)
T ss_dssp             HHHHHCCCGGGCEEEETTEECCTTSBTTTTTCCTTCEEEEECBC
T ss_pred             HHHHHCcChhHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEEC
Confidence            356789999999999999999999999999999 9999976654

>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=99.12  E-value=1.2e-11  Score=84.59  Aligned_cols=61  Identities=26%  Similarity=0.388  Sum_probs=47.0

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc--------cccccccccccccCCCCCCCceeeccccCcHHHH
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ--------ESTLHLGWRADFCKNPDPQNITLEVESSDTIDNV   67 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~--------~stl~L~~~~i~Vk~~~g~~~~l~V~~~~tV~~L   67 (133)
                      |+.++|||+++|||+|+|++|+|+.||++|||.        +++|||.++      .+|..-.+++.+-.+--+|
T Consensus        31 I~~~egIP~~qQrLi~~Gk~LeD~~TLsdy~I~~~~a~~q~~stL~L~lr------~~g~fe~l~i~~~s~pp~~   99 (118)
T 2fnj_B           31 VEGILKRPPEEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFR------ADDTFEALRIEPFSSPPEL   99 (118)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTSBHHHHTCCTTTSBTTBCEEEEEEEB------SSSCBCCCCBCCCCCCCC-
T ss_pred             HHHHhCCCHHHeEEEECCeECCCCCCHHHcCcccccccCCCCCEEEEEec------CCCceeeeEEecCCCCCCc
Confidence            467899999999999999999999999999998        578996554      4555555666555443333

>3v6c_B Ubiquitin; structural genomics, structural genomics consortium, SGC, UB protease, hydrolase-signaling protein complex; 1.70A {Homo sapiens} PDB: 3v6e_B

Probab=99.11  E-value=1.4e-11  Score=79.95  Aligned_cols=43  Identities=81%  Similarity=1.161  Sum_probs=39.5

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|||. +++|+|+++.
T Consensus        47 I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~rl   90 (91)
T 3v6c_B           47 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL   90 (91)
T ss_dssp             HHHHHCCCGGGCEEEETTEECCTTCBTGGGTCCTTCEEEEECCC
T ss_pred             HHhhhCCChhhEEEEECCeECCCcCcHHHCCCCCCCEEEEEEec
Confidence            356789999999999999999999999999999 9999988763

>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=99.10  E-value=4.1e-11  Score=82.80  Aligned_cols=42  Identities=36%  Similarity=0.531  Sum_probs=37.5

Q ss_pred             CcccCCCC--CCeEEEeCCEECCCCCCccccccc-c------ccccccccc
Q 040111            2 EDKEGIPP--GQQRSIFAGKQLEDGRTLADYKIQ-E------STLHLGWRA   43 (133)
Q Consensus         2 ~~~~gip~--~~Q~Li~~gk~L~D~~tL~~ygI~-~------stl~L~~~~   43 (133)
                      ++++|||+  ++|||||+||+|+|+.||++|+|. +      +++||+++.
T Consensus        53 ~dkegiP~~~~qQrLIy~GK~LeD~~TLsdy~I~~~~~~~~v~tmhlVlrl  103 (126)
T 1se9_A           53 REKENGPKTVKEVKLISAGKVLENSKTVKDYRSPVSNLAGAVTTMHVIIQA  103 (126)
T ss_dssp             TTCSSSCCSGGGEEEEETTEECCTTSBGGGGSCCTTSCTTCCEEEEEEECC
T ss_pred             cccccCCCChhhEEEEECCeECcCCCcHHHcCCCcCCccCCcEEEEEEecc
Confidence            46789997  799999999999999999999999 8      678977665

>2io1_B Small ubiquitin-related modifier 3 precursor; SUMO, SENP, ULP, complex, protein binding, hydrolase; 2.60A {Homo sapiens} SCOP: d.15.1.1

Probab=99.10  E-value=5.1e-11  Score=78.39  Aligned_cols=59  Identities=2%  Similarity=-0.079  Sum_probs=57.2

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCcccccccccc
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWF  102 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~  102 (133)
                      |+|++.+|+.+.++|.+++++..|++.++++.|+|+++|+|+|.|+.|.++.|+++|++
T Consensus        10 ikVk~~~g~~i~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~FdG~~l~~~~Tp~dl~m   68 (94)
T 2io1_B           10 LKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEM   68 (94)
T ss_dssp             EEEECTTSCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCTTTTTC
T ss_pred             EEEECCCCCEEEEEECCCCHHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCC
Confidence            78899999999999999999999999999999999999999999999999999999996

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

Probab=99.09  E-value=2.4e-11  Score=79.87  Aligned_cols=52  Identities=69%  Similarity=0.948  Sum_probs=39.1

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc-----cccCCCCCC
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA-----DFCKNPDPQ   52 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~-----i~Vk~~~g~   52 (133)
                      |++.+|+|+++|+|+|+|+.|+|+.+|++|||. +++|+|..+.     ++.++.+|+
T Consensus        30 I~~~~gi~~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~gG~~i~~~~v~~~   87 (98)
T 1yx5_B           30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGRDPNSSSVDKL   87 (98)
T ss_dssp             HHHHTCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCCCC-----------
T ss_pred             HHHHHCcChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEeCCCCCcCccccCCCc
Confidence            356789999999999999999999999999999 9999977664     455554443

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

Probab=99.09  E-value=3.3e-11  Score=75.92  Aligned_cols=43  Identities=42%  Similarity=0.696  Sum_probs=39.3

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++.+|+|+++|+|+|+|+.|+|+.+|++|||. +++|++.+++
T Consensus        37 i~~~~~i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~~   80 (81)
T 2dzi_A           37 VSEKLNVPVRQQRLLFKGKALADGKRLSDYSIGPNSKLNLVVKP   80 (81)
T ss_dssp             HHHHTCCCTTTCEEEETTEECCTTSBGGGGTCCSSBCCEEECCC
T ss_pred             HHHHHCcCHHHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            356789999999999999999999999999999 9999988764

>3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=99.09  E-value=2.2e-11  Score=81.55  Aligned_cols=43  Identities=16%  Similarity=0.304  Sum_probs=39.9

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|||+++|+|+|+|++|+|+.+|++|||. +++|+|+++.
T Consensus        31 I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~~i~~g~~i~lv~~~   74 (106)
T 3m62_B           31 LAQSISCEESQIKLIYSGKVLQDSKTVSECGLKDGDQVVFMVSQ   74 (106)
T ss_dssp             HHHTTTSCGGGCEEEETTEECCTTSBTTTTTCCTTCEEEEECCC
T ss_pred             HHHHHCCChhhEEEEECCEECCCcCCHHHcCCCCCCEEEEEEcC
Confidence            456789999999999999999999999999999 9999988775

>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=99.09  E-value=3.4e-11  Score=82.27  Aligned_cols=43  Identities=33%  Similarity=0.504  Sum_probs=38.5

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc--------cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ--------ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~--------~stl~L~~~~   43 (133)
                      |++++|||+++|||||+|++|+|+.||++|||.        +++|||.++.
T Consensus        31 I~~~~giPp~qQrLI~~Gk~LeD~kTL~dy~I~~~ta~~q~~atl~Lvlr~   81 (118)
T 4ajy_B           31 VEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRA   81 (118)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTSBTTTTTCCGGGSBTTBCEEEEEEECC
T ss_pred             HHHHHCCCHHHeEEEeCCeECCCcCCHHHcCCCcCcccCCCCCEEEEEEec
Confidence            467899999999999999999999999999985        4689987774

>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=99.08  E-value=1.5e-11  Score=81.01  Aligned_cols=43  Identities=19%  Similarity=0.416  Sum_probs=39.3

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|||+++|||+|+|++|+|+.||++|+|. +++|+|++++
T Consensus        51 i~~~~gip~~~qrLif~Gk~L~d~~tl~dy~i~~g~~I~l~~~~   94 (97)
T 1wyw_B           51 YCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQ   94 (97)
T ss_dssp             HHHHHTCCGGGEEEEETTEECCTTCCHHHHTCCTTCEEEEEESS
T ss_pred             HHHHHCCChhhEEEEECCeEcCCCCCHHHCCCCCCCEEEEEEec
Confidence            356789999999999999999999999999999 9999987653

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

Probab=99.08  E-value=2.3e-11  Score=78.22  Aligned_cols=42  Identities=33%  Similarity=0.609  Sum_probs=38.2

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCcccccccccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~~stl~L~~~   42 (133)
                      |++++|+|+++|+|+|+|++|+|+.+|++|||.+++|||++|
T Consensus        47 i~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i~g~~i~lv~R   88 (88)
T 4eew_A           47 IAASVSIPSEKQRLIYQGRVLQDDKKLQEYNVGGKVIHLVER   88 (88)
T ss_dssp             HHHHHTCCGGGEEEEETTEECCTTSBGGGGTCTTEEEEEEEC
T ss_pred             HHHHhCCCHHHEEEEECCEECCCCCcHHHcCCCCcEEEEEEC
Confidence            356789999999999999999999999999998889998764

>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=99.08  E-value=1.8e-11  Score=78.39  Aligned_cols=43  Identities=60%  Similarity=0.920  Sum_probs=39.0

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+|+++|+|+|+|++|+|+.+|++|+|. +++|+|.++.
T Consensus        42 i~~~~gip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~i~l~~rl   85 (88)
T 3dbh_I           42 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLRL   85 (88)
T ss_dssp             HHHHHCCCGGGCCEEETTEECCTTSBGGGGTCCTTCEEEECCCC
T ss_pred             HHHHHCcCHHHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            356789999999999999999999999999999 9999987653

>2daf_A FLJ35834 protein; hypothetical protein FLJ35834, ubiquitin-like domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.08  E-value=3.1e-11  Score=82.26  Aligned_cols=42  Identities=19%  Similarity=0.318  Sum_probs=39.4

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      ....++|+++|+|+|+||+|+|+.||.+|||+ +.++||+++.
T Consensus        47 s~~~~iP~e~qrLIy~GKiLKD~eTL~~~gIk~g~TIhLvi~s   89 (118)
T 2daf_A           47 SHLLGIPHSVLQIRYSGKILKNNETLVQHGVKPQEIVQVEIFS   89 (118)
T ss_dssp             HHHHTCCTTTEEEEETTEEECSSCCHHHHSCCSSCEEEEEEEE
T ss_pred             HhhhCCChHHEEEEECCeEcCCcchHHHcCCCCCCEEEEEEec
Confidence            34679999999999999999999999999999 9999999887

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.07  E-value=2.3e-11  Score=79.84  Aligned_cols=43  Identities=26%  Similarity=0.370  Sum_probs=38.7

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCC-CCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDG-RTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~-~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|||+++|+|+|+|++|+|+ .+|++|||. +++|+|+++.
T Consensus        44 I~~~~gip~~~QrLi~~Gk~L~D~~~tL~~ygI~~gstl~lv~r~   88 (94)
T 2kan_A           44 IHIVENTPIKRMQLYYSGIELADDYRNLNEYGITEFSEIVVFLKS   88 (94)
T ss_dssp             HHHHSSSCTTTEEEEETTEEECCTTSBHHHHTCCTTEEEEEEECC
T ss_pred             HHHHHCcCHHHEEEEECCEECCCCcccHHHCCCCCCCEEEEEEeC
Confidence            456789999999999999999999 999999999 9999976553

>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=98.64  E-value=1.6e-11  Score=76.73  Aligned_cols=43  Identities=33%  Similarity=0.621  Sum_probs=39.6

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++.+|+|+++|+|+|+|++|+|+.+|++|||. +++|||.++.
T Consensus        30 i~~~~gi~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~rl   73 (76)
T 3b1l_X           30 VAKQQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRP   73 (76)
Confidence            567899999999999999999999999999999 9999987753

>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling proteins; 1.15A {Saccharomyces cerevisiae} SCOP: d.15.1.1 PDB: 2bwe_S

Probab=99.06  E-value=3.7e-11  Score=75.00  Aligned_cols=42  Identities=40%  Similarity=0.664  Sum_probs=38.3

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |++.+|+|+++|+|+|+|+.|+|+.+|++|||. +++|++..+
T Consensus        33 i~~~~~i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~   75 (77)
T 2bwf_A           33 INKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS   75 (77)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEEC
T ss_pred             HHHHhCCCHHHEEEEECCeEcCCCCCHHHcCCCCCCEEEEEEc
Confidence            356789999999999999999999999999999 999998765

>1wm3_A Ubiquitin-like protein SMT3B; ubiquitin fold, half-open barrel, two helices, protein transport; 1.20A {Homo sapiens} SCOP: d.15.1.1 PDB: 1wm2_A 3uin_B 3uio_B 2ckh_B

Probab=99.06  E-value=1.7e-10  Score=72.11  Aligned_cols=63  Identities=2%  Similarity=-0.109  Sum_probs=58.6

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVG  106 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~  106 (133)
                      +.|++.+|+.+.+.+.++++++.|+...+++.|+|+++++++|.|+.|.++.|.++|++-...
T Consensus         4 lkV~~~~g~~v~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~~l~~~~Tp~~l~medgD   66 (72)
T 1wm3_A            4 LKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDED   66 (72)
T ss_dssp             EEEECTTSCEEEEEECTTSCTHHHHHHHHHHHTCCTTTCEEEETTEECCTTCCTTTTTCCTTE
T ss_pred             EEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcceEEEEECCEEcCCCCCHHHcCCCCCC
Confidence            678888999999999999999999999999999999999999999999999999999975433

>4hcn_B Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidase, NEDD8, protein binding; 2.60A {Saccharomyces cerevisiae}

Probab=99.06  E-value=3.5e-11  Score=79.22  Aligned_cols=43  Identities=81%  Similarity=1.161  Sum_probs=39.2

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+|+++|+|+|+|++|+|+.+|++|+|. +++|+|+++.
T Consensus        52 I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~i~l~~rl   95 (98)
T 4hcn_B           52 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL   95 (98)
T ss_dssp             HHHHHCCCGGGCEEEETTEECCTTCBSGGGTCCTTEEEEEECBC
T ss_pred             HHHHhCCChhHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEec
Confidence            456789999999999999999999999999999 9999987663

>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=99.05  E-value=3.4e-11  Score=76.54  Aligned_cols=43  Identities=70%  Similarity=1.023  Sum_probs=38.8

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++++|+++|+|+|+|++|+|+.+|++|+|. +++|++.++.
T Consensus        33 i~~~~~ip~~~qrL~~~g~~L~d~~tL~~~~i~~~~~i~l~~rl   76 (85)
T 3n3k_B           33 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIHNHSALYLLLKL   76 (85)
T ss_dssp             HHHHHCCCGGGEEEEETBEECCTTCBTTTTTCCTTCEEEEEECC
T ss_pred             HHHHHCCCHHHEEEEECCeECCCCCCHHHCCCCCCCEEEEEEec
Confidence            356789999999999999999999999999999 9999976653

>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=3.3e-11  Score=78.54  Aligned_cols=41  Identities=34%  Similarity=0.401  Sum_probs=37.0

Q ss_pred             Cccc--CCCCCCeEEEeCCEECCCCCCcccc--ccc-ccccccccc
Q 040111            2 EDKE--GIPPGQQRSIFAGKQLEDGRTLADY--KIQ-ESTLHLGWR   42 (133)
Q Consensus         2 ~~~~--gip~~~Q~Li~~gk~L~D~~tL~~y--gI~-~stl~L~~~   42 (133)
                      ++++  ++|+++|||+|+|++|+|+.+|++|  +|. +++|||+++
T Consensus        40 ~~~~~~~i~~~~QrLi~~Gk~L~D~~tL~~~~~~i~~~~~i~lv~~   85 (93)
T 1wgd_A           40 SRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVCN   85 (93)
T ss_dssp             HHHSTTCCCTTTCEEEETTEECCSSSCHHHHSCSSSCSEEEEEECC
T ss_pred             HHHhcCCCChHHeEEEECCEECcCcCCHHHHhcCCCCCCEEEEEeC
Confidence            3455  9999999999999999999999999  999 999997654

>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=99.05  E-value=3.8e-11  Score=74.47  Aligned_cols=42  Identities=60%  Similarity=0.909  Sum_probs=38.4

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|||. +++|++.++
T Consensus        30 i~~~~~i~~~~q~L~~~g~~L~d~~tL~~~~i~~g~~i~l~~~   72 (76)
T 1ndd_A           30 VEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLA   72 (76)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEEC
T ss_pred             HHHHHCcChHHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEe
Confidence            356789999999999999999999999999999 999998765

>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=99.05  E-value=4.5e-11  Score=76.15  Aligned_cols=39  Identities=28%  Similarity=0.483  Sum_probs=36.3

Q ss_pred             cCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            5 EGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         5 ~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      +|+|+++|+|+|+|++|+|+.+|++|||. +++|+|+.+.
T Consensus        42 ~gip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~i~l~~~~   81 (85)
T 2wyq_A           42 DAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTK   81 (85)
T ss_dssp             TTCCGGGEEEEETTEECCTTSBGGGGCCCTTSEEEEEEC-
T ss_pred             cCCCHHHeEEEECCEECcCCCCHHHcCCCCCCEEEEEEcC
Confidence            79999999999999999999999999999 9999987654

>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=99.05  E-value=4e-11  Score=77.16  Aligned_cols=43  Identities=35%  Similarity=0.491  Sum_probs=38.8

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+|+++|+|+|+|++|+|+.+|++|+|. +++|||+++.
T Consensus        39 i~~~~gip~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~~   82 (89)
T 1wy8_A           39 VWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVRP   82 (89)
T ss_dssp             HHHHSCCCTTTEEEEETTEECCSSSBHHHHTCCTTCEEEEEECC
T ss_pred             HHHHHCcChhhEEEEECCeECCCCCCHHHCCCCCCCEEEEEEeC
Confidence            356789999999999999999999999999999 9999976553

>2io0_B Small ubiquitin-related modifier 2 precursor; SUMO, SENP, ULP, complex, protein binding, hydrolase; 2.30A {Homo sapiens} SCOP: d.15.1.1

Probab=99.04  E-value=5.1e-10  Score=73.19  Aligned_cols=59  Identities=2%  Similarity=-0.079  Sum_probs=57.1

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCcccccccccc
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWF  102 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~  102 (133)
                      |.|++.+|+.+.++|.+++++..|+...+++.|+|+++++++|.|+.|.++.|.++|++
T Consensus         8 ikVk~~~g~~v~~~vk~~t~l~kl~~~y~~~~gi~~~~~rf~FdG~~l~~~~Tp~dl~m   66 (91)
T 2io0_B            8 LKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEM   66 (91)
T ss_dssp             EEEECTTSCEEEEEEETTSCTHHHHHHHHHHTTCCSTTEEEEETTEECCTTCCTTTTTC
T ss_pred             EEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCC
Confidence            78888999999999999999999999999999999999999999999999999999997

>4b6w_A Tubulin-specific chaperone; CAP-Gly, ubiquitin-like; HET: MSE; 2.35A {Trypanosoma brucei brucei strain 927}

Probab=99.04  E-value=2.5e-11  Score=78.62  Aligned_cols=42  Identities=17%  Similarity=0.234  Sum_probs=37.6

Q ss_pred             CCcccCCCCCCeEEEe-------CCEECCCCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIF-------AGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~-------~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |++++|||+++|||+|       .|++|+|+.+|++|||. |++|||+-+
T Consensus        34 i~~~~Gip~~~QrLi~~~~~~~~~g~~l~d~~tL~~Y~i~~g~~ihlvd~   83 (86)
T 4b6w_A           34 VFTHFATPPEYMQLQLIDDRGITIEKNMANDKQLGYYQCRDEFVIHVVDL   83 (86)
T ss_dssp             HHTTSCCCGGGEEEEEECTTSCEEESSCCTTSBGGGGTCCTTCEEEEEEC
T ss_pred             HHHHHCCCHHHEEEEEecCCCCceeeEcCCCCCHHHCCCCCCCEEEEEeC
Confidence            4678999999999996       58899999999999999 999998643

>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=99.04  E-value=4.5e-11  Score=76.52  Aligned_cols=43  Identities=42%  Similarity=0.557  Sum_probs=38.7

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+|+++|+|+|+|++|+|+.+|++|+|. +++|+|.++.
T Consensus        37 i~~~~gi~~~~qrL~~~Gk~L~d~~tL~~~~i~~g~~i~l~~~~   80 (87)
T 1wh3_A           37 IEDQQGLPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKK   80 (87)
T ss_dssp             HHHHTCCCTTTEEEEETTEECCSSSBHHHHTCCTTEEEEEEECS
T ss_pred             HHHHhCCChHHEEEEECCEEccCCCCHHHCCCCCCCEEEEEEec
Confidence            356789999999999999999999999999999 9999976553

>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=99.04  E-value=4.7e-11  Score=77.07  Aligned_cols=43  Identities=35%  Similarity=0.614  Sum_probs=38.7

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccccccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~~stl~L~~~~   43 (133)
                      |++++|+|+++|+|+|+|++|+|+.+|++|||.+++|||+++.
T Consensus        35 i~~~~gip~~~qrLi~~Gk~L~d~~tL~~~~i~g~~i~l~~~~   77 (90)
T 4dwf_A           35 IAASVSIPSEKQRLIYQGRVLQDDKKLQEYNVGGKVIHLVERA   77 (90)
T ss_dssp             HHHHHTCCGGGEEEEETTEECCTTSBGGGGTCTTEEEEEEECC
T ss_pred             HHHHhCCCHHHEEEEECCeECCCCCCHHHcCCCCcEEEEEecC
Confidence            4567899999999999999999999999999988899977664

>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure, northeast structural genomics consortium, protein structure initiative, NESG; NMR {Homo sapiens}

Probab=99.03  E-value=2.3e-11  Score=78.57  Aligned_cols=42  Identities=31%  Similarity=0.478  Sum_probs=38.3

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |++++|||+++|+|+|+|++|+|+.+|++|||. +++|+|..+
T Consensus        34 I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~~I~~g~~i~l~~~   76 (88)
T 2hj8_A           34 VSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLR   76 (88)
T ss_dssp             HHHHTCSCTTTEEEESSSSCCCTTSBHHHHHCSTTCEEEEEEC
T ss_pred             HHHHhCCChhHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEE
Confidence            356789999999999999999999999999999 999997554

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.02  E-value=7.6e-11  Score=75.85  Aligned_cols=42  Identities=26%  Similarity=0.332  Sum_probs=38.3

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |++.+|+|+++|+|+|+|++|+|+.+|++|||. +++|+|+.+
T Consensus        41 I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~l~l~~s   83 (85)
T 2kd0_A           41 LQPITNVLPRGQKLIFKGKVLVETSTLKQSDVGSGAKLMLMAS   83 (85)
T ss_dssp             HHHHHCCCTTTCEEEETTEECCTTCBTTTTTCCTTEEEEEECC
T ss_pred             HHHHHCcChHHEEEEECCeECCCcCCHHHCCCCCCCEEEEEEe
Confidence            356789999999999999999999999999999 999998764

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

Probab=99.02  E-value=5.6e-11  Score=78.97  Aligned_cols=42  Identities=40%  Similarity=0.664  Sum_probs=38.8

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |++++|+|+++|+|+|+|++|+|+.+|++|||. +++|+|+.+
T Consensus        57 I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~gI~~g~tI~lv~~   99 (101)
T 3m63_B           57 INKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS   99 (101)
T ss_dssp             HHHHHSCCSTTCCEEETTEECCTTSBTTTTTCCTTEEEEECCC
T ss_pred             HHHHHCcChHHEEEEECCEECCCcCcHHHCCCCCCCEEEEEeC
Confidence            356789999999999999999999999999999 999998765

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

Probab=99.02  E-value=3.3e-11  Score=78.78  Aligned_cols=43  Identities=35%  Similarity=0.516  Sum_probs=39.1

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+|+++|+|+|+|++|+|+.+|++|+|. +++|+|+++.
T Consensus        47 I~~~~gip~~~qrLi~~Gk~L~D~~tL~~y~I~~gstI~lv~rl   90 (93)
T 2l7r_A           47 VASLEGIAPEDQVVLLAGAPLEDEATLGQCGVEALTTLEVAGRM   90 (93)
T ss_dssp             HHHHHTCCGGGCEEEETTEECCTTSBHHHHTCCSSCEEEEECCC
T ss_pred             HHHHhCcChhHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEec
Confidence            456789999999999999999999999999999 9999987653

>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=99.02  E-value=1e-10  Score=76.58  Aligned_cols=39  Identities=31%  Similarity=0.508  Sum_probs=36.5

Q ss_pred             cCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            5 EGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         5 ~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      +|+|+++|+|+|+|++|+|+.+|++|||. +++|+|+++.
T Consensus        37 ~gip~~~qrLi~~Gk~L~D~~tL~~ygI~~g~~i~l~~~~   76 (95)
T 1uel_A           37 DAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTK   76 (95)
T ss_dssp             TTCCTTTEEEEETTEECCTTSBGGGGTCCSSSEEEEEESS
T ss_pred             CCCChhhEEEEECCEECCCcCcHHHCCCCCCCEEEEEEeC
Confidence            79999999999999999999999999999 9999976654

>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=99.02  E-value=6.3e-11  Score=75.17  Aligned_cols=42  Identities=79%  Similarity=1.079  Sum_probs=38.3

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |++++++|+++|+|+|+|+.|+|+.+|++|+|. +++|+|.++
T Consensus        33 i~~~~~i~~~~qrL~~~g~~L~d~~tL~~~~i~~~~~l~l~~r   75 (85)
T 3mtn_B           33 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKWSTLFLLLR   75 (85)
T ss_dssp             HHHHHCCCGGGCEEEETTEECCTTSBTGGGTCCTTCEEEEECC
T ss_pred             HHHHHCcChHHEEEEECCEECCCCCCHHHcCCCCCCEEEEEEE
Confidence            356789999999999999999999999999999 999997654

>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=99.01  E-value=7e-11  Score=77.03  Aligned_cols=43  Identities=81%  Similarity=1.161  Sum_probs=38.8

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|||. +++|+|+++.
T Consensus        31 i~~~~gip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~i~l~~r~   74 (96)
T 3k9o_B           31 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL   74 (96)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECC
T ss_pred             HHhhhCCChhHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEEc
Confidence            356789999999999999999999999999999 9999976554

>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=99.01  E-value=8.1e-11  Score=72.98  Aligned_cols=42  Identities=83%  Similarity=1.199  Sum_probs=38.3

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |++..|+|+++|+|+|+|+.|+|+.+|++|||. +++|++.++
T Consensus        30 i~~~~~i~~~~q~L~~~g~~L~d~~tL~~~~i~~g~~i~l~~~   72 (76)
T 3a9j_A           30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLR   72 (76)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTCBTGGGTCCTTCEEEEEEC
T ss_pred             HHHHHCcCHHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEEe
Confidence            356789999999999999999999999999999 999997765

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

Probab=99.01  E-value=7e-11  Score=76.35  Aligned_cols=42  Identities=83%  Similarity=1.199  Sum_probs=37.7

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |++++|+|+++|+|+|+|++|+|+.+|++|||. +++|+|.++
T Consensus        39 I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~r   81 (88)
T 1sif_A           39 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR   81 (88)
T ss_dssp             HHHHHCCCGGGCEEEETTEECCTTSBSGGGTCCTTCEEEEEC-
T ss_pred             HHHHHCcChhhEEEEECCEECCCCCcHHHcCCCCCCEEEEEEe
Confidence            356789999999999999999999999999999 999997654

>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=98.99  E-value=5.4e-11  Score=77.80  Aligned_cols=43  Identities=30%  Similarity=0.298  Sum_probs=38.8

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+|+++|+|+|+|++|+|+.+|++|+|. +++|||+++.
T Consensus        46 I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~   89 (96)
T 1wx8_A           46 ISKYLHCNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVRS   89 (96)
T ss_dssp             HHHHTCSCTTTBCCEETTEECCTTSCHHHHTCCTTEEEECCBCC
T ss_pred             HHHHhCCCHHHEEEEECCEECCCcCCHHHCCCCCCCEEEEEEeC
Confidence            356789999999999999999999999999999 9999976553

>1wgh_A Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: d.15.1.1

Probab=98.99  E-value=1.4e-10  Score=79.11  Aligned_cols=40  Identities=30%  Similarity=0.434  Sum_probs=35.2

Q ss_pred             ccCC--CCCCeEEEeCCEECCCCCCccccccc-c--ccccccccc
Q 040111            4 KEGI--PPGQQRSIFAGKQLEDGRTLADYKIQ-E--STLHLGWRA   43 (133)
Q Consensus         4 ~~gi--p~~~Q~Li~~gk~L~D~~tL~~ygI~-~--stl~L~~~~   43 (133)
                      ++++  |+++|||||+||+|+|+.||++|+|. +  +++||+++.
T Consensus        55 ke~~p~p~~qqrLIy~GK~LeD~~TL~~y~I~~~~~~tlhLvlr~   99 (116)
T 1wgh_A           55 EEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLVARE   99 (116)
T ss_dssp             SCCCCCCTTTEEEEETTEEECSSCBTTTTTCCSSCEEEEEEEECS
T ss_pred             ccCCCCChHHEEEEECCcCCCCCCcHHHcCCCCCCceEEEEEccC
Confidence            5675  69999999999999999999999997 5  688988776

>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=98.99  E-value=7.9e-11  Score=78.69  Aligned_cols=43  Identities=28%  Similarity=0.526  Sum_probs=39.1

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|||+++|+|+|+|++|+|+.+|++|||. +++|||+++.
T Consensus        53 I~~~~gip~~~qrLi~~Gk~L~D~~tL~~ygI~~g~ti~lv~~~   96 (106)
T 1ttn_A           53 LHAAEGVEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQ   96 (106)
T ss_dssp             HHHTTCCCSTTCEEEETTEECCTTSHHHHCCCSSSCEEEEECCC
T ss_pred             HHHHHCcCcccEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            356799999999999999999999999999999 9999987654

>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=98.98  E-value=1.1e-10  Score=78.63  Aligned_cols=43  Identities=81%  Similarity=1.161  Sum_probs=39.1

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+|+++|+|+|+|++|+|+.+|++|+|. +++|||+++.
T Consensus        65 I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~gI~~gs~I~l~~rl  108 (111)
T 3vdz_A           65 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  108 (111)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTSBTTTTTCCTTCEEEEEECC
T ss_pred             HHHHhCCChHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEec
Confidence            356789999999999999999999999999999 9999987663

>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=1e-10  Score=76.96  Aligned_cols=43  Identities=23%  Similarity=0.377  Sum_probs=39.2

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRAD   44 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~i   44 (133)
                      |++++|||+++|+|+|.|++|+|+ +|++|||. +++|+|+.+.-
T Consensus        37 I~~~tgip~~~QkLi~~Gk~L~D~-tL~~~~I~~g~~i~l~~~~~   80 (96)
T 1wgg_A           37 LFALTGVQPARQKVMVKGGTLKDD-DWGNIKMKNGMTVLMMGSAD   80 (96)
T ss_dssp             HHHHTCCCTTTSCCEETTEECCSS-CCCSCCCCSSCEEECCCCCC
T ss_pred             HHHHHCcCHHHeEEEECCcCCCCC-CHHHCCCCCCCEEEEEecch
Confidence            467899999999999999999999 99999999 99999987663

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A

Probab=98.97  E-value=1.1e-10  Score=78.26  Aligned_cols=42  Identities=21%  Similarity=0.188  Sum_probs=38.3

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCcccccc-c-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKI-Q-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI-~-~stl~L~~~   42 (133)
                      |++++|||+++|||+|+|+.++|+.||.+||| . |+++||.+.
T Consensus        56 I~~k~Gipp~~QRli~ggkll~D~~TL~~ygI~~~G~t~hL~l~   99 (105)
T 4dbg_A           56 VFLDYGFPPVLQQWVIGQRLARDQETLHSHGVRQNGDSAYLYLL   99 (105)
T ss_dssp             HHHHHCCCGGGEEEEETTEEECTTCBTGGGTCCSTTCEEEEEEC
T ss_pred             HHHHhCCCHHHEEEeccCeEccCcCcHHHcCCCCCCCEEEEEEE
Confidence            45789999999999999999999999999999 6 999998764

