Citrus Sinensis ID: 040824

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150----
Protein Sequence
MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGGL
Secondary Structure (PSIPRED)
cEEEEEcccccEEEEEEEccccHHHHHHHHHHHccccccccEEEEccEEccccccccccccccccEEEEEEEEcccEEEEEEEccccEEEEEcccccHHHHHHHHHHHHHcccccccEEEcccEEccccccccccccccccEEEEEEEcccccc
Secondary Structure Prediction (SSPRO)
cEEEEEEccccEEEEEcccccEHHHHHHHHHHHHcccHHHEEEEEccEEcccccEcHHHccccccEEEEEEccccccEEEEEcccccEEEEEcccccEHHHHHHHHHHHHcccHHHEEEEEccEEcccccEccccccccccEEEEEEccccccc
Coil and Loop (DISEMBL)
MQIFVKTltgktitlevessdtiDNVKAKiqdkegippdqQRLIFAGkqledgrtladyniqkeSTLHLVLRLRGgtmikvktltgkeieidieptDTIERIKERveekegippvQQRLIYAGKqladdktardynieggSVLHLVLALRGGGL
Flexible Loop (DISEMBL)
mqifvktltgktitlevessdtidnVKAKIqdkegippdqqRLIFAGKQLEDGRTLAdyniqkestlhlvlrlrggtmikvktltgkeieidieptdtiERIKErveekegippvqQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGGL
Low Complexity Region (SEG)
MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGTMIKVKTLTGKeieidieptdtierikerveekeGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGGL
Disordered region (IsUnstruct)
***FVKTLTGKTITLEV************************RLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERI***********PVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLAL*****
Disordered Region (DISOPRED)
MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG*
Disordered Region (DISEMBL)
MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGGL
Disordered Region (DISPRO)
MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRG***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGGL
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	154	2.2.26 [Sep-21-2011]
P0C031	153	Ubiquitin-NEDD8-like prot	yes	no	0.987	0.993	0.986	7e-81
P0C030	153	Ubiquitin-NEDD8-like prot	yes	no	0.987	0.993	0.986	9e-81
Q9SHE7	156	Ubiquitin-NEDD8-like prot	yes	no	0.987	0.974	0.986	9e-81
P0C073	153	Ubiquitin-NEDD8-like prot	N/A	no	0.987	0.993	0.980	1e-80
Q8RUC6	154	Ubiquitin-NEDD8-like prot	yes	no	1.0	1.0	0.974	5e-80
P0C032	154	Ubiquitin-like protein-NE	no	no	1.0	1.0	0.889	7e-74
Q1EC66	306	Polyubiquitin 3 OS=Arabid	no	no	1.0	0.503	0.792	8e-65
P0CH32	382	Polyubiquitin 4 OS=Arabid	no	no	1.0	0.403	0.792	8e-65
P0CG83	171	Polyubiquitin (Fragment)	N/A	no	0.987	0.888	0.802	1e-64
P69309	305	Polyubiquitin OS=Avena fa	N/A	no	0.987	0.498	0.802	1e-64

>sp|P0C031|RUB2_ORYSJ Ubiquitin-NEDD8-like protein RUB2 OS=Oryza sativa subsp. japonica GN=RUB2 PE=2 SV=2

 Score =  298 bits (764), Expect = 7e-81,   Method: Compositional matrix adjust.
 Identities = 150/152 (98%), Positives = 152/152 (100%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
           IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTI+RIKERVEEKEGIPPVQQRLI
Sbjct: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLI 120

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
           YAGKQLADDKTA+DYNIEGGSVLHLVLALRGG
Sbjct: 121 YAGKQLADDKTAKDYNIEGGSVLHLVLALRGG 152

NEDD8-like protein RUB2: Appears to function as a stable post-translational protein modifier.
Oryza sativa subsp. japonica (taxid: 39947)

>sp|P0C030|RUB1_ORYSJ Ubiquitin-NEDD8-like protein RUB1 OS=Oryza sativa subsp. japonica GN=RUB1 PE=2 SV=2

 Score =  298 bits (763), Expect = 9e-81,   Method: Compositional matrix adjust.
 Identities = 150/152 (98%), Positives = 152/152 (100%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
           IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTI+RIKERVEEKEGIPPVQQRLI
Sbjct: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLI 120

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
           YAGKQLADDKTA+DYNIEGGSVLHLVLALRGG
Sbjct: 121 YAGKQLADDKTAKDYNIEGGSVLHLVLALRGG 152

NEDD8-like protein RUB1: Appears to function as a stable post-translational protein modifier.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9SHE7|RUB1_ARATH Ubiquitin-NEDD8-like protein RUB1 OS=Arabidopsis thaliana GN=RUB1 PE=1 SV=3

 Score =  298 bits (763), Expect = 9e-81,   Method: Compositional matrix adjust.
 Identities = 150/152 (98%), Positives = 152/152 (100%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
           IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTI+RIKERVEEKEGIPPVQQRLI
Sbjct: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLI 120

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
           YAGKQLADDKTA+DYNIEGGSVLHLVLALRGG
Sbjct: 121 YAGKQLADDKTAKDYNIEGGSVLHLVLALRGG 152

NEDD8-like protein RUB1: Appears to function as a stable post-translational protein modifier. An AMP-RUB1 intermediate is formed by an activating enzyme, distinct from the ubiquitin activating enzyme E1, which is composed of an heterodimer AXR1/ECR1. Auxin response is mediated, at least in part, through modification of the cullin AtCUL1 by the attachment of RUB1 to 'Lys-692'.

Arabidopsis thaliana (taxid: 3702)

>sp|P0C073|RUB1_DESAN Ubiquitin-NEDD8-like protein RUB1 OS=Deschampsia antarctica GN=RUB1 PE=2 SV=2

 Score =  298 bits (762), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 149/152 (98%), Positives = 152/152 (100%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
           IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTI+R+KERVEEKEGIPPVQQRLI
Sbjct: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIDRVKERVEEKEGIPPVQQRLI 120

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
           YAGKQLADDKTA+DYNIEGGSVLHLVLALRGG
Sbjct: 121 YAGKQLADDKTAKDYNIEGGSVLHLVLALRGG 152

NEDD8-like protein RUB1: Probably function as a stable post-translational protein modifier. May be involved during cold acclimation.

Deschampsia antarctica (taxid: 159298)

>sp|Q8RUC6|RUB2_ARATH Ubiquitin-NEDD8-like protein RUB2 OS=Arabidopsis thaliana GN=RUB2 PE=1 SV=3

 Score =  296 bits (757), Expect = 5e-80,   Method: Compositional matrix adjust.
 Identities = 150/154 (97%), Positives = 152/154 (98%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
           IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTI+RIKERVEEKEGIPPVQQRLI
Sbjct: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLI 120

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGGGL 154
           YAGKQLADDKTA+DY IEGGSVLHLVLALRGG L
Sbjct: 121 YAGKQLADDKTAKDYAIEGGSVLHLVLALRGGLL 154

NEDD8-like protein RUB2: Appears to function as a stable post-translational protein modifier.

Arabidopsis thaliana (taxid: 3702)

>sp|P0C032|RUB3_ORYSJ Ubiquitin-like protein-NEDD8-like protein RUB3 OS=Oryza sativa subsp. japonica GN=RUB3 PE=3 SV=2

 Score =  275 bits (703), Expect = 7e-74,   Method: Compositional matrix adjust.
 Identities = 137/154 (88%), Positives = 144/154 (93%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTI NVKAK+QDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIQNVKAKVQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
           IQKESTLHLVLRLRGG  +KV+TLTGKEI+IDIE TDT++RIKERVEE+EGIPPVQQRLI
Sbjct: 61  IQKESTLHLVLRLRGGLNVKVRTLTGKEIDIDIEMTDTVDRIKERVEEREGIPPVQQRLI 120

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGGGL 154
           Y GKQLADDKTA DY IE GSVLHLVLALRGG  
Sbjct: 121 YGGKQLADDKTAHDYKIEAGSVLHLVLALRGGNF 154

NEDD8-like protein RUB3: Appears to function as a stable post-translational protein modifier.

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  245 bits (626), Expect = 8e-65,   Method: Compositional matrix adjust.
 Identities = 122/154 (79%), Positives = 135/154 (87%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 153 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 212

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
           IQKESTLHLVLRLRGG  I VKTLTGK I +++E +DTI+ +K ++++KEGIPP QQRLI
Sbjct: 213 IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI 272

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGGGL 154
           +AGKQL D +T  DYNI+  S LHLVL LRGG  
Sbjct: 273 FAGKQLEDGRTLADYNIQKESTLHLVLRLRGGSF 306

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

 Score =  245 bits (625), Expect = 8e-65,   Method: Compositional matrix adjust.
 Identities = 122/154 (79%), Positives = 135/154 (87%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 229 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 288

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
           IQKESTLHLVLRLRGG  I VKTLTGK I +++E +DTI+ +K ++++KEGIPP QQRLI
Sbjct: 289 IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI 348

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGGGL 154
           +AGKQL D +T  DYNI+  S LHLVL LRGG  
Sbjct: 349 FAGKQLEDGRTLADYNIQKESTLHLVLRLRGGSF 382

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

 Score =  244 bits (624), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 122/152 (80%), Positives = 135/152 (88%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 19  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 78

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
           IQKESTLHLVLRLRGG  I VKTLTGK I +++E +DTI+ +K ++++KEGIPP QQRLI
Sbjct: 79  IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI 138

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
           +AGKQL D +T  DYNI+  S LHLVL LRGG
Sbjct: 139 FAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 170

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

 Score =  244 bits (624), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 122/152 (80%), Positives = 135/152 (88%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
           IQKESTLHLVLRLRGG  I VKTLTGK I +++E +DTI+ +K ++++KEGIPP QQRLI
Sbjct: 61  IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI 120

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
           +AGKQL D +T  DYNI+  S LHLVL LRGG
Sbjct: 121 FAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 152

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

Avena fatua (taxid: 4499)

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	154
225465030	155	PREDICTED: ubiquitin-NEDD8-like protein	0.993	0.987	0.986	1e-79
222635996	208	hypothetical protein OsJ_22175 [Oryza sa	0.980	0.725	0.986	3e-79
297606280	177	Os06g0650100 [Oryza sativa Japonica Grou	0.987	0.858	0.986	4e-79
242093754	153	hypothetical protein SORBIDRAFT_10g02567	0.987	0.993	0.986	4e-79
115479211	153	Os09g0420800 [Oryza sativa Japonica Grou	0.987	0.993	0.986	5e-79
30692436	156	NEDD8-like protein RUB1 [Arabidopsis tha	0.987	0.974	0.986	5e-79
255544634	154	ubiquitin, putative [Ricinus communis] g	1.0	1.0	0.974	7e-79
302393764	153	RecName: Full=Ubiquitin-NEDD8-like prote	0.987	0.993	0.980	7e-79
224066593	154	predicted protein [Populus trichocarpa]	1.0	1.0	0.974	1e-78
356525758	154	PREDICTED: ubiquitin-NEDD8-like protein	0.987	0.987	0.980	1e-78

>gi|225465030|ref|XP_002265864.1| PREDICTED: ubiquitin-NEDD8-like protein RUB2 [Vitis vinifera] gi|297736166|emb|CBI24204.3| unnamed protein product [Vitis vinifera]

 Score =  300 bits (768), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 151/153 (98%), Positives = 152/153 (99%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
           IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTI+RIKERVEEKEGIPPVQQRLI
Sbjct: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLI 120

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGGG 153
           YAGKQL DDKTARDYNIEGGSVLHLVLALRGGG
Sbjct: 121 YAGKQLGDDKTARDYNIEGGSVLHLVLALRGGG 153

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222635996|gb|EEE66128.1| hypothetical protein OsJ_22175 [Oryza sativa Japonica Group]

 Score =  299 bits (765), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 149/151 (98%), Positives = 151/151 (100%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
           IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTI+RIKERVEEKEGIPPVQQRLI
Sbjct: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLI 120

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRG 151
           YAGKQLADDKTA+DYNIEGGSVLHLVLALRG
Sbjct: 121 YAGKQLADDKTAKDYNIEGGSVLHLVLALRG 151

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297606280|ref|NP_001058221.2| Os06g0650100 [Oryza sativa Japonica Group] gi|255677281|dbj|BAF20135.2| Os06g0650100, partial [Oryza sativa Japonica Group]

 Score =  298 bits (764), Expect = 4e-79,   Method: Compositional matrix adjust.
 Identities = 150/152 (98%), Positives = 152/152 (100%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 25  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 84

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
           IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTI+RIKERVEEKEGIPPVQQRLI
Sbjct: 85  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLI 144

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
           YAGKQLADDKTA+DYNIEGGSVLHLVLALRGG
Sbjct: 145 YAGKQLADDKTAKDYNIEGGSVLHLVLALRGG 176

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242093754|ref|XP_002437367.1| hypothetical protein SORBIDRAFT_10g025670 [Sorghum bicolor] gi|357123249|ref|XP_003563324.1| PREDICTED: ubiquitin-NEDD8-like protein RUB2-like [Brachypodium distachyon] gi|302393766|sp|P0C031.2|RUB2_ORYSJ RecName: Full=Ubiquitin-NEDD8-like protein RUB2; Contains: RecName: Full=Ubiquitin; Contains: RecName: Full=NEDD8-like protein RUB2; AltName: Full=OsRUB2; AltName: Full=Ubiquitin-related protein 2; Flags: Precursor gi|51534981|dbj|BAD38105.1| polyubiquitin 2 [Oryza sativa Japonica Group] gi|215692861|dbj|BAG88281.1| unnamed protein product [Oryza sativa Japonica Group] gi|218186299|gb|EEC68726.1| hypothetical protein OsI_37226 [Oryza sativa Indica Group] gi|218198663|gb|EEC81090.1| hypothetical protein OsI_23921 [Oryza sativa Indica Group] gi|241915590|gb|EER88734.1| hypothetical protein SORBIDRAFT_10g025670 [Sorghum bicolor]

 Score =  298 bits (764), Expect = 4e-79,   Method: Compositional matrix adjust.
 Identities = 150/152 (98%), Positives = 152/152 (100%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
           IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTI+RIKERVEEKEGIPPVQQRLI
Sbjct: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLI 120

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
           YAGKQLADDKTA+DYNIEGGSVLHLVLALRGG
Sbjct: 121 YAGKQLADDKTAKDYNIEGGSVLHLVLALRGG 152

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115479211|ref|NP_001063199.1| Os09g0420800 [Oryza sativa Japonica Group] gi|242044708|ref|XP_002460225.1| hypothetical protein SORBIDRAFT_02g024880 [Sorghum bicolor] gi|357158453|ref|XP_003578133.1| PREDICTED: ubiquitin-NEDD8-like protein RUB1-like [Brachypodium distachyon] gi|302393765|sp|P0C030.2|RUB1_ORYSJ RecName: Full=Ubiquitin-NEDD8-like protein RUB1; Contains: RecName: Full=Ubiquitin; Contains: RecName: Full=NEDD8-like protein RUB1; AltName: Full=OsRUB1; AltName: Full=Ubiquitin-related protein 1; Flags: Precursor gi|50725971|dbj|BAD33498.1| polyubiquitin 2 [Oryza sativa Japonica Group] gi|50726105|dbj|BAD33626.1| polyubiquitin 2 [Oryza sativa Japonica Group] gi|113631432|dbj|BAF25113.1| Os09g0420800 [Oryza sativa Japonica Group] gi|125563747|gb|EAZ09127.1| hypothetical protein OsI_31396 [Oryza sativa Indica Group] gi|215704536|dbj|BAG94169.1| unnamed protein product [Oryza sativa Japonica Group] gi|241923602|gb|EER96746.1| hypothetical protein SORBIDRAFT_02g024880 [Sorghum bicolor] gi|326513616|dbj|BAJ87827.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  298 bits (763), Expect = 5e-79,   Method: Compositional matrix adjust.
 Identities = 150/152 (98%), Positives = 152/152 (100%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
           IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTI+RIKERVEEKEGIPPVQQRLI
Sbjct: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLI 120

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
           YAGKQLADDKTA+DYNIEGGSVLHLVLALRGG
Sbjct: 121 YAGKQLADDKTAKDYNIEGGSVLHLVLALRGG 152

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30692436|ref|NP_564379.2| NEDD8-like protein RUB1 [Arabidopsis thaliana] gi|302393813|sp|Q9SHE7.3|RUB1_ARATH RecName: Full=Ubiquitin-NEDD8-like protein RUB1; Contains: RecName: Full=Ubiquitin; Contains: RecName: Full=NEDD8-like protein RUB1; AltName: Full=Ubiquitin-related protein 1; Short=AtRUB1; Flags: Precursor gi|6692129|gb|AAF24594.1|AC007654_10 T19E23.13 [Arabidopsis thaliana] gi|28973676|gb|AAO64156.1| putative ubiquitin (AtRUB1) [Arabidopsis thaliana] gi|29824269|gb|AAP04095.1| putative ubiquitin (AtRUB1) [Arabidopsis thaliana] gi|110737109|dbj|BAF00506.1| putative ubiquitin [Arabidopsis thaliana] gi|312283039|dbj|BAJ34385.1| unnamed protein product [Thellungiella halophila] gi|332193223|gb|AEE31344.1| NEDD8-like protein RUB1 [Arabidopsis thaliana]

 Score =  298 bits (763), Expect = 5e-79,   Method: Compositional matrix adjust.
 Identities = 150/152 (98%), Positives = 152/152 (100%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
           IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTI+RIKERVEEKEGIPPVQQRLI
Sbjct: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLI 120

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
           YAGKQLADDKTA+DYNIEGGSVLHLVLALRGG
Sbjct: 121 YAGKQLADDKTAKDYNIEGGSVLHLVLALRGG 152

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255544634|ref|XP_002513378.1| ubiquitin, putative [Ricinus communis] gi|223547286|gb|EEF48781.1| ubiquitin, putative [Ricinus communis]

 Score =  298 bits (762), Expect = 7e-79,   Method: Compositional matrix adjust.
 Identities = 150/154 (97%), Positives = 151/154 (98%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
           IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTI+RIKERVEEKEGIPPVQQRLI
Sbjct: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLI 120

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGGGL 154
           YAGKQL DDKTARDYNIEGGSVLHLVLALRGG  
Sbjct: 121 YAGKQLGDDKTARDYNIEGGSVLHLVLALRGGCF 154

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302393764|sp|P0C073.2|RUB1_DESAN RecName: Full=Ubiquitin-NEDD8-like protein RUB1; Contains: RecName: Full=Ubiquitin; Contains: RecName: Full=NEDD8-like protein RUB1; AltName: Full=DaRUB1; AltName: Full=Ubiquitin-related protein 1; Flags: Precursor gi|20562909|gb|AAM22748.1| polyubiquitin 2 [Deschampsia antarctica]

 Score =  298 bits (762), Expect = 7e-79,   Method: Compositional matrix adjust.
 Identities = 149/152 (98%), Positives = 152/152 (100%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
           IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTI+R+KERVEEKEGIPPVQQRLI
Sbjct: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIDRVKERVEEKEGIPPVQQRLI 120

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
           YAGKQLADDKTA+DYNIEGGSVLHLVLALRGG
Sbjct: 121 YAGKQLADDKTAKDYNIEGGSVLHLVLALRGG 152

Source: Deschampsia antarctica

Species: Deschampsia antarctica

Genus: Deschampsia

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224066593|ref|XP_002302153.1| predicted protein [Populus trichocarpa] gi|224082516|ref|XP_002306725.1| predicted protein [Populus trichocarpa] gi|118485172|gb|ABK94447.1| unknown [Populus trichocarpa] gi|222843879|gb|EEE81426.1| predicted protein [Populus trichocarpa] gi|222856174|gb|EEE93721.1| predicted protein [Populus trichocarpa]

 Score =  297 bits (760), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 150/154 (97%), Positives = 151/154 (98%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
           IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEP DTI+RIKERVEEKEGIPPVQQRLI
Sbjct: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPNDTIDRIKERVEEKEGIPPVQQRLI 120

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGGGL 154
           YAGKQL DDKTARDYNIEGGSVLHLVLALRGG L
Sbjct: 121 YAGKQLGDDKTARDYNIEGGSVLHLVLALRGGCL 154

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356525758|ref|XP_003531490.1| PREDICTED: ubiquitin-NEDD8-like protein RUB2-like [Glycine max] gi|356556999|ref|XP_003546806.1| PREDICTED: ubiquitin-NEDD8-like protein RUB2-like [Glycine max] gi|255627501|gb|ACU14095.1| unknown [Glycine max]

 Score =  297 bits (760), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 149/152 (98%), Positives = 152/152 (100%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
           IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTI+RIKERVEEKEGIPPVQQRLI
Sbjct: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLI 120

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
           YAGKQLADDKTA++YNIEGGSVLHLVLALRGG
Sbjct: 121 YAGKQLADDKTAKEYNIEGGSVLHLVLALRGG 152

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	154
TAIR|locus:2197525	156	RUB1 "AT1G31340" [Arabidopsis	1.0	0.987	0.838	9e-61
TAIR|locus:505006295	154	UBQ7 "AT2G35635" [Arabidopsis	0.987	0.987	0.835	8.1e-60
TAIR|locus:2115663	457	UBQ10 "AT4G05320" [Arabidopsis	0.987	0.332	0.75	1.3e-52
TAIR|locus:2180434	382	UBQ4 "AT5G20620" [Arabidopsis	0.987	0.397	0.75	1.3e-52
TAIR|locus:2143548	306	UBQ3 "AT5G03240" [Arabidopsis	0.987	0.496	0.75	1.3e-52
TAIR|locus:2140200	305	UBQ14 "AT4G02890" [Arabidopsis	0.987	0.498	0.75	1.3e-52
TAIR|locus:2138386	229	UBQ11 "AT4G05050" [Arabidopsis	0.987	0.663	0.75	1.3e-52
POMBASE|SPBC337.08c	382	ubi4 "ubiquitin" [Schizosaccha	0.987	0.397	0.736	5.6e-52
SGD|S000003962	381	UBI4 "Ubiquitin" [Saccharomyce	0.987	0.398	0.736	5.6e-52
UNIPROTKB|G4MY63	305	MGG_01282 "Polyubiquitin" [Mag	0.987	0.498	0.736	5.6e-52

TAIR|locus:2197525 RUB1 "AT1G31340" [Arabidopsis thaliana (taxid:3702)]

 Score = 622 (224.0 bits), Expect = 9.0e-61, P = 9.0e-61
 Identities = 130/155 (83%), Positives = 131/155 (84%)

Query:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
             MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query:    61 IQKESTLHLVLRLRGGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLI 120
             IQKESTLHLVLRLRGGTMIKVKTLTGK                       GIPPVQQRLI
Sbjct:    61 IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLI 120

Query:   121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG-GL 154
             YAGKQLADDKTA+DYNIEGGSVLHLVLALRGG GL
Sbjct:   121 YAGKQLADDKTAKDYNIEGGSVLHLVLALRGGFGL 155

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

GO:0045116 "protein neddylation" evidence=TAS

GO:0009693 "ethylene biosynthetic process" evidence=IMP

GO:0009790 "embryo development" evidence=IGI

GO:0005886 "plasma membrane" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0009733 "response to auxin stimulus" evidence=TAS

TAIR|locus:505006295 UBQ7 "AT2G35635" [Arabidopsis thaliana (taxid:3702)]

 Score = 613 (220.8 bits), Expect = 8.1e-60, P = 8.1e-60
 Identities = 127/152 (83%), Positives = 128/152 (84%)

Query:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
             MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60

Query:    61 IQKESTLHLVLRLRGGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLI 120
             IQKESTLHLVLRLRGGTMIKVKTLTGK                       GIPPVQQRLI
Sbjct:    61 IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLI 120

Query:   121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
             YAGKQLADDKTA+DY IEGGSVLHLVLALRGG
Sbjct:   121 YAGKQLADDKTAKDYAIEGGSVLHLVLALRGG 152

GO:0005622 "intracellular" evidence=TAS

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

GO:0005829 "cytosol" evidence=RCA

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

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

 Score = 545 (196.9 bits), Expect = 1.3e-52, P = 1.3e-52
 Identities = 114/152 (75%), Positives = 117/152 (76%)

Query:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
             MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct:   305 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 364

Query:    61 IQKESTLHLVLRLRGGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLI 120
             IQKESTLHLVLRLRGG  I VKTLTGK                       GIPP QQRLI
Sbjct:   365 IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI 424

Query:   121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
             +AGKQL D +T  DYNI+  S LHLVL LRGG
Sbjct:   425 FAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 456

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

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

GO:0007568 "aging" evidence=IEP

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

 Score = 545 (196.9 bits), Expect = 1.3e-52, P = 1.3e-52
 Identities = 114/152 (75%), Positives = 117/152 (76%)

Query:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
             MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct:   229 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 288

Query:    61 IQKESTLHLVLRLRGGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLI 120
             IQKESTLHLVLRLRGG  I VKTLTGK                       GIPP QQRLI
Sbjct:   289 IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI 348

Query:   121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
             +AGKQL D +T  DYNI+  S LHLVL LRGG
Sbjct:   349 FAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 380

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 = 545 (196.9 bits), Expect = 1.3e-52, P = 1.3e-52
 Identities = 114/152 (75%), Positives = 117/152 (76%)

Query:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
             MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct:   153 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 212

Query:    61 IQKESTLHLVLRLRGGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLI 120
             IQKESTLHLVLRLRGG  I VKTLTGK                       GIPP QQRLI
Sbjct:   213 IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI 272

Query:   121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
             +AGKQL D +T  DYNI+  S LHLVL LRGG
Sbjct:   273 FAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 304

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 = 545 (196.9 bits), Expect = 1.3e-52, P = 1.3e-52
 Identities = 114/152 (75%), Positives = 117/152 (76%)

Query:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
             MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct:   153 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 212

Query:    61 IQKESTLHLVLRLRGGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLI 120
             IQKESTLHLVLRLRGG  I VKTLTGK                       GIPP QQRLI
Sbjct:   213 IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI 272

Query:   121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
             +AGKQL D +T  DYNI+  S LHLVL LRGG
Sbjct:   273 FAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 304

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

GO:0005773 "vacuole" evidence=IDA

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

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

 Score = 545 (196.9 bits), Expect = 1.3e-52, P = 1.3e-52
 Identities = 114/152 (75%), Positives = 117/152 (76%)

Query:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
             MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN
Sbjct:    77 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 136

Query:    61 IQKESTLHLVLRLRGGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLI 120
             IQKESTLHLVLRLRGG  I VKTLTGK                       GIPP QQRLI
Sbjct:   137 IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI 196

Query:   121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
             +AGKQL D +T  DYNI+  S LHLVL LRGG
Sbjct:   197 FAGKQLEDGRTLADYNIQKESTLHLVLRLRGG 228

GO:0005622 "intracellular" evidence=TAS

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

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

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

 Score = 539 (194.8 bits), Expect = 5.6e-52, P = 5.6e-52
 Identities = 112/152 (73%), Positives = 117/152 (76%)

Query:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
             MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct:   229 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 288

Query:    61 IQKESTLHLVLRLRGGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLI 120
             IQKESTLHLVLRLRGG  I VKTLTGK                       GIPP QQRLI
Sbjct:   289 IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLI 348

Query:   121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
             +AGKQL D +T  DYNI+  S LHLVL LRGG
Sbjct:   349 FAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 380

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 = 539 (194.8 bits), Expect = 5.6e-52, P = 5.6e-52
 Identities = 112/152 (73%), Positives = 117/152 (76%)

Query:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
             MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct:   229 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 288

Query:    61 IQKESTLHLVLRLRGGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLI 120
             IQKESTLHLVLRLRGG  I VKTLTGK                       GIPP QQRLI
Sbjct:   289 IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLI 348

Query:   121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
             +AGKQL D +T  DYNI+  S LHLVL LRGG
Sbjct:   349 FAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 380

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 = 539 (194.8 bits), Expect = 5.6e-52, P = 5.6e-52
 Identities = 112/152 (73%), Positives = 117/152 (76%)

Query:     1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
             MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct:   153 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 212

Query:    61 IQKESTLHLVLRLRGGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLI 120
             IQKESTLHLVLRLRGG  I VKTLTGK                       GIPP QQRLI
Sbjct:   213 IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLI 272

Query:   121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
             +AGKQL D +T  DYNI+  S LHLVL LRGG
Sbjct:   273 FAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 304

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0043581 "mycelium development" evidence=IEP

---

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)
P62972	UBIQP_XENLA	No assigned EC number	0.7960	0.9870	0.9101	N/A	no
P0CG83	UBIQP_HORVU	No assigned EC number	0.8026	0.9870	0.8888	N/A	no
P62976	UBIQP_CRIGR	No assigned EC number	0.7960	0.9870	0.2310	yes	no
P0CG73	UBI1P_CANAX	No assigned EC number	0.7894	0.9870	0.6637	N/A	no
P0CG72	UBI4P_SCHPO	No assigned EC number	0.7894	0.9870	0.3979	yes	no
P0CG75	UBI4P_KLULA	No assigned EC number	0.7894	0.9870	0.3989	yes	no
P0CG50	UBC_MOUSE	No assigned EC number	0.7960	0.9870	0.2070	yes	no
P0CH28	UBC_BOVIN	No assigned EC number	0.7922	1.0	0.2231	yes	no
P0CG67	UBB_GORGO	No assigned EC number	0.7960	0.9870	0.6637	N/A	no
Q8RUC6	RUB2_ARATH	No assigned EC number	0.9740	1.0	1.0	yes	no
P0CG63	UBI4P_YEAST	No assigned EC number	0.7843	0.9935	0.4015	yes	no
Q8MKD1	UBB_HORSE	No assigned EC number	0.7960	0.9870	0.4983	yes	no
P0C073	RUB1_DESAN	No assigned EC number	0.9802	0.9870	0.9934	N/A	no
P0CG60	UBB_PONPY	No assigned EC number	0.7960	0.9870	0.6637	N/A	no
Q9SHE7	RUB1_ARATH	No assigned EC number	0.9868	0.9870	0.9743	yes	no
P0CG47	UBB_HUMAN	No assigned EC number	0.7960	0.9870	0.6637	yes	no
P0C030	RUB1_ORYSJ	No assigned EC number	0.9868	0.9870	0.9934	yes	no
Q63429	UBC_RAT	No assigned EC number	0.7960	0.9870	0.1876	yes	no
P0C032	RUB3_ORYSJ	No assigned EC number	0.8896	1.0	1.0	no	no
P0C031	RUB2_ORYSJ	No assigned EC number	0.9868	0.9870	0.9934	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	154
cd01803	76	cd01803, Ubiquitin, Ubiquitin	9e-48
cd01806	76	cd01806, Nedd8, Nebb8-like ubiquitin protein	6e-42
smart00213	72	smart00213, UBQ, Ubiquitin homologues	1e-30
pfam00240	69	pfam00240, ubiquitin, Ubiquitin family	1e-30
cd01803	76	cd01803, Ubiquitin, Ubiquitin	3e-28
cd01806	76	cd01806, Nedd8, Nebb8-like ubiquitin protein	6e-27
cd01769	69	cd01769, UBL, Ubiquitin-like domain of UBL	7e-27
pfam00240	69	pfam00240, ubiquitin, Ubiquitin family	2e-25
smart00213	72	smart00213, UBQ, Ubiquitin homologues	9e-25
PTZ00044	76	PTZ00044, PTZ00044, ubiquitin; Provisional	2e-23
cd01769	69	cd01769, UBL, Ubiquitin-like domain of UBL	1e-22
PTZ00044	76	PTZ00044, PTZ00044, ubiquitin; Provisional	2e-21
cd01802	103	cd01802, AN1_N, ubiquitin-like domain of AN1	7e-20
pfam11976	72	pfam11976, Rad60-SLD, Ubiquitin-2 like Rad60 SUMO-	2e-18
cd01805	77	cd01805, RAD23_N, Ubiquitin-like domain of RAD23	3e-16
cd01802	103	cd01802, AN1_N, ubiquitin-like domain of AN1	4e-16
cd01809	72	cd01809, Scythe_N, Ubiquitin-like domain of Scythe	5e-16
cd01809	72	cd01809, Scythe_N, Ubiquitin-like domain of Scythe	4e-15
pfam11976	72	pfam11976, Rad60-SLD, Ubiquitin-2 like Rad60 SUMO-	6e-15
cd00196	69	cd00196, UBQ, Ubiquitin-like proteins	6e-14
cd01798	70	cd01798, parkin_N, amino-terminal ubiquitin-like o	1e-13
cd01793	74	cd01793, Fubi, Fubi ubiquitin-like protein	2e-13
cd01805	77	cd01805, RAD23_N, Ubiquitin-like domain of RAD23	7e-13
TIGR00601	378	TIGR00601, rad23, UV excision repair protein Rad23	8e-13
cd01807	74	cd01807, GDX_N, ubiquitin-like domain of GDX	1e-12
cd00196	69	cd00196, UBQ, Ubiquitin-like proteins	2e-12
cd01800	76	cd01800, SF3a120_C, Ubiquitin-like domain of Mamma	1e-11
cd01798	70	cd01798, parkin_N, amino-terminal ubiquitin-like o	2e-11
cd01797	78	cd01797, NIRF_N, amino-terminal ubiquitin-like dom	7e-11
cd01810	74	cd01810, ISG15_repeat2, ISG15 ubiquitin-like prote	3e-10
TIGR00601	378	TIGR00601, rad23, UV excision repair protein Rad23	4e-10
cd01807	74	cd01807, GDX_N, ubiquitin-like domain of GDX	4e-10
COG5272	57	COG5272, UBI4, Ubiquitin [Posttranslational modifi	1e-09
cd01800	76	cd01800, SF3a120_C, Ubiquitin-like domain of Mamma	4e-08
cd01794	70	cd01794, DC_UbP_C, dendritic cell derived ubiquiti	2e-07
cd01797	78	cd01797, NIRF_N, amino-terminal ubiquitin-like dom	1e-06
cd01812	71	cd01812, BAG1_N, Ubiquitin-like domain of BAG1	3e-06
cd01794	70	cd01794, DC_UbP_C, dendritic cell derived ubiquiti	4e-06
cd12219	89	cd12219, UBL_TBK1_like, Ubiquitin-Like Domain Of H	4e-06
cd01808	71	cd01808, hPLIC_N, Ubiquitin-like domain of hPLIC-1	4e-06
cd01793	74	cd01793, Fubi, Fubi ubiquitin-like protein	1e-05
cd01796	71	cd01796, DDI1_N, DNA damage inducible protein 1 ub	2e-05
cd01792	80	cd01792, ISG15_repeat1, ISG15 ubiquitin-like prote	4e-05
cd01812	71	cd01812, BAG1_N, Ubiquitin-like domain of BAG1	7e-05
cd01808	71	cd01808, hPLIC_N, Ubiquitin-like domain of hPLIC-1	1e-04
cd01804	78	cd01804, midnolin_N, Ubiquitin-like domain of midn	2e-04
pfam13881	111	pfam13881, Rad60-SLD_2, Ubiquitin-2 like Rad60 SUM	4e-04
cd01804	78	cd01804, midnolin_N, Ubiquitin-like domain of midn	0.002
cd01763	87	cd01763, Sumo, Small ubiquitin-related modifier (S	0.002
cd01799	75	cd01799, Hoil1_N, Ubiquitin-like domain of HOIL1	0.002
cd01792	80	cd01792, ISG15_repeat1, ISG15 ubiquitin-like prote	0.003

>gnl|CDD|176398 cd01803, Ubiquitin, Ubiquitin

 Score =  148 bits (376), Expect = 9e-48
 Identities = 73/76 (96%), Positives = 75/76 (98%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

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

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

 Score =  134 bits (338), Expect = 6e-42
 Identities = 65/75 (86%), Positives = 70/75 (93%)

Query: 78  MIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNI 137
           +IKVKTLTGKEIEIDIEPTD +ERIKERVEEKEGIPP QQRLIY+GKQ+ DDKTA DY +
Sbjct: 2   LIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDDKTAADYKL 61

Query: 138 EGGSVLHLVLALRGG 152
           EGGSVLHLVLALRGG
Sbjct: 62  EGGSVLHLVLALRGG 76

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

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

 Score =  105 bits (264), Expect = 1e-30
 Identities = 47/72 (65%), Positives = 57/72 (79%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKTL GKTITLEV+ SDT+  +K KI +  GIPP+QQRLI+ GK LED RTLADY 
Sbjct: 1  IELTVKTLDGKTITLEVKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVLEDDRTLADYG 60

Query: 61 IQKESTLHLVLR 72
          IQ  ST+HLVLR
Sbjct: 61 IQDGSTIHLVLR 72

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

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

 Score =  105 bits (263), Expect = 1e-30
 Identities = 50/69 (72%), Positives = 57/69 (82%)

Query: 6  KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKES 65
          KTL GKTITLEV+ SDT+  +K KI+DKEGIP DQQRLIF+GK LED  TL++Y IQ  S
Sbjct: 1  KTLDGKTITLEVDPSDTVSELKEKIEDKEGIPVDQQRLIFSGKVLEDDTTLSEYGIQDGS 60

Query: 66 TLHLVLRLR 74
          TLHLVLRLR
Sbjct: 61 TLHLVLRLR 69

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

>gnl|CDD|176398 cd01803, Ubiquitin, Ubiquitin

 Score = 99.2 bits (247), Expect = 3e-28
 Identities = 48/74 (64%), Positives = 60/74 (81%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK I +++EP+DTIE +K ++++KEGIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62

Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 63  KESTLHLVLRLRGG 76

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

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

 Score = 96.0 bits (239), Expect = 6e-27
 Identities = 42/76 (55%), Positives = 59/76 (77%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ+ D +T ADY 
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDDKTAADYK 60

Query: 61 IQKESTLHLVLRLRGG 76
          ++  S LHLVL LRGG
Sbjct: 61 LEGGSVLHLVLALRGG 76

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

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

 Score = 95.4 bits (238), Expect = 7e-27
 Identities = 46/69 (66%), Positives = 54/69 (78%)

Query: 4  FVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQK 63
           VKTLTGKT  LEV   DT+  +KAKI  KEG+PP+QQRLI+AGK L+D +TL+DY IQ 
Sbjct: 1  TVKTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYAGKILKDDKTLSDYGIQD 60

Query: 64 ESTLHLVLR 72
           STLHLVLR
Sbjct: 61 GSTLHLVLR 69

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

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

 Score = 91.5 bits (228), Expect = 2e-25
 Identities = 39/69 (56%), Positives = 53/69 (76%)

Query: 82  KTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGS 141
           KTL GK I ++++P+DT+  +KE++E+KEGIP  QQRLI++GK L DD T  +Y I+ GS
Sbjct: 1   KTLDGKTITLEVDPSDTVSELKEKIEDKEGIPVDQQRLIFSGKVLEDDTTLSEYGIQDGS 60

Query: 142 VLHLVLALR 150
            LHLVL LR
Sbjct: 61  TLHLVLRLR 69

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

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

 Score = 90.4 bits (225), Expect = 9e-25
 Identities = 38/71 (53%), Positives = 51/71 (71%)

Query: 78  MIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNI 137
            + VKTL GK I ++++P+DT+  +KE++ E  GIPP QQRLIY GK L DD+T  DY I
Sbjct: 2   ELTVKTLDGKTITLEVKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVLEDDRTLADYGI 61

Query: 138 EGGSVLHLVLA 148
           + GS +HLVL 
Sbjct: 62  QDGSTIHLVLR 72

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

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

 Score = 86.8 bits (215), Expect = 2e-23
 Identities = 38/76 (50%), Positives = 52/76 (68%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQI +KTLTGK  +   E  +T+  VK  +Q+KEGI   Q RLI++GKQ+ D   L+DY 
Sbjct: 1  MQILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYSGKQMSDDLKLSDYK 60

Query: 61 IQKESTLHLVLRLRGG 76
          +   ST+H+VL+LRGG
Sbjct: 61 VVPGSTIHMVLQLRGG 76

Length = 76

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

 Score = 84.6 bits (210), Expect = 1e-22
 Identities = 41/68 (60%), Positives = 50/68 (73%)

Query: 80  KVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEG 139
            VKTLTGK  E+++ P DT+  +K ++  KEG+PP QQRLIYAGK L DDKT  DY I+ 
Sbjct: 1   TVKTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYAGKILKDDKTLSDYGIQD 60

Query: 140 GSVLHLVL 147
           GS LHLVL
Sbjct: 61  GSTLHLVL 68

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|185411 PTZ00044, PTZ00044, ubiquitin; Provisional

 Score = 82.2 bits (203), Expect = 2e-21
 Identities = 37/74 (50%), Positives = 53/74 (71%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I +KTLTGK+   + EP +T++++K  ++EKEGI   Q RLIY+GKQ++DD    DY + 
Sbjct: 3   ILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYSGKQMSDDLKLSDYKVV 62

Query: 139 GGSVLHLVLALRGG 152
            GS +H+VL LRGG
Sbjct: 63  PGSTIHMVLQLRGG 76

Length = 76

>gnl|CDD|176397 cd01802, AN1_N, ubiquitin-like domain of AN1

 Score = 78.8 bits (194), Expect = 7e-20
 Identities = 39/76 (51%), Positives = 50/76 (65%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           M++F++TLTG    L V   +T+ +VKAKIQ  EGIP  QQ LI+   +LED   L DYN
Sbjct: 28  MELFIETLTGTCFELRVSPFETVISVKAKIQRLEGIPVAQQHLIWNNMELEDEYCLNDYN 87

Query: 61  IQKESTLHLVLRLRGG 76
           I +  TL LVL +RGG
Sbjct: 88  ISEGCTLKLVLAMRGG 103

AN1 (also known as ANUBL1 and RSD-7) is ubiquitin-like protein with a testis-specific expression in rats that has an N-terminal ubiquitin-like domain and a C-terminal zinc-binding domain. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal ubiquitin-like domain of An1 does not undergo proteolytic processing. The function of AN1 is unknown. Length = 103

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

 Score = 73.7 bits (182), Expect = 2e-18
 Identities = 26/72 (36%), Positives = 46/72 (63%), Gaps = 1/72 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQ-RLIFAGKQLEDGRTLADY 59
          ++I +K   GK + ++V+ + T+  +    + K GIP DQQ RLIF G++L+   T+ADY
Sbjct: 1  IRIKLKGKDGKEVFIKVKPTTTLSKLINAYRKKRGIPADQQVRLIFDGERLDPNDTVADY 60

Query: 60 NIQKESTLHLVL 71
          +I+   T+ +V+
Sbjct: 61 DIEDGDTIDVVI 72

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|176400 cd01805, RAD23_N, Ubiquitin-like domain of RAD23

 Score = 68.5 bits (168), Expect = 3e-16
 Identities = 28/63 (44%), Positives = 44/63 (69%), Gaps = 2/63 (3%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLAD 58
          M+I  KTL  +T  +EV+  DT+  +K KI++++G   PP+QQ+LI++GK L+D  TL +
Sbjct: 1  MKITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKILKDDTTLEE 60

Query: 59 YNI 61
          Y I
Sbjct: 61 YKI 63

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

>gnl|CDD|176397 cd01802, AN1_N, ubiquitin-like domain of AN1

 Score = 69.1 bits (169), Expect = 4e-16
 Identities = 31/72 (43%), Positives = 45/72 (62%)

Query: 81  VKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGG 140
           ++TLTG   E+ + P +T+  +K +++  EGIP  QQ LI+   +L D+    DYNI  G
Sbjct: 32  IETLTGTCFELRVSPFETVISVKAKIQRLEGIPVAQQHLIWNNMELEDEYCLNDYNISEG 91

Query: 141 SVLHLVLALRGG 152
             L LVLA+RGG
Sbjct: 92  CTLKLVLAMRGG 103

AN1 (also known as ANUBL1 and RSD-7) is ubiquitin-like protein with a testis-specific expression in rats that has an N-terminal ubiquitin-like domain and a C-terminal zinc-binding domain. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal ubiquitin-like domain of An1 does not undergo proteolytic processing. The function of AN1 is unknown. Length = 103

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

 Score = 67.6 bits (166), Expect = 5e-16
 Identities = 31/68 (45%), Positives = 44/68 (64%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           IKVKTL  +     +E   T+  +KE++ E+ GIP  QQRLIY+G+ L DD+T  +Y +E
Sbjct: 3   IKVKTLDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYSGRVLKDDETLSEYKVE 62

Query: 139 GGSVLHLV 146
            G  +HLV
Sbjct: 63  DGHTIHLV 70

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

 Score = 65.7 bits (161), Expect = 4e-15
 Identities = 32/72 (44%), Positives = 50/72 (69%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          ++I VKTL  +T T  VE   T+ ++K KI ++ GIP +QQRLI++G+ L+D  TL++Y 
Sbjct: 1  IEIKVKTLDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYSGRVLKDDETLSEYK 60

Query: 61 IQKESTLHLVLR 72
          ++   T+HLV R
Sbjct: 61 VEDGHTIHLVKR 72

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

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

 Score = 64.9 bits (159), Expect = 6e-15
 Identities = 28/70 (40%), Positives = 44/70 (62%), Gaps = 1/70 (1%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQ-RLIYAGKQLADDKTARDYNI 137
           IK+K   GKE+ I ++PT T+ ++     +K GIP  QQ RLI+ G++L  + T  DY+I
Sbjct: 3   IKLKGKDGKEVFIKVKPTTTLSKLINAYRKKRGIPADQQVRLIFDGERLDPNDTVADYDI 62

Query: 138 EGGSVLHLVL 147
           E G  + +V+
Sbjct: 63  EDGDTIDVVI 72

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|176352 cd00196, UBQ, Ubiquitin-like proteins

 Score = 62.5 bits (152), Expect = 6e-14
 Identities = 32/69 (46%), Positives = 41/69 (59%)

Query: 4  FVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQK 63
           VK   GKT+ L V S  T+ ++K K+  K G+PP+QQRL+  GK L D  TL DY +Q 
Sbjct: 1  KVKLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGKILPDSLTLEDYGLQD 60

Query: 64 ESTLHLVLR 72
             L LV R
Sbjct: 61 GDELVLVPR 69

Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate. Length = 69

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

 Score = 61.7 bits (150), Expect = 1e-13
 Identities = 27/70 (38%), Positives = 46/70 (65%)

Query: 3  IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQ 62
          ++V+T TG T  +EV+    I  +K  +  ++G+PPDQ R+IFAGK+L +  T+ + ++ 
Sbjct: 1  VYVRTNTGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVIFAGKELRNTTTIQECDLG 60

Query: 63 KESTLHLVLR 72
          ++S LH V R
Sbjct: 61 QQSILHAVRR 70

parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain. Length = 70

>gnl|CDD|176388 cd01793, Fubi, Fubi ubiquitin-like protein

 Score = 61.3 bits (149), Expect = 2e-13
 Identities = 30/76 (39%), Positives = 43/76 (56%), Gaps = 2/76 (2%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQ+FV+     T TLEV   +T+ ++KA +   EGI  + Q L+ AG  LED  TL    
Sbjct: 1  MQLFVRAQ--NTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVLLLAGVPLEDDATLGQCG 58

Query: 61 IQKESTLHLVLRLRGG 76
          +++  TL +  RL GG
Sbjct: 59 VEELCTLEVAGRLLGG 74

Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8. Length = 74

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

 Score = 59.7 bits (145), Expect = 7e-13
 Identities = 28/62 (45%), Positives = 42/62 (67%), Gaps = 2/62 (3%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEG--IPPVQQRLIYAGKQLADDKTARDYN 136
           I  KTL  +   I+++P DT+  +KE++EE++G   PP QQ+LIY+GK L DD T  +Y 
Sbjct: 3   ITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKILKDDTTLEEYK 62

Query: 137 IE 138
           I+
Sbjct: 63  ID 64

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|233045 TIGR00601, rad23, UV excision repair protein Rad23

 Score = 64.1 bits (156), Expect = 8e-13
 Identities = 30/72 (41%), Positives = 50/72 (69%), Gaps = 4/72 (5%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEG---IPPVQQRLIYAGKQLADDKTARDY 135
           +  KTL  ++ +ID+EP +T++ +KE++E ++G    P  QQ+LIY+GK L+DDKT ++Y
Sbjct: 3   LTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVKEY 62

Query: 136 NI-EGGSVLHLV 146
            I E   V+ +V
Sbjct: 63  KIKEKDFVVVMV 74

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|176402 cd01807, GDX_N, ubiquitin-like domain of GDX

 Score = 59.5 bits (144), Expect = 1e-12
 Identities = 26/72 (36%), Positives = 45/72 (62%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M + VK L G+  +L+V   +++  +K  + +   +P +QQRL+F GK L D + L+DY+
Sbjct: 1  MFLTVKLLQGRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLLFKGKALADDKRLSDYS 60

Query: 61 IQKESTLHLVLR 72
          I   + L+LV+R
Sbjct: 61 IGPNAKLNLVVR 72

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|176352 cd00196, UBQ, Ubiquitin-like proteins

 Score = 58.3 bits (141), Expect = 2e-12
 Identities = 28/68 (41%), Positives = 40/68 (58%)

Query: 80  KVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEG 139
           KVK   GK +E+ +    T+  +KE++ +K G+PP QQRL+  GK L D  T  DY ++ 
Sbjct: 1   KVKLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGKILPDSLTLEDYGLQD 60

Query: 140 GSVLHLVL 147
           G  L LV 
Sbjct: 61  GDELVLVP 68

Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate. Length = 69

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

 Score = 56.7 bits (137), Expect = 1e-11
 Identities = 23/69 (33%), Positives = 42/69 (60%)

Query: 8  LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTL 67
          L G+ +   ++ SD +  +K KI ++ G+P  +Q+L + G  ++D  +LA YN+   + +
Sbjct: 5  LNGQMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQYEGIFIKDSNSLAYYNLANGTII 64

Query: 68 HLVLRLRGG 76
          HL L+ RGG
Sbjct: 65 HLQLKERGG 73

SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus. Length = 76

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

 Score = 55.9 bits (135), Expect = 2e-11
 Identities = 24/68 (35%), Positives = 46/68 (67%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           + V+T TG    ++++P   I+++KE V +++G+PP Q R+I+AGK+L +  T ++ ++ 
Sbjct: 1   VYVRTNTGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVIFAGKELRNTTTIQECDLG 60

Query: 139 GGSVLHLV 146
             S+LH V
Sbjct: 61  QQSILHAV 68

parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain. Length = 70

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

 Score = 54.8 bits (132), Expect = 7e-11
 Identities = 30/74 (40%), Positives = 47/74 (63%), Gaps = 2/74 (2%)

Query: 1  MQIFVKTLTGK-TITLEVESSDT-IDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLAD 58
          M I V+T+ GK T T++  S  T ++ ++ KIQ+   + P+ QRL + GKQ+EDG TL D
Sbjct: 1  MWIQVRTMDGKETRTVDSLSRLTKVEELREKIQELFNVEPECQRLFYRGKQMEDGHTLFD 60

Query: 59 YNIQKESTLHLVLR 72
          YN+     + L++R
Sbjct: 61 YNVGLNDIIQLLVR 74

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|176405 cd01810, ISG15_repeat2, ISG15 ubiquitin-like protein, second repeat of 2

 Score = 53.3 bits (128), Expect = 3e-10
 Identities = 24/74 (32%), Positives = 42/74 (56%)

Query: 3  IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQ 62
          I V+   G++   EV+ + T+  +K ++  +E +  DQ  L F G+ +ED   L +Y ++
Sbjct: 1  ILVRNDKGRSSIYEVQLTQTVATLKQQVSQRERVQADQFWLSFEGRPMEDEHPLGEYGLK 60

Query: 63 KESTLHLVLRLRGG 76
             T+ + LRLRGG
Sbjct: 61 PGCTVFMNLRLRGG 74

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. Length = 74

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

 Score = 56.4 bits (136), Expect = 4e-10
 Identities = 33/99 (33%), Positives = 53/99 (53%), Gaps = 10/99 (10%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLA 57
          M +  KTL  +   +++E  +T+  +K KI+ ++G    P  QQ+LI++GK L D +T+ 
Sbjct: 1  MTLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVK 60

Query: 58 DYNIQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPT 96
          +Y I KE    +V+      + K KT TGK       PT
Sbjct: 61 EYKI-KEKDFVVVM------VSKPKTGTGKVAPPAATPT 92

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|176402 cd01807, GDX_N, ubiquitin-like domain of GDX

 Score = 52.6 bits (126), Expect = 4e-10
 Identities = 26/69 (37%), Positives = 42/69 (60%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           + VK L G+E  + +   +++  +K+ V E   +P  QQRL++ GK LADDK   DY+I 
Sbjct: 3   LTVKLLQGRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLLFKGKALADDKRLSDYSIG 62

Query: 139 GGSVLHLVL 147
             + L+LV+
Sbjct: 63  PNAKLNLVV 71

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|227597 COG5272, UBI4, Ubiquitin [Posttranslational modification, protein turnover, chaperones]

 Score = 50.6 bits (121), Expect = 1e-09
 Identities = 10/56 (17%), Positives = 19/56 (33%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL 56
              +K  TG     E + +   D    K   ++    ++  L+   + LE  R  
Sbjct: 1  DAKPIKKATGGAAKPESQLAKAKDTRPEKQYAEQDSQLNEMALMDCERNLEASRIS 56

Length = 57

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

 Score = 47.4 bits (113), Expect = 4e-08
 Identities = 21/69 (30%), Positives = 40/69 (57%)

Query: 84  LTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVL 143
           L G+ +   ++ +D +  +K ++ E+ G+P  +Q+L Y G  + D  +   YN+  G+++
Sbjct: 5   LNGQMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQYEGIFIKDSNSLAYYNLANGTII 64

Query: 144 HLVLALRGG 152
           HL L  RGG
Sbjct: 65  HLQLKERGG 73

SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus. Length = 76

>gnl|CDD|176389 cd01794, DC_UbP_C, dendritic cell derived ubiquitin-like protein

 Score = 45.2 bits (107), Expect = 2e-07
 Identities = 25/67 (37%), Positives = 39/67 (58%)

Query: 5  VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKE 64
          V+  TGK + L V S DT+  +K ++Q  EG+ P  QR  F+GK L D   L +  IQK+
Sbjct: 3  VRLSTGKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWFFSGKLLTDKTRLQETKIQKD 62

Query: 65 STLHLVL 71
            + +++
Sbjct: 63 YVVQVIV 69

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. Length = 70

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

 Score = 43.7 bits (103), Expect = 1e-06
 Identities = 22/61 (36%), Positives = 35/61 (57%), Gaps = 2/61 (3%)

Query: 79  IKVKTLTGKEIEI--DIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYN 136
           I+V+T+ GKE      +     +E ++E+++E   + P  QRL Y GKQ+ D  T  DYN
Sbjct: 3   IQVRTMDGKETRTVDSLSRLTKVEELREKIQELFNVEPECQRLFYRGKQMEDGHTLFDYN 62

Query: 137 I 137
           +
Sbjct: 63  V 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|176407 cd01812, BAG1_N, Ubiquitin-like domain of BAG1

 Score = 42.3 bits (100), Expect = 3e-06
 Identities = 18/61 (29%), Positives = 32/61 (52%)

Query: 10 GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHL 69
          G++  L + S  T  ++K  +    G+ P  Q+LIF GK+ +D  TL    ++  S + L
Sbjct: 9  GESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIFKGKERDDAETLDMSGVKDGSKVML 68

Query: 70 V 70
          +
Sbjct: 69 L 69

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). Length = 71

>gnl|CDD|176389 cd01794, DC_UbP_C, dendritic cell derived ubiquitin-like protein

 Score = 41.8 bits (98), Expect = 4e-06
 Identities = 19/69 (27%), Positives = 43/69 (62%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           +KV+  TGK++++ +   DT+ ++K++++  EG+ P  QR  ++GK L D    ++  I+
Sbjct: 1   LKVRLSTGKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWFFSGKLLTDKTRLQETKIQ 60

Query: 139 GGSVLHLVL 147
              V+ +++
Sbjct: 61  KDYVVQVIV 69

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. Length = 70

>gnl|CDD|240618 cd12219, UBL_TBK1_like, Ubiquitin-Like Domain Of Human Tbk1 and similar proteins

 Score = 42.6 bits (101), Expect = 4e-06
 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 89  IEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKT--ARDYN 136
            ++ I P +T+   +E V E+  +PP  Q L+Y G+ L  + +  A+ Y 
Sbjct: 26  HKVYIHPEETLVNFQELVFEQTEVPPSNQELLYEGEHLVLEPSTPAKHYP 75

This family contains ubiquitin-like domain (UBL) found in TANK-binding kinase 1 (TBK1) and similar proteins. TBK1 regulates factors such as IRF3 and IRF7, promoting antiviral activity in the interferon signaling pathways. In addition to the central UBL, these proteins have an N-terminal kinase domain and a C-terminal elongated helical domain. The ubiquitin-like domain acts as a protein-protein interaction domain, and has been implicated in regulating kinase activity, which modulates interactions in the IFN pathway. Length = 89

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

 Score = 42.1 bits (99), Expect = 4e-06
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKT   K   +E+    ++ + K  +  K     +Q  LIFAGK L+D  TL  +N
Sbjct: 1  IKVTVKTPKDKE-EIEIAEDASVKDFKEAVSKKFKANQEQLVLIFAGKILKDTDTLTQHN 59

Query: 61 IQKESTLHLVLR 72
          I+   T+HLV++
Sbjct: 60 IKDGLTVHLVIK 71

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

>gnl|CDD|176388 cd01793, Fubi, Fubi ubiquitin-like protein

 Score = 40.9 bits (96), Expect = 1e-05
 Identities = 20/62 (32%), Positives = 28/62 (45%)

Query: 91  IDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALR 150
           +++   +T+  IK  V   EGI    Q L+ AG  L DD T     +E    L +   L 
Sbjct: 13  LEVTGQETVSDIKAHVAGLEGIDVEDQVLLLAGVPLEDDATLGQCGVEELCTLEVAGRLL 72

Query: 151 GG 152
           GG
Sbjct: 73  GG 74

Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8. Length = 74

>gnl|CDD|176391 cd01796, DDI1_N, DNA damage inducible protein 1 ubiquitin-like domain

 Score = 40.0 bits (94), Expect = 2e-05
 Identities = 19/54 (35%), Positives = 34/54 (62%), Gaps = 1/54 (1%)

Query: 10 GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQL-EDGRTLADYNIQ 62
            T +L+V+    ++N KA  + + GIP  QQ+LI+ G++L ++ R LA Y ++
Sbjct: 9  ETTFSLDVDPDLELENFKALCEAESGIPASQQQLIYNGRELVDNKRLLALYGVK 62

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. Length = 71

>gnl|CDD|176387 cd01792, ISG15_repeat1, ISG15 ubiquitin-like protein, first repeat of 2

 Score = 39.5 bits (92), Expect = 4e-05
 Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 2/70 (2%)

Query: 5  VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA--GKQLEDGRTLADYNIQ 62
          VK L G    + +  S T+  +K +I  K G+P  QQRL      + L+DG  L    + 
Sbjct: 7  VKMLGGNEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLAHLDSREVLQDGVPLVSQGLG 66

Query: 63 KESTLHLVLR 72
            ST+ LV++
Sbjct: 67 PGSTVLLVVQ 76

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. Length = 80

>gnl|CDD|176407 cd01812, BAG1_N, Ubiquitin-like domain of BAG1

 Score = 38.8 bits (91), Expect = 7e-05
 Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 1/68 (1%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           ++VK   G+  ++ I    T   +K+ +    G+ P  Q+LI+ GK+  D +T     ++
Sbjct: 3   VRVKH-GGESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIFKGKERDDAETLDMSGVK 61

Query: 139 GGSVLHLV 146
            GS + L+
Sbjct: 62  DGSKVMLL 69

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). Length = 71

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

 Score = 38.2 bits (89), Expect = 1e-04
 Identities = 27/69 (39%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           + VKT   KE EI+I    +++  KE V +K      Q  LI+AGK L D  T   +NI+
Sbjct: 3   VTVKTPKDKE-EIEIAEDASVKDFKEAVSKKFKANQEQLVLIFAGKILKDTDTLTQHNIK 61

Query: 139 GGSVLHLVL 147
            G  +HLV+
Sbjct: 62  DGLTVHLVI 70

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

>gnl|CDD|176399 cd01804, midnolin_N, Ubiquitin-like domain of midnolin

 Score = 37.8 bits (88), Expect = 2e-04
 Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 1/78 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M + + + TG    L V   +T++ +K +I  +  +P ++  L+    +L  G  L D  
Sbjct: 2  MNLNIHSTTGTRFDLSVPPDETVEGLKKRISQRLKVPKERLALLHRETRLSSG-KLQDLG 60

Query: 61 IQKESTLHLVLRLRGGTM 78
          +   S L LV  +  G M
Sbjct: 61 LGDGSKLTLVPTVEAGLM 78

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. Length = 78

>gnl|CDD|206052 pfam13881, Rad60-SLD_2, Ubiquitin-2 like Rad60 SUMO-like

 Score = 37.7 bits (88), Expect = 4e-04
 Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 13/68 (19%)

Query: 18 ESSDTIDNVKAKI-----QDKEGIP--PDQQRLIFAGKQLEDGRTLADYNI------QKE 64
            + T+ ++K K+     +DKE  P  P+  +LI AGK LE+ +TL +  +         
Sbjct: 21 SPATTVADLKEKVLAQWPKDKEEGPKSPNDVKLINAGKILENNKTLGECRLPAGETPGGV 80

Query: 65 STLHLVLR 72
            +H+V+R
Sbjct: 81 IVMHVVVR 88

Length = 111

>gnl|CDD|176399 cd01804, midnolin_N, Ubiquitin-like domain of midnolin

 Score = 35.2 bits (81), Expect = 0.002
 Identities = 18/74 (24%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           + + + TG   ++ + P +T+E +K+R+ ++  +P  +  L++   +L+  K  +D  + 
Sbjct: 4   LNIHSTTGTRFDLSVPPDETVEGLKKRISQRLKVPKERLALLHRETRLSSGKL-QDLGLG 62

Query: 139 GGSVLHLVLALRGG 152
            GS L LV  +  G
Sbjct: 63  DGSKLTLVPTVEAG 76

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. Length = 78

>gnl|CDD|176359 cd01763, Sumo, Small ubiquitin-related modifier (SUMO)

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 18/75 (24%), Positives = 41/75 (54%)

Query: 78  MIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNI 137
            +KVK   G E+   I+ +  ++++ E   +++G+     R ++ G+++ D++T  D  +
Sbjct: 13  NLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLFDGQRIRDNQTPDDLGM 72

Query: 138 EGGSVLHLVLALRGG 152
           E G  + ++L   GG
Sbjct: 73  EDGDEIEVMLEQTGG 87

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. Length = 87

>gnl|CDD|176394 cd01799, Hoil1_N, Ubiquitin-like domain of HOIL1

 Score = 35.2 bits (81), Expect = 0.002
 Identities = 16/51 (31%), Positives = 23/51 (45%)

Query: 12 TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQ 62
          TI L V    T+  +K K+    G PP  QR +   +   D  TL  + I+
Sbjct: 14 TIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRWVIGQRLARDQETLYSHGIR 64

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. Length = 75

>gnl|CDD|176387 cd01792, ISG15_repeat1, ISG15 ubiquitin-like protein, first repeat of 2

 Score = 34.9 bits (80), Expect = 0.003
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 2/71 (2%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYA--GKQLADDKTARDYN 136
           +KVK L G E  + +  + T+  +K+++ +K G+P  QQRL +    + L D        
Sbjct: 5   LKVKMLGGNEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLAHLDSREVLQDGVPLVSQG 64

Query: 137 IEGGSVLHLVL 147
           +  GS + LV+
Sbjct: 65  LGPGSTVLLVV 75

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. Length = 80

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	154
cd01802	103	AN1_N ubiquitin-like domain of AN1. AN1 (also know	99.9
cd01793	74	Fubi Fubi ubiquitin-like protein. Fubi is a ubiqui	99.85
PTZ00044	76	ubiquitin; Provisional	99.84
cd01806	76	Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also kn	99.83
cd01803	76	Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40	99.83
cd01810	74	ISG15_repeat2 ISG15 ubiquitin-like protein, second	99.83
cd01807	74	GDX_N ubiquitin-like domain of GDX. GDX contains a	99.83
cd01804	78	midnolin_N Ubiquitin-like domain of midnolin. midn	99.82
cd01807	74	GDX_N ubiquitin-like domain of GDX. GDX contains a	99.82
PTZ00044	76	ubiquitin; Provisional	99.8
cd01791	73	Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also know	99.79
cd01793	74	Fubi Fubi ubiquitin-like protein. Fubi is a ubiqui	99.79
cd01797	78	NIRF_N amino-terminal ubiquitin-like domain of Np9	99.79
cd01791	73	Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also know	99.79
cd01797	78	NIRF_N amino-terminal ubiquitin-like domain of Np9	99.79
cd01794	70	DC_UbP_C dendritic cell derived ubiquitin-like pro	99.79
cd01806	76	Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also kn	99.79
cd01802	103	AN1_N ubiquitin-like domain of AN1. AN1 (also know	99.78
cd01803	76	Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40	99.78
cd01805	77	RAD23_N Ubiquitin-like domain of RAD23. RAD23 belo	99.77
cd01800	76	SF3a120_C Ubiquitin-like domain of Mammalian splic	99.77
cd01804	78	midnolin_N Ubiquitin-like domain of midnolin. midn	99.77
cd01805	77	RAD23_N Ubiquitin-like domain of RAD23. RAD23 belo	99.77
cd01763	87	Sumo Small ubiquitin-related modifier (SUMO). Smal	99.77
cd01798	70	parkin_N amino-terminal ubiquitin-like of parkin p	99.76
cd01794	70	DC_UbP_C dendritic cell derived ubiquitin-like pro	99.76
cd01809	72	Scythe_N Ubiquitin-like domain of Scythe protein.	99.76
PF00240	69	ubiquitin: Ubiquitin family; InterPro: IPR000626 U	99.76
cd01809	72	Scythe_N Ubiquitin-like domain of Scythe protein.	99.76
cd01810	74	ISG15_repeat2 ISG15 ubiquitin-like protein, second	99.75
cd01792	80	ISG15_repeat1 ISG15 ubiquitin-like protein, first	99.74
cd01792	80	ISG15_repeat1 ISG15 ubiquitin-like protein, first	99.74
cd01798	70	parkin_N amino-terminal ubiquitin-like of parkin p	99.73
PF00240	69	ubiquitin: Ubiquitin family; InterPro: IPR000626 U	99.73
cd01808	71	hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC	99.72
cd01796	71	DDI1_N DNA damage inducible protein 1 ubiquitin-li	99.71
KOG0003	128	consensus Ubiquitin/60s ribosomal protein L40 fusi	99.71
cd01808	71	hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC	99.7
cd01812	71	BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-ter	99.7
cd01790	79	Herp_N Homocysteine-responsive endoplasmic reticul	99.69
cd01813	74	UBP_N UBP ubiquitin processing protease. The UBP (	99.69
KOG0004	156	consensus Ubiquitin/40S ribosomal protein S27a fus	99.69
cd01796	71	DDI1_N DNA damage inducible protein 1 ubiquitin-li	99.69
cd01812	71	BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-ter	99.68
KOG0005	70	consensus Ubiquitin-like protein [Cell cycle contr	99.68
cd01813	74	UBP_N UBP ubiquitin processing protease. The UBP (	99.68
cd01790	79	Herp_N Homocysteine-responsive endoplasmic reticul	99.67
cd01800	76	SF3a120_C Ubiquitin-like domain of Mammalian splic	99.66
cd01763	87	Sumo Small ubiquitin-related modifier (SUMO). Smal	99.62
KOG0005	70	consensus Ubiquitin-like protein [Cell cycle contr	99.62
smart00213	64	UBQ Ubiquitin homologues. Ubiquitin-mediated prote	99.61
smart00213	64	UBQ Ubiquitin homologues. Ubiquitin-mediated prote	99.59
cd01799	75	Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HO	99.57
KOG0004	156	consensus Ubiquitin/40S ribosomal protein S27a fus	99.56
KOG0003	128	consensus Ubiquitin/60s ribosomal protein L40 fusi	99.56
cd01799	75	Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HO	99.55
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	99.55
TIGR00601	378	rad23 UV excision repair protein Rad23. All protei	99.54
PF11976	72	Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; Inter	99.53
cd01815	75	BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC	99.52
cd01769	69	UBL Ubiquitin-like domain of UBL. UBLs function by	99.49
PF11976	72	Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; Inter	99.47
cd01795	107	USP48_C USP ubiquitin-specific protease. The USP (	99.44
cd01769	69	UBL Ubiquitin-like domain of UBL. UBLs function by	99.44
KOG0010	493	consensus Ubiquitin-like protein [Posttranslationa	99.43
cd01815	75	BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC	99.43
cd01795	107	USP48_C USP ubiquitin-specific protease. The USP (	99.42
KOG0010	493	consensus Ubiquitin-like protein [Posttranslationa	99.38
cd01814	113	NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and AT	99.38
cd01814	113	NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and AT	99.37
KOG0011	340	consensus Nucleotide excision repair factor NEF2,	99.35
KOG0011	340	consensus Nucleotide excision repair factor NEF2,	99.3
cd01789	84	Alp11_N Ubiquitin-like domain of Alp11 tubulin-fol	99.28
cd01789	84	Alp11_N Ubiquitin-like domain of Alp11 tubulin-fol	99.28
PF14560	87	Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2K	99.22
PF14560	87	Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2K	99.19
cd01811	80	OASL_repeat1 2'-5' oligoadenylate synthetase-like	99.18
cd01788	119	ElonginB Ubiquitin-like domain of Elongin B. Elong	99.16
KOG1769	99	consensus Ubiquitin-like proteins [Posttranslation	99.12
PLN02560	308	enoyl-CoA reductase	99.04
KOG0001	75	consensus Ubiquitin and ubiquitin-like proteins [P	99.03
PLN02560	308	enoyl-CoA reductase	99.02
PF11543	80	UN_NPL4: Nuclear pore localisation protein NPL4; I	99.01
KOG4248	1143	consensus Ubiquitin-like protein, regulator of apo	98.99
cd01788	119	ElonginB Ubiquitin-like domain of Elongin B. Elong	98.96
PF13881	111	Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB	98.95
KOG0001	75	consensus Ubiquitin and ubiquitin-like proteins [P	98.92
cd01801	77	Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-	98.89
PF13881	111	Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB	98.86
KOG4248	1143	consensus Ubiquitin-like protein, regulator of apo	98.83
cd01801	77	Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-	98.82
PF11543	80	UN_NPL4: Nuclear pore localisation protein NPL4; I	98.79
cd00196	69	UBQ Ubiquitin-like proteins. Ubiquitin homologs; I	98.71
KOG3493	73	consensus Ubiquitin-like protein [Posttranslationa	98.63
COG5227	103	SMT3 Ubiquitin-like protein (sentrin) [Posttransla	98.6
cd00196	69	UBQ Ubiquitin-like proteins. Ubiquitin homologs; I	98.56
KOG1769	99	consensus Ubiquitin-like proteins [Posttranslation	98.53
KOG3493	73	consensus Ubiquitin-like protein [Posttranslationa	98.46
KOG1872	473	consensus Ubiquitin-specific protease [Posttransla	98.36
cd01811	80	OASL_repeat1 2'-5' oligoadenylate synthetase-like	98.32
PF11470	65	TUG-UBL1: GLUT4 regulating protein TUG; InterPro:	98.3
KOG1872	473	consensus Ubiquitin-specific protease [Posttransla	98.23
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	98.2
KOG4495	110	consensus RNA polymerase II transcription elongati	98.18
PF13019	162	Telomere_Sde2: Telomere stability and silencing	98.07
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	98.02
PF08817	79	YukD: WXG100 protein secretion system (Wss), prote	97.99
KOG4495	110	consensus RNA polymerase II transcription elongati	97.98
PF08817	79	YukD: WXG100 protein secretion system (Wss), prote	97.89
PF00789	82	UBX: UBX domain; InterPro: IPR001012 The UBX domai	97.89
PF10302	97	DUF2407: DUF2407 ubiquitin-like domain; InterPro:	97.86
COG5227	103	SMT3 Ubiquitin-like protein (sentrin) [Posttransla	97.86
COG5417	81	Uncharacterized small protein [Function unknown]	97.79
smart00166	80	UBX Domain present in ubiquitin-regulatory protein	97.76
PF11470	65	TUG-UBL1: GLUT4 regulating protein TUG; InterPro:	97.75
PF00789	82	UBX: UBX domain; InterPro: IPR001012 The UBX domai	97.72
cd01772	79	SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-subst	97.6
cd01773	82	Faf1_like1_UBX Faf1 ike-1 UBX domain. Faf1_like1 i	97.56
smart00166	80	UBX Domain present in ubiquitin-regulatory protein	97.47
cd01767	77	UBX UBX (ubiquitin regulatory X) domain. The UBX (	97.42
cd01771	80	Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated fac	97.42
cd01774	85	Faf1_like2_UBX Faf1 ike-2 UBX domain. Faf1_like2 i	97.4
cd01770	79	p47_UBX p47-like ubiquitin domain. p47_UBX p47 is	97.35
COG5417	81	Uncharacterized small protein [Function unknown]	97.33
cd01772	79	SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-subst	97.26
PF14533	213	USP7_C2: Ubiquitin-specific protease C-terminal; P	97.24
KOG3206	234	consensus Alpha-tubulin folding cofactor B [Posttr	97.23
KOG1639	297	consensus Steroid reductase required for elongatio	97.21
PF10302	97	DUF2407: DUF2407 ubiquitin-like domain; InterPro:	97.18
KOG0013	231	consensus Uncharacterized conserved protein [Funct	97.17
PF12436	249	USP7_ICP0_bdg: ICP0-binding domain of Ubiquitin-sp	97.13
KOG0013	231	consensus Uncharacterized conserved protein [Funct	97.11
cd01770	79	p47_UBX p47-like ubiquitin domain. p47_UBX p47 is	97.1
cd01773	82	Faf1_like1_UBX Faf1 ike-1 UBX domain. Faf1_like1 i	97.1
cd01767	77	UBX UBX (ubiquitin regulatory X) domain. The UBX (	97.09
PF13019	162	Telomere_Sde2: Telomere stability and silencing	96.91
PRK06437	67	hypothetical protein; Provisional	96.91
KOG1639	297	consensus Steroid reductase required for elongatio	96.87
cd01774	85	Faf1_like2_UBX Faf1 ike-2 UBX domain. Faf1_like2 i	96.78
KOG3206	234	consensus Alpha-tubulin folding cofactor B [Posttr	96.76
cd01771	80	Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated fac	96.69
cd00754	80	MoaD Ubiquitin domain of MoaD-like proteins. MoaD	96.64
PF09379	80	FERM_N: FERM N-terminal domain ; InterPro: IPR0189	96.58
PF15044	76	CLU_N: Mitochondrial function, CLU-N-term	96.49
PF10790	76	DUF2604: Protein of Unknown function (DUF2604); In	96.45
PRK08364	70	sulfur carrier protein ThiS; Provisional	96.4
PF12754	309	Blt1: Cell-cycle control medial ring component; In	96.37
PRK06488	65	sulfur carrier protein ThiS; Validated	96.26
KOG4583	391	consensus Membrane-associated ER protein involved	96.25
cd06409	86	PB1_MUG70 The MUG70 protein is a product of the me	96.21
cd06407	82	PB1_NLP A PB1 domain is present in NIN like protei	95.96
cd06406	80	PB1_P67 A PB1 domain is present in p67 proteins wh	95.88
cd06406	80	PB1_P67 A PB1 domain is present in p67 proteins wh	95.74
PF11620	88	GABP-alpha: GA-binding protein alpha chain; InterP	95.7
cd00565	65	ThiS ThiaminS ubiquitin-like sulfur carrier protei	95.65
cd06407	82	PB1_NLP A PB1 domain is present in NIN like protei	95.63
PF09379	80	FERM_N: FERM N-terminal domain ; InterPro: IPR0189	95.6
cd06409	86	PB1_MUG70 The MUG70 protein is a product of the me	95.59
TIGR01683	64	thiS thiamine biosynthesis protein ThiS. This mode	95.5
TIGR01682	80	moaD molybdopterin converting factor, subunit 1, n	95.47
PLN02799	82	Molybdopterin synthase sulfur carrier subunit	95.45
PF14836	88	Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A	95.32
KOG4583	391	consensus Membrane-associated ER protein involved	95.31
PF02597	77	ThiS: ThiS family; InterPro: IPR003749 ThiS (thiam	95.28
TIGR01687	88	moaD_arch MoaD family protein, archaeal. Members o	95.23
PRK06437	67	hypothetical protein; Provisional	94.93
PF11620	88	GABP-alpha: GA-binding protein alpha chain; InterP	94.93
smart00666	81	PB1 PB1 domain. Phox and Bem1p domain, present in	94.79
smart00455	70	RBD Raf-like Ras-binding domain.	94.65
cd01760	72	RBD Ubiquitin-like domain of RBD-like S/T kinases.	94.46
PRK05863	65	sulfur carrier protein ThiS; Provisional	94.37
cd06408	86	PB1_NoxR The PB1 domain is present in the Epichloe	94.19
PF14836	88	Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A	94.17
smart00666	81	PB1 PB1 domain. Phox and Bem1p domain, present in	94.14
smart00295	207	B41 Band 4.1 homologues. Also known as ezrin/radix	94.02
PF15044	76	CLU_N: Mitochondrial function, CLU-N-term	93.83
PRK05659	66	sulfur carrier protein ThiS; Validated	93.5
PF10790	76	DUF2604: Protein of Unknown function (DUF2604); In	93.42
PRK06944	65	sulfur carrier protein ThiS; Provisional	93.18
KOG2982	418	consensus Uncharacterized conserved protein [Funct	93.17
PRK08053	66	sulfur carrier protein ThiS; Provisional	93.07
PRK06083	84	sulfur carrier protein ThiS; Provisional	92.99
PRK07696	67	sulfur carrier protein ThiS; Provisional	92.97
cd06408	86	PB1_NoxR The PB1 domain is present in the Epichloe	92.73
PRK07440	70	hypothetical protein; Provisional	92.66
KOG0012	380	consensus DNA damage inducible protein [Replicatio	92.64
cd01760	72	RBD Ubiquitin-like domain of RBD-like S/T kinases.	92.54
KOG2689	290	consensus Predicted ubiquitin regulatory protein [	92.28
KOG0012	380	consensus DNA damage inducible protein [Replicatio	92.27
cd00754	80	MoaD Ubiquitin domain of MoaD-like proteins. MoaD	92.16
smart00455	70	RBD Raf-like Ras-binding domain.	92.06
PF00564	84	PB1: PB1 domain; InterPro: IPR000270 The Phox and	92.05
PF02196	71	RBD: Raf-like Ras-binding domain; InterPro: IPR003	92.01
PF12754	309	Blt1: Cell-cycle control medial ring component; In	91.7
PRK08364	70	sulfur carrier protein ThiS; Provisional	91.33
cd06411	78	PB1_p51 The PB1 domain is present in the p51 prote	91.08
cd05992	81	PB1 The PB1 domain is a modular domain mediating s	91.07
KOG2086	380	consensus Protein tyrosine phosphatase SHP1/Cofact	90.95
cd05992	81	PB1 The PB1 domain is a modular domain mediating s	90.88
PF14453	57	ThiS-like: ThiS-like ubiquitin	90.85
PF00564	84	PB1: PB1 domain; InterPro: IPR000270 The Phox and	90.78
COG2104	68	ThiS Sulfur transfer protein involved in thiamine	90.75
KOG4261	1003	consensus Talin [Cytoskeleton]	90.68
TIGR02958	452	sec_mycoba_snm4 secretion protein snm4. Members of	90.67
PF14453	57	ThiS-like: ThiS-like ubiquitin	90.54
PLN02799	82	Molybdopterin synthase sulfur carrier subunit	90.08
cd06396	81	PB1_NBR1 The PB1 domain is an essential part of NB	90.08
COG5100	571	NPL4 Nuclear pore protein [Nuclear structure]	89.92
PF10209	122	DUF2340: Uncharacterized conserved protein (DUF234	89.81
cd06396	81	PB1_NBR1 The PB1 domain is an essential part of NB	89.8
cd01764	94	Urm1 Urm1-like ubuitin domain. Urm1 (Ubiquitin-Rel	89.55
cd06398	91	PB1_Joka2 The PB1 domain is present in the Nicotia	89.22
PF10209	122	DUF2340: Uncharacterized conserved protein (DUF234	89.21
PRK11130	81	moaD molybdopterin synthase small subunit; Provisi	88.91
cd01787	85	GRB7_RA RA (RAS-associated like) domain of Grb7. G	88.83
cd06411	78	PB1_p51 The PB1 domain is present in the p51 prote	88.39
cd01818	77	TIAM1_RBD Ubiquitin domain of Tiam1 guanine nucleo	88.25
KOG2086	380	consensus Protein tyrosine phosphatase SHP1/Cofact	88.23
cd01787	85	GRB7_RA RA (RAS-associated like) domain of Grb7. G	87.99
cd01766	82	Ufm1 Urm1-like ubiquitin domain. Ufm1 (ubiquitin-f	87.36
PF08825	84	E2_bind: E2 binding domain; InterPro: IPR014929 E1	87.14
PF02196	71	RBD: Raf-like Ras-binding domain; InterPro: IPR003	86.71
PF14451	81	Ub-Mut7C: Mut7-C ubiquitin	86.51
PF03671	76	Ufm1: Ubiquitin fold modifier 1 protein; InterPro:	86.47
cd01817	73	RGS12_RBD Ubiquitin domain of RGS12 and RGS14. RGS	86.33
PTZ00380	121	microtubule-associated protein (MAP); Provisional	86.27
PRK06488	65	sulfur carrier protein ThiS; Validated	85.95
TIGR02958	452	sec_mycoba_snm4 secretion protein snm4. Members of	85.75
smart00295	207	B41 Band 4.1 homologues. Also known as ezrin/radix	85.67
cd01777	87	SNX27_RA Ubiquitin domain of SNX27 (sorting nexin	85.58
cd06410	97	PB1_UP2 Uncharacterized protein 2. The PB1 domain	85.49
KOG4250	732	consensus TANK binding protein kinase TBK1 [Signal	85.18
cd01775	97	CYR1_RA Ubiquitin domain of CYR1 adenylate cyclase	85.16
cd01768	87	RA RA (Ras-associating) ubiquitin domain. The RA (	84.82
PF08825	84	E2_bind: E2 binding domain; InterPro: IPR014929 E1	84.8
TIGR01687	88	moaD_arch MoaD family protein, archaeal. Members o	84.6
KOG2689	290	consensus Predicted ubiquitin regulatory protein [	84.53
KOG4250	732	consensus TANK binding protein kinase TBK1 [Signal	84.47
PF08337	539	Plexin_cytopl: Plexin cytoplasmic RasGAP domain; I	84.42
PF02597	77	ThiS: ThiS family; InterPro: IPR003749 ThiS (thiam	84.27
PF00788	93	RA: Ras association (RalGDS/AF-6) domain; InterPro	84.17
PRK11840	326	bifunctional sulfur carrier protein/thiazole synth	83.23
KOG2982	418	consensus Uncharacterized conserved protein [Funct	83.02
cd01775	97	CYR1_RA Ubiquitin domain of CYR1 adenylate cyclase	82.7
PF12436	249	USP7_ICP0_bdg: ICP0-binding domain of Ubiquitin-sp	82.45
KOG4572	1424	consensus Predicted DNA-binding transcription fact	82.37
TIGR01682	80	moaD molybdopterin converting factor, subunit 1, n	82.35
KOG3439	116	consensus Protein conjugation factor involved in a	82.33
KOG2561	568	consensus Adaptor protein NUB1, contains UBA domai	82.26
cd00565	65	ThiS ThiaminS ubiquitin-like sulfur carrier protei	82.12
PF00788	93	RA: Ras association (RalGDS/AF-6) domain; InterPro	81.89
cd06398	91	PB1_Joka2 The PB1 domain is present in the Nicotia	81.66
cd06410	97	PB1_UP2 Uncharacterized protein 2. The PB1 domain	81.25
PF11834	69	DUF3354: Domain of unknown function (DUF3354); Int	81.01
TIGR01683	64	thiS thiamine biosynthesis protein ThiS. This mode	80.58
PF02017	78	CIDE-N: CIDE-N domain; InterPro: IPR003508 This do	80.4

>cd01802 AN1_N ubiquitin-like domain of AN1

Probab=99.90  E-value=5.8e-23  Score=129.12  Aligned_cols=97  Identities=35%  Similarity=0.577  Sum_probs=92.4

Q ss_pred             ecccccccccceeeeeeeecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCccccc
Q 040824           56 LADYNIQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDY  135 (154)
Q Consensus        56 l~~~~i~~~~~i~l~~~~~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~  135 (154)
                      .-.|++.+-.+++++++..+.|+|+|+...|+++.+++++++||++||++|++..|+|++.|+|+|+|+.|+|+.+|++|
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~~M~I~Vk~l~G~~~~leV~~~~TV~~lK~kI~~~~gip~~~QrLi~~Gk~L~D~~tL~dy   86 (103)
T cd01802           7 PPFFNEDNMGPFHYKLPFYDTMELFIETLTGTCFELRVSPFETVISVKAKIQRLEGIPVAQQHLIWNNMELEDEYCLNDY   86 (103)
T ss_pred             CCccccCCcceeEEeeccCCCEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEECCEECCCCCcHHHc
Confidence            34567778889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCEEEEEEeecCC
Q 040824          136 NIEGGSVLHLVLALRGG  152 (154)
Q Consensus       136 ~i~~~~~i~~~~~~~gg  152 (154)
                      +|++|++|++.++++||
T Consensus        87 ~I~~~stL~l~~~l~GG  103 (103)
T cd01802          87 NISEGCTLKLVLAMRGG  103 (103)
T ss_pred             CCCCCCEEEEEEecCCC
Confidence            99999999999999997

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.

>cd01793 Fubi Fubi ubiquitin-like protein

Probab=99.85  E-value=7.5e-21  Score=113.23  Aligned_cols=74  Identities=28%  Similarity=0.374  Sum_probs=70.2

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      |+|+|+.  ++++.+++++++||++||++|++..|+|++.|+|+|+|+.|+|+.+|++|+++++++|++.++++||
T Consensus         1 mqi~vk~--~~~~~l~v~~~~tV~~lK~~i~~~~gip~~~q~Li~~Gk~L~D~~tL~~~~i~~~~tl~l~~~l~GG   74 (74)
T cd01793           1 MQLFVRA--QNTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVLLLAGVPLEDDATLGQCGVEELCTLEVAGRLLGG   74 (74)
T ss_pred             CEEEEEC--CCEEEEEECCcCcHHHHHHHHHhhhCCCHHHEEEEECCeECCCCCCHHHcCCCCCCEEEEEEecCCC
Confidence            5788887  3678899999999999999999999999999999999999999999999999999999999999997

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

>PTZ00044 ubiquitin; Provisional

Probab=99.84  E-value=1.5e-20  Score=112.53  Aligned_cols=76  Identities=49%  Similarity=0.800  Sum_probs=74.0

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      |+|+|+..+|+++.+++++++||++||++|++.+|+|++.|+|+|+|+.|+|+.+|++|++++|++|++.++.+||
T Consensus         1 m~i~vk~~~G~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~gg   76 (76)
T PTZ00044          1 MQILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYSGKQMSDDLKLSDYKVVPGSTIHMVLQLRGG   76 (76)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEEccCCCcHHHcCCCCCCEEEEEEEccCC
Confidence            6799999999999999999999999999999999999999999999999999999999999999999999999987

>cd01806 Nedd8 Nebb8-like ubiquitin protein

Probab=99.83  E-value=4.7e-20  Score=110.39  Aligned_cols=76  Identities=86%  Similarity=1.265  Sum_probs=73.7

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      |+|+|+..+|+.+.++++++.||++||+++++.+|+|++.|+|+|+|+.|+|+.+|++|++++|++|++..+.+||
T Consensus         1 m~i~v~~~~g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~~~g~~L~d~~tl~~~~i~~g~~i~l~~~~~gg   76 (76)
T cd01806           1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDDKTAADYKLEGGSVLHLVLALRGG   76 (76)
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEEECCeEccCCCCHHHcCCCCCCEEEEEEEccCC
Confidence            6789999999999999999999999999999999999999999999999999999999999999999999999987

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.

>cd01803 Ubiquitin Ubiquitin

Probab=99.83  E-value=4.4e-20  Score=110.52  Aligned_cols=76  Identities=63%  Similarity=0.993  Sum_probs=73.8

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      |+|+|+..+|+.+.+++++++||++||++|++.+|+|++.|+|.|+|+.|+|+.+|++|++++|++|++.++++||
T Consensus         1 m~i~v~~~~g~~~~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~i~l~~~~~gg   76 (76)
T cd01803           1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   76 (76)
T ss_pred             CEEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCHHHeEEEECCEECCCCCcHHHcCCCCCCEEEEEEEccCC
Confidence            6789999999999999999999999999999999999999999999999999999999999999999999999987

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

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

Probab=99.83  E-value=4.6e-20  Score=109.82  Aligned_cols=74  Identities=26%  Similarity=0.515  Sum_probs=71.6

Q ss_pred             eeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           79 IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        79 i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      |+|+...|+++.+++++++||++||++|++..|+|+++|+|.|+|+.|+|+.+|++|||++++++++..+++||
T Consensus         1 i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~q~L~~~G~~L~D~~tL~~~~i~~~~tl~l~~~l~gg   74 (74)
T cd01810           1 ILVRNDKGRSSIYEVQLTQTVATLKQQVSQRERVQADQFWLSFEGRPMEDEHPLGEYGLKPGCTVFMNLRLRGG   74 (74)
T ss_pred             CEEECCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEECCEECCCCCCHHHcCCCCCCEEEEEEEccCC
Confidence            57889999999999999999999999999999999999999999999999999999999999999999999987

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.

>cd01807 GDX_N ubiquitin-like domain of GDX

Probab=99.83  E-value=3.4e-20  Score=110.42  Aligned_cols=73  Identities=36%  Similarity=0.653  Sum_probs=70.7

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|+++.|+|++.|+|+|+|+.|.|+.+|++|++++++++++.+++
T Consensus         1 m~i~vk~~~G~~~~l~v~~~~tV~~lK~~i~~~~gi~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~l~l~~~~   73 (74)
T cd01807           1 MFLTVKLLQGRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLLFKGKALADDKRLSDYSIGPNAKLNLVVRP   73 (74)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEECCCCCCHHHCCCCCCCEEEEEEcC
Confidence            8999999999999999999999999999999999999999999999999999999999999999999998764

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

>cd01804 midnolin_N Ubiquitin-like domain of midnolin

Probab=99.82  E-value=6.8e-20  Score=110.00  Aligned_cols=76  Identities=22%  Similarity=0.474  Sum_probs=73.3

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      +|+|+|+...|+.+.+++++++||++||++|++..++|+++|+|.|+|+.|+|+ +|++||+++|++|+++..++||
T Consensus         1 ~m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~~~~~~~qrL~~~Gk~L~d~-~L~~~gi~~~~~i~l~~~~~~~   76 (78)
T cd01804           1 PMNLNIHSTTGTRFDLSVPPDETVEGLKKRISQRLKVPKERLALLHRETRLSSG-KLQDLGLGDGSKLTLVPTVEAG   76 (78)
T ss_pred             CeEEEEEECCCCEEEEEECCcCHHHHHHHHHHHHhCCChHHEEEEECCcCCCCC-cHHHcCCCCCCEEEEEeecccc
Confidence            488999999999999999999999999999999999999999999999999998 9999999999999999999988

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.

>cd01807 GDX_N ubiquitin-like domain of GDX

Probab=99.82  E-value=5.4e-20  Score=109.53  Aligned_cols=73  Identities=36%  Similarity=0.606  Sum_probs=70.4

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEee
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      |+|+|+..+|+.+.+++++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++|||+++++|+++++.
T Consensus         1 m~i~vk~~~G~~~~l~v~~~~tV~~lK~~i~~~~gi~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~l~l~~~~   73 (74)
T cd01807           1 MFLTVKLLQGRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLLFKGKALADDKRLSDYSIGPNAKLNLVVRP   73 (74)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEECCCCCCHHHCCCCCCCEEEEEEcC
Confidence            6789999999999999999999999999999999999999999999999999999999999999999999875

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

>PTZ00044 ubiquitin; Provisional

Probab=99.80  E-value=2.6e-19  Score=107.14  Aligned_cols=75  Identities=49%  Similarity=0.803  Sum_probs=71.9

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|++..|+|++.|+|+|+|+.|+|+.+|++|++.+++++++.++..+
T Consensus         1 m~i~vk~~~G~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~g   75 (76)
T PTZ00044          1 MQILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYSGKQMSDDLKLSDYKVVPGSTIHMVLQLRG   75 (76)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEEccCCCcHHHcCCCCCCEEEEEEEccC
Confidence            899999999999999999999999999999999999999999999999999999999999999999999987643

>cd01791 Ubl5 UBL5 ubiquitin-like modifier

Probab=99.79  E-value=4.1e-19  Score=104.94  Aligned_cols=71  Identities=24%  Similarity=0.340  Sum_probs=67.9

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEE
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      |.|+|++..|+.+.+++++++||++||++|++..|+|+++|+|+|.|+.|+|+.+|++||+++|++||+..
T Consensus         2 ~~i~vkt~~Gk~~~~~v~~~~TV~~LK~~I~~~~~~~~~~qrLi~~Gk~L~D~~tL~~ygi~~~stv~l~~   72 (73)
T cd01791           2 IEVVCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFKDHISLGDYEIHDGMNLELYY   72 (73)
T ss_pred             EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEeCCcCCCCCCCHHHcCCCCCCEEEEEe
Confidence            67899999999999999999999999999999999999999999999999999999999999999999864

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.

>cd01793 Fubi Fubi ubiquitin-like protein

Probab=99.79  E-value=3.9e-19  Score=105.82  Aligned_cols=73  Identities=40%  Similarity=0.599  Sum_probs=68.8

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+||.  ++.+.+++++++||++||++|++..|+|++.|+|+|+|+.|+|+.+|++|++++++++++.++..+
T Consensus         1 mqi~vk~--~~~~~l~v~~~~tV~~lK~~i~~~~gip~~~q~Li~~Gk~L~D~~tL~~~~i~~~~tl~l~~~l~G   73 (74)
T cd01793           1 MQLFVRA--QNTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVLLLAGVPLEDDATLGQCGVEELCTLEVAGRLLG   73 (74)
T ss_pred             CEEEEEC--CCEEEEEECCcCcHHHHHHHHHhhhCCCHHHEEEEECCeECCCCCCHHHcCCCCCCEEEEEEecCC
Confidence            8999997  378999999999999999999999999999999999999999999999999999999999987654

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=99.79  E-value=5.3e-19  Score=105.94  Aligned_cols=73  Identities=33%  Similarity=0.587  Sum_probs=69.3

Q ss_pred             eeeeeeecCCce-EEEe-eCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEee
Q 040824           77 TMIKVKTLTGKE-IEID-IEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        77 ~~i~v~~~~~~~-~~~~-v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      |+|+|+..+|+. +.++ +.+++||++||++|++.+|+|++.|+|+|+|+.|+|+.+|++|||++|++|++++++
T Consensus         1 M~I~vk~~~G~~~~~l~~v~~~~TV~~lK~~i~~~~gi~~~~QrLi~~Gk~L~D~~tL~~y~i~~~~~i~l~~~~   75 (78)
T cd01797           1 MWIQVRTMDGKETRTVDSLSRLTKVEELREKIQELFNVEPECQRLFYRGKQMEDGHTLFDYNVGLNDIIQLLVRQ   75 (78)
T ss_pred             CEEEEEcCCCCEEEEeeccCCcCcHHHHHHHHHHHhCCCHHHeEEEeCCEECCCCCCHHHcCCCCCCEEEEEEec
Confidence            789999999987 6885 899999999999999999999999999999999999999999999999999999886

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

>cd01791 Ubl5 UBL5 ubiquitin-like modifier

Probab=99.79  E-value=3.2e-19  Score=105.40  Aligned_cols=70  Identities=24%  Similarity=0.383  Sum_probs=67.5

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~   70 (154)
                      |+|+|+++.|+.+.+++++++||++||++|+++.++|+++|+|.|.|+.|.|+.+|++||+.++++||+-
T Consensus         2 ~~i~vkt~~Gk~~~~~v~~~~TV~~LK~~I~~~~~~~~~~qrLi~~Gk~L~D~~tL~~ygi~~~stv~l~   71 (73)
T cd01791           2 IEVVCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFKDHISLGDYEIHDGMNLELY   71 (73)
T ss_pred             EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEeCCcCCCCCCCHHHcCCCCCCEEEEE
Confidence            7899999999999999999999999999999999999999999999999999999999999999999874

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.

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

Probab=99.79  E-value=4.7e-19  Score=106.16  Aligned_cols=74  Identities=36%  Similarity=0.634  Sum_probs=70.1

Q ss_pred             CEEEEEeCCCCE-EEEE-EeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeee
Q 040824            1 MQIFVKTLTGKT-ITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (154)
Q Consensus         1 m~v~v~~~~~~~-~~~~-v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~   74 (154)
                      |+|+|+..+|+. +.++ +.+++||.+||++|++..|+|++.|+|+|+|+.|+|+.+|++||+.++++|++.+++.
T Consensus         1 M~I~vk~~~G~~~~~l~~v~~~~TV~~lK~~i~~~~gi~~~~QrLi~~Gk~L~D~~tL~~y~i~~~~~i~l~~~~~   76 (78)
T cd01797           1 MWIQVRTMDGKETRTVDSLSRLTKVEELREKIQELFNVEPECQRLFYRGKQMEDGHTLFDYNVGLNDIIQLLVRQD   76 (78)
T ss_pred             CEEEEEcCCCCEEEEeeccCCcCcHHHHHHHHHHHhCCCHHHeEEEeCCEECCCCCCHHHcCCCCCCEEEEEEecC
Confidence            899999999986 7895 8999999999999999999999999999999999999999999999999999998764

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

>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein

Probab=99.79  E-value=5.1e-19  Score=103.86  Aligned_cols=69  Identities=28%  Similarity=0.591  Sum_probs=66.0

Q ss_pred             eeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEe
Q 040824           80 KVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        80 ~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      .|+..+|+++.+++++++||++||++|++..|+|++.|+|+|.|+.|+|+.+|++|+++++++|+++++
T Consensus         2 ~vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~Li~~G~~L~D~~~l~~~~i~~~~tv~~~~~   70 (70)
T cd01794           2 KVRLSTGKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWFFSGKLLTDKTRLQETKIQKDYVVQVIVN   70 (70)
T ss_pred             eEEcCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEECCeECCCCCCHHHcCCCCCCEEEEEeC
Confidence            567889999999999999999999999999999999999999999999999999999999999999874

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

>cd01806 Nedd8 Nebb8-like ubiquitin protein

Probab=99.79  E-value=9.7e-19  Score=104.64  Aligned_cols=75  Identities=55%  Similarity=0.948  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+..+|+.+.+++++++||.+||+++++..++|++.|+|+|+|+.|.|+.+|++|++.++++|++.++..+
T Consensus         1 m~i~v~~~~g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~~~g~~L~d~~tl~~~~i~~g~~i~l~~~~~g   75 (76)
T cd01806           1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDDKTAADYKLEGGSVLHLVLALRG   75 (76)
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEEECCeEccCCCCHHHcCCCCCCEEEEEEEccC
Confidence            899999999999999999999999999999999999999999999999999999999999999999999987543

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.

>cd01802 AN1_N ubiquitin-like domain of AN1

Probab=99.78  E-value=1e-18  Score=109.82  Aligned_cols=75  Identities=51%  Similarity=0.744  Sum_probs=71.8

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|++..|+|++.|+|+|+|+.|+|+.+|++|++.++++|++.++..+
T Consensus        28 M~I~Vk~l~G~~~~leV~~~~TV~~lK~kI~~~~gip~~~QrLi~~Gk~L~D~~tL~dy~I~~~stL~l~~~l~G  102 (103)
T cd01802          28 MELFIETLTGTCFELRVSPFETVISVKAKIQRLEGIPVAQQHLIWNNMELEDEYCLNDYNISEGCTLKLVLAMRG  102 (103)
T ss_pred             EEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEecCC
Confidence            799999999999999999999999999999999999999999999999999999999999999999999887543

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.

>cd01803 Ubiquitin Ubiquitin

Probab=99.78  E-value=1.4e-18  Score=103.95  Aligned_cols=75  Identities=96%  Similarity=1.311  Sum_probs=71.8

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+..+|+.+.+++++++||++||++|++.+++|++.|+|+|+|+.|.|+.+|++|++.++++|++.++..+
T Consensus         1 m~i~v~~~~g~~~~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~i~l~~~~~g   75 (76)
T cd01803           1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG   75 (76)
T ss_pred             CEEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCHHHeEEEECCEECCCCCcHHHcCCCCCCEEEEEEEccC
Confidence            899999999999999999999999999999999999999999999999999999999999999999999987643

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

>cd01805 RAD23_N Ubiquitin-like domain of RAD23

Probab=99.77  E-value=2.5e-18  Score=103.15  Aligned_cols=74  Identities=38%  Similarity=0.698  Sum_probs=70.5

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCC--CCCceeEEECCeecCCCCcccccccCCCCEEEEEEeec
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGI--PPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALR  150 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i--~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~  150 (154)
                      |+++|+..+|+.+.+++++++||++||++|++.+|+  |+++|+|+|+|+.|+|+.+|++||+++|++|+++++.+
T Consensus         1 m~i~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~i~~~~~~~   76 (77)
T cd01805           1 MKITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKILKDDTTLEEYKIDEKDFVVVMVSKP   76 (77)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEEECCEEccCCCCHHHcCCCCCCEEEEEEecC
Confidence            688999999999999999999999999999999999  99999999999999999999999999999999988754

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).

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

Probab=99.77  E-value=1.6e-18  Score=103.60  Aligned_cols=70  Identities=30%  Similarity=0.633  Sum_probs=67.3

Q ss_pred             cCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           84 LTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        84 ~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      .+|+++.+++++++||++||++|+..+|+|++.|+|+|+|+.|+|+.+|++|++++|++|+++++.+||+
T Consensus         5 l~g~~~~l~v~~~~TV~~lK~~i~~~~gip~~~q~L~~~G~~L~d~~tL~~~~i~~g~~l~v~~~~~gg~   74 (76)
T cd01800           5 LNGQMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQYEGIFIKDSNSLAYYNLANGTIIHLQLKERGGR   74 (76)
T ss_pred             cCCeEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCEEcCCCCcHHHcCCCCCCEEEEEEecCCCc
Confidence            3688999999999999999999999999999999999999999999999999999999999999999984

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.

>cd01804 midnolin_N Ubiquitin-like domain of midnolin

Probab=99.77  E-value=1.4e-18  Score=104.32  Aligned_cols=75  Identities=25%  Similarity=0.491  Sum_probs=70.8

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecc
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~   76 (154)
                      |+|+|+...|+.+.+++++++||.+||++|+++.++++++|+|.|.|+.|+|+ +|++||++++++|+++....++
T Consensus         2 m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~~~~~~~qrL~~~Gk~L~d~-~L~~~gi~~~~~i~l~~~~~~~   76 (78)
T cd01804           2 MNLNIHSTTGTRFDLSVPPDETVEGLKKRISQRLKVPKERLALLHRETRLSSG-KLQDLGLGDGSKLTLVPTVEAG   76 (78)
T ss_pred             eEEEEEECCCCEEEEEECCcCHHHHHHHHHHHHhCCChHHEEEEECCcCCCCC-cHHHcCCCCCCEEEEEeecccc
Confidence            79999999999999999999999999999999999999999999999999999 9999999999999998876543

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.

>cd01805 RAD23_N Ubiquitin-like domain of RAD23

Probab=99.77  E-value=3.4e-18  Score=102.56  Aligned_cols=73  Identities=38%  Similarity=0.705  Sum_probs=69.9

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCC--CCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGI--PPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~--~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|++..++  |+++|+|.|+|+.|+|+.+|++|++++++++++.++.
T Consensus         1 m~i~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~i~~~~~~   75 (77)
T cd01805           1 MKITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKILKDDTTLEEYKIDEKDFVVVMVSK   75 (77)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEEECCEEccCCCCHHHcCCCCCCEEEEEEec
Confidence            899999999999999999999999999999999999  9999999999999999999999999999999887754

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).

>cd01763 Sumo Small ubiquitin-related modifier (SUMO)

Probab=99.77  E-value=5.7e-18  Score=103.71  Aligned_cols=79  Identities=23%  Similarity=0.485  Sum_probs=75.8

Q ss_pred             ecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           74 RGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        74 ~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ...|.|+|++.+|+.+.+.+.+++|+..||++++++.|+|+++++|+|+|+.|+++.|+++|++++||+|+++++++||
T Consensus         9 ~~~i~I~v~~~~g~~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f~G~~L~~~~T~~~l~m~d~d~I~v~l~l~GG   87 (87)
T cd01763           9 SEHINLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLFDGQRIRDNQTPDDLGMEDGDEIEVMLEQTGG   87 (87)
T ss_pred             CCeEEEEEECCCCCEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEECCeECCCCCCHHHcCCCCCCEEEEEEecccC
Confidence            3457899999999999999999999999999999999999999999999999999999999999999999999999998

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.

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

Probab=99.76  E-value=2.8e-18  Score=101.05  Aligned_cols=70  Identities=34%  Similarity=0.666  Sum_probs=66.5

Q ss_pred             eeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEe
Q 040824           79 IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        79 i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      |+|+...|+.+.+++++++||+++|++|++.+|+|+++|+|+|+|++|+|+.+|++|||++|+++++..|
T Consensus         1 i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~q~Li~~G~~L~d~~~l~~~~i~~~stl~l~~~   70 (70)
T cd01798           1 VYVRTNTGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVIFAGKELRNTTTIQECDLGQQSILHAVRR   70 (70)
T ss_pred             CEEEcCCCCEEEEEECCCChHHHHHHHHHHHHCCCHHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEeC
Confidence            4678889999999999999999999999999999999999999999999999999999999999998764

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=99.76  E-value=1.6e-18  Score=101.71  Aligned_cols=69  Identities=36%  Similarity=0.587  Sum_probs=66.2

Q ss_pred             EEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeee
Q 040824            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (154)
Q Consensus         3 v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~   71 (154)
                      ++|+..+|+.+.+++++++||.+||++|++..|+|++.|+|+|.|+.|+|+.+|++|+++++++|++++
T Consensus         1 ~~vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~Li~~G~~L~D~~~l~~~~i~~~~tv~~~~   69 (70)
T cd01794           1 LKVRLSTGKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWFFSGKLLTDKTRLQETKIQKDYVVQVIV   69 (70)
T ss_pred             CeEEcCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEECCeECCCCCCHHHcCCCCCCEEEEEe
Confidence            468899999999999999999999999999999999999999999999999999999999999999875

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.

>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein

Probab=99.76  E-value=3.9e-18  Score=100.94  Aligned_cols=72  Identities=43%  Similarity=0.667  Sum_probs=68.7

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEe
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      |.|+|+..+|+.+.+++++++||++||+++++.+|+|++.|+|+|+|+.|+|+.+|++||+++|+++++..+
T Consensus         1 i~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~l~l~~~   72 (72)
T cd01809           1 IEIKVKTLDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYSGRVLKDDETLSEYKVEDGHTIHLVKR   72 (72)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCEECCCcCcHHHCCCCCCCEEEEEeC
Confidence            578999999999999999999999999999999999999999999999999999999999999999998753

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

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

Probab=99.76  E-value=3.9e-18  Score=100.19  Aligned_cols=69  Identities=52%  Similarity=0.943  Sum_probs=65.3

Q ss_pred             eecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeec
Q 040824           82 KTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALR  150 (154)
Q Consensus        82 ~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~  150 (154)
                      ++.+|+.+.+++++++||.+||++|++.+++|++.|+|+|+|+.|+|+.+|++||+.+|++|++.++.+
T Consensus         1 k~~~g~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~~G~~L~d~~tL~~~~i~~~~~I~l~~k~~   69 (69)
T PF00240_consen    1 KTLSGKTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLIYNGKELDDDKTLSDYGIKDGSTIHLVIKPR   69 (69)
T ss_dssp             EETTSEEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEETTEEESTTSBTGGGTTSTTEEEEEEESSE
T ss_pred             CCCCCcEEEEEECCCCCHHHhhhhcccccccccccceeeeeeecccCcCcHHHcCCCCCCEEEEEEecC
Confidence            456889999999999999999999999999999999999999999999999999999999999988754

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

>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein

Probab=99.76  E-value=3.9e-18  Score=100.97  Aligned_cols=71  Identities=44%  Similarity=0.692  Sum_probs=68.7

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~   71 (154)
                      |+|+|+..+|+.+.+++++++||.+||+++++..|+|++.|+|.|+|+.|+|+.+|++||+++++++++..
T Consensus         1 i~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~l~l~~   71 (72)
T cd01809           1 IEIKVKTLDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYSGRVLKDDETLSEYKVEDGHTIHLVK   71 (72)
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCEECCCcCcHHHCCCCCCCEEEEEe
Confidence            89999999999999999999999999999999999999999999999999999999999999999998875

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.

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

Probab=99.75  E-value=3.7e-18  Score=101.57  Aligned_cols=72  Identities=31%  Similarity=0.575  Sum_probs=68.8

Q ss_pred             EEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeee
Q 040824            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (154)
Q Consensus         3 v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~   74 (154)
                      |+|+...|+.+.+++++++||.+||++|+...|+|++.|+|.|+|+.|.|+.+|++||+++++++++.++..
T Consensus         1 i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~q~L~~~G~~L~D~~tL~~~~i~~~~tl~l~~~l~   72 (74)
T cd01810           1 ILVRNDKGRSSIYEVQLTQTVATLKQQVSQRERVQADQFWLSFEGRPMEDEHPLGEYGLKPGCTVFMNLRLR   72 (74)
T ss_pred             CEEECCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEECCEECCCCCCHHHcCCCCCCEEEEEEEcc
Confidence            579999999999999999999999999999999999999999999999999999999999999999987754

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.

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

Probab=99.74  E-value=9e-18  Score=101.35  Aligned_cols=73  Identities=29%  Similarity=0.424  Sum_probs=69.8

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeE--EECCeecCCCCcccccccCCCCEEEEEEee
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRL--IYAGKQLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l--~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      |.|+|+..+|+.+.+++++++||++||++|++..|+|+++|+|  .|+|+.|+|+.+|++||+++|++|++.++-
T Consensus         3 ~~i~Vk~~~G~~~~~~v~~~~TV~~lK~~I~~~~~i~~~~qrL~~~~~G~~L~D~~tL~~~gi~~gs~l~l~~~~   77 (80)
T cd01792           3 WDLKVKMLGGNEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLAHLDSREVLQDGVPLVSQGLGPGSTVLLVVQN   77 (80)
T ss_pred             eEEEEEeCCCCEEEEEcCCCCcHHHHHHHHHHHhCCCHHHEEEEeccCCCCCCCCCCHHHcCCCCCCEEEEEEEc
Confidence            7899999999999999999999999999999999999999999  799999999999999999999999999874

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.

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

Probab=99.74  E-value=7.2e-18  Score=101.75  Aligned_cols=73  Identities=32%  Similarity=0.431  Sum_probs=69.6

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEE--EEcceEeccCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRL--IFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L--~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|++..++|+++|+|  .|+|+.|+|+.+|++||+.+++++++.++.
T Consensus         3 ~~i~Vk~~~G~~~~~~v~~~~TV~~lK~~I~~~~~i~~~~qrL~~~~~G~~L~D~~tL~~~gi~~gs~l~l~~~~   77 (80)
T cd01792           3 WDLKVKMLGGNEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLAHLDSREVLQDGVPLVSQGLGPGSTVLLVVQN   77 (80)
T ss_pred             eEEEEEeCCCCEEEEEcCCCCcHHHHHHHHHHHhCCCHHHEEEEeccCCCCCCCCCCHHHcCCCCCCEEEEEEEc
Confidence            6899999999999999999999999999999999999999999  789999999999999999999999998874

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.

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

Probab=99.73  E-value=1.1e-17  Score=98.49  Aligned_cols=69  Identities=38%  Similarity=0.721  Sum_probs=66.4

Q ss_pred             EEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeee
Q 040824            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (154)
Q Consensus         3 v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~   71 (154)
                      |+|+..+|+.+.+++++++||.++|++|+++.|+|++.|+|+|+|+.|+|+.+|++|++.+++++|++.
T Consensus         1 i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~q~Li~~G~~L~d~~~l~~~~i~~~stl~l~~   69 (70)
T cd01798           1 VYVRTNTGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVIFAGKELRNTTTIQECDLGQQSILHAVR   69 (70)
T ss_pred             CEEEcCCCCEEEEEECCCChHHHHHHHHHHHHCCCHHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEe
Confidence            578999999999999999999999999999999999999999999999999999999999999999875

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.

>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=99.73  E-value=2.9e-17  Score=96.44  Aligned_cols=68  Identities=56%  Similarity=0.962  Sum_probs=64.6

Q ss_pred             EeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824            6 KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         6 ~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |+.+|+.+.+++++++||.+||++|+...++|++.|+|+|+|+.|+|+.+|++|++.++++|++.+++
T Consensus         1 k~~~g~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~~G~~L~d~~tL~~~~i~~~~~I~l~~k~   68 (69)
T PF00240_consen    1 KTLSGKTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLIYNGKELDDDKTLSDYGIKDGSTIHLVIKP   68 (69)
T ss_dssp             EETTSEEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEETTEEESTTSBTGGGTTSTTEEEEEEESS
T ss_pred             CCCCCcEEEEEECCCCCHHHhhhhcccccccccccceeeeeeecccCcCcHHHcCCCCCCEEEEEEec
Confidence            56789999999999999999999999999999999999999999999999999999999999988764

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

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

Probab=99.72  E-value=3.8e-17  Score=96.43  Aligned_cols=71  Identities=37%  Similarity=0.454  Sum_probs=65.6

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEe
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      +.|+++...|+ ..+++++++||++||++|++..|+|+++|+|.|+|+.|.|+.+|++||+++|++|++.++
T Consensus         1 ~~i~vk~~~g~-~~l~v~~~~TV~~lK~~I~~~~~i~~~~~~Li~~Gk~L~d~~tL~~~~i~~~stl~l~~~   71 (71)
T cd01808           1 IKVTVKTPKDK-EEIEIAEDASVKDFKEAVSKKFKANQEQLVLIFAGKILKDTDTLTQHNIKDGLTVHLVIK   71 (71)
T ss_pred             CEEEEEcCCCC-EEEEECCCChHHHHHHHHHHHhCCCHHHEEEEECCeEcCCCCcHHHcCCCCCCEEEEEEC
Confidence            35788888886 489999999999999999999999999999999999999999999999999999998764

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

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

Probab=99.71  E-value=5.3e-17  Score=95.74  Aligned_cols=68  Identities=32%  Similarity=0.588  Sum_probs=63.0

Q ss_pred             eeeeec-CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCC-CcccccccCCCCEEEEE
Q 040824           79 IKVKTL-TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADD-KTARDYNIEGGSVLHLV  146 (154)
Q Consensus        79 i~v~~~-~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~-~~L~~~~i~~~~~i~~~  146 (154)
                      |+|+.. +|+++.+++++++||++||++|++.+|+|++.|+|+|+|+.|+|+ .+|++||+++|++|++.
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            467788 889999999999999999999999999999999999999999987 68999999999999863

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.

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

Probab=99.71  E-value=1.3e-18  Score=106.35  Aligned_cols=77  Identities=61%  Similarity=0.955  Sum_probs=73.9

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      |.++++...|++..+++.+++||..+|++|....|+|++.|+|+|+|+.|+|+.|+++||++..|+|+++.+++||-
T Consensus         1 ~~~~~~~~~GKT~~le~EpS~ti~~vKA~i~~~~Gi~~~~~~L~~~~k~LED~~Tla~Y~i~~~~Tl~~~~rL~GG~   77 (128)
T KOG0003|consen    1 MQIFVKTLTGKTITLEVEPSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGI   77 (128)
T ss_pred             CcEEEEEeeCceEEEEecccchHHHHHHHhccccCCCHHHHHHHhcccccccCCcccccCccchhhhhhhHHHhcCC
Confidence            46788888999999999999999999999999999999999999999999999999999999999999999999983

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

Probab=99.70  E-value=6.3e-17  Score=95.52  Aligned_cols=71  Identities=34%  Similarity=0.489  Sum_probs=66.7

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      |+|+|+...|+ ..+++++++||.+||++|++..++++++|+|.|.|+.|.|+.+|++||++++++++++++
T Consensus         1 ~~i~vk~~~g~-~~l~v~~~~TV~~lK~~I~~~~~i~~~~~~Li~~Gk~L~d~~tL~~~~i~~~stl~l~~~   71 (71)
T cd01808           1 IKVTVKTPKDK-EEIEIAEDASVKDFKEAVSKKFKANQEQLVLIFAGKILKDTDTLTQHNIKDGLTVHLVIK   71 (71)
T ss_pred             CEEEEEcCCCC-EEEEECCCChHHHHHHHHHHHhCCCHHHEEEEECCeEcCCCCcHHHcCCCCCCEEEEEEC
Confidence            67999999887 589999999999999999999999999999999999999999999999999999998763

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.

>cd01812 BAG1_N Ubiquitin-like domain of BAG1

Probab=99.70  E-value=9.5e-17  Score=94.74  Aligned_cols=70  Identities=26%  Similarity=0.424  Sum_probs=65.5

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEE
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      +.|+|+.. |+.+.+++++++||++||+++++.+|+|+++|+|+|+|+.|+|+.+|++||+++|++|+++.
T Consensus         1 i~i~vk~~-g~~~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~l~d~~~L~~~~i~~g~~l~v~~   70 (71)
T cd01812           1 IRVRVKHG-GESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIFKGKERDDAETLDMSGVKDGSKVMLLE   70 (71)
T ss_pred             CEEEEEEC-CEEEEEEECCCCcHHHHHHHHHHhhCCChHHeEEeeCCcccCccCcHHHcCCCCCCEEEEec
Confidence            46788885 88899999999999999999999999999999999999999999999999999999998864

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=99.69  E-value=7.1e-17  Score=95.97  Aligned_cols=71  Identities=25%  Similarity=0.279  Sum_probs=63.2

Q ss_pred             CEEEEEeCCCCEE--EEEEeCCCcHHHHHHHHHhHhC--CCCCCeEEEEcceEeccCceecccc--cccccceeeee
Q 040824            1 MQIFVKTLTGKTI--TLEVESSDTIDNVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLADYN--IQKESTLHLVL   71 (154)
Q Consensus         1 m~v~v~~~~~~~~--~~~v~~~~tv~~lk~~i~~~~~--~~~~~q~L~~~g~~L~d~~~l~~~~--i~~~~~i~l~~   71 (154)
                      |.|+||.++++.+  .+++++++||.+||++|++..+  .+++.|+|+|.|+.|+|+.+|++|.  +.++.+|||+.
T Consensus         2 i~l~IK~~~~~~~~~~ve~~~~~TV~~lK~~i~~~~~~~~~~~~QrLIy~GKiLkD~~tL~~~~~~~~~~~tiHLV~   78 (79)
T cd01790           2 VTLLIKSPNQKYEDQTVSCFLNWTVGELKTHLSRVYPSKPLEQDQRLIYSGKLLPDHLKLRDVLRKQDEYHMVHLVC   78 (79)
T ss_pred             eEEEEECCCCCeEEEEEecCCcChHHHHHHHHHHhcCCCCChhHeEEEEcCeeccchhhHHHHhhcccCCceEEEEe
Confidence            5799999999884  5555899999999999998874  5689999999999999999999996  99999999875

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=99.69  E-value=1.3e-16  Score=94.63  Aligned_cols=69  Identities=22%  Similarity=0.350  Sum_probs=63.7

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEE---CCeecCCCCcccccccCCCCEEEEE
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIY---AGKQLADDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~---~g~~l~d~~~L~~~~i~~~~~i~~~  146 (154)
                      |.|.|+. .|+.+.+++++++||++||+++++.+|+|+++|+|+|   +|+.+.|+.+|++|++++|+.|+++
T Consensus         1 ~~i~vk~-~g~~~~v~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~~~~~Gk~l~D~~~L~~~~i~~g~~i~lm   72 (74)
T cd01813           1 VPVIVKW-GGQEYSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLGLKVKGKPAEDDVKISALKLKPNTKIMMM   72 (74)
T ss_pred             CEEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEeecccCCcCCCCcCHHHcCCCCCCEEEEE
Confidence            3566777 7788999999999999999999999999999999996   8999999999999999999999876

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

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

Probab=99.69  E-value=2.6e-17  Score=107.67  Aligned_cols=77  Identities=60%  Similarity=0.943  Sum_probs=74.6

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      |.|+|+...+++..+++.+++||..+|++|+...|||+++|+++|.|+.|+|+.+|+||+|+..++|++.++++||+
T Consensus         1 m~ifVk~l~~kti~~eve~~~ti~~~Kakiq~~egIp~dqqrlifag~qLedgrtlSDY~Iqkestl~l~l~l~Gg~   77 (156)
T KOG0004|consen    1 MQIFVKTLTGKTITLEVEANDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGA   77 (156)
T ss_pred             CccchhhccccceeeeecccccHHHHHHhhhcccCCCchhhhhhhhhcccccCCccccccccccceEEEEEEecCCc
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999984

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

Probab=99.69  E-value=9.2e-17  Score=94.71  Aligned_cols=68  Identities=35%  Similarity=0.543  Sum_probs=63.6

Q ss_pred             EEEEeC-CCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccC-ceecccccccccceeee
Q 040824            3 IFVKTL-TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDG-RTLADYNIQKESTLHLV   70 (154)
Q Consensus         3 v~v~~~-~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~-~~l~~~~i~~~~~i~l~   70 (154)
                      |+|+.. +|+.+.+++++++||++||++|++..|+|++.|+|+|+|+.|+|+ .+|++|++++++++++.
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            578888 899999999999999999999999999999999999999999987 58999999999999764

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.

>cd01812 BAG1_N Ubiquitin-like domain of BAG1

Probab=99.68  E-value=1.2e-16  Score=94.23  Aligned_cols=69  Identities=29%  Similarity=0.490  Sum_probs=65.6

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~   70 (154)
                      |+|+|++. |+.+.+++++++||.+||++|+..+++|+++|+|+|+|+.|.|+.+|++|++++++++++.
T Consensus         1 i~i~vk~~-g~~~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~g~~l~d~~~L~~~~i~~g~~l~v~   69 (71)
T cd01812           1 IRVRVKHG-GESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIFKGKERDDAETLDMSGVKDGSKVMLL   69 (71)
T ss_pred             CEEEEEEC-CEEEEEEECCCCcHHHHHHHHHHhhCCChHHeEEeeCCcccCccCcHHHcCCCCCCEEEEe
Confidence            68999985 8989999999999999999999999999999999999999999999999999999999775

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).

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

Probab=99.68  E-value=4.5e-17  Score=89.17  Aligned_cols=70  Identities=54%  Similarity=0.911  Sum_probs=67.5

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~   70 (154)
                      |.+.|++++|+.+.++++++++|..+|++++++.|+||..|+|+|.|+.++|+.+.++|++..|+.+|++
T Consensus         1 m~iKvktLt~KeIeidIep~DkverIKErvEEkeGIPp~qqrli~~gkqm~DD~tA~~Y~~~~GSVlHlv   70 (70)
T KOG0005|consen    1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYAGKQMNDDKTAAHYNLLGGSVLHLV   70 (70)
T ss_pred             CeeeEeeeccceEEEeeCcchHHHHHHHHhhhhcCCCchhhhhhhccccccccccHHHhhhccceeEeeC
Confidence            7799999999999999999999999999999999999999999999999999999999999999999864

>cd01813 UBP_N UBP ubiquitin processing protease

Probab=99.68  E-value=1.6e-16  Score=94.21  Aligned_cols=69  Identities=23%  Similarity=0.427  Sum_probs=64.6

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEE---cceEeccCceecccccccccceeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF---AGKQLEDGRTLADYNIQKESTLHLV   70 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~---~g~~L~d~~~l~~~~i~~~~~i~l~   70 (154)
                      |+|.|++ +|+.+++++++++||++||++|++.+++|+++|+|+|   .|+.+.|+.+|++|++++++.|.+.
T Consensus         1 ~~i~vk~-~g~~~~v~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~~~~~Gk~l~D~~~L~~~~i~~g~~i~lm   72 (74)
T cd01813           1 VPVIVKW-GGQEYSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLGLKVKGKPAEDDVKISALKLKPNTKIMMM   72 (74)
T ss_pred             CEEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEeecccCCcCCCCcCHHHcCCCCCCEEEEE
Confidence            6789996 7899999999999999999999999999999999996   8999999999999999999998765

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.

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

Probab=99.67  E-value=3.2e-16  Score=93.14  Aligned_cols=71  Identities=25%  Similarity=0.247  Sum_probs=62.9

Q ss_pred             ceeeeeeecCCce--EEEeeCCCchHHHHHHHHhhhcC--CCCCceeEEECCeecCCCCcccccc--cCCCCEEEEE
Q 040824           76 GTMIKVKTLTGKE--IEIDIEPTDTIERIKERVEEKEG--IPPVQQRLIYAGKQLADDKTARDYN--IEGGSVLHLV  146 (154)
Q Consensus        76 ~~~i~v~~~~~~~--~~~~v~~~~tv~~LK~~i~~~~~--i~~~~~~l~~~g~~l~d~~~L~~~~--i~~~~~i~~~  146 (154)
                      ++.++|+..+++.  +.+++++++||++||+++++..+  .|+++|+|+|+|+.|+|+.||++|.  +.+|.+||+.
T Consensus         1 ~i~l~IK~~~~~~~~~~ve~~~~~TV~~lK~~i~~~~~~~~~~~~QrLIy~GKiLkD~~tL~~~~~~~~~~~tiHLV   77 (79)
T cd01790           1 PVTLLIKSPNQKYEDQTVSCFLNWTVGELKTHLSRVYPSKPLEQDQRLIYSGKLLPDHLKLRDVLRKQDEYHMVHLV   77 (79)
T ss_pred             CeEEEEECCCCCeEEEEEecCCcChHHHHHHHHHHhcCCCCChhHeEEEEcCeeccchhhHHHHhhcccCCceEEEE
Confidence            3678999999988  45555899999999999999875  5689999999999999999999996  9999999986

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

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

Probab=99.66  E-value=2.3e-16  Score=94.23  Aligned_cols=68  Identities=32%  Similarity=0.655  Sum_probs=64.3

Q ss_pred             CCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            8 LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         8 ~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      .+|+.+++++++++||.+||++|+..+++|++.|+|+|+|+.|+|+.+|++|++.++++|++.++..+
T Consensus         5 l~g~~~~l~v~~~~TV~~lK~~i~~~~gip~~~q~L~~~G~~L~d~~tL~~~~i~~g~~l~v~~~~~g   72 (76)
T cd01800           5 LNGQMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQYEGIFIKDSNSLAYYNLANGTIIHLQLKERG   72 (76)
T ss_pred             cCCeEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCEEcCCCCcHHHcCCCCCCEEEEEEecCC
Confidence            37899999999999999999999999999999999999999999999999999999999999988654

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.

>cd01763 Sumo Small ubiquitin-related modifier (SUMO)

Probab=99.62  E-value=3e-15  Score=91.61  Aligned_cols=75  Identities=17%  Similarity=0.444  Sum_probs=71.3

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+..+|+.+.+++.+++|+..||++++++.++|++.|+|+|+|+.|+++.|+.+|++.++++|++.++..+
T Consensus        12 i~I~v~~~~g~~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f~G~~L~~~~T~~~l~m~d~d~I~v~l~l~G   86 (87)
T cd01763          12 INLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLFDGQRIRDNQTPDDLGMEDGDEIEVMLEQTG   86 (87)
T ss_pred             EEEEEECCCCCEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEECCeECCCCCCHHHcCCCCCCEEEEEEeccc
Confidence            679999999999999999999999999999999999999999999999999999999999999999999887643

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

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

Probab=99.62  E-value=5.9e-16  Score=84.79  Aligned_cols=70  Identities=84%  Similarity=1.209  Sum_probs=66.7

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEE
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~  146 (154)
                      |.+.+++.+|+.+.++++++++|..+|..++++.|+||.+|+|+|.|+.+.|+.|-++|++.-||.+|++
T Consensus         1 m~iKvktLt~KeIeidIep~DkverIKErvEEkeGIPp~qqrli~~gkqm~DD~tA~~Y~~~~GSVlHlv   70 (70)
T KOG0005|consen    1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYAGKQMNDDKTAAHYNLLGGSVLHLV   70 (70)
T ss_pred             CeeeEeeeccceEEEeeCcchHHHHHHHHhhhhcCCCchhhhhhhccccccccccHHHhhhccceeEeeC
Confidence            5678899999999999999999999999999999999999999999999999999999999999999863

>smart00213 UBQ Ubiquitin homologues

Probab=99.61  E-value=2.9e-15  Score=86.39  Aligned_cols=64  Identities=61%  Similarity=0.864  Sum_probs=60.9

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceeccccccccc
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKES   65 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~   65 (154)
                      |+|+|+..+ +.+.+++++++||++||++++..+++|++.|+|.|+|+.|.|+.+|++|++++++
T Consensus         1 ~~i~vk~~~-~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~~g~~L~d~~tL~~~~i~~~~   64 (64)
T smart00213        1 IELTVKTLD-GTITLEVKPSDTVSELKEKIAELTGIPVEQQRLIYKGKVLEDDRTLADYNIQDGS   64 (64)
T ss_pred             CEEEEEECC-ceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCEECCCCCCHHHcCCcCCC
Confidence            789999988 7899999999999999999999999999999999999999999999999998774

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

>smart00213 UBQ Ubiquitin homologues

Probab=99.59  E-value=5.1e-15  Score=85.37  Aligned_cols=64  Identities=50%  Similarity=0.826  Sum_probs=60.2

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGS  141 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~  141 (154)
                      |.|+|+..+ +.+.+++++++||++||++++..+|+|++.|+|+|+|+.|.|+.+|++||+.+|+
T Consensus         1 ~~i~vk~~~-~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~~g~~L~d~~tL~~~~i~~~~   64 (64)
T smart00213        1 IELTVKTLD-GTITLEVKPSDTVSELKEKIAELTGIPVEQQRLIYKGKVLEDDRTLADYNIQDGS   64 (64)
T ss_pred             CEEEEEECC-ceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCEECCCCCCHHHcCCcCCC
Confidence            578888887 6889999999999999999999999999999999999999999999999999885

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=99.57  E-value=8.4e-15  Score=86.95  Aligned_cols=63  Identities=29%  Similarity=0.429  Sum_probs=57.8

Q ss_pred             cCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecC-CCCcccccccC-CCCEEEEEE
Q 040824           84 LTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLA-DDKTARDYNIE-GGSVLHLVL  147 (154)
Q Consensus        84 ~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~-d~~~L~~~~i~-~~~~i~~~~  147 (154)
                      ..|.++.+++++++||++||+++++++|+|++.|+| |.|+.|. |+.+|++||+. +|+++++.+
T Consensus        10 ~~~~t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL-~~G~~L~dD~~tL~~ygi~~~g~~~~l~~   74 (75)
T cd01799          10 SHTVTIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRW-VIGQRLARDQETLYSHGIRTNGDSAFLYI   74 (75)
T ss_pred             cCCCeEEEEECCCCcHHHHHHHHHHHHCcCHHHEEE-EcCCeeCCCcCCHHHcCCCCCCCEEEEEe
Confidence            467788999999999999999999999999999999 9998885 77999999997 889999875

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

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

Probab=99.56  E-value=2.8e-15  Score=98.15  Aligned_cols=76  Identities=96%  Similarity=1.328  Sum_probs=73.3

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecc
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~   76 (154)
                      |+|+|+.+.+++..+++.+++||..+|++|+++.++|++.|+|+|.|+.|.|..+|+||+|...+++++++...++
T Consensus         1 m~ifVk~l~~kti~~eve~~~ti~~~Kakiq~~egIp~dqqrlifag~qLedgrtlSDY~Iqkestl~l~l~l~Gg   76 (156)
T KOG0004|consen    1 MQIFVKTLTGKTITLEVEANDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   76 (156)
T ss_pred             CccchhhccccceeeeecccccHHHHHHhhhcccCCCchhhhhhhhhcccccCCccccccccccceEEEEEEecCC
Confidence            8899999999999999999999999999999999999999999999999999999999999999999999987654

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

Probab=99.56  E-value=6.8e-16  Score=94.51  Aligned_cols=76  Identities=99%  Similarity=1.337  Sum_probs=72.3

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecc
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~   76 (154)
                      |+++++...|++..+++.+++||..+|+.|..+.|+||+.|+|.|+|+.|+|..++++||+...+++++.++..++
T Consensus         1 ~~~~~~~~~GKT~~le~EpS~ti~~vKA~i~~~~Gi~~~~~~L~~~~k~LED~~Tla~Y~i~~~~Tl~~~~rL~GG   76 (128)
T KOG0003|consen    1 MQIFVKTLTGKTITLEVEPSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (128)
T ss_pred             CcEEEEEeeCceEEEEecccchHHHHHHHhccccCCCHHHHHHHhcccccccCCcccccCccchhhhhhhHHHhcC
Confidence            6788999999999999999999999999999999999999999999999999999999999999999999887654

>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1

Probab=99.55  E-value=1.9e-14  Score=85.43  Aligned_cols=69  Identities=29%  Similarity=0.365  Sum_probs=60.2

Q ss_pred             EEEE--EeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEec-cCceecccccc-cccceeeee
Q 040824            2 QIFV--KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE-DGRTLADYNIQ-KESTLHLVL   71 (154)
Q Consensus         2 ~v~v--~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~-d~~~l~~~~i~-~~~~i~l~~   71 (154)
                      ++.|  +...|.++.+++++++||++||++++.++|+|++.|+| |.|+.|. |+.+|++|++. +|+++++.+
T Consensus         2 ~~~~~~~~~~~~t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL-~~G~~L~dD~~tL~~ygi~~~g~~~~l~~   74 (75)
T cd01799           2 NVSVEDAQSHTVTIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRW-VIGQRLARDQETLYSHGIRTNGDSAFLYI   74 (75)
T ss_pred             EEEEeccccCCCeEEEEECCCCcHHHHHHHHHHHHCcCHHHEEE-EcCCeeCCCcCCHHHcCCCCCCCEEEEEe
Confidence            4555  34467889999999999999999999999999999999 9998885 67899999998 779998764

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.

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=99.55  E-value=1.4e-14  Score=109.69  Aligned_cols=73  Identities=30%  Similarity=0.601  Sum_probs=70.0

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhC---CCCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~---~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |+|+||+..|+.+.+++++++||.+||++|+...+   ++++.|+|+|+|+.|+|+.+|++|+|+++++|++.+..
T Consensus         1 MkItVKtl~g~~~~IeV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLIy~GkiL~Dd~tL~dy~I~e~~~Ivvmv~k   76 (378)
T TIGR00601         1 MTLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVREYKIKEKDFVVVMVSK   76 (378)
T ss_pred             CEEEEEeCCCCEEEEEeCCcChHHHHHHHHHHhhCCCCCChhHeEEEECCEECCCCCcHHHcCCCCCCEEEEEecc
Confidence            89999999999999999999999999999999998   99999999999999999999999999999999888764

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).

>TIGR00601 rad23 UV excision repair protein Rad23

Probab=99.54  E-value=2.1e-14  Score=108.77  Aligned_cols=73  Identities=38%  Similarity=0.724  Sum_probs=69.7

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcC---CCCCceeEEECCeecCCCCcccccccCCCCEEEEEEee
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEG---IPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~---i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      |+|+||+.+|+.+.++|++++||.+||++|+...|   +|+++|+|+|+|+.|+|+.+|++|+|+++++|++++..
T Consensus         1 MkItVKtl~g~~~~IeV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLIy~GkiL~Dd~tL~dy~I~e~~~Ivvmv~k   76 (378)
T TIGR00601         1 MTLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVREYKIKEKDFVVVMVSK   76 (378)
T ss_pred             CEEEEEeCCCCEEEEEeCCcChHHHHHHHHHHhhCCCCCChhHeEEEECCEECCCCCcHHHcCCCCCCEEEEEecc
Confidence            68999999999999999999999999999999998   99999999999999999999999999999999988764

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).

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

Probab=99.53  E-value=6.1e-14  Score=82.92  Aligned_cols=71  Identities=39%  Similarity=0.735  Sum_probs=65.3

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCC-CceeEEECCeecCCCCcccccccCCCCEEEEEE
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPP-VQQRLIYAGKQLADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~-~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      |+|+|+..+|+.+.+.+.+++++..|++.+++..++|+ +.++|.|+|+.|+++.|++++|+++|++|++.+
T Consensus         1 I~i~v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~fdG~~L~~~~T~~~~~ied~d~Idv~I   72 (72)
T PF11976_consen    1 ITIKVRSQDGKEIKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLIFDGKRLDPNDTPEDLGIEDGDTIDVII   72 (72)
T ss_dssp             EEEEEEETTSEEEEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEEETTEEE-TTSCHHHHT-STTEEEEEE-
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCccceEEEEECCEEcCCCCCHHHCCCCCCCEEEEEC
Confidence            57889999999999999999999999999999999999 999999999999999999999999999999874

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 ....

>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP

Probab=99.52  E-value=2.1e-14  Score=84.25  Aligned_cols=54  Identities=26%  Similarity=0.441  Sum_probs=49.3

Q ss_pred             CCCchHHHHHHHHhhhc--CC-CCCceeEEECCeecCCCCcccccccCCCCEEEEEE
Q 040824           94 EPTDTIERIKERVEEKE--GI-PPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        94 ~~~~tv~~LK~~i~~~~--~i-~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      +.++||.+||++|+++.  ++ ++++|+|+|.|+.|+|+.||++|||++|++|+++.
T Consensus        18 ~~~~TV~~LK~kI~~~~~egi~~~dqQrLIy~GKiL~D~~TL~dygI~~gstlhLv~   74 (75)
T cd01815          18 PGGYQVSTLKQLIAAQLPDSLPDPELIDLIHCGRKLKDDQTLDFYGIQSGSTIHILR   74 (75)
T ss_pred             CccCcHHHHHHHHHHhhccCCCChHHeEEEeCCcCCCCCCcHHHcCCCCCCEEEEEe
Confidence            34789999999999996  46 59999999999999999999999999999999875

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.

>cd01769 UBL Ubiquitin-like domain of UBL

Probab=99.49  E-value=1.8e-13  Score=80.01  Aligned_cols=67  Identities=61%  Similarity=0.999  Sum_probs=62.5

Q ss_pred             eeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEE
Q 040824           81 VKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        81 v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      |+..+|+.+.+.+++++|+.+||++|++.+|+|++.|+|.|+|+.++|+.+|.+|++.+++.|+++.
T Consensus         2 v~~~~~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l~~~g~~l~d~~~l~~~~v~~~~~i~v~~   68 (69)
T cd01769           2 VKTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYAGKILKDDKTLSDYGIQDGSTLHLVL   68 (69)
T ss_pred             eEccCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCcCCCCcCCHHHCCCCCCCEEEEEE
Confidence            4566788999999999999999999999999999999999999999999999999999999998864

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.

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

Probab=99.47  E-value=3e-13  Score=79.94  Aligned_cols=71  Identities=34%  Similarity=0.633  Sum_probs=65.7

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCC-CCeEEEEcceEeccCceecccccccccceeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP-DQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~-~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~   71 (154)
                      |+|+|+..+|+.+.+.+.+++++..|++.+++..++++ +..+|.|+|+.|+++.|+++|++.+++.|++.+
T Consensus         1 I~i~v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~fdG~~L~~~~T~~~~~ied~d~Idv~I   72 (72)
T PF11976_consen    1 ITIKVRSQDGKEIKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLIFDGKRLDPNDTPEDLGIEDGDTIDVII   72 (72)
T ss_dssp             EEEEEEETTSEEEEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEEETTEEE-TTSCHHHHT-STTEEEEEE-
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCccceEEEEECCEEcCCCCCHHHCCCCCCCEEEEEC
Confidence            68999999999999999999999999999999999999 999999999999999999999999999998763

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 ....

>cd01795 USP48_C USP ubiquitin-specific protease

Probab=99.44  E-value=2.6e-13  Score=82.58  Aligned_cols=61  Identities=28%  Similarity=0.337  Sum_probs=56.5

Q ss_pred             EEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCc-eecccccccccceeeeee
Q 040824           12 TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGR-TLADYNIQKESTLHLVLR   72 (154)
Q Consensus        12 ~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~-~l~~~~i~~~~~i~l~~~   72 (154)
                      ...+++++++||.+||..|.++++++|.+|+|.++|+.|.|+. +|++||+.+++++.+.++
T Consensus        16 ~~~L~V~~~~TVg~LK~lImQ~f~V~P~dQkL~~dG~~L~DDsrTLssyGv~sgSvl~Llid   77 (107)
T cd01795          16 EKALLVSANQTLKELKIQIMHAFSVAPFDQNLSIDGKILSDDCATLGTLGVIPESVILLKAD   77 (107)
T ss_pred             CceEEeCccccHHHHHHHHHHHhcCCcccceeeecCceeccCCccHHhcCCCCCCEEEEEec
Confidence            4678999999999999999999999999999999999997755 999999999999988875

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,

>cd01769 UBL Ubiquitin-like domain of UBL

Probab=99.44  E-value=4e-13  Score=78.49  Aligned_cols=68  Identities=66%  Similarity=0.966  Sum_probs=63.1

Q ss_pred             EEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeee
Q 040824            4 FVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (154)
Q Consensus         4 ~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~   71 (154)
                      +|+..+|+.+.+++++++||.+||++|+..+++|+++|+|.|+|+.|+|+.+|.+|++.+++.|++..
T Consensus         1 ~v~~~~~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l~~~g~~l~d~~~l~~~~v~~~~~i~v~~   68 (69)
T cd01769           1 TVKTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYAGKILKDDKTLSDYGIQDGSTLHLVL   68 (69)
T ss_pred             CeEccCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCcCCCCcCCHHHCCCCCCCEEEEEE
Confidence            36777899999999999999999999999999999999999999999999999999999999987753

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

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

Probab=99.43  E-value=1.7e-13  Score=104.75  Aligned_cols=73  Identities=37%  Similarity=0.592  Sum_probs=69.3

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~   74 (154)
                      ++|+||+.++ .+.+.+..+.||.+||+.|.+.++.+++.++|+|.|++|+|+.+|..|||.+|.+|||+++..
T Consensus        16 irV~Vkt~~d-k~~~~V~~~ssV~qlKE~I~~~f~a~~dqlvLIfaGrILKD~dTL~~~gI~Dg~TvHLVik~~   88 (493)
T KOG0010|consen   16 IRVTVKTPKD-KYEVNVASDSSVLQLKELIAQRFGAPPDQLVLIYAGRILKDDDTLKQYGIQDGHTVHLVIKSQ   88 (493)
T ss_pred             eEEEEecCCc-ceeEecccchHHHHHHHHHHHhcCCChhHeeeeecCccccChhhHHHcCCCCCcEEEEEeccC
Confidence            4799999887 799999999999999999999999999999999999999999999999999999999999854

>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP

Probab=99.43  E-value=1.5e-13  Score=80.67  Aligned_cols=53  Identities=30%  Similarity=0.495  Sum_probs=48.4

Q ss_pred             CCCcHHHHHHHHHhHh--CC-CCCCeEEEEcceEeccCceecccccccccceeeee
Q 040824           19 SSDTIDNVKAKIQDKE--GI-PPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (154)
Q Consensus        19 ~~~tv~~lk~~i~~~~--~~-~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~   71 (154)
                      .++||.+||++|+++.  ++ +++.|+|+|.|+.|+|+.+|++|+|+++++||++.
T Consensus        19 ~~~TV~~LK~kI~~~~~egi~~~dqQrLIy~GKiL~D~~TL~dygI~~gstlhLv~   74 (75)
T cd01815          19 GGYQVSTLKQLIAAQLPDSLPDPELIDLIHCGRKLKDDQTLDFYGIQSGSTIHILR   74 (75)
T ss_pred             ccCcHHHHHHHHHHhhccCCCChHHeEEEeCCcCCCCCCcHHHcCCCCCCEEEEEe
Confidence            3779999999999996  46 49999999999999999999999999999999874

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=99.42  E-value=6.1e-13  Score=80.94  Aligned_cols=63  Identities=22%  Similarity=0.251  Sum_probs=57.7

Q ss_pred             eEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecC-CCCcccccccCCCCEEEEEEeec
Q 040824           88 EIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLA-DDKTARDYNIEGGSVLHLVLALR  150 (154)
Q Consensus        88 ~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~-d~~~L~~~~i~~~~~i~~~~~~~  150 (154)
                      ...+.|++++||.+||.+|.+.+++||++|+|+++|..|. |.+||++||+..++.|++.+..+
T Consensus        16 ~~~L~V~~~~TVg~LK~lImQ~f~V~P~dQkL~~dG~~L~DDsrTLssyGv~sgSvl~LlideP   79 (107)
T cd01795          16 EKALLVSANQTLKELKIQIMHAFSVAPFDQNLSIDGKILSDDCATLGTLGVIPESVILLKADEP   79 (107)
T ss_pred             CceEEeCccccHHHHHHHHHHHhcCCcccceeeecCceeccCCccHHhcCCCCCCEEEEEecCC
Confidence            4578899999999999999999999999999999999876 78899999999999999988653

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,

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

Probab=99.38  E-value=8.9e-13  Score=100.81  Aligned_cols=74  Identities=34%  Similarity=0.585  Sum_probs=69.9

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeec
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALR  150 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~  150 (154)
                      .++|+||+.+. .+.|.|..+.||.+||++|+..++.++++++|+|.|+.|+|+.||..|||+||.+||++++..
T Consensus        15 ~irV~Vkt~~d-k~~~~V~~~ssV~qlKE~I~~~f~a~~dqlvLIfaGrILKD~dTL~~~gI~Dg~TvHLVik~~   88 (493)
T KOG0010|consen   15 LIRVTVKTPKD-KYEVNVASDSSVLQLKELIAQRFGAPPDQLVLIYAGRILKDDDTLKQYGIQDGHTVHLVIKSQ   88 (493)
T ss_pred             eeEEEEecCCc-ceeEecccchHHHHHHHHHHHhcCCChhHeeeeecCccccChhhHHHcCCCCCcEEEEEeccC
Confidence            36788999877 899999999999999999999999999999999999999999999999999999999998864

>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4

Probab=99.38  E-value=5.5e-13  Score=83.45  Aligned_cols=73  Identities=25%  Similarity=0.351  Sum_probs=61.2

Q ss_pred             EEEEEeCCCCEE-EEEEeCCCcHHHHHHHHHhHh-----CCC--CCCeEEEEcceEeccCceecccc------cccccce
Q 040824            2 QIFVKTLTGKTI-TLEVESSDTIDNVKAKIQDKE-----GIP--PDQQRLIFAGKQLEDGRTLADYN------IQKESTL   67 (154)
Q Consensus         2 ~v~v~~~~~~~~-~~~v~~~~tv~~lk~~i~~~~-----~~~--~~~q~L~~~g~~L~d~~~l~~~~------i~~~~~i   67 (154)
                      .|+++..+|..+ +..+++++||.+||++|+...     ++|  ++.|+|+|.|+.|+|+.+|++|+      +....++
T Consensus         6 e~kfrl~dg~digp~~~~~sdTV~~lKekI~~~~p~~ke~~P~~~~~qKLIysGKiLeD~~TL~d~~~p~g~~~~~~~Tm   85 (113)
T cd01814           6 EIKFRLYDGSDIGPKRYPAATTVDFLKERVVSQWPKDKEVGPKTVNEVKLISAGKILENSKTVGECRSPVGDIAGGVITM   85 (113)
T ss_pred             EEEEEccCCCccCccccChhhHHHHHHHHHHHhcccccccCCCCHHHeEEEeCCeecCCCCcHHHhCCcccccCCCceEE
Confidence            466777788665 788899999999999999444     444  99999999999999999999999      5666788


Q ss_pred             eeeeeee
Q 040824           68 HLVLRLR   74 (154)
Q Consensus        68 ~l~~~~~   74 (154)
                      |+++++.
T Consensus        86 Hvvlr~~   92 (113)
T cd01814          86 HVVVQPP   92 (113)
T ss_pred             EEEecCC
Confidence            8888764

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

>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4

Probab=99.37  E-value=1.3e-12  Score=81.74  Aligned_cols=74  Identities=27%  Similarity=0.310  Sum_probs=61.4

Q ss_pred             eeeeeeecCCceE-EEeeCCCchHHHHHHHHhhhc-----CC--CCCceeEEECCeecCCCCcccccc------cCCCCE
Q 040824           77 TMIKVKTLTGKEI-EIDIEPTDTIERIKERVEEKE-----GI--PPVQQRLIYAGKQLADDKTARDYN------IEGGSV  142 (154)
Q Consensus        77 ~~i~v~~~~~~~~-~~~v~~~~tv~~LK~~i~~~~-----~i--~~~~~~l~~~g~~l~d~~~L~~~~------i~~~~~  142 (154)
                      +.|..+..+|..+ ++.+.+++||++||++|++..     ++  ++++|+|+|.|+.|+|+.||++|+      +....+
T Consensus         5 ~e~kfrl~dg~digp~~~~~sdTV~~lKekI~~~~p~~ke~~P~~~~~qKLIysGKiLeD~~TL~d~~~p~g~~~~~~~T   84 (113)
T cd01814           5 IEIKFRLYDGSDIGPKRYPAATTVDFLKERVVSQWPKDKEVGPKTVNEVKLISAGKILENSKTVGECRSPVGDIAGGVIT   84 (113)
T ss_pred             EEEEEEccCCCccCccccChhhHHHHHHHHHHHhcccccccCCCCHHHeEEEeCCeecCCCCcHHHhCCcccccCCCceE
Confidence            4455556677654 688999999999999999665     34  499999999999999999999999      677789


Q ss_pred             EEEEEeec
Q 040824          143 LHLVLALR  150 (154)
Q Consensus       143 i~~~~~~~  150 (154)
                      +|+.++..
T Consensus        85 mHvvlr~~   92 (113)
T cd01814          85 MHVVVQPP   92 (113)
T ss_pred             EEEEecCC
Confidence            99988764

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

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

Probab=99.35  E-value=1.8e-12  Score=94.59  Aligned_cols=74  Identities=38%  Similarity=0.657  Sum_probs=70.8

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhC--CCCCCeEEEEcceEeccCceecccccccccceeeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~--~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~   74 (154)
                      |+|+||++.++.|++++.+++||.++|.+|+...|  +|++.|+|+|+|++|.|+.++.+|+++.+..|.+.++..
T Consensus         1 m~lt~KtL~q~~F~iev~Pe~tV~evK~kIet~~g~dyP~~~QkLIy~GkiL~D~~tv~Eykv~E~~fiVvMlsK~   76 (340)
T KOG0011|consen    1 MKLTVKTLKQQTFTIEVKPEDTVVEVKKKIETEKGPDYPAEQQKLIYSGKILKDETTVGEYKVKEKKFIVVMLSKD   76 (340)
T ss_pred             CeeEeeeccCceeEeecCcchhHHHHHHHHHhccCCCCchhhheeeecceeccCCcchhhhccccCceEEEEEecC
Confidence            89999999999999999999999999999999998  999999999999999999999999999999998887654

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

Probab=99.30  E-value=7.9e-12  Score=91.30  Aligned_cols=74  Identities=32%  Similarity=0.632  Sum_probs=70.2

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcC--CCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeec
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEG--IPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALR  150 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~--i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~  150 (154)
                      |.|++|+..++.+.+++.+++||.++|++|+...|  +|.+.|+|+|+|+.|.|+.++.+|++..++.|-+++...
T Consensus         1 m~lt~KtL~q~~F~iev~Pe~tV~evK~kIet~~g~dyP~~~QkLIy~GkiL~D~~tv~Eykv~E~~fiVvMlsK~   76 (340)
T KOG0011|consen    1 MKLTVKTLKQQTFTIEVKPEDTVVEVKKKIETEKGPDYPAEQQKLIYSGKILKDETTVGEYKVKEKKFIVVMLSKD   76 (340)
T ss_pred             CeeEeeeccCceeEeecCcchhHHHHHHHHHhccCCCCchhhheeeecceeccCCcchhhhccccCceEEEEEecC
Confidence            67999999999999999999999999999999999  999999999999999999999999999999888887654

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

Probab=99.28  E-value=2.5e-11  Score=73.67  Aligned_cols=71  Identities=21%  Similarity=0.365  Sum_probs=58.4

Q ss_pred             EEEEEeCC-CCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEE-Ecce-----Ee-ccCceecccccccccceeeeee
Q 040824            2 QIFVKTLT-GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAGK-----QL-EDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         2 ~v~v~~~~-~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~-~~g~-----~L-~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      .|.|.... ....+.++++++||.+||++++..+|++|+.|+|. |.|+     .| +|+.+|++|++.+|.+||+.-.
T Consensus         3 ~v~i~~~~~~~~~ekr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~~~~~~~~~~l~~d~~~L~~y~~~dg~~IhVvD~   81 (84)
T cd01789           3 TVNITSSADSFSFEKKYSRGLTIAELKKKLELVVGTPASSMRLQLFDGDDKLVSKLDDDDALLGSYPVDDGCRIHVIDV   81 (84)
T ss_pred             EEEEEeCCCceeeeEecCCCCcHHHHHHHHHHHHCCCccceEEEEEcCCCCeEeecCCCccEeeeccCCCCCEEEEEeC
Confidence            56676644 23355679999999999999999999999999995 7776     45 6777999999999999988743

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.