>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=98.97  E-value=7.8e-11  Score=78.08  Aligned_cols=43  Identities=35%  Similarity=0.428  Sum_probs=38.9

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+|+++|+|+|+|++|+|+.+|++|||. +++|+|+++.
T Consensus        51 I~~~~gip~~~QrLi~~Gk~L~D~~tL~~ygI~~gstI~l~~r~   94 (100)
T 1yqb_A           51 ISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKR   94 (100)
T ss_dssp             HHHHHTCCGGGEEEEETTEECCTTSBHHHHTCCTTCEEEEEECC
T ss_pred             HHHHHCcChhhEEEEECCEECCCcCcHHHCCCCCCCEEEEEEcC
Confidence            356789999999999999999999999999999 9999977653

>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=98.96  E-value=1.2e-10  Score=78.38  Aligned_cols=42  Identities=29%  Similarity=0.371  Sum_probs=38.2

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |++.+|||+++|+|+|+|++|+|+.+|++|||. +++|+|+++
T Consensus        61 I~~~~gip~~~QrL~~~Gk~L~D~~tL~~y~I~~g~~l~l~~r  103 (111)
T 1we6_A           61 IAGEIQIPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLR  103 (111)
T ss_dssp             HHHHTTCCTTTSEEECSSSBCCTTSBTTTTTCSSSCEEEEECS
T ss_pred             HHHHHCCCHHHeEEEECCEECCCCCcHHHCCCCCCCEEEEEEE
Confidence            456789999999999999999999999999999 999996554

>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=98.96  E-value=1.2e-10  Score=78.83  Aligned_cols=42  Identities=29%  Similarity=0.644  Sum_probs=38.3

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |++.+|||+++|+|+|+|++|+|+.+|++|+|. +++|||+++
T Consensus        65 I~~~~gip~~~QrL~~~Gk~L~D~~tL~~y~i~~g~~i~lv~r  107 (115)
T 1we7_A           65 IHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMASGAVIHLALK  107 (115)
T ss_dssp             HHHHSSCCTTTEEEEETTEEECTTSBHHHHTCCSSCEEEEEEC
T ss_pred             HHHHHCCChHHEEEEECCEECCCCCCHHHCCCCCCCEEEEEEE
Confidence            356789999999999999999999999999999 999997654

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B

Probab=98.96  E-value=2e-10  Score=82.87  Aligned_cols=43  Identities=81%  Similarity=1.161  Sum_probs=40.4

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+|+++|+|+|+|++|+|+.+|++|||. +++|||+++.
T Consensus        30 I~~~~gip~~~QrLi~~Gk~L~D~~tL~~y~I~~gstI~Lvlrl   73 (169)
T 3l0w_B           30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL   73 (169)
T ss_dssp             HHHHHCCCTTTEEEEETTEECCTTSBGGGGTCCTTCEEEEEECC
T ss_pred             HHHHHCcCHHHEEEEECCccccCcCcHHHcCCCCCCEEEEEEEe
Confidence            456789999999999999999999999999999 9999999886

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=98.95  E-value=1.5e-10  Score=76.78  Aligned_cols=43  Identities=35%  Similarity=0.363  Sum_probs=38.8

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++.+|+|+++|+|+|+|++|+|+.+|++|||. +++|+|..+.
T Consensus        54 I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~gI~~g~~I~l~~~~   97 (101)
T 2klc_A           54 ISKRFKSHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKT   97 (101)
T ss_dssp             HHHHHTCCGGGEEEEETTEEECTTCCTGGGTCCTTCEEEEEECC
T ss_pred             HHHHHCcChhhEEEEECCEECCCcCcHHHcCCCCCCEEEEEEcC
Confidence            356789999999999999999999999999999 9999987653

>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=98.94  E-value=1.7e-10  Score=76.89  Aligned_cols=43  Identities=35%  Similarity=0.428  Sum_probs=39.0

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|||+++|+|+|+|+.|+|+.+|++|+|. +++|||+++.
T Consensus        46 I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~   89 (106)
T 1wx7_A           46 ISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKR   89 (106)
T ss_dssp             HHHHHTCCTTTEEEEETTEECCTTSCHHHHTCCTTEEEEEEECC
T ss_pred             HHHHHCcChhhEEEEECCEECCCcCcHHHcCCCCCCEEEEEEcC
Confidence            356789999999999999999999999999999 9999977654

>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=98.93  E-value=9.4e-11  Score=80.83  Aligned_cols=47  Identities=72%  Similarity=1.000  Sum_probs=0.5

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccccccCCCCCC
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRADFCKNPDPQ   52 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~i~Vk~~~g~   52 (133)
                      |++.+|||+++|+|+|+|++|+|+.||++|||. +++|+|+     ++...|.
T Consensus        30 I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~~I~~gsti~l~-----~rl~GG~   77 (128)
T 3u5e_m           30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV-----LRLRGGI   77 (128)
T ss_dssp             ----------------------------------------------------C
T ss_pred             HHHHhCcChHHEEEEECCEECCCCCchhhhccCCCCEEEEE-----EEcCCCC
Confidence            567899999999999999999999999999999 9999954     4555554

>3a4r_A Nfatc2-interacting protein; ubiquitin fold, coiled coil, cytoplasm, methylation, nucleus, transcription; 1.00A {Mus musculus} PDB: 3a4s_C 3rd2_A

Probab=98.93  E-value=6.4e-10  Score=70.74  Aligned_cols=63  Identities=2%  Similarity=-0.065  Sum_probs=58.2

Q ss_pred             cccCCCCCC-CceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeE
Q 040111           44 DFCKNPDPQ-NITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVG  106 (133)
Q Consensus        44 i~Vk~~~g~-~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~  106 (133)
                      |.|++.+|+ .+.+.|.+++++..|+...+++.|+++++++++|.|+.|.++.|.++|++-..-
T Consensus        10 ikV~~~~g~~~i~~~i~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~~l~~~~Tp~~l~medgD   73 (79)
T 3a4r_A           10 LRVQGKEKHQMLEISLSPDSPLKVLMSHYEEAMGLSGHKLSFFFDGTKLSGKELPADLGLESGD   73 (79)
T ss_dssp             EEEECSSTTCEEEEEECTTSCHHHHHHHHHHHHTCTTCCCEEEETTEECCSCCCHHHHTCCTTC
T ss_pred             EEEEeCCCCEEEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCC
Confidence            788899996 789999999999999999999999999999999999999999999999975433

>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=98.93  E-value=2.2e-10  Score=76.62  Aligned_cols=42  Identities=33%  Similarity=0.517  Sum_probs=38.1

Q ss_pred             Cccc--CCCCCC-eEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            2 EDKE--GIPPGQ-QRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         2 ~~~~--gip~~~-Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      ++++  |+|+++ |+|+|+|++|+|+.+|++|||. +++|||+.+.
T Consensus        55 ~~~~~~gip~~~~qrLi~~Gk~L~D~~tL~~y~i~~g~~i~lv~~~  100 (107)
T 1x1m_A           55 AGKLQESVPDPELIDLIYCGRKLKDDQTLDFYGIQPGSTVHVLRKS  100 (107)
T ss_dssp             HHHCTTTCCCSSSEEEEETTEECCTTCBHHHHTCCTTCEEEEEESS
T ss_pred             HHHhccCCChhhcEEEEECCeECCCCCcHHHcCCCCCCEEEEEeCC
Confidence            4556  999999 9999999999999999999999 9999987654

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=98.93  E-value=2.4e-10  Score=78.68  Aligned_cols=43  Identities=35%  Similarity=0.346  Sum_probs=38.5

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|||+++|+|+|+|++|+|+.+|.+|||. +++|+|+.+.
T Consensus        61 I~~~~gip~~~QrLi~~Gk~L~D~~tL~dygI~~gstI~lv~~~  104 (125)
T 1j8c_A           61 ISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIKR  104 (125)
T ss_dssp             HHHHHCSCSSSEEEEETTEEESTTSCGGGTTCSSSEEEEEEEC-
T ss_pred             HHHHHCcCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEEecc
Confidence            356789999999999999999999999999999 9999976654

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

Probab=98.92  E-value=2e-10  Score=84.40  Aligned_cols=43  Identities=81%  Similarity=1.161  Sum_probs=39.3

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|||+++|+|+|+|++|+|+.+|++|+|. +++|||+++.
T Consensus       135 I~~~~gIp~~~QrLi~~Gk~L~D~~tL~dygI~~gstI~Lvlrl  178 (189)
T 3q3f_A          135 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  178 (189)
T ss_dssp             HHHHHCCCGGGCCEEETTEECCTTCBGGGGTCCTTCEEEECCCC
T ss_pred             HHhccCCCHHHEEEEECCEECCCCCCHHHCCCCCCCEEEEEEEc
Confidence            456789999999999999999999999999999 9999977664

>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=98.92  E-value=2.2e-10  Score=74.38  Aligned_cols=43  Identities=19%  Similarity=0.357  Sum_probs=39.3

Q ss_pred             CCcccCCCCCCeEEE---eCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSI---FAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li---~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|||+++|+|+   |.|++|+|+.+|++|+|. +++|+|+...
T Consensus        37 I~~~~gip~~~QkLi~~k~~Gk~L~D~~~L~~~~i~~g~~l~l~~~~   83 (90)
T 1v5t_A           37 LKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMGTR   83 (90)
T ss_dssp             HHHHTCCCTTTCEEESCEETTEECCTTSBHHHHTCCTTEEEEEECCC
T ss_pred             HHHHHCcCHHHeEEEeeccCCcCcCCCCCHHHcCCCCCCEEEEEecC
Confidence            467899999999999   999999999999999999 9999987654

>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=98.91  E-value=1.3e-10  Score=82.71  Aligned_cols=43  Identities=81%  Similarity=1.161  Sum_probs=0.0

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++.+|||+++|+|+|+|++|+|+.+|++|||. +++|+|+++.
T Consensus        30 I~~~~gip~~~QrLi~~Gk~L~D~~tL~dygI~~gstL~Lvlrl   73 (152)
T 3u5c_f           30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL   73 (152)
T ss_dssp             --------------------------------------------
T ss_pred             HHHHhCCCHHHEEEEECCEEccccCcHHHcCCCCCCEEEEEeec
Confidence            577899999999999999999999999999999 9999988876

>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=98.88  E-value=1.5e-09  Score=71.12  Aligned_cols=62  Identities=2%  Similarity=-0.111  Sum_probs=58.0

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEe
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVV  105 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~  105 (133)
                      |.|++.+|+.+.+.|.+++++..|+...+++.|+++++++|+|.|+.|.++.|+++|++-..
T Consensus        20 ikV~~~~g~~i~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~~l~~~~Tp~dl~medg   81 (93)
T 2d07_B           20 LKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDE   81 (93)
T ss_dssp             EEEECTTSCEEEEEEETTSCHHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCTTTTTCCTT
T ss_pred             EEEECCCCCEEEEEEccCCHHHHHHHHHHHHhCCCccceEEEECCEEcCCCCCHHHcCCCCC
Confidence            78888899989999999999999999999999999999999999999999999999997433

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

Probab=98.88  E-value=5.7e-10  Score=75.03  Aligned_cols=43  Identities=81%  Similarity=1.161  Sum_probs=38.9

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+|+++|+|+|+|+.|+|+.+|++|||. +++|+|.++.
T Consensus        65 I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~gI~~gs~I~l~~rl  108 (111)
T 2ojr_A           65 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  108 (111)
T ss_dssp             HHHHHCCCTTTEEEEETTEECCSSCBTTTTTCCTTCEEEEEECC
T ss_pred             HHHHHCcCcccEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            356789999999999999999999999999999 9999987653

>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=98.88  E-value=3.4e-10  Score=73.42  Aligned_cols=43  Identities=30%  Similarity=0.455  Sum_probs=37.6

Q ss_pred             CCcccCCCCCCeEEEeCCEECCC-CCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLED-GRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D-~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+|+++|+|+|.|++|+| +.+|++|||. +++|+|+.+.
T Consensus        41 i~~~~gip~~~qrL~~~Gk~L~D~~~~L~~~~i~~g~~i~l~~~~   85 (92)
T 1wxv_A           41 VEEVIGVPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVMLIGKK   85 (92)
T ss_dssp             HHHHTCCCTTTCEEEETTEEECCSSSBHHHHTCCSSEEEEEESCC
T ss_pred             HHHHHCcCHHHEEEEECCeecCCCcccHHHCCCCCCCEEEEEecC
Confidence            35678999999999999999988 6689999999 9999986543

>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=98.87  E-value=2.3e-10  Score=75.90  Aligned_cols=43  Identities=19%  Similarity=0.363  Sum_probs=38.1

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCC-CCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDG-RTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~-~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|||+++|+|+|+|++|+|+ .+|++|||. +++|+|..+.
T Consensus        41 I~~~~gip~~~qrL~~~gk~L~D~~~tL~~ygI~~g~~l~l~~~~   85 (102)
T 1v5o_A           41 CELESGVPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVLLQKD   85 (102)
T ss_dssp             HHHHTCCCGGGBCEEETTEEECCSSSBHHHHTCCTTEEEEECBCC
T ss_pred             HHHHHCcChHHeEEEECCEECCCCcccHHHCCCCCCCEEEEEECC
Confidence            456789999999999999999987 699999999 9999976553

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens}

Probab=98.87  E-value=3.2e-10  Score=78.26  Aligned_cols=40  Identities=30%  Similarity=0.404  Sum_probs=35.3

Q ss_pred             ccCCC--CCCeEEEeCCEECCCCCCccccccc-cc--cccccccc
Q 040111            4 KEGIP--PGQQRSIFAGKQLEDGRTLADYKIQ-ES--TLHLGWRA   43 (133)
Q Consensus         4 ~~gip--~~~Q~Li~~gk~L~D~~tL~~ygI~-~s--tl~L~~~~   43 (133)
                      ++|+|  +++|||||+||+|+|+.||++|+|. ++  ++||+++.
T Consensus        56 ke~ip~~~~~qrLIy~GK~LeD~~TL~~y~I~~~~~~tlhlv~r~  100 (125)
T 2gow_A           56 EEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLVARE  100 (125)
T ss_dssp             CCCTTCCGGGEEEESSSSEEESSCBTGGGCCCTTSEEEEEEEECS
T ss_pred             ccCCCCChHHEEEEECCcCCCCCCcHHHcCCCCCCceEEEEEecC
Confidence            67885  8999999999999999999999998 65  78877766

>1wz0_A Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-like molecule, structural genomics, sentrin2, NPPFSA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=98.86  E-value=2e-09  Score=71.96  Aligned_cols=62  Identities=2%  Similarity=-0.111  Sum_probs=58.2

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEe
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVV  105 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~  105 (133)
                      |.|++.+|+.+.+.|.+++++..|+...+++.|+++++++|+|.|+.|.++.|+++|++-..
T Consensus        27 IkVk~~~g~~i~~kVk~~t~l~kL~~~y~ek~gi~~~~~rf~FdG~~l~~~~Tp~dl~medg   88 (104)
T 1wz0_A           27 LKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDE   88 (104)
T ss_dssp             EEEECSSSCEEEEEECTTSCHHHHHHHHHHHHTCCTTTSCEESSSSBCCTTSCTTTTTCCTT
T ss_pred             EEEECCCCCEEEEEEcCCChHHHHHHHHHHHhCCCcceEEEEECCEEcCCCCCHHHcCCCCC
Confidence            78888899999999999999999999999999999999999999999999999999997433

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens}

Probab=98.85  E-value=7.4e-10  Score=73.45  Aligned_cols=36  Identities=31%  Similarity=0.414  Sum_probs=32.9

Q ss_pred             cCCCC-CCeEEEeCCEECCCCCCcccc--ccc-ccccccc
Q 040111            5 EGIPP-GQQRSIFAGKQLEDGRTLADY--KIQ-ESTLHLG   40 (133)
Q Consensus         5 ~gip~-~~Q~Li~~gk~L~D~~tL~~y--gI~-~stl~L~   40 (133)
                      +|+|+ ++|||||+||+|+|+.+|++|  +|. +++|||+
T Consensus        60 ~g~pp~~~QrLIy~Gk~L~D~~tL~~y~~~I~~~~tihLv   99 (99)
T 2kdb_A           60 PSKPLTKDQRLVYSGRLLPDHLQLKDILRKQDEYHMVHLV   99 (99)
T ss_dssp             TTCCCTTTCCEEETTEEECTTSBTHHHHTTTCSEEEEEEC
T ss_pred             cCCCChhhEEEEECCEECCCCCCHHHHhcCCCCCCEEEeC
Confidence            56665 999999999999999999999  999 9999974

>2k8h_A Small ubiquitin protein; SUMO, post-translational modifier, signaling protein; NMR {Trypanosoma brucei}

Probab=98.84  E-value=1.8e-09  Score=72.93  Aligned_cols=63  Identities=10%  Similarity=-0.059  Sum_probs=58.7

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVG  106 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~  106 (133)
                      |.|++.+|+.+.+.|.+++++..|+...+++.|+|+++++|+|.|+.|.++.|+++|++-..-
T Consensus        29 IkVk~~~g~~i~fkVk~~t~l~kL~~ay~ek~gi~~~~~rfiFdG~~L~~~~Tp~dl~mEDgD   91 (110)
T 2k8h_A           29 VKVVNADGAEMFFRIKSRTALKKLIDTYCKKQGISRNSVRFLFDGTPIDETKTPEELGMEDDD   91 (110)
T ss_dssp             EEEEETTSCCEEEEECTTSSHHHHHHHHHHHHTCCSSSCEEESSSCBCCSSSHHHHHHCSSEE
T ss_pred             EEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCC
Confidence            788888999999999999999999999999999999999999999999999999999974333

>1wjn_A Tubulin-folding protein TBCE; ubiquitin-like domain, progressive motor neuropathy, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=98.84  E-value=1.7e-09  Score=71.02  Aligned_cols=60  Identities=15%  Similarity=0.098  Sum_probs=50.0

Q ss_pred             CCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCC-------ccc-CccccccccccEEeEEE
Q 040111           49 PDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKF-------PFF-FFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        49 ~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~g-------k~L-~d~~tL~dy~~~~~~~~  108 (133)
                      .+++.+...+++++||++||.+|+..+|+|+..|+|.|.+       ..| +|.++|++|++.....|
T Consensus        20 ~~~~~~e~~l~~~~TV~~LK~~i~~~~gip~~~q~L~~~~~~~~~~~~~L~~d~~~L~~y~i~~G~~I   87 (97)
T 1wjn_A           20 PERQILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCL   87 (97)
T ss_dssp             SSSCCEEEEEETTSBHHHHHHHHHTTTTCCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTCCTTCEE
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHCCChhHeEEEEEcCCCCceeeccCCCcccHhhcCCCCCCEE
Confidence            4677888999999999999999999999999999999873       224 56789999998644433

>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=98.79  E-value=3.6e-09  Score=70.99  Aligned_cols=62  Identities=3%  Similarity=-0.098  Sum_probs=57.8

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVG  106 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~  106 (133)
                      |.|++ +|+.+.+.|.+++++..|+...+++.|+++++++++|.|+.|.++.|.++|++-..-
T Consensus        34 IkV~~-~g~~i~fkIk~tt~l~kL~~ay~ek~gi~~~~~rF~FdG~rl~~~~Tp~dl~medgD   95 (106)
T 2eke_C           34 LKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDND   95 (106)
T ss_dssp             EEEEC-SSCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCTTTTTCCTTE
T ss_pred             EEEec-CCcEEEEEeCCCCHHHHHHHHHHHHhCCCcccEEEEECCeEcCCCCCHHHcCCCCCC
Confidence            78888 899999999999999999999999999999999999999999999999999975433

>2kjr_A CG11242; UBL, ubiquitin, ubiquitin-like, structural genomics, PSI-2, protein structure initiative; NMR {Drosophila melanogaster}

Probab=98.79  E-value=8.5e-10  Score=72.60  Aligned_cols=40  Identities=18%  Similarity=0.172  Sum_probs=35.2

Q ss_pred             CCcccCCCCCCeEEEeC--CE---EC-CCCCCccccccc-ccccccc
Q 040111            1 IEDKEGIPPGQQRSIFA--GK---QL-EDGRTLADYKIQ-ESTLHLG   40 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~--gk---~L-~D~~tL~~ygI~-~stl~L~   40 (133)
                      |++++|||+++|||+|.  |+   +| +|+.+|++|||. +++|+|+
T Consensus        47 I~~~~GiP~~~QrL~~~~~g~~~~~L~~D~~tL~~Y~i~~gstihlv   93 (95)
T 2kjr_A           47 LEILTGGCAGTMKVQVFKGDTCVSTMDNNDAQLGYYANSDGLRLHVV   93 (95)
T ss_dssp             HHHHHCSCTTTEEEEEEETTEEEEECCCTTSBHHHHCCSSSCEEEEE
T ss_pred             HHHHHCcCHHHeEEEEecCCcccceeCCCCCCHhHCCcCCCCEEEEE
Confidence            46789999999999998  55   55 899999999999 9999974

>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=8e-10  Score=73.03  Aligned_cols=40  Identities=18%  Similarity=0.123  Sum_probs=35.2

Q ss_pred             CCcccCCCCCCeEEEeCC---EE----CCCCCCccccccc-ccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAG---KQ----LEDGRTLADYKIQ-ESTLHLG   40 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~g---k~----L~D~~tL~~ygI~-~stl~L~   40 (133)
                      |++++|||+++|||+|.|   +.    ++|+.+|++|+|. +++|+|+
T Consensus        46 Ie~~~Gip~~~QrLi~~g~~g~~~~~L~~D~~tL~~Y~I~~g~~Ihlv   93 (97)
T 2kj6_A           46 LWKKCGTSVNSMALELYDDSGSKVAVLSDDSRPLGFFSPFDGFRLHII   93 (97)
T ss_dssp             HHHHHCCCTTSEEEEEECSSSCBCCCSSGGGSCHHHHCCCSCCEEEEE
T ss_pred             HHHHHCcCHHHeEEEEecCCCcccceecCCcCCHHHCCCCCCCEEEEE
Confidence            467899999999999998   33    4899999999999 9999975

>2dzj_A Synaptic glycoprotein SC2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.73  E-value=1.6e-09  Score=70.24  Aligned_cols=38  Identities=24%  Similarity=0.315  Sum_probs=34.2

Q ss_pred             Cc-ccCCCCCCeEEEeC--CEECCCCCCccccccc-cccccc
Q 040111            2 ED-KEGIPPGQQRSIFA--GKQLEDGRTLADYKIQ-ESTLHL   39 (133)
Q Consensus         2 ~~-~~gip~~~Q~Li~~--gk~L~D~~tL~~ygI~-~stl~L   39 (133)
                      ++ +.|+|+++|||+|.  |++|+|+.||++|||. +++|++
T Consensus        44 ~~~~~~i~~~~QrL~~~~~Gk~L~D~~tL~~y~i~~~stl~~   85 (88)
T 2dzj_A           44 TKTHPQWYPARQSLRLDPKGKSLKDEDVLQKLPVGTTATLYF   85 (88)
T ss_dssp             HHHCSSSCTTTCCEESSTTSCCCCTTCBTTTSSCCSEEEEEE
T ss_pred             HHHhcCCChHHeEEEecCCCcCcCCCCCHHHcCCCCCCEEEE
Confidence            44 58999999999987  9999999999999999 999875

>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=1.4e-09  Score=72.31  Aligned_cols=44  Identities=18%  Similarity=0.157  Sum_probs=38.4

Q ss_pred             CCcccCCCCCCeEEEe--CCEECCCCCCccccccc-cccccccccccc
Q 040111            1 IEDKEGIPPGQQRSIF--AGKQLEDGRTLADYKIQ-ESTLHLGWRADF   45 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~--~gk~L~D~~tL~~ygI~-~stl~L~~~~i~   45 (133)
                      |++++|||+++|+|+|  .|+ |+|+.+|++|+|+ +++|||++..+.
T Consensus        38 I~~~tgIpp~~QkLi~~~~gk-L~D~~tLs~~~I~~gstL~lvl~~~~   84 (100)
T 2dzm_A           38 LENELQIPVSKMLLKGWKTGD-VEDSTVLKSLHLPKNNSLYVLTPDLP   84 (100)
T ss_dssp             HHHHHCCCTTTCCEECCSSSC-CCTTSBHHHHCCCSEEEEEECCSSSC
T ss_pred             HHHHHCCChhHeEEEccCCCC-CCCcCCHHHcCCCCCCEEEEEecCCC
Confidence            4678999999999997  566 9999999999999 999998776643

>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=98.70  E-value=7.2e-09  Score=67.47  Aligned_cols=35  Identities=29%  Similarity=0.483  Sum_probs=32.8

Q ss_pred             CCCeEEEeCCEECCCC-CCccccccc-cccccccccc
Q 040111            9 PGQQRSIFAGKQLEDG-RTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         9 ~~~Q~Li~~gk~L~D~-~tL~~ygI~-~stl~L~~~~   43 (133)
                      +++|+|+|+|++|+|+ .+|++|||. +++|||+++.
T Consensus        42 ~~~qrLi~~Gk~L~D~~~tL~~y~i~~g~~i~l~~~~   78 (95)
T 1wia_A           42 ESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRSP   78 (95)
T ss_dssp             TTTCEEEETTEECCCSSCBTTTTTCCTTEEEEEECCC
T ss_pred             cCcEEEEECCEEccCCcCCHHHcCCCCCCEEEEEECC
Confidence            6999999999999999 999999999 9999987765

>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=98.68  E-value=8.6e-10  Score=72.30  Aligned_cols=42  Identities=24%  Similarity=0.449  Sum_probs=36.7

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|||+++|+|+|.|++|+ +.+|++|+|. +++|+|+.+.
T Consensus        46 I~~~tgip~~~QrL~~~Gk~Ld-d~tL~~~~i~~g~~i~lv~~~   88 (95)
T 1v86_A           46 IHSITGLPPAMQKVMYKGLVPE-DKTLREIKVTSGAKIMVVGST   88 (95)
T ss_dssp             HHHHHCSCSTTCCCBSSSBCCS-SSBHHHHCCCTTEEEEECCSS
T ss_pred             HHHHHCcCHHHeEEEECCeeCC-cCcHHHCCCCCCCEEEEEecc
Confidence            4567899999999999999994 5599999999 9999987654

>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=98.67  E-value=3e-09  Score=69.55  Aligned_cols=41  Identities=20%  Similarity=0.212  Sum_probs=35.6

Q ss_pred             CCcccCCCCCCeEEEeCC---EE----CCCCCCccccccc-cccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAG---KQ----LEDGRTLADYKIQ-ESTLHLGW   41 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~g---k~----L~D~~tL~~ygI~-~stl~L~~   41 (133)
                      |++++|||+++|||+|.|   +.    ++|+.+|++|||. +++||+.-
T Consensus        38 i~~~~gip~~~qrL~~~~~~g~~~~~l~~D~~tL~~y~i~~g~~l~v~d   86 (95)
T 1v6e_A           38 LELVVGSPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIHVID   86 (95)
T ss_dssp             HHHHTCSCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCEEEEBC
T ss_pred             HHHHHCCCHHHeEEEEeCCCCccccccCCCcCCHhHCCCCCCCEEEEEE
Confidence            467899999999999987   43    5899999999999 99999754

>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=98.64  E-value=9e-10  Score=73.83  Aligned_cols=34  Identities=24%  Similarity=0.322  Sum_probs=29.9

Q ss_pred             CCeEEEeCCEECC-CCCCccccccc-cccccccccc
Q 040111           10 GQQRSIFAGKQLE-DGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus        10 ~~Q~Li~~gk~L~-D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      ++|+|+|+|++|. |+.||++|||. +++|||+.+.
T Consensus        61 ~q~~Li~~Gk~L~dD~~tL~dygI~~g~~l~lv~~l   96 (105)
T 1v2y_A           61 RTYHLTSAGEKLTEDRKKLRDYGIRNRDEVSFIKKL   96 (105)
T ss_dssp             TTEEEESSSCEECCSSSBHHHHTCCSSEEEEEEECS
T ss_pred             eeEEEEeCCcCccCCcCCHHHcCCCCCCEEEEEehh
Confidence            5789999999996 67999999999 9999987654

>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=98.57  E-value=1.3e-08  Score=69.62  Aligned_cols=43  Identities=14%  Similarity=0.151  Sum_probs=36.7

Q ss_pred             CCcccCCCCCCeEEEeCC---E---E-CCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAG---K---Q-LEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~g---k---~-L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|||+++|||+|.|   +   + ++|+.+|++|||. +++|||.-..
T Consensus        37 i~~~~Gip~~~qrL~~~g~~~~~~~~l~~D~~tL~~y~i~~g~~ihvvd~~   87 (122)
T 1t0y_A           37 LELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHAVDVT   87 (122)
T ss_dssp             HHHHHCCCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEEEEEECT
T ss_pred             HHHHhCCCHHHeEEEEecCCCccccccCCCcCCHHHCCCCCCCEEEEEeCC
Confidence            467899999999999987   4   3 4899999999999 9999986543

>4efo_A Serine/threonine-protein kinase TBK1; ubiquitin like domain, transferase; 1.77A {Homo sapiens}

Probab=98.51  E-value=7.6e-08  Score=63.14  Aligned_cols=51  Identities=8%  Similarity=0.078  Sum_probs=43.4

Q ss_pred             CCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCc--ccccccc
Q 040111           50 DPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFF--EEVLSFF  100 (133)
Q Consensus        50 ~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d--~~tL~dy  100 (133)
                      .+..+.+.+.+++|+..+|++|++++||||++|+|+|+|+.|.-  ..+-+.|
T Consensus        22 ~a~~h~v~I~~~etv~~~ke~V~eqTgIp~~~Q~LL~eg~~l~l~p~~~a~~~   74 (94)
T 4efo_A           22 QMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLVLEPGRLAQHF   74 (94)
T ss_dssp             TTEEEEEEEETTCBHHHHHHHHHHHHCCCGGGEEEEETTEEECCCTTCBGGGS
T ss_pred             cceEEEEEeccchHHHHHHHHHHHHhCCCHHHHHHHhCCCccccCCCCccccC
Confidence            35668899999999999999999999999999999999988764  3444455

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

Probab=98.46  E-value=1.9e-08  Score=73.78  Aligned_cols=39  Identities=13%  Similarity=0.122  Sum_probs=0.0

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccccccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~~stl~L~~~~   43 (133)
                      |++.+|||+++|+|+|+|++|+|+.||+    .+++|||+++.
T Consensus        30 I~~keGIP~~qQRLIf~GK~LeD~~TLs----~~STLhLvlRL   68 (189)
T 2xzm_9           30 ISQDMGFEIDMMTLVNNGFIAPNTELVT----DDVTYYLSLKL   68 (189)
T ss_dssp             -------------------------------------------
T ss_pred             HHHHhCcChhHEEEEecCeECCCCCccc----CCCEEEEEEec
Confidence            6788999999999999999999999998    67899987765

>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=3.3e-08  Score=79.13  Aligned_cols=40  Identities=28%  Similarity=0.493  Sum_probs=35.4

Q ss_pred             ccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            4 KEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         4 ~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      ++|||+++|+|+|+||+|+|+.+|.+|||. +++|++++..
T Consensus        43 ~~gip~~~QrLiy~GK~L~D~~tL~dygI~~gstIv~lv~k   83 (368)
T 1oqy_A           43 RDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTK   83 (368)
T ss_dssp             SSSCCSTEEEEESSSSEECSSSBTTTTCCCTTSCEEEEEEC
T ss_pred             cCCCChhheEEEECCeecCCcCCHHHcCCCCCCEEEEEEec
Confidence            678999999999999999999999999999 9999444433

>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=98.43  E-value=7.8e-08  Score=62.99  Aligned_cols=42  Identities=21%  Similarity=0.353  Sum_probs=38.6

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      +++.|+|+++|||+|.|+.|+++.|+++|++. +++|++++++
T Consensus        38 ~~~~gi~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~~   80 (94)
T 2io1_B           38 CERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQ   80 (94)
T ss_dssp             HHHHTCCGGGEEEEETTEECCTTCCTTTTTCCTTCEEEEEECC
T ss_pred             HHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEec
Confidence            46789999999999999999999999999999 9999976654

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster}

Probab=98.35  E-value=3.9e-08  Score=77.33  Aligned_cols=43  Identities=19%  Similarity=0.318  Sum_probs=39.3

Q ss_pred             CCcccCCCCCCeEEE---eCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSI---FAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li---~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|||+++|+|+   |.|++|+|+.+|++|||+ |++|+|+.+.
T Consensus        34 I~~~tgVpp~~QkLi~~k~~Gk~l~D~~~L~~~~ik~g~~l~L~gs~   80 (320)
T 3shq_A           34 IFRKTQVRPERQKLLNLKYKGKTAADNVKISALELKPNFKLMMVGST   80 (320)
T ss_dssp             HHHHHCCCGGGCEETTCBSSSSBCCTTSBTTSSCCC--CEEEEECCC
T ss_pred             HHHHHCcCHHHeEEeecccCCcccCccccHHHcCCCCCCEEEEEccc
Confidence            467899999999999   899999999999999999 9999999876

>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=98.31  E-value=2.9e-07  Score=57.18  Aligned_cols=39  Identities=23%  Similarity=0.392  Sum_probs=36.3

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLG   40 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~   40 (133)
                      +++.|+|+++|||+|.|+.|.++.|.++|++. +++|++.
T Consensus        32 ~~~~gi~~~~~rf~fdG~~l~~~~Tp~~l~medgD~Idv~   71 (72)
T 1wm3_A           32 CERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVF   71 (72)
T ss_dssp             HHHHTCCTTTCEEEETTEECCTTCCTTTTTCCTTEEEEEE
T ss_pred             HHHhCCCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEE
Confidence            46789999999999999999999999999999 9999975

>3kyd_D Small ubiquitin-related modifier 1; SUMO, thioester, adenylation, inhibitor, TETR intermediate, ligase, nucleus, phosphoprotein; HET: VMX; 2.61A {Homo sapiens} SCOP: d.15.1.1

Probab=98.30  E-value=6.1e-07  Score=60.89  Aligned_cols=61  Identities=10%  Similarity=0.018  Sum_probs=57.4

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVV  104 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~  104 (133)
                      |.|+..+|..+.+.|.+++++..|+...+++.|+++++++++|.|+.|.++.|.+++++-.
T Consensus        43 LKV~~qdg~ev~fkIk~tt~L~KLm~aY~er~Gl~~~~irFlFDG~rI~~~~TP~dL~MED  103 (115)
T 3kyd_D           43 LKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEE  103 (115)
T ss_dssp             EEEECTTSCEEEEEEETTSCTHHHHHHHHHHHTCCTTSEEEEETTEECCTTCCTTTTTCCT
T ss_pred             EEEEcCCCCEEEEEEccCChHHHHHHHHHHHhCCChhhEEEEECCeECCCCCCHHHcCCCC
Confidence            7788888998999999999999999999999999999999999999999999999998743

>1wf9_A NPL4 family protein; beta-grAsp fold like domain, hypothetical protein, structural genomics, NPPSFA; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=98.28  E-value=5.8e-08  Score=64.81  Aligned_cols=42  Identities=17%  Similarity=0.225  Sum_probs=36.9

Q ss_pred             CCcccCCCCCCeEEEeCCE-----------E----CCCCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGK-----------Q----LEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk-----------~----L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |+++++||+++|+|+|.|+           +    ++|+.+|++|||. +++|||...
T Consensus        37 I~~~~gip~~~QrL~~~~~~~~~k~~~~~~~l~~~l~d~~tL~~~gi~~G~~L~l~~~   94 (107)
T 1wf9_A           37 IQDQLQIPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLAHGSMVYLAYE   94 (107)
T ss_dssp             HHHHSCCCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTCCCTTCEEECCCS
T ss_pred             HHHHhCcCcccCEEEECCccccccCccccccccccCCCCCCHHHCCCCCCCEEEEEeC
Confidence            4578999999999999988           4    5899999999999 999997654

>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=98.27  E-value=4.9e-07  Score=58.84  Aligned_cols=42  Identities=21%  Similarity=0.353  Sum_probs=38.2

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      +++.|+|++++||+|.|+.|.++.|+++|++. +++|++.+++
T Consensus        36 ~~~~gi~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~q   78 (91)
T 2io0_B           36 CERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQ   78 (91)
T ss_dssp             HHHTTCCSTTEEEEETTEECCTTCCTTTTTCCTTEEEEEEECC
T ss_pred             HHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEec
Confidence            46789999999999999999999999999999 9999976554

>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=98.18  E-value=6.2e-07  Score=58.46  Aligned_cols=42  Identities=21%  Similarity=0.353  Sum_probs=38.3

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      +++.|+|++++||+|.|+.|.++.|+++|++. +++|++.+++
T Consensus        48 ~~~~gi~~~~~rf~fdG~~l~~~~Tp~dl~medgD~Idv~~~q   90 (93)
T 2d07_B           48 CERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQ   90 (93)
T ss_dssp             HHHHTCCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECC
T ss_pred             HHHhCCCccceEEEECCEEcCCCCCHHHcCCCCCCEEEEEeec
Confidence            46789999999999999999999999999999 9999987654

>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative, hydrolase; NMR {Mus musculus}

Probab=98.11  E-value=4.8e-07  Score=57.85  Aligned_cols=41  Identities=34%  Similarity=0.428  Sum_probs=34.8

Q ss_pred             CCcccCCCCCCeEEEeC--CEECC---CCCCccccccc-cccccccc
Q 040111            1 IEDKEGIPPGQQRSIFA--GKQLE---DGRTLADYKIQ-ESTLHLGW   41 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~--gk~L~---D~~tL~~ygI~-~stl~L~~   41 (133)
                      |++++|||+++|+|+|+  +|+|+   |+.+|++|||. +++|++.-
T Consensus        30 I~~~~gi~~~~qrL~~~~p~k~l~l~~~~~tL~~~gl~~g~~l~v~~   76 (86)
T 2kzr_A           30 IAAITGIAPGSQRILVGYPPECLDLSDRDITLGDLPIQSGDMLIVEE   76 (86)
T ss_dssp             HHHHTCCCTTTCCCEESSCCCCCCCCCSSCBTTTSSCCTTCEEECCC
T ss_pred             HHHHhCCCccceEEEeCCCCcccccCCCCCCHHHcCCCCCCEEEEEe
Confidence            45678999999999997  47774   78999999999 99999653

>3pge_A SUMO-modified proliferating cell nuclear antigen; DNA replication, DNA binding protein; 2.80A {Saccharomyces cerevisiae}

Probab=98.10  E-value=1.8e-06  Score=63.78  Aligned_cols=58  Identities=3%  Similarity=-0.065  Sum_probs=54.1

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCcccccccccc
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWF  102 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~  102 (133)
                      |.|+. +|..+.+.+.+++++..|+...+++.|+|+.++|++|.|+.|.++.|.+++++
T Consensus        32 LkV~~-~g~~v~fkIk~~t~l~kL~~ay~er~Gi~~~~~RF~FdG~rI~~~~TP~dL~M   89 (200)
T 3pge_A           32 LKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDM   89 (200)
T ss_dssp             EEEEC-SSCEEEEEECTTSCTHHHHHHHHHHHSSCGGGEEEEETTEECCTTCCTTTTTC
T ss_pred             EEEec-CCCEEEEEEecCCHHHHHHHHHHHHhCCChhhEEEEECCEEcCCCCCHHHcCC
Confidence            55654 78889999999999999999999999999999999999999999999999996

>3a4r_A Nfatc2-interacting protein; ubiquitin fold, coiled coil, cytoplasm, methylation, nucleus, transcription; 1.00A {Mus musculus} PDB: 3a4s_C 3rd2_A

Probab=98.09  E-value=9.7e-07  Score=55.81  Aligned_cols=39  Identities=18%  Similarity=0.287  Sum_probs=36.0

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLG   40 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~   40 (133)
                      +++.|+|+++|||+|.|+.|.++.|.++|++. +++|++.
T Consensus        39 ~~~~gi~~~~~rf~fdG~~l~~~~Tp~~l~medgD~Idv~   78 (79)
T 3a4r_A           39 EEAMGLSGHKLSFFFDGTKLSGKELPADLGLESGDLIEVW   78 (79)
T ss_dssp             HHHHTCTTCCCEEEETTEECCSCCCHHHHTCCTTCEEEEE
T ss_pred             HHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEe
Confidence            46789999999999999999999999999999 9999864

>2pjh_A Protein NPL4, nuclear protein localization protein 4 homolog; UFD1, NPL4, AAA, protein binding, transport protein; NMR {Mus musculus}

Probab=98.07  E-value=1.1e-06  Score=55.76  Aligned_cols=60  Identities=8%  Similarity=-0.031  Sum_probs=50.4

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcc-----cCccccccccccEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPF-----FFFEEVLSFFWFVV  104 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~-----L~d~~tL~dy~~~~  104 (133)
                      +.||+.+| +..+++++++|+.+|+++|++..+++++.|.+.++..+     ...+.+|+++++..
T Consensus         7 lRvrs~~G-~~Ri~v~~~~t~~~L~~~I~~~~~i~~~~~~l~~~~~p~~~l~~~~~~~l~~lgl~h   71 (80)
T 2pjh_A            7 IRVQSPDG-VKRITATKRETAATFLKKVAKEFGFQNNGFSVYINRNKTGEITASSSKSLHLLKIKH   71 (80)
T ss_dssp             CEEECSSE-EEECCCCSSCCHHHHHHHHHHHTCCCTTTCCCCCSCCGGGGSSSCCCCTTTTTCCCT
T ss_pred             EEEECCCC-CEEEEcCCcChHHHHHHHHHHHcCCCCCcceEEecCCCCCcccCCCCCCHHHcCCCC
Confidence            66777776 55688999999999999999999999999999887776     34677899998864

>1wz0_A Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-like molecule, structural genomics, sentrin2, NPPFSA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=98.05  E-value=8.7e-07  Score=59.04  Aligned_cols=42  Identities=21%  Similarity=0.353  Sum_probs=38.0

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      +++.|+|+++|||+|.|+.|.++.|+.+|++. +++|++++++
T Consensus        55 ~ek~gi~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~q   97 (104)
T 1wz0_A           55 CERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQ   97 (104)
T ss_dssp             HHHHTCCTTTSCEESSSSBCCTTSCTTTTTCCTTEEEEECCCC
T ss_pred             HHHhCCCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEec
Confidence            46789999999999999999999999999999 9999976543

>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=98.05  E-value=1.6e-06  Score=57.98  Aligned_cols=42  Identities=12%  Similarity=0.288  Sum_probs=38.3

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      +++.|+|++++||+|.|+.|.++.|.++|++. +++|++.+++
T Consensus        61 ~ek~gi~~~~~rF~FdG~rl~~~~Tp~dl~medgD~Idv~~~q  103 (106)
T 2eke_C           61 AKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQ  103 (106)
T ss_dssp             HHHHTCCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECC
T ss_pred             HHHhCCCcccEEEEECCeEcCCCCCHHHcCCCCCCEEEEEeec
Confidence            46789999999999999999999999999999 9999987654

>2k8h_A Small ubiquitin protein; SUMO, post-translational modifier, signaling protein; NMR {Trypanosoma brucei}

Probab=97.92  E-value=1.2e-06  Score=58.93  Aligned_cols=42  Identities=17%  Similarity=0.355  Sum_probs=38.1

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      +++.|+|+++|||+|.|+.|.++.|+++|++. +++|++++.+
T Consensus        57 ~ek~gi~~~~~rfiFdG~~L~~~~Tp~dl~mEDgD~Idv~~~q   99 (110)
T 2k8h_A           57 CKKQGISRNSVRFLFDGTPIDETKTPEELGMEDDDVIDAMVEQ   99 (110)
T ss_dssp             HHHHTCCSSSCEEESSSCBCCSSSHHHHHHCSSEEEEEEECCC
T ss_pred             HHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEcc
Confidence            46789999999999999999999999999999 9999976554

>3goe_A DNA repair protein RAD60; SUMO-like domain, sumoylation, SUMO, genome stability, DNA damage, DNA recombination, nucleus; HET: DNA; 0.97A {Schizosaccharomyces pombe} PDB: 3rcz_A*

Probab=97.91  E-value=1.5e-05  Score=50.28  Aligned_cols=59  Identities=5%  Similarity=0.012  Sum_probs=53.3

Q ss_pred             ccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCC-ceEEEeCCcccCccccccccccE
Q 040111           45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPP-AEADLLKFPFFFFEEVLSFFWFV  103 (133)
Q Consensus        45 ~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~-~q~L~~~gk~L~d~~tL~dy~~~  103 (133)
                      ..++....-+.+.|.++++|.+|-+.-+.+.|||++ ..+|.|.|..|+.+++++||.++
T Consensus        13 ~~~~~~~~dl~f~I~~~t~v~kLi~ayc~~~~I~~~~~IrllFDGdRLdp~~tp~Dleme   72 (82)
T 3goe_A           13 LLRSSKSEDLRLSIPVDFTVKDLIKRYCTEVKISFHERIRLEFEGEWLDPNDQVQSTELE   72 (82)
T ss_dssp             EEEESSSCCEEEEEETTSBHHHHHHHHHHHHTCCCCTTCEEEETTEECCTTSBGGGSSCC
T ss_pred             hhhccCCCCeEEEecCCCCHHHHHHHHHHHcCCCcCceEEEEEcCcccCccCChhhhCCc
Confidence            445555667889999999999999999999999999 99999999999999999999874

>3tix_A Ubiquitin-like protein SMT3, RNA-induced transcri silencing complex protein TAS3; PIN, rossmann fold, SPOC, alpha-helical hairpin, heterochrom silencing, RITS, RNAI, argonaute; 2.90A {Saccharomyces cerevisiae}

Probab=97.89  E-value=5.9e-06  Score=60.70  Aligned_cols=60  Identities=3%  Similarity=-0.087  Sum_probs=54.9

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVV  104 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~  104 (133)
                      |.|+. +|..+.+.|.+++++..|+...+++.|+++.+++++|.|+.|.++.|.+++++-.
T Consensus        60 LKVk~-dG~eV~FKIKrtTpL~KLmeAYcERqGL~~~sIRFLFDGqRI~~ddTPeDLdMED  119 (207)
T 3tix_A           60 LKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLTFLYDGIEIQADQTPEDLDMED  119 (207)
T ss_dssp             EEEEC-SSCEEEEEEETTSCTHHHHHHHHHHTTCCGGGSCEEETTEECCSSCCTTTTTCCT
T ss_pred             EEEec-CCCEEEEEEccCChHHHHHHHHHHHhCCCcccEEEEECCeecCCCCCHHHcCCCC
Confidence            55653 7888999999999999999999999999999999999999999999999999733

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B*

Probab=97.87  E-value=3.2e-06  Score=66.11  Aligned_cols=36  Identities=78%  Similarity=1.212  Sum_probs=31.9

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCcccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQEST   36 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~~st   36 (133)
                      |++++|||+++|+|+|+|++|+|+.+|++|+|....
T Consensus       263 I~~~~GIp~~~QRLi~~Gk~L~D~~TLsdygI~~gs  298 (307)
T 3ai5_A          263 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKES  298 (307)
T ss_dssp             HHHHHCCCGGGCEEEETTEECCTTSBTGGGTCCTTC
T ss_pred             HHHHHCcChHHEEEEeCCeecCCCCCHHHcCCCCCC
Confidence            456789999999999999999999999999986444

>3v7o_A Minor nucleoprotein VP30; ssgcid, seattle structural genomics center for infectious disease, SMT, transcription; 2.25A {Reston ebolavirus}

Probab=97.74  E-value=4.1e-06  Score=62.29  Aligned_cols=64  Identities=5%  Similarity=-0.069  Sum_probs=0.0

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      |.| ..+|..+.+.|.++++...|+...+++.|++++++|++|.|+.+.++.|.+++++...-.|
T Consensus        24 LKV-~qdGseV~FKIKrtTpL~KLM~AYcERqGLs~~siRFLFDGqRI~dddTPadL~MEDGDtI   87 (227)
T 3v7o_A           24 LKV-SDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDII   87 (227)
T ss_dssp             -----------------------------------------------------------------
T ss_pred             EEE-eCCCCEEEEEEccCChHHHHHHHHHHHhCCCccceEEEECCEecCCCCCHHHcCCCCCCEE
Confidence            566 5678889999999999999999999999999999999999999999999999997544433

>1wjn_A Tubulin-folding protein TBCE; ubiquitin-like domain, progressive motor neuropathy, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=97.72  E-value=1.2e-05  Score=52.35  Aligned_cols=41  Identities=17%  Similarity=0.355  Sum_probs=34.3

Q ss_pred             CCcccCCCCCCeEEEeCC------E-EC-CCCCCccccccc-cccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAG------K-QL-EDGRTLADYKIQ-ESTLHLGW   41 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~g------k-~L-~D~~tL~~ygI~-~stl~L~~   41 (133)
                      |++.+|+|+.+|+|+|.+      . .| +|..+|+.||+. +++||+..
T Consensus        42 i~~~~gip~~~q~L~~~~~~~~~~~~~L~~d~~~L~~y~i~~G~~I~V~d   91 (97)
T 1wjn_A           42 LSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCLLVRW   91 (97)
T ss_dssp             HHTTTTCCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTCCTTCEEEEEC
T ss_pred             HHHHHCCChhHeEEEEEcCCCCceeeccCCCcccHhhcCCCCCCEEEEEe
Confidence            467899999999999873      2 36 678999999999 99999754

>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=97.46  E-value=7.3e-05  Score=50.57  Aligned_cols=42  Identities=19%  Similarity=0.431  Sum_probs=38.3

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      +++.|+|+.++|++|.|+.|.++.|..++++. +++|++.+.+
T Consensus        71 ~er~Gl~~~~irFlFDG~rI~~~~TP~dL~MEDgD~IdV~~~Q  113 (115)
T 3kyd_D           71 CQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQ  113 (115)
T ss_dssp             HHHHTCCTTSEEEEETTEECCTTCCTTTTTCCTTCEEEEEECC
T ss_pred             HHHhCCChhhEEEEECCeECCCCCCHHHcCCCCCCEEEEEeec
Confidence            35789999999999999999999999999999 9999987654

>3pge_A SUMO-modified proliferating cell nuclear antigen; DNA replication, DNA binding protein; 2.80A {Saccharomyces cerevisiae}

Probab=97.37  E-value=6.5e-05  Score=55.37  Aligned_cols=42  Identities=12%  Similarity=0.288  Sum_probs=39.9

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      +++.|+|+.++|++|.|+.|.++.|..++++. +++|++.+++
T Consensus        59 ~er~Gi~~~~~RF~FdG~rI~~~~TP~dL~MEdgD~Idv~~~q  101 (200)
T 3pge_A           59 AKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQ  101 (200)
T ss_dssp             HHHHSSCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECC
T ss_pred             HHHhCCChhhEEEEECCEEcCCCCCHHHcCCCCCCEEEEEecc
Confidence            46789999999999999999999999999999 9999999988

>3uf8_A Ubiquitin-like protein SMT3, peptidyl-prolyl CIS- isomerase; ssgcid, seattle structural genomics center for in disease; HET: FK5; 1.50A {Burkholderia pseudomallei} PDB: 4ggq_C* 3vaw_A* 3uqa_A* 4g50_A* 4fn2_A* 3uqb_A* 4giv_A* 1euv_B 3v60_A 3v61_A 3v62_A*

Probab=97.33  E-value=0.00014  Score=53.73  Aligned_cols=58  Identities=3%  Similarity=-0.065  Sum_probs=52.1

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCcccccccccc
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWF  102 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~  102 (133)
                      |.|+. ++..+.+.+.++++...|+...+++.|+|+++++++|.|+.+.++++..+..+
T Consensus        24 ikv~~-~~~~v~~~i~~~~~l~kl~~~y~~~~g~~~~~~~f~fdG~~i~~~~Tpk~L~~   81 (209)
T 3uf8_A           24 LKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDM   81 (209)
T ss_dssp             EEEEC-SSCEEEEEEETTSCTHHHHHHHHHHHTCCGGGCEEEETTEECCTTCCTTTTTC
T ss_pred             EEEEc-CCCEEEEEEeeCCHHHHHHHHHHHhhCCChheEEEEECCEeccCCCChHHhhh
Confidence            55665 67778899999999999999999999999999999999999999988888764

>2kc2_A Talin-1, F1; FERM, adhesion, cell membrane, cell projection, cytoplasm, cytoskeleton, membrane, phosphoprotein, structural protein; NMR {Mus musculus}

Probab=97.25  E-value=5.6e-05  Score=52.03  Aligned_cols=38  Identities=18%  Similarity=0.100  Sum_probs=35.5

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCC
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPP   80 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~   80 (133)
                      .+.|+.++|...++.|+.+.+|.+++..|+.+.||+..
T Consensus        13 ~LkV~llDg~~ktl~VD~S~~V~~lv~~Ic~kigI~n~   50 (128)
T 2kc2_A           13 PLKIRMLDGTVKTIMVDDSKTVTDMLMTICARIGITNH   50 (128)
T ss_dssp             EEEEECTTSCEEEEEEEECSSHHHHHHHHHHHHTCCCC
T ss_pred             cEEEEcCCCCEEEEEeCCCcCHHHHHHHHHHHhCCCCc
Confidence            48999999999999999999999999999999999754

>3qx1_A FAS-associated factor 1; UBX, protein binding, P97 binding; 1.60A {Homo sapiens} PDB: 3qwz_B* 3qc8_B 3qca_A 3qq8_B 3r3m_B 1h8c_A

Probab=97.16  E-value=0.001  Score=42.03  Aligned_cols=66  Identities=12%  Similarity=-0.020  Sum_probs=56.1

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEE--eCCcccC---ccccccccccEEeEEEEe
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADL--LKFPFFF---FEEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~--~~gk~L~---d~~tL~dy~~~~~~~~~~  110 (133)
                      |-||.++|+.+.-....++||.+|..-|.. .+.++....|+  |..+.+.   .+.+|.+.++.+.+++++
T Consensus        10 i~iRlpdG~r~~~~F~~~~tl~~v~~fv~~-~~~~~~~f~L~t~fPrk~l~~~d~~~TL~e~gL~p~a~L~v   80 (84)
T 3qx1_A           10 LRIRTPSGEFLERRFLASNKLQIVFDFVAS-KGFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFL   80 (84)
T ss_dssp             EEEECTTSCEEEEEEETTSBHHHHHHHHHH-TTCCTTTEEEECSSSCCBGGGSCTTSBTTTTTCCSEEEEEE
T ss_pred             EEEECCCCCEEEEEeCCCCCHHHHHHHHHH-cCCCCCCeEEEeCCCCCCCcCCCCCCCHHHCCCCCCCEEEE
Confidence            778999999888888999999999999988 67888889998  5678884   368999999987776664

>3ix6_A TS, tsase, thymidylate synthase; niaid, ssgcid, seattle structural center for infectious DISE brucellosis, orchitis, epididymitis, mastitis; 2.20A {Brucella melitensis}

Probab=97.12  E-value=6.9e-05  Score=59.69  Aligned_cols=62  Identities=3%  Similarity=-0.098  Sum_probs=0.0

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVG  106 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~  106 (133)
                      +.|+. +|..+.+.|.++++...|+...+++.|+++++++++|.|+.+.++.|.+++++...-
T Consensus        24 LKV~~-~g~~v~FkIk~~t~l~kLm~aY~~r~G~~~~~~rFlFdG~rI~~~~TP~~L~MEDgD   85 (360)
T 3ix6_A           24 LKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDND   85 (360)
T ss_dssp             ---------------------------------------------------------------
T ss_pred             EEEec-CCcEEEEEEecCChHHHHHHHHHHHhCCCcceEEEEECCeECCCCCChHHcCCCccc
Confidence            56665 577888999999999999999999999999999999999999999999999864433

>2jxx_A Nfatc2-interacting protein; nuclear factor of activated T-cells, cytoplasmic 2- interacting protein, ubiquitin like homologue; NMR {Homo sapiens}

Probab=97.11  E-value=0.00041  Score=45.45  Aligned_cols=61  Identities=2%  Similarity=-0.034  Sum_probs=54.5

Q ss_pred             cccCCCCCC-CceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEE
Q 040111           44 DFCKNPDPQ-NITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVV  104 (133)
Q Consensus        44 i~Vk~~~g~-~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~  104 (133)
                      |.|+..+|. .+.+.|.++++...|...-+++.|++++..+++|.|..+..+.|..++++-.
T Consensus        28 LkV~~~dg~~~v~fkIk~~t~l~kLm~aY~~~~g~~~~~vrF~FDG~rI~~~~TP~dLdMED   89 (97)
T 2jxx_A           28 LRVQGKEKHQTLEVSLSRDSPLKTLMSHYEEAMGLSGRKLSFFFDGTKLSGRELPADLGMES   89 (97)
T ss_dssp             EEEEESSSSCEEEEEEETTSCHHHHHHHHHHHTTCSSSCCEEEETTEECCSCSCHHHHTCCT
T ss_pred             EEEEcCCCCEEEEEEECCCChHHHHHHHHHHHHCCCcccEEEEECCEEcCCCCCHHHcCCCC
Confidence            566667774 6889999999999999999999999999999999999999999999988743

>2dzk_A UBX domain-containing protein 2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} PDB: 2kxj_A

Probab=97.04  E-value=0.0014  Score=43.55  Aligned_cols=78  Identities=8%  Similarity=-0.134  Sum_probs=63.9

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEE--eCCcccC--c-cccccccccEEeEEEEeCceeeeee
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADL--LKFPFFF--F-EEVLSFFWFVVVGVIFCGCRVNFWN  118 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~--~~gk~L~--d-~~tL~dy~~~~~~~~~~~~~~~~~~  118 (133)
                      |-||.++|..+.-....++||.+|.+-|....+.+.....|+  |..+.+.  | +.+|.+.++.+.+++++--.-++..
T Consensus        16 IqIRlpdG~rl~~rF~~~~tl~~v~~fV~~~~~~~~~~f~L~t~fPrk~l~~~d~~~TL~elgL~psa~L~v~~~~~~~~   95 (109)
T 2dzk_A           16 IQFRLPDGSSFTNQFPSDAPLEEARQFAAQTVGNTYGNFSLATMFPRREFTREDYKRRLLDLELAPSASVVLLPAGRPAT   95 (109)
T ss_dssp             EEEECSSSCEEEEEECTTSBHHHHHHHHHHHHTTSSCSCEEECSSSCCBCCTTTTTSBTGGGTCSSEEEEEEECCSSCCC
T ss_pred             EEEECCCCCEEEEEeCCCCCHHHHHHHHHhccCCCCCceEEEcCCCCcCCcccccCCCHHHCCCCCceEEEEEECcCCcc
Confidence            789999999888889999999999999999888877888888  6788887  3 6799999998878777665555555


Q ss_pred             ccc
Q 040111          119 ASL  121 (133)
Q Consensus       119 ~~~  121 (133)
                      +..
T Consensus        96 a~~   98 (109)
T 2dzk_A           96 SIV   98 (109)
T ss_dssp             CCC
T ss_pred             eee
Confidence            443

>3tix_A Ubiquitin-like protein SMT3, RNA-induced transcri silencing complex protein TAS3; PIN, rossmann fold, SPOC, alpha-helical hairpin, heterochrom silencing, RITS, RNAI, argonaute; 2.90A {Saccharomyces cerevisiae}

Probab=97.01  E-value=0.00022  Score=52.41  Aligned_cols=42  Identities=10%  Similarity=0.251  Sum_probs=39.1

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      +++.|+|+.+++++|.|+.|.++.|..++++. +++|++.+.+
T Consensus        87 cERqGL~~~sIRFLFDGqRI~~ddTPeDLdMEDGDtIDV~leQ  129 (207)
T 3tix_A           87 AKRQGKEMDSLTFLYDGIEIQADQTPEDLDMEDNDIIEAHREQ  129 (207)
T ss_dssp             HHHTTCCGGGSCEEETTEECCSSCCTTTTTCCTTEEEEECCCC
T ss_pred             HHHhCCCcccEEEEECCeecCCCCCHHHcCCCCCCEEEEEEec
Confidence            35789999999999999999999999999999 9999988777

>3v7o_A Minor nucleoprotein VP30; ssgcid, seattle structural genomics center for infectious disease, SMT, transcription; 2.25A {Reston ebolavirus}

Probab=96.79  E-value=0.0002  Score=53.23  Aligned_cols=42  Identities=12%  Similarity=0.288  Sum_probs=0.0

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      +++.|+|++++|++|.|+.+.++.|.+++++. +++|+++..+
T Consensus        51 cERqGLs~~siRFLFDGqRI~dddTPadL~MEDGDtIDV~leQ   93 (227)
T 3v7o_A           51 AKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQ   93 (227)
T ss_dssp             -------------------------------------------
T ss_pred             HHHhCCCccceEEEECCEecCCCCCHHHcCCCCCCEEEEEecc
Confidence            57889999999999999999999999999999 9999987766

>2al3_A TUG long isoform; TUG UBL1 insulin, endocytosis/exocytosis complex; NMR {Mus musculus} SCOP: d.15.1.2

Probab=96.78  E-value=0.0007  Score=43.76  Aligned_cols=63  Identities=11%  Similarity=0.026  Sum_probs=56.4

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVG  106 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~  106 (133)
                      +.|-.++++...+.|.|++++.++-+.-.++.|+.+++..|.|+++.++-..+++.-++++++
T Consensus        12 v~Vl~~n~rr~~VKvtp~t~L~~VL~eaC~K~gl~~~~~~Lkh~~k~lDLSlpfRlsgLpnnA   74 (90)
T 2al3_A           12 VSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQDFNPSEYDLKFQRTVLDLSLQWRFANLPNNA   74 (90)
T ss_dssp             EEEECTTSCEEEECCCTTSBHHHHHHHHHHHTTCCGGGCEEEETTEEESSSCBHHHHCCCSSC
T ss_pred             EEEEcCCCcEEEEEECCCCCHHHHHHHHHHHhCCChhhCeEEeCCEeccccceeEecCCCCCC
Confidence            667788899999999999999999999999999999999999999999888888888876443

>4efo_A Serine/threonine-protein kinase TBK1; ubiquitin like domain, transferase; 1.77A {Homo sapiens}

Probab=96.76  E-value=0.00041  Score=45.25  Aligned_cols=32  Identities=25%  Similarity=0.452  Sum_probs=24.1

Q ss_pred             CCcccCCCCCCeEEEeCCEEC--CCCCCcccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQL--EDGRTLADYKI   32 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L--~D~~tL~~ygI   32 (133)
                      |++++|||+++|+|+|.|+.|  +....-..|--
T Consensus        43 V~eqTgIp~~~Q~LL~eg~~l~l~p~~~a~~~p~   76 (94)
T 4efo_A           43 VYKQTKIISSNQELIYEGRRLVLEPGRLAQHFPK   76 (94)
T ss_dssp             HHHHHCCCGGGEEEEETTEEECCCTTCBGGGSCC
T ss_pred             HHHHhCCCHHHHHHHhCCCccccCCCCccccCCC
Confidence            467899999999999999875  44444445543

>4da1_A Protein phosphatase 1K, mitochondrial; metal-ION-assisted catalysis, dehydrogenase phosphatase, hydrolase; 2.38A {Homo sapiens} PDB: 3qht_A 1l2n_A