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

Probab=99.28  E-value=3.7e-11  Score=72.96  Aligned_cols=70  Identities=23%  Similarity=0.411  Sum_probs=57.4

Q ss_pred             eeeeecC-CceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEE-ECCe-----ec-CCCCcccccccCCCCEEEEEEe
Q 040824           79 IKVKTLT-GKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI-YAGK-----QL-ADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        79 i~v~~~~-~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~-~~g~-----~l-~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      +.|.... ....+..++++.||.+||++++..+|+|++.|+|. |.++     .| +|..+|++||+++|++|||.-.
T Consensus         4 v~i~~~~~~~~~ekr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~~~~~~~~~~l~~d~~~L~~y~~~dg~~IhVvD~   81 (84)
T cd01789           4 VNITSSADSFSFEKKYSRGLTIAELKKKLELVVGTPASSMRLQLFDGDDKLVSKLDDDDALLGSYPVDDGCRIHVIDV   81 (84)
T ss_pred             EEEEeCCCceeeeEecCCCCcHHHHHHHHHHHHCCCccceEEEEEcCCCCeEeecCCCccEeeeccCCCCCEEEEEeC
Confidence            4444422 33456679999999999999999999999999995 7777     35 6888999999999999998753

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.

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

Probab=99.22  E-value=6.2e-11  Score=72.51  Aligned_cols=70  Identities=27%  Similarity=0.480  Sum_probs=56.0

Q ss_pred             eeeeeecCC--ceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEEC----Ce---ec-CCCCcccccccCCCCEEEEEE
Q 040824           78 MIKVKTLTG--KEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYA----GK---QL-ADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        78 ~i~v~~~~~--~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~----g~---~l-~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      .|+|.....  ...+..++.+.||++||++++..+|+|++.|+|.+.    +.   .+ +|..+|.+||+.+|++|+|.-
T Consensus         3 ~l~It~~~~~~~~~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~~~~~~~~~~~~~dd~~~L~~y~~~dg~~i~V~D   82 (87)
T PF14560_consen    3 KLFITSSNSKQRSVEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLKSDKDDSKIEELDDDDATLGSYGIKDGMRIHVVD   82 (87)
T ss_dssp             EEEEEESSSSSSEEEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE-TSSSSEEEESSGSSSBCCHHT-STTEEEEEEE
T ss_pred             EEEEEeCCCCCeeEEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEEecCCCccccccCCCccEeecCCCCCCCEEEEEe
Confidence            455555443  478899999999999999999999999999999865    11   23 578999999999999999864

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

Probab=99.19  E-value=1.6e-10  Score=70.72  Aligned_cols=71  Identities=27%  Similarity=0.535  Sum_probs=56.9

Q ss_pred             EEEEEeCCC--CEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEc----c---eEe-ccCceecccccccccceeeee
Q 040824            2 QIFVKTLTG--KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA----G---KQL-EDGRTLADYNIQKESTLHLVL   71 (154)
Q Consensus         2 ~v~v~~~~~--~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~----g---~~L-~d~~~l~~~~i~~~~~i~l~~   71 (154)
                      +|.|.....  ...+.++++++||++||.+++..+|+|++.|+|.+.    +   ..+ +|+.+|.+||+.+|.+|++.-
T Consensus         3 ~l~It~~~~~~~~~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~~~~~~~~~~~~~dd~~~L~~y~~~dg~~i~V~D   82 (87)
T PF14560_consen    3 KLFITSSNSKQRSVEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLKSDKDDSKIEELDDDDATLGSYGIKDGMRIHVVD   82 (87)
T ss_dssp             EEEEEESSSSSSEEEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE-TSSSSEEEESSGSSSBCCHHT-STTEEEEEEE
T ss_pred             EEEEEeCCCCCeeEEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEEecCCCccccccCCCccEeecCCCCCCCEEEEEe
Confidence            577777655  378899999999999999999999999999999865    1   334 557799999999999998764


Q ss_pred             e
Q 040824           72 R   72 (154)
Q Consensus        72 ~   72 (154)
                      .
T Consensus        83 ~   83 (87)
T PF14560_consen   83 T   83 (87)
T ss_dssp             -
T ss_pred             C
Confidence            3

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

Probab=99.18  E-value=1.8e-10  Score=66.32  Aligned_cols=72  Identities=26%  Similarity=0.369  Sum_probs=64.2

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEc-----ceEeccCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA-----GKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~-----g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      ++|+|+.++...+.+.+++..+|.++|++|+...+++- .|+|.|.     .+.|++.++|++|||..+..|.+.-+.
T Consensus         1 iqVtV~q~g~~dl~l~vnPy~pI~k~K~kI~~~~~~~g-~qrLsfQepgg~rqlL~s~~sLA~yGiFs~~~i~lleT~   77 (80)
T cd01811           1 IQVTVEQTGYSDWILRVNPYSPIRKIKEKIRRSRNCSG-LQRLSFQEPGGERQLLSSRKSLADYGIFSKTNICLLETF   77 (80)
T ss_pred             CEEEeeecCCCceEEEeCCcchHHHHHHHHHHhhCccc-ceEEEeecCCcccccccccccHhhhcceeccEEEEEecC
Confidence            68999999999999999999999999999999999988 9999986     267899999999999988877665543

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=99.16  E-value=1.3e-10  Score=72.48  Aligned_cols=73  Identities=32%  Similarity=0.458  Sum_probs=62.1

Q ss_pred             CEEEEEeCCCCE-EEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceeccccc-------ccccceeeeee
Q 040824            1 MQIFVKTLTGKT-ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNI-------QKESTLHLVLR   72 (154)
Q Consensus         1 m~v~v~~~~~~~-~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i-------~~~~~i~l~~~   72 (154)
                      |.++++.+..++ +.+++.++.||.+||++|+.....||+.|+|+-.++.|+|+++|++||+       .+.+++-+.++
T Consensus         1 MdvFlmIrR~KTTiF~dakes~tVlelK~~iegI~k~pp~dQrL~kd~qvLeD~kTL~d~g~t~~~akaq~pA~vgLa~r   80 (119)
T cd01788           1 MDVFLMIRRHKTTIFTDAKESTTVYELKRIVEGILKRPPEDQRLYKDDQLLDDGKTLGDCGFTSQTARPQAPATVGLAFR   80 (119)
T ss_pred             CceEEEEEecceEEEeecCCcccHHHHHHHHHHHhcCChhHheeecCceeecccccHHHcCccccccccCCCCeEEEEEe
Confidence            567776665554 7789999999999999999999999999999977899999999999999       55677766665


Q ss_pred             e
Q 040824           73 L   73 (154)
Q Consensus        73 ~   73 (154)
                      .
T Consensus        81 ~   81 (119)
T cd01788          81 S   81 (119)
T ss_pred             c
Confidence            3

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.

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

Probab=99.12  E-value=9.7e-10  Score=67.11  Aligned_cols=78  Identities=21%  Similarity=0.408  Sum_probs=73.1

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      -+++.|+..++....|.+..+++...|+...|++.|++....+++|+|..+.+..|.++++.++||.|.++..+.||.
T Consensus        20 hi~LKV~gqd~~~~~Fkikr~t~LkKLM~aYc~r~Gl~~~s~RFlFdG~rI~~~~TP~~L~mEd~D~Iev~~~q~gG~   97 (99)
T KOG1769|consen   20 HINLKVKGQDGSVVVFKIKRHTPLKKLMKAYCERQGLSMNSLRFLFDGQRIRETHTPADLEMEDGDEIEVVQEQTGGF   97 (99)
T ss_pred             eEEEEEecCCCCEEEEEeecCChHHHHHHHHHHHcCCccceEEEEECCcCcCCCCChhhhCCcCCcEEEEEeecccCC
Confidence            366778887888899999999999999999999999999999999999999999999999999999999999999884

>PLN02560 enoyl-CoA reductase

Probab=99.04  E-value=8.9e-10  Score=81.87  Aligned_cols=69  Identities=25%  Similarity=0.512  Sum_probs=59.4

Q ss_pred             eeeeeeecCCceE---EEeeCCCchHHHHHHHHhhhcCC-CCCceeEEEC---C----eecCCCCcccccccCCCCEEEE
Q 040824           77 TMIKVKTLTGKEI---EIDIEPTDTIERIKERVEEKEGI-PPVQQRLIYA---G----KQLADDKTARDYNIEGGSVLHL  145 (154)
Q Consensus        77 ~~i~v~~~~~~~~---~~~v~~~~tv~~LK~~i~~~~~i-~~~~~~l~~~---g----~~l~d~~~L~~~~i~~~~~i~~  145 (154)
                      |.|+|+..+|+.+   .+++++++||++||++|++..+. ++++|+|.+.   |    ..++|+.+|+++|+++|++|++
T Consensus         1 M~I~Vk~~~Gk~i~~~~lev~~~aTV~dLK~~Isk~~~~~~~~RqRL~~~~~~gk~~g~~L~d~ktL~d~gv~~gstLy~   80 (308)
T PLN02560          1 MKVTVVSRSGREIIKGGLEVPDSATVADLKKAIHKRKKKYYPSRQRLTLPLPPGKTRPTVLDDSKSLKDYGLGDGGTVVF   80 (308)
T ss_pred             CEEEEEcCCCCeecceeEEcCCCCcHHHHHHHHHHHcCCCChhheEEEEecCCCCcCccccCCCCCHHhcCCCCCceEEE
Confidence            5677887778776   79999999999999999999986 8999999973   3    3788999999999999998654

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

Probab=99.03  E-value=4.1e-09  Score=61.65  Aligned_cols=73  Identities=59%  Similarity=0.944  Sum_probs=67.1

Q ss_pred             eeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecC
Q 040824           79 IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRG  151 (154)
Q Consensus        79 i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~g  151 (154)
                      +++....|+...+.+.+..++..+|.+++...++|+..|++.+.|+.|.|+.++.+|+|..++++++..+.++
T Consensus         2 ~~~~~~~gk~~~~~~~~~~~i~~~k~~i~~~~~~~~~~q~~~~~~~~l~d~~~l~~~~i~~~~~~~l~~~~~~   74 (75)
T KOG0001|consen    2 IFVKTLDGKTITLEVSPSDTIEVVKAKIRDKEGIPVDQQRLIFGGKPLEDGRTLADYNIQEGSTLHLVLSLRG   74 (75)
T ss_pred             EEEEecCCCEEEEEecCCCHHHHHHHHHHhhcCCCCeeEEEEECCEECcCCCcHHHhCCCCCCEEEEEEecCC
Confidence            3455678899999999999999999999999999999999999999999999999999999999999888764

>PLN02560 enoyl-CoA reductase

Probab=99.02  E-value=9.1e-10  Score=81.84  Aligned_cols=70  Identities=31%  Similarity=0.544  Sum_probs=61.7

Q ss_pred             CEEEEEeCCCCEE---EEEEeCCCcHHHHHHHHHhHhCC-CCCCeEEEEc---c----eEeccCceecccccccccceee
Q 040824            1 MQIFVKTLTGKTI---TLEVESSDTIDNVKAKIQDKEGI-PPDQQRLIFA---G----KQLEDGRTLADYNIQKESTLHL   69 (154)
Q Consensus         1 m~v~v~~~~~~~~---~~~v~~~~tv~~lk~~i~~~~~~-~~~~q~L~~~---g----~~L~d~~~l~~~~i~~~~~i~l   69 (154)
                      |+|+|+.++|+.+   .+++++++||++||++|+++.+. ++++|+|.+.   |    ..|+|+.+|+++|+++++++++
T Consensus         1 M~I~Vk~~~Gk~i~~~~lev~~~aTV~dLK~~Isk~~~~~~~~RqRL~~~~~~gk~~g~~L~d~ktL~d~gv~~gstLy~   80 (308)
T PLN02560          1 MKVTVVSRSGREIIKGGLEVPDSATVADLKKAIHKRKKKYYPSRQRLTLPLPPGKTRPTVLDDSKSLKDYGLGDGGTVVF   80 (308)
T ss_pred             CEEEEEcCCCCeecceeEEcCCCCcHHHHHHHHHHHcCCCChhheEEEEecCCCCcCccccCCCCCHHhcCCCCCceEEE
Confidence            8899999888886   79999999999999999999886 8999999973   3    4789999999999999998764


Q ss_pred             e
Q 040824           70 V   70 (154)
Q Consensus        70 ~   70 (154)
                      .
T Consensus        81 k   81 (308)
T PLN02560         81 K   81 (308)
T ss_pred             E
Confidence            4

>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=99.01  E-value=6.7e-10  Score=66.60  Aligned_cols=71  Identities=27%  Similarity=0.493  Sum_probs=44.5

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECC---eec--CCCCcccccccCCCCEEEEE
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAG---KQL--ADDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g---~~l--~d~~~L~~~~i~~~~~i~~~  146 (154)
                      ..|.|.|++.+| ...+++++++|+.+|+++|++.+++|...+.|..+.   ..+  +++.+|+++|++.||.|++.
T Consensus         3 ~~milRvrS~dG-~~Rie~~~~~t~~~L~~kI~~~l~~~~~~~~L~~~~~~~~~l~s~~~~tl~~lglkHGdmlyL~   78 (80)
T PF11543_consen    3 SSMILRVRSKDG-MKRIEVSPSSTLSDLKEKISEQLSIPDSSQSLSKDRNNKEELKSSDSKTLSSLGLKHGDMLYLK   78 (80)
T ss_dssp             ---EEEEE-SSE-EEEEEE-TTSBHHHHHHHHHHHS---TTT---BSSGGGGGCSSS-TT-CCCCT---TT-EEE--
T ss_pred             ccEEEEEECCCC-CEEEEcCCcccHHHHHHHHHHHcCCCCcceEEEecCCCCcccccCCcCCHHHcCCCCccEEEEe
Confidence            457888999887 778899999999999999999999999988886332   244  47889999999999999864

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.

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

Probab=98.99  E-value=7.8e-10  Score=91.04  Aligned_cols=74  Identities=34%  Similarity=0.579  Sum_probs=70.0

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecc
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~   76 (154)
                      .|+||+++.++.++.|...+||.+||+.+..+.+++.+.|+|+|.|+.|.|++++.+|++ +|.+|||+-++.++
T Consensus         4 ~v~vktld~r~~t~~ig~q~ti~~~~d~~r~~~ni~s~~qr~i~~grvl~~~k~vq~~~v-dgk~~hlverppp~   77 (1143)
T KOG4248|consen    4 NVLVKTLDSRTRTFIIGAQMTIKEFKDHIRASVNIPSEKQRLIYQGRVLQDDKKVQEYNV-DGKVIHLVERPPPQ   77 (1143)
T ss_pred             ceeeeecccceeEEEechHHHHHHHHHHHHHhcccccccceeeecceeeccchhhhhccC-CCeEEEeeccCCCC
Confidence            489999999999999999999999999999999999999999999999999999999999 99999999886543

>cd01788 ElonginB Ubiquitin-like domain of Elongin B

Probab=98.96  E-value=4.1e-09  Score=65.91  Aligned_cols=65  Identities=26%  Similarity=0.283  Sum_probs=57.2

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCccccccc-------CCCCEEEEEEee
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNI-------EGGSVLHLVLAL  149 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i-------~~~~~i~~~~~~  149 (154)
                      +..++.+++.++.||.+||++|+.....||++|+|+-.+..|+|++||++||+       ++-+++-+..+.
T Consensus        10 ~KTTiF~dakes~tVlelK~~iegI~k~pp~dQrL~kd~qvLeD~kTL~d~g~t~~~akaq~pA~vgLa~r~   81 (119)
T cd01788          10 HKTTIFTDAKESTTVYELKRIVEGILKRPPEDQRLYKDDQLLDDGKTLGDCGFTSQTARPQAPATVGLAFRS   81 (119)
T ss_pred             cceEEEeecCCcccHHHHHHHHHHHhcCChhHheeecCceeecccccHHHcCccccccccCCCCeEEEEEec
Confidence            44578899999999999999999999999999999966678999999999999       567777776664

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.

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

Probab=98.95  E-value=1.2e-08  Score=64.91  Aligned_cols=73  Identities=34%  Similarity=0.527  Sum_probs=54.1

Q ss_pred             eeeeeeecCCc-eEEEeeCCCchHHHHHHHHhhhcC-------CCCCceeEEECCeecCCCCcccccccCCCC------E
Q 040824           77 TMIKVKTLTGK-EIEIDIEPTDTIERIKERVEEKEG-------IPPVQQRLIYAGKQLADDKTARDYNIEGGS------V  142 (154)
Q Consensus        77 ~~i~v~~~~~~-~~~~~v~~~~tv~~LK~~i~~~~~-------i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~------~  142 (154)
                      +.|.....+|. ..++.+++++||++||+.|...+.       ..+..++|+|.|+.|+|+.+|+++++..|+      +
T Consensus         3 i~lkf~l~~G~d~~~~~~~~~~TV~~lKe~i~~~WP~d~~~~p~s~~~lRLI~~GriL~d~~tL~~~~~~~~~~~~~~~v   82 (111)
T PF13881_consen    3 IELKFRLADGKDIGPFRFDPSTTVADLKERIWAEWPEDWEERPKSPSDLRLIYAGRILEDNKTLSDCRLPSGETPGGPTV   82 (111)
T ss_dssp             EEEEEEETTS-EEEEEEE-TTSBHHHHHHHHHHSSSTTSSSTT-SGGGEEEEETTEEE-SSSBTGGGT--TTSETT--EE
T ss_pred             EEEEEEEeCCCcccccccCccChHHHHHHHHHHHCccccccCCCChhhEEEEeCCeecCCcCcHHHhCCCCCCCCCCCEE
Confidence            34444555888 788999999999999999998774       246678999999999999999999998777      4


Q ss_pred             EEEEEee
Q 040824          143 LHLVLAL  149 (154)
Q Consensus       143 i~~~~~~  149 (154)
                      +|+.++.
T Consensus        83 mHlvvrp   89 (111)
T PF13881_consen   83 MHLVVRP   89 (111)
T ss_dssp             EEEEE-S
T ss_pred             EEEEecC
Confidence            6666654

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

Probab=98.92  E-value=1e-08  Score=59.91  Aligned_cols=71  Identities=83%  Similarity=1.124  Sum_probs=65.7

Q ss_pred             EEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         3 v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      +.+....|+.+.+++....++..+|.+++...+++++.|++.+.|+.|.|+.++.+|+|..++++++..+.
T Consensus         2 ~~~~~~~gk~~~~~~~~~~~i~~~k~~i~~~~~~~~~~q~~~~~~~~l~d~~~l~~~~i~~~~~~~l~~~~   72 (75)
T KOG0001|consen    2 IFVKTLDGKTITLEVSPSDTIEVVKAKIRDKEGIPVDQQRLIFGGKPLEDGRTLADYNIQEGSTLHLVLSL   72 (75)
T ss_pred             EEEEecCCCEEEEEecCCCHHHHHHHHHHhhcCCCCeeEEEEECCEECcCCCcHHHhCCCCCCEEEEEEec
Confidence            45667889999999999999999999999999999999999999999999999999999999999887664

>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13

Probab=98.89  E-value=7.4e-09  Score=61.82  Aligned_cols=52  Identities=27%  Similarity=0.357  Sum_probs=46.9

Q ss_pred             CCCchHHHHHHHHhhhcC-CCCCceeEE--ECCeecCCCCcccccccCCCCEEEE
Q 040824           94 EPTDTIERIKERVEEKEG-IPPVQQRLI--YAGKQLADDKTARDYNIEGGSVLHL  145 (154)
Q Consensus        94 ~~~~tv~~LK~~i~~~~~-i~~~~~~l~--~~g~~l~d~~~L~~~~i~~~~~i~~  145 (154)
                      +++.||.+||..+++..+ +++++|+|.  +.|+.|.|+.+|.++|+.+|++||+
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            578999999999999886 589999886  7899999999999999999999876

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

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

Probab=98.86  E-value=2.2e-08  Score=63.68  Aligned_cols=72  Identities=31%  Similarity=0.505  Sum_probs=53.5

Q ss_pred             EEEEEeCCCC-EEEEEEeCCCcHHHHHHHHHhHh-------CCCCCCeEEEEcceEeccCceeccccccccc------ce
Q 040824            2 QIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKE-------GIPPDQQRLIFAGKQLEDGRTLADYNIQKES------TL   67 (154)
Q Consensus         2 ~v~v~~~~~~-~~~~~v~~~~tv~~lk~~i~~~~-------~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~------~i   67 (154)
                      .|+++..+|. .-++.+++++||.+||+.|...-       -..++..+|+|.|+.|+|+.+|+++.+..++      ++
T Consensus         4 ~lkf~l~~G~d~~~~~~~~~~TV~~lKe~i~~~WP~d~~~~p~s~~~lRLI~~GriL~d~~tL~~~~~~~~~~~~~~~vm   83 (111)
T PF13881_consen    4 ELKFRLADGKDIGPFRFDPSTTVADLKERIWAEWPEDWEERPKSPSDLRLIYAGRILEDNKTLSDCRLPSGETPGGPTVM   83 (111)
T ss_dssp             EEEEEETTS-EEEEEEE-TTSBHHHHHHHHHHSSSTTSSSTT-SGGGEEEEETTEEE-SSSBTGGGT--TTSETT--EEE
T ss_pred             EEEEEEeCCCcccccccCccChHHHHHHHHHHHCccccccCCCChhhEEEEeCCeecCCcCcHHHhCCCCCCCCCCCEEE
Confidence            5677777998 78899999999999999998652       2346779999999999999999999987655      45


Q ss_pred             eeeeee
Q 040824           68 HLVLRL   73 (154)
Q Consensus        68 ~l~~~~   73 (154)
                      |+++++
T Consensus        84 Hlvvrp   89 (111)
T PF13881_consen   84 HLVVRP   89 (111)
T ss_dssp             EEEE-S
T ss_pred             EEEecC
Confidence            666554

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

Probab=98.83  E-value=7.3e-09  Score=85.49  Aligned_cols=71  Identities=38%  Similarity=0.594  Sum_probs=67.7

Q ss_pred             eeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEee
Q 040824           78 MIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        78 ~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      .+.||+.+.+...|.+...+||.++|.++++...|+.+.|+++|.|+.|.|++++.+|++ +|-+||+.-|.
T Consensus         4 ~v~vktld~r~~t~~ig~q~ti~~~~d~~r~~~ni~s~~qr~i~~grvl~~~k~vq~~~v-dgk~~hlverp   74 (1143)
T KOG4248|consen    4 NVLVKTLDSRTRTFIIGAQMTIKEFKDHIRASVNIPSEKQRLIYQGRVLQDDKKVQEYNV-DGKVIHLVERP   74 (1143)
T ss_pred             ceeeeecccceeEEEechHHHHHHHHHHHHHhcccccccceeeecceeeccchhhhhccC-CCeEEEeeccC
Confidence            488999999999999999999999999999999999999999999999999999999999 99999998664

>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13

Probab=98.82  E-value=1.2e-08  Score=60.95  Aligned_cols=68  Identities=26%  Similarity=0.318  Sum_probs=53.7

Q ss_pred             EEEEEeCC-CCEEEEEE-eCCCcHHHHHHHHHhHhC-CCCCCeEEE--EcceEeccCceecccccccccceee
Q 040824            2 QIFVKTLT-GKTITLEV-ESSDTIDNVKAKIQDKEG-IPPDQQRLI--FAGKQLEDGRTLADYNIQKESTLHL   69 (154)
Q Consensus         2 ~v~v~~~~-~~~~~~~v-~~~~tv~~lk~~i~~~~~-~~~~~q~L~--~~g~~L~d~~~l~~~~i~~~~~i~l   69 (154)
                      .|.++..+ .....+++ +++.||.+||..+++..+ .++++|+|.  +.|+.|.|+.+|.+||+.+++++++
T Consensus         2 ~i~~~~~~~k~~~~~~~~~~~aTV~dlk~~i~~~~~~~~~~Rqrl~~~~~g~~L~d~~tL~~~gv~~g~~lyv   74 (77)
T cd01801           2 EILDAKRSDKPIGKLKVSSGDATIADLKKLIAKSSPQLTVNRQSLRLEPKGKSLKDDDTLVDLGVGAGATLYV   74 (77)
T ss_pred             eeeccccCcCceeecccCCCCccHHHHHHHHHHHcCCCCcceeEEEeCCCCcccCCcccHhhcCCCCCCEEEE
Confidence            45566655 33323444 478899999999998876 589999996  6799999999999999999998765

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.

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

Probab=98.79  E-value=1.1e-08  Score=61.38  Aligned_cols=69  Identities=29%  Similarity=0.434  Sum_probs=43.3

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcc---eEe--ccCceecccccccccceeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG---KQL--EDGRTLADYNIQKESTLHLV   70 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g---~~L--~d~~~l~~~~i~~~~~i~l~   70 (154)
                      |-|+|+..+| .+.+++++++|+.+|+++|.+.++++++.|.|+.+.   ..+  +++.+|+++|++.|+.+++.
T Consensus         5 milRvrS~dG-~~Rie~~~~~t~~~L~~kI~~~l~~~~~~~~L~~~~~~~~~l~s~~~~tl~~lglkHGdmlyL~   78 (80)
T PF11543_consen    5 MILRVRSKDG-MKRIEVSPSSTLSDLKEKISEQLSIPDSSQSLSKDRNNKEELKSSDSKTLSSLGLKHGDMLYLK   78 (80)
T ss_dssp             -EEEEE-SSE-EEEEEE-TTSBHHHHHHHHHHHS---TTT---BSSGGGGGCSSS-TT-CCCCT---TT-EEE--
T ss_pred             EEEEEECCCC-CEEEEcCCcccHHHHHHHHHHHcCCCCcceEEEecCCCCcccccCCcCCHHHcCCCCccEEEEe
Confidence            5678888764 588899999999999999999999999999987432   344  46779999999999998764

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

>cd00196 UBQ Ubiquitin-like proteins

Probab=98.71  E-value=1.1e-07  Score=53.39  Aligned_cols=63  Identities=40%  Similarity=0.652  Sum_probs=58.1

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEE
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      ++....+.+.++.|+.++++++++++|.+++.+.|.++|..+.+...+.++++.+++.|++..
T Consensus         6 ~~~~~~~~~~~~~tv~~l~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~   68 (69)
T cd00196           6 DGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGKILPDSLTLEDYGLQDGDELVLVP   68 (69)
T ss_pred             CCCEEEEEcCCCCcHHHHHHHHHHHHCcChHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEe
Confidence            677788999999999999999999999999999999999999988888899999999998764

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.

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

Probab=98.63  E-value=1.4e-08  Score=56.76  Aligned_cols=69  Identities=25%  Similarity=0.334  Sum_probs=61.1

Q ss_pred             eeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEE
Q 040824           78 MIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        78 ~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~  146 (154)
                      .+.+...-|+...+.+.+++||+++|+.+++.+|..++...|--.+..++|.-+|++|.+.+|-.+++.
T Consensus         3 ev~~nDrLGKKVRvKCn~dDtiGD~KKliaaQtGT~~~kivl~k~~~i~kd~I~L~dyeihdg~~lely   71 (73)
T KOG3493|consen    3 EVVLNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFKDHITLSDYEIHDGMNLELY   71 (73)
T ss_pred             eehhhhhcCceEEEEeCCcccccCHHHHHHHhhCCChhHhHHHhhhhhhhcccceeeEEeccCccEEEe
Confidence            344556678899999999999999999999999999999988877778999999999999999988775

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

Probab=98.60  E-value=4.8e-08  Score=58.37  Aligned_cols=78  Identities=23%  Similarity=0.398  Sum_probs=72.8

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      .+.+.|...++..+-|.+..+.+...|....+++.|-.-+..|++|+|+.++.++|..+++.++++.|++...+.||+
T Consensus        24 hinLkvv~qd~telfFkiKktT~f~klm~af~~rqGK~m~slRfL~dG~rI~~dqTP~dldmEdnd~iEav~eQvGG~  101 (103)
T COG5227          24 HINLKVVDQDGTELFFKIKKTTTFKKLMDAFSRRQGKNMSSLRFLFDGKRIDLDQTPGDLDMEDNDEIEAVTEQVGGA  101 (103)
T ss_pred             ccceEEecCCCCEEEEEEeccchHHHHHHHHHHHhCcCcceeEEEEcceecCCCCChhhcCCccchHHHHHHHHhcCc
Confidence            467778788899999999999999999999999999999999999999999999999999999999999988888885

>cd00196 UBQ Ubiquitin-like proteins

Probab=98.56  E-value=3.6e-07  Score=51.26  Aligned_cols=67  Identities=46%  Similarity=0.666  Sum_probs=59.2

Q ss_pred             EEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeee
Q 040824            5 VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (154)
Q Consensus         5 v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~   71 (154)
                      |+..++....+.+.+++|+.++++.+..+.+.+++.+.|+++|..+.+...+.++++.+++.+++..
T Consensus         2 v~~~~~~~~~~~~~~~~tv~~l~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~   68 (69)
T cd00196           2 VKLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGKILPDSLTLEDYGLQDGDELVLVP   68 (69)
T ss_pred             eEecCCCEEEEEcCCCCcHHHHHHHHHHHHCcChHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEe
Confidence            3444678888999999999999999999999999999999999999988888889999999887653

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.

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

Probab=98.53  E-value=9.9e-07  Score=54.04  Aligned_cols=74  Identities=15%  Similarity=0.400  Sum_probs=67.1

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~   74 (154)
                      ++|+|+..++....+.|..+++...|+....+..|++.+..+++|+|+.++...|.++++..+++.|.+.....
T Consensus        21 i~LKV~gqd~~~~~Fkikr~t~LkKLM~aYc~r~Gl~~~s~RFlFdG~rI~~~~TP~~L~mEd~D~Iev~~~q~   94 (99)
T KOG1769|consen   21 INLKVKGQDGSVVVFKIKRHTPLKKLMKAYCERQGLSMNSLRFLFDGQRIRETHTPADLEMEDGDEIEVVQEQT   94 (99)
T ss_pred             EEEEEecCCCCEEEEEeecCChHHHHHHHHHHHcCCccceEEEEECCcCcCCCCChhhhCCcCCcEEEEEeecc
Confidence            35777776778889999999999999999999999999999999999999999999999999999998776543

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

Probab=98.46  E-value=7e-08  Score=54.03  Aligned_cols=69  Identities=26%  Similarity=0.416  Sum_probs=60.0

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHL   69 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l   69 (154)
                      +++.+...-|+...+.+.+++||+++|..|...+|..++...|.--+..++|+-+|++|.+.++..+.+
T Consensus         2 iev~~nDrLGKKVRvKCn~dDtiGD~KKliaaQtGT~~~kivl~k~~~i~kd~I~L~dyeihdg~~lel   70 (73)
T KOG3493|consen    2 IEVVLNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFKDHITLSDYEIHDGMNLEL   70 (73)
T ss_pred             ceehhhhhcCceEEEEeCCcccccCHHHHHHHhhCCChhHhHHHhhhhhhhcccceeeEEeccCccEEE
Confidence            356677777899999999999999999999999999999988876667789999999999998876644

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

Probab=98.36  E-value=1.2e-06  Score=67.27  Aligned_cols=71  Identities=21%  Similarity=0.330  Sum_probs=63.5

Q ss_pred             eeeeeecCCceEEEe-eCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEee
Q 040824           78 MIKVKTLTGKEIEID-IEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        78 ~i~v~~~~~~~~~~~-v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      .+.|+. .|+.+.+. ++.++|...||+++...+|++|++|+++.+|..+.|+-.+....|++|.+++++-..
T Consensus         5 ~v~VKW-~gk~y~v~~l~~d~t~~vlKaqlf~LTgV~PeRQKv~vKGg~a~dd~~~~al~iKpn~~lmMmGt~   76 (473)
T KOG1872|consen    5 TVIVKW-GGKKYPVETLSTDETPSVLKAQLFALTGVPPERQKVMVKGGLAKDDVDWGALQIKPNETLMMMGTA   76 (473)
T ss_pred             eEeeee-cCccccceeccCCCchHHHHHHHHHhcCCCccceeEEEecccccccccccccccCCCCEEEeeccc
Confidence            355666 67788887 999999999999999999999999999999999999989999999999999887544

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

Probab=98.32  E-value=5.2e-06  Score=48.06  Aligned_cols=68  Identities=24%  Similarity=0.399  Sum_probs=57.5

Q ss_pred             eeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEEC---C--eecCCCCcccccccCCCCEEEEE
Q 040824           78 MIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYA---G--KQLADDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        78 ~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~---g--~~l~d~~~L~~~~i~~~~~i~~~  146 (154)
                      +++|+......+.+.|+|..+|..+|++|....+++- .|+|.|.   |  ..|.+..+|++|||-..-.|.++
T Consensus         2 qVtV~q~g~~dl~l~vnPy~pI~k~K~kI~~~~~~~g-~qrLsfQepgg~rqlL~s~~sLA~yGiFs~~~i~ll   74 (80)
T cd01811           2 QVTVEQTGYSDWILRVNPYSPIRKIKEKIRRSRNCSG-LQRLSFQEPGGERQLLSSRKSLADYGIFSKTNICLL   74 (80)
T ss_pred             EEEeeecCCCceEEEeCCcchHHHHHHHHHHhhCccc-ceEEEeecCCcccccccccccHhhhcceeccEEEEE
Confidence            5677777777899999999999999999999999875 8898874   2  26789999999999888777665

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.

>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=98.30  E-value=4e-06  Score=48.07  Aligned_cols=63  Identities=21%  Similarity=0.270  Sum_probs=47.0

Q ss_pred             ecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEE
Q 040824           83 TLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHL  145 (154)
Q Consensus        83 ~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~  145 (154)
                      ..+++...+.+.++.++.++-+..+++++++++...|.++++.++-+.+..-.|+.+|+.+++
T Consensus         3 ~~~~rr~~vkvtp~~~l~~VL~eac~k~~l~~~~~~L~h~~k~ldlslp~R~snL~n~akLeL   65 (65)
T PF11470_consen    3 CYNFRRFKVKVTPNTTLNQVLEEACKKFGLDPSSYDLKHNNKPLDLSLPFRLSNLPNNAKLEL   65 (65)
T ss_dssp             -TTS-EEEE---TTSBHHHHHHHHHHHTT--GGG-EEEETTEEESSS-BHHHH---SS-EEEE
T ss_pred             ccCCcEEEEEECCCCCHHHHHHHHHHHcCCCccceEEEECCEEeccccceeecCCCCCCEEeC
Confidence            346788999999999999999999999999999999999999999999999999999999875

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

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

Probab=98.23  E-value=2.9e-06  Score=65.29  Aligned_cols=70  Identities=24%  Similarity=0.431  Sum_probs=63.6

Q ss_pred             EEEEeCCCCEEEEE-EeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824            3 IFVKTLTGKTITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         3 v~v~~~~~~~~~~~-v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |.|+ |.|+.++++ ++.++|+..||+++...++++|++|++...|..+.|+..+....|+++.++++.-+.
T Consensus         6 v~VK-W~gk~y~v~~l~~d~t~~vlKaqlf~LTgV~PeRQKv~vKGg~a~dd~~~~al~iKpn~~lmMmGt~   76 (473)
T KOG1872|consen    6 VIVK-WGGKKYPVETLSTDETPSVLKAQLFALTGVPPERQKVMVKGGLAKDDVDWGALQIKPNETLMMMGTA   76 (473)
T ss_pred             Eeee-ecCccccceeccCCCchHHHHHHHHHhcCCCccceeEEEecccccccccccccccCCCCEEEeeccc
Confidence            5555 678889887 999999999999999999999999999999999999999999999999999888654

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

Probab=98.20  E-value=3e-06  Score=62.28  Aligned_cols=59  Identities=29%  Similarity=0.628  Sum_probs=54.5

Q ss_pred             eEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEE
Q 040824           88 EIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        88 ~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~  146 (154)
                      .++++|+.+.+|.+||+.++...|+|+++.+++|.|++|.++.++..+.+..-+.++++
T Consensus        15 ~l~v~v~~~t~I~~lke~Vak~~gvp~D~L~viFaGKeLs~~ttv~~cDL~qqs~~hi~   73 (446)
T KOG0006|consen   15 GLPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELSNDTTVQNCDLSQQSATHIM   73 (446)
T ss_pred             ceeEEEecCCCHHHHHHHHHHhhCCChhheEEEEeccccccCceeecccccccchhhhh
Confidence            47899999999999999999999999999999999999999999998888777777766

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

Probab=98.18  E-value=2.5e-06  Score=51.71  Aligned_cols=62  Identities=29%  Similarity=0.436  Sum_probs=51.5

Q ss_pred             CEEEEEeC-CCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEE-cc-eEeccCceecccccc
Q 040824            1 MQIFVKTL-TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF-AG-KQLEDGRTLADYNIQ   62 (154)
Q Consensus         1 m~v~v~~~-~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~-~g-~~L~d~~~l~~~~i~   62 (154)
                      |.++++.. +..++.+...++.||.+||++++....-|++.|+|+. +. +.|+|.++|+++|..
T Consensus         1 ~~~f~~VrR~kttif~da~es~tV~elK~~l~gi~~~Pvn~qrL~kmd~eqlL~D~ktL~d~gft   65 (110)
T KOG4495|consen    1 MDVFLRVRRHKTTIFTDAKESSTVFELKRKLEGILKRPVNEQRLYKMDTEQLLDDGKTLGDCGFT   65 (110)
T ss_pred             CceeeeeeecceeEEeecCccccHHHHHHHHHHHHhCCCcchheeecCHHHHhhccchhhhcccc
Confidence            44555444 4455788999999999999999999999999999996 33 889999999999864

>PF13019 Telomere_Sde2: Telomere stability and silencing

Probab=98.07  E-value=4e-05  Score=51.53  Aligned_cols=77  Identities=27%  Similarity=0.409  Sum_probs=58.7

Q ss_pred             eeeeeeecCC----ceEEEeeCCCchHHHHHHHHhhhcCCCCCce-eEEE-CCeec--CCCCcccccccCCC----CEEE
Q 040824           77 TMIKVKTLTG----KEIEIDIEPTDTIERIKERVEEKEGIPPVQQ-RLIY-AGKQL--ADDKTARDYNIEGG----SVLH  144 (154)
Q Consensus        77 ~~i~v~~~~~----~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~-~l~~-~g~~l--~d~~~L~~~~i~~~----~~i~  144 (154)
                      |+|+|...+|    .++.+.++++.||.+|+..+...++++...+ .|.. .+..+  .++..+.++.-.+.    -++.
T Consensus         1 i~Vlvss~~g~~lp~tl~~~lp~~ttv~dL~~~l~~~~~~~~~~~~~L~~~~n~~l~~~~~~~~s~l~~~~~~~~~~~l~   80 (162)
T PF13019_consen    1 INVLVSSFDGLTLPPTLSLSLPSTTTVSDLKDRLSERLPIPSSSQLYLTTNSNGQLSPSSDIPLSSLLSSSQDSDFITLR   80 (162)
T ss_pred             CeEEEecCCCCCCCCeEEeeCCCCCcHHHHHHHHHhhcCCCccceeEEEEeCCCeeCCCccccHHhhccCcCCCCceEEE
Confidence            4688888888    5788999999999999999999999998884 3443 34444  45556666654444    3788


Q ss_pred             EEEeecCCC
Q 040824          145 LVLALRGGG  153 (154)
Q Consensus       145 ~~~~~~gg~  153 (154)
                      +..+++||+
T Consensus        81 l~~rl~GGK   89 (162)
T PF13019_consen   81 LSLRLRGGK   89 (162)
T ss_pred             EEEeccCCC
Confidence            999999985

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

Probab=98.02  E-value=1.9e-05  Score=58.12  Aligned_cols=70  Identities=30%  Similarity=0.599  Sum_probs=60.2

Q ss_pred             CEEEEEeC---CCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeee
Q 040824            1 MQIFVKTL---TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (154)
Q Consensus         1 m~v~v~~~---~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~   70 (154)
                      |.+.|.+.   .-..++++++.+.+|.+||+-+++..|+|++..+++|.|+.|+++.++..+.+..-+.+|++
T Consensus         1 m~~lvqf~~~~~~h~l~v~v~~~t~I~~lke~Vak~~gvp~D~L~viFaGKeLs~~ttv~~cDL~qqs~~hi~   73 (446)
T KOG0006|consen    1 MIVLVQFNKTGSSHGLPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELSNDTTVQNCDLSQQSATHIM   73 (446)
T ss_pred             CeEEEEeCCccccCceeEEEecCCCHHHHHHHHHHhhCCChhheEEEEeccccccCceeecccccccchhhhh
Confidence            56677664   12447899999999999999999999999999999999999999999998888777777766

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

Probab=97.99  E-value=2.2e-05  Score=46.93  Aligned_cols=68  Identities=24%  Similarity=0.383  Sum_probs=48.1

Q ss_pred             eeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCC------ceeEE-ECCeecCCCCcccccccCCCCEEEE
Q 040824           78 MIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPV------QQRLI-YAGKQLADDKTARDYNIEGGSVLHL  145 (154)
Q Consensus        78 ~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~------~~~l~-~~g~~l~d~~~L~~~~i~~~~~i~~  145 (154)
                      +++|...+++.+.+.++.+.++++|...+.+..+.+..      ..+|. .+|..|+++.+|+++|+.+|+.+++
T Consensus         4 rVtv~~~~~~~~Dl~lP~~vpv~~li~~l~~~~~~~~~~~~~~~~~~L~~~~g~~L~~~~tL~~~gV~dGd~L~L   78 (79)
T PF08817_consen    4 RVTVDAGNGRQVDLALPADVPVAELIPELVELLGLPGDDPPGHGQWVLARAGGRPLDPDQTLADAGVRDGDVLVL   78 (79)
T ss_dssp             EEEEE-TT--EEEEEEETTSBTTHHHHHHHHHS---S---TT-E-EEEG-GGTEEEETTSBCGGGT--TT-EEEE
T ss_pred             EEEEEcCCCcEEEEEcCCCCcHHHHHHHHHHHhCCccCCCCCcceEEEEecCCcccCCcCcHhHcCCCCCCEEEe
Confidence            45555655688999999999999999999998886322      24444 5788999999999999999999976

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.

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

Probab=97.98  E-value=1.3e-05  Score=48.61  Aligned_cols=53  Identities=26%  Similarity=0.266  Sum_probs=46.7

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEE-CC-eecCCCCccccccc
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIY-AG-KQLADDKTARDYNI  137 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~-~g-~~l~d~~~L~~~~i  137 (154)
                      +..++.+...++.||-+||.+++....-|+.+|+|.. .. ..|+|+.+|+++|.
T Consensus        10 ~kttif~da~es~tV~elK~~l~gi~~~Pvn~qrL~kmd~eqlL~D~ktL~d~gf   64 (110)
T KOG4495|consen   10 HKTTIFTDAKESSTVFELKRKLEGILKRPVNEQRLYKMDTEQLLDDGKTLGDCGF   64 (110)
T ss_pred             cceeEEeecCccccHHHHHHHHHHHHhCCCcchheeecCHHHHhhccchhhhccc
Confidence            4567889999999999999999999999999999975 43 57899999999975

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

Probab=97.89  E-value=7.3e-05  Score=44.68  Aligned_cols=68  Identities=21%  Similarity=0.421  Sum_probs=47.1

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCe----EEE---EcceEeccCceecccccccccceee
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQ----RLI---FAGKQLEDGRTLADYNIQKESTLHL   69 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q----~L~---~~g~~L~d~~~l~~~~i~~~~~i~l   69 (154)
                      +|+|...++..+.+.++.+.+|.+|...+-+..+.+....    .|.   -+|..|+++.+|+++++.+|+.+.+
T Consensus         4 rVtv~~~~~~~~Dl~lP~~vpv~~li~~l~~~~~~~~~~~~~~~~~~L~~~~g~~L~~~~tL~~~gV~dGd~L~L   78 (79)
T PF08817_consen    4 RVTVDAGNGRQVDLALPADVPVAELIPELVELLGLPGDDPPGHGQWVLARAGGRPLDPDQTLADAGVRDGDVLVL   78 (79)
T ss_dssp             EEEEE-TT--EEEEEEETTSBTTHHHHHHHHHS---S---TT-E-EEEG-GGTEEEETTSBCGGGT--TT-EEEE
T ss_pred             EEEEEcCCCcEEEEEcCCCCcHHHHHHHHHHHhCCccCCCCCcceEEEEecCCcccCCcCcHhHcCCCCCCEEEe
Confidence            5677775568899999999999999999999887543221    233   3588999999999999999998865

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.

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

Probab=97.89  E-value=0.00016  Score=43.46  Aligned_cols=71  Identities=21%  Similarity=0.308  Sum_probs=59.3

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCc-eeEE--ECCeecCCC--CcccccccCCCCEEEE
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQ-QRLI--YAGKQLADD--KTARDYNIEGGSVLHL  145 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~-~~l~--~~g~~l~d~--~~L~~~~i~~~~~i~~  145 (154)
                      +...|.|+.++|+.+.-.+.+++|+.+|..-+......+... +.|.  |..+.+.+.  .||++.|+.++++|++
T Consensus         5 ~~~~I~vRlpdG~~l~~~F~~~~tl~~l~~~v~~~~~~~~~~~f~L~~~~Pr~~l~~~~~~tl~e~~l~p~~~l~v   80 (82)
T PF00789_consen    5 DVVRIQVRLPDGSRLQRRFPKSDTLQDLYDFVESQLFSPEESDFELITAFPRRELTDEDSKTLEEAGLLPSATLIV   80 (82)
T ss_dssp             SEEEEEEEETTSTEEEEEEETTSBHHHHHHHHHHHHHCTTTSSEEEEESSSTEECCSTTTSBTCCCTTSSCEEEEE
T ss_pred             CEEEEEEECCCCCEEEEEECCcchHHHHHHHHHHhcCCCCCccEEEEeCCCCcCCCccccccHHHhcCCCCeEEEE
Confidence            345788889999999999999999999999998888777665 7776  666777633  6999999999999876

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 ....

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

Probab=97.86  E-value=4.5e-05  Score=47.34  Aligned_cols=59  Identities=20%  Similarity=0.329  Sum_probs=47.0

Q ss_pred             EEEEEeCCC-CEEEEEEe--CCCcHHHHHHHHHhHhC--CCCCCeEEEEcceEeccCceecccc
Q 040824            2 QIFVKTLTG-KTITLEVE--SSDTIDNVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLADYN   60 (154)
Q Consensus         2 ~v~v~~~~~-~~~~~~v~--~~~tv~~lk~~i~~~~~--~~~~~q~L~~~g~~L~d~~~l~~~~   60 (154)
                      .|+|++.++ ..++++++  .+.||..||..|.+...  ....+++|+|+|+.|.|...|+.--
T Consensus         2 ~l~IRFs~sipDl~L~I~~~~~~Tv~~LK~lIR~~~p~~~s~~rLRlI~~Gr~L~d~t~l~~~l   65 (97)
T PF10302_consen    2 YLTIRFSDSIPDLPLDIPSPNTTTVAWLKQLIRERLPPEPSRRRLRLIYAGRLLNDHTDLSSEL   65 (97)
T ss_pred             eEEEEECCCCCCceeecCCCCcccHHHHHHHHHhhcCCCCccccEEeeecCcccCccchhhhhh
Confidence            477888874 45778777  78899999999999984  5566788889999999988766533

They contain a characteristic GFDRL sequence motif.

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

Probab=97.86  E-value=0.00013  Score=43.82  Aligned_cols=71  Identities=15%  Similarity=0.365  Sum_probs=64.1

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~   71 (154)
                      +.++|...++..+.+.+..+++...|.+......|-..+..+++|+|..++.+++..+++..+++.|..+.
T Consensus        25 inLkvv~qd~telfFkiKktT~f~klm~af~~rqGK~m~slRfL~dG~rI~~dqTP~dldmEdnd~iEav~   95 (103)
T COG5227          25 INLKVVDQDGTELFFKIKKTTTFKKLMDAFSRRQGKNMSSLRFLFDGKRIDLDQTPGDLDMEDNDEIEAVT   95 (103)
T ss_pred             cceEEecCCCCEEEEEEeccchHHHHHHHHHHHhCcCcceeEEEEcceecCCCCChhhcCCccchHHHHHH
Confidence            35677777888999999999999999999999999999999999999999999999999999998876544

>COG5417 Uncharacterized small protein [Function unknown]

Probab=97.79  E-value=0.00023  Score=41.28  Aligned_cols=66  Identities=18%  Similarity=0.229  Sum_probs=54.8

Q ss_pred             EEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCC-----CCCeEEEEcceEeccCceecccccccccceee
Q 040824            4 FVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIP-----PDQQRLIFAGKQLEDGRTLADYNIQKESTLHL   69 (154)
Q Consensus         4 ~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~-----~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l   69 (154)
                      -++.++|..+.++++...++..|...+.+...++     .+..+..-.++.|.++..|.+|++.+|+.+.+
T Consensus        10 D~t~y~g~~yDLrl~d~~pikklIdivwe~~kis~~~reg~~Ikv~nKa~llsgd~kL~d~~IadGD~Lei   80 (81)
T COG5417          10 DFTNYNGGTYDLRLPDYLPIKKLIDIVWESLKISIFDREGTQIKVMNKAQLLSGDDKLIDYQIADGDILEI   80 (81)
T ss_pred             EeEecCCceEEEeccccchHHHHHHHHHHHhhccccccCCCEEEEeccceEecCCceEEeccccCCCEEEe
Confidence            3467789999999999999999999998876533     34456667789999999999999999998754

>smart00166 UBX Domain present in ubiquitin-regulatory proteins

Probab=97.76  E-value=0.00029  Score=42.19  Aligned_cols=70  Identities=16%  Similarity=0.161  Sum_probs=57.5

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEE--ECCeecCC---CCcccccccCCCCEEEE
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI--YAGKQLAD---DKTARDYNIEGGSVLHL  145 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~--~~g~~l~d---~~~L~~~~i~~~~~i~~  145 (154)
                      ...|.|+.++|+.+.-.+++++|+.+|.+-+....+.+...+.|.  |..+.+.+   +.||.+.|+.+++++.+
T Consensus         4 ~~~I~iRlPdG~ri~~~F~~~~tl~~v~~~v~~~~~~~~~~f~L~t~~Prk~l~~~d~~~tL~e~gL~p~~~l~v   78 (80)
T smart00166        4 QCRLQIRLPDGSRLVRRFPSSDTLRTVYEFVSAALTDGNDPFTLNSPFPRRTFTKDDYSKTLLELALLPSSTLVL   78 (80)
T ss_pred             eEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHcccCCCCCEEEEeCCCCcCCccccccCCHHHCCCCCceEEEE
Confidence            356788889999999999999999999999977667766778886  66666753   57999999998888765

Present in FAF1 and Shp1p.

>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=97.75  E-value=0.00016  Score=41.44  Aligned_cols=63  Identities=19%  Similarity=0.252  Sum_probs=46.1

Q ss_pred             eCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceee
Q 040824            7 TLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHL   69 (154)
Q Consensus         7 ~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l   69 (154)
                      ..+++.+.+.+.+++++.++-+...++++++++.=.|.|+++.++.+.++...|+.+|+.+.+
T Consensus         3 ~~~~rr~~vkvtp~~~l~~VL~eac~k~~l~~~~~~L~h~~k~ldlslp~R~snL~n~akLeL   65 (65)
T PF11470_consen    3 CYNFRRFKVKVTPNTTLNQVLEEACKKFGLDPSSYDLKHNNKPLDLSLPFRLSNLPNNAKLEL   65 (65)
T ss_dssp             -TTS-EEEE---TTSBHHHHHHHHHHHTT--GGG-EEEETTEEESSS-BHHHH---SS-EEEE
T ss_pred             ccCCcEEEEEECCCCCHHHHHHHHHHHcCCCccceEEEECCEEeccccceeecCCCCCCEEeC
Confidence            357888999999999999999999999999999999999999999999999999999998753

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=97.72  E-value=0.00053  Score=41.12  Aligned_cols=68  Identities=24%  Similarity=0.361  Sum_probs=56.8

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCC-eEEE--EcceEeccC--ceecccccccccceee
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLI--FAGKQLEDG--RTLADYNIQKESTLHL   69 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~-q~L~--~~g~~L~d~--~~l~~~~i~~~~~i~l   69 (154)
                      .|.|+..+|+.+.-....++|+.+|.+-+......+... -.|.  |..+.+.++  .+|++.|+.+.+++.+
T Consensus         8 ~I~vRlpdG~~l~~~F~~~~tl~~l~~~v~~~~~~~~~~~f~L~~~~Pr~~l~~~~~~tl~e~~l~p~~~l~v   80 (82)
T PF00789_consen    8 RIQVRLPDGSRLQRRFPKSDTLQDLYDFVESQLFSPEESDFELITAFPRRELTDEDSKTLEEAGLLPSATLIV   80 (82)
T ss_dssp             EEEEEETTSTEEEEEEETTSBHHHHHHHHHHHHHCTTTSSEEEEESSSTEECCSTTTSBTCCCTTSSCEEEEE
T ss_pred             EEEEECCCCCEEEEEECCcchHHHHHHHHHHhcCCCCCccEEEEeCCCCcCCCccccccHHHhcCCCCeEEEE
Confidence            588999999999999999999999999999887766654 5565  567887665  5999999999988865

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 ....

>cd01772 SAKS1_UBX SAKS1-like UBX domain

Probab=97.60  E-value=0.00071  Score=40.41  Aligned_cols=68  Identities=18%  Similarity=0.327  Sum_probs=55.4

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEE--ECCeecCC---CCcccccccCCCCEEEE
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI--YAGKQLAD---DKTARDYNIEGGSVLHL  145 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~--~~g~~l~d---~~~L~~~~i~~~~~i~~  145 (154)
                      ..|.++.++|+.+.-.++.++|+.++.+-+....+-+ ....|+  |.-+.+.+   +.||.+.|+.+.+++.|
T Consensus         5 ~~i~iRlp~G~~~~~~F~~~~tl~~v~~fV~~~~~~~-~~f~L~t~fPrk~~~~~d~~~TL~elgL~Psa~L~v   77 (79)
T cd01772           5 TRIQIRLLDGTTLKQTFKAREQLAAVRLFVELNTGNG-GPFTLMTPFPRKVFTEDDMEKPLQELGLVPSAVLIV   77 (79)
T ss_pred             EEEEEECCCCCEEEEEeCCCChHHHHHHHHHHcCCCC-CCEEEEeCCCCeECCcccccCCHHHCCCCCceEEEE
Confidence            4677888899999999999999999999998765433 556776  67777753   57999999999998866

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.

>cd01773 Faf1_like1_UBX Faf1 ike-1 UBX domain

Probab=97.56  E-value=0.00096  Score=40.03  Aligned_cols=69  Identities=14%  Similarity=0.275  Sum_probs=58.9

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEE--ECCeecC---CCCcccccccCCCCEEEEE
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI--YAGKQLA---DDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~--~~g~~l~---d~~~L~~~~i~~~~~i~~~  146 (154)
                      -.|.|+.++|+...-.+..++++.+|..-+.. .|.+++.+.|+  |.-+.+.   .+.||.+.|+.+.+++.|-
T Consensus         6 t~i~vRlP~G~r~~rrF~~~~~L~~v~~fv~~-~g~~~~~f~L~t~FPRr~~~~~d~~~TL~e~GL~P~~~LfVq   79 (82)
T cd01773           6 ARLMLRYPDGKREQIALPEQAKLLALVRHVQS-KGYPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQ   79 (82)
T ss_pred             eEEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-cCCCCCCEEEecCCCCcccCCcccCCCHHHcCCCCCcEEEEe
Confidence            46888899999999999999999999999988 58888999998  6555553   4579999999999998764

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.

>smart00166 UBX Domain present in ubiquitin-regulatory proteins

Probab=97.47  E-value=0.0009  Score=40.01  Aligned_cols=68  Identities=22%  Similarity=0.260  Sum_probs=54.2

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEE--EcceEecc---Cceecccccccccceee
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLED---GRTLADYNIQKESTLHL   69 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~--~~g~~L~d---~~~l~~~~i~~~~~i~l   69 (154)
                      +|.|+..+|+.+.-..+.++|+.+|.+.+....+.....-.|.  |..+.+.+   +.+|.+.++.+.+++.+
T Consensus         6 ~I~iRlPdG~ri~~~F~~~~tl~~v~~~v~~~~~~~~~~f~L~t~~Prk~l~~~d~~~tL~e~gL~p~~~l~v   78 (80)
T smart00166        6 RLQIRLPDGSRLVRRFPSSDTLRTVYEFVSAALTDGNDPFTLNSPFPRRTFTKDDYSKTLLELALLPSSTLVL   78 (80)
T ss_pred             EEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHcccCCCCCEEEEeCCCCcCCccccccCCHHHCCCCCceEEEE
Confidence            5789999999999999999999999999966666555556665  56677754   46999999988887754

Present in FAF1 and Shp1p.

>cd01767 UBX UBX (ubiquitin regulatory X) domain

Probab=97.42  E-value=0.0017  Score=38.52  Aligned_cols=66  Identities=18%  Similarity=0.295  Sum_probs=51.5

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEE--ECCeecC---CCCcccccccCCCCEE
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI--YAGKQLA---DDKTARDYNIEGGSVL  143 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~--~~g~~l~---d~~~L~~~~i~~~~~i  143 (154)
                      ..|.++.++|+.+.-.++.++|+.+|.+-+.....- ...+.|.  |..+.+.   .+.||.+.|+.+++.+
T Consensus         3 t~i~iRlpdG~~~~~~F~~~~tl~~l~~fv~~~~~~-~~~f~L~t~~Pr~~~~~~~~~~TL~e~gL~~s~~~   73 (77)
T cd01767           3 TKIQIRLPDGKRLEQRFNSTHKLSDVRDFVESNGPP-AEPFTLMTSFPRRVLTDLDYELTLQEAGLVNEVVF   73 (77)
T ss_pred             EEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHcCCC-CCCEEEEeCCCCccCCCCCccCcHHHcCCccceEE
Confidence            467788899999999999999999999999866543 5567776  5566664   5889999999954443

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.

>cd01771 Faf1_UBX Faf1 UBX domain

Probab=97.42  E-value=0.0019  Score=38.64  Aligned_cols=69  Identities=19%  Similarity=0.261  Sum_probs=57.7

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEE--ECCeecC---CCCcccccccCCCCEEEE
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI--YAGKQLA---DDKTARDYNIEGGSVLHL  145 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~--~~g~~l~---d~~~L~~~~i~~~~~i~~  145 (154)
                      ..+|.++.++|+...-.+..++++.+|..-+... |.++..++|+  |.-+.+.   .+.||.+.|+.+.++|.|
T Consensus         4 ~~~i~iRlP~G~r~~rrF~~t~~L~~l~~fv~~~-~~~~~~f~L~t~fPRk~~~~~d~~~TL~e~gL~p~~~L~V   77 (80)
T cd01771           4 ISKLRVRTPSGDFLERRFLGDTPLQVLLNFVASK-GYPIDEYKLLSSWPRRDLTQLDPNFTLLELKLYPQETLIL   77 (80)
T ss_pred             eEEEEEECCCCCEEEEEeCCCCcHHHHHHHHHhc-CCCCCCEEEecCCCCCCCcCCCCCCcHHHcCCCCCcEEEE
Confidence            3567888899999999999999999999999875 7788888887  6666663   467999999999998866

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.

>cd01774 Faf1_like2_UBX Faf1 ike-2 UBX domain

Probab=97.40  E-value=0.002  Score=39.03  Aligned_cols=70  Identities=16%  Similarity=0.151  Sum_probs=56.4

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEEC--CeecC--------CCCcccccccCCCCEEEE
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYA--GKQLA--------DDKTARDYNIEGGSVLHL  145 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~--g~~l~--------d~~~L~~~~i~~~~~i~~  145 (154)
                      ...|.++.++|+...-.+..++|+++|..-+.. .+..++.+.|+.+  -+.+.        .+.||.+.|+.+.+++.|
T Consensus         4 ~~~I~iRlp~G~Rl~rrF~~~~tl~~l~~fv~~-~~~~~~~f~L~t~FPrr~~~~~~~~~~~~~~TL~eaGL~~s~~L~V   82 (85)
T cd01774           4 TVKIVFKLPNGTRVERRFLFTQSLRVIHDFLFS-LKETPEKFQIVTNFPRRVLPCLPSEGDPPPPTLLEAGLSNSEVLFV   82 (85)
T ss_pred             eEEEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-CCCCCCcEEEecCCCCccccccccccCcCCCCHHHcCCCCccEEEE
Confidence            357788889999999999999999999999964 4556788888843  36664        467999999998888765


Q ss_pred             E
Q 040824          146 V  146 (154)
Q Consensus       146 ~  146 (154)
                      -
T Consensus        83 ~   83 (85)
T cd01774          83 Q   83 (85)
T ss_pred             e
Confidence            3

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

>cd01770 p47_UBX p47-like ubiquitin domain

Probab=97.35  E-value=0.0021  Score=38.40  Aligned_cols=67  Identities=13%  Similarity=0.291  Sum_probs=53.2

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCC-CCCceeEE--ECCeecC-CCCcccccccCCCCEE
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGI-PPVQQRLI--YAGKQLA-DDKTARDYNIEGGSVL  143 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i-~~~~~~l~--~~g~~l~-d~~~L~~~~i~~~~~i  143 (154)
                      ..|.|+.++|+.+.-.++.++||++|.+-+....+- ....+.|.  |..+.+. ++.||.+.|+.+...+
T Consensus         5 t~iqiRlpdG~r~~~rF~~~~tv~~l~~~v~~~~~~~~~~~f~L~t~fP~k~l~~~~~Tl~eagL~~s~v~   75 (79)
T cd01770           5 TSIQIRLADGKRLVQKFNSSHRVSDVRDFIVNARPEFAARPFTLMTAFPVKELSDESLTLKEANLLNAVIV   75 (79)
T ss_pred             eEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHhCCCCCCCCEEEecCCCCcccCCCCCcHHHCCCcCcEEE
Confidence            467888899999999999999999999999876643 33556776  6777665 5789999999875544

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.

>COG5417 Uncharacterized small protein [Function unknown]

Probab=97.33  E-value=0.0026  Score=36.97  Aligned_cols=64  Identities=20%  Similarity=0.330  Sum_probs=53.0

Q ss_pred             eecCCceEEEeeCCCchHHHHHHHHhhhcCC---CCC--ceeEEECCeecCCCCcccccccCCCCEEEE
Q 040824           82 KTLTGKEIEIDIEPTDTIERIKERVEEKEGI---PPV--QQRLIYAGKQLADDKTARDYNIEGGSVLHL  145 (154)
Q Consensus        82 ~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i---~~~--~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~  145 (154)
                      +.-+|..+.++++...++..|-..+.+...+   +.+  ..+.+-+++.|.++..|.+|+|.+||.+.+
T Consensus        12 t~y~g~~yDLrl~d~~pikklIdivwe~~kis~~~reg~~Ikv~nKa~llsgd~kL~d~~IadGD~Lei   80 (81)
T COG5417          12 TNYNGGTYDLRLPDYLPIKKLIDIVWESLKISIFDREGTQIKVMNKAQLLSGDDKLIDYQIADGDILEI   80 (81)
T ss_pred             EecCCceEEEeccccchHHHHHHHHHHHhhccccccCCCEEEEeccceEecCCceEEeccccCCCEEEe
Confidence            3457889999999999999998888776664   222  357778899999999999999999999876

>cd01772 SAKS1_UBX SAKS1-like UBX domain

Probab=97.26  E-value=0.0026  Score=37.93  Aligned_cols=67  Identities=16%  Similarity=0.324  Sum_probs=53.1

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEE--EcceEecc---Cceecccccccccceee
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLED---GRTLADYNIQKESTLHL   69 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~--~~g~~L~d---~~~l~~~~i~~~~~i~l   69 (154)
                      +|.|+..+|+...-..+.++|+.++.+.+....+-. ..-.|.  |..+.+.+   +.+|.+.|+.+.+++.+
T Consensus         6 ~i~iRlp~G~~~~~~F~~~~tl~~v~~fV~~~~~~~-~~f~L~t~fPrk~~~~~d~~~TL~elgL~Psa~L~v   77 (79)
T cd01772           6 RIQIRLLDGTTLKQTFKAREQLAAVRLFVELNTGNG-GPFTLMTPFPRKVFTEDDMEKPLQELGLVPSAVLIV   77 (79)
T ss_pred             EEEEECCCCCEEEEEeCCCChHHHHHHHHHHcCCCC-CCEEEEeCCCCeECCcccccCCHHHCCCCCceEEEE
Confidence            578999999999999999999999999998665433 334454  66788864   46999999998887754

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.

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

Probab=97.24  E-value=0.0049  Score=43.85  Aligned_cols=101  Identities=23%  Similarity=0.343  Sum_probs=55.9

Q ss_pred             EEEEEEeCCCcHHHHHHHHHhHhCCCCC---CeEEE--Ecce---EeccCceecccccccccceeeeeeee---------
Q 040824           12 TITLEVESSDTIDNVKAKIQDKEGIPPD---QQRLI--FAGK---QLEDGRTLADYNIQKESTLHLVLRLR---------   74 (154)
Q Consensus        12 ~~~~~v~~~~tv~~lk~~i~~~~~~~~~---~q~L~--~~g~---~L~d~~~l~~~~i~~~~~i~l~~~~~---------   74 (154)
                      .+.+-++.+.||++|.+.+.++.+++.+   ..+|+  ++++   .+..+..+...+  +...+.+-.-+.         
T Consensus        35 ~~~~~vpk~~tV~Dll~~l~~k~~~~~~~~~~lrl~ev~~~ki~~~~~~d~~i~~l~--~~~~~r~E~ip~ee~~~~~~~  112 (213)
T PF14533_consen   35 EYELLVPKTGTVSDLLEELQKKVGFSEEGTGKLRLWEVSNHKIYKILSEDEPISSLN--DYITLRIEEIPEEELNLDDES  112 (213)
T ss_dssp             EEEE--BTT-BHHHHHHHHHTT----TT----EEEEEEETTEEEEEE-TTSBGGGS----TTEEEEEE--GGGSS--TT-
T ss_pred             EEEEEECCCCCHHHHHHHHHHHcCCCcCCcCcEEEEEeECCEEEeecCCCCchhhcc--CcceeeeecCChHHhhccccc
Confidence            4778899999999999999999998765   44444  4553   466677776652  222222221111         


Q ss_pred             -cceeeeeeec-------CCceEEEeeCCCchHHHHHHHHhhhcCCCC
Q 040824           75 -GGTMIKVKTL-------TGKEIEIDIEPTDTIERIKERVEEKEGIPP  114 (154)
Q Consensus        75 -~~~~i~v~~~-------~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~  114 (154)
                       +.+.|.|...       .|-.+.+.+.+.+|+.++|+.|++++|++-
T Consensus       113 ~~~~li~V~hf~k~~~~~hGiPF~f~v~~gE~f~~tK~Rl~~rlgv~~  160 (213)
T PF14533_consen  113 EGEKLIPVFHFHKDPSRTHGIPFLFVVKPGETFSDTKERLQKRLGVSD  160 (213)
T ss_dssp             -TEEEEEEEEESSSTT-EEEEEEEEEEETT--HHHHHHHHHHHH---H
T ss_pred             ccceEEEEEEEecCccccCCCCEEEEeeCCCcHHHHHHHHHHHhCCCh
Confidence             1233444332       356688999999999999999999999874

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

Probab=97.23  E-value=0.0023  Score=44.60  Aligned_cols=73  Identities=15%  Similarity=0.253  Sum_probs=56.1

Q ss_pred             EEEEEeCCC-CEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEE-Ecc-----eEecc-Cceecccccccccceeeeeee
Q 040824            2 QIFVKTLTG-KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAG-----KQLED-GRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         2 ~v~v~~~~~-~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~-~~g-----~~L~d-~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      +|.|.+... .....+++++.|+.+||.+++..+|.+++.+.|. |.|     ..|+| +..|..|...+|-.||++-..
T Consensus         3 ~v~Iss~~~~~~~Ekr~~~~ltl~q~K~KLe~~~G~~~~~M~l~l~~~~d~~~~~lsn~d~~lg~~~~~Dg~rihviD~~   82 (234)
T KOG3206|consen    3 RVVISSSLNDFRTEKRLSNSLTLAQFKDKLELLTGTEAESMELELYDGDDKKVSALSNEDADLGFYKVEDGLRIHVIDSN   82 (234)
T ss_pred             EEEEecccccchhhhhcCCcCcHHHHHhhhhhhhCCCccceEEEEEcCCCceeeeccCCcccccccCCCCceEEEEEecC
Confidence            455554432 2355678899999999999999999999999997 554     34554 558999999999999887654


Q ss_pred             e
Q 040824           74 R   74 (154)
Q Consensus        74 ~   74 (154)
                      .
T Consensus        83 ~   83 (234)
T KOG3206|consen   83 A   83 (234)
T ss_pred             c
Confidence            3

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

Probab=97.21  E-value=0.00062  Score=48.73  Aligned_cols=70  Identities=29%  Similarity=0.387  Sum_probs=52.8

Q ss_pred             CEEEEEeCCCCE-EE-EEEeCCCcHHHHHHHHHhH-hCCCCCCeEEE--E--cceEeccCceecccccccccceeee
Q 040824            1 MQIFVKTLTGKT-IT-LEVESSDTIDNVKAKIQDK-EGIPPDQQRLI--F--AGKQLEDGRTLADYNIQKESTLHLV   70 (154)
Q Consensus         1 m~v~v~~~~~~~-~~-~~v~~~~tv~~lk~~i~~~-~~~~~~~q~L~--~--~g~~L~d~~~l~~~~i~~~~~i~l~   70 (154)
                      |.|++.++++.. .. ..++...|+.|++.++.++ ....+.++++.  .  .|+.|.|+.+|++|+..+++++.+.
T Consensus         1 m~It~~srs~~~~~~~~~~s~~~ti~d~~~~~~~~~~k~~~~~~r~tlr~e~kgkpl~~~s~l~e~~~~s~~~i~vK   77 (297)
T KOG1639|consen    1 MEITIASRSKGLRIKEKDLSGSETIDDLLKAISAKNLKITPYRIRLTLRVEPKGKPLIDNSKLQEYGDGSGATIYVK   77 (297)
T ss_pred             CceeeeccCCCceeeeecCCCCCcHHHHHHHHHHhhhccCccchhheeeccCCCccccchhHHHHhccCCCCEEEEe
Confidence            788998877633 33 5667788999999777655 45777555554  3  4899999999999999999877543

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

Probab=97.18  E-value=0.0014  Score=40.70  Aligned_cols=48  Identities=29%  Similarity=0.401  Sum_probs=38.4

Q ss_pred             EEEeeC--CCchHHHHHHHHhhhcC--CCCCceeEEECCeecCCCCcccccc
Q 040824           89 IEIDIE--PTDTIERIKERVEEKEG--IPPVQQRLIYAGKQLADDKTARDYN  136 (154)
Q Consensus        89 ~~~~v~--~~~tv~~LK~~i~~~~~--i~~~~~~l~~~g~~l~d~~~L~~~~  136 (154)
                      ..++++  .+.|+..||++|.+..+  ..-.+++|+|+|+.|.|...|...-
T Consensus        14 l~L~I~~~~~~Tv~~LK~lIR~~~p~~~s~~rLRlI~~Gr~L~d~t~l~~~l   65 (97)
T PF10302_consen   14 LPLDIPSPNTTTVAWLKQLIRERLPPEPSRRRLRLIYAGRLLNDHTDLSSEL   65 (97)
T ss_pred             ceeecCCCCcccHHHHHHHHHhhcCCCCccccEEeeecCcccCccchhhhhh
Confidence            455555  78999999999999884  4566679999999999888766543

They contain a characteristic GFDRL sequence motif.

>KOG0013 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.17  E-value=0.00075  Score=47.07  Aligned_cols=63  Identities=29%  Similarity=0.448  Sum_probs=56.8

Q ss_pred             CCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeee
Q 040824            9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (154)
Q Consensus         9 ~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~   71 (154)
                      .++.+.+.....+|+.++|.+++...++.+..|+++|+|..+-+...|..+.+..+....+..
T Consensus       155 T~~d~~lta~~~Dtv~eik~~L~Aaeg~D~~sQrif~Sg~~l~dkt~LeEc~iekg~rYvlqv  217 (231)
T KOG0013|consen  155 TREDFWLTAPHYDTVGEIKRALRAAEGVDPLSQRIFFSGGVLVDKTDLEECKIEKGQRYVLQV  217 (231)
T ss_pred             hhhheeecccCcCcHHHHHHHHHHhhccchhhheeeccCCceeccccceeeeecCCCEEEEEE
Confidence            467788999999999999999999999999999999999999999999999999997665443

>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=97.13  E-value=0.0058  Score=44.53  Aligned_cols=106  Identities=17%  Similarity=0.353  Sum_probs=73.6

Q ss_pred             EEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcc------eEeccCceecccccccccceeeeeeee--------------
Q 040824           15 LEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG------KQLEDGRTLADYNIQKESTLHLVLRLR--------------   74 (154)
Q Consensus        15 ~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g------~~L~d~~~l~~~~i~~~~~i~l~~~~~--------------   74 (154)
                      +-++.+++|+++-..+.+..|.|++...++|.-      ..++.+.++....+.+|+.|.+-....              
T Consensus        89 ~~v~~~~~v~~l~~~i~~~~g~p~~t~l~lyEEi~~~~ie~i~~~~t~~~~el~~GdIi~fQ~~~~~~~~~~~~~~~v~~  168 (249)
T PF12436_consen   89 VYVPKNDKVSELVPLINERAGLPPDTPLLLYEEIKPNMIEPIDPNQTFEKAELQDGDIICFQRAPSEDLDKSSRYPDVKE  168 (249)
T ss_dssp             EEEETT-BGGGTHHHHHHHHT--TT--EEEEEEEETTEEEE--SSSBHHHTT--TTEEEEEEE--GG--GGGSSS-SHHH
T ss_pred             EEECCCCCHHHHHHHHHHHcCCCCCCceEEEEEeccceeeEcCCCCchhhcccCCCCEEEEEeccccccccccCCCCHHH
Confidence            568899999999999999999999887777752      457888899999999999987666432              


Q ss_pred             ------cceeeeeeec---CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEE
Q 040824           75 ------GGTMIKVKTL---TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI  120 (154)
Q Consensus        75 ------~~~~i~v~~~---~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~  120 (154)
                            ..+.|.++..   ....+.+.++...|-.+|-++|+++.+++|+..+|.
T Consensus       169 Yy~~l~nrv~V~f~~~~~~~~~~F~l~ls~~~tY~~la~~Va~~l~~dP~~lr~~  223 (249)
T PF12436_consen  169 YYDFLYNRVEVEFKPKDNPNDPEFTLWLSKKMTYDQLAEKVAEHLNVDPEHLRFF  223 (249)
T ss_dssp             HHHHHHHEEEEEEEETTSTT---EEEEEETT--HHHHHHHHHHHHTS-GGGEEEE
T ss_pred             HHHHHhCeEEEEEEECCCCCCCCEEEEECCCCCHHHHHHHHHHHHCCChHHEEEE
Confidence                  1245555442   334788999999999999999999999999999987

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.

>KOG0013 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.11  E-value=0.0015  Score=45.63  Aligned_cols=63  Identities=27%  Similarity=0.467  Sum_probs=56.4

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEE
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      .++.+.+....-+|+.++|.++.+..++++.-|+|+++|..+.+...|.+++++.|+...+.+
T Consensus       155 T~~d~~lta~~~Dtv~eik~~L~Aaeg~D~~sQrif~Sg~~l~dkt~LeEc~iekg~rYvlqv  217 (231)
T KOG0013|consen  155 TREDFWLTAPHYDTVGEIKRALRAAEGVDPLSQRIFFSGGVLVDKTDLEECKIEKGQRYVLQV  217 (231)
T ss_pred             hhhheeecccCcCcHHHHHHHHHHhhccchhhheeeccCCceeccccceeeeecCCCEEEEEE
Confidence            456788889999999999999999999999999999999999999999999999996554443

>cd01770 p47_UBX p47-like ubiquitin domain

Probab=97.10  E-value=0.0042  Score=37.07  Aligned_cols=64  Identities=23%  Similarity=0.326  Sum_probs=50.4

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCC-CCCCeEEE--EcceEecc-Cceeccccccccc
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGI-PPDQQRLI--FAGKQLED-GRTLADYNIQKES   65 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~-~~~~q~L~--~~g~~L~d-~~~l~~~~i~~~~   65 (154)
                      +|.|+..+|+.+.-+++.++||.+|.+-+....+- ....-.|.  |..+.+.+ +.||.+.|+.+..
T Consensus         6 ~iqiRlpdG~r~~~rF~~~~tv~~l~~~v~~~~~~~~~~~f~L~t~fP~k~l~~~~~Tl~eagL~~s~   73 (79)
T cd01770           6 SIQIRLADGKRLVQKFNSSHRVSDVRDFIVNARPEFAARPFTLMTAFPVKELSDESLTLKEANLLNAV   73 (79)
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHHhCCCCCCCCEEEecCCCCcccCCCCCcHHHCCCcCcE
Confidence            57899999999999999999999999999987542 22344554  66777765 5699999988644

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.

>cd01773 Faf1_like1_UBX Faf1 ike-1 UBX domain

Probab=97.10  E-value=0.0057  Score=36.72  Aligned_cols=67  Identities=16%  Similarity=0.363  Sum_probs=55.9

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEE--EcceEecc---Cceecccccccccceee
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLED---GRTLADYNIQKESTLHL   69 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~--~~g~~L~d---~~~l~~~~i~~~~~i~l   69 (154)
                      +|.|+.++|+...-+...++++.+|-..+.. .+.+++.-.|+  |-.+.+..   +.+|.+.|+.+.+++.+
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            5889999999999999999999999998887 46777777777  66777643   46999999998888754

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.

>cd01767 UBX UBX (ubiquitin regulatory X) domain

Probab=97.09  E-value=0.0036  Score=37.06  Aligned_cols=65  Identities=18%  Similarity=0.330  Sum_probs=50.1

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEE--EcceEecc---Cceecccccccccce
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLED---GRTLADYNIQKESTL   67 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~--~~g~~L~d---~~~l~~~~i~~~~~i   67 (154)
                      +|.|+..+|+.+.-+.+.++|+.+|.+-+.....- ...-.|.  |..+.+.+   +.+|.+.|+.+.+.+
T Consensus         4 ~i~iRlpdG~~~~~~F~~~~tl~~l~~fv~~~~~~-~~~f~L~t~~Pr~~~~~~~~~~TL~e~gL~~s~~~   73 (77)
T cd01767           4 KIQIRLPDGKRLEQRFNSTHKLSDVRDFVESNGPP-AEPFTLMTSFPRRVLTDLDYELTLQEAGLVNEVVF   73 (77)
T ss_pred             EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHcCCC-CCCEEEEeCCCCccCCCCCccCcHHHcCCccceEE
Confidence            57899999999999999999999999999876543 3344454  56677754   669999999854433

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.

>PF13019 Telomere_Sde2: Telomere stability and silencing

Probab=96.91  E-value=0.0091  Score=40.35  Aligned_cols=62  Identities=23%  Similarity=0.423  Sum_probs=47.6

Q ss_pred             CEEEEEeCCC----CEEEEEEeCCCcHHHHHHHHHhHhCCCCCCe-EEEE-cceEe--ccCceecccccc
Q 040824            1 MQIFVKTLTG----KTITLEVESSDTIDNVKAKIQDKEGIPPDQQ-RLIF-AGKQL--EDGRTLADYNIQ   62 (154)
Q Consensus         1 m~v~v~~~~~----~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q-~L~~-~g~~L--~d~~~l~~~~i~   62 (154)
                      |+|.|.+.+|    .++.+.++.++||.+|+..+....+.++..| .|.+ .++.+  .++..++.+.-.
T Consensus         1 i~Vlvss~~g~~lp~tl~~~lp~~ttv~dL~~~l~~~~~~~~~~~~~L~~~~n~~l~~~~~~~~s~l~~~   70 (162)
T PF13019_consen    1 INVLVSSFDGLTLPPTLSLSLPSTTTVSDLKDRLSERLPIPSSSQLYLTTNSNGQLSPSSDIPLSSLLSS   70 (162)
T ss_pred             CeEEEecCCCCCCCCeEEeeCCCCCcHHHHHHHHHhhcCCCccceeEEEEeCCCeeCCCccccHHhhccC
Confidence            7899999999    5788999999999999999999999998885 3444 34454  344456655543

>PRK06437 hypothetical protein; Provisional

Probab=96.91  E-value=0.015  Score=33.50  Aligned_cols=59  Identities=19%  Similarity=0.272  Sum_probs=45.7

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      .++...++++...|+++|-+.    .++++...-+..+|..+.     .++-+++||.|.++--.-||
T Consensus         9 g~~~~~~~i~~~~tv~dLL~~----Lgi~~~~vaV~vNg~iv~-----~~~~L~dgD~Veiv~~V~GG   67 (67)
T PRK06437          9 GHINKTIEIDHELTVNDIIKD----LGLDEEEYVVIVNGSPVL-----EDHNVKKEDDVLILEVFSGG   67 (67)
T ss_pred             CCcceEEEcCCCCcHHHHHHH----cCCCCccEEEEECCEECC-----CceEcCCCCEEEEEecccCC
Confidence            344567788888999998654    488888888889999886     66688999999877655554

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

Probab=96.87  E-value=0.0029  Score=45.42  Aligned_cols=73  Identities=25%  Similarity=0.383  Sum_probs=49.3

Q ss_pred             eeeeeeecCCc-eE-EEeeCCCchHHHHHHHHhhh-cCCCCCceeEE----ECCeecCCCCcccccccCCCCEEEEEEee
Q 040824           77 TMIKVKTLTGK-EI-EIDIEPTDTIERIKERVEEK-EGIPPVQQRLI----YAGKQLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        77 ~~i~v~~~~~~-~~-~~~v~~~~tv~~LK~~i~~~-~~i~~~~~~l~----~~g~~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      |.|++...++. .. ....+.++|+.|+++.+.++ ..+.+..+++.    -+|+++-|+.+|++|+..+|++|+  ++-
T Consensus         1 m~It~~srs~~~~~~~~~~s~~~ti~d~~~~~~~~~~k~~~~~~r~tlr~e~kgkpl~~~s~l~e~~~~s~~~i~--vKD   78 (297)
T KOG1639|consen    1 MEITIASRSKGLRIKEKDLSGSETIDDLLKAISAKNLKITPYRIRLTLRVEPKGKPLIDNSKLQEYGDGSGATIY--VKD   78 (297)
T ss_pred             CceeeeccCCCceeeeecCCCCCcHHHHHHHHHHhhhccCccchhheeeccCCCccccchhHHHHhccCCCCEEE--Eec
Confidence            34555554442 22 35677889999999777554 45666444333    468999999999999999997764  444


Q ss_pred             cC
Q 040824          150 RG  151 (154)
Q Consensus       150 ~g  151 (154)
                      +|
T Consensus        79 LG   80 (297)
T KOG1639|consen   79 LG   80 (297)
T ss_pred             cC
Confidence            44

>cd01774 Faf1_like2_UBX Faf1 ike-2 UBX domain

Probab=96.78  E-value=0.012  Score=35.60  Aligned_cols=67  Identities=13%  Similarity=0.236  Sum_probs=52.8

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEE--EcceEec--------cCceecccccccccceee
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE--------DGRTLADYNIQKESTLHL   69 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~--~~g~~L~--------d~~~l~~~~i~~~~~i~l   69 (154)
                      +|.|+.++|+.+.-+...++|+.+|.+-+.. .+..+..-.|.  |..+.+.        .+.||.+.|+.+.+++.+
T Consensus         6 ~I~iRlp~G~Rl~rrF~~~~tl~~l~~fv~~-~~~~~~~f~L~t~FPrr~~~~~~~~~~~~~~TL~eaGL~~s~~L~V   82 (85)
T cd01774           6 KIVFKLPNGTRVERRFLFTQSLRVIHDFLFS-LKETPEKFQIVTNFPRRVLPCLPSEGDPPPPTLLEAGLSNSEVLFV   82 (85)
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-CCCCCCcEEEecCCCCccccccccccCcCCCCHHHcCCCCccEEEE
Confidence            6889999999999999999999999999964 44555666666  5567775        356999999987776644

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.

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

Probab=96.76  E-value=0.0063  Score=42.48  Aligned_cols=60  Identities=23%  Similarity=0.382  Sum_probs=50.8

Q ss_pred             EEEeeCCCchHHHHHHHHhhhcCCCCCceeEE-ECC-----eec-CCCCcccccccCCCCEEEEEEe
Q 040824           89 IEIDIEPTDTIERIKERVEEKEGIPPVQQRLI-YAG-----KQL-ADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        89 ~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~-~~g-----~~l-~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      .....+++.|++++|.++...+|.+++.+.|. |+|     ..| +++..|..|...+|..||++-.
T Consensus        15 ~Ekr~~~~ltl~q~K~KLe~~~G~~~~~M~l~l~~~~d~~~~~lsn~d~~lg~~~~~Dg~rihviD~   81 (234)
T KOG3206|consen   15 TEKRLSNSLTLAQFKDKLELLTGTEAESMELELYDGDDKKVSALSNEDADLGFYKVEDGLRIHVIDS   81 (234)
T ss_pred             hhhhcCCcCcHHHHHhhhhhhhCCCccceEEEEEcCCCceeeeccCCcccccccCCCCceEEEEEec
Confidence            45678899999999999999999999999887 655     234 4778999999999999998744

>cd01771 Faf1_UBX Faf1 UBX domain

Probab=96.69  E-value=0.016  Score=34.69  Aligned_cols=67  Identities=21%  Similarity=0.343  Sum_probs=54.7

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEE--EcceEec---cCceecccccccccceee
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE---DGRTLADYNIQKESTLHL   69 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~--~~g~~L~---d~~~l~~~~i~~~~~i~l   69 (154)
                      +|.|+.++|+...-+...++++++|-.-+... +.++..-+|.  |-.+.+.   .+.+|.+.|+.+.+++.+
T Consensus         6 ~i~iRlP~G~r~~rrF~~t~~L~~l~~fv~~~-~~~~~~f~L~t~fPRk~~~~~d~~~TL~e~gL~p~~~L~V   77 (80)
T cd01771           6 KLRVRTPSGDFLERRFLGDTPLQVLLNFVASK-GYPIDEYKLLSSWPRRDLTQLDPNFTLLELKLYPQETLIL   77 (80)
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHhc-CCCCCCEEEecCCCCCCCcCCCCCCcHHHcCCCCCcEEEE
Confidence            68899999999999999999999999999764 6666667776  6677774   355999999988887754

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.

>cd00754 MoaD Ubiquitin domain of MoaD-like proteins

Probab=96.64  E-value=0.014  Score=34.49  Aligned_cols=60  Identities=17%  Similarity=0.304  Sum_probs=46.9

Q ss_pred             eEEEeeCCCchHHHHHHHHhhhcCC----CCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           88 EIEIDIEPTDTIERIKERVEEKEGI----PPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        88 ~~~~~v~~~~tv~~LK~~i~~~~~i----~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ...++++...|+.+|.+.+...++-    ......+..+|+...     .+.-+++||.|.++-..-||
T Consensus        17 ~~~~~~~~~~tv~~ll~~l~~~~~~~~~~~~~~~~v~vNg~~v~-----~~~~l~~gD~v~i~ppv~GG   80 (80)
T cd00754          17 EEELELPEGATVGELLDALEARYPGLLEELLARVRIAVNGEYVR-----LDTPLKDGDEVAIIPPVSGG   80 (80)
T ss_pred             eEEEECCCCCcHHHHHHHHHHHCchHHHhhhhcEEEEECCeEcC-----CCcccCCCCEEEEeCCCCCC
Confidence            3567888889999999999887653    344567778998876     45578999999888877776

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.

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

Probab=96.58  E-value=0.022  Score=33.67  Aligned_cols=67  Identities=24%  Similarity=0.315  Sum_probs=50.3

Q ss_pred             eeecCCceEEEeeCCCchHHHHHHHHhhhcCCC-CCceeEEE----CC--eecCCCCcccccccCCCC--EEEEEE
Q 040824           81 VKTLTGKEIEIDIEPTDTIERIKERVEEKEGIP-PVQQRLIY----AG--KQLADDKTARDYNIEGGS--VLHLVL  147 (154)
Q Consensus        81 v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~-~~~~~l~~----~g--~~l~d~~~L~~~~i~~~~--~i~~~~  147 (154)
                      |+.++|+...+.+++++|+.+|-..|+...++. .+-+-|.+    +|  ..|+.+++|.++....+.  ++++.+
T Consensus         1 V~llD~~~~~~~v~~~~t~~~l~~~v~~~l~l~e~~~FgL~~~~~~~~~~~wL~~~k~l~~q~~~~~~~~~l~frv   76 (80)
T PF09379_consen    1 VRLLDGTTKTFEVDPKTTGQDLLEQVCDKLGLKEKEYFGLQYQVDKDGEHHWLDLDKKLKKQLKKNNPPFTLYFRV   76 (80)
T ss_dssp             EEESSEEEEEEEEETTSBHHHHHHHHHHHHTTSSGGGEEEEE-EBTTSSEEEE-SSSBGGGSTBTSSSSEEEEEEE
T ss_pred             CCCcCCCcEEEEEcCCCcHHHHHHHHHHHcCCCCccEEEEEEeecCCCcceeccCcccHHHHcCCCCCCEEEEEEE
Confidence            456788899999999999999999999999984 44457777    22  367888999999877333  444433

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 ....

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

Probab=96.49  E-value=0.0079  Score=35.62  Aligned_cols=55  Identities=27%  Similarity=0.378  Sum_probs=46.9

Q ss_pred             eCCCchHHHHHHHHhhhcC-CCCCceeEEECCeecCCCCccccc-ccCCCCEEEEEE
Q 040824           93 IEPTDTIERIKERVEEKEG-IPPVQQRLIYAGKQLADDKTARDY-NIEGGSVLHLVL  147 (154)
Q Consensus        93 v~~~~tv~~LK~~i~~~~~-i~~~~~~l~~~g~~l~d~~~L~~~-~i~~~~~i~~~~  147 (154)
                      |.++++|.++++.+..... .....+.|.++|..|++...|+++ |+++|+.+.+.-
T Consensus         1 v~~~d~v~dvrq~L~~~~~t~~~Tn~~L~~~g~~L~~~~el~~i~~~~~~~~L~lve   57 (76)
T PF15044_consen    1 VSPTDTVQDVRQVLAESPETCYLTNFSLEHNGQRLDDFVELSEIEGIKDGCVLELVE   57 (76)
T ss_pred             CChhhHHHHHHHHHHhCccccceeEEEEEECCCccCCchhhhhhhCCCCCcEEEEEe
Confidence            5678999999999987765 567788999999999999999888 588899988764

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

Probab=96.45  E-value=0.024  Score=31.99  Aligned_cols=67  Identities=21%  Similarity=0.405  Sum_probs=52.6

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhcC---CCCCceeEE-ECCeecCCCCcccccccCCCCEEEEEEeecC
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKEG---IPPVQQRLI-YAGKQLADDKTARDYNIEGGSVLHLVLALRG  151 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~~---i~~~~~~l~-~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~g  151 (154)
                      +|+...++-+.+...--..++.-+.+|   -|+++..|. -.|..++-++.+++||+.+|-++++.++...
T Consensus         4 NGqPv~VEANvnaPLh~v~akALe~sgNvgQP~ENWElkDe~G~vlD~~kKveD~GftngvkLFLsLKAGv   74 (76)
T PF10790_consen    4 NGQPVQVEANVNAPLHPVRAKALEQSGNVGQPPENWELKDESGQVLDVNKKVEDFGFTNGVKLFLSLKAGV   74 (76)
T ss_pred             CCCceeeecCCCCcchHHHHHHHhhccccCCCcccceeeccCCcEeeccchhhhccccccceEEEEeeccc
Confidence            577777777777777666666655554   688888776 6788999999999999999999888777643

>PRK08364 sulfur carrier protein ThiS; Provisional

Probab=96.40  E-value=0.055  Score=31.40  Aligned_cols=56  Identities=21%  Similarity=0.306  Sum_probs=43.3

Q ss_pred             eEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           88 EIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        88 ~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ...+++++..|+.+|-+.+    ++++....+..+|..+..     +.-+++||.|.++-..-||
T Consensus        15 ~~~~~~~~~~tv~~ll~~l----~~~~~~v~v~vNg~iv~~-----~~~l~~gD~Veii~~V~GG   70 (70)
T PRK08364         15 EKEIEWRKGMKVADILRAV----GFNTESAIAKVNGKVALE-----DDPVKDGDYVEVIPVVSGG   70 (70)
T ss_pred             ceEEEcCCCCcHHHHHHHc----CCCCccEEEEECCEECCC-----CcCcCCCCEEEEEccccCC
Confidence            4567888889999998765    677777777899998853     5568999999887666555

>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=96.37  E-value=0.00088  Score=49.55  Aligned_cols=77  Identities=22%  Similarity=0.474  Sum_probs=0.0

Q ss_pred             eeeeeeecCCceEEEee--C---CCchHHHHHHHHhh----------hcCCCCCcee-----EEECCeecCCCCcccccc
Q 040824           77 TMIKVKTLTGKEIEIDI--E---PTDTIERIKERVEE----------KEGIPPVQQR-----LIYAGKQLADDKTARDYN  136 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v--~---~~~tv~~LK~~i~~----------~~~i~~~~~~-----l~~~g~~l~d~~~L~~~~  136 (154)
                      +.|.++......+.+.+  .   .+.+|.++|..+++          .+++|.+.++     |+|+-+++.|++||.+..
T Consensus        79 ItV~Lks~rnp~l~i~L~~~~plattSv~dlk~~v~~rv~~~~~~~~~~~vp~dKik~~~~~lL~~kkPv~~~ktl~e~l  158 (309)
T PF12754_consen   79 ITVHLKSLRNPPLDISLPNVPPLATTSVQDLKDAVQQRVHPSQATYDETRVPLDKIKNFRCRLLYKKKPVGDSKTLAEVL  158 (309)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EEEEeecCCCCCceeEeCCCCcCCcCcHHHHHHHHHhhhcccccccccccCCHHHhhhhhhhheecCccCCCcCcHHHHH
Confidence            34445554444433332  1   25889999999999          8899999999     999999999999988875


Q ss_pred             cC-------CCCEEEEEEeecCCC
Q 040824          137 IE-------GGSVLHLVLALRGGG  153 (154)
Q Consensus       137 i~-------~~~~i~~~~~~~gg~  153 (154)
                      -.       .+.++++.+...||+
T Consensus       159 ~~~~~~l~~~~~~vE~gvMVlGGa  182 (309)
T PF12754_consen  159 ADSESRLLSGGKEVEFGVMVLGGA  182 (309)
T ss_dssp             ------------------------
T ss_pred             hcccchhccCCceEEEEEEEECCc
Confidence            44       578888888888884

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.

>PRK06488 sulfur carrier protein ThiS; Validated

Probab=96.26  E-value=0.05  Score=30.99  Aligned_cols=60  Identities=12%  Similarity=0.291  Sum_probs=42.6

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      +|+.+.+  + ..|+.+|.+.+    ++++....+-.++..+.. ..-.+.-+++||.|.++-...||
T Consensus         6 Ng~~~~~--~-~~tl~~Ll~~l----~~~~~~vavavN~~iv~~-~~~~~~~L~dgD~Ieiv~~V~GG   65 (65)
T PRK06488          6 NGETLQT--E-ATTLALLLAEL----DYEGNWLATAVNGELVHK-EARAQFVLHEGDRIEILSPMQGG   65 (65)
T ss_pred             CCeEEEc--C-cCcHHHHHHHc----CCCCCeEEEEECCEEcCH-HHcCccccCCCCEEEEEEeccCC
Confidence            5666555  3 45899888765    566666667788987763 23456678999999887777665

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

Probab=96.25  E-value=0.0016  Score=48.58  Aligned_cols=72  Identities=24%  Similarity=0.341  Sum_probs=53.8

Q ss_pred             EEEEEeCCCCE--EEEEEeCCCcHHHHHHHHHhHhC--CCCCCeEEEEcceEeccCceeccccccc--ccceeeeeee
Q 040824            2 QIFVKTLTGKT--ITLEVESSDTIDNVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLADYNIQK--ESTLHLVLRL   73 (154)
Q Consensus         2 ~v~v~~~~~~~--~~~~v~~~~tv~~lk~~i~~~~~--~~~~~q~L~~~g~~L~d~~~l~~~~i~~--~~~i~l~~~~   73 (154)
                      .+.+|..+.+.  +.+..+..+||++||..++...-  --+.+|+|+|.|+.|.|+..+.+.=.+.  ...+||++..
T Consensus        11 ~lliks~Nq~y~dl~i~~dl~wtv~~Lk~hls~VyPskpl~~dqrliYsgkllld~qcl~d~lrkq~k~Hv~hlvcns   88 (391)
T KOG4583|consen   11 TLLIKSPNQSYKDLSISLDLKWTVGDLKVHLSQVYPSKPLELDQRLIYSGKLLLDHQCLTDWLRKQVKEHVKHLVCNS   88 (391)
T ss_pred             EEEecCCCccccceeeehhhhhhHHHHhhhHhhcCCCCCchhhHHHHhhccccccchhHHHHHHHHHHHHHHHHhcCC
Confidence            46778887755  55666778999999999998763  4466899999999999999988876533  2355555543

>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=96.21  E-value=0.021  Score=34.61  Aligned_cols=69  Identities=19%  Similarity=0.283  Sum_probs=48.8

Q ss_pred             eeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCC---CceeEEECC---e--ecCCCCccccc----ccCCCCEEEEEE
Q 040824           80 KVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPP---VQQRLIYAG---K--QLADDKTARDY----NIEGGSVLHLVL  147 (154)
Q Consensus        80 ~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~---~~~~l~~~g---~--~l~d~~~L~~~----~i~~~~~i~~~~  147 (154)
                      ..+.+.|+.+.+.+.+++.+.+|++.|+++.|...   ....|.|-.   .  .|..+.-|.++    ......+|.+.+
T Consensus         4 K~~~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~~~~~~L~YlDDEgD~VllT~D~DL~e~v~iar~~g~~~v~L~v   83 (86)
T cd06409           4 KFKDPKGRVHRFRLRPSESLEELRTLISQRLGDDDFETHLYALSYVDDEGDIVLITSDSDLVAAVLVARSAGLKKLDLHL   83 (86)
T ss_pred             EeeCCCCCEEEEEecCCCCHHHHHHHHHHHhCCccccCCcccEEEEcCCCCEEEEeccchHHHHHHHHHHcCCCEEEEEE
Confidence            45677899999999999999999999999999876   577888743   2  23333344444    234445555555


Q ss_pred             e
Q 040824          148 A  148 (154)
Q Consensus       148 ~  148 (154)
                      +
T Consensus        84 ~   84 (86)
T cd06409          84 H   84 (86)
T ss_pred             e
Confidence            4

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

>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=95.96  E-value=0.05  Score=32.67  Aligned_cols=64  Identities=16%  Similarity=0.304  Sum_probs=48.4

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhcCCCC-CceeEEECCe-----ecCCCCcccc----cccCCCCEEEEEEe
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKEGIPP-VQQRLIYAGK-----QLADDKTARD----YNIEGGSVLHLVLA  148 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~-~~~~l~~~g~-----~l~d~~~L~~----~~i~~~~~i~~~~~  148 (154)
                      ++..+.+.++++.+..+|++.+++++++.. ..+.|.|...     .+..+.-|.+    |.....++|.++++
T Consensus         8 ~~d~~r~~l~~~~~~~~L~~~i~~r~~~~~~~~f~LkY~Ddegd~v~ltsd~DL~eai~i~~~~~~~~v~l~v~   81 (82)
T cd06407           8 GEEKIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKYLDDDEEWVLLTCDADLEECIDVYRSSGSHTIRLLVH   81 (82)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEEECCCCCeEEeecHHHHHHHHHHHHHCCCCeEEEEee
Confidence            567889999999999999999999999865 6778887543     2334444555    45566778877765

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

>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=95.88  E-value=0.043  Score=32.67  Aligned_cols=43  Identities=19%  Similarity=0.262  Sum_probs=37.2

Q ss_pred             EEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcc
Q 040824            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG   47 (154)
Q Consensus         3 v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g   47 (154)
                      |+|.+. + ++.++++++.+..+|.++|.++.++|++...|.|..
T Consensus         5 vKV~f~-~-tIaIrvp~~~~y~~L~~ki~~kLkl~~e~i~LsYkd   47 (80)
T cd06406           5 VKVHFK-Y-TVAIQVARGLSYATLLQKISSKLELPAEHITLSYKS   47 (80)
T ss_pred             EEEEEE-E-EEEEEcCCCCCHHHHHHHHHHHhCCCchhcEEEecc
Confidence            456654 2 888999999999999999999999999999998864

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

>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=95.74  E-value=0.075  Score=31.66  Aligned_cols=38  Identities=13%  Similarity=0.288  Sum_probs=35.1

Q ss_pred             eEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCee
Q 040824           88 EIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQ  125 (154)
Q Consensus        88 ~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~  125 (154)
                      ++.+++++..+..+|..+|+++.++|++..+|.|+...
T Consensus        12 tIaIrvp~~~~y~~L~~ki~~kLkl~~e~i~LsYkde~   49 (80)
T cd06406          12 TVAIQVARGLSYATLLQKISSKLELPAEHITLSYKSEA   49 (80)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCchhcEEEeccCC
Confidence            88899999999999999999999999999999997653

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

>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=95.70  E-value=0.063  Score=32.19  Aligned_cols=61  Identities=18%  Similarity=0.305  Sum_probs=43.5

Q ss_pred             EEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEee
Q 040824           89 IEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        89 ~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      +...++-.++++.||..++++.+++.+...+...+..|+++++|-+.+++-...+.+.+-.
T Consensus         5 I~q~mDI~epl~~Lk~lLe~Rl~~~L~~~~f~LQD~~L~~~k~L~dQcVqgeGlVQlnvQi   65 (88)
T PF11620_consen    5 IMQHMDIREPLSTLKKLLERRLGISLSDYEFWLQDIQLEPHKSLVDQCVQGEGLVQLNVQI   65 (88)
T ss_dssp             EEEEEESSSBGGGHHHHSHHHH-S--SS-EEEETTEE--TTSBTTTSS----SEEEEEEEE
T ss_pred             EEEEEecCCcHHHHHHHHHHhhCCCcCCCeEEeccceecCCccHHHhhccccCEEEEEEEE
Confidence            4456677889999999999999999999999888878999999999999888888776544

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.

>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein

Probab=95.65  E-value=0.084  Score=30.05  Aligned_cols=57  Identities=19%  Similarity=0.381  Sum_probs=42.4

Q ss_pred             EeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           91 IDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        91 ~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ++++...|+.+|.+.+    ++++....+..+|+.+..+ .-.+.-+++||.|.++-..-||
T Consensus         9 ~~~~~~~tv~~ll~~l----~~~~~~i~V~vNg~~v~~~-~~~~~~L~~gD~V~ii~~v~GG   65 (65)
T cd00565           9 REVEEGATLAELLEEL----GLDPRGVAVALNGEIVPRS-EWASTPLQDGDRIEIVTAVGGG   65 (65)
T ss_pred             EEcCCCCCHHHHHHHc----CCCCCcEEEEECCEEcCHH-HcCceecCCCCEEEEEEeccCC
Confidence            4556778999998765    4677888888999887643 2334568999999888777666

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.

>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=95.63  E-value=0.11  Score=31.19  Aligned_cols=45  Identities=11%  Similarity=0.142  Sum_probs=36.2

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCC-CCeEEEEc
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP-DQQRLIFA   46 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~-~~q~L~~~   46 (154)
                      |+|++.. +|..+.+.++++.+..+|++.|.+++++.. ..-.|.|-
T Consensus         1 ~~vK~~~-~~d~~r~~l~~~~~~~~L~~~i~~r~~~~~~~~f~LkY~   46 (82)
T cd06407           1 VRVKATY-GEEKIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKYL   46 (82)
T ss_pred             CEEEEEe-CCeEEEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEEE
Confidence            4566665 667899999999999999999999999865 55566553

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

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

Probab=95.60  E-value=0.18  Score=29.72  Aligned_cols=58  Identities=24%  Similarity=0.301  Sum_probs=46.0

Q ss_pred             EEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCC-CCCeEEEE----c--ceEeccCceecccccc
Q 040824            5 VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIP-PDQQRLIF----A--GKQLEDGRTLADYNIQ   62 (154)
Q Consensus         5 v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~-~~~q~L~~----~--g~~L~d~~~l~~~~i~   62 (154)
                      |+.++|....++++.++|+.++-+.|.++.++. .+.--|.+    +  ...|+.+.++.++...
T Consensus         1 V~llD~~~~~~~v~~~~t~~~l~~~v~~~l~l~e~~~FgL~~~~~~~~~~~wL~~~k~l~~q~~~   65 (80)
T PF09379_consen    1 VRLLDGTTKTFEVDPKTTGQDLLEQVCDKLGLKEKEYFGLQYQVDKDGEHHWLDLDKKLKKQLKK   65 (80)
T ss_dssp             EEESSEEEEEEEEETTSBHHHHHHHHHHHHTTSSGGGEEEEE-EBTTSSEEEE-SSSBGGGSTBT
T ss_pred             CCCcCCCcEEEEEcCCCcHHHHHHHHHHHcCCCCccEEEEEEeecCCCcceeccCcccHHHHcCC
Confidence            567899999999999999999999999999965 33345556    1  2678888888888766

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 ....

>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=95.59  E-value=0.082  Score=32.01  Aligned_cols=37  Identities=14%  Similarity=0.296  Sum_probs=34.1

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCC
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP   38 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~   38 (154)
                      ..+++.+.|+.+.+.+.+++.+.+|++.|.++.+...
T Consensus         2 ~FK~~~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~   38 (86)
T cd06409           2 AFKFKDPKGRVHRFRLRPSESLEELRTLISQRLGDDD   38 (86)
T ss_pred             cEEeeCCCCCEEEEEecCCCCHHHHHHHHHHHhCCcc
Confidence            4678889999999999999999999999999999886

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

>TIGR01683 thiS thiamine biosynthesis protein ThiS

Probab=95.50  E-value=0.11  Score=29.45  Aligned_cols=61  Identities=20%  Similarity=0.388  Sum_probs=43.6

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      +|+.  ++++...|+.+|.+.+    +++++...+..+|..+..+ .-.++-+++||.|.++-..-||
T Consensus         4 Ng~~--~~~~~~~tv~~ll~~l----~~~~~~v~v~vN~~iv~~~-~~~~~~L~~gD~veii~~V~GG   64 (64)
T TIGR01683         4 NGEP--VEVEDGLTLAALLESL----GLDPRRVAVAVNGEIVPRS-EWDDTILKEGDRIEIVTFVGGG   64 (64)
T ss_pred             CCeE--EEcCCCCcHHHHHHHc----CCCCCeEEEEECCEEcCHH-HcCceecCCCCEEEEEEeccCC
Confidence            4544  4556678899988754    5667777788999887532 2344578999999888777665

This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.

>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal

Probab=95.47  E-value=0.16  Score=30.06  Aligned_cols=60  Identities=17%  Similarity=0.309  Sum_probs=44.9

Q ss_pred             eEEEeeCCC-chHHHHHHHHhhhcC-C--CCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           88 EIEIDIEPT-DTIERIKERVEEKEG-I--PPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        88 ~~~~~v~~~-~tv~~LK~~i~~~~~-i--~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ...++++.. .|+.+|...+.+.++ +  ......+..+++...+     +.-+++||.|.++-+.-||
T Consensus        17 ~~~~~~~~~~~tv~~L~~~L~~~~p~l~~~~~~~~v~vn~~~v~~-----~~~l~dgDevai~PpvsGG   80 (80)
T TIGR01682        17 EETLELPDESTTVGELKEHLAKEGPELAASRGQVMVAVNEEYVTD-----DALLNEGDEVAFIPPVSGG   80 (80)
T ss_pred             eEEEECCCCCcCHHHHHHHHHHhCchhhhhccceEEEECCEEcCC-----CcCcCCCCEEEEeCCCCCC
Confidence            356788876 899999999998875 1  1233566678887764     4678999999888777766

The C-terminal Gly-Gly of this model is critical to function.

>PLN02799 Molybdopterin synthase sulfur carrier subunit

Probab=95.45  E-value=0.096  Score=31.23  Aligned_cols=61  Identities=11%  Similarity=0.191  Sum_probs=42.8

Q ss_pred             ceEEEeeCCCchHHHHHHHHhhhcC-CCC--CceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           87 KEIEIDIEPTDTIERIKERVEEKEG-IPP--VQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        87 ~~~~~~v~~~~tv~~LK~~i~~~~~-i~~--~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ....++++...|+.+|.+.+...+. +..  ....+..+++...     .+.-+++||+|.++-..-||
T Consensus        19 ~~~~~~~~~~~tv~~L~~~l~~~~p~l~~~~~~~~vavN~~~v~-----~~~~l~dgDeVai~PpvsGG   82 (82)
T PLN02799         19 SDMTLELPAGSTTADCLAELVAKFPSLEEVRSCCVLALNEEYTT-----ESAALKDGDELAIIPPISGG   82 (82)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHChhHHHHhhCcEEEECCEEcC-----CCcCcCCCCEEEEeCCCCCC
Confidence            3456778888999999999977652 111  1234567887764     34467899999888777666

>PF14836 Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A3O_B 3PPA_A 3T9L_A 4A3P_A 3PV1_A

Probab=95.32  E-value=0.17  Score=30.74  Aligned_cols=62  Identities=19%  Similarity=0.207  Sum_probs=42.5

Q ss_pred             CEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEE-c---c-eEe-ccCceecccccccccceeeeeee
Q 040824           11 KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF-A---G-KQL-EDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus        11 ~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~-~---g-~~L-~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      ..+...++..+||+.+...+.+.+.+ +..-+|+- .   + ..| +.+.|+.+.++.+|..|.+-.+.
T Consensus        14 ~~~t~~FSk~DTI~~v~~~~rklf~i-~~E~RLW~~~~~~~~e~L~~~~~Tv~da~L~~gQ~vliE~rn   81 (88)
T PF14836_consen   14 SVLTKQFSKTDTIGFVEKEMRKLFNI-QEETRLWNKYSENSYELLNNPEITVEDAGLYDGQVVLIEERN   81 (88)
T ss_dssp             EEEEEEE-TTSBHHHHHHHHHHHCT--TS-EEEEEECTTTCEEEE--TTSBTTTTT--TTEEEEEEE--
T ss_pred             cHhHhhccccChHHHHHHHHHHHhCC-CccceehhccCCcchhhhCCCCccHHHccCcCCCEEEEEeec
Confidence            45778899999999999999999999 66677763 2   2 335 45679999999999877555443

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

Probab=95.31  E-value=0.0083  Score=44.88  Aligned_cols=60  Identities=25%  Similarity=0.384  Sum_probs=47.4

Q ss_pred             ceeeeeeecCC--ceEEEeeCCCchHHHHHHHHhhhcCC--CCCceeEEECCeecCCCCccccc
Q 040824           76 GTMIKVKTLTG--KEIEIDIEPTDTIERIKERVEEKEGI--PPVQQRLIYAGKQLADDKTARDY  135 (154)
Q Consensus        76 ~~~i~v~~~~~--~~~~~~v~~~~tv~~LK~~i~~~~~i--~~~~~~l~~~g~~l~d~~~L~~~  135 (154)
                      +..++++..+.  +...+..+...||++||..++..+.=  -+.+|||+|.|+.|.|...|.+.
T Consensus         9 ~v~lliks~Nq~y~dl~i~~dl~wtv~~Lk~hls~VyPskpl~~dqrliYsgkllld~qcl~d~   72 (391)
T KOG4583|consen    9 PVTLLIKSPNQSYKDLSISLDLKWTVGDLKVHLSQVYPSKPLELDQRLIYSGKLLLDHQCLTDW   72 (391)
T ss_pred             ceEEEecCCCccccceeeehhhhhhHHHHhhhHhhcCCCCCchhhHHHHhhccccccchhHHHH
Confidence            34566666654  45678888899999999999988863  24578999999999998888765

>PF02597 ThiS: ThiS family; InterPro: IPR003749 ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer

Probab=95.28  E-value=0.094  Score=30.62  Aligned_cols=63  Identities=19%  Similarity=0.302  Sum_probs=49.8

Q ss_pred             eEEEeeCCCchHHHHHHHHhhhcCC--CCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           88 EIEIDIEPTDTIERIKERVEEKEGI--PPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        88 ~~~~~v~~~~tv~~LK~~i~~~~~i--~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ...+.+....|+.+|.+.+...++-  ......+..+|+.+.+  .-.+.-+++||.|.++-..-||
T Consensus        13 ~~~~~~~~~~tv~~ll~~l~~~~p~~~~~~~~~v~vN~~~v~~--~~~~~~l~~gD~V~i~ppvsGG   77 (77)
T PF02597_consen   13 EEEIEVPEGSTVRDLLEALAERYPELALRDRVAVAVNGEIVPD--DGLDTPLKDGDEVAILPPVSGG   77 (77)
T ss_dssp             EEEEEESSTSBHHHHHHHHCHHTGGGHTTTTEEEEETTEEEGG--GTTTSBEETTEEEEEEESTSTS
T ss_pred             CeEEecCCCCcHHHHHHHHHhhccccccCccEEEEECCEEcCC--ccCCcCcCCCCEEEEECCCCCC
Confidence            5567889999999999999887742  3366788899998877  3566778999999887766665

ThiS is coded in the thiCEFSGH operon in Escherichia coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS []. MoaD, a protein involved in sulphur transfer during molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.; PDB: 1JW9_D 1JWB_D 1JWA_D 3BII_D 1NVI_D 1FMA_D 1FM0_D 2QIE_G 2Q5W_D 2K5P_A ....

>TIGR01687 moaD_arch MoaD family protein, archaeal

Probab=95.23  E-value=0.25  Score=29.75  Aligned_cols=61  Identities=16%  Similarity=0.262  Sum_probs=44.2

Q ss_pred             eEEEeeCCCchHHHHHHHHhhhcCC------C-----CCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           88 EIEIDIEPTDTIERIKERVEEKEGI------P-----PVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        88 ~~~~~v~~~~tv~~LK~~i~~~~~i------~-----~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ...++++ ..|+.+|.+.+.+.++-      .     .....+..+|+....+..   .-+++||.|.++-..-||
T Consensus        17 ~~~v~~~-~~tv~~l~~~l~~~~p~~~~~~l~~~~~~~~~~~v~vN~~~v~~~~~---~~l~dgdev~i~PpvsGG   88 (88)
T TIGR01687        17 SEEIEIE-GKTVGDLLNELMARYPKEFSELFKEGLGLVPNVIILVNGRNVDWGLG---TELKDGDVVAIFPPVSGG   88 (88)
T ss_pred             eEEEEeC-CCCHHHHHHHHHHHCcHHHHHhCccCCcccccEEEEECCEecCccCC---CCCCCCCEEEEeCCCcCC
Confidence            4566776 88999999999888741      1     123667788887764432   568999999888777766

Members of this family appear to be archaeal versions of MoaD, subunit 1 of molybdopterin converting factor. This model has been split from the bacterial/eukaryotic equivalog model TIGR01682 because the presence of two members of this family in a substantial number of archaeal species suggests that roles might not be interchangeable.

>PRK06437 hypothetical protein; Provisional

Probab=94.93  E-value=0.34  Score=27.84  Aligned_cols=59  Identities=17%  Similarity=0.329  Sum_probs=44.0

Q ss_pred             EEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeee
Q 040824            4 FVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (154)
Q Consensus         4 ~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~   71 (154)
                      +++-.+++...++++.+.|+.+|-+.    .++++...-+..+|..+.     .++-+++++.|.+..
T Consensus         4 ~~~v~g~~~~~~~i~~~~tv~dLL~~----Lgi~~~~vaV~vNg~iv~-----~~~~L~dgD~Veiv~   62 (67)
T PRK06437          4 MIRVKGHINKTIEIDHELTVNDIIKD----LGLDEEEYVVIVNGSPVL-----EDHNVKKEDDVLILE   62 (67)
T ss_pred             eEEecCCcceEEEcCCCCcHHHHHHH----cCCCCccEEEEECCEECC-----CceEcCCCCEEEEEe
Confidence            34443556688888889999998766    478888888888999886     455677788886654

>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=94.93  E-value=0.11  Score=31.16  Aligned_cols=59  Identities=20%  Similarity=0.330  Sum_probs=41.4

Q ss_pred             EEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeee
Q 040824           13 ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (154)
Q Consensus        13 ~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~   71 (154)
                      ....++-..+++.||..++.+.+++-+.-.++..+..|+++++|.+-+++....+.+.+
T Consensus         5 I~q~mDI~epl~~Lk~lLe~Rl~~~L~~~~f~LQD~~L~~~k~L~dQcVqgeGlVQlnv   63 (88)
T PF11620_consen    5 IMQHMDIREPLSTLKKLLERRLGISLSDYEFWLQDIQLEPHKSLVDQCVQGEGLVQLNV   63 (88)
T ss_dssp             EEEEEESSSBGGGHHHHSHHHH-S--SS-EEEETTEE--TTSBTTTSS----SEEEEEE
T ss_pred             EEEEEecCCcHHHHHHHHHHhhCCCcCCCeEEeccceecCCccHHHhhccccCEEEEEE
Confidence            44567778899999999999999998888898888779999999999998777775543

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.

>smart00666 PB1 PB1 domain

Probab=94.79  E-value=0.25  Score=29.23  Aligned_cols=44  Identities=16%  Similarity=0.341  Sum_probs=36.6

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEc
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA   46 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~   46 (154)
                      +++++. ++..+.+.++.+.|..+|+.+|.++++.+.....|.|.
T Consensus         3 ~vK~~~-~~~~~~~~~~~~~s~~dL~~~i~~~~~~~~~~~~l~Y~   46 (81)
T smart00666        3 DVKLRY-GGETRRLSVPRDISFEDLRSKVAKRFGLDNQSFTLKYQ   46 (81)
T ss_pred             cEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHhCCCCCCeEEEEE
Confidence            466666 66788999999999999999999999987766777664

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.

>smart00455 RBD Raf-like Ras-binding domain

Probab=94.65  E-value=0.15  Score=29.65  Aligned_cols=43  Identities=16%  Similarity=0.271  Sum_probs=38.7

Q ss_pred             eeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECC
Q 040824           81 VKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAG  123 (154)
Q Consensus        81 v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g  123 (154)
                      +..++|+...+.+.|..|+.++-..++++.|+.++...+...|
T Consensus         4 v~LP~~~~~~V~vrpg~tl~e~L~~~~~kr~l~~~~~~v~~~g   46 (70)
T smart00455        4 VHLPDNQRTVVKVRPGKTVRDALAKALKKRGLNPECCVVRLRG   46 (70)
T ss_pred             EECCCCCEEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEcC
Confidence            4456889999999999999999999999999999999998755

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

Probab=94.46  E-value=0.16  Score=29.75  Aligned_cols=44  Identities=16%  Similarity=0.334  Sum_probs=38.8

Q ss_pred             eeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECC
Q 040824           80 KVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAG  123 (154)
Q Consensus        80 ~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g  123 (154)
                      .|..++|+...+.+.+..|+.++-.+++++.|+.++..-+...|
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            45567899999999999999999999999999999999887654

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.

>PRK05863 sulfur carrier protein ThiS; Provisional

Probab=94.37  E-value=0.27  Score=28.00  Aligned_cols=60  Identities=17%  Similarity=0.323  Sum_probs=42.8

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      +|+.+  ++++..|+.+|-..    .++++...-+.+++..+..+.- ..+ +++||.|.++-...||
T Consensus         6 NG~~~--~~~~~~tl~~ll~~----l~~~~~~vav~~N~~iv~r~~~-~~~-L~~gD~ieIv~~VgGG   65 (65)
T PRK05863          6 NEEQV--EVDEQTTVAALLDS----LGFPEKGIAVAVDWSVLPRSDW-ATK-LRDGARLEVVTAVQGG   65 (65)
T ss_pred             CCEEE--EcCCCCcHHHHHHH----cCCCCCcEEEEECCcCcChhHh-hhh-cCCCCEEEEEeeccCC
Confidence            55544  44567788887653    5788888899999997764332 235 8999999887766655

>cd06408 PB1_NoxR The PB1 domain is present in the Epichloe festucae NoxR protein (NADPH oxidase regulator), a key regulator of NADPH oxidase isoform, NoxA

Probab=94.19  E-value=0.46  Score=28.78  Aligned_cols=44  Identities=16%  Similarity=0.289  Sum_probs=34.3

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEc
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA   46 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~   46 (154)
                      |+|+|.. +|....+.++++.+..+|.++|..++++. ....+.|.
T Consensus         3 ikVKv~~-~~Dv~~i~v~~~i~f~dL~~kIrdkf~~~-~~~~iKyk   46 (86)
T cd06408           3 IRVKVHA-QDDTRYIMIGPDTGFADFEDKIRDKFGFK-RRLKIKMK   46 (86)
T ss_pred             EEEEEEe-cCcEEEEEcCCCCCHHHHHHHHHHHhCCC-CceEEEEE
Confidence            3455554 67789999999999999999999999985 34455453

NoxA is essential for growth control of the fungal endophyte in plant tissue in the process of symbiotic interaction between a fungi and its plant host. The Epichloe festucae p67(phox)-like regulator, NoxR, dispensable in culture but essential in plants for the symbiotic interaction. Plants infected with a noxR deletion mutant show severe stunting and premature senescence, whereas hyphae in the meristematic tissues show increased branching leading to increased fungal colonization of pseudostem and leaf blade tissue. The PB1 domain is a modular domain mediating specific protein-protein interactions which a play 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

>PF14836 Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A3O_B 3PPA_A 3T9L_A 4A3P_A 3PV1_A

Probab=94.17  E-value=0.66  Score=28.20  Aligned_cols=65  Identities=20%  Similarity=0.216  Sum_probs=44.0

Q ss_pred             ceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEE-C---C-eec-CCCCcccccccCCCCEEEEEEeecCC
Q 040824           87 KEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIY-A---G-KQL-ADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        87 ~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~-~---g-~~l-~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ..+...++..+||..+...+++.+.+ .+..||-- .   + ..| +.+.|+.+.|+.+|..|.+=.+-.-|
T Consensus        14 ~~~t~~FSk~DTI~~v~~~~rklf~i-~~E~RLW~~~~~~~~e~L~~~~~Tv~da~L~~gQ~vliE~rn~DG   84 (88)
T PF14836_consen   14 SVLTKQFSKTDTIGFVEKEMRKLFNI-QEETRLWNKYSENSYELLNNPEITVEDAGLYDGQVVLIEERNEDG   84 (88)
T ss_dssp             EEEEEEE-TTSBHHHHHHHHHHHCT--TS-EEEEEECTTTCEEEE--TTSBTTTTT--TTEEEEEEE--TTS
T ss_pred             cHhHhhccccChHHHHHHHHHHHhCC-CccceehhccCCcchhhhCCCCccHHHccCcCCCEEEEEeeccCC
Confidence            45677899999999999999999999 66677742 1   2 245 45679999999999988766554333

>smart00666 PB1 PB1 domain

Probab=94.14  E-value=0.33  Score=28.67  Aligned_cols=45  Identities=16%  Similarity=0.348  Sum_probs=37.1

Q ss_pred             eeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCe
Q 040824           79 IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGK  124 (154)
Q Consensus        79 i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~  124 (154)
                      +.+.. ++....+.++++.|..+|+.+|+.+++.+.....|.|...
T Consensus         4 vK~~~-~~~~~~~~~~~~~s~~dL~~~i~~~~~~~~~~~~l~Y~De   48 (81)
T smart00666        4 VKLRY-GGETRRLSVPRDISFEDLRSKVAKRFGLDNQSFTLKYQDE   48 (81)
T ss_pred             EEEEE-CCEEEEEEECCCCCHHHHHHHHHHHhCCCCCCeEEEEECC
Confidence            34444 5677889999999999999999999999888888888753

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.

>smart00295 B41 Band 4

Probab=94.02  E-value=0.78  Score=31.85  Aligned_cols=73  Identities=25%  Similarity=0.297  Sum_probs=51.5

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCC-CceeEEEC---C---eecCCCCcccccccC-CCCEEEEEE
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPP-VQQRLIYA---G---KQLADDKTARDYNIE-GGSVLHLVL  147 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~-~~~~l~~~---g---~~l~d~~~L~~~~i~-~~~~i~~~~  147 (154)
                      ++.+.|...+|+...+.+++++|+.++...++.+.|++. ..+-|.+.   +   ..++...++.+.... ....+++..
T Consensus         3 ~~~~~V~l~dg~~~~~~~~~~~t~~ev~~~v~~~~~l~~~~~F~L~~~~~~~~~~~~l~~~~~l~~~~~~~~~~~l~fr~   82 (207)
T smart00295        3 PRVLKVYLLDGTTLEFEVDSSTTAEELLETVCRKLGIRESEYFGLQFEDPDEDLSHWLDPAKTLLDQDVKSEPLTLYFRV   82 (207)
T ss_pred             cEEEEEEecCCCEEEEEECCCCCHHHHHHHHHHHhCCCccceeEEEEEcCCCCcCeeCCCccCHHHhcCCCCCcEEEEEE
Confidence            456778888999999999999999999999999999853 22344421   1   346666677776654 334555444


Q ss_pred             e
Q 040824          148 A  148 (154)
Q Consensus       148 ~  148 (154)
                      +
T Consensus        83 r   83 (207)
T smart00295       83 K   83 (207)
T ss_pred             E
Confidence            4

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

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

Probab=93.83  E-value=0.085  Score=31.20  Aligned_cols=58  Identities=22%  Similarity=0.299  Sum_probs=43.6

Q ss_pred             EeCCCcHHHHHHHHHhHhC-CCCCCeEEEEcceEeccCceecccc-cccccceeeeeeee
Q 040824           17 VESSDTIDNVKAKIQDKEG-IPPDQQRLIFAGKQLEDGRTLADYN-IQKESTLHLVLRLR   74 (154)
Q Consensus        17 v~~~~tv~~lk~~i~~~~~-~~~~~q~L~~~g~~L~d~~~l~~~~-i~~~~~i~l~~~~~   74 (154)
                      ++++++|.++++.+..... ..-..-.|.++|+.|++...++++. +++++.+.+...+.
T Consensus         1 v~~~d~v~dvrq~L~~~~~t~~~Tn~~L~~~g~~L~~~~el~~i~~~~~~~~L~lve~pY   60 (76)
T PF15044_consen    1 VSPTDTVQDVRQVLAESPETCYLTNFSLEHNGQRLDDFVELSEIEGIKDGCVLELVEEPY   60 (76)
T ss_pred             CChhhHHHHHHHHHHhCccccceeEEEEEECCCccCCchhhhhhhCCCCCcEEEEEecCC
Confidence            4578899999999876643 3344556778999999888888876 77788887776554

>PRK05659 sulfur carrier protein ThiS; Validated

Probab=93.50  E-value=0.67  Score=26.25  Aligned_cols=61  Identities=20%  Similarity=0.387  Sum_probs=43.8

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      +|+.  +++++..|+.++-..    .++++...-+..+|..+... .-.+.-+++||.|.++-..-||
T Consensus         6 NG~~--~~~~~~~tl~~lL~~----l~~~~~~vav~vNg~iv~r~-~~~~~~l~~gD~vei~~~vgGG   66 (66)
T PRK05659          6 NGEP--RELPDGESVAALLAR----EGLAGRRVAVEVNGEIVPRS-QHASTALREGDVVEIVHALGGG   66 (66)
T ss_pred             CCeE--EEcCCCCCHHHHHHh----cCCCCCeEEEEECCeEeCHH-HcCcccCCCCCEEEEEEEecCC
Confidence            5554  456677888888654    57888888888999877633 2344568999999888776665

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

Probab=93.42  E-value=0.49  Score=26.80  Aligned_cols=65  Identities=23%  Similarity=0.473  Sum_probs=50.7

Q ss_pred             CCCEEEEEEeCCCcHHHHHHHHHhHhC---CCCCCeEEE-EcceEeccCceecccccccccceeeeeee
Q 040824            9 TGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLI-FAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         9 ~~~~~~~~v~~~~tv~~lk~~i~~~~~---~~~~~q~L~-~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      +|+...++.+.+++..-..++--+.++   -|++.=.|. -+|..++-++.+.+||+.++-++.+.++.
T Consensus         4 NGqPv~VEANvnaPLh~v~akALe~sgNvgQP~ENWElkDe~G~vlD~~kKveD~GftngvkLFLsLKA   72 (76)
T PF10790_consen    4 NGQPVQVEANVNAPLHPVRAKALEQSGNVGQPPENWELKDESGQVLDVNKKVEDFGFTNGVKLFLSLKA   72 (76)
T ss_pred             CCCceeeecCCCCcchHHHHHHHhhccccCCCcccceeeccCCcEeeccchhhhccccccceEEEEeec
Confidence            678888899999988888777655543   566665555 35889999999999999999988777654

>PRK06944 sulfur carrier protein ThiS; Provisional

Probab=93.18  E-value=0.86  Score=25.66  Aligned_cols=60  Identities=15%  Similarity=0.204  Sum_probs=40.1

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      +|+.  +++++..|+.+|.+.+.    ++ ....+..+|..+..+. -.+.-+++||.|.++-...||
T Consensus         6 Ng~~--~~~~~~~tl~~ll~~l~----~~-~~~~v~vN~~~v~~~~-~~~~~L~~gD~vei~~~v~GG   65 (65)
T PRK06944          6 NQQT--LSLPDGATVADALAAYG----AR-PPFAVAVNGDFVARTQ-HAARALAAGDRLDLVQPVAGG   65 (65)
T ss_pred             CCEE--EECCCCCcHHHHHHhhC----CC-CCeEEEECCEEcCchh-cccccCCCCCEEEEEeeccCC
Confidence            4554  45567789999988663    33 3456678888765321 234458899999888777665

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.17  E-value=0.18  Score=38.01  Aligned_cols=56  Identities=18%  Similarity=0.202  Sum_probs=45.4

Q ss_pred             EeeCCCchHHHHHHHHhhhcCCCCCceeEEE---CCe-----ecCCCCcccccccCCCCEEEEE
Q 040824           91 IDIEPTDTIERIKERVEEKEGIPPVQQRLIY---AGK-----QLADDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        91 ~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~---~g~-----~l~d~~~L~~~~i~~~~~i~~~  146 (154)
                      .-+.-.-||.+++..+..+.|+.+.+++|++   .|+     ...-+..|.+|+|++||.+.+-
T Consensus       352 ~~I~~~~TV~D~~~~Ld~~VGvk~trMkLf~L~eD~rt~~~ss~~~N~~L~~fkIedGDs~lvq  415 (418)
T KOG2982|consen  352 GLICMTRTVLDFMKILDPKVGVKFTRMKLFLLREDGRTDDFSSSDYNMPLHYFKIEDGDSFLVQ  415 (418)
T ss_pred             eEEEeehHHHHHHHHhccccccccceeEEEEEcccCccCCccccCCCCcceEEeccCCCEeeee
Confidence            3445567999999999999999999999985   233     3456778999999999998654

>PRK08053 sulfur carrier protein ThiS; Provisional

Probab=93.07  E-value=0.94  Score=25.77  Aligned_cols=61  Identities=11%  Similarity=0.208  Sum_probs=42.4

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      +|+.  +++.+..|+.+|.+.+    +.+.....+-.++..+..+ .-++.-+++||.|.++-..-||
T Consensus         6 Ng~~--~~~~~~~tl~~ll~~l----~~~~~~vaVavN~~iv~r~-~w~~~~L~~gD~Ieii~~v~GG   66 (66)
T PRK08053          6 NDQP--MQCAAGQTVHELLEQL----NQLQPGAALAINQQIIPRE-QWAQHIVQDGDQILLFQVIAGG   66 (66)
T ss_pred             CCeE--EEcCCCCCHHHHHHHc----CCCCCcEEEEECCEEeChH-HcCccccCCCCEEEEEEEccCC
Confidence            5554  4456678899888653    5555667777899887532 2344468999999888777665

>PRK06083 sulfur carrier protein ThiS; Provisional

Probab=92.99  E-value=0.78  Score=27.66  Aligned_cols=61  Identities=13%  Similarity=0.306  Sum_probs=45.1

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      +|+.  .++++..|+.+|-+.    .++++...-+-.+|..+.- ..-++.-+++||.|+++--..||
T Consensus        24 NG~~--~~~~~~~tl~~LL~~----l~~~~~~vAVevNg~iVpr-~~w~~t~L~egD~IEIv~~VgGG   84 (84)
T PRK06083         24 NDQS--IQVDISSSLAQIIAQ----LSLPELGCVFAINNQVVPR-SEWQSTVLSSGDAISLFQAIAGG   84 (84)
T ss_pred             CCeE--EEcCCCCcHHHHHHH----cCCCCceEEEEECCEEeCH-HHcCcccCCCCCEEEEEEEecCC
Confidence            5664  455677788888664    4778888888899998853 34566679999999888776665

>PRK07696 sulfur carrier protein ThiS; Provisional

Probab=92.97  E-value=1  Score=25.83  Aligned_cols=61  Identities=16%  Similarity=0.269  Sum_probs=43.0

Q ss_pred             CCceEEEeeCCC-chHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           85 TGKEIEIDIEPT-DTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        85 ~~~~~~~~v~~~-~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      +|+.+  +++.. .|+.+|-+    ..++++...-+-.++..+..+ .-++.-+++||.|+++--..||
T Consensus         6 NG~~~--~~~~~~~tv~~lL~----~l~~~~~~vav~vN~~iv~r~-~w~~~~L~~gD~iEIv~~VgGG   67 (67)
T PRK07696          6 NGNQI--EVPESVKTVAELLT----HLELDNKIVVVERNKDILQKD-DHTDTSVFDGDQIEIVTFVGGG   67 (67)
T ss_pred             CCEEE--EcCCCcccHHHHHH----HcCCCCCeEEEEECCEEeCHH-HcCceecCCCCEEEEEEEecCC
Confidence            55544  45554 57887765    457788888888999988643 3455678999999887766655

>cd06408 PB1_NoxR The PB1 domain is present in the Epichloe festucae NoxR protein (NADPH oxidase regulator), a key regulator of NADPH oxidase isoform, NoxA

Probab=92.73  E-value=1  Score=27.28  Aligned_cols=54  Identities=19%  Similarity=0.263  Sum_probs=40.3

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccc
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARD  134 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~  134 (154)
                      +.+.+.. +|-...+.++++.+..+|..+|..++++. ..+++-|...  .|-.|+.+
T Consensus         3 ikVKv~~-~~Dv~~i~v~~~i~f~dL~~kIrdkf~~~-~~~~iKykDE--GD~iti~s   56 (86)
T cd06408           3 IRVKVHA-QDDTRYIMIGPDTGFADFEDKIRDKFGFK-RRLKIKMKDD--GDMITMGD   56 (86)
T ss_pred             EEEEEEe-cCcEEEEEcCCCCCHHHHHHHHHHHhCCC-CceEEEEEcC--CCCccccC
Confidence            3444543 56688999999999999999999999995 5667777665  44444443

NoxA is essential for growth control of the fungal endophyte in plant tissue in the process of symbiotic interaction between a fungi and its plant host. The Epichloe festucae p67(phox)-like regulator, NoxR, dispensable in culture but essential in plants for the symbiotic interaction. Plants infected with a noxR deletion mutant show severe stunting and premature senescence, whereas hyphae in the meristematic tissues show increased branching leading to increased fungal colonization of pseudostem and leaf blade tissue. The PB1 domain is a modular domain mediating specific protein-protein interactions which a play 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

>PRK07440 hypothetical protein; Provisional

Probab=92.66  E-value=1.1  Score=25.92  Aligned_cols=61  Identities=18%  Similarity=0.323  Sum_probs=44.5

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      +|+.  .++....|+.+|-+    ..++++...-+-.+|..+.-+ .-.+.-+++||.|.++--..||
T Consensus        10 NG~~--~~~~~~~tl~~lL~----~l~~~~~~vav~~N~~iv~r~-~w~~~~L~~gD~IEIv~~v~GG   70 (70)
T PRK07440         10 NGET--RTCSSGTSLPDLLQ----QLGFNPRLVAVEYNGEILHRQ-FWEQTQVQPGDRLEIVTIVGGG   70 (70)
T ss_pred             CCEE--EEcCCCCCHHHHHH----HcCCCCCeEEEEECCEEeCHH-HcCceecCCCCEEEEEEEecCC
Confidence            5554  55667788888865    446788888888999888632 3455678999999887766665

>KOG0012 consensus DNA damage inducible protein [Replication, recombination and repair]

Probab=92.64  E-value=0.2  Score=38.07  Aligned_cols=75  Identities=20%  Similarity=0.298  Sum_probs=60.9

Q ss_pred             CEEEEEeC--CCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccC--ceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTL--TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDG--RTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~--~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~--~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |.++|-..  ....+++.+..+-....++..++...+++.+..-|+|+++.+..+  ..+.++|++.++.+.+-.+..+
T Consensus         1 M~~tvs~~l~~~~~~~i~v~~dg~L~nl~aL~~~d~g~~~~~~~li~n~~~l~s~~s~~l~Q~g~~~~dsl~lr~ks~d   79 (380)
T KOG0012|consen    1 MSLTVSVALNFEKKFPIPVTTDGELNNLAALCWKDTGIVYDPSDLIYNPRPLVSNESQGLTQIGLKDGDSLALRCKSSD   79 (380)
T ss_pred             CeEEEEEEecceeeeccccccccchhhHHHHHHHHhCcccchhhcccCCCccccchhhhhhhcccccceeEeccCCCCC
Confidence            44444333  456788999999999999999999999999999999999998765  4899999999998877665443

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

Probab=92.54  E-value=0.69  Score=27.01  Aligned_cols=45  Identities=22%  Similarity=0.315  Sum_probs=40.6

Q ss_pred             EEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcc
Q 040824            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG   47 (154)
Q Consensus         3 v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g   47 (154)
                      ++|..++|+.-.+.+.+++|+.++-+.+-++.|+.++.-.+++.|
T Consensus         2 ~~V~LPng~~t~V~vrpg~ti~d~L~~~c~kr~l~~~~~~v~~~~   46 (72)
T cd01760           2 CRVYLPNGQRTVVPVRPGMSVRDVLAKACKKRGLNPECCDVFLLG   46 (72)
T ss_pred             EEEECcCCCeEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEec
Confidence            567788999999999999999999999999999999988888654

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.

>KOG2689 consensus Predicted ubiquitin regulatory protein [Posttranslational modification, protein turnover, chaperones]

Probab=92.28  E-value=0.49  Score=34.72  Aligned_cols=69  Identities=10%  Similarity=0.193  Sum_probs=55.7

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEE--ECCeecC---CCCcccccccCCCCEEE
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI--YAGKQLA---DDKTARDYNIEGGSVLH  144 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~--~~g~~l~---d~~~L~~~~i~~~~~i~  144 (154)
                      .-.|.|+.++|+++...+++.+++..++.-+.-+.+...+...|+  |.-..+.   -.++|..+++.+.+++.
T Consensus       210 ~crlQiRl~DG~Tl~~tF~a~E~L~~VR~wVd~n~~~~~~P~~f~t~fPR~tf~edD~~KpLq~L~L~Psa~li  283 (290)
T KOG2689|consen  210 QCRLQIRLPDGQTLTQTFNARETLAAVRLWVDLNRGDGLDPYSFHTGFPRVTFTEDDELKPLQELDLVPSAVLI  283 (290)
T ss_pred             ceEEEEEcCCCCeeeeecCchhhHHHHHHHHHHhccCCCCCeeeecCCCceecccccccccHHHhccccchhee
Confidence            456778888999999999999999999999999999887777765  3333332   45689999998888764

>KOG0012 consensus DNA damage inducible protein [Replication, recombination and repair]

Probab=92.27  E-value=0.26  Score=37.54  Aligned_cols=61  Identities=18%  Similarity=0.279  Sum_probs=52.9

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCC--CCcccccccCCCCEEEE
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLAD--DKTARDYNIEGGSVLHL  145 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d--~~~L~~~~i~~~~~i~~  145 (154)
                      ....+++.+........|+..+...+|++.+..-++|+++++.+  .+.+..+|+.+++.+.+
T Consensus        11 ~~~~~~i~v~~dg~L~nl~aL~~~d~g~~~~~~~li~n~~~l~s~~s~~l~Q~g~~~~dsl~l   73 (380)
T KOG0012|consen   11 FEKKFPIPVTTDGELNNLAALCWKDTGIVYDPSDLIYNPRPLVSNESQGLTQIGLKDGDSLAL   73 (380)
T ss_pred             ceeeeccccccccchhhHHHHHHHHhCcccchhhcccCCCccccchhhhhhhcccccceeEec
Confidence            34567788888889999999999999999999999999998874  57899999999998754

>cd00754 MoaD Ubiquitin domain of MoaD-like proteins

Probab=92.16  E-value=0.92  Score=26.53  Aligned_cols=58  Identities=10%  Similarity=0.180  Sum_probs=39.4

Q ss_pred             CEEEEEEeCCCcHHHHHHHHHhHhCC----CCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824           11 KTITLEVESSDTIDNVKAKIQDKEGI----PPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus        11 ~~~~~~v~~~~tv~~lk~~i~~~~~~----~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      ....++++.+.|+.+|.+.+....+-    ......+..||+...     .+.-+++++.|.+....
T Consensus        16 ~~~~~~~~~~~tv~~ll~~l~~~~~~~~~~~~~~~~v~vNg~~v~-----~~~~l~~gD~v~i~ppv   77 (80)
T cd00754          16 DEEELELPEGATVGELLDALEARYPGLLEELLARVRIAVNGEYVR-----LDTPLKDGDEVAIIPPV   77 (80)
T ss_pred             ceEEEECCCCCcHHHHHHHHHHHCchHHHhhhhcEEEEECCeEcC-----CCcccCCCCEEEEeCCC
Confidence            34567777789999999999877532    223445556777765     34567888888766543

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.