Probab=96.68  E-value=0.00027  Score=56.36  Aligned_cols=61  Identities=3%  Similarity=-0.099  Sum_probs=0.0

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEe
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVV  105 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~  105 (133)
                      |.|+. ++..+.+.+.++++...|+...+++.|+++.++++.|.|+.+.++.|.+++++...
T Consensus        33 lkv~~-~~~~~~~~i~~~~~~~~l~~~y~~~~g~~~~~~~f~f~G~~i~~~~Tp~~l~med~   93 (389)
T 4da1_A           33 LKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQAPEDLDMEDN   93 (389)
T ss_dssp             --------------------------------------------------------------
T ss_pred             EEEec-CCcEEEEEECCCChHHHHHHHHHHHhCCCcceEEEEECCEEcCCCCCHHHcCCCCC
Confidence            55555 67778899999999999999999999999999999999999999999999986433

>2l76_A Nfatc2-interacting protein; ubiquitin-like domain, structural genomics, PSI-biology, Pro structure initiative; NMR {Homo sapiens}

Probab=95.98  E-value=0.0048  Score=40.16  Aligned_cols=59  Identities=8%  Similarity=-0.014  Sum_probs=53.0

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFV  103 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~  103 (133)
                      +.|+. .|..+.+.+..++....|....+++.|++++..+++|.|..+.++.|-++.++.
T Consensus        24 iKV~~-~g~ev~FkIK~tt~l~KL~~aYc~r~gv~~~sirFlfDG~rI~~~~TP~~L~me   82 (95)
T 2l76_A           24 LKIRC-RADLVRLPLRMSEPLQSVVDHMATHLGVSPSRILLLFGETELSPTATPRTLKLG   82 (95)
T ss_dssp             EEEEC-SSSEEEEEECSSSCTHHHHHHHHHHHTSCGGGEEEEETTEECCTTSCHHHHTCC
T ss_pred             EEEEc-CCcEEEEEEecCChHHHHHHHHHhhcCCChhhEEEEECCcCCCCCCCHhHcCCC
Confidence            55664 577888999999999999999999999999999999999999999998888764

>1wj4_A KIAA0794 protein; UBX domain, beta-grAsp fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: d.15.1.2

Probab=95.91  E-value=0.0054  Score=41.66  Aligned_cols=65  Identities=12%  Similarity=0.080  Sum_probs=54.5

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEE--eCCccc--Cc-cccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADL--LKFPFF--FF-EEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~--~~gk~L--~d-~~tL~dy~~~~~~~~~  109 (133)
                      |-||.++|..+.-....++||.+|..-|... +.++....|+  |-.+.|  .| +.+|.+.++.+.++++
T Consensus        46 IqIRlPdG~rl~~rF~~~~tl~~V~~fV~~~-~~~~~~F~L~t~fPrk~l~~~d~~~TL~e~gL~psa~Li  115 (124)
T 1wj4_A           46 LMLRYPDGKREQITLPEQAKLLALVKHVQSK-GYPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVF  115 (124)
T ss_dssp             EEEECTTSCEEEEEEETTSCHHHHHHHHHHH-HCCTTTEEEECSSSCCEETSSCSSSCTTTTTCCSSBCCE
T ss_pred             EEEECCCCCEEEEEeCCCCCHHHHHHHHHhc-CCCCCCeEEecCCCCcCCccCCCCCCHHHCCCCCceEEE
Confidence            8899999998888899999999999999886 8888888888  678888  34 6899999987655443

>3ivf_A Talin-1; FERM domain, cell membrane, cell projection, cytoskeleton, M phosphoprotein, cell adhesion, structural protein; 1.94A {Mus musculus} PDB: 2kma_A 2kc1_A

Probab=95.83  E-value=0.0092  Score=46.98  Aligned_cols=99  Identities=17%  Similarity=0.167  Sum_probs=71.5

Q ss_pred             CEECCCCCCccccccc-cccccccccc--cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCC-CCceEEEeCC-----
Q 040111           18 GKQLEDGRTLADYKIQ-ESTLHLGWRA--DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIP-PPAEADLLKF-----   88 (133)
Q Consensus        18 gk~L~D~~tL~~ygI~-~stl~L~~~~--i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp-~~~q~L~~~g-----   88 (133)
                      |+=|++++||+.|++. +..++..-+.  +.|..++|....+++++++|+.++-..|+++.|+. ++.--|.+..     
T Consensus        59 ~~Wl~~~~~l~~y~~~~~~~l~~~~~~~~~~V~l~dg~~~~~~vd~~tt~~el~~~v~~~l~L~e~~~FgL~~~~~~~~~  138 (371)
T 3ivf_A           59 GIWLEAGKALDYYMLRNGDTMEYRKKQRPLKIRMLDGTVKTIMVDDSKTVTDMLMTICARIGITNHDEYSLVRELMEEKK  138 (371)
T ss_dssp             CEECCTTSBGGGGTCCTTCEEEEEECEEEEEEECTTSCEEEEEEETTSBHHHHHHHHHHHTTCSCGGGEEEECCC-----
T ss_pred             CEeccCCCCHHHhCCCCCceeeccCceeEEEEECcCCCEEEEEECCCCCHHHHHHHHHHHcCCCCccccEEEEEeccccc
Confidence            3448888999999999 9998887666  77889999999999999999999999999999974 4445565532     


Q ss_pred             ----cccCccccccccccEE-eEEEEeCceeeeeec
Q 040111           89 ----PFFFFEEVLSFFWFVV-VGVIFCGCRVNFWNA  119 (133)
Q Consensus        89 ----k~L~d~~tL~dy~~~~-~~~~~~~~~~~~~~~  119 (133)
                          ..|+.++++.+-+... ..+.|   +++||-.
T Consensus       139 ~~~~~wL~~~k~l~~q~~~~~~~l~f---rvKf~~~  171 (371)
T 3ivf_A          139 DDELNWLDHGRTLREQGVEEHETLLL---RRKFFYS  171 (371)
T ss_dssp             -----CCCTTSBTGGGTCCTTCEEEE---EECCCCB
T ss_pred             chHHHHHhcCchhHhhCCCCCceEEE---EEEEecC
Confidence                3344455555543211 12222   5777753

>3goe_A DNA repair protein RAD60; SUMO-like domain, sumoylation, SUMO, genome stability, DNA damage, DNA recombination, nucleus; HET: DNA; 0.97A {Schizosaccharomyces pombe} PDB: 3rcz_A*

Probab=95.60  E-value=0.0077  Score=37.93  Aligned_cols=39  Identities=15%  Similarity=0.211  Sum_probs=34.9

Q ss_pred             cccCCCCC-CeEEEeCCEECCCCCCccccccc-cccccccc
Q 040111            3 DKEGIPPG-QQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGW   41 (133)
Q Consensus         3 ~~~gip~~-~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~   41 (133)
                      .+.|||++ .-+|.|.|..|+.+.++.+|++. +.-|.+++
T Consensus        41 ~~~~I~~~~~IrllFDGdRLdp~~tp~DlemeD~D~IDvmL   81 (82)
T 3goe_A           41 TEVKISFHERIRLEFEGEWLDPNDQVQSTELEDEDQVSVVL   81 (82)
T ss_dssp             HHHTCCCCTTCEEEETTEECCTTSBGGGSSCCTTCEEEEEC
T ss_pred             HHcCCCcCceEEEEEcCcccCccCChhhhCCcCCceeeeee
Confidence            45799999 89999999999999999999999 88887654

>3ix6_A TS, tsase, thymidylate synthase; niaid, ssgcid, seattle structural center for infectious DISE brucellosis, orchitis, epididymitis, mastitis; 2.20A {Brucella melitensis}

Probab=95.18  E-value=0.0034  Score=49.96  Aligned_cols=42  Identities=12%  Similarity=0.288  Sum_probs=0.0

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      +++.|++++++|++|.|+.+.++.|.+++++. +++|++..++
T Consensus        51 ~~r~G~~~~~~rFlFdG~rI~~~~TP~~L~MEDgD~Idv~~~Q   93 (360)
T 3ix6_A           51 AKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQ   93 (360)
T ss_dssp             -------------------------------------------
T ss_pred             HHHhCCCcceEEEEECCeECCCCCChHHcCCCccchhhhhhcc
Confidence            57889999999999999999999999999999 9999998887

>2bps_A YUKD protein; ubiquitin-like protein, ubiquitin; 2.7A {Bacillus subtilis}

Probab=95.13  E-value=0.012  Score=37.20  Aligned_cols=59  Identities=12%  Similarity=-0.097  Sum_probs=49.1

Q ss_pred             CCCCCCceeeccccCcHHHHHHHhhhhcCCCC-----CceEEEeCCcccCccccccccccEEeE
Q 040111           48 NPDPQNITLEVESSDTIDNVKAKIQDKKRIPP-----PAEADLLKFPFFFFEEVLSFFWFVVVG  106 (133)
Q Consensus        48 ~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~-----~~q~L~~~gk~L~d~~tL~dy~~~~~~  106 (133)
                      --.++.+.+.++...|+..|.+.+.+..+++.     .+.++.-.+..|.+++.|+||.+++..
T Consensus        13 ~y~~~~~DLRIP~~~tvK~Li~~l~ea~~l~~~~~~~~~irv~NK~~~L~~~~~L~d~~ItnGD   76 (81)
T 2bps_A           13 HYNGSVFDLRLSDYHPVKKVIDIAWQAQSVSMPPREGHWIRVVNKDKVFSGECKLSDCGITNGD   76 (81)
T ss_dssp             TTTCCEEEEEEETTSBTTHHHHHHHHHSCCCSCCCTTCEEEEGGGTEEEETTSBTGGGTCCTTC
T ss_pred             ccCCceEEEECCCchhHHHHHHHHHHHhCCCcCCCCCCEEEEecCCEEEcCCCEEeeCCcCCCC
Confidence            34688999999999999999999999998653     345666788889999999999987543

>2cr5_A Reproduction 8; UBX domain, D0H8S2298E protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.15.1.2

Probab=95.12  E-value=0.025  Score=37.32  Aligned_cols=66  Identities=8%  Similarity=-0.181  Sum_probs=54.4

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEE--eCCcccC-c-cccccccccEEeEEEEe
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADL--LKFPFFF-F-EEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~--~~gk~L~-d-~~tL~dy~~~~~~~~~~  110 (133)
                      |-||.++|+.+.-....++||.+|..-|... +..+....|+  |-.+.+. | +.||.+.++.+.+++++
T Consensus        26 IqiRlpdG~r~~rrF~~~~tl~~v~~fv~~~-~~~~~~f~L~t~fPrk~l~~d~~~TL~e~gL~p~a~L~V   95 (109)
T 2cr5_A           26 VALRCPNGRVLRRRFFKSWNSQVLLDWMMKV-GYHKSLYRLSTSFPRRALEVEGGSSLEDIGITVDTVLNV   95 (109)
T ss_dssp             EEEECTTSCEEEEEEESSSBTHHHHHHHHHH-TCCTTTEEEECSSSCCBCCCCSSCBHHHHTCSSCEEEEE
T ss_pred             EEEECCCCCEEEEEeCCCCCHHHHHHHHHhc-CCCCCCeEEEeCCCCcCCCCCCCCCHHHcCCCCCeEEEE
Confidence            7899999998888888999999999999964 6667778887  6678886 3 68999999887776654

>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=95.06  E-value=0.011  Score=43.47  Aligned_cols=42  Identities=12%  Similarity=0.288  Sum_probs=38.8

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      +++.|+|++++|++|.|+.+.++.|..+..+. +++|++...+
T Consensus        51 ~~~~g~~~~~~~f~fdG~~i~~~~Tpk~L~~ed~d~I~~~~eq   93 (209)
T 3uf8_A           51 AKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQ   93 (209)
T ss_dssp             HHHHTCCGGGCEEEETTEECCTTCCTTTTTCCTTEEEEEECSC
T ss_pred             HHhhCCChheEEEEECCEeccCCCChHHhhhcccccchhhccc
Confidence            46789999999999999999999999999999 9999977766

>1s3s_G P47 protein; AAA ATPase, protein-protein complex, UBX domain, protein binding; HET: ADP; 2.90A {Rattus norvegicus} SCOP: d.15.1.2 PDB: 1i42_A 1jru_A

Probab=94.73  E-value=0.019  Score=39.03  Aligned_cols=64  Identities=9%  Similarity=0.024  Sum_probs=52.8

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhc-CCCCCceEEE--eCCcccCc-cccccccccEEeEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKK-RIPPPAEADL--LKFPFFFF-EEVLSFFWFVVVGV  107 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~-gIp~~~q~L~--~~gk~L~d-~~tL~dy~~~~~~~  107 (133)
                      |-||.++|..+.-....++||.+|.+-|.... +.+.....|+  |-.+.+.| +.||.+.++.+.++
T Consensus        55 IqIRlpdG~rl~~rF~~~~tl~~v~~fV~~~~~~~~~~~f~L~t~fPrk~l~d~~~TL~eagL~psav  122 (127)
T 1s3s_G           55 IQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFPNKELADENQTLKEANLLNAVI  122 (127)
T ss_dssp             EEEEETTTTEEEEECCSSCBHHHHHHHHHHHCSGGGTSCEEEEETTTTEECCSTTCBHHHHTCSSCEE
T ss_pred             EEEECCCCCEEEEEeCCCCCHHHHHHHHHHhCcCCCCCCeEEecCCCCCCCCCCCCcHHHCCCcCceE
Confidence            88999999988888999999999999999863 4666778887  67888886 68999999865333

>2daj_A KIAA0977 protein, COBL-like 1; ubiquitin-like domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.65  E-value=0.031  Score=35.63  Aligned_cols=62  Identities=11%  Similarity=0.012  Sum_probs=51.5

Q ss_pred             ccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEe---CCcccCccccccccccEEeE
Q 040111           45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLL---KFPFFFFEEVLSFFWFVVVG  106 (133)
Q Consensus        45 ~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~---~gk~L~d~~tL~dy~~~~~~  106 (133)
                      .|+....+...+.|+|..+..++-..|.+++.+.|+.-.|..   .+.+|+-+.+|.||++.++-
T Consensus        14 vVNy~~tQKtVvRVSP~vpL~ellp~IC~Kcefdp~~~~Ll~d~~~~e~LdLskSLndlgirELy   78 (91)
T 2daj_A           14 VINFKKTQKTIVRVSPHASLQELAPIICSKCEFDPLHTLLLKDYQSQEPLDLTKSLNDLGLRELY   78 (91)
T ss_dssp             EEEETTTEEEEEEECSSSCTTTHHHHHHHHTTCCTTSEEEESCSSCCCBCCTTSCHHHHTCSEEE
T ss_pred             EEeecCcceeEEEeCCCCcHHHHHHHHhhcccCChhhEEEecCCCCCcccchhcchhhhhhhhhh
Confidence            344444566778999999999999999999999999999984   56677789999999997643

>4da1_A Protein phosphatase 1K, mitochondrial; metal-ION-assisted catalysis, dehydrogenase phosphatase, hydrolase; 2.38A {Homo sapiens} PDB: 3qht_A 1l2n_A

Probab=94.49  E-value=0.0066  Score=48.26  Aligned_cols=42  Identities=10%  Similarity=0.273  Sum_probs=0.0

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      +++.|+|+++++++|.|+.+.++.|..+.++. +.+|++...+
T Consensus        60 ~~~~g~~~~~~~f~f~G~~i~~~~Tp~~l~med~d~i~~~~~q  102 (389)
T 4da1_A           60 AKRQGKEMDSLRFLYDGIRIQADQAPEDLDMEDNDIIEAHREQ  102 (389)
T ss_dssp             -------------------------------------------
T ss_pred             HHHhCCCcceEEEEECCEEcCCCCCHHHcCCCCCCEeeeeecc
Confidence            46789999999999999999999999999999 9999977766

>2jxx_A Nfatc2-interacting protein; nuclear factor of activated T-cells, cytoplasmic 2- interacting protein, ubiquitin like homologue; NMR {Homo sapiens}

Probab=93.57  E-value=0.03  Score=36.47  Aligned_cols=37  Identities=16%  Similarity=0.308  Sum_probs=34.0

Q ss_pred             cccCCCCCCeEEEeCCEECCCCCCccccccc-cccccc
Q 040111            3 DKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL   39 (133)
Q Consensus         3 ~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L   39 (133)
                      ++.|++++.-+++|.|..|.++.|..+.++. +.+|.+
T Consensus        58 ~~~g~~~~~vrF~FDG~rI~~~~TP~dLdMEDgD~IDv   95 (97)
T 2jxx_A           58 EAMGLSGRKLSFFFDGTKLSGRELPADLGMESGDLIEV   95 (97)
T ss_dssp             HHTTCSSSCCEEEETTEECCSCSCHHHHTCCTTEEEEE
T ss_pred             HHHCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEE
Confidence            4678999999999999999999999999999 988875

>2kvr_A Ubiquitin carboxyl-terminal hydrolase 7; USP7, ubiquitin-like domain, UBL, ubiquitin specific protease, HOST-virus interaction, nucleus, protease; NMR {Homo sapiens}

Probab=92.76  E-value=0.077  Score=36.19  Aligned_cols=33  Identities=6%  Similarity=0.079  Sum_probs=30.4

Q ss_pred             CceeeccccCcHHHHHHHhhhhcCCCCCceEEE
Q 040111           53 NITLEVESSDTIDNVKAKIQDKKRIPPPAEADL   85 (133)
Q Consensus        53 ~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~   85 (133)
                      ..++.|..++|+.+++.+|++..|+|+++|||-
T Consensus        57 ~~~~rv~k~~~~~~~~~~va~~lg~~~~~~RlW   89 (130)
T 2kvr_A           57 YTVFKVLKNSSLAEFVQSLSQTMGFPQDQIRLW   89 (130)
T ss_dssp             CEEEECCTTSBHHHHHHHHHHHHCCCGGGCEEE
T ss_pred             cceEEEeccCcHHHHHHHHHHHhCCCcccEEEE
Confidence            356789999999999999999999999999986

>4e71_A Plexin-B2, MM1; transmembrane, signaling, RBD, structural genomics consortium, SGC, signaling protein; 2.26A {Homo sapiens}

Probab=92.42  E-value=0.14  Score=34.17  Aligned_cols=59  Identities=22%  Similarity=0.174  Sum_probs=40.9

Q ss_pred             CCCCceeeccccCcHHHHHHHhhhhc--CCC------CCceEEEe----CCcccCcc-------------ccccccccEE
Q 040111           50 DPQNITLEVESSDTIDNVKAKIQDKK--RIP------PPAEADLL----KFPFFFFE-------------EVLSFFWFVV  104 (133)
Q Consensus        50 ~g~~~~l~V~~~~tV~~LK~~I~~~~--gIp------~~~q~L~~----~gk~L~d~-------------~tL~dy~~~~  104 (133)
                      .++.+++.|-..+||.++|++|-+..  |.|      +++..|-+    +|+.|.|.             .||++|+|.+
T Consensus        22 ~~~~i~vkVLdCDTItQvKeKiLd~vyk~~pyS~rP~~~~~dLEwr~g~~~~iL~D~D~ts~~~~~wkrLNTL~HY~V~d  101 (111)
T 4e71_A           22 GVDAIPVKVLNCDTISQVKEKIIDQVYRGQPCSCWPRPDSVVLEWRPGSTAQILSDLDLTSQREGRWKRVNTLMHYNVRD  101 (111)
T ss_dssp             CCCCEEEEEETTCBHHHHHHHHHHHHTC---------CCSEEEEEC--CCCEECCSSCTTSCC---CCCCCBHHHHTCCT
T ss_pred             CCCceeeeeeccCcHHHHHHHHHHHHHcCCccccCCCCCceeeEEecCCCCccccccCccceecCcceEecchhhcCCCC
Confidence            34568888889999999999999884  554      46777876    34556552             3688888876


Q ss_pred             eEEE
Q 040111          105 VGVI  108 (133)
Q Consensus       105 ~~~~  108 (133)
                      .+.+
T Consensus       102 gatl  105 (111)
T 4e71_A          102 GATL  105 (111)
T ss_dssp             TCEE
T ss_pred             CCEE
Confidence            5544

>2juo_A GA-binding protein alpha chain; OST, ubiquitin, transcription factor, ensemble, DNA-binding, nucleus, transcription regulation; NMR {Mus musculus}

Probab=90.55  E-value=0.37  Score=30.56  Aligned_cols=55  Identities=13%  Similarity=0.049  Sum_probs=46.6

Q ss_pred             ceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           54 ITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        54 ~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      +.-+++-++++..||..++.+.|++.+...+...+.+|+.+++|.|=.+.-.|.|
T Consensus         5 i~qhmDI~epL~~Lk~LLe~Rl~i~L~~y~f~LQd~~L~~~k~LvdQcVqgeGlV   59 (89)
T 2juo_A            5 VSQAIDINEPIGNLKKLLEPRLQCSLDAHEICLQDIQLDPDRSLFDQGVKTDGTV   59 (89)
T ss_dssp             EEEEEESSSBGGGHHHHSHHHHCSCCSSCEEEETTEECCTTSBTTTSSCCCCSEE
T ss_pred             hhhhccccCcHHHHHHHHHHHhcCCcccCeEEeeccccCCCccHHHhhcccccEE
Confidence            3446677889999999999999999999999999999999999999876544443

>2l76_A Nfatc2-interacting protein; ubiquitin-like domain, structural genomics, PSI-biology, Pro structure initiative; NMR {Homo sapiens}

Probab=90.39  E-value=0.091  Score=34.07  Aligned_cols=39  Identities=15%  Similarity=0.212  Sum_probs=35.7

Q ss_pred             cccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccc
Q 040111            3 DKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGW   41 (133)
Q Consensus         3 ~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~   41 (133)
                      ++.|+++..-|++|.|..+.++.|..+.++. +.+|..++
T Consensus        52 ~r~gv~~~sirFlfDG~rI~~~~TP~~L~meD~DiID~~~   91 (95)
T 2l76_A           52 THLGVSPSRILLLFGETELSPTATPRTLKLGVADIIDCVV   91 (95)
T ss_dssp             HHHTSCGGGEEEEETTEECCTTSCHHHHTCCSSCEEEEEE
T ss_pred             hhcCCChhhEEEEECCcCCCCCCCHhHcCCCCCCEEEEEE
Confidence            5789999999999999999999999999999 99988654

>2pjh_A Protein NPL4, nuclear protein localization protein 4 homolog; UFD1, NPL4, AAA, protein binding, transport protein; NMR {Mus musculus}

Probab=88.89  E-value=0.066  Score=33.32  Aligned_cols=39  Identities=15%  Similarity=0.124  Sum_probs=30.3

Q ss_pred             CcccCCCCCCeEEEeCCEE-----CCCCCCccccccc-ccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQ-----LEDGRTLADYKIQ-ESTLHLG   40 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~-----L~D~~tL~~ygI~-~stl~L~   40 (133)
                      ++..++|++.|.+.++-.+     +.++.+|++.||. |++|.+.
T Consensus        34 ~~~~~i~~~~~~l~~~~~p~~~l~~~~~~~l~~lgl~hGd~l~l~   78 (80)
T 2pjh_A           34 AKEFGFQNNGFSVYINRNKTGEITASSSKSLHLLKIKHGDLLFLF   78 (80)
T ss_dssp             HHHTCCCTTTCCCCCSCCGGGGSSSCCCCTTTTTCCCTTCCEEC-
T ss_pred             HHHcCCCCCcceEEecCCCCCcccCCCCCCHHHcCCCCCCEEEEe
Confidence            4567899888888776443     3578899999999 9998864

>3h6n_A Plexin-D1; structural genomics consortium, SGC, membrane, transmembrane, receptor, alternative splicing, cell membrane, glycoprotein, polymorphism; 2.00A {Homo sapiens}

Probab=88.84  E-value=0.54  Score=31.94  Aligned_cols=59  Identities=14%  Similarity=0.128  Sum_probs=43.0

Q ss_pred             CCCCceeeccccCcHHHHHHHhhhhc--CCC------CCceEEEe-CC---c-ccCcc-------------ccccccccE
Q 040111           50 DPQNITLEVESSDTIDNVKAKIQDKK--RIP------PPAEADLL-KF---P-FFFFE-------------EVLSFFWFV  103 (133)
Q Consensus        50 ~g~~~~l~V~~~~tV~~LK~~I~~~~--gIp------~~~q~L~~-~g---k-~L~d~-------------~tL~dy~~~  103 (133)
                      ++..+++.|=..+||.++|++|-+..  |.|      +++..|-| .|   + .|.|.             .||++|+|.
T Consensus        15 ~~~~i~VkVLdCDTItQvKeKiLd~vyk~~p~S~rP~~~~~dLEwr~g~~~~~iL~D~D~ts~~~~~~krLNTL~HY~V~   94 (127)
T 3h6n_A           15 GMDSLSVRAMDTDTLTQVKEKILEAFCKNVPYSQWPRAEDVDLEWFASSTQSYILRDLDDTSVVEDGRKKLNTLAHYKIP   94 (127)
T ss_dssp             CCCCEEEEEETTSBHHHHHHHHHHHHSTTSCGGGSCCGGGEEEEEECSSSCEEECCSSSTTSCEETTEECCCBTTTTTCC
T ss_pred             CCCceeeeeeccCchhhhhHHHHHHHhccCCcccCCCCcccceEEecCCCCceEeecCCCcceecCceeEeccccccCCC
Confidence            45568888889999999999999884  554      46778886 33   3 35552             378999987


Q ss_pred             EeEEE
Q 040111          104 VVGVI  108 (133)
Q Consensus       104 ~~~~~  108 (133)
                      +.+.+
T Consensus        95 dgatv   99 (127)
T 3h6n_A           95 EGASL   99 (127)
T ss_dssp             TTCEE
T ss_pred             CCCEE
Confidence            66644

>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=88.76  E-value=0.24  Score=31.23  Aligned_cols=38  Identities=5%  Similarity=0.041  Sum_probs=35.3

Q ss_pred             CCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCc
Q 040111           52 QNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFP   89 (133)
Q Consensus        52 ~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk   89 (133)
                      -++.+.|++..+..+|+++|.++.++|++.-.|.|...
T Consensus        14 ~tvairvp~~~~y~~L~~~l~~kL~l~~~~~~LsYk~~   51 (83)
T 1oey_A           14 YTVVMKTQPGLPYSQVRDMVSKKLELRLEHTKLSYRPR   51 (83)
T ss_dssp             SEEEEEECTTCCHHHHHHHHHHHTTCCGGGCCEEECCT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhCCCcceeEEEeeCC
Confidence            57889999999999999999999999999999999775

>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=88.68  E-value=0.74  Score=39.27  Aligned_cols=67  Identities=15%  Similarity=0.144  Sum_probs=47.9

Q ss_pred             CCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCC-cccCcccccccccc-----------EEeEEEEeCceeee
Q 040111           50 DPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKF-PFFFFEEVLSFFWF-----------VVVGVIFCGCRVNF  116 (133)
Q Consensus        50 ~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~g-k~L~d~~tL~dy~~-----------~~~~~~~~~~~~~~  116 (133)
                      ..+...+.+.+++|+.+++..|++.+|||++.|.+++.+ -.+....+.+.|.+           ...-+.|..|..+|
T Consensus       320 ~~~~~~~~i~~~~tl~~l~~~i~~~T~i~~~~q~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  398 (676)
T 3qa8_A          320 SGRVHTYPVTENENLQNLKSWLQQDTGIPEEEQELLQASGLALNSAQPLTQYVIDCTVIDGRQGEGDLIFLFDNRKTVY  398 (676)
T ss_dssp             SSCCCEEECCTTCCHHHHHHHHHTTSCCCSTTCEEESSSSCCCCTTSCGGGSCCCSCC-------CCCEEECSSCC---
T ss_pred             ccccceeecCCCccHHHHHHHHHHHhCCCHHHHHHHhccCCCCCCCcchhhheeccccccccCCCCceEEEEecccccc
Confidence            455667888999999999999999999999999999754 44444556665431           22346777777777

>2l32_A Small archaeal modifier protein 2; protein BIN; NMR {Haloferax volcanii}

Probab=87.34  E-value=0.52  Score=28.78  Aligned_cols=51  Identities=8%  Similarity=0.012  Sum_probs=37.8

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCcccccc
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLS   98 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~   98 (133)
                      +.|+........+++++..|+++|-+.    .|+|++...+..+|+....+..+.
T Consensus         3 v~Vkl~g~~~~~~ev~~g~Tv~dLL~~----Lgl~~~~VvV~vNG~~v~~d~~l~   53 (74)
T 2l32_A            3 VTVEVVGEETSEVAVDDDGTYADLVRA----VDLSPHEVTVLVDGRPVPEDQSVE   53 (74)
T ss_dssp             EEEECSSSSEEEEECSTTCSHHHHHHT----TCCCSSCCCEECCCCCCCTTSSSC
T ss_pred             EEEEEeCccceeEEcCCCCcHHHHHHH----cCCCcceEEEEECCEECCHHHCCC
Confidence            344444333345789999999998754    899999998889999998777553

>4eut_A Serine/threonine-protein kinase TBK1; ATP binding, phosphorylation, transferase-transferas inhibitor complex; HET: BX7; 2.60A {Homo sapiens}

Probab=86.82  E-value=0.88  Score=35.25  Aligned_cols=63  Identities=8%  Similarity=-0.047  Sum_probs=43.6

Q ss_pred             CceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCccc--Ccccccccccc--EEeEEEEeCceee
Q 040111           53 NITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFF--FFEEVLSFFWF--VVVGVIFCGCRVN  115 (133)
Q Consensus        53 ~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L--~d~~tL~dy~~--~~~~~~~~~~~~~  115 (133)
                      ...+.+.+..|+.++++++++.++++++.|.+++.+..+  +...+.+.|.=  .+.-+++++..+|
T Consensus       323 ~~~~~~~~~~~~~~~~~~~~~~t~i~~~~q~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  389 (396)
T 4eut_A          323 AHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLVLEPGRLAQHFPKTTEENPIFVVSREGN  389 (396)
T ss_dssp             EEEEEECTTCBHHHHHHHHHHHHCCCSTTEEEESSSSEECCCSSCBTTSSCCCCSSSCEEEEECC--
T ss_pred             EEEEEcCchhHHHHHHHHHHHhcCCChhhhHHHhcCCCCCCCCCCccccCCCCCCCCCeEEEecCCC
Confidence            456677889999999999999999999999999988333  23455666642  2222455544443

>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=86.45  E-value=0.42  Score=32.95  Aligned_cols=56  Identities=21%  Similarity=0.204  Sum_probs=40.8

Q ss_pred             CCCceeeccccCcHHHHHHHhhhhc--CCC------CCceEEEe----CCc-ccCcc-------------ccccccccEE
Q 040111           51 PQNITLEVESSDTIDNVKAKIQDKK--RIP------PPAEADLL----KFP-FFFFE-------------EVLSFFWFVV  104 (133)
Q Consensus        51 g~~~~l~V~~~~tV~~LK~~I~~~~--gIp------~~~q~L~~----~gk-~L~d~-------------~tL~dy~~~~  104 (133)
                      .+.+++.|=..+||.++|++|-+..  |.|      +++.-|-+    +|+ .|.|.             .||+.|++..
T Consensus        40 ~~~i~VkVLdCDTItQvKeKiLDavYk~~PySqRP~~~d~dLEwr~g~~g~liL~D~D~tS~~~~~wkrLNTL~HY~V~D  119 (138)
T 2r2o_A           40 AQGVPVKVLDCDTISQAKEKMLDQLYKGVPLTQRPDPRTLDVEWRSGVAGHLILSDEDVTSEVQGLWRRLNTLQHYKVPD  119 (138)
T ss_dssp             CCCEEEEEETTCBHHHHHHHHHHHHTTTSCGGGCCCGGGEEEEEECSSSCEEEECSSSTTCCEETTEEECCBHHHHTCCT
T ss_pred             CCceeEEEeccccHHHHHHHHHHHHHcCCccccCCCccceeEEEecCCcCceEeeccCCcccccCCceeecchhccCCCC
Confidence            3568889999999999999999984  565      44556665    233 36653             3789999876


Q ss_pred             eE
Q 040111          105 VG  106 (133)
Q Consensus       105 ~~  106 (133)
                      .+
T Consensus       120 ga  121 (138)
T 2r2o_A          120 GA  121 (138)
T ss_dssp             TC
T ss_pred             CC
Confidence            55

>3jyu_A Ubiquitin carboxyl-terminal hydrolase; domain in ubiquitin-specific peptidases (DUSP), proto- oncogene, ubiquitin-fold, UBL, protease, thioesterase; HET: 1PS; 2.37A {Mus musculus}

Probab=85.19  E-value=1.5  Score=32.24  Aligned_cols=56  Identities=11%  Similarity=0.101  Sum_probs=43.1

Q ss_pred             ceeeccccCcHHHHHHHhhhhcCCCCC-ceEEEe-C----CcccCc-cccccccccEEeEEEE
Q 040111           54 ITLEVESSDTIDNVKAKIQDKKRIPPP-AEADLL-K----FPFFFF-EEVLSFFWFVVVGVIF  109 (133)
Q Consensus        54 ~~l~V~~~~tV~~LK~~I~~~~gIp~~-~q~L~~-~----gk~L~d-~~tL~dy~~~~~~~~~  109 (133)
                      ++..+...+||.+++..+....+|+++ ..||-. .    ...|.| +.+|.++++...-.|+
T Consensus       154 ~~~~~Sk~~ti~~l~~~~~~~~~i~~~~~~RLW~~~~~~~~~~L~~~~~tl~d~~L~~~Q~il  216 (231)
T 3jyu_A          154 LSCHFSKADTIATIEKEMRKLFNIPAERETRLWNKYMSNTYEQLSKLDNTIQDAGLYQGQVLV  216 (231)
T ss_dssp             EEEEECTTCBHHHHHHHHHHHTTCCTTSCEEEEECSSSSSCEECCCTTSBTTTTTCCTTEEEE
T ss_pred             EEEEecccCcHHHHHHHHHHHhCCCCCCeEEEEEecCCCCHhhhcCCCCCHHHhCCCCCCEEE
Confidence            445678999999999999999999997 688773 2    345665 5899999886555444

>1ryj_A Unknown; beta/alpha protein, structural genomics, protein structure initiative, OCSP, NESG, PSI; NMR {Methanothermococcusthermolithotrophicus} SCOP: d.15.3.2

Probab=84.11  E-value=2.3  Score=25.24  Aligned_cols=45  Identities=18%  Similarity=0.053  Sum_probs=34.2

Q ss_pred             eeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccE
Q 040111           55 TLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFV  103 (133)
Q Consensus        55 ~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~  103 (133)
                      .++++...|+.+|.+.+    ++++....+..+|.....+..|++=+-.
T Consensus        17 ~~~~~~~~tv~~Ll~~l----~~~~~~v~vavN~~~v~~~~~L~~gD~V   61 (70)
T 1ryj_A           17 ILESGAPRRIKDVLGEL----EIPIETVVVKKNGQIVIDEEEIFDGDII   61 (70)
T ss_dssp             EEEESSCCBHHHHHHHT----TCCTTTEEEEETTEECCTTSBCCTTCEE
T ss_pred             eEECCCCCcHHHHHHHh----CCCCCCEEEEECCEECCCcccCCCCCEE
Confidence            45666778999999875    6777777788899988877777776533

>2ylm_A Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70A {Homo sapiens}

Probab=83.06  E-value=0.72  Score=38.18  Aligned_cols=33  Identities=6%  Similarity=0.079  Sum_probs=30.3

Q ss_pred             CceeeccccCcHHHHHHHhhhhcCCCCCceEEE
Q 040111           53 NITLEVESSDTIDNVKAKIQDKKRIPPPAEADL   85 (133)
Q Consensus        53 ~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~   85 (133)
                      ..++.|..++|+.+|+.+|++..|+|+++|||-
T Consensus        37 ~~~~rv~k~~~~~~l~~~va~~lg~~~~~~RlW   69 (530)
T 2ylm_A           37 YTVFKVLKNSSLAEFVQSLSQTMGFPQDQIRLW   69 (530)
T ss_dssp             CEEEEEETTSBHHHHHHHHHHHHTSCGGGEEEE
T ss_pred             cceEEEcCcCCHHHHHHHHHHHhCcCcccEEEE
Confidence            456899999999999999999999999999985

>3ivf_A Talin-1; FERM domain, cell membrane, cell projection, cytoskeleton, M phosphoprotein, cell adhesion, structural protein; 1.94A {Mus musculus} PDB: 2kma_A 2kc1_A

Probab=80.86  E-value=1.1  Score=34.97  Aligned_cols=53  Identities=17%  Similarity=0.183  Sum_probs=44.2

Q ss_pred             CCCceeeccccCcHHHHHHHhhhhcC----CCCCceEEEe------CCcccCccccccccccE
Q 040111           51 PQNITLEVESSDTIDNVKAKIQDKKR----IPPPAEADLL------KFPFFFFEEVLSFFWFV  103 (133)
Q Consensus        51 g~~~~l~V~~~~tV~~LK~~I~~~~g----Ip~~~q~L~~------~gk~L~d~~tL~dy~~~  103 (133)
                      +.+.++..++++||.++-.+|.++..    .++++.-|..      .|+-|++.++|..|++.
T Consensus        12 ~~~~~~~f~~~~~v~~~~~~i~e~~~~~~~~~~~~y~l~~~~~~~~~~~Wl~~~~~l~~y~~~   74 (371)
T 3ivf_A           12 NVVKTMQFEPSTMVYDACRMIRERIPEALAGPPNDFGLFLSDDDPKKGIWLEAGKALDYYMLR   74 (371)
T ss_dssp             TEEEEEEECTTCBHHHHHHHHHTTCGGGGSSCGGGEEEEECCSSGGGCEECCTTSBGGGGTCC
T ss_pred             ceeEEEEECCCCCHHHHHHHHHHhcccccCCCHHHCeEeccCCCCCcCEeccCCCCHHHhCCC
Confidence            55677889999999999999988863    4788889988      45669999999999963

>2juo_A GA-binding protein alpha chain; OST, ubiquitin, transcription factor, ensemble, DNA-binding, nucleus, transcription regulation; NMR {Mus musculus}

Probab=80.85  E-value=1.8  Score=27.42  Aligned_cols=42  Identities=19%  Similarity=0.259  Sum_probs=35.6

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      +++.|++-+.=.+..++.+|+++.+|.|.+++ ...+.+.+.-
T Consensus        23 e~Rl~i~L~~y~f~LQd~~L~~~k~LvdQcVqgeGlVQinvqi   65 (89)
T 2juo_A           23 EPRLQCSLDAHEICLQDIQLDPDRSLFDQGVKTDGTVQLSVQV   65 (89)
T ss_dssp             HHHHCSCCSSCEEEETTEECCTTSBTTTSSCCCCSEEEEEEEE
T ss_pred             HHHhcCCcccCeEEeeccccCCCccHHHhhcccccEEEEEEEE
Confidence            56778888888888999999999999999999 8888765543

---

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	133
d1wx9a1	73	d.15.1.1 (A:8-80) Large proline-rich protein BAT3	2e-16
d1wx9a1	73	d.15.1.1 (A:8-80) Large proline-rich protein BAT3	4e-09
d1bt0a_	73	d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis t	5e-16
d1bt0a_	73	d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis t	4e-07
d2zeqa1	78	d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin	1e-15
d2zeqa1	78	d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin	3e-07
d2c9wb1	103	d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens)	2e-15
d2c9wb1	103	d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens)	9e-07
d1ogwa_	76	d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [Tax	5e-15
d1ogwa_	76	d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [Tax	4e-08
d2bwfa1	73	d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyc	6e-15
d2bwfa1	73	d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyc	1e-07
d1wh3a_	87	d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like	1e-14
d1wh3a_	87	d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like	3e-09
d1wgha_	116	d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mous	3e-14
d1wgha_	116	d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mous	5e-04
d1zkha1	86	d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-t	7e-14
d1zkha1	86	d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-t	2e-08
d1wy8a1	76	d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING fing	1e-13
d1wy8a1	76	d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING fing	4e-06
d2faza1	76	d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING fing	2e-13
d2faza1	76	d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING fing	1e-06
d1wgda_	93	d.15.1.1 (A:) Homocysteine-responsive endoplasmic	2e-13
d1wgda_	93	d.15.1.1 (A:) Homocysteine-responsive endoplasmic	4e-05
d1uela_	95	d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homol	7e-13
d1uela_	95	d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homol	5e-06
d1z2ma2	76	d.15.1.1 (A:79-154) Interferon-induced 15 kDa prot	9e-13
d1z2ma2	76	d.15.1.1 (A:79-154) Interferon-induced 15 kDa prot	5e-09
d1oqya4	77	d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 h	1e-12
d1oqya4	77	d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 h	4e-06
d1x1ma1	94	d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse	3e-12
d1uh6a_	100	d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mous	2e-11
d1uh6a_	100	d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mous	1e-07
d1wxva1	81	d.15.1.1 (A:7-87) Bag-family molecular chaperone r	3e-11
d1wxva1	81	d.15.1.1 (A:7-87) Bag-family molecular chaperone r	4e-04
d1ttna1	80	d.15.1.1 (A:21-100) Dendritic cell-derived ubiquit	9e-11
d1ttna1	80	d.15.1.1 (A:21-100) Dendritic cell-derived ubiquit	5e-06
d1se9a_	101	d.15.1.1 (A:) Hypothetical protein At3g01050 {Thal	1e-10
d1v6ea_	95	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	2e-10
d1v5ta_	90	d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus mu	5e-10
d1v5ta_	90	d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus mu	8e-05
d1t0ya_	90	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	7e-10
d1euvb_	79	d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yea	7e-10
d1v2ya_	105	d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik	1e-09
d1v2ya_	105	d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik	1e-06
d1wjna_	97	d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse	2e-09
d1wjna_	97	d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse	4e-08
d1j8ca_	103	d.15.1.1 (A:) Ubiquitin-like N-terminal domain of	6e-09
d1j8ca_	103	d.15.1.1 (A:) Ubiquitin-like N-terminal domain of	2e-06
d1z2ma1	76	d.15.1.1 (A:3-78) Interferon-induced 15 kDa protei	6e-09
d1z2ma1	76	d.15.1.1 (A:3-78) Interferon-induced 15 kDa protei	5e-06
d1wiaa_	95	d.15.1.1 (A:) Ubiquitin-like protein bab25500 (201	8e-09
d1wiaa_	95	d.15.1.1 (A:) Ubiquitin-like protein bab25500 (201	9e-06
d1wx8a1	83	d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus muscul	7e-08
d1wx8a1	83	d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus muscul	5e-05
d1we6a_	111	d.15.1.1 (A:) Splicing factor 3 subunit 1, C-termi	5e-07
d1we6a_	111	d.15.1.1 (A:) Splicing factor 3 subunit 1, C-termi	0.001
d1yqba1	84	d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapien	5e-07
d1yqba1	84	d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapien	1e-05
d2uyzb1	77	d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human	1e-06
d1v5oa_	102	d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus mu	1e-06
d1v5oa_	102	d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus mu	3e-06
d1v86a_	95	d.15.1.1 (A:) hypothetical D7wsu128e protein {Mous	5e-06
d1v86a_	95	d.15.1.1 (A:) hypothetical D7wsu128e protein {Mous	1e-04
d1m94a_	73	d.15.1.1 (A:) Ubiquitin-like modifier protein hub1	1e-05
d1m94a_	73	d.15.1.1 (A:) Ubiquitin-like modifier protein hub1	7e-05
d1wjua_	100	d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human	3e-05
d1wjua_	100	d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human	1e-04

>d1wx9a1 d.15.1.1 (A:8-80) Large proline-rich protein BAT3 {Human (Homo sapiens) [TaxId: 9606]} Length = 73

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Large proline-rich protein BAT3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.4 bits (162), Expect = 2e-16
 Identities = 13/39 (33%), Positives = 21/39 (53%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQESTLHL 39
          I     IP  +QR I+ G+ L+D + L +Y +    +HL
Sbjct: 30 IAASVSIPSEKQRLIYQGRVLQDDKKLQEYNVGGKVIHL 68

>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 = 47.9 bits (114), Expect = 4e-09
 Identities = 9/35 (25%), Positives = 11/35 (31%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
            K  D Q  T  V +   +   K  I     IP 
Sbjct: 4  LVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPS 38

>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 = 65.7 bits (160), Expect = 5e-16
 Identities = 25/40 (62%), Positives = 30/40 (75%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          +E+KEGIPP QQR I+AGKQL D +T  DY I+  S LHL
Sbjct: 30 VEEKEGIPPVQQRLIYAGKQLADDKTAKDYNIEGGSVLHL 69

>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 = 42.6 bits (100), Expect = 4e-07
 Identities = 12/35 (34%), Positives = 23/35 (65%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
            K    + I +++E +DTID +K ++++K+ IPP
Sbjct: 4  KVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPP 38

>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 = 64.5 bits (157), Expect = 1e-15
 Identities = 13/40 (32%), Positives = 26/40 (65%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          +  ++G+P  Q R IFAGK+L +  T+ +  ++ +S +H+
Sbjct: 32 VAKRQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHI 71

>d2zeqa1 d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of parkin
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.3 bits (102), Expect = 3e-07
 Identities = 7/35 (20%), Positives = 16/35 (45%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F +        +EV+S  +I  +K  +  ++ +P 
Sbjct: 6  FVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPA 40

>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 = 64.5 bits (157), Expect = 2e-15
 Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 8/52 (15%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKI--------QESTLHLGWRAD 44
          +E     PP +QR     + L+DG+TL +             +T+ L +RAD
Sbjct: 30 VEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRAD 81

>d2c9wb1 d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Elongin B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.1 bits (99), Expect = 9e-07
 Identities = 6/29 (20%), Positives = 13/29 (44%)

Query: 52 QNITLEVESSDTIDNVKAKIQDKKRIPPP 80
            I  + + S T+  +K  ++   + PP 
Sbjct: 11 TTIFTDAKESSTVFELKRIVEGILKRPPD 39

>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 = 63.0 bits (153), Expect = 5e-15
 Identities = 34/40 (85%), Positives = 36/40 (90%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          I+DKEGIPP QQR IFAGKQLEDGRTL+DY IQ ESTLHL
Sbjct: 30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHL 69

>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 = 45.3 bits (107), Expect = 4e-08
 Identities = 24/36 (66%), Positives = 27/36 (75%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPP 80
          F K    + ITLEVE SDTI+NVKAKIQDK+ IPP 
Sbjct: 4  FVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPD 39

>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 = 62.9 bits (153), Expect = 6e-15
 Identities = 17/40 (42%), Positives = 25/40 (62%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQE-STLHL 39
          I    GIP   QR I++GK L+D +T+  Y IQ+  ++HL
Sbjct: 30 INKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHL 69

>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 = 44.0 bits (104), Expect = 1e-07
 Identities = 7/35 (20%), Positives = 10/35 (28%), Gaps = 1/35 (2%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
            K+       + V    T+   K  I     IP 
Sbjct: 5  HIKSGQ-DKWEVNVAPESTVLQFKEAINKANGIPV 38

>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 = 62.3 bits (151), Expect = 1e-14
 Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 1/43 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          IED++G+P  QQ+  F G+ L+D   L  Y IQ   TL L  +
Sbjct: 37 IEDQQGLPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKK 79

>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 = 48.4 bits (115), Expect = 3e-09
 Identities = 10/35 (28%), Positives = 19/35 (54%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          F KNPD  +    +  +  I  +K +I+D++ +P 
Sbjct: 11 FVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPK 45

>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 = 62.3 bits (151), Expect = 3e-14
 Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 6/53 (11%)

Query: 2   EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQE---STLHLGWRADFCKNPDP 51
           E+++   P   R I+ G+ L    TL   K+     + +HL  R      P+P
Sbjct: 55  EEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLVARE---TLPEP 104

>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 = 35.3 bits (81), Expect = 5e-04
 Identities = 2/41 (4%), Positives = 12/41 (29%), Gaps = 8/41 (19%)

Query: 47 KNPDPQNITLEVESSDTIDNVKAKI--------QDKKRIPP 79
               +        +D+  ++   +        ++++   P
Sbjct: 22 ILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSP 62

>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 = 60.3 bits (146), Expect = 7e-14
 Identities = 12/40 (30%), Positives = 23/40 (57%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          I +  G+P G+Q+  + G  ++D  +LA Y +   + +HL
Sbjct: 41 IHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMANGAVIHL 80

>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 = 46.0 bits (109), Expect = 2e-08
 Identities = 6/28 (21%), Positives = 13/28 (46%)

Query: 52 QNITLEVESSDTIDNVKAKIQDKKRIPP 79
          Q +   +  +D +  +K KI +   +P 
Sbjct: 22 QVLVFTLPLTDQVSVIKVKIHEATGMPA 49

>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 = 59.5 bits (144), Expect = 1e-13
 Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 1/45 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRAD 44
          +     + P  QR  + GKQLE+G TL DY +     + L  R D
Sbjct: 32 VWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVRPD 76

>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 = 39.9 bits (93), Expect = 4e-06
 Identities = 6/29 (20%), Positives = 14/29 (48%), Gaps = 1/29 (3%)

Query: 52 QNITLE-VESSDTIDNVKAKIQDKKRIPP 79
          +  T+E V    TI+ ++ ++     + P
Sbjct: 12 KTCTIEDVSRKATIEELRERVWALFDVRP 40

>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 = 59.1 bits (143), Expect = 2e-13
 Identities = 18/43 (41%), Positives = 27/43 (62%), Gaps = 1/43 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          I++   + PG QR  + GKQ+EDG TL DY+++   T+ L  R
Sbjct: 32 IQELFHVEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLLVR 74

>d2faza1 d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING finger domain-containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like PHD and RING finger domain-containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.0 bits (96), Expect = 1e-06
 Identities = 6/29 (20%), Positives = 15/29 (51%), Gaps = 1/29 (3%)

Query: 52 QNITLE-VESSDTIDNVKAKIQDKKRIPP 79
          Q  T++ +     ++ ++ KIQ+   + P
Sbjct: 12 QTHTVDSLSRLTKVEELRRKIQELFHVEP 40

>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 = 59.5 bits (144), Expect = 2e-13
 Identities = 13/44 (29%), Positives = 19/44 (43%), Gaps = 5/44 (11%)

Query: 1  IEDKEG--IPPGQQRSIFAGKQLEDGRTLADYKIQE---STLHL 39
          +         P  QR I++GK L D + L D   ++     LHL
Sbjct: 39 LSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHL 82

>d1wgda_ d.15.1.1 (A:) Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.5 bits (87), Expect = 4e-05
 Identities = 7/38 (18%), Positives = 18/38 (47%), Gaps = 2/38 (5%)

Query: 47 KNPD--PQNITLEVESSDTIDNVKAKIQDKKRIPPPAE 82
          K+P+   +++ L  +   ++ ++KA +       P  E
Sbjct: 13 KSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPE 50

>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 = 58.1 bits (140), Expect = 7e-13
 Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 1/39 (2%)

Query: 2  EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          + K+  P   Q+ I+AGK L D   L +YKI  ++ + +
Sbjct: 34 KGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVV 72

>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 = 5e-06
 Identities = 9/51 (17%), Positives = 19/51 (37%), Gaps = 1/51 (1%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP-PAEADLLKFPFFFFE 94
            K    Q   ++++  +T+  +K KI+ +K     P     L +      
Sbjct: 4  TLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILN 54

>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 = 57.2 bits (138), Expect = 9e-13
 Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 1/43 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
          +   EG+        F GK LED   L +Y ++  ST+ +  R
Sbjct: 33 VSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLR 75

>d1z2ma2 d.15.1.1 (A:79-154) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.6 bits (113), Expect = 5e-09
 Identities = 6/35 (17%), Positives = 17/35 (48%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
            +N   ++ T EV  + T+ ++K ++   + +  
Sbjct: 7  LVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQD 41

>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 = 57.2 bits (138), Expect = 1e-12
 Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 4/43 (9%)

Query: 1  IEDKEG---IPPGQQRSIFAGKQLEDGRTLADYKIQE-STLHL 39
          IE ++G    P   Q+ I+AGK L D   + DY+I E + + +
Sbjct: 32 IEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVV 74

>d1oqya4 d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 homolog A (Hhr23a) {Human (Homo sapiens) [TaxId: 9606]} Length = 77

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of Rad23 homolog A (Hhr23a)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.8 bits (93), Expect = 4e-06
 Identities = 9/38 (23%), Positives = 16/38 (42%), Gaps = 3/38 (7%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKK---RIPP 79
            K    Q   + +E  +T+  +K KI+ +K     P 
Sbjct: 6  TLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPV 43

>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 = 56.4 bits (136), Expect = 3e-12
 Identities = 15/40 (37%), Positives = 25/40 (62%), Gaps = 2/40 (5%)

Query: 2  EDKEGIP-PGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          + +E +P P     I+ G++L+D +TL  Y IQ  ST+H+
Sbjct: 50 KLQESVPDPELIDLIYCGRKLKDDQTLDFYGIQPGSTVHV 89

>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 = 54.6 bits (131), Expect = 2e-11
 Identities = 9/43 (20%), Positives = 16/43 (37%), Gaps = 1/43 (2%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR 42
           I  + G    +          +D  +L DY+I     L L ++
Sbjct: 58  IAAQTGTRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLELYYQ 100

>d1uh6a_ d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 100

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 5, ubl5
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.6 bits (105), Expect = 1e-07
 Identities = 6/35 (17%), Positives = 15/35 (42%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
           C +   + + ++  + DTI ++K  I  +     
Sbjct: 32 VCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRW 66

>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 = 53.3 bits (128), Expect = 3e-11
 Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 2/41 (4%)

Query: 1  IEDKEGIPPGQQRSIFAGKQL-EDGRTLADYKIQE-STLHL 39
          +E+  G+P   Q+ IF GK L E    L+   IQ+   + L
Sbjct: 35 VEEVIGVPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVML 75

>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 = 34.8 bits (80), Expect = 4e-04
 Identities = 2/26 (7%), Positives = 11/26 (42%)

Query: 54 ITLEVESSDTIDNVKAKIQDKKRIPP 79
           + +  S   + ++   +++   +P 
Sbjct: 18 TSQQGSSEPVVQDLAQVVEEVIGVPQ 43

>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 = 52.2 bits (125), Expect = 9e-11
 Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
          +   EG+ PG QR  F+G+ L D     + KI  +  + +
Sbjct: 33 LHAAEGVEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQV 72

>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 = 39.9 bits (93), Expect = 5e-06
 Identities = 7/35 (20%), Positives = 19/35 (54%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
            +    +++ L V S+DT+ ++K ++   + + P
Sbjct: 7  RLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEP 41

>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 = 52.6 bits (126), Expect = 1e-10
 Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 9/46 (19%)

Query: 3  DKEGIP--PGQQRSIFAGKQLEDGRTLADYKIQ-------ESTLHL 39
          +KE  P    + + I AGK LE+ +T+ DY+          +T+H+
Sbjct: 45 EKENGPKTVKEVKLISAGKVLENSKTVKDYRSPVSNLAGAVTTMHV 90

>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 = 51.8 bits (124), Expect = 2e-10
 Identities = 7/47 (14%), Positives = 13/47 (27%), Gaps = 8/47 (17%)

Query: 1  IEDKEGIPPGQQRSIFAGKQ-------LEDGRTLADYKIQ-ESTLHL 39
          +E   G P         G          ++   L  Y +     +H+
Sbjct: 38 LELVVGSPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIHV 84

>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 = 50.8 bits (121), Expect = 5e-10
 Identities = 8/43 (18%), Positives = 20/43 (46%), Gaps = 4/43 (9%)

Query: 1  IEDKEGIPPGQQRSI---FAGKQLEDGRTLADYKIQE-STLHL 39
          ++   G+ P +Q+ +     GK  E+   L   K++  + + +
Sbjct: 37 LKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMM 79

>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 = 36.9 bits (85), Expect = 8e-05
 Identities = 5/33 (15%), Positives = 13/33 (39%)

Query: 47 KNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          K    +     +   DT+ ++K  ++    + P
Sbjct: 13 KWGGQEYSVTTLSEDDTVLDLKQFLKTLTGVLP 45

>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 = 50.3 bits (120), Expect = 7e-10
 Identities = 6/47 (12%), Positives = 13/47 (27%), Gaps = 8/47 (17%)

Query: 1  IEDKEGIPPGQQRSIFAGKQ-------LEDGRTLADYKIQ-ESTLHL 39
          +E   G      R               +  ++L D  ++    +H 
Sbjct: 35 LELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHA 81

>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 = 49.8 bits (119), Expect = 7e-10
 Identities = 5/40 (12%), Positives = 16/40 (40%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
             ++G      R ++ G +++  +T  D  ++    +  
Sbjct: 33 FAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEA 72

>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 = 50.1 bits (119), Expect = 1e-09
 Identities = 9/56 (16%), Positives = 18/56 (32%), Gaps = 17/56 (30%)

Query: 1  IEDKEGIPPGQQRS---------------IFAGKQLEDGR-TLADYKIQ-ESTLHL 39
          I+    +   ++                   AG++L + R  L DY I+    +  
Sbjct: 37 IQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLRDYGIRNRDEVSF 92

>d1v2ya_ d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik {Mouse (Mus musculus) [TaxId: 10090]} Length = 105

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3300001g02rik
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.3 bits (99), Expect = 1e-06
 Identities = 6/33 (18%), Positives = 15/33 (45%)

Query: 47 KNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
             D + + + V  + T+ ++K  IQ   ++  
Sbjct: 13 CKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQ 45

>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 = 49.5 bits (118), Expect = 2e-09
 Identities = 6/52 (11%), Positives = 16/52 (30%), Gaps = 9/52 (17%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLE--------DGRTLADYKIQ-ESTLHLGWRA 43
          +     +P  +    +   ++         D + L  Y ++    L + W  
Sbjct: 42 LSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCLLVRWSG 93

>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 = 45.7 bits (108), Expect = 4e-08
 Identities = 7/33 (21%), Positives = 15/33 (45%)

Query: 47 KNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
            P+ Q +  ++  S T+  VK  +    ++P 
Sbjct: 18 NQPERQILEKQLPDSMTVQKVKGLLSRLLKVPV 50

>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 = 48.1 bits (114), Expect = 6e-09
 Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 1/40 (2%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQE-STLHL 39
           I  +      Q   IFAGK L+D  TL  + I +  T+HL
Sbjct: 61  ISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHL 100

>d1j8ca_ d.15.1.1 (A:) Ubiquitin-like N-terminal domain of PLIC-2 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like N-terminal domain of PLIC-2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.5 bits (97), Expect = 2e-06
 Identities = 5/33 (15%), Positives = 11/33 (33%), Gaps = 1/33 (3%)

Query: 47 KNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          K P  +     V  + ++   K  I  + +   
Sbjct: 38 KTPK-EKEEFAVPENSSVQQFKEAISKRFKSQT 69

>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 = 47.2 bits (112), Expect = 6e-09
 Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 3/42 (7%)

Query: 1  IEDKEGIPPGQQRSIF--AGKQLEDGRTLADYKIQ-ESTLHL 39
          I  K G+   QQR     +G  L+D   LA   +   ST+ L
Sbjct: 30 ITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLL 71

>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 = 39.9 bits (93), Expect = 5e-06
 Identities = 7/33 (21%), Positives = 14/33 (42%)

Query: 47 KNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          K        + + SS ++  +KA+I  K  +  
Sbjct: 6  KMLAGNEFQVSLSSSMSVSELKAQITQKIGVHA 38

>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 = 47.6 bits (113), Expect = 8e-09
 Identities = 9/40 (22%), Positives = 15/40 (37%), Gaps = 2/40 (5%)

Query: 5  EGIPPGQQRSIFAGKQL-EDGRTLADYKIQ-ESTLHLGWR 42
                Q + I+ G+ L +  RTL+   I     +H    
Sbjct: 38 FPGQESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRS 77

>d1wiaa_ d.15.1.1 (A:) Ubiquitin-like protein bab25500 (2010008E23Rik) {Mouse (Mus musculus) [TaxId: 10090]} Length = 95

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein bab25500 (2010008E23Rik)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.5 bits (92), Expect = 9e-06
 Identities = 5/30 (16%), Positives = 9/30 (30%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDK 74
            K  +           DT+  +K+K    
Sbjct: 11 RLKFLNDTEELAVARPEDTVGTLKSKYFPG 40

>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 = 45.0 bits (106), Expect = 7e-08
 Identities = 12/40 (30%), Positives = 17/40 (42%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQE-STLHL 39
          I         +   IF GK L D   L+   I + ST+H+
Sbjct: 39 ISKYLHCNADRLVLIFTGKILRDQDILSQRGILDGSTVHV 78

>d1wx8a1 d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]} Length = 83

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 4931431F19Rik
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.3 bits (86), Expect = 5e-05
 Identities = 4/33 (12%), Positives = 8/33 (24%), Gaps = 1/33 (3%)

Query: 47 KNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
          K P        +  +  +   K +I        
Sbjct: 16 KTPQ-DCHEFFLAENSNVRRFKKQISKYLHCNA 47

>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 = 43.1 bits (101), Expect = 5e-07
 Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 1/40 (2%)

Query: 1   IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
           I  +  IP  +Q+       L+D  +LA Y +     L L
Sbjct: 61  IAGEIQIPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTL 100

>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 = 34.2 bits (78), Expect = 0.001
 Identities = 11/37 (29%), Positives = 20/37 (54%), Gaps = 2/37 (5%)

Query: 45 FCKN-PDPQNITLEVES-SDTIDNVKAKIQDKKRIPP 79
             N  D Q + + V+S S+ + ++K KI  + +IP 
Sbjct: 33 SKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPA 69

>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 = 42.3 bits (99), Expect = 5e-07
 Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQE-STLHL 39
          I  +    P Q   IFAGK L+D  +LA   +++  T+HL
Sbjct: 36 ISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHL 75

>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 = 38.8 bits (90), Expect = 1e-05
 Identities = 8/35 (22%), Positives = 13/35 (37%), Gaps = 1/35 (2%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPP 79
            K P        V  + TI  +K +I  + +  P
Sbjct: 11 TVKTPK-DKEDFSVTDTCTIQQLKEEISQRFKAHP 44

>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 = 41.3 bits (97), Expect = 1e-06
 Identities = 8/40 (20%), Positives = 20/40 (50%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL 39
             ++G+P    R +F G+++ D  T  +  ++ E  + +
Sbjct: 32 YCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEV 71

>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 = 41.9 bits (98), Expect = 1e-06
 Identities = 7/41 (17%), Positives = 20/41 (48%), Gaps = 2/41 (4%)

Query: 1  IEDKEGIPPGQQRSIFAGKQ-LEDGRTLADYKIQE-STLHL 39
           E + G+P  + + ++  +   +D  +L  Y +++   + L
Sbjct: 41 CELESGVPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVL 81

>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 = 41.2 bits (96), Expect = 3e-06
 Identities = 3/29 (10%), Positives = 11/29 (37%)

Query: 47 KNPDPQNITLEVESSDTIDNVKAKIQDKK 75
          ++      +L+V     + N +   + + 
Sbjct: 17 RDLTEVTFSLQVNPDFELSNFRVLCELES 45

>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 = 40.3 bits (94), Expect = 5e-06
 Identities = 7/28 (25%), Positives = 11/28 (39%)

Query: 52 QNITLEVESSDTIDNVKAKIQDKKRIPP 79
              ++V    T   +K KI     +PP
Sbjct: 27 TKHDVKVPLDSTGSELKQKIHSITGLPP 54