>smart00455 RBD Raf-like Ras-binding domain

Probab=92.06  E-value=0.92  Score=26.29  Aligned_cols=45  Identities=20%  Similarity=0.279  Sum_probs=40.5

Q ss_pred             EEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcc
Q 040824            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG   47 (154)
Q Consensus         3 v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g   47 (154)
                      .+|-.++|+.-.+.+.++.|+.|+-+.+-++.|+.++.-.+++.|
T Consensus         2 ~~v~LP~~~~~~V~vrpg~tl~e~L~~~~~kr~l~~~~~~v~~~g   46 (70)
T smart00455        2 CKVHLPDNQRTVVKVRPGKTVRDALAKALKKRGLNPECCVVRLRG   46 (70)
T ss_pred             eEEECCCCCEEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEcC
Confidence            456778999999999999999999999999999999988888755

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

Probab=92.05  E-value=1.1  Score=26.44  Aligned_cols=44  Identities=20%  Similarity=0.376  Sum_probs=34.7

Q ss_pred             eeeeecCCceEE-EeeCCCchHHHHHHHHhhhcCCCCCceeEEECC
Q 040824           79 IKVKTLTGKEIE-IDIEPTDTIERIKERVEEKEGIPPVQQRLIYAG  123 (154)
Q Consensus        79 i~v~~~~~~~~~-~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g  123 (154)
                      +.+.. .+.... +.+..+.|..+|+.++++.++.+....++.|..
T Consensus         4 vK~~~-~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~Y~D   48 (84)
T PF00564_consen    4 VKVRY-GGDIRRIISLPSDVSFDDLRSKIREKFGLLDEDFQLKYKD   48 (84)
T ss_dssp             EEEEE-TTEEEEEEEECSTSHHHHHHHHHHHHHTTSTSSEEEEEEE
T ss_pred             EEEEE-CCeeEEEEEcCCCCCHHHHHHHHHHHhCCCCccEEEEeeC
Confidence            34444 334444 889999999999999999999998888888854

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

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

Probab=92.01  E-value=0.72  Score=26.80  Aligned_cols=52  Identities=23%  Similarity=0.328  Sum_probs=38.3

Q ss_pred             eeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECC--eecCCCC
Q 040824           79 IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAG--KQLADDK  130 (154)
Q Consensus        79 i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g--~~l~d~~  130 (154)
                      +.|.-++|+...+.+.+..|+.+.-..++++.++.++...+...|  +.++-++
T Consensus         3 ~~v~LP~~q~t~V~vrpg~ti~d~L~~~~~kr~L~~~~~~V~~~~~~k~l~~~~   56 (71)
T PF02196_consen    3 CRVHLPNGQRTVVQVRPGMTIRDALSKACKKRGLNPECCDVRLVGEKKPLDWDQ   56 (71)
T ss_dssp             EEEEETTTEEEEEEE-TTSBHHHHHHHHHHTTT--CCCEEEEEEEEEEEE-TTS
T ss_pred             EEEECCCCCEEEEEEcCCCCHHHHHHHHHHHcCCCHHHEEEEEcCCCccccCCC
Confidence            345567899999999999999999999999999999988776443  3555433

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.

>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=91.70  E-value=0.051  Score=40.47  Aligned_cols=61  Identities=20%  Similarity=0.472  Sum_probs=0.0

Q ss_pred             EEEEEeCCCCEEEEEEe---C--CCcHHHHHHHHHh----------HhCCCCCCeE-----EEEcceEeccCceeccccc
Q 040824            2 QIFVKTLTGKTITLEVE---S--SDTIDNVKAKIQD----------KEGIPPDQQR-----LIFAGKQLEDGRTLADYNI   61 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~---~--~~tv~~lk~~i~~----------~~~~~~~~q~-----L~~~g~~L~d~~~l~~~~i   61 (154)
                      .|++|...+..+.+.+.   +  +.+|.++|..+.+          ..++|.+..+     |+|+.+.+.|..+|++..-
T Consensus        80 tV~Lks~rnp~l~i~L~~~~plattSv~dlk~~v~~rv~~~~~~~~~~~vp~dKik~~~~~lL~~kkPv~~~ktl~e~l~  159 (309)
T PF12754_consen   80 TVHLKSLRNPPLDISLPNVPPLATTSVQDLKDAVQQRVHPSQATYDETRVPLDKIKNFRCRLLYKKKPVGDSKTLAEVLA  159 (309)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EEEeecCCCCCceeEeCCCCcCCcCcHHHHHHHHHhhhcccccccccccCCHHHhhhhhhhheecCccCCCcCcHHHHHh
Confidence            45666666555555442   2  5789999999999          8889988888     9999999988888888764


Q ss_pred             c
Q 040824           62 Q   62 (154)
Q Consensus        62 ~   62 (154)
                      .
T Consensus       160 ~  160 (309)
T PF12754_consen  160 D  160 (309)
T ss_dssp             -
T ss_pred             c
Confidence            3

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.

>PRK08364 sulfur carrier protein ThiS; Provisional

Probab=91.33  E-value=1.8  Score=24.99  Aligned_cols=51  Identities=10%  Similarity=0.178  Sum_probs=36.8

Q ss_pred             EEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeee
Q 040824           12 TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (154)
Q Consensus        12 ~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~   71 (154)
                      ...++++.+.|+.+|-+.+    ++++....+..+|.....     +.-+++++.|.+..
T Consensus        15 ~~~~~~~~~~tv~~ll~~l----~~~~~~v~v~vNg~iv~~-----~~~l~~gD~Veii~   65 (70)
T PRK08364         15 EKEIEWRKGMKVADILRAV----GFNTESAIAKVNGKVALE-----DDPVKDGDYVEVIP   65 (70)
T ss_pred             ceEEEcCCCCcHHHHHHHc----CCCCccEEEEECCEECCC-----CcCcCCCCEEEEEc
Confidence            4677888889999988775    666666666688888753     44567788876654

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

Probab=91.08  E-value=0.78  Score=27.20  Aligned_cols=36  Identities=11%  Similarity=0.215  Sum_probs=32.7

Q ss_pred             CEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEc
Q 040824           11 KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA   46 (154)
Q Consensus        11 ~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~   46 (154)
                      -++.+.+.+..+..+|..+|.++...+++...|.|.
T Consensus         7 fTVai~v~~g~~y~~L~~~ls~kL~l~~~~~~LSY~   42 (78)
T cd06411           7 FTVALRAPRGADVSSLRALLSQALPQQAQRGQLSYR   42 (78)
T ss_pred             EEEEEEccCCCCHHHHHHHHHHHhcCChhhcEEEec
Confidence            357788899999999999999999999999999885

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

>cd05992 PB1 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

Probab=91.07  E-value=1.9  Score=25.25  Aligned_cols=43  Identities=23%  Similarity=0.348  Sum_probs=33.3

Q ss_pred             EEEEEeCCCCEEEEEEe-CCCcHHHHHHHHHhHhCCCCCCeEEEE
Q 040824            2 QIFVKTLTGKTITLEVE-SSDTIDNVKAKIQDKEGIPPDQQRLIF   45 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~-~~~tv~~lk~~i~~~~~~~~~~q~L~~   45 (154)
                      .|+++. +|..+.+.++ .+.+..+|+++|.++++.+...-.+.|
T Consensus         2 ~vK~~~-~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~y   45 (81)
T cd05992           2 RVKVKY-GGEIRRFVVVSRSISFEDLRSKIAEKFGLDAVSFKLKY   45 (81)
T ss_pred             cEEEEe-cCCCEEEEEecCCCCHHHHHHHHHHHhCCCCCcEEEEe
Confidence            466666 4577888888 899999999999999998754444444

A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, 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 a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.

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

Probab=90.95  E-value=0.62  Score=35.85  Aligned_cols=66  Identities=20%  Similarity=0.317  Sum_probs=52.2

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhC-CCCCCeEEE--EcceEeccC-ceecccccccccce
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG-IPPDQQRLI--FAGKQLEDG-RTLADYNIQKESTL   67 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~-~~~~~q~L~--~~g~~L~d~-~~l~~~~i~~~~~i   67 (154)
                      .|.|+..+|......++.+-||.+++..|..... .+...+.|.  |--+.|.|+ .||.+-|+.+...+
T Consensus       307 sIQIRLanG~RlV~~fN~sHTv~DIR~fI~~aRp~~~~~~F~L~~~FPpk~l~D~sqTle~AgL~Nsvlv  376 (380)
T KOG2086|consen  307 SIQIRLANGTRLVLKFNHSHTVSDIREFIDTARPGDSSTYFILMMAFPPKPLSDDSQTLEEAGLLNSVLV  376 (380)
T ss_pred             eEEEEecCCceeeeeccCcccHHHHHHHHHhcCCCCcCCceeeeecCCCcccCCcchhHHhccchhhhhh
Confidence            3678888999999999999999999999998876 444466666  667888764 49999998765543

>cd05992 PB1 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

Probab=90.88  E-value=1.1  Score=26.20  Aligned_cols=40  Identities=20%  Similarity=0.354  Sum_probs=32.9

Q ss_pred             CCceEEEeeC-CCchHHHHHHHHhhhcCCCCCceeEEECCe
Q 040824           85 TGKEIEIDIE-PTDTIERIKERVEEKEGIPPVQQRLIYAGK  124 (154)
Q Consensus        85 ~~~~~~~~v~-~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~  124 (154)
                      +|....+.++ .+.|..+|++++++.++.+.....+.|...
T Consensus         8 ~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~y~D~   48 (81)
T cd05992           8 GGEIRRFVVVSRSISFEDLRSKIAEKFGLDAVSFKLKYPDE   48 (81)
T ss_pred             cCCCEEEEEecCCCCHHHHHHHHHHHhCCCCCcEEEEeeCC
Confidence            3557788888 899999999999999999877777777653

A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, 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 a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.

>PF14453 ThiS-like: ThiS-like ubiquitin

Probab=90.85  E-value=1.7  Score=24.11  Aligned_cols=47  Identities=19%  Similarity=0.348  Sum_probs=35.3

Q ss_pred             EEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEE
Q 040824           90 EIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        90 ~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      ++++..+.|+.+||+++...      .-.++++|-...++.     -+++||.|.++-
T Consensus         9 ~~~~~~~~tl~~lr~~~k~~------~DI~I~NGF~~~~d~-----~L~e~D~v~~Ik   55 (57)
T PF14453_consen    9 EIETEENTTLFELRKESKPD------ADIVILNGFPTKEDI-----ELKEGDEVFLIK   55 (57)
T ss_pred             EEEcCCCcCHHHHHHhhCCC------CCEEEEcCcccCCcc-----ccCCCCEEEEEe
Confidence            46778888999999988753      335789998877665     567788886654

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

Probab=90.78  E-value=1.5  Score=25.92  Aligned_cols=44  Identities=20%  Similarity=0.382  Sum_probs=34.7

Q ss_pred             EEEEEeCCCCEEE-EEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEc
Q 040824            2 QIFVKTLTGKTIT-LEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA   46 (154)
Q Consensus         2 ~v~v~~~~~~~~~-~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~   46 (154)
                      .|++... +.... +.+..+.+..+|+.+|+..++.+.....|.|.
T Consensus         3 ~vK~~~~-~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~Y~   47 (84)
T PF00564_consen    3 RVKVRYG-GDIRRIISLPSDVSFDDLRSKIREKFGLLDEDFQLKYK   47 (84)
T ss_dssp             EEEEEET-TEEEEEEEECSTSHHHHHHHHHHHHHTTSTSSEEEEEE
T ss_pred             EEEEEEC-CeeEEEEEcCCCCCHHHHHHHHHHHhCCCCccEEEEee
Confidence            4556654 44444 89999999999999999999998777777774

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

>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]

Probab=90.75  E-value=2  Score=24.74  Aligned_cols=58  Identities=19%  Similarity=0.354  Sum_probs=43.5

Q ss_pred             EEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           90 EIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        90 ~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      +++++...|+.+|-+    ..+++++..-...+|..+..+. -++.-+++||.|.++--.-||
T Consensus        11 ~~e~~~~~tv~dLL~----~l~~~~~~vav~vNg~iVpr~~-~~~~~l~~gD~ievv~~v~GG   68 (68)
T COG2104          11 EVEIAEGTTVADLLA----QLGLNPEGVAVAVNGEIVPRSQ-WADTILKEGDRIEVVRVVGGG   68 (68)
T ss_pred             EEEcCCCCcHHHHHH----HhCCCCceEEEEECCEEccchh-hhhccccCCCEEEEEEeecCC
Confidence            456677789999865    5578888888889999887432 455677899999887666555

>KOG4261 consensus Talin [Cytoskeleton]

Probab=90.68  E-value=1.7  Score=36.66  Aligned_cols=101  Identities=24%  Similarity=0.315  Sum_probs=78.5

Q ss_pred             CCEEEEEEeCCCcHHHHHHHHHhHhCC---CCCCeEEEE------cceEeccCceecccccccccceeeeeeeecceeee
Q 040824           10 GKTITLEVESSDTIDNVKAKIQDKEGI---PPDQQRLIF------AGKQLEDGRTLADYNIQKESTLHLVLRLRGGTMIK   80 (154)
Q Consensus        10 ~~~~~~~v~~~~tv~~lk~~i~~~~~~---~~~~q~L~~------~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~~~i~   80 (154)
                      +-..++.+.|++.|.+-...|++++..   -+..-.|+.      .|-++++..++.+|-+.+++++...-+   .-.+.
T Consensus        12 ~v~ktmqfepst~vyda~~~ire~~~~~~~~a~~yglf~~de~~~k~~wle~grt~~~y~~~n~d~~ey~~k---~r~lk   88 (1003)
T KOG4261|consen   12 NVVKTMQFEPSTLVYDACKVIREKFAEADVGASEYGLFLSDEDPSKGIWLEAGRTLDYYMLRNGDTLEYKRK---QRPLK   88 (1003)
T ss_pred             ceeeeeeecCchHHHHHHHHHHHHhhhcccCchhcceeeecCCcccceeecCCccHHHHHHhcccccchhhh---cccce
Confidence            444678899999999999999888642   244444442      267789999999999999998843332   23467


Q ss_pred             eeecCCceEEEeeCCCchHHHHHHHHhhhcCCC
Q 040824           81 VKTLTGKEIEIDIEPTDTIERIKERVEEKEGIP  113 (154)
Q Consensus        81 v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~  113 (154)
                      ++..+|..-++.++.+.+|.+|.--|+.+.||.
T Consensus        89 vrmldg~vkti~vd~sq~v~~L~~~ic~~igIt  121 (1003)
T KOG4261|consen   89 VRMLDGAVKTIMVDDSQPVSQLMMTICNKIGIT  121 (1003)
T ss_pred             eeecccccceeeecccccHHHHHHHHHhccCcc
Confidence            778889888999999999999999999999973

>TIGR02958 sec_mycoba_snm4 secretion protein snm4

Probab=90.67  E-value=1.4  Score=35.08  Aligned_cols=70  Identities=16%  Similarity=0.217  Sum_probs=53.4

Q ss_pred             eeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCC------CCCceeEE-ECCeecCCCCcccccccCCCCEEEEEEe
Q 040824           78 MIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGI------PPVQQRLI-YAGKQLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        78 ~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i------~~~~~~l~-~~g~~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      +++|...+ +...+-++.+..+.+|--.+-+..+-      .+....|. ..|.+++.++||.+.|+.||+.+++.-.
T Consensus         4 RVtV~~~~-~~~DlaLPa~~PvaellP~ll~~~~~~~~~~~~~~~w~L~r~gG~pL~~~~sL~~~gV~DG~~L~L~p~   80 (452)
T TIGR02958         4 RVTVLAGR-RAVDVALPADVPVAELIPDLVDLLDDRGAAELGAVRWALARAGGSPLDPDASLAEAGVRDGELLVLVPA   80 (452)
T ss_pred             EEEEeeCC-eeeeeecCCCCcHHHHHHHHHHHhCcccccCCCCcceEEecCCCCCCCCCCCHHHcCCCCCCeEEEeeC
Confidence            35555533 45788899999999999998887764      22334554 5788999999999999999999987653

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

>PF14453 ThiS-like: ThiS-like ubiquitin

Probab=90.54  E-value=1.6  Score=24.30  Aligned_cols=47  Identities=15%  Similarity=0.270  Sum_probs=32.5

Q ss_pred             EEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeee
Q 040824           13 ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (154)
Q Consensus        13 ~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~   70 (154)
                      ..+++..+.|+.+||..+....      =.++++|-..+++..|+     +++.+.+.
T Consensus         8 k~~~~~~~~tl~~lr~~~k~~~------DI~I~NGF~~~~d~~L~-----e~D~v~~I   54 (57)
T PF14453_consen    8 KEIETEENTTLFELRKESKPDA------DIVILNGFPTKEDIELK-----EGDEVFLI   54 (57)
T ss_pred             EEEEcCCCcCHHHHHHhhCCCC------CEEEEcCcccCCccccC-----CCCEEEEE
Confidence            3567778889999998865532      25678888777666554     46666554

>PLN02799 Molybdopterin synthase sulfur carrier subunit

Probab=90.08  E-value=1.7  Score=25.77  Aligned_cols=67  Identities=16%  Similarity=0.192  Sum_probs=40.9

Q ss_pred             CEEEEEeCC------C-CEEEEEEeCCCcHHHHHHHHHhHhC-CCC--CCeEEEEcceEeccCceecccccccccceeee
Q 040824            1 MQIFVKTLT------G-KTITLEVESSDTIDNVKAKIQDKEG-IPP--DQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (154)
Q Consensus         1 m~v~v~~~~------~-~~~~~~v~~~~tv~~lk~~i~~~~~-~~~--~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~   70 (154)
                      |+|+|+.-.      | ....++++.+.|+.+|.+.+..... ...  ....+..|++...     .+.-++++++|.+.
T Consensus         2 m~i~V~~fa~~re~~g~~~~~~~~~~~~tv~~L~~~l~~~~p~l~~~~~~~~vavN~~~v~-----~~~~l~dgDeVai~   76 (82)
T PLN02799          2 VEIKVLFFARARELTGVSDMTLELPAGSTTADCLAELVAKFPSLEEVRSCCVLALNEEYTT-----ESAALKDGDELAII   76 (82)
T ss_pred             eEEEEEehHHHHHHhCCCeEEEECCCCCcHHHHHHHHHHHChhHHHHhhCcEEEECCEEcC-----CCcCcCCCCEEEEe
Confidence            556666542      3 4567788889999999999976541 111  1123445666653     33456778888665


Q ss_pred             ee
Q 040824           71 LR   72 (154)
Q Consensus        71 ~~   72 (154)
                      ..
T Consensus        77 Pp   78 (82)
T PLN02799         77 PP   78 (82)
T ss_pred             CC
Confidence            43

>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62

Probab=90.08  E-value=1.8  Score=25.86  Aligned_cols=35  Identities=14%  Similarity=0.253  Sum_probs=29.0

Q ss_pred             CCceEEEeeCC--CchHHHHHHHHhhhcCCCCCceeEEE
Q 040824           85 TGKEIEIDIEP--TDTIERIKERVEEKEGIPPVQQRLIY  121 (154)
Q Consensus        85 ~~~~~~~~v~~--~~tv~~LK~~i~~~~~i~~~~~~l~~  121 (154)
                      +|.+..+.+++  +.+..+|++.++..++++  .+.+-|
T Consensus         8 ~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~--~f~lKY   44 (81)
T cd06396           8 NGESQSFLVSDSENTTWASVEAMVKVSFGLN--DIQIKY   44 (81)
T ss_pred             CCeEEEEEecCCCCCCHHHHHHHHHHHhCCC--cceeEE
Confidence            66788888988  779999999999999999  554444

A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, 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. The NBR1 protein contains a type I PB1 domain.

>COG5100 NPL4 Nuclear pore protein [Nuclear structure]

Probab=89.92  E-value=1.4  Score=34.29  Aligned_cols=69  Identities=19%  Similarity=0.347  Sum_probs=51.7

Q ss_pred             eeeeeecCCceEEEeeCCCchHHHHHHHHhhhcC--CCCCceeEEEC----Cee--cCCCCcccccccCCCCEEEEEE
Q 040824           78 MIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEG--IPPVQQRLIYA----GKQ--LADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        78 ~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~--i~~~~~~l~~~----g~~--l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      .+.++...| ...+++.++++.+.|-.++-....  .+|++..+.-+    |..  +..++|+.+.|+..|+.+++-.
T Consensus         2 i~rfRsk~G-~~Rve~qe~d~lg~l~~kll~~~~~n~~~e~~svc~~p~~qG~~~s~l~dqt~~dlGL~hGqmLyl~y   78 (571)
T COG5100           2 IFRFRSKEG-QRRVEVQESDVLGMLSPKLLAFFEVNYSPEQISVCSAPDGQGEIFSLLKDQTPDDLGLRHGQMLYLEY   78 (571)
T ss_pred             eEEEecCCC-ceeeeccccchhhhhhHHHHhhhccCCCccceEEEeCCCCCceeeecccccChhhhccccCcEEEEEe
Confidence            455566555 568999999999999888866654  57778777643    221  3456899999999999998865

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

Probab=89.81  E-value=0.97  Score=29.13  Aligned_cols=55  Identities=22%  Similarity=0.395  Sum_probs=38.5

Q ss_pred             eCC-CchHHHHHHHHhhhcC----CCC------CceeEEEC----------------C-eec---CCCCcccccccCCCC
Q 040824           93 IEP-TDTIERIKERVEEKEG----IPP------VQQRLIYA----------------G-KQL---ADDKTARDYNIEGGS  141 (154)
Q Consensus        93 v~~-~~tv~~LK~~i~~~~~----i~~------~~~~l~~~----------------g-~~l---~d~~~L~~~~i~~~~  141 (154)
                      ++. +.|+.+|++.+.+...    ++|      +.+++...                . ..|   +++.+|.++|+.++.
T Consensus        22 vdL~~~Tv~~l~~~v~~~I~t~~~~~Pfrn~~yDtlKIy~~AHg~Kt~nLvInle~De~~iL~~~~~~~tL~~~gv~nET  101 (122)
T PF10209_consen   22 VDLKDTTVKDLKEQVKQDIKTRPGLPPFRNVKYDTLKIYTKAHGSKTNNLVINLEDDEDWILDVSDDDKTLKELGVENET  101 (122)
T ss_pred             CCcccCcHHHHHHHHHHHHhcCCCCCCceeeecceEEEEecCCCCCcCCceeeccCCcceeeecCCCCCcHHHcCCCccc
Confidence            665 8899999888876653    332      33444421                1 356   678899999999999


Q ss_pred             EEEEEE
Q 040824          142 VLHLVL  147 (154)
Q Consensus       142 ~i~~~~  147 (154)
                      .|-++.
T Consensus       102 EiSfF~  107 (122)
T PF10209_consen  102 EISFFN  107 (122)
T ss_pred             eeeeeC
Confidence            987764

>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62

Probab=89.80  E-value=2.9  Score=25.02  Aligned_cols=35  Identities=20%  Similarity=0.275  Sum_probs=29.6

Q ss_pred             EEEEEeCCCCEEEEEEeC--CCcHHHHHHHHHhHhCCC
Q 040824            2 QIFVKTLTGKTITLEVES--SDTIDNVKAKIQDKEGIP   37 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~--~~tv~~lk~~i~~~~~~~   37 (154)
                      +|++.. +|....+.+++  +.+..+|++.+...++++
T Consensus         2 ~vKaty-~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~   38 (81)
T cd06396           2 NLKVTY-NGESQSFLVSDSENTTWASVEAMVKVSFGLN   38 (81)
T ss_pred             EEEEEE-CCeEEEEEecCCCCCCHHHHHHHHHHHhCCC
Confidence            455665 67888888888  779999999999999999

A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, 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. The NBR1 protein contains a type I PB1 domain.

>cd01764 Urm1 Urm1-like ubuitin domain

Probab=89.55  E-value=0.88  Score=28.01  Aligned_cols=60  Identities=23%  Similarity=0.354  Sum_probs=35.4

Q ss_pred             EeeCCCchHHHHHHHHhhhcCCCCCceeEEEC-Ce------e-cCCC--Ccc--cccccCCCCEEEEEEeecCC
Q 040824           91 IDIEPTDTIERIKERVEEKEGIPPVQQRLIYA-GK------Q-LADD--KTA--RDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        91 ~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~-g~------~-l~d~--~~L--~~~~i~~~~~i~~~~~~~gg  152 (154)
                      +......||.+|-+.+++.+.  ..+..++.. |+      . +++.  ..+  .++-+++||.|.++-..-||
T Consensus        23 ~~~~~~~tV~dll~~L~~~~~--~~~~~lf~~~g~lr~~i~VlvN~~di~~l~g~~t~L~dgD~v~i~P~v~GG   94 (94)
T cd01764          23 LDGEKPVTVGDLLDYVASNLL--EERPDLFIEGGSVRPGIIVLINDTDWELLGEEDYILEDGDHVVFISTLHGG   94 (94)
T ss_pred             ccCCCCCcHHHHHHHHHHhCc--hhhhhhEecCCcccCCEEEEECCccccccCCcccCCCCcCEEEEECCCCCC
Confidence            444456799999999988773  223333321 11      1 1211  223  35678999999877665554

Urm1 (Ubiquitin-Related Modifier1) The Urm1 fold, like those of two closely related proteins MoaD (molybdopterin synthase) and ThiS (sulfur carrier protein), is similar to that of ubiquitin although there is little or no sequence similarity. The C-terminal glycines of Urm1 are conjugated to an E1-like protein Uba4 as part of a novel conjugation system in yeast. The Urm1 fold is found only in eukaryotes.

>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein

Probab=89.22  E-value=2.7  Score=25.74  Aligned_cols=65  Identities=20%  Similarity=0.286  Sum_probs=43.3

Q ss_pred             CCceEEEeeCC-----CchHHHHHHHHhhhcCCCC-CceeEEECCe-----ecCCCCccccc-----ccCCCCEEEEEEe
Q 040824           85 TGKEIEIDIEP-----TDTIERIKERVEEKEGIPP-VQQRLIYAGK-----QLADDKTARDY-----NIEGGSVLHLVLA  148 (154)
Q Consensus        85 ~~~~~~~~v~~-----~~tv~~LK~~i~~~~~i~~-~~~~l~~~g~-----~l~d~~~L~~~-----~i~~~~~i~~~~~  148 (154)
                      ++....|.++.     +.+..+|+++|++.+.+++ ....|.|...     .+.++.-|.++     .-+...++.+.+.
T Consensus         8 ~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~Dedgd~V~l~~D~DL~~a~~~~~~~~~~~~lrl~v~   87 (91)
T cd06398           8 GGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVVTLVDDNDLTDAIQYFCSGSRLNPLRIDVT   87 (91)
T ss_pred             CCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCEEEEccHHHHHHHHHHHhccCCCceEEEEEE
Confidence            45566667664     6899999999999999987 6677777543     23444444433     2235677776665


Q ss_pred             e
Q 040824          149 L  149 (154)
Q Consensus       149 ~  149 (154)
                      .
T Consensus        88 ~   88 (91)
T cd06398          88 V   88 (91)
T ss_pred             E
Confidence            4

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 domain, 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

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

Probab=89.21  E-value=0.9  Score=29.29  Aligned_cols=56  Identities=20%  Similarity=0.454  Sum_probs=38.5

Q ss_pred             EEeC-CCcHHHHHHHHHhHhC----CCC------CCeEEEEc-----------------ceEe---ccCceecccccccc
Q 040824           16 EVES-SDTIDNVKAKIQDKEG----IPP------DQQRLIFA-----------------GKQL---EDGRTLADYNIQKE   64 (154)
Q Consensus        16 ~v~~-~~tv~~lk~~i~~~~~----~~~------~~q~L~~~-----------------g~~L---~d~~~l~~~~i~~~   64 (154)
                      .++. ++|+.+|++.+.+...    ++|      +..++++.                 ...|   +++.+|.++|+.+.
T Consensus        21 ~vdL~~~Tv~~l~~~v~~~I~t~~~~~Pfrn~~yDtlKIy~~AHg~Kt~nLvInle~De~~iL~~~~~~~tL~~~gv~nE  100 (122)
T PF10209_consen   21 NVDLKDTTVKDLKEQVKQDIKTRPGLPPFRNVKYDTLKIYTKAHGSKTNNLVINLEDDEDWILDVSDDDKTLKELGVENE  100 (122)
T ss_pred             cCCcccCcHHHHHHHHHHHHhcCCCCCCceeeecceEEEEecCCCCCcCCceeeccCCcceeeecCCCCCcHHHcCCCcc
Confidence            4776 8899999999987743    433      22333322                 1567   67778999999888


Q ss_pred             cceeeee
Q 040824           65 STLHLVL   71 (154)
Q Consensus        65 ~~i~l~~   71 (154)
                      ..|.+..
T Consensus       101 TEiSfF~  107 (122)
T PF10209_consen  101 TEISFFN  107 (122)
T ss_pred             ceeeeeC
Confidence            8886654

>PRK11130 moaD molybdopterin synthase small subunit; Provisional

Probab=88.91  E-value=3.3  Score=24.49  Aligned_cols=52  Identities=13%  Similarity=0.217  Sum_probs=34.3

Q ss_pred             CchHHHHHHHHhhhcC-----CCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           96 TDTIERIKERVEEKEG-----IPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        96 ~~tv~~LK~~i~~~~~-----i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ..||.+|++.+.+++.     ......+...++.....     +.-+++||.|-++-+.-||
T Consensus        25 ~~tv~~l~~~L~~~~~~~~~~~~~~~~~~aVN~~~~~~-----~~~l~dgDeVai~PPVsGG   81 (81)
T PRK11130         25 FPTVEALRQHLAQKGDRWALALEDGKLLAAVNQTLVSF-----DHPLTDGDEVAFFPPVTGG   81 (81)
T ss_pred             CCCHHHHHHHHHHhCccHHhhhcCCCEEEEECCEEcCC-----CCCCCCCCEEEEeCCCCCC
Confidence            4799999999988863     12223344455544332     3468999999877776665

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

Probab=88.83  E-value=2.5  Score=25.55  Aligned_cols=55  Identities=22%  Similarity=0.253  Sum_probs=40.7

Q ss_pred             EEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEc-------ceEeccCceec
Q 040824            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA-------GKQLEDGRTLA   57 (154)
Q Consensus         3 v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~-------g~~L~d~~~l~   57 (154)
                      |+|-..+|....+.++..+|+.++.+.+..+.+...+.-.=++.       .+.++|+..+.
T Consensus         5 vkv~~~Dg~sK~l~V~~~~Ta~dV~~~L~~K~h~~~~~~W~LvE~~P~l~lER~~EDHE~vv   66 (85)
T cd01787           5 VKVYSEDGASKSLEVDERMTARDVCQLLVDKNHCQDDSSWTLVEHLPHLQLERLFEDHELVV   66 (85)
T ss_pred             EEEEecCCCeeEEEEcCCCcHHHHHHHHHHHhCCCCCCCeEEEEecchhhhhhhccchHHHH
Confidence            56677789999999999999999999999999876644433332       25566655433

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.

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

Probab=88.39  E-value=1.3  Score=26.21  Aligned_cols=36  Identities=6%  Similarity=0.148  Sum_probs=32.5

Q ss_pred             eEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECC
Q 040824           88 EIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAG  123 (154)
Q Consensus        88 ~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g  123 (154)
                      ++.+.+.+..+.++|..+|+++...+++..+|-|..
T Consensus         8 TVai~v~~g~~y~~L~~~ls~kL~l~~~~~~LSY~~   43 (78)
T cd06411           8 TVALRAPRGADVSSLRALLSQALPQQAQRGQLSYRA   43 (78)
T ss_pred             EEEEEccCCCCHHHHHHHHHHHhcCChhhcEEEecC
Confidence            566788999999999999999999999999999864

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

>cd01818 TIAM1_RBD Ubiquitin domain of Tiam1 guanine nucleotide exchange factor

Probab=88.25  E-value=2.1  Score=25.17  Aligned_cols=42  Identities=14%  Similarity=0.216  Sum_probs=35.5

Q ss_pred             eeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEEC
Q 040824           81 VKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYA  122 (154)
Q Consensus        81 v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~  122 (154)
                      |-.++|+...+.+.+.+|+.++-+..+++.++.|+..-|..+
T Consensus         4 V~lPn~~~~~v~vrp~~tv~dvLe~aCk~~~ldp~eh~Lrlk   45 (77)
T cd01818           4 VCLPDNQPVLTYLRPGMSVEDFLESACKRKQLDPMEHYLRLK   45 (77)
T ss_pred             EECCCCceEEEEECCCCCHHHHHHHHHHhcCCChhHheeEEE
Confidence            345688888999999999999999999999999888755533

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.

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

Probab=88.23  E-value=1  Score=34.70  Aligned_cols=67  Identities=16%  Similarity=0.309  Sum_probs=52.3

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCC-CCCceeEE--ECCeecC-CCCcccccccCCCCEE
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGI-PPVQQRLI--YAGKQLA-DDKTARDYNIEGGSVL  143 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i-~~~~~~l~--~~g~~l~-d~~~L~~~~i~~~~~i  143 (154)
                      -.|.|+..+|+..-..++.+.||.+++..|+..-.- +...+.|+  |..++|. ++.||++.|+.+...+
T Consensus       306 TsIQIRLanG~RlV~~fN~sHTv~DIR~fI~~aRp~~~~~~F~L~~~FPpk~l~D~sqTle~AgL~Nsvlv  376 (380)
T KOG2086|consen  306 TSIQIRLANGTRLVLKFNHSHTVSDIREFIDTARPGDSSTYFILMMAFPPKPLSDDSQTLEEAGLLNSVLV  376 (380)
T ss_pred             ceEEEEecCCceeeeeccCcccHHHHHHHHHhcCCCCcCCceeeeecCCCcccCCcchhHHhccchhhhhh
Confidence            467788888988888899999999999999876654 44455555  6678776 7789999999776544

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

Probab=87.99  E-value=2.5  Score=25.50  Aligned_cols=39  Identities=13%  Similarity=0.192  Sum_probs=33.2

Q ss_pred             eeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCc
Q 040824           78 MIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQ  116 (154)
Q Consensus        78 ~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~  116 (154)
                      .+.|...+|....+.|++.+|++++-+.++.+..+..+.
T Consensus         4 vvkv~~~Dg~sK~l~V~~~~Ta~dV~~~L~~K~h~~~~~   42 (85)
T cd01787           4 VVKVYSEDGASKSLEVDERMTARDVCQLLVDKNHCQDDS   42 (85)
T ss_pred             EEEEEecCCCeeEEEEcCCCcHHHHHHHHHHHhCCCCCC
Confidence            456667789999999999999999999999999975443

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.

>cd01766 Ufm1 Urm1-like ubiquitin domain

Probab=87.36  E-value=4.1  Score=23.77  Aligned_cols=63  Identities=19%  Similarity=0.270  Sum_probs=52.0

Q ss_pred             EEeeCCCchHHHHHHHHhhhcCCCCCceeEE-ECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           90 EIDIEPTDTIERIKERVEEKEGIPPVQQRLI-YAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        90 ~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~-~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      .++|+.+.....+-+-.++.+.+|+...-++ -.|-=++..++-...-++.|+.+.++-|-+-|
T Consensus        19 vlsVpE~aPftAvlkfaAEeFkv~~~TsAiiTndGvGINP~qtAGnvflkhgselrliPRDrvG   82 (82)
T cd01766          19 VLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAGNVFLKHGSELRLIPRDRVG   82 (82)
T ss_pred             EEeccccCchHHHHHHHHHhcCCCccceeEEecCccccChhhcccceeeecCCEeeecccccCC
Confidence            3678888888888888899999998887666 66777888999999999999999988776543

Ufm1 (ubiquitin-fold modifier 1) is a post-translational UBL (ubiquitin-like) modifier with a tertiary structure similar to that of ubiquitin. Ufm1 is initially expressed as a precursor which undergoes C-terminal cleavage to expose a conserved glycine residue that is required for the conjugation reactions involving Ufm1.

>PF08825 E2_bind: E2 binding domain; InterPro: IPR014929 E1 and E2 enzymes play a central role in ubiquitin and ubiquitin-like protein transfer cascades

Probab=87.14  E-value=1.3  Score=26.64  Aligned_cols=56  Identities=16%  Similarity=0.299  Sum_probs=39.8

Q ss_pred             EeeCCCchHHHHHHHHhhhcCCC-------CCceeEEECCe-ec------CCCCcccccccCCCCEEEEEE
Q 040824           91 IDIEPTDTIERIKERVEEKEGIP-------PVQQRLIYAGK-QL------ADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        91 ~~v~~~~tv~~LK~~i~~~~~i~-------~~~~~l~~~g~-~l------~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      +++++++|+.+|...+++...+.       .+.-.|++.+- .|      +-+++|.+. +.+|+.|.|.-
T Consensus         1 i~v~~~~TL~~lid~L~~~~~~qlk~PSlt~~~k~LYm~~pp~Lee~Tr~NL~k~l~eL-~~~g~ei~VtD   70 (84)
T PF08825_consen    1 IEVSPSWTLQDLIDSLCEKPEFQLKKPSLTTANKTLYMQSPPSLEEATRPNLSKKLKEL-LSDGEEITVTD   70 (84)
T ss_dssp             EEESTTSBSHHHHHHHHHSTTT--SS-EEESSEEEEEESSSHHHHHHTGGGGSSBTTTT-HHSSEEEEEEE
T ss_pred             CCcCccchHHHHHHHHHhChhhhcCCCcccCCCceEEEeCCHHHHHHhhhhhhhhHHHH-hcCCCEEEEEC
Confidence            57899999999999999885432       33345555442 12      346789999 99999998753

This is an E2 binding domain that is found on NEDD8 activating E1 enzyme. The protein resembles ubiquitin, and recruits the catalytic core of the E2 enzyme Ubc12 in a similar manner to that in which ubiquitin interacts with ubiquitin binding domains []. ; GO: 0005524 ATP binding, 0016881 acid-amino acid ligase activity, 0045116 protein neddylation; PDB: 3GZN_D 3DBL_F 1R4N_H 1R4M_D 2NVU_B 1TT5_D 3DBR_D 3DBH_H 1YOV_B 3FN1_A ....

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

Probab=86.71  E-value=4.4  Score=23.46  Aligned_cols=52  Identities=23%  Similarity=0.312  Sum_probs=39.5

Q ss_pred             EEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcc--eEeccCc
Q 040824            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG--KQLEDGR   54 (154)
Q Consensus         3 v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g--~~L~d~~   54 (154)
                      +.|.-++|+.-.+.+.++.|+.+.-..+-++.++.++.-.++..|  +.++.+.
T Consensus         3 ~~v~LP~~q~t~V~vrpg~ti~d~L~~~~~kr~L~~~~~~V~~~~~~k~l~~~~   56 (71)
T PF02196_consen    3 CRVHLPNGQRTVVQVRPGMTIRDALSKACKKRGLNPECCDVRLVGEKKPLDWDQ   56 (71)
T ss_dssp             EEEEETTTEEEEEEE-TTSBHHHHHHHHHHTTT--CCCEEEEEEEEEEEE-TTS
T ss_pred             EEEECCCCCEEEEEEcCCCCHHHHHHHHHHHcCCCHHHEEEEEcCCCccccCCC
Confidence            567888999999999999999999999999999999887777544  4454443

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.

>PF14451 Ub-Mut7C: Mut7-C ubiquitin

Probab=86.51  E-value=5.1  Score=23.95  Aligned_cols=55  Identities=20%  Similarity=0.387  Sum_probs=42.8

Q ss_pred             CceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEE-ECCeecCCCCcccccccCCCCEEEEEEee
Q 040824           86 GKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI-YAGKQLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        86 ~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~-~~g~~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      +..+...++...||.++-+    ..|+|.....++ .+|+..+-+     |-+++|+.|.+.-..
T Consensus        22 ~~~~~~~~~~~~tvkd~IE----sLGVP~tEV~~i~vNG~~v~~~-----~~~~~Gd~v~V~P~~   77 (81)
T PF14451_consen   22 GGPFTHPFDGGATVKDVIE----SLGVPHTEVGLILVNGRPVDFD-----YRLKDGDRVAVYPVF   77 (81)
T ss_pred             CCceEEecCCCCcHHHHHH----HcCCChHHeEEEEECCEECCCc-----ccCCCCCEEEEEecc
Confidence            4567889999999998854    679999998666 688877543     678899999887543

>PF03671 Ufm1: Ubiquitin fold modifier 1 protein; InterPro: IPR005375 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=86.47  E-value=4.6  Score=23.47  Aligned_cols=57  Identities=21%  Similarity=0.340  Sum_probs=44.6

Q ss_pred             EEeeCCCchHHHHHHHHhhhcCCCCCceeEE-ECCeecCCCCcccccccCCCCEEEEE
Q 040824           90 EIDIEPTDTIERIKERVEEKEGIPPVQQRLI-YAGKQLADDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        90 ~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~-~~g~~l~d~~~L~~~~i~~~~~i~~~  146 (154)
                      -++|+.+.....+-+-.++.+.+|+...-++ -.|--++..+|..+.-++.|+.+.++
T Consensus        19 v~sVPE~apftaVlkfaAeeF~vp~~tsaiItndG~GInP~QTag~vflKhGseLrli   76 (76)
T PF03671_consen   19 VISVPEEAPFTAVLKFAAEEFKVPPATSAIITNDGVGINPQQTAGNVFLKHGSELRLI   76 (76)
T ss_dssp             EEEEETTSBHHHHHHHHHHHTTS-SSSEEEEESSS-EE-TTSBHHHHHHHT-SEEEEE
T ss_pred             EEecCCCCchHHHHHHHHHHcCCCCceEEEEecCCcccccchhhhhhHhhcCcEeeeC
Confidence            4778888888888888899999999888777 45777889999999999999998764

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-like molecules (UBLs) can be divided into two subclasses: type-1 UBLs, which ligate to target proteins in a manner similar, but not identical, to the ubiquitylation pathway, such as SUMO, NEDD8, and UCRP/ISG15, and type-2 UBLs (also called UDPs, ubiquitin-domain proteins), which contain ubiquitin-like structure embedded in a variety of different classes of large proteins with apparently distinct functions, such as Rad23, Elongin B, Scythe, Parkin, and HOIL-1. This entry represents Ufm1 (ubiquitin-fold modifier), which is a ubiquitin-like protein with structural similarities to ubiquitin [, ]. Ufm1 is one of a number of ubiquitin-like modifiers that conjugate to target proteins in cells through Uba5 (E1) and Ufc1 (E2). The Ufm1-system is conserved in metazoa and plants, suggesting it has a potential role in multicellular organisms []. Human Ufm1 is synthesized as a precursor consisting of 85 amino-acid residues. Prior to activation by Uba5, the extra amino acids at the C-terminal region of Ufm1 are removed to expose Gly, which is necessary for conjugation to target molecule(s). C-terminal processing of Ufm1 requires two specific cysteine peptidases (IPR012462 from INTERPRO): UfSP1 and UfSP2; both peptidases are also able to release Ufm1 from Ufm1-conjugated cellular proteins. UfSP2 is present in most, if not all, of multi-cellular organisms including plant, nematode, fly, and mammal, whereas UfSP1 is not present in plants and nematodes []. For further information on ubiquitin, please see Protein of the Month [].; PDB: 1J0G_A 1WXS_A 1L7Y_A.

>cd01817 RGS12_RBD Ubiquitin domain of RGS12 and RGS14

Probab=86.33  E-value=3.6  Score=24.09  Aligned_cols=42  Identities=21%  Similarity=0.309  Sum_probs=37.0

Q ss_pred             ecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCe
Q 040824           83 TLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGK  124 (154)
Q Consensus        83 ~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~  124 (154)
                      -++|+.-.+.+.+..|+.++-.++.++-|++++..-++.-|.
T Consensus         6 LPdg~~T~V~vrpG~ti~d~L~kllekRgl~~~~~~vf~~g~   47 (73)
T cd01817           6 LPDGSTTVVPTRPGESIRDLLSGLCEKRGINYAAVDLFLVGG   47 (73)
T ss_pred             CCCCCeEEEEecCCCCHHHHHHHHHHHcCCChhHEEEEEecC
Confidence            458888899999999999999999999999999988875553

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.

>PTZ00380 microtubule-associated protein (MAP); Provisional

Probab=86.27  E-value=1  Score=29.11  Aligned_cols=46  Identities=17%  Similarity=0.221  Sum_probs=37.0

Q ss_pred             EE-eeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCccccc
Q 040824           90 EI-DIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDY  135 (154)
Q Consensus        90 ~~-~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~  135 (154)
                      .+ -|+.+.||+++...|.++.+++++..-|..++.....+.++++.
T Consensus        43 KfllVP~d~tV~qF~~iIRkrl~l~~~k~flfVnn~lp~~s~~mg~l   89 (121)
T PTZ00380         43 HFLALPRDATVAELEAAVRQALGTSAKKVTLAIEGSTPAVTATVGDI   89 (121)
T ss_pred             EEEEcCCCCcHHHHHHHHHHHcCCChhHEEEEECCccCCccchHHHH
Confidence            35 69999999999999999999999986555677666666677665

>PRK06488 sulfur carrier protein ThiS; Validated

Probab=85.95  E-value=4.4  Score=22.81  Aligned_cols=56  Identities=11%  Similarity=0.215  Sum_probs=36.2

Q ss_pred             CCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeee
Q 040824            9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         9 ~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      +|+.+.+   +..|+.+|.+.+    ++++....+-.++..+. .....+.-+++|+.|.++..
T Consensus         6 Ng~~~~~---~~~tl~~Ll~~l----~~~~~~vavavN~~iv~-~~~~~~~~L~dgD~Ieiv~~   61 (65)
T PRK06488          6 NGETLQT---EATTLALLLAEL----DYEGNWLATAVNGELVH-KEARAQFVLHEGDRIEILSP   61 (65)
T ss_pred             CCeEEEc---CcCcHHHHHHHc----CCCCCeEEEEECCEEcC-HHHcCccccCCCCEEEEEEe
Confidence            5666665   345899988764    56665555557777664 33344566888898876643

>TIGR02958 sec_mycoba_snm4 secretion protein snm4

Probab=85.75  E-value=4.3  Score=32.36  Aligned_cols=71  Identities=14%  Similarity=0.163  Sum_probs=54.8

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCC----CCCCeEEE---EcceEeccCceecccccccccceeeeeee
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGI----PPDQQRLI---FAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~----~~~~q~L~---~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      +|+|... .+..++.++.+.++.|+.-.+-+..+-    +.....+.   -+|..|+.+.||.+.++.+|+.+++....
T Consensus         4 RVtV~~~-~~~~DlaLPa~~PvaellP~ll~~~~~~~~~~~~~~~w~L~r~gG~pL~~~~sL~~~gV~DG~~L~L~p~~   81 (452)
T TIGR02958         4 RVTVLAG-RRAVDVALPADVPVAELIPDLVDLLDDRGAAELGAVRWALARAGGSPLDPDASLAEAGVRDGELLVLVPAS   81 (452)
T ss_pred             EEEEeeC-CeeeeeecCCCCcHHHHHHHHHHHhCcccccCCCCcceEEecCCCCCCCCCCCHHHcCCCCCCeEEEeeCC
Confidence            4667654 355788889999999999999888764    22233343   35789999999999999999999888643

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

>smart00295 B41 Band 4

Probab=85.67  E-value=3  Score=28.89  Aligned_cols=36  Identities=33%  Similarity=0.423  Sum_probs=33.4

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCC
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIP   37 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~   37 (154)
                      .+.|...+|....+.++..+|+.++.+.+..+.|++
T Consensus         5 ~~~V~l~dg~~~~~~~~~~~t~~ev~~~v~~~~~l~   40 (207)
T smart00295        5 VLKVYLLDGTTLEFEVDSSTTAEELLETVCRKLGIR   40 (207)
T ss_pred             EEEEEecCCCEEEEEECCCCCHHHHHHHHHHHhCCC
Confidence            578888999999999999999999999999999984

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

>cd01777 SNX27_RA Ubiquitin domain of SNX27 (sorting nexin protein 27)

Probab=85.58  E-value=2.1  Score=25.97  Aligned_cols=42  Identities=10%  Similarity=0.255  Sum_probs=36.1

Q ss_pred             eeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeE
Q 040824           78 MIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRL  119 (154)
Q Consensus        78 ~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l  119 (154)
                      .+.|--++|....+++..+++..++-+.++++.|+|.+.+.-
T Consensus         3 ~L~V~Lpdg~~i~V~v~~s~~a~~Vleav~~kl~L~~e~~~Y   44 (87)
T cd01777           3 ELRIALPDKATVTVRVRKNATTDQVYQALVAKAGMDSYTQNY   44 (87)
T ss_pred             EEEEEccCCCEEEEEEEEcccHHHHHHHHHHHhCCCHHHHhh
Confidence            455666789999999999999999999999999999877643

SNX27_RA SNX27 (sorting nexin protein 27) belongs to a large family of endosome-localized proteins related to sorting nexin1 which is implicated in regulating membrane traffic. The domain architecture of SNX27 includes an amino-terminal PDZ domain, a PX (PhoX homologous) domain, and a carboxy-terminal RA (RAS-associated) domain.

>cd06410 PB1_UP2 Uncharacterized protein 2

Probab=85.49  E-value=5.7  Score=24.63  Aligned_cols=39  Identities=18%  Similarity=0.240  Sum_probs=32.5

Q ss_pred             EeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEE
Q 040824            6 KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF   45 (154)
Q Consensus         6 ~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~   45 (154)
                      +-.+|++.-+.|+.+.+..+|+.++.+..+.+.. ..|.|
T Consensus        18 ~Y~GG~tr~i~V~r~~s~~el~~kl~~~~~~~~~-~~lky   56 (97)
T cd06410          18 RYVGGETRIVSVDRSISFKELVSKLSELFGAGVV-VTLKY   56 (97)
T ss_pred             EEcCCceEEEEEcCCCCHHHHHHHHHHHhCCCCc-eEEEE
Confidence            3457888999999999999999999999988875 55554

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.

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

Probab=85.18  E-value=3  Score=34.83  Aligned_cols=42  Identities=24%  Similarity=0.460  Sum_probs=37.8

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeec
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQL  126 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l  126 (154)
                      ++..+.+.++++.|+..++..|...+|+|.+.|.|+|.|...
T Consensus       323 ~~~~~~~~~~~~ntl~~~~~~I~~~Tgipe~~qeLL~e~~~~  364 (732)
T KOG4250|consen  323 QATSHEYYVHADNTLHSLIERISKQTGIPEGKQELLFEGGLS  364 (732)
T ss_pred             cceEEEEecChhhhHHHHHHHHHHhhCCCCccceeeeecCcc
Confidence            556788999999999999999999999999999999987643

>cd01775 CYR1_RA Ubiquitin domain of CYR1 adenylate cyclase

Probab=85.16  E-value=4.9  Score=24.87  Aligned_cols=42  Identities=17%  Similarity=0.184  Sum_probs=33.4

Q ss_pred             eeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCC-CceeEE
Q 040824           79 IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPP-VQQRLI  120 (154)
Q Consensus        79 i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~-~~~~l~  120 (154)
                      |.|-..++....+.++.+.||+++-..+++++.++. .+.+|.
T Consensus         5 IRIFr~D~Tf~Tls~~l~tTv~eli~~L~rK~~l~~~~ny~l~   47 (97)
T cd01775           5 IRVFRSDGTFTTLSCPLNTTVSELIPQLAKKFYLPSGGNYQLS   47 (97)
T ss_pred             EEEEecCCcEEEEEcCCcCcHHHHHHHHHHhhcCCCCCCeEEE
Confidence            334445677788999999999999999999999865 566665

CYR1 is a fungal adenylate cyclase with at least four domains, an N-terminal RA (Ras association) domain, a middle leucine-rich repeat domain, a catalytic domain. The N-terminal RA domain of CYR1 post-translationally modifies a small GTPase called Ras. The Ras-CYR1 pathway has been implicated in the transduction of a glucose-triggered signal to an intracellular environment where a protein phosphorylation cascade is initiated by cyclic AMP.

>cd01768 RA RA (Ras-associating) ubiquitin domain

Probab=84.82  E-value=4.6  Score=24.03  Aligned_cols=35  Identities=17%  Similarity=0.324  Sum_probs=30.0

Q ss_pred             CceEEEeeCCCchHHHHHHHHhhhcCCC--CCceeEE
Q 040824           86 GKEIEIDIEPTDTIERIKERVEEKEGIP--PVQQRLI  120 (154)
Q Consensus        86 ~~~~~~~v~~~~tv~~LK~~i~~~~~i~--~~~~~l~  120 (154)
                      +....+.++.++|..++-+.+.++++++  +..+.|+
T Consensus        12 ~~~kti~V~~~~t~~~Vi~~~l~k~~l~~~~~~y~L~   48 (87)
T cd01768          12 GTYKTLRVSKDTTAQDVIQQLLKKFGLDDDPEDYALV   48 (87)
T ss_pred             ccEEEEEECCCCCHHHHHHHHHHHhCCcCCcccEEEE
Confidence            5667899999999999999999999986  6666665

The RA (Ras-associating) domain is structurally similar to ubiquitin and is present in one or two copies in a number of signalling molecules that bind and regulate a small GTPase called Ras or the Ras-related GTPases, Ral and Rap. RA-containing proteins include RalGDS, AF6, RIN1, RASSF1, SNX27, CYR1, STE50, and phospholipase C epsilon.

>PF08825 E2_bind: E2 binding domain; InterPro: IPR014929 E1 and E2 enzymes play a central role in ubiquitin and ubiquitin-like protein transfer cascades

Probab=84.80  E-value=5.1  Score=24.12  Aligned_cols=56  Identities=13%  Similarity=0.219  Sum_probs=39.3

Q ss_pred             EEEeCCCcHHHHHHHHHhHhCC-------CCCCeEEEEcce-------EeccCceecccccccccceeeee
Q 040824           15 LEVESSDTIDNVKAKIQDKEGI-------PPDQQRLIFAGK-------QLEDGRTLADYNIQKESTLHLVL   71 (154)
Q Consensus        15 ~~v~~~~tv~~lk~~i~~~~~~-------~~~~q~L~~~g~-------~L~d~~~l~~~~i~~~~~i~l~~   71 (154)
                      +++++++|+.+|.+.+.+.-.+       ..+...|+..+-       .-+-+++|++. +.+|..|.+.-
T Consensus         1 i~v~~~~TL~~lid~L~~~~~~qlk~PSlt~~~k~LYm~~pp~Lee~Tr~NL~k~l~eL-~~~g~ei~VtD   70 (84)
T PF08825_consen    1 IEVSPSWTLQDLIDSLCEKPEFQLKKPSLTTANKTLYMQSPPSLEEATRPNLSKKLKEL-LSDGEEITVTD   70 (84)
T ss_dssp             EEESTTSBSHHHHHHHHHSTTT--SS-EEESSEEEEEESSSHHHHHHTGGGGSSBTTTT-HHSSEEEEEEE
T ss_pred             CCcCccchHHHHHHHHHhChhhhcCCCcccCCCceEEEeCCHHHHHHhhhhhhhhHHHH-hcCCCEEEEEC
Confidence            5789999999999999887432       345556666541       12336688888 88888886643

This is an E2 binding domain that is found on NEDD8 activating E1 enzyme. The protein resembles ubiquitin, and recruits the catalytic core of the E2 enzyme Ubc12 in a similar manner to that in which ubiquitin interacts with ubiquitin binding domains []. ; GO: 0005524 ATP binding, 0016881 acid-amino acid ligase activity, 0045116 protein neddylation; PDB: 3GZN_D 3DBL_F 1R4N_H 1R4M_D 2NVU_B 1TT5_D 3DBR_D 3DBH_H 1YOV_B 3FN1_A ....

>TIGR01687 moaD_arch MoaD family protein, archaeal

Probab=84.60  E-value=6.5  Score=23.47  Aligned_cols=59  Identities=10%  Similarity=0.244  Sum_probs=37.7

Q ss_pred             CEEEEEEeCCCcHHHHHHHHHhHhC-----CCC------CCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824           11 KTITLEVESSDTIDNVKAKIQDKEG-----IPP------DQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus        11 ~~~~~~v~~~~tv~~lk~~i~~~~~-----~~~------~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      ....++++ ..||.+|.+.+.....     +-.      ....+..+|+....+..   ..+++|+.|.+....
T Consensus        16 ~~~~v~~~-~~tv~~l~~~l~~~~p~~~~~~l~~~~~~~~~~~v~vN~~~v~~~~~---~~l~dgdev~i~Ppv   85 (88)
T TIGR01687        16 KSEEIEIE-GKTVGDLLNELMARYPKEFSELFKEGLGLVPNVIILVNGRNVDWGLG---TELKDGDVVAIFPPV   85 (88)
T ss_pred             ceEEEEeC-CCCHHHHHHHHHHHCcHHHHHhCccCCcccccEEEEECCEecCccCC---CCCCCCCEEEEeCCC
Confidence            34567776 8899999999987753     101      12444567776654321   567888888766543

Members of this family appear to be archaeal versions of MoaD, subunit 1 of molybdopterin converting factor. This model has been split from the bacterial/eukaryotic equivalog model TIGR01682 because the presence of two members of this family in a substantial number of archaeal species suggests that roles might not be interchangeable.

>KOG2689 consensus Predicted ubiquitin regulatory protein [Posttranslational modification, protein turnover, chaperones]

Probab=84.53  E-value=3.8  Score=30.25  Aligned_cols=67  Identities=15%  Similarity=0.257  Sum_probs=52.0

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEE--EcceEecc---Cceeccccccccccee
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLED---GRTLADYNIQKESTLH   68 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~--~~g~~L~d---~~~l~~~~i~~~~~i~   68 (154)
                      .+-|+..+|++...+++...++..++.-+.-..+..++.-.|.  |..+.+.+   .++|...++.+.+++.
T Consensus       212 rlQiRl~DG~Tl~~tF~a~E~L~~VR~wVd~n~~~~~~P~~f~t~fPR~tf~edD~~KpLq~L~L~Psa~li  283 (290)
T KOG2689|consen  212 RLQIRLPDGQTLTQTFNARETLAAVRLWVDLNRGDGLDPYSFHTGFPRVTFTEDDELKPLQELDLVPSAVLI  283 (290)
T ss_pred             EEEEEcCCCCeeeeecCchhhHHHHHHHHHHhccCCCCCeeeecCCCceecccccccccHHHhccccchhee
Confidence            4678999999999999999999999999998888777665554  44555533   3478888888777664

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

Probab=84.47  E-value=2.2  Score=35.64  Aligned_cols=42  Identities=24%  Similarity=0.460  Sum_probs=37.0

Q ss_pred             CCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEe
Q 040824            9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQL   50 (154)
Q Consensus         9 ~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L   50 (154)
                      ++..+.+-++++.|+..++++|+..+|+|.+.|.|+|.|...
T Consensus       323 ~~~~~~~~~~~~ntl~~~~~~I~~~Tgipe~~qeLL~e~~~~  364 (732)
T KOG4250|consen  323 QATSHEYYVHADNTLHSLIERISKQTGIPEGKQELLFEGGLS  364 (732)
T ss_pred             cceEEEEecChhhhHHHHHHHHHHhhCCCCccceeeeecCcc
Confidence            445678889999999999999999999999999999987553

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

Probab=84.42  E-value=4.7  Score=32.84  Aligned_cols=64  Identities=36%  Similarity=0.529  Sum_probs=42.5

Q ss_pred             CEEEEEEeCCCcHHHHHHHHHhHh--CCC------CCCeEEEE--c--ce-EeccCc-------------eecccccccc
Q 040824           11 KTITLEVESSDTIDNVKAKIQDKE--GIP------PDQQRLIF--A--GK-QLEDGR-------------TLADYNIQKE   64 (154)
Q Consensus        11 ~~~~~~v~~~~tv~~lk~~i~~~~--~~~------~~~q~L~~--~--g~-~L~d~~-------------~l~~~~i~~~   64 (154)
                      ..+++++-.-+||.++|++|-+..  +.|      ++..-|-+  +  |+ .|.|..             ||++|++.+|
T Consensus       202 ~~i~VkVLdCDTItQVKeKiLDavyk~~p~S~rp~~~d~dLEwr~~~~~~~iL~D~D~ts~~~~~wkrLNTL~HY~V~dg  281 (539)
T PF08337_consen  202 EEIPVKVLDCDTITQVKEKILDAVYKNTPYSQRPRADDVDLEWRQGRGGRLILQDEDSTSKVEGGWKRLNTLAHYKVPDG  281 (539)
T ss_dssp             TCEEEEEETTSBHHHHHHHHHHHHTTTS-GGGS--GGGEEEEEEETTSEEEEESSSSTTSEEETTEEE--BHHHHT--TT
T ss_pred             ceEEEEEEecCcccHHHHHHHHHHHcCCCCCCCCCccccceeeecCCCCcccccCCCCCcccCCCceEeccHhhcCCCCC
Confidence            558899999999999999997663  333      33444432  2  22 465542             5999999999


Q ss_pred             cceeeeeeee
Q 040824           65 STLHLVLRLR   74 (154)
Q Consensus        65 ~~i~l~~~~~   74 (154)
                      +++.++.+..
T Consensus       282 a~vaLv~k~~  291 (539)
T PF08337_consen  282 ATVALVPKQH  291 (539)
T ss_dssp             EEEEEEES--
T ss_pred             ceEEEeeccc
Confidence            9998887653

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

>PF02597 ThiS: ThiS family; InterPro: IPR003749 ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer

Probab=84.27  E-value=5.9  Score=22.75  Aligned_cols=60  Identities=12%  Similarity=0.190  Sum_probs=43.4

Q ss_pred             EEEEEEeCCCcHHHHHHHHHhHhCC--CCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824           12 TITLEVESSDTIDNVKAKIQDKEGI--PPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus        12 ~~~~~v~~~~tv~~lk~~i~~~~~~--~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      ...+.+....||.+|.+.+.....-  ....-.+..||+...+  .-.+.-++++++|.+....
T Consensus        13 ~~~~~~~~~~tv~~ll~~l~~~~p~~~~~~~~~v~vN~~~v~~--~~~~~~l~~gD~V~i~ppv   74 (77)
T PF02597_consen   13 EEEIEVPEGSTVRDLLEALAERYPELALRDRVAVAVNGEIVPD--DGLDTPLKDGDEVAILPPV   74 (77)
T ss_dssp             EEEEEESSTSBHHHHHHHHCHHTGGGHTTTTEEEEETTEEEGG--GTTTSBEETTEEEEEEEST
T ss_pred             CeEEecCCCCcHHHHHHHHHhhccccccCccEEEEECCEEcCC--ccCCcCcCCCCEEEEECCC
Confidence            4567888899999999999877531  2245666688888877  3556667889988776543

ThiS is coded in the thiCEFSGH operon in Escherichia coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS []. MoaD, a protein involved in sulphur transfer during molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.; PDB: 1JW9_D 1JWB_D 1JWA_D 3BII_D 1NVI_D 1FMA_D 1FM0_D 2QIE_G 2Q5W_D 2K5P_A ....

>PF00788 RA: Ras association (RalGDS/AF-6) domain; InterPro: IPR000159 Proteins with this domain are mostly RasGTP effectors and include guanine-nucleotide releasing factor in mammals []

Probab=84.17  E-value=5.2  Score=23.82  Aligned_cols=41  Identities=24%  Similarity=0.293  Sum_probs=32.0

Q ss_pred             eeeeecCCc----eEEEeeCCCchHHHHHHHHhhhcCC--CCCceeE
Q 040824           79 IKVKTLTGK----EIEIDIEPTDTIERIKERVEEKEGI--PPVQQRL  119 (154)
Q Consensus        79 i~v~~~~~~----~~~~~v~~~~tv~~LK~~i~~~~~i--~~~~~~l  119 (154)
                      |.|...++.    ...+.++.++|+.++-+.+.+++++  ++....|
T Consensus         5 lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~~~~~y~L   51 (93)
T PF00788_consen    5 LRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAEDPSDYCL   51 (93)
T ss_dssp             EEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSSSGGGEEE
T ss_pred             EEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCCCCCCEEE
Confidence            334444444    6789999999999999999999998  5566677

This factor stimulates the dissociation of GDP from the Ras-related RALA and RALB GTPases, which allows GTP binding and activation of the GTPases. It interacts and acts as an effector molecule for R-ras, K-Ras and Rap []. The domain is also present in a number of other proteins among them the sexual differentiation protein in yeast that is essential for mating and meiosis and yeast adenylate cyclase. These proteins contain repeated leucine-rich (LRR) segments.; GO: 0007165 signal transduction; PDB: 3EC8_A 2C5L_D 2BYF_A 2CS4_A 3KH0_A 2B3A_A 1RAX_A 2RGF_A 1WGR_A 1WXA_A ....

>PRK11840 bifunctional sulfur carrier protein/thiazole synthase protein; Provisional

Probab=83.23  E-value=6.4  Score=29.95  Aligned_cols=61  Identities=18%  Similarity=0.247  Sum_probs=46.3

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      +|+.  +++....|+.+|-+.    .+++++..-+..+|..+..+ .-.++-+++||.|.++--..||
T Consensus         6 NGk~--~el~e~~TL~dLL~~----L~i~~~~VAVeVNgeIVpr~-~w~~t~LkeGD~IEII~~VgGG   66 (326)
T PRK11840          6 NGEP--RQVPAGLTIAALLAE----LGLAPKKVAVERNLEIVPRS-EYGQVALEEGDELEIVHFVGGG   66 (326)
T ss_pred             CCEE--EecCCCCcHHHHHHH----cCCCCCeEEEEECCEECCHH-HcCccccCCCCEEEEEEEecCC
Confidence            5554  556677888888664    57888888888999988632 3456678999999998887776

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=83.02  E-value=3.2  Score=31.50  Aligned_cols=54  Identities=13%  Similarity=0.193  Sum_probs=41.1

Q ss_pred             EEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEc---ceE-----eccCceeccccccccccee
Q 040824           15 LEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA---GKQ-----LEDGRTLADYNIQKESTLH   68 (154)
Q Consensus        15 ~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~---g~~-----L~d~~~l~~~~i~~~~~i~   68 (154)
                      .-|...-||.++|..+..+.|+.+.+++|++-   |+.     .+.+..|..|+|.+|+.+.
T Consensus       352 ~~I~~~~TV~D~~~~Ld~~VGvk~trMkLf~L~eD~rt~~~ss~~~N~~L~~fkIedGDs~l  413 (418)
T KOG2982|consen  352 GLICMTRTVLDFMKILDPKVGVKFTRMKLFLLREDGRTDDFSSSDYNMPLHYFKIEDGDSFL  413 (418)
T ss_pred             eEEEeehHHHHHHHHhccccccccceeEEEEEcccCccCCccccCCCCcceEEeccCCCEee
Confidence            44556669999999999999999999999863   332     3345567777788888763

>cd01775 CYR1_RA Ubiquitin domain of CYR1 adenylate cyclase

Probab=82.70  E-value=6.3  Score=24.38  Aligned_cols=36  Identities=22%  Similarity=0.235  Sum_probs=29.9

Q ss_pred             EEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCC
Q 040824            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPP   38 (154)
Q Consensus         3 v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~   38 (154)
                      +.|-..++...++.++.++||+++-..+.+++.+++
T Consensus         5 IRIFr~D~Tf~Tls~~l~tTv~eli~~L~rK~~l~~   40 (97)
T cd01775           5 IRVFRSDGTFTTLSCPLNTTVSELIPQLAKKFYLPS   40 (97)
T ss_pred             EEEEecCCcEEEEEcCCcCcHHHHHHHHHHhhcCCC
Confidence            455555666678999999999999999999988766

CYR1 is a fungal adenylate cyclase with at least four domains, an N-terminal RA (Ras association) domain, a middle leucine-rich repeat domain, a catalytic domain. The N-terminal RA domain of CYR1 post-translationally modifies a small GTPase called Ras. The Ras-CYR1 pathway has been implicated in the transduction of a glucose-triggered signal to an intracellular environment where a protein phosphorylation cascade is initiated by cyclic AMP.

>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=82.45  E-value=1.7  Score=31.74  Aligned_cols=59  Identities=17%  Similarity=0.435  Sum_probs=40.6

Q ss_pred             EEeeCCCchHHHHHHHHhhhcCCCCCceeEEECC------eecCCCCcccccccCCCCEEEEEEe
Q 040824           90 EIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAG------KQLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        90 ~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g------~~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      .+-++.+++++++-..+.+..|.|++.--.+|..      ..++.+.|+....+.+||.|-+-..
T Consensus        88 h~~v~~~~~v~~l~~~i~~~~g~p~~t~l~lyEEi~~~~ie~i~~~~t~~~~el~~GdIi~fQ~~  152 (249)
T PF12436_consen   88 HVYVPKNDKVSELVPLINERAGLPPDTPLLLYEEIKPNMIEPIDPNQTFEKAELQDGDIICFQRA  152 (249)
T ss_dssp             EEEEETT-BGGGTHHHHHHHHT--TT--EEEEEEEETTEEEE--SSSBHHHTT--TTEEEEEEE-
T ss_pred             EEEECCCCCHHHHHHHHHHHcCCCCCCceEEEEEeccceeeEcCCCCchhhcccCCCCEEEEEec
Confidence            4678999999999999999999998766565543      3578899999999999999966543

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.

>KOG4572 consensus Predicted DNA-binding transcription factor, interacts with stathmin [Transcription; General function prediction only; Signal transduction mechanisms]

Probab=82.37  E-value=3.5  Score=35.19  Aligned_cols=64  Identities=17%  Similarity=0.330  Sum_probs=50.2

Q ss_pred             CCceEEEeeCC-CchHHHHHHHHhhhcCCCCCceeEEE-CCeecCCCCccccccc--CCCCEEEEEEe
Q 040824           85 TGKEIEIDIEP-TDTIERIKERVEEKEGIPPVQQRLIY-AGKQLADDKTARDYNI--EGGSVLHLVLA  148 (154)
Q Consensus        85 ~~~~~~~~v~~-~~tv~~LK~~i~~~~~i~~~~~~l~~-~g~~l~d~~~L~~~~i--~~~~~i~~~~~  148 (154)
                      .|+...|+... +.|+++||-+|++.+|....++.++- .|..+..++.+.+|.-  ++.+.|+++.+
T Consensus         3 rGqaltFDleaetqT~adLk~aiqke~~~aIq~~tfl~egGecmaadkrl~e~StaGTdTnPiffFnk   70 (1424)
T KOG4572|consen    3 RGQALTFDLEAETQTFADLKDAIQKEVGHAIQDLTFLDEGGECMAADKRLAEISTAGTDTNPIFFFNK   70 (1424)
T ss_pred             CCceeEEeecceeehHHHHHHHHHHHhchhhceeeeeecCCcCcccccchhhhccccCCCCceEEeeh
Confidence            46777777765 46999999999999999999998885 4567778888888863  55667777643

>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal

Probab=82.35  E-value=7.8  Score=22.71  Aligned_cols=57  Identities=14%  Similarity=0.226  Sum_probs=37.2

Q ss_pred             CEEEEEEeCC-CcHHHHHHHHHhHhC-CC--CCCeEEEEcceEeccCceecccccccccceeeeee
Q 040824           11 KTITLEVESS-DTIDNVKAKIQDKEG-IP--PDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus        11 ~~~~~~v~~~-~tv~~lk~~i~~~~~-~~--~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      ....++++.+ .|+.+|.+.+..... ..  .....+..+++...+     +.-+++++.|.+...
T Consensus        16 ~~~~~~~~~~~~tv~~L~~~L~~~~p~l~~~~~~~~v~vn~~~v~~-----~~~l~dgDevai~Pp   76 (80)
T TIGR01682        16 DEETLELPDESTTVGELKEHLAKEGPELAASRGQVMVAVNEEYVTD-----DALLNEGDEVAFIPP   76 (80)
T ss_pred             CeEEEECCCCCcCHHHHHHHHHHhCchhhhhccceEEEECCEEcCC-----CcCcCCCCEEEEeCC
Confidence            3356788766 899999999988753 11  122344566766653     445777888866654

The C-terminal Gly-Gly of this model is critical to function.

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

Probab=82.33  E-value=6.6  Score=24.87  Aligned_cols=48  Identities=8%  Similarity=0.234  Sum_probs=36.8

Q ss_pred             EEEEeCCC----CEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEe
Q 040824            3 IFVKTLTG----KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQL   50 (154)
Q Consensus         3 v~v~~~~~----~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L   50 (154)
                      |.++..++    +.-...|++++|++.+...+++..+++.+++...|-+...
T Consensus        33 i~l~aiG~~PilK~~k~~i~~t~tfa~vi~Flkk~Lkl~as~slflYVN~sF   84 (116)
T KOG3439|consen   33 IRLRAIGDAPILKKSKFKINPTQTFAKVILFLKKFLKLQASDSLFLYVNNSF   84 (116)
T ss_pred             EEEeccCCCcceecceEEeCcchhhHHHHHHHHHHhCCcccCeEEEEEcCcc
Confidence            44454443    2245789999999999999999999999999888755443

>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=82.26  E-value=0.39  Score=37.75  Aligned_cols=59  Identities=19%  Similarity=0.142  Sum_probs=50.1

Q ss_pred             EEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEe
Q 040824           90 EIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        90 ~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      .+..+..-|-++|...++++.|++-...+.+.+|+.++..+||.+.|++.+....+.+.
T Consensus        53 l~k~sL~i~Gselqa~iakklgi~enhvKci~~~Kils~~ktlaeQglk~nq~~mv~~~  111 (568)
T KOG2561|consen   53 LKKCSLHITGSELQALIAKKLGIKENHVKCIINGKILSCRKTLAEQGLKINQELMVAVG  111 (568)
T ss_pred             hhhcccccccHHHHHHHHHHcCCchhhhheeeccceeecccchhhhhhhhhhHHHHHhc
Confidence            44555566789999999999999998999999999999999999999988876655543

>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein

Probab=82.12  E-value=6.9  Score=21.96  Aligned_cols=55  Identities=18%  Similarity=0.337  Sum_probs=36.6

Q ss_pred             EEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824           14 TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus        14 ~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      .++++...|+.+|.+.+    +++++...+..+|+.+..+ .-.++-+++++.|.+....
T Consensus         8 ~~~~~~~~tv~~ll~~l----~~~~~~i~V~vNg~~v~~~-~~~~~~L~~gD~V~ii~~v   62 (65)
T cd00565           8 PREVEEGATLAELLEEL----GLDPRGVAVALNGEIVPRS-EWASTPLQDGDRIEIVTAV   62 (65)
T ss_pred             EEEcCCCCCHHHHHHHc----CCCCCcEEEEECCEEcCHH-HcCceecCCCCEEEEEEec
Confidence            34555678999988775    4667777777888776433 2233457888888766543

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.

>PF00788 RA: Ras association (RalGDS/AF-6) domain; InterPro: IPR000159 Proteins with this domain are mostly RasGTP effectors and include guanine-nucleotide releasing factor in mammals []

Probab=81.89  E-value=8.6  Score=22.86  Aligned_cols=39  Identities=28%  Similarity=0.253  Sum_probs=30.8

Q ss_pred             EEEEeCCCC----EEEEEEeCCCcHHHHHHHHHhHhCCCCCCe
Q 040824            3 IFVKTLTGK----TITLEVESSDTIDNVKAKIQDKEGIPPDQQ   41 (154)
Q Consensus         3 v~v~~~~~~----~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q   41 (154)
                      |+|-..++.    ...+.++.++|+.++.+.+-++++++.+..
T Consensus         5 lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~~~~   47 (93)
T PF00788_consen    5 LRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAEDPS   47 (93)
T ss_dssp             EEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSSSGG
T ss_pred             EEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCCCCC
Confidence            445555555    788999999999999999999999844444

This factor stimulates the dissociation of GDP from the Ras-related RALA and RALB GTPases, which allows GTP binding and activation of the GTPases. It interacts and acts as an effector molecule for R-ras, K-Ras and Rap []. The domain is also present in a number of other proteins among them the sexual differentiation protein in yeast that is essential for mating and meiosis and yeast adenylate cyclase. These proteins contain repeated leucine-rich (LRR) segments.; GO: 0007165 signal transduction; PDB: 3EC8_A 2C5L_D 2BYF_A 2CS4_A 3KH0_A 2B3A_A 1RAX_A 2RGF_A 1WGR_A 1WXA_A ....

>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein

Probab=81.66  E-value=9.6  Score=23.29  Aligned_cols=43  Identities=16%  Similarity=0.292  Sum_probs=31.8

Q ss_pred             EEEEEeCCCCEEEEEEeC-----CCcHHHHHHHHHhHhCCCC-CCeEEEE
Q 040824            2 QIFVKTLTGKTITLEVES-----SDTIDNVKAKIQDKEGIPP-DQQRLIF   45 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~-----~~tv~~lk~~i~~~~~~~~-~~q~L~~   45 (154)
                      .|++.. +|....+.++.     +.+..+|+++|.+.+++++ ..-.|.|
T Consensus         2 ~vKv~y-~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y   50 (91)
T cd06398           2 VVKVKY-GGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTY   50 (91)
T ss_pred             EEEEEe-CCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEE
Confidence            355665 56667777774     6899999999999999987 4444445

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 domain, 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

>cd06410 PB1_UP2 Uncharacterized protein 2

Probab=81.25  E-value=7.6  Score=24.05  Aligned_cols=45  Identities=11%  Similarity=0.220  Sum_probs=34.0

Q ss_pred             eecCCceEEEeeCCCchHHHHHHHHhhhcCCCCC-ceeEEECCeec
Q 040824           82 KTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPV-QQRLIYAGKQL  126 (154)
Q Consensus        82 ~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~-~~~l~~~g~~l  126 (154)
                      +-..|.+.-+.|+.+.|..+|++++++.++++.. ..++...+..+
T Consensus        18 ~Y~GG~tr~i~V~r~~s~~el~~kl~~~~~~~~~~~lky~Lp~edl   63 (97)
T cd06410          18 RYVGGETRIVSVDRSISFKELVSKLSELFGAGVVVTLKYQLPDEDL   63 (97)
T ss_pred             EEcCCceEEEEEcCCCCHHHHHHHHHHHhCCCCceEEEEEcCCCCc
Confidence            3446788889999999999999999999998875 23333345444

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.

>PF11834 DUF3354: Domain of unknown function (DUF3354); InterPro: IPR021789 Potassium channels take part in important processes of higher plants, including opening and closing of stomatal pores and leaf movement

Probab=81.01  E-value=2.7  Score=24.36  Aligned_cols=43  Identities=28%  Similarity=0.362  Sum_probs=30.0

Q ss_pred             chHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEE
Q 040824           97 DTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHL  145 (154)
Q Consensus        97 ~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~  145 (154)
                      .|+++|.+..++++|++ ...-+.-+|.+++|=.     -|.+||.+++
T Consensus        26 ~SleeLl~ia~~kfg~~-~~~v~~~dgaeIdDI~-----~IRDgD~L~~   68 (69)
T PF11834_consen   26 DSLEELLKIASEKFGFS-ATKVLNEDGAEIDDID-----VIRDGDHLYL   68 (69)
T ss_pred             ccHHHHHHHHHHHhCCC-ceEEEcCCCCEEeEEE-----EEEcCCEEEE
Confidence            69999999999999997 3333444555554422     3578888876

Inward rectifying potassium (K(+)in) channels play an important role in turgor regulation and ion uptake in higher plants. All of them comprise, from their N-terminal to their C-terminal ends: a short hydrophilic region, a hydrophobic region structurally analogous and partially homologous to the transmembrane domain of voltage-gated animal channels from the Shaker superfamily, a putative cyclic nucleotide-binding domain, and a conserved C-terminal KHA domain. Between these last two regions, some of them (AKT1, AKT2 and SKT1) contain an ankyrin-repeat domain with six repeats homologous to those of human erythrocyte ankyrin. This entry represents the KHA domain which is unique to plant K(+)in channels. The KHA domain contains two high-homology blocks enriched for hydrophobic and acidic residues, respectively. The KHA domain is essential for interaction of plant K(+)in channels. The KHA domain mediates tetramerization and/or stabilisation of the heteromers [, , ].

>TIGR01683 thiS thiamine biosynthesis protein ThiS

Probab=80.58  E-value=8  Score=21.66  Aligned_cols=57  Identities=18%  Similarity=0.341  Sum_probs=36.8

Q ss_pred             CCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeee
Q 040824            9 TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         9 ~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      +|+.+  ++..+.|+.+|.+.+    +++++...+..+|..+.. ..-.++-+++++.|.+...
T Consensus         4 Ng~~~--~~~~~~tv~~ll~~l----~~~~~~v~v~vN~~iv~~-~~~~~~~L~~gD~veii~~   60 (64)
T TIGR01683         4 NGEPV--EVEDGLTLAALLESL----GLDPRRVAVAVNGEIVPR-SEWDDTILKEGDRIEIVTF   60 (64)
T ss_pred             CCeEE--EcCCCCcHHHHHHHc----CCCCCeEEEEECCEEcCH-HHcCceecCCCCEEEEEEe
Confidence            45544  445677899988764    566666666678877632 2233456788888876654

This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.

>PF02017 CIDE-N: CIDE-N domain; InterPro: IPR003508 This domain consists of caspase-activated (CAD) nucleases, which induce DNA fragmentation and chromatin condensation during apoptosis, and the cell death activator proteins CIDE-A and CIDE-B, which are inhibitors of CAD nuclease

Probab=80.40  E-value=6.2  Score=23.43  Aligned_cols=34  Identities=24%  Similarity=0.504  Sum_probs=27.3

Q ss_pred             chHHHHHHHHhhhcCCCCCceeEEE--CCeecCCCC
Q 040824           97 DTIERIKERVEEKEGIPPVQQRLIY--AGKQLADDK  130 (154)
Q Consensus        97 ~tv~~LK~~i~~~~~i~~~~~~l~~--~g~~l~d~~  130 (154)
                      .+..+|+.+.+..++++.+..+|..  .|..++|+.
T Consensus        21 ~sL~eL~~K~~~~l~~~~~~~~lvL~eDGT~VddEe   56 (78)
T PF02017_consen   21 SSLEELLEKACDKLQLPEEPVRLVLEEDGTEVDDEE   56 (78)
T ss_dssp             SSHHHHHHHHHHHHT-SSSTCEEEETTTTCBESSCH
T ss_pred             CCHHHHHHHHHHHhCCCCcCcEEEEeCCCcEEccHH
Confidence            5899999999999999988888875  677777654

The two proteins interact through the region defined by the method signatures.; GO: 0006915 apoptosis, 0005622 intracellular; PDB: 1IBX_A 2EEL_A 1F2R_I 1C9F_A 1D4B_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	154
3b08_A	152	Crystal Structure Of The Mouse Hoil1-L-Nzf In Compl		9e-56
2zvn_A	154	Nemo Cozi Domain Incomplex With Diubiquitin In P212		9e-56
3u30_A	172	Crystal Structure Of A Linear-Specific Ubiquitin Fa		1e-55
2w9n_A	152	Crystal Structure Of Linear Di-Ubiquitin Length = 1		5e-55
2y5b_B	152	Structure Of Usp21 In Complex With Linear Diubiquit		2e-54
3u5e_m	128	The Structure Of The Eukaryotic Ribosome At 3.0 A R		3e-38
3u5e_m	128	The Structure Of The Eukaryotic Ribosome At 3.0 A R		2e-12
3u5g_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		4e-38
3u5g_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		2e-12
3zf7_s	128	High-resolution Cryo-electron Microscopy Structure		5e-38
3zf7_s	128	High-resolution Cryo-electron Microscopy Structure		6e-12
3olm_D	79	Structure And Function Of A Ubiquitin Binding Site		8e-38
3olm_D	79	Structure And Function Of A Ubiquitin Binding Site		1e-12
4a18_K	129	T.Thermophila 60s Ribosomal Subunit In Complex With		1e-37
4a18_K	129	T.Thermophila 60s Ribosomal Subunit In Complex With		2e-13
1otr_B	76	Solution Structure Of A Cue-Ubiquitin Complex Lengt		1e-37
1otr_B	76	Solution Structure Of A Cue-Ubiquitin Complex Lengt		1e-12
3l0w_B	169	Structure Of Split Monoubiquitinated Pcna With Ubiq		1e-37
3l0w_B	169	Structure Of Split Monoubiquitinated Pcna With Ubiq		4e-13
4ii3_B	96	Crystal Structure Of S. Pombe Ubiquitin Activating		2e-37
4ii3_B	96	Crystal Structure Of S. Pombe Ubiquitin Activating		1e-12
4hcn_B	98	Crystal Structure Of Burkholderia Pseudomallei Effe		2e-37
4hcn_B	98	Crystal Structure Of Burkholderia Pseudomallei Effe		2e-12
1yx5_B	98	Solution Structure Of S5a Uim-1UBIQUITIN COMPLEX Le		4e-37
1yx5_B	98	Solution Structure Of S5a Uim-1UBIQUITIN COMPLEX Le		2e-12
2kdi_A	114	Solution Structure Of A UbiquitinUIM FUSION PROTEIN		5e-37
2kdi_A	114	Solution Structure Of A UbiquitinUIM FUSION PROTEIN		3e-12
2jwz_A	76	Mutations In The Hydrophobic Core Of Ubiquitin Diff		6e-37
2jwz_A	76	Mutations In The Hydrophobic Core Of Ubiquitin Diff		6e-12
3nob_A	78	Structure Of K11-Linked Di-Ubiquitin Length = 78		7e-37
3nob_A	78	Structure Of K11-Linked Di-Ubiquitin Length = 78		2e-12
1aar_A	76	Structure Of A Diubiquitin Conjugate And A Model Fo		8e-37
1aar_A	76	Structure Of A Diubiquitin Conjugate And A Model Fo		2e-12
2khw_B	79	Solution Structure Of The Human Polymerase Iota Ubm		9e-37
2khw_B	79	Solution Structure Of The Human Polymerase Iota Ubm		2e-12
4ap4_C	80	Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Le		9e-37
4ap4_C	80	Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Le		9e-13
2ld9_A	77	Backbone Structure Of Ubiquitin Determined Using Ba		1e-36
2ld9_A	77	Backbone Structure Of Ubiquitin Determined Using Ba		7e-13
3jvz_X	81	E2~ubiquitin-Hect Length = 81		1e-36
3jvz_X	81	E2~ubiquitin-Hect Length = 81		5e-13
2znv_C	77	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		1e-36
2znv_C	77	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		2e-12
3dvg_X	80	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		1e-36
3dvg_X	80	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		2e-12
4ii2_B	83	Crystal Structure Of Ubiquitin Activating Enzyme 1		1e-36
4ii2_B	83	Crystal Structure Of Ubiquitin Activating Enzyme 1		1e-11
3vdz_A	111	Tailoring Encodable Lanthanide-Binding Tags As Mri		2e-36
3vdz_A	111	Tailoring Encodable Lanthanide-Binding Tags As Mri		3e-12
2ojr_A	111	Structure Of Ubiquitin Solved By Sad Using The Lant		2e-36
2ojr_A	111	Structure Of Ubiquitin Solved By Sad Using The Lant		3e-12
2znv_B	76	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		2e-36
2znv_B	76	Crystal Structure Of Human Amsh-Lp Dub Domain In Co		2e-12
1zgu_B	76	Solution Structure Of The Human Mms2-Ubiquitin Comp		2e-36
1zgu_B	76	Solution Structure Of The Human Mms2-Ubiquitin Comp		3e-12
3dvg_Y	79	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		2e-36
3dvg_Y	79	Crystal Structure Of K63-Specific Fab Apu.3a8 Bound		2e-12
3q3f_A	189	Engineering Domain-Swapped Binding Interfaces By Mu		2e-36
3q3f_A	189	Engineering Domain-Swapped Binding Interfaces By Mu		4e-13
1yiw_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		3e-36
1yiw_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		2e-12
2k6d_B	76	Cin85 Sh3-C Domain In Complex With Ubiquitin Length		3e-36
2k6d_B	76	Cin85 Sh3-C Domain In Complex With Ubiquitin Length		7e-12
1xd3_B	75	Crystal Structure Of Uchl3-Ubvme Complex Length = 7		3e-36
1xd3_B	75	Crystal Structure Of Uchl3-Ubvme Complex Length = 7		7e-12
1cmx_B	76	Structural Basis For The Specificity Of Ubiquitin C		3e-36
1cmx_B	76	Structural Basis For The Specificity Of Ubiquitin C		7e-12
3rul_A	79	New Strategy To Analyze Structures Of Glycopeptide-		3e-36
3rul_A	79	New Strategy To Analyze Structures Of Glycopeptide-		7e-12
2o6v_D	76	Crystal Structure And Solution Nmr Studies Of Lys48		3e-36
2o6v_D	76	Crystal Structure And Solution Nmr Studies Of Lys48		4e-12
2xk5_B	76	Crystal Structure Of K6-Linked Diubiquitin Length =		4e-36
2xk5_B	76	Crystal Structure Of K6-Linked Diubiquitin Length =		1e-12
1s1q_B	76	Tsg101(Uev) Domain In Complex With Ubiquitin Length		5e-36
1s1q_B	76	Tsg101(Uev) Domain In Complex With Ubiquitin Length		2e-12
3k9o_B	96	The Crystal Structure Of E2-25k And Ubb+1 Complex L		6e-36
3k9o_B	96	The Crystal Structure Of E2-25k And Ubb+1 Complex L		4e-12
2o6v_B	76	Crystal Structure And Solution Nmr Studies Of Lys48		8e-36
2o6v_B	76	Crystal Structure And Solution Nmr Studies Of Lys48		9e-12
2k25_A	103	Automated Nmr Structure Of The Ubb By Fapsy Length		1e-35
2k25_A	103	Automated Nmr Structure Of The Ubb By Fapsy Length		3e-12
1ogw_A	76	Synthetic Ubiquitin With Fluoro-Leu At 50 And 67 Le		1e-35
1ogw_A	76	Synthetic Ubiquitin With Fluoro-Leu At 50 And 67 Le		3e-11
3ai5_A	307	Crystal Structure Of Yeast Enhanced Green Fluoresce		2e-35
3ai5_A	307	Crystal Structure Of Yeast Enhanced Green Fluoresce		2e-11
1yj1_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		2e-35
1yj1_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		1e-11
2fcs_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		2e-35
2fcs_A	76	X-Ray Crystal Structure Of A Chemically Synthesized		1e-11
2gbr_A	81	Crystal Structure Of The 35-36 Moad Insertion Mutan		4e-35
2gbr_A	81	Crystal Structure Of The 35-36 Moad Insertion Mutan		1e-10
2zcb_A	76	Crystal Structure Of Ubiquitin P37aP38A Length = 76		4e-35
2zcb_A	76	Crystal Structure Of Ubiquitin P37aP38A Length = 76		2e-10
3ldz_F	73	Crystal Structure Of Human Stam1 Vhs Domain In Comp		6e-35
3ldz_F	73	Crystal Structure Of Human Stam1 Vhs Domain In Comp		1e-10
1ud7_A	76	Solution Structure Of The Designed Hydrophobic Core		8e-35
1ud7_A	76	Solution Structure Of The Designed Hydrophobic Core		1e-11
3h7s_B	76	Crystal Structures Of K63-Linked Di- And Tri-Ubiqui		9e-35
3h7s_B	76	Crystal Structures Of K63-Linked Di- And Tri-Ubiqui		2e-10
2gbk_A	83	Crystal Structure Of The 9-10 Moad Insertion Mutant		1e-34
2gbk_A	83	Crystal Structure Of The 9-10 Moad Insertion Mutant		3e-11
3u5c_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		1e-34
3u5c_f	152	The Structure Of The Eukaryotic Ribosome At 3.0 A R		1e-09
3ons_A	72	Crystal Structure Of Human Ubiquitin In A New Cryst		2e-34
3ons_A	72	Crystal Structure Of Human Ubiquitin In A New Cryst		3e-10
1c3t_A	76	Rotamer Strain As A Determinant Of Protein Structur		3e-34
1c3t_A	76	Rotamer Strain As A Determinant Of Protein Structur		1e-11
1zw7_A	82	Elimination Of The C-Cap In Ubiquitin Structure, Dy		3e-34
1zw7_A	82	Elimination Of The C-Cap In Ubiquitin Structure, Dy		2e-11
4gsw_A	80	Crystal Structure Of Ubiquitin From Entamoeba Histo		3e-34
4gsw_A	80	Crystal Structure Of Ubiquitin From Entamoeba Histo		3e-12
3v6e_B	91	Crystal Structure Of Usp2 And A Mutant Form Of Ubiq		3e-34
3v6e_B	91	Crystal Structure Of Usp2 And A Mutant Form Of Ubiq		2e-11
1sif_A	88	Crystal Structure Of A Multiple Hydrophobic Core Mu		4e-34
1sif_A	88	Crystal Structure Of A Multiple Hydrophobic Core Mu		2e-13
2gbj_A	84	Crystal Structure Of The 9-10 8 Glycine Insertion M		7e-34
2gbj_A	84	Crystal Structure Of The 9-10 8 Glycine Insertion M		2e-11
2gbm_A	84	Crystal Structure Of The 35-36 8 Glycine Insertion		7e-34
2gbm_A	84	Crystal Structure Of The 35-36 8 Glycine Insertion		1e-10
3v6c_B	91	Crystal Structure Of Usp2 In Complex With Mutated U		7e-34
3v6c_B	91	Crystal Structure Of Usp2 In Complex With Mutated U		4e-11
4hjk_A	77	U7ub7 Disulfide Variant Length = 77		6e-33
4hjk_A	77	U7ub7 Disulfide Variant Length = 77		3e-10
4i6l_B	76	Crystal Structure Of Otub1 In Complex With Ubiquiti		5e-32
4i6l_B	76	Crystal Structure Of Otub1 In Complex With Ubiquiti		3e-09
3mtn_B	85	Usp21 In Complex With A Ubiquitin-based, Usp21-spec		2e-30
3mtn_B	85	Usp21 In Complex With A Ubiquitin-based, Usp21-spec		7e-08
2jvc_A	82	Nmr Solution Structure Of Ubiquitin Like Protein Le		2e-30
2jvc_A	82	Nmr Solution Structure Of Ubiquitin Like Protein Le		4e-11
4hk2_A	78	U7ub25.2540 Length = 78		9e-30
4hk2_A	78	U7ub25.2540 Length = 78		3e-07
3n3k_B	85	The Catalytic Domain Of Usp8 In Complex With A Usp8		7e-26
3n3k_B	85	The Catalytic Domain Of Usp8 In Complex With A Usp8		2e-06
1gjz_A	53	Solution Structure Of A Dimeric N-Terminal Fragment		5e-22
1bt0_A	76	Structure Of Ubiquitin-Like Protein, Rub1 Length =		8e-22
1bt0_A	76	Structure Of Ubiquitin-Like Protein, Rub1 Length =		1e-20
3dbh_I	88	Structural Dissection Of A Gating Mechanism Prevent		1e-20
3dbh_I	88	Structural Dissection Of A Gating Mechanism Prevent		8e-16
3dbl_I	88	Structural Dissection Of A Gating Mechanism Prevent		6e-20
3dbl_I	88	Structural Dissection Of A Gating Mechanism Prevent		7e-16
4hcp_B	78	Crystal Structure Of Burkholderia Pseudomallei Effe		1e-19
4hcp_B	78	Crystal Structure Of Burkholderia Pseudomallei Effe		3e-16
2nvu_I	81	Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C1		1e-19
2nvu_I	81	Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C1		2e-16
2bkr_B	77	Nedd8 Nedp1 Complex Length = 77		1e-19
2bkr_B	77	Nedd8 Nedp1 Complex Length = 77		3e-16
1ndd_B	76	Structure Of Nedd8 Length = 76		1e-19
1ndd_B	76	Structure Of Nedd8 Length = 76		4e-16
4f8c_B	88	Structure Of The Cif:nedd8 Complex - Yersinia Pseud		1e-19
4f8c_B	88	Structure Of The Cif:nedd8 Complex - Yersinia Pseud		1e-16
3gzn_I	82	Structure Of Nedd8-Activating Enzyme In Complex Wit		1e-19
3gzn_I	82	Structure Of Nedd8-Activating Enzyme In Complex Wit		4e-16
3dqv_A	81	Structural Insights Into Nedd8 Activation Of Cullin		4e-19
3dqv_A	81	Structural Insights Into Nedd8 Activation Of Cullin		2e-16
2dzi_A	81	2dziSOLUTION STRUCTURE OF THE N-Terminal Ubiquitin-		1e-10
2knb_A	81	Solution Nmr Structure Of The Parkin Ubl Domain In		2e-08
2zeq_A	78	Crystal Structure Of Ubiquitin-Like Domain Of Murin		3e-08
1iyf_A	81	Solution Structure Of Ubiquitin-Like Domain Of Huma		3e-08
3b1l_X	76	Crystal Structure Of Parkin Ubiquitin-Like Domain R		5e-08
3rt3_B	159	Complex Of Influenza Virus Protein With Host Anti-V		1e-07
3sdl_C	164	Crystal Structure Of Human Isg15 In Complex With Ns		1e-07
3r66_C	164	Crystal Structure Of Human Isg15 In Complex With Ns		1e-07
2hj8_A	88	Solution Nmr Structure Of The C-Terminal Domain Of		1e-07
2l7r_A	93	Solution Nmr Structure Of N-Terminal Ubiquitin-Like		2e-07
2faz_A	78	Ubiquitin-Like Domain Of Human Nuclear Zinc Finger		4e-07
3pse_B	156	Structure Of A Viral Otu Domain Protease Bound To I		5e-07
3phx_B	79	Otu Domain Of Crimean Congo Hemorrhagic Fever Virus		7e-07
1wy8_A	89	Solution Structure Of The N-Terminal Ubiquitin-Like		8e-07
1zkh_A	86	Solution Structure Of A Human Ubiquitin-Like Domain		2e-06
1z2m_A	155	Crystal Structure Of Isg15, The Interferon-Induced		3e-06
1wh3_A	87	Solution Structure Of C-Terminal Ubiquitin Like Dom		4e-06
1wx9_A	86	Solution Structure Of The N-Terminal Ubiquitin-Like		5e-06
1wx9_A	86	Solution Structure Of The N-Terminal Ubiquitin-Like		9e-05
1we7_A	115	Solution Structure Of Ubiquitin-Like Domain In Sf3a		7e-06
4dwf_A	90	Crystal Structure Of A Hla-B Associated Transcript		8e-06
4dwf_A	90	Crystal Structure Of A Hla-B Associated Transcript		1e-04
2bwe_S	77	The Crystal Structure Of The Complex Between The Ub		1e-05
3m63_B	101	Crystal Structure Of Ufd2 In Complex With The Ubiqu		2e-05
4eew_A	88	Crystal Structure Of The Ubl Domain Of Bag6 Length		2e-05
4eew_A	88	Crystal Structure Of The Ubl Domain Of Bag6 Length		6e-05
1ttn_A	106	Solution Structure Of The Ubiquitin-Like Domain Of		3e-05
1p1a_A	85	Nmr Structure Of Ubiquitin-Like Domain Of Hhr23b Le		8e-05
1uel_A	95	Solution Structure Of Ubiquitin-Like Domain Of Hhr2		1e-04
2wyq_A	85	The Crystal Structure Of The Ubiquitin-Like (Ubl) D		7e-04
1yqb_A	100	Human Ubiquilin 3 Length = 100		7e-04

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

Iteration: 1
 Score =  212 bits (539), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 111/152 (73%), Positives = 116/152 (76%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1   MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLI 120
           IQKESTLHLVLRLRGG  I VKTLTGK                       GIPP QQRLI
Sbjct: 61  IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI 120
Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
           +AGKQL D +T  DYNI+  S LHLVL LRGG
Sbjct: 121 FAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 152

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

Iteration: 1
 Score =  211 bits (538), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 111/152 (73%), Positives = 116/152 (76%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 3   MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 62
Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLI 120
           IQKESTLHLVLRLRGG  I VKTLTGK                       GIPP QQRLI
Sbjct: 63  IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI 122
Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
           +AGKQL D +T  DYNI+  S LHLVL LRGG
Sbjct: 123 FAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 154

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

Iteration: 1
 Score =  211 bits (537), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 111/152 (73%), Positives = 116/152 (76%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 21  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 80
Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLI 120
           IQKESTLHLVLRLRGG  I VKTLTGK                       GIPP QQRLI
Sbjct: 81  IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI 140
Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
           +AGKQL D +T  DYNI+  S LHLVL LRGG
Sbjct: 141 FAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 172

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

Iteration: 1
 Score =  209 bits (532), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 110/151 (72%), Positives = 115/151 (76%)
Query: 2   QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNI 61
           QIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYNI
Sbjct: 2   QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNI 61
Query: 62  QKESTLHLVLRLRGGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIY 121
           QKESTLHLVLRLRGG  I VKTLTGK                       GIPP QQRLI+
Sbjct: 62  QKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF 121
Query: 122 AGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
           AGKQL D +T  DYNI+  S LHLVL LRGG
Sbjct: 122 AGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 152

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

Iteration: 1
 Score =  207 bits (527), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 109/151 (72%), Positives = 114/151 (75%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1   MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLI 120
           IQKESTLHLVLRLRG   I VKTLTGK                       GIPP QQRLI
Sbjct: 61  IQKESTLHLVLRLRGHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI 120
Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRG 151
           +AGKQL D +T  DYNI+  S LHLVL LRG
Sbjct: 121 FAGKQLEDGRTLSDYNIQKESTLHLVLRLRG 151

>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 =  154 bits (388), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 74/76 (97%), Positives = 76/76 (100%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

>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 = 68.2 bits (165), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 41/74 (55%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 63  KESTLHLVLRLRGG 76

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

Iteration: 1
 Score =  153 bits (386), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 74/76 (97%), Positives = 76/76 (100%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

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

Iteration: 1
 Score = 67.8 bits (164), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 41/74 (55%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 63  KESTLHLVLRLRGG 76

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

Iteration: 1
 Score =  152 bits (385), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 73/78 (93%), Positives = 76/78 (97%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTI LEVE+SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLE+GRTLADYN
Sbjct: 1  MQIFVKTLTGKTIALEVEASDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEEGRTLADYN 60
Query: 61 IQKESTLHLVLRLRGGTM 78
          IQKESTLHLVLRLRGG M
Sbjct: 61 IQKESTLHLVLRLRGGVM 78

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

Iteration: 1
 Score = 66.2 bits (160), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 37/74 (50%), Positives = 41/74 (55%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL + +T  DYNI+
Sbjct: 3   IFVKTLTGKTIALEVEASDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEEGRTLADYNIQ 62
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 63  KESTLHLVLRLRGG 76

>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 =  152 bits (384), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 74/76 (97%), Positives = 76/76 (100%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 4  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 63
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 64 IQKESTLHLVLRLRGG 79

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

Iteration: 1
 Score = 68.9 bits (167), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 41/74 (55%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 6   IFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 65
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 66  KESTLHLVLRLRGG 79

>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 =  151 bits (382), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 73/78 (93%), Positives = 77/78 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITL+VE+SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLDVEASDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGGTM 78
          IQKESTLHLVLRLRGG M
Sbjct: 61 IQKESTLHLVLRLRGGGM 78

>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 = 71.2 bits (173), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 39/76 (51%), Positives = 43/76 (56%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLDVEASDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRGGGL 154
             S LHLVL LRGGG+
Sbjct: 63  KESTLHLVLRLRGGGM 78

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

Iteration: 1
 Score =  151 bits (382), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 74/76 (97%), Positives = 76/76 (100%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

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

Iteration: 1
 Score = 68.6 bits (166), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 41/74 (55%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 63  KESTLHLVLRLRGG 76

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

Iteration: 1
 Score =  151 bits (382), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 74/76 (97%), Positives = 76/76 (100%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

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

Iteration: 1
 Score = 70.1 bits (170), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 39/75 (52%), Positives = 42/75 (56%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRGGG 153
             S LHLVL LRGGG
Sbjct: 63  KESTLHLVLRLRGGG 77

>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 =  151 bits (381), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 74/76 (97%), Positives = 76/76 (100%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 21 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 80
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 81 IQKESTLHLVLRLRGG 96

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

Iteration: 1
 Score = 68.9 bits (167), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 41/80 (51%), Positives = 44/80 (55%), Gaps = 1/80 (1%)
Query: 74  RGGTM-IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTA 132
           RG  M I VKTLTGK                       GIPP QQRLI+AGKQL D +T 
Sbjct: 17  RGSHMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTL 76
Query: 133 RDYNIEGGSVLHLVLALRGG 152
            DYNI+  S LHLVL LRGG
Sbjct: 77  SDYNIQKESTLHLVLRLRGG 96

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

Iteration: 1
 Score =  150 bits (380), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 74/76 (97%), Positives = 76/76 (100%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 23 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 82
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 83 IQKESTLHLVLRLRGG 98

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

Iteration: 1
 Score = 67.8 bits (164), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 41/83 (49%), Positives = 45/83 (54%), Gaps = 1/83 (1%)
Query: 71  LRLRGGTM-IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADD 129
           L  +G  M I VKTLTGK                       GIPP QQRLI+AGKQL D 
Sbjct: 16  LYFQGRPMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDG 75
Query: 130 KTARDYNIEGGSVLHLVLALRGG 152
           +T  DYNI+  S LHLVL LRGG
Sbjct: 76  RTLSDYNIQKESTLHLVLRLRGG 98

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

Iteration: 1
 Score =  150 bits (378), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

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

Iteration: 1
 Score = 68.6 bits (166), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 41/74 (55%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 63  KESTLHLVLRLRGG 76

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

Iteration: 1
 Score =  149 bits (377), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 71/78 (91%), Positives = 76/78 (97%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           QIF KTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLI+AGKQLEDGRTL+DYN
Sbjct: 10 FQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLEDGRTLSDYN 69
Query: 61 IQKESTLHLVLRLRGGTM 78
          IQ+ESTLHLVLRLRGG+M
Sbjct: 70 IQRESTLHLVLRLRGGSM 87

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

Iteration: 1
 Score = 67.8 bits (164), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/80 (47%), Positives = 42/80 (52%)
Query: 75  GGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARD 134
           G   I  KTLTGK                       GIPP QQRLI+AGKQL D +T  D
Sbjct: 8   GEFQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLEDGRTLSD 67
Query: 135 YNIEGGSVLHLVLALRGGGL 154
           YNI+  S LHLVL LRGG +
Sbjct: 68  YNIQRESTLHLVLRLRGGSM 87

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

Iteration: 1
 Score =  149 bits (376), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLH VLRLRGG
Sbjct: 61 IQKESTLHSVLRLRGG 76

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

Iteration: 1
 Score = 66.2 bits (160), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 37/74 (50%), Positives = 40/74 (54%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRGG 152
             S LH VL LRGG
Sbjct: 63  KESTLHSVLRLRGG 76

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

Iteration: 1
 Score =  149 bits (375), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 3  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 62
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 63 IQKESTLHLVLRLRGG 78

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 41/74 (55%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 5   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 64
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 65  KESTLHLVLRLRGG 78

>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 =  149 bits (375), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 41/74 (55%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 63  KESTLHLVLRLRGG 76

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

Iteration: 1
 Score =  149 bits (375), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 63
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 64 IQKESTLHLVLRLRGG 79

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 41/74 (55%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 6   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 65
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 66  KESTLHLVLRLRGG 79

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

Iteration: 1
 Score =  148 bits (374), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 5  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 64
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 65 IQKESTLHLVLRLRGG 80

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

Iteration: 1
 Score = 69.3 bits (168), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 42/77 (54%)
Query: 76  GTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDY 135
           G  I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DY
Sbjct: 4   GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY 63
Query: 136 NIEGGSVLHLVLALRGG 152
           NI+  S LHLVL LRGG
Sbjct: 64  NIQKESTLHLVLRLRGG 80

>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 =  148 bits (374), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 2  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 61
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 62 IQKESTLHLVLRLRGG 77

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

Iteration: 1
 Score = 69.7 bits (169), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 42/77 (54%)
Query: 76  GTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDY 135
           G  I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DY
Sbjct: 1   GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY 60
Query: 136 NIEGGSVLHLVLALRGG 152
           NI+  S LHLVL LRGG
Sbjct: 61  NIQKESTLHLVLRLRGG 77

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

Iteration: 1
 Score =  148 bits (374), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 6  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 65
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 66 IQKESTLHLVLRLRGG 81

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

Iteration: 1
 Score = 70.1 bits (170), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 41/79 (51%), Positives = 45/79 (56%), Gaps = 1/79 (1%)
Query: 75  GGTM-IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTAR 133
           GG+M I VKTLTGK                       GIPP QQRLI+AGKQL D +T  
Sbjct: 3   GGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLS 62
Query: 134 DYNIEGGSVLHLVLALRGG 152
           DYNI+  S LHLVL LRGG
Sbjct: 63  DYNIQKESTLHLVLRLRGG 81

>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 =  148 bits (374), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 41/74 (55%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 63  KESTLHLVLRLRGG 76

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

Iteration: 1
 Score =  148 bits (374), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 63
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 64 IQKESTLHLVLRLRGG 79

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

Iteration: 1
 Score = 67.8 bits (164), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 41/74 (55%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 6   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 65
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 66  KESTLHLVLRLRGG 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 =  148 bits (373), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 69/76 (90%), Positives = 76/76 (100%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFV+TLTG+TITLEVESSDTIDNV+A+IQD+EGIPPDQQRLIFAG+QLEDGRTLADYN
Sbjct: 8  MQIFVRTLTGRTITLEVESSDTIDNVRARIQDREGIPPDQQRLIFAGRQLEDGRTLADYN 67
Query: 61 IQKESTLHLVLRLRGG 76
          IQ+ESTLHLVLRLRGG
Sbjct: 68 IQRESTLHLVLRLRGG 83

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

Iteration: 1
 Score = 65.5 bits (158), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 35/74 (47%), Positives = 41/74 (55%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I V+TLTG+                       GIPP QQRLI+AG+QL D +T  DYNI+
Sbjct: 10  IFVRTLTGRTITLEVESSDTIDNVRARIQDREGIPPDQQRLIFAGRQLEDGRTLADYNIQ 69
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 70  RESTLHLVLRLRGG 83

>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 =  148 bits (373), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 36  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 95
Query: 61  IQKESTLHLVLRLRGG 76
           IQKESTLHLVLRLRGG
Sbjct: 96  IQKESTLHLVLRLRGG 111

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

Iteration: 1
 Score = 67.4 bits (163), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 41/74 (55%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 38  IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 97
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 98  KESTLHLVLRLRGG 111

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

Iteration: 1
 Score =  148 bits (373), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 73/76 (96%), Positives = 75/76 (98%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 36  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 95
Query: 61  IQKESTLHLVLRLRGG 76
           IQKESTLHLVLRLRGG
Sbjct: 96  IQKESTLHLVLRLRGG 111

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

Iteration: 1
 Score = 67.4 bits (163), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 41/74 (55%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 38  IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 97
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 98  KESTLHLVLRLRGG 111

>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 =  147 bits (372), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 72/76 (94%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQ+ESTLHLVLRLRGG
Sbjct: 61 IQRESTLHLVLRLRGG 76

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

Iteration: 1
 Score = 67.8 bits (164), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 41/74 (55%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 63  RESTLHLVLRLRGG 76

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

Iteration: 1
 Score =  147 bits (372), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 72/76 (94%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAG+QLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGRQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

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

Iteration: 1
 Score = 67.4 bits (163), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 37/74 (50%), Positives = 41/74 (55%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AG+QL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGRQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 63  KESTLHLVLRLRGG 76

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

Iteration: 1
 Score =  147 bits (372), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 72/76 (94%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 63
Query: 61 IQKESTLHLVLRLRGG 76
          IQ+ESTLHLVLRLRGG
Sbjct: 64 IQRESTLHLVLRLRGG 79

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

Iteration: 1
 Score = 67.8 bits (164), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 41/74 (55%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 6   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 65
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 66  RESTLHLVLRLRGG 79

>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 =  147 bits (371), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 74/83 (89%), Positives = 78/83 (93%), Gaps = 2/83 (2%)
Query: 2   QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNI 61
           QIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYNI
Sbjct: 107 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNI 166
Query: 62  QKESTLHLVLRLRGG--TMIKVK 82
           QKESTLHLVLRLRGG  T  K++
Sbjct: 167 QKESTLHLVLRLRGGGQTFTKIR 189

>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 = 70.1 bits (170), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 40/78 (51%), Positives = 43/78 (55%)
Query: 76  GTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDY 135
           G  I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DY
Sbjct: 105 GGQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY 164
Query: 136 NIEGGSVLHLVLALRGGG 153
           NI+  S LHLVL LRGGG
Sbjct: 165 NIQKESTLHLVLRLRGGG 182

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

Iteration: 1
 Score =  147 bits (371), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 72/76 (94%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +QIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  LQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 41/74 (55%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 63  KESTLHLVLRLRGG 76

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

Iteration: 1
 Score =  147 bits (370), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 72/75 (96%), Positives = 74/75 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRG 75
          IQKESTLHLVLRLRG
Sbjct: 61 IQKESTLHLVLRLRG 75

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

Iteration: 1
 Score = 66.2 bits (160), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 37/73 (50%), Positives = 40/73 (54%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRG 151
             S LHLVL LRG
Sbjct: 63  KESTLHLVLRLRG 75

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

Iteration: 1
 Score =  147 bits (370), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 72/75 (96%), Positives = 74/75 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRG 75
          IQKESTLHLVLRLRG
Sbjct: 61 IQKESTLHLVLRLRG 75

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

Iteration: 1
 Score = 66.2 bits (160), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 37/73 (50%), Positives = 40/73 (54%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRG 151
             S LHLVL LRG
Sbjct: 63  KESTLHLVLRLRG 75

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

Iteration: 1
 Score =  147 bits (370), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 72/75 (96%), Positives = 74/75 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRG 75
          IQKESTLHLVLRLRG
Sbjct: 61 IQKESTLHLVLRLRG 75

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

Iteration: 1
 Score = 66.2 bits (160), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 37/73 (50%), Positives = 40/73 (54%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRG 151
             S LHLVL LRG
Sbjct: 63  KESTLHLVLRLRG 75

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

Iteration: 1
 Score =  147 bits (370), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 72/75 (96%), Positives = 74/75 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRG 75
          IQKESTLHLVLRLRG
Sbjct: 61 IQKESTLHLVLRLRG 75

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

Iteration: 1
 Score = 66.2 bits (160), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 37/73 (50%), Positives = 40/73 (54%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRG 151
             S LHLVL LRG
Sbjct: 63  KESTLHLVLRLRG 75

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

Iteration: 1
 Score =  147 bits (370), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAG+QLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGRQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQ+ESTLHLVLRLRGG
Sbjct: 61 IQRESTLHLVLRLRGG 76

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

Iteration: 1
 Score = 67.0 bits (162), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 37/74 (50%), Positives = 41/74 (55%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AG+QL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGRQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 63  RESTLHLVLRLRGG 76

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

Iteration: 1
 Score =  146 bits (369), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 72/76 (94%), Positives = 74/76 (97%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPP QQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPQQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

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

Iteration: 1
 Score = 68.6 bits (166), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 41/74 (55%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPQQQRLIFAGKQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 63  KESTLHLVLRLRGG 76

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

Iteration: 1
 Score =  146 bits (368), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 72/75 (96%), Positives = 74/75 (98%)
Query: 2  QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNI 61
          QIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYNI
Sbjct: 2  QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNI 61
Query: 62 QKESTLHLVLRLRGG 76
          QKESTLHLVLRLRGG
Sbjct: 62 QKESTLHLVLRLRGG 76

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 41/74 (55%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 63  KESTLHLVLRLRGG 76

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

Iteration: 1
 Score =  146 bits (368), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 72/75 (96%), Positives = 74/75 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 2  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 61
Query: 61 IQKESTLHLVLRLRG 75
          IQKESTLHLVLRLRG
Sbjct: 62 IQKESTLHLVLRLRG 76

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

Iteration: 1
 Score = 67.0 bits (162), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 38/76 (50%), Positives = 41/76 (53%)
Query: 76  GTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDY 135
           G  I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DY
Sbjct: 1   GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY 60
Query: 136 NIEGGSVLHLVLALRG 151
           NI+  S LHLVL LRG
Sbjct: 61  NIQKESTLHLVLRLRG 76

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

Iteration: 1
 Score =  145 bits (366), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 74/76 (97%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAG QLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGXQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQ+ESTLHLVLRLRGG
Sbjct: 61 IQRESTLHLVLRLRGG 76

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

Iteration: 1
 Score = 65.9 bits (159), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 37/74 (50%), Positives = 40/74 (54%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AG QL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGXQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 63  RESTLHLVLRLRGG 76

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

Iteration: 1
 Score =  144 bits (364), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 71/75 (94%), Positives = 74/75 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL++YN
Sbjct: 9  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSEYN 68
Query: 61 IQKESTLHLVLRLRG 75
          IQKESTLHLVLRLRG
Sbjct: 69 IQKESTLHLVLRLRG 83

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

Iteration: 1
 Score = 67.4 bits (163), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/78 (48%), Positives = 42/78 (53%)
Query: 74  RGGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTAR 133
           RG   I VKTLTGK                       GIPP QQRLI+AGKQL D +T  
Sbjct: 6   RGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLS 65
Query: 134 DYNIEGGSVLHLVLALRG 151
           +YNI+  S LHLVL LRG
Sbjct: 66  EYNIQKESTLHLVLRLRG 83

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

Iteration: 1
 Score =  144 bits (364), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 73/76 (96%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQ EDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQXEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKEST HLVLRLRGG
Sbjct: 61 IQKESTXHLVLRLRGG 76

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 36/74 (48%), Positives = 39/74 (52%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQ  D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQXEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRGG 152
             S  HLVL LRGG
Sbjct: 63  KESTXHLVLRLRGG 76

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

Iteration: 1
 Score =  144 bits (364), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 71/74 (95%), Positives = 73/74 (98%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 234 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 293
Query: 61  IQKESTLHLVLRLR 74
           IQKESTLHLVLRLR
Sbjct: 294 IQKESTLHLVLRLR 307

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

Iteration: 1
 Score = 65.1 bits (157), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 37/78 (47%), Positives = 41/78 (52%)
Query: 73  LRGGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTA 132
           + G   I VKTLTGK                       GIPP QQRLI+AGKQL D +T 
Sbjct: 230 ITGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL 289
Query: 133 RDYNIEGGSVLHLVLALR 150
            DYNI+  S LHLVL LR
Sbjct: 290 SDYNIQKESTLHLVLRLR 307

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

Iteration: 1
 Score =  144 bits (364), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 74/76 (97%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +QIFVKTLTGKTITLEVE SDTI+NVKAKIQDKE IPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  LQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEXIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

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

Iteration: 1
 Score = 65.5 bits (158), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 37/74 (50%), Positives = 40/74 (54%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                        IPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEXIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 63  KESTLHLVLRLRGG 76

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

Iteration: 1
 Score =  144 bits (364), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 74/76 (97%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +QIFVKTLTGKTITLEVE SDTI+NVKAKIQDKE IPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  LQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEQIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

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

Iteration: 1
 Score = 65.5 bits (158), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 37/74 (50%), Positives = 40/74 (54%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                        IPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEQIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 63  KESTLHLVLRLRGG 76

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

Iteration: 1
 Score =  143 bits (360), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 73/81 (90%), Positives = 75/81 (92%), Gaps = 5/81 (6%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG-----IPPDQQRLIFAGKQLEDGRT 55
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEG     IPPDQQRLIFAGKQLEDGRT
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGRWALAIPPDQQRLIFAGKQLEDGRT 60
Query: 56 LADYNIQKESTLHLVLRLRGG 76
          L+DYNIQKESTLHLVLRLRGG
Sbjct: 61 LSDYNIQKESTLHLVLRLRGG 81

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

Iteration: 1
 Score = 62.0 bits (149), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 29/42 (69%), Positives = 32/42 (76%)
Query: 111 GIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
            IPP QQRLI+AGKQL D +T  DYNI+  S LHLVL LRGG
Sbjct: 40  AIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 81

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

Iteration: 1
 Score =  143 bits (360), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 71/76 (93%), Positives = 73/76 (96%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGI  DQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIAADQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

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

Iteration: 1
 Score = 61.6 bits (148), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 36/74 (48%), Positives = 39/74 (52%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GI   QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIAADQQRLIFAGKQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 63  KESTLHLVLRLRGG 76

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

Iteration: 1
 Score =  142 bits (359), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 70/73 (95%), Positives = 72/73 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRL 73
          IQKESTLHLVLRL
Sbjct: 61 IQKESTLHLVLRL 73

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

Iteration: 1
 Score = 62.0 bits (149), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 35/71 (49%), Positives = 38/71 (53%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLAL 149
             S LHLVL L
Sbjct: 63  KESTLHLVLRL 73

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

Iteration: 1
 Score =  142 bits (358), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 66/76 (86%), Positives = 74/76 (97%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQ+F+KTLTGKT+T+EVE SDT++N KAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQVFLKTLTGKTVTIEVEPSDTVENFKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKEST+HLVLRLRGG
Sbjct: 61 IQKESTIHLVLRLRGG 76

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

Iteration: 1
 Score = 65.9 bits (159), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 35/72 (48%), Positives = 40/72 (55%)
Query: 81  VKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIEGG 140
           +KTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+  
Sbjct: 5   LKTLTGKTVTIEVEPSDTVENFKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKE 64
Query: 141 SVLHLVLALRGG 152
           S +HLVL LRGG
Sbjct: 65  STIHLVLRLRGG 76

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

Iteration: 1
 Score =  142 bits (357), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 73/83 (87%), Positives = 75/83 (90%), Gaps = 7/83 (8%)
Query: 1  MQIFVKTLT-------GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDG 53
          MQIFVKTLT       GKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDG
Sbjct: 1  MQIFVKTLTQVRELVGGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDG 60
Query: 54 RTLADYNIQKESTLHLVLRLRGG 76
          RTL+DYNIQKESTLHLVLRLRGG
Sbjct: 61 RTLSDYNIQKESTLHLVLRLRGG 83

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

Iteration: 1
 Score = 63.9 bits (154), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 30/42 (71%), Positives = 33/42 (78%)
Query: 111 GIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
           GIPP QQRLI+AGKQL D +T  DYNI+  S LHLVL LRGG
Sbjct: 42  GIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 83

>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 =  141 bits (356), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 68/70 (97%), Positives = 70/70 (100%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLV 70
          IQKESTLHLV
Sbjct: 61 IQKESTLHLV 70

>pdb|3U5C|FF Chain f, The Structure Of The Eukaryotic Ribosome At 3.0 A Resolution. This Entry Contains Proteins Of The 40s Subunit, Ribosome A Length = 152

Iteration: 1
 Score = 58.9 bits (141), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 33/68 (48%), Positives = 36/68 (52%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLV 146
             S LHLV
Sbjct: 63  KESTLHLV 70

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

Iteration: 1
 Score =  141 bits (355), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 69/72 (95%), Positives = 71/72 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLR 72
          IQKESTLHLVLR
Sbjct: 61 IQKESTLHLVLR 72

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

Iteration: 1
 Score = 60.8 bits (146), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 34/69 (49%), Positives = 37/69 (53%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVL 147
             S LHLVL
Sbjct: 63  KESTLHLVL 71

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

Iteration: 1
 Score =  140 bits (353), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 65/76 (85%), Positives = 75/76 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQ+FVKTLTGKT+T+E+E SDT++N+KAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQLFVKTLTGKTLTVELEPSDTVENLKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          +QKEST+HLVLRLRGG
Sbjct: 61 LQKESTIHLVLRLRGG 76

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

Iteration: 1
 Score = 65.5 bits (158), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 35/72 (48%), Positives = 40/72 (55%)
Query: 81  VKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIEGG 140
           VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYN++  
Sbjct: 5   VKTLTGKTLTVELEPSDTVENLKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNLQKE 64
Query: 141 SVLHLVLALRGG 152
           S +HLVL LRGG
Sbjct: 65  STIHLVLRLRGG 76

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

Iteration: 1
 Score =  140 bits (353), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 69/76 (90%), Positives = 71/76 (93%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTG TITLEVESSDTIDNVK+KIQ   GIPPDQQ LIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGATITLEVESSDTIDNVKSKIQAAPGIPPDQQELIFAGKQLEDGRTLSDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 36/74 (48%), Positives = 39/74 (52%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTG                        GIPP QQ LI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGATITLEVESSDTIDNVKSKIQAAPGIPPDQQELIFAGKQLEDGRTLSDYNIQ 62
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 63  KESTLHLVLRLRGG 76

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

Iteration: 1
 Score =  140 bits (353), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 67/76 (88%), Positives = 74/76 (97%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE +D+ID +KAKIQ+KEGIPPDQQRLIFAGKQLE+G+TL+DYN
Sbjct: 4  MQIFVKTLTGKTITLEVEPNDSIDAIKAKIQEKEGIPPDQQRLIFAGKQLEEGKTLSDYN 63
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 64 IQKESTLHLVLRLRGG 79

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

Iteration: 1
 Score = 67.4 bits (163), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 41/74 (55%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL + KT  DYNI+
Sbjct: 6   IFVKTLTGKTITLEVEPNDSIDAIKAKIQEKEGIPPDQQRLIFAGKQLEEGKTLSDYNIQ 65
Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 66  KESTLHLVLRLRGG 79

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

Iteration: 1
 Score =  140 bits (352), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 68/74 (91%), Positives = 71/74 (95%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFV TL+GK ITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 18 MQIFVNTLSGKHITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 77
Query: 61 IQKESTLHLVLRLR 74
          IQKESTLHLVLRLR
Sbjct: 78 IQKESTLHLVLRLR 91

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

Iteration: 1
 Score = 64.7 bits (156), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 36/77 (46%), Positives = 40/77 (51%)
Query: 74  RGGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTAR 133
           RG   I V TL+GK                       GIPP QQRLI+AGKQL D +T  
Sbjct: 15  RGSMQIFVNTLSGKHITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLS 74
Query: 134 DYNIEGGSVLHLVLALR 150
           DYNI+  S LHLVL LR
Sbjct: 75  DYNIQKESTLHLVLRLR 91

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

Iteration: 1
 Score =  140 bits (352), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 66/76 (86%), Positives = 74/76 (97%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +Q+F+KTLTGKT T+E+E SDTI+N+KAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 10 LQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 69
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 70 IQKESTLHLVLRLRGG 85

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

Iteration: 1
 Score = 71.6 bits (174), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 39/79 (49%), Positives = 44/79 (55%)
Query: 76  GTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDY 135
           G  + +KTLTGK                       GIPP QQRLI+AGKQL D +T  DY
Sbjct: 9   GLQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY 68
Query: 136 NIEGGSVLHLVLALRGGGL 154
           NI+  S LHLVL LRGGGL
Sbjct: 69  NIQKESTLHLVLRLRGGGL 87

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

Iteration: 1
 Score =  139 bits (350), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 73/84 (86%), Positives = 75/84 (89%), Gaps = 8/84 (9%)
Query: 1  MQIFVKTLTG--------KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLED 52
          MQIFVKTLTG        KTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLED
Sbjct: 1  MQIFVKTLTGGGGGGGGGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLED 60
Query: 53 GRTLADYNIQKESTLHLVLRLRGG 76
          GRTL+DYNIQKESTLHLVLRLRGG
Sbjct: 61 GRTLSDYNIQKESTLHLVLRLRGG 84

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 30/42 (71%), Positives = 33/42 (78%)
Query: 111 GIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
           GIPP QQRLI+AGKQL D +T  DYNI+  S LHLVL LRGG
Sbjct: 43  GIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 84

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

Iteration: 1
 Score =  139 bits (350), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 73/84 (86%), Positives = 75/84 (89%), Gaps = 8/84 (9%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG--------IPPDQQRLIFAGKQLED 52
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEG        IPPDQQRLIFAGKQLED
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGGGGGGGGGIPPDQQRLIFAGKQLED 60
Query: 53 GRTLADYNIQKESTLHLVLRLRGG 76
          GRTL+DYNIQKESTLHLVLRLRGG
Sbjct: 61 GRTLSDYNIQKESTLHLVLRLRGG 84

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

Iteration: 1
 Score = 62.0 bits (149), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 29/41 (70%), Positives = 32/41 (78%)
Query: 112 IPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
           IPP QQRLI+AGKQL D +T  DYNI+  S LHLVL LRGG
Sbjct: 44  IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 84

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

Iteration: 1
 Score =  139 bits (349), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 68/74 (91%), Positives = 70/74 (94%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFV TLTG  ITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 18 MQIFVNTLTGTHITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 77
Query: 61 IQKESTLHLVLRLR 74
          IQKESTLHLVLRLR
Sbjct: 78 IQKESTLHLVLRLR 91

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

Iteration: 1
 Score = 63.5 bits (153), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 36/77 (46%), Positives = 39/77 (50%)
Query: 74  RGGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTAR 133
           RG   I V TLTG                        GIPP QQRLI+AGKQL D +T  
Sbjct: 15  RGSMQIFVNTLTGTHITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLS 74
Query: 134 DYNIEGGSVLHLVLALR 150
           DYNI+  S LHLVL LR
Sbjct: 75  DYNIQKESTLHLVLRLR 91

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

Iteration: 1
 Score =  136 bits (342), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 67/76 (88%), Positives = 69/76 (90%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVK LTGKT TLEVE SDTI+NVKAKIQDK G PPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 2  MQIFVKCLTGKTNTLEVEPSDTIENVKAKIQDKIGYPPDQQRLIFAGKQLEDGRTLSDYN 61
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLH V RLRGG
Sbjct: 62 IQKESTLHCVRRLRGG 77

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

Iteration: 1
 Score = 60.8 bits (146), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 34/74 (45%), Positives = 37/74 (50%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VK LTGK                       G PP QQRLI+AGKQL D +T  DYNI+
Sbjct: 4   IFVKCLTGKTNTLEVEPSDTIENVKAKIQDKIGYPPDQQRLIFAGKQLEDGRTLSDYNIQ 63
Query: 139 GGSVLHLVLALRGG 152
             S LH V  LRGG
Sbjct: 64  KESTLHCVRRLRGG 77

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

Iteration: 1
 Score =  133 bits (334), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 65/74 (87%), Positives = 70/74 (94%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQ+L+FA KQLEDGRTL+DYN
Sbjct: 3  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQKLLFARKQLEDGRTLSDYN 62
Query: 61 IQKESTLHLVLRLR 74
          I KES L+LVLRLR
Sbjct: 63 IHKESFLYLVLRLR 76

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 33/76 (43%), Positives = 38/76 (50%)
Query: 75  GGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARD 134
           G   I VKTLTGK                       GIPP QQ+L++A KQL D +T  D
Sbjct: 1   GSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQKLLFARKQLEDGRTLSD 60
Query: 135 YNIEGGSVLHLVLALR 150
           YNI   S L+LVL LR
Sbjct: 61  YNIHKESFLYLVLRLR 76

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

Iteration: 1
 Score =  128 bits (321), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 63/67 (94%), Positives = 65/67 (97%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 63
Query: 61 IQKESTL 67
          IQK STL
Sbjct: 64 IQKWSTL 70

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 33/65 (50%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK                       GIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 6   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 65
Query: 139 GGSVL 143
             S L
Sbjct: 66  KWSTL 70

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

Iteration: 1
 Score =  127 bits (319), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 60/76 (78%), Positives = 68/76 (89%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTIT++V+ +DT+  VKAKI DKEGIPPDQQRLIF GKQLED   ++DYN
Sbjct: 6  MQIFVKTLTGKTITIDVDHADTVGAVKAKIYDKEGIPPDQQRLIFGGKQLEDSNAMSDYN 65
Query: 61 IQKESTLHLVLRLRGG 76
          +QKESTLHLVLRLRGG
Sbjct: 66 VQKESTLHLVLRLRGG 81

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

Iteration: 1
 Score = 63.9 bits (154), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 36/78 (46%), Positives = 39/78 (50%)
Query: 75  GGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARD 134
           G   I VKTLTGK                       GIPP QQRLI+ GKQL D     D
Sbjct: 4   GSMQIFVKTLTGKTITIDVDHADTVGAVKAKIYDKEGIPPDQQRLIFGGKQLEDSNAMSD 63
Query: 135 YNIEGGSVLHLVLALRGG 152
           YN++  S LHLVL LRGG
Sbjct: 64  YNVQKESTLHLVLRLRGG 81

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

Iteration: 1
 Score =  125 bits (314), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 64/76 (84%), Positives = 67/76 (88%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVK  TGKT TLEVE SDTI+NVKAKIQDK GIPPDQQ LIFAGK+LEDGRTL+DYN
Sbjct: 3  MQIFVKFRTGKTYTLEVEPSDTIENVKAKIQDKLGIPPDQQWLIFAGKRLEDGRTLSDYN 62
Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTL  V RLRGG
Sbjct: 63 IQKESTLRGVRRLRGG 78

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 32/78 (41%), Positives = 36/78 (46%)
Query: 75  GGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARD 134
           G   I VK  TGK                       GIPP QQ LI+AGK+L D +T  D
Sbjct: 1   GSMQIFVKFRTGKTYTLEVEPSDTIENVKAKIQDKLGIPPDQQWLIFAGKRLEDGRTLSD 60
Query: 135 YNIEGGSVLHLVLALRGG 152
           YNI+  S L  V  LRGG
Sbjct: 61  YNIQKESTLRGVRRLRGG 78

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

Iteration: 1
 Score =  112 bits (281), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 54/66 (81%), Positives = 58/66 (87%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M+I VKTL G+TI LEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 4  MRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 63
Query: 61 IQKEST 66
          I   S 
Sbjct: 64 IHNHSA 69

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/63 (42%), Positives = 30/63 (47%)
Query: 79  IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTL G+                       GIPP QQRLI+AGKQL D +T  DYNI 
Sbjct: 6   IVVKTLMGRTIILEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIH 65
Query: 139 GGS 141
             S
Sbjct: 66  NHS 68

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

Iteration: 1
 Score = 99.8 bits (247), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 49/51 (96%), Positives = 50/51 (98%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE 51
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLE
Sbjct: 3  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLE 53

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

Iteration: 1
 Score = 99.4 bits (246), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 48/76 (63%), Positives = 60/76 (78%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +DTID +K ++++KEGIPP QQRLI+AGKQL D +T  DYN
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLIYAGKQLADDKTAKDYN 60
Query: 61 IQKESTLHLVLRLRGG 76
          I+  S LHLVL LRGG
Sbjct: 61 IEGGSVLHLVLALRGG 76

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

Iteration: 1
 Score = 95.5 bits (236), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 50/75 (66%), Positives = 52/75 (69%)
Query: 78  MIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNI 137
           +IKVKTLTGK                       GIPPVQQRLIYAGKQLADDKTA+DYNI
Sbjct: 2   LIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLIYAGKQLADDKTAKDYNI 61
Query: 138 EGGSVLHLVLALRGG 152
           EGGSVLHLVLALRGG
Sbjct: 62  EGGSVLHLVLALRGG 76

>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 = 95.1 bits (235), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 44/76 (57%), Positives = 59/76 (77%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ+ D +T ADY 
Sbjct: 13 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK 72
Query: 61 IQKESTLHLVLRLRGG 76
          I   S LHLVLRLRGG
Sbjct: 73 ILGGSVLHLVLRLRGG 88

>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 = 79.3 bits (194), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 45/79 (56%), Positives = 49/79 (62%), Gaps = 1/79 (1%)
Query: 75  GGTM-IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTAR 133
           GG+M IKVKTLTGK                       GIPP QQRLIY+GKQ+ D+KTA 
Sbjct: 10  GGSMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAA 69
Query: 134 DYNIEGGSVLHLVLALRGG 152
           DY I GGSVLHLVL LRGG
Sbjct: 70  DYKILGGSVLHLVLRLRGG 88

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

Iteration: 1
 Score = 93.2 bits (230), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 43/76 (56%), Positives = 59/76 (77%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ+ D +T ADY 
Sbjct: 13 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK 72
Query: 61 IQKESTLHLVLRLRGG 76
          I   S LHLVL+LRGG
Sbjct: 73 ILGGSVLHLVLQLRGG 88

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

Iteration: 1
 Score = 79.3 bits (194), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 45/79 (56%), Positives = 49/79 (62%), Gaps = 1/79 (1%)
Query: 75  GGTM-IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTAR 133
           GG+M IKVKTLTGK                       GIPP QQRLIY+GKQ+ D+KTA 
Sbjct: 10  GGSMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAA 69
Query: 134 DYNIEGGSVLHLVLALRGG 152
           DY I GGSVLHLVL LRGG
Sbjct: 70  DYKILGGSVLHLVLQLRGG 88

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

Iteration: 1
 Score = 92.4 bits (228), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 43/76 (56%), Positives = 58/76 (76%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ+ D +T ADY 
Sbjct: 3  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK 62
Query: 61 IQKESTLHLVLRLRGG 76
          I   S LHLVL LRGG
Sbjct: 63 ILGGSVLHLVLALRGG 78

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

Iteration: 1
 Score = 80.5 bits (197), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 43/78 (55%), Positives = 47/78 (60%)
Query: 75  GGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARD 134
              +IKVKTLTGK                       GIPP QQRLIY+GKQ+ D+KTA D
Sbjct: 1   AAMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAAD 60
Query: 135 YNIEGGSVLHLVLALRGG 152
           Y I GGSVLHLVLALRGG
Sbjct: 61  YKILGGSVLHLVLALRGG 78

>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 = 92.0 bits (227), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 43/76 (56%), Positives = 58/76 (76%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ+ D +T ADY 
Sbjct: 6  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK 65
Query: 61 IQKESTLHLVLRLRGG 76
          I   S LHLVL LRGG
Sbjct: 66 ILGGSVLHLVLALRGG 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 = 81.6 bits (200), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 46/79 (58%), Positives = 50/79 (63%), Gaps = 1/79 (1%)
Query: 75  GGTM-IKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTAR 133
           GG+M IKVKTLTGK                       GIPP QQRLIY+GKQ+ D+KTA 
Sbjct: 3   GGSMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAA 62
Query: 134 DYNIEGGSVLHLVLALRGG 152
           DY I GGSVLHLVLALRGG
Sbjct: 63  DYKILGGSVLHLVLALRGG 81

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

Iteration: 1
 Score = 92.0 bits (227), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 43/76 (56%), Positives = 58/76 (76%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ+ D +T ADY 
Sbjct: 2  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK 61
Query: 61 IQKESTLHLVLRLRGG 76
          I   S LHLVL LRGG
Sbjct: 62 ILGGSVLHLVLALRGG 77

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

Iteration: 1
 Score = 80.5 bits (197), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 43/75 (57%), Positives = 47/75 (62%)
Query: 78  MIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNI 137
           +IKVKTLTGK                       GIPP QQRLIY+GKQ+ D+KTA DY I
Sbjct: 3   LIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKI 62
Query: 138 EGGSVLHLVLALRGG 152
            GGSVLHLVLALRGG
Sbjct: 63  LGGSVLHLVLALRGG 77

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

Iteration: 1
 Score = 92.0 bits (227), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 43/76 (56%), Positives = 58/76 (76%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ+ D +T ADY 
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK 60
Query: 61 IQKESTLHLVLRLRGG 76
          I   S LHLVL LRGG
Sbjct: 61 ILGGSVLHLVLALRGG 76

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

Iteration: 1
 Score = 80.5 bits (197), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 43/75 (57%), Positives = 47/75 (62%)
Query: 78  MIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNI 137
           +IKVKTLTGK                       GIPP QQRLIY+GKQ+ D+KTA DY I
Sbjct: 2   LIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKI 61
Query: 138 EGGSVLHLVLALRGG 152
            GGSVLHLVLALRGG
Sbjct: 62  LGGSVLHLVLALRGG 76

>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 = 92.0 bits (227), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 43/76 (56%), Positives = 58/76 (76%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ+ D +T ADY 
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK 60
Query: 61 IQKESTLHLVLRLRGG 76
          I   S LHLVL LRGG
Sbjct: 61 ILGGSVLHLVLALRGG 76

>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 = 82.0 bits (201), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 44/76 (57%), Positives = 48/76 (63%)
Query: 78  MIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNI 137
           +IKVKTLTGK                       GIPP QQRLIY+GKQ+ D+KTA DY I
Sbjct: 2   LIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKI 61
Query: 138 EGGSVLHLVLALRGGG 153
            GGSVLHLVLALRGGG
Sbjct: 62  LGGSVLHLVLALRGGG 77

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

Iteration: 1
 Score = 92.0 bits (227), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 43/76 (56%), Positives = 58/76 (76%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ+ D +T ADY 
Sbjct: 7  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK 66
Query: 61 IQKESTLHLVLRLRGG 76
          I   S LHLVL LRGG
Sbjct: 67 ILGGSVLHLVLALRGG 82

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

Iteration: 1
 Score = 80.5 bits (197), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 43/75 (57%), Positives = 47/75 (62%)
Query: 78  MIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARDYNI 137
           +IKVKTLTGK                       GIPP QQRLIY+GKQ+ D+KTA DY I
Sbjct: 8   LIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKI 67
Query: 138 EGGSVLHLVLALRGG 152
            GGSVLHLVLALRGG
Sbjct: 68  LGGSVLHLVLALRGG 82

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

Iteration: 1
 Score = 90.1 bits (222), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 42/74 (56%), Positives = 56/74 (75%)
Query: 3  IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQ 62
          I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ  D +T ADY I 
Sbjct: 8  IKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQXNDEKTAADYKIX 67
Query: 63 KESTLHLVLRLRGG 76
            S LHLVL LRGG
Sbjct: 68 GGSVLHLVLALRGG 81

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

Iteration: 1
 Score = 80.9 bits (198), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 44/78 (56%), Positives = 47/78 (60%)
Query: 75  GGTMIKVKTLTGKXXXXXXXXXXXXXXXXXXXXXXXGIPPVQQRLIYAGKQLADDKTARD 134
           G  +IKVKTLTGK                       GIPP QQRLIY+GKQ  D+KTA D
Sbjct: 4   GSXLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQXNDEKTAAD 63
Query: 135 YNIEGGSVLHLVLALRGG 152
           Y I GGSVLHLVLALRGG
Sbjct: 64  YKIXGGSVLHLVLALRGG 81

>pdb|2DZI|A Chain A, 2dziSOLUTION STRUCTURE OF THE N-Terminal Ubiquitin-Like Domain In Human Ubiquitin-Like Protein 4a (Gdx) Length = 81

Iteration: 1
 Score = 62.0 bits (149), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 29/72 (40%), Positives = 46/72 (63%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQ+ VK L G+  +L+V   + +  +K  + +K  +P  QQRL+F GK L DG+ L+DY+
Sbjct: 8  MQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLNVPVRQQRLLFKGKALADGKRLSDYS 67
Query: 61 IQKESTLHLVLR 72
          I   S L+LV++
Sbjct: 68 IGPNSKLNLVVK 79

>pdb|2KNB|A Chain A, Solution Nmr Structure Of The Parkin Ubl Domain In Complex With The Endophilin-A1 Sh3 Domain Length = 81

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 48/72 (66%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M +FV+  +     +EV+S  +I  +K  +  ++G+P DQ R+IFAGK+L++  T+ + +
Sbjct: 6  MIVFVRFNSSYGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELQNHLTVQNCD 65
Query: 61 IQKESTLHLVLR 72
          ++++S +H+V R
Sbjct: 66 LEQQSIVHIVQR 77

>pdb|2ZEQ|A Chain A, Crystal Structure Of Ubiquitin-Like Domain Of Murine Parkin Length = 78

Iteration: 1
 Score = 54.3 bits (129), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 48/74 (64%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M +FV+  +     +EV+S  +I  +K  +  ++G+P DQ R+IFAGK+L +  T+ + +
Sbjct: 3  MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVIFAGKELPNHLTVQNCD 62
Query: 61 IQKESTLHLVLRLR 74
          ++++S +H+V R R
Sbjct: 63 LEQQSIVHIVQRPR 76

>pdb|1IYF|A Chain A, Solution Structure Of Ubiquitin-Like Domain Of Human Parkin Length = 81

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 46/72 (63%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M +FV+  +     +EV+S  +I  +K  +  ++G+P DQ R+IFAGK+L +  T+ + +
Sbjct: 6  MIVFVRFNSSHGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELRNDWTVQNCD 65
Query: 61 IQKESTLHLVLR 72
          + ++S +H+V R
Sbjct: 66 LDQQSIVHIVQR 77

>pdb|3B1L|X Chain X, Crystal Structure Of Parkin Ubiquitin-Like Domain R33q Mutant Length = 76

Iteration: 1
 Score = 53.5 bits (127), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 48/74 (64%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M +FV+  +     +EV+S  +I  +K  +  ++G+P DQ R+IFAGK+L +  T+ + +
Sbjct: 1  MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKQQGVPADQLRVIFAGKELPNHLTVQNCD 60
Query: 61 IQKESTLHLVLRLR 74
          ++++S +H+V R R
Sbjct: 61 LEQQSIVHIVQRPR 74

>pdb|3RT3|B Chain B, Complex Of Influenza Virus Protein With Host Anti-Viral Factor Length = 159

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 44/76 (57%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           + I V+   G++ T EV  + T+ ++K ++   EG+  D   L F GK LED   L +Y 
Sbjct: 82  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 141
Query: 61  IQKESTLHLVLRLRGG 76
           ++  ST+ + LRLRGG
Sbjct: 142 LKPLSTVFMNLRLRGG 157

>pdb|3SDL|C Chain C, Crystal Structure Of Human Isg15 In Complex With Ns1 N-Terminal Region From Influenza B Virus, Northeast Structural Genomics Consortium Target Ids Hx6481, Hr2873, And Or2 Length = 164

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 44/76 (57%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           + I V+   G++ T EV  + T+ ++K ++   EG+  D   L F GK LED   L +Y 
Sbjct: 89  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 148
Query: 61  IQKESTLHLVLRLRGG 76
           ++  ST+ + LRLRGG
Sbjct: 149 LKPLSTVFMNLRLRGG 164

>pdb|3R66|C Chain C, Crystal Structure Of Human Isg15 In Complex With Ns1 N-Terminal Region From Influenza Virus B, Northeast Structural Genomics Consortium Target Ids Hx6481, Hr2873, And Or2 Length = 164

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 44/76 (57%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           + I V+   G++ T EV  + T+ ++K ++   EG+  D   L F GK LED   L +Y 
Sbjct: 89  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 148
Query: 61  IQKESTLHLVLRLRGG 76
           ++  ST+ + LRLRGG
Sbjct: 149 LKPLSTVFMNLRLRGG 164