>d1v86a_ d.15.1.1 (A:) hypothetical D7wsu128e protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 95

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: hypothetical D7wsu128e protein
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.5 bits (84), Expect = 1e-04
 Identities = 8/40 (20%), Positives = 19/40 (47%), Gaps = 2/40 (5%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQE-STLHL 39
          I    G+PP  Q+ +     + + +TL + K+   + + +
Sbjct: 46 IHSITGLPPAMQK-VMYKGLVPEDKTLREIKVTSGAKIMV 84

>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 = 38.5 bits (89), Expect = 1e-05
 Identities = 10/40 (25%), Positives = 19/40 (47%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQE-STLHL 39
          +  + G  P +      G  L+D  +L DY++ + + L L
Sbjct: 31 LSLQIGTQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLEL 70

>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 = 36.6 bits (84), Expect = 7e-05
 Identities = 3/36 (8%), Positives = 14/36 (38%)

Query: 45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPP 80
             +   + + ++  + D++ + K  +  +    P 
Sbjct: 5  VVNDRLGKKVRVKCLAEDSVGDFKKVLSLQIGTQPN 40

>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 = 38.4 bits (89), Expect = 3e-05
 Identities = 5/34 (14%), Positives = 12/34 (35%)

Query: 47 KNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPP 80
          +    +   LE     T   +++KI +   +   
Sbjct: 25 RLKKDRKNLLETRLHITGRELRSKIAETFGLQEN 58

>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 = 36.5 bits (84), Expect = 1e-04
 Identities = 8/40 (20%), Positives = 17/40 (42%), Gaps = 1/40 (2%)

Query: 1  IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQE-STLHL 39
          I +  G+     + +   KQL+ G+TL +  +       +
Sbjct: 49 IAETFGLQENYIKIVINKKQLQLGKTLEEQGVAHNVKAMV 88

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	133
d1bt0a_	73	Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxI	99.77
d2zeqa1	78	Ubiquitin-like domain of parkin {Mouse (Mus muscul	99.76
d1z2ma2	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.76
d1wh3a_	87	2'-5'-oligoadenylate synthetase-like protein, OASL	99.75
d1ogwa_	76	Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}	99.74
d1ttna1	80	Dendritic cell-derived ubiquitin-like protein {Hum	99.73
d1wx9a1	73	Large proline-rich protein BAT3 {Human (Homo sapie	99.73
d1z2ma1	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.73
d1oqya4	77	Ubiquitin-like domain of Rad23 homolog A (Hhr23a)	99.72
d1m94a_	73	Ubiquitin-like modifier protein hub1 {Baker's yeas	99.72
d2faza1	76	Ubiquitin-like PHD and RING finger domain-containi	99.7
d1uh6a_	100	Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculu	99.69
d1uela_	95	Ubiquitin-like domain of Rad23 homolog B (Hhr23B)	99.69
d1wy8a1	76	Ubiquitin-like PHD and RING finger domain-containi	99.68
d2bwfa1	73	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.67
d1yqba1	84	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	99.63
d1zkha1	86	Splicing factor 3 subunit 1, C-terminal domain {Hu	99.62
d1wjua_	100	NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens	99.62
d1wx8a1	83	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	99.6
d1wgha_	116	Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculu	99.6
d1we6a_	111	Splicing factor 3 subunit 1, C-terminal domain {Th	99.59
d1j8ca_	103	Ubiquitin-like N-terminal domain of PLIC-2 {Human	99.59
d2c9wb1	103	Elongin B {Human (Homo sapiens) [TaxId: 9606]}	99.59
d1v5oa_	102	1700011n24rik protein {Mouse (Mus musculus) [TaxId	99.55
d1se9a_	101	Hypothetical protein At3g01050 {Thale cress (Arabi	99.54
d1wgga_	96	Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (M	99.54
d1wiaa_	95	Ubiquitin-like protein bab25500 (2010008E23Rik) {M	99.47
d1wgda_	93	Homocysteine-responsive endoplasmic reticulum-resi	99.47
d1v5ta_	90	8430435i17rik protein {Mouse (Mus musculus) [TaxId	99.46
d1v2ya_	105	Ubiquitin-like protein 3300001g02rik {Mouse (Mus m	99.46
d1v86a_	95	hypothetical D7wsu128e protein {Mouse (Mus musculu	99.46
d1wxva1	81	Bag-family molecular chaperone regulator-1 {Human	99.41
d2faza1	76	Ubiquitin-like PHD and RING finger domain-containi	99.38
d1z2ma2	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.36
d1bt0a_	73	Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxI	99.36
d2zeqa1	78	Ubiquitin-like domain of parkin {Mouse (Mus muscul	99.35
d1wy8a1	76	Ubiquitin-like PHD and RING finger domain-containi	99.34
d2bwfa1	73	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.33
d1wh3a_	87	2'-5'-oligoadenylate synthetase-like protein, OASL	99.33
d1ttna1	80	Dendritic cell-derived ubiquitin-like protein {Hum	99.29
d1wx9a1	73	Large proline-rich protein BAT3 {Human (Homo sapie	99.26
d1ogwa_	76	Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}	99.25
d1z2ma1	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.24
d1zkha1	86	Splicing factor 3 subunit 1, C-terminal domain {Hu	99.23
d1yqba1	84	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	99.22
d1v6ea_	95	Ubiquitin-like domain of tubulin folding cofactor	99.22
d1wjna_	97	Tubulin-folding protein TbcE {Mouse (Mus musculus)	99.22
d1wx8a1	83	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	99.21
d1x1ma1	94	Ubiquitin-like protein 7 {Mouse (Mus musculus) [Ta	99.2
d1m94a_	73	Ubiquitin-like modifier protein hub1 {Baker's yeas	99.18
d1j8ca_	103	Ubiquitin-like N-terminal domain of PLIC-2 {Human	99.17
d1we6a_	111	Splicing factor 3 subunit 1, C-terminal domain {Th	99.17
d1se9a_	101	Hypothetical protein At3g01050 {Thale cress (Arabi	99.14
d1oqya4	77	Ubiquitin-like domain of Rad23 homolog A (Hhr23a)	99.12
d1uela_	95	Ubiquitin-like domain of Rad23 homolog B (Hhr23B)	99.11
d1uh6a_	100	Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculu	99.1
d1euvb_	79	SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomy	99.06
d1wgha_	116	Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculu	99.04
d1x1ma1	94	Ubiquitin-like protein 7 {Mouse (Mus musculus) [Ta	99.04
d1t0ya_	90	Ubiquitin-like domain of tubulin folding cofactor	99.03
d1wjua_	100	NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens	98.97
d1wxva1	81	Bag-family molecular chaperone regulator-1 {Human	98.97
d1wgga_	96	Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (M	98.97
d2c9wb1	103	Elongin B {Human (Homo sapiens) [TaxId: 9606]}	98.97
d1v5oa_	102	1700011n24rik protein {Mouse (Mus musculus) [TaxId	98.95
d1v5ta_	90	8430435i17rik protein {Mouse (Mus musculus) [TaxId	98.91
d2uyzb1	77	SUMO-1 (smt3 homologue) {Human (Homo sapiens) [Tax	98.87
d1wgda_	93	Homocysteine-responsive endoplasmic reticulum-resi	98.82
d1v86a_	95	hypothetical D7wsu128e protein {Mouse (Mus musculu	98.78
d1wiaa_	95	Ubiquitin-like protein bab25500 (2010008E23Rik) {M	98.74
d1euvb_	79	SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomy	98.67
d1v2ya_	105	Ubiquitin-like protein 3300001g02rik {Mouse (Mus m	98.62
d1v6ea_	95	Ubiquitin-like domain of tubulin folding cofactor	98.55
d1wjna_	97	Tubulin-folding protein TbcE {Mouse (Mus musculus)	98.36
d1t0ya_	90	Ubiquitin-like domain of tubulin folding cofactor	98.31
d1wf9a1	94	NPL4-like protein 1 {Thale cress (Arabidopsis thal	98.2
d2uyzb1	77	SUMO-1 (smt3 homologue) {Human (Homo sapiens) [Tax	98.14
d1wm3a_	72	SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}	97.97
d2al3a1	76	Tether containing UBX domain for GLUT4 (Tug) {Mous	97.06
d1i42a_	89	p47 {Rat (Rattus norvegicus) [TaxId: 10116]}	96.54
d1h8ca_	82	Fas-associated factor 1, Faf1 {Human (Homo sapiens	96.47
d1wm3a_	72	SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}	96.1
d1wj4a_	124	Hypothetical protein KIAA0794 {Human (Homo sapiens	94.7
d2cr5a1	96	UBX domain-containing protein 6 (Reproduction 8) {	94.66
d1wf9a1	94	NPL4-like protein 1 {Thale cress (Arabidopsis thal	94.33
d1wxma1	73	A-Raf proto-oncogene serine/threonine-protein kina	92.1
d1c1yb_	77	c-Raf1 RBD {Human (Homo sapiens) [TaxId: 9606]}	88.39
d1wgra_	100	Growth factor receptor-bound protein 7, GRB-7 {Hum	85.23
d1oeya_	82	Neutrophil cytosol factor 2 (p67phox component of	84.7

>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=99.77  E-value=1.1e-19  Score=113.31  Aligned_cols=66  Identities=20%  Similarity=0.256  Sum_probs=62.2

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      .|+||+++|++++++|++++||+++|++|+++.|+||++|+|+|+|++|+|+.+|++|+|.+.+.|
T Consensus         2 ~I~Vk~~~G~~~~l~V~~~~tV~~lK~~i~~~~gi~~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti   67 (73)
T d1bt0a_           2 LIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLIYAGKQLADDKTAKDYNIEGGSVL   67 (73)
T ss_dssp             EEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEE
T ss_pred             EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhCCChHHEEEEECCeEcCCCCcHHHcCCCCCCEE
Confidence            378999999999999999999999999999999999999999999999999999999999766654

>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=99.76  E-value=1.2e-19  Score=114.56  Aligned_cols=68  Identities=10%  Similarity=0.076  Sum_probs=63.5

Q ss_pred             cccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           42 RADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        42 ~~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      ..||||+.+|++++++|++++||++||++|++++|+||++|+|+|+|++|+|+.+|++|+|...+.|.
T Consensus         3 M~I~Vk~~~g~t~~l~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~   70 (78)
T d2zeqa1           3 MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVH   70 (78)
T ss_dssp             EEEEEESSSSSCEEEEECTTCBHHHHHHHHHHHHTCCGGGEEEEETTEEECTTCBGGGSSCCTTCEEE
T ss_pred             eEEEEEcCCCCEEEEEEcccccHHHHHHHHHHHHCcChhHeEEEEeeeEcCCCCCHHHcCCCCCCEEE
Confidence            34899999999999999999999999999999999999999999999999999999999997666553

>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=99.76  E-value=1.6e-19  Score=113.22  Aligned_cols=67  Identities=12%  Similarity=0.067  Sum_probs=63.2

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      +|+||+.+|++++++|++++||++||++|+++.|+|+++|+|+|+|+.|+|+.+|++|+|...+.|.
T Consensus         5 qi~Vk~~~G~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~qrL~~~gk~L~d~~tL~~y~I~~~sti~   71 (76)
T d1z2ma2           5 SILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVF   71 (76)
T ss_dssp             EEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEE
T ss_pred             EEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHhcCChhHeEEEECCeECCCCCcHHHcCCCCCCEEE
Confidence            3899999999999999999999999999999999999999999999999999999999997766654

>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=99.75  E-value=2.3e-19  Score=115.36  Aligned_cols=66  Identities=17%  Similarity=0.187  Sum_probs=62.4

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      |+||+++|++++++|++++||.+||++|++++|||+++|+|+|+|+.|+|+.+|++|+|...+++.
T Consensus        10 I~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~~tL~~y~I~~~stl~   75 (87)
T d1wh3a_          10 VFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLI   75 (87)
T ss_dssp             EEEEETTTEEEEEEECSSSBHHHHHHHHHHHTCCCTTTEEEEETTEECCSSSBHHHHTCCTTEEEE
T ss_pred             EEEECCCCCEEEEEECCcCcHHHHHHHHHHHHCcChHHeEEEeeceEcCCCCcHHHcCCCCCCEEE
Confidence            899999999999999999999999999999999999999999999999999999999997666554

>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=99.74  E-value=3.8e-19  Score=111.56  Aligned_cols=67  Identities=39%  Similarity=0.399  Sum_probs=63.0

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      +|+||+++|++++++|++++||++||++|+++.|+|+++|+|+|+|++|+|+.+|++|++.+.++|.
T Consensus         2 qI~Vk~l~G~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~qrL~~~Gk~L~d~~tL~~y~i~~~s~I~   68 (76)
T d1ogwa_           2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLH   68 (76)
T ss_dssp             EEEEEETTSCEEEEECCTTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEE
T ss_pred             EEEEEcCCCCEEEEEECCCCcHHHHHHhhhhhcCCChHHEEeEECCeEcCCCCCHHHcCCCCCCEEE
Confidence            4899999999999999999999999999999999999999999999999999999999997766554

>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=99.73  E-value=3.7e-19  Score=112.74  Aligned_cols=66  Identities=12%  Similarity=0.039  Sum_probs=62.7

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      ++||+.+|+++.++|++++||++||++|++++|+|+++|+|+|+|++|+|+.+|++|+|...++|.
T Consensus         6 i~Vk~~~G~~~~l~V~~~~tV~~lK~~I~~~~~ip~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~   71 (80)
T d1ttna1           6 LRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQ   71 (80)
T ss_dssp             EEEEETTTEEEEEEECTTSHHHHHHHHHHHTTCCCSTTCEEEETTEECCTTSHHHHCCCSSSCEEE
T ss_pred             EEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCcccEEEEECceEcCCCCcHHHcCCCCCCEEE
Confidence            899999999999999999999999999999999999999999999999999999999998766554

>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=99.73  E-value=5.2e-19  Score=110.25  Aligned_cols=61  Identities=16%  Similarity=0.122  Sum_probs=58.8

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFV  103 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~  103 (133)
                      +|+||+++|+++.++|++++||++||++|+++.|+|+++|+|+|+|+.|+|+.+|+||++.
T Consensus         2 ~I~Vk~~~g~~~~l~V~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~~tL~dy~i~   62 (73)
T d1wx9a1           2 EVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYNVG   62 (73)
T ss_dssp             EEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHCCCTTTCCCEETTEECCSSSBHHHHTCT
T ss_pred             EEEEEcCCCCEEEEEECCCChHHHHHHHHHHHhCCChHHEEEEECCeEccCCCCHHHhCCC
Confidence            3789999999999999999999999999999999999999999999999999999999984

>d1z2ma1 d.15.1.1 (A:3-78) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=9e-19  Score=109.99  Aligned_cols=66  Identities=12%  Similarity=-0.039  Sum_probs=61.5

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEe--CCcccCccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLL--KFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~--~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      +.||+++|+.+.++|++++||+++|++|++++|+||++|+|+|  +|+.|+|+.+|++|+|.+.+.|.
T Consensus         3 l~Vk~l~G~~~~v~V~~~~tV~~lK~~I~~~~gip~~~QrLi~~~~Gk~L~D~~tL~~y~i~~g~~i~   70 (76)
T d1z2ma1           3 LTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVL   70 (76)
T ss_dssp             EEEEESSSCEEEEECCSSCCHHHHHHHHHHHHCCCGGGEEEEEETTCCBCCSSSCSGGGTCCTTCEEE
T ss_pred             EEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhccCCccEEEEEcCCCeeccCCCcHHHcCCCCCCEEE
Confidence            6799999999999999999999999999999999999999999  79999999999999997666543

>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=99.72  E-value=6.1e-19  Score=110.92  Aligned_cols=67  Identities=13%  Similarity=0.143  Sum_probs=62.1

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcC---CCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKR---IPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~g---Ip~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      +|+||+++|+++.++|++++||++||++|+++.|   +||++|||+|+|+.|+|+.+|++|+|...++|+
T Consensus         4 ~i~vk~l~g~~~~l~v~~~~TV~~lK~~i~~~~g~~~i~~~~qrLi~~Gk~L~D~~tL~~y~I~~~s~i~   73 (77)
T d1oqya4           4 TITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVV   73 (77)
T ss_dssp             CEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSSEECSSSBTTTTCCCTTSCEE
T ss_pred             EEEEECCCCCEEEEEECCCCcHHHHHHHHHHhcCCCCCChHHEEeEECCcCccCCCcHHHcCCCCCCEEE
Confidence            3789999999999999999999999999999987   999999999999999999999999998766444

>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=99.72  E-value=7.7e-19  Score=109.51  Aligned_cols=66  Identities=6%  Similarity=-0.075  Sum_probs=62.0

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      .|+|++..|+++.++|++++||++||++|++++|+||++|+|+|+|+.|+|+.+|++|+|.+.+.+
T Consensus         3 ~i~vk~~~Gk~~~v~V~~~~tV~~lK~~I~~~~~i~~~~q~Li~~Gk~L~d~~tL~~y~I~~gstl   68 (73)
T d1m94a_           3 EVVVNDRLGKKVRVKCLAEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHISLEDYEVHDQTNL   68 (73)
T ss_dssp             EEEEEETTTEEEEEEECTTSBHHHHHHHHHHHHCCTTTSEEEESSSCEECTTSBHHHHTCCTTEEE
T ss_pred             EEEEECCCCCEEEEEECCcCcHHHHHHHHHHhhcccccEEEEEEEeEEecccCcHHHcCCCCCCEE
Confidence            378999999999999999999999999999999999999999999999999999999999766654

>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=99.70  E-value=2.2e-18  Score=108.30  Aligned_cols=66  Identities=12%  Similarity=0.062  Sum_probs=60.3

Q ss_pred             ccccCCCCCC-Cceee-ccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           43 ADFCKNPDPQ-NITLE-VESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        43 ~i~Vk~~~g~-~~~l~-V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      .|+||+++|+ +++++ +++++||++||++|+++.|+|+++|+|+|+|+.|+|+.+|++|++...+.|
T Consensus         2 ~I~Vktl~Gk~t~~l~~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~y~I~~~sti   69 (76)
T d2faza1           2 WIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTI   69 (76)
T ss_dssp             EEEEEETTSSCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTTTTTCCTTCEE
T ss_pred             EEEEEeCCCCcEEEEecCCCCCCHHHHHHHHHHHHCcChHHeEEEEeeEeccCCCcHHHcCCCCCCEE
Confidence            4899999996 68885 899999999999999999999999999999999999999999999766654

>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=99.69  E-value=4.8e-18  Score=111.93  Aligned_cols=65  Identities=12%  Similarity=0.042  Sum_probs=62.0

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      |+|++..|+.+.++|++++||++||++|++++|+|+++|+|+|+|+.|+|+.+|++|+|.+.+.|
T Consensus        31 V~V~~~~Gk~~~v~V~p~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~dygI~~GstI   95 (100)
T d1uh6a_          31 VVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNL   95 (100)
T ss_dssp             EEEECSSSSCEEEEEETTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCSSCBHHHHTCCTTEEE
T ss_pred             EEEECCCCCEEEEEECCcChHHHHHHHHHHHHCCCcceEEEEEEeecccCcCCHHHcCCCCCCEE
Confidence            89999999999999999999999999999999999999999999999999999999999866654

>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=99.69  E-value=6.6e-18  Score=109.96  Aligned_cols=68  Identities=13%  Similarity=0.185  Sum_probs=62.4

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcC---CCCCceEEEeCCcccCccccccccccEEeEEEEe
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKR---IPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~g---Ip~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~~  110 (133)
                      +|+||+.+|+++.++|++++||.+||++|+++.|   +|+++|+|+|+|+.|+|+.+|++|+|.+.++|.+
T Consensus         2 ~I~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~~~~i~~~~qrLi~~Gk~L~d~~tL~~y~I~~~s~i~l   72 (95)
T d1uela_           2 QVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVV   72 (95)
T ss_dssp             EEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEETTEECCTTSBGGGGTCCSSSEEEE
T ss_pred             EEEEEeCCCCEEEEEECCCccHHHHHHHHHhhhcccCCCccceEEEECCeEccCCCcHHHcCCCCCCEEEE
Confidence            4789999999999999999999999999999875   8999999999999999999999999987765543

>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=99.68  E-value=7e-18  Score=105.91  Aligned_cols=67  Identities=12%  Similarity=0.045  Sum_probs=60.3

Q ss_pred             ccccCCCCCC-Ccee-eccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           43 ADFCKNPDPQ-NITL-EVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        43 ~i~Vk~~~g~-~~~l-~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      .|+||+.+|+ ++.+ +|++++||++||++|+++.|||+++|+|+|+|++|+|+.+|++|+|...+.+.
T Consensus         2 ~I~Vk~l~G~~t~~~~~v~~~~TV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~~tL~~y~I~~~s~i~   70 (76)
T d1wy8a1           2 WIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQ   70 (76)
T ss_dssp             EEEEEETTCSCEEEEEEECTTCBHHHHHHHHHHHSCCCTTTEEEEETTEECCSSSBHHHHTCCTTCEEE
T ss_pred             EEEEEeCCCCceEEEeccCCCChHHHHHHHHHHHHCCCchhcEEEEEeeEecCCCCHHHcCCCCCCEEE
Confidence            3789999985 6777 59999999999999999999999999999999999999999999997666543

>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=99.67  E-value=9.5e-18  Score=104.37  Aligned_cols=64  Identities=11%  Similarity=0.081  Sum_probs=58.0

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      |+|++. ++.+.++|++++||++||++|++++|+|+++|+|+|+|+.|+|+.+|++|+|.+.+.+
T Consensus         4 I~Vk~~-~~~~~i~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~I~~g~~i   67 (73)
T d2bwfa1           4 IHIKSG-QDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSV   67 (73)
T ss_dssp             EEEEET-TEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEE
T ss_pred             EEEEeC-CeEEEEEECCCChHHHHHHHHHHHHCcChHHeEEEECCeEccCCCcHHHCCCCCCCEE
Confidence            677775 4568999999999999999999999999999999999999999999999999866654

>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=99.63  E-value=3.7e-17  Score=104.28  Aligned_cols=65  Identities=14%  Similarity=0.060  Sum_probs=59.8

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      |+|+++++ .+.++|++++||++||++|++++|+|+++|+|+|+|+.|+|+.+|++|+|.+.+.|.
T Consensus        10 I~Vkt~~~-~~~~~V~~~~tV~~lK~~i~~~~gi~~~~qrL~~~Gk~L~D~~tL~~y~i~~gsti~   74 (84)
T d1yqba1          10 VTVKTPKD-KEDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVH   74 (84)
T ss_dssp             EEEECSSC-EEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBHHHHTCCTTCEEE
T ss_pred             EEEEcCCC-cEEEEECCCCcHHHHHHHHHHHHCcCchhEEEEEeeeeccccCcHHHcCCCCCCEEE
Confidence            88999755 579999999999999999999999999999999999999999999999997766654

>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=99.62  E-value=1.3e-16  Score=102.16  Aligned_cols=61  Identities=16%  Similarity=0.220  Sum_probs=56.9

Q ss_pred             CCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           49 PDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        49 ~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      ++|++++++|++++||++||++|++++|+|+++|+|+|+|+.|+|+.+|++|+|.+.+.|.
T Consensus        19 L~G~~~~l~v~~~~tV~~lK~~I~~~~~ip~~~q~Li~~Gk~L~D~~tL~dY~I~~gsti~   79 (86)
T d1zkha1          19 LNGQVLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMANGAVIH   79 (86)
T ss_dssp             CSSCEEEEEECTTSBHHHHHHHHHHHTCCCTTTEEEEETTEEECTTSBHHHHTCCTTEEEE
T ss_pred             cCCeEEEEEECCCChHHHHHHHHHhhhcCChHHEEEEeCCcCcCCCCCHHHcCCCCCCEEE
Confidence            5799999999999999999999999999999999999999999999999999997666543

>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=99.62  E-value=2e-16  Score=104.02  Aligned_cols=66  Identities=9%  Similarity=-0.098  Sum_probs=61.0

Q ss_pred             ccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEEe
Q 040111           45 FCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        45 ~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~~  110 (133)
                      ..+...|+.+.++|++++||++||.+|+++.|+|+++|+|+|+|+.|+|+.+|++|+|.+.+.|++
T Consensus        23 ~~~~~~g~~~~lev~~~~TV~~LK~~I~~~~gi~~~~qkLi~~Gk~L~d~~tL~~~gI~~~s~i~v   88 (100)
T d1wjua_          23 PPRLKKDRKNLLETRLHITGRELRSKIAETFGLQENYIKIVINKKQLQLGKTLEEQGVAHNVKAMV   88 (100)
T ss_dssp             CTTTCCSSSEEEEEESSSBHHHHHHHHHHHTTCCSTTCEEEETTEECCTTSBHHHHTCCSSEEEEE
T ss_pred             eeccCCCeEEEEEECCCcHHHHHHHHHHHHHCCCCeeEEEEEcccCcCCCcCHHHcCCCCCCEEEE
Confidence            337788999999999999999999999999999999999999999999999999999988886653

>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=99.60  E-value=9.6e-17  Score=102.07  Aligned_cols=66  Identities=9%  Similarity=0.007  Sum_probs=60.2

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEEe
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~~  110 (133)
                      |+|+++++ .+.++|++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+|.+.+.|..
T Consensus        13 v~Vk~~~~-~~~i~v~~~~tV~~lK~~I~~~~~v~~~~qrL~f~Gk~L~d~~tL~~~gI~~gs~I~l   78 (83)
T d1wx8a1          13 VSVKTPQD-CHEFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQDILSQRGILDGSTVHV   78 (83)
T ss_dssp             EEEECSSS-EEEEEEETTCCHHHHHHHHHHHTCSCTTTBCCEETTEECCTTSCHHHHTCCTTEEEEC
T ss_pred             EEEEcCCC-cEEEEECCCChHHHHHHHHHHHhCCChhHEEEEEEhhccccCCcHHHcCCCCCCEEEE
Confidence            88898765 4689999999999999999999999999999999999999999999999987776653

>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=99.60  E-value=2.2e-16  Score=106.40  Aligned_cols=63  Identities=6%  Similarity=-0.010  Sum_probs=59.0

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHh--------hhhcCCCCCceEEEeCCcccCccccccccccEEeE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKI--------QDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVG  106 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I--------~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~  106 (133)
                      |+|++++|+++.++|++++||.+||++|        +++.|+||++|||+|.|+.|+|+.+|++|+|....
T Consensus        19 i~v~~l~Gk~~~~~v~p~~TV~~lK~~I~~~~p~~~~e~~~~~~~~qRLiy~Gk~L~D~~tL~~~~i~~g~   89 (116)
T d1wgha_          19 LRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGK   89 (116)
T ss_dssp             EEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEEETTEEECSSCBTTTTTCCSSC
T ss_pred             EEEEEcCCCEEEEEECCcchHHHHHHHHHhhcccccccccCCChHHeEEEECCEEecCCCCHHHcCCCCCC
Confidence            8899999999999999999999999999        57789999999999999999999999999996554

>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=99.59  E-value=5.7e-16  Score=103.58  Aligned_cols=67  Identities=21%  Similarity=0.165  Sum_probs=59.5

Q ss_pred             cccCCC-CCCCceeeccc-cCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEEe
Q 040111           44 DFCKNP-DPQNITLEVES-SDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        44 i~Vk~~-~g~~~~l~V~~-~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~~  110 (133)
                      |+|++. +|++++++|.+ ++||++||++|++++|+|+++|+|+|+|+.|+|+.+|++|+|...+.|..
T Consensus        32 V~v~~~~~G~~i~l~v~~~sdtV~~lK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~ynI~~gsti~L  100 (111)
T d1we6a_          32 VSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTL  100 (111)
T ss_dssp             ECCTTCSSSCCEEEEESCSSSBHHHHHHHHHHHTTCCTTTSEEECSSSBCCTTSBTTTTTCSSSCEEEE
T ss_pred             EEcccCCCCeEEEEEecCCccHHHHHHHHHHHHHCCCccceEEEEeeEEccccCCHHHcCCCCCCEEEE
Confidence            566654 58999999987 89999999999999999999999999999999999999999976665543

>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=99.59  E-value=4.1e-16  Score=102.81  Aligned_cols=65  Identities=9%  Similarity=0.014  Sum_probs=59.7

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      |+|+++++ .+.++|++++||.+||++|++++|+|+++|+|+|+|+.|+|+.+|++|+|.+.++|.
T Consensus        35 V~Vk~~~~-~~~i~V~~~~tV~~LK~~I~~~~gi~~~~qrLi~~Gk~L~D~~tL~~~~I~~g~~I~   99 (103)
T d1j8ca_          35 VTVKTPKE-KEEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVH   99 (103)
T ss_dssp             EEEECSSC-EEEEEECTTCCHHHHHHHHHHHHCSCSSSEEEEETTEEESTTSCGGGTTCSSSEEEE
T ss_pred             EEEECCCc-cEEEEECCCChHHHHHHHHHHHHCcCHHHeeeeeeeecccCCCcHHHcCCCCCCEEE
Confidence            88888765 578999999999999999999999999999999999999999999999998766654

>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=99.59  E-value=1.1e-16  Score=105.86  Aligned_cols=60  Identities=15%  Similarity=0.081  Sum_probs=54.2

Q ss_pred             cccCCCCCC-CceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccE
Q 040111           44 DFCKNPDPQ-NITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFV  103 (133)
Q Consensus        44 i~Vk~~~g~-~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~  103 (133)
                      |||+...++ ++.++|++++||.+||++|++++|||+++|+|+|+|++|+|+++|+||+|+
T Consensus         2 ifv~i~~~k~Ti~l~v~~~~TV~~lK~~I~~~~gip~~~QrLi~~Gk~L~D~~TL~dYgI~   62 (103)
T d2c9wb1           2 VFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFT   62 (103)
T ss_dssp             EEEEEEEBTEEEEEEECTTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBHHHHTCC
T ss_pred             EEEEEeCCCEEEEEEeCCCCcHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCC
Confidence            455555554 678999999999999999999999999999999999999999999999995

>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=99.55  E-value=9.7e-16  Score=101.02  Aligned_cols=64  Identities=8%  Similarity=0.062  Sum_probs=58.5

Q ss_pred             CCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccC-ccccccccccEEeEEEEe
Q 040111           47 KNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFF-FEEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        47 k~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~-d~~tL~dy~~~~~~~~~~  110 (133)
                      +..++.+++++|++++||.+||++|+++.|||+++|+|+|+|+.|. |..+|++|+|....+|..
T Consensus        17 ~~~~~~t~~l~V~~~~tV~~LK~~Ie~~~gip~~~Q~Li~~Gk~L~dd~~tL~~~gI~~g~~i~l   81 (102)
T d1v5oa_          17 RDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVL   81 (102)
T ss_dssp             CCCCCCEEEEEECTTCBHHHHHHHHHHHTCCCGGGBCEEETTEEECCSSSBHHHHTCCTTEEEEE
T ss_pred             cCCCCCEEEEEECCcccHHHHHHHHHHHhCCCcceEEEEeCCeEeecccCCHHHcCCCCCCEEEE
Confidence            7888999999999999999999999999999999999999999996 557999999987776554

>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=99.54  E-value=3.3e-15  Score=98.12  Aligned_cols=60  Identities=8%  Similarity=-0.011  Sum_probs=55.3