>pdb|2HJ8|A Chain A, Solution Nmr Structure Of The C-Terminal Domain Of The Interferon Alpha-Inducible Isg15 Protein From Homo Sapiens. Northeast Structural Genomics Target Hr2873b Length = 88

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 44/76 (57%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + I V+   G++ T EV  + T+ ++K ++   EG+  D   L F GK LED   L +Y 
Sbjct: 5  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 64
Query: 61 IQKESTLHLVLRLRGG 76
          ++  ST+ + LRLRGG
Sbjct: 65 LKPLSTVFMNLRLRGG 80

>pdb|2L7R|A Chain A, Solution Nmr Structure Of N-Terminal Ubiquitin-Like Domain Of Fubi, A Ribosomal Protein S30 Precursor From Homo Sapiens. Northeast Structural Genomics Consortium (Nesg) Target Hr6166 Length = 93

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 2/76 (2%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQ+FV+    +  T EV   +T+  +KA +   EGI P+ Q ++ AG  LED  TL    
Sbjct: 20 MQLFVRAQ--ELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAGAPLEDEATLGQCG 77
Query: 61 IQKESTLHLVLRLRGG 76
          ++  +TL +  R+ GG
Sbjct: 78 VEALTTLEVAGRMLGG 93

>pdb|2FAZ|A Chain A, Ubiquitin-Like Domain Of Human Nuclear Zinc Finger Protein Np95 Length = 78

Iteration: 1
 Score = 50.4 bits (119), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 47/74 (63%), Gaps = 2/74 (2%)
Query: 1  MQIFVKTLTGK-TITLEVESSDT-IDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLAD 58
          M I V+T+ G+ T T++  S  T ++ ++ KIQ+   + P  QRL + GKQ+EDG TL D
Sbjct: 3  MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFD 62
Query: 59 YNIQKESTLHLVLR 72
          Y ++   T+ L++R
Sbjct: 63 YEVRLNDTIQLLVR 76

>pdb|3PSE|B Chain B, Structure Of A Viral Otu Domain Protease Bound To Interferon- Stimulated Gene 15 (Isg15) Length = 156

Iteration: 1
 Score = 50.1 bits (118), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 27/75 (36%), Positives = 43/75 (57%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           + I V+   G++ T EV  + T+ ++K ++   EG+  D   L F GK LED   L +Y 
Sbjct: 82  LNILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 141
Query: 61  IQKESTLHLVLRLRG 75
           ++  ST+ + LRLRG
Sbjct: 142 LKPLSTVFMNLRLRG 156

>pdb|3PHX|B Chain B, Otu Domain Of Crimean Congo Hemorrhagic Fever Virus In Complex With Isg15 Length = 79

Iteration: 1
 Score = 49.7 bits (117), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 27/75 (36%), Positives = 43/75 (57%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + I V+   G++ T EV  + T+ ++K ++   EG+  D   L F GK LED   L +Y 
Sbjct: 5  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 64
Query: 61 IQKESTLHLVLRLRG 75
          ++  ST+ + LRLRG
Sbjct: 65 LKPLSTVFMNLRLRG 79

>pdb|1WY8|A Chain A, Solution Structure Of The N-Terminal Ubiquitin-Like Domain In Human Np95ICBP90-Like Ring Finger Protein (Nirf) Length = 89

Iteration: 1
 Score = 49.3 bits (116), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 29/78 (37%), Positives = 46/78 (58%), Gaps = 2/78 (2%)
Query: 1  MQIFVKTLTG-KTITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLAD 58
          M I V+T+ G KT T+E V    TI+ ++ ++     + P+ QRL + GKQLE+G TL D
Sbjct: 8  MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFD 67
Query: 59 YNIQKESTLHLVLRLRGG 76
          Y++     + L++R   G
Sbjct: 68 YDVGLNDIIQLLVRPDSG 85

>pdb|1ZKH|A Chain A, Solution Structure Of A Human Ubiquitin-Like Domain In Sf3a1 Length = 86

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/68 (30%), Positives = 39/68 (57%)
Query: 8  LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTL 67
          L G+ +   +  +D +  +K KI +  G+P  +Q+L + G  ++D  +LA YN+   + +
Sbjct: 19 LNGQVLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMANGAVI 78
Query: 68 HLVLRLRG 75
          HL L+ RG
Sbjct: 79 HLALKERG 86

>pdb|1Z2M|A Chain A, Crystal Structure Of Isg15, The Interferon-Induced Ubiquitin Cross Reactive Protein Length = 155

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 42/74 (56%)
Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           + I V+   G++ T EV  + T+ ++K ++   EG+  D   L F GK LED   L +Y 
Sbjct: 82  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 141
Query: 61  IQKESTLHLVLRLR 74
           ++  ST+ + LRLR
Sbjct: 142 LKPLSTVFMNLRLR 155

>pdb|1WH3|A Chain A, Solution Structure Of C-Terminal Ubiquitin Like Domain Of Human 2'-5'-Oligoadenylate Synthetase-Like Protain (P59 Oasl) Length = 87

Iteration: 1
 Score = 47.0 bits (110), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 39/69 (56%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +Q+FVK   G +    +  +  I  +K +I+D++G+P  QQ+L F G+ L+D   L  Y 
Sbjct: 8  IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGLGIYG 67
Query: 61 IQKESTLHL 69
          IQ   TL L
Sbjct: 68 IQDSDTLIL 76

>pdb|1WX9|A Chain A, Solution Structure Of The N-Terminal Ubiquitin-Like Domain In The Human Bat3 Protein Length = 86

Iteration: 1
 Score = 46.6 bits (109), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKTL  +T T  V +   +   K  I     IP ++QRLI+ G+ L+D + L +YN
Sbjct: 8  LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYN 67
Query: 61 IQKESTLHLVLRLRGG 76
          +  +  +HLV R   G
Sbjct: 68 VGGK-VIHLVERAPSG 82

>pdb|1WX9|A Chain A, Solution Structure Of The N-Terminal Ubiquitin-Like Domain In The Human Bat3 Protein Length = 86

Iteration: 1
 Score = 42.7 bits (99), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 20/35 (57%), Positives = 26/35 (74%), Gaps = 1/35 (2%)
Query: 112 IPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLV 146
           IP  +QRLIY G+ L DDK  ++YN+ GG V+HLV
Sbjct: 43  IPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVIHLV 76

>pdb|1WE7|A Chain A, Solution Structure Of Ubiquitin-Like Domain In Sf3a120 Length = 115

Iteration: 1
 Score = 46.2 bits (108), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 21/69 (30%), Positives = 39/69 (56%)
Query: 8   LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTL 67
           L G+ +   +  +D +  +K KI +  G+P  +Q+L + G  ++D  +LA YN+   + +
Sbjct: 43  LNGQGLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMASGAVI 102
Query: 68  HLVLRLRGG 76
           HL L+ R G
Sbjct: 103 HLALKERSG 111

>pdb|4DWF|A Chain A, Crystal Structure Of A Hla-B Associated Transcript 3 (Bat3) From Homo Sapiens At 1.80 A Resolution Length = 90

Iteration: 1
 Score = 46.2 bits (108), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKTL  +T T  V +   +   K  I     IP ++QRLI+ G+ L+D + L +YN
Sbjct: 6  LEVLVKTLDSQTRTFIVGAQXNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYN 65
Query: 61 IQKESTLHLVLR 72
          +  +  +HLV R
Sbjct: 66 VGGK-VIHLVER 76

>pdb|4DWF|A Chain A, Crystal Structure Of A Hla-B Associated Transcript 3 (Bat3) From Homo Sapiens At 1.80 A Resolution Length = 90

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/36 (55%), Positives = 26/36 (72%), Gaps = 1/36 (2%)
Query: 111 GIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLV 146
            IP  +QRLIY G+ L DDK  ++YN+ GG V+HLV
Sbjct: 40  SIPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVIHLV 74

>pdb|2BWE|S Chain S, The Crystal Structure Of The Complex Between The Uba And Ubl Domains Of Dsk2 Length = 77

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 20/36 (55%), Positives = 25/36 (69%)
Query: 111 GIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLV 146
           GIP   QRLIY+GK L DD+T   Y+I+ G  +HLV
Sbjct: 38  GIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLV 73

>pdb|3M63|B Chain B, Crystal Structure Of Ufd2 In Complex With The Ubiquitin-Like (Ubl) Domain Of Dsk2 Length = 101

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/36 (55%), Positives = 25/36 (69%)
Query: 111 GIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLV 146
           GIP   QRLIY+GK L DD+T   Y+I+ G  +HLV
Sbjct: 62  GIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLV 97

>pdb|4EEW|A Chain A, Crystal Structure Of The Ubl Domain Of Bag6 Length = 88

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKTL  +T T  V +   +   K  I     IP ++QRLI+ G+ L+D + L +YN
Sbjct: 18 LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYN 77
Query: 61 IQKESTLHLVLR 72
          +  +  +HLV R
Sbjct: 78 VGGK-VIHLVER 88

>pdb|4EEW|A Chain A, Crystal Structure Of The Ubl Domain Of Bag6 Length = 88

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 20/36 (55%), Positives = 26/36 (72%), Gaps = 1/36 (2%)
Query: 111 GIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLV 146
            IP  +QRLIY G+ L DDK  ++YN+ GG V+HLV
Sbjct: 52  SIPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVIHLV 86

>pdb|1TTN|A Chain A, Solution Structure Of The Ubiquitin-Like Domain Of Human Dc- Ubp From Dendritic Cells Length = 106

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/71 (29%), Positives = 40/71 (56%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           Q+ ++  TGK + L V S+DT+ ++K ++   EG+ P  QR  F+G+ L D     +  
Sbjct: 24 CQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKFEELK 83
Query: 61 IQKESTLHLVL 71
          I K+  + +++
Sbjct: 84 IPKDYVVQVIV 94

>pdb|1P1A|A Chain A, Nmr Structure Of Ubiquitin-Like Domain Of Hhr23b Length = 85

Iteration: 1
 Score = 42.7 bits (99), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 23/68 (33%), Positives = 42/68 (61%), Gaps = 3/68 (4%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLA 57
          MQ+ +KTL  +T  ++++  +T+  +K KI+ ++G    P   Q+LI+AGK L D   L 
Sbjct: 4  MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 63
Query: 58 DYNIQKES 65
          +Y I +++
Sbjct: 64 EYKIDEKN 71

>pdb|1UEL|A Chain A, Solution Structure Of Ubiquitin-Like Domain Of Hhr23b Complexed With Ubiquitin-Interacting Motif Of Proteasome Subunit S5a Length = 95

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/68 (33%), Positives = 41/68 (60%), Gaps = 3/68 (4%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQD---KEGIPPDQQRLIFAGKQLEDGRTLA 57
          MQ+ +KTL  +T  ++++  +T+  +K KI+    K+  P   Q+LI+AGK L D   L 
Sbjct: 1  MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 60
Query: 58 DYNIQKES 65
          +Y I +++
Sbjct: 61 EYKIDEKN 68

>pdb|2WYQ|A Chain A, The Crystal Structure Of The Ubiquitin-Like (Ubl) Domain Of Hhr23a (Human Homologue A Of Rad23) Length = 85

Iteration: 1
 Score = 39.7 bits (91), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 4/78 (5%)
Query: 3  IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLADY 59
          I +KTL  +T  + +E  +T+  +K KI+ ++G    P   Q+LI+AGK L D   + DY
Sbjct: 8  ITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDY 67
Query: 60 NI-QKESTLHLVLRLRGG 76
           I +K   + +V + + G
Sbjct: 68 RIDEKNFVVVMVTKTKAG 85

>pdb|1YQB|A Chain A, Human Ubiquilin 3 Length = 100

Iteration: 1
 Score = 39.7 bits (91), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKT   K     V  + TI  +K +I  +    PDQ  LIFAGK L+D  +LA   
Sbjct: 23 IKVTVKTPKDKE-DFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCG 81
Query: 61 IQKESTLHLVLRLRGGTM 78
          ++   T+HLV++ +   M
Sbjct: 82 VRDGLTVHLVIKRQHRAM 99

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	154
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	2e-73
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	8e-73
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	1e-71
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	4e-23
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	1e-62
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	1e-54
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	3e-39
3u5c_F	225	RP14, S2, YS8, 40S ribosomal protein S5; translati	2e-53
3u5c_F	225	RP14, S2, YS8, 40S ribosomal protein S5; translati	4e-40
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	2e-52
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	2e-39
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	4e-52
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	1e-39
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	6e-52
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	1e-37
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	3e-51
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	2e-36
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	4e-50
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	3e-37
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	1e-49
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	2e-39
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	1e-49
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	2e-40
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	2e-49
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	9e-39
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	2e-49
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	2e-37
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	3e-49
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	9e-39
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	8e-49
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	5e-35
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	1e-48
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	7e-37
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	2e-48
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	1e-36
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	2e-48
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	3e-35
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	3e-48
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	4e-39
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	4e-48
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	5e-36
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	2e-46
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	2e-34
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	3e-46
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	5e-34
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	4e-46
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	3e-44
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	2e-45
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	5e-34
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	2e-45
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	3e-33
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	2e-45
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	5e-31
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	3e-45
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	7e-33
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	3e-45
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	2e-33
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	7e-45
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	3e-33
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	2e-44
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	4e-34
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	3e-44
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	7e-34
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	9e-44
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	2e-35
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	2e-42
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	7e-34
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	3e-42
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	7e-32
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	4e-42
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	4e-32
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	5e-42
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	4e-29
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	1e-41
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	2e-30
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	2e-41
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	1e-30
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	5e-41
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	2e-31
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	9e-41
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	3e-36
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	9e-10
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	6e-04
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	3e-40
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	3e-32
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	2e-36
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	9e-25
1we6_A	111	Splicing factor, putative; structural genomics, ub	4e-36
1we6_A	111	Splicing factor, putative; structural genomics, ub	5e-29
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	1e-31
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	2e-25
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	1e-30
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	3e-25
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	3e-24
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	1e-16
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	6e-22
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	3e-12
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	1e-19
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	3e-13
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	4e-16
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	7e-09
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	7e-15
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	4e-14
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	2e-14
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	4e-14
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	4e-14
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	8e-13
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	8e-14
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	5e-12
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	9e-14
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	1e-09
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	2e-13
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	2e-11
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	4e-13
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	8e-12
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	1e-12
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	6e-12
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	1e-12
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	4e-12
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	1e-12
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	6e-09
2k8h_A	110	Small ubiquitin protein; SUMO, post-translational	5e-12
2k8h_A	110	Small ubiquitin protein; SUMO, post-translational	1e-06
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	6e-12
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	9e-12
2io0_B	91	Small ubiquitin-related modifier 2 precursor; SUMO	8e-11
2io0_B	91	Small ubiquitin-related modifier 2 precursor; SUMO	7e-06
1wyw_B	97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	9e-10
1wyw_B	97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	6e-05
1wz0_A	104	Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-li	7e-09
1wz0_A	104	Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-li	2e-04
2uyz_B	79	Small ubiquitin-related modifier 1; sumoylation, c	8e-09
2io1_B	94	Small ubiquitin-related modifier 3 precursor; SUMO	9e-09
2io1_B	94	Small ubiquitin-related modifier 3 precursor; SUMO	5e-04
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	3e-08
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	5e-08
2d07_B	93	Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Ho	5e-08
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	1e-07
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	6e-06
2kj6_A	97	Tubulin folding cofactor B; methods development, N	4e-07
2kj6_A	97	Tubulin folding cofactor B; methods development, N	1e-06
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	6e-07
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	3e-06
2kzr_A	86	Ubiquitin thioesterase OTU1; structural genomics,	1e-06
2kzr_A	86	Ubiquitin thioesterase OTU1; structural genomics,	2e-05
1wxv_A	92	BAG-family molecular chaperone regulator-1; struct	3e-06
1wxv_A	92	BAG-family molecular chaperone regulator-1; struct	3e-05
1v6e_A	95	Cytoskeleton-associated protein 1; tubulin-specifi	4e-06
1v6e_A	95	Cytoskeleton-associated protein 1; tubulin-specifi	5e-05
1se9_A	126	Ubiquitin family; ubiquitin-like, cell-free, wheat	4e-06
1se9_A	126	Ubiquitin family; ubiquitin-like, cell-free, wheat	2e-05
3tix_A	207	Ubiquitin-like protein SMT3, RNA-induced transcri	5e-06
2eke_C	106	Ubiquitin-like protein SMT3; UBC9, SUMO binding mo	1e-05
2kjr_A	95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	1e-04
2kjr_A	95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	6e-04
4efo_A	94	Serine/threonine-protein kinase TBK1; ubiquitin li	5e-04

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

 Score =  216 bits (552), Expect = 2e-73
 Identities = 121/152 (79%), Positives = 135/152 (88%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 21  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 80

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
           IQKESTLHLVLRLRGG  I VKTLTGK I +++EP+DTIE +K ++++KEGIPP QQRLI
Sbjct: 81  IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI 140

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
           +AGKQL D +T  DYNI+  S LHLVL LRGG
Sbjct: 141 FAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 172

>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 =  214 bits (546), Expect = 8e-73
 Identities = 121/152 (79%), Positives = 135/152 (88%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1   MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
           IQKESTLHLVLRLRGG  I VKTLTGK I +++EP+DTIE +K ++++KEGIPP QQRLI
Sbjct: 61  IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI 120

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
           +AGKQL D +T  DYNI+  S LHLVL LRGG
Sbjct: 121 FAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 152

>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 =  211 bits (538), Expect = 1e-71
 Identities = 46/156 (29%), Positives = 74/156 (47%), Gaps = 3/156 (1%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF--AGKQLEDGRTLAD 58
             + VK L G    + + SS ++  +KA+I  K G+   QQRL    +G  L+D   LA 
Sbjct: 3   WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLAS 62

Query: 59  YNIQKESTLHLV-LRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQ 117
             +   ST+ LV  +      I V+   G+    ++  T T+  +K++V   EG+     
Sbjct: 63  QGLGPGSTVLLVVDKSDEPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLF 122

Query: 118 RLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG 153
            L + GK L D     +Y ++  S + + L LRGGG
Sbjct: 123 WLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRGGG 158

>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 = 88.1 bits (218), Expect = 4e-23
 Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 2/73 (2%)

Query: 76  GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIY--AGKQLADDKTAR 133
           G  + VK L G E ++ +  + ++  +K ++ +K G+   QQRL    +G  L D     
Sbjct: 2   GWDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLA 61

Query: 134 DYNIEGGSVLHLV 146
              +  GS + LV
Sbjct: 62  SQGLGPGSTVLLV 74

>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 =  189 bits (481), Expect = 1e-62
 Identities = 87/163 (53%), Positives = 103/163 (63%), Gaps = 12/163 (7%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIE---IDIEPTDTIERIKERVEEKEGIPPVQQ 117
           IQKESTLHLVLRLRGG    +K +   +I    + I+P   +E  +  ++ +   P    
Sbjct: 61  IQKESTLHLVLRLRGGGGETIKFVADGDIGSGSVIIKPFVDMEHPETSIKLEMDQPV--- 117

Query: 118 RLIYAGKQLADDKTAR------DYNIEGGSVLHLVLALRGGGL 154
            L +  K L D              +   +       L+ G L
Sbjct: 118 DLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKSGFL 160

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

 Score =  169 bits (429), Expect = 1e-54
 Identities = 61/153 (39%), Positives = 80/153 (52%), Gaps = 10/153 (6%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
                    GK+I       D   N + K+  K G    +  + +        R L   +
Sbjct: 40  KGNLADVAPGKSIG-----GDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSD 94

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
                 L        G  I VKTLTGK I +++EP+DTIE +K ++++KEGIPP QQRLI
Sbjct: 95  -----WLIYKTTDHYGGQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI 149

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGGG 153
           +AGKQL D +T  DYNI+  S LHLVL LRGGG
Sbjct: 150 FAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGG 182

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

 Score =  130 bits (328), Expect = 3e-39
 Identities = 73/82 (89%), Positives = 75/82 (91%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
            QIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 106 GQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 165

Query: 61  IQKESTLHLVLRLRGGTMIKVK 82
           IQKESTLHLVLRLRGG     K
Sbjct: 166 IQKESTLHLVLRLRGGGQTFTK 187

>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 =  164 bits (418), Expect = 2e-53
 Identities = 5/76 (6%), Positives = 19/76 (25%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M      +  +     VE    +       ++ +    + +       +  + +  +  +
Sbjct: 1  MSDTEAPVEVQEDFEVVEEFTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVD 60

Query: 61 IQKESTLHLVLRLRGG 76
            +      V    G 
Sbjct: 61 YVQVRQPIFVAHTAGR 76

>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 =  131 bits (331), Expect = 4e-40
 Identities = 8/75 (10%), Positives = 17/75 (22%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
                +  +E    +E    +       EE +      +       +  + K A   +  
Sbjct: 3   DTEAPVEVQEDFEVVEEFTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVDYV 62

Query: 139 GGSVLHLVLALRGGG 153
                  V    G  
Sbjct: 63  QVRQPIFVAHTAGRY 77

>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 =  160 bits (407), Expect = 2e-52
 Identities = 44/87 (50%), Positives = 61/87 (70%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ+ D +T ADY 
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK 60

Query: 61 IQKESTLHLVLRLRGGTMIKVKTLTGK 87
          I   S LHLVL LRGG  ++ K     
Sbjct: 61 ILGGSVLHLVLALRGGGGLRQKHHHHH 87

>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 =  127 bits (320), Expect = 2e-39
 Identities = 65/76 (85%), Positives = 70/76 (92%)

Query: 78  MIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNI 137
           +IKVKTLTGKEIEIDIEPTD +ERIKERVEEKEGIPP QQRLIY+GKQ+ D+KTA DY I
Sbjct: 2   LIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKI 61

Query: 138 EGGSVLHLVLALRGGG 153
            GGSVLHLVLALRGGG
Sbjct: 62  LGGSVLHLVLALRGGG 77

>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 =  159 bits (404), Expect = 4e-52
 Identities = 43/76 (56%), Positives = 58/76 (76%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ+ D +T ADY 
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK 60

Query: 61 IQKESTLHLVLRLRGG 76
          I   S LHLVL LRGG
Sbjct: 61 ILGGSVLHLVLALRGG 76

>1ndd_A NEDD8, protein (ubiquitin-like protein NEDD8); proteolysis, signaling protei; 1.60A {Homo sapiens} SCOP: d.15.1.1 PDB: 1r4m_I 1r4n_I* 1xt9_B 2ko3_A 3gzn_I* 2bkr_B 2nvu_I* 3dqv_A 1bt0_A Length = 76

 Score =  127 bits (322), Expect = 1e-39
 Identities = 64/75 (85%), Positives = 69/75 (92%)

Query: 78  MIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNI 137
           +IKVKTLTGKEIEIDIEPTD +ERIKERVEEKEGIPP QQRLIY+GKQ+ D+KTA DY I
Sbjct: 2   LIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKI 61

Query: 138 EGGSVLHLVLALRGG 152
            GGSVLHLVLALRGG
Sbjct: 62  LGGSVLHLVLALRGG 76

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

 Score =  159 bits (405), Expect = 6e-52
 Identities = 75/100 (75%), Positives = 85/100 (85%), Gaps = 3/100 (3%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
            QIF KTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLI+AGKQLEDGRTL+DYN
Sbjct: 10  FQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLEDGRTLSDYN 69

Query: 61  IQKESTLHLVLRLRGGTM---IKVKTLTGKEIEIDIEPTD 97
           IQ+ESTLHLVLRLRGG+M      + L  K IE+ ++ + 
Sbjct: 70  IQRESTLHLVLRLRGGSMGGAADEEELIRKAIELSLKESR 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 =  123 bits (310), Expect = 1e-37
 Identities = 46/84 (54%), Positives = 60/84 (71%)

Query: 71  LRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDK 130
               G   I  KTLTGK I +++E +DTI+ +K ++++KEGIPP QQRLI+AGKQL D +
Sbjct: 4   HHHHGEFQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLEDGR 63

Query: 131 TARDYNIEGGSVLHLVLALRGGGL 154
           T  DYNI+  S LHLVL LRGG +
Sbjct: 64  TLSDYNIQRESTLHLVLRLRGGSM 87

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

 Score =  157 bits (399), Expect = 3e-51
 Identities = 73/95 (76%), Positives = 79/95 (83%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query: 61 IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEP 95
          IQKESTLHLVLRLRGG      ++      ++   
Sbjct: 61 IQKESTLHLVLRLRGGRDPNSSSVDKLAAALEHHH 95

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

 Score =  120 bits (302), Expect = 2e-36
 Identities = 48/75 (64%), Positives = 60/75 (80%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK I +++EP+DTIE +K ++++KEGIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62

Query: 139 GGSVLHLVLALRGGG 153
             S LHLVL LRGG 
Sbjct: 63  KESTLHLVLRLRGGR 77

>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 =  155 bits (393), Expect = 4e-50
 Identities = 22/82 (26%), Positives = 42/82 (51%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
            Q+ ++  TGK + L V S+DT+ ++K ++   EG+ P  QR  F+G+ L D     +  
Sbjct: 24  CQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKFEELK 83

Query: 61  IQKESTLHLVLRLRGGTMIKVK 82
           I K+  + +++         V+
Sbjct: 84  IPKDYVVQVIVSQPVQNPTPVE 105

>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 =  122 bits (307), Expect = 3e-37
 Identities = 19/81 (23%), Positives = 41/81 (50%), Gaps = 1/81 (1%)

Query: 74  RGGTM-IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTA 132
            G    ++++  TGK++++ +  TDT+  +K R+   EG+ P  QR  ++G+ L D    
Sbjct: 20  SGYECQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKF 79

Query: 133 RDYNIEGGSVLHLVLALRGGG 153
            +  I    V+ ++++     
Sbjct: 80  EELKIPKDYVVQVIVSQPVQN 100

>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 =  153 bits (388), Expect = 1e-49
 Identities = 70/76 (92%), Positives = 73/76 (96%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 4  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 63

Query: 61 IQKESTLHLVLRLRGG 76
          IQK STL L+LRLRGG
Sbjct: 64 IQKWSTLFLLLRLRGG 79

>3mtn_B UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquitin-specific protease activity, hydrolase, ubiquitin B structural genomics consortium, SGC; 2.70A {Homo sapiens} Length = 85

 Score =  127 bits (321), Expect = 2e-39
 Identities = 49/80 (61%), Positives = 62/80 (77%), Gaps = 1/80 (1%)

Query: 75  GGTM-IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTAR 133
           G  M I VKTLTGK I +++EP+DTIE +K ++++KEGIPP QQRLI+AGKQL D +T  
Sbjct: 1   GSHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLS 60

Query: 134 DYNIEGGSVLHLVLALRGGG 153
           DYNI+  S L L+L LRGGG
Sbjct: 61  DYNIQKWSTLFLLLRLRGGG 80

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

 Score =  153 bits (388), Expect = 1e-49
 Identities = 66/78 (84%), Positives = 75/78 (96%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +Q+F+KTLTGKT T+E+E SDTI+N+KAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 10 LQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 69

Query: 61 IQKESTLHLVLRLRGGTM 78
          IQKESTLHLVLRLRGG +
Sbjct: 70 IQKESTLHLVLRLRGGGL 87

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

 Score =  129 bits (327), Expect = 2e-40
 Identities = 49/87 (56%), Positives = 63/87 (72%)

Query: 68  HLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLA 127
           H       G  + +KTLTGK   +++EP+DTIE +K ++++KEGIPP QQRLI+AGKQL 
Sbjct: 1   HHHHHHLQGLQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEGIPPDQQRLIFAGKQLE 60

Query: 128 DDKTARDYNIEGGSVLHLVLALRGGGL 154
           D +T  DYNI+  S LHLVL LRGGGL
Sbjct: 61  DGRTLSDYNIQKESTLHLVLRLRGGGL 87

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

 Score =  152 bits (386), Expect = 2e-49
 Identities = 61/76 (80%), Positives = 68/76 (89%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M+I VKTL G+TI LEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 4  MRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 63

Query: 61 IQKESTLHLVLRLRGG 76
          I   S L+L+L+LRGG
Sbjct: 64 IHNHSALYLLLKLRGG 79

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

 Score =  125 bits (316), Expect = 9e-39
 Identities = 47/80 (58%), Positives = 61/80 (76%), Gaps = 1/80 (1%)

Query: 75  GGTM-IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTAR 133
           G  M I VKTL G+ I +++EP+DTIE +K ++++KEGIPP QQRLI+AGKQL D +T  
Sbjct: 1   GSHMRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLS 60

Query: 134 DYNIEGGSVLHLVLALRGGG 153
           DYNI   S L+L+L LRGGG
Sbjct: 61  DYNIHNHSALYLLLKLRGGG 80

>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 =  152 bits (385), Expect = 2e-49
 Identities = 72/76 (94%), Positives = 75/76 (98%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query: 61 IQKESTLHLVLRLRGG 76
          IQ+ESTLHLVLRLRGG
Sbjct: 61 IQRESTLHLVLRLRGG 76

>3a9j_A Ubiquitin; protein complex, cytoplasm, isopeptide bond, metal-binding, zinc; 1.18A {Mus musculus} PDB: 3a1q_B 2znv_B 3a9k_A 3h7p_A 3jsv_A 3dvg_Y 3dvn_Y 3nob_A 2o6v_D* 3jw0_X 3jvz_X 3nhe_B* 1aar_A 1d3z_A 1f9j_A 1fxt_B 1g6j_A 1nbf_C 1cmx_B 1q5w_B ... Length = 76

 Score =  122 bits (307), Expect = 2e-37
 Identities = 48/74 (64%), Positives = 60/74 (81%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK I +++EP+DTIE +K ++++KEGIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62

Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 63  RESTLHLVLRLRGG 76

>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 =  152 bits (386), Expect = 3e-49
 Identities = 44/76 (57%), Positives = 59/76 (77%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +D ++ +K ++++KEGIPP QQRLI++GKQ+ D +T ADY 
Sbjct: 13 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK 72

Query: 61 IQKESTLHLVLRLRGG 76
          I   S LHLVLRLRGG
Sbjct: 73 ILGGSVLHLVLRLRGG 88

>3dbh_I NEDD8; cell cycle, activating enzyme, apoptosis, membrane, UBL conjugation pathway, ATP-binding, ligase, nucleotide- binding, polymorphism; 2.85A {Homo sapiens} SCOP: k.45.1.1 PDB: 3dbr_I 3dbl_I Length = 88

 Score =  125 bits (316), Expect = 9e-39
 Identities = 66/79 (83%), Positives = 71/79 (89%), Gaps = 1/79 (1%)

Query: 75  GGTM-IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTAR 133
           GG+M IKVKTLTGKEIEIDIEPTD +ERIKERVEEKEGIPP QQRLIY+GKQ+ D+KTA 
Sbjct: 10  GGSMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAA 69

Query: 134 DYNIEGGSVLHLVLALRGG 152
           DY I GGSVLHLVL LRGG
Sbjct: 70  DYKILGGSVLHLVLRLRGG 88

>4dwf_A HLA-B-associated transcript 3; ubiquitin-like domain, BAT3 protein, PF00240, structural GEN joint center for structural genomics, JCSG; 1.80A {Homo sapiens} PDB: 1wx9_A Length = 90

 Score =  151 bits (383), Expect = 8e-49
 Identities = 27/86 (31%), Positives = 45/86 (52%), Gaps = 1/86 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKTL  +T T  V +   +   K  I     IP ++QRLI+ G+ L+D + L +YN
Sbjct: 6  LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYN 65

Query: 61 IQKESTLHLVLRLRGGTMIKVKTLTG 86
          +  +  +HLV R    T +     +G
Sbjct: 66 VGGK-VIHLVERAPPQTHLPSGASSG 90

>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 =  116 bits (292), Expect = 5e-35
 Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 2/78 (2%)

Query: 76  GTM-IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARD 134
            ++ + VKTL  +     +     ++  KE +     IP  +QRLIY G+ L DDK  ++
Sbjct: 4   DSLEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQE 63

Query: 135 YNIEGGSVLHLVLALRGG 152
           YN+  G V+HLV      
Sbjct: 64  YNVG-GKVIHLVERAPPQ 80

>3k9o_B Ubiquitin, UBB+1; E2-25K, complex structure, ATP-binding, isopeptide BO ligase, nucleotide-binding, UBL conjugation pathway; 1.80A {Homo sapiens} PDB: 2k25_A 2kx0_A Length = 96

 Score =  150 bits (381), Expect = 1e-48
 Identities = 72/83 (86%), Positives = 76/83 (91%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 2  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 61

Query: 61 IQKESTLHLVLRLRGGTMIKVKT 83
          IQKESTLHLVLRLRG   ++   
Sbjct: 62 IQKESTLHLVLRLRGYADLREDP 84

>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 =  121 bits (304), Expect = 7e-37
 Identities = 48/78 (61%), Positives = 60/78 (76%)

Query: 76  GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDY 135
           G  I VKTLTGK I +++EP+DTIE +K ++++KEGIPP QQRLI+AGKQL D +T  DY
Sbjct: 1   GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY 60

Query: 136 NIEGGSVLHLVLALRGGG 153
           NI+  S LHLVL LRG  
Sbjct: 61  NIQKESTLHLVLRLRGYA 78

>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 =  150 bits (380), Expect = 2e-48
 Identities = 25/75 (33%), Positives = 48/75 (64%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M +FV+  +     +EV+S  +I  +K  +  ++G+P DQ R+IFAGK+L +  T+ + +
Sbjct: 1  MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKQQGVPADQLRVIFAGKELPNHLTVQNCD 60

Query: 61 IQKESTLHLVLRLRG 75
          ++++S +H+V R R 
Sbjct: 61 LEQQSIVHIVQRPRR 75

>3b1l_X E3 ubiquitin-protein ligase parkin; proteasome, ALFA-beta-protein; 1.85A {Mus musculus} PDB: 1mg8_A 2zeq_A 2knb_A 1iyf_A Length = 76

 Score =  120 bits (302), Expect = 1e-36
 Identities = 20/74 (27%), Positives = 46/74 (62%)

Query: 78  MIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNI 137
           ++ V+  +     ++++   +I ++KE V +++G+P  Q R+I+AGK+L +  T ++ ++
Sbjct: 2   IVFVRFNSSYGFPVEVDSDTSILQLKEVVAKQQGVPADQLRVIFAGKELPNHLTVQNCDL 61

Query: 138 EGGSVLHLVLALRG 151
           E  S++H+V   R 
Sbjct: 62  EQQSIVHIVQRPRR 75

>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 =  150 bits (380), Expect = 2e-48
 Identities = 28/82 (34%), Positives = 44/82 (53%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + I V+   G++ T EV  + T+ ++K ++   EG+  D   L F GK LED   L +Y 
Sbjct: 5  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 64

Query: 61 IQKESTLHLVLRLRGGTMIKVK 82
          ++  ST+ + LRLRGG      
Sbjct: 65 LKPLSTVFMNLRLRGGLEHHHH 86

>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 =  116 bits (293), Expect = 3e-35
 Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 1/78 (1%)

Query: 77  TM-IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDY 135
            + I V+   G+    ++  T T+  +K++V   EG+      L + GK L D     +Y
Sbjct: 4   PLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEY 63

Query: 136 NIEGGSVLHLVLALRGGG 153
            ++  S + + L LRGG 
Sbjct: 64  GLKPLSTVFMNLRLRGGL 81

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

 Score =  150 bits (380), Expect = 3e-48
 Identities = 73/76 (96%), Positives = 75/76 (98%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 36  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 95

Query: 61  IQKESTLHLVLRLRGG 76
           IQKESTLHLVLRLRGG
Sbjct: 96  IQKESTLHLVLRLRGG 111

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

 Score =  127 bits (320), Expect = 4e-39
 Identities = 53/111 (47%), Positives = 67/111 (60%), Gaps = 6/111 (5%)

Query: 43  LIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGTM-IKVKTLTGKEIEIDIEPTDTIER 101
                  +E      D N         +L      M I VKTLTGK I +++EP+DTIE 
Sbjct: 6   DTNNDGWIEGDELYIDTNNDGWIEGDELL-----AMQIFVKTLTGKTITLEVEPSDTIEN 60

Query: 102 IKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
           +K ++++KEGIPP QQRLI+AGKQL D +T  DYNI+  S LHLVL LRGG
Sbjct: 61  VKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 111

>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 =  149 bits (378), Expect = 4e-48
 Identities = 26/77 (33%), Positives = 41/77 (53%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +Q+FVK   G +    +  +  I  +K +I+D++G+P  QQ+L F G+ L+D   L  Y 
Sbjct: 8  IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGLGIYG 67

Query: 61 IQKESTLHLVLRLRGGT 77
          IQ   TL L  +   G 
Sbjct: 68 IQDSDTLILSKKKGSGP 84

>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 =  118 bits (298), Expect = 5e-36
 Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 1/79 (1%)

Query: 75  GGTM-IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTAR 133
              + + VK   G      I P   I  +K+++E+++G+P  QQ+L + G+ L D     
Sbjct: 5   SSGIQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGLG 64

Query: 134 DYNIEGGSVLHLVLALRGG 152
            Y I+    L L      G
Sbjct: 65  IYGIQDSDTLILSKKKGSG 83

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

 Score =  145 bits (367), Expect = 2e-46
 Identities = 29/73 (39%), Positives = 46/73 (63%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQ+ VK L G+  +L+V   + +  +K  + +K  +P  QQRL+F GK L DG+ L+DY+
Sbjct: 8  MQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLNVPVRQQRLLFKGKALADGKRLSDYS 67

Query: 61 IQKESTLHLVLRL 73
          I   S L+LV++ 
Sbjct: 68 IGPNSKLNLVVKP 80

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

 Score =  114 bits (288), Expect = 2e-34
 Identities = 28/76 (36%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 75  GGTM-IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTAR 133
              M + VK L G+E  + +   + +  +K+ V EK  +P  QQRL++ GK LAD K   
Sbjct: 5   SSGMQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLNVPVRQQRLLFKGKALADGKRLS 64

Query: 134 DYNIEGGSVLHLVLAL 149
           DY+I   S L+LV+  
Sbjct: 65  DYSIGPNSKLNLVVKP 80

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

 Score =  144 bits (365), Expect = 3e-46
 Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKTL  +T T  V +   +   K  I     IP ++QRLI+ G+ L+D + L +YN
Sbjct: 18 LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYN 77

Query: 61 IQKESTLHLVLR 72
          +  +  +HLV R
Sbjct: 78 VGGK-VIHLVER 88

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

 Score =  113 bits (286), Expect = 5e-34
 Identities = 25/87 (28%), Positives = 41/87 (47%), Gaps = 1/87 (1%)

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
           ++   +    +       + VKTL  +     +     ++  KE +     IP  +QRLI
Sbjct: 2   MEPNDSTSTAVEEPDSLEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLI 61

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVL 147
           Y G+ L DDK  ++YN+  G V+HLV 
Sbjct: 62  YQGRVLQDDKKLQEYNVG-GKVIHLVE 87

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

 Score =  144 bits (366), Expect = 4e-46
 Identities = 32/101 (31%), Positives = 54/101 (53%), Gaps = 5/101 (4%)

Query: 48  KQLEDGRTLADYNIQKESTLHLVLRLRGGTMIKVKTLTGKE-IEIDIEPTDTIERIKERV 106
           K       ++DY+I     L+     +G   + +   +G++  E+++ P  T+ + KE +
Sbjct: 2   KHHHHHHPMSDYDIPTTENLYF----QGAMSLNIHIKSGQDKWEVNVAPESTVLQFKEAI 57

Query: 107 EEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVL 147
            +  GIP   QRLIY+GK L DD+T   Y+I+ G  +HLV 
Sbjct: 58  NKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVK 98

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

 Score =  140 bits (354), Expect = 3e-44
 Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 1  MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADY 59
          M + +   +G+    + V    T+   K  I    GIP   QRLI++GK L+D +T+  Y
Sbjct: 27 MSLNIHIKSGQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESY 86

Query: 60 NIQKESTLHLVLR 72
          +IQ   ++HLV  
Sbjct: 87 HIQDGHSVHLVKS 99

>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 =  142 bits (361), Expect = 2e-45
 Identities = 29/78 (37%), Positives = 46/78 (58%), Gaps = 2/78 (2%)

Query: 1  MQIFVKTLTG-KTITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLAD 58
          M I V+T+ G KT T+E V    TI+ ++ ++     + P+ QRL + GKQLE+G TL D
Sbjct: 8  MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFD 67

Query: 59 YNIQKESTLHLVLRLRGG 76
          Y++     + L++R   G
Sbjct: 68 YDVGLNDIIQLLVRPDSG 85

>1wy8_A NP95-like ring finger protein, isoform A; ubiquitin-like domain, NP95/ICBP90-like ring finger (NIRF), ubiquitin ligase, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 89

 Score =  113 bits (285), Expect = 5e-34
 Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 3/82 (3%)

Query: 74  RGGTM-IKVKTLTGKEIEI--DIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDK 130
               M I+V+T+ G +     D+    TIE ++ERV     + P  QRL Y GKQL +  
Sbjct: 4   GSSGMWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGY 63

Query: 131 TARDYNIEGGSVLHLVLALRGG 152
           T  DY++    ++ L++    G
Sbjct: 64  TLFDYDVGLNDIIQLLVRPDSG 85

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

 Score =  142 bits (359), Expect = 2e-45
 Identities = 27/75 (36%), Positives = 43/75 (57%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + I V+   G++ T EV  + T+ ++K ++   EG+  D   L F GK LED   L +Y 
Sbjct: 5  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 64

Query: 61 IQKESTLHLVLRLRG 75
          ++  ST+ + LRLRG
Sbjct: 65 LKPLSTVFMNLRLRG 79

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

 Score =  111 bits (279), Expect = 3e-33
 Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 77  TM-IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDY 135
            + I V+   G+    ++  T T+  +K++V   EG+      L + GK L D     +Y
Sbjct: 4   PLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEY 63

Query: 136 NIEGGSVLHLVLALRG 151
            ++  S + + L LRG
Sbjct: 64  GLKPLSTVFMNLRLRG 79

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

 Score =  146 bits (368), Expect = 2e-45
 Identities = 24/91 (26%), Positives = 40/91 (43%), Gaps = 5/91 (5%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQ+ VKTL G+T    +E   ++ ++K++I    G   D   L+  G    +   + D  
Sbjct: 1  MQVQVKTLEGETKIYTLEQGTSVLDLKSQISQDMGFEIDMMTLVNNGFIAPNTELVTDD- 59

Query: 61 IQKESTLHLVLRLRGGTMIKVKTLTGKEIEI 91
               T +L L+L GG   K K     + + 
Sbjct: 60 ----VTYYLSLKLLGGKKKKKKKSYTTKKKT 86

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

 Score =  109 bits (273), Expect = 5e-31
 Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 5/74 (6%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           ++VKTL G+     +E   ++  +K ++ +  G       L+  G    + +   D    
Sbjct: 3   VQVKTLEGETKIYTLEQGTSVLDLKSQISQDMGFEIDMMTLVNNGFIAPNTELVTDD--- 59

Query: 139 GGSVLHLVLALRGG 152
                +L L L GG
Sbjct: 60  --VTYYLSLKLLGG 71

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

 Score =  142 bits (360), Expect = 3e-45
 Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 2/76 (2%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQ+FV+    +  T EV   +T+  +KA +   EGI P+ Q ++ AG  LED  TL    
Sbjct: 20 MQLFVRA--QELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAGAPLEDEATLGQCG 77

Query: 61 IQKESTLHLVLRLRGG 76
          ++  +TL +  R+ GG
Sbjct: 78 VEALTTLEVAGRMLGG 93

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

 Score =  111 bits (278), Expect = 7e-33
 Identities = 22/92 (23%), Positives = 39/92 (42%), Gaps = 3/92 (3%)

Query: 62  QKESTLHLVLRLRGGTM-IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
                 H    +  G+M + V+    +    ++   +T+ +IK  V   EGI P  Q ++
Sbjct: 4   SHHHHHHSSGLVPRGSMQLFVRA--QELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVL 61

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVLALRGG 152
            AG  L D+ T     +E  + L +   + GG
Sbjct: 62  LAGAPLEDEATLGQCGVEALTTLEVAGRMLGG 93

>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 =  142 bits (360), Expect = 3e-45
 Identities = 23/80 (28%), Positives = 46/80 (57%), Gaps = 3/80 (3%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLA 57
          MQ+ +KTL  +T  ++++  +T+  +K KI+ ++G    P   Q+LI+AGK L D   L 
Sbjct: 1  MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 60

Query: 58 DYNIQKESTLHLVLRLRGGT 77
          +Y I +++ + +++      
Sbjct: 61 EYKIDEKNFVVVMVTKPKAV 80

>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 =  112 bits (281), Expect = 2e-33
 Identities = 25/78 (32%), Positives = 47/78 (60%), Gaps = 3/78 (3%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEG---IPPVQQRLIYAGKQLADDKTARDY 135
           + +KTL  +  +IDI+P +T++ +KE++E ++G    P   Q+LIYAGK L DD   ++Y
Sbjct: 3   VTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEY 62

Query: 136 NIEGGSVLHLVLALRGGG 153
            I+  + + +++      
Sbjct: 63  KIDEKNFVVVMVTKPKAV 80

>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 =  141 bits (358), Expect = 7e-45
 Identities = 28/86 (32%), Positives = 44/86 (51%), Gaps = 1/86 (1%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           +++ VKT   K     V  + TI  +K +I  +    PDQ  LIFAGK L+D  +LA   
Sbjct: 18  IKVTVKTPKDKE-DFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCG 76

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTG 86
           ++   T+HLV++ +   M      +G
Sbjct: 77  VRDGLTVHLVIKRQHRAMGNECPASG 102

>1wx7_A Ubiquilin 3; ubiquitin-like domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 106

 Score =  112 bits (281), Expect = 3e-33
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           + VKT   KE +  +  T TI+++KE + ++    P Q  LI+AGK L D  +     + 
Sbjct: 20  VTVKTPKDKE-DFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVR 78

Query: 139 GGSVLHLVLALRGGG 153
            G  +HLV+  +   
Sbjct: 79  DGLTVHLVIKRQHRA 93

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

 Score =  140 bits (354), Expect = 2e-44
 Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQ-LEDGRTLADY 59
          M+  V+ L G +  LEV+  DT+  VK KI+  + IP  +Q LI  G   L +  T+   
Sbjct: 11 MKFLVENLNGSSFELEVDYRDTLLVVKQKIERSQHIPVSKQTLIVDGIVILREDLTVEQC 70

Query: 60 NIQKESTLHLVL 71
           I   S + L +
Sbjct: 71 QIVPTSDIQLEV 82

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

 Score =  113 bits (286), Expect = 4e-34
 Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 2/77 (2%)

Query: 74  RGGTM-IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQ-LADDKT 131
               M   V+ L G   E++++  DT+  +K+++E  + IP  +Q LI  G   L +D T
Sbjct: 7   HHSHMKFLVENLNGSSFELEVDYRDTLLVVKQKIERSQHIPVSKQTLIVDGIVILREDLT 66

Query: 132 ARDYNIEGGSVLHLVLA 148
                I   S + L ++
Sbjct: 67  VEQCQIVPTSDIQLEVS 83

>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 =  139 bits (352), Expect = 3e-44
 Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 1  MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADY 59
          M + +   +G+    + V    T+   K  I    GIP   QRLI++GK L+D +T+  Y
Sbjct: 3  MSLNIHIKSGQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESY 62

Query: 60 NIQKESTLHLVLR 72
          +IQ   ++HLV  
Sbjct: 63 HIQDGHSVHLVKS 75

>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling proteins; 1.15A {Saccharomyces cerevisiae} SCOP: d.15.1.1 PDB: 2bwe_S Length = 77

 Score =  113 bits (284), Expect = 7e-34
 Identities = 26/70 (37%), Positives = 43/70 (61%), Gaps = 1/70 (1%)

Query: 79  IKVKTLTGKE-IEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNI 137
           + +   +G++  E+++ P  T+ + KE + +  GIP   QRLIY+GK L DD+T   Y+I
Sbjct: 5   LNIHIKSGQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHI 64

Query: 138 EGGSVLHLVL 147
           + G  +HLV 
Sbjct: 65  QDGHSVHLVK 74

>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 =  139 bits (352), Expect = 9e-44
 Identities = 21/75 (28%), Positives = 39/75 (52%)

Query: 2   QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNI 61
                 L G+ +   +  +D +  +K KI +  G+P  +Q+L + G  ++D  +LA YN+
Sbjct: 37  DKTEWKLNGQGLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNM 96

Query: 62  QKESTLHLVLRLRGG 76
              + +HL L+ R G
Sbjct: 97  ASGAVIHLALKERSG 111

>1we7_A SF3A1 protein; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: d.15.1.1 PDB: 1zkh_A Length = 115

 Score =  117 bits (296), Expect = 2e-35
 Identities = 23/71 (32%), Positives = 37/71 (52%)

Query: 82  KTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGS 141
             L G+ +   +  TD +  IK ++ E  G+P  +Q+L Y G  + D  +   YN+  G+
Sbjct: 41  WKLNGQGLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMASGA 100

Query: 142 VLHLVLALRGG 152
           V+HL L  R G
Sbjct: 101 VIHLALKERSG 111

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens} Length = 101

 Score =  135 bits (342), Expect = 2e-42
 Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M++ VKT   K     V  + ++   K +I  +     DQ  LIFAGK L+D  TL+ + 
Sbjct: 26 MKVTVKTPKEK-EEFAVPENSSVQQFKEEISKRFKSHTDQLVLIFAGKILKDQDTLSQHG 84

Query: 61 IQKESTLHLVLR 72
          I    T+HLV++
Sbjct: 85 IHDGLTVHLVIK 96

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens} Length = 101

 Score =  113 bits (285), Expect = 7e-34
 Identities = 23/91 (25%), Positives = 40/91 (43%), Gaps = 2/91 (2%)

Query: 58  DYNIQKESTLHLVLRLRGGTM-IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQ 116
            ++       +L  +     M + VKT   K  E  +    ++++ KE + ++      Q
Sbjct: 6   HHHHHSSGRENLYFQGHPKIMKVTVKTPKEK-EEFAVPENSSVQQFKEEISKRFKSHTDQ 64

Query: 117 QRLIYAGKQLADDKTARDYNIEGGSVLHLVL 147
             LI+AGK L D  T   + I  G  +HLV+
Sbjct: 65  LVLIFAGKILKDQDTLSQHGIHDGLTVHLVI 95

>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 =  134 bits (339), Expect = 3e-42
 Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 2/75 (2%)

Query: 1  MQIFVKTLTGKTIT--LEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLAD 58
          M I V+T+ G+       +     ++ ++ KIQ+   + P  QRL + GKQ+EDG TL D
Sbjct: 3  MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFD 62

Query: 59 YNIQKESTLHLVLRL 73
          Y ++   T+ L++R 
Sbjct: 63 YEVRLNDTIQLLVRQ 77

>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 =  107 bits (270), Expect = 7e-32
 Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 3/77 (3%)

Query: 76  GTM-IKVKTLTGKEIEI--DIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTA 132
           G+M I+V+T+ G++      +     +E ++ +++E   + P  QRL Y GKQ+ D  T 
Sbjct: 1   GSMWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTL 60

Query: 133 RDYNIEGGSVLHLVLAL 149
            DY +     + L++  
Sbjct: 61  FDYEVRLNDTIQLLVRQ 77

>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 =  134 bits (340), Expect = 4e-42
 Identities = 27/78 (34%), Positives = 42/78 (53%), Gaps = 1/78 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKT   K     V  + TI  +K +I  +    PDQ  LIFAGK L+D  +LA   
Sbjct: 23 IKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCG 81

Query: 61 IQKESTLHLVLRLRGGTM 78
          ++   T+HLV++ +   M
Sbjct: 82 VRDGLTVHLVIKRQHRAM 99

>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 =  108 bits (273), Expect = 4e-32
 Identities = 25/87 (28%), Positives = 41/87 (47%), Gaps = 2/87 (2%)

Query: 62  QKESTLHLVLRLRGGTM-IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI 120
               +  LV R     + + VKT   K  +  +  T TI+++KE + ++    P Q  LI
Sbjct: 7   HHHHSSGLVPRGSPHLIKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLI 65

Query: 121 YAGKQLADDKTARDYNIEGGSVLHLVL 147
           +AGK L D  +     +  G  +HLV+
Sbjct: 66  FAGKILKDPDSLAQCGVRDGLTVHLVI 92

>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 =  135 bits (341), Expect = 5e-42
 Identities = 76/118 (64%), Positives = 85/118 (72%), Gaps = 3/118 (2%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVESSDTIDNVK+KIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1   MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query: 61  IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQR 118
           IQKESTLHLVLRLRGG +         +   D        +   R+  +      ++ 
Sbjct: 61  IQKESTLHLVLRLRGGIIEPSLKALASKYNCDKS---VCRKCYARLPPRATNCRKRKC 115

>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 =  102 bits (255), Expect = 4e-29
 Identities = 45/73 (61%), Positives = 58/73 (79%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK I +++E +DTI+ +K ++++KEGIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62

Query: 139 GGSVLHLVLALRG 151
             S LHLVL LRG
Sbjct: 63  KESTLHLVLRLRG 75

>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 =  133 bits (336), Expect = 1e-41
 Identities = 24/80 (30%), Positives = 47/80 (58%), Gaps = 4/80 (5%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLA 57
          + I +KTL  +T  + +E  +T+  +K KI+ ++G    P   Q+LI+AGK L D   + 
Sbjct: 6  VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIR 65

Query: 58 DYNIQKESTLHLVL-RLRGG 76
          DY I +++ + +++ + + G
Sbjct: 66 DYRIDEKNFVVVMVTKTKAG 85

>2wyq_A HHR23A, UV excision repair protein RAD23 homolog A; DNA binding protein, DNA excision repair, proteasomal degrad polyubiquitin; 1.65A {Homo sapiens} PDB: 1p98_A 1p9d_U 1p1a_A Length = 85

 Score =  104 bits (261), Expect = 2e-30
 Identities = 28/78 (35%), Positives = 48/78 (61%), Gaps = 3/78 (3%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEG---IPPVQQRLIYAGKQLADDKTARDY 135
           I +KTL  +  +I +EP +T++ +KE++E ++G    P   Q+LIYAGK L+DD   RDY
Sbjct: 8   ITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDY 67

Query: 136 NIEGGSVLHLVLALRGGG 153
            I+  + + +++     G
Sbjct: 68  RIDEKNFVVVMVTKTKAG 85

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 125

 Score =  133 bits (337), Expect = 2e-41
 Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 1/77 (1%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           +++ VKT   K     V  + ++   K  I  +     DQ  LIFAGK L+D  TL  + 
Sbjct: 33  IKVTVKTPKEK-EEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLIQHG 91

Query: 61  IQKESTLHLVLRLRGGT 77
           I    T+HLV++    +
Sbjct: 92  IHDGLTVHLVIKRDPNS 108

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 125

 Score =  106 bits (266), Expect = 1e-30
 Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           + VKT   K  E  +    ++++ KE + ++      Q  LI+AGK L D  T   + I 
Sbjct: 35  VTVKTPKEK-EEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIH 93

Query: 139 GGSVLHLVL 147
            G  +HLV+
Sbjct: 94  DGLTVHLVI 102

>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 =  131 bits (332), Expect = 5e-41
 Identities = 21/77 (27%), Positives = 33/77 (42%), Gaps = 1/77 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKT         +  +  +   K +I        D+  LIF GK L D   L+   
Sbjct: 18 IRVSVKTPQDCH-EFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQDILSQRG 76

Query: 61 IQKESTLHLVLRLRGGT 77
          I   ST+H+V+R   G 
Sbjct: 77 ILDGSTVHVVVRSHSGP 93

>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 =  107 bits (269), Expect = 2e-31
 Identities = 18/74 (24%), Positives = 30/74 (40%), Gaps = 1/74 (1%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           + VKT      E  +     + R K+++ +       +  LI+ GK L D        I 
Sbjct: 20  VSVKTPQDCH-EFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQDILSQRGIL 78

Query: 139 GGSVLHLVLALRGG 152
            GS +H+V+    G
Sbjct: 79  DGSTVHVVVRSHSG 92

>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 =  137 bits (346), Expect = 9e-41
 Identities = 71/74 (95%), Positives = 73/74 (98%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 234 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 293

Query: 61  IQKESTLHLVLRLR 74
           IQKESTLHLVLRLR
Sbjct: 294 IQKESTLHLVLRLR 307

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B* Length = 307

 Score =  126 bits (316), Expect = 3e-36
 Identities = 54/156 (34%), Positives = 83/156 (53%), Gaps = 6/156 (3%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF-AGKQLEDGRTLADY 59
             +  K   G  +  ++  +    +V+     ++  P     ++      L     L+  
Sbjct: 152 YIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKD 211

Query: 60  NIQKESTLHLVLRLRGGTM-----IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPP 114
             +K   + L+  +    +     I VKTLTGK I +++EP+DTIE +K ++++KEGIPP
Sbjct: 212 PNEKRDHMVLLEFVTAAGITGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP 271

Query: 115 VQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALR 150
            QQRLI+AGKQL D +T  DYNI+  S LHLVL LR
Sbjct: 272 DQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 307

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B* Length = 307

 Score = 54.8 bits (131), Expect = 9e-10
 Identities = 12/112 (10%), Positives = 32/112 (28%), Gaps = 5/112 (4%)

Query: 30  IQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKEST-LHLVLRLRGGTMIKV----KTL 84
               +G    +  + F G  L +   L   + +++   L   L     +        K  
Sbjct: 100 FFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQK 159

Query: 85  TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYN 136
            G ++   I        ++     ++  P     ++         ++A   +
Sbjct: 160 NGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKD 211

>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 = 37.9 bits (87), Expect = 6e-04
 Identities = 7/46 (15%), Positives = 17/46 (36%), Gaps = 1/46 (2%)

Query: 108 EKEGIPPVQQRLIYAGKQLADDKTARDYNI-EGGSVLHLVLALRGG 152
           + +G    +  + + G  L +    +  +  E G++L   L     
Sbjct: 102 KDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYN 147

>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 =  130 bits (328), Expect = 3e-40
 Identities = 16/72 (22%), Positives = 37/72 (51%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + +  K    + + L++E S+TI   K K+         Q +LI++GK L+D +T+++  
Sbjct: 2  VSLTFKNFKKEKVPLDLEPSNTILETKTKLAQSISCEESQIKLIYSGKVLQDSKTVSECG 61

Query: 61 IQKESTLHLVLR 72
          ++    +  ++ 
Sbjct: 62 LKDGDQVVFMVS 73

>3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} Length = 106

 Score =  109 bits (275), Expect = 3e-32
 Identities = 18/70 (25%), Positives = 38/70 (54%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           +  K    +++ +D+EP++TI   K ++ +       Q +LIY+GK L D KT  +  ++
Sbjct: 4   LTFKNFKKEKVPLDLEPSNTILETKTKLAQSISCEESQIKLIYSGKVLQDSKTVSECGLK 63

Query: 139 GGSVLHLVLA 148
            G  +  +++
Sbjct: 64  DGDQVVFMVS 73

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} Length = 94

 Score =  120 bits (302), Expect = 2e-36
 Identities = 22/78 (28%), Positives = 42/78 (53%), Gaps = 2/78 (2%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQL-EDGRTLADY 59
          + + VK    K  T+EV+ ++T+ ++K KI   E  P  + +L ++G +L +D R L +Y
Sbjct: 16 IHVTVKFP-SKQFTVEVDRTETVSSLKDKIHIVENTPIKRMQLYYSGIELADDYRNLNEY 74

Query: 60 NIQKESTLHLVLRLRGGT 77
           I + S + + L+     
Sbjct: 75 GITEFSEIVVFLKSINRA 92

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} Length = 94

 Score = 90.5 bits (225), Expect = 9e-25
 Identities = 19/70 (27%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADD-KTARDYNI 137
           + VK    K+  ++++ T+T+  +K+++   E  P  + +L Y+G +LADD +   +Y I
Sbjct: 18  VTVKFP-SKQFTVEVDRTETVSSLKDKIHIVENTPIKRMQLYYSGIELADDYRNLNEYGI 76

Query: 138 EGGSVLHLVL 147
              S + + L
Sbjct: 77  TEFSEIVVFL 86

>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 =  119 bits (301), Expect = 4e-36
 Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 2/78 (2%)

Query: 1   MQIFVKT-LTGKTITLEVES-SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLAD 58
           +++       G+ + + V+S S+ + ++K KI  +  IP ++Q+L      L+D  +LA 
Sbjct: 30  IRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSLAH 89

Query: 59  YNIQKESTLHLVLRLRGG 76
           YN+     L L LR R G
Sbjct: 90  YNVGAGEILTLSLRERSG 107

>1we6_A Splicing factor, putative; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: d.15.1.1 Length = 111

 Score =  101 bits (254), Expect = 5e-29
 Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 4/82 (4%)

Query: 75  GGTMIKVK---TLTGKEIEIDIEP-TDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDK 130
           G   I+V       G+ +EI ++  ++ +  +KE++  +  IP  +Q+L      L D+ 
Sbjct: 26  GPATIRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNM 85

Query: 131 TARDYNIEGGSVLHLVLALRGG 152
           +   YN+  G +L L L  R G
Sbjct: 86  SLAHYNVGAGEILTLSLRERSG 107

>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 =  115 bits (288), Expect = 1e-31
 Identities = 23/80 (28%), Positives = 44/80 (55%), Gaps = 3/80 (3%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLA 57
          + I +KTL  +T  + +E  +T+  +K KI+ ++G    P   Q+LI+AGK L D   + 
Sbjct: 8  VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIR 67

Query: 58 DYNIQKESTLHLVLRLRGGT 77
          DY I +++ + +++      
Sbjct: 68 DYRIDEKNFVVVMVTKTKAG 87

>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 = 98.5 bits (244), Expect = 2e-25
 Identities = 29/86 (33%), Positives = 50/86 (58%), Gaps = 4/86 (4%)

Query: 72  RLRGGTM-IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEG---IPPVQQRLIYAGKQLA 127
            L    + I +KTL  +  +I +EP +T++ +KE++E ++G    P   Q+LIYAGK L+
Sbjct: 2   PLGSSAVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILS 61

Query: 128 DDKTARDYNIEGGSVLHLVLALRGGG 153
           DD   RDY I+  + + +++     G
Sbjct: 62  DDVPIRDYRIDEKNFVVVMVTKTKAG 87

>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 =  105 bits (263), Expect = 1e-30
 Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 1/70 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VK   GK+I L V    T+ ++K+++Q    + P  Q+LIF GK L +  TL   +
Sbjct: 13 IKLTVK-FGGKSIPLSVSPDCTVKDLKSQLQPITNVLPRGQKLIFKGKVLVETSTLKQSD 71

Query: 61 IQKESTLHLV 70
          +   + L L+
Sbjct: 72 VGSGAKLMLM 81

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana} Length = 85

 Score = 91.6 bits (228), Expect = 3e-25
 Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           + VK   GK I + + P  T++ +K +++    + P  Q+LI+ GK L +  T +  ++ 
Sbjct: 15  LTVK-FGGKSIPLSVSPDCTVKDLKSQLQPITNVLPRGQKLIFKGKVLVETSTLKQSDVG 73

Query: 139 GGSVLHLV 146
            G+ L L+
Sbjct: 74  SGAKLMLM 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 = 89.3 bits (221), Expect = 3e-24
 Identities = 19/91 (20%), Positives = 42/91 (46%), Gaps = 5/91 (5%)

Query: 1  MQIFVKT----LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQL-EDGRT 55
          M I V      LT  T +L+V     + N +   + + G+P ++ ++++  + L +D  +
Sbjct: 8  MLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLTDDHCS 67

Query: 56 LADYNIQKESTLHLVLRLRGGTMIKVKTLTG 86
          L  Y ++    + L+ +   G     +T +G
Sbjct: 68 LGSYGLKDGDMVVLLQKDNVGLRTPGRTPSG 98

>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 = 70.0 bits (171), Expect = 1e-16
 Identities = 17/82 (20%), Positives = 35/82 (42%), Gaps = 5/82 (6%)

Query: 76  GTMIKVKT----LTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADD-K 130
           G +I V      LT     + + P   +   +   E + G+P  + +++Y  + L DD  
Sbjct: 7   GMLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLTDDHC 66

Query: 131 TARDYNIEGGSVLHLVLALRGG 152
           +   Y ++ G ++ L+     G
Sbjct: 67  SLGSYGLKDGDMVVLLQKDNVG 88

>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 = 83.6 bits (206), Expect = 6e-22
 Identities = 13/72 (18%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-FAGKQLEDGRTLADY 59
          M  F      + + + +E + T+  +K  ++++  IP  +  L  +    +ED   L   
Sbjct: 9  MLDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGDVEDSTVLKSL 68

Query: 60 NIQKESTLHLVL 71
          ++ K ++L+++ 
Sbjct: 69 HLPKNNSLYVLT 80

>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 = 58.6 bits (141), Expect = 3e-12
 Identities = 12/81 (14%), Positives = 32/81 (39%), Gaps = 1/81 (1%)

Query: 74  RGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI-YAGKQLADDKTA 132
            G  +        + +++ +E T T+  IK+ +E +  IP  +  L  +    + D    
Sbjct: 6   SGRMLDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGDVEDSTVL 65

Query: 133 RDYNIEGGSVLHLVLALRGGG 153
           +  ++   + L+++       
Sbjct: 66  KSLHLPKNNSLYVLTPDLPPP 86

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A Length = 105

 Score = 77.4 bits (190), Expect = 1e-19
 Identities = 15/72 (20%), Positives = 31/72 (43%), Gaps = 1/72 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + +    +   TI L V    T+ ++K  +    G PP  Q+ +   +   D  TL  + 
Sbjct: 27 VSVEDAQMHTVTIWLTVRPDMTVASLKDMVFLDYGFPPVLQQWVIGQRLARDQETLHSHG 86

Query: 61 IQKE-STLHLVL 71
          +++   + +L L
Sbjct: 87 VRQNGDSAYLYL 98

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A Length = 105

 Score = 61.2 bits (148), Expect = 3e-13
 Identities = 15/70 (21%), Positives = 30/70 (42%), Gaps = 1/70 (1%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           ++   +    I + + P  T+  +K+ V    G PPV Q+ +   +   D +T   + + 
Sbjct: 29  VEDAQMHTVTIWLTVRPDMTVASLKDMVFLDYGFPPVLQQWVIGQRLARDQETLHSHGVR 88

Query: 139 G-GSVLHLVL 147
             G   +L L
Sbjct: 89  QNGDSAYLYL 98

>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 = 68.9 bits (168), Expect = 4e-16
 Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 8/83 (9%)

Query: 1  MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADY 59
          M +F+     K TI  + + S T+  +K  ++     PP++QRL    + L+DG+TL + 
Sbjct: 1  MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPEEQRLYKDDQLLDDGKTLGEC 60

Query: 60 NI-------QKESTLHLVLRLRG 75
                   Q  +T+ L  R   
Sbjct: 61 GFTSQTARPQAPATVGLAFRADD 83

>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 = 50.0 bits (119), Expect = 7e-09
 Identities = 21/81 (25%), Positives = 31/81 (38%), Gaps = 8/81 (9%)

Query: 78  MIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNI 137
           MI+    T   I  D + + T+  +K  VE     PP +QRL    + L D KT  +   
Sbjct: 6   MIRRHKTT---IFTDAKESSTVFELKRIVEGILKRPPEEQRLYKDDQLLDDGKTLGECGF 62

Query: 138 EGGSVL-----HLVLALRGGG 153
              +        + LA R   
Sbjct: 63  TSQTARPQAPATVGLAFRADD 83

>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 = 65.0 bits (158), Expect = 7e-15
 Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 6/82 (7%)

Query: 1  MQIFVKT--LTGKTITLEVESSDTIDNVKAKIQDK--EGIPPDQQRLIFAGKQLEDGRTL 56
          + + VK+     + + L  +   ++ ++KA +     E   P+ QRLI++GK L D + L
Sbjct: 8  VTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCL 67

Query: 57 ADYNIQKES--TLHLVLRLRGG 76
           D   ++E    LHLV  ++ G
Sbjct: 68 RDLLPKQEKRHVLHLVCNVKSG 89

>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 = 63.1 bits (153), Expect = 4e-14
 Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 4/78 (5%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEK--EGIPPVQQRLIYAGKQLADDKTARDY- 135
           +K      +++E+  +   ++  +K  +     E   P  QRLIY+GK L D +  RD  
Sbjct: 12  VKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLL 71

Query: 136 -NIEGGSVLHLVLALRGG 152
              E   VLHLV  ++ G
Sbjct: 72  PKQEKRHVLHLVCNVKSG 89

>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 = 64.0 bits (156), Expect = 2e-14
 Identities = 13/70 (18%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + + +         ++V    T   +K KI    G+PP  Q++++ G  + + +TL +  
Sbjct: 18 VDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGL-VPEDKTLREIK 75

Query: 61 IQKESTLHLV 70
          +   + + +V
Sbjct: 76 VTSGAKIMVV 85

>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 = 63.3 bits (154), Expect = 4e-14
 Identities = 16/73 (21%), Positives = 38/73 (52%), Gaps = 2/73 (2%)

Query: 75  GGTMIKVK-TLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTAR 133
           G  ++ +K      + ++ +    T   +K+++    G+PP  Q+++Y G  + +DKT R
Sbjct: 14  GKELVDLKIIWNKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGL-VPEDKTLR 72

Query: 134 DYNIEGGSVLHLV 146
           +  +  G+ + +V
Sbjct: 73  EIKVTSGAKIMVV 85

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens} Length = 125

 Score = 63.9 bits (155), Expect = 4e-14
 Identities = 17/82 (20%), Positives = 36/82 (43%), Gaps = 10/82 (12%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKI--------QDKEGIPPDQQRLIFAGKQLED 52
          + + +  ++GKT       +D+  ++   +        ++++   P+  RLI+ G+ L  
Sbjct: 18 INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHG 77

Query: 53 GRTLADYNIQKEST--LHLVLR 72
            TL    +    T  +HLV R
Sbjct: 78 NVTLGALKLPFGKTTVMHLVAR 99

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens} Length = 125

 Score = 60.4 bits (146), Expect = 8e-13
 Identities = 20/80 (25%), Positives = 33/80 (41%), Gaps = 8/80 (10%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERV--------EEKEGIPPVQQRLIYAGKQLADDK 130
           +++  ++GK  E    P D+   I + V        EE++   P   RLIY G+ L  + 
Sbjct: 20  LRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNV 79

Query: 131 TARDYNIEGGSVLHLVLALR 150
           T     +  G    + L  R
Sbjct: 80  TLGALKLPFGKTTVMHLVAR 99

>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 = 62.2 bits (151), Expect = 8e-14
 Identities = 13/70 (18%), Positives = 32/70 (45%), Gaps = 1/70 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
            + VK    K   +E+ + +     KA++    G+ P +Q+++  G  L+D     +  
Sbjct: 8  YSVTVKWGKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLKDD-DWGNIK 66

Query: 61 IQKESTLHLV 70
          ++   T+ ++
Sbjct: 67 MKNGMTVLMM 76

>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 = 57.6 bits (139), Expect = 5e-12
 Identities = 12/68 (17%), Positives = 30/68 (44%), Gaps = 1/68 (1%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           + VK    K   +++   +     K ++    G+ P +Q+++  G  L DD    +  ++
Sbjct: 10  VTVKWGKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLKDD-DWGNIKMK 68

Query: 139 GGSVLHLV 146
            G  + ++
Sbjct: 69  NGMTVLMM 76

>3plu_A Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-1, SNU66, peptide binding protein; 1.40A {Saccharomyces cerevisiae} PDB: 3plv_A 1m94_A 1p0r_A Length = 93

 Score = 62.3 bits (151), Expect = 9e-14
 Identities = 16/69 (23%), Positives = 34/69 (49%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ V    GK + ++    D++ + K  +  + G  P++  L   G  L+D  +L DY 
Sbjct: 22 IEVVVNDRLGKKVRVKCLGEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHISLEDYE 81

Query: 61 IQKESTLHL 69
          +  ++ L L
Sbjct: 82 VHDQTNLEL 90

>3plu_A Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-1, SNU66, peptide binding protein; 1.40A {Saccharomyces cerevisiae} PDB: 3plv_A 1m94_A 1p0r_A Length = 93

 Score = 51.1 bits (122), Expect = 1e-09
 Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 2/74 (2%)

Query: 74  RGGTMIKV--KTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKT 131
           RG  MI+V      GK++ +     D++   K+ +  + G  P +  L   G  L D  +
Sbjct: 17  RGSHMIEVVVNDRLGKKVRVKCLGEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHIS 76

Query: 132 ARDYNIEGGSVLHL 145
             DY +   + L L
Sbjct: 77  LEDYEVHDQTNLEL 90

>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 = 62.0 bits (150), Expect = 2e-13
 Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 10/82 (12%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQD-------KEGIP-PDQQRLIFAGKQLED 52
          + + +  ++GKT       +D+  ++   + D       +E +  P+  RLI+ G+ L  
Sbjct: 17 INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHG 76

Query: 53 GRTLADYNIQ--KESTLHLVLR 72
            TL    +   K + +HLV R
Sbjct: 77 NVTLGALKLPFGKTTVMHLVAR 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 = 57.0 bits (137), Expect = 2e-11
 Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 10/79 (12%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERV--------EEKEGIPPVQQRLIYAGKQLADDK 130
           +++  ++GK  E    P D+   I + V        EE++   P   RLIY G+ L  + 
Sbjct: 19  LRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNV 78

Query: 131 TARDYNIEGGS--VLHLVL 147
           T     +  G   V+HLV 
Sbjct: 79  TLGALKLPFGKTTVMHLVA 97

>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 = 61.1 bits (148), Expect = 4e-13
 Identities = 13/82 (15%), Positives = 30/82 (36%), Gaps = 12/82 (14%)

Query: 1  MQIFVK---TLTGKTITLE--VESSDTIDNVKAKIQDKEGIPPDQQRLI-------FAGK 48
          M        T       +E    +  +++++K K++   G   D  R+          G+
Sbjct: 3  MTEVYDLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGE 62

Query: 49 QLEDGRTLADYNIQKESTLHLV 70
            +  ++L D  ++    +H V
Sbjct: 63 LTDGAKSLKDLGVRDGYRIHAV 84

>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 = 57.6 bits (139), Expect = 8e-12
 Identities = 12/80 (15%), Positives = 28/80 (35%), Gaps = 10/80 (12%)

Query: 77  TMIKVK---TLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIY-------AGKQL 126
            +  ++     T   +E       ++  +K+++E   G      R+          G+  
Sbjct: 5   EVYDLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGELT 64

Query: 127 ADDKTARDYNIEGGSVLHLV 146
              K+ +D  +  G  +H V
Sbjct: 65  DGAKSLKDLGVRDGYRIHAV 84

>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 = 59.8 bits (144), Expect = 1e-12
 Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 11/83 (13%)

Query: 1  MQIFVKTLTGKTITLEVE--------SSDTIDNVKAKIQDKEGI---PPDQQRLIFAGKQ 49
          +++  + L  K+I    E           +I  +K  I  K       P+   LI+ G++
Sbjct: 17 VKLADQPLAPKSILQLPETELGEYSLGGYSISFLKQLIAGKLQESVPDPELIDLIYCGRK 76

Query: 50 LEDGRTLADYNIQKESTLHLVLR 72
          L+D +TL  Y IQ  ST+H++ +
Sbjct: 77 LKDDQTLDFYGIQPGSTVHVLRK 99

>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 = 57.9 bits (139), Expect = 6e-12
 Identities = 24/87 (27%), Positives = 40/87 (45%), Gaps = 5/87 (5%)

Query: 65  STLHLVLRLRGGTMIKVKTLTGKEIEI-DIEPTD-TIERIKERVEEKEGI---PPVQQRL 119
           S  HL ++L    +     L   E E+ +      +I  +K+ +  K       P    L
Sbjct: 11  SDWHLAVKLADQPLAPKSILQLPETELGEYSLGGYSISFLKQLIAGKLQESVPDPELIDL 70

Query: 120 IYAGKQLADDKTARDYNIEGGSVLHLV 146
           IY G++L DD+T   Y I+ GS +H++
Sbjct: 71  IYCGRKLKDDQTLDFYGIQPGSTVHVL 97

>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 = 59.3 bits (143), Expect = 1e-12
 Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 4/69 (5%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADD-KTARDYNI 137
           +++K L   E      P DT+  +K +    +     Q +LIY G+ L D  +T    NI
Sbjct: 10  VRLKFLNDTEELAVARPEDTVGTLKSKYFPGQ---ESQMKLIYQGRLLQDPARTLSSLNI 66

Query: 138 EGGSVLHLV 146
               V+H  
Sbjct: 67  TNNCVIHCH 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 = 57.7 bits (139), Expect = 4e-12
 Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 4/73 (5%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQL-EDGRTLADY 59
          + + +K L            DT+  +K+K    +     Q +LI+ G+ L +  RTL+  
Sbjct: 8  INVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQ---ESQMKLIYQGRLLQDPARTLSSL 64

Query: 60 NIQKESTLHLVLR 72
          NI     +H    
Sbjct: 65 NITNNCVIHCHRS 77

>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 Length = 100

 Score = 59.3 bits (143), Expect = 1e-12
 Identities = 16/69 (23%), Positives = 30/69 (43%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++      GK + ++  + DTI ++K  I  + G   ++  L       +D  +L DY 
Sbjct: 29 IEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSLGDYE 88

Query: 61 IQKESTLHL 69
          I     L L
Sbjct: 89 IHDGMNLEL 97

>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 Length = 100

 Score = 49.7 bits (118), Expect = 6e-09
 Identities = 19/73 (26%), Positives = 29/73 (39%), Gaps = 2/73 (2%)

Query: 75  GGTMIKV--KTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTA 132
             TMI+V      GK++ +     DTI  +K+ +  + G    +  L        D  + 
Sbjct: 25  AATMIEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSL 84

Query: 133 RDYNIEGGSVLHL 145
            DY I  G  L L
Sbjct: 85  GDYEIHDGMNLEL 97

>2k8h_A Small ubiquitin protein; SUMO, post-translational modifier, signaling protein; NMR {Trypanosoma brucei} Length = 110

 Score = 58.0 bits (140), Expect = 5e-12
 Identities = 16/75 (21%), Positives = 35/75 (46%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           +KV    G E+   I+    ++++ +   +K+GI     R ++ G  + + KT  +  +E
Sbjct: 29  VKVVNADGAEMFFRIKSRTALKKLIDTYCKKQGISRNSVRFLFDGTPIDETKTPEELGME 88

Query: 139 GGSVLHLVLALRGGG 153
              V+  ++   GG 
Sbjct: 89  DDDVIDAMVEQTGGL 103

>2k8h_A Small ubiquitin protein; SUMO, post-translational modifier, signaling protein; NMR {Trypanosoma brucei} Length = 110

 Score = 43.8 bits (103), Expect = 1e-06
 Identities = 12/76 (15%), Positives = 33/76 (43%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           + + V    G  +   ++S   +  +      K+GI  +  R +F G  +++ +T  +  
Sbjct: 27  VAVKVVNADGAEMFFRIKSRTALKKLIDTYCKKQGISRNSVRFLFDGTPIDETKTPEELG 86

Query: 61  IQKESTLHLVLRLRGG 76
           ++ +  +  ++   GG
Sbjct: 87  MEDDDVIDAMVEQTGG 102

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens} Length = 99

 Score = 57.6 bits (139), Expect = 6e-12
 Identities = 16/76 (21%), Positives = 31/76 (40%), Gaps = 6/76 (7%)

Query: 1  MQIFVKTLTGK--TITLEVESSDTIDNVKAKIQDK--EGIPPDQQRLIFAGKQLEDGRTL 56
          + + +K    K    T+    + T+  +K  + +          QRL+++G+ L D   L
Sbjct: 24 VTLIIKAPNQKYSDQTISCFLNWTVGKLKTHLSNVYPSKPLTKDQRLVYSGRLLPDHLQL 83

Query: 57 AD--YNIQKESTLHLV 70
           D      +   +HLV
Sbjct: 84 KDILRKQDEYHMVHLV 99

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens} Length = 99

 Score = 57.3 bits (138), Expect = 9e-12
 Identities = 16/72 (22%), Positives = 28/72 (38%), Gaps = 4/72 (5%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEK--EGIPPVQQRLIYAGKQLADDKTARD-- 134
           IK       +  I      T+ ++K  +            QRL+Y+G+ L D    +D  
Sbjct: 28  IKAPNQKYSDQTISCFLNWTVGKLKTHLSNVYPSKPLTKDQRLVYSGRLLPDHLQLKDIL 87

Query: 135 YNIEGGSVLHLV 146
              +   ++HLV
Sbjct: 88  RKQDEYHMVHLV 99

>2io0_B Small ubiquitin-related modifier 2 precursor; SUMO, SENP, ULP, complex, protein binding, hydrolase; 2.30A {Homo sapiens} SCOP: d.15.1.1 Length = 91

 Score = 54.4 bits (131), Expect = 8e-11
 Identities = 13/74 (17%), Positives = 31/74 (41%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           +KV    G  ++  I+    + ++ +   E++G+   Q R  + G+ + +  T     +E
Sbjct: 8   LKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEME 67

Query: 139 GGSVLHLVLALRGG 152
               + +     GG
Sbjct: 68  DEDTIDVFQQQTGG 81

>2io0_B Small ubiquitin-related modifier 2 precursor; SUMO, SENP, ULP, complex, protein binding, hydrolase; 2.30A {Homo sapiens} SCOP: d.15.1.1 Length = 91

 Score = 41.3 bits (97), Expect = 7e-06
 Identities = 13/80 (16%), Positives = 35/80 (43%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + + V    G  +  +++    +  +     +++G+   Q R  F G+ + +  T A   
Sbjct: 6  INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLE 65

Query: 61 IQKESTLHLVLRLRGGTMIK 80
          ++ E T+ +  +  GG  ++
Sbjct: 66 MEDEDTIDVFQQQTGGVYLE 85

>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 Length = 97

 Score = 51.8 bits (124), Expect = 9e-10
 Identities = 18/74 (24%), Positives = 40/74 (54%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           +KV      EI   ++ T  ++++KE   +++G+P    R ++ G+++AD+ T ++  +E
Sbjct: 24  LKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGME 83

Query: 139 GGSVLHLVLALRGG 152
              V+ +     GG
Sbjct: 84  EEDVIEVYQEQTGG 97

>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 Length = 97

 Score = 39.1 bits (91), Expect = 6e-05
 Identities = 14/76 (18%), Positives = 36/76 (47%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ V       I  +V+ +  +  +K     ++G+P +  R +F G+++ D  T  +  
Sbjct: 22 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELG 81

Query: 61 IQKESTLHLVLRLRGG 76
          +++E  + +     GG
Sbjct: 82 MEEEDVIEVYQEQTGG 97

>1wz0_A Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-like molecule, structural genomics, sentrin2, NPPFSA; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 104

 Score = 49.5 bits (118), Expect = 7e-09
 Identities = 12/75 (16%), Positives = 30/75 (40%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           +KV    G  ++  I+    + ++ +   E++G+   Q R  + G+ + +  T     +E
Sbjct: 27  LKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEME 86

Query: 139 GGSVLHLVLALRGGG 153
               + +      G 
Sbjct: 87  DEDTIDVFQQQTSGP 101

>1wz0_A Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-like molecule, structural genomics, sentrin2, NPPFSA; NMR {Homo sapiens} SCOP: d.15.1.1 Length = 104

 Score = 37.5 bits (87), Expect = 2e-04
 Identities = 12/76 (15%), Positives = 32/76 (42%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           + + V    G  +  +++    +  +     +++G+   Q R  F G+ + +  T A   
Sbjct: 25  INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLE 84

Query: 61  IQKESTLHLVLRLRGG 76
           ++ E T+ +  +   G
Sbjct: 85  MEDEDTIDVFQQQTSG 100

>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 Length = 79

 Score = 49.0 bits (117), Expect = 8e-09
 Identities = 18/74 (24%), Positives = 40/74 (54%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           +KV      EI   ++ T  ++++KE   +++G+P    R ++ G+++AD+ T ++  +E
Sbjct: 6   LKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGME 65

Query: 139 GGSVLHLVLALRGG 152
              V+ +     GG
Sbjct: 66  EEDVIEVYQEQTGG 79

>2io1_B Small ubiquitin-related modifier 3 precursor; SUMO, SENP, ULP, complex, protein binding, hydrolase; 2.60A {Homo sapiens} SCOP: d.15.1.1 Length = 94

 Score = 49.1 bits (117), Expect = 9e-09
 Identities = 13/75 (17%), Positives = 31/75 (41%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           +KV    G  ++  I+    + ++ +   E++G+   Q R  + G+ + +  T     +E
Sbjct: 10  LKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEME 69

Query: 139 GGSVLHLVLALRGGG 153
               + +     GG 
Sbjct: 70  DEDTIDVFQQQTGGV 84

>2io1_B Small ubiquitin-related modifier 3 precursor; SUMO, SENP, ULP, complex, protein binding, hydrolase; 2.60A {Homo sapiens} SCOP: d.15.1.1 Length = 94

 Score = 36.3 bits (84), Expect = 5e-04
 Identities = 13/76 (17%), Positives = 33/76 (43%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + + V    G  +  +++    +  +     +++G+   Q R  F G+ + +  T A   
Sbjct: 8  INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLE 67

Query: 61 IQKESTLHLVLRLRGG 76
          ++ E T+ +  +  GG
Sbjct: 68 MEDEDTIDVFQQQTGG 83

>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 Length = 90

 Score = 47.6 bits (113), Expect = 3e-08
 Identities = 15/74 (20%), Positives = 37/74 (50%), Gaps = 5/74 (6%)

Query: 1  MQIFVKTLTGKTITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLI---FAGKQLEDGRTL 56
          + I VK   G+  ++  +   DT+ ++K  ++   G+ P++Q+L+     GK  E+   L
Sbjct: 8  LPIIVKW-GGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKL 66

Query: 57 ADYNIQKESTLHLV 70
              ++  + + ++
Sbjct: 67 GALKLKPNTKIMMM 80

>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 Length = 90

 Score = 46.8 bits (111), Expect = 5e-08
 Identities = 15/72 (20%), Positives = 34/72 (47%), Gaps = 5/72 (6%)

Query: 79  IKVKTLTGKEIEID-IEPTDTIERIKERVEEKEGIPPVQQRLIY---AGKQLADDKTARD 134
           I VK   G+E  +  +   DT+  +K+ ++   G+ P +Q+L+     GK   +D     
Sbjct: 10  IIVKW-GGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGA 68

Query: 135 YNIEGGSVLHLV 146
             ++  + + ++
Sbjct: 69  LKLKPNTKIMMM 80

>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 Length = 93

 Score = 47.1 bits (112), Expect = 5e-08
 Identities = 13/74 (17%), Positives = 31/74 (41%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           +KV    G  ++  I+    + ++ +   E++G+   Q R  + G+ + +  T     +E
Sbjct: 20  LKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEME 79

Query: 139 GGSVLHLVLALRGG 152
               + +     GG
Sbjct: 80  DEDTIDVFQQQTGG 93

>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 Length = 105

 Score = 46.1 bits (109), Expect = 1e-07
 Identities = 19/91 (20%), Positives = 39/91 (42%), Gaps = 16/91 (17%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQR---------------LIF 45
          M + V  + G+ + + V  + T+ ++K  IQ    +  +++                L  
Sbjct: 8  MTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTS 67

Query: 46 AGKQL-EDGRTLADYNIQKESTLHLVLRLRG 75
          AG++L ED + L DY I+    +  + +L  
Sbjct: 68 AGEKLTEDRKKLRDYGIRNRDEVSFIKKLGQ 98

>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 Length = 105

 Score = 41.9 bits (98), Expect = 6e-06
 Identities = 15/91 (16%), Positives = 35/91 (38%), Gaps = 16/91 (17%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQR---------------LIYAG 123
           ++V  + G+ + + +    T+  +K+ ++    +   ++                L  AG
Sbjct: 10  VRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAG 69

Query: 124 KQLADD-KTARDYNIEGGSVLHLVLALRGGG 153
           ++L +D K  RDY I     +  +  L    
Sbjct: 70  EKLTEDRKKLRDYGIRNRDEVSFIKKLGQKS 100

>2kj6_A Tubulin folding cofactor B; methods development, NESG, solution PSI-2, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} Length = 97

 Score = 44.9 bits (106), Expect = 4e-07
 Identities = 13/76 (17%), Positives = 25/76 (32%), Gaps = 7/76 (9%)

Query: 78  MIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIY-------AGKQLADDK 130
            I    L     +    P  ++E +KE++ +K G       L               D +
Sbjct: 18  HITHANLKSFSADARFSPQMSVEAVKEKLWKKCGTSVNSMALELYDDSGSKVAVLSDDSR 77

Query: 131 TARDYNIEGGSVLHLV 146
               ++   G  LH++
Sbjct: 78  PLGFFSPFDGFRLHII 93

>2kj6_A Tubulin folding cofactor B; methods development, NESG, solution PSI-2, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} Length = 97

 Score = 43.7 bits (103), Expect = 1e-06
 Identities = 12/72 (16%), Positives = 23/72 (31%), Gaps = 7/72 (9%)

Query: 6  KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-------FAGKQLEDGRTLAD 58
            L   +         +++ VK K+  K G   +   L              +D R L  
Sbjct: 22 ANLKSFSADARFSPQMSVEAVKEKLWKKCGTSVNSMALELYDDSGSKVAVLSDDSRPLGF 81

Query: 59 YNIQKESTLHLV 70
          ++      LH++
Sbjct: 82 FSPFDGFRLHII 93

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster} Length = 320

 Score = 46.7 bits (110), Expect = 6e-07
 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 3/61 (4%)

Query: 86  GKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYA---GKQLADDKTARDYNIEGGSV 142
           GKE  +D+   DT+E ++  +  K  + P +Q+L+     GK  AD+       ++    
Sbjct: 14  GKEYPVDLTDQDTVEVLRHEIFRKTQVRPERQKLLNLKYKGKTAADNVKISALELKPNFK 73

Query: 143 L 143
           L
Sbjct: 74  L 74

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster} Length = 320

 Score = 44.4 bits (104), Expect = 3e-06
 Identities = 13/61 (21%), Positives = 31/61 (50%), Gaps = 3/61 (4%)

Query: 10 GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI---FAGKQLEDGRTLADYNIQKEST 66
          GK   +++   DT++ ++ +I  K  + P++Q+L+   + GK   D   ++   ++    
Sbjct: 14 GKEYPVDLTDQDTVEVLRHEIFRKTQVRPERQKLLNLKYKGKTAADNVKISALELKPNFK 73

Query: 67 L 67
          L
Sbjct: 74 L 74

>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative, hydrolase; NMR {Mus musculus} Length = 86

 Score = 43.3 bits (102), Expect = 1e-06
 Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 5/71 (7%)

Query: 2  QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE---DGRTL 56
          ++  K   G  +   + S   +  ++ +I    GI P  QR++  +  + L+      TL
Sbjct: 2  RVRCKAKGGTHLLQGLSSRTRLRELQGQIAAITGIAPGSQRILVGYPPECLDLSDRDITL 61

Query: 57 ADYNIQKESTL 67
           D  IQ    L
Sbjct: 62 GDLPIQSGDML 72

>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative, hydrolase; NMR {Mus musculus} Length = 86

 Score = 40.2 bits (94), Expect = 2e-05
 Identities = 15/70 (21%), Positives = 29/70 (41%), Gaps = 5/70 (7%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI--YAGKQLA---DDKTAR 133
           ++ K   G  +   +     +  ++ ++    GI P  QR++  Y  + L     D T  
Sbjct: 3   VRCKAKGGTHLLQGLSSRTRLRELQGQIAAITGIAPGSQRILVGYPPECLDLSDRDITLG 62

Query: 134 DYNIEGGSVL 143
           D  I+ G +L
Sbjct: 63  DLPIQSGDML 72

>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 Length = 92

 Score = 42.4 bits (99), Expect = 3e-06
 Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 1/56 (1%)

Query: 92  DIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLAD-DKTARDYNIEGGSVLHLV 146
                  ++ + + VEE  G+P   Q+LI+ GK L + +       I+ G  + L+
Sbjct: 27  QGSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVMLI 82

>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 Length = 92

 Score = 39.7 bits (92), Expect = 3e-05
 Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 19 SSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQL-EDGRTLADYNIQKESTLHLV 70
          S   + ++   +++  G+P   Q+LIF GK L E    L+   IQ    + L+
Sbjct: 30 SEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVMLI 82

>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 Length = 95

 Score = 42.2 bits (99), Expect = 4e-06
 Identities = 14/71 (19%), Positives = 24/71 (33%), Gaps = 7/71 (9%)

Query: 83  TLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIY-------AGKQLADDKTARDY 135
           +L     E     + TI   K ++E   G P     L           K   +D     Y
Sbjct: 15  SLNSFRSEKRYSRSLTIAEFKCKLELVVGSPASCMELELYGADDKFYSKLDQEDALLGSY 74

Query: 136 NIEGGSVLHLV 146
            ++ G  +H++
Sbjct: 75  PVDDGCRIHVI 85

>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 Length = 95

 Score = 39.1 bits (91), Expect = 5e-05
 Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 7/58 (12%)

Query: 20 SDTIDNVKAKIQDKEGIPPDQQRLI-------FAGKQLEDGRTLADYNIQKESTLHLV 70
          S TI   K K++   G P     L        F  K  ++   L  Y +     +H++
Sbjct: 28 SLTIAEFKCKLELVVGSPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIHVI 85

>1se9_A Ubiquitin family; ubiquitin-like, cell-free, wheat GERM, structural genomics, protein structure initiative, CESG; NMR {Arabidopsis thaliana} SCOP: d.15.1.1 Length = 126

 Score = 42.7 bits (100), Expect = 4e-06
 Identities = 25/97 (25%), Positives = 39/97 (40%), Gaps = 22/97 (22%)

Query: 64  ESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERV-----EEKEGIP--PVQ 116
            + L +  RL  G+ I  K               T+  +KE V      EKE  P    +
Sbjct: 14  HNQLEIKFRLTDGSDIGPKA---------FPDATTVSALKETVISEWPREKENGPKTVKE 64

Query: 117 QRLIYAGKQLADDKTARDYNI------EGGSVLHLVL 147
            +LI AGK L + KT +DY           + +H+++
Sbjct: 65  VKLISAGKVLENSKTVKDYRSPVSNLAGAVTTMHVII 101

>1se9_A Ubiquitin family; ubiquitin-like, cell-free, wheat GERM, structural genomics, protein structure initiative, CESG; NMR {Arabidopsis thaliana} SCOP: d.15.1.1 Length = 126

 Score = 41.2 bits (96), Expect = 2e-05
 Identities = 17/67 (25%), Positives = 34/67 (50%), Gaps = 13/67 (19%)

Query: 19  SSDTIDNVKAKI-----QDKEGIP--PDQQRLIFAGKQLEDGRTLADYNIQ------KES 65
            + T+  +K  +     ++KE  P    + +LI AGK LE+ +T+ DY           +
Sbjct: 36  DATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSKTVKDYRSPVSNLAGAVT 95

Query: 66  TLHLVLR 72
           T+H++++
Sbjct: 96  TMHVIIQ 102

>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} Length = 207

 Score = 43.6 bits (102), Expect = 5e-06
 Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 1/74 (1%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           +KV      EI   I+ T  + R+ E   +++G        +Y G ++  D+T  D ++E
Sbjct: 60  LKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLTFLYDGIEIQADQTPEDLDME 118

Query: 139 GGSVLHLVLALRGG 152
              ++       GG
Sbjct: 119 DNDIIEAHREQIGG 132

>2eke_C Ubiquitin-like protein SMT3; UBC9, SUMO binding motif, SBM, ligase/protein binding complex; 1.90A {Saccharomyces cerevisiae} SCOP: d.15.1.1 Length = 106

 Score = 41.1 bits (96), Expect = 1e-05
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 1/74 (1%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           +KV      EI   I+ T  + R+ E   +++G      R +Y G ++  D+T  D ++E
Sbjct: 34  LKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDME 92

Query: 139 GGSVLHLVLALRGG 152
              ++       GG
Sbjct: 93  DNDIIEAHREQIGG 106

>2kjr_A CG11242; UBL, ubiquitin, ubiquitin-like, structural genomics, PSI-2, protein structure initiative; NMR {Drosophila melanogaster} Length = 95

 Score = 38.3 bits (89), Expect = 1e-04
 Identities = 12/75 (16%), Positives = 26/75 (34%), Gaps = 6/75 (8%)

Query: 78  MIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRL-IYAGKQLA-----DDKT 131
            +          E+ +    T+ ++K ++E   G      ++ ++ G         +D  
Sbjct: 19  NVSNSHNDAVAFEVKLAKDLTVAQLKTKLEILTGGCAGTMKVQVFKGDTCVSTMDNNDAQ 78

Query: 132 ARDYNIEGGSVLHLV 146
              Y    G  LH+V
Sbjct: 79  LGYYANSDGLRLHVV 93

>2kjr_A CG11242; UBL, ubiquitin, ubiquitin-like, structural genomics, PSI-2, protein structure initiative; NMR {Drosophila melanogaster} Length = 95

 Score = 36.4 bits (84), Expect = 6e-04
 Identities = 9/55 (16%), Positives = 17/55 (30%), Gaps = 6/55 (10%)

Query: 22 TIDNVKAKIQDKEGIPPDQQRLI------FAGKQLEDGRTLADYNIQKESTLHLV 70
          T+  +K K++   G      ++              +   L  Y       LH+V
Sbjct: 39 TVAQLKTKLEILTGGCAGTMKVQVFKGDTCVSTMDNNDAQLGYYANSDGLRLHVV 93

>4efo_A Serine/threonine-protein kinase TBK1; ubiquitin like domain, transferase; 1.77A {Homo sapiens} Length = 94

 Score = 36.4 bits (84), Expect = 5e-04
 Identities = 13/51 (25%), Positives = 21/51 (41%), Gaps = 2/51 (3%)

Query: 87  KEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGK--QLADDKTARDY 135
              +I I   +T     E V ++  I    Q LIY G+   L   + A+ +
Sbjct: 24  TAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLVLEPGRLAQHF 74

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	154
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	100.0
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	100.0
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	100.0
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	99.88
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	99.88
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	99.87
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	99.87
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	99.86
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	99.86
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	99.86
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	99.86
4hcn_B	98	Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidas	99.86
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	99.86
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	99.86
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	99.86
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	99.85
2uyz_B	79	Small ubiquitin-related modifier 1; sumoylation, c	99.85
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	99.85
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	99.85
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	99.85
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	99.84
1wyw_B	97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	99.84
3vdz_A	111	Ubiquitin-40S ribosomal protein S27A; gadolinium,	99.84
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	99.84
3phx_B	79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	99.84
4fbj_B	88	NEDD8; effector-HOST target complex, glutamine dea	99.83
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	99.83
1we6_A	111	Splicing factor, putative; structural genomics, ub	99.83
3v6c_B	91	Ubiquitin; structural genomics, structural genomic	99.83
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	99.83
3plu_A	93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	99.83
1yx5_B	98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	99.83
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	99.82
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	99.82
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	99.81
1ndd_A	76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	99.81
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	99.81
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	99.81
2kk8_A	84	Uncharacterized protein AT4G05270; solution arabid	99.81
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	99.81
3a9j_A	76	Ubiquitin; protein complex, cytoplasm, isopeptide	99.81
4hcn_B	98	Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidas	99.81
3v6c_B	91	Ubiquitin; structural genomics, structural genomic	99.81
3dbh_I	88	NEDD8; cell cycle, activating enzyme, apoptosis, m	99.81
2kdi_A	114	Ubiquitin, vacuolar protein sorting-associated pro	99.81
3k9o_B	96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	99.81
1sif_A	88	Ubiquitin; hydrophobic mutants, folding, stability	99.8
3n3k_B	85	Ubiquitin; hydrolase, protease, thiol protease, DU	99.8
4dwf_A	90	HLA-B-associated transcript 3; ubiquitin-like doma	99.8
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	99.8
3mtn_B	85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	99.8
2lxa_A	87	Ubiquitin-like protein MDY2; ubiquitin-like domain	99.8
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	99.8
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	99.8
4eew_A	88	Large proline-rich protein BAG6; ubiquitin-like fo	99.8
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	99.8
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	99.8
2uyz_B	79	Small ubiquitin-related modifier 1; sumoylation, c	99.8
1uh6_A	100	Ubiquitin-like 5; beta-grAsp fold, structural geno	99.79
2faz_A	78	Ubiquitin-like containing PHD and ring finger DOM	99.79
2hj8_A	88	Interferon-induced 17 kDa protein; HR2873B, human	99.79
3l0w_B	169	Monoubiquitinated proliferating cell nuclear antig	99.79
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	99.79
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	99.79
2dzi_A	81	Ubiquitin-like protein 4A; GDX, structural genomic	99.79
1wh3_A	87	59 kDa 2'-5'-oligoadenylate synthetase like protei	99.79
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	99.79
2lxa_A	87	Ubiquitin-like protein MDY2; ubiquitin-like domain	99.79
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	99.66
1uel_A	95	HHR23B, UV excision repair protein RAD23 homolog B	99.79
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	99.79
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	99.78
3m62_B	106	UV excision repair protein RAD23; armadillo-like r	99.78
3vdz_A	111	Ubiquitin-40S ribosomal protein S27A; gadolinium,	99.78
4a20_A	98	Ubiquitin-like protein MDY2; protein binding, GET-	99.78
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	99.78
2wyq_A	85	HHR23A, UV excision repair protein RAD23 homolog A	99.78
2kan_A	94	Uncharacterized protein AR3433A; ubiquitin fold, a	99.78
1wy8_A	89	NP95-like ring finger protein, isoform A; ubiquiti	99.78
3q3f_A	189	Ribonuclease/ubiquitin chimeric protein; domain SW	99.78
1wju_A	100	NEDD8 ultimate buster-1; ubiquitin-like domain, st	99.78
4a20_A	98	Ubiquitin-like protein MDY2; protein binding, GET-	99.78
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	99.77
2bwf_A	77	Ubiquitin-like protein DSK2; signaling protein, UB	99.77
1wyw_B	97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	99.77
3u5c_f	152	40S ribosomal protein S31; translation, ribosome,	99.77
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	99.77
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	99.77
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	99.77
2l7r_A	93	Ubiquitin-like protein FUBI; structural genomics,	99.76
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	99.76
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	99.76
3b1l_X	76	E3 ubiquitin-protein ligase parkin; proteasome, AL	99.62
3u30_A	172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.76
1wgd_A	93	Homocysteine-responsive endoplasmic reticulum- res	99.76
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	99.75
2ojr_A	111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	99.75
1se9_A	126	Ubiquitin family; ubiquitin-like, cell-free, wheat	99.75
4ajy_B	118	Transcription elongation factor B polypeptide 2; E	99.75
1ttn_A	106	DC-UBP, dendritic cell-derived ubiquitin-like prot	99.75
4ajy_B	118	Transcription elongation factor B polypeptide 2; E	99.74
1yqb_A	100	Ubiquilin 3; structural genomics consortium, ubiqu	99.74
2klc_A	101	Ubiquilin-1; ubiquitin-like, structural genomics,	99.74
1wx8_A	96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	99.74
3rt3_B	159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.73
2fnj_B	118	Transcription elongation factor B polypeptide 2; b	99.73
1v2y_A	105	3300001G02RIK protein; hypothetical protein, ubiqu	99.73
1j8c_A	125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	99.73
1wju_A	100	NEDD8 ultimate buster-1; ubiquitin-like domain, st	99.73
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	99.73
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	99.73
1wx7_A	106	Ubiquilin 3; ubiquitin-like domain, structural gen	99.72
1we6_A	111	Splicing factor, putative; structural genomics, ub	99.72
1v5o_A	102	1700011N24RIK protein; hypothetical protein, ubiqu	99.72
3m63_B	101	Ubiquitin domain-containing protein DSK2; armadill	99.72
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	99.71
3u5e_m	128	60S ribosomal protein L40; translation, ribosome,	99.71
3b08_A	152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.71
2daf_A	118	FLJ35834 protein; hypothetical protein FLJ35834, u	99.71
2io1_B	94	Small ubiquitin-related modifier 3 precursor; SUMO	99.71
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	99.71
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	99.71
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	99.7
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	99.7
2kd0_A	85	LRR repeats and ubiquitin-like domain-containing p	99.7
1wgh_A	116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	99.7
4dbg_A	105	Ranbp-type and C3HC4-type zinc finger-containing;	99.7
1v5t_A	90	8430435I17RIK protein; hypothetical protein, ubiqu	99.7
2kdb_A	99	Homocysteine-responsive endoplasmic reticulum- res	99.7
3u5c_f	152	40S ribosomal protein S31; translation, ribosome,	99.69
2io0_B	91	Small ubiquitin-related modifier 2 precursor; SUMO	99.69
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	99.69
1se9_A	126	Ubiquitin family; ubiquitin-like, cell-free, wheat	99.69
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	99.68
1we7_A	115	SF3A1 protein; structural genomics, ubiquitin-like	99.68
1wgg_A	96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	99.68
1wia_A	95	Hypothetical ubiquitin-like protein (riken cDNA 20	99.68
1x1m_A	107	Ubiquitin-like protein SB132; structural genomics,	99.68
2gow_A	125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	99.68
1wxv_A	92	BAG-family molecular chaperone regulator-1; struct	99.68
2daf_A	118	FLJ35834 protein; hypothetical protein FLJ35834, u	99.67
1wxv_A	92	BAG-family molecular chaperone regulator-1; struct	99.66
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	99.66
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	99.65
2d07_B	93	Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Ho	99.65
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	99.65
4b6w_A	86	Tubulin-specific chaperone; CAP-Gly, ubiquitin-lik	99.65
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	99.65
2kjr_A	95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	99.64
2kjr_A	95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	99.64
1v86_A	95	DNA segment, CHR 7, wayne state university 128, ex	99.64
1wz0_A	104	Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-li	99.63
2dzj_A	88	Synaptic glycoprotein SC2; ubiquitin-like fold, st	99.63
2dzj_A	88	Synaptic glycoprotein SC2; ubiquitin-like fold, st	99.63
2dzm_A	100	FAS-associated factor 1; ubiquitin-like domain, HF	99.62
2eke_C	106	Ubiquitin-like protein SMT3; UBC9, SUMO binding mo	99.62
3ai5_A	307	Yeast enhanced green fluorescent protein, ubiquit;	99.61
2kj6_A	97	Tubulin folding cofactor B; methods development, N	99.6
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	99.6
4b6w_A	86	Tubulin-specific chaperone; CAP-Gly, ubiquitin-lik	99.59
2k8h_A	110	Small ubiquitin protein; SUMO, post-translational	99.59
2kj6_A	97	Tubulin folding cofactor B; methods development, N	99.58
1wm3_A	72	Ubiquitin-like protein SMT3B; ubiquitin fold, half	99.58
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	99.57
2io1_B	94	Small ubiquitin-related modifier 3 precursor; SUMO	99.57
1v6e_A	95	Cytoskeleton-associated protein 1; tubulin-specifi	99.57
1v6e_A	95	Cytoskeleton-associated protein 1; tubulin-specifi	99.56
1wf9_A	107	NPL4 family protein; beta-grAsp fold like domain,	99.55
1oqy_A	368	HHR23A, UV excision repair protein RAD23 homolog A	99.55
2xzm_9	189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	99.55
1wf9_A	107	NPL4 family protein; beta-grAsp fold like domain,	99.54
1t0y_A	122	Tubulin folding cofactor B; ubiquitin-like, cytosk	99.54
3a4r_A	79	Nfatc2-interacting protein; ubiquitin fold, coiled	99.53
2io0_B	91	Small ubiquitin-related modifier 2 precursor; SUMO	99.53
1wm3_A	72	Ubiquitin-like protein SMT3B; ubiquitin fold, half	99.52
2kzr_A	86	Ubiquitin thioesterase OTU1; structural genomics,	99.5
2d07_B	93	Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Ho	99.48
2kzr_A	86	Ubiquitin thioesterase OTU1; structural genomics,	99.48
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	99.46
3shq_A	320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	99.45
3kyd_D	115	Small ubiquitin-related modifier 1; SUMO, thioeste	99.44
3a4r_A	79	Nfatc2-interacting protein; ubiquitin fold, coiled	99.44
1wz0_A	104	Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-li	99.44
2k8h_A	110	Small ubiquitin protein; SUMO, post-translational	99.42
2eke_C	106	Ubiquitin-like protein SMT3; UBC9, SUMO binding mo	99.41
1wjn_A	97	Tubulin-folding protein TBCE; ubiquitin-like domai	99.38
3tix_A	207	Ubiquitin-like protein SMT3, RNA-induced transcri	99.36
3pge_A	200	SUMO-modified proliferating cell nuclear antigen;	99.35
1wjn_A	97	Tubulin-folding protein TBCE; ubiquitin-like domai	99.33
3v7o_A	227	Minor nucleoprotein VP30; ssgcid, seattle structur	99.24
3kyd_D	115	Small ubiquitin-related modifier 1; SUMO, thioeste	99.23
3goe_A	82	DNA repair protein RAD60; SUMO-like domain, sumoyl	99.18
3goe_A	82	DNA repair protein RAD60; SUMO-like domain, sumoyl	99.13
3pge_A	200	SUMO-modified proliferating cell nuclear antigen;	99.07
2jxx_A	97	Nfatc2-interacting protein; nuclear factor of acti	99.06
3tix_A	207	Ubiquitin-like protein SMT3, RNA-induced transcri	99.02
2pjh_A	80	Protein NPL4, nuclear protein localization protein	99.0
3uf8_A	209	Ubiquitin-like protein SMT3, peptidyl-prolyl CIS-	99.0
3ivf_A	371	Talin-1; FERM domain, cell membrane, cell projecti	98.96
2l76_A	95	Nfatc2-interacting protein; ubiquitin-like domain,	98.94
3ix6_A	360	TS, tsase, thymidylate synthase; niaid, ssgcid, se	98.9
2pjh_A	80	Protein NPL4, nuclear protein localization protein	98.83
2jxx_A	97	Nfatc2-interacting protein; nuclear factor of acti	98.83
3v7o_A	227	Minor nucleoprotein VP30; ssgcid, seattle structur	98.81
4da1_A	389	Protein phosphatase 1K, mitochondrial; metal-ION-a	98.7
2l76_A	95	Nfatc2-interacting protein; ubiquitin-like domain,	98.69
2al3_A	90	TUG long isoform; TUG UBL1 insulin, endocytosis/ex	98.66
3ix6_A	360	TS, tsase, thymidylate synthase; niaid, ssgcid, se	98.46
3uf8_A	209	Ubiquitin-like protein SMT3, peptidyl-prolyl CIS-	98.44
4efo_A	94	Serine/threonine-protein kinase TBK1; ubiquitin li	98.43
4efo_A	94	Serine/threonine-protein kinase TBK1; ubiquitin li	98.41
2al3_A	90	TUG long isoform; TUG UBL1 insulin, endocytosis/ex	98.28
2kc2_A	128	Talin-1, F1; FERM, adhesion, cell membrane, cell p	98.24
2kc2_A	128	Talin-1, F1; FERM, adhesion, cell membrane, cell p	98.24
2bps_A	81	YUKD protein; ubiquitin-like protein, ubiquitin; 2	98.19
4da1_A	389	Protein phosphatase 1K, mitochondrial; metal-ION-a	98.15
2bps_A	81	YUKD protein; ubiquitin-like protein, ubiquitin; 2	98.14
3qx1_A	84	FAS-associated factor 1; UBX, protein binding, P97	98.08
3qx1_A	84	FAS-associated factor 1; UBX, protein binding, P97	97.84
2dzk_A	109	UBX domain-containing protein 2; ubiquitin-like fo	97.75
1wj4_A	124	KIAA0794 protein; UBX domain, beta-grAsp fold, str	97.74
2dzk_A	109	UBX domain-containing protein 2; ubiquitin-like fo	97.51
1wj4_A	124	KIAA0794 protein; UBX domain, beta-grAsp fold, str	97.45
2cr5_A	109	Reproduction 8; UBX domain, D0H8S2298E protein, st	97.29
2ylm_A	530	Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70	97.17
2daj_A	91	KIAA0977 protein, COBL-like 1; ubiquitin-like doma	97.15
1ryj_A	70	Unknown; beta/alpha protein, structural genomics,	97.12
2ylm_A	530	Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70	97.06
1s3s_G	127	P47 protein; AAA ATPase, protein-protein complex,	97.04
3ivf_A	371	Talin-1; FERM domain, cell membrane, cell projecti	96.86
2l32_A	74	Small archaeal modifier protein 2; protein BIN; NM	96.78
2cr5_A	109	Reproduction 8; UBX domain, D0H8S2298E protein, st	96.77
1s3s_G	127	P47 protein; AAA ATPase, protein-protein complex,	96.56
2daj_A	91	KIAA0977 protein, COBL-like 1; ubiquitin-like doma	96.51
4e71_A	111	Plexin-B2, MM1; transmembrane, signaling, RBD, str	96.47
4a3p_A	217	Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {H	96.4
3jyu_A	231	Ubiquitin carboxyl-terminal hydrolase; domain in u	96.34
1vjk_A	98	Molybdopterin converting factor, subunit 1; struct	96.24
2juo_A	89	GA-binding protein alpha chain; OST, ubiquitin, tr	96.19
2r2o_A	138	Plexin-B1; effector domain, structural genomics, s	96.17
1oey_A	83	P67-PHOX, neutrophil cytosol factor 2; immune syst	96.05
1tyg_B	87	YJBS; alpha beta barrel, protein-protein complex,	95.87
4e71_A	111	Plexin-B2, MM1; transmembrane, signaling, RBD, str	95.85
2k5p_A	78	THis protein, thiamine-biosynthesis protein; NESG,	95.84
2l32_A	74	Small archaeal modifier protein 2; protein BIN; NM	95.83
3rpf_C	74	Molybdopterin converting factor, subunit 1 (MOAD);	95.8
2r2o_A	138	Plexin-B1; effector domain, structural genomics, s	95.72
3jyu_A	231	Ubiquitin carboxyl-terminal hydrolase; domain in u	95.48
1oey_A	83	P67-PHOX, neutrophil cytosol factor 2; immune syst	95.46
2kl0_A	73	Putative thiamin biosynthesis THis; structural gen	95.39
3po0_A	89	Small archaeal modifier protein 1; ubiquitin-like	95.39
4a3p_A	217	Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {H	95.36
3h6n_A	127	Plexin-D1; structural genomics consortium, SGC, me	95.29
1fm0_D	81	Molybdopterin convertin factor, subunit 1; molybde	95.28
2q5w_D	77	Molybdopterin converting factor, subunit 1; MOCO,	95.21
2cu3_A	64	Unknown function protein; thermus thermophilus HB8	94.91
3kuz_A	126	Plexin-C1; structural genomics, structural genomic	94.87
1f0z_A	66	THis protein; ubiquitin fold, transport protein; N	94.77
2juo_A	89	GA-binding protein alpha chain; OST, ubiquitin, tr	94.69
1ef1_A	294	Moesin; membrane, FERM domain, tail domain, membra	94.5
1vd2_A	89	Protein kinase C, IOTA type; PB1 domain, OPCA moti	94.4
3h6n_A	127	Plexin-D1; structural genomics consortium, SGC, me	94.36
1ryj_A	70	Unknown; beta/alpha protein, structural genomics,	94.25
2kvr_A	130	Ubiquitin carboxyl-terminal hydrolase 7; USP7, ubi	94.16
4e74_A	117	Plexin-A4; RBD, structural genomics, structural ge	93.91
2kvr_A	130	Ubiquitin carboxyl-terminal hydrolase 7; USP7, ubi	93.88
4e74_A	117	Plexin-A4; RBD, structural genomics, structural ge	93.86
1h4r_A	314	Merlin; FERM, neurofibromatosis, NF2, structural p	93.83
1rws_A	77	Hypothetical protein PF1061; residual dipolar coup	93.56
3rpf_C	74	Molybdopterin converting factor, subunit 1 (MOAD);	93.41
3dwg_C	93	9.5 kDa culture filtrate antigen CFP10A; sulfur ca	93.13
2i1j_A	575	Moesin; FERM, coiled-coil, C-ermad, ERM, radixin,	93.02
2g1e_A	90	Hypothetical protein TA0895; MOAD, molybdopterin,	92.92
3kuz_A	126	Plexin-C1; structural genomics, structural genomic	92.23
1vd2_A	89	Protein kinase C, IOTA type; PB1 domain, OPCA moti	91.67
3qij_A	296	Protein 4.1; cytoskeleton, structural genomics, st	91.65
1j0g_A	92	Hypothetical protein 1810045K17; ubiquitin-like fo	91.39
1y8x_B	98	Ubiquitin-activating enzyme E1C; ubiquitin-conjuga	90.89
1wgk_A	114	Riken cDNA 2900073H19 protein; THis domain, ubiqut	90.79
1vjk_A	98	Molybdopterin converting factor, subunit 1; struct	90.67
1wgy_A	104	RAP guanine nucleotide exchange factor 5; ubiquiti	90.53
1wgr_A	100	Growth factor receptor-bound protein 7; RA domain,	90.49
3hm6_X	644	Plexin-B1; structural genomics consortium, SGC, me	89.51
3u52_E	119	Phenol hydroxylase component PHO; 4-helix bundle,	89.43
1wgr_A	100	Growth factor receptor-bound protein 7; RA domain,	89.31
1wgy_A	104	RAP guanine nucleotide exchange factor 5; ubiquiti	89.21
1ef1_A	294	Moesin; membrane, FERM domain, tail domain, membra	88.9
2kmc_A	102	Fermitin family homolog 1; kindlin, cytoskeleton,	88.72
1h4r_A	314	Merlin; FERM, neurofibromatosis, NF2, structural p	88.64
3hm6_X	644	Plexin-B1; structural genomics consortium, SGC, me	88.03
1tyg_B	87	YJBS; alpha beta barrel, protein-protein complex,	87.82
3ig3_A	627	Plxna3 protein; plexin intracellular GAP RBD inact	87.64
2qjl_A	99	URM1, ubiquitin-related modifier 1; ubiquitin-like	87.53
1y8x_B	98	Ubiquitin-activating enzyme E1C; ubiquitin-conjuga	87.37
2kmc_A	102	Fermitin family homolog 1; kindlin, cytoskeleton,	87.01
3qij_A	296	Protein 4.1; cytoskeleton, structural genomics, st	86.89
2i1j_A	575	Moesin; FERM, coiled-coil, C-ermad, ERM, radixin,	86.82
2k9x_A	110	Tburm1, uncharacterized protein; unknown function;	86.71
1q1o_A	98	Cell division control protein 24; PB1 domain, PCCR	86.4
2hj1_A	97	Hypothetical protein; structural genomics, PSI, pr	85.95
1ip9_A	85	BEM1 protein; ubiquitin alpha/beta roll, signaling	85.83
3ig3_A	627	Plxna3 protein; plexin intracellular GAP RBD inact	85.41
2inc_C	83	TOUB protein; DIIRON, 4-helix bundle, carboxylate	85.37
3onh_A	127	Ubiquitin-activating enzyme E1-like; ligase, SUMO	85.0
2kmm_A	73	Guanosine-3',5'-BIS(diphosphate) 3'- pyrophosphohy	84.63
4eut_A	396	Serine/threonine-protein kinase TBK1; ATP binding,	84.55
3ge3_C	84	Toluene-4-monooxygenase system protein B; DIIRON h	83.09
2kmm_A	73	Guanosine-3',5'-BIS(diphosphate) 3'- pyrophosphohy	82.96
2l52_A	99	Methanosarcina acetivorans SAMP1 homolog; beta-grA	82.38
4eut_A	396	Serine/threonine-protein kinase TBK1; ATP binding,	82.34
1v8c_A	168	MOAD related protein; riken structural genomics/pr	81.99
3dwg_C	93	9.5 kDa culture filtrate antigen CFP10A; sulfur ca	81.15
2dhz_A	120	RAP guanine nucleotide exchange factor (GEF)- like	81.01
1fm0_D	81	Molybdopterin convertin factor, subunit 1; molybde	80.78
3onh_A	127	Ubiquitin-activating enzyme E1-like; ligase, SUMO	80.26

>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=100.00  E-value=4.1e-42  Score=232.66  Aligned_cols=153  Identities=30%  Similarity=0.429  Sum_probs=147.0

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEE-E-cceEeccCceecccccccccceeeeee-eecce
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI-F-AGKQLEDGRTLADYNIQKESTLHLVLR-LRGGT   77 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~-~-~g~~L~d~~~l~~~~i~~~~~i~l~~~-~~~~~   77 (154)
                      |+|+|+.++|+.+.+++++++||.+||++|+..+++|++.|+|+ | +|+.|+|+.+|++|++.+++++++.++ ..++|
T Consensus         3 m~i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~QrL~~~~~g~~L~d~~tL~~y~i~~~~~l~l~~~~~~~~m   82 (159)
T 3rt3_B            3 WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDKSDEPL   82 (159)
T ss_dssp             CEEEEEETTSCEEEEECCTTCCHHHHHHHHHHHHCCCGGGEEEEEETTCCBCCTTSCGGGGTCCTTCEEEEEECCCCCCE
T ss_pred             eEEEEEECCCCEEEEEeCCCCcHHHHHHHHHHHhCCCHHHEEEEEcCCCCCCCCCCCHHHcCCCCCCEEEEEccCCCCcE
Confidence            78999999999999999999999999999999999999999999 9 799999999999999999999999999 58899


Q ss_pred             eeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           78 MIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        78 ~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      .|+|+..+|+.+.+++++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+|++|++|++.++++||+
T Consensus        83 ~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~q~L~~~G~~L~d~~tL~~y~i~~g~~l~l~~rl~GG~  158 (159)
T 3rt3_B           83 SILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRGGG  158 (159)
T ss_dssp             EEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCC---
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCHHHEEEEECCeecCCCCCHHHcCCCCCCEEEEEEecCCCC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999995

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

Probab=100.00  E-value=2.7e-41  Score=231.28  Aligned_cols=152  Identities=80%  Similarity=1.158  Sum_probs=145.0

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecceeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGTMIK   80 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~~~i~   80 (154)
                      |+|+|+.++|+.+.+++++++||.+||++|+..+++|+++|+|+|+|+.|+|+.+|++|++.+++++++.++..++|.++
T Consensus        21 m~i~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~QrL~~~g~~L~d~~tL~~~~i~~~~~l~l~~~~~gg~~i~  100 (172)
T 3u30_A           21 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIF  100 (172)
T ss_dssp             EEEEEEETTTEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTGGGTCCTTCEEEEEECCCCCEEEE
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCccccccCCHhHcCCcccceeeeeecccccccce
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           81 VKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        81 v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      |+..+|+++.+++++++||.+||++|+..+|+|+++|+|+|+|+.|+|+.+|++|+|++|++|++.++++||
T Consensus       101 Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~q~L~~~g~~L~D~~tL~~y~i~~g~tl~l~~rlrgG  172 (172)
T 3u30_A          101 VKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  172 (172)
T ss_dssp             EEESSCCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCCEEETTEECCTTSBSGGGTCCTTCEEEECC-----
T ss_pred             eecccCcceeEEecCCCCHHHHHHHHHHHhCCCceeEEEEECCccCCCCCcHHHhCCCCCCEEEEEEecCCC
Confidence            999999999999999999999999999999999999999999999999999999999999999999999998

>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=100.00  E-value=6.2e-40  Score=220.28  Aligned_cols=152  Identities=80%  Similarity=1.158  Sum_probs=148.4

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecceeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGTMIK   80 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~~~i~   80 (154)
                      |+|+|+.++|+.+.+++++++||.+||++|+..+++|+++|+|+|+|+.|+|+.+|++|++.+++++++..+..++|.++
T Consensus         1 M~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gip~~~q~L~~~g~~L~d~~tL~~~~i~~~~~l~l~~~~~~~~~i~   80 (152)
T 3b08_A            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIF   80 (152)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCTTCEEEE
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHHHHHCcChHHeEEEECCeECcCcccHHHhccCCCCeeEEEeeccccccee
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           81 VKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        81 v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      |+..+|+.+.+++++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++|++++|++|++.++++||
T Consensus        81 Vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~qrL~~~g~~L~d~~tL~~~~i~~~~~i~l~~r~~GG  152 (152)
T 3b08_A           81 VKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  152 (152)
T ss_dssp             EEESSSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCCC-
T ss_pred             eeecCCCEEEEEeCCCCcHHHHHHHHHHHhCcChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEecCCC
Confidence            999999999999999999999999999999999999999999999999999999999999999999999998

>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=99.88  E-value=2.1e-22  Score=123.02  Aligned_cols=77  Identities=84%  Similarity=1.246  Sum_probs=72.5

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      |+|+|+..+|+.+.+++++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+|++|++|++.++++||+
T Consensus         1 M~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~l~l~~rl~Gg~   77 (88)
T 4fbj_B            1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGGG   77 (88)
T ss_dssp             CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBTTTTTCCTTCEEEEECBCC---
T ss_pred             CEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHCcChhHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEECCCCC
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999996

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

Probab=99.88  E-value=5.1e-22  Score=118.94  Aligned_cols=77  Identities=26%  Similarity=0.391  Sum_probs=74.8

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecC
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRG  151 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~g  151 (154)
                      ++|+|+|+..+|+.+.+++++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+|++|++|++.++++|
T Consensus         3 ~~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~l~l~~rl~G   79 (79)
T 3phx_B            3 EPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRG   79 (79)
T ss_dssp             CCEEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCBC
T ss_pred             CCEEEEEEeCCCCEEEEEECCcChHHHHHHHHHhhcCCCHHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCC
Confidence            56999999999999999999999999999999999999999999999999999999999999999999999999987

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

Probab=99.87  E-value=7.7e-22  Score=120.50  Aligned_cols=80  Identities=60%  Similarity=0.987  Sum_probs=70.1

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCCC
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGGL  154 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~~  154 (154)
                      .+|+|+++..+|+.+.+++++++||++||++|++.+|+|++.|+|+|+|+.|+|+.+|++|++.+|++|++.++.+||++
T Consensus         8 ~~~~i~v~~~~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~r~~GG~~   87 (88)
T 1sif_A            8 QGLQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGGL   87 (88)
T ss_dssp             --CEEEEEETTSCEEEEECCTTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBSGGGTCCTTCEEEEEC-------
T ss_pred             cceEEEEEeCCCCEEEEEECCCChHHHHHHHHHHHHCcChhhEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCCCCC
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999974

>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=99.87  E-value=1.3e-21  Score=119.16  Aligned_cols=80  Identities=28%  Similarity=0.390  Sum_probs=77.2

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCCC
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGGL  154 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~~  154 (154)
                      ..|+|+|+..+|+.+.+++++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|.++++|++.++++||++
T Consensus         6 ~~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~qrL~~~Gk~L~d~~tL~~~~i~~g~~i~l~~~~~GG~~   85 (87)
T 1wh3_A            6 SGIQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKGSGPS   85 (87)
T ss_dssp             SSEEEEEEETTTEEEEEEECSSSBHHHHHHHHHHHTCCCTTTEEEEETTEECCSSSBHHHHTCCTTEEEEEEECSCCCSC
T ss_pred             CCEEEEEEcCCCCEEEEEeCCCChHHHHHHHHHHHhCCChHHEEEEECCEEccCCCCHHHCCCCCCCEEEEEEeccCCCC
Confidence            56899999999999999999999999999999999999999999999999999999999999999999999999999975

>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=99.86  E-value=1e-21  Score=119.16  Aligned_cols=78  Identities=58%  Similarity=0.925  Sum_probs=72.7

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      .|+|+|+..+|+.+.+++++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|+++++|+++++++||+
T Consensus         3 ~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~~ip~~~qrL~~~g~~L~d~~tL~~~~i~~~~~i~l~~rl~GG~   80 (85)
T 3n3k_B            3 HMRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIHNHSALYLLLKLRGGG   80 (85)
T ss_dssp             -CEEEEECGGGCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETBEECCTTCBTTTTTCCTTCEEEEEECCC---
T ss_pred             eEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCeECCCCCCHHHCCCCCCCEEEEEEeccCCC
Confidence            588999999999999999999999999999999999999999999999999999999999999999999999999985

>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=99.86  E-value=1.2e-21  Score=119.63  Aligned_cols=79  Identities=81%  Similarity=1.200  Sum_probs=76.2

Q ss_pred             ecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           74 RGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        74 ~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ...|.|+|+..+|+.+.+++++++||.+||++|++.+|+|++.|+|+|+|+.|+|+.+|++|+|++|++|+++++++||
T Consensus        10 ~~~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~i~l~~rl~GG   88 (88)
T 3dbh_I           10 GGSMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLRLRGG   88 (88)
T ss_dssp             CCCEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCCEEETTEECCTTSBGGGGTCCTTCEEEECCCCCCC
T ss_pred             CCcEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHCcCHHHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEeCCCC
Confidence            3568999999999999999999999999999999999999999999999999999999999999999999999999998

>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=99.86  E-value=2.1e-21  Score=115.24  Aligned_cols=76  Identities=84%  Similarity=1.234  Sum_probs=72.1

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|++.+|+|++.|+|+|+|+.|+|+.+|++|++++|++|++.++++||
T Consensus         1 M~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~~i~~~~q~L~~~g~~L~d~~tL~~~~i~~g~~i~l~~~~~GG   76 (76)
T 1ndd_A            1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG   76 (76)
T ss_dssp             CEEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCC--
T ss_pred             CEEEEECCCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCCC
Confidence            6889999999999999999999999999999999999999999999999999999999999999999999999998

>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=99.86  E-value=2.4e-21  Score=117.43  Aligned_cols=78  Identities=60%  Similarity=0.943  Sum_probs=75.1

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      .|+|+|+..+|+.+.+++++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|+++++|+++++++||+
T Consensus         3 ~m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~~i~~~~qrL~~~g~~L~d~~tL~~~~i~~~~~l~l~~r~~GG~   80 (85)
T 3mtn_B            3 HMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKWSTLFLLLRLRGGG   80 (85)
T ss_dssp             CEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBTGGGTCCTTCEEEEECCCCCC-
T ss_pred             eEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHCcChHHEEEEECCEECCCCCCHHHcCCCCCCEEEEEEECcCCC
Confidence            589999999999999999999999999999999999999999999999999999999999999999999999999985

>4hcn_B Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidase, NEDD8, protein binding; 2.60A {Saccharomyces cerevisiae}

Probab=99.86  E-value=1.9e-21  Score=120.99  Aligned_cols=79  Identities=58%  Similarity=0.907  Sum_probs=75.3

Q ss_pred             ecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           74 RGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        74 ~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ...|+|+|+..+|+.+.+++++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|++|++|+++++++||
T Consensus        20 ~~~m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~i~l~~rl~GG   98 (98)
T 4hcn_B           20 GRPMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   98 (98)
T ss_dssp             --CCEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTCBSGGGTCCTTEEEEEECBCSCC
T ss_pred             CCeEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCCC
Confidence            3468999999999999999999999999999999999999999999999999999999999999999999999999998

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

Probab=99.86  E-value=2.3e-21  Score=118.41  Aligned_cols=87  Identities=30%  Similarity=0.503  Sum_probs=71.5

Q ss_pred             cccccceeeeeeeecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCC
Q 040824           61 IQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGG  140 (154)
Q Consensus        61 i~~~~~i~l~~~~~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~  140 (154)
                      ..+++.+++.+.....|.|+|+..+|+.+.+++++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+| +|
T Consensus         2 ~~~~~~~~~~~~~~~~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i-~g   80 (88)
T 4eew_A            2 MEPNDSTSTAVEEPDSLEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYNV-GG   80 (88)
T ss_dssp             -------------CCEEEEEEEETTSCEEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGGTC-TT
T ss_pred             CCCCCceEEeecCCCeEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEECCCCCcHHHcCC-CC
Confidence            45677888888888889999999999999999999999999999999999999999999999999999999999999 89


Q ss_pred             CEEEEEEe
Q 040824          141 SVLHLVLA  148 (154)
Q Consensus       141 ~~i~~~~~  148 (154)
                      ++|+++.|
T Consensus        81 ~~i~lv~R   88 (88)
T 4eew_A           81 KVIHLVER   88 (88)
T ss_dssp             EEEEEEEC
T ss_pred             cEEEEEEC
Confidence            99999865

>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=99.86  E-value=4e-21  Score=114.03  Aligned_cols=76  Identities=63%  Similarity=0.993  Sum_probs=73.8

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      |+|+|+..+|+.+.+++++++||++||++|++.+++|++.|+|+|+|+.|+|+.+|++|++.+|++|++.++++||
T Consensus         1 M~i~vk~~~g~~~~i~v~~~~tv~~lK~~i~~~~~i~~~~q~L~~~g~~L~d~~tL~~~~i~~g~~i~l~~~~~GG   76 (76)
T 3a9j_A            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRGG   76 (76)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTGGGTCCTTCEEEEEECCCCC
T ss_pred             CEEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEEeCCCC
Confidence            6889999999999999999999999999999999999999999999999999999999999999999999999998

>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=99.86  E-value=3.1e-21  Score=116.98  Aligned_cols=76  Identities=21%  Similarity=0.270  Sum_probs=70.4

Q ss_pred             eeecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEE
Q 040824           72 RLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        72 ~~~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      ...+.|+|+|++..|+++.+++.+++||.+||++|+++.|+|+++|+|+|+|+.|+|+.||++|+|++|++|++..
T Consensus        17 ~~~~mIqI~Vk~~~Gkk~~v~v~p~DTI~~LK~~I~~k~Gip~~qQrLif~Gk~LkD~~TL~dY~I~dgstLhL~~   92 (93)
T 3plu_A           17 RGSHMIEVVVNDRLGKKVRVKCLGEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLELYY   92 (93)
T ss_dssp             ---CEEEEEEECTTSCEEEEEEETTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEE
T ss_pred             CCCceEEEEEECCCCCEEEEEECCcCHHHHHHHHHHHHhCCCHHHEEEEeCCEEccCcCCHHHcCCCCCCEEEEEe
Confidence            3456689999999999999999999999999999999999999999999999999999999999999999999863

>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=99.85  E-value=4.2e-21  Score=119.02  Aligned_cols=78  Identities=62%  Similarity=0.953  Sum_probs=73.7

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      +|+|+|+..+|+.+.+++++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|.+|++|+++++++||+
T Consensus         1 gm~i~vk~~~g~~~~~~v~~~~TV~~LK~~i~~~~gip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~i~l~~r~~gG~   78 (96)
T 3k9o_B            1 GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGYA   78 (96)
T ss_dssp             -CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCCC--
T ss_pred             CcEEEEEeCCCCEEEEEECCCCCHHHHHHHHHhhhCCChhHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEEcCCCC
Confidence            488999999999999999999999999999999999999999999999999999999999999999999999999984

>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=99.85  E-value=2e-21  Score=116.35  Aligned_cols=77  Identities=23%  Similarity=0.476  Sum_probs=74.0

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      .|.|+|+..+|+.+.+++.+++||.+||++++++.|+|+++|+|+|+|+.|+|+.||++|++++|++|+++++++||
T Consensus         3 ~m~i~vk~~~g~~~~~~v~~~~tv~~lk~~i~~~~gi~~~~qrL~~~G~~L~d~~tl~~~~i~~~~~i~l~~~~~GG   79 (79)
T 2uyz_B            3 YIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGG   79 (79)
T ss_dssp             EEEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCHHHHTCCTTEEEEEEECCCC-
T ss_pred             eEEEEEECCCCCEEEEEECCCChHHHHHHHHHHHHCCCcccEEEEECCEEeCCCCCHHHcCCCCCCEEEEEEeccCC
Confidence            48899999999999999999999999999999999999999999999999999999999999999999999999998

>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure, northeast structural genomics consortium, protein structure initiative, NESG; NMR {Homo sapiens}

Probab=99.85  E-value=2.8e-21  Score=118.03  Aligned_cols=79  Identities=27%  Similarity=0.391  Sum_probs=71.7

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      ..|.|+|+..+|+.+.+++++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+|++|++|++..+.+||+
T Consensus         3 ~~m~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~~I~~g~~i~l~~~~~gg~   81 (88)
T 2hj8_A            3 EPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRGGL   81 (88)
T ss_dssp             CEEEEEEEETTSCEEEEEEESSSBHHHHHHHHHHHTCSCTTTEEEESSSSCCCTTSBHHHHHCSTTCEEEEEEC-----
T ss_pred             ccEEEEEECCCCCEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEEcCCCc
Confidence            4589999999999999999999999999999999999999999999999999999999999999999999999999985

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

Probab=99.85  E-value=3.2e-22  Score=127.67  Aligned_cols=101  Identities=74%  Similarity=1.030  Sum_probs=93.6

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecceeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGTMIK   80 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~~~i~   80 (154)
                      ++|+|+.++|+.+.+++++++||.+||++|+...++|++.|+|+|+|+.|+|+.+|++|++.++++|++..+..+++.++
T Consensus        10 ~~i~vk~l~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~ygI~~gstI~l~~~~~GG~~~~   89 (114)
T 2kdi_A           10 FQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLEDGRTLSDYNIQRESTLHLVLRLRGGSMGG   89 (114)
T ss_dssp             CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTTTTTCCSSCEEEEEECCCSSCCCS
T ss_pred             EEEEEEeCCCcEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEEcCCCceee
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             eee---cCCceEEEeeCCCchHHH
Q 040824           81 VKT---LTGKEIEIDIEPTDTIER  101 (154)
Q Consensus        81 v~~---~~~~~~~~~v~~~~tv~~  101 (154)
                      ++.   ..|+++.+++.+++||.+
T Consensus        90 ~~~~~~~~g~~~~~~v~~~~~~~~  113 (114)
T 2kdi_A           90 AADEEELIRKAIELSLKESRNSGG  113 (114)
T ss_dssp             SCSSSHHHHHHHHSSSHHHHHGGG
T ss_pred             ccccccccCceEEEEeccccccCC
Confidence            883   467888888888888763

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

Probab=99.85  E-value=1e-20  Score=120.22  Aligned_cols=92  Identities=53%  Similarity=0.780  Sum_probs=81.8

Q ss_pred             cccccceeeeeee--------ecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcc
Q 040824           61 IQKESTLHLVLRL--------RGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTA  132 (154)
Q Consensus        61 i~~~~~i~l~~~~--------~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L  132 (154)
                      +.+|+++++....        ...|.|+|+..+|+.+.+++++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|
T Consensus        12 ~~~~~~~~~~~~~~~~~~g~~~~~m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL   91 (111)
T 2ojr_A           12 WIEGDELYIDTNNDGWIEGDELLAMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL   91 (111)
T ss_dssp             SCCGGGBCCCTTCSSSCCGGGSSCEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHCCCTTTEEEEETTEECCSSCBT
T ss_pred             eecCCEEEEeecccccccCCCCCeEEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHHHCcCcccEEEEECCEECCCCCcH
Confidence            4555666555442        24699999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccCCCCEEEEEEeecCC
Q 040824          133 RDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus       133 ~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ++|++.+|++|+++++++||
T Consensus        92 ~~~gI~~gs~I~l~~rl~GG  111 (111)
T 2ojr_A           92 SDYNIQKESTLHLVLRLRGG  111 (111)
T ss_dssp             TTTTCCTTCEEEEEECCCC-
T ss_pred             HHcCCCCCCEEEEEEeCCCC
Confidence            99999999999999999998

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.84  E-value=8.8e-21  Score=117.03  Aligned_cols=79  Identities=23%  Similarity=0.382  Sum_probs=75.1

Q ss_pred             ecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCC-CcccccccCCCCEEEEEEeecCC
Q 040824           74 RGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADD-KTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        74 ~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~-~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ...|+|+|+..++ .+.+++++++||.+||++|++.+|+|+++|+|+|+|+.|+|+ .+|++|+|++|++|++.++.+||
T Consensus        13 ~~~~~I~Vk~~~~-~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~~tL~~ygI~~gstl~lv~r~~gg   91 (94)
T 2kan_A           13 VRKIHVTVKFPSK-QFTVEVDRTETVSSLKDKIHIVENTPIKRMQLYYSGIELADDYRNLNEYGITEFSEIVVFLKSINR   91 (94)
T ss_dssp             SCCEEEEEECSSC-EEEEEECTTCBHHHHHHHHHHHSSSCTTTEEEEETTEEECCTTSBHHHHTCCTTEEEEEEECCCSS
T ss_pred             CCCEEEEEEcCCc-EEEEEECCCCcHHHHHHHHHHHHCcCHHHEEEEECCEECCCCcccHHHCCCCCCCEEEEEEeCCCC
Confidence            4568999999877 889999999999999999999999999999999999999999 99999999999999999999998


Q ss_pred             C
Q 040824          153 G  153 (154)
Q Consensus       153 ~  153 (154)
                      +
T Consensus        92 ~   92 (94)
T 2kan_A           92 A   92 (94)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.84  E-value=5.8e-21  Score=118.58  Aligned_cols=79  Identities=23%  Similarity=0.456  Sum_probs=76.1

Q ss_pred             ecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           74 RGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        74 ~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ...|.|+|+..+|+.+.+.+.+++||.+||++|+++.|+|+++|+|+|+|+.|+|+.||++|+|++|++|+++++++||
T Consensus        19 ~~~m~I~Vk~~~g~~~~l~v~~~~tv~~lK~~i~~~~gip~~~qrLif~Gk~L~d~~tl~dy~i~~g~~I~l~~~~~GG   97 (97)
T 1wyw_B           19 GEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGG   97 (97)
T ss_dssp             CCEEEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCHHHHTCCTTCEEEEEESSSCC
T ss_pred             CCcEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCChhhEEEEECCeEcCCCCCHHHCCCCCCCEEEEEEecCCC
Confidence            3458999999999999999999999999999999999999999999999999999999999999999999999999998

>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=99.84  E-value=1.4e-20  Score=119.57  Aligned_cols=78  Identities=62%  Similarity=0.951  Sum_probs=74.7

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ..|+|+|+..+|+.+.+++++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|++|++|+++++++||
T Consensus        34 ~~m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~gI~~gs~I~l~~rl~GG  111 (111)
T 3vdz_A           34 LAMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  111 (111)
T ss_dssp             GCEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTTTTTCCTTCEEEEEECCCC-
T ss_pred             ccEEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHhCCChHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCCC
Confidence            358999999999999999999999999999999999999999999999999999999999999999999999999998

>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=99.84  E-value=2.2e-20  Score=114.26  Aligned_cols=79  Identities=35%  Similarity=0.547  Sum_probs=75.3

Q ss_pred             cceeeeeeecCC-ceEEE-eeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           75 GGTMIKVKTLTG-KEIEI-DIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        75 ~~~~i~v~~~~~-~~~~~-~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ..|+|+|+..+| +.+.+ ++++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|.+|++|+++++.+||
T Consensus         6 ~~m~i~Vk~~~g~~~~~l~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~~~gG   85 (89)
T 1wy8_A            6 SGMWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVRPDSG   85 (89)
T ss_dssp             SCEEEEEEETTCSCEEEEEEECTTCBHHHHHHHHHHHSCCCTTTEEEEETTEECCSSSBHHHHTCCTTCEEEEEECCCCS
T ss_pred             CcEEEEEEECCCCceEEEEecCCCCCHHHHHHHHHHHHCcChhhEEEEECCeECCCCCCHHHCCCCCCCEEEEEEeCCCC
Confidence            468999999988 68999 5999999999999999999999999999999999999999999999999999999999998


Q ss_pred             C
Q 040824          153 G  153 (154)
Q Consensus       153 ~  153 (154)
                      +
T Consensus        86 ~   86 (89)
T 1wy8_A           86 P   86 (89)
T ss_dssp             S
T ss_pred             C
Confidence            5

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

Probab=99.84  E-value=1.5e-20  Score=112.55  Aligned_cols=74  Identities=35%  Similarity=0.574  Sum_probs=71.3

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~   74 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|+...++|++.|+|+|+|+.|+|+.+|++|++.++++|++.++..
T Consensus         5 m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~l~l~~rl~   78 (79)
T 3phx_B            5 LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLR   78 (79)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCB
T ss_pred             EEEEEEeCCCCEEEEEECCcChHHHHHHHHHhhcCCCHHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecC
Confidence            78999999999999999999999999999999999999999999999999999999999999999999998754

>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=99.83  E-value=1.9e-20  Score=114.30  Aligned_cols=77  Identities=56%  Similarity=0.934  Sum_probs=72.3

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecce
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGT   77 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~~   77 (154)
                      |+|+|+.++|+.+.+++++++||.+||++|++..++|++.|+|+|+|+.|+|+.+|++|++.++++|++.++..++.
T Consensus         1 M~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~l~l~~rl~Gg~   77 (88)
T 4fbj_B            1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGGG   77 (88)
T ss_dssp             CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBTTTTTCCTTCEEEEECBCC---
T ss_pred             CEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHCcChhHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEECCCCC
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999877653

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

Probab=99.83  E-value=1.3e-20  Score=116.18  Aligned_cols=77  Identities=27%  Similarity=0.442  Sum_probs=71.9

Q ss_pred             ecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           74 RGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        74 ~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ...|+|+|+.  |+.+.+++++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+|++|++|++.++++||
T Consensus        17 ~~~m~I~Vk~--g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~y~I~~gstI~lv~rl~GG   93 (93)
T 2l7r_A           17 RGSMQLFVRA--QELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAGAPLEDEATLGQCGVEALTTLEVAGRMLGG   93 (93)
T ss_dssp             ---CEEEEES--SSEEEEECCSSCBHHHHHHHHHHHHTCCGGGCEEEETTEECCTTSBHHHHTCCSSCEEEEECCCCCC
T ss_pred             CCcEEEEEEC--CCEEEEEeCCCCcHHHHHHHHHHHhCcChhHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCCC
Confidence            3458899998  7889999999999999999999999999999999999999999999999999999999999999998

>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=99.83  E-value=1.8e-20  Score=119.12  Aligned_cols=82  Identities=27%  Similarity=0.443  Sum_probs=77.6

Q ss_pred             eecceeeeeeec---CCceEEEeeCC-CchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEe
Q 040824           73 LRGGTMIKVKTL---TGKEIEIDIEP-TDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        73 ~~~~~~i~v~~~---~~~~~~~~v~~-~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      ..+.|.|+|+..   +|+.+.+++++ ++||.+||++|+..+|+|+++|+|+|+|+.|+|+.+|++|+|.+|++|+++++
T Consensus        24 ~~~~i~i~Vk~~~~~~g~~~~l~v~~l~~TV~~LK~~I~~~~gip~~~QrL~~~Gk~L~D~~tL~~y~I~~g~~l~l~~r  103 (111)
T 1we6_A           24 HPGPATIRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLR  103 (111)
T ss_dssp             CCSCEEEEECCTTCSSSCCEEEEESCSSSBHHHHHHHHHHHTTCCTTTSEEECSSSBCCTTSBTTTTTCSSSCEEEEECS
T ss_pred             CCCcEEEEEEecccCCCcEEEEEecCCCCcHHHHHHHHHHHHCCCHHHeEEEECCEECCCCCcHHHCCCCCCCEEEEEEE
Confidence            456789999998   78899999998 99999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 040824          149 LRGGGL  154 (154)
Q Consensus       149 ~~gg~~  154 (154)
                      ++||++
T Consensus       104 ~~GGk~  109 (111)
T 1we6_A          104 ERSGPS  109 (111)
T ss_dssp             SCCSSC
T ss_pred             cCCCCC
Confidence            999975

>3v6c_B Ubiquitin; structural genomics, structural genomics consortium, SGC, UB protease, hydrolase-signaling protein complex; 1.70A {Homo sapiens} PDB: 3v6e_B

Probab=99.83  E-value=3.2e-20  Score=113.97  Aligned_cols=77  Identities=60%  Similarity=0.952  Sum_probs=73.5

Q ss_pred             ecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeec
Q 040824           74 RGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALR  150 (154)
Q Consensus        74 ~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~  150 (154)
                      ...|+|+|+..+|+.+.+++++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|||++|++|++++++|
T Consensus        15 ~~~m~i~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~rlr   91 (91)
T 3v6c_B           15 RGSMQIFVNTLTGTHITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR   91 (91)
T ss_dssp             CCSEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTCBTGGGTCCTTCEEEEECCCC
T ss_pred             CCeEEEEEEeCCCCEEEEEECCCCCHHHHHHHHHhhhCCChhhEEEEECCeECCCcCcHHHCCCCCCCEEEEEEecC
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999875

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

Probab=99.83  E-value=4.6e-20  Score=114.77  Aligned_cols=77  Identities=62%  Similarity=0.976  Sum_probs=73.9

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      |+|+|+..+|+.+.+++++++||++||++|++.+|+|++.|+|+|+|+.|+|+.+|++|||.+|++|++..+.+||+
T Consensus         1 M~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~gi~~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~gG~   77 (98)
T 1yx5_B            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGR   77 (98)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHTCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCCCC-
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEeCCCCC
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999884

>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=99.83  E-value=2.8e-20  Score=112.77  Aligned_cols=70  Identities=23%  Similarity=0.433  Sum_probs=67.9

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~   70 (154)
                      |+|+|+.+.|+.+.+++++++||.+||++|+++.|+|++.|+|.|.|+.|+|+.+|++|+|.+++++++-
T Consensus        22 IqI~Vk~~~Gkk~~v~v~p~DTI~~LK~~I~~k~Gip~~qQrLif~Gk~LkD~~TL~dY~I~dgstLhL~   91 (93)
T 3plu_A           22 IEVVVNDRLGKKVRVKCLGEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLELY   91 (93)
T ss_dssp             EEEEEECTTSCEEEEEEETTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEE
T ss_pred             EEEEEECCCCCEEEEEECCcCHHHHHHHHHHHHhCCCHHHEEEEeCCEEccCcCCHHHcCCCCCCEEEEE
Confidence            6899999999999999999999999999999999999999999999999999999999999999999874

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

Probab=99.83  E-value=3.8e-20  Score=115.16  Aligned_cols=88  Identities=83%  Similarity=1.120  Sum_probs=74.1

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecceeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGTMIK   80 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~~~i~   80 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|+...++|++.|+|+|+|+.|+|+.+|++|++.++++|++..+..++..++
T Consensus         1 M~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~gi~~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~gG~~i~   80 (98)
T 1yx5_B            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGRDPN   80 (98)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHTCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCCCC----
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEeCCCCCcCc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999998888888


Q ss_pred             eeecCCce
Q 040824           81 VKTLTGKE   88 (154)
Q Consensus        81 v~~~~~~~   88 (154)
                      .++.+|..
T Consensus        81 ~~~v~~~~   88 (98)
T 1yx5_B           81 SSSVDKLA   88 (98)
T ss_dssp             --------
T ss_pred             cccCCCch
Confidence            88877654

>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=99.82  E-value=5.4e-20  Score=112.71  Aligned_cols=77  Identities=34%  Similarity=0.538  Sum_probs=73.1

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ..|+|+|+..+|+.+.+++++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+| +|++|+++++.+++
T Consensus         4 ~~m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~d~~tL~~~~i-~g~~i~l~~~~~~~   80 (90)
T 4dwf_A            4 DSLEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVIHLVERAPPQ   80 (90)
T ss_dssp             CEEEEEEEETTCCEEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGGTC-TTEEEEEEECCCC-
T ss_pred             cEEEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCeECCCCCCHHHcCC-CCcEEEEEecCCCC
Confidence            468999999999999999999999999999999999999999999999999999999999999 89999999998765

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

Probab=99.82  E-value=3.2e-20  Score=112.19  Aligned_cols=73  Identities=33%  Similarity=0.473  Sum_probs=70.1

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceE-eccCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQ-LEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~-L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |+|+|+.++|+.+.+++++++||.+||++|++..|+|+++|+|+|+|+. |+|+.+|++|++.++++|++.+++
T Consensus        11 ~~i~vk~l~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~lL~D~~tL~~y~I~~gs~i~lv~~p   84 (84)
T 2kk8_A           11 MKFLVENLNGSSFELEVDYRDTLLVVKQKIERSQHIPVSKQTLIVDGIVILREDLTVEQCQIVPTSDIQLEVSS   84 (84)
T ss_dssp             EEEEEEETTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCCSSSBHHHHTCCTTSCEEEEECC
T ss_pred             eEEEEEecCCcEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCEEecCCcCCHHHcCCCCCCEEEEEEcC
Confidence            7899999999999999999999999999999999999999999999999 999999999999999999988753

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B

Probab=99.81  E-value=1.1e-19  Score=123.38  Aligned_cols=77  Identities=61%  Similarity=0.975  Sum_probs=73.6

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+|++|++|++.++++||+
T Consensus         1 MqI~Vk~~~Gk~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~y~I~~gstI~Lvlrl~GG~   77 (169)
T 3l0w_B            1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGG   77 (169)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHCCCTTTEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCCC--
T ss_pred             CEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHHCcCHHHEEEEECCccccCcCcHHHcCCCCCCEEEEEEEecccc
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999984

>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=99.81  E-value=1.2e-19  Score=107.64  Aligned_cols=75  Identities=56%  Similarity=0.935  Sum_probs=71.3

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|++..++|++.|+|+|+|+.|+|+.+|++|++.++++|++.++..+
T Consensus         1 M~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~~i~~~~q~L~~~g~~L~d~~tL~~~~i~~g~~i~l~~~~~G   75 (76)
T 1ndd_A            1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRG   75 (76)
T ss_dssp             CEEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCC-
T ss_pred             CEEEEECCCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCC
Confidence            899999999999999999999999999999999999999999999999999999999999999999999887653

>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=99.81  E-value=7.1e-20  Score=112.84  Aligned_cols=79  Identities=30%  Similarity=0.458  Sum_probs=73.6

Q ss_pred             cceeeeeeecCCc--eEEEeeCCCchHHHHHHHHhhhc--CCCCCceeEEECCeecCCCCccccc--ccCCCCEEEEEEe
Q 040824           75 GGTMIKVKTLTGK--EIEIDIEPTDTIERIKERVEEKE--GIPPVQQRLIYAGKQLADDKTARDY--NIEGGSVLHLVLA  148 (154)
Q Consensus        75 ~~~~i~v~~~~~~--~~~~~v~~~~tv~~LK~~i~~~~--~i~~~~~~l~~~g~~l~d~~~L~~~--~i~~~~~i~~~~~  148 (154)
                      ..|.|+|+..+++  .+.+++++++||.+||++|++.+  ++|+++|+|+|+|+.|+|+.+|++|  +|+++++|+++++
T Consensus         6 ~~m~i~Vk~~~~~~~~~~v~v~~~~TV~~lK~~I~~~~~~~i~~~~QrLi~~Gk~L~D~~tL~~~~~~i~~~~~i~lv~~   85 (93)
T 1wgd_A            6 SGVTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVCN   85 (93)
T ss_dssp             CCCEEEEECSSSSCCCEEEECCTTSCHHHHHHHHHHHSTTCCCTTTCEEEETTEECCSSSCHHHHSCSSSCSEEEEEECC
T ss_pred             cEEEEEEEeCCCCeEEEEEecCCCCcHHHHHHHHHHHhcCCCChHHeEEEECCEECcCcCCHHHHhcCCCCCCEEEEEeC
Confidence            4588999998887  57777889999999999999999  9999999999999999999999999  9999999999999


Q ss_pred             ecCCC
Q 040824          149 LRGGG  153 (154)
Q Consensus       149 ~~gg~  153 (154)
                      .+||+
T Consensus        86 ~~gg~   90 (93)
T 1wgd_A           86 VKSGP   90 (93)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            99985

>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=99.81  E-value=1.5e-19  Score=107.79  Aligned_cols=75  Identities=28%  Similarity=0.554  Sum_probs=70.6

Q ss_pred             cceeeeeeecCCceE-EEe-eCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEee
Q 040824           75 GGTMIKVKTLTGKEI-EID-IEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~-~~~-v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      ++|+|+|+..+|+.+ .++ +++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++||+.+|++|++.++.
T Consensus         1 g~m~i~Vk~~~g~~~~~l~~v~~~~tv~~lK~~i~~~~gip~~~qrL~~~g~~L~d~~tL~~~~i~~g~~i~l~~r~   77 (78)
T 2faz_A            1 GSMWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLLVRQ   77 (78)
T ss_dssp             -CEEEEEEETTSSCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTTTTTCCTTCEEEEEECC
T ss_pred             CcEEEEEEECCCCEEEEEeccCCCCCHHHHHHHHHHHHCcChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEeC
Confidence            468999999999885 899 999999999999999999999999999999999999999999999999999999875

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

Probab=99.81  E-value=9.2e-20  Score=110.17  Aligned_cols=74  Identities=27%  Similarity=0.412  Sum_probs=70.9

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCee-cCCCCcccccccCCCCEEEEEEe
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQ-LADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~-l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      .-|+|+++..+|+.+.+++++++||++||++|++.+|+|+++|+|+|+|+. |+|+.+|++|+|++|++|+++++
T Consensus         9 ~~~~i~vk~l~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~lL~D~~tL~~y~I~~gs~i~lv~~   83 (84)
T 2kk8_A            9 SHMKFLVENLNGSSFELEVDYRDTLLVVKQKIERSQHIPVSKQTLIVDGIVILREDLTVEQCQIVPTSDIQLEVS   83 (84)
T ss_dssp             CCEEEEEEETTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCCSSSBHHHHTCCTTSCEEEEEC
T ss_pred             CceEEEEEecCCcEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEECCEEecCCcCCHHHcCCCCCCEEEEEEc
Confidence            458999999999999999999999999999999999999999999999999 99999999999999999999875

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

Probab=99.81  E-value=1.2e-19  Score=124.62  Aligned_cols=80  Identities=63%  Similarity=0.982  Sum_probs=77.0

Q ss_pred             ecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           74 RGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        74 ~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      ...|+|+|+..+|+++.+++++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+|++|++|+++++++||+
T Consensus       103 ~~eMqI~VKtl~Gkt~~l~V~~s~TV~~LK~kI~~~~gIp~~~QrLi~~Gk~L~D~~tL~dygI~~gstI~LvlrlrGG~  182 (189)
T 3q3f_A          103 HYGGQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGG  182 (189)
T ss_dssp             CCCEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCCEEETTEECCTTCBGGGGTCCTTCEEEECCCCCCCC
T ss_pred             ccceeeeeecCCCCEEEEEeCCCCcHHHHHHHHHhccCCCHHHEEEEECCEECCCCCCHHHCCCCCCCEEEEEEEcCCCC
Confidence            34699999999999999999999999999999999999999999999999999999999999999999999999999984

>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=99.81  E-value=1.9e-19  Score=106.74  Aligned_cols=75  Identities=95%  Similarity=1.308  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|++..++|++.|+|+|+|+.|+|+.+|++|++.++++|++.++..+
T Consensus         1 M~i~vk~~~g~~~~i~v~~~~tv~~lK~~i~~~~~i~~~~q~L~~~g~~L~d~~tL~~~~i~~g~~i~l~~~~~G   75 (76)
T 3a9j_A            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRG   75 (76)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTGGGTCCTTCEEEEEECCCC
T ss_pred             CEEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEEeCCC
Confidence            899999999999999999999999999999999999999999999999999999999999999999999887654

>4hcn_B Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidase, NEDD8, protein binding; 2.60A {Saccharomyces cerevisiae}

Probab=99.81  E-value=1.4e-19  Score=112.55  Aligned_cols=75  Identities=97%  Similarity=1.322  Sum_probs=72.0

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+.++|+.+.+++++++||.+||++|++..++|++.|+|+|+|+.|+|+.+|++|++.++++|+++++..+
T Consensus        23 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~i~l~~rl~G   97 (98)
T 4hcn_B           23 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG   97 (98)
T ss_dssp             CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTCBSGGGTCCTTEEEEEECBCSC
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCC
Confidence            799999999999999999999999999999999999999999999999999999999999999999999987654

>3v6c_B Ubiquitin; structural genomics, structural genomics consortium, SGC, UB protease, hydrolase-signaling protein complex; 1.70A {Homo sapiens} PDB: 3v6e_B

Probab=99.81  E-value=1.2e-19  Score=111.36  Aligned_cols=73  Identities=92%  Similarity=1.257  Sum_probs=70.4

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|++.+++|++.|+|+|+|+.|+|+.+|++||+.++++|++.++.
T Consensus        18 m~i~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~rl   90 (91)
T 3v6c_B           18 MQIFVNTLTGTHITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL   90 (91)
T ss_dssp             EEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTCBTGGGTCCTTCEEEEECCC
T ss_pred             EEEEEEeCCCCEEEEEECCCCCHHHHHHHHHhhhCCChhhEEEEECCeECCCcCcHHHCCCCCCCEEEEEEec
Confidence            7899999999999999999999999999999999999999999999999999999999999999999998764

>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=99.81  E-value=1.2e-19  Score=110.72  Aligned_cols=75  Identities=57%  Similarity=0.958  Sum_probs=71.8

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+.++|+.+.+++++++||.+||++|++..++|++.|+|+|+|+.|+|+.+|++|++.++++|++.++..+
T Consensus        13 m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~i~l~~rl~G   87 (88)
T 3dbh_I           13 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLRLRG   87 (88)
T ss_dssp             EEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCCEEETTEECCTTSBGGGGTCCTTCEEEECCCCCC
T ss_pred             EEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHCcCHHHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEeCCC
Confidence            789999999999999999999999999999999999999999999999999999999999999999999987654

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

Probab=99.81  E-value=2.5e-19  Score=114.22  Aligned_cols=80  Identities=58%  Similarity=0.915  Sum_probs=76.6

Q ss_pred             ecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           74 RGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        74 ~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      .++.+|+++..+|+.+.+++++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+|.+|++|++..+.+||.
T Consensus         7 ~~~~~i~vk~l~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~ygI~~gstI~l~~~~~GG~   86 (114)
T 2kdi_A            7 HGEFQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLEDGRTLSDYNIQRESTLHLVLRLRGGS   86 (114)
T ss_dssp             CCCCEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTTTTTCCSSCEEEEEECCCSSC
T ss_pred             CCcEEEEEEeCCCcEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEEcCCCc
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999984

>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=99.81  E-value=2.1e-19  Score=111.31  Aligned_cols=79  Identities=91%  Similarity=1.229  Sum_probs=73.1

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecceee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGTMI   79 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~~~i   79 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|++.++++|++.++..++...
T Consensus         2 m~i~vk~~~g~~~~~~v~~~~TV~~LK~~i~~~~gip~~~qrL~~~G~~L~d~~tL~~~~i~~~~~i~l~~r~~gG~~~   80 (96)
T 3k9o_B            2 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGYADL   80 (96)
T ss_dssp             CEEEEEETTCCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCCC----
T ss_pred             cEEEEEeCCCCEEEEEECCCCCHHHHHHHHHhhhCCChhHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEEcCCCCcc
Confidence            8999999999999999999999999999999999999999999999999999999999999999999999988776553

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

Probab=99.80  E-value=2e-19  Score=109.74  Aligned_cols=75  Identities=87%  Similarity=1.259  Sum_probs=69.6

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+.++|+.+.+++++++||.+||++|++.+++|++.|+|+|+|+.|+|+.+|++|++.++++|++.++..+
T Consensus        10 ~~i~v~~~~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~r~~G   84 (88)
T 1sif_A           10 LQLFIKTLTGKTFTVEMEPSDTIENLKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG   84 (88)
T ss_dssp             CEEEEEETTSCEEEEECCTTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBSGGGTCCTTCEEEEEC----
T ss_pred             eEEEEEeCCCCEEEEEECCCChHHHHHHHHHHHHCcChhhEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCC
Confidence            899999999999999999999999999999999999999999999999999999999999999999999887654

>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=99.80  E-value=1.5e-19  Score=109.43  Aligned_cols=75  Identities=80%  Similarity=1.153  Sum_probs=71.6

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+.++|+.+.+++++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|++.++++|++.++..+
T Consensus         4 m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~~ip~~~qrL~~~g~~L~d~~tL~~~~i~~~~~i~l~~rl~G   78 (85)
T 3n3k_B            4 MRIVVKTLMGRTIILEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIHNHSALYLLLKLRG   78 (85)
T ss_dssp             CEEEEECGGGCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETBEECCTTCBTTTTTCCTTCEEEEEECCC-
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEECCeECCCCCCHHHCCCCCCCEEEEEEeccC
Confidence            899999999999999999999999999999999999999999999999999999999999999999999988654

>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=99.80  E-value=2.5e-19  Score=109.72  Aligned_cols=74  Identities=34%  Similarity=0.585  Sum_probs=70.7

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|+.+.++|++.|+|+|+|+.|+|+.+|++|++ ++++|+++++..+
T Consensus         6 m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~d~~tL~~~~i-~g~~i~l~~~~~~   79 (90)
T 4dwf_A            6 LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVIHLVERAPP   79 (90)
T ss_dssp             EEEEEEETTCCEEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGGTC-TTEEEEEEECCCC
T ss_pred             EEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCeECCCCCCHHHcCC-CCcEEEEEecCCC
Confidence            7899999999999999999999999999999999999999999999999999999999999 8999999988653

>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=99.80  E-value=2.5e-19  Score=114.52  Aligned_cols=80  Identities=33%  Similarity=0.547  Sum_probs=72.9

Q ss_pred             cceeeeeeec----------CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEE
Q 040824           75 GGTMIKVKTL----------TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLH  144 (154)
Q Consensus        75 ~~~~i~v~~~----------~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~  144 (154)
                      +++.|.|+.+          +|+.+.+++++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+|.+|++|+
T Consensus        24 ~~i~l~V~~p~~~~~~~~~L~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrL~~~Gk~L~D~~tL~~y~i~~g~~i~  103 (115)
T 1we7_A           24 GPVSIKVQVPNMQDKTEWKLNGQGLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMASGAVIH  103 (115)
T ss_dssp             SCEEEEEEECCCSSSCSSCCSSEEEEEEECSCSBTHHHHHHHHHHSSCCTTTEEEEETTEEECTTSBHHHHTCCSSCEEE
T ss_pred             CCEEEEEEcCCCccccccccCCeEEEEEECCCCCHHHHHHHHHHHHCCChHHEEEEECCEECCCCCCHHHCCCCCCCEEE
Confidence            4456666654          477899999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeecCCCC
Q 040824          145 LVLALRGGGL  154 (154)
Q Consensus       145 ~~~~~~gg~~  154 (154)
                      +.++++||++
T Consensus       104 lv~rl~GGk~  113 (115)
T 1we7_A          104 LALKERSGPS  113 (115)
T ss_dssp             EEECCCSCCS
T ss_pred             EEEEcCCCCC
Confidence            9999999974

>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=99.80  E-value=3.2e-19  Score=108.01  Aligned_cols=75  Identities=92%  Similarity=1.241  Sum_probs=72.0

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|++.++++|++.++..+
T Consensus         4 m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~~i~~~~qrL~~~g~~L~d~~tL~~~~i~~~~~l~l~~r~~G   78 (85)
T 3mtn_B            4 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKWSTLFLLLRLRG   78 (85)
T ss_dssp             EEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBTGGGTCCTTCEEEEECCCCC
T ss_pred             EEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHHCcChHHEEEEECCEECCCCCCHHHcCCCCCCEEEEEEECcC
Confidence            789999999999999999999999999999999999999999999999999999999999999999999987654

>2lxa_A Ubiquitin-like protein MDY2; ubiquitin-like domain, protein-protein interaction, SGT2 BIN domain, GET pathway, protein binding; NMR {Saccharomyces cerevisiae}

Probab=99.80  E-value=1.4e-19  Score=109.72  Aligned_cols=73  Identities=22%  Similarity=0.429  Sum_probs=68.8

Q ss_pred             CEEEEEeCCCCEEEEEEe--CCCcHHHHHHHH-HhHhCCCCCCeEEEEcceEeccCceeccccc-ccccceeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVE--SSDTIDNVKAKI-QDKEGIPPDQQRLIFAGKQLEDGRTLADYNI-QKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~--~~~tv~~lk~~i-~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i-~~~~~i~l~~~~   73 (154)
                      |+|+||+.+|+.+.++++  +++||.+||++| +...|+|+++|+|+|.|+.|+|+.+|++|++ .++++|++..++
T Consensus         2 mqI~VKtl~g~~~~i~v~v~~~~TV~~lK~~I~~~~~gip~~~QrLi~~Gk~L~D~~tL~~y~I~~~~stl~v~~~~   78 (87)
T 2lxa_A            2 VHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKP   78 (87)
T ss_dssp             CEEEEEECSSSCEECCEECCTTCBHHHHHHHHHHTTSCSSSTTEEEEETTEECCTTCBHHHHCCCGGGCEEEEEECC
T ss_pred             EEEEEEcCCCCEEEEEEcCCCCCcHHHHHHHHHHHhcCCChHHEEEEECCEECcCcCCHHHcCCCCCCCEEEEEcCC
Confidence            899999999999988766  999999999999 9999999999999999999999999999999 799999988875

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

Probab=99.80  E-value=3.6e-19  Score=106.85  Aligned_cols=76  Identities=37%  Similarity=0.578  Sum_probs=71.8

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeec
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALR  150 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~  150 (154)
                      ..|.|+|+..+|+.+.+++++++||++||++|++.+|+|++.|+|+|+|+.|+|+.+|++||+.+|++|+++++++
T Consensus         6 ~~m~i~vk~~~g~~~~~~v~~~~tV~~LK~~i~~~~~i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~~~   81 (81)
T 2dzi_A            6 SGMQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLNVPVRQQRLLFKGKALADGKRLSDYSIGPNSKLNLVVKPL   81 (81)
T ss_dssp             SSEEEEEEETTSCEEEEEECSSCBHHHHHHHHHHHTCCCTTTCEEEETTEECCTTSBGGGGTCCSSBCCEEECCCC
T ss_pred             CcEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEeCC
Confidence            4589999998899999999999999999999999999999999999999999999999999999999999988753

>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=99.80  E-value=6.9e-19  Score=108.78  Aligned_cols=76  Identities=32%  Similarity=0.627  Sum_probs=71.3

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhh---cCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEK---EGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~---~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|++.   +|+|+++|+|+|+|+.|+|+.+|++|||.+|++|+++++...|
T Consensus         1 M~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~~~~gip~~~qrLi~~Gk~L~D~~tL~~ygI~~g~~i~l~~~~~~~   79 (95)
T 1uel_A            1 MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKPKA   79 (95)
T ss_dssp             CEEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEETTEECCTTSBGGGGTCCSSSEEEEEESSCCC
T ss_pred             CEEEEEeCCCCEEEEEECCCCHHHHHHHHHHhhcccCCCChhhEEEEECCEECCCcCcHHHCCCCCCCEEEEEEeCCCC
Confidence            689999999999999999999999999999999   7899999999999999999999999999999999999876543

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

Probab=99.80  E-value=3.9e-19  Score=108.43  Aligned_cols=71  Identities=35%  Similarity=0.627  Sum_probs=68.0

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|++..++|++.|+|+|+|+.|+|+.+|++|++ ++++||++++
T Consensus        18 m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i-~g~~i~lv~R   88 (88)
T 4eew_A           18 LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVIHLVER   88 (88)
T ss_dssp             EEEEEEETTSCEEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGGTC-TTEEEEEEEC
T ss_pred             EEEEEEcCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEECCCCCcHHHcCC-CCcEEEEEEC
Confidence            6899999999999999999999999999999999999999999999999999999999999 8999998764

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

Probab=99.80  E-value=7.5e-20  Score=114.23  Aligned_cols=92  Identities=35%  Similarity=0.615  Sum_probs=67.2

Q ss_pred             ceecccccccccceeeeeeeecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCccc
Q 040824           54 RTLADYNIQKESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTAR  133 (154)
Q Consensus        54 ~~l~~~~i~~~~~i~l~~~~~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~  133 (154)
                      ...++|.+.  ++.++.....-.+.|+|+. +|+.+.+++++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|+
T Consensus         8 ~~~~~~~~~--~t~~l~l~~~m~i~I~Vk~-~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~   84 (101)
T 3m63_B            8 HPMSDYDIP--TTENLYFQGAMSLNIHIKS-GQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVE   84 (101)
T ss_dssp             -----------------------CCEEEEC-SSCCCCBCCCTTSBHHHHHHHHHHHHSCCSTTCCEEETTEECCTTSBTT
T ss_pred             CCccccCCC--cceeecccCCcEEEEEEEE-CCEEEEEEeCCCCCHHHHHHHHHHHHCcChHHEEEEECCEECCCcCcHH
Confidence            467889885  4555555555557788887 8889999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCEEEEEEe
Q 040824          134 DYNIEGGSVLHLVLA  148 (154)
Q Consensus       134 ~~~i~~~~~i~~~~~  148 (154)
                      +|||++|++|+++.+
T Consensus        85 ~~gI~~g~tI~lv~~   99 (101)
T 3m63_B           85 SYHIQDGHSVHLVKS   99 (101)
T ss_dssp             TTTCCTTEEEEECCC
T ss_pred             HCCCCCCCEEEEEeC
Confidence            999999999998765

>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=99.80  E-value=1.5e-19  Score=111.54  Aligned_cols=70  Identities=23%  Similarity=0.328  Sum_probs=67.9

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~   70 (154)
                      |+|+|+.+.|+.+.+++++++||.+||++|+++.|+|+++|+|+|.|+.|+|+.+|++|+|.++++|+|.
T Consensus        29 m~I~VKtl~Gk~i~lev~p~dTV~~lK~~Ia~k~Gip~~qQrLi~~Gk~L~D~~TL~dygI~~gstlhL~   98 (100)
T 1uh6_A           29 IEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLELY   98 (100)
T ss_dssp             EEEEEECSSSSCEEEEEETTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCSSCBHHHHTCCTTEEEEEE
T ss_pred             EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhCCCHHHEEEEECCEECCCCCCHHHcCCCCCCEEEEE
Confidence            7899999999999999999999999999999999999999999999999999999999999999999876

>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=99.80  E-value=2.1e-19  Score=107.49  Aligned_cols=75  Identities=17%  Similarity=0.425  Sum_probs=71.6

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+..+|+.+.+++++++||.+||++++++.++|++.|+|+|+|+.|+|+.+|++|++.++++|++.++..+
T Consensus         4 m~i~vk~~~g~~~~~~v~~~~tv~~lk~~i~~~~gi~~~~qrL~~~G~~L~d~~tl~~~~i~~~~~i~l~~~~~G   78 (79)
T 2uyz_B            4 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTG   78 (79)
T ss_dssp             EEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCHHHHTCCTTEEEEEEECCCC
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHHCCCcccEEEEECCEEeCCCCCHHHcCCCCCCEEEEEEeccC
Confidence            689999999999999999999999999999999999999999999999999999999999999999999987654

>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=99.79  E-value=2.2e-19  Score=110.85  Aligned_cols=72  Identities=21%  Similarity=0.227  Sum_probs=69.0

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEE
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      .|.|+|++..|+.+.+++.+++||.+||++|+++.|+|+++|+|+|.|+.|+|+.+|++|+|.++++|++..
T Consensus        28 mm~I~VKtl~Gk~i~lev~p~dTV~~lK~~Ia~k~Gip~~qQrLi~~Gk~L~D~~TL~dygI~~gstlhL~~   99 (100)
T 1uh6_A           28 MIEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLELYY   99 (100)
T ss_dssp             EEEEEEECSSSSCEEEEEETTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCSSCBHHHHTCCTTEEEEEEC
T ss_pred             eEEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhCCCHHHEEEEECCEECCCCCCHHHcCCCCCCEEEEEe
Confidence            389999999999999999999999999999999999999999999999999999999999999999998863

>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=99.79  E-value=3.4e-19  Score=106.27  Aligned_cols=73  Identities=36%  Similarity=0.643  Sum_probs=69.4

Q ss_pred             CEEEEEeCCCCEE-EEE-EeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTGKTI-TLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~~~-~~~-v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |+|+|+..+|+.+ .++ +++++||.+||++|+...++|+++|+|+|+|+.|+|+.+|++|++.++++|++.+++
T Consensus         3 m~i~Vk~~~g~~~~~l~~v~~~~tv~~lK~~i~~~~gip~~~qrL~~~g~~L~d~~tL~~~~i~~g~~i~l~~r~   77 (78)
T 2faz_A            3 MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLLVRQ   77 (78)
T ss_dssp             EEEEEEETTSSCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTTTTTCCTTCEEEEEECC
T ss_pred             EEEEEEECCCCEEEEEeccCCCCCHHHHHHHHHHHHCcChhhEEEEECCEECCCCCCHHHcCCCCCCEEEEEEeC
Confidence            7899999999885 899 999999999999999999999999999999999999999999999999999998764

>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure, northeast structural genomics consortium, protein structure initiative, NESG; NMR {Homo sapiens}

Probab=99.79  E-value=1.9e-19  Score=109.77  Aligned_cols=75  Identities=36%  Similarity=0.595  Sum_probs=69.9

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|+...++|+++|+|+|+|+.|+|+.+|++|++.++++|++..+..+
T Consensus         5 m~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~~I~~g~~i~l~~~~~g   79 (88)
T 2hj8_A            5 LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRG   79 (88)
T ss_dssp             EEEEEEETTSCEEEEEEESSSBHHHHHHHHHHHTCSCTTTEEEESSSSCCCTTSBHHHHHCSTTCEEEEEEC---
T ss_pred             EEEEEECCCCCEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEECCEECCCCCcHHHcCCCCCCEEEEEEEcCC
Confidence            689999999999999999999999999999999999999999999999999999999999999999999887654

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B

Probab=99.79  E-value=1.4e-18  Score=117.90  Aligned_cols=83  Identities=90%  Similarity=1.208  Sum_probs=75.6

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecceeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGTMIK   80 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~~~i~   80 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|++.++++|++.++..++..-.
T Consensus         1 MqI~Vk~~~Gk~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~y~I~~gstI~Lvlrl~GG~k~~   80 (169)
T 3l0w_B            1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGGGET   80 (169)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHCCCTTTEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCCC---CC
T ss_pred             CEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHHCcCHHHEEEEECCccccCcCcHHHcCCCCCCEEEEEEEeccccccc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999987765544


Q ss_pred             eee
Q 040824           81 VKT   83 (154)
Q Consensus        81 v~~   83 (154)
                      |+.
T Consensus        81 vkf   83 (169)
T 3l0w_B           81 IKF   83 (169)
T ss_dssp             EEE
T ss_pred             ccc
Confidence            443

>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=99.79  E-value=4.2e-19  Score=110.67  Aligned_cols=79  Identities=28%  Similarity=0.369  Sum_probs=74.0

Q ss_pred             ecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           74 RGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        74 ~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      ...|.|+|+..+|+ +.+++++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+|++|++|+++++.+||+
T Consensus        20 ~~~m~I~Vk~~~g~-~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~ygI~~gstI~l~~r~~~~p   98 (100)
T 1yqb_A           20 PHLIKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHRA   98 (100)
T ss_dssp             TTEEEEEEECSSCE-EEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBHHHHTCCTTCEEEEEECCCCSC
T ss_pred             CCeEEEEEEcCCCc-EEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEECCCcCcHHHCCCCCCCEEEEEEcCCCCC
Confidence            34589999998886 68999999999999999999999999999999999999999999999999999999999999874

>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=99.79  E-value=6.5e-21  Score=124.05  Aligned_cols=78  Identities=59%  Similarity=0.927  Sum_probs=1.1

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCCC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGGL  154 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~~  154 (154)
                      |+|+|+..+|+++.+++++++||++||++|++.+|+|++.|+|+|+|+.|+|+.+|++|||.+|++|+++++++||.+
T Consensus         1 M~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~~I~~gsti~l~~rl~GG~~   78 (128)
T 3u5e_m            1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGII   78 (128)
T ss_dssp             ----------------------------------------------------------------------------CC
T ss_pred             CEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHhCcChHHEEEEECCEECCCCCchhhhccCCCCEEEEEEEcCCCCC
Confidence            678999999999999999999999999999999999999999999999999999999999999999999999999964

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

Probab=99.79  E-value=7.3e-19  Score=105.49  Aligned_cols=73  Identities=40%  Similarity=0.690  Sum_probs=69.8

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |+|+|+.++|+.+.+++++++||.+||++|++..++|++.|+|+|+|+.|+|+.+|++|++.++++|++.+++
T Consensus         8 m~i~vk~~~g~~~~~~v~~~~tV~~LK~~i~~~~~i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~~   80 (81)
T 2dzi_A            8 MQLTVKALQGRECSLQVPEDELVSTLKQLVSEKLNVPVRQQRLLFKGKALADGKRLSDYSIGPNSKLNLVVKP   80 (81)
T ss_dssp             EEEEEEETTSCEEEEEECSSCBHHHHHHHHHHHTCCCTTTCEEEETTEECCTTSBGGGGTCCSSBCCEEECCC
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHEEEEECCeECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            7899999999999999999999999999999999999999999999999999999999999999999988764

>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=99.79  E-value=4.9e-19  Score=107.71  Aligned_cols=76  Identities=34%  Similarity=0.532  Sum_probs=72.4

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecc
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~   76 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|++.++++|++.++..++
T Consensus         8 m~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~qrL~~~Gk~L~d~~tL~~~~i~~g~~i~l~~~~~GG   83 (87)
T 1wh3_A            8 IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKGSG   83 (87)
T ss_dssp             EEEEEEETTTEEEEEEECSSSBHHHHHHHHHHHTCCCTTTEEEEETTEECCSSSBHHHHTCCTTEEEEEEECSCCC
T ss_pred             EEEEEEcCCCCEEEEEeCCCChHHHHHHHHHHHhCCChHHEEEEECCEEccCCCCHHHCCCCCCCEEEEEEeccCC
Confidence            7899999999999999999999999999999999999999999999999999999999999999999999887654

>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=99.79  E-value=1.7e-19  Score=111.78  Aligned_cols=78  Identities=23%  Similarity=0.274  Sum_probs=74.3

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      ..|.|+|+.. |+.+.+++++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|.+|++|+++++.+||+
T Consensus        16 ~~m~i~Vk~~-g~~~~~~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~~g~   93 (96)
T 1wx8_A           16 RIIRVSVKTP-QDCHEFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVRSHSGP   93 (96)
T ss_dssp             CEEEEEEECS-SSEEEEEEETTCCHHHHHHHHHHHTCSCTTTBCCEETTEECCTTSCHHHHTCCTTEEEECCBCCSSCS
T ss_pred             CcEEEEEEEC-CeEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEECCCcCCHHHCCCCCCCEEEEEEeCCCCC
Confidence            4588999997 88999999999999999999999999999999999999999999999999999999999999999985

>2lxa_A Ubiquitin-like protein MDY2; ubiquitin-like domain, protein-protein interaction, SGT2 BIN domain, GET pathway, protein binding; NMR {Saccharomyces cerevisiae}

Probab=99.79  E-value=2.9e-19  Score=108.33  Aligned_cols=73  Identities=22%  Similarity=0.404  Sum_probs=68.3

Q ss_pred             eeeeeeecCCceEEEeeC--CCchHHHHHHHH-hhhcCCCCCceeEEECCeecCCCCccccccc-CCCCEEEEEEee
Q 040824           77 TMIKVKTLTGKEIEIDIE--PTDTIERIKERV-EEKEGIPPVQQRLIYAGKQLADDKTARDYNI-EGGSVLHLVLAL  149 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~--~~~tv~~LK~~i-~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i-~~~~~i~~~~~~  149 (154)
                      |+|+|++.+|+++.++++  +++||.+||++| ++..|+|+++|+|+|+|+.|+|+.+|++|+| ++|++|++....
T Consensus         2 mqI~VKtl~g~~~~i~v~v~~~~TV~~lK~~I~~~~~gip~~~QrLi~~Gk~L~D~~tL~~y~I~~~~stl~v~~~~   78 (87)
T 2lxa_A            2 VHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKP   78 (87)
T ss_dssp             CEEEEEECSSSCEECCEECCTTCBHHHHHHHHHHTTSCSSSTTEEEEETTEECCTTCBHHHHCCCGGGCEEEEEECC
T ss_pred             EEEEEEcCCCCEEEEEEcCCCCCcHHHHHHHHHHHhcCCChHHEEEEECCEECcCcCCHHHcCCCCCCCEEEEEcCC
Confidence            789999999998888755  999999999999 9999999999999999999999999999999 799999998764

>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=99.66  E-value=7.2e-21  Score=113.04  Aligned_cols=75  Identities=27%  Similarity=0.511  Sum_probs=72.4

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRG  151 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~g  151 (154)
                      |+|+|+..+|+.+.+++++++||++||+++++.+|+|++.|+|+|+|+.|+|+.+|++||+.+|++|++.++++|
T Consensus         1 M~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~rlrg   75 (76)
T 3b1l_X            1 MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKQQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRR   75 (76)
Confidence            678999999999999999999999999999999999999999999999999999999999999999999999987

>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=99.79  E-value=1.2e-18  Score=107.72  Aligned_cols=74  Identities=30%  Similarity=0.585  Sum_probs=70.4

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhH---hCCCCCCeEEEEcceEeccCceecccccccccceeeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDK---EGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~---~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~   74 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|+..   .++|+++|+|+|+|+.|+|+.+|++|++.++++|++..+..
T Consensus         1 M~I~Vk~~~g~~~~~~v~~~~TV~~LK~~I~~~~~~~gip~~~qrLi~~Gk~L~D~~tL~~ygI~~g~~i~l~~~~~   77 (95)
T 1uel_A            1 MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKP   77 (95)
T ss_dssp             CEEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEETTEECCTTSBGGGGTCCSSSEEEEEESSC
T ss_pred             CEEEEEeCCCCEEEEEECCCCHHHHHHHHHHhhcccCCCChhhEEEEECCEECCCcCcHHHCCCCCCCEEEEEEeCC
Confidence            899999999999999999999999999999999   78999999999999999999999999999999999887643

>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=99.79  E-value=1.6e-18  Score=105.00  Aligned_cols=76  Identities=34%  Similarity=0.610  Sum_probs=70.6

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhh---cCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeec
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEK---EGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALR  150 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~---~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~  150 (154)
                      ..|.|+|+..+|+.+.+++++++||.+||++|++.   +|+|+++|+|+|+|+.|+|+.+|++|+|.+|++|+++.+..
T Consensus         4 ~~m~i~vk~~~g~~~~~~v~~~~TV~~lK~~i~~~~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~i~l~~~~~   82 (85)
T 2wyq_A            4 MAVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTKT   82 (85)
T ss_dssp             CCEEEEEEETTSCEEEEEECTTSBHHHHHHHHHHHHCTTTCCGGGEEEEETTEECCTTSBGGGGCCCTTSEEEEEEC--
T ss_pred             ceEEEEEEECCCCEEEEEECCCCCHHHHHHHHHhhccccCCCHHHeEEEECCEECcCCCCHHHcCCCCCCEEEEEEcCC
Confidence            46899999999999999999999999999999998   89999999999999999999999999999999999987653

>3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=99.78  E-value=5.6e-19  Score=111.26  Aligned_cols=74  Identities=24%  Similarity=0.483  Sum_probs=69.7

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeec
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALR  150 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~  150 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|||++|++|+++++..
T Consensus         2 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~~i~~g~~i~lv~~~~   75 (106)
T 3m62_B            2 VSLTFKNFKKEKVPLDLEPSNTILETKTKLAQSISCEESQIKLIYSGKVLQDSKTVSECGLKDGDQVVFMVSQK   75 (106)
T ss_dssp             -CEEEECTTCCEEEECCCTTSBHHHHHHHHHHTTTSCGGGCEEEETTEECCTTSBTTTTTCCTTCEEEEECCC-
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCChhhEEEEECCEECCCcCCHHHcCCCCCCEEEEEEcCC
Confidence            78999999999999999999999999999999999999999999999999999999999999999999998753

>3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=99.78  E-value=3e-19  Score=112.50  Aligned_cols=74  Identities=22%  Similarity=0.437  Sum_probs=70.1

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~   74 (154)
                      |+|+|+.++|+.+.+++++++||.+||++|+...++|+++|+|+|+|+.|+|+.+|++|+++++++|+++++..
T Consensus         2 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~~i~~g~~i~lv~~~~   75 (106)
T 3m62_B            2 VSLTFKNFKKEKVPLDLEPSNTILETKTKLAQSISCEESQIKLIYSGKVLQDSKTVSECGLKDGDQVVFMVSQK   75 (106)
T ss_dssp             -CEEEECTTCCEEEECCCTTSBHHHHHHHHHHTTTSCGGGCEEEETTEECCTTSBTTTTTCCTTCEEEEECCC-
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCChhhEEEEECCEECCCcCCHHHcCCCCCCEEEEEEcCC
Confidence            78999999999999999999999999999999999999999999999999999999999999999999998754

>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=99.78  E-value=7.4e-19  Score=111.56  Aligned_cols=75  Identities=96%  Similarity=1.311  Sum_probs=72.0

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+.++|+.+.+++++++||.+||++|+...++|++.|+|+|+|+.|.|+.+|++|++.++++|++.++..+
T Consensus        36 m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~gI~~gs~I~l~~rl~G  110 (111)
T 3vdz_A           36 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG  110 (111)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTTTTTCCTTCEEEEEECCCC
T ss_pred             EEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHhCCChHHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCC
Confidence            789999999999999999999999999999999999999999999999999999999999999999999988654

>4a20_A Ubiquitin-like protein MDY2; protein binding, GET-pathway, tail-anchored proteins; 1.78A {Saccharomyces cerevisiae} PDB: 2lxc_A 4goc_A

Probab=99.78  E-value=9.6e-19  Score=108.26  Aligned_cols=76  Identities=22%  Similarity=0.406  Sum_probs=69.4

Q ss_pred             ecceeeeeeecCCceEEE--eeCCCchHHHHHHHH-hhhcCCCCCceeEEECCeecCCCCccccccc-CCCCEEEEEEee
Q 040824           74 RGGTMIKVKTLTGKEIEI--DIEPTDTIERIKERV-EEKEGIPPVQQRLIYAGKQLADDKTARDYNI-EGGSVLHLVLAL  149 (154)
Q Consensus        74 ~~~~~i~v~~~~~~~~~~--~v~~~~tv~~LK~~i-~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i-~~~~~i~~~~~~  149 (154)
                      ...|.|+|++.+|+.+.+  ++++++||++||++| ++..|+|+++|+|+|+|+.|+|+.+|++|+| ++|++|++++..
T Consensus        17 ~~~m~I~VKtl~g~~~~i~v~v~~~~TV~~lK~~I~~~~~gip~~~QrLi~~Gk~L~D~~tL~dy~I~~~g~ti~lmvsk   96 (98)
T 4a20_A           17 NAAVHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKP   96 (98)
T ss_dssp             -CCEEEEEEECSSSCEEEEEEECTTCBHHHHHHHHHHTTSCSCGGGEEEEETTEEECTTCBGGGSCCBTTBCEEEEEECC
T ss_pred             CCCEEEEEEcCCCCEEEEEEecCCCChHHHHHHHHHHHhcCCChhhEEEEECCEECcCcCCHHHcCcCCCCCEEEEEEeC
Confidence            456999999999987766  566999999999999 8889999999999999999999999999999 999999998864

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.78  E-value=1.2e-18  Score=112.65  Aligned_cols=78  Identities=26%  Similarity=0.319  Sum_probs=70.2

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      ..|.|+|+.. |+.+.+++++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+|++|++|+++.+.+||+
T Consensus        31 ~~m~I~Vk~~-g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~dygI~~gstI~lv~~~~gg~  108 (125)
T 1j8c_A           31 KIIKVTVKTP-KEKEEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIKRDPNS  108 (125)
T ss_dssp             CCEEEEEECS-SCEEEEEECTTCCHHHHHHHHHHHHCSCSSSEEEEETTEEESTTSCGGGTTCSSSEEEEEEEC-----
T ss_pred             CcEEEEEEeC-CeEEEEEECCCCcHHHHHHHHHHHHCcCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEEeccCCCC
Confidence            4588999998 88999999999999999999999999999999999999999999999999999999999999999985

>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=99.78  E-value=1.2e-18  Score=105.54  Aligned_cols=74  Identities=30%  Similarity=0.531  Sum_probs=69.2

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhH---hCCCCCCeEEEEcceEeccCceecccccccccceeeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDK---EGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~---~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~   74 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|+..   .++|+++|+|+|+|+.|+|+.+|++|++.++++|++..+..
T Consensus         6 m~i~vk~~~g~~~~~~v~~~~TV~~lK~~i~~~~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~i~~g~~i~l~~~~~   82 (85)
T 2wyq_A            6 VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTKT   82 (85)
T ss_dssp             EEEEEEETTSCEEEEEECTTSBHHHHHHHHHHHHCTTTCCGGGEEEEETTEECCTTSBGGGGCCCTTSEEEEEEC--
T ss_pred             EEEEEEECCCCEEEEEECCCCCHHHHHHHHHhhccccCCCHHHeEEEECCEECcCCCCHHHcCCCCCCEEEEEEcCC
Confidence            789999999999999999999999999999998   88999999999999999999999999999999999987653

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.78  E-value=9.8e-19  Score=107.81  Aligned_cols=75  Identities=28%  Similarity=0.461  Sum_probs=70.5

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccC-ceecccccccccceeeeeeeecc
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDG-RTLADYNIQKESTLHLVLRLRGG   76 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~-~~l~~~~i~~~~~i~l~~~~~~~   76 (154)
                      |+|+|+..++ .+.+++++++||.+||++|+...++|+++|+|+|+|+.|+|+ .+|++|+++++++|+++++..++
T Consensus        16 ~~I~Vk~~~~-~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~~tL~~ygI~~gstl~lv~r~~gg   91 (94)
T 2kan_A           16 IHVTVKFPSK-QFTVEVDRTETVSSLKDKIHIVENTPIKRMQLYYSGIELADDYRNLNEYGITEFSEIVVFLKSINR   91 (94)
T ss_dssp             EEEEEECSSC-EEEEEECTTCBHHHHHHHHHHHSSSCTTTEEEEETTEEECCTTSBHHHHTCCTTEEEEEEECCCSS
T ss_pred             EEEEEEcCCc-EEEEEECCCCcHHHHHHHHHHHHCcCHHHEEEEECCEECCCCcccHHHCCCCCCCEEEEEEeCCCC
Confidence            6899999877 899999999999999999999999999999999999999999 99999999999999999887653

>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=99.78  E-value=1.2e-18  Score=106.47  Aligned_cols=76  Identities=37%  Similarity=0.627  Sum_probs=71.5

Q ss_pred             CEEEEEeCCC-CEEEE-EEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecc
Q 040824            1 MQIFVKTLTG-KTITL-EVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (154)
Q Consensus         1 m~v~v~~~~~-~~~~~-~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~   76 (154)
                      |+|+|+..+| +.+.+ ++++++||.+||++|+...++|+++|+|+|+|+.|+|+.+|++|++.++++|++.++..++
T Consensus         8 m~i~Vk~~~g~~~~~l~~v~~~~tV~~lK~~i~~~~gip~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~~~gG   85 (89)
T 1wy8_A            8 MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVRPDSG   85 (89)
T ss_dssp             EEEEEEETTCSCEEEEEEECTTCBHHHHHHHHHHHSCCCTTTEEEEETTEECCSSSBHHHHTCCTTCEEEEEECCCCS
T ss_pred             EEEEEEECCCCceEEEEecCCCCCHHHHHHHHHHHHCcChhhEEEEECCeECCCCCCHHHCCCCCCCEEEEEEeCCCC
Confidence            7899999999 79999 5999999999999999999999999999999999999999999999999999999887644

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

Probab=99.78  E-value=5.7e-19  Score=121.21  Aligned_cols=83  Identities=88%  Similarity=1.166  Sum_probs=79.1

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecceeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGTMIK   80 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~~~i~   80 (154)
                      |+|+|+..+|+++.+++++++||.+||++|++..++|++.|+|+|+|+.|+|+.+|++|++.++++|+++++..++..++
T Consensus       106 MqI~VKtl~Gkt~~l~V~~s~TV~~LK~kI~~~~gIp~~~QrLi~~Gk~L~D~~tL~dygI~~gstI~LvlrlrGG~~~f  185 (189)
T 3q3f_A          106 GQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGGQTF  185 (189)
T ss_dssp             EEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCCEEETTEECCTTCBGGGGTCCTTCEEEECCCCCCCCCCC
T ss_pred             eeeeeecCCCCEEEEEeCCCCcHHHHHHHHHhccCCCHHHEEEEECCEECCCCCCHHHCCCCCCCEEEEEEEcCCCCcce
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999998887777


Q ss_pred             eee
Q 040824           81 VKT   83 (154)
Q Consensus        81 v~~   83 (154)
                      |+.
T Consensus       186 vk~  188 (189)
T 3q3f_A          186 TKI  188 (189)
T ss_dssp             CCC
T ss_pred             Eec
Confidence            653

>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=99.78  E-value=8.7e-19  Score=108.16  Aligned_cols=66  Identities=17%  Similarity=0.221  Sum_probs=62.7

Q ss_pred             CceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           86 GKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        86 ~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ++.+.+++++++||.+||++|+++.|+|+++|+|+|+|+.|+|+.||++|+|++|++| ++++++|.
T Consensus        29 ~~~~~lev~~~~TV~~lK~kI~~k~gip~~qQrLI~~GKiL~D~~TL~~y~I~~gsti-~vl~lrg~   94 (100)
T 1wju_A           29 DRKNLLETRLHITGRELRSKIAETFGLQENYIKIVINKKQLQLGKTLEEQGVAHNVKA-MVLELKQS   94 (100)
T ss_dssp             SSSEEEEEESSSBHHHHHHHHHHHTTCCSTTCEEEETTEECCTTSBHHHHTCCSSEEE-EEECCCCC
T ss_pred             CcEEEEEeCCcCHHHHHHHHHHHHHCcCHHHeEEEeCCeECCCCCcHHHcCCCCCCEE-EEEEECCC
Confidence            6789999999999999999999999999999999999999999999999999999999 77777764

>4a20_A Ubiquitin-like protein MDY2; protein binding, GET-pathway, tail-anchored proteins; 1.78A {Saccharomyces cerevisiae} PDB: 2lxc_A 4goc_A

Probab=99.78  E-value=1e-18  Score=108.17  Aligned_cols=73  Identities=21%  Similarity=0.423  Sum_probs=67.6

Q ss_pred             CEEEEEeCCCCEEEE--EEeCCCcHHHHHHHH-HhHhCCCCCCeEEEEcceEeccCceeccccc-ccccceeeeeee
Q 040824            1 MQIFVKTLTGKTITL--EVESSDTIDNVKAKI-QDKEGIPPDQQRLIFAGKQLEDGRTLADYNI-QKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~~~~~--~v~~~~tv~~lk~~i-~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i-~~~~~i~l~~~~   73 (154)
                      |+|+||+.+|+.|.+  ++++++||.+||++| +...++|+++|+|+|+|+.|+|+.+|++|+| +++++|++.++.
T Consensus        20 m~I~VKtl~g~~~~i~v~v~~~~TV~~lK~~I~~~~~gip~~~QrLi~~Gk~L~D~~tL~dy~I~~~g~ti~lmvsk   96 (98)
T 4a20_A           20 VHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKP   96 (98)
T ss_dssp             EEEEEEECSSSCEEEEEEECTTCBHHHHHHHHHHTTSCSCGGGEEEEETTEEECTTCBGGGSCCBTTBCEEEEEECC
T ss_pred             EEEEEEcCCCCEEEEEEecCCCChHHHHHHHHHHHhcCCChhhEEEEECCEECcCcCCHHHcCcCCCCCEEEEEEeC
Confidence            789999999998777  556999999999999 8888999999999999999999999999999 999999998764

>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling proteins; 1.15A {Saccharomyces cerevisiae} SCOP: d.15.1.1 PDB: 2bwe_S

Probab=99.77  E-value=2.6e-18  Score=102.06  Aligned_cols=71  Identities=38%  Similarity=0.684  Sum_probs=67.8

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEe
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      |.|+|+. +|+.+.+++++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++||+++|++|++..+
T Consensus         5 m~i~vk~-~g~~~~~~v~~~~tV~~LK~~i~~~~~i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~   75 (77)
T 2bwf_A            5 LNIHIKS-GQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS   75 (77)
T ss_dssp             EEEEEEE-TTEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEEC
T ss_pred             EEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHhCCCHHHEEEEECCeEcCCCCCHHHcCCCCCCEEEEEEc
Confidence            7889998 8999999999999999999999999999999999999999999999999999999999998764

>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling proteins; 1.15A {Saccharomyces cerevisiae} SCOP: d.15.1.1 PDB: 2bwe_S

Probab=99.77  E-value=1.6e-18  Score=103.04  Aligned_cols=72  Identities=33%  Similarity=0.559  Sum_probs=68.0

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |+|+|+. +|+.+.+++++++||.+||++|+...++|++.|+|+|+|+.|+|+.+|++|++.++++|++..++
T Consensus         5 m~i~vk~-~g~~~~~~v~~~~tV~~LK~~i~~~~~i~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~~~   76 (77)
T 2bwf_A            5 LNIHIKS-GQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKSQ   76 (77)
T ss_dssp             EEEEEEE-TTEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECC
T ss_pred             EEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHhCCCHHHEEEEECCeEcCCCCCHHHcCCCCCCEEEEEEcC
Confidence            6789998 89999999999999999999999999999999999999999999999999999999999887653

>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=99.77  E-value=8e-19  Score=108.87  Aligned_cols=75  Identities=17%  Similarity=0.425  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+..+|+.+.+++.+++||.+||++|+.+.++|++.|+|+|+|+.|.|+.+|++|++.++++|++.++..+
T Consensus        22 m~I~Vk~~~g~~~~l~v~~~~tv~~lK~~i~~~~gip~~~qrLif~Gk~L~d~~tl~dy~i~~g~~I~l~~~~~G   96 (97)
T 1wyw_B           22 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTG   96 (97)
T ss_dssp             EEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCHHHHTCCTTCEEEEEESSSC
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCChhhEEEEECCeEcCCCCCHHHCCCCCCCEEEEEEecCC
Confidence            689999999999999999999999999999999999999999999999999999999999999999999987654

>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=99.77  E-value=1.9e-20  Score=124.66  Aligned_cols=77  Identities=61%  Similarity=0.975  Sum_probs=0.0

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+|++|++|+++++++||+
T Consensus         1 MqI~VK~l~G~~~~l~V~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~dygI~~gstL~Lvlrl~GGg   77 (152)
T 3u5c_f            1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGG   77 (152)
T ss_dssp             -----------------------------------------------------------------------------
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEEccccCcHHHcCCCCCCEEEEEeeccCCC
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999985

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=99.77  E-value=3.3e-18  Score=106.81  Aligned_cols=79  Identities=25%  Similarity=0.325  Sum_probs=73.0

Q ss_pred             eecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           73 LRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        73 ~~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ....|.|+|+.. |+.+.+++++++||.+||++|++.+|+|++.|+|+|+|+.|+|+.+|++|||.+|++|+++.+.++.
T Consensus        22 ~~~~m~I~Vk~~-g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~gI~~g~~I~l~~~~~~~  100 (101)
T 2klc_A           22 HPKIMKVTVKTP-KEKEEFAVPENSSVQQFKEEISKRFKSHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQNR  100 (101)
T ss_dssp             -CCCEEEEEECS-SCEEEEEECSCCCHHHHHHHHHHHHTCCGGGEEEEETTEEECTTCCTGGGTCCTTCEEEEEECCSSC
T ss_pred             CCCeEEEEEEeC-CcEEEEEECCCCCHHHHHHHHHHHHCcChhhEEEEECCEECCCcCcHHHcCCCCCCEEEEEEcCCCC
Confidence            345689999997 7889999999999999999999999999999999999999999999999999999999999988754

>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=99.77  E-value=2.4e-18  Score=108.35  Aligned_cols=79  Identities=23%  Similarity=0.434  Sum_probs=74.1

Q ss_pred             ecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           74 RGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        74 ~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ...|.|+|+..+|+.+.+++++++||.+||++|+..+|+|+++|+|+|+|+.|+|+.+|++|||.+|++|+++.+...+
T Consensus        21 ~~~m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~ygI~~g~ti~lv~~~~~~   99 (106)
T 1ttn_A           21 GYECQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQPVQ   99 (106)
T ss_dssp             CCSEEEEEEETTTEEEEEEECTTSHHHHHHHHHHHTTCCCSTTCEEEETTEECCTTSHHHHCCCSSSCEEEEECCCSSC
T ss_pred             CCeEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHHCcCcccEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCCC
Confidence            3568999999999999999999999999999999999999999999999999999999999999999999999887654

>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=99.77  E-value=1.9e-18  Score=108.84  Aligned_cols=78  Identities=28%  Similarity=0.378  Sum_probs=73.3

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      ..|.|+|+..+++ +.+++++++||.+||++|++.+++|+++|+|+|+|+.|+|+.+|++|+|.+|++|+++++.+||+
T Consensus        16 ~~m~I~Vk~~~g~-~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~~~~   93 (106)
T 1wx7_A           16 HLIKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHRA   93 (106)
T ss_dssp             SEEEEEEECSSCE-EEEEEETTCCHHHHHHHHHHHHTCCTTTEEEEETTEECCTTSCHHHHTCCTTEEEEEEECCCCCS
T ss_pred             ceEEEEEEeCCCc-EEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEECCCcCcHHHcCCCCCCEEEEEEcCCCCC
Confidence            4488999998876 78999999999999999999999999999999999999999999999999999999999999875

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

Probab=99.76  E-value=1.8e-18  Score=106.52  Aligned_cols=73  Identities=36%  Similarity=0.599  Sum_probs=69.2

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+.  |+.+.+++++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|++.++++|+++++..+
T Consensus        20 m~I~Vk~--g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~y~I~~gstI~lv~rl~G   92 (93)
T 2l7r_A           20 MQLFVRA--QELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAGAPLEDEATLGQCGVEALTTLEVAGRMLG   92 (93)
T ss_dssp             CEEEEES--SSEEEEECCSSCBHHHHHHHHHHHHTCCGGGCEEEETTEECCTTSBHHHHTCCSSCEEEEECCCCC
T ss_pred             EEEEEEC--CCEEEEEeCCCCcHHHHHHHHHHHhCcChhHEEEEECCEECCCCCcHHHCCCCCCCEEEEEEecCC
Confidence            7899997  799999999999999999999999999999999999999999999999999999999999987654

>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=99.76  E-value=1.8e-18  Score=108.28  Aligned_cols=79  Identities=19%  Similarity=0.387  Sum_probs=72.2

Q ss_pred             cceeeeeeecCC----ceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCC-CcccccccCCCCEEEEEEee
Q 040824           75 GGTMIKVKTLTG----KEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADD-KTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        75 ~~~~i~v~~~~~----~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~-~~L~~~~i~~~~~i~~~~~~  149 (154)
                      ..|+|+|+..++    +.+.+++++++||.+||++|++.+|+|+++|+|+|+|+.|+|+ .+|++|+|++|++|++..+.
T Consensus         6 ~~m~I~Vk~~~~~~~~~~~~i~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~gk~L~D~~~tL~~ygI~~g~~l~l~~~~   85 (102)
T 1v5o_A            6 SGMLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVLLQKD   85 (102)
T ss_dssp             CCEEEEEEECCCCCCCCEEEEEECTTCBHHHHHHHHHHHTCCCGGGBCEEETTEEECCSSSBHHHHTCCTTEEEEECBCC
T ss_pred             CeEEEEEEECCCCcCceEEEEEcCCCCCHHHHHHHHHHHHCcChHHeEEEECCEECCCCcccHHHCCCCCCCEEEEEECC
Confidence            348888888644    6889999999999999999999999999999999999999877 69999999999999999999


Q ss_pred             cCCC
Q 040824          150 RGGG  153 (154)
Q Consensus       150 ~gg~  153 (154)
                      +||.
T Consensus        86 ~gg~   89 (102)
T 1v5o_A           86 NVGL   89 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9873

>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=99.76  E-value=2e-18  Score=109.48  Aligned_cols=76  Identities=22%  Similarity=0.215  Sum_probs=67.5

Q ss_pred             eeeeeeecCCc-eEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccC-------CCCEEEEEEe
Q 040824           77 TMIKVKTLTGK-EIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE-------GGSVLHLVLA  148 (154)
Q Consensus        77 ~~i~v~~~~~~-~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~-------~~~~i~~~~~  148 (154)
                      |.++++...++ ++.+++.+++||.+||++|+.+.|+|+++|+|+|+|+.|+|++||++|||+       ++++|++.++
T Consensus         1 M~mfl~ir~~ktti~lev~~sdTV~~lK~kI~~~egIP~~qQrLi~~Gk~LeD~~TLsdy~I~~~~a~~q~~stL~L~lr   80 (118)
T 2fnj_B            1 MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPEEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFR   80 (118)
T ss_dssp             CEEEEEEEEBTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBHHHHTCCTTTSBTTBCEEEEEEEB
T ss_pred             CcEEEEEecCCEEEEEEeCCcChHHHHHHHHHHHhCCCHHHeEEEECCeECCCCCCHHHcCcccccccCCCCCEEEEEec
Confidence            34555555554 588999999999999999999999999999999999999999999999999       7999999999


Q ss_pred             ecCCC
Q 040824          149 LRGGG  153 (154)
Q Consensus       149 ~~gg~  153 (154)
                       .||.
T Consensus        81 -~~g~   84 (118)
T 2fnj_B           81 -ADDT   84 (118)
T ss_dssp             -SSSC
T ss_pred             -CCCc
Confidence             6663

>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=99.62  E-value=4.1e-20  Score=109.77  Aligned_cols=75  Identities=33%  Similarity=0.588  Sum_probs=71.5

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|++..++|++.|+|+|+|+.|+|+.+|++|++.++++|++.++.++
T Consensus         1 M~i~Vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~qrL~~~gk~L~d~~tL~~~~i~~g~~i~l~~rlrg   75 (76)
T 3b1l_X            1 MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKQQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRR   75 (76)
Confidence            899999999999999999999999999999999999999999999999999999999999999999999887653

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

Probab=99.76  E-value=5e-18  Score=115.70  Aligned_cols=79  Identities=61%  Similarity=0.947  Sum_probs=75.4

Q ss_pred             ecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           74 RGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        74 ~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ...|+|+|+..+|+.+.+++++++||.+||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+|.+|++|+++++++||
T Consensus        18 ~~~m~i~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~QrL~~~g~~L~d~~tL~~~~i~~~~~l~l~~~~~gg   96 (172)
T 3u30_A           18 GSHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   96 (172)
T ss_dssp             -CCEEEEEEETTTEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTGGGTCCTTCEEEEEECCCCC
T ss_pred             CCcEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCccccccCCHhHcCCcccceeeeeeccccc
Confidence            4569999999999999999999999999999999999999999999999999999999999999999999999998876

>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=99.76  E-value=2.6e-18  Score=105.82  Aligned_cols=75  Identities=28%  Similarity=0.459  Sum_probs=69.2

Q ss_pred             CEEEEEeCCCC--EEEEEEeCCCcHHHHHHHHHhHh--CCCCCCeEEEEcceEeccCceeccc--ccccccceeeeeeee
Q 040824            1 MQIFVKTLTGK--TITLEVESSDTIDNVKAKIQDKE--GIPPDQQRLIFAGKQLEDGRTLADY--NIQKESTLHLVLRLR   74 (154)
Q Consensus         1 m~v~v~~~~~~--~~~~~v~~~~tv~~lk~~i~~~~--~~~~~~q~L~~~g~~L~d~~~l~~~--~i~~~~~i~l~~~~~   74 (154)
                      |+|+|+..+++  .+.+++++++||.+||++|++..  ++|+++|+|+|.|+.|+|+.+|++|  ++.++++||++++..
T Consensus         8 m~i~Vk~~~~~~~~~~v~v~~~~TV~~lK~~I~~~~~~~i~~~~QrLi~~Gk~L~D~~tL~~~~~~i~~~~~i~lv~~~~   87 (93)
T 1wgd_A            8 VTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVCNVK   87 (93)
T ss_dssp             CEEEEECSSSSCCCEEEECCTTSCHHHHHHHHHHHSTTCCCTTTCEEEETTEECCSSSCHHHHSCSSSCSEEEEEECCCC
T ss_pred             EEEEEEeCCCCeEEEEEecCCCCcHHHHHHHHHHHhcCCCChHHeEEEECCEECcCcCCHHHHhcCCCCCCEEEEEeCCC
Confidence            78999999888  56677779999999999999998  9999999999999999999999999  999999999998765


Q ss_pred             c
Q 040824           75 G   75 (154)
Q Consensus        75 ~   75 (154)
                      +
T Consensus        88 g   88 (93)
T 1wgd_A           88 S   88 (93)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.75  E-value=1e-18  Score=109.10  Aligned_cols=77  Identities=21%  Similarity=0.355  Sum_probs=71.4

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCC---------------ceeEEECCeecC-CCCcccccccCC
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPV---------------QQRLIYAGKQLA-DDKTARDYNIEG  139 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~---------------~~~l~~~g~~l~-d~~~L~~~~i~~  139 (154)
                      .|.|+|+..+|+.+.++|.+++||++||++|+++.++|+.               +|+|+|+|+.|. |+.||++|||++
T Consensus         7 ~M~I~Vk~l~g~~~~v~V~~~~TV~dLK~~I~~~~~i~~~~q~g~~~isw~~~w~q~~Li~~Gk~L~dD~~tL~dygI~~   86 (105)
T 1v2y_A            7 GMTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLRDYGIRN   86 (105)
T ss_dssp             SEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHHHHHHHTTCCCCCCHHHHHTTEEEESSSCEECCSSSBHHHHTCCS
T ss_pred             cEEEEEEecCCCEEEEEECCCChHHHHHHHHHHHhCCCcccccCcceeeeeecceeEEEEeCCcCccCCcCCHHHcCCCC
Confidence            4899999999999999999999999999999999999873               569999999996 679999999999


Q ss_pred             CCEEEEEEeecCC
Q 040824          140 GSVLHLVLALRGG  152 (154)
Q Consensus       140 ~~~i~~~~~~~gg  152 (154)
                      |++|+++.+++|.
T Consensus        87 g~~l~lv~~lr~~   99 (105)
T 1v2y_A           87 RDEVSFIKKLGQK   99 (105)
T ss_dssp             SEEEEEEECSCSC
T ss_pred             CCEEEEEehhccC
Confidence            9999999999874

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

Probab=99.75  E-value=8.2e-18  Score=106.77  Aligned_cols=75  Identities=96%  Similarity=1.311  Sum_probs=71.4

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|++..++|++.|+|+|+|+.|+|+.+|++|++.++++|++.++..+
T Consensus        36 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~gI~~gs~I~l~~rl~G  110 (111)
T 2ojr_A           36 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG  110 (111)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHCCCTTTEEEEETTEECCSSCBTTTTTCCTTCEEEEEECCCC
T ss_pred             EEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHHHCcCcccEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCCC
Confidence            789999999999999999999999999999999999999999999999999999999999999999999987654

>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=99.75  E-value=9.4e-18  Score=107.52  Aligned_cols=79  Identities=29%  Similarity=0.412  Sum_probs=71.8

Q ss_pred             cceeeeeeecCCceE-EEeeCCCchHHHHHHHH-----hhhcCCCC--CceeEEECCeecCCCCcccccccCCC------
Q 040824           75 GGTMIKVKTLTGKEI-EIDIEPTDTIERIKERV-----EEKEGIPP--VQQRLIYAGKQLADDKTARDYNIEGG------  140 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~-~~~v~~~~tv~~LK~~i-----~~~~~i~~--~~~~l~~~g~~l~d~~~L~~~~i~~~------  140 (154)
                      ..|.|+++..+|+.+ ++++++++||.+||++|     +.+.++|+  ++|+|+|.|+.|+|+.||++|+|+.|      
T Consensus        15 ~~~~i~~kt~~G~~i~~l~v~psdTV~~lK~kI~~~~p~dkegiP~~~~qQrLIy~GK~LeD~~TLsdy~I~~~~~~~~v   94 (126)
T 1se9_A           15 NQLEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSKTVKDYRSPVSNLAGAV   94 (126)
T ss_dssp             CCEEEEEEETTSCEEEEEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEEETTEECCTTSBGGGGSCCTTSCTTCC
T ss_pred             ccEEEEEEECCCCEEEeeecCccCHHHHHHHHHHhhcccccccCCCChhhEEEEECCeECcCCCcHHHcCCCcCCccCCc
Confidence            568999999999888 79999999999999999     45667886  89999999999999999999999998      


Q ss_pred             CEEEEEEeecCCC
Q 040824          141 SVLHLVLALRGGG  153 (154)
Q Consensus       141 ~~i~~~~~~~gg~  153 (154)
                      .++++.++++||+
T Consensus        95 ~tmhlVlrl~g~~  107 (126)
T 1se9_A           95 TTMHVIIQAPVTE  107 (126)
T ss_dssp             EEEEEEECCCSSC
T ss_pred             EEEEEEeccCCcc
Confidence            6899999999874

>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=99.75  E-value=5.9e-18  Score=106.87  Aligned_cols=75  Identities=29%  Similarity=0.437  Sum_probs=70.1

Q ss_pred             CEEEEEeCCCC-EEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceeccccccc-------ccceeeeee
Q 040824            1 MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQK-------ESTLHLVLR   72 (154)
Q Consensus         1 m~v~v~~~~~~-~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~-------~~~i~l~~~   72 (154)
                      |.++++.+.++ ++.+++.+++||.+||++|+.+.|+|++.|+|+|+|+.|+|+.+|++|||.+       +++++++++
T Consensus         1 m~vFl~Ikr~ktTI~ldve~sdTV~~lK~kI~~~~giPp~qQrLI~~Gk~LeD~kTL~dy~I~~~ta~~q~~atl~Lvlr   80 (118)
T 4ajy_B            1 MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFR   80 (118)
T ss_dssp             CEEEEEEEEBTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTTTTTCCGGGSBTTBCEEEEEEEC
T ss_pred             CceEEEEecCCEEEEEEcCCCChHHHHHHHHHHHHCCCHHHeEEEeCCeECCCcCCHHHcCCCcCcccCCCCCEEEEEEe
Confidence            78899888777 6889999999999999999999999999999999999999999999999999       999999998


Q ss_pred             eec
Q 040824           73 LRG   75 (154)
Q Consensus        73 ~~~   75 (154)
                      ..+
T Consensus        81 ~~~   83 (118)
T 4ajy_B           81 ADD   83 (118)
T ss_dssp             CSS
T ss_pred             cCC
Confidence            643

>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=99.75  E-value=3.9e-18  Score=107.40  Aligned_cols=74  Identities=28%  Similarity=0.525  Sum_probs=70.7

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~   74 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|+...++++++|+|+|+|+.|+|+.+|++|++.++++|+++.+..
T Consensus        24 m~I~Vk~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~ygI~~g~ti~lv~~~~   97 (106)
T 1ttn_A           24 CQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQP   97 (106)
T ss_dssp             EEEEEEETTTEEEEEEECTTSHHHHHHHHHHHTTCCCSTTCEEEETTEECCTTSHHHHCCCSSSCEEEEECCCS
T ss_pred             EEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHHCcCcccEEEEECCEECCCCCcHHHcCCCCCCEEEEEEeCC
Confidence            78999999999999999999999999999999999999999999999999999999999999999999988654

>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=99.74  E-value=7.8e-18  Score=106.31  Aligned_cols=75  Identities=23%  Similarity=0.215  Sum_probs=67.2

Q ss_pred             eeeeeeecCCc-eEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCC-------CCEEEEEEe
Q 040824           77 TMIKVKTLTGK-EIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEG-------GSVLHLVLA  148 (154)
Q Consensus        77 ~~i~v~~~~~~-~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~-------~~~i~~~~~  148 (154)
                      |.++++...++ ++.+++.+++||.+||++|+.+.|+|+++|+|+|.|+.|+|++||++|||++       +++|++.++
T Consensus         1 m~vFl~Ikr~ktTI~ldve~sdTV~~lK~kI~~~~giPp~qQrLI~~Gk~LeD~kTL~dy~I~~~ta~~q~~atl~Lvlr   80 (118)
T 4ajy_B            1 MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFR   80 (118)
T ss_dssp             CEEEEEEEEBTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTTTTTCCGGGSBTTBCEEEEEEEC
T ss_pred             CceEEEEecCCEEEEEEcCCCChHHHHHHHHHHHHCCCHHHeEEEeCCeECCCcCCHHHcCCCcCcccCCCCCEEEEEEe
Confidence            34555555454 7889999999999999999999999999999999999999999999999999       999999999


Q ss_pred             ecCC
Q 040824          149 LRGG  152 (154)
Q Consensus       149 ~~gg  152 (154)
                      . ||
T Consensus        81 ~-~~   83 (118)
T 4ajy_B           81 A-DD   83 (118)
T ss_dssp             C-SS
T ss_pred             c-CC
Confidence            7 44

>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=99.74  E-value=5.2e-18  Score=105.69  Aligned_cols=74  Identities=35%  Similarity=0.490  Sum_probs=69.6

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+..+|+ +.+++++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|++.++++|++..+..+
T Consensus        23 m~I~Vk~~~g~-~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~ygI~~gstI~l~~r~~~   96 (100)
T 1yqb_A           23 IKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQH   96 (100)
T ss_dssp             EEEEEECSSCE-EEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBHHHHTCCTTCEEEEEECCCC
T ss_pred             EEEEEEcCCCc-EEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEECCCcCcHHHCCCCCCCEEEEEEcCCC
Confidence            68999998886 799999999999999999999999999999999999999999999999999999999887654

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens}

Probab=99.74  E-value=9.9e-18  Score=104.63  Aligned_cols=73  Identities=33%  Similarity=0.450  Sum_probs=69.2

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~   74 (154)
                      |+|+|+.. |+.+.+++++++||.+||++|+...++|++.|+|+|+|+.|+|+.+|++|++.++++|++..+..
T Consensus        26 m~I~Vk~~-g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~gI~~g~~I~l~~~~~   98 (101)
T 2klc_A           26 MKVTVKTP-KEKEEFAVPENSSVQQFKEEISKRFKSHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQ   98 (101)
T ss_dssp             EEEEEECS-SCEEEEEECSCCCHHHHHHHHHHHHTCCGGGEEEEETTEEECTTCCTGGGTCCTTCEEEEEECCS
T ss_pred             EEEEEEeC-CcEEEEEECCCCCHHHHHHHHHHHHCcChhhEEEEECCEECCCcCcHHHcCCCCCCEEEEEEcCC
Confidence            68999998 88899999999999999999999999999999999999999999999999999999999988754

>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=99.74  E-value=3.9e-18  Score=105.60  Aligned_cols=74  Identities=27%  Similarity=0.349  Sum_probs=70.2

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+.. |+.+.+++++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|++.++++|++.++..+
T Consensus        18 m~i~Vk~~-g~~~~~~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~~   91 (96)
T 1wx8_A           18 IRVSVKTP-QDCHEFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVRSHS   91 (96)
T ss_dssp             EEEEEECS-SSEEEEEEETTCCHHHHHHHHHHHTCSCTTTBCCEETTEECCTTSCHHHHTCCTTEEEECCBCCSS
T ss_pred             EEEEEEEC-CeEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEECCCcCCHHHCCCCCCCEEEEEEeCCC
Confidence            68999998 899999999999999999999999999999999999999999999999999999999999887654

>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=99.73  E-value=1.1e-17  Score=112.56  Aligned_cols=76  Identities=37%  Similarity=0.616  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecc
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~   76 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|+.+.++|++.|+|+|+|+.|+|+.+|++|++.+++++++.++..++
T Consensus        82 m~i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gip~~~q~L~~~G~~L~d~~tL~~y~i~~g~~l~l~~rl~GG  157 (159)
T 3rt3_B           82 LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRGG  157 (159)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECCC--
T ss_pred             EEEEEECCCCCEEEEEeCCCCCHHHHHHHHHHHHCCCHHHEEEEECCeecCCCCCHHHcCCCCCCEEEEEEecCCC
Confidence            6899999999999999999999999999999999999999999999999999999999999999999999987654

>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=99.73  E-value=8.7e-18  Score=106.51  Aligned_cols=72  Identities=29%  Similarity=0.451  Sum_probs=67.5

Q ss_pred             CEEEEEeCCCC-EEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccc-------cccceeeeee
Q 040824            1 MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQ-------KESTLHLVLR   72 (154)
Q Consensus         1 m~v~v~~~~~~-~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~-------~~~~i~l~~~   72 (154)
                      |+++|+.+.++ ++.+++.+++||.+||++|+.+.|+|++.|+|+|+|+.|+|+.+|++|||.       ++++++++++
T Consensus         1 M~mfl~ir~~ktti~lev~~sdTV~~lK~kI~~~egIP~~qQrLi~~Gk~LeD~~TLsdy~I~~~~a~~q~~stL~L~lr   80 (118)
T 2fnj_B            1 MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPEEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFR   80 (118)
T ss_dssp             CEEEEEEEEBTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBHHHHTCCTTTSBTTBCEEEEEEEB
T ss_pred             CcEEEEEecCCEEEEEEeCCcChHHHHHHHHHHHhCCCHHHeEEEECCeECCCCCCHHHcCcccccccCCCCCEEEEEec
Confidence            78888887776 589999999999999999999999999999999999999999999999999       7999999888

>1v2y_A 3300001G02RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.73  E-value=2.6e-18  Score=107.24  Aligned_cols=75  Identities=24%  Similarity=0.395  Sum_probs=69.0

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCC---------------CeEEEEcceEec-cCceecccccccc
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD---------------QQRLIFAGKQLE-DGRTLADYNIQKE   64 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~---------------~q~L~~~g~~L~-d~~~l~~~~i~~~   64 (154)
                      |+|+|+..+|+.+++++++++||.+||++|+++.++|+.               .|+|+|+|+.|. |+.+|++|+|.++
T Consensus         8 M~I~Vk~l~g~~~~v~V~~~~TV~dLK~~I~~~~~i~~~~q~g~~~isw~~~w~q~~Li~~Gk~L~dD~~tL~dygI~~g   87 (105)
T 1v2y_A            8 MTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLRDYGIRNR   87 (105)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHHHHHHHTTCCCCCCHHHHHTTEEEESSSCEECCSSSBHHHHTCCSS
T ss_pred             EEEEEEecCCCEEEEEECCCChHHHHHHHHHHHhCCCcccccCcceeeeeecceeEEEEeCCcCccCCcCCHHHcCCCCC
Confidence            799999999999999999999999999999999998874               569999999996 6689999999999


Q ss_pred             cceeeeeeeec
Q 040824           65 STLHLVLRLRG   75 (154)
Q Consensus        65 ~~i~l~~~~~~   75 (154)
                      ++|+++.+.++
T Consensus        88 ~~l~lv~~lr~   98 (105)
T 1v2y_A           88 DEVSFIKKLGQ   98 (105)
T ss_dssp             EEEEEEECSCS
T ss_pred             CEEEEEehhcc
Confidence            99999988654

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.73  E-value=2.2e-17  Score=106.75  Aligned_cols=74  Identities=31%  Similarity=0.405  Sum_probs=68.5

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+.. |+.+.+++++++||.+||++|+...++++++|+|+|+|+.|+|+.+|++|+|.++++|+++.+..+
T Consensus        33 m~I~Vk~~-g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~dygI~~gstI~lv~~~~g  106 (125)
T 1j8c_A           33 IKVTVKTP-KEKEEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIKRDP  106 (125)
T ss_dssp             EEEEEECS-SCEEEEEECTTCCHHHHHHHHHHHHCSCSSSEEEEETTEEESTTSCGGGTTCSSSEEEEEEEC---
T ss_pred             EEEEEEeC-CeEEEEEECCCCcHHHHHHHHHHHHCcCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEEeccCC
Confidence            68999998 899999999999999999999999999999999999999999999999999999999999887654

>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=99.73  E-value=1.4e-17  Score=102.76  Aligned_cols=69  Identities=20%  Similarity=0.255  Sum_probs=63.3

Q ss_pred             EEEEEeCC----CCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeee
Q 040824            2 QIFVKTLT----GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (154)
Q Consensus         2 ~v~v~~~~----~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~   70 (154)
                      .+.|+.++    ++.+.+++++++||.+||++|+++.++|++.|+|+|+|+.|+|+.+|++|+|+++++|+++
T Consensus        17 ti~V~~~~~~~~~~~~~lev~~~~TV~~lK~kI~~k~gip~~qQrLI~~GKiL~D~~TL~~y~I~~gsti~vl   89 (100)
T 1wju_A           17 TIEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFGLQENYIKIVINKKQLQLGKTLEEQGVAHNVKAMVL   89 (100)
T ss_dssp             EEEEECCTTTCCSSSEEEEEESSSBHHHHHHHHHHHTTCCSTTCEEEETTEECCTTSBHHHHTCCSSEEEEEE
T ss_pred             EEEEEecCCCCCCcEEEEEeCCcCHHHHHHHHHHHHHCcCHHHeEEEeCCeECCCCCcHHHcCCCCCCEEEEE
Confidence            36677776    6789999999999999999999999999999999999999999999999999999999443

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A

Probab=99.73  E-value=3.7e-17  Score=101.66  Aligned_cols=72  Identities=22%  Similarity=0.311  Sum_probs=66.1

Q ss_pred             eeeeeeecCC--ceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCccccccc-CCCCEEEEEEe
Q 040824           77 TMIKVKTLTG--KEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNI-EGGSVLHLVLA  148 (154)
Q Consensus        77 ~~i~v~~~~~--~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i-~~~~~i~~~~~  148 (154)
                      |.++|++..+  ..+.+++.+++||++||++|++++|+|++.|||++.|+.++|+.||.+||| ++|+++++++-
T Consensus        25 l~v~v~d~~s~~~~i~l~V~ps~TV~~LK~~I~~k~Gipp~~QRli~ggkll~D~~TL~~ygI~~~G~t~hL~l~   99 (105)
T 4dbg_A           25 LWVSVEDAQMHTVTIWLTVRPDMTVASLKDMVFLDYGFPPVLQQWVIGQRLARDQETLHSHGVRQNGDSAYLYLL   99 (105)
T ss_dssp             EEEEEEESSSCCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEEECTTCBTGGGTCCSTTCEEEEEEC
T ss_pred             EEEEEEccCCCCceEEEEECCcChHHHHHHHHHHHhCCCHHHEEEeccCeEccCcCcHHHcCCCCCCCEEEEEEE
Confidence            6677888764  679999999999999999999999999999999999999999999999999 69999998874

>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=99.73  E-value=4.1e-17  Score=103.57  Aligned_cols=80  Identities=26%  Similarity=0.334  Sum_probs=70.1

Q ss_pred             eecceeeeeeecCCceEEEeeCCCchHHHHHHHHhh------hcCC--CCCceeEEECCeecCCCCcccccccCCC--CE
Q 040824           73 LRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEE------KEGI--PPVQQRLIYAGKQLADDKTARDYNIEGG--SV  142 (154)
Q Consensus        73 ~~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~------~~~i--~~~~~~l~~~g~~l~d~~~L~~~~i~~~--~~  142 (154)
                      +...|.|+++..+|+++.+++++++||.+||++|+.      +.++  |+++|+|+|.|+.|+|+.||++|+|..+  .+
T Consensus        13 ~~~~m~I~vKtl~G~t~~lev~~s~TV~~lK~kI~~~~p~dwke~~p~p~~qqrLIy~GK~LeD~~TL~~y~I~~~~~~t   92 (116)
T 1wgh_A           13 PADMINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTV   92 (116)
T ss_dssp             CSSSEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEEETTEEECSSCBTTTTTCCSSCEEE
T ss_pred             CCCeEEEEEEeCCCCEEEEEECCcCHHHHHHHHHHHhcccccccCCCCChHHEEEEECCcCCCCCCcHHHcCCCCCCceE
Confidence            445699999999999999999999999999999998      5564  6999999999999999999999999877  46


Q ss_pred             EEEEEeecCC
Q 040824          143 LHLVLALRGG  152 (154)
Q Consensus       143 i~~~~~~~gg  152 (154)
                      +|+.++..+.
T Consensus        93 lhLvlr~~~~  102 (116)
T 1wgh_A           93 MHLVARETLP  102 (116)
T ss_dssp             EEEEECSSCS
T ss_pred             EEEEccCCCC
Confidence            7777776543

>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=99.72  E-value=1.8e-17  Score=104.33  Aligned_cols=74  Identities=35%  Similarity=0.490  Sum_probs=69.4

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+..+++ +.+++++++||.+||++|++..++++++|+|+|+|+.|+|+.+|++|+|.++++|++..+..+
T Consensus        18 m~I~Vk~~~g~-~~l~v~~~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~gi~~g~~i~l~~~~~~   91 (106)
T 1wx7_A           18 IKVTVKTPKDK-EDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQH   91 (106)
T ss_dssp             EEEEEECSSCE-EEEEEETTCCHHHHHHHHHHHHTCCTTTEEEEETTEECCTTSCHHHHTCCTTEEEEEEECCCC
T ss_pred             EEEEEEeCCCc-EEEEECCCCcHHHHHHHHHHHHCcChhhEEEEECCEECCCcCcHHHcCCCCCCEEEEEEcCCC
Confidence            78999998876 799999999999999999999999999999999999999999999999999999999987653

>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=99.72  E-value=1.1e-17  Score=106.21  Aligned_cols=76  Identities=33%  Similarity=0.468  Sum_probs=71.1

Q ss_pred             CEEEEEeC---CCCEEEEEEeC-CCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecc
Q 040824            1 MQIFVKTL---TGKTITLEVES-SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (154)
Q Consensus         1 m~v~v~~~---~~~~~~~~v~~-~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~   76 (154)
                      |+|+|+..   +|+.+.+++++ ++||.+||++|+..+++|++.|+|+|+|+.|+|+.+|++|++.++++|++.++..++
T Consensus        28 i~i~Vk~~~~~~g~~~~l~v~~l~~TV~~LK~~I~~~~gip~~~QrL~~~Gk~L~D~~tL~~y~I~~g~~l~l~~r~~GG  107 (111)
T 1we6_A           28 ATIRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLRERSG  107 (111)
T ss_dssp             EEEEECCTTCSSSCCEEEEESCSSSBHHHHHHHHHHHTTCCTTTSEEECSSSBCCTTSBTTTTTCSSSCEEEEECSSCCS
T ss_pred             EEEEEEecccCCCcEEEEEecCCCCcHHHHHHHHHHHHCCCHHHeEEEECCEECCCCCcHHHCCCCCCCEEEEEEEcCCC
Confidence            68999998   78899999997 999999999999999999999999999999999999999999999999999886643

>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=99.72  E-value=2.1e-17  Score=103.38  Aligned_cols=75  Identities=19%  Similarity=0.352  Sum_probs=68.8

Q ss_pred             CEEEEEeCCC----CEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccC-ceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTG----KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDG-RTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~----~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~-~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+..++    +.+.+++++++||.+||++|+..+++|+++|+|+|+|+.|+|+ .+|++|+|+++++|++..+..+
T Consensus         8 m~I~Vk~~~~~~~~~~~~i~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~gk~L~D~~~tL~~ygI~~g~~l~l~~~~~g   87 (102)
T 1v5o_A            8 MLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVLLQKDNV   87 (102)
T ss_dssp             EEEEEEECCCCCCCCEEEEEECTTCBHHHHHHHHHHHTCCCGGGBCEEETTEEECCSSSBHHHHTCCTTEEEEECBCCCC
T ss_pred             EEEEEEECCCCcCceEEEEEcCCCCCHHHHHHHHHHHHCcChHHeEEEECCEECCCCcccHHHCCCCCCCEEEEEECCCC
Confidence            7899998754    6899999999999999999999999999999999999999987 6999999999999999887654

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

Probab=99.72  E-value=5.5e-18  Score=105.73  Aligned_cols=71  Identities=34%  Similarity=0.574  Sum_probs=66.8

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      |+|+|++ +|+.+.+++++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|+++++++|+++.+
T Consensus        29 i~I~Vk~-~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~gI~~g~tI~lv~~   99 (101)
T 3m63_B           29 LNIHIKS-GQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS   99 (101)
T ss_dssp             CCEEEEC-SSCCCCBCCCTTSBHHHHHHHHHHHHSCCSTTCCEEETTEECCTTSBTTTTTCCTTEEEEECCC
T ss_pred             EEEEEEE-CCEEEEEEeCCCCCHHHHHHHHHHHHCcChHHEEEEECCEECCCcCcHHHCCCCCCCEEEEEeC
Confidence            4678886 8888999999999999999999999999999999999999999999999999999999998865

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens}

Probab=99.71  E-value=3e-17  Score=105.58  Aligned_cols=78  Identities=27%  Similarity=0.348  Sum_probs=70.5

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhh------hcCC--CCCceeEEECCeecCCCCcccccccCCCC--EEE
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEE------KEGI--PPVQQRLIYAGKQLADDKTARDYNIEGGS--VLH  144 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~------~~~i--~~~~~~l~~~g~~l~d~~~L~~~~i~~~~--~i~  144 (154)
                      ..|.|+++..+|+++.+++++++||.+||++|++      +.++  ++++|+|+|.|+.|+|+.||++|+|+.++  +++
T Consensus        16 ~~m~I~vktl~G~~~~lev~~s~TV~~lK~~I~~~~p~dwke~ip~~~~~qrLIy~GK~LeD~~TL~~y~I~~~~~~tlh   95 (125)
T 2gow_A           16 DMINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMH   95 (125)
T ss_dssp             TCEEEEEECTTSCEEEEEECTTSBHHHHHHHHHSSCCCSCCCCTTCCGGGEEEESSSSEEESSCBTGGGCCCTTSEEEEE
T ss_pred             CeEEEEEEeCCCCEEEEEeCCccHHHHHHHHHHHHCCcccccCCCCChHHEEEEECCcCCCCCCcHHHcCCCCCCceEEE
Confidence            3488999999999999999999999999999998      6677  48999999999999999999999999776  788


Q ss_pred             EEEeecCC
Q 040824          145 LVLALRGG  152 (154)
Q Consensus       145 ~~~~~~gg  152 (154)
                      +.++.+++
T Consensus        96 lv~r~~~~  103 (125)
T 2gow_A           96 LVARETLP  103 (125)
T ss_dssp             EEECSCCS
T ss_pred             EEecCCCC
Confidence            88888775

>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=99.71  E-value=4.8e-19  Score=115.17  Aligned_cols=76  Identities=97%  Similarity=1.333  Sum_probs=0.0

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecc
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~   76 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|++.+++|++.|+|+|+|+.|+|+.+|++|+|.++++|++.++..++
T Consensus         1 M~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~~~I~~gsti~l~~rl~GG   76 (128)
T 3u5e_m            1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   76 (128)
T ss_dssp             ----------------------------------------------------------------------------
T ss_pred             CEEEEEeCCCCEEEEEeCCCCCHHHHHHHHHHHhCcChHHEEEEECCEECCCCCchhhhccCCCCEEEEEEEcCCC
Confidence            8999999999999999999999999999999999999999999999999999999999999999999999886643

>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=99.71  E-value=5.5e-17  Score=108.20  Aligned_cols=76  Identities=63%  Similarity=0.993  Sum_probs=72.7

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      |.|+|+..+|+.+.+++++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++|++.+|++|++..+.+||
T Consensus         1 M~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gip~~~q~L~~~g~~L~d~~tL~~~~i~~~~~l~l~~~~~~~   76 (152)
T 3b08_A            1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   76 (152)
T ss_dssp             CEEEEEETTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCTTC
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHHHHHCcChHHeEEEECCeECcCcccHHHhccCCCCeeEEEeecccc
Confidence            6899999999999999999999999999999999999999999999999999999999999999999999888765

>2daf_A FLJ35834 protein; hypothetical protein FLJ35834, ubiquitin-like domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=3.1e-17  Score=103.03  Aligned_cols=77  Identities=16%  Similarity=0.298  Sum_probs=70.2

Q ss_pred             EEEEE-eCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeeccee
Q 040824            2 QIFVK-TLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGTM   78 (154)
Q Consensus         2 ~v~v~-~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~~~   78 (154)
                      .|+|+ ..+++.+.++++++.||.+||+.++..+++|++.|+|.|+|+.|+|+.+|++||++++.+|||.++..++-.
T Consensus        17 tvkv~l~~~~~k~tv~v~~d~TV~dLKe~ls~~~~iP~e~qrLIy~GKiLKD~eTL~~~gIk~g~TIhLvi~s~~p~~   94 (118)
T 2daf_A           17 TVKVVLIPVGQEIVIPFKVDTILKYLKDHFSHLLGIPHSVLQIRYSGKILKNNETLVQHGVKPQEIVQVEIFSTNPDL   94 (118)
T ss_dssp             EEEEEETTTCCEEEEEECSSSCSHHHHHHHHHHHTCCTTTEEEEETTEEECSSCCHHHHSCCSSCEEEEEEEESCTTT
T ss_pred             EEEEEEcCCCcEEEEEeCCCCcHHHHHHHHHhhhCCChHHEEEEECCeEcCCcchHHHcCCCCCCEEEEEEecCCCcc
Confidence            46666 557888999999999999999999999999999999999999999999999999999999999998765533

>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=99.71  E-value=5.3e-17  Score=99.75  Aligned_cols=79  Identities=16%  Similarity=0.336  Sum_probs=75.8

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      ..|.|.|+..+|+.+.+.+.+++++..|+++++++.|+|++.++|+|.|+.|.++.|+++|++++||+|+++.+++||.
T Consensus         6 ~~i~ikVk~~~g~~i~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~~~GG~   84 (94)
T 2io1_B            6 DHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGGV   84 (94)
T ss_dssp             CEEEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCTTTTTCCTTCEEEEEECCEESC
T ss_pred             CeEEEEEECCCCCEEEEEECCCCHHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEeccCCC
Confidence            4588999999999999999999999999999999999999999999999999999999999999999999999999984

>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=99.71  E-value=4.4e-17  Score=99.64  Aligned_cols=74  Identities=22%  Similarity=0.345  Sum_probs=68.4

Q ss_pred             cceeeeeeecCCceEEE-eeCCCchHHHHHHHHhhhcCCCCCceeEE---ECCeecCCCCcccccccCCCCEEEEEEee
Q 040824           75 GGTMIKVKTLTGKEIEI-DIEPTDTIERIKERVEEKEGIPPVQQRLI---YAGKQLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~-~v~~~~tv~~LK~~i~~~~~i~~~~~~l~---~~g~~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      ..|.|+|+. .|+.+.+ ++++++||.+||++|++.+|+|+++|+|+   |+|+.|+|+.+|++|+|.+|++|+++...
T Consensus         6 ~~m~i~Vk~-~g~~~~i~~v~~~~TV~~lK~~I~~~~gip~~~QkLi~~k~~Gk~L~D~~~L~~~~i~~g~~l~l~~~~   83 (90)
T 1v5t_A            6 SGLPIIVKW-GGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMGTR   83 (90)
T ss_dssp             CSCCEEEEE-TTEEEEECSCCSSSBHHHHHHHHHHHTCCCTTTCEEESCEETTEECCTTSBHHHHTCCTTEEEEEECCC
T ss_pred             ceEEEEEEE-CCEEEEEEEeCCCCCHHHHHHHHHHHHCcCHHHeEEEeeccCCcCcCCCCCHHHcCCCCCCEEEEEecC
Confidence            358899987 7889999 99999999999999999999999999999   99999999999999999999999887543

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens}

Probab=99.71  E-value=2.7e-17  Score=101.93  Aligned_cols=70  Identities=24%  Similarity=0.383  Sum_probs=63.3

Q ss_pred             CEEEEEeCCCC--EEEEEEeCCCcHHHHHHHHHhHh-CCC-CCCeEEEEcceEeccCceeccc--ccccccceeee
Q 040824            1 MQIFVKTLTGK--TITLEVESSDTIDNVKAKIQDKE-GIP-PDQQRLIFAGKQLEDGRTLADY--NIQKESTLHLV   70 (154)
Q Consensus         1 m~v~v~~~~~~--~~~~~v~~~~tv~~lk~~i~~~~-~~~-~~~q~L~~~g~~L~d~~~l~~~--~i~~~~~i~l~   70 (154)
                      |+|+||..+++  .+.+++++++||.+||++|+++. +.| ++.|+|+|.|+.|+|+.+|++|  ++.++++|+++
T Consensus        24 m~I~VK~~~g~~~~i~l~v~~~~TV~~LK~~I~~~~~g~pp~~~QrLIy~Gk~L~D~~tL~~y~~~I~~~~tihLv   99 (99)
T 2kdb_A           24 VTLIIKAPNQKYSDQTISCFLNWTVGKLKTHLSNVYPSKPLTKDQRLVYSGRLLPDHLQLKDILRKQDEYHMVHLV   99 (99)
T ss_dssp             EEEEEECTTSSSCCEEEEECTTSBHHHHHHHHHHHSTTCCCTTTCCEEETTEEECTTSBTHHHHTTTCSEEEEEEC
T ss_pred             EEEEEEcCCCCEEEEEEEcCCCCHHHHHHHHHHHHhcCCCChhhEEEEECCEECCCCCCHHHHhcCCCCCCEEEeC
Confidence            68999999887  67899999999999999999864 555 5999999999999999999999  99999999874

>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=99.70  E-value=3e-17  Score=101.44  Aligned_cols=72  Identities=17%  Similarity=0.287  Sum_probs=67.0

Q ss_pred             CEEEEEeCCCCEE-EEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeee
Q 040824            1 MQIFVKTLTGKTI-TLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (154)
Q Consensus         1 m~v~v~~~~~~~~-~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~   74 (154)
                      |+|+|+. .|+.+ .+++++++||.+||++|++.+++|+++|+|+|.|+.|+|+ +|++|+|+++++|+++....
T Consensus         8 m~i~Vk~-~g~~~~~l~v~~~~TV~~lK~~I~~~tgip~~~QkLi~~Gk~L~D~-tL~~~~I~~g~~i~l~~~~~   80 (96)
T 1wgg_A            8 YSVTVKW-GKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLKDD-DWGNIKMKNGMTVLMMGSAD   80 (96)
T ss_dssp             EEEEEEE-TTEEEEEEEEESSSCHHHHHHHHHHHTCCCTTTSCCEETTEECCSS-CCCSCCCCSSCEEECCCCCC
T ss_pred             EEEEEEE-CCEEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCcCCCCC-CHHHCCCCCCCEEEEEecch
Confidence            6899995 78889 6999999999999999999999999999999999999999 99999999999999887654

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.70  E-value=8.4e-17  Score=97.34  Aligned_cols=69  Identities=25%  Similarity=0.474  Sum_probs=63.7

Q ss_pred             eeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEe
Q 040824           80 KVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        80 ~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      .++..+|+.+.+++++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+|++|++|+++..
T Consensus        15 ~~~~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~l~l~~s   83 (85)
T 2kd0_A           15 LTVKFGGKSIPLSVSPDCTVKDLKSQLQPITNVLPRGQKLIFKGKVLVETSTLKQSDVGSGAKLMLMAS   83 (85)
T ss_dssp             EEEEETTEEEEEEECTTSBHHHHHHHHHHHHCCCTTTCEEEETTEECCTTCBTTTTTCCTTEEEEEECC
T ss_pred             EEEEECCEEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCeECCCcCCHHHCCCCCCCEEEEEEe
Confidence            344558889999999999999999999999999999999999999999999999999999999988753

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana}

Probab=99.70  E-value=7.6e-17  Score=97.53  Aligned_cols=70  Identities=29%  Similarity=0.452  Sum_probs=65.0

Q ss_pred             EEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeee
Q 040824            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         3 v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      ..++.++|+.+.+++++++||.+||++|+...++|+++|+|+|+|+.|+|+.+|++|+++++++|++...
T Consensus        14 ~~~~~~~g~~~~l~v~~~~TV~~LK~~I~~~~gip~~~qrL~~~Gk~L~D~~tL~~~gi~~g~~l~l~~s   83 (85)
T 2kd0_A           14 KLTVKFGGKSIPLSVSPDCTVKDLKSQLQPITNVLPRGQKLIFKGKVLVETSTLKQSDVGSGAKLMLMAS   83 (85)
T ss_dssp             EEEEEETTEEEEEEECTTSBHHHHHHHHHHHHCCCTTTCEEEETTEECCTTCBTTTTTCCTTEEEEEECC
T ss_pred             EEEEEECCEEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEECCeECCCcCCHHHCCCCCCCEEEEEEe
Confidence            3456678999999999999999999999999999999999999999999999999999999999988764

>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=99.70  E-value=9.4e-17  Score=101.93  Aligned_cols=74  Identities=24%  Similarity=0.419  Sum_probs=66.3

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHh------HhCC--CCCCeEEEEcceEeccCceecccccccc--cceeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQD------KEGI--PPDQQRLIFAGKQLEDGRTLADYNIQKE--STLHLV   70 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~------~~~~--~~~~q~L~~~g~~L~d~~~l~~~~i~~~--~~i~l~   70 (154)
                      |+|+|++.+|+++++++++++||.+||++|+.      +.++  +++.|+|+|.|+.|+|+.+|++|+|..+  .++|++
T Consensus        17 m~I~vKtl~G~t~~lev~~s~TV~~lK~kI~~~~p~dwke~~p~p~~qqrLIy~GK~LeD~~TL~~y~I~~~~~~tlhLv   96 (116)
T 1wgh_A           17 INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLV   96 (116)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEEETTEEECSSCBTTTTTCCSSCEEEEEEE
T ss_pred             EEEEEEeCCCCEEEEEECCcCHHHHHHHHHHHhcccccccCCCCChHHEEEEECCcCCCCCCcHHHcCCCCCCceEEEEE
Confidence            68999999999999999999999999999998      5564  6999999999999999999999999755  578888


Q ss_pred             eeee
Q 040824           71 LRLR   74 (154)
Q Consensus        71 ~~~~   74 (154)
                      ++..
T Consensus        97 lr~~  100 (116)
T 1wgh_A           97 ARET  100 (116)
T ss_dssp             ECSS
T ss_pred             ccCC
Confidence            7654

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A

Probab=99.70  E-value=9.3e-17  Score=99.85  Aligned_cols=73  Identities=23%  Similarity=0.240  Sum_probs=67.4

Q ss_pred             CEEEEEeCCC--CEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceeccccc-ccccceeeeeee
Q 040824            1 MQIFVKTLTG--KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNI-QKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~--~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i-~~~~~i~l~~~~   73 (154)
                      |+|+|+...+  ..+.+++++++||.+||++|+++.|+||+.|+|+|+|+.++|+.+|++||| .+|++++|.+..
T Consensus        25 l~v~v~d~~s~~~~i~l~V~ps~TV~~LK~~I~~k~Gipp~~QRli~ggkll~D~~TL~~ygI~~~G~t~hL~l~~  100 (105)
T 4dbg_A           25 LWVSVEDAQMHTVTIWLTVRPDMTVASLKDMVFLDYGFPPVLQQWVIGQRLARDQETLHSHGVRQNGDSAYLYLLS  100 (105)
T ss_dssp             EEEEEEESSSCCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEEECTTCBTGGGTCCSTTCEEEEEECC
T ss_pred             EEEEEEccCCCCceEEEEECCcChHHHHHHHHHHHhCCCHHHEEEeccCeEccCcCcHHHcCCCCCCCEEEEEEEe
Confidence            5789998874  678999999999999999999999999999999999999999999999999 599999998754

>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=99.70  E-value=3.6e-17  Score=100.03  Aligned_cols=73  Identities=21%  Similarity=0.408  Sum_probs=68.1

Q ss_pred             CEEEEEeCCCCEEEE-EEeCCCcHHHHHHHHHhHhCCCCCCeEEE---EcceEeccCceecccccccccceeeeeeee
Q 040824            1 MQIFVKTLTGKTITL-EVESSDTIDNVKAKIQDKEGIPPDQQRLI---FAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (154)
Q Consensus         1 m~v~v~~~~~~~~~~-~v~~~~tv~~lk~~i~~~~~~~~~~q~L~---~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~   74 (154)
                      |+|+|+. +|+.+.+ ++++++||.+||++|++.+++|+++|+|+   |.|+.|+|+.+|++|+++++++|+++....
T Consensus         8 m~i~Vk~-~g~~~~i~~v~~~~TV~~lK~~I~~~~gip~~~QkLi~~k~~Gk~L~D~~~L~~~~i~~g~~l~l~~~~~   84 (90)
T 1v5t_A            8 LPIIVKW-GGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMGTRE   84 (90)
T ss_dssp             CCEEEEE-TTEEEEECSCCSSSBHHHHHHHHHHHTCCCTTTCEEESCEETTEECCTTSBHHHHTCCTTEEEEEECCCS
T ss_pred             EEEEEEE-CCEEEEEEEeCCCCCHHHHHHHHHHHHCcCHHHeEEEeeccCCcCcCCCCCHHHcCCCCCCEEEEEecCc
Confidence            7899996 7899999 99999999999999999999999999999   999999999999999999999998876643

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens}

Probab=99.70  E-value=4.4e-17  Score=101.02  Aligned_cols=72  Identities=24%  Similarity=0.348  Sum_probs=64.1

Q ss_pred             cceeeeeeecCCc--eEEEeeCCCchHHHHHHHHhhh-cCCC-CCceeEEECCeecCCCCccccc--ccCCCCEEEEE
Q 040824           75 GGTMIKVKTLTGK--EIEIDIEPTDTIERIKERVEEK-EGIP-PVQQRLIYAGKQLADDKTARDY--NIEGGSVLHLV  146 (154)
Q Consensus        75 ~~~~i~v~~~~~~--~~~~~v~~~~tv~~LK~~i~~~-~~i~-~~~~~l~~~g~~l~d~~~L~~~--~i~~~~~i~~~  146 (154)
                      ..|.|+|+..+++  .+.+++++++||.+||++|++. .|.| +++|+|+|.|+.|+|+.+|++|  +|+++++|++.
T Consensus        22 ~~m~I~VK~~~g~~~~i~l~v~~~~TV~~LK~~I~~~~~g~pp~~~QrLIy~Gk~L~D~~tL~~y~~~I~~~~tihLv   99 (99)
T 2kdb_A           22 HPVTLIIKAPNQKYSDQTISCFLNWTVGKLKTHLSNVYPSKPLTKDQRLVYSGRLLPDHLQLKDILRKQDEYHMVHLV   99 (99)
T ss_dssp             -CEEEEEECTTSSSCCEEEEECTTSBHHHHHHHHHHHSTTCCCTTTCCEEETTEEECTTSBTHHHHTTTCSEEEEEEC
T ss_pred             CeEEEEEEcCCCCEEEEEEEcCCCCHHHHHHHHHHHHhcCCCChhhEEEEECCEECCCCCCHHHHhcCCCCCCEEEeC
Confidence            4589999998887  5788999999999999999986 4655 5999999999999999999999  99999999873

>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=99.69  E-value=1.4e-18  Score=115.61  Aligned_cols=76  Identities=97%  Similarity=1.333  Sum_probs=0.0

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecc
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~   76 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|++..++|++.|+|+|+|+.|+|+.+|++|+|.++++|+++++..++
T Consensus         1 MqI~VK~l~G~~~~l~V~~~~TV~~LK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~dygI~~gstL~Lvlrl~GG   76 (152)
T 3u5c_f            1 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   76 (152)
T ss_dssp             ----------------------------------------------------------------------------
T ss_pred             CEEEEEeCCCCEEEEEECCCCCHHHHHHHHHHHhCCCHHHEEEEECCEEccccCcHHHcCCCCCCEEEEEeeccCC
Confidence            8999999999999999999999999999999999999999999999999999999999999999999999987654

>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=99.69  E-value=2e-16  Score=96.54  Aligned_cols=79  Identities=16%  Similarity=0.336  Sum_probs=75.7

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      ..|.|.|+..+|+.+.+.+.+++++..|+.+++++.|+|++.++|+|+|+.|.++.|++++++++||+|+++..++||.
T Consensus         4 ~~i~ikVk~~~g~~v~~~vk~~t~l~kl~~~y~~~~gi~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~q~gg~   82 (91)
T 2io0_B            4 DHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGGV   82 (91)
T ss_dssp             CEEEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHTTCCSTTEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCCCCC
T ss_pred             CeEEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEeccCCc
Confidence            4578999999999999999999999999999999999999999999999999999999999999999999999999995

>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=99.69  E-value=1.3e-16  Score=98.43  Aligned_cols=74  Identities=28%  Similarity=0.407  Sum_probs=69.1

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCC-CcccccccCCCCEEEEEEeecC
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADD-KTARDYNIEGGSVLHLVLALRG  151 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~-~~L~~~~i~~~~~i~~~~~~~g  151 (154)
                      ..|.|+|+..+|+.+.+++++++||.+||++|+..+   +++|+|+|+|+.|+|+ .+|++|+|.+|++|+++.+..+
T Consensus         6 ~~m~i~Vk~~~g~~~~~~v~~~~TV~~LK~~i~~~~---~~~qrLi~~Gk~L~D~~~tL~~y~i~~g~~i~l~~~~~~   80 (95)
T 1wia_A            6 SGINVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQ---ESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRSPPG   80 (95)
T ss_dssp             CSEEEEEEETTTEEEEEEECSSSBHHHHHHHHSSST---TTTCEEEETTEECCCSSCBTTTTTCCTTEEEEEECCCCC
T ss_pred             CeEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHhhC---cCcEEEEECCEEccCCcCCHHHcCCCCCCEEEEEECCCC
Confidence            458999999999999999999999999999999987   8999999999999999 9999999999999999988755

>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=99.69  E-value=1.3e-16  Score=102.29  Aligned_cols=75  Identities=27%  Similarity=0.469  Sum_probs=67.0

Q ss_pred             CEEEEEeCCCCEE-EEEEeCCCcHHHHHHHH-----HhHhCCCC--CCeEEEEcceEeccCceecccccccc------cc
Q 040824            1 MQIFVKTLTGKTI-TLEVESSDTIDNVKAKI-----QDKEGIPP--DQQRLIFAGKQLEDGRTLADYNIQKE------ST   66 (154)
Q Consensus         1 m~v~v~~~~~~~~-~~~v~~~~tv~~lk~~i-----~~~~~~~~--~~q~L~~~g~~L~d~~~l~~~~i~~~------~~   66 (154)
                      |+|+|+..+|+.+ ++++++++||.+||++|     +.+.++|+  +.|+|+|.|+.|+|+.+|++|+|..+      .+
T Consensus        17 ~~i~~kt~~G~~i~~l~v~psdTV~~lK~kI~~~~p~dkegiP~~~~qQrLIy~GK~LeD~~TLsdy~I~~~~~~~~v~t   96 (126)
T 1se9_A           17 LEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSKTVKDYRSPVSNLAGAVTT   96 (126)
T ss_dssp             EEEEEEETTSCEEEEEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEEETTEECCTTSBGGGGSCCTTSCTTCCEE
T ss_pred             EEEEEEECCCCEEEeeecCccCHHHHHHHHHHhhcccccccCCCChhhEEEEECCeECcCCCcHHHcCCCcCCccCCcEE
Confidence            6899999999888 79999999999999999     45667886  89999999999999999999999988      57


Q ss_pred             eeeeeeeec
Q 040824           67 LHLVLRLRG   75 (154)
Q Consensus        67 i~l~~~~~~   75 (154)
                      ++++++..+
T Consensus        97 mhlVlrl~g  105 (126)
T 1se9_A           97 MHVIIQAPV  105 (126)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEeccCC
Confidence            888887654

>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=99.68  E-value=1.7e-16  Score=99.96  Aligned_cols=76  Identities=25%  Similarity=0.361  Sum_probs=69.1

Q ss_pred             cceeeeeeecCC---ceEEEeeCC---------CchHHHHHHHHhhhc--CCCCCc-eeEEECCeecCCCCcccccccCC
Q 040824           75 GGTMIKVKTLTG---KEIEIDIEP---------TDTIERIKERVEEKE--GIPPVQ-QRLIYAGKQLADDKTARDYNIEG  139 (154)
Q Consensus        75 ~~~~i~v~~~~~---~~~~~~v~~---------~~tv~~LK~~i~~~~--~i~~~~-~~l~~~g~~l~d~~~L~~~~i~~  139 (154)
                      ..|.|+|+..++   +.+.+++++         ++||.+||++|++.+  |+|+++ |+|+|+|+.|+|+.+|++|+|++
T Consensus        11 ~~~~i~Vk~~~~~~~~~~~l~v~~~~~~~v~~~~~TV~~LK~~i~~~~~~gip~~~~qrLi~~Gk~L~D~~tL~~y~i~~   90 (107)
T 1x1m_A           11 SDWHLAVKLADQPLAPKSILQLPETELGEYSLGGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDFYGIQP   90 (107)
T ss_dssp             CSCCEEEEETTCTTSCCEEECCCCCSSCSSCCCCCBHHHHHHHHHHHCTTTCCCSSSEEEEETTEECCTTCBHHHHTCCT
T ss_pred             CceEEEEEeCCCCCccEEEEEecCccccccCcccCCHHHHHHHHHHHhccCCChhhcEEEEECCeECCCCCcHHHcCCCC
Confidence            458899999888   788899554         499999999999999  999999 99999999999999999999999


Q ss_pred             CCEEEEEEeec
Q 040824          140 GSVLHLVLALR  150 (154)
Q Consensus       140 ~~~i~~~~~~~  150 (154)
                      |++|+++.+..
T Consensus        91 g~~i~lv~~~~  101 (107)
T 1x1m_A           91 GSTVHVLRKSW  101 (107)
T ss_dssp             TCEEEEEESSC
T ss_pred             CCEEEEEeCCC
Confidence            99999988764

>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=99.68  E-value=1.1e-16  Score=102.09  Aligned_cols=76  Identities=29%  Similarity=0.577  Sum_probs=69.2

Q ss_pred             CEEEEEeCC----------CCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeee
Q 040824            1 MQIFVKTLT----------GKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (154)
Q Consensus         1 m~v~v~~~~----------~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~   70 (154)
                      ++|.|+.++          |+.+.+++++++||.+||++|+...++|+++|+|+|.|+.|+|+.+|++|++.++++|+++
T Consensus        26 i~l~V~~p~~~~~~~~~L~G~~~~l~v~~~~TV~~LK~~I~~~~gip~~~QrL~~~Gk~L~D~~tL~~y~i~~g~~i~lv  105 (115)
T 1we7_A           26 VSIKVQVPNMQDKTEWKLNGQGLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMASGAVIHLA  105 (115)
T ss_dssp             EEEEEEECCCSSSCSSCCSSEEEEEEECSCSBTHHHHHHHHHHSSCCTTTEEEEETTEEECTTSBHHHHTCCSSCEEEEE
T ss_pred             EEEEEEcCCCccccccccCCeEEEEEECCCCCHHHHHHHHHHHHCCChHHEEEEECCEECCCCCCHHHCCCCCCCEEEEE
Confidence            467777764          6789999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeecc
Q 040824           71 LRLRGG   76 (154)
Q Consensus        71 ~~~~~~   76 (154)
                      ++..++
T Consensus       106 ~rl~GG  111 (115)
T 1we7_A          106 LKERSG  111 (115)
T ss_dssp             ECCCSC
T ss_pred             EEcCCC
Confidence            887654

>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=99.68  E-value=9.2e-17  Score=99.26  Aligned_cols=71  Identities=17%  Similarity=0.333  Sum_probs=65.8

Q ss_pred             ceeeeeeecCCceE-EEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEe
Q 040824           76 GTMIKVKTLTGKEI-EIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        76 ~~~i~v~~~~~~~~-~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      .|.|+|+. .|+.+ .+++++++||.+||++|++.+|+|+++|+|+|+|+.|+|+ +|++|+|++|++|+++..
T Consensus         7 ~m~i~Vk~-~g~~~~~l~v~~~~TV~~lK~~I~~~tgip~~~QkLi~~Gk~L~D~-tL~~~~I~~g~~i~l~~~   78 (96)
T 1wgg_A            7 GYSVTVKW-GKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLKDD-DWGNIKMKNGMTVLMMGS   78 (96)
T ss_dssp             EEEEEEEE-TTEEEEEEEEESSSCHHHHHHHHHHHTCCCTTTSCCEETTEECCSS-CCCSCCCCSSCEEECCCC
T ss_pred             EEEEEEEE-CCEEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCcCCCCC-CHHHCCCCCCCEEEEEec
Confidence            47888986 67889 6999999999999999999999999999999999999999 999999999999988754

>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=99.68  E-value=1.1e-16  Score=98.83  Aligned_cols=71  Identities=25%  Similarity=0.364  Sum_probs=67.0

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccC-ceecccccccccceeeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDG-RTLADYNIQKESTLHLVLRLR   74 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~-~~l~~~~i~~~~~i~l~~~~~   74 (154)
                      |+|+|+..+|+.+.+++++++||.+||++|+...   +++|+|+|+|+.|+|+ .+|++|++.++++|+++.+..
T Consensus         8 m~i~Vk~~~g~~~~~~v~~~~TV~~LK~~i~~~~---~~~qrLi~~Gk~L~D~~~tL~~y~i~~g~~i~l~~~~~   79 (95)
T 1wia_A            8 INVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQ---ESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRSPP   79 (95)
T ss_dssp             EEEEEEETTTEEEEEEECSSSBHHHHHHHHSSST---TTTCEEEETTEECCCSSCBTTTTTCCTTEEEEEECCCC
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHhhC---cCcEEEEECCEEccCCcCCHHHcCCCCCCEEEEEECCC
Confidence            7899999999999999999999999999999887   8999999999999999 999999999999999988754

>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=99.68  E-value=9.1e-17  Score=101.27  Aligned_cols=74  Identities=28%  Similarity=0.401  Sum_probs=68.1

Q ss_pred             CEEEEEeCCC---CEEEEEEeC---------CCcHHHHHHHHHhHh--CCCCCC-eEEEEcceEeccCceeccccccccc
Q 040824            1 MQIFVKTLTG---KTITLEVES---------SDTIDNVKAKIQDKE--GIPPDQ-QRLIFAGKQLEDGRTLADYNIQKES   65 (154)
Q Consensus         1 m~v~v~~~~~---~~~~~~v~~---------~~tv~~lk~~i~~~~--~~~~~~-q~L~~~g~~L~d~~~l~~~~i~~~~   65 (154)
                      |+|+||..++   +.+.+++++         ++||.+||++|+...  ++|++. |+|+|.|+.|+|+.+|++|++++++
T Consensus        13 ~~i~Vk~~~~~~~~~~~l~v~~~~~~~v~~~~~TV~~LK~~i~~~~~~gip~~~~qrLi~~Gk~L~D~~tL~~y~i~~g~   92 (107)
T 1x1m_A           13 WHLAVKLADQPLAPKSILQLPETELGEYSLGGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDFYGIQPGS   92 (107)
T ss_dssp             CCEEEEETTCTTSCCEEECCCCCSSCSSCCCCCBHHHHHHHHHHHCTTTCCCSSSEEEEETTEECCTTCBHHHHTCCTTC
T ss_pred             eEEEEEeCCCCCccEEEEEecCccccccCcccCCHHHHHHHHHHHhccCCChhhcEEEEECCeECCCCCcHHHcCCCCCC
Confidence            6899999988   789999554         599999999999999  999999 9999999999999999999999999


Q ss_pred             ceeeeeeee
Q 040824           66 TLHLVLRLR   74 (154)
Q Consensus        66 ~i~l~~~~~   74 (154)
                      +|+++.+..
T Consensus        93 ~i~lv~~~~  101 (107)
T 1x1m_A           93 TVHVLRKSW  101 (107)
T ss_dssp             EEEEEESSC
T ss_pred             EEEEEeCCC
Confidence            999988754

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens}

Probab=99.68  E-value=9.9e-17  Score=103.17  Aligned_cols=74  Identities=24%  Similarity=0.412  Sum_probs=66.6

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHh------HhCC--CCCCeEEEEcceEeccCceeccccccccc--ceeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQD------KEGI--PPDQQRLIFAGKQLEDGRTLADYNIQKES--TLHLV   70 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~------~~~~--~~~~q~L~~~g~~L~d~~~l~~~~i~~~~--~i~l~   70 (154)
                      |.|+|++.+|+++++++++++||.+||++|+.      +.++  +++.|+|+|.|+.|+|+.+|++|+|..++  +++++
T Consensus        18 m~I~vktl~G~~~~lev~~s~TV~~lK~~I~~~~p~dwke~ip~~~~~qrLIy~GK~LeD~~TL~~y~I~~~~~~tlhlv   97 (125)
T 2gow_A           18 INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLV   97 (125)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHSSCCCSCCCCTTCCGGGEEEESSSSEEESSCBTGGGCCCTTSEEEEEEE
T ss_pred             EEEEEEeCCCCEEEEEeCCccHHHHHHHHHHHHCCcccccCCCCChHHEEEEECCcCCCCCCcHHHcCCCCCCceEEEEE
Confidence            67899999999999999999999999999998      6777  48999999999999999999999998665  67777


Q ss_pred             eeee
Q 040824           71 LRLR   74 (154)
Q Consensus        71 ~~~~   74 (154)
                      ++..
T Consensus        98 ~r~~  101 (125)
T 2gow_A           98 ARET  101 (125)
T ss_dssp             ECSC
T ss_pred             ecCC
Confidence            7764

>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=99.68  E-value=2e-16  Score=97.06  Aligned_cols=73  Identities=23%  Similarity=0.429  Sum_probs=66.5

Q ss_pred             CEEEEEeCCCCEEEEEEeCC-----CcHHHHHHHHHhHhCCCCCCeEEEEcceEecc-Cceecccccccccceeeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESS-----DTIDNVKAKIQDKEGIPPDQQRLIFAGKQLED-GRTLADYNIQKESTLHLVLRLR   74 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~-----~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d-~~~l~~~~i~~~~~i~l~~~~~   74 (154)
                      |+|+|++ .++.+.++++++     +||.+||++|+..+++|+++|+|+|.|+.|.| +.+|++|+++++++|+++....
T Consensus         8 ~~v~Vk~-~~~~~~i~v~~~~~~~~~TV~~LK~~i~~~~gip~~~qrL~~~Gk~L~D~~~~L~~~~i~~g~~i~l~~~~~   86 (92)
T 1wxv_A            8 LTVTVTH-SNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVMLIGKKN   86 (92)
T ss_dssp             EEEEEEC-SSSEEEEEECCCSSSSSCBHHHHHHHHHHHTCCCTTTCEEEETTEEECCSSSBHHHHTCCSSEEEEEESCCS
T ss_pred             EEEEEEE-CCEEEEEEECCCcCcccCcHHHHHHHHHHHHCcCHHHEEEEECCeecCCCcccHHHCCCCCCCEEEEEecCC
Confidence            6899998 578899999985     99999999999999999999999999999998 5689999999999999887654

>2daf_A FLJ35834 protein; hypothetical protein FLJ35834, ubiquitin-like domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=4.2e-16  Score=97.88  Aligned_cols=73  Identities=21%  Similarity=0.343  Sum_probs=67.1

Q ss_pred             eeeeee-ecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEee
Q 040824           77 TMIKVK-TLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        77 ~~i~v~-~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      +.+.|+ ...++.+.++++++.||.+||++++...++|++.|+|+|+|+.|+|+.||.+|||++|.+||+.++.
T Consensus        16 itvkv~l~~~~~k~tv~v~~d~TV~dLKe~ls~~~~iP~e~qrLIy~GKiLKD~eTL~~~gIk~g~TIhLvi~s   89 (118)
T 2daf_A           16 ATVKVVLIPVGQEIVIPFKVDTILKYLKDHFSHLLGIPHSVLQIRYSGKILKNNETLVQHGVKPQEIVQVEIFS   89 (118)
T ss_dssp             EEEEEEETTTCCEEEEEECSSSCSHHHHHHHHHHHTCCTTTEEEEETTEEECSSCCHHHHSCCSSCEEEEEEEE
T ss_pred             EEEEEEEcCCCcEEEEEeCCCCcHHHHHHHHHhhhCCChHHEEEEECCeEcCCcchHHHcCCCCCCEEEEEEec
Confidence            455655 4567889999999999999999999999999999999999999999999999999999999999875

>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=99.66  E-value=3.9e-16  Score=95.78  Aligned_cols=74  Identities=22%  Similarity=0.432  Sum_probs=66.9

Q ss_pred             cceeeeeeecCCceEEEeeCCC-----chHHHHHHHHhhhcCCCCCceeEEECCeecCC-CCcccccccCCCCEEEEEEe
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPT-----DTIERIKERVEEKEGIPPVQQRLIYAGKQLAD-DKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~-----~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d-~~~L~~~~i~~~~~i~~~~~  148 (154)
                      ..|.|+|+. .++.+.++++++     +||.+||++|++.+|+|+++|+|+|+|+.|+| +.+|++|+|.+|++|+++.+
T Consensus         6 ~~~~v~Vk~-~~~~~~i~v~~~~~~~~~TV~~LK~~i~~~~gip~~~qrL~~~Gk~L~D~~~~L~~~~i~~g~~i~l~~~   84 (92)
T 1wxv_A            6 SGLTVTVTH-SNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVMLIGK   84 (92)
T ss_dssp             SSEEEEEEC-SSSEEEEEECCCSSSSSCBHHHHHHHHHHHTCCCTTTCEEEETTEEECCSSSBHHHHTCCSSEEEEEESC
T ss_pred             CeEEEEEEE-CCEEEEEEECCCcCcccCcHHHHHHHHHHHHCcCHHHEEEEECCeecCCCcccHHHCCCCCCCEEEEEec
Confidence            357888988 577889999995     99999999999999999999999999999998 66899999999999998865


Q ss_pred             e
Q 040824          149 L  149 (154)
Q Consensus       149 ~  149 (154)
                      .
T Consensus        85 ~   85 (92)
T 1wxv_A           85 K   85 (92)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.66  E-value=7e-18  Score=115.16  Aligned_cols=73  Identities=21%  Similarity=0.270  Sum_probs=1.1

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCCC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGGL  154 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~~  154 (154)
                      |+|+|++.+|+++.++|++++||.+||++|+...|+|+++|+|+|.|+.|+|+.+|+     ++++|+++++++||+.
T Consensus         1 MqI~VKtL~GktitLeV~~sdTV~~LK~kI~~keGIP~~qQRLIf~GK~LeD~~TLs-----~~STLhLvlRLrGG~~   73 (189)
T 2xzm_9            1 MQVQVKTLEGETKIYTLEQGTSVLDLKSQISQDMGFEIDMMTLVNNGFIAPNTELVT-----DDVTYYLSLKLLGGKK   73 (189)
T ss_dssp             ----------------------------------------------------------------------------CC
T ss_pred             CEEEEEcCCCCEEEEEECCcChHHHHHHHHHHHhCcChhHEEEEecCeECCCCCccc-----CCCEEEEEEecCCCcc
Confidence            689999999999999999999999999999999999999999999999999999998     8999999999999963

>2dzm_A FAS-associated factor 1; ubiquitin-like domain, HFAF1, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=3e-16  Score=97.21  Aligned_cols=73  Identities=19%  Similarity=0.284  Sum_probs=65.7

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEE--cceEeccCceecccccccccceeeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF--AGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~--~g~~L~d~~~l~~~~i~~~~~i~l~~~~~   74 (154)
                      |..+++.++|+.+.+++++++||.+||++|++++|+||++|+|++  .|+ |+|+.+|++|+|++++++++++...
T Consensus         9 m~~~~vk~~Gk~~~v~v~~~~TV~~LK~~I~~~tgIpp~~QkLi~~~~gk-L~D~~tLs~~~I~~gstL~lvl~~~   83 (100)
T 2dzm_A            9 MLDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGD-VEDSTVLKSLHLPKNNSLYVLTPDL   83 (100)
T ss_dssp             EEEEEEECSSCEEEEEEETTSBHHHHHHHHHHHHCCCTTTCCEECCSSSC-CCTTSBHHHHCCCSEEEEEECCSSS
T ss_pred             eEEEEEEeCCeEEEEEECCCCcHHHHHHHHHHHHCCChhHeEEEccCCCC-CCCcCCHHHcCCCCCCEEEEEecCC
Confidence            456677789999999999999999999999999999999999985  455 8999999999999999999987654

>2d07_B Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Homo sapiens} SCOP: d.15.1.1 PDB: 2rpq_A 2awt_A 2io3_B 2iyd_B 1u4a_A 2k1f_A

Probab=99.65  E-value=8.7e-16  Score=94.21  Aligned_cols=78  Identities=17%  Similarity=0.354  Sum_probs=72.0

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ..|.|.|+..+|+.+.+.+.+++++..|+..++++.|++++.++|+|.|+.|.++.|+++|++.+|++|+++.+++||
T Consensus        16 ~~i~ikV~~~~g~~i~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~~l~~~~Tp~dl~medgD~Idv~~~q~GG   93 (93)
T 2d07_B           16 DHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGG   93 (93)
T ss_dssp             CEEEEEEECTTSCEEEEEEETTSCHHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECC---
T ss_pred             CeEEEEEECCCCCEEEEEEccCCHHHHHHHHHHHHhCCCccceEEEECCEEcCCCCCHHHcCCCCCCEEEEEeeccCC
Confidence            457888999899999999999999999999999999999999999999999999999999999999999999999998

>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=99.65  E-value=9.6e-17  Score=99.03  Aligned_cols=71  Identities=18%  Similarity=0.328  Sum_probs=64.8

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |+|+|+. +++.+.+++++++||.+||++|+..+++|+++|+|+|.|+.| |+.+|++|+++++++|+++...
T Consensus        18 ~~i~Vk~-~g~~~~i~v~~~~TV~~LK~~I~~~tgip~~~QrL~~~Gk~L-dd~tL~~~~i~~g~~i~lv~~~   88 (95)
T 1v86_A           18 VDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGLVP-EDKTLREIKVTSGAKIMVVGST   88 (95)
T ss_dssp             EEEEEEE-TTEEEEEEECTTSBHHHHHHHHHHHHCSCSTTCCCBSSSBCC-SSSBHHHHCCCTTEEEEECCSS
T ss_pred             EEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCeeC-CcCcHHHCCCCCCCEEEEEecc
Confidence            5788984 688999999999999999999999999999999999999999 4559999999999999887654

>4b6w_A Tubulin-specific chaperone; CAP-Gly, ubiquitin-like; HET: MSE; 2.35A {Trypanosoma brucei brucei strain 927}

Probab=99.65  E-value=4.8e-16  Score=94.00  Aligned_cols=66  Identities=29%  Similarity=0.260  Sum_probs=59.5

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEEC-------CeecCCCCcccccccCCCCEEEEEEeec
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYA-------GKQLADDKTARDYNIEGGSVLHLVLALR  150 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~-------g~~l~d~~~L~~~~i~~~~~i~~~~~~~  150 (154)
                      ..+.++.++++++||.+||++|+..+|+|+++|+|+|.       |+.++|+++|++|||++|++||++-..+
T Consensus        13 ~~~~~E~r~~~s~TI~~lK~ki~~~~Gip~~~QrLi~~~~~~~~~g~~l~d~~tL~~Y~i~~g~~ihlvd~~P   85 (86)
T 4b6w_A           13 RMRVPEKRYGLAQTIESIKENVFTHFATPPEYMQLQLIDDRGITIEKNMANDKQLGYYQCRDEFVIHVVDLQP   85 (86)
T ss_dssp             SCCEEEEEEETTSBHHHHHHHHHTTSCCCGGGEEEEEECTTSCEEESSCCTTSBGGGGTCCTTCEEEEEECCC
T ss_pred             CCeEEEEEcCccCcHHHHHHHHHHHHCCCHHHEEEEEecCCCCceeeEcCCCCCHHHCCCCCCCEEEEEeCCC
Confidence            44567899999999999999999999999999999974       7789999999999999999999986543

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B*

Probab=99.65  E-value=9.4e-16  Score=112.23  Aligned_cols=78  Identities=60%  Similarity=0.952  Sum_probs=71.9

Q ss_pred             eecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeec
Q 040824           73 LRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALR  150 (154)
Q Consensus        73 ~~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~  150 (154)
                      ....|+|+|+..+|+.+.+++++++||++||++|++.+|+|+++|+|+|+|+.|+|+.+|++|+|++|++|++++++|
T Consensus       230 ~~~~MqI~VKtl~Gk~~~leV~~s~TV~dLK~kI~~~~GIp~~~QRLi~~Gk~L~D~~TLsdygI~~gstL~LvlRLr  307 (307)
T 3ai5_A          230 ITGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR  307 (307)
T ss_dssp             SCCCEEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBTGGGTCCTTCEEEEEC---
T ss_pred             CCCeEEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEeCCeecCCCCCHHHcCCCCCCEEEEEEeCC
Confidence            346799999999999999999999999999999999999999999999999999999999999999999999998874

>2kjr_A CG11242; UBL, ubiquitin, ubiquitin-like, structural genomics, PSI-2, protein structure initiative; NMR {Drosophila melanogaster}

Probab=99.64  E-value=6.3e-16  Score=95.12  Aligned_cols=72  Identities=17%  Similarity=0.159  Sum_probs=62.0

Q ss_pred             cceeeeeeecCC--ceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEEC--Ce---e-cCCCCcccccccCCCCEEEEE
Q 040824           75 GGTMIKVKTLTG--KEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYA--GK---Q-LADDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        75 ~~~~i~v~~~~~--~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~--g~---~-l~d~~~L~~~~i~~~~~i~~~  146 (154)
                      +.+.|+|+...+  ..+.+++++++||++||++|+..+|+|+++|+|+|.  |+   . ++|+.+|++|+|++|++|++.
T Consensus        14 ~~v~l~It~s~~~~~~~~~~v~~~~TV~~LK~kI~~~~GiP~~~QrL~~~~~g~~~~~L~~D~~tL~~Y~i~~gstihlv   93 (95)
T 2kjr_A           14 DFIKVNVSNSHNDAVAFEVKLAKDLTVAQLKTKLEILTGGCAGTMKVQVFKGDTCVSTMDNNDAQLGYYANSDGLRLHVV   93 (95)
T ss_dssp             CEEEEEEEESSCSCEEEEEEEETTCBHHHHHHHHHHHHCSCTTTEEEEEEETTEEEEECCCTTSBHHHHCCSSSCEEEEE
T ss_pred             CeEEEEEEECCCCceEEEEEeCccCHHHHHHHHHHHHHCcCHHHeEEEEecCCcccceeCCCCCCHhHCCcCCCCEEEEE
Confidence            335666776554  478899999999999999999999999999999997  44   3 489999999999999999886

>2kjr_A CG11242; UBL, ubiquitin, ubiquitin-like, structural genomics, PSI-2, protein structure initiative; NMR {Drosophila melanogaster}

Probab=99.64  E-value=9.4e-16  Score=94.34  Aligned_cols=70  Identities=14%  Similarity=0.222  Sum_probs=61.8

Q ss_pred             CEEEEEeCCCC--EEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEc--ce---Ee-ccCceecccccccccceeee
Q 040824            1 MQIFVKTLTGK--TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA--GK---QL-EDGRTLADYNIQKESTLHLV   70 (154)
Q Consensus         1 m~v~v~~~~~~--~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~--g~---~L-~d~~~l~~~~i~~~~~i~l~   70 (154)
                      ++|+|+..+++  .+++++++++||.+||++|+.++|+||+.|+|+|.  |+   .| +|+.+|++|++.++++|+++
T Consensus        16 v~l~It~s~~~~~~~~~~v~~~~TV~~LK~kI~~~~GiP~~~QrL~~~~~g~~~~~L~~D~~tL~~Y~i~~gstihlv   93 (95)
T 2kjr_A           16 IKVNVSNSHNDAVAFEVKLAKDLTVAQLKTKLEILTGGCAGTMKVQVFKGDTCVSTMDNNDAQLGYYANSDGLRLHVV   93 (95)
T ss_dssp             EEEEEEESSCSCEEEEEEEETTCBHHHHHHHHHHHHCSCTTTEEEEEEETTEEEEECCCTTSBHHHHCCSSSCEEEEE
T ss_pred             EEEEEEECCCCceEEEEEeCccCHHHHHHHHHHHHHCcCHHHeEEEEecCCcccceeCCCCCCHhHCCcCCCCEEEEE
Confidence            36788877664  78999999999999999999999999999999997  44   34 88999999999999999875

>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=99.64  E-value=2.7e-16  Score=96.99  Aligned_cols=72  Identities=21%  Similarity=0.380  Sum_probs=64.9

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEee
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      .|.|+|+. .++.+.+++++++||.+||++|++.+|+|+++|+|+|+|+.|+| .+|++|+|++|++|+++...
T Consensus        17 ~~~i~Vk~-~g~~~~i~v~~~~TV~~LK~~I~~~tgip~~~QrL~~~Gk~Ldd-~tL~~~~i~~g~~i~lv~~~   88 (95)
T 1v86_A           17 LVDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGLVPED-KTLREIKVTSGAKIMVVGST   88 (95)
T ss_dssp             CEEEEEEE-TTEEEEEEECTTSBHHHHHHHHHHHHCSCSTTCCCBSSSBCCSS-SBHHHHCCCTTEEEEECCSS
T ss_pred             eEEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEECCeeCCc-CcHHHCCCCCCCEEEEEecc
Confidence            47788885 68889999999999999999999999999999999999999955 59999999999999987543

>1wz0_A Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-like molecule, structural genomics, sentrin2, NPPFSA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.63  E-value=1.1e-15  Score=95.42  Aligned_cols=79  Identities=15%  Similarity=0.317  Sum_probs=75.8

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      ..|.|.|+..+|+.+.+.+.+++++..|+.+++++.|+++..++|+|.|+.|.++.|+.+|++.+|++|+++.+++||.
T Consensus        23 ~~I~IkVk~~~g~~i~~kVk~~t~l~kL~~~y~ek~gi~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~q~GG~  101 (104)
T 1wz0_A           23 DHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTSGP  101 (104)
T ss_dssp             CCEEEEEECSSSCEEEEEECTTSCHHHHHHHHHHHHTCCTTTSCEESSSSBCCTTSCTTTTTCCTTEEEEECCCCCCCS
T ss_pred             CeEEEEEECCCCCEEEEEEcCCChHHHHHHHHHHHhCCCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEeccCCC
Confidence            4588999998999999999999999999999999999999999999999999999999999999999999999999996

>2dzj_A Synaptic glycoprotein SC2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=7.2e-16  Score=93.67  Aligned_cols=70  Identities=21%  Similarity=0.300  Sum_probs=63.1

Q ss_pred             ceeeeeeecCCceE--EE-eeCCCchHHHHHHHHhh-hcCCCCCceeEEEC--CeecCCCCcccccccCCCCEEEE
Q 040824           76 GTMIKVKTLTGKEI--EI-DIEPTDTIERIKERVEE-KEGIPPVQQRLIYA--GKQLADDKTARDYNIEGGSVLHL  145 (154)
Q Consensus        76 ~~~i~v~~~~~~~~--~~-~v~~~~tv~~LK~~i~~-~~~i~~~~~~l~~~--g~~l~d~~~L~~~~i~~~~~i~~  145 (154)
                      .|.|+|++..|+.+  .+ ++++++||.+||++|++ ..++|+++|+|+|.  |+.|+|+.+|++|+|.+|++|++
T Consensus        10 ~M~I~Vk~~~g~~~~~~l~~v~~~~TV~~lK~~I~~~~~~i~~~~QrL~~~~~Gk~L~D~~tL~~y~i~~~stl~~   85 (88)
T 2dzj_A           10 HYEVEILDAKTREKLCFLDKVEPHATIAEIKNLFTKTHPQWYPARQSLRLDPKGKSLKDEDVLQKLPVGTTATLYF   85 (88)
T ss_dssp             CEEEEEEESSSCCCCEEEEEECSSCBHHHHHHHHHHHCSSSCTTTCCEESSTTSCCCCTTCBTTTSSCCSEEEEEE
T ss_pred             EEEEEEECCCCCEEeeEEeEcCCCCcHHHHHHHHHHHhcCCChHHeEEEecCCCcCcCCCCCHHHcCCCCCCEEEE
Confidence            38899999987664  58 99999999999999999 48999999999976  89999999999999999999765

>2dzj_A Synaptic glycoprotein SC2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=3.9e-16  Score=94.84  Aligned_cols=69  Identities=23%  Similarity=0.303  Sum_probs=62.8

Q ss_pred             CEEEEEeCCCCEE--EE-EEeCCCcHHHHHHHHHhH-hCCCCCCeEEEEc--ceEeccCceecccccccccceee
Q 040824            1 MQIFVKTLTGKTI--TL-EVESSDTIDNVKAKIQDK-EGIPPDQQRLIFA--GKQLEDGRTLADYNIQKESTLHL   69 (154)
Q Consensus         1 m~v~v~~~~~~~~--~~-~v~~~~tv~~lk~~i~~~-~~~~~~~q~L~~~--g~~L~d~~~l~~~~i~~~~~i~l   69 (154)
                      |+|+|+.+.|+.+  .+ ++++++||.+||++|++. .++||++|+|.|.  |+.|+|+.+|++|++.++++|++
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            7899999988664  58 999999999999999995 7999999999976  89999999999999999998765

>2dzm_A FAS-associated factor 1; ubiquitin-like domain, HFAF1, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=6.5e-16  Score=95.69  Aligned_cols=75  Identities=15%  Similarity=0.151  Sum_probs=65.7

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEE-CCeecCCCCcccccccCCCCEEEEEEeec
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIY-AGKQLADDKTARDYNIEGGSVLHLVLALR  150 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~-~g~~l~d~~~L~~~~i~~~~~i~~~~~~~  150 (154)
                      +|.++++..+|+.+.+++++++||.+||++|++++|+||++|+|++ ++..++|+.+|++|+|++|++|++..+-.
T Consensus         8 ~m~~~~vk~~Gk~~~v~v~~~~TV~~LK~~I~~~tgIpp~~QkLi~~~~gkL~D~~tLs~~~I~~gstL~lvl~~~   83 (100)
T 2dzm_A            8 RMLDFRVEYRDRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGDVEDSTVLKSLHLPKNNSLYVLTPDL   83 (100)
T ss_dssp             CEEEEEEECSSCEEEEEEETTSBHHHHHHHHHHHHCCCTTTCCEECCSSSCCCTTSBHHHHCCCSEEEEEECCSSS
T ss_pred             ceEEEEEEeCCeEEEEEECCCCcHHHHHHHHHHHHCCChhHeEEEccCCCCCCCcCCHHHcCCCCCCEEEEEecCC
Confidence            4666666678999999999999999999999999999999999985 44448999999999999999999876543

>2eke_C Ubiquitin-like protein SMT3; UBC9, SUMO binding motif, SBM, ligase/protein binding complex; 1.90A {Saccharomyces cerevisiae} SCOP: d.15.1.1

Probab=99.62  E-value=2.4e-15  Score=93.90  Aligned_cols=78  Identities=23%  Similarity=0.388  Sum_probs=71.8

Q ss_pred             ecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           74 RGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        74 ~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ...|.|.|+. +|+.+.+.+.+++++..|+.+++++.|++++.++|+|.|+.|.++.|+++|++++||+|+++.+++||
T Consensus        29 ~~~I~IkV~~-~g~~i~fkIk~tt~l~kL~~ay~ek~gi~~~~~rF~FdG~rl~~~~Tp~dl~medgD~Idv~~~q~GG  106 (106)
T 2eke_C           29 ETHINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGG  106 (106)
T ss_dssp             CSEEEEEEEC-SSCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECC---
T ss_pred             CCeEEEEEec-CCcEEEEEeCCCCHHHHHHHHHHHHhCCCcccEEEEECCeEcCCCCCHHHcCCCCCCEEEEEeecccC
Confidence            3458899999 99999999999999999999999999999999999999999999999999999999999999999998

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B*

Probab=99.61  E-value=2.1e-15  Score=110.34  Aligned_cols=73  Identities=96%  Similarity=1.295  Sum_probs=68.9

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |+|+|+.++|+.+.+++++++||.+||++|++..++|+++|+|+|+|+.|+|+.+|++|+|+++++|+++++.
T Consensus       234 MqI~VKtl~Gk~~~leV~~s~TV~dLK~kI~~~~GIp~~~QRLi~~Gk~L~D~~TLsdygI~~gstL~LvlRL  306 (307)
T 3ai5_A          234 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  306 (307)
T ss_dssp             EEEEEECTTSCEEEEEECTTCBHHHHHHHHHHHHCCCGGGCEEEETTEECCTTSBTGGGTCCTTCEEEEEC--
T ss_pred             EEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcChHHEEEEeCCeecCCCCCHHHcCCCCCCEEEEEEeC
Confidence            6899999999999999999999999999999999999999999999999999999999999999999998764

>2kj6_A Tubulin folding cofactor B; methods development, NESG, solution PSI-2, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.60  E-value=2.8e-15  Score=92.46  Aligned_cols=71  Identities=15%  Similarity=0.175  Sum_probs=60.7

Q ss_pred             eeeeeeecCC--ceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCe---e----cCCCCcccccccCCCCEEEEEE
Q 040824           77 TMIKVKTLTG--KEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGK---Q----LADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        77 ~~i~v~~~~~--~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~---~----l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      +.+.|+....  ..+.+++++++||++||++|+..+|+|++.|+|+|.|+   .    ++|+++|++|+|++|++|++.-
T Consensus        15 v~l~It~s~~~~~~~e~~v~~~~TV~~LK~kIe~~~Gip~~~QrLi~~g~~g~~~~~L~~D~~tL~~Y~I~~g~~Ihlvd   94 (97)
T 2kj6_A           15 VHLHITHANLKSFSADARFSPQMSVEAVKEKLWKKCGTSVNSMALELYDDSGSKVAVLSDDSRPLGFFSPFDGFRLHIID   94 (97)
T ss_dssp             EEEEEEETTSSCCCEEEEECTTCCHHHHHHHHHHHHCCCTTSEEEEEECSSSCBCCCSSGGGSCHHHHCCCSCCEEEEEE
T ss_pred             EEEEEEECCCCceEEEEEeCCCChHHHHHHHHHHHHCcCHHHeEEEEecCCCcccceecCCcCCHHHCCCCCCCEEEEEe
Confidence            4555555433  46889999999999999999999999999999999873   3    4899999999999999998864

>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=99.60  E-value=2e-15  Score=113.31  Aligned_cols=79  Identities=35%  Similarity=0.646  Sum_probs=72.3

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhh---hcCCCCCceeEEECCeecCCCCcccccccCCCCEE-EEEEeec
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEE---KEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVL-HLVLALR  150 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~---~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i-~~~~~~~  150 (154)
                      ..|.|+|+..+|+.+.++|++++||.+||++|+.   +.|+|+++|+|+|+|+.|+|+++|++|+|++|++| ++..+.+
T Consensus         6 ~~M~I~VKtl~Gk~~~leV~~~~TV~~LK~~I~~~~~~~gip~~~QrLiy~GK~L~D~~tL~dygI~~gstIv~lv~k~~   85 (368)
T 1oqy_A            6 SAVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTKTK   85 (368)
T ss_dssp             CCCCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSSEECSSSBTTTTCCCTTSCEEEEEECCC
T ss_pred             ceEEEEEEeCCCCEEEEEeCCCChHHHHHHHHHHHhCcCCCChhheEEEECCeecCCcCCHHHcCCCCCCEEEEEEecCC
Confidence            4589999999999999999999999999999999   67799999999999999999999999999999998 6777777