Q ss_pred             cccCCCCCCCc-eeeccccCcHHHHHHHhhhh-----cCCC--CCceEEEeCCcccCccccccccccE
Q 040111           44 DFCKNPDPQNI-TLEVESSDTIDNVKAKIQDK-----KRIP--PPAEADLLKFPFFFFEEVLSFFWFV  103 (133)
Q Consensus        44 i~Vk~~~g~~~-~l~V~~~~tV~~LK~~I~~~-----~gIp--~~~q~L~~~gk~L~d~~tL~dy~~~  103 (133)
                      |.+|+.+|+.+ ++.+++++||.+||++|++.     .|+|  +++|||+|+|+.|+|+++|++|++.
T Consensus        10 I~~r~~~G~~i~~~~v~~s~TV~~lK~~I~~~~~~~k~~iP~~~~~qRLIf~Gk~L~D~~tL~dy~i~   77 (101)
T d1se9a_          10 IKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSKTVKDYRSP   77 (101)
T ss_dssp             EEEEETTSCEEEEEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEEETTEECCTTSBGGGGSCC
T ss_pred             EEEEeCCCCeecceecCccCHHHHHHHHHHHhccccccCCCCCcccEEEEECCeEecCCCCHHHcCCC
Confidence            88999999976 79999999999999999875     6898  7899999999999999999999983

>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=99.54  E-value=6.8e-16  Score=100.64  Aligned_cols=66  Identities=9%  Similarity=-0.061  Sum_probs=59.9

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEEe
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~~  110 (133)
                      |.||..+++.+.++|++++||.+||++|++.+|+|+++|+|+|+|+.|+|+ +|++|+|.....|++
T Consensus        10 I~VK~~~~~~~~v~v~~~~tV~~lK~~i~~~~gvp~~~QkLi~~Gk~L~d~-tL~~~gi~~g~~i~l   75 (96)
T d1wgga_          10 VTVKWGKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLKDD-DWGNIKMKNGMTVLM   75 (96)
T ss_dssp             EEEEETTEEEEEEEEESSSCHHHHHHHHHHHTCCCTTTSCCEETTEECCSS-CCCSCCCCSSCEEEC
T ss_pred             EEEEeCCCCEEEEEECCCCcHHHHHHHhhhhcCccceeeEEeecCcccCCC-cHHHCCCCCCCEEEE
Confidence            788998888889999999999999999999999999999999999999986 799999987664443

>d1wiaa_ d.15.1.1 (A:) Ubiquitin-like protein bab25500 (2010008E23Rik) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein bab25500 (2010008E23Rik)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.47  E-value=9.9e-15  Score=94.95  Aligned_cols=64  Identities=16%  Similarity=0.016  Sum_probs=57.9

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccC-ccccccccccEEeEEEEe
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFF-FEEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~-d~~tL~dy~~~~~~~~~~  110 (133)
                      |+||+++|+.+.++|++++||.+||++|+   .+++++|+|+|+|+.|. |.++|++|+|.+..+|.+
T Consensus        10 i~vK~l~~~~~~v~v~~~~TV~~lK~~i~---~~~~~~qrLi~~Gk~L~dd~~tL~~y~i~~g~~v~l   74 (95)
T d1wiaa_          10 VRLKFLNDTEELAVARPEDTVGTLKSKYF---PGQESQMKLIYQGRLLQDPARTLSSLNITNNCVIHC   74 (95)
T ss_dssp             EEEEETTTEEEEEEECSSSBHHHHHHHHS---SSTTTTCEEEETTEECCCSSCBTTTTTCCTTEEEEE
T ss_pred             EEEEcCCCCEEEEEECCcCcHHHHHHHHh---cCCcceeEEEECCEEcccCCCCHHHcCCCCCCEEEE
Confidence            89999999999999999999999999987   45889999999999997 568999999988877655

>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=99.47  E-value=1.7e-14  Score=93.38  Aligned_cols=59  Identities=12%  Similarity=0.146  Sum_probs=53.4

Q ss_pred             cccCCCCCCC--ceeeccccCcHHHHHHHhhhhcC--CCCCceEEEeCCcccCcccccccccc
Q 040111           44 DFCKNPDPQN--ITLEVESSDTIDNVKAKIQDKKR--IPPPAEADLLKFPFFFFEEVLSFFWF  102 (133)
Q Consensus        44 i~Vk~~~g~~--~~l~V~~~~tV~~LK~~I~~~~g--Ip~~~q~L~~~gk~L~d~~tL~dy~~  102 (133)
                      ++|++++++.  +.+++++++||.+||++|++..+  +|+++|||+|+|+.|+|+.+|++|..
T Consensus        10 l~Ik~~~~~~~~~~~~v~~~~TV~~LK~~I~~~~~~~~~~~~qrLIy~Gk~L~D~~~L~d~~~   72 (93)
T d1wgda_          10 LLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLP   72 (93)
T ss_dssp             EEEECSSSSCCCEEEECCTTSCHHHHHHHHHHHSTTCCCTTTCEEEETTEECCSSSCHHHHSC
T ss_pred             EEEECCCCCceeEEEEcCCCCcHHHHHHHHHHHcCCCCChHHEEEEECCeEccCCCCHHHhCc
Confidence            7788887654  78889999999999999999965  99999999999999999999999964

>d1v5ta_ d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 8430435i17rik protein
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.46  E-value=8e-15  Score=94.25  Aligned_cols=65  Identities=15%  Similarity=0.039  Sum_probs=56.6

Q ss_pred             cccCCCCCCCcee-eccccCcHHHHHHHhhhhcCCCCCceEEE---eCCcccCccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITL-EVESSDTIDNVKAKIQDKKRIPPPAEADL---LKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l-~V~~~~tV~~LK~~I~~~~gIp~~~q~L~---~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      |+||.. ++.+.+ +|++++||.+||++|++++|+||++|+|+   |.|+.|+|+.+|++|+|.....|+
T Consensus        10 i~Vk~~-~~~~~i~~v~~~~tV~~LK~~i~~~t~vp~~~QkLi~~~~~Gk~L~D~~tL~~~~i~~g~~i~   78 (90)
T d1v5ta_          10 IIVKWG-GQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIM   78 (90)
T ss_dssp             EEEEET-TEEEEECSCCSSSBHHHHHHHHHHHTCCCTTTCEEESCEETTEECCTTSBHHHHTCCTTEEEE
T ss_pred             EEEEEC-CeEEEEEEeCCCCcHHHHHHHHHHHHcCCHHHhhhhhhccCCcCCCCcCcHHHcCCCCCCEEE
Confidence            778864 455555 79999999999999999999999999999   599999999999999998666444

>d1v2ya_ d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3300001g02rik
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.46  E-value=1.5e-15  Score=100.60  Aligned_cols=65  Identities=12%  Similarity=-0.039  Sum_probs=60.1

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceE---------------EEeCCcccCcc-ccccccccEEeEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEA---------------DLLKFPFFFFE-EVLSFFWFVVVGV  107 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~---------------L~~~gk~L~d~-~tL~dy~~~~~~~  107 (133)
                      |+|++.+|+.++++|++++||++||++|+++.++|+++|+               |+|+|+.|.|+ .+|++|+|.....
T Consensus        10 v~Vk~~~G~~~~v~V~~~~TV~~LK~~I~~~~~ip~~~Qr~~~~~~~~~~~~~~~Li~~G~~L~d~~~tL~~~gI~~g~~   89 (105)
T d1v2ya_          10 VRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLRDYGIRNRDE   89 (105)
T ss_dssp             EEEECSSSCEEEEEECTTCBHHHHHHHHHHHHHHHHHHTTCCCCCCHHHHHTTEEEESSSCEECCSSSBHHHHTCCSSEE
T ss_pred             EEEEeCCCCEEEEEECCCChHHHHHHHHHHHHCcCHHHhcccccccccccccceEEEECCEECcccCCCHHHcCCCCCCE
Confidence            8899999999999999999999999999999999999997               99999999876 5899999976665


Q ss_pred             E
Q 040111          108 I  108 (133)
Q Consensus       108 ~  108 (133)
                      |
T Consensus        90 l   90 (105)
T d1v2ya_          90 V   90 (105)
T ss_dssp             E
T ss_pred             E
Confidence            4

>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=99.46  E-value=6.9e-15  Score=95.61  Aligned_cols=64  Identities=16%  Similarity=0.044  Sum_probs=56.8

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~~  109 (133)
                      +.|+ .+++++.++|++++||++||++|++.+|+|+++|+|+|+|+ |+|+.+|++|+|...+.|+
T Consensus        20 v~V~-~~~k~~~i~v~~~~TV~~LK~~I~~~tgvp~~~q~Li~~g~-l~D~~tL~~~~I~~gs~i~   83 (95)
T d1v86a_          20 LKII-WNKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGL-VPEDKTLREIKVTSGAKIM   83 (95)
T ss_dssp             EEEE-ETTEEEEEEECTTSBHHHHHHHHHHHHCSCSTTCCCBSSSB-CCSSSBHHHHCCCTTEEEE
T ss_pred             EEEE-ECCEEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEeccc-ccCCCcHHHCCCCCCCEEE
Confidence            4555 36788999999999999999999999999999999999997 9999999999997776443

>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=99.41  E-value=6.8e-14  Score=88.30  Aligned_cols=66  Identities=12%  Similarity=0.083  Sum_probs=54.0

Q ss_pred             cccCCCCCCCceeec-----cccCcHHHHHHHhhhhcCCCCCceEEEeCCcccC-ccccccccccEEeEEEEe
Q 040111           44 DFCKNPDPQNITLEV-----ESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFF-FEEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V-----~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~-d~~tL~dy~~~~~~~~~~  110 (133)
                      |.|+. .++.+.+++     ++++||++||++|++.+|+|+++|+|+|+|+.|. |+.+|++|++.+.+.+++
T Consensus         4 i~V~~-~~~~~~i~v~~~~~~~~~Tv~~LK~~I~~~tgvp~~~QkL~~~G~~L~~d~~tL~~~gi~~g~~i~l   75 (81)
T d1wxva1           4 VTVTH-SNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVML   75 (81)
T ss_dssp             EEEEC-SSSEEEEEECCCSSSSSCBHHHHHHHHHHHTCCCTTTCEEEETTEEECCSSSBHHHHTCCSSEEEEE
T ss_pred             EEEEE-CCeeEEEEEecCCCCCccHHHHHHHHHHHHHCcCHHHEEeeecCeEeCcCCCChHHCCCCCCCEEEE
Confidence            34443 455566666     5789999999999999999999999999999996 568999999987775543

>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=99.38  E-value=3.7e-14  Score=88.54  Aligned_cols=43  Identities=42%  Similarity=0.696  Sum_probs=40.2

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|||+++|+|+|+|++|+|+.+|++|||. +++|||++|+
T Consensus        32 I~~~~gip~~~qrLi~~Gk~L~D~~tL~~y~I~~~sti~lv~r~   75 (76)
T d2faza1          32 IQELFHVEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLLVRQ   75 (76)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTCBTTTTTCCTTCEEEEEECC
T ss_pred             HHHHHCcChHHeEEEEeeEeccCCCcHHHcCCCCCCEEEEEEEc
Confidence            467899999999999999999999999999999 9999998874

>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=99.36  E-value=5.8e-14  Score=87.33  Aligned_cols=43  Identities=30%  Similarity=0.458  Sum_probs=40.0

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|||+++|+|+|+|++|+|+.||++|||. +++|||++|.
T Consensus        33 I~~~~gi~~~~qrL~~~gk~L~d~~tL~~y~I~~~sti~l~lRL   76 (76)
T d1z2ma2          33 VSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRL   76 (76)
T ss_dssp             HHHHHTCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECC
T ss_pred             HHHHhcCChhHeEEEECCeECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            467899999999999999999999999999999 9999998773

>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=99.36  E-value=6.6e-14  Score=86.48  Aligned_cols=43  Identities=58%  Similarity=0.866  Sum_probs=39.9

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+|+++|+|+|+|++|+|+.||++|||. +++|||++|.
T Consensus        30 i~~~~gi~~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lvlrL   73 (73)
T d1bt0a_          30 VEEKEGIPPVQQRLIYAGKQLADDKTAKDYNIEGGSVLHLVLAL   73 (73)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECC
T ss_pred             HHHHhCCChHHEEEEECCeEcCCCCcHHHcCCCCCCEEEEEeeC
Confidence            356789999999999999999999999999999 9999998874

>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=99.35  E-value=6.7e-14  Score=87.70  Aligned_cols=43  Identities=33%  Similarity=0.630  Sum_probs=39.6

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|||+++|+|+|+|++|+|+.+|++|||. +++|||..|+
T Consensus        32 i~~~~gip~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lv~R~   75 (78)
T d2zeqa1          32 VAKRQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRP   75 (78)
T ss_dssp             HHHHHTCCGGGEEEEETTEEECTTCBGGGSSCCTTCEEEEEESS
T ss_pred             HHHHHCcChhHeEEEEeeeEcCCCCCHHHcCCCCCCEEEEEecc
Confidence            456799999999999999999999999999999 9999997764

>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=99.34  E-value=9.1e-14  Score=86.75  Aligned_cols=43  Identities=35%  Similarity=0.491  Sum_probs=40.2

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|||+++|+|+|+|++|+|+.||++|||. +++|||++|+
T Consensus        32 I~~~~gip~~~qrLi~~Gk~L~d~~tL~~y~I~~~s~i~lv~rp   75 (76)
T d1wy8a1          32 VWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVRP   75 (76)
T ss_dssp             HHHHSCCCTTTEEEEETTEECCSSSBHHHHTCCTTCEEEEEECC
T ss_pred             HHHHHCCCchhcEEEEEeeEecCCCCHHHcCCCCCCEEEEEEcc
Confidence            467899999999999999999999999999999 9999998874

>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=99.33  E-value=1.2e-13  Score=85.46  Aligned_cols=43  Identities=40%  Similarity=0.647  Sum_probs=39.5

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |+.++|+|+++|+|+|+|++|+|+.+|++|||. +++|||+.++
T Consensus        30 I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~I~~g~~i~lV~~~   73 (73)
T d2bwfa1          30 INKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKSQ   73 (73)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECC
T ss_pred             HHHHHCcChHHeEEEECCeEccCCCcHHHCCCCCCCEEEEEeeC
Confidence            456789999999999999999999999999999 9999998763

>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=99.33  E-value=1.1e-13  Score=88.34  Aligned_cols=43  Identities=42%  Similarity=0.557  Sum_probs=39.5

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|||+++|+|+|+||+|+|+.||++|+|. +++|||..+.
T Consensus        37 I~~~~gip~~~qrLi~~Gk~L~d~~tL~~y~I~~~stl~l~~r~   80 (87)
T d1wh3a_          37 IEDQQGLPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKK   80 (87)
T ss_dssp             HHHHTCCCTTTEEEEETTEECCSSSBHHHHTCCTTEEEEEEECS
T ss_pred             HHHHHCcChHHeEEEeeceEcCCCCcHHHcCCCCCCEEEEEecC
Confidence            467899999999999999999999999999999 9999986653

>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=99.29  E-value=2.1e-13  Score=85.69  Aligned_cols=43  Identities=28%  Similarity=0.526  Sum_probs=39.9

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+|+++|+|+|+|++|+|+.||++|||. +++|||++++
T Consensus        33 I~~~~~ip~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lvi~~   76 (80)
T d1ttna1          33 LHAAEGVEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQ   76 (80)
T ss_dssp             HHHTTCCCSTTCEEEETTEECCTTSHHHHCCCSSSCEEEEECCC
T ss_pred             HHHHhCCCcccEEEEECceEcCCCCcHHHcCCCCCCEEEEEecC
Confidence            457899999999999999999999999999999 9999988764

>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=99.26  E-value=2.3e-13  Score=84.10  Aligned_cols=43  Identities=35%  Similarity=0.614  Sum_probs=39.0

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccccccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~~stl~L~~~~   43 (133)
                      |++++|||+++|||+|+|++|+|+.+|++|+|.++++||+.+.
T Consensus        30 I~~~~gip~~~qrLi~~Gk~L~d~~tL~dy~i~~~ti~lv~r~   72 (73)
T d1wx9a1          30 IAASVSIPSEKQRLIYQGRVLQDDKKLQEYNVGGKVIHLVERA   72 (73)
T ss_dssp             HHHHHCCCTTTCCCEETTEECCSSSBHHHHTCTTEEEBCCCSS
T ss_pred             HHHHhCCChHHEEEEECCeEccCCCCHHHhCCCCCEEEEEecC
Confidence            4678999999999999999999999999999997799988764

>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=99.25  E-value=6.1e-13  Score=82.61  Aligned_cols=42  Identities=83%  Similarity=1.199  Sum_probs=39.0

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |+.+.|+|+++|+|+|+|++|+|+.||++|||. +++|+|.++
T Consensus        30 I~~~~gi~~~~qrL~~~Gk~L~d~~tL~~y~i~~~s~I~L~~r   72 (76)
T d1ogwa_          30 IQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR   72 (76)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEEC
T ss_pred             hhhhcCCChHHEEeEECCeEcCCCCCHHHcCCCCCCEEEEEEe
Confidence            356789999999999999999999999999999 999998776

>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=99.24  E-value=5.5e-13  Score=82.99  Aligned_cols=43  Identities=33%  Similarity=0.286  Sum_probs=39.4

Q ss_pred             CCcccCCCCCCeEEEe--CCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIF--AGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~--~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|||+++|+|+|  .|++|+|+.+|++|||. +++|+|++++
T Consensus        30 I~~~~gip~~~QrLi~~~~Gk~L~D~~tL~~y~i~~g~~i~lv~~~   75 (76)
T d1z2ma1          30 ITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDK   75 (76)
T ss_dssp             HHHHHCCCGGGEEEEEETTCCBCCSSSCSGGGTCCTTCEEEEEECC
T ss_pred             HHHHhccCCccEEEEEcCCCeeccCCCcHHHcCCCCCCEEEEEEEC
Confidence            4568899999999999  69999999999999999 9999998764

>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=99.23  E-value=7.7e-13  Score=84.28  Aligned_cols=43  Identities=28%  Similarity=0.629  Sum_probs=39.8

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+|+++|+|+|+|+.|+|+.||++|||. +++|||+++.
T Consensus        41 I~~~~~ip~~~q~Li~~Gk~L~D~~tL~dY~I~~gsti~l~~r~   84 (86)
T d1zkha1          41 IHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMANGAVIHLALKE   84 (86)
T ss_dssp             HHHHTCCCTTTEEEEETTEEECTTSBHHHHTCCTTEEEEEEESC
T ss_pred             HHhhhcCChHHEEEEeCCcCcCCCCCHHHcCCCCCCEEEEEEec
Confidence            467899999999999999999999999999999 9999988763

>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=99.22  E-value=5.8e-13  Score=84.35  Aligned_cols=43  Identities=35%  Similarity=0.428  Sum_probs=39.5

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++++|+|+++|+|+|+|++|+|+.+|++|||. +++|||+++.
T Consensus        36 i~~~~gi~~~~qrL~~~Gk~L~D~~tL~~y~i~~gsti~lv~r~   79 (84)
T d1yqba1          36 ISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKR   79 (84)
T ss_dssp             HHHHHTCCGGGEEEEETTEECCTTSBHHHHTCCTTCEEEEEECC
T ss_pred             HHHHHCcCchhEEEEEeeeeccccCcHHHcCCCCCCEEEEEECC
Confidence            456899999999999999999999999999999 9999987664

>d1v6ea_ d.15.1.1 (A:) Ubiquitin-like domain of tubulin folding cofactor B {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of tubulin folding cofactor B
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.22  E-value=2.3e-12  Score=83.48  Aligned_cols=64  Identities=14%  Similarity=-0.061  Sum_probs=54.2

Q ss_pred             cccCCC-CCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCc-------ccCccccccccccEEeEE
Q 040111           44 DFCKNP-DPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFP-------FFFFEEVLSFFWFVVVGV  107 (133)
Q Consensus        44 i~Vk~~-~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk-------~L~d~~tL~dy~~~~~~~  107 (133)
                      ++|++. ++......++++.||.+||++|+..+|+||++|+|+|.|+       .++|+++|++|++.....
T Consensus        10 v~I~s~~~~~~~E~r~~~~~TV~~LK~kle~~tGip~~~qrL~~~~~~~~~~~~l~~d~~~L~~y~i~dg~~   81 (95)
T d1v6ea_          10 VFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVGSPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCR   81 (95)
T ss_dssp             EEEEETTSSSCEEEEECTTSBHHHHHHHHHHHTCSCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCE
T ss_pred             EEEEECCCCcEEEEEeCCCCCHHHHHHHHHHHhCcCchhEEEEEeCCCCceeecccCCcCCHHHCCCCCCCE
Confidence            566663 5556778899999999999999999999999999999887       578899999999864443

>d1wjna_ d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Tubulin-folding protein TbcE
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.22  E-value=6e-12  Score=81.65  Aligned_cols=63  Identities=14%  Similarity=0.123  Sum_probs=54.9

Q ss_pred             CCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcc-------cC-ccccccccccEEeEEEEe
Q 040111           48 NPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPF-------FF-FEEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        48 ~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~-------L~-d~~tL~dy~~~~~~~~~~  110 (133)
                      ..+++.+.+++++++||.+||.+|+..+|+|+++|+|+|.|+.       |+ |+++|.+|+|.+...|++
T Consensus        19 ~~~~~~~~~kv~~~~TV~~LK~~i~~~~gip~~~qrL~y~~~~~~~~~~~l~~d~~tL~~YgI~dg~~I~V   89 (97)
T d1wjna_          19 QPERQILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCLLV   89 (97)
T ss_dssp             CSSSCCEEEEEETTSBHHHHHHHHHTTTTCCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTCCTTCEEEE
T ss_pred             CCCCceEEEEcCCCCCHHHHHHHHHHHHCcChHHeEEEecCCCCCcccceecCCCcCHhhccCCCCCEEEE
Confidence            3457788999999999999999999999999999999999884       44 678999999987776664

>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=99.21  E-value=7.3e-13  Score=83.71  Aligned_cols=43  Identities=30%  Similarity=0.298  Sum_probs=39.5

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++.+++|+++|+|+|+|++|+|+.+|++|||. +++|||++|.
T Consensus        39 I~~~~~v~~~~qrL~f~Gk~L~d~~tL~~~gI~~gs~I~lv~r~   82 (83)
T d1wx8a1          39 ISKYLHCNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVRS   82 (83)
T ss_dssp             HHHHTCSCTTTBCCEETTEECCTTSCHHHHTCCTTEEEECCBCC
T ss_pred             HHHHhCCChhHEEEEEEhhccccCCcHHHcCCCCCCEEEEEEeC
Confidence            356789999999999999999999999999999 9999988763

>d1x1ma1 d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 7
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.20  E-value=4.6e-12  Score=81.85  Aligned_cols=63  Identities=14%  Similarity=0.065  Sum_probs=47.9

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhc--CCC-CCceEEEeCCcccCccccccccccEEeEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKK--RIP-PPAEADLLKFPFFFFEEVLSFFWFVVVGV  107 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~--gIp-~~~q~L~~~gk~L~d~~tL~dy~~~~~~~  107 (133)
                      ..++.++.+. ...+..+.||.+||++|+++.  ++| |++|+|+|+|+.|+|+.+|++|+|...++
T Consensus        21 ~~i~~p~~~~-~~~~~~~~tV~~lK~~i~~~~~~~~P~p~~~rLIy~Gk~L~D~~tL~~y~I~~gst   86 (94)
T d1x1ma1          21 SILQLPETEL-GEYSLGGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDFYGIQPGST   86 (94)
T ss_dssp             EEECCCCCSS-CSSCCCCCBHHHHHHHHHHHCTTTCCCSSSEEEEETTEECCTTCBHHHHTCCTTCE
T ss_pred             ceEECCCCcc-CccCCCccCHHHHHHHHHHHcccCCCChhheEEEECCeEECCCccHHHcCCCCCCE
Confidence            3455554332 223355789999999999886  454 79999999999999999999999975443

>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=99.18  E-value=1.2e-12  Score=80.90  Aligned_cols=40  Identities=25%  Similarity=0.379  Sum_probs=37.4

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLG   40 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~   40 (133)
                      |++++|+|+++|+|+|+|++|+|+.||++|||. |++|+|.
T Consensus        31 I~~~~~i~~~~q~Li~~Gk~L~d~~tL~~y~I~~gstl~L~   71 (73)
T d1m94a_          31 LSLQIGTQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLELY   71 (73)
T ss_dssp             HHHHHCCTTTSEEEESSSCEECTTSBHHHHTCCTTEEEEEE
T ss_pred             HHHhhcccccEEEEEEEeEEecccCcHHHcCCCCCCEEEEE
Confidence            456889999999999999999999999999999 9999985

>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=99.17  E-value=2.6e-12  Score=84.17  Aligned_cols=42  Identities=36%  Similarity=0.359  Sum_probs=39.1

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |++++|+|+++|+|+|+|++|+|+.+|++|||. +++|||++|
T Consensus        61 I~~~~gi~~~~qrLi~~Gk~L~D~~tL~~~~I~~g~~I~lvlr  103 (103)
T d1j8ca_          61 ISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIK  103 (103)
T ss_dssp             HHHHHCSCSSSEEEEETTEEESTTSCGGGTTCSSSEEEEEEEC
T ss_pred             HHHHHCcCHHHeeeeeeeecccCCCcHHHcCCCCCCEEEEEEC
Confidence            456789999999999999999999999999999 999999875

>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=99.17  E-value=2.1e-12  Score=85.88  Aligned_cols=42  Identities=29%  Similarity=0.371  Sum_probs=39.0

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |++++|||+++|+|+|.|+.|+|+.||++|+|. +++|||.++
T Consensus        61 I~~~~gip~~~QrLi~~Gk~L~D~~tL~~ynI~~gsti~L~lr  103 (111)
T d1we6a_          61 IAGEIQIPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLR  103 (111)
T ss_dssp             HHHHTTCCTTTSEEECSSSBCCTTSBTTTTTCSSSCEEEEECS
T ss_pred             HHHHHCCCccceEEEEeeEEccccCCHHHcCCCCCCEEEEEee
Confidence            467899999999999999999999999999999 999997665

>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=99.14  E-value=9.2e-12  Score=81.40  Aligned_cols=41  Identities=37%  Similarity=0.526  Sum_probs=37.0

Q ss_pred             cccCCC--CCCeEEEeCCEECCCCCCccccccc-cc------cccccccc
Q 040111            3 DKEGIP--PGQQRSIFAGKQLEDGRTLADYKIQ-ES------TLHLGWRA   43 (133)
Q Consensus         3 ~~~gip--~~~Q~Li~~gk~L~D~~tL~~ygI~-~s------tl~L~~~~   43 (133)
                      +++|||  +++|||||+||+|+|+.||++|+|. |.      ++||++|+
T Consensus        45 ~k~~iP~~~~~qRLIf~Gk~L~D~~tL~dy~i~~g~~~~~~~tmHlVvrp   94 (101)
T d1se9a_          45 EKENGPKTVKEVKLISAGKVLENSKTVKDYRSPVSNLAGAVTTMHVIIQA   94 (101)
T ss_dssp             TCSSSCCSGGGEEEEETTEECCTTSBGGGGSCCTTSCTTCCEEEEEEECC
T ss_pred             cccCCCCCcccEEEEECCeEecCCCCHHHcCCCCCCcCCCceEEEEEeCC
Confidence            358999  7799999999999999999999999 86      99988875

>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=99.12  E-value=4.4e-12  Score=78.88  Aligned_cols=38  Identities=29%  Similarity=0.499  Sum_probs=34.9

Q ss_pred             cCCCCCCeEEEeCCEECCCCCCccccccc-ccccccccc
Q 040111            5 EGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         5 ~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      ..+|+++|||+|+|++|+|+.||++|||. +++++++++
T Consensus        39 ~~i~~~~qrLi~~Gk~L~D~~tL~~y~I~~~s~i~~~vs   77 (77)
T d1oqya4          39 DAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVT   77 (77)
T ss_dssp             SSCCSTEEEEESSSSEECSSSBTTTTCCCTTSCEEEEEE
T ss_pred             CCCChHHEEeEECCcCccCCCcHHHcCCCCCCEEEEEEC
Confidence            34999999999999999999999999999 999998763

>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=99.11  E-value=1e-11  Score=80.00  Aligned_cols=39  Identities=31%  Similarity=0.508  Sum_probs=36.1

Q ss_pred             cCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            5 EGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         5 ~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      .+||+++|+|+|+|++|+|+.+|++|||. +++|+|+++.
T Consensus        37 ~~i~~~~qrLi~~Gk~L~d~~tL~~y~I~~~s~i~lv~~~   76 (95)
T d1uela_          37 DAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTK   76 (95)
T ss_dssp             TTCCTTTEEEEETTEECCTTSBGGGGTCCSSSEEEEEESS
T ss_pred             cCCCccceEEEECCeEccCCCcHHHcCCCCCCEEEEEECC
Confidence            45999999999999999999999999999 9999987764

>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=99.10  E-value=4.3e-12  Score=82.91  Aligned_cols=41  Identities=22%  Similarity=0.185  Sum_probs=38.3

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGW   41 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~   41 (133)
                      |++++|+|+++|+|+|+|++|+|+.||++|||. |++|+|..
T Consensus        58 I~~~~gip~~~qrLi~~Gk~L~D~~tL~dygI~~GstI~L~~   99 (100)
T d1uh6a_          58 IAAQTGTRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLELYY   99 (100)
T ss_dssp             HHHHHCCCGGGCEEEETTEECCSSCBHHHHTCCTTEEEEEEC
T ss_pred             HHHHHCCCcceEEEEEEeecccCcCCHHHcCCCCCCEEEEEE
Confidence            467899999999999999999999999999999 99999865

>d1euvb_ d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-1 (smt3 homologue)
species: Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932]

Probab=99.06  E-value=5.3e-11  Score=74.19  Aligned_cols=64  Identities=5%  Similarity=-0.058  Sum_probs=56.1

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEeEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVVGVI  108 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~~~~  108 (133)
                      |.|+. +|+.+.+.|.++++++.|+..++++.|+|+++|+|+|+|+.|.++.|+++|++....+|
T Consensus         7 ikv~~-~~~~~~f~v~~~~~~~~l~~~~~~~~~i~~~~~~l~f~G~~l~~~~T~~~~~i~dgd~I   70 (79)
T d1euvb_           7 LKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDII   70 (79)
T ss_dssp             EEEES-SSCEEEEEEETTSCTHHHHHHHHHHTTCCGGGEEEEETTEECCTTCCTTTTTCCTTEEE
T ss_pred             EEECC-CCeEEEEEECCCCcHHHHHHHHHHHhCCChHhEEEEECCEEeCCCCCHHHCCCCCCCEE
Confidence            44554 57778899999999999999999999999999999999999999999999998544433

>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=99.04  E-value=5.7e-11  Score=79.40  Aligned_cols=42  Identities=31%  Similarity=0.438  Sum_probs=37.3

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCccccccc-ccc--ccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-EST--LHLGWRA   43 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~st--l~L~~~~   43 (133)
                      +++.++|+++|||||+||+|+|+.+|++|+|. +++  |||+++.
T Consensus        55 ~e~~~~~~~~qRLiy~Gk~L~D~~tL~~~~i~~g~~~~lhlv~r~   99 (116)
T d1wgha_          55 EEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLVARE   99 (116)
T ss_dssp             SCCCCCCTTTEEEEETTEEECSSCBTTTTTCCSSCEEEEEEEECS
T ss_pred             ccccCCChHHeEEEECCEEecCCCCHHHcCCCCCCEEEEEEEeCC
Confidence            46789999999999999999999999999999 876  7766664

>d1x1ma1 d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 7
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.04  E-value=4.1e-11  Score=77.30  Aligned_cols=38  Identities=39%  Similarity=0.639  Sum_probs=34.5

Q ss_pred             cCCC-CCCeEEEeCCEECCCCCCccccccc-ccccccccc
Q 040111            5 EGIP-PGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         5 ~gip-~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      +++| +++|+|||+||+|+|+.+|++|||. +++|||+.|
T Consensus        53 ~~~P~p~~~rLIy~Gk~L~D~~tL~~y~I~~gstihLV~r   92 (94)
T d1x1ma1          53 ESVPDPELIDLIYCGRKLKDDQTLDFYGIQPGSTVHVLRK   92 (94)
T ss_dssp             TTCCCSSSEEEEETTEECCTTCBHHHHTCCTTCEEEEEES
T ss_pred             cCCCChhheEEEECCeEECCCccHHHcCCCCCCEEEEEEe
Confidence            3565 5899999999999999999999999 999999876

>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=99.03  E-value=1.7e-10  Score=73.63  Aligned_cols=58  Identities=9%  Similarity=-0.170  Sum_probs=49.3

Q ss_pred             CCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCc-------ccCccccccccccEEeEEEE
Q 040111           52 QNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFP-------FFFFEEVLSFFWFVVVGVIF  109 (133)
Q Consensus        52 ~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk-------~L~d~~tL~dy~~~~~~~~~  109 (133)
                      ......++++.||.+||.+|+..+|+||+.|+|+|.|+       ..+|+++|++|++...+.|.
T Consensus        16 ~~~E~r~~~~~TV~~LK~kle~~~Gip~~~q~L~~~~~~~~~~~~l~dd~~~L~~ygi~dG~~Ih   80 (90)
T d1t0ya_          16 FPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIH   80 (90)
T ss_dssp             SCEEEEEETTSBHHHHHHHHHHHHCCCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEEE
T ss_pred             cEEEEecCCCCCHHHHHHHHHHHHCCChhheEEEEeCCCCCcccccccCCCCHHHCCCCCCCEEE
Confidence            34566689999999999999999999999999999887       34578999999998666553

>d1wjua_ d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: NEDD8 ultimate buster-1, NUB1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.97  E-value=5.1e-11  Score=77.67  Aligned_cols=41  Identities=20%  Similarity=0.236  Sum_probs=37.6

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGW   41 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~   41 (133)
                      |+++.|+|+++|+|+|+|++|+|+.||++|||. +++|+++.
T Consensus        49 I~~~~gi~~~~qkLi~~Gk~L~d~~tL~~~gI~~~s~i~vi~   90 (100)
T d1wjua_          49 IAETFGLQENYIKIVINKKQLQLGKTLEEQGVAHNVKAMVLE   90 (100)
T ss_dssp             HHHHTTCCSTTCEEEETTEECCTTSBHHHHTCCSSEEEEEEC
T ss_pred             HHHHHCCCCeeEEEEEcccCcCCCcCHHHcCCCCCCEEEEEE
Confidence            457899999999999999999999999999999 99998753

>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=98.97  E-value=4.5e-11  Score=75.00  Aligned_cols=43  Identities=30%  Similarity=0.411  Sum_probs=38.3

Q ss_pred             CCcccCCCCCCeEEEeCCEECC-CCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLE-DGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~-D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |+..+|+|+++|+|+|+|+.|. |+.+|++|||. +++|+|+.+.
T Consensus        35 I~~~tgvp~~~QkL~~~G~~L~~d~~tL~~~gi~~g~~i~lv~~~   79 (81)
T d1wxva1          35 VEEVIGVPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVMLIGKK   79 (81)
T ss_dssp             HHHHTCCCTTTCEEEETTEEECCSSSBHHHHTCCSSEEEEEESCC
T ss_pred             HHHHHCcCHHHEEeeecCeEeCcCCCChHHCCCCCCCEEEEEEec
Confidence            4567999999999999999995 67899999999 9999987764

>d1wgga_ d.15.1.1 (A:) Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin carboxyl-terminal hydrolase 14
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.97  E-value=5.3e-11  Score=76.95  Aligned_cols=42  Identities=21%  Similarity=0.349  Sum_probs=37.7

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++.+|||+++|+|+|.|++|+|+ +|++|||. +++|+|+.+.
T Consensus        37 i~~~~gvp~~~QkLi~~Gk~L~d~-tL~~~gi~~g~~i~lv~t~   79 (96)
T d1wgga_          37 LFALTGVQPARQKVMVKGGTLKDD-DWGNIKMKNGMTVLMMGSA   79 (96)
T ss_dssp             HHHHTCCCTTTSCCEETTEECCSS-CCCSCCCCSSCEEECCCCC
T ss_pred             hhhhcCccceeeEEeecCcccCCC-cHHHCCCCCCCEEEEEeeC
Confidence            457799999999999999999986 79999999 9999987654

>d2c9wb1 d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Elongin B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.97  E-value=3.5e-11  Score=78.87  Aligned_cols=35  Identities=29%  Similarity=0.471  Sum_probs=32.2

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ES   35 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~s   35 (133)
                      |++++|||+++|||+|+|++|+|+.||++|||. ++
T Consensus        30 I~~~~gip~~~QrLi~~Gk~L~D~~TL~dYgI~~~~   65 (103)
T d2c9wb1          30 VEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQT   65 (103)
T ss_dssp             HHHHHCCCGGGEEEEETTEECCTTSBHHHHTCCTTT
T ss_pred             HHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCccc
Confidence            467899999999999999999999999999996 54

>d1v5oa_ d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 1700011n24rik protein
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.95  E-value=3.4e-11  Score=78.78  Aligned_cols=43  Identities=19%  Similarity=0.352  Sum_probs=38.0

Q ss_pred             CCcccCCCCCCeEEEeCCEECC-CCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLE-DGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~-D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |+.++|||+++|+|+|+|++|. |+.||++|||. +++|+|+.+.
T Consensus        41 Ie~~~gip~~~Q~Li~~Gk~L~dd~~tL~~~gI~~g~~i~l~~r~   85 (102)
T d1v5oa_          41 CELESGVPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVLLQKD   85 (102)
T ss_dssp             HHHHTCCCGGGBCEEETTEEECCSSSBHHHHTCCTTEEEEECBCC
T ss_pred             HHHHhCCCcceEEEEeCCeEeecccCCHHHcCCCCCCEEEEEECC
Confidence            4678999999999999999995 66899999999 9999987654

>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=98.91  E-value=1.2e-10  Score=74.22  Aligned_cols=42  Identities=19%  Similarity=0.370  Sum_probs=38.3

Q ss_pred             CCcccCCCCCCeEEE---eCCEECCCCCCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQRSI---FAGKQLEDGRTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~Li---~~gk~L~D~~tL~~ygI~-~stl~L~~~   42 (133)
                      |++++|+|+++|+|+   |.|++|+|+.+|.+|+|. +++|+|+.+
T Consensus        37 i~~~t~vp~~~QkLi~~~~~Gk~L~D~~tL~~~~i~~g~~i~lv~s   82 (90)
T d1v5ta_          37 LKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMGT   82 (90)
T ss_dssp             HHHHTCCCTTTCEEESCEETTEECCTTSBHHHHTCCTTEEEEEECC
T ss_pred             HHHHHcCCHHHhhhhhhccCCcCCCCcCcHHHcCCCCCCEEEEEee
Confidence            467899999999999   689999999999999999 999998654

>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=98.87  E-value=4.2e-10  Score=69.67  Aligned_cols=61  Identities=10%  Similarity=0.018  Sum_probs=57.7

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVV  104 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~  104 (133)
                      |.|++.+|+.+.+.|.++++++.|+...+++.|+|+++++|+|.|+.|.++.|+++|++-.
T Consensus         5 ikv~~~dg~~v~f~v~~~t~l~kl~~~y~~~~~~~~~~~~f~fdG~~l~~~~T~~~l~~ed   65 (77)
T d2uyzb1           5 LKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEE   65 (77)
T ss_dssp             EEEECTTCCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCHHHHTCCT
T ss_pred             EEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCChhHEEEEECCEECCCCCCHHHcCCCC
Confidence            6788899999999999999999999999999999999999999999999999999999743

>d1wgda_ d.15.1.1 (A:) Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.82  E-value=3.8e-10  Score=72.45  Aligned_cols=39  Identities=38%  Similarity=0.466  Sum_probs=33.5

Q ss_pred             cCCCCCCeEEEeCCEECCCCCCccccccc-c--ccccccccc
Q 040111            5 EGIPPGQQRSIFAGKQLEDGRTLADYKIQ-E--STLHLGWRA   43 (133)
Q Consensus         5 ~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~--stl~L~~~~   43 (133)
                      ..+|+++|||||+||+|+|+.+|++|... +  .+|||+.+.
T Consensus        45 ~~~~~~~qrLIy~Gk~L~D~~~L~d~~~~~~~~~viHLV~~~   86 (93)
T d1wgda_          45 ERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVCNV   86 (93)
T ss_dssp             TCCCTTTCEEEETTEECCSSSCHHHHSCSSSCSEEEEEECCC
T ss_pred             CCCChHHEEEEECCeEccCCCCHHHhCcccCCCCEEEEEecC
Confidence            35999999999999999999999999876 4  489987543

>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=98.78  E-value=1.6e-10  Score=74.43  Aligned_cols=42  Identities=21%  Similarity=0.483  Sum_probs=37.7

Q ss_pred             CCcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |++.+|||+++|+|+|+|+ |+|+.+|++|+|. +++|+|+.+.
T Consensus        46 I~~~tgvp~~~q~Li~~g~-l~D~~tL~~~~I~~gs~i~lvgs~   88 (95)
T d1v86a_          46 IHSITGLPPAMQKVMYKGL-VPEDKTLREIKVTSGAKIMVVGST   88 (95)
T ss_dssp             HHHHHCSCSTTCCCBSSSB-CCSSSBHHHHCCCTTEEEEECCSS
T ss_pred             HHHHhCCChhHEEEEeccc-ccCCCcHHHCCCCCCCEEEEEecC
Confidence            4678999999999999997 9999999999999 9999987543

>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=98.74  E-value=2e-09  Score=69.31  Aligned_cols=39  Identities=23%  Similarity=0.319  Sum_probs=34.5

Q ss_pred             cCCCCCCeEEEeCCEECC-CCCCccccccc-cccccccccc
Q 040111            5 EGIPPGQQRSIFAGKQLE-DGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         5 ~gip~~~Q~Li~~gk~L~-D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      +.+|+++|+|+|+|++|. |..+|++|+|. +++|||++++
T Consensus        38 ~~~~~~~qrLi~~Gk~L~dd~~tL~~y~i~~g~~v~l~~~~   78 (95)
T d1wiaa_          38 FPGQESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRSP   78 (95)
T ss_dssp             SSSTTTTCEEEETTEECCCSSCBTTTTTCCTTEEEEEECCC
T ss_pred             hcCCcceeEEEECCEEcccCCCCHHHcCCCCCCEEEEEEcC
Confidence            467889999999999996 66899999999 9999987654

>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=98.67  E-value=4e-09  Score=65.39  Aligned_cols=42  Identities=12%  Similarity=0.288  Sum_probs=38.7

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      +++.|+|+++|+|+|+|+.|+++.|+++|+|. +++|++.+++
T Consensus        34 ~~~~~i~~~~~~l~f~G~~l~~~~T~~~~~i~dgd~I~v~~~q   76 (79)
T d1euvb_          34 AKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQ   76 (79)
T ss_dssp             HHHTTCCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECC
T ss_pred             HHHhCCChHhEEEEECCEEeCCCCCHHHCCCCCCCEEEEEEec
Confidence            46789999999999999999999999999999 9999987664

>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=98.62  E-value=1.7e-10  Score=75.63  Aligned_cols=42  Identities=19%  Similarity=0.310  Sum_probs=36.2

Q ss_pred             CCcccCCCCCCeE---------------EEeCCEECCCC-CCccccccc-ccccccccc
Q 040111            1 IEDKEGIPPGQQR---------------SIFAGKQLEDG-RTLADYKIQ-ESTLHLGWR   42 (133)
Q Consensus         1 I~~~~gip~~~Q~---------------Li~~gk~L~D~-~tL~~ygI~-~stl~L~~~   42 (133)
                      |+++++||+++||               |+|+|+.|.|+ .||.+|||. +++|||+.+
T Consensus        37 I~~~~~ip~~~Qr~~~~~~~~~~~~~~~Li~~G~~L~d~~~tL~~~gI~~g~~l~lv~r   95 (105)
T d1v2ya_          37 IQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLRDYGIRNRDEVSFIKK   95 (105)
T ss_dssp             HHHHHHHHHHHTTCCCCCCHHHHHTTEEEESSSCEECCSSSBHHHHTCCSSEEEEEEEC
T ss_pred             HHHHHCcCHHHhcccccccccccccceEEEECCEECcccCCCHHHcCCCCCCEEEEEEe
Confidence            4567889999987               99999999765 699999999 999998755

>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=98.55  E-value=4.2e-09  Score=67.71  Aligned_cols=43  Identities=16%  Similarity=0.196  Sum_probs=37.1

Q ss_pred             CCcccCCCCCCeEEEeCCE-------ECCCCCCccccccc-cccccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGK-------QLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk-------~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      |+..+|+|+++|+|+|.|+       .++|+.+|.+|+|. +++|||+-+.
T Consensus        38 le~~tGip~~~qrL~~~~~~~~~~~~l~~d~~~L~~y~i~dg~~ihlvd~~   88 (95)
T d1v6ea_          38 LELVVGSPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIHVIDHS   88 (95)
T ss_dssp             HHHHTCSCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCEEEEBCCS
T ss_pred             HHHHhCcCchhEEEEEeCCCCceeecccCCcCCHHHCCCCCCCEEEEEeCC
Confidence            3567999999999999887       47899999999999 9999976543

>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=98.36  E-value=3.9e-08  Score=63.15  Aligned_cols=40  Identities=18%  Similarity=0.259  Sum_probs=34.5

Q ss_pred             CCcccCCCCCCeEEEeCCE-------ECC-CCCCccccccc-ccccccc
Q 040111            1 IEDKEGIPPGQQRSIFAGK-------QLE-DGRTLADYKIQ-ESTLHLG   40 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~gk-------~L~-D~~tL~~ygI~-~stl~L~   40 (133)
                      |++.+|||+++|+|+|.|+       +|+ |+.+|.+|||. +++|++.
T Consensus        42 i~~~~gip~~~qrL~y~~~~~~~~~~~l~~d~~tL~~YgI~dg~~I~V~   90 (97)
T d1wjna_          42 LSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCLLVR   90 (97)
T ss_dssp             HHTTTTCCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTCCTTCEEEEE
T ss_pred             HHHHHCcChHHeEEEecCCCCCcccceecCCCcCHhhccCCCCCEEEEE
Confidence            4678999999999999886       254 78999999999 9999964

>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=98.31  E-value=5.6e-08  Score=61.59  Aligned_cols=39  Identities=15%  Similarity=0.148  Sum_probs=34.2

Q ss_pred             CcccCCCCCCeEEEeCCE-------ECCCCCCccccccc-ccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGK-------QLEDGRTLADYKIQ-ESTLHLG   40 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk-------~L~D~~tL~~ygI~-~stl~L~   40 (133)
                      +..+|+|++.|+|+|.|+       .++|+.+|.+|||. |++||++
T Consensus        36 e~~~Gip~~~q~L~~~~~~~~~~~~l~dd~~~L~~ygi~dG~~Ihvv   82 (90)
T d1t0ya_          36 ELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHAV   82 (90)
T ss_dssp             HHHHCCCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEEEEE
T ss_pred             HHHHCCChhheEEEEeCCCCCcccccccCCCCHHHCCCCCCCEEEEE
Confidence            567899999999999886       35789999999999 9999963

>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=98.20  E-value=2.5e-07  Score=58.50  Aligned_cols=69  Identities=16%  Similarity=0.125  Sum_probs=53.9

Q ss_pred             cccCCCCCCCceeeccc-cCcHHHHHHHhhhhcCCCCCceEEEe--------------CCcccCcc-ccccccccEEeEE
Q 040111           44 DFCKNPDPQNITLEVES-SDTIDNVKAKIQDKKRIPPPAEADLL--------------KFPFFFFE-EVLSFFWFVVVGV  107 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~-~~tV~~LK~~I~~~~gIp~~~q~L~~--------------~gk~L~d~-~tL~dy~~~~~~~  107 (133)
                      |.+|+-+|.. .++|+. +.|+.+||.+|++..++|.+.|.|..              +...|.|+ .+|+++++...++
T Consensus         3 iRiRsrdG~e-Rv~v~~~~~Tl~~LK~~Ie~~L~VPv~~Q~LSl~~~llL~k~P~~~~~~~~l~d~~~~L~sl~i~hGsi   81 (94)
T d1wf9a1           3 LRVRSRDGLE-RVSVDGPHITVSQLKTLIQDQLQIPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLAHGSM   81 (94)
T ss_dssp             EEEECSSCEE-EEEECCTTSBHHHHHHHHHHHSCCCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTCCCTTCE
T ss_pred             EEEEecCCce-EEEecCCCCcHHHHHHHHHHHhCCCcccceeecChhhhccCCccccchhhhccCCccCHHHcCccCceE
Confidence            3466666544 577864 78999999999999999999999954              45567764 6799999988778


Q ss_pred             EEeCce
Q 040111          108 IFCGCR  113 (133)
Q Consensus       108 ~~~~~~  113 (133)
                      |++...
T Consensus        82 vyL~y~   87 (94)
T d1wf9a1          82 VYLAYE   87 (94)
T ss_dssp             EECCCS
T ss_pred             EEEEee
Confidence            887543

>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=98.14  E-value=2.5e-07  Score=56.75  Aligned_cols=42  Identities=19%  Similarity=0.431  Sum_probs=38.3

Q ss_pred             CcccCCCCCCeEEEeCCEECCCCCCccccccc-cccccccccc
Q 040111            2 EDKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHLGWRA   43 (133)
Q Consensus         2 ~~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L~~~~   43 (133)
                      +++.|+|+++++|+|+|+.|.++.|++++++. +++|++.+++
T Consensus        33 ~~~~~~~~~~~~f~fdG~~l~~~~T~~~l~~edgD~Idv~~~q   75 (77)
T d2uyzb1          33 CQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQ   75 (77)
T ss_dssp             HHHHTCCGGGEEEEETTEECCTTCCHHHHTCCTTEEEEEEECC
T ss_pred             HHHhCCChhHEEEEECCEECCCCCCHHHcCCCCCCEEEEEEec
Confidence            35689999999999999999999999999999 9999987764

>d1wm3a_ d.15.1.1 (A:) SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.97  E-value=5e-06  Score=50.14  Aligned_cols=60  Identities=2%  Similarity=-0.088  Sum_probs=55.5

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFV  103 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~  103 (133)
                      +.|+..+|+.+.+.|.++++...|...-+++.|+++...+++|.|..+..+.|.+++++-
T Consensus         4 lkv~~~~g~~v~f~vk~~t~l~kl~~~y~~~~~~~~~~~~f~fdG~~i~~~~Tp~~l~me   63 (72)
T d1wm3a_           4 LKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEME   63 (72)
T ss_dssp             EEEECTTSCEEEEEECTTSCTHHHHHHHHHHHTCCTTTCEEEETTEECCTTCCTTTTTCC
T ss_pred             EEEECCCCCEEEEEEcCCChHHHHHHHHHHHhCCCccceEEEECCEEcCCCCCHHHcCCC
Confidence            456777889999999999999999999999999999999999999999999999999874

>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=97.06  E-value=0.00014  Score=44.09  Aligned_cols=62  Identities=11%  Similarity=0.023  Sum_probs=55.6

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeCCcccCccccccccccEEe
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLKFPFFFFEEVLSFFWFVVV  105 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~gk~L~d~~tL~dy~~~~~  105 (133)
                      +.|=.++|+..++.|.|++++.++-+...++.|+.+++..|.|++++++-..++...++.++
T Consensus         3 V~Vl~~~~rR~~VKvtP~t~l~~VL~eaC~k~~~~~~~~~Lkh~~k~ldLsl~~R~sgLpnn   64 (76)
T d2al3a1           3 VSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQDFNPSEYDLKFQRTVLDLSLQWRFANLPNN   64 (76)
T ss_dssp             EEEECTTSCEEEECCCTTSBHHHHHHHHHHHTTCCGGGCEEEETTEEESSSCBHHHHCCCSS
T ss_pred             EEEECCCCcEEEEEeCCCcCHHHHHHHHHHHhCCChhHceeeeCCEEcCccceeeecCCCCC
Confidence            44567889999999999999999999999999999999999999999999888888877643

>d1i42a_ d.15.1.2 (A:) p47 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: p47
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.54  E-value=0.0018  Score=39.90  Aligned_cols=63  Identities=10%  Similarity=-0.010  Sum_probs=52.2

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhc-CCCCCceEEEe--CCcccCc-cccccccccEEeE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKK-RIPPPAEADLL--KFPFFFF-EEVLSFFWFVVVG  106 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~-gIp~~~q~L~~--~gk~L~d-~~tL~dy~~~~~~  106 (133)
                      |.||.++|..+.....++++|.+|..-+.... +.+.....|+.  ..+.+.| +.||.+.++.+.+
T Consensus        17 I~iRlPdG~~~~~~F~~~~tl~dv~~~v~~~~~~~~~~~f~L~t~~Prr~l~d~~~TL~e~gL~~s~   83 (89)
T d1i42a_          17 IQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFPNKELADENQTLKEANLLNAV   83 (89)
T ss_dssp             EEEEETTTCCEEEEECSSSCGGGHHHHHHHHCTTTSSCCEEEEETTTTEECCCCSSCSGGGTTCCSE
T ss_pred             EEEEcCCCCEEEEEECCchhHHHHHHHHHHhCccCCCCCEEEecCCCCcccCCCcCcHHHCCCcCce
Confidence            77899999999999999999999999998754 67777788885  4667865 6899999987433

>d1h8ca_ d.15.1.2 (A:) Fas-associated factor 1, Faf1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: Fas-associated factor 1, Faf1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.47  E-value=0.0021  Score=38.86  Aligned_cols=67  Identities=12%  Similarity=-0.022  Sum_probs=55.1

Q ss_pred             ccccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEE--eCCcccC---ccccccccccEEeEEEEe
Q 040111           43 ADFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADL--LKFPFFF---FEEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        43 ~i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~--~~gk~L~---d~~tL~dy~~~~~~~~~~  110 (133)
                      .|.||.++|..+.-...+++|+.++.+-+.. .+.++....|+  |..+.+.   .+.||.+.++...+.++.
T Consensus         7 ~i~iRlPdG~~~~~~F~~~~tl~~v~~~v~~-~~~~~~~~~l~~~~Pr~~l~~~d~~~TL~e~gL~p~~~L~v   78 (82)
T d1h8ca_           7 KLRIRTPSGEFLERRFLASNKLQIVFDFVAS-KGFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFL   78 (82)
T ss_dssp             EEEEECTTSCEEEEEECTTSBHHHHHHHHHH-HTCCSSSEEEEETTTTEETTTCCTTSBHHHHCCCSEEEEEE
T ss_pred             EEEEECCCCCEEEEEECCCCcHHHHHHHHHh-cCCCCCceEEEecCcccccccccccCCHHHCCCCCCCEEEE
Confidence            3778999999998899999999999999987 57788888888  5777774   357999999876666654

>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=96.10  E-value=0.0017  Score=38.43  Aligned_cols=37  Identities=24%  Similarity=0.487  Sum_probs=33.6

Q ss_pred             cccCCCCCCeEEEeCCEECCCCCCccccccc-cccccc
Q 040111            3 DKEGIPPGQQRSIFAGKQLEDGRTLADYKIQ-ESTLHL   39 (133)
Q Consensus         3 ~~~gip~~~Q~Li~~gk~L~D~~tL~~ygI~-~stl~L   39 (133)
                      ++.++|+...+++|.|..+.++.|.++.++. +.+|.+
T Consensus        33 ~~~~~~~~~~~f~fdG~~i~~~~Tp~~l~med~D~Idv   70 (72)
T d1wm3a_          33 ERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDV   70 (72)
T ss_dssp             HHHTCCTTTCEEEETTEECCTTCCTTTTTCCTTEEEEE
T ss_pred             HHhCCCccceEEEECCEEcCCCCCHHHcCCCCCCEEEE
Confidence            4568999999999999999999999999999 988874

>d1wj4a_ d.15.1.2 (A:) Hypothetical protein KIAA0794 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: Hypothetical protein KIAA0794
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.70  E-value=0.011  Score=38.40  Aligned_cols=65  Identities=12%  Similarity=0.056  Sum_probs=52.2

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEE--eCCcccC--c-cccccccccEEeEEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADL--LKFPFFF--F-EEVLSFFWFVVVGVIF  109 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~--~~gk~L~--d-~~tL~dy~~~~~~~~~  109 (133)
                      |.||.++|+.+......++||.+|.+.+... +.+.....|+  |--+.|.  | +.+|.+.++...++++
T Consensus        46 l~iRlPdG~r~~r~F~~~~tl~~l~~~v~~~-~~~~~~~~L~~~fPr~~l~~~d~~~TL~e~gL~P~~~L~  115 (124)
T d1wj4a_          46 LMLRYPDGKREQITLPEQAKLLALVKHVQSK-GYPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVF  115 (124)
T ss_dssp             EEEECTTSCEEEEEEETTSCHHHHHHHHHHH-HCCTTTEEEECSSSCCEETSSCSSSCTTTTTCCSSBCCE
T ss_pred             EEEECCCCCEEEEEeCCCCcHHHHHHHHHhc-ccCCcceEEeecccccccccccccCcHHHcCCCCCCEEE
Confidence            8899999999989999999999999999774 5667777777  5667774  3 5799999886555544

>d2cr5a1 d.15.1.2 (A:8-103) UBX domain-containing protein 6 (Reproduction 8) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: UBX domain-containing protein 6 (Reproduction 8)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.66  E-value=0.019  Score=35.24  Aligned_cols=66  Identities=8%  Similarity=-0.181  Sum_probs=52.4

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEE--eCCcccC-c-cccccccccEEeEEEEe
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADL--LKFPFFF-F-EEVLSFFWFVVVGVIFC  110 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~--~~gk~L~-d-~~tL~dy~~~~~~~~~~  110 (133)
                      |-||.++|+.+.-...+++||.+|..-+... +..+...+|+  |-.+.+. | +.||.+.++...+++++
T Consensus        19 i~iRlPdG~r~~r~F~~~dtl~~l~~fv~~~-~~~~~~f~l~~~~Pr~~~~~d~~~TL~e~gl~p~~~L~v   88 (96)
T d2cr5a1          19 VALRCPNGRVLRRRFFKSWNSQVLLDWMMKV-GYHKSLYRLSTSFPRRALEVEGGSSLEDIGITVDTVLNV   88 (96)
T ss_dssp             EEEECTTSCEEEEEEESSSBTHHHHHHHHHH-TCCTTTEEEECSSSCCBCCCCSSCBHHHHTCSSCEEEEE
T ss_pred             EEEECCCCCEEEEEECCcccHHHHHHHHHHh-ccCcccceeecCCCceecCccCCCcHHHCCCCCCCEEEE
Confidence            7889999999888899999999999998764 5566777777  4446664 3 57999999977776665

>d1wf9a1 d.15.1.1 (A:8-101) NPL4-like protein 1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: NPL4-like protein 1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=94.33  E-value=0.0023  Score=39.89  Aligned_cols=41  Identities=20%  Similarity=0.297  Sum_probs=31.7

Q ss_pred             CCcccCCCCCCeEEEeC-------------C-EECCC-CCCccccccc-cccccccc
Q 040111            1 IEDKEGIPPGQQRSIFA-------------G-KQLED-GRTLADYKIQ-ESTLHLGW   41 (133)
Q Consensus         1 I~~~~gip~~~Q~Li~~-------------g-k~L~D-~~tL~~ygI~-~stl~L~~   41 (133)
                      |++..+||++.|+|..+             . ..|.| ..+|+.+||. |+.++|..
T Consensus        30 Ie~~L~VPv~~Q~LSl~~~llL~k~P~~~~~~~~l~d~~~~L~sl~i~hGsivyL~y   86 (94)
T d1wf9a1          30 IQDQLQIPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLAHGSMVYLAY   86 (94)
T ss_dssp             HHHHSCCCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTCCCTTCEEECCC
T ss_pred             HHHHhCCCcccceeecChhhhccCCccccchhhhccCCccCHHHcCccCceEEEEEe
Confidence            56789999999999653             1 23554 5679999999 99999754

>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=92.10  E-value=0.094  Score=30.87  Aligned_cols=43  Identities=9%  Similarity=-0.004  Sum_probs=38.0

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEe
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLL   86 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~   86 (133)
                      +.|..++|+...+.+.|..|+.++-.++.++.|++++.-.++.
T Consensus         3 iRv~LPngq~T~V~vrpG~tir~~L~k~l~kRgl~~~~~~V~~   45 (73)
T d1wxma1           3 VKVYLPNKQRTVVTVRDGMSVYDSLDKALKVRGLNQDCCVVYR   45 (73)
T ss_dssp             EEEECSSSCEEEEECCSSCBSHHHHHHHHHTTTCCSSSEEEEE
T ss_pred             EEEEcCCCCeEEEEecCCCCHHHHHHHHHHHcCCCHHHEEEEE
Confidence            3456788999999999999999999999999999999888764

>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=88.39  E-value=0.14  Score=30.42  Aligned_cols=43  Identities=14%  Similarity=0.118  Sum_probs=38.2

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCCceEEEe
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLL   86 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~   86 (133)
                      +.|..++|+...+++.|..|+.++-.++.++.|++++.-.++-
T Consensus         4 iRv~LPngq~T~V~vrpG~tird~L~k~l~kRgl~~~~c~V~~   46 (77)
T d1c1yb_           4 IRVFLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVFR   46 (77)
T ss_dssp             EEEEETTTEEEEEECCTTCBHHHHHHHHHHTTTCCGGGEEEEE
T ss_pred             EEEECCCCCeEEEEecCCCCHHHHHHHHHHHcCCCHHHEEEEE
Confidence            4456688999999999999999999999999999999888864

>d1wgra_ d.15.1.5 (A:) Growth factor receptor-bound protein 7, GRB-7 {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: Growth factor receptor-bound protein 7, GRB-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.23  E-value=0.21  Score=30.64  Aligned_cols=42  Identities=12%  Similarity=0.006  Sum_probs=33.2

Q ss_pred             cccCCCCCCCceeeccccCcHHHHHHHhhhhcCCCCC-ceEEE
Q 040111           44 DFCKNPDPQNITLEVESSDTIDNVKAKIQDKKRIPPP-AEADL   85 (133)
Q Consensus        44 i~Vk~~~g~~~~l~V~~~~tV~~LK~~I~~~~gIp~~-~q~L~   85 (133)
                      +.|-..+|.+.++.|++++|+.++-+.+.++.++..+ ...|+
T Consensus        12 vkv~~~dg~~k~l~V~~~tTa~eV~~~l~~K~~~~~~~~f~L~   54 (100)
T d1wgra_          12 VKVYSEDGACRSVEVAAGATARHVCEMLVQRAHALSDETWGLV   54 (100)
T ss_dssp             EEEEETTSCEEEEEECTTCCHHHHHHHHHCSSSCCCCCCCCEE
T ss_pred             EEEEecCCCEEEEEECCCCcHHHHHHHHHHHhCCCCCCCeEEE
Confidence            4444577888999999999999999999999997543 33444

>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=84.70  E-value=0.52  Score=28.12  Aligned_cols=36  Identities=6%  Similarity=0.086  Sum_probs=33.4

Q ss_pred             CCceeeccccCcHHHHHHHhhhhcCCCCCceEEEeC
Q 040111           52 QNITLEVESSDTIDNVKAKIQDKKRIPPPAEADLLK   87 (133)
Q Consensus        52 ~~~~l~V~~~~tV~~LK~~I~~~~gIp~~~q~L~~~   87 (133)
                      =++.+++.+....++|.++|+++...+|+.-+|.|+
T Consensus        14 fTVal~v~~G~~y~~L~~lvs~KL~l~~~~~~LSY~   49 (82)
T d1oeya_          14 YTVVMKTQPGLPYSQVRDMVSKKLELRLEHTKLSYR   49 (82)
T ss_dssp             SEEEEEECTTCCHHHHHHHHHHHTTCCGGGCCEEEC
T ss_pred             EEEEEEccCCCCHHHHHHHHHHHhCCChhheEEEec
Confidence            367788999999999999999999999999999996