Q ss_pred             CCC
Q 040824          151 GGG  153 (154)
Q Consensus       151 gg~  153 (154)
                      ||.
T Consensus        86 ~~~   88 (368)
T 1oqy_A           86 AGQ   88 (368)
T ss_dssp             SSS
T ss_pred             CCC
Confidence            653

>4b6w_A Tubulin-specific chaperone; CAP-Gly, ubiquitin-like; HET: MSE; 2.35A {Trypanosoma brucei brucei strain 927}

Probab=99.59  E-value=2.3e-15  Score=90.98  Aligned_cols=72  Identities=17%  Similarity=0.266  Sum_probs=62.5

Q ss_pred             EEEEEeC--CCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEE-------cceEeccCceecccccccccceeeeee
Q 040824            2 QIFVKTL--TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF-------AGKQLEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         2 ~v~v~~~--~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~-------~g~~L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      .|.|.+.  +.+.++.++++++||.+||++|+.++|+||+.|+|+|       .|+.++|+.+|++|++.+|++||++-.
T Consensus         4 ~v~iths~~~~~~~E~r~~~s~TI~~lK~ki~~~~Gip~~~QrLi~~~~~~~~~g~~l~d~~tL~~Y~i~~g~~ihlvd~   83 (86)
T 4b6w_A            4 KVSLTHSASRMRVPEKRYGLAQTIESIKENVFTHFATPPEYMQLQLIDDRGITIEKNMANDKQLGYYQCRDEFVIHVVDL   83 (86)
T ss_dssp             EEEEEETTCSCCEEEEEEETTSBHHHHHHHHHTTSCCCGGGEEEEEECTTSCEEESSCCTTSBGGGGTCCTTCEEEEEEC
T ss_pred             EEEEEEcCCCCeEEEEEcCccCcHHHHHHHHHHHHCCCHHHEEEEEecCCCCceeeEcCCCCCHHHCCCCCCCEEEEEeC
Confidence            4556543  3466789999999999999999999999999999996       478899999999999999999999865


Q ss_pred             e
Q 040824           73 L   73 (154)
Q Consensus        73 ~   73 (154)
                      .
T Consensus        84 ~   84 (86)
T 4b6w_A           84 Q   84 (86)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2k8h_A Small ubiquitin protein; SUMO, post-translational modifier, signaling protein; NMR {Trypanosoma brucei}

Probab=99.59  E-value=2.8e-15  Score=94.25  Aligned_cols=79  Identities=20%  Similarity=0.417  Sum_probs=75.5

Q ss_pred             ecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           74 RGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        74 ~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ...|.|.|+..+|+.+.+.+.+++++..|+.+++++.|++++.++|+|.|..|.++.|+++|++.+||+|+++..++||
T Consensus        24 ~~~I~IkVk~~~g~~i~fkVk~~t~l~kL~~ay~ek~gi~~~~~rfiFdG~~L~~~~Tp~dl~mEDgD~Idv~~~q~Gg  102 (110)
T 2k8h_A           24 TALVAVKVVNADGAEMFFRIKSRTALKKLIDTYCKKQGISRNSVRFLFDGTPIDETKTPEELGMEDDDVIDAMVEQTGG  102 (110)
T ss_dssp             CCCEEEEEEETTSCCEEEEECTTSSHHHHHHHHHHHHTCCSSSCEEESSSCBCCSSSHHHHHHCSSEEEEEEECCCCCC
T ss_pred             CCeEEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEcccCc
Confidence            3458899999999999999999999999999999999999999999999999999999999999999999999999988

>2kj6_A Tubulin folding cofactor B; methods development, NESG, solution PSI-2, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}

Probab=99.58  E-value=4.2e-15  Score=91.67  Aligned_cols=71  Identities=15%  Similarity=0.188  Sum_probs=61.9

Q ss_pred             EEEEEeCCC--CEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcc---eE----eccCceecccccccccceeeeee
Q 040824            2 QIFVKTLTG--KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG---KQ----LEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         2 ~v~v~~~~~--~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g---~~----L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      .|.|+..+.  ..+++++++++||.+||++|+.++|+||+.|+|+|.|   +.    ++|+.+|++|++.++++|+++-.
T Consensus        16 ~l~It~s~~~~~~~e~~v~~~~TV~~LK~kIe~~~Gip~~~QrLi~~g~~g~~~~~L~~D~~tL~~Y~I~~g~~Ihlvd~   95 (97)
T 2kj6_A           16 HLHITHANLKSFSADARFSPQMSVEAVKEKLWKKCGTSVNSMALELYDDSGSKVAVLSDDSRPLGFFSPFDGFRLHIIDL   95 (97)
T ss_dssp             EEEEEETTSSCCCEEEEECTTCCHHHHHHHHHHHHCCCTTSEEEEEECSSSCBCCCSSGGGSCHHHHCCCSCCEEEEEEC
T ss_pred             EEEEEECCCCceEEEEEeCCCChHHHHHHHHHHHHCcCHHHeEEEEecCCCcccceecCCcCCHHHCCCCCCCEEEEEeC
Confidence            577777554  4689999999999999999999999999999999987   33    58899999999999999988743

>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=99.58  E-value=1.2e-14  Score=84.99  Aligned_cols=70  Identities=16%  Similarity=0.355  Sum_probs=67.4

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEE
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~  146 (154)
                      |.|.|+..+|+.+.+.+.+++++..|+.+++++.|+|++.++|+|.|+.|.++.|++++++++|++|+++
T Consensus         2 i~lkV~~~~g~~v~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~~l~~~~Tp~~l~medgD~Idv~   71 (72)
T 1wm3_A            2 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVF   71 (72)
T ss_dssp             EEEEEECTTSCEEEEEECTTSCTHHHHHHHHHHHTCCTTTCEEEETTEECCTTCCTTTTTCCTTEEEEEE
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEE
Confidence            6788999999999999999999999999999999999999999999999999999999999999999986

>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=99.57  E-value=1.1e-14  Score=93.67  Aligned_cols=73  Identities=14%  Similarity=0.223  Sum_probs=63.2

Q ss_pred             CEEEEEeCCCC-EEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcc---eE----eccCceecccccccccceeeeee
Q 040824            1 MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG---KQ----LEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         1 m~v~v~~~~~~-~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g---~~----L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      |.|+|+..++. .+.+++++++||.+||++|+.++|+|++.|+|.|.|   +.    ++|+.+|++||+.+|++||++..
T Consensus         7 v~l~V~~~~~~~~~e~~v~~~~TV~~lK~ki~~~~Gip~~~qrL~~~g~~~~~~~~l~~D~~tL~~y~i~~g~~ihvvd~   86 (122)
T 1t0y_A            7 YDLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHAVDV   86 (122)
T ss_dssp             EEEEEEESSCCSCEEEEEETTSBHHHHHHHHHHHHCCCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEEEEEEC
T ss_pred             EEEEEEECCCCccEEEEeCCCCcHHHHHHHHHHHhCCCHHHeEEEEecCCCccccccCCCcCCHHHCCCCCCCEEEEEeC
Confidence            46778876553 588999999999999999999999999999999976   32    47889999999999999998864


Q ss_pred             e
Q 040824           73 L   73 (154)
Q Consensus        73 ~   73 (154)
                      .
T Consensus        87 ~   87 (122)
T 1t0y_A           87 T   87 (122)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.57  E-value=1.5e-14  Score=88.78  Aligned_cols=76  Identities=17%  Similarity=0.403  Sum_probs=72.1

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecc
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~   76 (154)
                      |+|+|+..+|+.+.+++.+++++..|+++++++.+++++.++|+|+|+.|+++.|+++|++.++++|++.+...++
T Consensus         8 i~ikVk~~~g~~i~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~~~GG   83 (94)
T 2io1_B            8 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGG   83 (94)
T ss_dssp             EEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCTTTTTCCTTCEEEEEECCEES
T ss_pred             EEEEEECCCCCEEEEEECCCCHHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEeccCC
Confidence            6789999999999999999999999999999999999999999999999999999999999999999999887654

>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=99.57  E-value=1.2e-14  Score=89.58  Aligned_cols=71  Identities=21%  Similarity=0.253  Sum_probs=61.1

Q ss_pred             eeeeeeecCCc-eEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECC---ee----cCCCCcccccccCCCCEEEEEE
Q 040824           77 TMIKVKTLTGK-EIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAG---KQ----LADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        77 ~~i~v~~~~~~-~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g---~~----l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      +.+.|+..... .+.+++++++||++||++|+..+|+|+++|+|+|.|   +.    ++|+.+|++|||.+|++|++.-
T Consensus         8 v~l~I~~~~~~~~~~~~v~~~~TV~~lK~ki~~~~gip~~~qrL~~~~~~g~~~~~l~~D~~tL~~y~i~~g~~l~v~d   86 (95)
T 1v6e_A            8 VMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVGSPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIHVID   86 (95)
T ss_dssp             EEEEEEETTSSSCEEEEECTTSBHHHHHHHHHHHTCSCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCEEEEBC
T ss_pred             EEEEEEECCCCeeEEEEcCccCHHHHHHHHHHHHHCCCHHHeEEEEeCCCCccccccCCCcCCHhHCCCCCCCEEEEEE
Confidence            55666665443 688999999999999999999999999999999976   43    5899999999999999998864

>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=99.56  E-value=1.1e-14  Score=89.84  Aligned_cols=72  Identities=19%  Similarity=0.278  Sum_probs=62.5

Q ss_pred             CEEEEEeCCCC-EEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcc---eE----eccCceecccccccccceeeeee
Q 040824            1 MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG---KQ----LEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         1 m~v~v~~~~~~-~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g---~~----L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      +.|+|+..+.. .+.+++++++||.+||++|+.++|+|++.|+|+|.|   +.    ++|+.+|++|++.++++||+.-.
T Consensus         8 v~l~I~~~~~~~~~~~~v~~~~TV~~lK~ki~~~~gip~~~qrL~~~~~~g~~~~~l~~D~~tL~~y~i~~g~~l~v~d~   87 (95)
T 1v6e_A            8 VMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVGSPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIHVIDH   87 (95)
T ss_dssp             EEEEEEETTSSSCEEEEECTTSBHHHHHHHHHHHTCSCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCEEEEBCC
T ss_pred             EEEEEEECCCCeeEEEEcCccCHHHHHHHHHHHHHCCCHHHeEEEEeCCCCccccccCCCcCCHhHCCCCCCCEEEEEEC
Confidence            35778876553 688999999999999999999999999999999976   43    58999999999999999988753

>1wf9_A NPL4 family protein; beta-grAsp fold like domain, hypothetical protein, structural genomics, NPPSFA; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=99.55  E-value=4.2e-15  Score=93.56  Aligned_cols=72  Identities=21%  Similarity=0.252  Sum_probs=65.3

Q ss_pred             CEEEEEeCCCCEEEEEEe-CCCcHHHHHHHHHhHhCCCCCCeEEEEcce-----------E----eccCceecccccccc
Q 040824            1 MQIFVKTLTGKTITLEVE-SSDTIDNVKAKIQDKEGIPPDQQRLIFAGK-----------Q----LEDGRTLADYNIQKE   64 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~-~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~-----------~----L~d~~~l~~~~i~~~   64 (154)
                      |.|+|++.+|.. .++++ +++||.+||++|+.++++|++.|+|.+.|+           .    ++|+.+|++|++++|
T Consensus         8 M~irvrs~~G~~-~v~v~~~~~Tv~~LK~kI~~~~gip~~~QrL~~~~~~~~~k~~~~~~~l~~~l~d~~tL~~~gi~~G   86 (107)
T 1wf9_A            8 TMLRVRSRDGLE-RVSVDGPHITVSQLKTLIQDQLQIPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLAHG   86 (107)
T ss_dssp             EEEEEECSSCEE-EEEECCTTSBHHHHHHHHHHHSCCCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTCCCTT
T ss_pred             EEEEEECCCCCE-EEEECCCCCcHHHHHHHHHHHhCcCcccCEEEECCccccccCccccccccccCCCCCCHHHCCCCCC
Confidence            789999998865 78999 999999999999999999999999998877           3    588889999999999


Q ss_pred             cceeeeeee
Q 040824           65 STLHLVLRL   73 (154)
Q Consensus        65 ~~i~l~~~~   73 (154)
                      ++||+....
T Consensus        87 ~~L~l~~~~   95 (107)
T 1wf9_A           87 SMVYLAYEG   95 (107)
T ss_dssp             CEEECCCSS
T ss_pred             CEEEEEeCC
Confidence            999988764

>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=99.55  E-value=7.2e-15  Score=110.31  Aligned_cols=74  Identities=31%  Similarity=0.566  Sum_probs=68.1

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHh---HhCCCCCCeEEEEcceEeccCceecccccccccce-eeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQD---KEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTL-HLVLRLR   74 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~---~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i-~l~~~~~   74 (154)
                      |+|+||..+|+.+.+++++++||.+||++|+.   +.++++++|+|+|.|+.|+|+.+|++|+|+++++| +++.+..
T Consensus         8 M~I~VKtl~Gk~~~leV~~~~TV~~LK~~I~~~~~~~gip~~~QrLiy~GK~L~D~~tL~dygI~~gstIv~lv~k~~   85 (368)
T 1oqy_A            8 VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMVTKTK   85 (368)
T ss_dssp             CCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSSEECSSSBTTTTCCCTTSCEEEEEECCC
T ss_pred             EEEEEEeCCCCEEEEEeCCCChHHHHHHHHHHHhCcCCCChhheEEEECCeecCCcCCHHHcCCCCCCEEEEEEecCC
Confidence            78999999999999999999999999999999   56799999999999999999999999999999998 5555543

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

Probab=99.55  E-value=4e-16  Score=106.50  Aligned_cols=71  Identities=30%  Similarity=0.415  Sum_probs=0.0

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecc
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~   76 (154)
                      |+|+|++++|+++.+++++++||.+||++|+...++|++.|+|+|+|+.|+|+.+|+     ++++|+|+++..++
T Consensus         1 MqI~VKtL~GktitLeV~~sdTV~~LK~kI~~keGIP~~qQRLIf~GK~LeD~~TLs-----~~STLhLvlRLrGG   71 (189)
T 2xzm_9            1 MQVQVKTLEGETKIYTLEQGTSVLDLKSQISQDMGFEIDMMTLVNNGFIAPNTELVT-----DDVTYYLSLKLLGG   71 (189)
T ss_dssp             ----------------------------------------------------------------------------
T ss_pred             CEEEEEcCCCCEEEEEECCcChHHHHHHHHHHHhCcChhHEEEEecCeECCCCCccc-----CCCEEEEEEecCCC
Confidence            899999999999999999999999999999999999999999999999999999998     78999999987654

>1wf9_A NPL4 family protein; beta-grAsp fold like domain, hypothetical protein, structural genomics, NPPSFA; NMR {Arabidopsis thaliana} SCOP: d.15.1.1

Probab=99.54  E-value=8.2e-15  Score=92.22  Aligned_cols=72  Identities=24%  Similarity=0.410  Sum_probs=64.9

Q ss_pred             ceeeeeeecCCceEEEeeC-CCchHHHHHHHHhhhcCCCCCceeEEECCe-----------e----cCCCCcccccccCC
Q 040824           76 GTMIKVKTLTGKEIEIDIE-PTDTIERIKERVEEKEGIPPVQQRLIYAGK-----------Q----LADDKTARDYNIEG  139 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~-~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~-----------~----l~d~~~L~~~~i~~  139 (154)
                      .|.|+|+..+|.. .++++ +++||.+||++|++.+++|+++|+|.+.++           .    ++|+.+|++|||++
T Consensus         7 ~M~irvrs~~G~~-~v~v~~~~~Tv~~LK~kI~~~~gip~~~QrL~~~~~~~~~k~~~~~~~l~~~l~d~~tL~~~gi~~   85 (107)
T 1wf9_A            7 GTMLRVRSRDGLE-RVSVDGPHITVSQLKTLIQDQLQIPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLAH   85 (107)
T ss_dssp             CEEEEEECSSCEE-EEEECCTTSBHHHHHHHHHHHSCCCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTCCCT
T ss_pred             eEEEEEECCCCCE-EEEECCCCCcHHHHHHHHHHHhCcCcccCEEEECCccccccCccccccccccCCCCCCHHHCCCCC
Confidence            3889999998865 78999 999999999999999999999999998887           3    58999999999999


Q ss_pred             CCEEEEEEe
Q 040824          140 GSVLHLVLA  148 (154)
Q Consensus       140 ~~~i~~~~~  148 (154)
                      |++||+...
T Consensus        86 G~~L~l~~~   94 (107)
T 1wf9_A           86 GSMVYLAYE   94 (107)
T ss_dssp             TCEEECCCS
T ss_pred             CCEEEEEeC
Confidence            999988654

>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=99.54  E-value=3.1e-14  Score=91.56  Aligned_cols=72  Identities=15%  Similarity=0.193  Sum_probs=62.0

Q ss_pred             ceeeeeeecCCc-eEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECC---e---e-cCCCCcccccccCCCCEEEEEE
Q 040824           76 GTMIKVKTLTGK-EIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAG---K---Q-LADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        76 ~~~i~v~~~~~~-~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g---~---~-l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      .+.|.|+...+. .+.+++++++||++||++|+..+|+|+++|+|+|.|   +   . ++|+.+|++|||.+|++||+..
T Consensus         6 ~v~l~V~~~~~~~~~e~~v~~~~TV~~lK~ki~~~~Gip~~~qrL~~~g~~~~~~~~l~~D~~tL~~y~i~~g~~ihvvd   85 (122)
T 1t0y_A            6 VYDLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHAVD   85 (122)
T ss_dssp             EEEEEEEESSCCSCEEEEEETTSBHHHHHHHHHHHHCCCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEEEEEE
T ss_pred             EEEEEEEECCCCccEEEEeCCCCcHHHHHHHHHHHhCCCHHHeEEEEecCCCccccccCCCcCCHHHCCCCCCCEEEEEe
Confidence            356667765443 688999999999999999999999999999999977   3   2 4799999999999999999875

>3a4r_A Nfatc2-interacting protein; ubiquitin fold, coiled coil, cytoplasm, methylation, nucleus, transcription; 1.00A {Mus musculus} PDB: 3a4s_C 3rd2_A

Probab=99.53  E-value=7.4e-14  Score=83.08  Aligned_cols=72  Identities=17%  Similarity=0.373  Sum_probs=68.3

Q ss_pred             cceeeeeeecCCc-eEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEE
Q 040824           75 GGTMIKVKTLTGK-EIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        75 ~~~~i~v~~~~~~-~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~  146 (154)
                      ..|.|.|+..+|+ .+.+.+.+++++..|+.+++++.|++++.++|+|.|..|.++.|++++++++||+|+++
T Consensus         6 ~~i~ikV~~~~g~~~i~~~i~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~~l~~~~Tp~~l~medgD~Idv~   78 (79)
T 3a4r_A            6 QELRLRVQGKEKHQMLEISLSPDSPLKVLMSHYEEAMGLSGHKLSFFFDGTKLSGKELPADLGLESGDLIEVW   78 (79)
T ss_dssp             CCEEEEEECSSTTCEEEEEECTTSCHHHHHHHHHHHHTCTTCCCEEEETTEECCSCCCHHHHTCCTTCEEEEE
T ss_pred             CEEEEEEEeCCCCEEEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEe
Confidence            4578999999996 89999999999999999999999999999999999999999999999999999999986

>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=99.53  E-value=7e-14  Score=85.19  Aligned_cols=76  Identities=17%  Similarity=0.403  Sum_probs=71.7

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecc
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~   76 (154)
                      |+|+|+..+|+.+.+++.+++++..|+++++++.|++++.++|+|+|+.|+++.|+++|++.++++|++.+...++
T Consensus         6 i~ikVk~~~g~~v~~~vk~~t~l~kl~~~y~~~~gi~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~q~gg   81 (91)
T 2io0_B            6 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGG   81 (91)
T ss_dssp             EEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHTTCCSTTEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCCCC
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEeccCC
Confidence            5789999999999999999999999999999999999999999999999999999999999999999999876544

>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=99.52  E-value=8e-14  Score=81.53  Aligned_cols=70  Identities=16%  Similarity=0.384  Sum_probs=67.3

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~   70 (154)
                      |+|+|+..+|+.+.+++.+++++..|+++++++.|++++.++|+|+|+.|.++.|+++|++.++++|++.
T Consensus         2 i~lkV~~~~g~~v~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~~l~~~~Tp~~l~medgD~Idv~   71 (72)
T 1wm3_A            2 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVF   71 (72)
T ss_dssp             EEEEEECTTSCEEEEEECTTSCTHHHHHHHHHHHTCCTTTCEEEETTEECCTTCCTTTTTCCTTEEEEEE
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEE
Confidence            6799999999999999999999999999999999999999999999999999999999999999999875

>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative, hydrolase; NMR {Mus musculus}

Probab=99.50  E-value=4.2e-14  Score=85.58  Aligned_cols=70  Identities=20%  Similarity=0.337  Sum_probs=61.5

Q ss_pred             eeeeeeecCCceEEEe-eCCCchHHHHHHHHhhhcCCCCCceeEEEC--CeecC---CCCcccccccCCCCEEEEEE
Q 040824           77 TMIKVKTLTGKEIEID-IEPTDTIERIKERVEEKEGIPPVQQRLIYA--GKQLA---DDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~-v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~--g~~l~---d~~~L~~~~i~~~~~i~~~~  147 (154)
                      |.|+|+..+|+. .+. +++++||.+||+.|++.+|+|+++|+|+|.  ++.++   ++.+|++|||.+|++|++..
T Consensus         1 m~i~vr~~~G~~-~v~~l~~~~Tv~~Lk~~I~~~~gi~~~~qrL~~~~p~k~l~l~~~~~tL~~~gl~~g~~l~v~~   76 (86)
T 2kzr_A            1 WRVRCKAKGGTH-LLQGLSSRTRLRELQGQIAAITGIAPGSQRILVGYPPECLDLSDRDITLGDLPIQSGDMLIVEE   76 (86)
T ss_dssp             CCEEEEETTEEE-EECSCCTTCBHHHHHHHHHHHTCCCTTTCCCEESSCCCCCCCCCSSCBTTTSSCCTTCEEECCC
T ss_pred             CEEEEEcCCCCE-EeeecCCCCCHHHHHHHHHHHhCCCccceEEEeCCCCcccccCCCCCCHHHcCCCCCCEEEEEe
Confidence            678999999865 477 999999999999999999999999999976  47764   78899999999999998754

>2d07_B Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Homo sapiens} SCOP: d.15.1.1 PDB: 2rpq_A 2awt_A 2io3_B 2iyd_B 1u4a_A 2k1f_A

Probab=99.48  E-value=2.2e-13  Score=83.39  Aligned_cols=75  Identities=16%  Similarity=0.379  Sum_probs=69.6

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+..+|+.+.+++..++++..|+++++++.+++++.++|+|+|+.|.++.|+++|++.++++|++.+...+
T Consensus        18 i~ikV~~~~g~~i~~~v~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~~l~~~~Tp~dl~medgD~Idv~~~q~G   92 (93)
T 2d07_B           18 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTG   92 (93)
T ss_dssp             EEEEEECTTSCEEEEEEETTSCHHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECC--
T ss_pred             EEEEEECCCCCEEEEEEccCCHHHHHHHHHHHHhCCCccceEEEECCEEcCCCCCHHHcCCCCCCEEEEEeeccC
Confidence            578899889999999999999999999999999999999999999999999999999999999999999887543

>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative, hydrolase; NMR {Mus musculus}

Probab=99.48  E-value=4.3e-14  Score=85.54  Aligned_cols=71  Identities=24%  Similarity=0.352  Sum_probs=62.8

Q ss_pred             CEEEEEeCCCCEEEEE-EeCCCcHHHHHHHHHhHhCCCCCCeEEEEc--ceEec---cCceecccccccccceeeeee
Q 040824            1 MQIFVKTLTGKTITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFA--GKQLE---DGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~-v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~--g~~L~---d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      |+|+|+..+|+. .++ +++++||.+||++|++++++++++|+|.|+  ++.+.   ++.+|++||+.+|++|++...
T Consensus         1 m~i~vr~~~G~~-~v~~l~~~~Tv~~Lk~~I~~~~gi~~~~qrL~~~~p~k~l~l~~~~~tL~~~gl~~g~~l~v~~~   77 (86)
T 2kzr_A            1 WRVRCKAKGGTH-LLQGLSSRTRLRELQGQIAAITGIAPGSQRILVGYPPECLDLSDRDITLGDLPIQSGDMLIVEED   77 (86)
T ss_dssp             CCEEEEETTEEE-EECSCCTTCBHHHHHHHHHHHTCCCTTTCCCEESSCCCCCCCCCSSCBTTTSSCCTTCEEECCCC
T ss_pred             CEEEEEcCCCCE-EeeecCCCCCHHHHHHHHHHHhCCCccceEEEeCCCCcccccCCCCCCHHHcCCCCCCEEEEEeC
Confidence            889999999964 477 999999999999999999999999999986  47764   678999999999999987754

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster}

Probab=99.46  E-value=9.6e-14  Score=102.70  Aligned_cols=72  Identities=28%  Similarity=0.451  Sum_probs=64.9

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEE---ECCeecCCCCcccccccCCCCEEEEEEe
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI---YAGKQLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~---~~g~~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      .+.++|+. +|+.+.+++++++||++||++|++.+|+|+++|+|+   |+|+.++|+.+|++|+|++|++|+++..
T Consensus         5 ~i~i~Vk~-~g~~~~v~v~~~~Tv~~lK~~I~~~tgVpp~~QkLi~~k~~Gk~l~D~~~L~~~~ik~g~~l~L~gs   79 (320)
T 3shq_A            5 EVVVIVKW-SGKEYPVDLTDQDTVEVLRHEIFRKTQVRPERQKLLNLKYKGKTAADNVKISALELKPNFKLMMVGS   79 (320)
T ss_dssp             EEEEEEEE-TTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGCEETTCBSSSSBCCTTSBTTSSCCC--CEEEEECC
T ss_pred             eEEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEeecccCCcccCccccHHHcCCCCCCEEEEEcc
Confidence            46788887 788999999999999999999999999999999999   8999999999999999999999988743

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster}

Probab=99.45  E-value=7.5e-14  Score=103.27  Aligned_cols=74  Identities=22%  Similarity=0.437  Sum_probs=66.5

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEE---EcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI---FAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~---~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+. +|+.+.+++++++||++||++|++.+|+||++|+|+   |.|+.|+|+.+|++|+|++|++|+++-+...
T Consensus         6 i~i~Vk~-~g~~~~v~v~~~~Tv~~lK~~I~~~tgVpp~~QkLi~~k~~Gk~l~D~~~L~~~~ik~g~~l~L~gs~~~   82 (320)
T 3shq_A            6 VVVIVKW-SGKEYPVDLTDQDTVEVLRHEIFRKTQVRPERQKLLNLKYKGKTAADNVKISALELKPNFKLMMVGSTEA   82 (320)
T ss_dssp             EEEEEEE-TTEEEEEEEETTSBHHHHHHHHHHHHCCCGGGCEETTCBSSSSBCCTTSBTTSSCCC--CEEEEECCCC-
T ss_pred             EEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEeecccCCcccCccccHHHcCCCCCCEEEEEccchh
Confidence            5788995 789999999999999999999999999999999999   8999999999999999999999999877654

>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=99.44  E-value=9e-13  Score=83.04  Aligned_cols=77  Identities=22%  Similarity=0.435  Sum_probs=72.5

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecC
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRG  151 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~g  151 (154)
                      ..+.|.|+..+|+.+.|.+.+++++..|+..++++.|+++..++++|.|..|.++.|++++++++||+|+++..+.|
T Consensus        39 ~~I~LKV~~qdg~ev~fkIk~tt~L~KLm~aY~er~Gl~~~~irFlFDG~rI~~~~TP~dL~MEDgD~IdV~~~Q~G  115 (115)
T 3kyd_D           39 EYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQCG  115 (115)
T ss_dssp             CEEEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHHTCCTTSEEEEETTEECCTTCCTTTTTCCTTCEEEEEECCCC
T ss_pred             CeEEEEEEcCCCCEEEEEEccCChHHHHHHHHHHHhCCChhhEEEEECCeECCCCCCHHHcCCCCCCEEEEEeeccC
Confidence            34788888888999999999999999999999999999999999999999999999999999999999999998865

>3a4r_A Nfatc2-interacting protein; ubiquitin fold, coiled coil, cytoplasm, methylation, nucleus, transcription; 1.00A {Mus musculus} PDB: 3a4s_C 3rd2_A

Probab=99.44  E-value=5.8e-13  Score=79.16  Aligned_cols=70  Identities=10%  Similarity=0.274  Sum_probs=66.5

Q ss_pred             CEEEEEeCCCC-EEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeee
Q 040824            1 MQIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (154)
Q Consensus         1 m~v~v~~~~~~-~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~   70 (154)
                      |+|+|+..+|+ .+.+++.+++++..|+++++++.|++++.++|+|+|+.|.++.|+++|++.++++|++.
T Consensus         8 i~ikV~~~~g~~~i~~~i~~~t~l~kl~~~y~~~~gi~~~~~rf~fdG~~l~~~~Tp~~l~medgD~Idv~   78 (79)
T 3a4r_A            8 LRLRVQGKEKHQMLEISLSPDSPLKVLMSHYEEAMGLSGHKLSFFFDGTKLSGKELPADLGLESGDLIEVW   78 (79)
T ss_dssp             EEEEEECSSTTCEEEEEECTTSCHHHHHHHHHHHHTCTTCCCEEEETTEECCSCCCHHHHTCCTTCEEEEE
T ss_pred             EEEEEEeCCCCEEEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEe
Confidence            57899999995 89999999999999999999999999999999999999999999999999999999874

>1wz0_A Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-like molecule, structural genomics, sentrin2, NPPFSA; NMR {Homo sapiens} SCOP: d.15.1.1

Probab=99.44  E-value=3.5e-13  Score=83.97  Aligned_cols=75  Identities=15%  Similarity=0.352  Sum_probs=70.8

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+..+|+.+.++|..++++..|+++++++.+++++.++|+|+|+.|.++.|+.+|++.++++|++.+...+
T Consensus        25 I~IkVk~~~g~~i~~kVk~~t~l~kL~~~y~ek~gi~~~~~rf~FdG~~l~~~~Tp~dl~medgD~Idv~~~q~G   99 (104)
T 1wz0_A           25 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTS   99 (104)
T ss_dssp             EEEEEECSSSCEEEEEECTTSCHHHHHHHHHHHHTCCTTTSCEESSSSBCCTTSCTTTTTCCTTEEEEECCCCCC
T ss_pred             EEEEEECCCCCEEEEEEcCCChHHHHHHHHHHHhCCCcceEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEeccC
Confidence            578999999999999999999999999999999999999999999999999999999999999999999887654

>2k8h_A Small ubiquitin protein; SUMO, post-translational modifier, signaling protein; NMR {Trypanosoma brucei}

Probab=99.42  E-value=3.1e-13  Score=84.95  Aligned_cols=77  Identities=16%  Similarity=0.410  Sum_probs=72.2

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecce
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGT   77 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~~   77 (154)
                      |+|+|+..+|+.+.+++.+++++..|+++++++.+++++.++|+|+|+.|.++.|+++|++.++++|++.+...+++
T Consensus        27 I~IkVk~~~g~~i~fkVk~~t~l~kL~~ay~ek~gi~~~~~rfiFdG~~L~~~~Tp~dl~mEDgD~Idv~~~q~Gg~  103 (110)
T 2k8h_A           27 VAVKVVNADGAEMFFRIKSRTALKKLIDTYCKKQGISRNSVRFLFDGTPIDETKTPEELGMEDDDVIDAMVEQTGGL  103 (110)
T ss_dssp             EEEEEEETTSCCEEEEECTTSSHHHHHHHHHHHHTCCSSSCEEESSSCBCCSSSHHHHHHCSSEEEEEEECCCCCC-
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEEEcccCcc
Confidence            57899999999999999999999999999999999999999999999999999999999999999999998876654

>2eke_C Ubiquitin-like protein SMT3; UBC9, SUMO binding motif, SBM, ligase/protein binding complex; 1.90A {Saccharomyces cerevisiae} SCOP: d.15.1.1

Probab=99.41  E-value=1e-12  Score=81.96  Aligned_cols=74  Identities=12%  Similarity=0.314  Sum_probs=68.7

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+. +|+...+++..++++..|+++++++.+++++.++|+|+|+.|.++.|+++|++.++++|++.+...+
T Consensus        32 I~IkV~~-~g~~i~fkIk~tt~l~kL~~ay~ek~gi~~~~~rF~FdG~rl~~~~Tp~dl~medgD~Idv~~~q~G  105 (106)
T 2eke_C           32 INLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIG  105 (106)
T ss_dssp             EEEEEEC-SSCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECC--
T ss_pred             EEEEEec-CCcEEEEEeCCCCHHHHHHHHHHHHhCCCcccEEEEECCeEcCCCCCHHHcCCCCCCEEEEEeeccc
Confidence            5788998 8999999999999999999999999999999999999999999999999999999999999887543

>1wjn_A Tubulin-folding protein TBCE; ubiquitin-like domain, progressive motor neuropathy, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.38  E-value=2.9e-12  Score=79.14  Aligned_cols=74  Identities=19%  Similarity=0.262  Sum_probs=61.8

Q ss_pred             eeeeeee---cCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECC-------eec-CCCCcccccccCCCCEEEE
Q 040824           77 TMIKVKT---LTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAG-------KQL-ADDKTARDYNIEGGSVLHL  145 (154)
Q Consensus        77 ~~i~v~~---~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g-------~~l-~d~~~L~~~~i~~~~~i~~  145 (154)
                      +.|.|+.   .++..+...+++++||++||.+|++.+|+|+..|+|.|.+       ..| +|..+|++|++.+|++|+|
T Consensus        10 v~l~I~~~~~~~~~~~e~~l~~~~TV~~LK~~i~~~~gip~~~q~L~~~~~~~~~~~~~L~~d~~~L~~y~i~~G~~I~V   89 (97)
T 1wjn_A           10 LTLKIKCSNQPERQILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCLLV   89 (97)
T ss_dssp             EEEEEEESSCSSSCCEEEEEETTSBHHHHHHHHHTTTTCCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTCCTTCEEEE
T ss_pred             EEEEEEecCCCCCcEEEEECCCCCCHHHHHHHHHHHHCCChhHeEEEEEcCCCCceeeccCCCcccHhhcCCCCCCEEEE
Confidence            4455554   3677889999999999999999999999999999999763       124 6889999999999999999


Q ss_pred             EEeec
Q 040824          146 VLALR  150 (154)
Q Consensus       146 ~~~~~  150 (154)
                      ....+
T Consensus        90 ~d~~p   94 (97)
T 1wjn_A           90 RWSGP   94 (97)
T ss_dssp             ECCSS
T ss_pred             EecCC
Confidence            87543

>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=99.36  E-value=1.8e-12  Score=87.78  Aligned_cols=79  Identities=22%  Similarity=0.345  Sum_probs=73.7

Q ss_pred             ecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           74 RGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        74 ~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      ...+.|.|+. +|+.+.|.|.+++++..|+..++++.|+++..++++|+|..|.++.|++++++.+||+|+++..+.||.
T Consensus        55 ~e~InLKVk~-dG~eV~FKIKrtTpL~KLmeAYcERqGL~~~sIRFLFDGqRI~~ddTPeDLdMEDGDtIDV~leQ~GG~  133 (207)
T 3tix_A           55 ETHINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLTFLYDGIEIQADQTPEDLDMEDNDIIEAHREQIGGL  133 (207)
T ss_dssp             CCEEEEEEEC-SSCEEEEEEETTSCTHHHHHHHHHHTTCCGGGSCEEETTEECCSSCCTTTTTCCTTEEEEECCCCCTTG
T ss_pred             CCcEEEEEec-CCCEEEEEEccCChHHHHHHHHHHHhCCCcccEEEEECCeecCCCCCHHHcCCCCCCEEEEEEeccCCC
Confidence            3447778864 888999999999999999999999999999999999999999999999999999999999999999984

>3pge_A SUMO-modified proliferating cell nuclear antigen; DNA replication, DNA binding protein; 2.80A {Saccharomyces cerevisiae}

Probab=99.35  E-value=5e-12  Score=87.09  Aligned_cols=79  Identities=24%  Similarity=0.411  Sum_probs=73.4

Q ss_pred             ecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           74 RGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        74 ~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      ..-++|.|+. +|+.+.|.+.+++++..|+..++++.|+++..++++|.|+.+.++.|++++++.+||+|+++..+.||.
T Consensus        27 ~~~I~LkV~~-~g~~v~fkIk~~t~l~kL~~ay~er~Gi~~~~~RF~FdG~rI~~~~TP~dL~MEdgD~Idv~~~q~gg~  105 (200)
T 3pge_A           27 ETHINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGG  105 (200)
T ss_dssp             CCCEEEEEEC-SSCEEEEEECTTSCTHHHHHHHHHHHSSCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCSCCC
T ss_pred             CCeEEEEEec-CCCEEEEEEecCCHHHHHHHHHHHHhCCChhhEEEEECCEEcCCCCCHHHcCCCCCCEEEEEeccCcCc
Confidence            3446777864 888999999999999999999999999999999999999999999999999999999999999999983

>1wjn_A Tubulin-folding protein TBCE; ubiquitin-like domain, progressive motor neuropathy, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1

Probab=99.33  E-value=6.7e-12  Score=77.48  Aligned_cols=71  Identities=17%  Similarity=0.238  Sum_probs=60.4

Q ss_pred             EEEEEe---CCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcc-------eEe-ccCceecccccccccceeee
Q 040824            2 QIFVKT---LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG-------KQL-EDGRTLADYNIQKESTLHLV   70 (154)
Q Consensus         2 ~v~v~~---~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g-------~~L-~d~~~l~~~~i~~~~~i~l~   70 (154)
                      +|+|+.   .+++.+..++++++||++||.+|+..+|+|+..|+|.|.+       ..| +|..+|++|++.+|++|++.
T Consensus        11 ~l~I~~~~~~~~~~~e~~l~~~~TV~~LK~~i~~~~gip~~~q~L~~~~~~~~~~~~~L~~d~~~L~~y~i~~G~~I~V~   90 (97)
T 1wjn_A           11 TLKIKCSNQPERQILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCLLVR   90 (97)
T ss_dssp             EEEEEESSCSSSCCEEEEEETTSBHHHHHHHHHTTTTCCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTCCTTCEEEEE
T ss_pred             EEEEEecCCCCCcEEEEECCCCCCHHHHHHHHHHHHCCChhHeEEEEEcCCCCceeeccCCCcccHhhcCCCCCCEEEEE
Confidence            466665   3677899999999999999999999999999999999862       225 56779999999999999887


Q ss_pred             ee
Q 040824           71 LR   72 (154)
Q Consensus        71 ~~   72 (154)
                      ..
T Consensus        91 d~   92 (97)
T 1wjn_A           91 WS   92 (97)
T ss_dssp             CC
T ss_pred             ec
Confidence            64

>3v7o_A Minor nucleoprotein VP30; ssgcid, seattle structural genomics center for infectious disease, SMT, transcription; 2.25A {Reston ebolavirus}

Probab=99.24  E-value=7e-13  Score=90.94  Aligned_cols=83  Identities=22%  Similarity=0.338  Sum_probs=1.4

Q ss_pred             eeeeecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEee
Q 040824           70 VLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        70 ~~~~~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      ...+...|.|.| ..+|+.+.|.+.+++++..|++.++++.|+++..++++|+|..+.++.|++++++++||+|+++..+
T Consensus        15 ~~~p~e~InLKV-~qdGseV~FKIKrtTpL~KLM~AYcERqGLs~~siRFLFDGqRI~dddTPadL~MEDGDtIDV~leQ   93 (227)
T 3v7o_A           15 EVKPETHINLKV-SDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQ   93 (227)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCCCCCeEEEEE-eCCCCEEEEEEccCChHHHHHHHHHHHhCCCccceEEEECCEecCCCCCHHHcCCCCCCEEEEEecc
Confidence            344455678888 6688899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 040824          150 RGGG  153 (154)
Q Consensus       150 ~gg~  153 (154)
                      .||.
T Consensus        94 ~GG~   97 (227)
T 3v7o_A           94 IGGL   97 (227)
T ss_dssp             --CC
T ss_pred             cCCc
Confidence            9995

>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=99.23  E-value=7.9e-11  Score=74.17  Aligned_cols=73  Identities=16%  Similarity=0.408  Sum_probs=68.5

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |+|+|+..+|....+.|..++++..|+..+.++.|++++.++++|+|+.|+++.|..++++.++++|.+....
T Consensus        41 I~LKV~~qdg~ev~fkIk~tt~L~KLm~aY~er~Gl~~~~irFlFDG~rI~~~~TP~dL~MEDgD~IdV~~~Q  113 (115)
T 3kyd_D           41 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQ  113 (115)
T ss_dssp             EEEEEECTTSCEEEEEEETTSCTHHHHHHHHHHHTCCTTSEEEEETTEECCTTCCTTTTTCCTTCEEEEEECC
T ss_pred             EEEEEEcCCCCEEEEEEccCChHHHHHHHHHHHhCCChhhEEEEECCeECCCCCCHHHcCCCCCCEEEEEeec
Confidence            4688888889999999999999999999999999999999999999999999999999999999999987653

>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=99.18  E-value=3.3e-10  Score=65.39  Aligned_cols=71  Identities=15%  Similarity=0.261  Sum_probs=64.4

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCC-ceeEEECCeecCCCCcccccccCCCCEEEEEE
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPV-QQRLIYAGKQLADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~-~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      +.+.++......+.+.++++.+|.+|.+..+.+.++|++ ..+|.|.|..|+.+.++.+|++.+||.|.+++
T Consensus        10 ~~~~~~~~~~~dl~f~I~~~t~v~kLi~ayc~~~~I~~~~~IrllFDGdRLdp~~tp~DlemeD~D~IDvmL   81 (82)
T 3goe_A           10 ITLLLRSSKSEDLRLSIPVDFTVKDLIKRYCTEVKISFHERIRLEFEGEWLDPNDQVQSTELEDEDQVSVVL   81 (82)
T ss_dssp             EEEEEEESSSCCEEEEEETTSBHHHHHHHHHHHHTCCCCTTCEEEETTEECCTTSBGGGSSCCTTCEEEEEC
T ss_pred             HHHhhhccCCCCeEEEecCCCCHHHHHHHHHHHcCCCcCceEEEEEcCcccCccCChhhhCCcCCceeeeee
Confidence            345556666677999999999999999999999999999 89999999999999999999999999999875

>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=99.13  E-value=6.6e-10  Score=64.15  Aligned_cols=70  Identities=16%  Similarity=0.316  Sum_probs=64.5

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCC-CeEEEEcceEeccCceecccccccccceeeee
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD-QQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~-~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~   71 (154)
                      .+.++......+.+++.++++|.+|......+.+++++ ..+|.|.|..|+++.++.+|++.+++.|.+.+
T Consensus        11 ~~~~~~~~~~dl~f~I~~~t~v~kLi~ayc~~~~I~~~~~IrllFDGdRLdp~~tp~DlemeD~D~IDvmL   81 (82)
T 3goe_A           11 TLLLRSSKSEDLRLSIPVDFTVKDLIKRYCTEVKISFHERIRLEFEGEWLDPNDQVQSTELEDEDQVSVVL   81 (82)
T ss_dssp             EEEEEESSSCCEEEEEETTSBHHHHHHHHHHHHTCCCCTTCEEEETTEECCTTSBGGGSSCCTTCEEEEEC
T ss_pred             HHhhhccCCCCeEEEecCCCCHHHHHHHHHHHcCCCcCceEEEEEcCcccCccCChhhhCCcCCceeeeee
Confidence            45667776778999999999999999999999999999 99999999999999999999999999998765

>3pge_A SUMO-modified proliferating cell nuclear antigen; DNA replication, DNA binding protein; 2.80A {Saccharomyces cerevisiae}

Probab=99.07  E-value=1.9e-09  Score=74.22  Aligned_cols=74  Identities=12%  Similarity=0.314  Sum_probs=69.0

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+. +|+...+.|..++++..|+..+.++.|++++.++++|+|+.|.++.|..++++.++++|++.....+
T Consensus        30 I~LkV~~-~g~~v~fkIk~~t~l~kL~~ay~er~Gi~~~~~RF~FdG~rI~~~~TP~dL~MEdgD~Idv~~~q~g  103 (200)
T 3pge_A           30 INLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIG  103 (200)
T ss_dssp             EEEEEEC-SSCEEEEEECTTSCTHHHHHHHHHHHSSCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCSC
T ss_pred             EEEEEec-CCCEEEEEEecCCHHHHHHHHHHHHhCCChhhEEEEECCEEcCCCCCHHHcCCCCCCEEEEEeccCc
Confidence            4678874 8899999999999999999999999999999999999999999999999999999999999988654

>2jxx_A Nfatc2-interacting protein; nuclear factor of activated T-cells, cytoplasmic 2- interacting protein, ubiquitin like homologue; NMR {Homo sapiens}

Probab=99.06  E-value=1.2e-09  Score=66.92  Aligned_cols=72  Identities=14%  Similarity=0.344  Sum_probs=66.8

Q ss_pred             cceeeeeeecCCc-eEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEE
Q 040824           75 GGTMIKVKTLTGK-EIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        75 ~~~~i~v~~~~~~-~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~  146 (154)
                      ..+.|.|+..+++ .+.+.+..++++..|....+++.|+++...+++|.|..+..+.|..++++++||+|.++
T Consensus        24 ~~I~LkV~~~dg~~~v~fkIk~~t~l~kLm~aY~~~~g~~~~~vrF~FDG~rI~~~~TP~dLdMEDgD~IDv~   96 (97)
T 2jxx_A           24 QQLQLRVQGKEKHQTLEVSLSRDSPLKTLMSHYEEAMGLSGRKLSFFFDGTKLSGRELPADLGMESGDLIEVW   96 (97)
T ss_dssp             SEEEEEEEESSSSCEEEEEEETTSCHHHHHHHHHHHTTCSSSCCEEEETTEECCSCSCHHHHTCCTTEEEEEE
T ss_pred             CeEEEEEEcCCCCEEEEEEECCCChHHHHHHHHHHHHCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEe
Confidence            4477888888885 78999999999999999999999999999999999999999999999999999999885

>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=99.02  E-value=8.7e-10  Score=74.75  Aligned_cols=75  Identities=12%  Similarity=0.318  Sum_probs=69.9

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecc
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~   76 (154)
                      |+|+|+. +|....+.|..++++..|+..+.++.+++++.++++|+|+.|+++.|..++++.++++|++.+...++
T Consensus        58 InLKVk~-dG~eV~FKIKrtTpL~KLmeAYcERqGL~~~sIRFLFDGqRI~~ddTPeDLdMEDGDtIDV~leQ~GG  132 (207)
T 3tix_A           58 INLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLTFLYDGIEIQADQTPEDLDMEDNDIIEAHREQIGG  132 (207)
T ss_dssp             EEEEEEC-SSCEEEEEEETTSCTHHHHHHHHHHTTCCGGGSCEEETTEECCSSCCTTTTTCCTTEEEEECCCCCTT
T ss_pred             EEEEEec-CCCEEEEEEccCChHHHHHHHHHHHhCCCcccEEEEECCeecCCCCCHHHcCCCCCCEEEEEEeccCC
Confidence            4678864 88999999999999999999999999999999999999999999999999999999999999987765

>2pjh_A Protein NPL4, nuclear protein localization protein 4 homolog; UFD1, NPL4, AAA, protein binding, transport protein; NMR {Mus musculus}

Probab=99.00  E-value=4.5e-10  Score=66.68  Aligned_cols=70  Identities=17%  Similarity=0.267  Sum_probs=58.3

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCee---c--CCCCcccccccCCCCEEEEE
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQ---L--ADDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~---l--~d~~~L~~~~i~~~~~i~~~  146 (154)
                      .|.|.++..+| ++.+++++++|+.+|+++|++.++++++.+.+.+...+   +  ..+.+|+++|+++||+|++.
T Consensus         4 ~m~lRvrs~~G-~~Ri~v~~~~t~~~L~~~I~~~~~i~~~~~~l~~~~~p~~~l~~~~~~~l~~lgl~hGd~l~l~   78 (80)
T 2pjh_A            4 SIIIRVQSPDG-VKRITATKRETAATFLKKVAKEFGFQNNGFSVYINRNKTGEITASSSKSLHLLKIKHGDLLFLF   78 (80)
T ss_dssp             CCCCEEECSSE-EEECCCCSSCCHHHHHHHHHHHTCCCTTTCCCCCSCCGGGGSSSCCCCTTTTTCCCTTCCEEC-
T ss_pred             cEEEEEECCCC-CEEEEcCCcChHHHHHHHHHHHcCCCCCcceEEecCCCCCcccCCCCCCHHHcCCCCCCEEEEe
Confidence            47888999887 67788999999999999999999999888877644332   3  37789999999999999864

>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=99.00  E-value=1.6e-09  Score=75.65  Aligned_cols=83  Identities=22%  Similarity=0.357  Sum_probs=73.8

Q ss_pred             eeeeeecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEe
Q 040824           69 LVLRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        69 l~~~~~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      ..+.+...+.|.|+. +++.+.|.+..++++..|+..+|++.|+++..++++|.|..+.++.|..++.+.++|+|.++..
T Consensus        14 ~~~~~~~~i~ikv~~-~~~~v~~~i~~~~~l~kl~~~y~~~~g~~~~~~~f~fdG~~i~~~~Tpk~L~~ed~d~I~~~~e   92 (209)
T 3uf8_A           14 PEVKPETHINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHRE   92 (209)
T ss_dssp             ----CCSEEEEEEEC-SSCEEEEEEETTSCTHHHHHHHHHHHTCCGGGCEEEETTEECCTTCCTTTTTCCTTEEEEEECS
T ss_pred             ceeCCCCcEEEEEEc-CCCEEEEEEeeCCHHHHHHHHHHHhhCCChheEEEEECCEeccCCCChHHhhhcccccchhhcc
Confidence            344455567788877 7778899999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCC
Q 040824          149 LRGG  152 (154)
Q Consensus       149 ~~gg  152 (154)
                      +.||
T Consensus        93 q~Gg   96 (209)
T 3uf8_A           93 QIGG   96 (209)
T ss_dssp             CTTC
T ss_pred             cccc
Confidence            9987

>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=98.96  E-value=8.7e-08  Score=72.30  Aligned_cols=143  Identities=20%  Similarity=0.269  Sum_probs=112.6

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhC----CCCCCeEEEE------cceEeccCceecccccccccceeeee
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG----IPPDQQRLIF------AGKQLEDGRTLADYNIQKESTLHLVL   71 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~----~~~~~q~L~~------~g~~L~d~~~l~~~~i~~~~~i~l~~   71 (154)
                      .++|... +-+..+.+++++||.+....|.++..    .+.++--|+.      .|++|.+..+|..|++.+++.+....
T Consensus         5 ~~~~~~~-~~~~~~~f~~~~~v~~~~~~i~e~~~~~~~~~~~~y~l~~~~~~~~~~~Wl~~~~~l~~y~~~~~~~l~~~~   83 (371)
T 3ivf_A            5 SLKISIG-NVVKTMQFEPSTMVYDACRMIRERIPEALAGPPNDFGLFLSDDDPKKGIWLEAGKALDYYMLRNGDTMEYRK   83 (371)
T ss_dssp             EEEEEET-TEEEEEEECTTCBHHHHHHHHHTTCGGGGSSCGGGEEEEECCSSGGGCEECCTTSBGGGGTCCTTCEEEEEE
T ss_pred             EEEEEec-ceeEEEEECCCCCHHHHHHHHHHhcccccCCCHHHCeEeccCCCCCcCEeccCCCCHHHhCCCCCceeeccC
Confidence            4566655 67788999999999999999988874    3567777877      46889999999999999999886554


Q ss_pred             eeecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCC-CCceeEEECC---------eecCCCCcccccccCCCC
Q 040824           72 RLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIP-PVQQRLIYAG---------KQLADDKTARDYNIEGGS  141 (154)
Q Consensus        72 ~~~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~-~~~~~l~~~g---------~~l~d~~~L~~~~i~~~~  141 (154)
                      +   .+.+.|..++|+...+.+++++|+.++-..++...|+. .+.+-|.+..         ..|+.++++.+.+.....
T Consensus        84 ~---~~~~~V~l~dg~~~~~~vd~~tt~~el~~~v~~~l~L~e~~~FgL~~~~~~~~~~~~~~wL~~~k~l~~q~~~~~~  160 (371)
T 3ivf_A           84 K---QRPLKIRMLDGTVKTIMVDDSKTVTDMLMTICARIGITNHDEYSLVRELMEEKKDDELNWLDHGRTLREQGVEEHE  160 (371)
T ss_dssp             C---EEEEEEECTTSCEEEEEEETTSBHHHHHHHHHHHTTCSCGGGEEEECCC----------CCCTTSBTGGGTCCTTC
T ss_pred             c---eeEEEEECcCCCEEEEEECCCCCHHHHHHHHHHHcCCCCccccEEEEEecccccchHHHHHhcCchhHhhCCCCCc
Confidence            4   46888999999999999999999999999999999974 4455665431         356667788887776666


Q ss_pred             EEEEEEe
Q 040824          142 VLHLVLA  148 (154)
Q Consensus       142 ~i~~~~~  148 (154)
                      .+++.++
T Consensus       161 ~l~frvK  167 (371)
T 3ivf_A          161 TLLLRRK  167 (371)
T ss_dssp             EEEEEEC
T ss_pred             eEEEEEE
Confidence            7665544

>2l76_A Nfatc2-interacting protein; ubiquitin-like domain, structural genomics, PSI-biology, Pro structure initiative; NMR {Homo sapiens}

Probab=98.94  E-value=7.5e-09  Score=62.43  Aligned_cols=71  Identities=11%  Similarity=0.324  Sum_probs=66.4

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEE
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      .+.|.|+. +|....|.+..++....|....|++.|+++...+++|.|..+.++.|..++++++||+|.+++
T Consensus        21 ~IniKV~~-~g~ev~FkIK~tt~l~KL~~aYc~r~gv~~~sirFlfDG~rI~~~~TP~~L~meD~DiID~~~   91 (95)
T 2l76_A           21 LFPLKIRC-RADLVRLPLRMSEPLQSVVDHMATHLGVSPSRILLLFGETELSPTATPRTLKLGVADIIDCVV   91 (95)
T ss_dssp             CEEEEEEC-SSSEEEEEECSSSCTHHHHHHHHHHHTSCGGGEEEEETTEECCTTSCHHHHTCCSSCEEEEEE
T ss_pred             eEEEEEEc-CCcEEEEEEecCChHHHHHHHHHhhcCCChhhEEEEECCcCCCCCCCHhHcCCCCCCEEEEEE
Confidence            37778885 688899999999999999999999999999999999999999999999999999999999875

>3ix6_A TS, tsase, thymidylate synthase; niaid, ssgcid, seattle structural center for infectious DISE brucellosis, orchitis, epididymitis, mastitis; 2.20A {Brucella melitensis}

Probab=98.90  E-value=1.5e-10  Score=86.16  Aligned_cols=81  Identities=22%  Similarity=0.383  Sum_probs=0.0

Q ss_pred             eeeecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeec
Q 040824           71 LRLRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALR  150 (154)
Q Consensus        71 ~~~~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~  150 (154)
                      ..+...+.|.|+. +|+...+.+..++++..|++.++++.|++++.++++|+|..+.++.|.+++++++||+|+++..+.
T Consensus        16 ~~~~~~I~LKV~~-~g~~v~FkIk~~t~l~kLm~aY~~r~G~~~~~~rFlFdG~rI~~~~TP~~L~MEDgD~Idv~~~Q~   94 (360)
T 3ix6_A           16 VKPETHINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQI   94 (360)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCCCCeEEEEEec-CCcEEEEEEecCChHHHHHHHHHHHhCCCcceEEEEECCeECCCCCChHHcCCCccchhhhhhccC
Confidence            3344557788877 677889999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CC
Q 040824          151 GG  152 (154)
Q Consensus       151 gg  152 (154)
                      ||
T Consensus        95 g~   96 (360)
T 3ix6_A           95 GG   96 (360)
T ss_dssp             --
T ss_pred             ch
Confidence            98

>2pjh_A Protein NPL4, nuclear protein localization protein 4 homolog; UFD1, NPL4, AAA, protein binding, transport protein; NMR {Mus musculus}

Probab=98.83  E-value=1.7e-09  Score=64.17  Aligned_cols=69  Identities=14%  Similarity=0.229  Sum_probs=57.1

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceE---e--ccCceecccccccccceeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQ---L--EDGRTLADYNIQKESTLHLV   70 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~---L--~d~~~l~~~~i~~~~~i~l~   70 (154)
                      |.|+|++.+| .+.+++++++|+.+|+++|.+.++++++.|.+++....   |  .++.+|+++|+++|+.+++.
T Consensus         5 m~lRvrs~~G-~~Ri~v~~~~t~~~L~~~I~~~~~i~~~~~~l~~~~~p~~~l~~~~~~~l~~lgl~hGd~l~l~   78 (80)
T 2pjh_A            5 IIIRVQSPDG-VKRITATKRETAATFLKKVAKEFGFQNNGFSVYINRNKTGEITASSSKSLHLLKIKHGDLLFLF   78 (80)
T ss_dssp             CCCEEECSSE-EEECCCCSSCCHHHHHHHHHHHTCCCTTTCCCCCSCCGGGGSSSCCCCTTTTTCCCTTCCEEC-
T ss_pred             EEEEEECCCC-CEEEEcCCcChHHHHHHHHHHHcCCCCCcceEEecCCCCCcccCCCCCCHHHcCCCCCCEEEEe
Confidence            5688998876 57888999999999999999999999988888754322   3  36779999999999999764

>2jxx_A Nfatc2-interacting protein; nuclear factor of activated T-cells, cytoplasmic 2- interacting protein, ubiquitin like homologue; NMR {Homo sapiens}

Probab=98.83  E-value=2.7e-08  Score=60.88  Aligned_cols=70  Identities=13%  Similarity=0.300  Sum_probs=64.3

Q ss_pred             CEEEEEeCCC-CEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeee
Q 040824            1 MQIFVKTLTG-KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (154)
Q Consensus         1 m~v~v~~~~~-~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~   70 (154)
                      +.|+|+..+| +.+.+.+..++++..|...+.++.+++++..+++|+|..+.++.|..++++.++++|.+.
T Consensus        26 I~LkV~~~dg~~~v~fkIk~~t~l~kLm~aY~~~~g~~~~~vrF~FDG~rI~~~~TP~dLdMEDgD~IDv~   96 (97)
T 2jxx_A           26 LQLRVQGKEKHQTLEVSLSRDSPLKTLMSHYEEAMGLSGRKLSFFFDGTKLSGRELPADLGMESGDLIEVW   96 (97)
T ss_dssp             EEEEEEESSSSCEEEEEEETTSCHHHHHHHHHHHTTCSSSCCEEEETTEECCSCSCHHHHTCCTTEEEEEE
T ss_pred             EEEEEEcCCCCEEEEEEECCCChHHHHHHHHHHHHCCCcccEEEEECCEEcCCCCCHHHcCCCCCCEEEEe
Confidence            4677888888 478999999999999999999999999999999999999999999999999999999763

>3v7o_A Minor nucleoprotein VP30; ssgcid, seattle structural genomics center for infectious disease, SMT, transcription; 2.25A {Reston ebolavirus}

Probab=98.81  E-value=4.4e-10  Score=77.18  Aligned_cols=76  Identities=13%  Similarity=0.318  Sum_probs=0.9

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecce
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGT   77 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~~   77 (154)
                      |+|+| ..+|+...++|..++++..|++.+.++.|++++.+++.|+|+.++++.|.+++++.++++|++.....++.
T Consensus        22 InLKV-~qdGseV~FKIKrtTpL~KLM~AYcERqGLs~~siRFLFDGqRI~dddTPadL~MEDGDtIDV~leQ~GG~   97 (227)
T 3v7o_A           22 INLKV-SDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGL   97 (227)
T ss_dssp             ---------------------------------------------------------------------------CC
T ss_pred             EEEEE-eCCCCEEEEEEccCChHHHHHHHHHHHhCCCccceEEEECCEecCCCCCHHHcCCCCCCEEEEEecccCCc
Confidence            56778 66888899999999999999999999999999999999999999999999999999999999998876653

>4da1_A Protein phosphatase 1K, mitochondrial; metal-ION-assisted catalysis, dehydrogenase phosphatase, hydrolase; 2.38A {Homo sapiens} PDB: 3qht_A 1l2n_A

Probab=98.70  E-value=1.7e-09  Score=82.15  Aligned_cols=78  Identities=22%  Similarity=0.375  Sum_probs=0.0

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      ..+.|.|+. +++...|.+..++++..|++.++++.|+++..++++|+|+.+.++.|.+++++++|++|.++..+.||.
T Consensus        29 ~~i~lkv~~-~~~~~~~~i~~~~~~~~l~~~y~~~~g~~~~~~~f~f~G~~i~~~~Tp~~l~med~d~i~~~~~q~gg~  106 (389)
T 4da1_A           29 THINLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQAPEDLDMEDNDIIEAHREQIGGE  106 (389)
T ss_dssp             -------------------------------------------------------------------------------
T ss_pred             CcEEEEEec-CCcEEEEEECCCChHHHHHHHHHHHhCCCcceEEEEECCEEcCCCCCHHHcCCCCCCEeeeeecccccc
Confidence            346677776 677888999999999999999999999999999999999999999999999999999999999999983

>2l76_A Nfatc2-interacting protein; ubiquitin-like domain, structural genomics, PSI-biology, Pro structure initiative; NMR {Homo sapiens}

Probab=98.69  E-value=8.5e-08  Score=57.83  Aligned_cols=72  Identities=14%  Similarity=0.280  Sum_probs=66.2

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      +.|+|+ .+|....+.+..++....|.+.+.++.|++++..+++|+|..++++.|..+.++.++++|.+....
T Consensus        22 IniKV~-~~g~ev~FkIK~tt~l~KL~~aYc~r~gv~~~sirFlfDG~rI~~~~TP~~L~meD~DiID~~~~~   93 (95)
T 2l76_A           22 FPLKIR-CRADLVRLPLRMSEPLQSVVDHMATHLGVSPSRILLLFGETELSPTATPRTLKLGVADIIDCVVLT   93 (95)
T ss_dssp             EEEEEE-CSSSEEEEEECSSSCTHHHHHHHHHHHTSCGGGEEEEETTEECCTTSCHHHHTCCSSCEEEEEECC
T ss_pred             EEEEEE-cCCcEEEEEEecCChHHHHHHHHHhhcCCChhhEEEEECCcCCCCCCCHhHcCCCCCCEEEEEEec
Confidence            467888 478889999999999999999999999999999999999999999999999999999999887643

>2al3_A TUG long isoform; TUG UBL1 insulin, endocytosis/exocytosis complex; NMR {Mus musculus} SCOP: d.15.1.2

Probab=98.66  E-value=1.8e-07  Score=55.94  Aligned_cols=76  Identities=17%  Similarity=0.278  Sum_probs=68.6

Q ss_pred             ecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEee
Q 040824           74 RGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        74 ~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      ..+|.+.|-..+++...+.+.++.++.++-+..++++|+++++..|.|+++.++-+.++.-.|+.+|+.+++....
T Consensus         7 ~~~m~v~Vl~~n~rr~~VKvtp~t~L~~VL~eaC~K~gl~~~~~~Lkh~~k~lDLSlpfRlsgLpnnAkLELv~~s   82 (90)
T 2al3_A            7 GGGSAVSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQDFNPSEYDLKFQRTVLDLSLQWRFANLPNNAKLEMVPVS   82 (90)
T ss_dssp             ---CCEEEECTTSCEEEECCCTTSBHHHHHHHHHHHTTCCGGGCEEEETTEEESSSCBHHHHCCCSSCEEEEECSS
T ss_pred             CCccEEEEEcCCCcEEEEEECCCCCHHHHHHHHHHHhCCChhhCeEEeCCEeccccceeEecCCCCCCEEEEEEcc
Confidence            3467888888899999999999999999999999999999999999999999999999999999999999987543

>3ix6_A TS, tsase, thymidylate synthase; niaid, ssgcid, seattle structural center for infectious DISE brucellosis, orchitis, epididymitis, mastitis; 2.20A {Brucella melitensis}

Probab=98.46  E-value=1.8e-08  Score=75.02  Aligned_cols=76  Identities=13%  Similarity=0.332  Sum_probs=0.4

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecce
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGT   77 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~~   77 (154)
                      ++|+|+. +|+...+++..++++..|++++.++.|++++.+++.|+|+.+.++.|.+++++.+|++|++.....++|
T Consensus        22 I~LKV~~-~g~~v~FkIk~~t~l~kLm~aY~~r~G~~~~~~rFlFdG~rI~~~~TP~~L~MEDgD~Idv~~~Q~g~~   97 (360)
T 3ix6_A           22 INLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGM   97 (360)
T ss_dssp             ----------------------------------------------------------------------------C
T ss_pred             EEEEEec-CCcEEEEEEecCChHHHHHHHHHHHhCCCcceEEEEECCeECCCCCChHHcCCCccchhhhhhccCchH
Confidence            4577776 567788999999999999999999999999999999999999999999999999999999998876654

>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=98.44  E-value=2e-06  Score=59.89  Aligned_cols=74  Identities=12%  Similarity=0.314  Sum_probs=67.4

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      +.|+|+. +++...+++..++++..|+++++++.|++++.++++|+|+.+.++.+..+.++.+++.|.+.....+
T Consensus        22 i~ikv~~-~~~~v~~~i~~~~~l~kl~~~y~~~~g~~~~~~~f~fdG~~i~~~~Tpk~L~~ed~d~I~~~~eq~G   95 (209)
T 3uf8_A           22 INLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIG   95 (209)
T ss_dssp             EEEEEEC-SSCEEEEEEETTSCTHHHHHHHHHHHTCCGGGCEEEETTEECCTTCCTTTTTCCTTEEEEEECSCTT
T ss_pred             EEEEEEc-CCCEEEEEEeeCCHHHHHHHHHHHhhCCChheEEEEECCEeccCCCChHHhhhcccccchhhccccc
Confidence            3577776 6778899999999999999999999999999999999999999999999999999999998877654

>4efo_A Serine/threonine-protein kinase TBK1; ubiquitin like domain, transferase; 1.77A {Homo sapiens}

Probab=98.43  E-value=1.4e-06  Score=52.75  Aligned_cols=64  Identities=22%  Similarity=0.266  Sum_probs=50.4

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeec--CCCCccccccc-CCCCEEEEEEe
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQL--ADDKTARDYNI-EGGSVLHLVLA  148 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l--~d~~~L~~~~i-~~~~~i~~~~~  148 (154)
                      .+..+.+.+.+++|+..+|++|++++|+|+++|+|+|.|+.+  +.+..-..|.- ....-|.++.+
T Consensus        22 ~a~~h~v~I~~~etv~~~ke~V~eqTgIp~~~Q~LL~eg~~l~l~p~~~a~~~p~Tt~~~Pl~L~s~   88 (94)
T 4efo_A           22 QMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLVLEPGRLAQHFPKTTEENPIFVVSL   88 (94)
T ss_dssp             TTEEEEEEEETTCBHHHHHHHHHHHHCCCGGGEEEEETTEEECCCTTCBGGGSCCCBTTBCEEEEEC
T ss_pred             cceEEEEEeccchHHHHHHHHHHHHhCCCHHHHHHHhCCCccccCCCCccccCCCCCCCCCEEEEec
Confidence            567789999999999999999999999999999999999754  45555555543 44455655544

>4efo_A Serine/threonine-protein kinase TBK1; ubiquitin like domain, transferase; 1.77A {Homo sapiens}

Probab=98.41  E-value=2.3e-06  Score=51.78  Aligned_cols=59  Identities=22%  Similarity=0.300  Sum_probs=46.4

Q ss_pred             EEEEeC-CCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEec--cCceeccccc
Q 040824            3 IFVKTL-TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE--DGRTLADYNI   61 (154)
Q Consensus         3 v~v~~~-~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~--d~~~l~~~~i   61 (154)
                      |+|-.. .+..+.+.+.+++|+..+|++|++++|+|++.|+|+|.|+.+.  ++.....|.-
T Consensus        15 vHVf~~~~a~~h~v~I~~~etv~~~ke~V~eqTgIp~~~Q~LL~eg~~l~l~p~~~a~~~p~   76 (94)
T 4efo_A           15 IHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLVLEPGRLAQHFPK   76 (94)
T ss_dssp             EEEEETTTTEEEEEEEETTCBHHHHHHHHHHHHCCCGGGEEEEETTEEECCCTTCBGGGSCC
T ss_pred             EEEEEcccceEEEEEeccchHHHHHHHHHHHHhCCCHHHHHHHhCCCccccCCCCccccCCC
Confidence            344333 4567889999999999999999999999999999999996654  4445555553

>2al3_A TUG long isoform; TUG UBL1 insulin, endocytosis/exocytosis complex; NMR {Mus musculus} SCOP: d.15.1.2

Probab=98.28  E-value=3.7e-06  Score=50.23  Aligned_cols=73  Identities=18%  Similarity=0.186  Sum_probs=67.8

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |.|.|-..+++...+.+.+++++.++-+...++++++++.-.|.|+++.|+-...+..-|+.+++.+.++...
T Consensus        10 m~v~Vl~~n~rr~~VKvtp~t~L~~VL~eaC~K~gl~~~~~~Lkh~~k~lDLSlpfRlsgLpnnAkLELv~~s   82 (90)
T 2al3_A           10 SAVSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQDFNPSEYDLKFQRTVLDLSLQWRFANLPNNAKLEMVPVS   82 (90)
T ss_dssp             CCEEEECTTSCEEEECCCTTSBHHHHHHHHHHHTTCCGGGCEEEETTEEESSSCBHHHHCCCSSCEEEEECSS
T ss_pred             cEEEEEcCCCcEEEEEECCCCCHHHHHHHHHHHhCCChhhCeEEeCCEeccccceeEecCCCCCCEEEEEEcc
Confidence            5788998999999999999999999999999999999999999999999999999999999999999887654

>2kc2_A Talin-1, F1; FERM, adhesion, cell membrane, cell projection, cytoplasm, cytoskeleton, membrane, phosphoprotein, structural protein; NMR {Mus musculus}

Probab=98.24  E-value=1.7e-06  Score=55.30  Aligned_cols=70  Identities=21%  Similarity=0.269  Sum_probs=56.8

Q ss_pred             eeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCC-------------------------------------ceeEE
Q 040824           78 MIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPV-------------------------------------QQRLI  120 (154)
Q Consensus        78 ~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~-------------------------------------~~~l~  120 (154)
                      .+.|+.++|+...+.|+.+.+|.+++..||.+.|++..                                     .++|-
T Consensus        13 ~LkV~llDg~~ktl~VD~S~~V~~lv~~Ic~kigI~n~~ey~L~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~k~kL~   92 (128)
T 2kc2_A           13 PLKIRMLDGTVKTIMVDDSKTVTDMLMTICARIGITNHDEYSLVRELMEEKKDEGTGTLRKDKTLLRDEKKMEKLKQKLH   92 (128)
T ss_dssp             EEEEECTTSCEEEEEEEECSSHHHHHHHHHHHHTCCCCSSEEEEEECCCCCCCCCSSCCSSSSSCSCCSCCSCSSCCSCC
T ss_pred             cEEEEcCCCCEEEEEeCCCcCHHHHHHHHHHHhCCCCcccccccccccccccccCchhhccccccccchhHHHHHHHHhc
Confidence            58889999999999999999999999999999998643                                     22221


Q ss_pred             E--CCeecCCCCcccccccCCCCEEEEEE
Q 040824          121 Y--AGKQLADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus       121 ~--~g~~l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      .  .+..|+++.||.++||..++++.+--
T Consensus        93 ~dd~~~WLD~srtL~EQGI~e~~tllLRr  121 (128)
T 2kc2_A           93 TDDELNWLDHGRTLREQGVEEHETLLLRR  121 (128)
T ss_dssp             CSSSEEEECSSSCHHHHTCCTTSEEEEEE
T ss_pred             ccCCCCcccCCCcHHHcCCCCCCEEEEEE
Confidence            1  12577889999999999999975543

>2kc2_A Talin-1, F1; FERM, adhesion, cell membrane, cell projection, cytoplasm, cytoskeleton, membrane, phosphoprotein, structural protein; NMR {Mus musculus}

Probab=98.24  E-value=2.7e-06  Score=54.34  Aligned_cols=70  Identities=27%  Similarity=0.386  Sum_probs=58.8

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCC-------------------------------------CeEEE
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD-------------------------------------QQRLI   44 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~-------------------------------------~q~L~   44 (154)
                      .++|+.++|...++.|+.+.+|++++..|.++.|++..                                     .|+|.
T Consensus        13 ~LkV~llDg~~ktl~VD~S~~V~~lv~~Ic~kigI~n~~ey~L~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~k~kL~   92 (128)
T 2kc2_A           13 PLKIRMLDGTVKTIMVDDSKTVTDMLMTICARIGITNHDEYSLVRELMEEKKDEGTGTLRKDKTLLRDEKKMEKLKQKLH   92 (128)
T ss_dssp             EEEEECTTSCEEEEEEEECSSHHHHHHHHHHHHTCCCCSSEEEEEECCCCCCCCCSSCCSSSSSCSCCSCCSCSSCCSCC
T ss_pred             cEEEEcCCCCEEEEEeCCCcCHHHHHHHHHHHhCCCCcccccccccccccccccCchhhccccccccchhHHHHHHHHhc
Confidence            48899999999999999999999999999999998854                                     34443


Q ss_pred             E--cceEeccCceecccccccccceeeee
Q 040824           45 F--AGKQLEDGRTLADYNIQKESTLHLVL   71 (154)
Q Consensus        45 ~--~g~~L~d~~~l~~~~i~~~~~i~l~~   71 (154)
                      .  ...+|++..+|.++|+.+++++.|-.
T Consensus        93 ~dd~~~WLD~srtL~EQGI~e~~tllLRr  121 (128)
T 2kc2_A           93 TDDELNWLDHGRTLREQGVEEHETLLLRR  121 (128)
T ss_dssp             CSSSEEEECSSSCHHHHTCCTTSEEEEEE
T ss_pred             ccCCCCcccCCCcHHHcCCCCCCEEEEEE
Confidence            2  23788999999999999999875544

>2bps_A YUKD protein; ubiquitin-like protein, ubiquitin; 2.7A {Bacillus subtilis}

Probab=98.19  E-value=5.7e-06  Score=48.68  Aligned_cols=69  Identities=14%  Similarity=0.233  Sum_probs=56.3

Q ss_pred             CEEEEEe--CCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCC-----CeEEEEcceEeccCceecccccccccceee
Q 040824            1 MQIFVKT--LTGKTITLEVESSDTIDNVKAKIQDKEGIPPD-----QQRLIFAGKQLEDGRTLADYNIQKESTLHL   69 (154)
Q Consensus         1 m~v~v~~--~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~-----~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l   69 (154)
                      +.|++..  ..++.+.++++...|+.+|++.+.+..+++..     ..+..-.+..|.++..|++|++.+|+.+.+
T Consensus         5 I~ITidl~~y~~~~~DLRIP~~~tvK~Li~~l~ea~~l~~~~~~~~~irv~NK~~~L~~~~~L~d~~ItnGD~Lei   80 (81)
T 2bps_A            5 IDITIDLKHYNGSVFDLRLSDYHPVKKVIDIAWQAQSVSMPPREGHWIRVVNKDKVFSGECKLSDCGITNGDRLEI   80 (81)
T ss_dssp             EEEEEECTTTTCCEEEEEEETTSBTTHHHHHHHHHSCCCSCCCTTCEEEEGGGTEEEETTSBTGGGTCCTTCEEEE
T ss_pred             EEEEEEeeccCCceEEEECCCchhHHHHHHHHHHHhCCCcCCCCCCEEEEecCCEEEcCCCEEeeCCcCCCCEEEE
Confidence            3566664  67899999999999999999999999886642     233335678999999999999999998854

>4da1_A Protein phosphatase 1K, mitochondrial; metal-ION-assisted catalysis, dehydrogenase phosphatase, hydrolase; 2.38A {Homo sapiens} PDB: 3qht_A 1l2n_A

Probab=98.15  E-value=2.6e-07  Score=70.12  Aligned_cols=74  Identities=12%  Similarity=0.324  Sum_probs=0.0

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecc
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~   76 (154)
                      .|+|+. ++....+++..++++..|+..+.++.+++++.+++.|+|+.+.++.|..++++.++++|.+.....++
T Consensus        32 ~lkv~~-~~~~~~~~i~~~~~~~~l~~~y~~~~g~~~~~~~f~f~G~~i~~~~Tp~~l~med~d~i~~~~~q~gg  105 (389)
T 4da1_A           32 NLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQAPEDLDMEDNDIIEAHREQIGG  105 (389)
T ss_dssp             ---------------------------------------------------------------------------
T ss_pred             EEEEec-CCcEEEEEECCCChHHHHHHHHHHHhCCCcceEEEEECCEEcCCCCCHHHcCCCCCCEeeeeeccccc
Confidence            466665 66778899999999999999999999999999999999999999999999999999999999876544

>2bps_A YUKD protein; ubiquitin-like protein, ubiquitin; 2.7A {Bacillus subtilis}

Probab=98.14  E-value=6.9e-06  Score=48.32  Aligned_cols=62  Identities=11%  Similarity=0.256  Sum_probs=53.0

Q ss_pred             cCCceEEEeeCCCchHHHHHHHHhhhcCCCCC-----ceeEEECCeecCCCCcccccccCCCCEEEE
Q 040824           84 LTGKEIEIDIEPTDTIERIKERVEEKEGIPPV-----QQRLIYAGKQLADDKTARDYNIEGGSVLHL  145 (154)
Q Consensus        84 ~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~-----~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~  145 (154)
                      -.++.+.++++...|+.+|...+.+.++++..     ..++.-++..|.++.+|++|++.+||.|.+
T Consensus        14 y~~~~~DLRIP~~~tvK~Li~~l~ea~~l~~~~~~~~~irv~NK~~~L~~~~~L~d~~ItnGD~Lei   80 (81)
T 2bps_A           14 YNGSVFDLRLSDYHPVKKVIDIAWQAQSVSMPPREGHWIRVVNKDKVFSGECKLSDCGITNGDRLEI   80 (81)
T ss_dssp             TTCCEEEEEEETTSBTTHHHHHHHHHSCCCSCCCTTCEEEEGGGTEEEETTSBTGGGTCCTTCEEEE
T ss_pred             cCCceEEEECCCchhHHHHHHHHHHHhCCCcCCCCCCEEEEecCCEEEcCCCEEeeCCcCCCCEEEE
Confidence            36889999999999999999999999997542     234446788999999999999999999976

>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=98.08  E-value=2.4e-05  Score=46.50  Aligned_cols=69  Identities=14%  Similarity=0.307  Sum_probs=58.9

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEE--ECCeec---CCCCcccccccCCCCEEEEE
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI--YAGKQL---ADDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~--~~g~~l---~d~~~L~~~~i~~~~~i~~~  146 (154)
                      ..|.|+.++|+.+.-.+..++|+.+|..-+.. .+.++..+.|.  |..+.+   +.+.||.+.|+.++++|.|-
T Consensus         8 ~~i~iRlpdG~r~~~~F~~~~tl~~v~~fv~~-~~~~~~~f~L~t~fPrk~l~~~d~~~TL~e~gL~p~a~L~ve   81 (84)
T 3qx1_A            8 SKLRIRTPSGEFLERRFLASNKLQIVFDFVAS-KGFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLE   81 (84)
T ss_dssp             EEEEEECTTSCEEEEEEETTSBHHHHHHHHHH-TTCCTTTEEEECSSSCCBGGGSCTTSBTTTTTCCSEEEEEEE
T ss_pred             EEEEEECCCCCEEEEEeCCCCCHHHHHHHHHH-cCCCCCCeEEEeCCCCCCCcCCCCCCCHHHCCCCCCCEEEEE
Confidence            56788889999888889999999999999987 57788888888  566777   45789999999999998764

>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=97.84  E-value=0.00013  Score=43.23  Aligned_cols=68  Identities=19%  Similarity=0.369  Sum_probs=57.0

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEE--EcceEec---cCceecccccccccceeee
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE---DGRTLADYNIQKESTLHLV   70 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~--~~g~~L~---d~~~l~~~~i~~~~~i~l~   70 (154)
                      +|.|+..+|+.+.-....++||.+|.+.|.. .+.++....|.  |..+.+.   .+.+|.+.|+.+.+++.+-
T Consensus         9 ~i~iRlpdG~r~~~~F~~~~tl~~v~~fv~~-~~~~~~~f~L~t~fPrk~l~~~d~~~TL~e~gL~p~a~L~ve   81 (84)
T 3qx1_A            9 KLRIRTPSGEFLERRFLASNKLQIVFDFVAS-KGFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLE   81 (84)
T ss_dssp             EEEEECTTSCEEEEEEETTSBHHHHHHHHHH-TTCCTTTEEEECSSSCCBGGGSCTTSBTTTTTCCSEEEEEEE
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHH-cCCCCCCeEEEeCCCCCCCcCCCCCCCHHHCCCCCCCEEEEE
Confidence            5789999999999999999999999999987 56677777887  5578774   4679999999999888654

>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=97.75  E-value=0.00023  Score=44.36  Aligned_cols=72  Identities=10%  Similarity=0.142  Sum_probs=60.7

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEE--ECCeecC---CCCcccccccCCCCEEEEEE
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI--YAGKQLA---DDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~--~~g~~l~---d~~~L~~~~i~~~~~i~~~~  147 (154)
                      ...|.|+.++|+.+.-.++.++|+.+|..-+....+.+...+.|+  |.-+.+.   .++||.+.|+.+.+++.+.-
T Consensus        13 ~t~IqIRlpdG~rl~~rF~~~~tl~~v~~fV~~~~~~~~~~f~L~t~fPrk~l~~~d~~~TL~elgL~psa~L~v~~   89 (109)
T 2dzk_A           13 IARIQFRLPDGSSFTNQFPSDAPLEEARQFAAQTVGNTYGNFSLATMFPRREFTREDYKRRLLDLELAPSASVVLLP   89 (109)
T ss_dssp             CEEEEEECSSSCEEEEEECTTSBHHHHHHHHHHHHTTSSCSCEEECSSSCCBCCTTTTTSBTGGGTCSSEEEEEEEC
T ss_pred             cEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHhccCCCCCceEEEcCCCCcCCcccccCCCHHHCCCCCceEEEEEE
Confidence            357888899999999999999999999999998888777788887  5667775   47899999999998886653

>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=97.74  E-value=0.00014  Score=46.35  Aligned_cols=71  Identities=15%  Similarity=0.265  Sum_probs=60.2

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEE--ECCeec---CCCCcccccccCCCCEEEEE
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI--YAGKQL---ADDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~--~~g~~l---~d~~~L~~~~i~~~~~i~~~  146 (154)
                      +...|.|+.++|..+.-.+..++|+.+|..-|... +.++..+.|+  |..+.+   +.+.||.+.|+.+.+.|.|.
T Consensus        42 ~~t~IqIRlPdG~rl~~rF~~~~tl~~V~~fV~~~-~~~~~~F~L~t~fPrk~l~~~d~~~TL~e~gL~psa~Liv~  117 (124)
T 1wj4_A           42 PKAQLMLRYPDGKREQITLPEQAKLLALVKHVQSK-GYPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQ  117 (124)
T ss_dssp             CEEEEEEECTTSCEEEEEEETTSCHHHHHHHHHHH-HCCTTTEEEECSSSCCEETSSCSSSCTTTTTCCSSBCCEEE
T ss_pred             CcEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHhc-CCCCCCeEEecCCCCcCCccCCCCCCHHHCCCCCceEEEEE
Confidence            44678889999999899999999999999999887 7788888887  667777   34789999999998887664

>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=97.51  E-value=0.00078  Score=41.88  Aligned_cols=71  Identities=17%  Similarity=0.269  Sum_probs=59.0

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEE--EcceEec--c-Cceecccccccccceeeeee
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE--D-GRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~--~~g~~L~--d-~~~l~~~~i~~~~~i~l~~~   72 (154)
                      +|.|+..+|..+.-+.+.++||.+|.+.|....+.+...-.|.  |..+.+.  | +.+|.+.|+.+.+.+.+...
T Consensus        15 ~IqIRlpdG~rl~~rF~~~~tl~~v~~fV~~~~~~~~~~f~L~t~fPrk~l~~~d~~~TL~elgL~psa~L~v~~~   90 (109)
T 2dzk_A           15 RIQFRLPDGSSFTNQFPSDAPLEEARQFAAQTVGNTYGNFSLATMFPRREFTREDYKRRLLDLELAPSASVVLLPA   90 (109)
T ss_dssp             EEEEECSSSCEEEEEECTTSBHHHHHHHHHHHHTTSSCSCEEECSSSCCBCCTTTTTSBTGGGTCSSEEEEEEECC
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHhccCCCCCceEEEcCCCCcCCcccccCCCHHHCCCCCceEEEEEEC
Confidence            5789999999999999999999999999998877766666676  5677776  3 56999999999888866543

>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=97.45  E-value=0.00088  Score=42.62  Aligned_cols=68  Identities=21%  Similarity=0.372  Sum_probs=56.9

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEE--EcceEe--cc-Cceecccccccccceeee
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQL--ED-GRTLADYNIQKESTLHLV   70 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~--~~g~~L--~d-~~~l~~~~i~~~~~i~l~   70 (154)
                      +|.|+..+|..+.-++..++||.+|.+.|... +.++..-.|.  |..+.+  .| +.+|.+.++.+.+.+.+.
T Consensus        45 ~IqIRlPdG~rl~~rF~~~~tl~~V~~fV~~~-~~~~~~F~L~t~fPrk~l~~~d~~~TL~e~gL~psa~Liv~  117 (124)
T 1wj4_A           45 QLMLRYPDGKREQITLPEQAKLLALVKHVQSK-GYPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQ  117 (124)
T ss_dssp             EEEEECTTSCEEEEEEETTSCHHHHHHHHHHH-HCCTTTEEEECSSSCCEETSSCSSSCTTTTTCCSSBCCEEE
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHhc-CCCCCCeEEecCCCCcCCccCCCCCCHHHCCCCCceEEEEE
Confidence            58899999999999999999999999999876 6666677776  668888  33 679999999988887654

>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=97.29  E-value=0.0013  Score=40.91  Aligned_cols=70  Identities=13%  Similarity=0.168  Sum_probs=57.4

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEE--ECCeecC--CCCcccccccCCCCEEEEE
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI--YAGKQLA--DDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~--~~g~~l~--d~~~L~~~~i~~~~~i~~~  146 (154)
                      ...|.|+..+|+.+.-.+..++|+.+|..-+... +..+..+.|+  |..+.+.  .+.||.+.|+.+.++|.|-
T Consensus        23 ~~~IqiRlpdG~r~~rrF~~~~tl~~v~~fv~~~-~~~~~~f~L~t~fPrk~l~~d~~~TL~e~gL~p~a~L~Ve   96 (109)
T 2cr5_A           23 VVTVALRCPNGRVLRRRFFKSWNSQVLLDWMMKV-GYHKSLYRLSTSFPRRALEVEGGSSLEDIGITVDTVLNVE   96 (109)
T ss_dssp             EEEEEEECTTSCEEEEEEESSSBTHHHHHHHHHH-TCCTTTEEEECSSSCCBCCCCSSCBHHHHTCSSCEEEEEE
T ss_pred             cEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHhc-CCCCCCeEEEeCCCCcCCCCCCCCCHHHcCCCCCeEEEEE
Confidence            3578888889998888899999999999999865 5566778887  5666665  5789999999999998664

>2ylm_A Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70A {Homo sapiens}

Probab=97.17  E-value=0.002  Score=50.75  Aligned_cols=135  Identities=14%  Similarity=0.239  Sum_probs=90.1

Q ss_pred             EEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEc-----c--eE-e-c----cCceeccccc-ccccceeeeeee-----
Q 040824           13 ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA-----G--KQ-L-E----DGRTLADYNI-QKESTLHLVLRL-----   73 (154)
Q Consensus        13 ~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~-----g--~~-L-~----d~~~l~~~~i-~~~~~i~l~~~~-----   73 (154)
                      ..+++..++|+.+|++.+.+.+|+++++|+|+.-     +  +. + .    .+.++.++.- .+.-++++-...     
T Consensus        38 ~~~rv~k~~~~~~l~~~va~~lg~~~~~~RlW~~~~RqN~T~Rp~~~~~~~~~~~~~~~~~~~~~~~~lflE~~~~~~~~  117 (530)
T 2ylm_A           38 TVFKVLKNSSLAEFVQSLSQTMGFPQDQIRLWPMQARSNGTKRPAMLDNEADGNKTMIELSDNENPWTIFLETVDPELAA  117 (530)
T ss_dssp             EEEEEETTSBHHHHHHHHHHHHTSCGGGEEEEEEEECTTSCEEECCCCHHHHTTSBHHHHHTSCSSEEEEEEECCHHHHT
T ss_pred             ceEEEcCcCCHHHHHHHHHHHhCcCcccEEEEEEEcCCCCccCCccCCccccHHHHHHHHhccCCceEEEEEecccccCC
Confidence            4689999999999999999999999999999832     1  11 1 1    0112222211 111233332210     


Q ss_pred             ----------ecceeeeeeecC--CceE----EEeeCCCchHHHHHHHHhhhcCCCCCceeEEEC----C--eecC-CCC
Q 040824           74 ----------RGGTMIKVKTLT--GKEI----EIDIEPTDTIERIKERVEEKEGIPPVQQRLIYA----G--KQLA-DDK  130 (154)
Q Consensus        74 ----------~~~~~i~v~~~~--~~~~----~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~----g--~~l~-d~~  130 (154)
                                ...+.|++|.-+  .+.+    .+.++.+.+|++|-..+.+..|+|++.--.+|.    +  ..|+ .+.
T Consensus       118 ~~~~l~~~~~~~~iLlFlK~yDp~~q~L~~~G~~~v~~~~kv~~l~~~i~~~~g~p~dt~l~lyEEi~~~~ie~l~~~~~  197 (530)
T 2ylm_A          118 SGATLPKFDKDHDVMLFLKMYDPKTRSLNYCGHIYTPISCKIRDLLPVMCDRAGFIQDTSLILYEEVKPNLTERIQDYDV  197 (530)
T ss_dssp             TTCCCCCCCTTTEEEEEEEEEETTTTEEEEEEEEEEETTCBGGGTHHHHHHHHTCCTTCCEEEEEEEETTEEEECCCSSS
T ss_pred             ccccCCCCCCCCcEEEEEEeeCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHcCCCCCCceEEEEecCCCceeEcccccc
Confidence                      112566776643  2332    366899999999999999999999877655554    2  3566 678


Q ss_pred             ccccc--ccCCCCEEEEEE
Q 040824          131 TARDY--NIEGGSVLHLVL  147 (154)
Q Consensus       131 ~L~~~--~i~~~~~i~~~~  147 (154)
                      |+.+.  .+.+|+.|-+-.
T Consensus       198 t~~~~~~eL~~GdII~fQ~  216 (530)
T 2ylm_A          198 SLDKALDELMDGDIIVFQK  216 (530)
T ss_dssp             BHHHHSTTCCTTEEEEEEE
T ss_pred             cHHHHHhcccCCCEEEEEe
Confidence            99999  999999986543

>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=97.15  E-value=0.0016  Score=38.13  Aligned_cols=64  Identities=11%  Similarity=0.214  Sum_probs=54.6

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEE---CCeecCCCCcccccccCC
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIY---AGKQLADDKTARDYNIEG  139 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~---~g~~l~d~~~L~~~~i~~  139 (154)
                      ..++.|.....+..-++|+|..++.+|--.||+++.++|++..|..   .+.+|+-+++|.+|||..
T Consensus        10 TvRLvVNy~~tQKtVvRVSP~vpL~ellp~IC~Kcefdp~~~~Ll~d~~~~e~LdLskSLndlgirE   76 (91)
T 2daj_A           10 TVRVVINFKKTQKTIVRVSPHASLQELAPIICSKCEFDPLHTLLLKDYQSQEPLDLTKSLNDLGLRE   76 (91)
T ss_dssp             CEEEEEEETTTEEEEEEECSSSCTTTHHHHHHHHTTCCTTSEEEESCSSCCCBCCTTSCHHHHTCSE
T ss_pred             EEEEEEeecCcceeEEEeCCCCcHHHHHHHHhhcccCChhhEEEecCCCCCcccchhcchhhhhhhh
Confidence            3455566666778889999999999999999999999999999984   456899999999999965

>1ryj_A Unknown; beta/alpha protein, structural genomics, protein structure initiative, OCSP, NESG, PSI; NMR {Methanothermococcusthermolithotrophicus} SCOP: d.15.3.2

Probab=97.12  E-value=0.0088  Score=33.91  Aligned_cols=67  Identities=19%  Similarity=0.330  Sum_probs=49.4

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      .|++++....+ ...++++...|+.+|.+.+    ++++....+..+|..+..+.     -+++||.|.++-..-||
T Consensus         4 ~m~i~vNg~~~-~~~~~~~~~~tv~~Ll~~l----~~~~~~v~vavN~~~v~~~~-----~L~~gD~V~ii~~V~GG   70 (70)
T 1ryj_A            4 GMKFTVITDDG-KKILESGAPRRIKDVLGEL----EIPIETVVVKKNGQIVIDEE-----EIFDGDIIEVIRVIYGG   70 (70)
T ss_dssp             CEEEEEEETTE-EEEEEESSCCBHHHHHHHT----TCCTTTEEEEETTEECCTTS-----BCCTTCEEEEEECTTCC
T ss_pred             eEEEEEeCccC-ceeEECCCCCcHHHHHHHh----CCCCCCEEEEECCEECCCcc-----cCCCCCEEEEEeccccC
Confidence            36777766432 3456777889999998876    56677777779999887554     68999999887766655

>2ylm_A Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70A {Homo sapiens}

Probab=97.06  E-value=0.0062  Score=47.98  Aligned_cols=119  Identities=12%  Similarity=0.193  Sum_probs=77.1

Q ss_pred             EEEEEEeCCCcHHHHHHHHHhHhCCC---CCCeEEE--Ecc---eEeccCceecccccccccceeeeeeeec--------
Q 040824           12 TITLEVESSDTIDNVKAKIQDKEGIP---PDQQRLI--FAG---KQLEDGRTLADYNIQKESTLHLVLRLRG--------   75 (154)
Q Consensus        12 ~~~~~v~~~~tv~~lk~~i~~~~~~~---~~~q~L~--~~g---~~L~d~~~l~~~~i~~~~~i~l~~~~~~--------   75 (154)
                      .+.+-++.+.||++|.+.+.++.+++   ....+++  +++   +.+.++.+++..+-.....+.+-.-+..        
T Consensus       353 ~~~l~vpK~gtV~Dll~~l~k~~~~~~~~~~~lRl~ev~~~ki~ki~~~~~~i~~i~d~~~~~~rieeip~ee~~~~~~~  432 (530)
T 2ylm_A          353 EITLYPDKHGCVRDLLEECKKAVELGEKASGKLRLLEIVSYKIIGVHQEDELLECLSPATSRTFRIEEIPLDQVDIDKEN  432 (530)
T ss_dssp             EEEECCBTTCBHHHHHHHHHTTCCCCTTCCCCEEEEEEETTEEEEEECTTSBGGGSCCCTTCEEEEEECCGGGSSCCTTT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHhcCCCcCCcccEEEEEEECCEEEEecCCCcccccccccccceEEEEECCHHHhccCCCC
Confidence            46677888999999999999999887   3556664  566   4466777776544211333333222211        


Q ss_pred             ceeeeeeec-------CCceEEEeeCCCchHHHHHHHHhhhcCCCCC---ceeE--EECC--eecCCCC
Q 040824           76 GTMIKVKTL-------TGKEIEIDIEPTDTIERIKERVEEKEGIPPV---QQRL--IYAG--KQLADDK  130 (154)
Q Consensus        76 ~~~i~v~~~-------~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~---~~~l--~~~g--~~l~d~~  130 (154)
                      .+.|.|...       .|..+.+.+.+.+|+.++|+.|++++|++..   ..++  +-.+  ..++|+.
T Consensus       433 ~~li~V~hf~k~~~~~~G~PF~~~v~~gEt~~~~k~Rl~~rlgv~~keF~K~Kfa~v~~~~~~yl~d~d  501 (530)
T 2ylm_A          433 EMLVTVAHFHKEVFGTFGIPFLLRIHQGEHFREVMKRIQSLLDIQEKEFEKFKFAIVMMGRHQYINEDE  501 (530)
T ss_dssp             EEEEEEEEESSSTTCEEEEEEEEEEETTCCHHHHHHHHHHHHCCCHHHHTTCEEEEEETTEEEECCTTT
T ss_pred             cEEEEEEEeccCcccccCCCeEEEecCCCcHHHHHHHHHHHhCCCHhhhhhEEEEEEECCcccccCCcc
Confidence            122333221       3677889999999999999999999999744   3443  3334  3466544

>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=97.04  E-value=0.0026  Score=40.61  Aligned_cols=69  Identities=16%  Similarity=0.316  Sum_probs=56.2

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhc-CCCCCceeEE--ECCeecC-CCCcccccccCCCCEE
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKE-GIPPVQQRLI--YAGKQLA-DDKTARDYNIEGGSVL  143 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~-~i~~~~~~l~--~~g~~l~-d~~~L~~~~i~~~~~i  143 (154)
                      +...|.|+..+|+.+.-.++.++||.+|..-|.... +.+...+.|+  |..+.++ ++.||.+.|+.+.+.+
T Consensus        51 ~~t~IqIRlpdG~rl~~rF~~~~tl~~v~~fV~~~~~~~~~~~f~L~t~fPrk~l~d~~~TL~eagL~psavl  123 (127)
T 1s3s_G           51 PTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFPNKELADENQTLKEANLLNAVIV  123 (127)
T ss_dssp             CCCCEEEEETTTTEEEEECCSSCBHHHHHHHHHHHCSGGGTSCEEEEETTTTEECCSTTCBHHHHTCSSCEEE
T ss_pred             CcEEEEEECCCCCEEEEEeCCCCCHHHHHHHHHHhCcCCCCCCeEEecCCCCCCCCCCCCcHHHCCCcCceEE
Confidence            346788999999999999999999999999998864 3556677777  6677786 4689999999886554

>3ivf_A Talin-1; FERM domain, cell membrane, cell projection, cytoskeleton, M phosphoprotein, cell adhesion, structural protein; 1.94A {Mus musculus} PDB: 2kma_A 2kc1_A

Probab=96.86  E-value=0.01  Score=44.51  Aligned_cols=61  Identities=18%  Similarity=0.247  Sum_probs=52.3

Q ss_pred             CceEEEeeCCCchHHHHHHHHhhhcC----CCCCceeEEE------CCeecCCCCcccccccCCCCEEEEE
Q 040824           86 GKEIEIDIEPTDTIERIKERVEEKEG----IPPVQQRLIY------AGKQLADDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        86 ~~~~~~~v~~~~tv~~LK~~i~~~~~----i~~~~~~l~~------~g~~l~d~~~L~~~~i~~~~~i~~~  146 (154)
                      +.+-.+.+++++||.+....|.++..    .++++.-|.+      +|..|++.+||..|++.+|+.++..
T Consensus        12 ~~~~~~~f~~~~~v~~~~~~i~e~~~~~~~~~~~~y~l~~~~~~~~~~~Wl~~~~~l~~y~~~~~~~l~~~   82 (371)
T 3ivf_A           12 NVVKTMQFEPSTMVYDACRMIRERIPEALAGPPNDFGLFLSDDDPKKGIWLEAGKALDYYMLRNGDTMEYR   82 (371)
T ss_dssp             TEEEEEEECTTCBHHHHHHHHHTTCGGGGSSCGGGEEEEECCSSGGGCEECCTTSBGGGGTCCTTCEEEEE
T ss_pred             ceeEEEEECCCCCHHHHHHHHHHhcccccCCCHHHCeEeccCCCCCcCEeccCCCCHHHhCCCCCceeecc
Confidence            55678999999999999999988885    3688888887      4567898999999999999998765

>2l32_A Small archaeal modifier protein 2; protein BIN; NMR {Haloferax volcanii}

Probab=96.78  E-value=0.0058  Score=35.16  Aligned_cols=66  Identities=14%  Similarity=0.297  Sum_probs=47.4

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      |+++|+........+++++..|+++|-+    ..++|++..-+..+|+.+..+.      +.+||.|.++ ++.||+
T Consensus         1 M~v~Vkl~g~~~~~~ev~~g~Tv~dLL~----~Lgl~~~~VvV~vNG~~v~~d~------~l~GD~VeIv-~~V~G~   66 (74)
T 2l32_A            1 MNVTVEVVGEETSEVAVDDDGTYADLVR----AVDLSPHEVTVLVDGRPVPEDQ------SVEVDRVKVL-RLIKGG   66 (74)
T ss_dssp             CEEEEECSSSSEEEEECSTTCSHHHHHH----TTCCCSSCCCEECCCCCCCTTS------SSCCCCEEEC-SSCSCC
T ss_pred             CEEEEEEeCccceeEEcCCCCcHHHHHH----HcCCCcceEEEEECCEECCHHH------CCCCCEEEEE-Eeeccc
Confidence            4566666533445688999999999854    7799999998888999887555      3358999665 444444

>2cr5_A Reproduction 8; UBX domain, D0H8S2298E protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.15.1.2

Probab=96.77  E-value=0.0065  Score=37.65  Aligned_cols=69  Identities=19%  Similarity=0.243  Sum_probs=55.2

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEE--EcceEec--cCceecccccccccceeeee
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE--DGRTLADYNIQKESTLHLVL   71 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~--~~g~~L~--d~~~l~~~~i~~~~~i~l~~   71 (154)
                      +|.|+..+|+.+.-+...++||.+|..-|... +..+..-.|.  |..+.+.  .+.+|.+.|+.+.+++.+..
T Consensus        25 ~IqiRlpdG~r~~rrF~~~~tl~~v~~fv~~~-~~~~~~f~L~t~fPrk~l~~d~~~TL~e~gL~p~a~L~Ve~   97 (109)
T 2cr5_A           25 TVALRCPNGRVLRRRFFKSWNSQVLLDWMMKV-GYHKSLYRLSTSFPRRALEVEGGSSLEDIGITVDTVLNVEE   97 (109)
T ss_dssp             EEEEECTTSCEEEEEEESSSBTHHHHHHHHHH-TCCTTTEEEECSSSCCBCCCCSSCBHHHHTCSSCEEEEEEE
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHhc-CCCCCCeEEEeCCCCcCCCCCCCCCHHHcCCCCCeEEEEEe
Confidence            58899999999999999999999999999855 4455556665  5677775  36799999999888886543

>1s3s_G P47 protein; AAA ATPase, protein-protein complex, UBX domain, protein binding; HET: ADP; 2.90A {Rattus norvegicus} SCOP: d.15.1.2 PDB: 1i42_A 1jru_A

Probab=96.56  E-value=0.007  Score=38.59  Aligned_cols=66  Identities=21%  Similarity=0.370  Sum_probs=52.9

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHh-CCCCCCeEEE--EcceEecc-Cceecccccccccce
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKE-GIPPDQQRLI--FAGKQLED-GRTLADYNIQKESTL   67 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~-~~~~~~q~L~--~~g~~L~d-~~~l~~~~i~~~~~i   67 (154)
                      +|.|+..+|..+.-+++.++||.+|.+.|.... +.....-.|.  |..+.+.| +.+|.+.|+.+.+.+
T Consensus        54 ~IqIRlpdG~rl~~rF~~~~tl~~v~~fV~~~~~~~~~~~f~L~t~fPrk~l~d~~~TL~eagL~psavl  123 (127)
T 1s3s_G           54 NIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFPNKELADENQTLKEANLLNAVIV  123 (127)
T ss_dssp             CEEEEETTTTEEEEECCSSCBHHHHHHHHHHHCSGGGTSCEEEEETTTTEECCSTTCBHHHHTCSSCEEE
T ss_pred             EEEEECCCCCEEEEEeCCCCCHHHHHHHHHHhCcCCCCCCeEEecCCCCCCCCCCCCcHHHCCCcCceEE
Confidence            578999999999999999999999999998864 3445556666  56788875 579999999875543

>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=96.51  E-value=0.0048  Score=36.10  Aligned_cols=62  Identities=13%  Similarity=0.232  Sum_probs=53.7

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEc---ceEeccCceeccccccc
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA---GKQLEDGRTLADYNIQK   63 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~---g~~L~d~~~l~~~~i~~   63 (154)
                      ++.|....-+...+++++..++++|--.|.++-.+.|+.-.|...   +..|+-+++|.+|||+.
T Consensus        12 RLvVNy~~tQKtVvRVSP~vpL~ellp~IC~Kcefdp~~~~Ll~d~~~~e~LdLskSLndlgirE   76 (91)
T 2daj_A           12 RVVINFKKTQKTIVRVSPHASLQELAPIICSKCEFDPLHTLLLKDYQSQEPLDLTKSLNDLGLRE   76 (91)
T ss_dssp             EEEEEETTTEEEEEEECSSSCTTTHHHHHHHHTTCCTTSEEEESCSSCCCBCCTTSCHHHHTCSE
T ss_pred             EEEEeecCcceeEEEeCCCCcHHHHHHHHhhcccCChhhEEEecCCCCCcccchhcchhhhhhhh
Confidence            466676666778899999999999999999999999999988843   57799999999999984

>4e71_A Plexin-B2, MM1; transmembrane, signaling, RBD, structural genomics consortium, SGC, signaling protein; 2.26A {Homo sapiens}

Probab=96.47  E-value=0.025  Score=34.97  Aligned_cols=62  Identities=39%  Similarity=0.503  Sum_probs=43.7

Q ss_pred             CCEEEEEEeCCCcHHHHHHHHHhHh--CCC------CCCeEEEEc----ceEeccCc-------------eecccccccc
Q 040824           10 GKTITLEVESSDTIDNVKAKIQDKE--GIP------PDQQRLIFA----GKQLEDGR-------------TLADYNIQKE   64 (154)
Q Consensus        10 ~~~~~~~v~~~~tv~~lk~~i~~~~--~~~------~~~q~L~~~----g~~L~d~~-------------~l~~~~i~~~   64 (154)
                      ++.+++.+-.-+||.++|++|-...  |.|      ++...|-+.    |+.|.|..             ||++|++.+|
T Consensus        23 ~~~i~vkVLdCDTItQvKeKiLd~vyk~~pyS~rP~~~~~dLEwr~g~~~~iL~D~D~ts~~~~~wkrLNTL~HY~V~dg  102 (111)
T 4e71_A           23 VDAIPVKVLNCDTISQVKEKIIDQVYRGQPCSCWPRPDSVVLEWRPGSTAQILSDLDLTSQREGRWKRVNTLMHYNVRDG  102 (111)
T ss_dssp             CCCEEEEEETTCBHHHHHHHHHHHHTC---------CCSEEEEEC--CCCEECCSSCTTSCC---CCCCCBHHHHTCCTT
T ss_pred             CCceeeeeeccCcHHHHHHHHHHHHHcCCccccCCCCCceeeEEecCCCCccccccCccceecCcceEecchhhcCCCCC
Confidence            3558889999999999999997663  444      345556552    45666522             5899999999


Q ss_pred             cceeeee
Q 040824           65 STLHLVL   71 (154)
Q Consensus        65 ~~i~l~~   71 (154)
                      +++.++.
T Consensus       103 atl~l~~  109 (111)
T 4e71_A          103 ATLILSK  109 (111)
T ss_dssp             CEEEEEE
T ss_pred             CEEEEEe
Confidence            9987654

>4a3p_A Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {Homo sapiens} PDB: 4a3o_A 3pv1_A 3ppa_A* 3t9l_A 3lmn_A

Probab=96.40  E-value=0.011  Score=41.13  Aligned_cols=65  Identities=26%  Similarity=0.394  Sum_probs=52.1

Q ss_pred             eEEEeeCCCchHHHHHHHHhhhcCCCCC-ceeEE--E-CC--eecCC-CCcccccccCCCCEEEEEEeecCC
Q 040824           88 EIEIDIEPTDTIERIKERVEEKEGIPPV-QQRLI--Y-AG--KQLAD-DKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        88 ~~~~~v~~~~tv~~LK~~i~~~~~i~~~-~~~l~--~-~g--~~l~d-~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      .+.+.++..+|+.+|++.+++.++++++ ..||-  + .+  ..|++ +.||.++++.++..|.+-++-..|
T Consensus       141 ~~~~~~Sk~~ti~~l~~~~~~~~~i~~~~~~RlW~~~~~~~~~~L~~~~~tl~~~~l~~~Q~illE~r~~dg  212 (217)
T 4a3p_A          141 VVTRRFSKADTIDTIEKEIRKIFSIPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLVIEQKNEDG  212 (217)
T ss_dssp             EEEEEECTTSBHHHHHHHHHHHTTCCTTSCEEEEEEEETTEEEECCCTTSBHHHHTCCTTCEEEEEECCCC-
T ss_pred             ceEEEEcccchHHHHHHHHHHHhCCCCCCceEEEEecCCCCeeecCCCCCCHHHhCCCCCCEEEEEEecCCC
Confidence            3567889999999999999999999987 67775  2 22  35555 579999999999999887776555

>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=96.34  E-value=0.024  Score=39.78  Aligned_cols=65  Identities=26%  Similarity=0.324  Sum_probs=52.5

Q ss_pred             eEEEeeCCCchHHHHHHHHhhhcCCCCC-ceeEEE-C----CeecCC-CCcccccccCCCCEEEEEEeecCC
Q 040824           88 EIEIDIEPTDTIERIKERVEEKEGIPPV-QQRLIY-A----GKQLAD-DKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        88 ~~~~~v~~~~tv~~LK~~i~~~~~i~~~-~~~l~~-~----g~~l~d-~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      .+.+.++..+|+.+|++.++..++++++ ..||-. .    ...|.+ +.||.++++.++..|.+=++-..|
T Consensus       153 ~~~~~~Sk~~ti~~l~~~~~~~~~i~~~~~~RLW~~~~~~~~~~L~~~~~tl~d~~L~~~Q~illE~r~~dg  224 (231)
T 3jyu_A          153 VLSCHFSKADTIATIEKEMRKLFNIPAERETRLWNKYMSNTYEQLSKLDNTIQDAGLYQGQVLVIEPQNEDG  224 (231)
T ss_dssp             EEEEEECTTCBHHHHHHHHHHHTTCCTTSCEEEEECSSSSSCEECCCTTSBTTTTTCCTTEEEEEEECCTTS
T ss_pred             eEEEEecccCcHHHHHHHHHHHhCCCCCCeEEEEEecCCCCHhhhcCCCCCHHHhCCCCCCEEEEEEecCCC
Confidence            3557789999999999999999999997 688863 3    235664 589999999999999887775544

>1vjk_A Molybdopterin converting factor, subunit 1; structural genomics, PSI, protein structure INI southeast collaboratory for structural genomics; 1.51A {Pyrococcus furiosus} SCOP: d.15.3.1

Probab=96.24  E-value=0.069  Score=32.17  Aligned_cols=73  Identities=21%  Similarity=0.419  Sum_probs=47.8

Q ss_pred             cceeeeeeecC------C-ceEEEeeCCCchHHHHHHHHhhhcC-C----------CCCceeEEECCeecCCCCcccccc
Q 040824           75 GGTMIKVKTLT------G-KEIEIDIEPTDTIERIKERVEEKEG-I----------PPVQQRLIYAGKQLADDKTARDYN  136 (154)
Q Consensus        75 ~~~~i~v~~~~------~-~~~~~~v~~~~tv~~LK~~i~~~~~-i----------~~~~~~l~~~g~~l~d~~~L~~~~  136 (154)
                      +.|.++|+...      | ....++++...||.+|.+.+...+. +          ......+..+|+....     +.-
T Consensus         8 ~~~~v~V~~FA~lre~~g~~~~~~e~~~~~Tv~~Ll~~L~~~~p~l~~~l~~~~g~~~~~v~v~VNg~~v~~-----~~~   82 (98)
T 1vjk_A            8 GSVKVKVKYFARFRQLAGVDEEEIELPEGARVRDLIEEIKKRHEKFKEEVFGEGYDEDADVNIAVNGRYVSW-----DEE   82 (98)
T ss_dssp             -CEEEEEEECTHHHHHHSSSEEEEEECTTCBHHHHHHHHHHHCGGGGGSCBCSSSCTTSSBEEEETTBCCCT-----TCB
T ss_pred             CcEEEEEEEhHHHHHHhCCCeEEEECCCCCCHHHHHHHHHhHChhHHHHhhccccccCCcEEEEECCEECCC-----CCC
Confidence            34555555532      2 3556788788999999999987652 1          1244567788887753     567


Q ss_pred             cCCCCEEEEEEeecCC
Q 040824          137 IEGGSVLHLVLALRGG  152 (154)
Q Consensus       137 i~~~~~i~~~~~~~gg  152 (154)
                      +++||.|.++-..-||
T Consensus        83 L~dGDeV~i~ppv~GG   98 (98)
T 1vjk_A           83 LKDGDVVGVFPPVSGG   98 (98)
T ss_dssp             CCTTCEEEEESCC---
T ss_pred             CCCCCEEEEECCCCCC
Confidence            8999999887666554

>2juo_A GA-binding protein alpha chain; OST, ubiquitin, transcription factor, ensemble, DNA-binding, nucleus, transcription regulation; NMR {Mus musculus}

Probab=96.19  E-value=0.036  Score=32.31  Aligned_cols=61  Identities=15%  Similarity=0.234  Sum_probs=53.0

Q ss_pred             EEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEee
Q 040824           89 IEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        89 ~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      +.-.++-++++..||+.++++.+++.+...+...+..|+++++|-+.+++-...+.+.+-.
T Consensus         5 i~qhmDI~epL~~Lk~LLe~Rl~i~L~~y~f~LQd~~L~~~k~LvdQcVqgeGlVQinvqi   65 (89)
T 2juo_A            5 VSQAIDINEPIGNLKKLLEPRLQCSLDAHEICLQDIQLDPDRSLFDQGVKTDGTVQLSVQV   65 (89)
T ss_dssp             EEEEEESSSBGGGHHHHSHHHHCSCCSSCEEEETTEECCTTSBTTTSSCCCCSEEEEEEEE
T ss_pred             hhhhccccCcHHHHHHHHHHHhcCCcccCeEEeeccccCCCccHHHhhcccccEEEEEEEE
Confidence            3445666788999999999999999999999888888999999999999888888877654

>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=96.17  E-value=0.036  Score=35.55  Aligned_cols=63  Identities=29%  Similarity=0.560  Sum_probs=45.0

Q ss_pred             ceEEEeeCCCchHHHHHHHHhhhc--CCC------CCceeEEE----CCe-ecCCC-------------CcccccccCCC
Q 040824           87 KEIEIDIEPTDTIERIKERVEEKE--GIP------PVQQRLIY----AGK-QLADD-------------KTARDYNIEGG  140 (154)
Q Consensus        87 ~~~~~~v~~~~tv~~LK~~i~~~~--~i~------~~~~~l~~----~g~-~l~d~-------------~~L~~~~i~~~  140 (154)
                      ..+++.|-.++||.++|++|-...  |.|      ++.+-|-|    .|+ .|.|.             .||+.|++.+|
T Consensus        41 ~~i~VkVLdCDTItQvKeKiLDavYk~~PySqRP~~~d~dLEwr~g~~g~liL~D~D~tS~~~~~wkrLNTL~HY~V~Dg  120 (138)
T 2r2o_A           41 QGVPVKVLDCDTISQAKEKMLDQLYKGVPLTQRPDPRTLDVEWRSGVAGHLILSDEDVTSEVQGLWRRLNTLQHYKVPDG  120 (138)
T ss_dssp             CCEEEEEETTCBHHHHHHHHHHHHTTTSCGGGCCCGGGEEEEEECSSSCEEEECSSSTTCCEETTEEECCBHHHHTCCTT
T ss_pred             CceeEEEeccccHHHHHHHHHHHHHcCCccccCCCccceeEEEecCCcCceEeeccCCcccccCCceeecchhccCCCCC
Confidence            568899999999999999995444  344      34456655    233 24432             28999999999


Q ss_pred             CEEEEEEee
Q 040824          141 SVLHLVLAL  149 (154)
Q Consensus       141 ~~i~~~~~~  149 (154)
                      +++.++-+.
T Consensus       121 a~l~l~~~~  129 (138)
T 2r2o_A          121 ATVALVPCL  129 (138)
T ss_dssp             CEEEEEEC-
T ss_pred             CEEEEEECC
Confidence            999887654

>1oey_A P67-PHOX, neutrophil cytosol factor 2; immune system, PB1 heterodimer/complex, NADPH oxidase, PB1 D heterodimerization; 2.0A {Homo sapiens} SCOP: d.15.2.2

Probab=96.05  E-value=0.022  Score=33.40  Aligned_cols=45  Identities=11%  Similarity=0.187  Sum_probs=39.3

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcc
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAG   47 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g   47 (154)
                      |.|+|...  .++.++++.+.+..+|.++|.++.+++++...|.|..
T Consensus         6 ~~VKV~~~--~tvairvp~~~~y~~L~~~l~~kL~l~~~~~~LsYk~   50 (83)
T 1oey_A            6 YTLKVHYK--YTVVMKTQPGLPYSQVRDMVSKKLELRLEHTKLSYRP   50 (83)
T ss_dssp             EEEEEESS--SEEEEEECTTCCHHHHHHHHHHHTTCCGGGCCEEECC
T ss_pred             EEEEEEEE--EEEEEECCCCCCHHHHHHHHHHHhCCCcceeEEEeeC
Confidence            35667765  6899999999999999999999999999999998864

>1tyg_B YJBS; alpha beta barrel, protein-protein complex, THis, BIOS protein; 3.15A {Bacillus subtilis} SCOP: d.15.3.2

Probab=95.87  E-value=0.045  Score=32.40  Aligned_cols=67  Identities=13%  Similarity=0.247  Sum_probs=46.2

Q ss_pred             ceeeeeeecCCceEEEeeCCC-chHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           76 GTMIKVKTLTGKEIEIDIEPT-DTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~-~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      .|.|++   +|+.  ++++.. .|+.+|.+.+    ++++....+..+|..+..+ ...+.-+++||.|.++-...||
T Consensus        20 ~M~I~v---NGe~--~el~~~~~Tv~dLL~~L----~~~~~~vaVavNg~iV~~~-~~~~~~L~dGD~Vei~~~V~GG   87 (87)
T 1tyg_B           20 RHMLQL---NGKD--VKWKKDTGTIQDLLASY----QLENKIVIVERNKEIIGKE-RYHEVELCDRDVIEIVHFVGGG   87 (87)
T ss_dssp             --CEEE---TTEE--ECCSSSCCBHHHHHHHT----TCTTSCCEEEETTEEECGG-GTTTSBCCSSSEEEEEEECCC-
T ss_pred             ceEEEE---CCEE--EECCCCCCcHHHHHHHh----CCCCCCEEEEECCEECChh-hcCCcCCCCCCEEEEEcccccC
Confidence            355544   5554  456676 8999998866    5677777788999887643 3445679999999888766655

>4e71_A Plexin-B2, MM1; transmembrane, signaling, RBD, structural genomics consortium, SGC, signaling protein; 2.26A {Homo sapiens}

Probab=95.85  E-value=0.073  Score=32.90  Aligned_cols=62  Identities=29%  Similarity=0.449  Sum_probs=43.0

Q ss_pred             CceEEEeeCCCchHHHHHHHHhhhc--CCC------CCceeEEEC----CeecCC-------------CCcccccccCCC
Q 040824           86 GKEIEIDIEPTDTIERIKERVEEKE--GIP------PVQQRLIYA----GKQLAD-------------DKTARDYNIEGG  140 (154)
Q Consensus        86 ~~~~~~~v~~~~tv~~LK~~i~~~~--~i~------~~~~~l~~~----g~~l~d-------------~~~L~~~~i~~~  140 (154)
                      +..+++.+-.++||.++|++|-...  |.|      ++.+.|-|.    |+.|.|             =.||+.|++.+|
T Consensus        23 ~~~i~vkVLdCDTItQvKeKiLd~vyk~~pyS~rP~~~~~dLEwr~g~~~~iL~D~D~ts~~~~~wkrLNTL~HY~V~dg  102 (111)
T 4e71_A           23 VDAIPVKVLNCDTISQVKEKIIDQVYRGQPCSCWPRPDSVVLEWRPGSTAQILSDLDLTSQREGRWKRVNTLMHYNVRDG  102 (111)
T ss_dssp             CCCEEEEEETTCBHHHHHHHHHHHHTC---------CCSEEEEEC--CCCEECCSSCTTSCC---CCCCCBHHHHTCCTT
T ss_pred             CCceeeeeeccCcHHHHHHHHHHHHHcCCccccCCCCCceeeEEecCCCCccccccCccceecCcceEecchhhcCCCCC
Confidence            4568889999999999999994433  343      355666663    334433             137999999999


Q ss_pred             CEEEEEE
Q 040824          141 SVLHLVL  147 (154)
Q Consensus       141 ~~i~~~~  147 (154)
                      +++.+.-
T Consensus       103 atl~l~~  109 (111)
T 4e71_A          103 ATLILSK  109 (111)
T ss_dssp             CEEEEEE
T ss_pred             CEEEEEe
Confidence            9997653

>2k5p_A THis protein, thiamine-biosynthesis protein; NESG, GMR137, structural genomics, PSI-2, protein structure initiative; NMR {Geobacter metallireducens gs-15} PDB: 3cwi_A

Probab=95.84  E-value=0.019  Score=33.25  Aligned_cols=64  Identities=13%  Similarity=0.254  Sum_probs=46.5

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhcCCC-CCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKEGIP-PVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~~i~-~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      +|+.+.+......|+.+|.+.+    +++ +...-+..+|..+..+ ...+.-+++||.|.++-...||.
T Consensus         6 NGe~~e~~~~~~~Tl~~LL~~l----~~~~~~~vAVavNg~iVpr~-~~~~~~L~dGD~IEIv~~VgGG~   70 (78)
T 2k5p_A            6 NGKPSTVDGAESLNVTELLSAL----KVAQAEYVTVELNGEVLERE-AFDATTVKDGDAVEFLYFMGGGK   70 (78)
T ss_dssp             TTEEEECSSCSCEEHHHHHHHH----TCSCTTTCCEEETTEECCTT-HHHHCEECSSBCEEECCCCCCSC
T ss_pred             CCEEEEcCCCCCCcHHHHHHHc----CCCCCCcEEEEECCEECChH-HcCcccCCCCCEEEEEeeecCCC
Confidence            5664443221678999997754    677 7777888999988653 45567889999999888777774

>2l32_A Small archaeal modifier protein 2; protein BIN; NMR {Haloferax volcanii}

Probab=95.83  E-value=0.044  Score=31.39  Aligned_cols=62  Identities=11%  Similarity=0.273  Sum_probs=46.1

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      |+|+|+--+.....++++++.|+.+|-+.    .+++++.-....||+.+..+.      +.+|+.+.+..-
T Consensus         1 M~v~Vkl~g~~~~~~ev~~g~Tv~dLL~~----Lgl~~~~VvV~vNG~~v~~d~------~l~GD~VeIv~~   62 (74)
T 2l32_A            1 MNVTVEVVGEETSEVAVDDDGTYADLVRA----VDLSPHEVTVLVDGRPVPEDQ------SVEVDRVKVLRL   62 (74)
T ss_dssp             CEEEEECSSSSEEEEECSTTCSHHHHHHT----TCCCSSCCCEECCCCCCCTTS------SSCCCCEEECSS
T ss_pred             CEEEEEEeCccceeEEcCCCCcHHHHHHH----cCCCcceEEEEECCEECCHHH------CCCCCEEEEEEe
Confidence            89999987545566899999999998755    789988887778888776555      223777765543

>3rpf_C Molybdopterin converting factor, subunit 1 (MOAD); MCSG, PSI-biology, structural genomics, midwest center for S genomics, transferase; 1.90A {Helicobacter pylori}

Probab=95.80  E-value=0.057  Score=30.73  Aligned_cols=57  Identities=18%  Similarity=0.359  Sum_probs=40.6

Q ss_pred             EeeCCCchHHHHHHHHhhhcCCCC--CceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           91 IDIEPTDTIERIKERVEEKEGIPP--VQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        91 ~~v~~~~tv~~LK~~i~~~~~i~~--~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      +++ ...|+.+|.+.+....++..  ....+..+|+.+.+    .+.-+++||.|.++-..-||
T Consensus        16 ~e~-~~~tv~~ll~~L~~~~~l~~~l~~~~vavN~~~v~~----~~~~l~~gDeV~i~PpvsGG   74 (74)
T 3rpf_C           16 FFI-KANDLKELRAILQEKEGLKEWLGVCAIALNDHLIDN----LNTPLKDGDVISLLPPVCGG   74 (74)
T ss_dssp             EEE-ECSSHHHHHHHHHTCTTTTTTTTTCEEEESSSEECC----TTCCCCTTCEEEEECCBCCC
T ss_pred             Eee-CCCcHHHHHHHHHHCcCHHHHhhccEEEECCEEcCC----CCcCCCCCCEEEEECCCCCC
Confidence            455 56799999999987544322  45666778877432    34568999999888777766

>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=95.72  E-value=0.073  Score=34.12  Aligned_cols=63  Identities=32%  Similarity=0.533  Sum_probs=45.6

Q ss_pred             CEEEEEEeCCCcHHHHHHHHHhHh--CCC------CCCeEEEE-c---ce-EeccC-------------ceecccccccc
Q 040824           11 KTITLEVESSDTIDNVKAKIQDKE--GIP------PDQQRLIF-A---GK-QLEDG-------------RTLADYNIQKE   64 (154)
Q Consensus        11 ~~~~~~v~~~~tv~~lk~~i~~~~--~~~------~~~q~L~~-~---g~-~L~d~-------------~~l~~~~i~~~   64 (154)
                      +.+++.+-.-+||.++|++|-+..  +.|      +++..|-+ .   |+ .|.|.             .||+.|++.+|
T Consensus        41 ~~i~VkVLdCDTItQvKeKiLDavYk~~PySqRP~~~d~dLEwr~g~~g~liL~D~D~tS~~~~~wkrLNTL~HY~V~Dg  120 (138)
T 2r2o_A           41 QGVPVKVLDCDTISQAKEKMLDQLYKGVPLTQRPDPRTLDVEWRSGVAGHLILSDEDVTSEVQGLWRRLNTLQHYKVPDG  120 (138)
T ss_dssp             CCEEEEEETTCBHHHHHHHHHHHHTTTSCGGGCCCGGGEEEEEECSSSCEEEECSSSTTCCEETTEEECCBHHHHTCCTT
T ss_pred             CceeEEEeccccHHHHHHHHHHHHHcCCccccCCCccceeEEEecCCcCceEeeccCCcccccCCceeecchhccCCCCC
Confidence            458899999999999999998664  444      33445544 2   33 36654             27999999999


Q ss_pred             cceeeeeee
Q 040824           65 STLHLVLRL   73 (154)
Q Consensus        65 ~~i~l~~~~   73 (154)
                      +++.++.+.
T Consensus       121 a~l~l~~~~  129 (138)
T 2r2o_A          121 ATVALVPCL  129 (138)
T ss_dssp             CEEEEEEC-
T ss_pred             CEEEEEECC
Confidence            999887654

>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=95.48  E-value=0.067  Score=37.52  Aligned_cols=61  Identities=20%  Similarity=0.286  Sum_probs=49.4

Q ss_pred             EEEEEeCCCcHHHHHHHHHhHhCCCCC-CeEEEE-c----ceEecc-Cceecccccccccceeeeeee
Q 040824           13 ITLEVESSDTIDNVKAKIQDKEGIPPD-QQRLIF-A----GKQLED-GRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus        13 ~~~~v~~~~tv~~lk~~i~~~~~~~~~-~q~L~~-~----g~~L~d-~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      +...++..+|+.+|++++.+.++++++ ..+|+. .    ...|.+ +.+|.++++.++..|.+-.+.
T Consensus       154 ~~~~~Sk~~ti~~l~~~~~~~~~i~~~~~~RLW~~~~~~~~~~L~~~~~tl~d~~L~~~Q~illE~r~  221 (231)
T 3jyu_A          154 LSCHFSKADTIATIEKEMRKLFNIPAERETRLWNKYMSNTYEQLSKLDNTIQDAGLYQGQVLVIEPQN  221 (231)
T ss_dssp             EEEEECTTCBHHHHHHHHHHHTTCCTTSCEEEEECSSSSSCEECCCTTSBTTTTTCCTTEEEEEEECC
T ss_pred             EEEEecccCcHHHHHHHHHHHhCCCCCCeEEEEEecCCCCHhhhcCCCCCHHHhCCCCCCEEEEEEec
Confidence            456779999999999999999999997 688874 3    255665 579999999999988666554

>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=95.46  E-value=0.057  Score=31.64  Aligned_cols=46  Identities=15%  Similarity=0.244  Sum_probs=39.9

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCe
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGK  124 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~  124 (154)
                      +.|.|+..  -++.+.+++..+..+|..+|+++.+++++..+|.|+..
T Consensus         6 ~~VKV~~~--~tvairvp~~~~y~~L~~~l~~kL~l~~~~~~LsYk~~   51 (83)
T 1oey_A            6 YTLKVHYK--YTVVMKTQPGLPYSQVRDMVSKKLELRLEHTKLSYRPR   51 (83)
T ss_dssp             EEEEEESS--SEEEEEECTTCCHHHHHHHHHHHTTCCGGGCCEEECCT
T ss_pred             EEEEEEEE--EEEEEECCCCCCHHHHHHHHHHHhCCCcceeEEEeeCC
Confidence            55666664  58889999999999999999999999999999999763

>3po0_A Small archaeal modifier protein 1; ubiquitin-like protein, protein binding; 1.55A {Haloferax volcanii} PDB: 2l83_A

Probab=95.39  E-value=0.12  Score=30.29  Aligned_cols=61  Identities=15%  Similarity=0.252  Sum_probs=45.2

Q ss_pred             ceEEEeeCCCchHHHHHHHHhhhcC-C-----CC-----CceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           87 KEIEIDIEPTDTIERIKERVEEKEG-I-----PP-----VQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        87 ~~~~~~v~~~~tv~~LK~~i~~~~~-i-----~~-----~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ....++++...||.+|.+.+...+. +     ..     ....+..+|+....     +.-+++||.|.++-..-||
T Consensus        18 ~~~~~~~~~~~Tv~~ll~~L~~~~p~~~~~~l~~~g~l~~~~~v~VN~~~v~~-----~~~l~~gDeV~i~Ppv~GG   89 (89)
T 3po0_A           18 RTVRVDVDGDATVGDALDALVGAHPALESRVFGDDGELYDHINVLRNGEAAAL-----GEATAAGDELALFPPVSGG   89 (89)
T ss_dssp             SEEEEECCTTCBHHHHHHHHHHHCGGGHHHHBCTTSCBCTTSEEEETTEECCT-----TSBCCTTCEEEEECCCSCC
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHCcHHHHHHhccCCcccccEEEEECCEECCC-----CcccCCCCEEEEECCCCCC
Confidence            4567788888899999999988763 1     10     23577788887764     4568999999888777666

>4a3p_A Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {Homo sapiens} PDB: 4a3o_A 3pv1_A 3ppa_A* 3t9l_A 3lmn_A

Probab=95.36  E-value=0.058  Score=37.48  Aligned_cols=61  Identities=23%  Similarity=0.339  Sum_probs=49.2

Q ss_pred             EEEEEeCCCcHHHHHHHHHhHhCCCCC-CeEEEE-c--c--eEecc-Cceecccccccccceeeeeee
Q 040824           13 ITLEVESSDTIDNVKAKIQDKEGIPPD-QQRLIF-A--G--KQLED-GRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus        13 ~~~~v~~~~tv~~lk~~i~~~~~~~~~-~q~L~~-~--g--~~L~d-~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      ..+.++..+|+.+|++++.+.++++++ ..+|+. .  +  ..|.+ +.+|.++++.++..|.+-.+.
T Consensus       142 ~~~~~Sk~~ti~~l~~~~~~~~~i~~~~~~RlW~~~~~~~~~~L~~~~~tl~~~~l~~~Q~illE~r~  209 (217)
T 4a3p_A          142 VTRRFSKADTIDTIEKEIRKIFSIPDEKETRLWNKYMSNTFEPLNKPDSTIQDAGLYQGQVLVIEQKN  209 (217)
T ss_dssp             EEEEECTTSBHHHHHHHHHHHTTCCTTSCEEEEEEEETTEEEECCCTTSBHHHHTCCTTCEEEEEECC
T ss_pred             eEEEEcccchHHHHHHHHHHHhCCCCCCceEEEEecCCCCeeecCCCCCCHHHhCCCCCCEEEEEEec
Confidence            567789999999999999999999987 688873 2  2  45666 569999999999988666554

>3h6n_A Plexin-D1; structural genomics consortium, SGC, membrane, transmembrane, receptor, alternative splicing, cell membrane, glycoprotein, polymorphism; 2.00A {Homo sapiens}

Probab=95.29  E-value=0.26  Score=31.11  Aligned_cols=64  Identities=25%  Similarity=0.351  Sum_probs=45.2

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhc--CCC------CCceeEEEC-C---ee-cCC-------------CCcccccccC
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKE--GIP------PVQQRLIYA-G---KQ-LAD-------------DKTARDYNIE  138 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~--~i~------~~~~~l~~~-g---~~-l~d-------------~~~L~~~~i~  138 (154)
                      ++..+++.+-.++||.++|++|-...  +.|      ++.+.|-|. |   .. |.|             =.||+.|++.
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            44568889999999999999995433  344      456667662 2   22 432             1379999999


Q ss_pred             CCCEEEEEEe
Q 040824          139 GGSVLHLVLA  148 (154)
Q Consensus       139 ~~~~i~~~~~  148 (154)
                      +|+++.+..+
T Consensus        95 dgatv~l~~~  104 (127)
T 3h6n_A           95 EGASLAMSLI  104 (127)
T ss_dssp             TTCEEEEEEC
T ss_pred             CCCEEEEEEc
Confidence            9999987643

>1fm0_D Molybdopterin convertin factor, subunit 1; molybdenum cofactor biosynthesis, transferase; 1.45A {Escherichia coli} SCOP: d.15.3.1 PDB: 1fma_D 1jw9_D 1jwa_D* 1jwb_D* 3bii_D 1nvi_D

Probab=95.28  E-value=0.067  Score=30.81  Aligned_cols=59  Identities=12%  Similarity=0.205  Sum_probs=42.2

Q ss_pred             eEEEeeCCCchHHHHHHHHhhhcC-----CCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           88 EIEIDIEPTDTIERIKERVEEKEG-----IPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        88 ~~~~~v~~~~tv~~LK~~i~~~~~-----i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ...++ ....|+.+|.+.+...+.     ++.....+..+|+....     +.-+++||.|.++-..-||
T Consensus        18 ~~~~~-~~~~tv~~ll~~L~~~~p~~~~~l~~~~~~v~vN~~~v~~-----~~~l~~gD~V~i~Ppv~GG   81 (81)
T 1fm0_D           18 ATEVA-ADFPTVEALRQHMAAQSDRWALALEDGKLLAAVNQTLVSF-----DHPLTDGDEVAFFPPVTGG   81 (81)
T ss_dssp             EEEEC-SCCSBHHHHHHHHHTTCHHHHHHHCCTTCEEEETTEECCT-----TCBCCTTCEEEEECCCCCC
T ss_pred             eEEEc-CCCCCHHHHHHHHHHHChhHHHHhcCCCEEEEECCEECCC-----CCCCCCCCEEEEeCCCCCC
Confidence            34555 567899999999986642     33345567789987753     4578999999887766665

>2q5w_D Molybdopterin converting factor, subunit 1; MOCO, MPT synthase, MOAD, MOAE, transferase, molybdenum cofactor biosynthesis; 2.00A {Staphylococcus aureus} PDB: 2qie_B*

Probab=95.21  E-value=0.062  Score=30.66  Aligned_cols=59  Identities=14%  Similarity=0.204  Sum_probs=42.6

Q ss_pred             eEEEeeCCCchHHHHHHHHhhhcCCCCCce--eEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           88 EIEIDIEPTDTIERIKERVEEKEGIPPVQQ--RLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        88 ~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~--~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ...+++....|+.+|.+.+...+. .....  .+..+|+....+     .-+++||.|.++-..-||
T Consensus        17 ~~~~~~~~~~tv~~ll~~l~~~~p-~~~~v~~~v~vNg~~v~~~-----~~L~~gD~V~i~ppv~GG   77 (77)
T 2q5w_D           17 QEDIVLEQALTVQQFEDLLFERYP-QINNKKFQVAVNEEFVQKS-----DFIQPNDTVALIPPVSGG   77 (77)
T ss_dssp             EEECCCSSCEEHHHHHHHHHHHCG-GGTTCCCEEEETTEEECTT-----SEECTTCEEEEECSCCCC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHCc-chhcceEEEEECCEECCCC-----CCcCCCCEEEEECCCCCC
Confidence            456677778899999999977642 11233  677899877643     578999999887666555

>2cu3_A Unknown function protein; thermus thermophilus HB8, structural genomics, riken structu genomics/proteomics initiative, RSGI, NPPSFA; 1.70A {Thermus thermophilus} SCOP: d.15.3.2 PDB: 2htm_E

Probab=94.91  E-value=0.11  Score=28.63  Aligned_cols=60  Identities=17%  Similarity=0.339  Sum_probs=42.3

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      +|+.+  ++ ...|+.+|.+.+    ++++....+..+|..+..+ .-.+.-+++||.|.++-..-||
T Consensus         5 Ng~~~--~~-~~~tv~~ll~~l----~~~~~~v~vavN~~~v~~~-~~~~~~L~dgD~v~i~~~V~GG   64 (64)
T 2cu3_A            5 NGEPR--PL-EGKTLKEVLEEM----GVELKGVAVLLNEEAFLGL-EVPDRPLRDGDVVEVVALMQGG   64 (64)
T ss_dssp             TTEEE--CC-TTCCHHHHHHHH----TBCGGGEEEEETTEEEEGG-GCCCCCCCTTCEEEEEECCCC-
T ss_pred             CCEEE--Ec-CCCcHHHHHHHc----CCCCCcEEEEECCEECCcc-ccCCcCCCCCCEEEEEeecccC
Confidence            55554  45 668999998877    4567777777899877543 2344578999999888766555

>3kuz_A Plexin-C1; structural genomics, structural genomics consortium, SGC; 2.30A {Homo sapiens}

Probab=94.87  E-value=0.4  Score=30.19  Aligned_cols=61  Identities=30%  Similarity=0.440  Sum_probs=41.5

Q ss_pred             ceEEEeeCCCchHHHHHHHHh-hhc---CCCC----CceeEEEC-C---eec----------CCC----CcccccccCCC
Q 040824           87 KEIEIDIEPTDTIERIKERVE-EKE---GIPP----VQQRLIYA-G---KQL----------ADD----KTARDYNIEGG  140 (154)
Q Consensus        87 ~~~~~~v~~~~tv~~LK~~i~-~~~---~i~~----~~~~l~~~-g---~~l----------~d~----~~L~~~~i~~~  140 (154)
                      ..+++.+-.++||.++|++|- ..+   +.|.    +.+.|-|. |   ..|          +++    .||+.|++.+|
T Consensus        39 ~~v~VkVLdCDTItQVKEKILdavYk~k~~pys~r~~d~dLEwr~g~~~~~L~D~D~tS~~~e~~wkrLNTL~HY~V~Dg  118 (126)
T 3kuz_A           39 RNISVNVLDCDTIGQAKEKIFQAFLSKNGSPYGLQLNEIGLELQMGTRQKELLDIDSSSVILEDGITKLNTIGHYEISNG  118 (126)
T ss_dssp             CEEEEEEETTCBHHHHHHHHHHHHHHHHSSCCSSCGGGEEEEEEETTEEEEECSSCTTCCBCTTSCBCCCBTGGGTCCTT
T ss_pred             CceEeeeecCCcHHHHHHHHHHHHhccCCCcCCCCccccceEEecCCCcceeeccCCcceEecCCeeEeccccccCCCCC
Confidence            458888999999999999983 333   6553    44555542 1   111          221    37899999999


Q ss_pred             CEEEEEE
Q 040824          141 SVLHLVL  147 (154)
Q Consensus       141 ~~i~~~~  147 (154)
                      +++.++-
T Consensus       119 atlal~k  125 (126)
T 3kuz_A          119 STIKVFK  125 (126)
T ss_dssp             CEEEEEE
T ss_pred             CEEEEee
Confidence            9997764

>1f0z_A THis protein; ubiquitin fold, transport protein; NMR {Escherichia coli} SCOP: d.15.3.2 PDB: 1zud_2

Probab=94.77  E-value=0.065  Score=29.77  Aligned_cols=61  Identities=11%  Similarity=0.222  Sum_probs=43.5

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      +|+.  +++....|+.+|.+.+    ++++....+..+|..+... ...+.-+++||.|.++-..-||
T Consensus         6 Ng~~--~~~~~~~tv~~ll~~l----~~~~~~v~vavN~~~v~~~-~~~~~~L~~gD~v~i~~~V~GG   66 (66)
T 1f0z_A            6 NDQA--MQCAAGQTVHELLEQL----DQRQAGAALAINQQIVPRE-QWAQHIVQDGDQILLFQVIAGG   66 (66)
T ss_dssp             SSCE--ECCCTTCCHHHHHHHH----TCCCSSEEEEETTEEECHH-HHTTCCCCTTEEECEEESCCCC
T ss_pred             CCEE--EEcCCCCcHHHHHHHc----CCCCCCEEEEECCEECCch-hcCCcCCCCCCEEEEEeecccC
Confidence            4554  4566778999998877    5667777777899877532 2234578999999887766554

>2juo_A GA-binding protein alpha chain; OST, ubiquitin, transcription factor, ensemble, DNA-binding, nucleus, transcription regulation; NMR {Mus musculus}

Probab=94.69  E-value=0.14  Score=29.84  Aligned_cols=59  Identities=19%  Similarity=0.378  Sum_probs=49.9

Q ss_pred             EEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeee
Q 040824           13 ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (154)
Q Consensus        13 ~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~   71 (154)
                      +.-.++-..++..||..++.+.+++-+.-.++..+..|+++++|.+-+++....+.+.+
T Consensus         5 i~qhmDI~epL~~Lk~LLe~Rl~i~L~~y~f~LQd~~L~~~k~LvdQcVqgeGlVQinv   63 (89)
T 2juo_A            5 VSQAIDINEPIGNLKKLLEPRLQCSLDAHEICLQDIQLDPDRSLFDQGVKTDGTVQLSV   63 (89)
T ss_dssp             EEEEEESSSBGGGHHHHSHHHHCSCCSSCEEEETTEECCTTSBTTTSSCCCCSEEEEEE
T ss_pred             hhhhccccCcHHHHHHHHHHHhcCCcccCeEEeeccccCCCccHHHhhcccccEEEEEE
Confidence            34456778899999999999999999998998888779999999999998777765544

>1ef1_A Moesin; membrane, FERM domain, tail domain, membrane protein; 1.90A {Homo sapiens} SCOP: a.11.2.1 b.55.1.5 d.15.1.4 PDB: 1sgh_A 1j19_A 2emt_A 2ems_A 2d10_A 2d11_A 2yvc_A 2d2q_A 2zpy_A 1gc7_A 1gc6_A 1ni2_A

Probab=94.50  E-value=0.33  Score=34.93  Aligned_cols=71  Identities=23%  Similarity=0.295  Sum_probs=52.3

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCC-CceeEEE---CCe--ecCCCCcccccccCCCCEEEEEEe
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPP-VQQRLIY---AGK--QLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~-~~~~l~~---~g~--~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      +.+.|..++| ++.+.+++++|+.++-..+++..|+.. +-+-|.+   +|.  .|+.++++.+.++..+....+..+
T Consensus         2 i~~~V~l~d~-~~~~~v~~~tt~~el~~~v~~~l~L~e~~~FgL~~~~~~~~~~wLd~~~~l~~q~~~~~~~~~l~fr   78 (294)
T 1ef1_A            2 ISVRVTTMDA-ELEFAIQPNTTGKQLFDQVVKTIGLREVWFFGLQYQDTKGFSTWLKLNKKVTAQDVRKESPLLFKFR   78 (294)
T ss_dssp             EEEEEEETTE-EEEEEECTTCBHHHHHHHHHHHHTCCCGGGEEEEEEBTTSCEEECCSSSBGGGSCBCCCSSEEEEEE
T ss_pred             EEEEEEECCc-eEEEEECCCCcHHHHHHHHHHHcCCCCcceeEEEEECCCCceeecccccCHHhhccCCCCCEEEEEE
Confidence            5677778887 678999999999999999999999854 3345554   332  577788888887655555544443

>1vd2_A Protein kinase C, IOTA type; PB1 domain, OPCA motif, APKC, ZIP/P62, MEK5, molecular recognition, transferase; NMR {Homo sapiens} SCOP: d.15.2.2 PDB: 1wmh_A

Probab=94.40  E-value=0.3  Score=28.92  Aligned_cols=48  Identities=15%  Similarity=0.194  Sum_probs=37.4

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCc-eeEEECCee
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQ-QRLIYAGKQ  125 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~-~~l~~~g~~  125 (154)
                      +.+.+.. +|....+.++++.+..+|.+++...++++..+ +.+.|....
T Consensus         7 vkvK~~~-~gdi~~~~v~~~i~~~~L~~kv~~~~~~~~~~~f~lky~DEe   55 (89)
T 1vd2_A            7 VRVKAYY-RGDIMITHFEPSISFEGLCNEVRDMCSFDNEQLFTMKWIDEE   55 (89)
T ss_dssp             EEEEEES-SSCEEEEEECTTCCHHHHHHHHHHHTTCCSSCCEEEEECCSS
T ss_pred             EEEEEEe-CCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCeEEEEEECCC
Confidence            3444434 56688899999999999999999999987544 788887653

>3h6n_A Plexin-D1; structural genomics consortium, SGC, membrane, transmembrane, receptor, alternative splicing, cell membrane, glycoprotein, polymorphism; 2.00A {Homo sapiens}

Probab=94.36  E-value=0.42  Score=30.15  Aligned_cols=64  Identities=28%  Similarity=0.421  Sum_probs=45.8

Q ss_pred             CCCEEEEEEeCCCcHHHHHHHHHhHh--CCC------CCCeEEEE-cc---e-EeccC-------------ceecccccc
Q 040824            9 TGKTITLEVESSDTIDNVKAKIQDKE--GIP------PDQQRLIF-AG---K-QLEDG-------------RTLADYNIQ   62 (154)
Q Consensus         9 ~~~~~~~~v~~~~tv~~lk~~i~~~~--~~~------~~~q~L~~-~g---~-~L~d~-------------~~l~~~~i~   62 (154)
                      ++..+++.+-.-+||.++|++|-+..  ++|      ++...|-| .|   + .|.|.             .||++|++.
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            34568899999999999999997663  444      34566654 22   3 25542             258999999


Q ss_pred             cccceeeeee
Q 040824           63 KESTLHLVLR   72 (154)
Q Consensus        63 ~~~~i~l~~~   72 (154)
                      +|+++.+..+
T Consensus        95 dgatv~l~~~  104 (127)
T 3h6n_A           95 EGASLAMSLI  104 (127)
T ss_dssp             TTCEEEEEEC
T ss_pred             CCCEEEEEEc
Confidence            9999977654

>1ryj_A Unknown; beta/alpha protein, structural genomics, protein structure initiative, OCSP, NESG, PSI; NMR {Methanothermococcusthermolithotrophicus} SCOP: d.15.3.2

Probab=94.25  E-value=0.36  Score=27.03  Aligned_cols=62  Identities=19%  Similarity=0.211  Sum_probs=42.2

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      |+++|.-.. ....++++...|+.+|.+.+    ++++....+..+|..+..+.     -+++|+.|.+...
T Consensus         5 m~i~vNg~~-~~~~~~~~~~~tv~~Ll~~l----~~~~~~v~vavN~~~v~~~~-----~L~~gD~V~ii~~   66 (70)
T 1ryj_A            5 MKFTVITDD-GKKILESGAPRRIKDVLGEL----EIPIETVVVKKNGQIVIDEE-----EIFDGDIIEVIRV   66 (70)
T ss_dssp             EEEEEEETT-EEEEEEESSCCBHHHHHHHT----TCCTTTEEEEETTEECCTTS-----BCCTTCEEEEEEC
T ss_pred             EEEEEeCcc-CceeEECCCCCcHHHHHHHh----CCCCCCEEEEECCEECCCcc-----cCCCCCEEEEEec
Confidence            455555432 23567788889999999875    55666666668888876554     5677888866543

>2kvr_A Ubiquitin carboxyl-terminal hydrolase 7; USP7, ubiquitin-like domain, UBL, ubiquitin specific protease, HOST-virus interaction, nucleus, protease; NMR {Homo sapiens}

Probab=94.16  E-value=0.069  Score=34.06  Aligned_cols=33  Identities=21%  Similarity=0.340  Sum_probs=30.5

Q ss_pred             EEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEE
Q 040824           13 ITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF   45 (154)
Q Consensus        13 ~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~   45 (154)
                      ..+.|..++|+.+|+..+.+.+|+|++.|+|+.
T Consensus        58 ~~~rv~k~~~~~~~~~~va~~lg~~~~~~RlW~   90 (130)
T 2kvr_A           58 TVFKVLKNSSLAEFVQSLSQTMGFPQDQIRLWP   90 (130)
T ss_dssp             EEEECCTTSBHHHHHHHHHHHHCCCGGGCEEEE
T ss_pred             ceEEEeccCcHHHHHHHHHHHhCCCcccEEEEE
Confidence            467888999999999999999999999999984

>4e74_A Plexin-A4; RBD, structural genomics, structural genomics consor SGC, signaling protein; 1.58A {Homo sapiens} PDB: 3q3j_A*

Probab=93.91  E-value=0.35  Score=30.13  Aligned_cols=64  Identities=30%  Similarity=0.482  Sum_probs=44.5

Q ss_pred             CceEEEeeCCCchHHHHHHHHhhhc--CCC------CCceeEEE-CC---e-ecCC-------------CCcccccccCC
Q 040824           86 GKEIEIDIEPTDTIERIKERVEEKE--GIP------PVQQRLIY-AG---K-QLAD-------------DKTARDYNIEG  139 (154)
Q Consensus        86 ~~~~~~~v~~~~tv~~LK~~i~~~~--~i~------~~~~~l~~-~g---~-~l~d-------------~~~L~~~~i~~  139 (154)
                      ...+++.+-.++||.++|++|-...  +.|      ++.+.|-| .|   . .|.|             =.||+.|++.+
T Consensus        26 ~~~i~VkVLdCDTItQvKeKiLd~vyk~~p~S~rP~~~~~dLEwr~g~~~~~iL~D~D~ts~~~~~wkrLNTL~HY~V~d  105 (117)
T 4e74_A           26 SPEVPVKILNCDTITQVKEKILDAIFKNVPCSHRPKAADMDLEWRQGSGARMILQDEDITTKIENDWKRLNTLAHYQVPD  105 (117)
T ss_dssp             CCCEEEEEETTSBHHHHHHHHHHHHTTTSCGGGSCCGGGEEEEEECTTSCEEEECSSSTTCCC---CCCCCBHHHHTCCT
T ss_pred             CCceEeeeecCCchHHHHHHHHHHHhcCCCcccCCCCCceeEEEecCCCCceEeecCCCccEecCcceEeccccccCCCC
Confidence            3458888999999999999994433  344      34556665 23   2 2322             13799999999


Q ss_pred             CCEEEEEEee
Q 040824          140 GSVLHLVLAL  149 (154)
Q Consensus       140 ~~~i~~~~~~  149 (154)
                      |+++.++-+.
T Consensus       106 gatl~l~~~~  115 (117)
T 4e74_A          106 GSVVALVSKQ  115 (117)
T ss_dssp             TCEEEEEECC
T ss_pred             CCEEEEEeCC
Confidence            9999887654

>2kvr_A Ubiquitin carboxyl-terminal hydrolase 7; USP7, ubiquitin-like domain, UBL, ubiquitin specific protease, HOST-virus interaction, nucleus, protease; NMR {Homo sapiens}

Probab=93.88  E-value=0.067  Score=34.12  Aligned_cols=32  Identities=16%  Similarity=0.281  Sum_probs=29.6

Q ss_pred             EEEeeCCCchHHHHHHHHhhhcCCCCCceeEE
Q 040824           89 IEIDIEPTDTIERIKERVEEKEGIPPVQQRLI  120 (154)
Q Consensus        89 ~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~  120 (154)
                      ..+.|..++|+.+|+..+++.+|+|++.++|-
T Consensus        58 ~~~rv~k~~~~~~~~~~va~~lg~~~~~~RlW   89 (130)
T 2kvr_A           58 TVFKVLKNSSLAEFVQSLSQTMGFPQDQIRLW   89 (130)
T ss_dssp             EEEECCTTSBHHHHHHHHHHHHCCCGGGCEEE
T ss_pred             ceEEEeccCcHHHHHHHHHHHhCCCcccEEEE
Confidence            45799999999999999999999999999886

>4e74_A Plexin-A4; RBD, structural genomics, structural genomics consor SGC, signaling protein; 1.58A {Homo sapiens} PDB: 3q3j_A*

Probab=93.86  E-value=0.32  Score=30.34  Aligned_cols=62  Identities=32%  Similarity=0.521  Sum_probs=43.8

Q ss_pred             CEEEEEEeCCCcHHHHHHHHHhHh--CCC------CCCeEEEE-cc---e-EeccC-------------ceecccccccc
Q 040824           11 KTITLEVESSDTIDNVKAKIQDKE--GIP------PDQQRLIF-AG---K-QLEDG-------------RTLADYNIQKE   64 (154)
Q Consensus        11 ~~~~~~v~~~~tv~~lk~~i~~~~--~~~------~~~q~L~~-~g---~-~L~d~-------------~~l~~~~i~~~   64 (154)
                      ..+++.+-.-+||.++|++|-+..  +.|      ++...|-+ .|   + .|.|.             .||++|++.+|
T Consensus        27 ~~i~VkVLdCDTItQvKeKiLd~vyk~~p~S~rP~~~~~dLEwr~g~~~~~iL~D~D~ts~~~~~wkrLNTL~HY~V~dg  106 (117)
T 4e74_A           27 PEVPVKILNCDTITQVKEKILDAIFKNVPCSHRPKAADMDLEWRQGSGARMILQDEDITTKIENDWKRLNTLAHYQVPDG  106 (117)
T ss_dssp             CCEEEEEETTSBHHHHHHHHHHHHTTTSCGGGSCCGGGEEEEEECTTSCEEEECSSSTTCCC---CCCCCBHHHHTCCTT
T ss_pred             CceEeeeecCCchHHHHHHHHHHHhcCCCcccCCCCCceeEEEecCCCCceEeecCCCccEecCcceEeccccccCCCCC
Confidence            447888989999999999997653  444      33455554 22   2 35542             25899999999


Q ss_pred             cceeeeee
Q 040824           65 STLHLVLR   72 (154)
Q Consensus        65 ~~i~l~~~   72 (154)
                      +++.++.+
T Consensus       107 atl~l~~~  114 (117)
T 4e74_A          107 SVVALVSK  114 (117)
T ss_dssp             CEEEEEEC
T ss_pred             CEEEEEeC
Confidence            99987654

>1h4r_A Merlin; FERM, neurofibromatosis, NF2, structural protein, cytoskeleton, anti-oncogene; 1.8A {Homo sapiens} SCOP: a.11.2.1 b.55.1.5 d.15.1.4 PDB: 1isn_A 3u8z_A

Probab=93.83  E-value=0.53  Score=34.23  Aligned_cols=74  Identities=16%  Similarity=0.133  Sum_probs=54.2

Q ss_pred             ecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCC-CceeEEE--CCe--ecCCCCcccccccCCCCEEEEEEe
Q 040824           74 RGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPP-VQQRLIY--AGK--QLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        74 ~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~-~~~~l~~--~g~--~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      ...+.+.|..++| ++.+.+++++|+.+|-..+++..|+.. +-+-|.+  +|.  .|+.+.++.+.+...+....+..+
T Consensus        20 ~~~~~~~V~lldg-~~~~~v~~~t~~~el~~~v~~~l~L~e~~~FgL~~~~~~~~~wL~~~~~i~~q~~~~~~~~~l~fr   98 (314)
T 1h4r_A           20 PKTFTVRIVTMDA-EMEFNCEMKWKGKDLFDLVCRTLGLRETWFFGLQYTIKDTVAWLKMDKKVLDHDVSKEEPVTFHFL   98 (314)
T ss_dssp             -CEEEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHTCCCGGGEEEEEEETTEEEECCTTSBGGGSSCCCSSSEEEEEE
T ss_pred             CCeeEEEEEeCCc-eEEEEeCCCCcHHHHHHHHHHHhCCCCCccceEEEEeCCcCeeCCCccCHHHcCCCCCCCEEEEEE
Confidence            3456777888888 788999999999999999999999853 3345554  443  577888888887655555444433

>1rws_A Hypothetical protein PF1061; residual dipolar couplings, structural genomics, unknown FUN; NMR {Pyrococcus furiosus} SCOP: d.15.3.2 PDB: 1sf0_A

Probab=93.56  E-value=0.027  Score=32.43  Aligned_cols=54  Identities=20%  Similarity=0.348  Sum_probs=40.7

Q ss_pred             EEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           90 EIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        90 ~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      .+++++..|+.+|.+.+    ++++....+..+|+.+..+     .-+++||.|.++-..-||
T Consensus        24 ~~~~~~~~Tv~dLl~~L----~~~~~~v~VavNg~~v~~~-----~~L~dGD~V~i~ppv~GG   77 (77)
T 1rws_A           24 EIEWREGMKVRDILRAV----GFNTESAIAKVNGKVVLED-----DEVKDGDFVEVIPVVSGG   77 (77)
T ss_dssp             CCCCCSSCCHHHHHHTT----TCSSCSSCEEETTEEECSS-----SCCCSSCCCBCSCCCCCC
T ss_pred             EEECCCCCcHHHHHHHh----CCCCcCEEEEECCEECCCC-----CCcCCCCEEEEEcccccC
Confidence            34666778999998765    4667777788999988654     578999999877666555

>3rpf_C Molybdopterin converting factor, subunit 1 (MOAD); MCSG, PSI-biology, structural genomics, midwest center for S genomics, transferase; 1.90A {Helicobacter pylori}

Probab=93.41  E-value=0.52  Score=26.58  Aligned_cols=68  Identities=13%  Similarity=0.292  Sum_probs=42.0

Q ss_pred             CEEEEEeCCC-CEEEEEEeCCCcHHHHHHHHHhHhCCCC--CCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTG-KTITLEVESSDTIDNVKAKIQDKEGIPP--DQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~-~~~~~~v~~~~tv~~lk~~i~~~~~~~~--~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |.++|+.... +.-.+++ ...|+.+|.+.+...-++..  ....+.-||+...+    .+.-+++|+.|.+....
T Consensus         1 M~v~V~~fa~l~~~~~e~-~~~tv~~ll~~L~~~~~l~~~l~~~~vavN~~~v~~----~~~~l~~gDeV~i~Ppv   71 (74)
T 3rpf_C            1 MMVEVRFFGPIKEENFFI-KANDLKELRAILQEKEGLKEWLGVCAIALNDHLIDN----LNTPLKDGDVISLLPPV   71 (74)
T ss_dssp             CEEEEEECTTCCCCCEEE-ECSSHHHHHHHHHTCTTTTTTTTTCEEEESSSEECC----TTCCCCTTCEEEEECCB
T ss_pred             CEEEEEEEeecceeEEee-CCCcHHHHHHHHHHCcCHHHHhhccEEEECCEEcCC----CCcCCCCCCEEEEECCC
Confidence            7788877643 1134566 67899999999986433221  23344456665432    24557888988776543

>3dwg_C 9.5 kDa culture filtrate antigen CFP10A; sulfur carrier protein complex, beta-grAsp fold, amino-acid biosynthesis; HET: PLP; 1.53A {Mycobacterium tuberculosis} PDB: 3dwm_A

Probab=93.13  E-value=0.75  Score=27.07  Aligned_cols=61  Identities=13%  Similarity=0.153  Sum_probs=41.7

Q ss_pred             EEeeCCCchHHHHHHHHhhhcCC------C-------CCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           90 EIDIEPTDTIERIKERVEEKEGI------P-------PVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        90 ~~~v~~~~tv~~LK~~i~~~~~i------~-------~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      .++. +..||.+|.+.+..++.-      .       .....+..+|.......- .+.-+++||.|.++-..-||
T Consensus        20 ~~~~-~~~Tv~~ll~~L~~~~p~l~~~l~~~~~~g~~~~~~~v~VN~~~v~~~~~-~~~~L~~gDeV~i~Ppv~GG   93 (93)
T 3dwg_C           20 SVSA-SGDTLGAVISDLEANYSGISERLMDPSSPGKLHRFVNIYVNDEDVRFSGG-LATAIADGDSVTILPAVAGG   93 (93)
T ss_dssp             EEEE-CCSBHHHHHHHHHHHSTTHHHHHBCSSSTTSBCTTEEEEETTEEGGGTTG-GGCBCCTTCEEEEEECCTTC
T ss_pred             EEec-CCCCHHHHHHHHHHHChhHHHHHhccccCCcccCCEEEEECCEEccCcCC-CCcCCCCCCEEEEECCCCCC
Confidence            4554 457999999999887631      1       113567788887754222 24568999999888777766

>2i1j_A Moesin; FERM, coiled-coil, C-ermad, ERM, radixin, ezrin, MER actin binding, masking, regulation, SELF-inhibition, cell A membrane protein; 2.10A {Spodoptera frugiperda} PDB: 2i1k_A 1e5w_A

Probab=93.02  E-value=0.53  Score=37.45  Aligned_cols=73  Identities=19%  Similarity=0.250  Sum_probs=54.2

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCC-CCceeEEEC---C--eecCCCCcccccccCCCCEEEEEEe
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIP-PVQQRLIYA---G--KQLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~-~~~~~l~~~---g--~~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      .++.+.|..++| ++.+.+++++|+.+|-..|+...|+. .+-+-|.+.   |  ..|+.+.++.+.++..+....+..+
T Consensus         3 k~i~v~V~llDg-t~e~~vd~~tt~~ell~~V~~~LgL~e~~~FGL~~~d~~~~~~WLd~~k~i~~q~~~~~~~~~L~FR   81 (575)
T 2i1j_A            3 KSMNVRVTTMDA-ELEFAIQQTTTGKQLFDQVVKTIGLREVWFFGLQYTDSKGDLTWIKLYKKVMQQDVKKENPLQFKFR   81 (575)
T ss_dssp             CEEEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHTCCCGGGEEEEEEBTTSCEEECCTTSBGGGSCBCCCSSEEEEEE
T ss_pred             ceEEEEEEeCCC-eEEEEECCCCCHHHHHHHHHHHcCCCCccceeEEEEecCcchhHhhccccHHHhcccCCCCeEEEEE
Confidence            346677888888 67899999999999999999999985 344566542   2  3677788888887766665555444

>2g1e_A Hypothetical protein TA0895; MOAD, molybdopterin, transferase; NMR {Thermoplasma acidophilum} PDB: 2k22_A

Probab=92.92  E-value=0.52  Score=27.46  Aligned_cols=61  Identities=16%  Similarity=0.265  Sum_probs=40.4

Q ss_pred             EeeCCCchHHHHHHHHhhhcC------C-----CCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           91 IDIEPTDTIERIKERVEEKEG------I-----PPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        91 ~~v~~~~tv~~LK~~i~~~~~------i-----~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ++++...|+.+|.+.+...+.      +     ......+..+|+..... .-.+.-+++||.|.++-..-||
T Consensus        19 ~~~~~~~tv~~ll~~l~~~~p~~~~~~l~~~~g~~~~v~v~vN~~~v~~~-~~~~~~l~~gD~V~i~ppv~GG   90 (90)
T 2g1e_A           19 ETFNGISKISELLERLKVEYGSEFTKQMYDGNNLFKNVIILVNGNNITSM-KGLDTEIKDDDKIDLFPPVAGG   90 (90)
T ss_dssp             EEESSCCBHHHHHHHHHHHSCHHHHHHHCCSSCSTTTCEEEESSSBGGGT-CSSSCBCCTTCEEEEECCTTCC
T ss_pred             EEcCCCCcHHHHHHHHHHHCcchhhhccccccCcCcceEEEECCEEcccc-CCCCcCCCCCCEEEEeCCCCCC
Confidence            455566899999999987752      1     01345677888766522 1234468999999887665554

>3kuz_A Plexin-C1; structural genomics, structural genomics consortium, SGC; 2.30A {Homo sapiens}

Probab=92.23  E-value=1.3  Score=27.78  Aligned_cols=60  Identities=33%  Similarity=0.496  Sum_probs=40.5

Q ss_pred             CEEEEEEeCCCcHHHHHHHHHhH----hCCCC----CCeEEEE-cc---eEeccC--------------ceecccccccc
Q 040824           11 KTITLEVESSDTIDNVKAKIQDK----EGIPP----DQQRLIF-AG---KQLEDG--------------RTLADYNIQKE   64 (154)
Q Consensus        11 ~~~~~~v~~~~tv~~lk~~i~~~----~~~~~----~~q~L~~-~g---~~L~d~--------------~~l~~~~i~~~   64 (154)
                      +.+++.+-.-+||.++|++|-..    .++|.    ++..|-| .|   ..|.|.              .||+.|++.+|
T Consensus        39 ~~v~VkVLdCDTItQVKEKILdavYk~k~~pys~r~~d~dLEwr~g~~~~~L~D~D~tS~~~e~~wkrLNTL~HY~V~Dg  118 (126)
T 3kuz_A           39 RNISVNVLDCDTIGQAKEKIFQAFLSKNGSPYGLQLNEIGLELQMGTRQKELLDIDSSSVILEDGITKLNTIGHYEISNG  118 (126)
T ss_dssp             CEEEEEEETTCBHHHHHHHHHHHHHHHHSSCCSSCGGGEEEEEEETTEEEEECSSCTTCCBCTTSCBCCCBTGGGTCCTT
T ss_pred             CceEeeeecCCcHHHHHHHHHHHHhccCCCcCCCCccccceEEecCCCcceeeccCCcceEecCCeeEeccccccCCCCC
Confidence            46889999999999999999644    36654    3444443 22   333331              25778899999


Q ss_pred             cceeee
Q 040824           65 STLHLV   70 (154)
Q Consensus        65 ~~i~l~   70 (154)
                      +++.++
T Consensus       119 atlal~  124 (126)
T 3kuz_A          119 STIKVF  124 (126)
T ss_dssp             CEEEEE
T ss_pred             CEEEEe
Confidence            988654

>1vd2_A Protein kinase C, IOTA type; PB1 domain, OPCA motif, APKC, ZIP/P62, MEK5, molecular recognition, transferase; NMR {Homo sapiens} SCOP: d.15.2.2 PDB: 1wmh_A

Probab=91.67  E-value=1.2  Score=26.37  Aligned_cols=44  Identities=11%  Similarity=0.180  Sum_probs=33.9

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCC-eEEEEc
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLIFA   46 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~-q~L~~~   46 (154)
                      +|++.. +|..+.+.++++.+..+|.+++....+++... ..+.|.
T Consensus         8 kvK~~~-~gdi~~~~v~~~i~~~~L~~kv~~~~~~~~~~~f~lky~   52 (89)
T 1vd2_A            8 RVKAYY-RGDIMITHFEPSISFEGLCNEVRDMCSFDNEQLFTMKWI   52 (89)
T ss_dssp             EEEEES-SSCEEEEEECTTCCHHHHHHHHHHHTTCCSSCCEEEEEC
T ss_pred             EEEEEe-CCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCeEEEEEE
Confidence            344444 56788999999999999999999999987533 555554

>3qij_A Protein 4.1; cytoskeleton, structural genomics, structural genomics conso SGC; 1.80A {Homo sapiens} PDB: 1gg3_A 3bin_A 2he7_A 2rq1_A

Probab=91.65  E-value=0.71  Score=33.38  Aligned_cols=73  Identities=15%  Similarity=-0.041  Sum_probs=51.7

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCC-CceeEEEC---C--eecCCCCcccccccCCCCEEEEEE
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPP-VQQRLIYA---G--KQLADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~-~~~~l~~~---g--~~l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      ..+.+.|..++|....+.+++++|+.+|-..+++..|+.. +-+-|.+.   |  ..|+.++++.+........+++.+
T Consensus        16 ~~~~~~V~lldgt~~~~~vd~~tt~~el~~~v~~~l~L~e~~~FgL~~~~~~~~~~wLd~~k~i~~q~~~~~~~l~frv   94 (296)
T 3qij_A           16 FQGHCKVSLLDDTVYECVVEKHAKGQDLLKRVCEHLNLLEEDYFGLAIWDNATSKTWLDSAKEIKKQVRGVPWNFTFNV   94 (296)
T ss_dssp             -CCEEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHTCSSGGGEEEEEEEETTEEEECCTTSBHHHHC---CCEEEEEE
T ss_pred             ceEEEEEEccCCCEEEEEECCCCCHHHHHHHHHHHcCCCCcceeEEEEEcCCCccchhccchhHHHhcCCCCcEEEEEE
Confidence            4577888889999999999999999999999999999853 33555542   3  357777777776533334454443

>1j0g_A Hypothetical protein 1810045K17; ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: d.15.1.6 PDB: 1wxs_A 1l7y_A

Probab=91.39  E-value=1.2  Score=25.60  Aligned_cols=64  Identities=17%  Similarity=0.259  Sum_probs=54.8

Q ss_pred             EEeeCCCchHHHHHHHHhhhcCCCCCceeEEE-CCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           90 EIDIEPTDTIERIKERVEEKEGIPPVQQRLIY-AGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        90 ~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~-~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      .+.|+.......+-+-.++.+.+|+...-++. .|-=++..++-...-++.|+.+.++-|-|-|.
T Consensus        27 vlsVPE~~PftAVlkfaaEeF~vp~~TsAiiT~dGiGInP~QtAGnvFlKhGseLrlIPRDRVG~   91 (92)
T 1j0g_A           27 VLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAGNVFLKHGSELRIIPRDRVGS   91 (92)
T ss_dssp             EEEEETTSBHHHHHHHHHHHTTCCSSSEEEECTTSCCCCCSSBHHHHHHHTCSEEEEEECCSSCC
T ss_pred             EEecCccCchHHHHHHHHHHcCCCccceEEEecCCcccChhhccchhhhhcCceeEecccccccC
Confidence            47788888888888889999999998887774 56678888999999999999999998887775

>1y8x_B Ubiquitin-activating enzyme E1C; ubiquitin-conjugating enzyme E2 M, ligase; 2.40A {Homo sapiens} SCOP: c.111.1.2 PDB: 3fn1_A

Probab=90.89  E-value=0.33  Score=29.30  Aligned_cols=59  Identities=12%  Similarity=0.284  Sum_probs=40.9

Q ss_pred             eEEEeeCCCchHHHHHHHHhhhcCCCC---C--------ceeEEECC-eecC------CCCcccccccCCCCEEEEE
Q 040824           88 EIEIDIEPTDTIERIKERVEEKEGIPP---V--------QQRLIYAG-KQLA------DDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        88 ~~~~~v~~~~tv~~LK~~i~~~~~i~~---~--------~~~l~~~g-~~l~------d~~~L~~~~i~~~~~i~~~  146 (154)
                      ...++++++.|+.+|...+++.-.+..   +        .-.|++.+ ..|+      -+++|.+.|+.+|+.|+|.
T Consensus         6 ~~~l~v~~~~TL~~lid~L~~~p~~qlk~PSltt~~~~~~k~LYmq~pp~Lee~Tr~NL~k~l~eLgl~~g~ei~Vt   82 (98)
T 1y8x_B            6 PQNIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYMQSVTSIEERTRPNLSKTLKELGLVDGQELAVA   82 (98)
T ss_dssp             CCCEECCTTCBHHHHHHHHHHCTTCCCSSCEEEEEETTEEEEEECSSCHHHHHHHHHHHHSBSGGGTCCTTCEEEEE
T ss_pred             cEEEEECCchhHHHHHHHHHhChHhhccCCeeeeecCCCCCeEEEeCcHHHHHHhHhhhhCCHHHhCCCCCCEEEEE
Confidence            456889999999999999988543221   1        33444333 1222      3567999999999999885

>1wgk_A Riken cDNA 2900073H19 protein; THis domain, ubiqutin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.3.3 PDB: 1xo3_A

Probab=90.79  E-value=1.9  Score=26.65  Aligned_cols=64  Identities=9%  Similarity=0.104  Sum_probs=37.4

Q ss_pred             eEEEeeCC---CchHHHHHHHHhhhcC-CC----------CCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           88 EIEIDIEP---TDTIERIKERVEEKEG-IP----------PVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        88 ~~~~~v~~---~~tv~~LK~~i~~~~~-i~----------~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ...++++.   ..||.+|...+++.+. ..          .....++.++....-- -=.++-+++||.|.++-..-||
T Consensus        31 ~~~vel~~~~~~~TV~~Ll~~L~~~~~~~~~~lf~~~g~lr~~i~VlVN~~di~~l-~gldt~L~dGDeV~iip~vaGG  108 (114)
T 1wgk_A           31 KHQVALPGQEEPWDIRNLLVWIKKNLLKERPELFIQGDSVRPGILVLINDADWELL-GELDYQLQDQDSILFISTLHGG  108 (114)
T ss_dssp             EEEEEECCCSSCCBHHHHHHHHTTTTCCSCHHHHCCSSSCCSSEEEEESSSBHHHH-CTTTCBCCSSEEEEEEECSCCC
T ss_pred             EEEEEeCCCCCCCCHHHHHHHHHHHccchhHhhCccCCcccCCeEEEECCeeeecc-CCcCcCCCCCCEEEEeCCCCCC
Confidence            45677773   3699999999998762 11          0112233344321100 1135679999999776665555

>1vjk_A Molybdopterin converting factor, subunit 1; structural genomics, PSI, protein structure INI southeast collaboratory for structural genomics; 1.51A {Pyrococcus furiosus} SCOP: d.15.3.1

Probab=90.67  E-value=1.7  Score=25.88  Aligned_cols=67  Identities=10%  Similarity=0.242  Sum_probs=42.9

Q ss_pred             CEEEEEeCC------C-CEEEEEEeCCCcHHHHHHHHHhHhC-C----------CCCCeEEEEcceEeccCceecccccc
Q 040824            1 MQIFVKTLT------G-KTITLEVESSDTIDNVKAKIQDKEG-I----------PPDQQRLIFAGKQLEDGRTLADYNIQ   62 (154)
Q Consensus         1 m~v~v~~~~------~-~~~~~~v~~~~tv~~lk~~i~~~~~-~----------~~~~q~L~~~g~~L~d~~~l~~~~i~   62 (154)
                      |+|+|+.-.      | ....++++...||.+|.+.+..... +          ......+..||+....     ++.++
T Consensus        10 ~~v~V~~FA~lre~~g~~~~~~e~~~~~Tv~~Ll~~L~~~~p~l~~~l~~~~g~~~~~v~v~VNg~~v~~-----~~~L~   84 (98)
T 1vjk_A           10 VKVKVKYFARFRQLAGVDEEEIELPEGARVRDLIEEIKKRHEKFKEEVFGEGYDEDADVNIAVNGRYVSW-----DEELK   84 (98)
T ss_dssp             EEEEEEECTHHHHHHSSSEEEEEECTTCBHHHHHHHHHHHCGGGGGSCBCSSSCTTSSBEEEETTBCCCT-----TCBCC
T ss_pred             EEEEEEEhHHHHHHhCCCeEEEECCCCCCHHHHHHHHHhHChhHHHHhhccccccCCcEEEEECCEECCC-----CCCCC
Confidence            456666542      3 4567888888999999999976631 1          0123445566666542     55678


Q ss_pred             cccceeeeee
Q 040824           63 KESTLHLVLR   72 (154)
Q Consensus        63 ~~~~i~l~~~   72 (154)
                      +|+.|.+...
T Consensus        85 dGDeV~i~pp   94 (98)
T 1vjk_A           85 DGDVVGVFPP   94 (98)
T ss_dssp             TTCEEEEESC
T ss_pred             CCCEEEEECC
Confidence            8888876543

>1wgy_A RAP guanine nucleotide exchange factor 5; ubiquitin fold, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.5

Probab=90.53  E-value=1.9  Score=26.24  Aligned_cols=71  Identities=13%  Similarity=0.175  Sum_probs=50.8

Q ss_pred             eeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEE---ECCe--ecCCCCcccccccCCCCEEEEEEe
Q 040824           78 MIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI---YAGK--QLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        78 ~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~---~~g~--~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      ...|-..+.+...+.++.+.|+.+++..++.+.+...+.+.|.   ++|.  .++++..--.-.+.-+..|++..+
T Consensus        11 ~~~Vy~~Dhsy~tvr~~v~~sa~eIl~~va~kl~~~~e~l~Lv~v~ssGEk~~lqp~d~si~tsL~~NgRLfvc~k   86 (104)
T 1wgy_A           11 FCHVYITEHSYVSVKAKVSSIAQEILKVVAEKIQYAEEDLALVAITFSGEKHELQPNDLVISKSLEASGRIYVYRK   86 (104)
T ss_dssp             CEEEECSSSCEEEECCCTTCBSHHHHHHHHHHHTSCGGGEEEEEECSSCCCCBCCTTSBSSCCSSCSSCEEEEEEC
T ss_pred             EEEEEeccCceEEEEEeccchHHHHHHHHHHHhcCCccceEEEEEccCCcEeecCCcceEEEeeccccceEEEeeh
Confidence            3344455667788899999999999999999999887778776   5665  345544444445566777777654

>1wgr_A Growth factor receptor-bound protein 7; RA domain, GRB7, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.15.1.5

Probab=90.49  E-value=0.82  Score=27.66  Aligned_cols=60  Identities=13%  Similarity=0.174  Sum_probs=42.5

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCC-ceeEE--EC----CeecCCCCcccc
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPV-QQRLI--YA----GKQLADDKTARD  134 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~-~~~l~--~~----g~~l~d~~~L~~  134 (154)
                      .+..+.+-..+|+...+.|++++|+.++-+.++.+.++..+ ...|+  +.    .+.++|...+-+
T Consensus         8 ~k~vvkvf~~Dgssksi~V~~~~Ta~dv~~~L~~K~~~~~~~~WaLvE~~P~L~~ER~~EDHE~vve   74 (100)
T 1wgr_A            8 RPHVVKVYSEDGACRSVEVAAGATARHVCEMLVQRAHALSDETWGLVECHPHLALERGLEDHESVVE   74 (100)
T ss_dssp             SCEEEEEEETTSCEEEEEECTTCCHHHHHHHHHCSSSCCCCCCCCEEEEETTTTEEEEECSSSCHHH
T ss_pred             CCEEEEEEecCCCEEEEEECCCCcHHHHHHHHHHHcCCCCCCCeEEEEecCCCCcEEeccCchhHHH
Confidence            34566777789999999999999999999999999987533 33333  22    135566554443

>3hm6_X Plexin-B1; structural genomics consortium, SGC, membrane, transmembrane receptor, cell membrane, glycoprotein, phosphoprotein; 2.40A {Homo sapiens} PDB: 3sua_D* 3su8_X*

Probab=89.51  E-value=2.1  Score=34.24  Aligned_cols=63  Identities=30%  Similarity=0.478  Sum_probs=44.5

Q ss_pred             CEEEEEEeCCCcHHHHHHHHHhHh--CCCC------CCeEEEE-c---ce-EeccCc-------------eecccccccc
Q 040824           11 KTITLEVESSDTIDNVKAKIQDKE--GIPP------DQQRLIF-A---GK-QLEDGR-------------TLADYNIQKE   64 (154)
Q Consensus        11 ~~~~~~v~~~~tv~~lk~~i~~~~--~~~~------~~q~L~~-~---g~-~L~d~~-------------~l~~~~i~~~   64 (154)
                      +..++.+-.-+||.++|++|-+..  |+|.      +...|-| .   |+ .|.|..             ||++|++++|
T Consensus       274 ~~i~VkVLdCDTItQVKeKiLDavYk~~pyS~rP~~~~~dLEwr~g~~g~~iL~D~D~ts~~~~~wkrLNTL~HY~V~dg  353 (644)
T 3hm6_X          274 QGVPVKVLDCDTISQAKEKMLDQLYKGVPLTQRPDPRTLDVEWRSGVAGHLILSDEDVTSEVQGLWRRLNTLQHYKVPDG  353 (644)
T ss_dssp             CCEEEEEETTSBHHHHHHHHHHHHTTTSCGGGSCCGGGEEEEEECSSSCEEEECSSSTTCCEETTEEECCBTTTTTCCTT
T ss_pred             CceeeEeeccCcHHHHHHHHHHHHHcCCCcccCCCCCCcceEEeeCCCCceeecccCccceecCcceeecchhhcCCCCC
Confidence            447889999999999999997552  4443      4455554 2   33 355532             6999999999


Q ss_pred             cceeeeeee
Q 040824           65 STLHLVLRL   73 (154)
Q Consensus        65 ~~i~l~~~~   73 (154)
                      +++.++.+.
T Consensus       354 a~v~L~p~~  362 (644)
T 3hm6_X          354 ATVALVPCL  362 (644)
T ss_dssp             CEEEEEEC-
T ss_pred             cEEEEEecc
Confidence            999877654

>3u52_E Phenol hydroxylase component PHO; 4-helix bundle, dioxygen, hydrocarbons, oxidore; HET: MPO EPE; 1.95A {Pseudomonas stutzeri} PDB: 2inn_E* 2inp_E

Probab=89.43  E-value=2  Score=26.61  Aligned_cols=62  Identities=10%  Similarity=0.228  Sum_probs=49.4

Q ss_pred             ceEEEeeCCCchHHHHHHHH-hhhcC-------CCCCceeEEECCeecC--CCCcccccccCCCCEEEEEEe
Q 040824           87 KEIEIDIEPTDTIERIKERV-EEKEG-------IPPVQQRLIYAGKQLA--DDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        87 ~~~~~~v~~~~tv~~LK~~i-~~~~~-------i~~~~~~l~~~g~~l~--d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      ..+.+.+++.++.++|-+.+ ...++       ++.+.-+|..+|++..  .+++|++.|+...|.|.+.-.
T Consensus        38 ap~~~p~pP~mpFg~lv~~vl~~~~~~hPDfa~idws~v~W~l~g~pftPD~~kSLaenG~~HKs~lrf~TP  109 (119)
T 3u52_E           38 APFALLVQPGMTFSALVDEILKPATAAHPDSAKADFLNAEWLLNDEPFTPKADASLKEQGIDHKSMLTVTTP  109 (119)
T ss_dssp             SCEEEEECTTSBHHHHHHHTHHHHTTTSTTGGGCCTTSSEEEETTEEECCCTTSBTTTTTCCTTEEEEEECT
T ss_pred             CceeecCCCCCCHHHHHHHhcchhhhcCCccccCCcchheEEECCccCCCChhhhHHHcCCCchheEEEeCC
Confidence            55789999999999998776 33333       5666778999999875  678999999999999876543

>1wgr_A Growth factor receptor-bound protein 7; RA domain, GRB7, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.15.1.5

Probab=89.31  E-value=1.1  Score=27.03  Aligned_cols=56  Identities=18%  Similarity=0.235  Sum_probs=40.9

Q ss_pred             EEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEE---c----ceEeccCceecc
Q 040824            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF---A----GKQLEDGRTLAD   58 (154)
Q Consensus         3 v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~---~----g~~L~d~~~l~~   58 (154)
                      |+|-..+|....+.|++++|+.++.+.+..+.++..+.-.=++   .    -+.++|+..+-+
T Consensus        12 vkvf~~Dgssksi~V~~~~Ta~dv~~~L~~K~~~~~~~~WaLvE~~P~L~~ER~~EDHE~vve   74 (100)
T 1wgr_A           12 VKVYSEDGACRSVEVAAGATARHVCEMLVQRAHALSDETWGLVECHPHLALERGLEDHESVVE   74 (100)
T ss_dssp             EEEEETTSCEEEEEECTTCCHHHHHHHHHCSSSCCCCCCCCEEEEETTTTEEEEECSSSCHHH
T ss_pred             EEEEecCCCEEEEEECCCCcHHHHHHHHHHHcCCCCCCCeEEEEecCCCCcEEeccCchhHHH
Confidence            5677789999999999999999999999999986644332211   1    266777665433

>1wgy_A RAP guanine nucleotide exchange factor 5; ubiquitin fold, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.5

Probab=89.21  E-value=1.8  Score=26.36  Aligned_cols=68  Identities=10%  Similarity=0.228  Sum_probs=47.7

Q ss_pred             EEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEE---Ecc--eEeccCceecccccccccceeeeee
Q 040824            5 VKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI---FAG--KQLEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         5 v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~---~~g--~~L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      |=..+...+.+.+..+.|+.+++..+.++.+...+.+.|.   ++|  ..|+++..--.-.+..+..++++.+
T Consensus        14 Vy~~Dhsy~tvr~~v~~sa~eIl~~va~kl~~~~e~l~Lv~v~ssGEk~~lqp~d~si~tsL~~NgRLfvc~k   86 (104)
T 1wgy_A           14 VYITEHSYVSVKAKVSSIAQEILKVVAEKIQYAEEDLALVAITFSGEKHELQPNDLVISKSLEASGRIYVYRK   86 (104)
T ss_dssp             EECSSSCEEEECCCTTCBSHHHHHHHHHHHTSCGGGEEEEEECSSCCCCBCCTTSBSSCCSSCSSCEEEEEEC
T ss_pred             EEeccCceEEEEEeccchHHHHHHHHHHHhcCCccceEEEEEccCCcEeecCCcceEEEeeccccceEEEeeh
Confidence            4344567788899999999999999999999877678776   456  3355555433334555566666654

>1ef1_A Moesin; membrane, FERM domain, tail domain, membrane protein; 1.90A {Homo sapiens} SCOP: a.11.2.1 b.55.1.5 d.15.1.4 PDB: 1sgh_A 1j19_A 2emt_A 2ems_A 2d10_A 2d11_A 2yvc_A 2d2q_A 2zpy_A 1gc7_A 1gc6_A 1ni2_A

Probab=88.90  E-value=3.2  Score=29.69  Aligned_cols=68  Identities=16%  Similarity=0.273  Sum_probs=49.3

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCC-eEEEE---cc--eEeccCceecccccccccceee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLIF---AG--KQLEDGRTLADYNIQKESTLHL   69 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~-q~L~~---~g--~~L~d~~~l~~~~i~~~~~i~l   69 (154)
                      |.+.|...+| +..+.++..+|+.++-+.+....|+.... =-|.+   +|  ..|+.+..+.+.+.+.+....+
T Consensus         2 i~~~V~l~d~-~~~~~v~~~tt~~el~~~v~~~l~L~e~~~FgL~~~~~~~~~~wLd~~~~l~~q~~~~~~~~~l   75 (294)
T 1ef1_A            2 ISVRVTTMDA-ELEFAIQPNTTGKQLFDQVVKTIGLREVWFFGLQYQDTKGFSTWLKLNKKVTAQDVRKESPLLF   75 (294)
T ss_dssp             EEEEEEETTE-EEEEEECTTCBHHHHHHHHHHHHTCCCGGGEEEEEEBTTSCEEECCSSSBGGGSCBCCCSSEEE
T ss_pred             EEEEEEECCc-eEEEEECCCCcHHHHHHHHHHHcCCCCcceeEEEEECCCCceeecccccCHHhhccCCCCCEEE
Confidence            4688899887 67899999999999999999999976533 23333   23  4577778887766544444433

>2kmc_A Fermitin family homolog 1; kindlin, cytoskeleton, integrin, N-terminal, talin, cell adhesion, cell junction, cell membrane, cell projection; NMR {Mus musculus}

Probab=88.72  E-value=2.6  Score=25.29  Aligned_cols=71  Identities=23%  Similarity=0.243  Sum_probs=54.7

Q ss_pred             EEEEEeCCC---CEEEEEEeCCCcHHHHHHHHHhHhCCC--CCCeEEEEcc---eEeccCceecccccccccceeeeee
Q 040824            2 QIFVKTLTG---KTITLEVESSDTIDNVKAKIQDKEGIP--PDQQRLIFAG---KQLEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         2 ~v~v~~~~~---~~~~~~v~~~~tv~~lk~~i~~~~~~~--~~~q~L~~~g---~~L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      +|+|...+.   ....++|.-+.-|+.+..++-++..++  =++.-|.+.-   ..++...+|..||+..++.+++...
T Consensus        21 ~V~V~d~~~~~~~~~~lrV~GdlHIGGvmlklVEki~i~~dWSDhaLWW~~k~~WLlkt~~tLDkygiqADa~L~ftp~   99 (102)
T 2kmc_A           21 VVRVDHANGEQQTEITLRVSGDLHIGGVMLKLVEQMNIAQDWSDYALWWEQKRCWLLKTHWTLDKCGVQADANLLFTPQ   99 (102)
T ss_dssp             EEEEECTTSSCEEEEEEEECSCCBHHHHHHHHHHHHCCSSCCSSEEEEETTTTEEECCTTSBHHHHTCCTTSCEEEEEC
T ss_pred             EEEEecCCcccCccEEEEEeeccccchhhhhhhhhcccccchHHhhhhhhhhchhhhhhhhhhhhhceeeeeeeeccCC
Confidence            577777554   457889988899999999998777655  3456666542   5578889999999999998876654

>1h4r_A Merlin; FERM, neurofibromatosis, NF2, structural protein, cytoskeleton, anti-oncogene; 1.8A {Homo sapiens} SCOP: a.11.2.1 b.55.1.5 d.15.1.4 PDB: 1isn_A 3u8z_A

Probab=88.64  E-value=3.6  Score=29.77  Aligned_cols=66  Identities=12%  Similarity=0.160  Sum_probs=48.8

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCC-eEEEE--cc--eEeccCceecccccccccce
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLIF--AG--KQLEDGRTLADYNIQKESTL   67 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~-q~L~~--~g--~~L~d~~~l~~~~i~~~~~i   67 (154)
                      +.+.|...+| .+.++++..+|+.++-+.|....++.... --|.+  +|  .+|+.+..+.+.+.+.+...
T Consensus        23 ~~~~V~lldg-~~~~~v~~~t~~~el~~~v~~~l~L~e~~~FgL~~~~~~~~~wL~~~~~i~~q~~~~~~~~   93 (314)
T 1h4r_A           23 FTVRIVTMDA-EMEFNCEMKWKGKDLFDLVCRTLGLRETWFFGLQYTIKDTVAWLKMDKKVLDHDVSKEEPV   93 (314)
T ss_dssp             EEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHTCCCGGGEEEEEEETTEEEECCTTSBGGGSSCCCSSSE
T ss_pred             eEEEEEeCCc-eEEEEeCCCCcHHHHHHHHHHHhCCCCCccceEEEEeCCcCeeCCCccCHHHcCCCCCCCE
Confidence            3578888888 78899999999999999999999977422 23433  33  45788888888765444444

>3hm6_X Plexin-B1; structural genomics consortium, SGC, membrane, transmembrane receptor, cell membrane, glycoprotein, phosphoprotein; 2.40A {Homo sapiens} PDB: 3sua_D* 3su8_X*

Probab=88.03  E-value=2.5  Score=33.80  Aligned_cols=63  Identities=27%  Similarity=0.566  Sum_probs=43.4

Q ss_pred             ceEEEeeCCCchHHHHHHHHhhh--cCCC------CCceeEEEC----Ce-ecCCC-------------CcccccccCCC
Q 040824           87 KEIEIDIEPTDTIERIKERVEEK--EGIP------PVQQRLIYA----GK-QLADD-------------KTARDYNIEGG  140 (154)
Q Consensus        87 ~~~~~~v~~~~tv~~LK~~i~~~--~~i~------~~~~~l~~~----g~-~l~d~-------------~~L~~~~i~~~  140 (154)
                      ..+++.|-.++||.++|++|-..  .|.|      ++.+-|-|.    |. .|.|.             .||+.|++.+|
T Consensus       274 ~~i~VkVLdCDTItQVKeKiLDavYk~~pyS~rP~~~~~dLEwr~g~~g~~iL~D~D~ts~~~~~wkrLNTL~HY~V~dg  353 (644)
T 3hm6_X          274 QGVPVKVLDCDTISQAKEKMLDQLYKGVPLTQRPDPRTLDVEWRSGVAGHLILSDEDVTSEVQGLWRRLNTLQHYKVPDG  353 (644)
T ss_dssp             CCEEEEEETTSBHHHHHHHHHHHHTTTSCGGGSCCGGGEEEEEECSSSCEEEECSSSTTCCEETTEEECCBTTTTTCCTT
T ss_pred             CceeeEeeccCcHHHHHHHHHHHHHcCCCcccCCCCCCcceEEeeCCCCceeecccCccceecCcceeecchhhcCCCCC
Confidence            45889999999999999999532  2344      345556652    22 23331             37999999999


Q ss_pred             CEEEEEEee
Q 040824          141 SVLHLVLAL  149 (154)
Q Consensus       141 ~~i~~~~~~  149 (154)
                      +++.++-+.
T Consensus       354 a~v~L~p~~  362 (644)
T 3hm6_X          354 ATVALVPCL  362 (644)
T ss_dssp             CEEEEEEC-
T ss_pred             cEEEEEecc
Confidence            999876443

>1tyg_B YJBS; alpha beta barrel, protein-protein complex, THis, BIOS protein; 3.15A {Bacillus subtilis} SCOP: d.15.3.2

Probab=87.82  E-value=1.6  Score=25.57  Aligned_cols=57  Identities=11%  Similarity=0.137  Sum_probs=37.7

Q ss_pred             CCCEEEEEEeCC-CcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeee
Q 040824            9 TGKTITLEVESS-DTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         9 ~~~~~~~~v~~~-~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      ||+  +++++.. .||.+|.+.+    ++++....+..||..+.. ....+.-+++|+.|.++..
T Consensus        26 NGe--~~el~~~~~Tv~dLL~~L----~~~~~~vaVavNg~iV~~-~~~~~~~L~dGD~Vei~~~   83 (87)
T 1tyg_B           26 NGK--DVKWKKDTGTIQDLLASY----QLENKIVIVERNKEIIGK-ERYHEVELCDRDVIEIVHF   83 (87)
T ss_dssp             TTE--EECCSSSCCBHHHHHHHT----TCTTSCCEEEETTEEECG-GGTTTSBCCSSSEEEEEEE
T ss_pred             CCE--EEECCCCCCcHHHHHHHh----CCCCCCEEEEECCEECCh-hhcCCcCCCCCCEEEEEcc
Confidence            454  3445666 8999998875    566666666678877642 2333456888998876643

>3ig3_A Plxna3 protein; plexin intracellular GAP RBD inactive, membrane, transmembra membrane protein, signaling protein; 1.99A {Mus musculus} PDB: 3ryt_A*

Probab=87.64  E-value=3.8  Score=32.74  Aligned_cols=72  Identities=25%  Similarity=0.425  Sum_probs=48.3

Q ss_pred             EEEEEeCC---CCEEEEEEeCCCcHHHHHHHHHhHh--CCC------CCCeEEEE-c---ce-EeccC------------
Q 040824            2 QIFVKTLT---GKTITLEVESSDTIDNVKAKIQDKE--GIP------PDQQRLIF-A---GK-QLEDG------------   53 (154)
Q Consensus         2 ~v~v~~~~---~~~~~~~v~~~~tv~~lk~~i~~~~--~~~------~~~q~L~~-~---g~-~L~d~------------   53 (154)
                      .|+|-..+   .+..++.+-.-+||.++|++|-+..  ++|      ++...|-| .   |+ .|.|.            
T Consensus       235 tL~v~~~~~~~~~~i~vkVLdCDTItQVKeKiLdavYk~~pyS~rP~~~~~dLEwr~g~~g~~iL~D~D~ts~~~~~wkr  314 (627)
T 3ig3_A          235 TLHCVCPESEGSAQVPVKVLNCDSITQAKDKLLDTVYKGIPYSQRPKAEDMDLEWRQGRMARIILQDEDITTKIECDWKR  314 (627)
T ss_dssp             EEEEECTTTC--CEEEEEEETTCBHHHHHHHHHHHHTTTSCGGGSCCGGGEEEEEESCSSCEEEECSSSTTCCEETTEEE
T ss_pred             EEEEeccCCCCCCceeeEeeccCcHHHHHHHHHHHHHcCCCcccCCCCCccceeEeeCCCCceeeccCCccccccCceeE
Confidence            34444433   2558899999999999999997653  444      44455554 2   22 34442            


Q ss_pred             -ceecccccccccceeeeeee
Q 040824           54 -RTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus        54 -~~l~~~~i~~~~~i~l~~~~   73 (154)
                       .||++|++++|+++.++.+.
T Consensus       315 LNTL~HY~V~Dga~v~L~p~~  335 (627)
T 3ig3_A          315 VNSLAHYQVTDGSLVALVPKQ  335 (627)
T ss_dssp             CCBTTTTTCCTTCEEEEEEC-
T ss_pred             ecchhhcCCCCCceEEEEecc
Confidence             26999999999999887654

>2qjl_A URM1, ubiquitin-related modifier 1; ubiquitin-like protein, signaling protein; 1.44A {Saccharomyces cerevisiae} PDB: 2pko_A 2ax5_A

Probab=87.53  E-value=3.1  Score=24.75  Aligned_cols=65  Identities=15%  Similarity=0.281  Sum_probs=39.3

Q ss_pred             ceEEEeeC--CCchHHHHHHHHhhhcCCCCC-------------ceeEEECCeecCCCCcccccccCCCCEEEEEEeecC
Q 040824           87 KEIEIDIE--PTDTIERIKERVEEKEGIPPV-------------QQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRG  151 (154)
Q Consensus        87 ~~~~~~v~--~~~tv~~LK~~i~~~~~i~~~-------------~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~g  151 (154)
                      +...++++  +..||.+|.+.+.+++.-...             ...+..++....-. .=.++-+++||.|.++-..-|
T Consensus        20 ~~~~~~l~~~~~~Tv~~L~~~L~~~~~~~~~~l~~~~~~~~lr~~~~v~VN~~~~~~~-~~~d~~L~dgDeVa~~Ppv~G   98 (99)
T 2qjl_A           20 RVHKIKMDKEDPVTVGDLIDHIVSTMINNPNDVSIFIEDDSIRPGIITLINDTDWELE-GEKDYILEDGDIISFTSTLHG   98 (99)
T ss_dssp             CEEEEEECSCSCCBHHHHHHHHHHHTCSSGGGHHHHEETTEECTTEEEEETTEEGGGG-TGGGCBCCTTCEEEEEECTTC
T ss_pred             cEEEEecCCCCCCcHHHHHHHHHHHCchhhHHHhhhccCCccccCeEEEECCEEcccc-CCCCcCcCCCCEEEEECCCCC
Confidence            34556666  678999999999887732111             11234555432100 013557899999987766655


Q ss_pred             C
Q 040824          152 G  152 (154)
Q Consensus       152 g  152 (154)
                      |
T Consensus        99 G   99 (99)
T 2qjl_A           99 G   99 (99)
T ss_dssp             C
T ss_pred             C
Confidence            5

>1y8x_B Ubiquitin-activating enzyme E1C; ubiquitin-conjugating enzyme E2 M, ligase; 2.40A {Homo sapiens} SCOP: c.111.1.2 PDB: 3fn1_A

Probab=87.37  E-value=3.1  Score=25.00  Aligned_cols=59  Identities=10%  Similarity=0.235  Sum_probs=40.3

Q ss_pred             EEEEEEeCCCcHHHHHHHHHhHhCCCCC-----------CeEEEEcc-eEe------ccCceecccccccccceeee
Q 040824           12 TITLEVESSDTIDNVKAKIQDKEGIPPD-----------QQRLIFAG-KQL------EDGRTLADYNIQKESTLHLV   70 (154)
Q Consensus        12 ~~~~~v~~~~tv~~lk~~i~~~~~~~~~-----------~q~L~~~g-~~L------~d~~~l~~~~i~~~~~i~l~   70 (154)
                      ...+++++++|+.+|.+.+.+.-.+.-.           ...|+..+ ..|      +-+++|.+.|+.+|..|++.
T Consensus         6 ~~~l~v~~~~TL~~lid~L~~~p~~qlk~PSltt~~~~~~k~LYmq~pp~Lee~Tr~NL~k~l~eLgl~~g~ei~Vt   82 (98)
T 1y8x_B            6 PQNIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYMQSVTSIEERTRPNLSKTLKELGLVDGQELAVA   82 (98)
T ss_dssp             CCCEECCTTCBHHHHHHHHHHCTTCCCSSCEEEEEETTEEEEEECSSCHHHHHHHHHHHHSBSGGGTCCTTCEEEEE
T ss_pred             cEEEEECCchhHHHHHHHHHhChHhhccCCeeeeecCCCCCeEEEeCcHHHHHHhHhhhhCCHHHhCCCCCCEEEEE
Confidence            4568999999999999999885332222           34555443 111      12557899999999988765

>2kmc_A Fermitin family homolog 1; kindlin, cytoskeleton, integrin, N-terminal, talin, cell adhesion, cell junction, cell membrane, cell projection; NMR {Mus musculus}

Probab=87.01  E-value=3.4  Score=24.77  Aligned_cols=70  Identities=17%  Similarity=0.209  Sum_probs=53.0

Q ss_pred             eeeeeeecCC---ceEEEeeCCCchHHHHHHHHhhhcCC--CCCceeEEECCe---ecCCCCcccccccCCCCEEEEE
Q 040824           77 TMIKVKTLTG---KEIEIDIEPTDTIERIKERVEEKEGI--PPVQQRLIYAGK---QLADDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        77 ~~i~v~~~~~---~~~~~~v~~~~tv~~LK~~i~~~~~i--~~~~~~l~~~g~---~l~d~~~L~~~~i~~~~~i~~~  146 (154)
                      +.|+|...+.   ....++|..+..|+.+..++-+...+  +.++.-|-+..+   .+.-..||..|||+..+.+++.
T Consensus        20 L~V~V~d~~~~~~~~~~lrV~GdlHIGGvmlklVEki~i~~dWSDhaLWW~~k~~WLlkt~~tLDkygiqADa~L~ft   97 (102)
T 2kmc_A           20 LVVRVDHANGEQQTEITLRVSGDLHIGGVMLKLVEQMNIAQDWSDYALWWEQKRCWLLKTHWTLDKCGVQADANLLFT   97 (102)
T ss_dssp             EEEEEECTTSSCEEEEEEEECSCCBHHHHHHHHHHHHCCSSCCSSEEEEETTTTEEECCTTSBHHHHTCCTTSCEEEE
T ss_pred             EEEEEecCCcccCccEEEEEeeccccchhhhhhhhhcccccchHHhhhhhhhhchhhhhhhhhhhhhceeeeeeeecc
Confidence            4566666443   45788999899999999999877765  455566665543   6778899999999999988764

>3qij_A Protein 4.1; cytoskeleton, structural genomics, structural genomics conso SGC; 1.80A {Homo sapiens} PDB: 1gg3_A 3bin_A 2he7_A 2rq1_A

Probab=86.89  E-value=3.1  Score=30.00  Aligned_cols=60  Identities=10%  Similarity=0.061  Sum_probs=46.4

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCC-eEEEEc---c--eEeccCceecccc
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLIFA---G--KQLEDGRTLADYN   60 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~-q~L~~~---g--~~L~d~~~l~~~~   60 (154)
                      |.+.|...+|....++++..+|+.+|-+.|.++.|+.... --|.+.   |  ..|+.+..+.+..
T Consensus        18 ~~~~V~lldgt~~~~~vd~~tt~~el~~~v~~~l~L~e~~~FgL~~~~~~~~~~wLd~~k~i~~q~   83 (296)
T 3qij_A           18 GHCKVSLLDDTVYECVVEKHAKGQDLLKRVCEHLNLLEEDYFGLAIWDNATSKTWLDSAKEIKKQV   83 (296)
T ss_dssp             CEEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHTCSSGGGEEEEEEEETTEEEECCTTSBHHHHC
T ss_pred             EEEEEEccCCCEEEEEECCCCCHHHHHHHHHHHcCCCCcceeEEEEEcCCCccchhccchhHHHhc
Confidence            5688999999999999999999999999999999976432 344432   2  5577777766653

>2i1j_A Moesin; FERM, coiled-coil, C-ermad, ERM, radixin, ezrin, MER actin binding, masking, regulation, SELF-inhibition, cell A membrane protein; 2.10A {Spodoptera frugiperda} PDB: 2i1k_A 1e5w_A

Probab=86.82  E-value=4.8  Score=31.99  Aligned_cols=68  Identities=15%  Similarity=0.273  Sum_probs=49.8

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCC-CeEEEEc---c--eEeccCceecccccccccceee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPD-QQRLIFA---G--KQLEDGRTLADYNIQKESTLHL   69 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~-~q~L~~~---g--~~L~d~~~l~~~~i~~~~~i~l   69 (154)
                      |.+.|...+| ++.+.++..+|+.+|-..|....|+... .--|+|.   |  .+|+.+.++.+.+++.+..+.+
T Consensus         5 i~v~V~llDg-t~e~~vd~~tt~~ell~~V~~~LgL~e~~~FGL~~~d~~~~~~WLd~~k~i~~q~~~~~~~~~L   78 (575)
T 2i1j_A            5 MNVRVTTMDA-ELEFAIQQTTTGKQLFDQVVKTIGLREVWFFGLQYTDSKGDLTWIKLYKKVMQQDVKKENPLQF   78 (575)
T ss_dssp             EEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHTCCCGGGEEEEEEBTTSCEEECCTTSBGGGSCBCCCSSEEE
T ss_pred             EEEEEEeCCC-eEEEEECCCCCHHHHHHHHHHHcCCCCccceeEEEEecCcchhHhhccccHHHhcccCCCCeEE
Confidence            4678888888 6789999999999999999999997643 3344442   2  5677788888776555544433

>2k9x_A Tburm1, uncharacterized protein; unknown function; NMR {Trypanosoma brucei}

Probab=86.71  E-value=0.85  Score=28.06  Aligned_cols=63  Identities=11%  Similarity=0.249  Sum_probs=35.8

Q ss_pred             ceEEEeeCC----CchHHHHHHHHhhhcCCCCCcee---------------EEECCeecCCCCcccccccCCCCEEEEEE
Q 040824           87 KEIEIDIEP----TDTIERIKERVEEKEGIPPVQQR---------------LIYAGKQLADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        87 ~~~~~~v~~----~~tv~~LK~~i~~~~~i~~~~~~---------------l~~~g~~l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      +...++++.    ..||.+|-..+++.+.-  .+-.               ++.||+..+-. -=.++-+++||.|.++-
T Consensus        21 ~~~~v~l~~~~g~~~TV~dLl~~L~~~~~~--~r~~lf~~~g~~~lrpgIlVLVNg~d~e~l-~gldt~L~dgD~V~fis   97 (110)
T 2k9x_A           21 KQTSLQLDGVVPTGTNLNGLVQLLKTNYVK--ERPDLLVDQTGQTLRPGILVLVNSCDAEVV-GGMDYVLNDGDTVEFIS   97 (110)
T ss_dssp             SCSEECCCCSCGGGCCHHHHHHHHTTTTCC--SCHHHHBCSSSSSBCTTEEEEESSSBHHHH-TSSCCCCCSSCEEEEEE
T ss_pred             CeEEEEeCCcCCCCccHHHHHHHHHHHccc--cchhhEecCCCcccCCCeEEEECCeeeecc-CCcccCCCCcCEEEEeC
Confidence            345677763    35999999999887631  1222               22333221100 01356799999987765


Q ss_pred             eecCC
Q 040824          148 ALRGG  152 (154)
Q Consensus       148 ~~~gg  152 (154)
                      .+-||
T Consensus        98 tlhg~  102 (110)
T 2k9x_A           98 TLHGG  102 (110)
T ss_dssp             CCCCC
T ss_pred             CCccc
Confidence            55444

>1q1o_A Cell division control protein 24; PB1 domain, PCCR, PC motif, OPCA motif, yeast, cell polarity, protein-protein interaction; NMR {Saccharomyces cerevisiae} SCOP: d.15.2.2 PDB: 2kfj_A 2kfk_B

Probab=86.40  E-value=1.3  Score=26.66  Aligned_cols=36  Identities=19%  Similarity=0.113  Sum_probs=28.8

Q ss_pred             EEEEEeCC-------CCEEEEEEeCCCcHHHHHHHHHhHhCCC
Q 040824            2 QIFVKTLT-------GKTITLEVESSDTIDNVKAKIQDKEGIP   37 (154)
Q Consensus         2 ~v~v~~~~-------~~~~~~~v~~~~tv~~lk~~i~~~~~~~   37 (154)
                      +|+|...+       +..+.+.++++.+..+|..+|..+++.+
T Consensus         7 kVKv~y~~~~~~~~~~d~~~i~V~~~i~f~~L~~kI~~Kl~~~   49 (98)
T 1q1o_A            7 LFRISYNNNSNNTSSSEIFTLLVEKVWNFDDLIMAINSKISNT   49 (98)
T ss_dssp             EEEEEECSSCSSCCCCEEEEEEECTTCCHHHHHHHHHHHHHHH
T ss_pred             EEEEEecCcccccccCcEEEEEecCCCCHHHHHHHHHHHHcCC
Confidence            45666542       4568999999999999999999998754

>2hj1_A Hypothetical protein; structural genomics, PSI, protein structure initiative, NEW research center for structural genomics, nysgxrc; 2.10A {Haemophilus influenzae} SCOP: d.15.3.4

Probab=85.95  E-value=1.8  Score=25.94  Aligned_cols=58  Identities=7%  Similarity=0.054  Sum_probs=42.9

Q ss_pred             ceEEEeeCCCchHHHHHHHHhh--h-cCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEee
Q 040824           87 KEIEIDIEPTDTIERIKERVEE--K-EGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        87 ~~~~~~v~~~~tv~~LK~~i~~--~-~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      ..+.+++++..||.++-+...-  . ..+..+...+..+|+...     .+.-+++||.|.++-.+
T Consensus        26 ~~~~~~v~~g~TV~daI~~~gi~~~~peIdl~~~~V~Vng~~v~-----~d~~L~dGDRVEIyrpl   86 (97)
T 2hj1_A           26 YLKSFQVDEGITVQTAITQSGILSQFPEIDLSTNKIGIFSRPIK-----LTDVLKEGDRIEIYRPL   86 (97)
T ss_dssp             EEEEEEEETTCBHHHHHHHHTHHHHCTTCCTTTSEEEEEECSCC-----TTCBCCTTCEEEECCCC
T ss_pred             EEEEEEcCCCCcHHHHHHHcCCCccCCcccccccEEEEcCEECC-----CCccCCCCCEEEEEecc
Confidence            3467888999999999888753  2 245566677888888776     44568999999987443

>1ip9_A BEM1 protein; ubiquitin alpha/beta roll, signaling protein; NMR {Saccharomyces cerevisiae} SCOP: d.15.2.2 PDB: 1ipg_A 2kfk_A

Probab=85.83  E-value=3.6  Score=23.94  Aligned_cols=35  Identities=14%  Similarity=0.209  Sum_probs=28.7

Q ss_pred             EEEEeC-CCCEEEEEEeCCCcHHHHHHHHHhHhCCC
Q 040824            3 IFVKTL-TGKTITLEVESSDTIDNVKAKIQDKEGIP   37 (154)
Q Consensus         3 v~v~~~-~~~~~~~~v~~~~tv~~lk~~i~~~~~~~   37 (154)
                      ++||.. ++..|.+.++.+.+..+|+.+|..+..+.
T Consensus        13 ~KVK~yy~DDIiAIrvP~di~~~~L~dKi~~RLk~~   48 (85)
T 1ip9_A           13 TKIKFYYKDDIFALMLKGDTTYKELRSKIAPRIDTD   48 (85)
T ss_dssp             EEEEECBTTCCEEEEECSCCCHHHHHHHHHHHHTSS
T ss_pred             eEEEEEecCcEEEEECCCCCCHHHHHHHHHHHhccc
Confidence            344444 45679999999999999999999999883

>3ig3_A Plxna3 protein; plexin intracellular GAP RBD inactive, membrane, transmembra membrane protein, signaling protein; 1.99A {Mus musculus} PDB: 3ryt_A*

Probab=85.41  E-value=3.3  Score=33.05  Aligned_cols=64  Identities=22%  Similarity=0.424  Sum_probs=44.0

Q ss_pred             CceEEEeeCCCchHHHHHHHHhhhc--CCC------CCceeEEEC----Ce-ecCC-------------CCcccccccCC
Q 040824           86 GKEIEIDIEPTDTIERIKERVEEKE--GIP------PVQQRLIYA----GK-QLAD-------------DKTARDYNIEG  139 (154)
Q Consensus        86 ~~~~~~~v~~~~tv~~LK~~i~~~~--~i~------~~~~~l~~~----g~-~l~d-------------~~~L~~~~i~~  139 (154)
                      ...+++.|-.++||.++|++|-...  +.|      ++.+-|-|.    |+ .|.|             =.||+.|++.+
T Consensus       246 ~~~i~vkVLdCDTItQVKeKiLdavYk~~pyS~rP~~~~~dLEwr~g~~g~~iL~D~D~ts~~~~~wkrLNTL~HY~V~D  325 (627)
T 3ig3_A          246 SAQVPVKVLNCDSITQAKDKLLDTVYKGIPYSQRPKAEDMDLEWRQGRMARIILQDEDITTKIECDWKRVNSLAHYQVTD  325 (627)
T ss_dssp             -CEEEEEEETTCBHHHHHHHHHHHHTTTSCGGGSCCGGGEEEEEESCSSCEEEECSSSTTCCEETTEEECCBTTTTTCCT
T ss_pred             CCceeeEeeccCcHHHHHHHHHHHHHcCCCcccCCCCCccceeEeeCCCCceeeccCCccccccCceeEecchhhcCCCC
Confidence            3568899999999999999994433  333      455566552    22 2322             13799999999


Q ss_pred             CCEEEEEEee
Q 040824          140 GSVLHLVLAL  149 (154)
Q Consensus       140 ~~~i~~~~~~  149 (154)
                      |+++.++-+.
T Consensus       326 ga~v~L~p~~  335 (627)
T 3ig3_A          326 GSLVALVPKQ  335 (627)
T ss_dssp             TCEEEEEEC-
T ss_pred             CceEEEEecc
Confidence            9999887554

>2inc_C TOUB protein; DIIRON, 4-helix bundle, carboxylate bridge, metalloenzyme, oxidoreductase; HET: P6G; 1.85A {Pseudomonas stutzeri} SCOP: d.15.12.1 PDB: 2ind_C* 3n20_C* 1t0r_C 1t0s_C 1t0q_C* 3n1x_C 3n1y_C* 3n1z_C* 2rdb_C* 3rn9_C* 3rna_C 3rnb_C 3rnc_C 3rne_C 3rnf_C* 3rng_C

Probab=85.37  E-value=3.8  Score=23.71  Aligned_cols=60  Identities=12%  Similarity=0.248  Sum_probs=48.5

Q ss_pred             EEEeeCCCchHHHHHHHHhhhc-C--C--CCC-ceeEEECC--eecCCCCcccccccCCCCEEEEEEe
Q 040824           89 IEIDIEPTDTIERIKERVEEKE-G--I--PPV-QQRLIYAG--KQLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        89 ~~~~v~~~~tv~~LK~~i~~~~-~--i--~~~-~~~l~~~g--~~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      .-+.++..+|..++-++++... |  +  .|. ..+..++|  ..+..+.|+++.||.+-+.|.+...
T Consensus        15 ~LV~VDt~dTmdqVA~kvA~HsVGrRV~p~p~~~~rVr~~G~~~~~pr~~tvae~gl~P~e~vev~~~   82 (83)
T 2inc_C           15 QLVPVDTEDTMDQVAEKCAYHSINRRVHPQPEKILRVRRHEDGTLFPRGMIVSDAGLRPTETLDIIFM   82 (83)
T ss_dssp             EEEEECTTCBHHHHHHHHHTTTBTTTBCCCTTSEEEEEETTTCCEECTTCBGGGSCCCTTCEEEEEEE
T ss_pred             EEEEecCCCcHHHHHHHHhhhhcceecCCCCCCeEEEEecCCccCCCCCCEeeccCCCCceEEEEEEc
Confidence            4578999999999999997655 3  3  222 46777888  8899999999999999999988753

>3onh_A Ubiquitin-activating enzyme E1-like; ligase, SUMO conjugation, UBC9; 1.60A {Saccharomyces cerevisiae} PDB: 3ong_A

Probab=85.00  E-value=3.8  Score=25.78  Aligned_cols=50  Identities=20%  Similarity=0.312  Sum_probs=35.7

Q ss_pred             CchHHHHHHHHhhhcCCCCCce--------eEEECCee-cCCCCcccccccCCCCEEEEE
Q 040824           96 TDTIERIKERVEEKEGIPPVQQ--------RLIYAGKQ-LADDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        96 ~~tv~~LK~~i~~~~~i~~~~~--------~l~~~g~~-l~d~~~L~~~~i~~~~~i~~~  146 (154)
                      ..|..+|-..+..++|.+- .+        +|+|..-. =+-.++|++.|+++|+.|.+.
T Consensus        19 ~~TL~dLV~~l~~~~gy~~-eiSV~~~~~~rLLyD~DfDDnl~k~L~dLgv~~gsfLtv~   77 (127)
T 3onh_A           19 KMKLSDFVVLIREKYSYPQ-DISLLDASNQRLLFDYDFEDLNDRTLSEINLGNGSIILFS   77 (127)
T ss_dssp             HCBHHHHHHHHHHHHTCCS-SEEEEETTTTEEEEETTBCTTTTSBTTTTTCCTTCEEEEE
T ss_pred             ccCHHHHHHHHHHhcCCCC-cEEEEecCCCCeEeCCCccccccCcHHHcCcCCCcEEEEE
Confidence            4689998888888888753 44        44433321 124679999999999999876

>2kmm_A Guanosine-3',5'-BIS(diphosphate) 3'- pyrophosphohydrolase; methods development, TGS domain, predominantly beta-sheet structure; NMR {Porphyromonas gingivalis}

Probab=84.63  E-value=3.5  Score=22.68  Aligned_cols=61  Identities=13%  Similarity=0.155  Sum_probs=38.1

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~   70 (154)
                      |.++|...+|+.  .+++.+.|+.++-..+....+  ....-...+|+...-+     +.+.+++.|.++
T Consensus         1 m~i~i~~p~g~~--~~~~~g~T~~dla~~i~~~l~--~~~vaa~vNg~lvdl~-----~~L~~~~~Veiv   61 (73)
T 2kmm_A            1 MEVMVFTPKGEI--KRLPQGATALDFAYSLHSDLG--DHCIGAKVNHKLVPLS-----YVLNSGDQVEVL   61 (73)
T ss_dssp             CCEEEECTTCCE--EEECTTCBHHHHHHHHCSHHH--HTEEEEEETTEECCTT-----CBCCSSSBEEEE
T ss_pred             CeEEEEcCCCCE--EEcCCCCcHHHHHHHHhhccc--cceEEEEECCEEeCCC-----cCcCCCCEEEEE
Confidence            788898888875  566788999999888743321  1112223577665443     445566766554

>4eut_A Serine/threonine-protein kinase TBK1; ATP binding, phosphorylation, transferase-transferas inhibitor complex; HET: BX7; 2.60A {Homo sapiens}

Probab=84.55  E-value=3.6  Score=30.55  Aligned_cols=50  Identities=22%  Similarity=0.365  Sum_probs=39.5

Q ss_pred             CEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceE--eccCceecccc
Q 040824           11 KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQ--LEDGRTLADYN   60 (154)
Q Consensus        11 ~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~--L~d~~~l~~~~   60 (154)
                      ....+.+++..|+.++++++++.++++++.|.|++.+..  ++.......|.
T Consensus       322 ~~~~~~~~~~~~~~~~~~~~~~~t~i~~~~q~~l~~~~~~~~~~~~~~~~~~  373 (396)
T 4eut_A          322 TAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLVLEPGRLAQHFP  373 (396)
T ss_dssp             EEEEEEECTTCBHHHHHHHHHHHHCCCSTTEEEESSSSEECCCSSCBTTSSC
T ss_pred             eEEEEEcCchhHHHHHHHHHHHhcCCChhhhHHHhcCCCCCCCCCCccccCC
Confidence            446678889999999999999999999999999998733  34444555544

>3ge3_C Toluene-4-monooxygenase system protein B; DIIRON hydroxylase, effector protein, T201A, aromatic hydrocarbons catabolism, FAD, flavoprotein; 1.52A {Pseudomonas mendocina} SCOP: d.15.12.0 PDB: 3dhh_C* 3dhg_C* 3dhi_C 3ge8_C 3i5j_C 3i63_C 3q14_C 3q2a_C* 3q3m_C* 3q3n_C* 3q3o_C* 3rmk_C* 3ri7_C*

Probab=83.09  E-value=5  Score=23.24  Aligned_cols=59  Identities=14%  Similarity=0.222  Sum_probs=48.1

Q ss_pred             EEEeeCCCchHHHHHHHHhhhc-C--C--CCCceeEEECCee--cCCCCcccccccCCCCEEEEEE
Q 040824           89 IEIDIEPTDTIERIKERVEEKE-G--I--PPVQQRLIYAGKQ--LADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        89 ~~~~v~~~~tv~~LK~~i~~~~-~--i--~~~~~~l~~~g~~--l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      .-+.++..+|..++-++++... |  +  .|...+...+|..  +..+.|+++.||.+-+.|.++.
T Consensus        17 ~Lv~VDt~dtmdqVA~k~A~h~VGrrv~p~pg~lrVr~~G~~~~~Pr~mtVaeaGl~Pme~vev~~   82 (84)
T 3ge3_C           17 QLVVVDLNDSMDQVAEKVAYHCVNRRVAPREGVMRVRKHRSTELFPRDMTIAESGLNPTEVIDVVF   82 (84)
T ss_dssp             EEEEEETTCBHHHHHHHHHHTTBTTTBCCCSSCEEEEETTCSCBCCTTCBHHHHCCCTTCEEEEEE
T ss_pred             EEEEecCCCcHHHHHHHHhhhhcceeeCCCCCcEEEEECCCcccCCCCCEeeccCCCcceEEEEEE
Confidence            4578899999999999987654 3  2  2335677889987  9999999999999999998875

>2kmm_A Guanosine-3',5'-BIS(diphosphate) 3'- pyrophosphohydrolase; methods development, TGS domain, predominantly beta-sheet structure; NMR {Porphyromonas gingivalis}

Probab=82.96  E-value=4.2  Score=22.33  Aligned_cols=63  Identities=13%  Similarity=0.066  Sum_probs=38.9

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEe
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      |.+.|..++|+.  .+++...|+.++-+.+....+  ....-...+|+..+-+     +-+.+|+.|.++-.
T Consensus         1 m~i~i~~p~g~~--~~~~~g~T~~dla~~i~~~l~--~~~vaa~vNg~lvdl~-----~~L~~~~~Veivt~   63 (73)
T 2kmm_A            1 MEVMVFTPKGEI--KRLPQGATALDFAYSLHSDLG--DHCIGAKVNHKLVPLS-----YVLNSGDQVEVLSS   63 (73)
T ss_dssp             CCEEEECTTCCE--EEECTTCBHHHHHHHHCSHHH--HTEEEEEETTEECCTT-----CBCCSSSBEEEEEC
T ss_pred             CeEEEEcCCCCE--EEcCCCCcHHHHHHHHhhccc--cceEEEEECCEEeCCC-----cCcCCCCEEEEEEC
Confidence            456666667765  456678999999887743321  1122234688766543     45567888877643

>2l52_A Methanosarcina acetivorans SAMP1 homolog; beta-grAsp fold, protein binding, E1-like, SAMP activator, ELSA, adenylation, ubiquitin; NMR {Methanosarcina acetivorans}

Probab=82.38  E-value=3.3  Score=24.63  Aligned_cols=56  Identities=7%  Similarity=0.191  Sum_probs=36.1

Q ss_pred             CchHHHHHHHHhhhcC-CCC---------Cce-------eEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           96 TDTIERIKERVEEKEG-IPP---------VQQ-------RLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        96 ~~tv~~LK~~i~~~~~-i~~---------~~~-------~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ..|+.+|.+.+...+. +..         ...       .+..+|+...... -.+.-+++||.|.++-..-||
T Consensus        27 ~~tv~~ll~~L~~~~p~l~~~l~~~g~l~~~v~~~~~~~~v~VNg~~v~~~~-~~~~~L~~gD~V~i~ppv~GG   99 (99)
T 2l52_A           27 GEKVIDVLLSLTDKYPALKYVIFEKGDEKSEILILCGSINILINGNNIRHLE-GLETLLKDSDEIGILPPVSGG   99 (99)
T ss_dssp             CSSHHHHHHHHHHHCGGGTTTSBCSCCTTSSCCCBCSSCEEEETTSCGGGTT-STTSCCCTTEEEEEECCCSCC
T ss_pred             CCcHHHHHHHHHHHChhHHHHHhcccccccceeccccccEEEECCEEccccC-CCCCCCCCCCEEEEECCCCCC
Confidence            5899999999987752 111         123       5667887653221 234468999999887666555

>4eut_A Serine/threonine-protein kinase TBK1; ATP binding, phosphorylation, transferase-transferas inhibitor complex; HET: BX7; 2.60A {Homo sapiens}

Probab=82.34  E-value=5.1  Score=29.69  Aligned_cols=52  Identities=25%  Similarity=0.308  Sum_probs=40.8

Q ss_pred             CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCe--ecCCCCcccccc
Q 040824           85 TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGK--QLADDKTARDYN  136 (154)
Q Consensus        85 ~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~--~l~d~~~L~~~~  136 (154)
                      ......+.+.+..|+.++++.+++.++++++.|.+++.+.  .++.......+.
T Consensus       320 ~~~~~~~~~~~~~~~~~~~~~~~~~t~i~~~~q~~l~~~~~~~~~~~~~~~~~~  373 (396)
T 4eut_A          320 QMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLVLEPGRLAQHFP  373 (396)
T ss_dssp             TTEEEEEEECTTCBHHHHHHHHHHHHCCCSTTEEEESSSSEECCCSSCBTTSSC
T ss_pred             cceEEEEEcCchhHHHHHHHHHHHhcCCChhhhHHHhcCCCCCCCCCCccccCC
Confidence            3455678899999999999999999999999999999873  334444444444

>1v8c_A MOAD related protein; riken structural genomics/proteomics initiative, RSGI, structural genomics, protein binding; 1.60A {Thermus thermophilus} SCOP: d.15.3.1 d.129.5.1

Probab=81.99  E-value=5.2  Score=26.44  Aligned_cols=62  Identities=15%  Similarity=0.298  Sum_probs=42.1

Q ss_pred             EEeeCCCchHHHHHHHHhhhcC-CC---------CCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           90 EIDIEPTDTIERIKERVEEKEG-IP---------PVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        90 ~~~v~~~~tv~~LK~~i~~~~~-i~---------~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      .++++. .||.+|.+.+...+. +.         .....+..||....... -.+.-+++||.|.++-..-||.
T Consensus        17 ~~ev~~-~TV~dLl~~L~~~~p~l~~~l~~~~~l~~~v~VaVNg~~v~~~~-~~dt~L~dGDeVai~PpVsGG~   88 (168)
T 1v8c_A           17 QLELPG-ATVGEVLENLVRAYPALKEELFEGEGLAERVSVFLEGRDVRYLQ-GLSTPLSPGATLDLFPPVAGGG   88 (168)
T ss_dssp             EEECCC-SBHHHHHHHHHHHCGGGHHHHEETTEECTTCEEEETTEEGGGTT-GGGCBCCTTCEEEEECSCCSEE
T ss_pred             eEEECC-CcHHHHHHHHHhhChhhhhhhhcccccCCcEEEEECCEECCCcC-CCccCCCCCCEEEEECcccccc
Confidence            345555 899999999987652 10         23456778888775422 2345689999998887777663

>3dwg_C 9.5 kDa culture filtrate antigen CFP10A; sulfur carrier protein complex, beta-grAsp fold, amino-acid biosynthesis; HET: PLP; 1.53A {Mycobacterium tuberculosis} PDB: 3dwm_A

Probab=81.15  E-value=6.1  Score=22.97  Aligned_cols=71  Identities=14%  Similarity=0.222  Sum_probs=40.9

Q ss_pred             CEEEEEeCC------CCEEEEEEeCCCcHHHHHHHHHhHhC-----C-C---CC----CeEEEEcceEeccCceeccccc
Q 040824            1 MQIFVKTLT------GKTITLEVESSDTIDNVKAKIQDKEG-----I-P---PD----QQRLIFAGKQLEDGRTLADYNI   61 (154)
Q Consensus         1 m~v~v~~~~------~~~~~~~v~~~~tv~~lk~~i~~~~~-----~-~---~~----~q~L~~~g~~L~d~~~l~~~~i   61 (154)
                      |+|+|+...      |....++. ...||.+|.+.+.....     + .   ..    ...+..||+......- .+.-+
T Consensus         1 M~v~V~~fa~lr~~~g~~~~~~~-~~~Tv~~ll~~L~~~~p~l~~~l~~~~~~g~~~~~~~v~VN~~~v~~~~~-~~~~L   78 (93)
T 3dwg_C            1 MNVTVSIPTILRPHTGGQKSVSA-SGDTLGAVISDLEANYSGISERLMDPSSPGKLHRFVNIYVNDEDVRFSGG-LATAI   78 (93)
T ss_dssp             -CEEEECCGGGGGGTTTCSEEEE-CCSBHHHHHHHHHHHSTTHHHHHBCSSSTTSBCTTEEEEETTEEGGGTTG-GGCBC
T ss_pred             CEEEEEEeHHHHHHhCCCeEEec-CCCCHHHHHHHHHHHChhHHHHHhccccCCcccCCEEEEECCEEccCcCC-CCcCC
Confidence            667776542      32234564 56899999999987642     0 1   01    2345566766543221 24467


Q ss_pred             ccccceeeeeee
Q 040824           62 QKESTLHLVLRL   73 (154)
Q Consensus        62 ~~~~~i~l~~~~   73 (154)
                      ++|+.|.+....
T Consensus        79 ~~gDeV~i~Ppv   90 (93)
T 3dwg_C           79 ADGDSVTILPAV   90 (93)
T ss_dssp             CTTCEEEEEECC
T ss_pred             CCCCEEEEECCC
Confidence            889988776543

>2dhz_A RAP guanine nucleotide exchange factor (GEF)- like 1; LINK guanine nucleotide exchange factor II, LINK-gefii, RA domain, structural genomics; NMR {Homo sapiens}

Probab=81.01  E-value=5.6  Score=24.79  Aligned_cols=70  Identities=16%  Similarity=0.081  Sum_probs=45.2

Q ss_pred             eeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCC------ceeEE---ECCe--ecCCCCcccccccCCCCEEEEE
Q 040824           78 MIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPV------QQRLI---YAGK--QLADDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        78 ~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~------~~~l~---~~g~--~l~d~~~L~~~~i~~~~~i~~~  146 (154)
                      ...|-..+.+.+.+.++.+.|+.+++..++.+.+..-+      .+.|.   ++|.  .++++..--.-.+.-+..|++.
T Consensus        11 ~~~VY~~Dhsy~tvr~~v~~sa~eIl~~va~kl~~~e~~~~~~~~l~Lv~V~ssGEk~vlqp~d~sv~tsL~~NgRLfvc   90 (120)
T 2dhz_A           11 FCRVYMPDHSYVTIRSRLSASVQDILGSVTEKLQYSEEPAGREDSLILVAVSSSGEKVLLQPTEDCVFTALGINSHLFAC   90 (120)
T ss_dssp             EECEECTTSCCCCEEECTTCCHHHHHHHHHHHSTTCSSTTSCCSCCEEEEEETTCCCEECCTTCSCHHHHSCSSEEEEEE
T ss_pred             EEEEEeccCceEEEEEeccccHHHHHHHHHHHhccccccccccCceEEEEEccCCcEeecCCcceEEEeeccccceEEEe
Confidence            33344456667778899999999999999999987544      56665   5665  3444433333334455566554


Q ss_pred             E
Q 040824          147 L  147 (154)
Q Consensus       147 ~  147 (154)
                      .
T Consensus        91 ~   91 (120)
T 2dhz_A           91 T   91 (120)
T ss_dssp             C
T ss_pred             e
Confidence            3

>1fm0_D Molybdopterin convertin factor, subunit 1; molybdenum cofactor biosynthesis, transferase; 1.45A {Escherichia coli} SCOP: d.15.3.1 PDB: 1fma_D 1jw9_D 1jwa_D* 1jwb_D* 3bii_D 1nvi_D

Probab=80.78  E-value=5.2  Score=22.49  Aligned_cols=56  Identities=4%  Similarity=0.077  Sum_probs=35.8

Q ss_pred             CEEEEEEeCCCcHHHHHHHHHhHhC-----CCCCCeEEEEcceEeccCceecccccccccceeeeee
Q 040824           11 KTITLEVESSDTIDNVKAKIQDKEG-----IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus        11 ~~~~~~v~~~~tv~~lk~~i~~~~~-----~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      ....++ ....||.+|.+.+.....     ++.....+..||+....     +..+++|+.|.+...
T Consensus        17 ~~~~~~-~~~~tv~~ll~~L~~~~p~~~~~l~~~~~~v~vN~~~v~~-----~~~l~~gD~V~i~Pp   77 (81)
T 1fm0_D           17 DATEVA-ADFPTVEALRQHMAAQSDRWALALEDGKLLAAVNQTLVSF-----DHPLTDGDEVAFFPP   77 (81)
T ss_dssp             SEEEEC-SCCSBHHHHHHHHHTTCHHHHHHHCCTTCEEEETTEECCT-----TCBCCTTCEEEEECC
T ss_pred             CeEEEc-CCCCCHHHHHHHHHHHChhHHHHhcCCCEEEEECCEECCC-----CCCCCCCCEEEEeCC
Confidence            345555 567899999999875421     22333456677876643     446778888876643

>3onh_A Ubiquitin-activating enzyme E1-like; ligase, SUMO conjugation, UBC9; 1.60A {Saccharomyces cerevisiae} PDB: 3ong_A

Probab=80.26  E-value=6.6  Score=24.69  Aligned_cols=51  Identities=22%  Similarity=0.264  Sum_probs=36.6

Q ss_pred             CCcHHHHHHHHHhHhCCCCCCeEEEE--cceEecc-------Cceecccccccccceeeee
Q 040824           20 SDTIDNVKAKIQDKEGIPPDQQRLIF--AGKQLED-------GRTLADYNIQKESTLHLVL   71 (154)
Q Consensus        20 ~~tv~~lk~~i~~~~~~~~~~q~L~~--~g~~L~d-------~~~l~~~~i~~~~~i~l~~   71 (154)
                      .+|..+|-+.+..+.|++. ...+.-  +.+.|.|       +++|++.|+++|+.+.+.-
T Consensus        19 ~~TL~dLV~~l~~~~gy~~-eiSV~~~~~~rLLyD~DfDDnl~k~L~dLgv~~gsfLtv~D   78 (127)
T 3onh_A           19 KMKLSDFVVLIREKYSYPQ-DISLLDASNQRLLFDYDFEDLNDRTLSEINLGNGSIILFSD   78 (127)
T ss_dssp             HCBHHHHHHHHHHHHTCCS-SEEEEETTTTEEEEETTBCTTTTSBTTTTTCCTTCEEEEEE
T ss_pred             ccCHHHHHHHHHHhcCCCC-cEEEEecCCCCeEeCCCccccccCcHHHcCcCCCcEEEEEc
Confidence            4699999988988888864 444432  2344433       5689999999999886654

---

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	154
d1ogwa_	76	d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [Tax	1e-39
d1ogwa_	76	d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [Tax	2e-29
d1wh3a_	87	d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like	4e-39
d1wh3a_	87	d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like	4e-26
d2zeqa1	78	d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin	8e-39
d2zeqa1	78	d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin	9e-28
d1bt0a_	73	d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis t	5e-37
d1bt0a_	73	d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis t	3e-27
d1z2ma2	76	d.15.1.1 (A:79-154) Interferon-induced 15 kDa prot	1e-35
d1z2ma2	76	d.15.1.1 (A:79-154) Interferon-induced 15 kDa prot	1e-23
d1wx9a1	73	d.15.1.1 (A:8-80) Large proline-rich protein BAT3	8e-34
d1wx9a1	73	d.15.1.1 (A:8-80) Large proline-rich protein BAT3	3e-24
d2c9wb1	103	d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens)	1e-33
d2c9wb1	103	d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens)	7e-22
d1uela_	95	d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homol	2e-33
d1uela_	95	d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homol	3e-23
d1zkha1	86	d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-t	3e-33
d1zkha1	86	d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-t	2e-25
d2faza1	76	d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING fing	5e-32
d2faza1	76	d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING fing	5e-22
d1wgha_	116	d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mous	3e-31
d1wgha_	116	d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mous	3e-25
d1v2ya_	105	d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik	3e-31
d1v2ya_	105	d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik	2e-23
d1uh6a_	100	d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mous	8e-31
d1uh6a_	100	d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mous	2e-24
d1oqya4	77	d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 h	1e-30
d1oqya4	77	d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 h	1e-22
d1wy8a1	76	d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING fing	2e-30
d1wy8a1	76	d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING fing	9e-22
d1ttna1	80	d.15.1.1 (A:21-100) Dendritic cell-derived ubiquit	2e-30
d1ttna1	80	d.15.1.1 (A:21-100) Dendritic cell-derived ubiquit	6e-22
d2bwfa1	73	d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyc	1e-29
d2bwfa1	73	d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyc	2e-23
d1z2ma1	76	d.15.1.1 (A:3-78) Interferon-induced 15 kDa protei	1e-29
d1z2ma1	76	d.15.1.1 (A:3-78) Interferon-induced 15 kDa protei	3e-23
d1v5oa_	102	d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus mu	2e-29
d1v5oa_	102	d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus mu	5e-20
d1wgda_	93	d.15.1.1 (A:) Homocysteine-responsive endoplasmic	5e-29
d1wgda_	93	d.15.1.1 (A:) Homocysteine-responsive endoplasmic	6e-23
d1wiaa_	95	d.15.1.1 (A:) Ubiquitin-like protein bab25500 (201	2e-27
d1wiaa_	95	d.15.1.1 (A:) Ubiquitin-like protein bab25500 (201	1e-21
d1wx8a1	83	d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus muscul	7e-26
d1wx8a1	83	d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus muscul	2e-19
d1j8ca_	103	d.15.1.1 (A:) Ubiquitin-like N-terminal domain of	1e-25
d1j8ca_	103	d.15.1.1 (A:) Ubiquitin-like N-terminal domain of	1e-19
d1we6a_	111	d.15.1.1 (A:) Splicing factor 3 subunit 1, C-termi	2e-25
d1we6a_	111	d.15.1.1 (A:) Splicing factor 3 subunit 1, C-termi	1e-17
d1v5ta_	90	d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus mu	2e-25
d1v5ta_	90	d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus mu	5e-17
d1yqba1	84	d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapien	5e-25
d1yqba1	84	d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapien	9e-18
d1m94a_	73	d.15.1.1 (A:) Ubiquitin-like modifier protein hub1	1e-24
d1m94a_	73	d.15.1.1 (A:) Ubiquitin-like modifier protein hub1	1e-17
d1se9a_	101	d.15.1.1 (A:) Hypothetical protein At3g01050 {Thal	2e-23
d1se9a_	101	d.15.1.1 (A:) Hypothetical protein At3g01050 {Thal	1e-19
d1v6ea_	95	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	4e-23
d1v6ea_	95	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	3e-17
d1wjua_	100	d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human	2e-22
d1wjua_	100	d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human	7e-18
d1wjna_	97	d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse	2e-22
d1wjna_	97	d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse	6e-17
d1x1ma1	94	d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse	3e-22
d1x1ma1	94	d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse	2e-20
d1euvb_	79	d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yea	3e-20
d1euvb_	79	d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yea	5e-20
d1v86a_	95	d.15.1.1 (A:) hypothetical D7wsu128e protein {Mous	6e-20
d1v86a_	95	d.15.1.1 (A:) hypothetical D7wsu128e protein {Mous	6e-17
d1wgga_	96	d.15.1.1 (A:) Ubiquitin carboxyl-terminal hydrolas	8e-20
d1wgga_	96	d.15.1.1 (A:) Ubiquitin carboxyl-terminal hydrolas	2e-15
d2uyzb1	77	d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human	2e-19
d2uyzb1	77	d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human	9e-19
d1t0ya_	90	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	1e-18
d1t0ya_	90	d.15.1.1 (A:) Ubiquitin-like domain of tubulin fol	2e-16
d1wxva1	81	d.15.1.1 (A:7-87) Bag-family molecular chaperone r	2e-18
d1wxva1	81	d.15.1.1 (A:7-87) Bag-family molecular chaperone r	6e-15
d1wm3a_	72	d.15.1.1 (A:) SUMO-2 {Human (Homo sapiens) [TaxId:	3e-08

>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 =  126 bits (318), Expect = 1e-39
 Identities = 73/76 (96%), Positives = 75/76 (98%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          MQIFVKTLTGKTITLEVE SDTI+NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL+DYN
Sbjct: 1  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60

Query: 61 IQKESTLHLVLRLRGG 76
          IQKESTLHLVLRLRGG
Sbjct: 61 IQKESTLHLVLRLRGG 76

>d1ogwa_ d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  100 bits (250), Expect = 2e-29
 Identities = 48/74 (64%), Positives = 60/74 (81%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I VKTLTGK I +++EP+DTIE +K ++++KEGIPP QQRLI+AGKQL D +T  DYNI+
Sbjct: 3   IFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQ 62

Query: 139 GGSVLHLVLALRGG 152
             S LHLVL LRGG
Sbjct: 63  KESTLHLVLRLRGG 76

>d1wh3a_ d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like protein, OASL {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 2'-5'-oligoadenylate synthetase-like protein, OASL
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  125 bits (315), Expect = 4e-39
 Identities = 26/76 (34%), Positives = 41/76 (53%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +Q+FVK   G +    +  +  I  +K +I+D++G+P  QQ+L F G+ L+D   L  Y 
Sbjct: 8  IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGLGIYG 67

Query: 61 IQKESTLHLVLRLRGG 76
          IQ   TL L  +   G
Sbjct: 68 IQDSDTLILSKKKGSG 83

>d1wh3a_ d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like protein, OASL {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 2'-5'-oligoadenylate synthetase-like protein, OASL
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 92.7 bits (230), Expect = 4e-26
 Identities = 21/74 (28%), Positives = 34/74 (45%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           + VK   G      I P   I  +K+++E+++G+P  QQ+L + G+ L D      Y I+
Sbjct: 10  VFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGLGIYGIQ 69

Query: 139 GGSVLHLVLALRGG 152
               L L      G
Sbjct: 70  DSDTLILSKKKGSG 83

>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 =  124 bits (313), Expect = 8e-39
 Identities = 25/75 (33%), Positives = 48/75 (64%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M +FV+  +     +EV+S  +I  +K  +  ++G+P DQ R+IFAGK+L +  T+ + +
Sbjct: 3  MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVIFAGKELPNHLTVQNCD 62

Query: 61 IQKESTLHLVLRLRG 75
          ++++S +H+V R R 
Sbjct: 63 LEQQSIVHIVQRPRR 77

>d2zeqa1 d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of parkin
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 96.5 bits (240), Expect = 9e-28
 Identities = 21/76 (27%), Positives = 47/76 (61%)

Query: 76  GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDY 135
           G ++ V+  +     ++++   +I ++KE V +++G+P  Q R+I+AGK+L +  T ++ 
Sbjct: 2   GMIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVIFAGKELPNHLTVQNC 61

Query: 136 NIEGGSVLHLVLALRG 151
           ++E  S++H+V   R 
Sbjct: 62  DLEQQSIVHIVQRPRR 77

>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 =  119 bits (300), Expect = 5e-37
 Identities = 45/73 (61%), Positives = 57/73 (78%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          M I VKTLTGK I +++E +DTID +K ++++KEGIPP QQRLI+AGKQL D +T  DYN
Sbjct: 1  MLIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLIYAGKQLADDKTAKDYN 60

Query: 61 IQKESTLHLVLRL 73
          I+  S LHLVL L
Sbjct: 61 IEGGSVLHLVLAL 73

>d1bt0a_ d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 73

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Rub1
species: Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 94.9 bits (236), Expect = 3e-27
 Identities = 69/71 (97%), Positives = 71/71 (100%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           IKVKTLTGKEIEIDIEPTDTI+RIKERVEEKEGIPPVQQRLIYAGKQLADDKTA+DYNIE
Sbjct: 3   IKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLIYAGKQLADDKTAKDYNIE 62

Query: 139 GGSVLHLVLAL 149
           GGSVLHLVLAL
Sbjct: 63  GGSVLHLVLAL 73

>d1z2ma2 d.15.1.1 (A:79-154) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  116 bits (291), Expect = 1e-35
 Identities = 25/73 (34%), Positives = 41/73 (56%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + I V+   G++ T EV  + T+ ++K ++   EG+  D   L F GK LED   L +Y 
Sbjct: 4  LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYG 63

Query: 61 IQKESTLHLVLRL 73
          ++  ST+ + LRL
Sbjct: 64 LKPLSTVFMNLRL 76

>d1z2ma2 d.15.1.1 (A:79-154) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 86.1 bits (213), Expect = 1e-23
 Identities = 18/71 (25%), Positives = 33/71 (46%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I V+   G+    ++  T T+  +K++V   EG+      L + GK L D     +Y ++
Sbjct: 6   ILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLK 65

Query: 139 GGSVLHLVLAL 149
             S + + L L
Sbjct: 66  PLSTVFMNLRL 76

>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 =  111 bits (279), Expect = 8e-34
 Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKTL  +T T  V +   +   K  I     IP ++QRLI+ G+ L+D + L +YN
Sbjct: 1  LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYN 60

Query: 61 IQKESTLHLVLR 72
          +     +HLV R
Sbjct: 61 VGG-KVIHLVER 71

>d1wx9a1 d.15.1.1 (A:8-80) Large proline-rich protein BAT3 {Human (Homo sapiens) [TaxId: 9606]} Length = 73

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Large proline-rich protein BAT3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 87.6 bits (217), Expect = 3e-24
 Identities = 25/69 (36%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           + VKTL  +     +     ++  KE +     IP  +QRLIY G+ L DDK  ++YN+ 
Sbjct: 3   VLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYNVG 62

Query: 139 GGSVLHLVL 147
            G V+HLV 
Sbjct: 63  -GKVIHLVE 70

>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 =  112 bits (281), Expect = 1e-33
 Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 8/83 (9%)

Query: 2  QIFVKTLTGK-TITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           +F+     K TI  + + S T+  +K  ++     PPD+QRL    + L+DG+TL +  
Sbjct: 1  DVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECG 60

Query: 61 I-------QKESTLHLVLRLRGG 76
                  Q  +T+ L  R    
Sbjct: 61 FTSQTARPQAPATVGLAFRADDT 83

>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 = 82.2 bits (203), Expect = 7e-22
 Identities = 17/82 (20%), Positives = 29/82 (35%), Gaps = 8/82 (9%)

Query: 79  IKVKTLTGKE-IEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNI 137
           + +     K  I  D + + T+  +K  VE     PP +QRL    + L D KT  +   
Sbjct: 2   VFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGF 61

Query: 138 -------EGGSVLHLVLALRGG 152
                  +  + + L       
Sbjct: 62  TSQTARPQAPATVGLAFRADDT 83

>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 =  111 bits (279), Expect = 2e-33
 Identities = 22/80 (27%), Positives = 45/80 (56%), Gaps = 3/80 (3%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDK---EGIPPDQQRLIFAGKQLEDGRTLA 57
          MQ+ +KTL  +T  ++++  +T+  +K KI+ +   +  P   Q+LI+AGK L D   L 
Sbjct: 1  MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALK 60

Query: 58 DYNIQKESTLHLVLRLRGGT 77
          +Y I +++ + +++      
Sbjct: 61 EYKIDEKNFVVVMVTKPKAV 80

>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 = 85.5 bits (211), Expect = 3e-23
 Identities = 24/72 (33%), Positives = 46/72 (63%), Gaps = 3/72 (4%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEK---EGIPPVQQRLIYAGKQLADDKTARDY 135
           + +KTL  +  +IDI+P +T++ +KE++E +   +  P   Q+LIYAGK L DD   ++Y
Sbjct: 3   VTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEY 62

Query: 136 NIEGGSVLHLVL 147
            I+  + + +++
Sbjct: 63  KIDEKNFVVVMV 74

>d1zkha1 d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Splicing factor 3 subunit 1, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  110 bits (276), Expect = 3e-33
 Identities = 21/68 (30%), Positives = 39/68 (57%)

Query: 8  LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTL 67
          L G+ +   +  +D +  +K KI +  G+P  +Q+L + G  ++D  +LA YN+   + +
Sbjct: 19 LNGQVLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMANGAVI 78

Query: 68 HLVLRLRG 75
          HL L+ RG
Sbjct: 79 HLALKERG 86

>d1zkha1 d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Splicing factor 3 subunit 1, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 90.3 bits (224), Expect = 2e-25
 Identities = 23/68 (33%), Positives = 37/68 (54%)

Query: 84  LTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVL 143
           L G+ +   +  TD +  IK ++ E  G+P  +Q+L Y G  + D  +   YN+  G+V+
Sbjct: 19  LNGQVLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMANGAVI 78

Query: 144 HLVLALRG 151
           HL L  RG
Sbjct: 79  HLALKERG 86

>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 =  107 bits (268), Expect = 5e-32
 Identities = 27/75 (36%), Positives = 46/75 (61%), Gaps = 2/75 (2%)

Query: 1  MQIFVKTLTGK-TITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLAD 58
          M I V+T+ G+ T T++ +     ++ ++ KIQ+   + P  QRL + GKQ+EDG TL D
Sbjct: 1  MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFD 60

Query: 59 YNIQKESTLHLVLRL 73
          Y ++   T+ L++R 
Sbjct: 61 YEVRLNDTIQLLVRQ 75

>d2faza1 d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING finger domain-containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like PHD and RING finger domain-containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 81.5 bits (201), Expect = 5e-22
 Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 2/73 (2%)

Query: 79  IKVKTLTGKEIEI--DIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYN 136
           I+V+T+ G++      +     +E ++ +++E   + P  QRL Y GKQ+ D  T  DY 
Sbjct: 3   IQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFDYE 62

Query: 137 IEGGSVLHLVLAL 149
           +     + L++  
Sbjct: 63  VRLNDTIQLLVRQ 75

>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 =  106 bits (266), Expect = 3e-31
 Identities = 15/84 (17%), Positives = 34/84 (40%), Gaps = 8/84 (9%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKI--------QDKEGIPPDQQRLIFAGKQLED 52
           + + +  ++GKT       +D+  ++   +        ++++   P+  RLI+ G+ L  
Sbjct: 17  INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHG 76

Query: 53  GRTLADYNIQKESTLHLVLRLRGG 76
             TL    +    T  + L  R  
Sbjct: 77  NVTLGALKLPFGKTTVMHLVARET 100

>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 = 91.2 bits (226), Expect = 3e-25
 Identities = 20/82 (24%), Positives = 33/82 (40%), Gaps = 8/82 (9%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERV--------EEKEGIPPVQQRLIYAGKQLADDK 130
           +++  ++GK  E    P D+   I + V        EE++   P   RLIY G+ L  + 
Sbjct: 19  LRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNV 78

Query: 131 TARDYNIEGGSVLHLVLALRGG 152
           T     +  G    + L  R  
Sbjct: 79  TLGALKLPFGKTTVMHLVARET 100

>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 =  105 bits (264), Expect = 3e-31
 Identities = 18/92 (19%), Positives = 38/92 (41%), Gaps = 16/92 (17%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQR---------------LIF 45
          M + V  + G+ + + V  + T+ ++K  IQ    +  +++                L  
Sbjct: 8  MTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTS 67

Query: 46 AGKQLEDGR-TLADYNIQKESTLHLVLRLRGG 76
          AG++L + R  L DY I+    +  + +L   
Sbjct: 68 AGEKLTEDRKKLRDYGIRNRDEVSFIKKLGQK 99

>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 = 86.3 bits (213), Expect = 2e-23
 Identities = 15/94 (15%), Positives = 36/94 (38%), Gaps = 16/94 (17%)

Query: 76  GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQR---------------LI 120
           G  ++V  + G+ + + +    T+  +K+ ++    +   ++                L 
Sbjct: 7   GMTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLT 66

Query: 121 YAGKQLADDK-TARDYNIEGGSVLHLVLALRGGG 153
            AG++L +D+   RDY I     +  +  L    
Sbjct: 67  SAGEKLTEDRKKLRDYGIRNRDEVSFIKKLGQKS 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 =  105 bits (262), Expect = 8e-31
 Identities = 16/72 (22%), Positives = 31/72 (43%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           +++      GK + ++  + DTI ++K  I  + G   ++  L       +D  +L DY 
Sbjct: 29  IEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSLGDYE 88

Query: 61  IQKESTLHLVLR 72
           I     L L  +
Sbjct: 89  IHDGMNLELYYQ 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 = 88.5 bits (219), Expect = 2e-24
 Identities = 23/98 (23%), Positives = 37/98 (37%), Gaps = 4/98 (4%)

Query: 54  RTLADYNIQKESTLHLVLRLRGG--TMIK--VKTLTGKEIEIDIEPTDTIERIKERVEEK 109
           +  + ++    S   LV R   G  TMI+       GK++ +     DTI  +K+ +  +
Sbjct: 2   KGSSHHHHHHSSGASLVPRGSEGAATMIEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQ 61

Query: 110 EGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVL 147
            G    +  L        D  +  DY I  G  L L  
Sbjct: 62  TGTRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLELYY 99

>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 =  103 bits (259), Expect = 1e-30
 Identities = 23/74 (31%), Positives = 44/74 (59%), Gaps = 3/74 (4%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLA 57
          + I +KTL  +T  + +E  +T+  +K KI+ ++G    P   Q+LI+AGK L D   + 
Sbjct: 3  VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIR 62

Query: 58 DYNIQKESTLHLVL 71
          DY I +++ + +++
Sbjct: 63 DYRIDEKNFVVVMV 76

>d1oqya4 d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 homolog A (Hhr23a) {Human (Homo sapiens) [TaxId: 9606]} Length = 77

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of Rad23 homolog A (Hhr23a)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 83.0 bits (205), Expect = 1e-22
 Identities = 27/72 (37%), Positives = 47/72 (65%), Gaps = 3/72 (4%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEG---IPPVQQRLIYAGKQLADDKTARDY 135
           I +KTL  +  +I +EP +T++ +KE++E ++G    P   Q+LIYAGK L+DD   RDY
Sbjct: 5   ITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDY 64

Query: 136 NIEGGSVLHLVL 147
            I+  + + +++
Sbjct: 65  RIDEKNFVVVMV 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 =  103 bits (258), Expect = 2e-30
 Identities = 28/74 (37%), Positives = 45/74 (60%), Gaps = 2/74 (2%)

Query: 1  MQIFVKTLTG-KTITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLAD 58
          M I V+T+ G KT T+E V    TI+ ++ ++     + P+ QRL + GKQLE+G TL D
Sbjct: 1  MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFD 60

Query: 59 YNIQKESTLHLVLR 72
          Y++     + L++R
Sbjct: 61 YDVGLNDIIQLLVR 74

>d1wy8a1 d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING finger domain-containing protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like PHD and RING finger domain-containing protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 81.1 bits (200), Expect = 9e-22
 Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 2/71 (2%)

Query: 79  IKVKTLTGKEIEI--DIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYN 136
           I+V+T+ G +     D+    TIE ++ERV     + P  QRL Y GKQL +  T  DY+
Sbjct: 3   IQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYD 62

Query: 137 IEGGSVLHLVL 147
           +    ++ L++
Sbjct: 63  VGLNDIIQLLV 73

>d1ttna1 d.15.1.1 (A:21-100) Dendritic cell-derived ubiquitin-like protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Dendritic cell-derived ubiquitin-like protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  103 bits (258), Expect = 2e-30
 Identities = 21/73 (28%), Positives = 40/73 (54%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           Q+ ++  TGK + L V S+DT+ ++K ++   EG+ P  QR  F+G+ L D     +  
Sbjct: 4  CQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKFEELK 63

Query: 61 IQKESTLHLVLRL 73
          I K+  + +++  
Sbjct: 64 IPKDYVVQVIVSQ 76

>d1ttna1 d.15.1.1 (A:21-100) Dendritic cell-derived ubiquitin-like protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Dendritic cell-derived ubiquitin-like protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 81.5 bits (201), Expect = 6e-22
 Identities = 18/71 (25%), Positives = 40/71 (56%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           ++++  TGK++++ +  TDT+  +K R+   EG+ P  QR  ++G+ L D     +  I 
Sbjct: 6   LRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKFEELKIP 65

Query: 139 GGSVLHLVLAL 149
              V+ ++++ 
Sbjct: 66  KDYVVQVIVSQ 76

>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 =  100 bits (252), Expect = 1e-29
 Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + I +K+       + V    T+   K  I    GIP   QRLI++GK L+D +T+  Y+
Sbjct: 2  LNIHIKSG-QDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYH 60

Query: 61 IQKESTLHLVLR 72
          IQ   ++HLV  
Sbjct: 61 IQDGHSVHLVKS 72

>d2bwfa1 d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 73

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: DSK2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 85.2 bits (211), Expect = 2e-23
 Identities = 28/70 (40%), Positives = 43/70 (61%), Gaps = 1/70 (1%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           I +K+   K  E+++ P  T+ + KE + +  GIP   QRLIY+GK L DD+T   Y+I+
Sbjct: 4   IHIKSGQDK-WEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHIQ 62

Query: 139 GGSVLHLVLA 148
            G  +HLV +
Sbjct: 63  DGHSVHLVKS 72

>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 =  101 bits (252), Expect = 1e-29
 Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 2/73 (2%)

Query: 2  QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF--AGKQLEDGRTLADY 59
           + VK L G    + + SS ++  +KA+I  K G+   QQRL    +G  L+D   LA  
Sbjct: 2  DLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQ 61

Query: 60 NIQKESTLHLVLR 72
           +   ST+ LV+ 
Sbjct: 62 GLGPGSTVLLVVD 74

>d1z2ma1 d.15.1.1 (A:3-78) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Interferon-induced 15 kDa protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 84.6 bits (209), Expect = 3e-23
 Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 2/71 (2%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIY--AGKQLADDKTARDYN 136
           + VK L G E ++ +  + ++  +K ++ +K G+   QQRL    +G  L D        
Sbjct: 3   LTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQG 62

Query: 137 IEGGSVLHLVL 147
           +  GS + LV+
Sbjct: 63  LGPGSTVLLVV 73

>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 =  101 bits (252), Expect = 2e-29
 Identities = 18/91 (19%), Positives = 42/91 (46%), Gaps = 5/91 (5%)

Query: 1  MQIFV----KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQ-LEDGRT 55
          M I V    + LT  T +L+V     + N +   + + G+P ++ ++++  +   +D  +
Sbjct: 8  MLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLTDDHCS 67

Query: 56 LADYNIQKESTLHLVLRLRGGTMIKVKTLTG 86
          L  Y ++    + L+ +   G     +T +G
Sbjct: 68 LGSYGLKDGDMVVLLQKDNVGLRTPGRTPSG 98

>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 = 77.4 bits (190), Expect = 5e-20
 Identities = 13/77 (16%), Positives = 31/77 (40%), Gaps = 1/77 (1%)

Query: 78  MIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLAD-DKTARDYN 136
               + LT     + + P   +   +   E + G+P  + +++Y  + L D   +   Y 
Sbjct: 13  YCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLTDDHCSLGSYG 72

Query: 137 IEGGSVLHLVLALRGGG 153
           ++ G ++ L+     G 
Sbjct: 73  LKDGDMVVLLQKDNVGL 89

>d1wgda_ d.15.1.1 (A:) Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1
species: Human (Homo sapiens) [TaxId: 9606]

 Score =   99 bits (249), Expect = 5e-29
 Identities = 22/82 (26%), Positives = 41/82 (50%), Gaps = 6/82 (7%)

Query: 1  MQIFVKTLTGK--TITLEVESSDTIDNVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTL 56
          + + VK+   +   + L  +   ++ ++KA +         P+ QRLI++GK L D + L
Sbjct: 8  VTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCL 67

Query: 57 ADYNIQKES--TLHLVLRLRGG 76
           D   ++E    LHLV  ++ G
Sbjct: 68 RDLLPKQEKRHVLHLVCNVKSG 89

>d1wgda_ d.15.1.1 (A:) Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 84.5 bits (209), Expect = 6e-23
 Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 6/80 (7%)

Query: 79  IKVKTLTGK--EIEIDIEPTDTIERIKERVEEKEG--IPPVQQRLIYAGKQLADDKTARD 134
           + VK+   +  ++E+  +   ++  +K  +         P  QRLIY+GK L D +  RD
Sbjct: 10  LLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRD 69

Query: 135 YNI--EGGSVLHLVLALRGG 152
                E   VLHLV  ++ G
Sbjct: 70  LLPKQEKRHVLHLVCNVKSG 89

>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 = 96.1 bits (239), Expect = 2e-27
 Identities = 18/78 (23%), Positives = 31/78 (39%), Gaps = 4/78 (5%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQL-EDGRTLADY 59
          + + +K L            DT+  +K+K    +     Q +LI+ G+ L +  RTL+  
Sbjct: 8  INVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQ---ESQMKLIYQGRLLQDPARTLSSL 64

Query: 60 NIQKESTLHLVLRLRGGT 77
          NI     +H      G  
Sbjct: 65 NITNNCVIHCHRSPPGAA 82

>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 = 81.5 bits (201), Expect = 1e-21
 Identities = 20/79 (25%), Positives = 32/79 (40%), Gaps = 4/79 (5%)

Query: 75  GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQL-ADDKTAR 133
            G  +++K L   E      P DT+  +K +    +     Q +LIY G+ L    +T  
Sbjct: 6   SGINVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQES---QMKLIYQGRLLQDPARTLS 62

Query: 134 DYNIEGGSVLHLVLALRGG 152
             NI    V+H   +  G 
Sbjct: 63  SLNITNNCVIHCHRSPPGA 81

>d1wx8a1 d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]} Length = 83

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 4931431F19Rik
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 92.0 bits (228), Expect = 7e-26
 Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 1/72 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKT         +  +  +   K +I        D+  LIF GK L D   L+   
Sbjct: 11 IRVSVKTPQDCH-EFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQDILSQRG 69

Query: 61 IQKESTLHLVLR 72
          I   ST+H+V+R
Sbjct: 70 ILDGSTVHVVVR 81

>d1wx8a1 d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]} Length = 83

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 4931431F19Rik
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 75.4 bits (185), Expect = 2e-19
 Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 1/69 (1%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           + VKT      E  +     + R K+++ +       +  LI+ GK L D        I 
Sbjct: 13  VSVKTPQDCH-EFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQDILSQRGIL 71

Query: 139 GGSVLHLVL 147
            GS +H+V+
Sbjct: 72  DGSTVHVVV 80

>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 = 92.0 bits (228), Expect = 1e-25
 Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 1   MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
           +++ VKT   K     V  + ++   K  I  +     DQ  LIFAGK L+D  TL  + 
Sbjct: 33  IKVTVKTPKEK-EEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLIQHG 91

Query: 61  IQKESTLHLVLR 72
           I    T+HLV++
Sbjct: 92  IHDGLTVHLVIK 103

>d1j8ca_ d.15.1.1 (A:) Ubiquitin-like N-terminal domain of PLIC-2 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like N-terminal domain of PLIC-2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 76.6 bits (188), Expect = 1e-19
 Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 1/69 (1%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           + VKT   KE E  +    ++++ KE + ++      Q  LI+AGK L D  T   + I 
Sbjct: 35  VTVKTPKEKE-EFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIH 93

Query: 139 GGSVLHLVL 147
            G  +HLV+
Sbjct: 94  DGLTVHLVI 102

>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 = 91.6 bits (227), Expect = 2e-25
 Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 2/78 (2%)

Query: 1   MQIFVKTLT-GKTITLEVES-SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLAD 58
           +++       G+ + + V+S S+ + ++K KI  +  IP ++Q+L      L+D  +LA 
Sbjct: 30  IRVSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSLAH 89

Query: 59  YNIQKESTLHLVLRLRGG 76
           YN+     L L LR R G
Sbjct: 90  YNVGAGEILTLSLRERSG 107

>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 = 71.2 bits (174), Expect = 1e-17
 Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 2/76 (2%)

Query: 79  IKVKTLT-GKEIEIDIEP-TDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYN 136
           +       G+ +EI ++  ++ +  +KE++  +  IP  +Q+L      L D+ +   YN
Sbjct: 32  VSKPNENDGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSLAHYN 91

Query: 137 IEGGSVLHLVLALRGG 152
           +  G +L L L  R G
Sbjct: 92  VGAGEILTLSLRERSG 107

>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 = 90.4 bits (224), Expect = 2e-25
 Identities = 15/79 (18%), Positives = 35/79 (44%), Gaps = 3/79 (3%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI---FAGKQLEDGRTLA 57
          + I VK    +     +   DT+ ++K  ++   G+ P++Q+L+     GK  E+   L 
Sbjct: 8  LPIIVKWGGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLG 67

Query: 58 DYNIQKESTLHLVLRLRGG 76
             ++  + + ++     G
Sbjct: 68 ALKLKPNTKIMMMGTRESG 86

>d1v5ta_ d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 90

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: 8430435i17rik protein
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 69.3 bits (169), Expect = 5e-17
 Identities = 14/77 (18%), Positives = 32/77 (41%), Gaps = 3/77 (3%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIY---AGKQLADDKTARDY 135
           I VK    +     +   DT+  +K+ ++   G+ P +Q+L+     GK   +D      
Sbjct: 10  IIVKWGGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGAL 69

Query: 136 NIEGGSVLHLVLALRGG 152
            ++  + + ++     G
Sbjct: 70  KLKPNTKIMMMGTRESG 86

>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 = 89.7 bits (222), Expect = 5e-25
 Identities = 27/78 (34%), Positives = 42/78 (53%), Gaps = 1/78 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ VKT   K     V  + TI  +K +I  +    PDQ  LIFAGK L+D  +LA   
Sbjct: 8  IKVTVKTPKDKE-DFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCG 66

Query: 61 IQKESTLHLVLRLRGGTM 78
          ++   T+HLV++ +   M
Sbjct: 67 VRDGLTVHLVIKRQHRAM 84

>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 = 71.2 bits (174), Expect = 9e-18
 Identities = 23/69 (33%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           + VKT   KE +  +  T TI+++KE + ++    P Q  LI+AGK L D  +     + 
Sbjct: 10  VTVKTPKDKE-DFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVR 68

Query: 139 GGSVLHLVL 147
            G  +HLV+
Sbjct: 69  DGLTVHLVI 77

>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 = 88.6 bits (219), Expect = 1e-24
 Identities = 16/69 (23%), Positives = 35/69 (50%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ V    GK + ++  + D++ + K  +  + G  P++  L   G  L+D  +L DY 
Sbjct: 2  IEVVVNDRLGKKVRVKCLAEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHISLEDYE 61

Query: 61 IQKESTLHL 69
          +  ++ L L
Sbjct: 62 VHDQTNLEL 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 = 70.5 bits (172), Expect = 1e-17
 Identities = 15/67 (22%), Positives = 28/67 (41%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           + V    GK++ +     D++   K+ +  + G  P +  L   G  L D  +  DY + 
Sbjct: 4   VVVNDRLGKKVRVKCLAEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHISLEDYEVH 63

Query: 139 GGSVLHL 145
             + L L
Sbjct: 64  DQTNLEL 70

>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 = 86.1 bits (213), Expect = 2e-23
 Identities = 20/86 (23%), Positives = 38/86 (44%), Gaps = 14/86 (16%)

Query: 1  MQIFVKTLTGKTIT-LEVESSDTIDNVKAKIQD-----KEGIP--PDQQRLIFAGKQLED 52
          ++I  +   G  I       + T+  +K  +       KE  P    + +LI AGK LE+
Sbjct: 8  LEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLEN 67

Query: 53 GRTLADYNI------QKESTLHLVLR 72
           +T+ DY           +T+H++++
Sbjct: 68 SKTVKDYRSPVSNLAGAVTTMHVIIQ 93

>d1se9a_ d.15.1.1 (A:) Hypothetical protein At3g01050 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 101

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Hypothetical protein At3g01050
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 76.5 bits (188), Expect = 1e-19
 Identities = 22/83 (26%), Positives = 35/83 (42%), Gaps = 14/83 (16%)

Query: 79  IKVKTLTGKEI-EIDIEPTDTIERIKERVEE-----KEGIP--PVQQRLIYAGKQLADDK 130
           IK +   G +I         T+  +KE V       KE  P    + +LI AGK L + K
Sbjct: 10  IKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSK 69

Query: 131 TARDYNIEGG------SVLHLVL 147
           T +DY           + +H+++
Sbjct: 70  TVKDYRSPVSNLAGAVTTMHVII 92

>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 = 85.0 bits (210), Expect = 4e-23
 Identities = 15/84 (17%), Positives = 27/84 (32%), Gaps = 8/84 (9%)

Query: 1  MQIFVKT-LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQ-------LED 52
          + +F+ + L           S TI   K K++   G P     L   G          ++
Sbjct: 8  VMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVGSPASCMELELYGADDKFYSKLDQE 67

Query: 53 GRTLADYNIQKESTLHLVLRLRGG 76
             L  Y +     +H++     G
Sbjct: 68 DALLGSYPVDDGCRIHVIDHSGSG 91

>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 = 69.9 bits (171), Expect = 3e-17
 Identities = 14/71 (19%), Positives = 24/71 (33%), Gaps = 7/71 (9%)

Query: 83  TLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQ-------LADDKTARDY 135
           +L     E     + TI   K ++E   G P     L   G           +D     Y
Sbjct: 15  SLNSFRSEKRYSRSLTIAEFKCKLELVVGSPASCMELELYGADDKFYSKLDQEDALLGSY 74

Query: 136 NIEGGSVLHLV 146
            ++ G  +H++
Sbjct: 75  PVDDGCRIHVI 85

>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 = 83.9 bits (207), Expect = 2e-22
 Identities = 13/79 (16%), Positives = 35/79 (44%), Gaps = 2/79 (2%)

Query: 1  MQIFV--KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLAD 58
          +++F+  +    +   LE     T   +++KI +  G+  +  +++   KQL+ G+TL +
Sbjct: 18 IEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFGLQENYIKIVINKKQLQLGKTLEE 77

Query: 59 YNIQKESTLHLVLRLRGGT 77
            +       ++   +   
Sbjct: 78 QGVAHNVKAMVLELKQSSG 96

>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 = 71.5 bits (175), Expect = 7e-18
 Identities = 9/75 (12%), Positives = 28/75 (37%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           +  +    ++  ++     T   ++ ++ E  G+     +++   KQL   KT  +  + 
Sbjct: 22  LPPRLKKDRKNLLETRLHITGRELRSKIAETFGLQENYIKIVINKKQLQLGKTLEEQGVA 81

Query: 139 GGSVLHLVLALRGGG 153
                 ++   +  G
Sbjct: 82  HNVKAMVLELKQSSG 96

>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 = 83.0 bits (205), Expect = 2e-22
 Identities = 10/73 (13%), Positives = 26/73 (35%), Gaps = 8/73 (10%)

Query: 6  KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE--------DGRTLA 57
               + +  ++  S T+  VK  +     +P  +  L +   ++         D + L 
Sbjct: 18 NQPERQILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQ 77

Query: 58 DYNIQKESTLHLV 70
           Y+++    L + 
Sbjct: 78 FYSVENGDCLLVR 90

>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 = 69.2 bits (169), Expect = 6e-17
 Identities = 13/85 (15%), Positives = 34/85 (40%), Gaps = 13/85 (15%)

Query: 75  GGTMIKVK-----TLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLA-- 127
            G ++ +K         + +E  +  + T++++K  +     +P  +  L Y   ++   
Sbjct: 6   SGQLLTLKIKCSNQPERQILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSKMPGR 65

Query: 128 ------DDKTARDYNIEGGSVLHLV 146
                 D +  + Y++E G  L + 
Sbjct: 66  EIELENDLQPLQFYSVENGDCLLVR 90

>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 = 82.6 bits (204), Expect = 3e-22
 Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 3/69 (4%)

Query: 7  TLTGKTITLEVESSDTIDNVKAKIQDK--EGIP-PDQQRLIFAGKQLEDGRTLADYNIQK 63
           L    +        +I  +K  I  K  E +P P+   LI+ G++L+D +TL  Y IQ 
Sbjct: 24 QLPETELGEYSLGGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDFYGIQP 83

Query: 64 ESTLHLVLR 72
           ST+H++ +
Sbjct: 84 GSTVHVLRK 92

>d1x1ma1 d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 7
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 78.4 bits (193), Expect = 2e-20
 Identities = 26/89 (29%), Positives = 42/89 (47%), Gaps = 5/89 (5%)

Query: 64  ESTLHLVLRLRGGTMIKVKTLTGKEIEIDIEP--TDTIERIKERVEEK--EGIP-PVQQR 118
            S  HL ++L    +     L   E E+        +I  +K+ +  K  E +P P    
Sbjct: 3   LSDWHLAVKLADQPLAPKSILQLPETELGEYSLGGYSISFLKQLIAGKLQESVPDPELID 62

Query: 119 LIYAGKQLADDKTARDYNIEGGSVLHLVL 147
           LIY G++L DD+T   Y I+ GS +H++ 
Sbjct: 63  LIYCGRKLKDDQTLDFYGIQPGSTVHVLR 91

>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 = 77.2 bits (190), Expect = 3e-20
 Identities = 10/76 (13%), Positives = 30/76 (39%), Gaps = 1/76 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + + V       I  +++ +  +  +      ++G   D  R ++ G +++  +T  D +
Sbjct: 5  INLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLD 63

Query: 61 IQKESTLHLVLRLRGG 76
          ++    +       GG
Sbjct: 64 MEDNDIIEAHREQIGG 79

>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 = 76.8 bits (189), Expect = 5e-20
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 1/74 (1%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           +KV      EI   I+ T  + R+ E   +++G      R +Y G ++  D+T  D ++E
Sbjct: 7   LKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDME 65

Query: 139 GGSVLHLVLALRGG 152
              ++       GG
Sbjct: 66  DNDIIEAHREQIGG 79

>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 = 76.9 bits (189), Expect = 6e-20
 Identities = 13/76 (17%), Positives = 32/76 (42%), Gaps = 2/76 (2%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          + + +         ++V    T   +K KI    G+PP  Q++++    + + +TL +  
Sbjct: 18 VDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMY-KGLVPEDKTLREIK 75

Query: 61 IQKESTLHLVLRLRGG 76
          +   + + +V     G
Sbjct: 76 VTSGAKIMVVGSTISG 91

>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 = 69.2 bits (169), Expect = 6e-17
 Identities = 16/79 (20%), Positives = 40/79 (50%), Gaps = 2/79 (2%)

Query: 75  GGTMIKVKTLT-GKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTAR 133
           G  ++ +K +    + ++ +    T   +K+++    G+PP  Q+++Y    + +DKT R
Sbjct: 14  GKELVDLKIIWNKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMY-KGLVPEDKTLR 72

Query: 134 DYNIEGGSVLHLVLALRGG 152
           +  +  G+ + +V +   G
Sbjct: 73  EIKVTSGAKIMVVGSTISG 91

>d1wgga_ d.15.1.1 (A:) Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (Mus musculus) [TaxId: 10090]} Length = 96

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin carboxyl-terminal hydrolase 14
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 76.6 bits (188), Expect = 8e-20
 Identities = 13/70 (18%), Positives = 32/70 (45%), Gaps = 1/70 (1%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
            + VK    K   +E+ + +     KA++    G+ P +Q+++  G  L+D     +  
Sbjct: 8  YSVTVKWGKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLKDD-DWGNIK 66

Query: 61 IQKESTLHLV 70
          ++   T+ ++
Sbjct: 67 MKNGMTVLMM 76

>d1wgga_ d.15.1.1 (A:) Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (Mus musculus) [TaxId: 10090]} Length = 96

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin carboxyl-terminal hydrolase 14
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 65.4 bits (159), Expect = 2e-15
 Identities = 12/68 (17%), Positives = 30/68 (44%), Gaps = 1/68 (1%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           + VK    K   +++   +     K ++    G+ P +Q+++  G  L DD    +  ++
Sbjct: 10  VTVKWGKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLKDD-DWGNIKMK 68

Query: 139 GGSVLHLV 146
            G  + ++
Sbjct: 69  NGMTVLMM 76

>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 = 74.8 bits (184), Expect = 2e-19
 Identities = 17/73 (23%), Positives = 39/73 (53%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           +KV      EI   ++ T  ++++KE   +++G+P    R ++ G+++AD+ T ++  +E
Sbjct: 5   LKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGME 64

Query: 139 GGSVLHLVLALRG 151
              V+ +     G
Sbjct: 65  EEDVIEVYQEQTG 77

>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 = 73.2 bits (180), Expect = 9e-19
 Identities = 13/75 (17%), Positives = 35/75 (46%)

Query: 1  MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYN 60
          +++ V       I  +V+ +  +  +K     ++G+P +  R +F G+++ D  T  +  
Sbjct: 3  IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELG 62

Query: 61 IQKESTLHLVLRLRG 75
          +++E  + +     G
Sbjct: 63 MEEEDVIEVYQEQTG 77

>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 = 73.4 bits (180), Expect = 1e-18
 Identities = 11/76 (14%), Positives = 28/76 (36%), Gaps = 7/76 (9%)

Query: 7  TLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQ-------LEDGRTLADY 59
            T   +  +  +  +++++K K++   G   D  R+              +  ++L D 
Sbjct: 12 NATDFPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDL 71

Query: 60 NIQKESTLHLVLRLRG 75
           ++    +H V    G
Sbjct: 72 GVRDGYRIHAVDVTGG 87

>d1t0ya_ d.15.1.1 (A:) Ubiquitin-like domain of tubulin folding cofactor B {Nematode (Caenorhabditis elegans) [TaxId: 6239]} Length = 90

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like domain of tubulin folding cofactor B
species: Nematode (Caenorhabditis elegans) [TaxId: 6239]

 Score = 68.0 bits (166), Expect = 2e-16
 Identities = 13/85 (15%), Positives = 29/85 (34%), Gaps = 11/85 (12%)

Query: 78  MIKVK---TLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQ-------LA 127
           +  ++     T   +E       ++  +K+++E   G      R+               
Sbjct: 4   VYDLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGELTD 63

Query: 128 DDKTARDYNIEGGSVLHLVLALRGG 152
             K+ +D  +  G  +H V  + GG
Sbjct: 64  GAKSLKDLGVRDGYRIHAV-DVTGG 87

>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 = 72.6 bits (178), Expect = 2e-18
 Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 7/78 (8%)

Query: 1  MQIFVKTLTGKTITLEVE-----SSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQL-EDGR 54
          + + V   + +   L V      S   + ++   +++  G+P   Q+LIF GK L E   
Sbjct: 2  LTVTVTH-SNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLKEMET 60

Query: 55 TLADYNIQKESTLHLVLR 72
           L+   IQ    + L+ +
Sbjct: 61 PLSALGIQDGCRVMLIGK 78

>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 = 63.7 bits (155), Expect = 6e-15
 Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 7/74 (9%)

Query: 79  IKVKTLTGKEIEIDIEP-----TDTIERIKERVEEKEGIPPVQQRLIYAGKQLA-DDKTA 132
           + V   + ++ ++ +          ++ + + VEE  G+P   Q+LI+ GK L   +   
Sbjct: 4   VTVTH-SNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLKEMETPL 62

Query: 133 RDYNIEGGSVLHLV 146
               I+ G  + L+
Sbjct: 63  SALGIQDGCRVMLI 76

>d1wm3a_ d.15.1.1 (A:) SUMO-2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

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]

 Score = 45.9 bits (109), Expect = 3e-08
 Identities = 11/65 (16%), Positives = 28/65 (43%)

Query: 79  IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIE 138
           +KV    G  ++  I+    + ++ +   E++G+   Q R  + G+ + +  T     +E
Sbjct: 4   LKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEME 63

Query: 139 GGSVL 143
               +
Sbjct: 64  DEDTI 68

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	154
d1ogwa_	76	Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}	99.91
d2zeqa1	78	Ubiquitin-like domain of parkin {Mouse (Mus muscul	99.89
d1wh3a_	87	2'-5'-oligoadenylate synthetase-like protein, OASL	99.88
d1bt0a_	73	Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxI	99.88
d1ogwa_	76	Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}	99.88
d2zeqa1	78	Ubiquitin-like domain of parkin {Mouse (Mus muscul	99.88
d1z2ma2	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.87
d1bt0a_	73	Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxI	99.87
d1z2ma2	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.86
d1wh3a_	87	2'-5'-oligoadenylate synthetase-like protein, OASL	99.85
d1ttna1	80	Dendritic cell-derived ubiquitin-like protein {Hum	99.85
d1ttna1	80	Dendritic cell-derived ubiquitin-like protein {Hum	99.84
d1wx9a1	73	Large proline-rich protein BAT3 {Human (Homo sapie	99.84
d2faza1	76	Ubiquitin-like PHD and RING finger domain-containi	99.84
d1m94a_	73	Ubiquitin-like modifier protein hub1 {Baker's yeas	99.84
d2faza1	76	Ubiquitin-like PHD and RING finger domain-containi	99.84
d1wy8a1	76	Ubiquitin-like PHD and RING finger domain-containi	99.84
d1m94a_	73	Ubiquitin-like modifier protein hub1 {Baker's yeas	99.83
d1wy8a1	76	Ubiquitin-like PHD and RING finger domain-containi	99.83
d1z2ma1	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.83
d1wx9a1	73	Large proline-rich protein BAT3 {Human (Homo sapie	99.83
d1z2ma1	76	Interferon-induced 15 kDa protein {Human (Homo sap	99.82
d1zkha1	86	Splicing factor 3 subunit 1, C-terminal domain {Hu	99.82
d1oqya4	77	Ubiquitin-like domain of Rad23 homolog A (Hhr23a)	99.82
d2bwfa1	73	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.82
d1yqba1	84	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	99.82
d1uela_	95	Ubiquitin-like domain of Rad23 homolog B (Hhr23B)	99.82
d1oqya4	77	Ubiquitin-like domain of Rad23 homolog A (Hhr23a)	99.81
d2bwfa1	73	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.81
d1uela_	95	Ubiquitin-like domain of Rad23 homolog B (Hhr23B)	99.81
d1we6a_	111	Splicing factor 3 subunit 1, C-terminal domain {Th	99.81
d1uh6a_	100	Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculu	99.81
d1yqba1	84	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	99.8
d1uh6a_	100	Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculu	99.79
d1j8ca_	103	Ubiquitin-like N-terminal domain of PLIC-2 {Human	99.78
d1j8ca_	103	Ubiquitin-like N-terminal domain of PLIC-2 {Human	99.78
d1wx8a1	83	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	99.78
d1wx8a1	83	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	99.78
d1v5oa_	102	1700011n24rik protein {Mouse (Mus musculus) [TaxId	99.77
d1zkha1	86	Splicing factor 3 subunit 1, C-terminal domain {Hu	99.76
d1v5oa_	102	1700011n24rik protein {Mouse (Mus musculus) [TaxId	99.75
d1se9a_	101	Hypothetical protein At3g01050 {Thale cress (Arabi	99.74
d1wiaa_	95	Ubiquitin-like protein bab25500 (2010008E23Rik) {M	99.74
d1wgga_	96	Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (M	99.73
d1se9a_	101	Hypothetical protein At3g01050 {Thale cress (Arabi	99.73
d1v2ya_	105	Ubiquitin-like protein 3300001g02rik {Mouse (Mus m	99.73
d1v2ya_	105	Ubiquitin-like protein 3300001g02rik {Mouse (Mus m	99.73
d1wgha_	116	Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculu	99.73
d1euvb_	79	SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomy	99.73
d1wgga_	96	Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (M	99.73
d1wiaa_	95	Ubiquitin-like protein bab25500 (2010008E23Rik) {M	99.72
d1wgha_	116	Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculu	99.71
d1wxva1	81	Bag-family molecular chaperone regulator-1 {Human	99.71
d1wjua_	100	NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens	99.71
d1v86a_	95	hypothetical D7wsu128e protein {Mouse (Mus musculu	99.71
d1we6a_	111	Splicing factor 3 subunit 1, C-terminal domain {Th	99.7
d1v5ta_	90	8430435i17rik protein {Mouse (Mus musculus) [TaxId	99.7
d1wjua_	100	NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens	99.7
d1wxva1	81	Bag-family molecular chaperone regulator-1 {Human	99.69
d1v86a_	95	hypothetical D7wsu128e protein {Mouse (Mus musculu	99.69
d1v5ta_	90	8430435i17rik protein {Mouse (Mus musculus) [TaxId	99.68
d1wgda_	93	Homocysteine-responsive endoplasmic reticulum-resi	99.66
d1wgda_	93	Homocysteine-responsive endoplasmic reticulum-resi	99.65
d2uyzb1	77	SUMO-1 (smt3 homologue) {Human (Homo sapiens) [Tax	99.63
d2c9wb1	103	Elongin B {Human (Homo sapiens) [TaxId: 9606]}	99.63
d1v6ea_	95	Ubiquitin-like domain of tubulin folding cofactor	99.62
d2c9wb1	103	Elongin B {Human (Homo sapiens) [TaxId: 9606]}	99.61
d1v6ea_	95	Ubiquitin-like domain of tubulin folding cofactor	99.58
d1euvb_	79	SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomy	99.57
d1wjna_	97	Tubulin-folding protein TbcE {Mouse (Mus musculus)	99.51
d2uyzb1	77	SUMO-1 (smt3 homologue) {Human (Homo sapiens) [Tax	99.51
d1x1ma1	94	Ubiquitin-like protein 7 {Mouse (Mus musculus) [Ta	99.5
d1wjna_	97	Tubulin-folding protein TbcE {Mouse (Mus musculus)	99.45
d1t0ya_	90	Ubiquitin-like domain of tubulin folding cofactor	99.45
d1t0ya_	90	Ubiquitin-like domain of tubulin folding cofactor	99.43
d1x1ma1	94	Ubiquitin-like protein 7 {Mouse (Mus musculus) [Ta	99.35
d1wm3a_	72	SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}	99.27
d1wm3a_	72	SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}	99.1
d1wf9a1	94	NPL4-like protein 1 {Thale cress (Arabidopsis thal	98.9
d1wf9a1	94	NPL4-like protein 1 {Thale cress (Arabidopsis thal	98.68
d2al3a1	76	Tether containing UBX domain for GLUT4 (Tug) {Mous	98.54
d2al3a1	76	Tether containing UBX domain for GLUT4 (Tug) {Mous	98.1
d1h8ca_	82	Fas-associated factor 1, Faf1 {Human (Homo sapiens	97.85
d1h8ca_	82	Fas-associated factor 1, Faf1 {Human (Homo sapiens	97.68
d1i42a_	89	p47 {Rat (Rattus norvegicus) [TaxId: 10116]}	97.49
d1i42a_	89	p47 {Rat (Rattus norvegicus) [TaxId: 10116]}	97.31
d1wj4a_	124	Hypothetical protein KIAA0794 {Human (Homo sapiens	97.27
d2cr5a1	96	UBX domain-containing protein 6 (Reproduction 8) {	97.25
d1wj4a_	124	Hypothetical protein KIAA0794 {Human (Homo sapiens	97.14
d2cr5a1	96	UBX domain-containing protein 6 (Reproduction 8) {	96.87
d1ef1a3	84	Moesin {Human (Homo sapiens) [TaxId: 9606]}	94.89
d1vjka_	88	Molybdopterin synthase subunit MoaD {Pyrococcus fu	94.67
d1zud21	65	Thiamin biosynthesis sulfur carrier protein ThiS {	94.55
d1ef1a3	84	Moesin {Human (Homo sapiens) [TaxId: 9606]}	94.48
d1wgya_	104	Rap guanine nucleotide exchange factor 5, RapGEF5	94.24
d1oeya_	82	Neutrophil cytosol factor 2 (p67phox component of	93.65
d1oeya_	82	Neutrophil cytosol factor 2 (p67phox component of	93.43
d1wxma1	73	A-Raf proto-oncogene serine/threonine-protein kina	93.29
d1vjka_	88	Molybdopterin synthase subunit MoaD {Pyrococcus fu	93.06
d1gg3a3	81	Erythroid membrane protein 4.1R {Human (Homo sapie	92.83
d1xo3a_	101	C9orf74 homolog {Mouse (Mus musculus) [TaxId: 1009	92.48
d1wgra_	100	Growth factor receptor-bound protein 7, GRB-7 {Hum	92.33
d1h4ra3	84	Merlin {Human (Homo sapiens) [TaxId: 9606]}	92.23
d1ip9a_	85	Bud emergence mediator Bemp1 {Baker's yeast (Sacch	91.46
d1wgya_	104	Rap guanine nucleotide exchange factor 5, RapGEF5	91.24
d1c1yb_	77	c-Raf1 RBD {Human (Homo sapiens) [TaxId: 9606]}	90.96
d1wgra_	100	Growth factor receptor-bound protein 7, GRB-7 {Hum	90.71
d1fm0d_	81	Molybdopterin synthase subunit MoaD {Escherichia c	90.38
d1h4ra3	84	Merlin {Human (Homo sapiens) [TaxId: 9606]}	89.95
d1ip9a_	85	Bud emergence mediator Bemp1 {Baker's yeast (Sacch	89.84
d1gg3a3	81	Erythroid membrane protein 4.1R {Human (Homo sapie	88.56
d1xo3a_	101	C9orf74 homolog {Mouse (Mus musculus) [TaxId: 1009	88.38
d1y8xb1	92	UBA3 {Human (Homo sapiens) [TaxId: 9606]}	88.02
d1v8ca1	87	MoaD-related protein, N-terminal domain {Thermus t	86.88
d1j0ga_	92	Hypothetical protein 1810045k17 {Mouse (Mus muscul	86.18
d1wxma1	73	A-Raf proto-oncogene serine/threonine-protein kina	85.56
d1tygb_	65	Thiamin biosynthesis sulfur carrier protein ThiS {	85.05
d1c1yb_	77	c-Raf1 RBD {Human (Homo sapiens) [TaxId: 9606]}	82.73
d2incc1	83	Toluene, o-xylene monooxygenase oxygenase subunit	81.18

>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=99.91  E-value=2.9e-24  Score=126.30  Aligned_cols=76  Identities=63%  Similarity=0.993  Sum_probs=74.7

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      |+|+|+..+|+++.+++++++||.+||++|+.+.|+|++.|+|+|+|+.|+|+.+|++|||++|++|++++|++||
T Consensus         1 MqI~Vk~l~G~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~qrL~~~Gk~L~d~~tL~~y~i~~~s~I~L~~rlrgG   76 (76)
T d1ogwa_           1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG   76 (76)
T ss_dssp             CEEEEEETTSCEEEEECCTTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECTTCC
T ss_pred             CEEEEEcCCCCEEEEEECCCCcHHHHHHhhhhhcCCChHHEEeEECCeEcCCCCCHHHcCCCCCCEEEEEEecCCC
Confidence            7899999999999999999999999999999999999999999999999999999999999999999999999998

>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=99.89  E-value=2.8e-23  Score=122.41  Aligned_cols=76  Identities=28%  Similarity=0.538  Sum_probs=74.1

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecC
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRG  151 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~g  151 (154)
                      +|.|+|+..+|+++++++++++||++||++|++++|+|++.|+|+|+|+.|+|+.+|++|+|+++++|+++.|++|
T Consensus         2 ~M~I~Vk~~~g~t~~l~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lv~R~rg   77 (78)
T d2zeqa1           2 GMIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRR   77 (78)
T ss_dssp             CEEEEEESSSSSCEEEEECTTCBHHHHHHHHHHHHTCCGGGEEEEETTEEECTTCBGGGSSCCTTCEEEEEESSCC
T ss_pred             ceEEEEEcCCCCEEEEEEcccccHHHHHHHHHHHHCcChhHeEEEEeeeEcCCCCCHHHcCCCCCCEEEEEeccCC
Confidence            4899999999999999999999999999999999999999999999999999999999999999999999999987

>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=99.88  E-value=8.7e-23  Score=122.82  Aligned_cols=80  Identities=28%  Similarity=0.398  Sum_probs=76.9

Q ss_pred             ecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           74 RGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        74 ~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      ...|+|+|+..+|+.+.+++++++||.+||++|+.++|+|+++|+|+|+|+.|+|+.+|++|+|.++++|++..+.+||+
T Consensus         5 s~~mqI~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~~tL~~y~I~~~stl~l~~r~~~gp   84 (87)
T d1wh3a_           5 SSGIQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKGSGP   84 (87)
T ss_dssp             SSSEEEEEEETTTEEEEEEECSSSBHHHHHHHHHHHTCCCTTTEEEEETTEECCSSSBHHHHTCCTTEEEEEEECSCCCS
T ss_pred             CCcEEEEEECCCCCEEEEEECCcCcHHHHHHHHHHHHCcChHHeEEEeeceEcCCCCcHHHcCCCCCCEEEEEecCCCCC
Confidence            35699999999999999999999999999999999999999999999999999999999999999999999999999885

>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=99.88  E-value=1.5e-22  Score=117.98  Aligned_cols=73  Identities=95%  Similarity=1.327  Sum_probs=70.9

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEee
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      |.|+|++.+|+++.++|++++||++||++++++.|+|+++|+|+|+|+.|+|+.+|++|||++|++|++++|+
T Consensus         1 M~I~Vk~~~G~~~~l~V~~~~tV~~lK~~i~~~~gi~~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lvlrL   73 (73)
T d1bt0a_           1 MLIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLIYAGKQLADDKTAKDYNIEGGSVLHLVLAL   73 (73)
T ss_dssp             CEEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhCCChHHEEEEECCeEcCCCCcHHHcCCCCCCEEEEEeeC
Confidence            7899999999999999999999999999999999999999999999999999999999999999999999874

>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=99.88  E-value=1.5e-22  Score=118.92  Aligned_cols=75  Identities=96%  Similarity=1.311  Sum_probs=72.6

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+||+.+|+++.+++++++||.+||++|+.+.++|++.|+|+|+|+.|+|+.+|++|++.++++|++.++.++
T Consensus         1 MqI~Vk~l~G~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~qrL~~~Gk~L~d~~tL~~y~i~~~s~I~L~~rlrg   75 (76)
T d1ogwa_           1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG   75 (76)
T ss_dssp             CEEEEEETTSCEEEEECCTTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECTTC
T ss_pred             CEEEEEcCCCCEEEEEECCCCcHHHHHHhhhhhcCCChHHEEeEECCeEcCCCCCHHHcCCCCCCEEEEEEecCC
Confidence            899999999999999999999999999999999999999999999999999999999999999999999988654

>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=99.88  E-value=1.1e-22  Score=119.74  Aligned_cols=75  Identities=33%  Similarity=0.593  Sum_probs=72.6

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+..+|+++++++++++||.+||++|+++.++|++.|+|+|+|+.|+|+.+|++|+|.++++||++.++++
T Consensus         3 M~I~Vk~~~g~t~~l~v~~~~tV~~lK~~i~~~~gip~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lv~R~rg   77 (78)
T d2zeqa1           3 MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRR   77 (78)
T ss_dssp             EEEEEESSSSSCEEEEECTTCBHHHHHHHHHHHHTCCGGGEEEEETTEEECTTCBGGGSSCCTTCEEEEEESSCC
T ss_pred             eEEEEEcCCCCEEEEEEcccccHHHHHHHHHHHHCcChhHeEEEEeeeEcCCCCCHHHcCCCCCCEEEEEeccCC
Confidence            799999999999999999999999999999999999999999999999999999999999999999999988764

>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=99.87  E-value=3.4e-22  Score=117.32  Aligned_cols=75  Identities=24%  Similarity=0.352  Sum_probs=72.3

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEee
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      .+|+|+|+..+|+++.+++++++||.+||++|+++.|+|++.|+|+|+|+.|+|+.+|++|||++|++|++++|+
T Consensus         2 ~~~qi~Vk~~~G~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~qrL~~~gk~L~d~~tL~~y~I~~~sti~l~lRL   76 (76)
T d1z2ma2           2 EPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRL   76 (76)
T ss_dssp             CCEEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEECC
T ss_pred             CCEEEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHhcCChhHeEEEECCeECCCCCcHHHcCCCCCCEEEEEEeC
Confidence            468999999999999999999999999999999999999999999999999999999999999999999999874

>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=99.87  E-value=2.3e-22  Score=117.18  Aligned_cols=72  Identities=61%  Similarity=0.938  Sum_probs=70.5

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      |+|+||+++|+++++++++++||.+||++|+++.|+|++.|+|+|+|+.|+|+.+|++|+|.++++|+++++
T Consensus         1 M~I~Vk~~~G~~~~l~V~~~~tV~~lK~~i~~~~gi~~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lvlr   72 (73)
T d1bt0a_           1 MLIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLIYAGKQLADDKTAKDYNIEGGSVLHLVLA   72 (73)
T ss_dssp             CEEEEECTTSCEEEEECCTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEEC
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhCCChHHEEEEECCeEcCCCCcHHHcCCCCCCEEEEEee
Confidence            899999999999999999999999999999999999999999999999999999999999999999999876

>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=99.86  E-value=7.7e-22  Score=115.79  Aligned_cols=72  Identities=33%  Similarity=0.549  Sum_probs=70.2

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      |+|+|+..+|+++++++++++||.+||++|+.+.|+|++.|+|+|+|+.|+|+.+|++|||+++++|++.++
T Consensus         4 ~qi~Vk~~~G~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~qrL~~~gk~L~d~~tL~~y~I~~~sti~l~lR   75 (76)
T d1z2ma2           4 LSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLR   75 (76)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBGGGGTCCTTCEEEEEEC
T ss_pred             EEEEEEcCCCCEEEEEECCCCcHHHHHHHHHHHhcCChhHeEEEECCeECCCCCcHHHcCCCCCCEEEEEEe
Confidence            789999999999999999999999999999999999999999999999999999999999999999999875

>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=99.85  E-value=1.1e-21  Score=117.87  Aligned_cols=75  Identities=33%  Similarity=0.510  Sum_probs=72.1

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|+.++|+.+.+++++++||.+||++|+.+.++|++.|+|+|+|+.|+|+.+|++|+|.++++|++..+..+
T Consensus         8 mqI~Vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~~tL~~y~I~~~stl~l~~r~~~   82 (87)
T d1wh3a_           8 IQVFVKNPDGGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKKKGS   82 (87)
T ss_dssp             EEEEEEETTTEEEEEEECSSSBHHHHHHHHHHHTCCCTTTEEEEETTEECCSSSBHHHHTCCTTEEEEEEECSCC
T ss_pred             EEEEEECCCCCEEEEEECCcCcHHHHHHHHHHHHCcChHHeEEEeeceEcCCCCcHHHcCCCCCCEEEEEecCCC
Confidence            799999999999999999999999999999999999999999999999999999999999999999999987653

>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=99.85  E-value=1.9e-21  Score=115.13  Aligned_cols=77  Identities=23%  Similarity=0.454  Sum_probs=73.5

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecC
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRG  151 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~g  151 (154)
                      .+++|+|+..+|+++.+++++++||++||++|++++|+|+++|+|+|+|+.|+|+.+|++|+|++|++|+++++.+.
T Consensus         2 ~e~qi~Vk~~~G~~~~l~V~~~~tV~~lK~~I~~~~~ip~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lvi~~p~   78 (80)
T d1ttna1           2 YECQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQPV   78 (80)
T ss_dssp             CSEEEEEEETTTEEEEEEECTTSHHHHHHHHHHHTTCCCSTTCEEEETTEECCTTSHHHHCCCSSSCEEEEECCCSS
T ss_pred             CeEEEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCcccEEEEECceEcCCCCcHHHcCCCCCCEEEEEecCCC
Confidence            35889999999999999999999999999999999999999999999999999999999999999999999988764

>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=99.84  E-value=2.1e-21  Score=114.87  Aligned_cols=74  Identities=28%  Similarity=0.525  Sum_probs=71.2

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~   74 (154)
                      |+|+||..+|+++.+++++++||.+||++|+.+.++|++.|+|+|+|+.|+|+.+|++|+|.++++|+++++.+
T Consensus         4 ~qi~Vk~~~G~~~~l~V~~~~tV~~lK~~I~~~~~ip~~~qrLi~~Gk~L~d~~tL~~y~I~~~sti~lvi~~p   77 (80)
T d1ttna1           4 CQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQP   77 (80)
T ss_dssp             EEEEEEETTTEEEEEEECTTSHHHHHHHHHHHTTCCCSTTCEEEETTEECCTTSHHHHCCCSSSCEEEEECCCS
T ss_pred             EEEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCcccEEEEECceEcCCCCcHHHcCCCCCCEEEEEecCC
Confidence            68999999999999999999999999999999999999999999999999999999999999999999988754

>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=99.84  E-value=1.4e-21  Score=113.67  Aligned_cols=72  Identities=35%  Similarity=0.613  Sum_probs=68.6

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |+|+|++.+|+.+.+++++++||.+||++|+++.|+|++.|+|+|+|+.|+|+.+|++|++ ++++||++.+.
T Consensus         1 m~I~Vk~~~g~~~~l~V~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~~tL~dy~i-~~~ti~lv~r~   72 (73)
T d1wx9a1           1 LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVIHLVERA   72 (73)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHCCCTTTCCCEETTEECCSSSBHHHHTC-TTEEEBCCCSS
T ss_pred             CEEEEEcCCCCEEEEEECCCChHHHHHHHHHHHhCCChHHEEEEECCeEccCCCCHHHhCC-CCCEEEEEecC
Confidence            7999999999999999999999999999999999999999999999999999999999999 57899988764

>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=99.84  E-value=7.3e-21  Score=111.24  Aligned_cols=73  Identities=27%  Similarity=0.522  Sum_probs=69.0

Q ss_pred             eeeeeeecCCc-eEEEe-eCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEee
Q 040824           77 TMIKVKTLTGK-EIEID-IEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        77 ~~i~v~~~~~~-~~~~~-v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      |+|+|+..+|+ ++.+. +++++||++||++|+++.|+|++.|+|+|+|+.|+|+.+|++|||++|++|++.+|.
T Consensus         1 M~I~Vktl~Gk~t~~l~~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~y~I~~~sti~lv~r~   75 (76)
T d2faza1           1 MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLLVRQ   75 (76)
T ss_dssp             EEEEEEETTSSCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTTTTTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCcEEEEecCCCCCCHHHHHHHHHHHHCcChHHeEEEEeeEeccCCCcHHHcCCCCCCEEEEEEEc
Confidence            78999999996 67775 899999999999999999999999999999999999999999999999999999875

>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=99.84  E-value=4.1e-21  Score=111.63  Aligned_cols=71  Identities=21%  Similarity=0.320  Sum_probs=68.5

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEE
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      |+|+|++..|+.+.+++++++||++||++|+.++|+|+++|+|+|+|+.|+|+.+|++|||++|++|+++.
T Consensus         2 i~i~vk~~~Gk~~~v~V~~~~tV~~lK~~I~~~~~i~~~~q~Li~~Gk~L~d~~tL~~y~I~~gstl~L~~   72 (73)
T d1m94a_           2 IEVVVNDRLGKKVRVKCLAEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLELYY   72 (73)
T ss_dssp             EEEEEEETTTEEEEEEECTTSBHHHHHHHHHHHHCCTTTSEEEESSSCEECTTSBHHHHTCCTTEEEEEEE
T ss_pred             eEEEEECCCCCEEEEEECCcCcHHHHHHHHHHhhcccccEEEEEEEeEEecccCcHHHcCCCCCCEEEEEE
Confidence            67899999999999999999999999999999999999999999999999999999999999999999864

>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=99.84  E-value=6.6e-21  Score=111.44  Aligned_cols=73  Identities=37%  Similarity=0.647  Sum_probs=69.2

Q ss_pred             CEEEEEeCCCC-EEEEE-EeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTGK-TITLE-VESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~-~~~~~-v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |+|+|++++|+ ++++. +++++||++||++|+++.|+|++.|+|+|+|+.|.|+.+|++||+.++++||++++.
T Consensus         1 M~I~Vktl~Gk~t~~l~~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~y~I~~~sti~lv~r~   75 (76)
T d2faza1           1 MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLLVRQ   75 (76)
T ss_dssp             EEEEEEETTSSCEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTCBTTTTTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCcEEEEecCCCCCCHHHHHHHHHHHHCcChHHeEEEEeeEeccCCCcHHHcCCCCCCEEEEEEEc
Confidence            89999999995 78885 899999999999999999999999999999999999999999999999999998864

>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=99.84  E-value=6e-21  Score=111.61  Aligned_cols=73  Identities=37%  Similarity=0.622  Sum_probs=69.2

Q ss_pred             CEEEEEeCCC-CEEEE-EEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTG-KTITL-EVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~-~~~~~-~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |+|+|+..+| +++.+ .+++++||.+||++|+.+.|+|++.|+|+|+|+.|+|+.+|++|||.++++|++++++
T Consensus         1 M~I~Vk~l~G~~t~~~~~v~~~~TV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~~tL~~y~I~~~s~i~lv~rp   75 (76)
T d1wy8a1           1 MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVRP   75 (76)
T ss_dssp             EEEEEEETTCSCEEEEEEECTTCBHHHHHHHHHHHSCCCTTTEEEEETTEECCSSSBHHHHTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCceEEEeccCCCChHHHHHHHHHHHHCCCchhcEEEEEeeEecCCCCHHHcCCCCCCEEEEEEcc
Confidence            8999999998 57877 5999999999999999999999999999999999999999999999999999999874

>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=99.83  E-value=6.6e-21  Score=110.74  Aligned_cols=70  Identities=23%  Similarity=0.437  Sum_probs=68.1

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLV   70 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~   70 (154)
                      |+|+|+...|+.+.+++++++||.+||++|+.++++|++.|+|+|+|+.|+|+.+|++|+|++|+++++.
T Consensus         2 i~i~vk~~~Gk~~~v~V~~~~tV~~lK~~I~~~~~i~~~~q~Li~~Gk~L~d~~tL~~y~I~~gstl~L~   71 (73)
T d1m94a_           2 IEVVVNDRLGKKVRVKCLAEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHISLEDYEVHDQTNLELY   71 (73)
T ss_dssp             EEEEEEETTTEEEEEEECTTSBHHHHHHHHHHHHCCTTTSEEEESSSCEECTTSBHHHHTCCTTEEEEEE
T ss_pred             eEEEEECCCCCEEEEEECCcCcHHHHHHHHHHhhcccccEEEEEEEeEEecccCcHHHcCCCCCCEEEEE
Confidence            6899999999999999999999999999999999999999999999999999999999999999999875

>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=99.83  E-value=1.9e-20  Score=109.45  Aligned_cols=73  Identities=36%  Similarity=0.537  Sum_probs=68.5

Q ss_pred             eeeeeeecCC-ceEEE-eeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEee
Q 040824           77 TMIKVKTLTG-KEIEI-DIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        77 ~~i~v~~~~~-~~~~~-~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      |+|+|+..+| +++.+ ++++++||++||++|+++.|+|++.|+|+|+|+.|+|+.+|++|||++|++|++++|.
T Consensus         1 M~I~Vk~l~G~~t~~~~~v~~~~TV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~~tL~~y~I~~~s~i~lv~rp   75 (76)
T d1wy8a1           1 MWIQVRTIDGSKTCTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVRP   75 (76)
T ss_dssp             EEEEEEETTCSCEEEEEEECTTCBHHHHHHHHHHHSCCCTTTEEEEETTEECCSSSBHHHHTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCceEEEeccCCCChHHHHHHHHHHHHCCCchhcEEEEEeeEecCCCCHHHcCCCCCCEEEEEEcc
Confidence            7899999998 46776 6999999999999999999999999999999999999999999999999999999874

>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=99.83  E-value=2e-20  Score=109.46  Aligned_cols=73  Identities=26%  Similarity=0.417  Sum_probs=69.2

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEE--CCeecCCCCcccccccCCCCEEEEEEee
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIY--AGKQLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~--~g~~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      ++|+|+..+|+.+.+++++++||.+||++|+..+|+|++.|+|+|  +|+.|+|+.+|++|||.+|++|+++++.
T Consensus         1 ~~l~Vk~l~G~~~~v~V~~~~tV~~lK~~I~~~~gip~~~QrLi~~~~Gk~L~D~~tL~~y~i~~g~~i~lv~~~   75 (76)
T d1z2ma1           1 WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDK   75 (76)
T ss_dssp             CEEEEEESSSCEEEEECCSSCCHHHHHHHHHHHHCCCGGGEEEEEETTCCBCCSSSCSGGGTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhccCCccEEEEEcCCCeeccCCCcHHHcCCCCCCEEEEEEEC
Confidence            368899999999999999999999999999999999999999999  7999999999999999999999998763

>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=99.83  E-value=2.9e-21  Score=112.32  Aligned_cols=72  Identities=36%  Similarity=0.589  Sum_probs=68.3

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEee
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      |+|+|+..+|+.+.++|++++||++||++|+++.|+|+++|+|+|+|+.|+|+.+|++|+| ++++|+++.+.
T Consensus         1 m~I~Vk~~~g~~~~l~V~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~d~~tL~dy~i-~~~ti~lv~r~   72 (73)
T d1wx9a1           1 LEVLVKTLDSQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRLIYQGRVLQDDKKLQEYNV-GGKVIHLVERA   72 (73)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHHHHCCCTTTCCCEETTEECCSSSBHHHHTC-TTEEEBCCCSS
T ss_pred             CEEEEEcCCCCEEEEEECCCChHHHHHHHHHHHhCCChHHEEEEECCeEccCCCCHHHhCC-CCCEEEEEecC
Confidence            6899999999999999999999999999999999999999999999999999999999999 58999887764

>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=99.82  E-value=2.1e-20  Score=109.40  Aligned_cols=73  Identities=33%  Similarity=0.428  Sum_probs=69.4

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEE--cceEeccCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF--AGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~--~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      .+|+||.++|+.+.+++++++||.+||++|+.+.|+|++.|+|+|  .|+.|.|+.+|++|||.+|++|+++++.
T Consensus         1 ~~l~Vk~l~G~~~~v~V~~~~tV~~lK~~I~~~~gip~~~QrLi~~~~Gk~L~D~~tL~~y~i~~g~~i~lv~~~   75 (76)
T d1z2ma1           1 WDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTVLLVVDK   75 (76)
T ss_dssp             CEEEEEESSSCEEEEECCSSCCHHHHHHHHHHHHCCCGGGEEEEEETTCCBCCSSSCSGGGTCCTTCEEEEEECC
T ss_pred             CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHhccCCccEEEEEcCCCeeccCCCcHHHcCCCCCCEEEEEEEC
Confidence            379999999999999999999999999999999999999999999  5999999999999999999999998763

>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=99.82  E-value=3.2e-20  Score=110.93  Aligned_cols=68  Identities=34%  Similarity=0.608  Sum_probs=66.1

Q ss_pred             cCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecC
Q 040824           84 LTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRG  151 (154)
Q Consensus        84 ~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~g  151 (154)
                      .+|+.+.+++++++||++||++|++++|+|+++|+|+|+|+.|+|+.+|++|||.+|++|++.++.||
T Consensus        19 L~G~~~~l~v~~~~tV~~lK~~I~~~~~ip~~~q~Li~~Gk~L~D~~tL~dY~I~~gsti~l~~r~RG   86 (86)
T d1zkha1          19 LNGQVLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMANGAVIHLALKERG   86 (86)
T ss_dssp             CSSCEEEEEECTTSBHHHHHHHHHHHTCCCTTTEEEEETTEEECTTSBHHHHTCCTTEEEEEEESCCC
T ss_pred             cCCeEEEEEECCCChHHHHHHHHHhhhcCChHHEEEEeCCcCcCCCCCHHHcCCCCCCEEEEEEecCC
Confidence            47899999999999999999999999999999999999999999999999999999999999999987

>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=99.82  E-value=2.3e-20  Score=109.61  Aligned_cols=72  Identities=38%  Similarity=0.689  Sum_probs=68.8

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcC---CCCCceeEEECCeecCCCCcccccccCCCCEEEEEE
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEG---IPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~---i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      .|.|+|+..+|+.+.+++++++||++||+++++..|   +|+++|+|+|+|+.|+|+.+|++|||++|++|.+++
T Consensus         2 ~~~i~vk~l~g~~~~l~v~~~~TV~~lK~~i~~~~g~~~i~~~~qrLi~~Gk~L~D~~tL~~y~I~~~s~i~~~v   76 (77)
T d1oqya4           2 AVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMV   76 (77)
T ss_dssp             CCCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSSEECSSSBTTTTCCCTTSCEEEEE
T ss_pred             cEEEEEECCCCCEEEEEECCCCcHHHHHHHHHHhcCCCCCChHHEEeEECCcCccCCCcHHHcCCCCCCEEEEEE
Confidence            478999999999999999999999999999999988   899999999999999999999999999999998876

>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=99.82  E-value=6.6e-20  Score=106.51  Aligned_cols=71  Identities=38%  Similarity=0.669  Sum_probs=66.3

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEe
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      |.|+|+.. ++.+.+++++++||.+||++|+..+|+|+++|+|+|+|+.|+|+.+|++|||++|++|+++.+
T Consensus         2 i~I~Vk~~-~~~~~i~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~I~~g~~i~lV~~   72 (73)
T d2bwfa1           2 LNIHIKSG-QDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS   72 (73)
T ss_dssp             EEEEEEET-TEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEEC
T ss_pred             EEEEEEeC-CeEEEEEECCCChHHHHHHHHHHHHCcChHHeEEEECCeEccCCCcHHHCCCCCCCEEEEEee
Confidence            67888884 557899999999999999999999999999999999999999999999999999999998765

>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=99.82  E-value=3.7e-20  Score=110.40  Aligned_cols=78  Identities=27%  Similarity=0.387  Sum_probs=71.9

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCCC
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGGL  154 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~~  154 (154)
                      .|+|+|++.++ .+.++|++++||.+||++|++++|+|++.|+|+|+|+.|+|+.+|++|||.+|++|+++++....++
T Consensus         7 ~i~I~Vkt~~~-~~~~~V~~~~tV~~lK~~i~~~~gi~~~~qrL~~~Gk~L~D~~tL~~y~i~~gsti~lv~r~~~~a~   84 (84)
T d1yqba1           7 LIKVTVKTPKD-KEDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHRAM   84 (84)
T ss_dssp             EEEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBHHHHTCCTTCEEEEEECCCCSCC
T ss_pred             EEEEEEEcCCC-cEEEEECCCCcHHHHHHHHHHHHCcCchhEEEEEeeeeccccCcHHHcCCCCCCEEEEEECCCCCCC
Confidence            48899999755 5799999999999999999999999999999999999999999999999999999999998876543

>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=99.82  E-value=6.4e-20  Score=111.91  Aligned_cols=74  Identities=31%  Similarity=0.606  Sum_probs=70.0

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhC---CCCCCeEEEEcceEeccCceecccccccccceeeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~---~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~   74 (154)
                      |+|+||..+|+++.+++++++||.+||++|+++.+   +|++.|+|+|+|+.|+|+.+|++|+|.++++|+++++..
T Consensus         1 M~I~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~~~~i~~~~qrLi~~Gk~L~d~~tL~~y~I~~~s~i~lv~~~~   77 (95)
T d1uela_           1 MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKP   77 (95)
T ss_dssp             CEEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEETTEECCTTSBGGGGTCCSSSEEEEEESSC
T ss_pred             CEEEEEeCCCCEEEEEECCCccHHHHHHHHHhhhcccCCCccceEEEECCeEccCCCcHHHcCCCCCCEEEEEECCC
Confidence            89999999999999999999999999999998875   889999999999999999999999999999999987643

>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=99.81  E-value=2.4e-20  Score=109.53  Aligned_cols=71  Identities=32%  Similarity=0.587  Sum_probs=67.9

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhC---CCCCCeEEEEcceEeccCceecccccccccceeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEG---IPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~---~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~   71 (154)
                      |+|+||..+|+.+.+++++++||.+||++++.+.|   +|++.|+|+|+|+.|+|+.+|++|+|+++++|.+.+
T Consensus         3 ~~i~vk~l~g~~~~l~v~~~~TV~~lK~~i~~~~g~~~i~~~~qrLi~~Gk~L~D~~tL~~y~I~~~s~i~~~v   76 (77)
T d1oqya4           3 VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKNFVVVMV   76 (77)
T ss_dssp             CCEEEEETTTEEEEECCCTTCBHHHHHHHHHHHTCSSSCCSTEEEEESSSSEECSSSBTTTTCCCTTSCEEEEE
T ss_pred             EEEEEECCCCCEEEEEECCCCcHHHHHHHHHHhcCCCCCChHHEEeEECCcCccCCCcHHHcCCCCCCEEEEEE
Confidence            78999999999999999999999999999999887   899999999999999999999999999999998765

>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=99.81  E-value=4.8e-20  Score=107.12  Aligned_cols=71  Identities=34%  Similarity=0.558  Sum_probs=66.6

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      |+|+|++. ++.+.+++++++||.+||++|+...|+|++.|+|+|+|+.|+|+.+|++|++.+|++|+++.+
T Consensus         2 i~I~Vk~~-~~~~~i~v~~~~tV~~lK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~~~~I~~g~~i~lV~~   72 (73)
T d2bwfa1           2 LNIHIKSG-QDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS   72 (73)
T ss_dssp             EEEEEEET-TEEEEEEECTTCBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEEC
T ss_pred             EEEEEEeC-CeEEEEEECCCChHHHHHHHHHHHHCcChHHeEEEECCeEccCCCcHHHCCCCCCCEEEEEee
Confidence            68999974 567999999999999999999999999999999999999999999999999999999998764

>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=99.81  E-value=9.4e-20  Score=111.15  Aligned_cols=75  Identities=33%  Similarity=0.654  Sum_probs=70.6

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcC---CCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEG---IPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRG  151 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~---i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~g  151 (154)
                      |.|+|+..+|+++.++|++++||.+||++|+++.|   +|+++|+|+|+|+.|+|+.+|++|||.+|++|+++++...
T Consensus         1 M~I~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~~~~i~~~~qrLi~~Gk~L~d~~tL~~y~I~~~s~i~lv~~~~~   78 (95)
T d1uela_           1 MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKPK   78 (95)
T ss_dssp             CEEEEEETTCCEEEEECCTTSBHHHHHHHHHHHHCTTTCCTTTEEEEETTEECCTTSBGGGGTCCSSSEEEEEESSCC
T ss_pred             CEEEEEeCCCCEEEEEECCCccHHHHHHHHHhhhcccCCCccceEEEECCeEccCCCcHHHcCCCCCCEEEEEECCCC
Confidence            78999999999999999999999999999999876   8999999999999999999999999999999999887654

>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=99.81  E-value=4.9e-20  Score=114.86  Aligned_cols=69  Identities=28%  Similarity=0.486  Sum_probs=66.8

Q ss_pred             CCceEEEeeCC-CchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           85 TGKEIEIDIEP-TDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        85 ~~~~~~~~v~~-~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      +|+++.+.+.+ ++||.+||++|++++|+|++.|+|+|.|+.|+|+.+|++|+|++|++|++.+|.|||.
T Consensus        39 ~G~~i~l~v~~~sdtV~~lK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~ynI~~gsti~L~lr~rGG~  108 (111)
T d1we6a_          39 DGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLRERSGP  108 (111)
T ss_dssp             SSCCEEEEESCSSSBHHHHHHHHHHHTTCCTTTSEEECSSSBCCTTSBTTTTTCSSSCEEEEECSSCCSS
T ss_pred             CCeEEEEEecCCccHHHHHHHHHHHHHCCCccceEEEEeeEEccccCCHHHcCCCCCCEEEEEeeCCCCC
Confidence            58899999987 9999999999999999999999999999999999999999999999999999999995

>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=99.81  E-value=3e-20  Score=113.71  Aligned_cols=71  Identities=21%  Similarity=0.246  Sum_probs=68.9

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEE
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      ++|+|++..|+.+.++|.+++||.+||++|++++|+|+++|+|+|+|+.|+|+.+|++|||++|++|+++.
T Consensus        29 i~V~V~~~~Gk~~~v~V~p~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~dygI~~GstI~L~~   99 (100)
T d1uh6a_          29 IEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLELYY   99 (100)
T ss_dssp             EEEEEECSSSSCEEEEEETTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCSSCBHHHHTCCTTEEEEEEC
T ss_pred             EEEEEECCCCCEEEEEECCcChHHHHHHHHHHHHCCCcceEEEEEEeecccCcCCHHHcCCCCCCEEEEEE
Confidence            68999999999999999999999999999999999999999999999999999999999999999999875

>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=99.80  E-value=6.2e-20  Score=109.41  Aligned_cols=74  Identities=34%  Similarity=0.476  Sum_probs=69.1

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |+|+|++.++ .+.+++++++||.+||++|++.+++|++.|+|+|+|+.|+|+.+|++|||.+|++|+++++...
T Consensus         8 i~I~Vkt~~~-~~~~~V~~~~tV~~lK~~i~~~~gi~~~~qrL~~~Gk~L~D~~tL~~y~i~~gsti~lv~r~~~   81 (84)
T d1yqba1           8 IKVTVKTPKD-KEDFSVTDTCTIQQLKEEISQRFKAHPDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQH   81 (84)
T ss_dssp             EEEEEECSSC-EEEEEEETTCBHHHHHHHHHHHHTCCGGGEEEEETTEECCTTSBHHHHTCCTTCEEEEEECCCC
T ss_pred             EEEEEEcCCC-cEEEEECCCCcHHHHHHHHHHHHCcCchhEEEEEeeeeccccCcHHHcCCCCCCEEEEEECCCC
Confidence            6899999754 5899999999999999999999999999999999999999999999999999999999987653

>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=99.79  E-value=1.1e-19  Score=111.14  Aligned_cols=71  Identities=23%  Similarity=0.324  Sum_probs=68.4

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL   71 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~   71 (154)
                      |+|+|+...|+.+.+++++++||.+||++|+.+.++|++.|+|+|+|+.|.|+.+|++|+|++|++|+|..
T Consensus        29 i~V~V~~~~Gk~~~v~V~p~~TV~~LK~~I~~~~gip~~~qrLi~~Gk~L~D~~tL~dygI~~GstI~L~~   99 (100)
T d1uh6a_          29 IEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLELYY   99 (100)
T ss_dssp             EEEEEECSSSSCEEEEEETTSBHHHHHHHHHHHHCCCGGGCEEEETTEECCSSCBHHHHTCCTTEEEEEEC
T ss_pred             EEEEEECCCCCEEEEEECCcChHHHHHHHHHHHHCCCcceEEEEEEeecccCcCCHHHcCCCCCCEEEEEE
Confidence            48999999999999999999999999999999999999999999999999999999999999999998864

>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=99.78  E-value=3.9e-19  Score=109.82  Aligned_cols=71  Identities=32%  Similarity=0.437  Sum_probs=66.8

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      |+|+|++.++ .+.+++++++||.+||++|+..++++++.|+|+|+|+.|+|+.+|++|+|.+|++|+|+++
T Consensus        33 i~V~Vk~~~~-~~~i~V~~~~tV~~LK~~I~~~~gi~~~~qrLi~~Gk~L~D~~tL~~~~I~~g~~I~lvlr  103 (103)
T d1j8ca_          33 IKVTVKTPKE-KEEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIK  103 (103)
T ss_dssp             EEEEEECSSC-EEEEEECTTCCHHHHHHHHHHHHCSCSSSEEEEETTEEESTTSCGGGTTCSSSEEEEEEEC
T ss_pred             EEEEEECCCc-cEEEEECCCChHHHHHHHHHHHHCcCHHHeeeeeeeecccCCCcHHHcCCCCCCEEEEEEC
Confidence            6899998765 5899999999999999999999999999999999999999999999999999999999864

>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=99.78  E-value=4.9e-19  Score=109.35  Aligned_cols=72  Identities=28%  Similarity=0.362  Sum_probs=67.7

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEe
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      .|+|+|++.++ .+.++|++++||.+||++|+..+|+|++.|+|+|+|+.|+|+.+|++|||++|++|++++|
T Consensus        32 ~i~V~Vk~~~~-~~~i~V~~~~tV~~LK~~I~~~~gi~~~~qrLi~~Gk~L~D~~tL~~~~I~~g~~I~lvlr  103 (103)
T d1j8ca_          32 IIKVTVKTPKE-KEEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIK  103 (103)
T ss_dssp             CEEEEEECSSC-EEEEEECTTCCHHHHHHHHHHHHCSCSSSEEEEETTEEESTTSCGGGTTCSSSEEEEEEEC
T ss_pred             eEEEEEECCCc-cEEEEECCCChHHHHHHHHHHHHCcCHHHeeeeeeeecccCCCcHHHcCCCCCCEEEEEEC
Confidence            48899998765 5789999999999999999999999999999999999999999999999999999999875

>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=99.78  E-value=1.7e-19  Score=107.29  Aligned_cols=72  Identities=28%  Similarity=0.356  Sum_probs=67.2

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |+|+|++.++ .+.+++++++||.+||++|++.+++|++.|+|+|+|+.|.|+.+|++|||.+|++|+++++.
T Consensus        11 i~v~Vk~~~~-~~~i~v~~~~tV~~lK~~I~~~~~v~~~~qrL~f~Gk~L~d~~tL~~~gI~~gs~I~lv~r~   82 (83)
T d1wx8a1          11 IRVSVKTPQD-CHEFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVRS   82 (83)
T ss_dssp             EEEEEECSSS-EEEEEEETTCCHHHHHHHHHHHTCSCTTTBCCEETTEECCTTSCHHHHTCCTTEEEECCBCC
T ss_pred             EEEEEEcCCC-cEEEEECCCChHHHHHHHHHHHhCCChhHEEEEEEhhccccCCcHHHcCCCCCCEEEEEEeC
Confidence            6899998654 57899999999999999999999999999999999999999999999999999999988763

>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=99.78  E-value=1.3e-19  Score=107.79  Aligned_cols=73  Identities=23%  Similarity=0.278  Sum_probs=67.8

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEe
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      ..|+|+|+..++ .+.+++++++||.+||++|++.+++|+++|+|+|+|+.|.|+.+|++|||++|++|++++|
T Consensus         9 ~~i~v~Vk~~~~-~~~i~v~~~~tV~~lK~~I~~~~~v~~~~qrL~f~Gk~L~d~~tL~~~gI~~gs~I~lv~r   81 (83)
T d1wx8a1           9 RIIRVSVKTPQD-CHEFFLAENSNVRRFKKQISKYLHCNADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVR   81 (83)
T ss_dssp             CEEEEEEECSSS-EEEEEEETTCCHHHHHHHHHHHTCSCTTTBCCEETTEECCTTSCHHHHTCCTTEEEECCBC
T ss_pred             CeEEEEEEcCCC-cEEEEECCCChHHHHHHHHHHHhCCChhHEEEEEEhhccccCCcHHHcCCCCCCEEEEEEe
Confidence            458899998665 5689999999999999999999999999999999999999999999999999999998876

>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=99.77  E-value=4.6e-19  Score=108.99  Aligned_cols=78  Identities=21%  Similarity=0.437  Sum_probs=70.0

Q ss_pred             cceeeee----eecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecC-CCCcccccccCCCCEEEEEEee
Q 040824           75 GGTMIKV----KTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLA-DDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        75 ~~~~i~v----~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~-d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      ..|.|+|    +..++.++.++|++++||.+||++|+.++++|++.|+|+|+|+.|. |..+|++|||++|++|+++.+.
T Consensus         6 ~~m~itV~~~~~~~~~~t~~l~V~~~~tV~~LK~~Ie~~~gip~~~Q~Li~~Gk~L~dd~~tL~~~gI~~g~~i~l~~r~   85 (102)
T d1v5oa_           6 SGMLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVLLQKD   85 (102)
T ss_dssp             CCEEEEEEECCCCCCCCEEEEEECTTCBHHHHHHHHHHHTCCCGGGBCEEETTEEECCSSSBHHHHTCCTTEEEEECBCC
T ss_pred             CCEEEEEEecccCCCCCEEEEEECCcccHHHHHHHHHHHhCCCcceEEEEeCCeEeecccCCHHHcCCCCCCEEEEEECC
Confidence            3577787    5667899999999999999999999999999999999999999995 6789999999999999988776


Q ss_pred             cCC
Q 040824          150 RGG  152 (154)
Q Consensus       150 ~gg  152 (154)
                      .++
T Consensus        86 ~~~   88 (102)
T d1v5oa_          86 NVG   88 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            554

>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=99.76  E-value=1.7e-18  Score=103.31  Aligned_cols=67  Identities=30%  Similarity=0.623  Sum_probs=64.0

Q ss_pred             CCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeee
Q 040824            8 LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (154)
Q Consensus         8 ~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~   74 (154)
                      .+|+.+.+++++++||.+||++|+.++++|++.|+|+|+|+.|.|+.+|++|||.++++|++.++.+
T Consensus        19 L~G~~~~l~v~~~~tV~~lK~~I~~~~~ip~~~q~Li~~Gk~L~D~~tL~dY~I~~gsti~l~~r~R   85 (86)
T d1zkha1          19 LNGQVLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMANGAVIHLALKER   85 (86)
T ss_dssp             CSSCEEEEEECTTSBHHHHHHHHHHHTCCCTTTEEEEETTEEECTTSBHHHHTCCTTEEEEEEESCC
T ss_pred             cCCeEEEEEECCCChHHHHHHHHHhhhcCChHHEEEEeCCcCcCCCCCHHHcCCCCCCEEEEEEecC
Confidence            5789999999999999999999999999999999999999999999999999999999999988754

>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=99.75  E-value=1.3e-18  Score=106.91  Aligned_cols=75  Identities=21%  Similarity=0.391  Sum_probs=68.3

Q ss_pred             CEEEE----EeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEec-cCceecccccccccceeeeeeeec
Q 040824            1 MQIFV----KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE-DGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v----~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~-d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |.|+|    +..++.++++++++++||.+||+.|+.+.++|++.|+|+|+|+.|. |..+|++|||+++++|++..+...
T Consensus         8 m~itV~~~~~~~~~~t~~l~V~~~~tV~~LK~~Ie~~~gip~~~Q~Li~~Gk~L~dd~~tL~~~gI~~g~~i~l~~r~~~   87 (102)
T d1v5oa_           8 MLITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLTDDHCSLGSYGLKDGDMVVLLQKDNV   87 (102)
T ss_dssp             EEEEEEECCCCCCCCEEEEEECTTCBHHHHHHHHHHHTCCCGGGBCEEETTEEECCSSSBHHHHTCCTTEEEEECBCCCC
T ss_pred             EEEEEEecccCCCCCEEEEEECCcccHHHHHHHHHHHhCCCcceEEEEeCCeEeecccCCHHHcCCCCCCEEEEEECCCC
Confidence            67888    6777899999999999999999999999999999999999999995 567999999999999998876543

>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=99.74  E-value=1.3e-17  Score=101.38  Aligned_cols=78  Identities=27%  Similarity=0.384  Sum_probs=70.2

Q ss_pred             ecceeeeeeecCCceE-EEeeCCCchHHHHHHHHhhh-----cCCC--CCceeEEECCeecCCCCcccccccCCCC----
Q 040824           74 RGGTMIKVKTLTGKEI-EIDIEPTDTIERIKERVEEK-----EGIP--PVQQRLIYAGKQLADDKTARDYNIEGGS----  141 (154)
Q Consensus        74 ~~~~~i~v~~~~~~~~-~~~v~~~~tv~~LK~~i~~~-----~~i~--~~~~~l~~~g~~l~d~~~L~~~~i~~~~----  141 (154)
                      ..+|.|.++..+|+.+ ++.+++++||.+||++|++.     .|+|  +++|+|+|.|+.|+|+.||++|++.+|+    
T Consensus         5 ~~~i~I~~r~~~G~~i~~~~v~~s~TV~~lK~~I~~~~~~~k~~iP~~~~~qRLIf~Gk~L~D~~tL~dy~i~~g~~~~~   84 (101)
T d1se9a_           5 HNQLEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSKTVKDYRSPVSNLAGA   84 (101)
T ss_dssp             CCCEEEEEEETTSCEEEEEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEEETTEECCTTSBGGGGSCCTTSCTTC
T ss_pred             cceEEEEEEeCCCCeecceecCccCHHHHHHHHHHHhccccccCCCCCcccEEEEECCeEecCCCCHHHcCCCCCCcCCC
Confidence            3568999999999876 79999999999999999875     5677  7899999999999999999999999998    


Q ss_pred             --EEEEEEeecC
Q 040824          142 --VLHLVLALRG  151 (154)
Q Consensus       142 --~i~~~~~~~g  151 (154)
                        ++|++++...
T Consensus        85 ~~tmHlVvrpp~   96 (101)
T d1se9a_          85 VTTMHVIIQAPV   96 (101)
T ss_dssp             CEEEEEEECCCS
T ss_pred             ceEEEEEeCCCC
Confidence              9999998753

>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=99.74  E-value=7.7e-18  Score=102.02  Aligned_cols=76  Identities=26%  Similarity=0.348  Sum_probs=69.2

Q ss_pred             ecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecC-CCCcccccccCCCCEEEEEEeecCC
Q 040824           74 RGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLA-DDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        74 ~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~-d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ..+|.|+||..+|+.+.+++++++||.+||++++   ..++++|+|+|+|+.|. |.++|++|+|.+|++|+++++.+++
T Consensus         5 ~s~m~i~vK~l~~~~~~v~v~~~~TV~~lK~~i~---~~~~~~qrLi~~Gk~L~dd~~tL~~y~i~~g~~v~l~~~~~~~   81 (95)
T d1wiaa_           5 SSGINVRLKFLNDTEELAVARPEDTVGTLKSKYF---PGQESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRSPPGA   81 (95)
T ss_dssp             CCSEEEEEEETTTEEEEEEECSSSBHHHHHHHHS---SSTTTTCEEEETTEECCCSSCBTTTTTCCTTEEEEEECCCCCC
T ss_pred             CCcEEEEEEcCCCCEEEEEECCcCcHHHHHHHHh---cCCcceeEEEECCEEcccCCCCHHHcCCCCCCEEEEEEcCCCC
Confidence            3579999999999999999999999999999986   46889999999999996 6789999999999999999887765

>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=99.73  E-value=3.2e-18  Score=104.25  Aligned_cols=72  Identities=18%  Similarity=0.256  Sum_probs=66.9

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |+|+||+.+++.+.+++++++||.+||++|++.+++|+++|+|+|+|+.|+|+ +|++|+|++|++|+++.+.
T Consensus         8 ~~I~VK~~~~~~~~v~v~~~~tV~~lK~~i~~~~gvp~~~QkLi~~Gk~L~d~-tL~~~gi~~g~~i~lv~t~   79 (96)
T d1wgga_           8 YSVTVKWGKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLKDD-DWGNIKMKNGMTVLMMGSA   79 (96)
T ss_dssp             EEEEEEETTEEEEEEEEESSSCHHHHHHHHHHHTCCCTTTSCCEETTEECCSS-CCCSCCCCSSCEEECCCCC
T ss_pred             eEEEEEeCCCCEEEEEECCCCcHHHHHHHhhhhcCccceeeEEeecCcccCCC-cHHHCCCCCCCEEEEEeeC
Confidence            57999998888788999999999999999999999999999999999999986 7999999999999987653

>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=99.73  E-value=9e-18  Score=102.06  Aligned_cols=74  Identities=26%  Similarity=0.447  Sum_probs=67.3

Q ss_pred             CEEEEEeCCCCEE-EEEEeCCCcHHHHHHHHHhH-----hCCC--CCCeEEEEcceEeccCceeccccccccc------c
Q 040824            1 MQIFVKTLTGKTI-TLEVESSDTIDNVKAKIQDK-----EGIP--PDQQRLIFAGKQLEDGRTLADYNIQKES------T   66 (154)
Q Consensus         1 m~v~v~~~~~~~~-~~~v~~~~tv~~lk~~i~~~-----~~~~--~~~q~L~~~g~~L~d~~~l~~~~i~~~~------~   66 (154)
                      |+|++|..+|+.+ ++.+++++||.+||++|+..     .++|  ++.|+|+|.|+.|+|+.+|++|++.+|+      +
T Consensus         8 i~I~~r~~~G~~i~~~~v~~s~TV~~lK~~I~~~~~~~k~~iP~~~~~qRLIf~Gk~L~D~~tL~dy~i~~g~~~~~~~t   87 (101)
T d1se9a_           8 LEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLENSKTVKDYRSPVSNLAGAVTT   87 (101)
T ss_dssp             EEEEEEETTSCEEEEEEECTTCBHHHHHHHHHHHSCTTCSSSCCSGGGEEEEETTEECCTTSBGGGGSCCTTSCTTCCEE
T ss_pred             EEEEEEeCCCCeecceecCccCHHHHHHHHHHHhccccccCCCCCcccEEEEECCeEecCCCCHHHcCCCCCCcCCCceE
Confidence            6899999999876 79999999999999999875     5777  7899999999999999999999999997      8


Q ss_pred             eeeeeeee
Q 040824           67 LHLVLRLR   74 (154)
Q Consensus        67 i~l~~~~~   74 (154)
                      +|+++++.
T Consensus        88 mHlVvrpp   95 (101)
T d1se9a_          88 MHVIIQAP   95 (101)
T ss_dssp             EEEEECCC
T ss_pred             EEEEeCCC
Confidence            99988764

>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=99.73  E-value=7.2e-19  Score=108.74  Aligned_cols=77  Identities=21%  Similarity=0.392  Sum_probs=71.3

Q ss_pred             ecceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCcee---------------EEECCeecCCC-Cccccccc
Q 040824           74 RGGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQR---------------LIYAGKQLADD-KTARDYNI  137 (154)
Q Consensus        74 ~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~---------------l~~~g~~l~d~-~~L~~~~i  137 (154)
                      ...|.|+|+..+|+.+.++|++++||.+||++|++.+++|+++|+               |+|+|+.|.|+ .+|.+|||
T Consensus         5 ss~M~v~Vk~~~G~~~~v~V~~~~TV~~LK~~I~~~~~ip~~~Qr~~~~~~~~~~~~~~~Li~~G~~L~d~~~tL~~~gI   84 (105)
T d1v2ya_           5 SSGMTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLRDYGI   84 (105)
T ss_dssp             CCSEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHHHHHHHTTCCCCCCHHHHHTTEEEESSSCEECCSSSBHHHHTC
T ss_pred             CCcEEEEEEeCCCCEEEEEECCCChHHHHHHHHHHHHCcCHHHhcccccccccccccceEEEECCEECcccCCCHHHcCC
Confidence            356999999999999999999999999999999999999999998               99999999755 69999999


Q ss_pred             CCCCEEEEEEeec
Q 040824          138 EGGSVLHLVLALR  150 (154)
Q Consensus       138 ~~~~~i~~~~~~~  150 (154)
                      .+|++|+++.+++
T Consensus        85 ~~g~~l~lv~r~~   97 (105)
T d1v2ya_          85 RNRDEVSFIKKLG   97 (105)
T ss_dssp             CSSEEEEEEECSC
T ss_pred             CCCCEEEEEEecC
Confidence            9999999998874

>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=99.73  E-value=5.4e-19  Score=109.33  Aligned_cols=74  Identities=23%  Similarity=0.416  Sum_probs=69.4

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeE---------------EEEcceEeccC-ceecccccccc
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQR---------------LIFAGKQLEDG-RTLADYNIQKE   64 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~---------------L~~~g~~L~d~-~~l~~~~i~~~   64 (154)
                      |+|+|+..+|+.++++|++++||.+||++|++.+++|+++|+               |+|+|+.|.|+ .+|++|+|.++
T Consensus         8 M~v~Vk~~~G~~~~v~V~~~~TV~~LK~~I~~~~~ip~~~Qr~~~~~~~~~~~~~~~Li~~G~~L~d~~~tL~~~gI~~g   87 (105)
T d1v2ya_           8 MTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLRDYGIRNR   87 (105)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHHHHHHHTTCCCCCCHHHHHTTEEEESSSCEECCSSSBHHHHTCCSS
T ss_pred             EEEEEEeCCCCEEEEEECCCChHHHHHHHHHHHHCcCHHHhcccccccccccccceEEEECCEECcccCCCHHHcCCCCC
Confidence            789999999999999999999999999999999999999997               99999999766 59999999999


Q ss_pred             cceeeeeeee
Q 040824           65 STLHLVLRLR   74 (154)
Q Consensus        65 ~~i~l~~~~~   74 (154)
                      ++|+++.+.+
T Consensus        88 ~~l~lv~r~~   97 (105)
T d1v2ya_          88 DEVSFIKKLG   97 (105)
T ss_dssp             EEEEEEECSC
T ss_pred             CEEEEEEecC
Confidence            9999987753

>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=99.73  E-value=1.5e-17  Score=104.06  Aligned_cols=77  Identities=25%  Similarity=0.317  Sum_probs=68.2

Q ss_pred             eecceeeeeeecCCceEEEeeCCCchHHHHHHHH--------hhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEE
Q 040824           73 LRGGTMIKVKTLTGKEIEIDIEPTDTIERIKERV--------EEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLH  144 (154)
Q Consensus        73 ~~~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i--------~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~  144 (154)
                      +...|.|+++..+|+.+.+.|++++||.+||++|        ++..++|++.|||+|.|+.|+|+.+|++|+|.+|+++.
T Consensus        13 ~~~~i~i~v~~l~Gk~~~~~v~p~~TV~~lK~~I~~~~p~~~~e~~~~~~~~qRLiy~Gk~L~D~~tL~~~~i~~g~~~~   92 (116)
T d1wgha_          13 PADMINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTV   92 (116)
T ss_dssp             CSSSEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEEETTEEECSSCBTTTTTCCSSCEEE
T ss_pred             CCCeEEEEEEEcCCCEEEEEECCcchHHHHHHHHHhhcccccccccCCChHHeEEEECCEEecCCCCHHHcCCCCCCEEE
Confidence            3456889999999999999999999999999999        56778999999999999999999999999999999855


Q ss_pred             EEEee
Q 040824          145 LVLAL  149 (154)
Q Consensus       145 ~~~~~  149 (154)
                      +.+..
T Consensus        93 lhlv~   97 (116)
T d1wgha_          93 MHLVA   97 (116)
T ss_dssp             EEEEE
T ss_pred             EEEEe
Confidence            54433

>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=99.73  E-value=1.3e-17  Score=98.08  Aligned_cols=75  Identities=24%  Similarity=0.413  Sum_probs=70.3

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      +.|.|+. +++.+.+.+..++++..|+..++++.++++++++|+|+|+.|.++.|+++|++++||+|+++++++||
T Consensus         5 I~ikv~~-~~~~~~f~v~~~~~~~~l~~~~~~~~~i~~~~~~l~f~G~~l~~~~T~~~~~i~dgd~I~v~~~q~GG   79 (79)
T d1euvb_           5 INLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGG   79 (79)
T ss_dssp             EEEEEES-SSCEEEEEEETTSCTHHHHHHHHHHTTCCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCBCC
T ss_pred             EEEEECC-CCeEEEEEECCCCcHHHHHHHHHHHhCCChHhEEEEECCEEeCCCCCHHHCCCCCCCEEEEEEeccCC
Confidence            5566665 67778899999999999999999999999999999999999999999999999999999999999998

>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=99.73  E-value=4.9e-18  Score=103.41  Aligned_cols=73  Identities=18%  Similarity=0.282  Sum_probs=67.4

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEe
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      ..+.|+|+..+++.+.+++++++||.+||++|++.+|+|+++|+|+|+|+.|+|+ +|++|||++|++|+++..
T Consensus         6 ~~~~I~VK~~~~~~~~v~v~~~~tV~~lK~~i~~~~gvp~~~QkLi~~Gk~L~d~-tL~~~gi~~g~~i~lv~t   78 (96)
T d1wgga_           6 SGYSVTVKWGKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVKGGTLKDD-DWGNIKMKNGMTVLMMGS   78 (96)
T ss_dssp             CEEEEEEEETTEEEEEEEEESSSCHHHHHHHHHHHTCCCTTTSCCEETTEECCSS-CCCSCCCCSSCEEECCCC
T ss_pred             CceEEEEEeCCCCEEEEEECCCCcHHHHHHHhhhhcCccceeeEEeecCcccCCC-cHHHCCCCCCCEEEEEee
Confidence            4588999998887788999999999999999999999999999999999999986 799999999999988743

>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=99.72  E-value=1e-17  Score=101.51  Aligned_cols=71  Identities=24%  Similarity=0.319  Sum_probs=65.0

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEec-cCceecccccccccceeeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE-DGRTLADYNIQKESTLHLVLRLR   74 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~-d~~~l~~~~i~~~~~i~l~~~~~   74 (154)
                      |+|+||+.+|+.+.+++++++||.+||++++   .++++.|+|+|+|+.|. |..+|++|+|.++++||++++..
T Consensus         8 m~i~vK~l~~~~~~v~v~~~~TV~~lK~~i~---~~~~~~qrLi~~Gk~L~dd~~tL~~y~i~~g~~v~l~~~~~   79 (95)
T d1wiaa_           8 INVRLKFLNDTEELAVARPEDTVGTLKSKYF---PGQESQMKLIYQGRLLQDPARTLSSLNITNNCVIHCHRSPP   79 (95)
T ss_dssp             EEEEEEETTTEEEEEEECSSSBHHHHHHHHS---SSTTTTCEEEETTEECCCSSCBTTTTTCCTTEEEEEECCCC
T ss_pred             EEEEEEcCCCCEEEEEECCcCcHHHHHHHHh---cCCcceeEEEECCEEcccCCCCHHHcCCCCCCEEEEEEcCC
Confidence            7899999999999999999999999999886   46889999999999996 56799999999999999988654

>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=99.71  E-value=1.8e-17  Score=103.67  Aligned_cols=72  Identities=24%  Similarity=0.436  Sum_probs=65.9

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHH--------HhHhCCCCCCeEEEEcceEeccCceecccccccccc--eeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKI--------QDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKEST--LHLV   70 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i--------~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~--i~l~   70 (154)
                      |+|+|+..+|+++.+.+++++||.+||++|        +++.+++++.|+|+|.|+.|.|+.+|++|+|.+|++  +|++
T Consensus        17 i~i~v~~l~Gk~~~~~v~p~~TV~~lK~~I~~~~p~~~~e~~~~~~~~qRLiy~Gk~L~D~~tL~~~~i~~g~~~~lhlv   96 (116)
T d1wgha_          17 INLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLV   96 (116)
T ss_dssp             EEEEEECSSSCEEEEEECTTCBHHHHHHHHHHSSSCCSSCCCCCCTTTEEEEETTEEECSSCBTTTTTCCSSCEEEEEEE
T ss_pred             EEEEEEEcCCCEEEEEECCcchHHHHHHHHHhhcccccccccCCChHHeEEEECCEEecCCCCHHHcCCCCCCEEEEEEE
Confidence            579999999999999999999999999999        467889999999999999999999999999999987  5555


Q ss_pred             ee
Q 040824           71 LR   72 (154)
Q Consensus        71 ~~   72 (154)
                      ++
T Consensus        97 ~r   98 (116)
T d1wgha_          97 AR   98 (116)
T ss_dssp             EC
T ss_pred             eC
Confidence            54

>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=99.71  E-value=1.9e-17  Score=97.68  Aligned_cols=73  Identities=22%  Similarity=0.411  Sum_probs=63.8

Q ss_pred             ceeeeeeecCCceEEEee-----CCCchHHHHHHHHhhhcCCCCCceeEEECCeecC-CCCcccccccCCCCEEEEEEee
Q 040824           76 GTMIKVKTLTGKEIEIDI-----EPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLA-DDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v-----~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~-d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      +|.|+|+. .+..+.+++     ++++||++||++|++.+|+|+++|+|+|+|+.|. |+.+|++|||++|++|+++.+.
T Consensus         1 gi~i~V~~-~~~~~~i~v~~~~~~~~~Tv~~LK~~I~~~tgvp~~~QkL~~~G~~L~~d~~tL~~~gi~~g~~i~lv~~~   79 (81)
T d1wxva1           1 GLTVTVTH-SNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVMLIGKK   79 (81)
T ss_dssp             SEEEEEEC-SSSEEEEEECCCSSSSSCBHHHHHHHHHHHTCCCTTTCEEEETTEEECCSSSBHHHHTCCSSEEEEEESCC
T ss_pred             CEEEEEEE-CCeeEEEEEecCCCCCccHHHHHHHHHHHHHCcCHHHEEeeecCeEeCcCCCChHHCCCCCCCEEEEEEec
Confidence            36777766 556777777     4688999999999999999999999999999995 6789999999999999988764

>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=99.71  E-value=1.1e-17  Score=102.39  Aligned_cols=73  Identities=11%  Similarity=0.101  Sum_probs=65.5

Q ss_pred             eeeee--eecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEee
Q 040824           77 TMIKV--KTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        77 ~~i~v--~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      +.+++  +...++.+.+++++++||.+||++|+++.|+|++.|+|+|+|+.|+|+.||++|||+++++|+++...
T Consensus        18 i~V~~~~~~~~g~~~~lev~~~~TV~~LK~~I~~~~gi~~~~qkLi~~Gk~L~d~~tL~~~gI~~~s~i~vi~~~   92 (100)
T d1wjua_          18 IEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFGLQENYIKIVINKKQLQLGKTLEEQGVAHNVKAMVLELK   92 (100)
T ss_dssp             EEEECCTTTCCSSSEEEEEESSSBHHHHHHHHHHHTTCCSTTCEEEETTEECCTTSBHHHHTCCSSEEEEEECCC
T ss_pred             EEEEEeeccCCCeEEEEEECCCcHHHHHHHHHHHHHCCCCeeEEEEEcccCcCCCcCHHHcCCCCCCEEEEEEcC
Confidence            34444  44578899999999999999999999999999999999999999999999999999999999877544

>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=99.71  E-value=5.7e-18  Score=102.90  Aligned_cols=76  Identities=21%  Similarity=0.411  Sum_probs=69.0

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      .|.+.|+. +++.+.++|++++||.+||++|+..+++|+++|+|+|+|+ |.|+.+|++|+|++|++|+++....+|.
T Consensus        17 ~i~v~V~~-~~k~~~i~v~~~~TV~~LK~~I~~~tgvp~~~q~Li~~g~-l~D~~tL~~~~I~~gs~i~lvgs~~~gp   92 (95)
T d1v86a_          17 LVDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGL-VPEDKTLREIKVTSGAKIMVVGSTISGP   92 (95)
T ss_dssp             CEEEEEEE-TTEEEEEEECTTSBHHHHHHHHHHHHCSCSTTCCCBSSSB-CCSSSBHHHHCCCTTEEEEECCSSCCCC
T ss_pred             EEEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEeccc-ccCCCcHHHCCCCCCCEEEEEecCCCCC
Confidence            46777775 7889999999999999999999999999999999999996 8999999999999999999987776653

>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=99.70  E-value=5.5e-18  Score=105.45  Aligned_cols=68  Identities=34%  Similarity=0.516  Sum_probs=64.3

Q ss_pred             CCCEEEEEEeC-CCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeecc
Q 040824            9 TGKTITLEVES-SDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGG   76 (154)
Q Consensus         9 ~~~~~~~~v~~-~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~~   76 (154)
                      +|+++.+++.+ ++||.+||++|++++++|++.|+|+|.|+.|+|+.+|++|||.++++|++.++.+++
T Consensus        39 ~G~~i~l~v~~~sdtV~~lK~~I~~~~gip~~~QrLi~~Gk~L~D~~tL~~ynI~~gsti~L~lr~rGG  107 (111)
T d1we6a_          39 DGQFMEITVQSLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLRERSG  107 (111)
T ss_dssp             SSCCEEEEESCSSSBHHHHHHHHHHHTTCCTTTSEEECSSSBCCTTSBTTTTTCSSSCEEEEECSSCCS
T ss_pred             CCeEEEEEecCCccHHHHHHHHHHHHHCCCccceEEEEeeEEccccCCHHHcCCCCCCEEEEEeeCCCC
Confidence            58899999976 899999999999999999999999999999999999999999999999999987754

>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=99.70  E-value=2.5e-17  Score=99.21  Aligned_cols=77  Identities=22%  Similarity=0.363  Sum_probs=68.6

Q ss_pred             cceeeeeeecCCceEEE-eeCCCchHHHHHHHHhhhcCCCCCceeEE---ECCeecCCCCcccccccCCCCEEEEEEeec
Q 040824           75 GGTMIKVKTLTGKEIEI-DIEPTDTIERIKERVEEKEGIPPVQQRLI---YAGKQLADDKTARDYNIEGGSVLHLVLALR  150 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~-~v~~~~tv~~LK~~i~~~~~i~~~~~~l~---~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~  150 (154)
                      ..|.|+|+. .++.+.+ ++++++||.+||++|++.+++|+++|+|+   |+|+.|+|+.+|.+|+|++|++|+++....
T Consensus         6 ~~~~i~Vk~-~~~~~~i~~v~~~~tV~~LK~~i~~~t~vp~~~QkLi~~~~~Gk~L~D~~tL~~~~i~~g~~i~lv~s~~   84 (90)
T d1v5ta_           6 SGLPIIVKW-GGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMGTRE   84 (90)
T ss_dssp             CSCCEEEEE-TTEEEEECSCCSSSBHHHHHHHHHHHTCCCTTTCEEESCEETTEECCTTSBHHHHTCCTTEEEEEECCCS
T ss_pred             CcEEEEEEE-CCeEEEEEEeCCCCcHHHHHHHHHHHHcCCHHHhhhhhhccCCcCCCCcCcHHHcCCCCCCEEEEEeeCC
Confidence            468899998 5566666 79999999999999999999999999999   689999999999999999999999987655


Q ss_pred             CC
Q 040824          151 GG  152 (154)
Q Consensus       151 gg  152 (154)
                      .|
T Consensus        85 ~~   86 (90)
T d1v5ta_          85 SG   86 (90)
T ss_dssp             SS
T ss_pred             CC
Confidence            44

>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=99.70  E-value=1.1e-17  Score=102.45  Aligned_cols=73  Identities=18%  Similarity=0.294  Sum_probs=66.0

Q ss_pred             CEEEE--EeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824            1 MQIFV--KTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v--~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |+|++  +...|+.+.+++.+++||.+||++|+++.++|++.|+|+|+|+.|+|+.+|++|+|+++++|+++...
T Consensus        18 i~V~~~~~~~~g~~~~lev~~~~TV~~LK~~I~~~~gi~~~~qkLi~~Gk~L~d~~tL~~~gI~~~s~i~vi~~~   92 (100)
T d1wjua_          18 IEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETFGLQENYIKIVINKKQLQLGKTLEEQGVAHNVKAMVLELK   92 (100)
T ss_dssp             EEEECCTTTCCSSSEEEEEESSSBHHHHHHHHHHHTTCCSTTCEEEETTEECCTTSBHHHHTCCSSEEEEEECCC
T ss_pred             EEEEEeeccCCCeEEEEEECCCcHHHHHHHHHHHHHCCCCeeEEEEEcccCcCCCcCHHHcCCCCCCEEEEEEcC
Confidence            34555  44578999999999999999999999999999999999999999999999999999999999877643

>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=99.69  E-value=4.8e-17  Score=95.94  Aligned_cols=72  Identities=24%  Similarity=0.409  Sum_probs=64.2

Q ss_pred             CEEEEEeCCCCEEEEEE-----eCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEec-cCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTGKTITLEV-----ESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLE-DGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v-----~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~-d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |+|+|++ +++.+++++     ++++||++||++|+..+|+|+++|+|+|+|+.|. |+.+|++|++++|++|+++.+.
T Consensus         2 i~i~V~~-~~~~~~i~v~~~~~~~~~Tv~~LK~~I~~~tgvp~~~QkL~~~G~~L~~d~~tL~~~gi~~g~~i~lv~~~   79 (81)
T d1wxva1           2 LTVTVTH-SNEKHDLHVTSQQGSSEPVVQDLAQVVEEVIGVPQSFQKLIFKGKSLKEMETPLSALGIQDGCRVMLIGKK   79 (81)
T ss_dssp             EEEEEEC-SSSEEEEEECCCSSSSSCBHHHHHHHHHHHTCCCTTTCEEEETTEEECCSSSBHHHHTCCSSEEEEEESCC
T ss_pred             EEEEEEE-CCeeEEEEEecCCCCCccHHHHHHHHHHHHHCcCHHHEEeeecCeEeCcCCCChHHCCCCCCCEEEEEEec
Confidence            6789976 668889888     4688999999999999999999999999999996 5679999999999999887653

>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=99.69  E-value=1.1e-17  Score=101.61  Aligned_cols=71  Identities=18%  Similarity=0.352  Sum_probs=65.8

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |+|+|++ +++.+.+++++++||.+||++|++.+++|+++|+|+|+|+ |.|+.+|++|+|+++++|+|+...
T Consensus        18 i~v~V~~-~~k~~~i~v~~~~TV~~LK~~I~~~tgvp~~~q~Li~~g~-l~D~~tL~~~~I~~gs~i~lvgs~   88 (95)
T d1v86a_          18 VDLKIIW-NKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKGL-VPEDKTLREIKVTSGAKIMVVGST   88 (95)
T ss_dssp             EEEEEEE-TTEEEEEEECTTSBHHHHHHHHHHHHCSCSTTCCCBSSSB-CCSSSBHHHHCCCTTEEEEECCSS
T ss_pred             EEEEEEE-CCEEEEEEECCCCcHHHHHHHHHHHhCCChhHEEEEeccc-ccCCCcHHHCCCCCCCEEEEEecC
Confidence            5788884 8899999999999999999999999999999999999987 899999999999999999988654

>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=99.68  E-value=2.5e-17  Score=99.15  Aligned_cols=73  Identities=21%  Similarity=0.408  Sum_probs=66.5

Q ss_pred             CEEEEEeCCCCEEEE-EEeCCCcHHHHHHHHHhHhCCCCCCeEEE---EcceEeccCceecccccccccceeeeeeee
Q 040824            1 MQIFVKTLTGKTITL-EVESSDTIDNVKAKIQDKEGIPPDQQRLI---FAGKQLEDGRTLADYNIQKESTLHLVLRLR   74 (154)
Q Consensus         1 m~v~v~~~~~~~~~~-~v~~~~tv~~lk~~i~~~~~~~~~~q~L~---~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~   74 (154)
                      |+|+|++ .++.+.+ ++++++||.+||++|++++++|++.|+|+   |.|+.|+|+.+|++|+++++++|+++.+..
T Consensus         8 ~~i~Vk~-~~~~~~i~~v~~~~tV~~LK~~i~~~t~vp~~~QkLi~~~~~Gk~L~D~~tL~~~~i~~g~~i~lv~s~~   84 (90)
T d1v5ta_           8 LPIIVKW-GGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKIMMMGTRE   84 (90)
T ss_dssp             CCEEEEE-TTEEEEECSCCSSSBHHHHHHHHHHHTCCCTTTCEEESCEETTEECCTTSBHHHHTCCTTEEEEEECCCS
T ss_pred             EEEEEEE-CCeEEEEEEeCCCCcHHHHHHHHHHHHcCCHHHhhhhhhccCCcCCCCcCcHHHcCCCCCCEEEEEeeCC
Confidence            7899996 6677777 79999999999999999999999999999   689999999999999999999999887643

>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=99.66  E-value=1.8e-16  Score=95.75  Aligned_cols=74  Identities=28%  Similarity=0.445  Sum_probs=64.7

Q ss_pred             CEEEEEeCCCCE--EEEEEeCCCcHHHHHHHHHhHhC--CCCCCeEEEEcceEeccCceecccccccc--cceeeeeeee
Q 040824            1 MQIFVKTLTGKT--ITLEVESSDTIDNVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLADYNIQKE--STLHLVLRLR   74 (154)
Q Consensus         1 m~v~v~~~~~~~--~~~~v~~~~tv~~lk~~i~~~~~--~~~~~q~L~~~g~~L~d~~~l~~~~i~~~--~~i~l~~~~~   74 (154)
                      |+|+|+.++++.  +.+++++++||.+||++|++..+  +|++.|+|+|.|+.|.|+.+|++|....+  .+||++++..
T Consensus         8 i~l~Ik~~~~~~~~~~~~v~~~~TV~~LK~~I~~~~~~~~~~~~qrLIy~Gk~L~D~~~L~d~~~~~~~~~viHLV~~~~   87 (93)
T d1wgda_           8 VTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVCNVK   87 (93)
T ss_dssp             CEEEEECSSSSCCCEEEECCTTSCHHHHHHHHHHHSTTCCCTTTCEEEETTEECCSSSCHHHHSCSSSCSEEEEEECCCC
T ss_pred             EEEEEECCCCCceeEEEEcCCCCcHHHHHHHHHHHcCCCCChHHEEEEECCeEccCCCCHHHhCcccCCCCEEEEEecCC
Confidence            789999988754  88899999999999999999864  99999999999999999999999976544  4898887654

>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=99.65  E-value=3.9e-16  Score=94.24  Aligned_cols=77  Identities=30%  Similarity=0.443  Sum_probs=66.6

Q ss_pred             ceeeeeeecCCc--eEEEeeCCCchHHHHHHHHhhhcC--CCCCceeEEECCeecCCCCcccccccC--CCCEEEEEEee
Q 040824           76 GTMIKVKTLTGK--EIEIDIEPTDTIERIKERVEEKEG--IPPVQQRLIYAGKQLADDKTARDYNIE--GGSVLHLVLAL  149 (154)
Q Consensus        76 ~~~i~v~~~~~~--~~~~~v~~~~tv~~LK~~i~~~~~--i~~~~~~l~~~g~~l~d~~~L~~~~i~--~~~~i~~~~~~  149 (154)
                      .|.|+|+..+++  .+.+++++++||.+||++|++..+  +|+++|+|+|+|+.|+|+.+|++|...  ++.+||++.+.
T Consensus         7 ~i~l~Ik~~~~~~~~~~~~v~~~~TV~~LK~~I~~~~~~~~~~~~qrLIy~Gk~L~D~~~L~d~~~~~~~~~viHLV~~~   86 (93)
T d1wgda_           7 GVTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVCNV   86 (93)
T ss_dssp             CCEEEEECSSSSCCCEEEECCTTSCHHHHHHHHHHHSTTCCCTTTCEEEETTEECCSSSCHHHHSCSSSCSEEEEEECCC
T ss_pred             cEEEEEECCCCCceeEEEEcCCCCcHHHHHHHHHHHcCCCCChHHEEEEECCeEccCCCCHHHhCcccCCCCEEEEEecC
Confidence            478888888765  488999999999999999999975  899999999999999999999999764  44599998877


Q ss_pred             cCC
Q 040824          150 RGG  152 (154)
Q Consensus       150 ~gg  152 (154)
                      ..+
T Consensus        87 ~~~   89 (93)
T d1wgda_          87 KSG   89 (93)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>d2uyzb1 d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-1 (smt3 homologue)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=6.6e-16  Score=90.17  Aligned_cols=75  Identities=23%  Similarity=0.477  Sum_probs=72.1

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRG  151 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~g  151 (154)
                      +.|.|+..+|+.+.+.+.+++++..|+.+++++.++|+..++|+|+|..|.++.|++++++++|++|++++++.|
T Consensus         3 I~ikv~~~dg~~v~f~v~~~t~l~kl~~~y~~~~~~~~~~~~f~fdG~~l~~~~T~~~l~~edgD~Idv~~~q~G   77 (77)
T d2uyzb1           3 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTG   77 (77)
T ss_dssp             EEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCHHHHTCCTTEEEEEEECCCC
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCChhHEEEEECCEECCCCCCHHHcCCCCCCEEEEEEecCC
Confidence            678899999999999999999999999999999999999999999999999999999999999999999998876

>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=99.63  E-value=6e-16  Score=94.53  Aligned_cols=74  Identities=22%  Similarity=0.214  Sum_probs=62.9

Q ss_pred             eeeeec-CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCC-------CCEEEEEEeec
Q 040824           79 IKVKTL-TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEG-------GSVLHLVLALR  150 (154)
Q Consensus        79 i~v~~~-~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~-------~~~i~~~~~~~  150 (154)
                      |+++.. .+.++.+++++++||.+||++|+++.|+|+++|+|+|+|+.|+|+.||++|||.+       .+++.+.++..
T Consensus         2 ifv~i~~~k~Ti~l~v~~~~TV~~lK~~I~~~~gip~~~QrLi~~Gk~L~D~~TL~dYgI~~~~~~~~~~~~~~l~~~~~   81 (103)
T d2c9wb1           2 VFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRAD   81 (103)
T ss_dssp             EEEEEEEBTEEEEEEECTTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBHHHHTCCTTTSBTTBCEEEEEEEEET
T ss_pred             EEEEEeCCCEEEEEEeCCCCcHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCcccccccCCcEEEEEEecC
Confidence            344443 3357889999999999999999999999999999999999999999999999954       45788877776


Q ss_pred             CC
Q 040824          151 GG  152 (154)
Q Consensus       151 gg  152 (154)
                      |+
T Consensus        82 ~~   83 (103)
T d2c9wb1          82 DT   83 (103)
T ss_dssp             TE
T ss_pred             CC
Confidence            64

>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=99.62  E-value=7.1e-16  Score=93.37  Aligned_cols=77  Identities=21%  Similarity=0.258  Sum_probs=68.2

Q ss_pred             ceeeeeeec-CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCe-------ecCCCCcccccccCCCCEEEEEE
Q 040824           76 GTMIKVKTL-TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGK-------QLADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        76 ~~~i~v~~~-~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~-------~l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      .+.|+|++. ++...+.++++++||.+||++++..+|+|++.|+|+|.|+       .++|+.+|.+|++.+|++||+..
T Consensus         7 ~v~v~I~s~~~~~~~E~r~~~~~TV~~LK~kle~~tGip~~~qrL~~~~~~~~~~~~l~~d~~~L~~y~i~dg~~ihlvd   86 (95)
T d1v6ea_           7 GVMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVGSPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIHVID   86 (95)
T ss_dssp             CEEEEEEETTSSSCEEEEECTTSBHHHHHHHHHHHTCSCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCEEEEBC
T ss_pred             cEEEEEEECCCCcEEEEEeCCCCCHHHHHHHHHHHhCcCchhEEEEEeCCCCceeecccCCcCCHHHCCCCCCCEEEEEe
Confidence            467788774 5556889999999999999999999999999999998776       57899999999999999999998


Q ss_pred             eecCC
Q 040824          148 ALRGG  152 (154)
Q Consensus       148 ~~~gg  152 (154)
                      +.++|
T Consensus        87 ~~p~~   91 (95)
T d1v6ea_          87 HSGSG   91 (95)
T ss_dssp             CSCCS
T ss_pred             CCCCC
Confidence            87765

>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=99.61  E-value=6.8e-16  Score=94.29  Aligned_cols=64  Identities=27%  Similarity=0.423  Sum_probs=56.8

Q ss_pred             EEEEEeCCC-CEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceeccccccccc
Q 040824            2 QIFVKTLTG-KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKES   65 (154)
Q Consensus         2 ~v~v~~~~~-~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~   65 (154)
                      +|+|+...+ .++.+++++++||.+||++|+++.|++++.|+|+|+|+.|.|+.+|++|||.+.+
T Consensus         1 qifv~i~~~k~Ti~l~v~~~~TV~~lK~~I~~~~gip~~~QrLi~~Gk~L~D~~TL~dYgI~~~~   65 (103)
T d2c9wb1           1 DVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQT   65 (103)
T ss_dssp             CEEEEEEEBTEEEEEEECTTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBHHHHTCCTTT
T ss_pred             CEEEEEeCCCEEEEEEeCCCCcHHHHHHHHHHHhCCCcccEEEEECCEEcCCCCCHHHcCCCccc
Confidence            356665555 4688999999999999999999999999999999999999999999999996554

>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=99.58  E-value=1.8e-15  Score=91.57  Aligned_cols=74  Identities=18%  Similarity=0.238  Sum_probs=65.6

Q ss_pred             CEEEEEeC-CCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcce-------EeccCceecccccccccceeeeee
Q 040824            1 MQIFVKTL-TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGK-------QLEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         1 m~v~v~~~-~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~-------~L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      |.|+|+.. ++...+.++++++||.+||++++..+|+|++.|+|+|.|+       .++|+.+|++|++.+|++||++.+
T Consensus         8 v~v~I~s~~~~~~~E~r~~~~~TV~~LK~kle~~tGip~~~qrL~~~~~~~~~~~~l~~d~~~L~~y~i~dg~~ihlvd~   87 (95)
T d1v6ea_           8 VMVFISSSLNSFRSEKRYSRSLTIAEFKCKLELVVGSPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIHVIDH   87 (95)
T ss_dssp             EEEEEEETTSSSCEEEEECTTSBHHHHHHHHHHHTCSCTTTCBCEEECSSSCEEEECCCSSSBTTSSSCCTTCEEEEBCC
T ss_pred             EEEEEEECCCCcEEEEEeCCCCCHHHHHHHHHHHhCcCchhEEEEEeCCCCceeecccCCcCCHHHCCCCCCCEEEEEeC
Confidence            57888874 4556889999999999999999999999999999998775       578899999999999999999876


Q ss_pred             ee
Q 040824           73 LR   74 (154)
Q Consensus        73 ~~   74 (154)
                      .+
T Consensus        88 ~p   89 (95)
T d1v6ea_          88 SG   89 (95)
T ss_dssp             SC
T ss_pred             CC
Confidence            54

>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=99.57  E-value=6.1e-15  Score=86.40  Aligned_cols=74  Identities=12%  Similarity=0.314  Sum_probs=67.6

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeeeec
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRG   75 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~~~   75 (154)
                      |.|+|+. +|+...+.+..++++..|++.++++.+++++.++|+|+|+.|.++.|+++|++.++++|++.++..+
T Consensus         5 I~ikv~~-~~~~~~f~v~~~~~~~~l~~~~~~~~~i~~~~~~l~f~G~~l~~~~T~~~~~i~dgd~I~v~~~q~G   78 (79)
T d1euvb_           5 INLKVSD-GSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIG   78 (79)
T ss_dssp             EEEEEES-SSCEEEEEEETTSCTHHHHHHHHHHTTCCGGGEEEEETTEECCTTCCTTTTTCCTTEEEEEEECCBC
T ss_pred             EEEEECC-CCeEEEEEECCCCcHHHHHHHHHHHhCCChHhEEEEECCEEeCCCCCHHHCCCCCCCEEEEEEeccC
Confidence            3566765 6788889999999999999999999999999999999999999999999999999999999987654

>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=99.51  E-value=3.8e-14  Score=86.02  Aligned_cols=70  Identities=20%  Similarity=0.315  Sum_probs=59.7

Q ss_pred             eeeeeec---CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCee-------cC-CCCcccccccCCCCEEEEE
Q 040824           78 MIKVKTL---TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQ-------LA-DDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        78 ~i~v~~~---~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~-------l~-d~~~L~~~~i~~~~~i~~~  146 (154)
                      .|.|+..   +++.++..+++++||.+||.+++..+|+|++.|+|+|.|+.       |+ |+++|.+|||++|++|+|.
T Consensus        11 ti~i~~~~~~~~~~~~~kv~~~~TV~~LK~~i~~~~gip~~~qrL~y~~~~~~~~~~~l~~d~~tL~~YgI~dg~~I~V~   90 (97)
T d1wjna_          11 TLKIKCSNQPERQILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCLLVR   90 (97)
T ss_dssp             EEEEEESSCSSSCCEEEEEETTSBHHHHHHHHHTTTTCCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTCCTTCEEEEE
T ss_pred             EEEEEeCCCCCCceEEEEcCCCCCHHHHHHHHHHHHCcChHHeEEEecCCCCCcccceecCCCcCHhhccCCCCCEEEEE
Confidence            4444443   46778999999999999999999999999999999998762       44 7899999999999999875


Q ss_pred             E
Q 040824          147 L  147 (154)
Q Consensus       147 ~  147 (154)
                      .
T Consensus        91 ~   91 (97)
T d1wjna_          91 W   91 (97)
T ss_dssp             C
T ss_pred             e
Confidence            4

>d2uyzb1 d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: SUMO-1 (smt3 homologue)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=3.3e-14  Score=82.80  Aligned_cols=73  Identities=16%  Similarity=0.408  Sum_probs=69.7

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeeee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRL   73 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~~   73 (154)
                      |+|+|+..+|+.+.+.+..++++..|++.++++.+++++.++|+|+|+.|.++.|++++++.+|++|++....
T Consensus         3 I~ikv~~~dg~~v~f~v~~~t~l~kl~~~y~~~~~~~~~~~~f~fdG~~l~~~~T~~~l~~edgD~Idv~~~q   75 (77)
T d2uyzb1           3 IKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQ   75 (77)
T ss_dssp             EEEEEECTTCCEEEEEEETTSCTHHHHHHHHHHHTCCGGGEEEEETTEECCTTCCHHHHTCCTTEEEEEEECC
T ss_pred             EEEEEECCCCCEEEEEECCCChHHHHHHHHHHHhCCChhHEEEEECCEECCCCCCHHHcCCCCCCEEEEEEec
Confidence            5789999999999999999999999999999999999999999999999999999999999999999988754

>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=99.50  E-value=2.6e-14  Score=85.49  Aligned_cols=83  Identities=27%  Similarity=0.338  Sum_probs=61.6

Q ss_pred             cceeeeeeeecc---eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcC--C-CCCceeEEECCeecCCCCcccccccC
Q 040824           65 STLHLVLRLRGG---TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEG--I-PPVQQRLIYAGKQLADDKTARDYNIE  138 (154)
Q Consensus        65 ~~i~l~~~~~~~---~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~--i-~~~~~~l~~~g~~l~d~~~L~~~~i~  138 (154)
                      ++.|++++..++   ....++..+. .....+..+.||.+||++|+++..  . +|++|+|+|.|+.|+|+.+|++|||+
T Consensus         4 s~~~~~~~l~~~p~~pk~~i~~p~~-~~~~~~~~~~tV~~lK~~i~~~~~~~~P~p~~~rLIy~Gk~L~D~~tL~~y~I~   82 (94)
T d1x1ma1           4 SDWHLAVKLADQPLAPKSILQLPET-ELGEYSLGGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDFYGIQ   82 (94)
T ss_dssp             CSCCEEEEETTCTTSCCEEECCCCC-SSCSSCCCCCBHHHHHHHHHHHCTTTCCCSSSEEEEETTEECCTTCBHHHHTCC
T ss_pred             ccceEEEEEccCCCCCcceEECCCC-ccCccCCCccCHHHHHHHHHHHcccCCCChhheEEEECCeEECCCccHHHcCCC
Confidence            355666665433   2334444332 112234568899999999998875  4 47999999999999999999999999


Q ss_pred             CCCEEEEEEe
Q 040824          139 GGSVLHLVLA  148 (154)
Q Consensus       139 ~~~~i~~~~~  148 (154)
                      +|++||++.|
T Consensus        83 ~gstihLV~r   92 (94)
T d1x1ma1          83 PGSTVHVLRK   92 (94)
T ss_dssp             TTCEEEEEES
T ss_pred             CCCEEEEEEe
Confidence            9999999876

>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=99.45  E-value=1.1e-13  Score=83.95  Aligned_cols=70  Identities=19%  Similarity=0.266  Sum_probs=60.0

Q ss_pred             EEEEEeC---CCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcce-------Eec-cCceecccccccccceeee
Q 040824            2 QIFVKTL---TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGK-------QLE-DGRTLADYNIQKESTLHLV   70 (154)
Q Consensus         2 ~v~v~~~---~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~-------~L~-d~~~l~~~~i~~~~~i~l~   70 (154)
                      +|+|+..   +++.+.++++.++||.+||.+++..+|+|++.|+|+|.|+       .|+ |+.+|.+|++.+|++|++.
T Consensus        11 ti~i~~~~~~~~~~~~~kv~~~~TV~~LK~~i~~~~gip~~~qrL~y~~~~~~~~~~~l~~d~~tL~~YgI~dg~~I~V~   90 (97)
T d1wjna_          11 TLKIKCSNQPERQILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCLLVR   90 (97)
T ss_dssp             EEEEEESSCSSSCCEEEEEETTSBHHHHHHHHHTTTTCCTTTCEEEEECTTSCSCEEECCCSSSBSGGGTCCTTCEEEEE
T ss_pred             EEEEEeCCCCCCceEEEEcCCCCCHHHHHHHHHHHHCcChHHeEEEecCCCCCcccceecCCCcCHhhccCCCCCEEEEE
Confidence            5666644   4577899999999999999999999999999999999875       244 6789999999999999875


Q ss_pred             e
Q 040824           71 L   71 (154)
Q Consensus        71 ~   71 (154)
                      .
T Consensus        91 ~   91 (97)
T d1wjna_          91 W   91 (97)
T ss_dssp             C
T ss_pred             e
Confidence            4

>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=99.45  E-value=2.3e-13  Score=81.38  Aligned_cols=72  Identities=17%  Similarity=0.181  Sum_probs=59.7

Q ss_pred             eeeeeec-CCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCe-------ecCCCCcccccccCCCCEEEEEEee
Q 040824           78 MIKVKTL-TGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGK-------QLADDKTARDYNIEGGSVLHLVLAL  149 (154)
Q Consensus        78 ~i~v~~~-~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~-------~l~d~~~L~~~~i~~~~~i~~~~~~  149 (154)
                      .+.|... ++...+..++++.||.+||++++..+|+|++.|+|+|.++       ..+|+.+|.+||+.+|++|||.-..
T Consensus         6 ~l~it~~~t~~~~E~r~~~~~TV~~LK~kle~~~Gip~~~q~L~~~~~~~~~~~~l~dd~~~L~~ygi~dG~~Ihvvd~~   85 (90)
T d1t0ya_           6 DLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHAVDVT   85 (90)
T ss_dssp             EEEEEESSCCSCEEEEEETTSBHHHHHHHHHHHHCCCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEEEEEECT
T ss_pred             EEEEEECCCccEEEEecCCCCCHHHHHHHHHHHHCCChhheEEEEeCCCCCcccccccCCCCHHHCCCCCCCEEEEEeCC
Confidence            4444442 3344678899999999999999999999999999998775       4568999999999999999985543

>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=99.43  E-value=3.1e-13  Score=80.78  Aligned_cols=71  Identities=15%  Similarity=0.221  Sum_probs=59.1

Q ss_pred             EEEEEeC-CCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcce-------EeccCceecccccccccceeeeee
Q 040824            2 QIFVKTL-TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGK-------QLEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         2 ~v~v~~~-~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~-------~L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      .|.|.+. .+...+.++++++||.+||++++..+|+|++.|+|+|.|+       ..+|+.+|.+||+.+|++||++-.
T Consensus         6 ~l~it~~~t~~~~E~r~~~~~TV~~LK~kle~~~Gip~~~q~L~~~~~~~~~~~~l~dd~~~L~~ygi~dG~~Ihvvd~   84 (90)
T d1t0ya_           6 DLEITTNATDFPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHAVDV   84 (90)
T ss_dssp             EEEEEESSCCSCEEEEEETTSBHHHHHHHHHHHHCCCTTTEEEEEECSSSSEEEECCCCSSBTTTTTCCSSEEEEEEEC
T ss_pred             EEEEEECCCccEEEEecCCCCCHHHHHHHHHHHHCCChhheEEEEeCCCCCcccccccCCCCHHHCCCCCCCEEEEEeC
Confidence            3555542 3344688899999999999999999999999999998764       456788999999999999998654

>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=99.35  E-value=5.8e-13  Score=79.52  Aligned_cols=54  Identities=33%  Similarity=0.516  Sum_probs=48.6

Q ss_pred             CCCcHHHHHHHHHhHhC--C-CCCCeEEEEcceEeccCceecccccccccceeeeee
Q 040824           19 SSDTIDNVKAKIQDKEG--I-PPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus        19 ~~~tv~~lk~~i~~~~~--~-~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      .++||.+||+.|..+..  . +|+.|+|+|+|+.|+|+.+|++|+|.+|++||++.+
T Consensus        36 ~~~tV~~lK~~i~~~~~~~~P~p~~~rLIy~Gk~L~D~~tL~~y~I~~gstihLV~r   92 (94)
T d1x1ma1          36 GGYSISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDFYGIQPGSTVHVLRK   92 (94)
T ss_dssp             CCCBHHHHHHHHHHHCTTTCCCSSSEEEEETTEECCTTCBHHHHTCCTTCEEEEEES
T ss_pred             CccCHHHHHHHHHHHcccCCCChhheEEEECCeEECCCccHHHcCCCCCCEEEEEEe
Confidence            36799999999988864  4 479999999999999999999999999999999876

>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=99.27  E-value=2.1e-11  Score=69.61  Aligned_cols=70  Identities=16%  Similarity=0.355  Sum_probs=66.1

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEE
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~  146 (154)
                      +.|.|+..+|+.+.+.+..++++..|....++..++++...+++|+|..+..+.|.+++++++|++|.++
T Consensus         2 I~lkv~~~~g~~v~f~vk~~t~l~kl~~~y~~~~~~~~~~~~f~fdG~~i~~~~Tp~~l~med~D~Idv~   71 (72)
T d1wm3a_           2 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVF   71 (72)
T ss_dssp             EEEEEECTTSCEEEEEECTTSCTHHHHHHHHHHHTCCTTTCEEEETTEECCTTCCTTTTTCCTTEEEEEE
T ss_pred             EEEEEECCCCCEEEEEEcCCChHHHHHHHHHHHhCCCccceEEEECCEEcCCCCCHHHcCCCCCCEEEEE
Confidence            4677888899999999999999999999999999999999999999999999999999999999999875

>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=99.10  E-value=2.9e-10  Score=64.79  Aligned_cols=69  Identities=16%  Similarity=0.389  Sum_probs=65.7

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceee
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHL   69 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l   69 (154)
                      |.|+|+..+|+.+.+.+..++++..|..+..+..+++++..+++|+|+.+.++.|.+++++.+++.|.+
T Consensus         2 I~lkv~~~~g~~v~f~vk~~t~l~kl~~~y~~~~~~~~~~~~f~fdG~~i~~~~Tp~~l~med~D~Idv   70 (72)
T d1wm3a_           2 INLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDV   70 (72)
T ss_dssp             EEEEEECTTSCEEEEEECTTSCTHHHHHHHHHHHTCCTTTCEEEETTEECCTTCCTTTTTCCTTEEEEE
T ss_pred             EEEEEECCCCCEEEEEEcCCChHHHHHHHHHHHhCCCccceEEEECCEEcCCCCCHHHcCCCCCCEEEE
Confidence            478899999999999999999999999999999999999999999999999999999999999999875

>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=98.90  E-value=1.6e-09  Score=62.97  Aligned_cols=69  Identities=20%  Similarity=0.363  Sum_probs=55.2

Q ss_pred             eeeeecCCceEEEeeC-CCchHHHHHHHHhhhcCCCCCceeEEECC--------------eecC-CCCcccccccCCCCE
Q 040824           79 IKVKTLTGKEIEIDIE-PTDTIERIKERVEEKEGIPPVQQRLIYAG--------------KQLA-DDKTARDYNIEGGSV  142 (154)
Q Consensus        79 i~v~~~~~~~~~~~v~-~~~tv~~LK~~i~~~~~i~~~~~~l~~~g--------------~~l~-d~~~L~~~~i~~~~~  142 (154)
                      |.+++.+| +..++++ ++.|+.+||.+|++..++|.+.|.|..+.              ..+. |..+|+++||.+|+.
T Consensus         3 iRiRsrdG-~eRv~v~~~~~Tl~~LK~~Ie~~L~VPv~~Q~LSl~~~llL~k~P~~~~~~~~l~d~~~~L~sl~i~hGsi   81 (94)
T d1wf9a1           3 LRVRSRDG-LERVSVDGPHITVSQLKTLIQDQLQIPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLAHGSM   81 (94)
T ss_dssp             EEEECSSC-EEEEEECCTTSBHHHHHHHHHHHSCCCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTCCCTTCE
T ss_pred             EEEEecCC-ceEEEecCCCCcHHHHHHHHHHHhCCCcccceeecChhhhccCCccccchhhhccCCccCHHHcCccCceE
Confidence            56677676 6678885 47899999999999999999999995431              2243 667799999999999


Q ss_pred             EEEEEe
Q 040824          143 LHLVLA  148 (154)
Q Consensus       143 i~~~~~  148 (154)
                      ||+...
T Consensus        82 vyL~y~   87 (94)
T d1wf9a1          82 VYLAYE   87 (94)
T ss_dssp             EECCCS
T ss_pred             EEEEee
Confidence            998654

>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=98.68  E-value=1.8e-08  Score=58.49  Aligned_cols=69  Identities=23%  Similarity=0.325  Sum_probs=55.0

Q ss_pred             EEEEeCCCCEEEEEEeC-CCcHHHHHHHHHhHhCCCCCCeEEEEc-------------c-eEecc-Cceecccccccccc
Q 040824            3 IFVKTLTGKTITLEVES-SDTIDNVKAKIQDKEGIPPDQQRLIFA-------------G-KQLED-GRTLADYNIQKEST   66 (154)
Q Consensus         3 v~v~~~~~~~~~~~v~~-~~tv~~lk~~i~~~~~~~~~~q~L~~~-------------g-~~L~d-~~~l~~~~i~~~~~   66 (154)
                      |+|+..+| +..++++. +.|+.+||.+|++..++|.+.|.|..+             + ..+.| ...|+++|+.+|+.
T Consensus         3 iRiRsrdG-~eRv~v~~~~~Tl~~LK~~Ie~~L~VPv~~Q~LSl~~~llL~k~P~~~~~~~~l~d~~~~L~sl~i~hGsi   81 (94)
T d1wf9a1           3 LRVRSRDG-LERVSVDGPHITVSQLKTLIQDQLQIPIHNQTLSTNRNLLLAKSPSDFLAFTDMADPNLRISSLNLAHGSM   81 (94)
T ss_dssp             EEEECSSC-EEEEEECCTTSBHHHHHHHHHHHSCCCTTTCCCBSSGGGGTCCSHHHHTTCCSSCCTTCBGGGTCCCTTCE
T ss_pred             EEEEecCC-ceEEEecCCCCcHHHHHHHHHHHhCCCcccceeecChhhhccCCccccchhhhccCCccCHHHcCccCceE
Confidence            67888765 46788854 779999999999999999999999653             1 22444 45799999999999


Q ss_pred             eeeeee
Q 040824           67 LHLVLR   72 (154)
Q Consensus        67 i~l~~~   72 (154)
                      +++...
T Consensus        82 vyL~y~   87 (94)
T d1wf9a1          82 VYLAYE   87 (94)
T ss_dssp             EECCCS
T ss_pred             EEEEee
Confidence            987654

>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=98.54  E-value=3.3e-07  Score=51.52  Aligned_cols=69  Identities=16%  Similarity=0.253  Sum_probs=64.4

Q ss_pred             eeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEE
Q 040824           79 IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        79 i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      +.|-..+|+...+.+.|++|+.++-+..++++|+++++..|.|+++.++-+.+..-.|+.+|+.++++-
T Consensus         3 V~Vl~~~~rR~~VKvtP~t~l~~VL~eaC~k~~~~~~~~~Lkh~~k~ldLsl~~R~sgLpnnakLELv~   71 (76)
T d2al3a1           3 VSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQDFNPSEYDLKFQRTVLDLSLQWRFANLPNNAKLEMVP   71 (76)
T ss_dssp             EEEECTTSCEEEECCCTTSBHHHHHHHHHHHTTCCGGGCEEEETTEEESSSCBHHHHCCCSSCEEEEEC
T ss_pred             EEEECCCCcEEEEEeCCCcCHHHHHHHHHHHhCCChhHceeeeCCEEcCccceeeecCCCCCCEEEEEE
Confidence            456677899999999999999999999999999999999999999999999999999999999999864

>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=98.10  E-value=8.3e-06  Score=45.65  Aligned_cols=70  Identities=19%  Similarity=0.211  Sum_probs=65.4

Q ss_pred             EEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEcceEeccCceecccccccccceeeeee
Q 040824            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         3 v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      |.|=..+|+...+.+.+++++.++-+...+++|+.++.-.|.|+++.++-...+...|+.+++.+.++..
T Consensus         3 V~Vl~~~~rR~~VKvtP~t~l~~VL~eaC~k~~~~~~~~~Lkh~~k~ldLsl~~R~sgLpnnakLELv~~   72 (76)
T d2al3a1           3 VSVLAPNGRRHTVKVTPSTVLLQVLEDTCRRQDFNPSEYDLKFQRTVLDLSLQWRFANLPNNAKLEMVPV   72 (76)
T ss_dssp             EEEECTTSCEEEECCCTTSBHHHHHHHHHHHTTCCGGGCEEEETTEEESSSCBHHHHCCCSSCEEEEECS
T ss_pred             EEEECCCCcEEEEEeCCCcCHHHHHHHHHHHhCCChhHceeeeCCEEcCccceeeecCCCCCCEEEEEEc
Confidence            6777889999999999999999999999999999999999999999999999999999999999987654

>d1h8ca_ d.15.1.2 (A:) Fas-associated factor 1, Faf1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: Fas-associated factor 1, Faf1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.85  E-value=5.1e-05  Score=43.41  Aligned_cols=69  Identities=16%  Similarity=0.316  Sum_probs=58.4

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEE--ECCeec---CCCCcccccccCCCCEEEEE
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI--YAGKQL---ADDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~--~~g~~l---~d~~~L~~~~i~~~~~i~~~  146 (154)
                      ..|.++.++|+.+.-.+.+++|+.+|..-+... +.++..+.|.  |..+.+   +.+.||.+.|+.+.++|+|-
T Consensus         6 ~~i~iRlPdG~~~~~~F~~~~tl~~v~~~v~~~-~~~~~~~~l~~~~Pr~~l~~~d~~~TL~e~gL~p~~~L~vq   79 (82)
T d1h8ca_           6 SKLRIRTPSGEFLERRFLASNKLQIVFDFVASK-GFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLE   79 (82)
T ss_dssp             EEEEEECTTSCEEEEEECTTSBHHHHHHHHHHH-TCCSSSEEEEETTTTEETTTCCTTSBHHHHCCCSEEEEEEE
T ss_pred             EEEEEECCCCCEEEEEECCCCcHHHHHHHHHhc-CCCCCceEEEecCcccccccccccCCHHHCCCCCCCEEEEE
Confidence            468888999999999999999999999999874 7788888887  566766   35789999999999998764

>d1h8ca_ d.15.1.2 (A:) Fas-associated factor 1, Faf1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: Fas-associated factor 1, Faf1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.68  E-value=0.00014  Score=41.52  Aligned_cols=68  Identities=21%  Similarity=0.379  Sum_probs=56.3

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEE--EcceEec---cCceecccccccccceeee
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE---DGRTLADYNIQKESTLHLV   70 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~--~~g~~L~---d~~~l~~~~i~~~~~i~l~   70 (154)
                      +|.|+.++|..+.-..+.++|+.+|.+-+... +.++..-.|+  |..+.+.   .+.||.+.|+.+.+++++-
T Consensus         7 ~i~iRlPdG~~~~~~F~~~~tl~~v~~~v~~~-~~~~~~~~l~~~~Pr~~l~~~d~~~TL~e~gL~p~~~L~vq   79 (82)
T d1h8ca_           7 KLRIRTPSGEFLERRFLASNKLQIVFDFVASK-GFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLE   79 (82)
T ss_dssp             EEEEECTTSCEEEEEECTTSBHHHHHHHHHHH-TCCSSSEEEEETTTTEETTTCCTTSBHHHHCCCSEEEEEEE
T ss_pred             EEEEECCCCCEEEEEECCCCcHHHHHHHHHhc-CCCCCceEEEecCcccccccccccCCHHHCCCCCCCEEEEE
Confidence            58899999999999999999999999999864 6677777776  5677773   4569999999888887653

>d1i42a_ d.15.1.2 (A:) p47 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: p47
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.49  E-value=0.00033  Score=40.53  Aligned_cols=65  Identities=15%  Similarity=0.274  Sum_probs=53.0

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhc-CCCCCceeEEE--CCeec-CCCCcccccccCCCC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKE-GIPPVQQRLIY--AGKQL-ADDKTARDYNIEGGS  141 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~-~i~~~~~~l~~--~g~~l-~d~~~L~~~~i~~~~  141 (154)
                      ..|.|+.++|+.+...+.+++|+.+|..-+.... +.+...+.|..  .-+.+ +++.||.+.|+.+..
T Consensus        15 t~I~iRlPdG~~~~~~F~~~~tl~dv~~~v~~~~~~~~~~~f~L~t~~Prr~l~d~~~TL~e~gL~~s~   83 (89)
T d1i42a_          15 TNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFPNKELADENQTLKEANLLNAV   83 (89)
T ss_dssp             EEEEEEETTTCCEEEEECSSSCGGGHHHHHHHHCTTTSSCCEEEEETTTTEECCCCSSCSGGGTTCCSE
T ss_pred             EEEEEEcCCCCEEEEEECCchhHHHHHHHHHHhCccCCCCCEEEecCCCCcccCCCcCcHHHCCCcCce
Confidence            4678889999999999999999999999997754 56777788874  45666 477899999998643

>d1i42a_ d.15.1.2 (A:) p47 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: p47
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.31  E-value=0.00043  Score=39.97  Aligned_cols=64  Identities=22%  Similarity=0.375  Sum_probs=51.5

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHh-CCCCCCeEEE--EcceEecc-Cceeccccccccc
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKE-GIPPDQQRLI--FAGKQLED-GRTLADYNIQKES   65 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~-~~~~~~q~L~--~~g~~L~d-~~~l~~~~i~~~~   65 (154)
                      .|.|+..+|..+...+..+++|.+|.+.+.... +.+...-.|.  |..+.+.| +.+|.+.|+.+.+
T Consensus        16 ~I~iRlPdG~~~~~~F~~~~tl~dv~~~v~~~~~~~~~~~f~L~t~~Prr~l~d~~~TL~e~gL~~s~   83 (89)
T d1i42a_          16 NIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFPNKELADENQTLKEANLLNAV   83 (89)
T ss_dssp             EEEEEETTTCCEEEEECSSSCGGGHHHHHHHHCTTTSSCCEEEEETTTTEECCCCSSCSGGGTTCCSE
T ss_pred             EEEEEcCCCCEEEEEECCchhHHHHHHHHHHhCccCCCCCEEEecCCCCcccCCCcCcHHHCCCcCce
Confidence            578999999999999999999999999998764 4566566776  34677754 6699999998654

>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=97.27  E-value=0.00044  Score=42.49  Aligned_cols=69  Identities=16%  Similarity=0.286  Sum_probs=56.5

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEE--ECCeec---CCCCcccccccCCCCEEEEE
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI--YAGKQL---ADDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~--~~g~~l---~d~~~L~~~~i~~~~~i~~~  146 (154)
                      ..|.++.++|+.+.-.+..++|+.+|..-+... +.+...+.|.  |.-+.+   +.+.||.+.|+.+.++|+|-
T Consensus        44 ~~l~iRlPdG~r~~r~F~~~~tl~~l~~~v~~~-~~~~~~~~L~~~fPr~~l~~~d~~~TL~e~gL~P~~~L~ve  117 (124)
T d1wj4a_          44 AQLMLRYPDGKREQITLPEQAKLLALVKHVQSK-GYPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQ  117 (124)
T ss_dssp             EEEEEECTTSCEEEEEEETTSCHHHHHHHHHHH-HCCTTTEEEECSSSCCEETSSCSSSCTTTTTCCSSBCCEEE
T ss_pred             eEEEEECCCCCEEEEEeCCCCcHHHHHHHHHhc-ccCCcceEEeecccccccccccccCcHHHcCCCCCCEEEEE
Confidence            578888899999999999999999999999765 5666777777  555566   45789999999999998654

>d2cr5a1 d.15.1.2 (A:8-103) UBX domain-containing protein 6 (Reproduction 8) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: UBX domain
domain: UBX domain-containing protein 6 (Reproduction 8)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.25  E-value=0.00074  Score=39.45  Aligned_cols=70  Identities=13%  Similarity=0.170  Sum_probs=55.4

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEE--ECCeec--CCCCcccccccCCCCEEEEEE
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI--YAGKQL--ADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~--~~g~~l--~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      ..|.++.++|+.+.-.+..++|+.+|..-+... +.......|.  |..+.+  +.+.||.++|+.+.++|+|--
T Consensus        17 ~~i~iRlPdG~r~~r~F~~~dtl~~l~~fv~~~-~~~~~~f~l~~~~Pr~~~~~d~~~TL~e~gl~p~~~L~v~~   90 (96)
T d2cr5a1          17 VTVALRCPNGRVLRRRFFKSWNSQVLLDWMMKV-GYHKSLYRLSTSFPRRALEVEGGSSLEDIGITVDTVLNVEE   90 (96)
T ss_dssp             EEEEEECTTSCEEEEEEESSSBTHHHHHHHHHH-TCCTTTEEEECSSSCCBCCCCSSCBHHHHTCSSCEEEEEEE
T ss_pred             EEEEEECCCCCEEEEEECCcccHHHHHHHHHHh-ccCcccceeecCCCceecCccCCCcHHHCCCCCCCEEEEec
Confidence            567888889999888999999999999998764 4556777776  444555  357899999999999887643

>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=97.14  E-value=0.0014  Score=40.12  Aligned_cols=68  Identities=18%  Similarity=0.314  Sum_probs=54.3

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEE--EcceEec---cCceecccccccccceeee
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE---DGRTLADYNIQKESTLHLV   70 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~--~~g~~L~---d~~~l~~~~i~~~~~i~l~   70 (154)
                      +|.||..+|+.+...+..++||.+|.+.+.... .....-.|+  |..+.|.   .+.+|.+.|+.+.++|++-
T Consensus        45 ~l~iRlPdG~r~~r~F~~~~tl~~l~~~v~~~~-~~~~~~~L~~~fPr~~l~~~d~~~TL~e~gL~P~~~L~ve  117 (124)
T d1wj4a_          45 QLMLRYPDGKREQITLPEQAKLLALVKHVQSKG-YPNERFELLTNFPRRKLSHLDYDITLQEAGLCPQETVFVQ  117 (124)
T ss_dssp             EEEEECTTSCEEEEEEETTSCHHHHHHHHHHHH-CCTTTEEEECSSSCCEETSSCSSSCTTTTTCCSSBCCEEE
T ss_pred             EEEEECCCCCEEEEEeCCCCcHHHHHHHHHhcc-cCCcceEEeecccccccccccccCcHHHcCCCCCCEEEEE
Confidence            588999999999999999999999999997653 455555565  5567773   4569999999988888554

>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=96.87  E-value=0.0016  Score=37.90  Aligned_cols=69  Identities=19%  Similarity=0.243  Sum_probs=53.3

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEE--EcceEec--cCceecccccccccceeeee
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI--FAGKQLE--DGRTLADYNIQKESTLHLVL   71 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~--~~g~~L~--d~~~l~~~~i~~~~~i~l~~   71 (154)
                      +|.|+..+|+.+.-....++||.+|..-+... +.....-.|+  |..+.+.  .+.||.+.|+.+.+++.+--
T Consensus        18 ~i~iRlPdG~r~~r~F~~~dtl~~l~~fv~~~-~~~~~~f~l~~~~Pr~~~~~d~~~TL~e~gl~p~~~L~v~~   90 (96)
T d2cr5a1          18 TVALRCPNGRVLRRRFFKSWNSQVLLDWMMKV-GYHKSLYRLSTSFPRRALEVEGGSSLEDIGITVDTVLNVEE   90 (96)
T ss_dssp             EEEEECTTSCEEEEEEESSSBTHHHHHHHHHH-TCCTTTEEEECSSSCCBCCCCSSCBHHHHTCSSCEEEEEEE
T ss_pred             EEEEECCCCCEEEEEECCcccHHHHHHHHHHh-ccCcccceeecCCCceecCccCCCcHHHCCCCCCCEEEEec
Confidence            68899999999999999999999999999765 3444555565  4445553  35699999999888876543

>d1ef1a3 d.15.1.4 (A:4-87) Moesin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: First domain of FERM
domain: Moesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.89  E-value=0.13  Score=28.66  Aligned_cols=64  Identities=16%  Similarity=0.251  Sum_probs=49.0

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCC-CCCeEEEEc---c--eEeccCceeccccccccc
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIP-PDQQRLIFA---G--KQLEDGRTLADYNIQKES   65 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~-~~~q~L~~~---g--~~L~d~~~l~~~~i~~~~   65 (154)
                      |+|.|..+++ .+.+.++..++..+|=+.+.+..++. .+.--|.|.   |  .+|+.++.+..+..+.+.
T Consensus         2 ~~v~V~~LD~-~~~~~v~~~a~G~~l~~~Vc~~l~L~E~dYFGL~y~d~~~~~~WLd~~k~l~kq~~~~~~   71 (84)
T d1ef1a3           2 ISVRVTTMDA-ELEFAIQPNTTGKQLFDQVVKTIGLREVWFFGLQYQDTKGFSTWLKLNKKVTAQDVRKES   71 (84)
T ss_dssp             EEEEEEETTE-EEEEEECTTCBHHHHHHHHHHHHTCCCGGGEEEEEEBTTSCEEECCSSSBGGGSCBCCCS
T ss_pred             EEEEEEEcCC-EEEEEEcCCChHHHHHHHHHHHcCCcccccceEEEECCCCCeEeccCCCchhhhccCCCC
Confidence            6789999987 48999999999999999999999965 333444432   2  568888888887655444

>d1vjka_ d.15.3.1 (A:) Molybdopterin synthase subunit MoaD {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: MoaD/ThiS
family: MoaD
domain: Molybdopterin synthase subunit MoaD
species: Pyrococcus furiosus [TaxId: 2261]

Probab=94.67  E-value=0.15  Score=28.36  Aligned_cols=55  Identities=15%  Similarity=0.303  Sum_probs=40.6

Q ss_pred             ceEEEeeCCCchHHHHHHHHhhhcCC-----------CCCceeEEECCeecCCCCcccccccCCCCEEEEE
Q 040824           87 KEIEIDIEPTDTIERIKERVEEKEGI-----------PPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        87 ~~~~~~v~~~~tv~~LK~~i~~~~~i-----------~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~  146 (154)
                      ....++++...||.+|.+.+.++++-           .....++..+|+...++     +-+++||.|-++
T Consensus        19 ~~~~~~~~~~~Tv~~l~~~L~~~~~~~~~~l~~~~~~~~~~i~iavN~~~~~~d-----~~L~~gDevai~   84 (88)
T d1vjka_          19 DEEEIELPEGARVRDLIEEIKKRHEKFKEEVFGEGYDEDADVNIAVNGRYVSWD-----EELKDGDVVGVF   84 (88)
T ss_dssp             SEEEEEECTTCBHHHHHHHHHHHCGGGGGSCBCSSSCTTSSBEEEETTBCCCTT-----CBCCTTCEEEEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHChHHHHHhhhccccccccEEEEEcceEcCCC-----cCcCCCCEEEEe
Confidence            46678899999999999999887641           12345666788776543     457899998765

>d1zud21 d.15.3.2 (2:2-66) Thiamin biosynthesis sulfur carrier protein ThiS {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: MoaD/ThiS
family: ThiS
domain: Thiamin biosynthesis sulfur carrier protein ThiS
species: Escherichia coli [TaxId: 562]

Probab=94.55  E-value=0.13  Score=27.13  Aligned_cols=58  Identities=12%  Similarity=0.195  Sum_probs=44.7

Q ss_pred             EEeeCCCchHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           90 EIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        90 ~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ++++++..|+.+|-+.    .++++...-+-.++..+.-+ .-.+.-+++||.|.++-...||
T Consensus         8 ~~~~~~~~tl~~ll~~----l~~~~~~vaV~vN~~ivpk~-~~~~~~L~~gD~ieIv~~v~GG   65 (65)
T d1zud21           8 AMQCAAGQTVHELLEQ----LDQRQAGAALAINQQIVPRE-QWAQHIVQDGDQILLFQVIAGG   65 (65)
T ss_dssp             EECCCTTCBHHHHHHH----HTCCCTTEEEEETTEECCGG-GTTTCBCCTTCEEEEEECCCCC
T ss_pred             EEEcCCCCcHHHHHHH----cCCCCCcEEEEECCEEcCHH-HHhhccCCCCCEEEEEEEecCC
Confidence            3567788899998764    57888888888999887643 4566788999999888777665

>d1ef1a3 d.15.1.4 (A:4-87) Moesin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: First domain of FERM
domain: Moesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.48  E-value=0.18  Score=28.15  Aligned_cols=70  Identities=24%  Similarity=0.347  Sum_probs=52.5

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCc-eeEEEC---C--eecCCCCcccccccCCCCEEEEEE
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQ-QRLIYA---G--KQLADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~-~~l~~~---g--~~l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      |.+.|...++ .+.+.+++.++..+|-.++++..++.... +-|.|-   |  ..|+.++.+..+..+.+....+..
T Consensus         2 ~~v~V~~LD~-~~~~~v~~~a~G~~l~~~Vc~~l~L~E~dYFGL~y~d~~~~~~WLd~~k~l~kq~~~~~~~~~l~F   77 (84)
T d1ef1a3           2 ISVRVTTMDA-ELEFAIQPNTTGKQLFDQVVKTIGLREVWFFGLQYQDTKGFSTWLKLNKKVTAQDVRKESPLLFKF   77 (84)
T ss_dssp             EEEEEEETTE-EEEEEECTTCBHHHHHHHHHHHHTCCCGGGEEEEEEBTTSCEEECCSSSBGGGSCBCCCSSEEEEE
T ss_pred             EEEEEEEcCC-EEEEEEcCCChHHHHHHHHHHHcCCcccccceEEEECCCCCeEeccCCCchhhhccCCCCCEEEEE
Confidence            5778888887 48999999999999999999999985333 455443   2  268888899888766666544443

>d1wgya_ d.15.1.5 (A:) Rap guanine nucleotide exchange factor 5, RapGEF5 {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: Rap guanine nucleotide exchange factor 5, RapGEF5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.24  E-value=0.23  Score=28.74  Aligned_cols=73  Identities=12%  Similarity=0.164  Sum_probs=52.0

Q ss_pred             ceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEE---ECCe--ecCCCCcccccccCCCCEEEEEEe
Q 040824           76 GTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLI---YAGK--QLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        76 ~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~---~~g~--~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      .+...|...+.+...+.++-+.|+.++++.++++.+.+.+++.|.   .+|.  .++++..--.-.+.-+..+++..+
T Consensus         9 ei~~~VY~~Dhsy~tlr~~v~~sa~eI~~~vaeKl~~~~e~L~LV~V~SsGEr~~lkp~d~sV~TsL~lN~rLFvc~~   86 (104)
T d1wgya_           9 EIFCHVYITEHSYVSVKAKVSSIAQEILKVVAEKIQYAEEDLALVAITFSGEKHELQPNDLVISKSLEASGRIYVYRK   86 (104)
T ss_dssp             CCCEEEECSSSCEEEECCCTTCBSHHHHHHHHHHHTSCGGGEEEEEECSSCCCCBCCTTSBSSCCSSCSSCEEEEEEC
T ss_pred             eEEEEEEecCCcEEEEEeeccCcHHHHHHHHHHHhCCCCCceEEEEEccCCcEEeeCccceeEEeeeeecceEEEech
Confidence            344455566778889999999999999999999999998887665   5665  344433333334556677766654

>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=93.65  E-value=0.12  Score=28.69  Aligned_cols=36  Identities=11%  Similarity=0.254  Sum_probs=34.1

Q ss_pred             CEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEEc
Q 040824           11 KTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFA   46 (154)
Q Consensus        11 ~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~~   46 (154)
                      -++.+++.+..+..+|.++|.++...+++..+|.|.
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            778899999999999999999999999999999995

>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=93.43  E-value=0.16  Score=28.13  Aligned_cols=38  Identities=13%  Similarity=0.232  Sum_probs=34.7

Q ss_pred             CceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECC
Q 040824           86 GKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAG  123 (154)
Q Consensus        86 ~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g  123 (154)
                      .-++.+.+.+....++|.++|+++...+++..+|-|+.
T Consensus        13 ~fTVal~v~~G~~y~~L~~lvs~KL~l~~~~~~LSY~~   50 (82)
T d1oeya_          13 KYTVVMKTQPGLPYSQVRDMVSKKLELRLEHTKLSYRP   50 (82)
T ss_dssp             SSEEEEEECTTCCHHHHHHHHHHHTTCCGGGCCEEECC
T ss_pred             EEEEEEEccCCCCHHHHHHHHHHHhCCChhheEEEecc
Confidence            35788899999999999999999999999999999963

>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=93.29  E-value=0.29  Score=26.50  Aligned_cols=43  Identities=7%  Similarity=0.024  Sum_probs=38.2

Q ss_pred             eeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEE
Q 040824           79 IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIY  121 (154)
Q Consensus        79 i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~  121 (154)
                      +.+.-++|+.-.+.+.+..|+.++-.++.++-|++++...++.
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            4555678999899999999999999999999999999988864

>d1vjka_ d.15.3.1 (A:) Molybdopterin synthase subunit MoaD {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: MoaD/ThiS
family: MoaD
domain: Molybdopterin synthase subunit MoaD
species: Pyrococcus furiosus [TaxId: 2261]

Probab=93.06  E-value=0.35  Score=26.80  Aligned_cols=65  Identities=11%  Similarity=0.250  Sum_probs=42.8

Q ss_pred             CEEEEEeCC------C-CEEEEEEeCCCcHHHHHHHHHhHhCC-----------CCCCeEEEEcceEeccCceecccccc
Q 040824            1 MQIFVKTLT------G-KTITLEVESSDTIDNVKAKIQDKEGI-----------PPDQQRLIFAGKQLEDGRTLADYNIQ   62 (154)
Q Consensus         1 m~v~v~~~~------~-~~~~~~v~~~~tv~~lk~~i~~~~~~-----------~~~~q~L~~~g~~L~d~~~l~~~~i~   62 (154)
                      |+|+|+.-.      | ....++++...||.+|.+.+..+..-           ......+..+|+...+     ++-++
T Consensus         2 mkI~v~~Fa~lre~~G~~~~~~~~~~~~Tv~~l~~~L~~~~~~~~~~l~~~~~~~~~~i~iavN~~~~~~-----d~~L~   76 (88)
T d1vjka_           2 VKVKVKYFARFRQLAGVDEEEIELPEGARVRDLIEEIKKRHEKFKEEVFGEGYDEDADVNIAVNGRYVSW-----DEELK   76 (88)
T ss_dssp             EEEEEEECTHHHHHHSSSEEEEEECTTCBHHHHHHHHHHHCGGGGGSCBCSSSCTTSSBEEEETTBCCCT-----TCBCC
T ss_pred             eEEEEEEhHHHHHHhCCCeEEEECCCCCCHHHHHHHHHHHChHHHHHhhhccccccccEEEEEcceEcCC-----CcCcC
Confidence            677777663      3 56788999999999999999876421           1122344455555443     34567


Q ss_pred             cccceeee
Q 040824           63 KESTLHLV   70 (154)
Q Consensus        63 ~~~~i~l~   70 (154)
                      +|+.|.+.
T Consensus        77 ~gDevai~   84 (88)
T d1vjka_          77 DGDVVGVF   84 (88)
T ss_dssp             TTCEEEEE
T ss_pred             CCCEEEEe
Confidence            78887654

>d1gg3a3 d.15.1.4 (A:1-81) Erythroid membrane protein 4.1R {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: First domain of FERM
domain: Erythroid membrane protein 4.1R
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.83  E-value=0.22  Score=27.52  Aligned_cols=59  Identities=12%  Similarity=0.119  Sum_probs=44.3

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCC-eEEEEc---c--eEeccCceeccc
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLIFA---G--KQLEDGRTLADY   59 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~-q~L~~~---g--~~L~d~~~l~~~   59 (154)
                      |..+|..++|..+.+.++..++..+|=+++.+..++...+ --|.|-   |  ..|+.++.+...
T Consensus         1 ~~C~V~lLD~~~~~~~v~~~~~G~~l~~~Vc~~l~l~E~~YFGL~y~d~~~~~~WLd~~K~i~kq   65 (81)
T d1gg3a3           1 MHCKVSLLDDTVYECVVEKHAKGQDLLKRVCEHLNLLEEDYFGLAIWDNATSKTWLDSAKEIKKQ   65 (81)
T ss_dssp             CEEEEECTTSCEEEEECCTTCCHHHHHHHHHHHHTTCSCCSSSCEEECCSSSCCBCCTTSCHHHH
T ss_pred             CEEEEEecCCCEEEEEECCCCcHHHHHHHHHHHcCCcccccceEEEECCCCceEecccccchhhh
Confidence            7889999999999999999999999999999999866432 222221   2  456666665543

>d1xo3a_ d.15.3.3 (A:) C9orf74 homolog {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: MoaD/ThiS
family: C9orf74 homolog
domain: C9orf74 homolog
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.48  E-value=0.26  Score=28.32  Aligned_cols=74  Identities=14%  Similarity=0.178  Sum_probs=44.8

Q ss_pred             ceeeeeeecCC--------ceEEEeeCC---CchHHHHHHHHhhhcCCCCCc-----------eeEEECCeecCCCCcc-
Q 040824           76 GTMIKVKTLTG--------KEIEIDIEP---TDTIERIKERVEEKEGIPPVQ-----------QRLIYAGKQLADDKTA-  132 (154)
Q Consensus        76 ~~~i~v~~~~~--------~~~~~~v~~---~~tv~~LK~~i~~~~~i~~~~-----------~~l~~~g~~l~d~~~L-  132 (154)
                      +|.|+|+...|        +...+.++.   ..||.+|-..++++++-....           ..++.+|....   .+ 
T Consensus         4 ~m~V~V~F~g~L~~lf~~~r~~~v~l~~~~~~~TV~dll~~L~~~~p~~~~~l~~~~~~lr~~v~v~vN~~di~---~l~   80 (101)
T d1xo3a_           4 PLCVKVEFGGGAELLFDGVKKHQVALPGQEEPWDIRNLLVWIKKNLLKERPELFIQGDSVRPGILVLINDADWE---LLG   80 (101)
T ss_dssp             SCEEEEEECSSGGGGGTTCCCEEEECCSSSCCCCHHHHHHHHHHHHCCSCGGGSCCTTSCCSSEEEEETTEEHH---HHT
T ss_pred             CeEEEEEEechHHHHhCCcceEEEEcCCCCCCcCHHHHHHHHHHhCCcchhhhhccCcCeeeeEEEEEcCccee---ccC
Confidence            45555555322        334555543   479999999999888633221           23334444321   12 


Q ss_pred             -cccccCCCCEEEEEEeecCC
Q 040824          133 -RDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus       133 -~~~~i~~~~~i~~~~~~~gg  152 (154)
                       .++.+++||.|.++-..-||
T Consensus        81 gl~t~l~dgDeV~~~p~v~GG  101 (101)
T d1xo3a_          81 ELDYQLQDQDSILFISTLHGG  101 (101)
T ss_dssp             TTSCCCCTTCEEEEEETTCCC
T ss_pred             CCccCcCCCCEEEEeCCCCCC
Confidence             25689999999888777665

>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=92.33  E-value=0.19  Score=28.93  Aligned_cols=59  Identities=14%  Similarity=0.179  Sum_probs=42.7

Q ss_pred             cceeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCc-eeEE--EC--C--eecCCCCccc
Q 040824           75 GGTMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQ-QRLI--YA--G--KQLADDKTAR  133 (154)
Q Consensus        75 ~~~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~-~~l~--~~--g--~~l~d~~~L~  133 (154)
                      .+..+.|-.++|.+..+.|++++|+.++-+.++++.+++... .-|+  +.  |  +.|.|...+-
T Consensus         8 ~~~vvkv~~~dg~~k~l~V~~~tTa~eV~~~l~~K~~~~~~~~f~L~E~~~~~~leR~L~d~E~vl   73 (100)
T d1wgra_           8 RPHVVKVYSEDGACRSVEVAAGATARHVCEMLVQRAHALSDETWGLVECHPHLALERGLEDHESVV   73 (100)
T ss_dssp             SCEEEEEEETTSCEEEEEECTTCCHHHHHHHHHCSSSCCCCCCCCEEEEETTTTEEEEECSSSCHH
T ss_pred             CceEEEEEecCCCEEEEEECCCCcHHHHHHHHHHHhCCCCCCCeEEEEecCCCcceeecCchHhHH
Confidence            345677777899999999999999999999999999975433 3333  22  2  5566655433

>d1h4ra3 d.15.1.4 (A:20-103) Merlin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: First domain of FERM
domain: Merlin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.23  E-value=0.47  Score=26.29  Aligned_cols=66  Identities=12%  Similarity=0.166  Sum_probs=48.5

Q ss_pred             CEEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCC-eEEEE--cc--eEeccCceecccccccccce
Q 040824            1 MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQ-QRLIF--AG--KQLEDGRTLADYNIQKESTL   67 (154)
Q Consensus         1 m~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~-q~L~~--~g--~~L~d~~~l~~~~i~~~~~i   67 (154)
                      |.|.|..++++ ..+++...++..+|=+.+.+..++...+ --|.|  .|  .+|+.++.+..+..+.+..+
T Consensus         3 ~~v~V~lLD~~-le~~v~~~a~G~~L~d~Vc~~L~L~E~~YFGL~y~~~~~~~WLd~~k~l~kq~~~~~~~~   73 (84)
T d1h4ra3           3 FTVRIVTMDAE-MEFNCEMKWKGKDLFDLVCRTLGLRETWFFGLQYTIKDTVAWLKMDKKVLDHDVSKEEPV   73 (84)
T ss_dssp             EEEEEECSSCE-EEEEEETTCBHHHHHHHHHHHHTCCCGGGEEEEEEETTEEEECCTTSBGGGSSCCCSSSE
T ss_pred             EEEEEEEcCCc-EEEEEcCCChHHHHHHHHHHHcCCcccccceEEEecCCceEEccCCCchhhhccCCCCCE
Confidence            46889999875 7999999999999999999999965432 23332  23  56788888887765544433

>d1ip9a_ d.15.2.2 (A:) Bud emergence mediator Bemp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: CAD & PB1 domains
family: PB1 domain
domain: Bud emergence mediator Bemp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.46  E-value=0.46  Score=26.35  Aligned_cols=41  Identities=15%  Similarity=0.184  Sum_probs=31.6

Q ss_pred             EEEEeC-CCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEE
Q 040824            3 IFVKTL-TGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF   45 (154)
Q Consensus         3 v~v~~~-~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~   45 (154)
                      ++||.. ++..+.+.++++.+..+|+++|+++++..  ...|.|
T Consensus        13 ikVKv~~~~D~~~~~l~~~it~~dL~~kI~~rf~~~--~~~lkY   54 (85)
T d1ip9a_          13 TKIKFYYKDDIFALMLKGDTTYKELRSKIAPRIDTD--NFKLQT   54 (85)
T ss_dssp             EEEEECBTTCCEEEEECSCCCHHHHHHHHHHHHTSS--CEEEEE
T ss_pred             EEEEEEECCcEEEEEeCCCCCHHHHHHHHHHHhCCC--ceEEEE
Confidence            455555 56778999999999999999999998754  344544

>d1wgya_ d.15.1.5 (A:) Rap guanine nucleotide exchange factor 5, RapGEF5 {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: Rap guanine nucleotide exchange factor 5, RapGEF5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.24  E-value=0.41  Score=27.65  Aligned_cols=69  Identities=10%  Similarity=0.224  Sum_probs=47.3

Q ss_pred             EEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEE---Ecc--eEeccCceecccccccccceeeeee
Q 040824            4 FVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLI---FAG--KQLEDGRTLADYNIQKESTLHLVLR   72 (154)
Q Consensus         4 ~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~---~~g--~~L~d~~~l~~~~i~~~~~i~l~~~   72 (154)
                      .|-..+....++.++.+.|+.++++.+.++.+.+.++..|.   .+|  ..|+++..--.-.+.-+..++++.+
T Consensus        13 ~VY~~Dhsy~tlr~~v~~sa~eI~~~vaeKl~~~~e~L~LV~V~SsGEr~~lkp~d~sV~TsL~lN~rLFvc~~   86 (104)
T d1wgya_          13 HVYITEHSYVSVKAKVSSIAQEILKVVAEKIQYAEEDLALVAITFSGEKHELQPNDLVISKSLEASGRIYVYRK   86 (104)
T ss_dssp             EEECSSSCEEEECCCTTCBSHHHHHHHHHHHTSCGGGEEEEEECSSCCCCBCCTTSBSSCCSSCSSCEEEEEEC
T ss_pred             EEEecCCcEEEEEeeccCcHHHHHHHHHHHhCCCCCceEEEEEccCCcEEeeCccceeEEeeeeecceEEEech
Confidence            45555667788999999999999999999999988887776   445  3355444322223444556655544

>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=90.96  E-value=0.46  Score=25.92  Aligned_cols=43  Identities=9%  Similarity=0.122  Sum_probs=38.4

Q ss_pred             eeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEE
Q 040824           79 IKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIY  121 (154)
Q Consensus        79 i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~  121 (154)
                      +.+.-++|+.-.+.+.+..|+.++-.++.++-|++++...++.
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            4566778999899999999999999999999999999998864

>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=90.71  E-value=0.4  Score=27.46  Aligned_cols=38  Identities=18%  Similarity=0.209  Sum_probs=32.8

Q ss_pred             EEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCC
Q 040824            3 IFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQ   40 (154)
Q Consensus         3 v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~   40 (154)
                      |.|-..+|....+.|+.++|+.++.+.+.++.++..+.
T Consensus        12 vkv~~~dg~~k~l~V~~~tTa~eV~~~l~~K~~~~~~~   49 (100)
T d1wgra_          12 VKVYSEDGACRSVEVAAGATARHVCEMLVQRAHALSDE   49 (100)
T ss_dssp             EEEEETTSCEEEEEECTTCCHHHHHHHHHCSSSCCCCC
T ss_pred             EEEEecCCCEEEEEECCCCcHHHHHHHHHHHhCCCCCC
Confidence            45666788999999999999999999999999976654

>d1fm0d_ d.15.3.1 (D:) Molybdopterin synthase subunit MoaD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: MoaD/ThiS
family: MoaD
domain: Molybdopterin synthase subunit MoaD
species: Escherichia coli [TaxId: 562]

Probab=90.38  E-value=0.64  Score=25.33  Aligned_cols=59  Identities=12%  Similarity=0.236  Sum_probs=40.8

Q ss_pred             eEEEeeCCCchHHHHHHHHhhhcC-----CCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           88 EIEIDIEPTDTIERIKERVEEKEG-----IPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        88 ~~~~~v~~~~tv~~LK~~i~~~~~-----i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      ...++.+ ..|+.+|++.+.+++.     +.....++..+++....+.     -+++||.|-++-+.-||
T Consensus        18 ~~~~~~~-~~tv~~l~~~L~~~~~~~~~~l~~~~~~vavn~~~~~~~~-----~l~~gdevAi~PPVsGG   81 (81)
T d1fm0d_          18 ATEVAAD-FPTVEALRQHMAAQSDRWALALEDGKLLAAVNQTLVSFDH-----PLTDGDEVAFFPPVTGG   81 (81)
T ss_dssp             EEEECSC-CSBHHHHHHHHHTTCHHHHHHHCCTTCEEEETTEECCTTC-----BCCTTCEEEEECCCCCC
T ss_pred             eEEecCC-CCCHHHHHHHHHHhCchHHHHhcCCcEEEecCceecCCCC-----CcCCCCEEEEECCCCCC
Confidence            4455544 4589999999987764     3345566667877665443     57899999777766665

>d1h4ra3 d.15.1.4 (A:20-103) Merlin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: First domain of FERM
domain: Merlin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.95  E-value=0.85  Score=25.16  Aligned_cols=71  Identities=15%  Similarity=0.154  Sum_probs=52.1

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCc-eeEEE--CCe--ecCCCCcccccccCCCCEEEEEEe
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQ-QRLIY--AGK--QLADDKTARDYNIEGGSVLHLVLA  148 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~-~~l~~--~g~--~l~d~~~L~~~~i~~~~~i~~~~~  148 (154)
                      +.+.|...+++ ..++++..++..+|-.++++..++.... +-|.|  +|.  .|+.+++|..+..+.+..+.+..+
T Consensus         3 ~~v~V~lLD~~-le~~v~~~a~G~~L~d~Vc~~L~L~E~~YFGL~y~~~~~~~WLd~~k~l~kq~~~~~~~~~~~F~   78 (84)
T d1h4ra3           3 FTVRIVTMDAE-MEFNCEMKWKGKDLFDLVCRTLGLRETWFFGLQYTIKDTVAWLKMDKKVLDHDVSKEEPVTFHFL   78 (84)
T ss_dssp             EEEEEECSSCE-EEEEEETTCBHHHHHHHHHHHHTCCCGGGEEEEEEETTEEEECCTTSBGGGSSCCCSSSEEEEEE
T ss_pred             EEEEEEEcCCc-EEEEEcCCChHHHHHHHHHHHcCCcccccceEEEecCCceEEccCCCchhhhccCCCCCEEEEEE
Confidence            45677788875 7999999999999999999999985333 23333  343  677888898887766665554433

>d1ip9a_ d.15.2.2 (A:) Bud emergence mediator Bemp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: CAD & PB1 domains
family: PB1 domain
domain: Bud emergence mediator Bemp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.84  E-value=0.62  Score=25.80  Aligned_cols=44  Identities=11%  Similarity=0.099  Sum_probs=33.8

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCceeEEECC
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQQRLIYAG  123 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~~~g  123 (154)
                      +.|.+.. ++..+.+.++++.+..+|+++|+++++.  ..++|.|..
T Consensus        13 ikVKv~~-~~D~~~~~l~~~it~~dL~~kI~~rf~~--~~~~lkY~D   56 (85)
T d1ip9a_          13 TKIKFYY-KDDIFALMLKGDTTYKELRSKIAPRIDT--DNFKLQTKL   56 (85)
T ss_dssp             EEEEECB-TTCCEEEEECSCCCHHHHHHHHHHHHTS--SCEEEEECC
T ss_pred             EEEEEEE-CCcEEEEEeCCCCCHHHHHHHHHHHhCC--CceEEEEEc
Confidence            3444433 5567889999999999999999999975  457777764

>d1gg3a3 d.15.1.4 (A:1-81) Erythroid membrane protein 4.1R {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: First domain of FERM
domain: Erythroid membrane protein 4.1R
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.56  E-value=0.61  Score=25.60  Aligned_cols=59  Identities=20%  Similarity=0.111  Sum_probs=44.0

Q ss_pred             eeeeeeecCCceEEEeeCCCchHHHHHHHHhhhcCCCCCc-eeEEE---CC--eecCCCCccccc
Q 040824           77 TMIKVKTLTGKEIEIDIEPTDTIERIKERVEEKEGIPPVQ-QRLIY---AG--KQLADDKTARDY  135 (154)
Q Consensus        77 ~~i~v~~~~~~~~~~~v~~~~tv~~LK~~i~~~~~i~~~~-~~l~~---~g--~~l~d~~~L~~~  135 (154)
                      |.-.|...+|+...+.++..++..+|=.++++..++.... +-|.|   .|  ..|+.++++...
T Consensus         1 ~~C~V~lLD~~~~~~~v~~~~~G~~l~~~Vc~~l~l~E~~YFGL~y~d~~~~~~WLd~~K~i~kq   65 (81)
T d1gg3a3           1 MHCKVSLLDDTVYECVVEKHAKGQDLLKRVCEHLNLLEEDYFGLAIWDNATSKTWLDSAKEIKKQ   65 (81)
T ss_dssp             CEEEEECTTSCEEEEECCTTCCHHHHHHHHHHHHTTCSCCSSSCEEECCSSSCCBCCTTSCHHHH
T ss_pred             CEEEEEecCCCEEEEEECCCCcHHHHHHHHHHHcCCcccccceEEEECCCCceEecccccchhhh
Confidence            4556778899999999999999999999999999985433 23332   22  256666777665

>d1xo3a_ d.15.3.3 (A:) C9orf74 homolog {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: MoaD/ThiS
family: C9orf74 homolog
domain: C9orf74 homolog
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.38  E-value=0.5  Score=27.03  Aligned_cols=70  Identities=17%  Similarity=0.197  Sum_probs=41.7

Q ss_pred             CEEEEEeCCC--------CEEEEEEe---CCCcHHHHHHHHHhHhCCCCCC-----------eEEEEcceEeccCcee--
Q 040824            1 MQIFVKTLTG--------KTITLEVE---SSDTIDNVKAKIQDKEGIPPDQ-----------QRLIFAGKQLEDGRTL--   56 (154)
Q Consensus         1 m~v~v~~~~~--------~~~~~~v~---~~~tv~~lk~~i~~~~~~~~~~-----------q~L~~~g~~L~d~~~l--   56 (154)
                      |+|+|++.++        +...++++   ...||.+|-+.+.+...-....           ..++.+|+...   .+  
T Consensus         5 m~V~V~F~g~L~~lf~~~r~~~v~l~~~~~~~TV~dll~~L~~~~p~~~~~l~~~~~~lr~~v~v~vN~~di~---~l~g   81 (101)
T d1xo3a_           5 LCVKVEFGGGAELLFDGVKKHQVALPGQEEPWDIRNLLVWIKKNLLKERPELFIQGDSVRPGILVLINDADWE---LLGE   81 (101)
T ss_dssp             CEEEEEECSSGGGGGTTCCCEEEECCSSSCCCCHHHHHHHHHHHHCCSCGGGSCCTTSCCSSEEEEETTEEHH---HHTT
T ss_pred             eEEEEEEechHHHHhCCcceEEEEcCCCCCCcCHHHHHHHHHHhCCcchhhhhccCcCeeeeEEEEEcCccee---ccCC
Confidence            7899998652        33566664   3579999999998775422111           22233443321   11  


Q ss_pred             cccccccccceeeeeee
Q 040824           57 ADYNIQKESTLHLVLRL   73 (154)
Q Consensus        57 ~~~~i~~~~~i~l~~~~   73 (154)
                      -++.+++|+.|.+....
T Consensus        82 l~t~l~dgDeV~~~p~v   98 (101)
T d1xo3a_          82 LDYQLQDQDSILFISTL   98 (101)
T ss_dssp             TSCCCCTTCEEEEEETT
T ss_pred             CccCcCCCCEEEEeCCC
Confidence            14568889988776543

>d1y8xb1 c.111.1.2 (B:349-440) UBA3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Activating enzymes of the ubiquitin-like proteins
superfamily: Activating enzymes of the ubiquitin-like proteins
family: Ubiquitin activating enzymes (UBA)
domain: UBA3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.02  E-value=0.7  Score=26.04  Aligned_cols=57  Identities=12%  Similarity=0.279  Sum_probs=39.3

Q ss_pred             EEeeCCCchHHHHHHHHhhhcCCCCCc----------e-eEEECCe-ecC------CCCcccccccCCCCEEEEE
Q 040824           90 EIDIEPTDTIERIKERVEEKEGIPPVQ----------Q-RLIYAGK-QLA------DDKTARDYNIEGGSVLHLV  146 (154)
Q Consensus        90 ~~~v~~~~tv~~LK~~i~~~~~i~~~~----------~-~l~~~g~-~l~------d~~~L~~~~i~~~~~i~~~  146 (154)
                      .++++++.|..+|-..+++.-.+....          . .|++.+- .|+      -.++|.+.|+.+|+.|.|.
T Consensus         4 ~l~~~~~~TL~~li~~L~e~p~~qlk~Psltt~~~g~~ktLYm~~pp~Lee~Tr~NL~k~L~eLgl~dG~ei~Vt   78 (92)
T d1y8xb1           4 NIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYMQSVTSIEERTRPNLSKTLKELGLVDGQELAVA   78 (92)
T ss_dssp             CEECCTTCBHHHHHHHHHHCTTCCCSSCEEEEEETTEEEEEECSSCHHHHHHHHHHHHSBSGGGTCCTTCEEEEE
T ss_pred             eEEcCCCCcHHHHHHHHhhChHhhccCCceeeecCCCccEEEecCcHHHHHHhhhccccCHHHhCCcCCCEEEEe
Confidence            467899999999999999874332211          2 2333221 132      3578999999999999876

>d1v8ca1 d.15.3.1 (A:1-87) MoaD-related protein, N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: MoaD/ThiS
family: MoaD
domain: MoaD-related protein, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=86.88  E-value=1.2  Score=24.43  Aligned_cols=61  Identities=13%  Similarity=0.258  Sum_probs=41.1

Q ss_pred             EEeeCCCchHHHHHHHHhhhcC-C---------CCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           90 EIDIEPTDTIERIKERVEEKEG-I---------PPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        90 ~~~v~~~~tv~~LK~~i~~~~~-i---------~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      +++++. .||.+|...+.+.+. +         ......+..+|+.+.+.. -.+.-+++||.|.++-..-||
T Consensus        17 e~~v~~-~Tv~~ll~~L~~~~p~l~~~l~~~~~~~~~v~i~vng~~i~~~~-~~~~~l~~gdeV~i~PpvsGG   87 (87)
T d1v8ca1          17 QLELPG-ATVGEVLENLVRAYPALKEELFEGEGLAERVSVFLEGRDVRYLQ-GLSTPLSPGATLDLFPPVAGG   87 (87)
T ss_dssp             EEECCC-SBHHHHHHHHHHHCGGGHHHHEETTEECTTCEEEETTEEGGGTT-GGGCBCCTTCEEEEECSCCSE
T ss_pred             EEEEcC-CCHHHHHHHHHHHCHHHHHHhcccccccceEEEEEcCeeeeccc-CCcccCCCCCEEEEECCCCCC
Confidence            456654 699999999988774 1         123356777887664322 234468999999888777665

>d1j0ga_ d.15.1.6 (A:) Hypothetical protein 1810045k17 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: BM-002-like
domain: Hypothetical protein 1810045k17
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.18  E-value=1.6  Score=23.80  Aligned_cols=64  Identities=17%  Similarity=0.262  Sum_probs=54.3

Q ss_pred             EEeeCCCchHHHHHHHHhhhcCCCCCceeEE-ECCeecCCCCcccccccCCCCEEEEEEeecCCC
Q 040824           90 EIDIEPTDTIERIKERVEEKEGIPPVQQRLI-YAGKQLADDKTARDYNIEGGSVLHLVLALRGGG  153 (154)
Q Consensus        90 ~~~v~~~~tv~~LK~~i~~~~~i~~~~~~l~-~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg~  153 (154)
                      -+.|+.......+-+-.++.+.+|+...-++ -.|-=++..++-...-++.|+.+.++-|-|-|.
T Consensus        27 vlsVpE~aPftAVlkfaAEeFkV~~~TSAiITndGvGINP~QtAg~vFlKhGselrliPRDRVG~   91 (92)
T d1j0ga_          27 VLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPAQTAGNVFLKHGSELRIIPRDRVGS   91 (92)
T ss_dssp             EEEEETTSBHHHHHHHHHHHTTCCSSSEEEECTTSCCCCCSSBHHHHHHHTCSEEEEEECCSSCC
T ss_pred             EEecCccCchHHHHHHHHHHcCCCccceeEEecCccccChhhccchhhhhcCceeeecccccccC
Confidence            3678888888888888999999999888776 567778888999999999999999998887764

>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=85.56  E-value=1.6  Score=23.36  Aligned_cols=44  Identities=11%  Similarity=0.046  Sum_probs=39.1

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEE
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF   45 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~   45 (154)
                      .++|..++|+.-.+.+.++.|+.+.-.++-++.|+.++.-.++.
T Consensus         2 ~iRv~LPngq~T~V~vrpG~tir~~L~k~l~kRgl~~~~~~V~~   45 (73)
T d1wxma1           2 TVKVYLPNKQRTVVTVRDGMSVYDSLDKALKVRGLNQDCCVVYR   45 (73)
T ss_dssp             EEEEECSSSCEEEEECCSSCBSHHHHHHHHHTTTCCSSSEEEEE
T ss_pred             eEEEEcCCCCeEEEEecCCCCHHHHHHHHHHHcCCCHHHEEEEE
Confidence            36788889998889999999999999999999999998877764

>d1tygb_ d.15.3.2 (B:) Thiamin biosynthesis sulfur carrier protein ThiS {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: MoaD/ThiS
family: ThiS
domain: Thiamin biosynthesis sulfur carrier protein ThiS
species: Bacillus subtilis [TaxId: 1423]

Probab=85.05  E-value=1.5  Score=22.70  Aligned_cols=60  Identities=13%  Similarity=0.224  Sum_probs=43.3

Q ss_pred             CCceEEEeeCCC-chHHHHHHHHhhhcCCCCCceeEEECCeecCCCCcccccccCCCCEEEEEEeecCC
Q 040824           85 TGKEIEIDIEPT-DTIERIKERVEEKEGIPPVQQRLIYAGKQLADDKTARDYNIEGGSVLHLVLALRGG  152 (154)
Q Consensus        85 ~~~~~~~~v~~~-~tv~~LK~~i~~~~~i~~~~~~l~~~g~~l~d~~~L~~~~i~~~~~i~~~~~~~gg  152 (154)
                      +|+.  .+++++ .|+.+|-+.    .++++...-+-+++..+.-+ .-.++-+++||.|+++- +.||
T Consensus         5 NG~~--~~~~~~~~tl~~LL~~----l~~~~~~vAVevN~~iv~k~-~~~~~~L~~gD~IEIv~-~vgG   65 (65)
T d1tygb_           5 NGKD--VKWKKDTGTIQDLLAS----YQLENKIVIVERNKEIIGKE-RYHEVELCDRDVIEIVH-FVGG   65 (65)
T ss_dssp             TTEE--ECCSSSCCBHHHHHHH----TTCTTSCCEEEETTEEECGG-GTTTSBCCSSSEEEEEE-ECCC
T ss_pred             CCEE--EEcCCCcccHHHHHHH----cCCCCCcEEEEECCEEcCHH-HcCcccCCCCCEEEEEE-eecC
Confidence            5554  456555 589998553    57888888888999887643 46677899999998776 4444

>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=82.73  E-value=2.3  Score=22.95  Aligned_cols=44  Identities=14%  Similarity=0.154  Sum_probs=38.9

Q ss_pred             EEEEEeCCCCEEEEEEeCCCcHHHHHHHHHhHhCCCCCCeEEEE
Q 040824            2 QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIF   45 (154)
Q Consensus         2 ~v~v~~~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~q~L~~   45 (154)
                      .++|..++|+.-.+.+.++.|+.+.-.++-++.|+.++.-.++.
T Consensus         3 ~iRv~LPngq~T~V~vrpG~tird~L~k~l~kRgl~~~~c~V~~   46 (77)
T d1c1yb_           3 TIRVFLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVFR   46 (77)
T ss_dssp             EEEEEETTTEEEEEECCTTCBHHHHHHHHHHTTTCCGGGEEEEE
T ss_pred             eEEEECCCCCeEEEEecCCCCHHHHHHHHHHHcCCCHHHEEEEE
Confidence            46788889998889999999999999999999999988777764

>d2incc1 d.15.12.1 (C:3-85) Toluene, o-xylene monooxygenase oxygenase subunit TouB {Pseudomonas stutzeri [TaxId: 316]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: TmoB-like
family: TmoB-like
domain: Toluene, o-xylene monooxygenase oxygenase subunit TouB
species: Pseudomonas stutzeri [TaxId: 316]

Probab=81.18  E-value=2.7  Score=22.76  Aligned_cols=59  Identities=14%  Similarity=0.311  Sum_probs=45.0

Q ss_pred             EEEeeCCCchHHHHHHHHhhhc-C--CCCC--ce-eEE--ECCeecCCCCcccccccCCCCEEEEEE
Q 040824           89 IEIDIEPTDTIERIKERVEEKE-G--IPPV--QQ-RLI--YAGKQLADDKTARDYNIEGGSVLHLVL  147 (154)
Q Consensus        89 ~~~~v~~~~tv~~LK~~i~~~~-~--i~~~--~~-~l~--~~g~~l~d~~~L~~~~i~~~~~i~~~~  147 (154)
                      .-+.|+..+|..++-++++... |  +.|.  .. +..  .+|..+..+.++++.||.+-+.|++..
T Consensus        15 qLVaVDt~dtmdqVA~k~A~HsVGRRv~p~P~~~~rvr~~~~ge~~pr~~tv~~~gi~P~e~iev~f   81 (83)
T d2incc1          15 QLVPVDTEDTMDQVAEKCAYHSINRRVHPQPEKILRVRRHEDGTLFPRGMIVSDAGLRPTETLDIIF   81 (83)
T ss_dssp             EEEEECTTCBHHHHHHHHHTTTBTTTBCCCTTSEEEEEETTTCCEECTTCBGGGSCCCTTCEEEEEE
T ss_pred             EEEEEcCCCcHHHHHHHHHHHhhccccCCCCCCccEEEEcCCCcCCCCCCChhhcCCCCceEEEEEE
Confidence            3477899999999999998665 3  4332  22 333  368899999999999999999998763